Use 'repr' instead of 'str' in Interval string representation.

Otherwise timestamps get truncated to 2 decimal places.

.coveragerc

@@ -0,0 +1,9 @@
+# -*- conf -*-
+
+[run]
+# branch = True
+
+[report]
+exclude_lines =
+	pragma: no cover
+	if 0:

.gitignore

@@ -0,0 +1,4 @@
+db/
+tests/*testdb/
+.coverage
+*.pyc

Makefile

@@ -1,2 +1,20 @@
-all:
+all: test
+
+tool:
+	python nilmtool.py  --help
+	python nilmtool.py list --help
+	python nilmtool.py -u asfdadsf list
+
+lint:
+	pylint -f parseable nilmdb
+
+test:
 	nosetests
+
+profile:
+	nosetests --with-profile 
+
+clean::
+	find . -name '*pyc' | xargs rm -f
+	rm -f .coverage
+	rm -rf tests/*testdb*

README.txt

@@ -1,4 +1,4 @@
-To install, 
-
-   python seutp.py install
+sudo apt-get install python-nose python-coverage
+sudo apt-get install python-tables python-cherrypy3
+sudo apt-get install cython # 0.17.1-1 or newer
 

TODO

@@ -0,0 +1 @@
+- Merge adjacent intervals on insert (maybe with client help?)

bin/nilm-test.py

@@ -1,26 +0,0 @@
-#!/usr/bin/python
-
-from nilmdb import Interval
-from optparse import OptionParser
-import sys
-
-version = "1.0"
-
-parser = OptionParser()
-parser.add_option("-d", "--db", dest="database", metavar="DATABASE",
-                  help="location of sqlite database")
-parser.add_option("-V", "--version", dest="version", default=False, action="store_true",
-                  help="print version then exit")
-
-(options, args) = parser.parse_args()
-
-if (options.version):
-    print "This script version: " + version
-    sys.exit(0)
-
-if options.database is None:
-    print "Error: database is mandatory"
-    sys.exit(1)
-
-print "Database is " + options.database
-

datetime_tz/__init__.py

@@ -0,0 +1,710 @@
+#!/usr/bin/python
+#
+# Copyright 2009 Google Inc.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+#
+# Disable the invalid name warning as we are inheriting from a standard library
+# object.
+# pylint: disable-msg=C6409,W0212
+
+"""A version of the datetime module which *cares* about timezones.
+
+This module will never return a naive datetime object. This requires the module
+know your local timezone, which it tries really hard to figure out.
+
+You can override the detection by using the datetime.tzaware.defaulttz_set
+method. It the module is unable to figure out the timezone itself this method
+*must* be called before the normal module is imported. If done before importing
+it can also speed up the time taken to import as the defaulttz will no longer
+try and do the detection.
+"""
+
+__author__ = "tansell@google.com (Tim Ansell)"
+
+import calendar
+import datetime
+import os
+import os.path
+import re
+import time
+import warnings
+import dateutil.parser
+import dateutil.relativedelta
+import dateutil.tz
+import pytz
+import pytz_abbr
+
+
+try:
+  # pylint: disable-msg=C6204
+  import functools
+except ImportError, e:
+
+  class functools(object):
+    """Fake replacement for a full functools."""
+
+    # pylint: disable-msg=W0613
+    @staticmethod
+    def wraps(f, *args, **kw):
+      return f
+
+
+# Need to patch pytz.utc to have a _utcoffset so you can normalize/localize
+# using it.
+pytz.utc._utcoffset = datetime.timedelta()
+
+
+timedelta = datetime.timedelta
+
+
+def _tzinfome(tzinfo):
+  """Gets a tzinfo object from a string.
+
+  Args:
+    tzinfo: A string (or string like) object, or a datetime.tzinfo object.
+
+  Returns:
+    An datetime.tzinfo object.
+
+  Raises:
+    UnknownTimeZoneError: If the timezone given can't be decoded.
+  """
+  if not isinstance(tzinfo, datetime.tzinfo):
+    try:
+      tzinfo = pytz.timezone(tzinfo)
+    except AttributeError:
+      raise pytz.UnknownTimeZoneError("Unknown timezone! %s" % tzinfo)
+  return tzinfo
+
+
+# Our "local" timezone
+_localtz = None
+
+
+def localtz():
+  """Get the local timezone.
+
+  Returns:
+    The localtime timezone as a tzinfo object.
+  """
+  # pylint: disable-msg=W0603
+  global _localtz
+  if _localtz is None:
+    _localtz = detect_timezone()
+  return _localtz
+
+
+def localtz_set(timezone):
+  """Set the local timezone."""
+  # pylint: disable-msg=W0603
+  global _localtz
+  _localtz = _tzinfome(timezone)
+
+
+def detect_timezone():
+  """Try and detect the timezone that Python is currently running in.
+
+  We have a bunch of different methods for trying to figure this out (listed in
+  order they are attempted).
+    * Try TZ environment variable.
+    * Try and find /etc/timezone file (with timezone name).
+    * Try and find /etc/localtime file (with timezone data).
+    * Try and match a TZ to the current dst/offset/shortname.
+
+  Returns:
+    The detected local timezone as a tzinfo object
+
+  Raises:
+    pytz.UnknownTimeZoneError: If it was unable to detect a timezone.
+  """
+  # First we try the TZ variable
+  tz = _detect_timezone_environ()
+  if tz is not None:
+    return tz
+
+  # Second we try /etc/timezone and use the value in that
+  tz = _detect_timezone_etc_timezone()
+  if tz is not None:
+    return tz
+
+  # Next we try and see if something matches the tzinfo in /etc/localtime
+  tz = _detect_timezone_etc_localtime()
+  if tz is not None:
+    return tz
+
+  # Next we try and use a similiar method to what PHP does.
+  # We first try to search on time.tzname, time.timezone, time.daylight to
+  # match a pytz zone.
+  warnings.warn("Had to fall back to worst detection method (the 'PHP' "
+                "method).")
+
+  tz = _detect_timezone_php()
+  if tz is not None:
+    return tz
+
+  raise pytz.UnknownTimeZoneError("Unable to detect your timezone!")
+
+
+def _detect_timezone_environ():
+  if "TZ" in os.environ:
+    try:
+      return pytz.timezone(os.environ["TZ"])
+    except (IOError, pytz.UnknownTimeZoneError):
+      warnings.warn("You provided a TZ environment value (%r) we did not "
+                    "understand!" % os.environ["TZ"])
+
+
+def _detect_timezone_etc_timezone():
+  if os.path.exists("/etc/timezone"):
+    try:
+      tz = file("/etc/timezone").read().strip()
+      try:
+        return pytz.timezone(tz)
+      except (IOError, pytz.UnknownTimeZoneError), ei:
+        warnings.warn("Your /etc/timezone file references a timezone (%r) that"
+                      " is not valid (%r)." % (tz, ei))
+
+    # Problem reading the /etc/timezone file
+    except IOError, eo:
+      warnings.warn("Could not access your /etc/timezone file: %s" % eo)
+
+
+def _detect_timezone_etc_localtime():
+  matches = []
+  if os.path.exists("/etc/localtime"):
+    localtime = pytz.tzfile.build_tzinfo("/etc/localtime",
+                                         file("/etc/localtime"))
+
+    # See if we can find a "Human Name" for this..
+    for tzname in pytz.all_timezones:
+      tz = _tzinfome(tzname)
+
+      if dir(tz) != dir(localtime):
+        continue
+
+      for attrib in dir(tz):
+        # Ignore functions and specials
+        if callable(getattr(tz, attrib)) or attrib.startswith("__"):
+          continue
+
+        # This will always be different
+        if attrib == "zone" or attrib == "_tzinfos":
+          continue
+
+        if getattr(tz, attrib) != getattr(localtime, attrib):
+          break
+
+      # We get here iff break didn't happen, i.e. no meaningful attributes
+      # differ between tz and localtime
+      else:
+        matches.append(tzname)
+
+    if len(matches) == 1:
+      return _tzinfome(matches[0])
+    else:
+      # Warn the person about this!
+      warning = "Could not get a human name for your timezone: "
+      if len(matches) > 1:
+        warning += ("We detected multiple matches for your /etc/localtime. "
+                    "(Matches where %s)" % matches)
+        return _tzinfome(matches[0])
+      else:
+        warning += "We detected no matches for your /etc/localtime."
+      warnings.warn(warning)
+
+      # Register /etc/localtime as the timezone loaded.
+      pytz._tzinfo_cache['/etc/localtime'] = localtime
+      return localtime
+
+
+def _detect_timezone_php():
+  tomatch = (time.tzname[0], time.timezone, time.daylight)
+  now = datetime.datetime.now()
+
+  matches = []
+  for tzname in pytz.all_timezones:
+    try:
+      tz = pytz.timezone(tzname)
+    except IOError:
+      continue
+
+    try:
+      indst = tz.localize(now).timetuple()[-1]
+
+      if tomatch == (tz._tzname, -tz._utcoffset.seconds, indst):
+        matches.append(tzname)
+
+    # pylint: disable-msg=W0704
+    except AttributeError:
+      pass
+
+  if len(matches) > 1:
+    warnings.warn("We detected multiple matches for the timezone, choosing "
+                  "the first %s. (Matches where %s)" % (matches[0], matches))
+    return pytz.timezone(matches[0])
+
+
+class datetime_tz(datetime.datetime):
+  """An extension of the inbuilt datetime adding more functionality.
+
+  The extra functionality includes:
+    * Partial parsing support (IE 2006/02/30 matches %Y/%M/%D %H:%M)
+    * Full integration with pytz (just give it the string of the timezone!)
+    * Proper support for going to/from Unix timestamps (which are in UTC!).
+  """
+  __slots__ = ["is_dst"]
+
+  def __new__(cls, *args, **kw):
+    args = list(args)
+    if not args:
+      raise TypeError("Not enough arguments given.")
+
+    # See if we are given a tzinfo object...
+    tzinfo = None
+    if isinstance(args[-1], (datetime.tzinfo, basestring)):
+      tzinfo = _tzinfome(args.pop(-1))
+    elif kw.get("tzinfo", None) is not None:
+      tzinfo = _tzinfome(kw.pop("tzinfo"))
+
+    # Create a datetime object if we don't have one
+    if isinstance(args[0], datetime.datetime):
+      # Convert the datetime instance to a datetime object.
+      newargs = (list(args[0].timetuple()[0:6]) +
+                 [args[0].microsecond, args[0].tzinfo])
+      dt = datetime.datetime(*newargs)
+
+      if tzinfo is None and dt.tzinfo is None:
+        raise TypeError("Must specify a timezone!")
+
+      if tzinfo is not None and dt.tzinfo is not None:
+        raise TypeError("Can not give a timezone with timezone aware"
+                        " datetime object! (Use localize.)")
+    else:
+      dt = datetime.datetime(*args, **kw)
+
+    if dt.tzinfo is not None:
+      # Re-normalize the dt object
+      dt = dt.tzinfo.normalize(dt)
+
+    else:
+      if tzinfo is None:
+        tzinfo = localtz()
+
+      try:
+        dt = tzinfo.localize(dt, is_dst=None)
+      except pytz.AmbiguousTimeError:
+        is_dst = None
+        if "is_dst" in kw:
+          is_dst = kw.pop("is_dst")
+
+        try:
+          dt = tzinfo.localize(dt, is_dst)
+        except IndexError:
+          raise pytz.AmbiguousTimeError("No such time exists!")
+
+    newargs = list(dt.timetuple()[0:6])+[dt.microsecond, dt.tzinfo]
+    obj = datetime.datetime.__new__(cls, *newargs)
+    obj.is_dst = obj.dst() != datetime.timedelta(0)
+    return obj
+
+  def asdatetime(self, naive=True):
+    """Return this datetime_tz as a datetime object.
+
+    Args:
+      naive: Return *without* any tz info.
+
+    Returns:
+      This datetime_tz as a datetime object.
+    """
+    args = list(self.timetuple()[0:6])+[self.microsecond]
+    if not naive:
+      args.append(self.tzinfo)
+    return datetime.datetime(*args)
+
+  def asdate(self):
+    """Return this datetime_tz as a date object.
+
+    Returns:
+      This datetime_tz as a date object.
+    """
+    return datetime.date(self.year, self.month, self.day)
+
+  def totimestamp(self):
+    """Convert this datetime object back to a unix timestamp.
+
+    The Unix epoch is the time 00:00:00 UTC on January 1, 1970.
+
+    Returns:
+      Unix timestamp.
+    """
+    return calendar.timegm(self.utctimetuple())+1e-6*self.microsecond
+
+  def astimezone(self, tzinfo):
+    """Returns a version of this timestamp converted to the given timezone.
+
+    Args:
+      tzinfo: Either a datetime.tzinfo object or a string (which will be looked
+              up in pytz.
+
+    Returns:
+      A datetime_tz object in the given timezone.
+    """
+    # Assert we are not a naive datetime object
+    assert self.tzinfo is not None
+
+    tzinfo = _tzinfome(tzinfo)
+
+    d = self.asdatetime(naive=False).astimezone(tzinfo)
+    return datetime_tz(d)
+
+  # pylint: disable-msg=C6113
+  def replace(self, **kw):
+    """Return datetime with new specified fields given as arguments.
+
+    For example, dt.replace(days=4) would return a new datetime_tz object with
+    exactly the same as dt but with the days attribute equal to 4.
+
+    Any attribute can be replaced, but tzinfo can not be set to None.
+
+    Args:
+      Any datetime_tz attribute.
+
+    Returns:
+      A datetime_tz object with the attributes replaced.
+
+    Raises:
+      TypeError: If the given replacement is invalid.
+    """
+    if "tzinfo" in kw:
+      if kw["tzinfo"] is None:
+        raise TypeError("Can not remove the timezone use asdatetime()")
+
+    is_dst = None
+    if "is_dst" in kw:
+      is_dst = kw["is_dst"]
+      del kw["is_dst"]
+    else:
+      # Use our own DST setting..
+      is_dst = self.is_dst
+
+    replaced = self.asdatetime().replace(**kw)
+
+    return datetime_tz(replaced, tzinfo=self.tzinfo.zone, is_dst=is_dst)
+
+  # pylint: disable-msg=C6310
+  @classmethod
+  def smartparse(cls, toparse, tzinfo=None):
+    """Method which uses dateutil.parse and extras to try and parse the string.
+
+    Valid dates are found at:
+     http://labix.org/python-dateutil#head-1443e0f14ad5dff07efd465e080d1110920673d8-2
+
+    Other valid formats include:
+      "now" or "today"
+      "yesterday"
+      "tommorrow"
+      "5 minutes ago"
+      "10 hours ago"
+      "10h5m ago"
+      "start of yesterday"
+      "end of tommorrow"
+      "end of 3rd of March"
+
+    Args:
+      toparse: The string to parse.
+      tzinfo: Timezone for the resultant datetime_tz object should be in.
+              (Defaults to your local timezone.)
+
+    Returns:
+      New datetime_tz object.
+
+    Raises:
+      ValueError: If unable to make sense of the input.
+    """
+    # Default for empty fields are:
+    #  year/month/day == now
+    #  hour/minute/second/microsecond == 0
+    toparse = toparse.strip()
+
+    if tzinfo is None:
+      dt = cls.now()
+    else:
+      dt = cls.now(tzinfo)
+
+    default = dt.replace(hour=0, minute=0, second=0, microsecond=0)
+
+    # Remove "start of " and "end of " prefix in the string
+    if toparse.lower().startswith("end of "):
+      toparse = toparse[7:].strip()
+
+      dt += datetime.timedelta(days=1)
+      dt = dt.replace(hour=0, minute=0, second=0, microsecond=0)
+      dt -= datetime.timedelta(microseconds=1)
+
+      default = dt
+
+    elif toparse.lower().startswith("start of "):
+      toparse = toparse[9:].strip()
+
+      dt = dt.replace(hour=0, minute=0, second=0, microsecond=0)
+      default = dt
+
+    # Handle strings with "now", "today", "yesterday", "tomorrow" and "ago".
+    # Need to use lowercase
+    toparselower = toparse.lower()
+
+    if toparselower in ["now", "today"]:
+      pass
+
+    elif toparselower == "yesterday":
+      dt -= datetime.timedelta(days=1)
+
+    elif toparselower == "tommorrow":
+      dt += datetime.timedelta(days=1)
+
+    elif "ago" in toparselower:
+      # Remove the "ago" bit
+      toparselower = toparselower[:-3]
+      # Replace all "a day and an hour" with "1 day 1 hour"
+      toparselower = toparselower.replace("a ", "1 ")
+      toparselower = toparselower.replace("an ", "1 ")
+      toparselower = toparselower.replace(" and ", " ")
+
+      # Match the following
+      # 1 hour ago
+      # 1h ago
+      # 1 h ago
+      # 1 hour ago
+      # 2 hours ago
+      # Same with minutes, seconds, etc.
+
+      tocheck = ("seconds", "minutes", "hours", "days", "weeks", "months",
+                 "years")
+      result = {}
+      for match in re.finditer("([0-9]+)([^0-9]*)", toparselower):
+        amount = int(match.group(1))
+        unit = match.group(2).strip()
+
+        for bit in tocheck:
+          regex = "^([%s]|((%s)s?))$" % (
+              bit[0], bit[:-1])
+
+          bitmatch = re.search(regex, unit)
+          if bitmatch:
+            result[bit] = amount
+            break
+        else:
+          raise ValueError("Was not able to parse date unit %r!" % unit)
+
+      delta = dateutil.relativedelta.relativedelta(**result)
+      dt -= delta
+
+    else:
+      # Handle strings with normal datetime format, use original case.
+      dt = dateutil.parser.parse(toparse, default=default.asdatetime(),
+                                 tzinfos=pytz_abbr.tzinfos)
+      if dt is None:
+        raise ValueError("Was not able to parse date!")
+
+      if dt.tzinfo is pytz_abbr.unknown:
+        dt = dt.replace(tzinfo=None)
+
+      if dt.tzinfo is None:
+        if tzinfo is None:
+          tzinfo = localtz()
+        dt = cls(dt, tzinfo)
+      else:
+        if isinstance(dt.tzinfo, pytz_abbr.tzabbr):
+          abbr = dt.tzinfo
+          dt = dt.replace(tzinfo=None)
+          dt = cls(dt, abbr.zone, is_dst=abbr.dst)
+
+        dt = cls(dt)
+
+    return dt
+
+  @classmethod
+  def utcfromtimestamp(cls, timestamp):
+    """Returns a datetime object of a given timestamp (in UTC)."""
+    obj = datetime.datetime.utcfromtimestamp(timestamp)
+    obj = pytz.utc.localize(obj)
+    return cls(obj)
+
+  @classmethod
+  def fromtimestamp(cls, timestamp):
+    """Returns a datetime object of a given timestamp (in local tz)."""
+    d = cls.utcfromtimestamp(timestamp)
+    return d.astimezone(localtz())
+
+  @classmethod
+  def utcnow(cls):
+    """Return a new datetime representing UTC day and time."""
+    obj = datetime.datetime.utcnow()
+    obj = cls(obj, tzinfo=pytz.utc)
+    return obj
+
+  @classmethod
+  def now(cls, tzinfo=None):
+    """[tz] -> new datetime with tz's local day and time."""
+    obj = cls.utcnow()
+    if tzinfo is None:
+      tzinfo = localtz()
+    return obj.astimezone(tzinfo)
+
+  today = now
+
+  @staticmethod
+  def fromordinal(ordinal):
+    raise SyntaxError("Not enough information to create a datetime_tz object "
+                      "from an ordinal. Please use datetime.date.fromordinal")
+
+
+class iterate(object):
+  """Helpful iterators for working with datetime_tz objects."""
+
+  @staticmethod
+  def between(start, delta, end=None):
+    """Return an iterator between this date till given end point.
+
+    Example usage:
+      >>> d = datetime_tz.smartparse("5 days ago")
+      2008/05/12 11:45
+      >>> for i in d.between(timedelta(days=1), datetime_tz.now()):
+      >>>    print i
+      2008/05/12 11:45
+      2008/05/13 11:45
+      2008/05/14 11:45
+      2008/05/15 11:45
+      2008/05/16 11:45
+
+    Args:
+      start: The date to start at.
+      delta: The interval to iterate with.
+      end: (Optional) Date to end at. If not given the iterator will never
+           terminate.
+
+    Yields:
+      datetime_tz objects.
+    """
+    toyield = start
+    while end is None or toyield < end:
+      yield toyield
+      toyield += delta
+
+  @staticmethod
+  def weeks(start, end=None):
+    """Iterate over the weeks between the given datetime_tzs.
+
+    Args:
+      start: datetime_tz to start from.
+      end: (Optional) Date to end at, if not given the iterator will never
+           terminate.
+
+    Returns:
+      An iterator which generates datetime_tz objects a week apart.
+    """
+    return iterate.between(start, datetime.timedelta(days=7), end)
+
+  @staticmethod
+  def days(start, end=None):
+    """Iterate over the days between the given datetime_tzs.
+
+    Args:
+      start: datetime_tz to start from.
+      end: (Optional) Date to end at, if not given the iterator will never
+           terminate.
+
+    Returns:
+      An iterator which generates datetime_tz objects a day apart.
+    """
+    return iterate.between(start, datetime.timedelta(days=1), end)
+
+  @staticmethod
+  def hours(start, end=None):
+    """Iterate over the hours between the given datetime_tzs.
+
+    Args:
+      start: datetime_tz to start from.
+      end: (Optional) Date to end at, if not given the iterator will never
+           terminate.
+
+    Returns:
+      An iterator which generates datetime_tz objects a hour apart.
+    """
+    return iterate.between(start, datetime.timedelta(hours=1), end)
+
+  @staticmethod
+  def minutes(start, end=None):
+    """Iterate over the minutes between the given datetime_tzs.
+
+    Args:
+      start: datetime_tz to start from.
+      end: (Optional) Date to end at, if not given the iterator will never
+           terminate.
+
+    Returns:
+      An iterator which generates datetime_tz objects a minute apart.
+    """
+    return iterate.between(start, datetime.timedelta(minutes=1), end)
+
+  @staticmethod
+  def seconds(start, end=None):
+    """Iterate over the seconds between the given datetime_tzs.
+
+    Args:
+      start: datetime_tz to start from.
+      end: (Optional) Date to end at, if not given the iterator will never
+           terminate.
+
+    Returns:
+      An iterator which generates datetime_tz objects a second apart.
+    """
+    return iterate.between(start, datetime.timedelta(minutes=1), end)
+
+
+def _wrap_method(name):
+  """Wrap a method.
+
+  Patch a method which might return a datetime.datetime to return a
+  datetime_tz.datetime_tz instead.
+
+  Args:
+    name: The name of the method to patch
+  """
+  method = getattr(datetime.datetime, name)
+
+  # Have to give the second argument as method has no __module__ option.
+  @functools.wraps(method, ("__name__", "__doc__"), ())
+  def wrapper(*args, **kw):
+    r = method(*args, **kw)
+
+    if isinstance(r, datetime.datetime) and not isinstance(r, datetime_tz):
+      r = datetime_tz(r)
+    return r
+
+  setattr(datetime_tz, name, wrapper)
+
+for methodname in ["__add__", "__radd__", "__rsub__", "__sub__", "combine"]:
+
+  # Make sure we have not already got an override for this method
+  assert methodname not in datetime_tz.__dict__
+
+  _wrap_method(methodname)
+
+
+__all__ = ['datetime_tz', 'detect_timezone', 'iterate', 'localtz',
+    'localtz_set', 'timedelta', '_detect_timezone_environ',
+    '_detect_timezone_etc_localtime', '_detect_timezone_etc_timezone',
+    '_detect_timezone_php']

datetime_tz/pytz_abbr.py

@@ -0,0 +1,230 @@
+#!/usr/bin/python2.4
+# -*- coding: utf-8 -*-
+#
+# Copyright 2010 Google Inc. All Rights Reserved.
+#
+
+"""
+Common time zone acronyms/abbreviations for use with the datetime_tz module.
+
+*WARNING*: There are lots of caveats when using this module which are listed
+below.
+
+CAVEAT 1: The acronyms/abbreviations are not globally unique, they are not even
+unique within a region. For example, EST can mean any of,
+  Eastern Standard Time in Australia (which is 10 hour ahead of UTC)
+  Eastern Standard Time in North America (which is 5 hours behind UTC)
+
+Where there are two abbreviations the more popular one will appear in the all
+dictionary, while the less common one will only appear in that countries region
+dictionary. IE If using all, EST will be mapped to Eastern Standard Time in
+North America.
+
+CAVEAT 2: Many of the acronyms don't map to a neat Oslon timezones. For example,
+Eastern European Summer Time (EEDT) is used by many different countries in
+Europe *at different times*! If the acronym does not map neatly to one zone it
+is mapped to the Etc/GMT+-XX Oslon zone. This means that any date manipulations
+can end up with idiot things like summer time in the middle of winter.
+
+CAVEAT 3: The Summer/Standard time difference is really important! For an hour
+each year it is needed to determine which time you are actually talking about.
+    2002-10-27 01:20:00 EST != 2002-10-27 01:20:00 EDT
+"""
+
+import datetime
+import pytz
+import pytz.tzfile
+
+
+class tzabbr(datetime.tzinfo):
+  """A timezone abbreviation.
+
+  *WARNING*: This is not a tzinfo implementation! Trying to use this as tzinfo
+  object will result in failure.  We inherit from datetime.tzinfo so we can get
+  through the dateutil checks.
+  """
+  pass
+
+
+# A "marker" tzinfo object which is used to signify an unknown timezone.
+unknown = datetime.tzinfo(0)
+
+
+regions = {'all': {}, 'military': {}}
+# Create a special alias for the all and military regions
+all = regions['all']
+military = regions['military']
+
+
+def tzabbr_register(abbr, name, region, zone, dst):
+  """Register a new timezone abbreviation in the global registry.
+
+  If another abbreviation with the same name has already been registered it new
+  abbreviation will only be registered in region specific dictionary.
+  """
+  newabbr = tzabbr()
+  newabbr.abbr = abbr
+  newabbr.name = name
+  newabbr.region = region
+  newabbr.zone = zone
+  newabbr.dst = dst
+
+  if abbr not in all:
+    all[abbr] = newabbr
+
+  if not region in regions:
+    regions[region] = {}
+
+  assert abbr not in regions[region]
+  regions[region][abbr] = newabbr
+
+
+def tzinfos_create(use_region):
+  abbrs = regions[use_region]
+
+  def tzinfos(abbr, offset):
+    if abbr:
+      if abbr in abbrs:
+        result = abbrs[abbr]
+        if offset:
+          # FIXME: Check the offset matches the abbreviation we just selected.
+          pass
+        return result
+      else:
+        raise ValueError, "Unknown timezone found %s" % abbr
+    if offset == 0:
+      return pytz.utc
+    if offset:
+      return pytz.FixedOffset(offset/60)
+    return unknown
+
+  return tzinfos
+
+
+# Create a special alias for the all tzinfos
+tzinfos = tzinfos_create('all')
+
+
+# Create the abbreviations.
+# *WARNING*: Order matters!
+tzabbr_register("A", u"Alpha Time Zone", u"Military", "Etc/GMT-1", False)
+tzabbr_register("ACDT", u"Australian Central Daylight Time", u"Australia",
+                "Australia/Adelaide", True)
+tzabbr_register("ACST", u"Australian Central Standard Time", u"Australia",
+                "Australia/Adelaide", False)
+tzabbr_register("ADT", u"Atlantic Daylight Time", u"North America",
+                "America/Halifax", True)
+tzabbr_register("AEDT", u"Australian Eastern Daylight Time", u"Australia",
+                "Australia/Sydney", True)
+tzabbr_register("AEST", u"Australian Eastern Standard Time", u"Australia",
+                "Australia/Sydney", False)
+tzabbr_register("AKDT", u"Alaska Daylight Time", u"North America",
+                "US/Alaska", True)
+tzabbr_register("AKST", u"Alaska Standard Time", u"North America",
+                "US/Alaska", False)
+tzabbr_register("AST", u"Atlantic Standard Time", u"North America",
+                "America/Halifax", False)
+tzabbr_register("AWDT", u"Australian Western Daylight Time", u"Australia",
+                "Australia/West", True)
+tzabbr_register("AWST", u"Australian Western Standard Time", u"Australia",
+                "Australia/West", False)
+tzabbr_register("B", u"Bravo Time Zone", u"Military", "Etc/GMT-2", False)
+tzabbr_register("BST", u"British Summer Time", u"Europe", "Europe/London", True)
+tzabbr_register("C", u"Charlie Time Zone", u"Military", "Etc/GMT-2", False)
+tzabbr_register("CDT", u"Central Daylight Time", u"North America",
+                "US/Central", True)
+tzabbr_register("CEDT", u"Central European Daylight Time", u"Europe",
+                "Etc/GMT+2", True)
+tzabbr_register("CEST", u"Central European Summer Time", u"Europe",
+                "Etc/GMT+2", True)
+tzabbr_register("CET", u"Central European Time", u"Europe", "Etc/GMT+1", False)
+tzabbr_register("CST", u"Central Standard Time", u"North America",
+                "US/Central", False)
+tzabbr_register("CXT", u"Christmas Island Time", u"Australia",
+                "Indian/Christmas", False)
+tzabbr_register("D", u"Delta Time Zone", u"Military", "Etc/GMT-2", False)
+tzabbr_register("E", u"Echo Time Zone", u"Military", "Etc/GMT-2", False)
+tzabbr_register("EDT", u"Eastern Daylight Time", u"North America",
+                "US/Eastern", True)
+tzabbr_register("EEDT", u"Eastern European Daylight Time", u"Europe",
+                "Etc/GMT+3", True)
+tzabbr_register("EEST", u"Eastern European Summer Time", u"Europe",
+                "Etc/GMT+3", True)
+tzabbr_register("EET", u"Eastern European Time", u"Europe", "Etc/GMT+2", False)
+tzabbr_register("EST", u"Eastern Standard Time", u"North America",
+                "US/Eastern", False)
+tzabbr_register("F", u"Foxtrot Time Zone", u"Military", "Etc/GMT-6", False)
+tzabbr_register("G", u"Golf Time Zone", u"Military", "Etc/GMT-7", False)
+tzabbr_register("GMT", u"Greenwich Mean Time", u"Europe", pytz.utc, False)
+tzabbr_register("H", u"Hotel Time Zone", u"Military", "Etc/GMT-8", False)
+#tzabbr_register("HAA", u"Heure Avancée de l'Atlantique", u"North America", u"UTC - 3 hours")
+#tzabbr_register("HAC", u"Heure Avancée du Centre", u"North America", u"UTC - 5 hours")
+tzabbr_register("HADT", u"Hawaii-Aleutian Daylight Time", u"North America",
+                "Pacific/Honolulu", True)
+#tzabbr_register("HAE", u"Heure Avancée de l'Est", u"North America", u"UTC - 4 hours")
+#tzabbr_register("HAP", u"Heure Avancée du Pacifique", u"North America", u"UTC - 7 hours")
+#tzabbr_register("HAR", u"Heure Avancée des Rocheuses", u"North America", u"UTC - 6 hours")
+tzabbr_register("HAST", u"Hawaii-Aleutian Standard Time", u"North America",
+                "Pacific/Honolulu", False)
+#tzabbr_register("HAT", u"Heure Avancée de Terre-Neuve", u"North America", u"UTC - 2:30 hours")
+#tzabbr_register("HAY", u"Heure Avancée du Yukon", u"North America", u"UTC - 8 hours")
+tzabbr_register("HDT", u"Hawaii Daylight Time", u"North America",
+                "Pacific/Honolulu", True)
+#tzabbr_register("HNA", u"Heure Normale de l'Atlantique", u"North America", u"UTC - 4 hours")
+#tzabbr_register("HNC", u"Heure Normale du Centre", u"North America", u"UTC - 6 hours")
+#tzabbr_register("HNE", u"Heure Normale de l'Est", u"North America", u"UTC - 5 hours")
+#tzabbr_register("HNP", u"Heure Normale du Pacifique", u"North America", u"UTC - 8 hours")
+#tzabbr_register("HNR", u"Heure Normale des Rocheuses", u"North America", u"UTC - 7 hours")
+#tzabbr_register("HNT", u"Heure Normale de Terre-Neuve", u"North America", u"UTC - 3:30 hours")
+#tzabbr_register("HNY", u"Heure Normale du Yukon", u"North America", u"UTC - 9 hours")
+tzabbr_register("HST", u"Hawaii Standard Time", u"North America",
+                "Pacific/Honolulu", False)
+tzabbr_register("I", u"India Time Zone", u"Military", "Etc/GMT-9", False)
+tzabbr_register("IST", u"Irish Summer Time", u"Europe", "Europe/Dublin", True)
+tzabbr_register("K", u"Kilo Time Zone", u"Military", "Etc/GMT-10", False)
+tzabbr_register("L", u"Lima Time Zone", u"Military", "Etc/GMT-11", False)
+tzabbr_register("M", u"Mike Time Zone", u"Military", "Etc/GMT-12", False)
+tzabbr_register("MDT", u"Mountain Daylight Time", u"North America",
+                "US/Mountain", True)
+#tzabbr_register("MESZ", u"Mitteleuroäische Sommerzeit", u"Europe", u"UTC + 2 hours")
+#tzabbr_register("MEZ", u"Mitteleuropäische Zeit", u"Europe", u"UTC + 1 hour")
+tzabbr_register("MSD", u"Moscow Daylight Time", u"Europe",
+                "Europe/Moscow", True)
+tzabbr_register("MSK", u"Moscow Standard Time", u"Europe",
+                "Europe/Moscow", False)
+tzabbr_register("MST", u"Mountain Standard Time", u"North America",
+                "US/Mountain", False)
+tzabbr_register("N", u"November Time Zone", u"Military", "Etc/GMT+1", False)
+tzabbr_register("NDT", u"Newfoundland Daylight Time", u"North America",
+                "America/St_Johns", True)
+tzabbr_register("NFT", u"Norfolk (Island) Time", u"Australia",
+                "Pacific/Norfolk", False)
+tzabbr_register("NST", u"Newfoundland Standard Time", u"North America",
+                "America/St_Johns", False)
+tzabbr_register("O", u"Oscar Time Zone", u"Military", "Etc/GMT+2", False)
+tzabbr_register("P", u"Papa Time Zone", u"Military", "Etc/GMT+3", False)
+tzabbr_register("PDT", u"Pacific Daylight Time", u"North America",
+                "US/Pacific", True)
+tzabbr_register("PST", u"Pacific Standard Time", u"North America",
+                "US/Pacific", False)
+tzabbr_register("Q", u"Quebec Time Zone", u"Military", "Etc/GMT+4", False)
+tzabbr_register("R", u"Romeo Time Zone", u"Military", "Etc/GMT+5", False)
+tzabbr_register("S", u"Sierra Time Zone", u"Military", "Etc/GMT+6", False)
+tzabbr_register("T", u"Tango Time Zone", u"Military", "Etc/GMT+7", False)
+tzabbr_register("U", u"Uniform Time Zone", u"Military", "Etc/GMT+8", False)
+tzabbr_register("UTC", u"Coordinated Universal Time", u"Europe",
+                pytz.utc, False)
+tzabbr_register("V", u"Victor Time Zone", u"Military", "Etc/GMT+9", False)
+tzabbr_register("W", u"Whiskey Time Zone", u"Military", "Etc/GMT+10", False)
+tzabbr_register("WDT", u"Western Daylight Time", u"Australia",
+                "Australia/West", True)
+tzabbr_register("WEDT", u"Western European Daylight Time", u"Europe",
+                "Etc/GMT+1", True)
+tzabbr_register("WEST", u"Western European Summer Time", u"Europe",
+                "Etc/GMT+1", True)
+tzabbr_register("WET", u"Western European Time", u"Europe", pytz.utc, False)
+tzabbr_register("WST", u"Western Standard Time", u"Australia",
+                "Australia/West", False)
+tzabbr_register("X", u"X-ray Time Zone", u"Military", "Etc/GMT+11", False)
+tzabbr_register("Y", u"Yankee Time Zone", u"Military", "Etc/GMT+12", False)
+tzabbr_register("Z", u"Zulu Time Zone", u"Military", pytz.utc, False)

design.md

@@ -0,0 +1,193 @@
+Structure
+---------
+nilmdb.nilmdb is the NILM database interface.  It tracks a PyTables
+database holds actual rows of data, and a SQL database tracks metadata
+and ranges.
+
+Access to the nilmdb must be single-threaded.  This is handled with
+the nilmdb.serializer class.
+
+nilmdb.server is a HTTP server that provides an interface to talk,
+thorugh the serialization layer, to the nilmdb object.
+
+nilmdb.client is a HTTP client that connects to this.
+
+Sqlite performance
+------------------
+
+Committing a transaction in the default sync mode (PRAGMA synchronous=FULL)
+takes about 125msec.  sqlite3 will commit transactions at 3 times:
+
+  1: explicit con.commit()
+
+  2: between a series of DML commands and non-DML commands, e.g.
+   after a series of INSERT, SELECT, but before a CREATE TABLE or
+   PRAGMA.
+
+3: at the end of an explicit transaction, e.g. "with self.con as con:"
+
+To speed up testing, or if this transaction speed becomes an issue,
+the sync=False option to NilmDB will set PRAGMA synchronous=OFF.
+
+
+Inserting streams
+-----------------
+
+We need to send the contents of "data" as POST.  Do we need chunked
+transfer?
+
+- Don't know the size in advance, so we would need to use chunked if
+  we send the entire thing in one request.
+- But we shouldn't send one chunk per line, so we need to buffer some
+  anyway; why not just make new requests?
+- Consider the infinite-streaming case, we might want to send it
+  immediately?  Not really -- server still should do explicit inserts
+  of fixed-size chunks.
+- Even chunked encoding needs the size of each chunk beforehand, so
+  everything still gets buffered.  Just a tradeoff of buffer size.
+
+Before timestamps are added:
+- Raw data is about 440 kB/s    (9 channels)
+- Prep data is about 12.5 kB/s  (1 phase)
+- How do we know how much data to send?
+
+  - Remember that we can only do maybe 8-50 transactions per second on
+    the sqlite database.  So if one block of inserted data is one
+    transaction, we'd need the raw case to be around 64kB per request,
+	ideally more.
+  - Maybe use a range, based on how long it's taking to read the data
+    - If no more data, send it
+    - If data > 1 MB, send it
+	- If more than 10 seconds have elapsed, send it
+  - Should those numbers come from the server?
+
+Converting from ASCII to PyTables:
+- For each row getting added, we need to set attributes on a PyTables
+  Row object and call table.append().  This means that there isn't a
+  particularly efficient way of converting from ascii.
+- Could create a function like nilmdb.layout.Layout("foo".fillRow(asciiline)
+  - But this means we're doing parsing on the serialized side
+  - Let's keep parsing on the threaded server side so we can detect
+    errors better, and not block the serialized nilmdb for a slow
+    parsing process.
+- Client sends ASCII data
+- Server converts this ACSII data to a list of values
+  - Maybe:
+
+		# threaded side creates this object
+		parser = nilmdb.layout.Parser("layout_name")
+		# threaded side parses and fills it with data
+		parser.parse(textdata)
+		# serialized side pulls out rows
+		for n in xrange(parser.nrows):
+		    parser.fill_row(rowinstance, n)
+			table.append()
+
+
+Inserting streams, inside nilmdb
+--------------------------------
+
+- First check that the new stream doesn't overlap.
+  - Get minimum timestamp, maximum timestamp from data parser.
+    - (extend parser to verify monotonicity and track extents)
+  - Get all intervals for this stream in the database
+  - See if new interval overlaps any existing ones
+    - If so, bail
+  - Question: should we cache intervals inside NilmDB?
+    - Assume database is fast for now, and always rebuild fom DB.
+	- Can add a caching layer later if we need to.
+  - `stream_get_ranges(path)` -> return IntervalSet?
+
+Speed
+-----
+
+- First approach was quadratic.  Adding four hours of data:
+
+    $ time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s 20110513-110000 /bpnilm/1/raw
+	real    24m31.093s
+	$ time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s 20110513-120001 /bpnilm/1/raw
+	real    43m44.528s
+	$ time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s 20110513-130002 /bpnilm/1/raw
+	real    93m29.713s
+	$ time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s 20110513-140003 /bpnilm/1/raw
+	real    166m53.007s
+
+- Disabling pytables indexing didn't help:
+
+    real    31m21.492s
+	real    52m51.963s
+	real    102m8.151s
+	real    176m12.469s
+
+- Server RAM usage is constant.
+
+- Speed problems were due to IntervalSet speed, of parsing intervals
+  from the database and adding the new one each time.
+
+  - First optimization is to cache result of `nilmdb:_get_intervals`,
+    which gives the best speedup.
+
+  - Also switched to internally using bxInterval from bx-python package.
+    Speed of `tests/test_interval:TestIntervalSpeed` is pretty decent
+	and seems to be growing logarithmically now.  About 85μs per insertion
+	for inserting 131k entries.
+
+  - Storing the interval data in SQL might be better, with a scheme like:
+    http://www.logarithmic.net/pfh/blog/01235197474
+
+- Next slowdown target is nilmdb.layout.Parser.parse().
+  - Rewrote parsers using cython and sscanf
+  - Stats (rev 10831), with _add_interval disabled
+     layout.pyx.Parser.parse:128        6303 sec, 262k calls
+	 layout.pyx.parse:63               13913 sec, 5.1g calls
+	 numpy:records.py.fromrecords:569   7410 sec, 262k calls
+  - Probably OK for now.
+
+IntervalSet speed
+-----------------
+- Initial implementation was pretty slow, even with binary search in
+  sorted list
+
+- Replaced with bxInterval; now takes about log n time for an insertion
+  - TestIntervalSpeed with range(17,18) and profiling
+    - 85 μs each
+    - 131072 calls to `__iadd__`
+    - 131072 to bx.insert_interval
+    - 131072 to bx.insert:395
+    - 2355835 to bx.insert:106  (18x as many?)
+
+- Tried blist too, worse than bxinterval.
+
+- Might be algorithmic improvements to be made in Interval.py,
+  like in `__and__`
+
+- Replaced again with rbtree.  Seems decent.  Numbers are time per
+  insert for 2**17 insertions, followed by total wall time and RAM
+  usage for running "make test" with `test_rbtree` and `test_interval`
+  with range(5,20):
+  - old values with bxinterval:
+    20.2 μS, total 20 s, 177 MB RAM
+  - rbtree, plain python:
+    97 μS, total 105 s, 846 MB RAM
+  - rbtree converted to cython:
+    26 μS, total 29 s, 320 MB RAM
+  - rbtree and interval converted to cython:
+    8.4 μS, total 12 s, 134 MB RAM
+
+Layouts
+-------
+Current/old design has specific layouts: RawData, PrepData, RawNotchedData.
+Let's get rid of this entirely and switch to simpler data types that are
+just collections and counts of a single type.  We'll still use strings
+to describe them, with format:
+
+    type_count
+
+where type is "uint16", "float32", or "float64", and count is an integer.
+
+nilmdb.layout.named() will parse these strings into the appropriate
+handlers.  For compatibility:
+
+    "RawData" == "uint16_6"
+    "RawNotchedData" == "uint16_9"
+    "PrepData" == "float32_8"

nilmdb/RedBlackTree.cc

@@ -0,0 +1,605 @@
+
+
+
+// The RedBlackEntry class is an Abstract Base Class.  This means that no
+// instance of the RedBlackEntry class can exist.  Only classes which
+// inherit from the RedBlackEntry class can exist.  Furthermore any class
+// which inherits from the RedBlackEntry class must define the member
+// function GetKey().  The Print() member function does not have to
+// be defined because a default definition exists.
+//
+// The GetKey() function should return an integer key for that entry.
+// The key for an entry should never change otherwise bad things might occur.
+
+class RedBlackEntry {
+public:
+  RedBlackEntry();
+  virtual ~RedBlackEntry();
+  virtual int GetKey() const = 0;
+  virtual void Print() const;
+};
+
+class RedBlackTreeNode {
+  friend class RedBlackTree;
+public:
+  void Print(RedBlackTreeNode*,
+	     RedBlackTreeNode*) const;
+  RedBlackTreeNode();
+  RedBlackTreeNode(RedBlackEntry *);
+  RedBlackEntry * GetEntry() const;
+  ~RedBlackTreeNode();
+protected:
+  RedBlackEntry * storedEntry;
+  int key;
+  int red; /* if red=0 then the node is black */
+  RedBlackTreeNode * left;
+  RedBlackTreeNode * right;
+  RedBlackTreeNode * parent;
+};
+
+
+
+class RedBlackTree {
+public:
+  RedBlackTree();
+  ~RedBlackTree();
+  void Print() const;
+  RedBlackEntry * DeleteNode(RedBlackTreeNode *);
+  RedBlackTreeNode * Insert(RedBlackEntry *);
+  RedBlackTreeNode * GetPredecessorOf(RedBlackTreeNode *) const;
+  RedBlackTreeNode * GetSuccessorOf(RedBlackTreeNode *) const;
+  RedBlackTreeNode * Search(int key);
+  TemplateStack<RedBlackTreeNode *> * Enumerate(int low, int high) ;
+  void CheckAssumptions() const;
+protected:
+  /*  A sentinel is used for root and for nil.  These sentinels are */
+  /*  created when RedBlackTreeCreate is caled.  root->left should always */
+  /*  point to the node which is the root of the tree.  nil points to a */
+  /*  node which should always be black but has aribtrary children and */
+  /*  parent and no key or info.  The point of using these sentinels is so */
+  /*  that the root and nil nodes do not require special cases in the code */
+  RedBlackTreeNode * root;
+  RedBlackTreeNode * nil;
+  void LeftRotate(RedBlackTreeNode *);
+  void RightRotate(RedBlackTreeNode *);
+  void TreeInsertHelp(RedBlackTreeNode *);
+  void TreePrintHelper(RedBlackTreeNode *) const;
+  void FixUpMaxHigh(RedBlackTreeNode *);
+  void DeleteFixUp(RedBlackTreeNode *);
+};
+
+const int MIN_INT=-MAX_INT;
+
+RedBlackTreeNode::RedBlackTreeNode(){
+};
+
+RedBlackTreeNode::RedBlackTreeNode(RedBlackEntry * newEntry)
+  : storedEntry (newEntry) , key(newEntry->GetKey()) {
+};
+
+RedBlackTreeNode::~RedBlackTreeNode(){
+};
+
+RedBlackEntry * RedBlackTreeNode::GetEntry() const {return storedEntry;}
+
+RedBlackEntry::RedBlackEntry(){
+};
+RedBlackEntry::~RedBlackEntry(){
+};
+void RedBlackEntry::Print() const {
+  cout << "No Print Method defined. Using Default: " << GetKey() << endl;
+}
+
+RedBlackTree::RedBlackTree()
+{
+  nil = new RedBlackTreeNode;
+  nil->left = nil->right = nil->parent = nil;
+  nil->red = 0;
+  nil->key = MIN_INT;
+  nil->storedEntry = NULL;
+
+  root = new RedBlackTreeNode;
+  root->parent = root->left = root->right = nil;
+  root->key = MAX_INT;
+  root->red=0;
+  root->storedEntry = NULL;
+}
+
+/***********************************************************************/
+/*  FUNCTION:  LeftRotate */
+/**/
+/*  INPUTS:  the node to rotate on */
+/**/
+/*  OUTPUT:  None */
+/**/
+/*  Modifies Input: this, x */
+/**/
+/*  EFFECTS:  Rotates as described in _Introduction_To_Algorithms by */
+/*            Cormen, Leiserson, Rivest (Chapter 14).  Basically this */
+/*            makes the parent of x be to the left of x, x the parent of */
+/*            its parent before the rotation and fixes other pointers */
+/*            accordingly.  */
+/***********************************************************************/
+
+void RedBlackTree::LeftRotate(RedBlackTreeNode* x) {
+  RedBlackTreeNode* y;
+
+  /*  I originally wrote this function to use the sentinel for */
+  /*  nil to avoid checking for nil.  However this introduces a */
+  /*  very subtle bug because sometimes this function modifies */
+  /*  the parent pointer of nil.  This can be a problem if a */
+  /*  function which calls LeftRotate also uses the nil sentinel */
+  /*  and expects the nil sentinel's parent pointer to be unchanged */
+  /*  after calling this function.  For example, when DeleteFixUP */
+  /*  calls LeftRotate it expects the parent pointer of nil to be */
+  /*  unchanged. */
+
+  y=x->right;
+  x->right=y->left;
+
+  if (y->left != nil) y->left->parent=x; /* used to use sentinel here */
+  /* and do an unconditional assignment instead of testing for nil */
+
+  y->parent=x->parent;
+
+  /* instead of checking if x->parent is the root as in the book, we */
+  /* count on the root sentinel to implicitly take care of this case */
+  if( x == x->parent->left) {
+    x->parent->left=y;
+  } else {
+    x->parent->right=y;
+  }
+  y->left=x;
+  x->parent=y;
+}
+
+/***********************************************************************/
+/*  FUNCTION:  RighttRotate */
+/**/
+/*  INPUTS:  node to rotate on */
+/**/
+/*  OUTPUT:  None */
+/**/
+/*  Modifies Input?: this, y */
+/**/
+/*  EFFECTS:  Rotates as described in _Introduction_To_Algorithms by */
+/*            Cormen, Leiserson, Rivest (Chapter 14).  Basically this */
+/*            makes the parent of x be to the left of x, x the parent of */
+/*            its parent before the rotation and fixes other pointers */
+/*            accordingly.  */
+/***********************************************************************/
+
+void RedBlackTree::RightRotate(RedBlackTreeNode* y) {
+  RedBlackTreeNode* x;
+
+  /*  I originally wrote this function to use the sentinel for */
+  /*  nil to avoid checking for nil.  However this introduces a */
+  /*  very subtle bug because sometimes this function modifies */
+  /*  the parent pointer of nil.  This can be a problem if a */
+  /*  function which calls LeftRotate also uses the nil sentinel */
+  /*  and expects the nil sentinel's parent pointer to be unchanged */
+  /*  after calling this function.  For example, when DeleteFixUP */
+  /*  calls LeftRotate it expects the parent pointer of nil to be */
+  /*  unchanged. */
+
+  x=y->left;
+  y->left=x->right;
+
+  if (nil != x->right)  x->right->parent=y; /*used to use sentinel here */
+  /* and do an unconditional assignment instead of testing for nil */
+
+  /* instead of checking if x->parent is the root as in the book, we */
+  /* count on the root sentinel to implicitly take care of this case */
+  x->parent=y->parent;
+  if( y == y->parent->left) {
+    y->parent->left=x;
+  } else {
+    y->parent->right=x;
+  }
+  x->right=y;
+  y->parent=x;
+}
+
+/***********************************************************************/
+/*  FUNCTION:  TreeInsertHelp  */
+/**/
+/*  INPUTS:  z is the node to insert */
+/**/
+/*  OUTPUT:  none */
+/**/
+/*  Modifies Input:  this, z */
+/**/
+/*  EFFECTS:  Inserts z into the tree as if it were a regular binary tree */
+/*            using the algorithm described in _Introduction_To_Algorithms_ */
+/*            by Cormen et al.  This funciton is only intended to be called */
+/*            by the Insert function and not by the user */
+/***********************************************************************/
+
+void RedBlackTree::TreeInsertHelp(RedBlackTreeNode* z) {
+  /*  This function should only be called by RedBlackTree::Insert */
+  RedBlackTreeNode* x;
+  RedBlackTreeNode* y;
+
+  z->left=z->right=nil;
+  y=root;
+  x=root->left;
+  while( x != nil) {
+    y=x;
+    if ( x->key > z->key) {
+      x=x->left;
+    } else { /* x->key <= z->key */
+      x=x->right;
+    }
+  }
+  z->parent=y;
+  if ( (y == root) ||
+       (y->key > z->key) ) {
+    y->left=z;
+  } else {
+    y->right=z;
+  }
+}
+
+/*  Before calling InsertNode  the node x should have its key set */
+
+/***********************************************************************/
+/*  FUNCTION:  InsertNode */
+/**/
+/*  INPUTS:  newEntry is the entry to insert*/
+/**/
+/*  OUTPUT:  This function returns a pointer to the newly inserted node */
+/*           which is guarunteed to be valid until this node is deleted. */
+/*           What this means is if another data structure stores this */
+/*           pointer then the tree does not need to be searched when this */
+/*           is to be deleted. */
+/**/
+/*  Modifies Input: tree */
+/**/
+/*  EFFECTS:  Creates a node node which contains the appropriate key and */
+/*            info pointers and inserts it into the tree. */
+/***********************************************************************/
+/* jim */
+RedBlackTreeNode * RedBlackTree::Insert(RedBlackEntry * newEntry)
+{
+  RedBlackTreeNode * y;
+  RedBlackTreeNode * x;
+  RedBlackTreeNode * newNode;
+
+  x = new RedBlackTreeNode(newEntry);
+  TreeInsertHelp(x);
+  newNode = x;
+  x->red=1;
+  while(x->parent->red) { /* use sentinel instead of checking for root */
+    if (x->parent == x->parent->parent->left) {
+      y=x->parent->parent->right;
+      if (y->red) {
+	x->parent->red=0;
+	y->red=0;
+	x->parent->parent->red=1;
+	x=x->parent->parent;
+      } else {
+	if (x == x->parent->right) {
+	  x=x->parent;
+	  LeftRotate(x);
+	}
+	x->parent->red=0;
+	x->parent->parent->red=1;
+	RightRotate(x->parent->parent);
+      }
+    } else { /* case for x->parent == x->parent->parent->right */
+             /* this part is just like the section above with */
+             /* left and right interchanged */
+      y=x->parent->parent->left;
+      if (y->red) {
+	x->parent->red=0;
+	y->red=0;
+	x->parent->parent->red=1;
+	x=x->parent->parent;
+      } else {
+	if (x == x->parent->left) {
+	  x=x->parent;
+	  RightRotate(x);
+	}
+	x->parent->red=0;
+	x->parent->parent->red=1;
+	LeftRotate(x->parent->parent);
+      }
+    }
+  }
+  root->left->red=0;
+  return(newNode);
+}
+
+/***********************************************************************/
+/*  FUNCTION:  GetSuccessorOf  */
+/**/
+/*    INPUTS:  x is the node we want the succesor of */
+/**/
+/*    OUTPUT:  This function returns the successor of x or NULL if no */
+/*             successor exists. */
+/**/
+/*    Modifies Input: none */
+/**/
+/*    Note:  uses the algorithm in _Introduction_To_Algorithms_ */
+/***********************************************************************/
+
+RedBlackTreeNode * RedBlackTree::GetSuccessorOf(RedBlackTreeNode * x) const
+{
+  RedBlackTreeNode* y;
+
+  if (nil != (y = x->right)) { /* assignment to y is intentional */
+    while(y->left != nil) { /* returns the minium of the right subtree of x */
+      y=y->left;
+    }
+    return(y);
+  } else {
+    y=x->parent;
+    while(x == y->right) { /* sentinel used instead of checking for nil */
+      x=y;
+      y=y->parent;
+    }
+    if (y == root) return(nil);
+    return(y);
+  }
+}
+
+/***********************************************************************/
+/*  FUNCTION:  GetPredecessorOf  */
+/**/
+/*    INPUTS:  x is the node to get predecessor of */
+/**/
+/*    OUTPUT:  This function returns the predecessor of x or NULL if no */
+/*             predecessor exists. */
+/**/
+/*    Modifies Input: none */
+/**/
+/*    Note:  uses the algorithm in _Introduction_To_Algorithms_ */
+/***********************************************************************/
+
+RedBlackTreeNode * RedBlackTree::GetPredecessorOf(RedBlackTreeNode * x) const {
+  RedBlackTreeNode* y;
+
+  if (nil != (y = x->left)) { /* assignment to y is intentional */
+    while(y->right != nil) { /* returns the maximum of the left subtree of x */
+      y=y->right;
+    }
+    return(y);
+  } else {
+    y=x->parent;
+    while(x == y->left) {
+      if (y == root) return(nil);
+      x=y;
+      y=y->parent;
+    }
+    return(y);
+  }
+}
+
+/***********************************************************************/
+/*  FUNCTION:  Print */
+/**/
+/*    INPUTS:  none */
+/**/
+/*    OUTPUT:  none  */
+/**/
+/*    EFFECTS:  This function recursively prints the nodes of the tree */
+/*              inorder. */
+/**/
+/*    Modifies Input: none */
+/**/
+/*    Note:    This function should only be called from ITTreePrint */
+/***********************************************************************/
+
+void RedBlackTreeNode::Print(RedBlackTreeNode * nil,
+			     RedBlackTreeNode * root) const {
+  storedEntry->Print();
+  printf(", key=%i ",key);
+  printf("  l->key=");
+  if( left == nil) printf("NULL"); else printf("%i",left->key);
+  printf("  r->key=");
+  if( right == nil) printf("NULL"); else printf("%i",right->key);
+  printf("  p->key=");
+  if( parent == root) printf("NULL"); else printf("%i",parent->key);
+  printf("  red=%i\n",red);
+}
+
+void RedBlackTree::TreePrintHelper( RedBlackTreeNode* x) const {
+
+  if (x != nil) {
+    TreePrintHelper(x->left);
+    x->Print(nil,root);
+    TreePrintHelper(x->right);
+  }
+}
+
+/***********************************************************************/
+/*  FUNCTION:  Print */
+/**/
+/*    INPUTS:  none */
+/**/
+/*    OUTPUT:  none */
+/**/
+/*    EFFECT:  This function recursively prints the nodes of the tree */
+/*             inorder. */
+/**/
+/*    Modifies Input: none */
+/**/
+/***********************************************************************/
+
+void RedBlackTree::Print() const {
+  TreePrintHelper(root->left);
+}
+
+/***********************************************************************/
+/*  FUNCTION:  DeleteFixUp */
+/**/
+/*    INPUTS:  x is the child of the spliced */
+/*             out node in DeleteNode. */
+/**/
+/*    OUTPUT:  none */
+/**/
+/*    EFFECT:  Performs rotations and changes colors to restore red-black */
+/*             properties after a node is deleted */
+/**/
+/*    Modifies Input: this, x */
+/**/
+/*    The algorithm from this function is from _Introduction_To_Algorithms_ */
+/***********************************************************************/
+
+void RedBlackTree::DeleteFixUp(RedBlackTreeNode* x) {
+  RedBlackTreeNode * w;
+  RedBlackTreeNode * rootLeft = root->left;
+
+  while( (!x->red) && (rootLeft != x)) {
+    if (x == x->parent->left) {
+
+//
+      w=x->parent->right;
+      if (w->red) {
+	w->red=0;
+	x->parent->red=1;
+	LeftRotate(x->parent);
+	w=x->parent->right;
+      }
+      if ( (!w->right->red) && (!w->left->red) ) {
+	w->red=1;
+	x=x->parent;
+      } else {
+	if (!w->right->red) {
+	  w->left->red=0;
+	  w->red=1;
+	  RightRotate(w);
+	  w=x->parent->right;
+	}
+	w->red=x->parent->red;
+	x->parent->red=0;
+	w->right->red=0;
+	LeftRotate(x->parent);
+	x=rootLeft; /* this is to exit while loop */
+      }
+//
+
+    } else { /* the code below is has left and right switched from above */
+      w=x->parent->left;
+      if (w->red) {
+	w->red=0;
+	x->parent->red=1;
+	RightRotate(x->parent);
+	w=x->parent->left;
+      }
+      if ( (!w->right->red) && (!w->left->red) ) {
+	w->red=1;
+	x=x->parent;
+      } else {
+	if (!w->left->red) {
+	  w->right->red=0;
+	  w->red=1;
+	  LeftRotate(w);
+	  w=x->parent->left;
+	}
+	w->red=x->parent->red;
+	x->parent->red=0;
+	w->left->red=0;
+	RightRotate(x->parent);
+	x=rootLeft; /* this is to exit while loop */
+      }
+    }
+  }
+  x->red=0;
+
+}
+
+
+/***********************************************************************/
+/*  FUNCTION:  DeleteNode */
+/**/
+/*    INPUTS:  tree is the tree to delete node z from */
+/**/
+/*    OUTPUT:  returns the RedBlackEntry stored at deleted node */
+/**/
+/*    EFFECT:  Deletes z from tree and but don't call destructor */
+/**/
+/*    Modifies Input:  z */
+/**/
+/*    The algorithm from this function is from _Introduction_To_Algorithms_ */
+/***********************************************************************/
+
+RedBlackEntry * RedBlackTree::DeleteNode(RedBlackTreeNode * z){
+  RedBlackTreeNode* y;
+  RedBlackTreeNode* x;
+  RedBlackEntry * returnValue = z->storedEntry;
+
+  y= ((z->left == nil) || (z->right == nil)) ? z : GetSuccessorOf(z);
+  x= (y->left == nil) ? y->right : y->left;
+  if (root == (x->parent = y->parent)) { /* assignment of y->p to x->p is intentional */
+    root->left=x;
+  } else {
+    if (y == y->parent->left) {
+      y->parent->left=x;
+    } else {
+      y->parent->right=x;
+    }
+  }
+  if (y != z) { /* y should not be nil in this case */
+
+    /* y is the node to splice out and x is its child */
+
+    y->left=z->left;
+    y->right=z->right;
+    y->parent=z->parent;
+    z->left->parent=z->right->parent=y;
+    if (z == z->parent->left) {
+      z->parent->left=y;
+    } else {
+      z->parent->right=y;
+    }
+    if (!(y->red)) {
+      y->red = z->red;
+      DeleteFixUp(x);
+    } else
+      y->red = z->red;
+    delete z;
+  } else {
+    if (!(y->red)) DeleteFixUp(x);
+    delete y;
+  }
+  return returnValue;
+}
+
+
+/***********************************************************************/
+/*  FUNCTION:  Enumerate */
+/**/
+/*    INPUTS:  tree is the tree to look for keys between [low,high] */
+/**/
+/*    OUTPUT:  stack containing pointers to the nodes between [low,high] */
+/**/
+/*    Modifies Input: none */
+/**/
+/*    EFFECT:  Returns a stack containing pointers to nodes containing */
+/*             keys which in [low,high]/ */
+/**/
+/***********************************************************************/
+
+TemplateStack<RedBlackTreeNode *> * RedBlackTree::Enumerate(int low,
+							    int high)  {
+  TemplateStack<RedBlackTreeNode *> * enumResultStack =
+    new TemplateStack<RedBlackTreeNode *>(4);
+
+  RedBlackTreeNode* x=root->left;
+  RedBlackTreeNode* lastBest=NULL;
+
+  while(nil != x) {
+    if ( x->key > high ) {
+      x=x->left;
+    } else {
+      lastBest=x;
+      x=x->right;
+    }
+  }
+  while ( (lastBest) && (low <= lastBest->key) ) {
+    enumResultStack->Push(lastBest);
+    lastBest=GetPredecessorOf(lastBest);
+  }
+  return(enumResultStack);
+}

nilmdb/__init__.py

@@ -1,2 +1,16 @@
-from nilmdb.interval import *
-from nilmdb.fileinterval import *
+"""Main NilmDB import"""
+
+from .nilmdb import NilmDB
+from .server import Server
+from .client import Client
+from .timer import Timer
+
+import cmdline
+
+import pyximport; pyximport.install()
+import layout
+
+import serializer
+import timestamper
+import interval
+import du

nilmdb/bxintersect.pyx

@@ -0,0 +1,495 @@
+# cython: profile=False
+# This is from bx-python 554:07aca5a9f6fc (BSD licensed), modified to
+# store interval ranges as doubles rather than 32-bit integers.
+
+"""
+Data structure for performing intersect queries on a set of intervals which
+preserves all information about the intervals (unlike bitset projection methods).
+
+:Authors: James Taylor (james@jamestaylor.org),
+          Ian Schenk (ian.schenck@gmail.com),
+          Brent Pedersen (bpederse@gmail.com)
+"""
+
+# Historical note:
+#    This module original contained an implementation based on sorted endpoints
+#    and a binary search, using an idea from Scott Schwartz and Piotr Berman.
+#    Later an interval tree implementation was implemented by Ian for Galaxy's
+#    join tool (see `bx.intervals.operations.quicksect.py`). This was then
+#    converted to Cython by Brent, who also added support for
+#    upstream/downstream/neighbor queries. This was modified by James to
+#    handle half-open intervals strictly, to maintain sort order, and to
+#    implement the same interface as the original Intersecter.
+
+#cython: cdivision=True
+
+import operator
+
+cdef extern from "stdlib.h":
+    int ceil(float f)
+    float log(float f)
+    int RAND_MAX
+    int rand()
+    int strlen(char *)
+    int iabs(int)
+
+cdef inline double dmax2(double a, double b):
+    if b > a: return b
+    return a
+
+cdef inline double dmax3(double a, double b, double c):
+    if b > a:
+        if c > b:
+            return c
+        return b
+    if a > c:
+        return a
+    return c
+
+cdef inline double dmin3(double a, double b, double c):
+    if b < a:
+        if c < b:
+            return c
+        return b
+    if a < c:
+        return a
+    return c
+
+cdef inline double dmin2(double a, double b):
+    if b < a: return b
+    return a
+
+cdef float nlog = -1.0 / log(0.5)
+
+cdef class IntervalNode:
+    """
+    A single node of an `IntervalTree`.
+
+    NOTE: Unless you really know what you are doing, you probably should us
+          `IntervalTree` rather than using this directly.
+    """
+    cdef float priority
+    cdef public object interval
+    cdef public double start, end
+    cdef double minend, maxend, minstart
+    cdef IntervalNode cleft, cright, croot
+
+    property left_node:
+        def __get__(self):
+            return self.cleft if self.cleft is not EmptyNode else None
+    property right_node:
+        def __get__(self):
+            return self.cright if self.cright is not EmptyNode else None
+    property root_node:
+        def __get__(self):
+            return self.croot if self.croot is not EmptyNode else None
+
+    def __repr__(self):
+        return "IntervalNode(%g, %g)" % (self.start, self.end)
+
+    def __cinit__(IntervalNode self, double start, double end, object interval):
+        # Python lacks the binomial distribution, so we convert a
+        # uniform into a binomial because it naturally scales with
+        # tree size.  Also, python's uniform is perfect since the
+        # upper limit is not inclusive, which gives us undefined here.
+        self.priority = ceil(nlog * log(-1.0/(1.0 * rand()/RAND_MAX - 1)))
+        self.start    = start
+        self.end      = end
+        self.interval = interval
+        self.maxend   = end
+        self.minstart = start
+        self.minend   = end
+        self.cleft    = EmptyNode
+        self.cright   = EmptyNode
+        self.croot    = EmptyNode
+
+    cpdef IntervalNode insert(IntervalNode self, double start, double end, object interval):
+        """
+        Insert a new IntervalNode into the tree of which this node is
+        currently the root. The return value is the new root of the tree (which
+        may or may not be this node!)
+        """
+        cdef IntervalNode croot = self
+        # If starts are the same, decide which to add interval to based on
+        # end, thus maintaining sortedness relative to start/end
+        cdef double decision_endpoint = start
+        if start == self.start:
+            decision_endpoint = end
+
+        if decision_endpoint > self.start:
+            # insert to cright tree
+            if self.cright is not EmptyNode:
+                self.cright = self.cright.insert( start, end, interval )
+            else:
+                self.cright = IntervalNode( start, end, interval )
+            # rebalance tree
+            if self.priority < self.cright.priority:
+                croot = self.rotate_left()
+        else:
+            # insert to cleft tree
+            if self.cleft is not EmptyNode:
+                self.cleft = self.cleft.insert( start, end, interval)
+            else:
+                self.cleft = IntervalNode( start, end, interval)
+            # rebalance tree
+            if self.priority < self.cleft.priority:
+                croot = self.rotate_right()
+
+        croot.set_ends()
+        self.cleft.croot  = croot
+        self.cright.croot = croot
+        return croot
+
+    cdef IntervalNode rotate_right(IntervalNode self):
+        cdef IntervalNode croot = self.cleft
+        self.cleft  = self.cleft.cright
+        croot.cright = self
+        self.set_ends()
+        return croot
+
+    cdef IntervalNode rotate_left(IntervalNode self):
+        cdef IntervalNode croot = self.cright
+        self.cright = self.cright.cleft
+        croot.cleft  = self
+        self.set_ends()
+        return croot
+
+    cdef inline void set_ends(IntervalNode self):
+        if self.cright is not EmptyNode and self.cleft is not EmptyNode:
+            self.maxend = dmax3(self.end, self.cright.maxend, self.cleft.maxend)
+            self.minend = dmin3(self.end, self.cright.minend, self.cleft.minend)
+            self.minstart = dmin3(self.start, self.cright.minstart, self.cleft.minstart)
+        elif self.cright is not EmptyNode:
+            self.maxend = dmax2(self.end, self.cright.maxend)
+            self.minend = dmin2(self.end, self.cright.minend)
+            self.minstart = dmin2(self.start, self.cright.minstart)
+        elif self.cleft is not EmptyNode:
+            self.maxend = dmax2(self.end, self.cleft.maxend)
+            self.minend = dmin2(self.end, self.cleft.minend)
+            self.minstart = dmin2(self.start, self.cleft.minstart)
+
+
+    def intersect( self, double start, double end, sort=True ):
+        """
+        given a start and a end, return a list of features
+        falling within that range
+        """
+        cdef list results = []
+        self._intersect( start, end, results )
+        if sort:
+            results = sorted(results)
+        return results
+
+    find = intersect
+
+    cdef void _intersect( IntervalNode self, double start, double end, list results):
+        # Left subtree
+        if self.cleft is not EmptyNode and self.cleft.maxend > start:
+            self.cleft._intersect( start, end, results )
+        # This interval
+        if ( self.end > start ) and ( self.start < end ):
+            results.append( self.interval )
+        # Right subtree
+        if self.cright is not EmptyNode and self.start < end:
+            self.cright._intersect( start, end, results )
+
+
+    cdef void _seek_left(IntervalNode self, double position, list results, int n, double max_dist):
+        # we know we can bail in these 2 cases.
+        if self.maxend + max_dist < position:
+            return
+        if self.minstart > position:
+            return
+
+        # the ordering of these 3 blocks makes it so the results are
+        # ordered nearest to farest from the query position
+        if self.cright is not EmptyNode:
+            self.cright._seek_left(position, results, n, max_dist)
+
+        if -1 < position - self.end < max_dist:
+            results.append(self.interval)
+
+        # TODO: can these conditionals be more stringent?
+        if self.cleft is not EmptyNode:
+                self.cleft._seek_left(position, results, n, max_dist)
+
+
+
+    cdef void _seek_right(IntervalNode self, double position, list results, int n, double max_dist):
+        # we know we can bail in these 2 cases.
+        if self.maxend < position: return
+        if self.minstart - max_dist > position: return
+
+        #print "SEEK_RIGHT:",self, self.cleft, self.maxend, self.minstart, position
+
+        # the ordering of these 3 blocks makes it so the results are
+        # ordered nearest to farest from the query position
+        if self.cleft is not EmptyNode:
+                self.cleft._seek_right(position, results, n, max_dist)
+
+        if -1 < self.start - position < max_dist:
+            results.append(self.interval)
+
+        if self.cright is not EmptyNode:
+                self.cright._seek_right(position, results, n, max_dist)
+
+
+    cpdef left(self, position, int n=1, double max_dist=2500):
+        """
+        find n features with a start > than `position`
+        f: a Interval object (or anything with an `end` attribute)
+        n: the number of features to return
+        max_dist: the maximum distance to look before giving up.
+        """
+        cdef list results = []
+        # use start - 1 becuase .left() assumes strictly left-of
+        self._seek_left( position - 1, results, n, max_dist )
+        if len(results) == n: return results
+        r = results
+        r.sort(key=operator.attrgetter('end'), reverse=True)
+        return r[:n]
+
+    cpdef right(self, position, int n=1, double max_dist=2500):
+        """
+        find n features with a end < than position
+        f: a Interval object (or anything with a `start` attribute)
+        n: the number of features to return
+        max_dist: the maximum distance to look before giving up.
+        """
+        cdef list results = []
+        # use end + 1 becuase .right() assumes strictly right-of
+        self._seek_right(position + 1, results, n, max_dist)
+        if len(results) == n: return results
+        r = results
+        r.sort(key=operator.attrgetter('start'))
+        return r[:n]
+
+    def traverse(self):
+        if self.cleft is not EmptyNode:
+            for node in self.cleft.traverse():
+                yield node
+        yield self.interval
+        if self.cright is not EmptyNode:
+            for node in self.cright.traverse():
+                yield node
+
+cdef IntervalNode EmptyNode = IntervalNode( 0, 0, Interval(0, 0))
+
+## ---- Wrappers that retain the old interface -------------------------------
+
+cdef class Interval:
+    """
+    Basic feature, with required integer start and end properties.
+    Also accepts optional strand as +1 or -1 (used for up/downstream queries),
+    a name, and any arbitrary data is sent in on the info keyword argument
+
+    >>> from bx.intervals.intersection import Interval
+
+    >>> f1 = Interval(23, 36)
+    >>> f2 = Interval(34, 48, value={'chr':12, 'anno':'transposon'})
+    >>> f2
+    Interval(34, 48, value={'anno': 'transposon', 'chr': 12})
+
+    """
+    cdef public double start, end
+    cdef public object value, chrom, strand
+
+    def __init__(self, double start, double end, object value=None, object chrom=None, object strand=None ):
+        assert start <= end, "start must be less than end"
+        self.start  = start
+        self.end   = end
+        self.value = value
+        self.chrom = chrom
+        self.strand = strand
+
+    def __repr__(self):
+        fstr = "Interval(%g, %g" % (self.start, self.end)
+        if not self.value is None:
+            fstr += ", value=" + str(self.value)
+        fstr += ")"
+        return fstr
+
+    def __richcmp__(self, other, op):
+        if op == 0:
+            # <
+            return self.start < other.start or self.end < other.end
+        elif op == 1:
+            # <=
+            return self == other or self < other
+        elif op == 2:
+            # ==
+            return self.start == other.start and self.end == other.end
+        elif op == 3:
+            # !=
+            return self.start != other.start or self.end != other.end
+        elif op == 4:
+            # >
+            return self.start > other.start or self.end > other.end
+        elif op == 5:
+            # >=
+            return self == other or self > other
+
+cdef class IntervalTree:
+    """
+    Data structure for performing window intersect queries on a set of
+    of possibly overlapping 1d intervals.
+
+    Usage
+    =====
+
+    Create an empty IntervalTree
+
+    >>> from bx.intervals.intersection import Interval, IntervalTree
+    >>> intersecter = IntervalTree()
+
+    An interval is a start and end position and a value (possibly None).
+    You can add any object as an interval:
+
+    >>> intersecter.insert( 0, 10, "food" )
+    >>> intersecter.insert( 3, 7, dict(foo='bar') )
+
+    >>> intersecter.find( 2, 5 )
+    ['food', {'foo': 'bar'}]
+
+    If the object has start and end attributes (like the Interval class) there
+    is are some shortcuts:
+
+    >>> intersecter = IntervalTree()
+    >>> intersecter.insert_interval( Interval( 0, 10 ) )
+    >>> intersecter.insert_interval( Interval( 3, 7 ) )
+    >>> intersecter.insert_interval( Interval( 3, 40 ) )
+    >>> intersecter.insert_interval( Interval( 13, 50 ) )
+
+    >>> intersecter.find( 30, 50 )
+    [Interval(3, 40), Interval(13, 50)]
+    >>> intersecter.find( 100, 200 )
+    []
+
+    Before/after for intervals
+
+    >>> intersecter.before_interval( Interval( 10, 20 ) )
+    [Interval(3, 7)]
+    >>> intersecter.before_interval( Interval( 5, 20 ) )
+    []
+
+    Upstream/downstream
+
+    >>> intersecter.upstream_of_interval(Interval(11, 12))
+    [Interval(0, 10)]
+    >>> intersecter.upstream_of_interval(Interval(11, 12, strand="-"))
+    [Interval(13, 50)]
+
+    >>> intersecter.upstream_of_interval(Interval(1, 2, strand="-"), num_intervals=3)
+    [Interval(3, 7), Interval(3, 40), Interval(13, 50)]
+
+
+    """
+
+    cdef IntervalNode root
+
+    def __cinit__( self ):
+        root = None
+
+    # ---- Position based interfaces -----------------------------------------
+
+    def insert( self, double start, double end, object value=None ):
+        """
+        Insert the interval [start,end) associated with value `value`.
+        """
+        if self.root is None:
+            self.root = IntervalNode( start, end, value )
+        else:
+            self.root = self.root.insert( start, end, value )
+
+    add = insert
+
+
+    def find( self, start, end ):
+        """
+        Return a sorted list of all intervals overlapping [start,end).
+        """
+        if self.root is None:
+            return []
+        return self.root.find( start, end )
+
+    def before( self, position, num_intervals=1, max_dist=2500 ):
+        """
+        Find `num_intervals` intervals that lie before `position` and are no
+        further than `max_dist` positions away
+        """
+        if self.root is None:
+            return []
+        return self.root.left( position, num_intervals, max_dist )
+
+    def after( self, position, num_intervals=1, max_dist=2500 ):
+        """
+        Find `num_intervals` intervals that lie after `position` and are no
+        further than `max_dist` positions away
+        """
+        if self.root is None:
+            return []
+        return self.root.right( position, num_intervals, max_dist )
+
+    # ---- Interval-like object based interfaces -----------------------------
+
+    def insert_interval( self, interval ):
+        """
+        Insert an "interval" like object (one with at least start and end
+        attributes)
+        """
+        self.insert( interval.start, interval.end, interval )
+
+    add_interval = insert_interval
+
+    def before_interval( self, interval, num_intervals=1, max_dist=2500 ):
+        """
+        Find `num_intervals` intervals that lie completely before `interval`
+        and are no further than `max_dist` positions away
+        """
+        if self.root is None:
+            return []
+        return self.root.left( interval.start, num_intervals, max_dist )
+
+    def after_interval( self, interval, num_intervals=1, max_dist=2500 ):
+        """
+        Find `num_intervals` intervals that lie completely after `interval` and
+        are no further than `max_dist` positions away
+        """
+        if self.root is None:
+            return []
+        return self.root.right( interval.end, num_intervals, max_dist )
+
+    def upstream_of_interval( self, interval, num_intervals=1, max_dist=2500 ):
+        """
+        Find `num_intervals` intervals that lie completely upstream of
+        `interval` and are no further than `max_dist` positions away
+        """
+        if self.root is None:
+            return []
+        if interval.strand == -1 or interval.strand == "-":
+            return self.root.right( interval.end, num_intervals, max_dist )
+        else:
+            return self.root.left( interval.start, num_intervals, max_dist )
+
+    def downstream_of_interval( self, interval, num_intervals=1, max_dist=2500 ):
+        """
+        Find `num_intervals` intervals that lie completely downstream of
+        `interval` and are no further than `max_dist` positions away
+        """
+        if self.root is None:
+            return []
+        if interval.strand == -1 or interval.strand == "-":
+            return self.root.left( interval.start, num_intervals, max_dist )
+        else:
+            return self.root.right( interval.end, num_intervals, max_dist )
+
+    def traverse(self):
+        """
+        iterator that traverses the tree
+        """
+        if self.root is None:
+            return iter([])
+        return self.root.traverse()
+
+# For backward compatibility
+Intersecter = IntervalTree

nilmdb/client.py

@@ -0,0 +1,157 @@
+"""Class for performing HTTP client requests via libcurl"""
+
+from __future__ import absolute_import
+from nilmdb.printf import *
+
+import time
+import sys
+import re
+import os
+import simplejson as json
+
+import nilmdb.httpclient
+
+# Other functions expect to see these in the nilmdb.client namespace
+from nilmdb.httpclient import ClientError, ServerError, Error
+
+version = "1.0"
+
+class Client(object):
+    """Main client interface to the Nilm database."""
+
+    client_version = version
+
+    def __init__(self, url):
+        self.http = nilmdb.httpclient.HTTPClient(url)
+
+    def _json_param(self, data):
+        """Return compact json-encoded version of parameter"""
+        return json.dumps(data, separators=(',',':'))
+
+    def close(self):
+        self.http.close()
+
+    def geturl(self):
+        """Return the URL we're using"""
+        return self.http.baseurl
+
+    def version(self):
+        """Return server version"""
+        return self.http.get("version")
+
+    def dbpath(self):
+        """Return server database path"""
+        return self.http.get("dbpath")
+
+    def dbsize(self):
+        """Return server database size as human readable string"""
+        return self.http.get("dbsize")
+
+    def stream_list(self, path = None, layout = None):
+        params = {}
+        if path is not None:
+            params["path"] = path
+        if layout is not None:
+            params["layout"] = layout
+        return self.http.get("stream/list", params)
+
+    def stream_get_metadata(self, path, keys = None):
+        params = { "path": path }
+        if keys is not None:
+            params["key"] = keys
+        return self.http.get("stream/get_metadata", params)
+
+    def stream_set_metadata(self, path, data):
+        """Set stream metadata from a dictionary, replacing all existing
+        metadata."""
+        params = {
+            "path": path,
+            "data": self._json_param(data)
+            }
+        return self.http.get("stream/set_metadata", params)
+
+    def stream_update_metadata(self, path, data):
+        """Update stream metadata from a dictionary"""
+        params = {
+            "path": path,
+            "data": self._json_param(data)
+            }
+        return self.http.get("stream/update_metadata", params)
+
+    def stream_create(self, path, layout):
+        """Create a new stream"""
+        params = { "path": path,
+                   "layout" : layout }
+        return self.http.get("stream/create", params)
+
+    def stream_destroy(self, path):
+        """Delete stream and its contents"""
+        params = { "path": path }
+        return self.http.get("stream/destroy", params)
+
+    def stream_insert(self, path, data):
+        """Insert data into a stream.  data should be a file-like object
+        that provides ASCII data that matches the database layout for path."""
+        params = { "path": path }
+
+        # See design.md for a discussion of how much data to send.
+        # These are soft limits -- actual data might be rounded up.
+        max_data = 1048576
+        max_time = 30
+
+        def sendit():
+            result = self.http.put("stream/insert", send_data, params)
+            params["old_timestamp"] = result[1]
+            return result
+
+        result = None
+        start = time.time()
+        send_data = ""
+        for line in data:
+            elapsed = time.time() - start
+            send_data += line
+
+            if (len(send_data) > max_data) or (elapsed > max_time):
+                result = sendit()
+                send_data = ""
+                start = time.time()
+        if len(send_data):
+            result = sendit()
+
+        # Return the most recent JSON result we got back, or None if
+        # we didn't make any requests.
+        return result
+
+    def stream_intervals(self, path, start = None, end = None):
+        """
+        Return a generator that yields each stream interval.
+        """
+        params = {
+            "path": path
+        }
+        if start is not None:
+            params["start"] = repr(start)  # use repr to keep precision
+        if end is not None:
+            params["end"] = repr(end)
+        return self.http.get_gen("stream/intervals", params, retjson = True)
+
+    def stream_extract(self, path, start = None, end = None, count = False):
+        """
+        Extract data from a stream.  Returns a generator that yields
+        lines of ASCII-formatted data that matches the database
+        layout for the given path.
+
+        Specify count=True to just get a count of values rather than
+        the actual data.
+        """
+        params = {
+            "path": path,
+        }
+        if start is not None:
+            params["start"] = repr(start)  # use repr to keep precision
+        if end is not None:
+            params["end"] = repr(end)
+        if count:
+            params["count"] = 1
+
+        return self.http.get_gen("stream/extract", params, retjson = False)

nilmdb/cmdline/__init__.py

@@ -0,0 +1 @@
+from .cmdline import Cmdline

nilmdb/cmdline/cmdline.py

@@ -0,0 +1,148 @@
+"""Command line client functionality"""
+
+from __future__ import absolute_import
+from nilmdb.printf import *
+import nilmdb.client
+
+import datetime_tz
+import dateutil.parser
+import sys
+import re
+import argparse
+from argparse import ArgumentDefaultsHelpFormatter as def_form
+
+version = "0.1"
+
+# Valid subcommands.  Defined in separate files just to break
+# things up -- they're still called with Cmdline as self.
+subcommands = [ "info", "create", "list", "metadata", "insert", "extract",
+                "destroy" ]
+
+# Import the subcommand modules.  Equivalent way of doing this would be
+# from . import info as cmd_info
+subcmd_mods = {}
+for cmd in subcommands:
+    subcmd_mods[cmd] = __import__("nilmdb.cmdline." + cmd, fromlist = [ cmd ])
+
+class Cmdline(object):
+
+    def __init__(self, argv):
+        self.argv = argv
+
+    def arg_time(self, toparse):
+        """Parse a time string argument"""
+        try:
+            return self.parse_time(toparse).totimestamp()
+        except ValueError as e:
+            raise argparse.ArgumentTypeError(sprintf("%s \"%s\"",
+                                                     str(e), toparse))
+
+    def parse_time(self, toparse):
+        """
+        Parse a free-form time string and return a datetime_tz object.
+        If the string doesn't contain a timestamp, the current local
+        timezone is assumed (e.g. from the TZ env var).
+        """
+        # If string doesn't contain at least 6 digits, consider it
+        # invalid.  smartparse might otherwise accept empty strings
+        # and strings with just separators.
+        if len(re.findall(r"\d", toparse)) < 6:
+            raise ValueError("not enough digits for a timestamp")
+
+        # Try to just parse the time as given
+        try:
+            return datetime_tz.datetime_tz.smartparse(toparse)
+        except ValueError:
+            pass
+
+        # Try to extract a substring in a condensed format that we expect
+        # to see in a filename or header comment
+        res = re.search(r"(^|[^\d])("            # non-numeric or SOL
+                        r"(199\d|2\d\d\d)"       # year
+                        r"[-/]?"                 # separator
+                        r"(0[1-9]|1[012])"       # month
+                        r"[-/]?"                 # separator
+                        r"([012]\d|3[01])"       # day
+                        r"[-T ]?"                # separator
+                        r"([01]\d|2[0-3])"       # hour
+                        r"[:]?"                  # separator
+                        r"([0-5]\d)"             # minute
+                        r"[:]?"                  # separator
+                        r"([0-5]\d)?"            # second
+                        r"([-+]\d\d\d\d)?"       # timezone
+                        r")", toparse)
+        if res is not None:
+            try:
+                return datetime_tz.datetime_tz.smartparse(res.group(2))
+            except ValueError:
+                pass
+
+        # Could also try to successively parse substrings, but let's
+        # just give up for now.
+        raise ValueError("unable to parse timestamp")
+
+    def time_string(self, timestamp):
+        """
+        Convert a Unix timestamp to a string for printing, using the
+        local timezone for display (e.g. from the TZ env var).
+        """
+        dt = datetime_tz.datetime_tz.fromtimestamp(timestamp)
+        return dt.strftime("%a, %d %b %Y %H:%M:%S.%f %z")
+
+    def parser_setup(self):
+        version_string = sprintf("nilmtool %s, client library %s",
+                                 version, nilmdb.Client.client_version)
+
+        self.parser = argparse.ArgumentParser(add_help = False,
+                                              formatter_class = def_form)
+
+        group = self.parser.add_argument_group("General options")
+        group.add_argument("-h", "--help", action='help',
+                           help='show this help message and exit')
+        group.add_argument("-V", "--version", action="version",
+                           version=version_string)
+
+        group = self.parser.add_argument_group("Server")
+        group.add_argument("-u", "--url", action="store",
+                           default="http://localhost:12380/",
+                           help="NilmDB server URL (default: %(default)s)")
+
+        sub = self.parser.add_subparsers(title="Commands",
+                                         dest="command",
+                                         description="Specify --help after "
+                                         "the command for command-specific "
+                                         "options.")
+
+        # Set up subcommands (defined in separate files)
+        for cmd in subcommands:
+            subcmd_mods[cmd].setup(self, sub)
+
+    def die(self, formatstr, *args):
+        fprintf(sys.stderr, formatstr + "\n", *args)
+        self.client.close()
+        sys.exit(-1)
+
+    def run(self):
+        # Clear cached timezone, so that we can pick up timezone changes
+        # while running this from the test suite.
+        datetime_tz._localtz = None
+
+        # Run parser
+        self.parser_setup()
+        self.args = self.parser.parse_args(self.argv)
+
+        self.client = nilmdb.Client(self.args.url)
+
+        # Make a test connection to make sure things work
+        try:
+            server_version = self.client.version()
+        except nilmdb.client.Error as e:
+            self.die("Error connecting to server: %s", str(e))
+
+        # Now dispatch client request to appropriate function.  Parser
+        # should have ensured that we don't have any unknown commands
+        # here.
+        retval = self.args.handler(self) or 0
+
+        self.client.close()
+        sys.exit(retval)

nilmdb/cmdline/create.py

@@ -0,0 +1,27 @@
+from __future__ import absolute_import
+from nilmdb.printf import *
+import nilmdb.client
+
+from argparse import ArgumentDefaultsHelpFormatter as def_form
+
+def setup(self, sub):
+    cmd = sub.add_parser("create", help="Create a new stream",
+                         formatter_class = def_form,
+                         description="""
+                         Create a new empty stream at the
+                         specified path and with the specifed
+                         layout type.
+                         """)
+    cmd.set_defaults(handler = cmd_create)
+    group = cmd.add_argument_group("Required arguments")
+    group.add_argument("path",
+                       help="Path (in database) of new stream, e.g. /foo/bar")
+    group.add_argument("layout",
+                       help="Layout type for new stream, e.g. float32_8")
+
+def cmd_create(self):
+    """Create new stream"""
+    try:
+        self.client.stream_create(self.args.path, self.args.layout)
+    except nilmdb.client.ClientError as e:
+        self.die("Error creating stream: %s", str(e))

nilmdb/cmdline/destroy.py

@@ -0,0 +1,25 @@
+from __future__ import absolute_import
+from nilmdb.printf import *
+import nilmdb.client
+
+from argparse import ArgumentDefaultsHelpFormatter as def_form
+
+def setup(self, sub):
+    cmd = sub.add_parser("destroy", help="Delete a stream and all data",
+                         formatter_class = def_form,
+                         description="""
+                         Destroy the stream at the specified path.  All
+                         data and metadata related to the stream is
+                         permanently deleted.
+                         """)
+    cmd.set_defaults(handler = cmd_destroy)
+    group = cmd.add_argument_group("Required arguments")
+    group.add_argument("path",
+                       help="Path of the stream to delete, e.g. /foo/bar")
+
+def cmd_destroy(self):
+    """Destroy stream"""
+    try:
+        self.client.stream_destroy(self.args.path)
+    except nilmdb.client.ClientError as e:
+        self.die("Error deleting stream: %s", str(e))

nilmdb/cmdline/extract.py

@@ -0,0 +1,61 @@
+from __future__ import absolute_import
+from nilmdb.printf import *
+import nilmdb.client
+import nilmdb.layout
+import sys
+
+def setup(self, sub):
+    cmd = sub.add_parser("extract", help="Extract data",
+                         description="""
+                         Extract data from a stream.
+                         """)
+    cmd.set_defaults(handler = cmd_extract)
+
+    group = cmd.add_argument_group("Data selection")
+    group.add_argument("path",
+                       help="Path of stream, e.g. /foo/bar")
+    group.add_argument("-s", "--start", required=True,
+                       metavar="TIME", type=self.arg_time,
+                       help="Starting timestamp (free-form)")
+    group.add_argument("-e", "--end", required=True,
+                       metavar="TIME", type=self.arg_time,
+                       help="Ending timestamp (free-form)")
+
+    group = cmd.add_argument_group("Output format")
+    group.add_argument("-b", "--bare", action="store_true",
+                       help="Exclude timestamps from output lines")
+    group.add_argument("-a", "--annotate", action="store_true",
+                       help="Include comments with some information "
+                       "about the stream")
+    group.add_argument("-c", "--count", action="store_true",
+                       help="Just output a count of matched data points")
+
+def cmd_extract(self):
+    streams = self.client.stream_list(self.args.path)
+    if len(streams) != 1:
+        self.die("Error getting stream info for path %s", self.args.path)
+    layout = streams[0][1]
+
+    if self.args.annotate:
+        printf("# path: %s\n", self.args.path)
+        printf("# layout: %s\n", layout)
+        printf("# start: %s\n", self.time_string(self.args.start))
+        printf("# end: %s\n", self.time_string(self.args.end))
+
+    printed = False
+    for dataline in self.client.stream_extract(self.args.path,
+                                               self.args.start,
+                                               self.args.end,
+                                               self.args.count):
+        if self.args.bare and not self.args.count:
+            # Strip timestamp (first element).  Doesn't make sense
+            # if we are only returning a count.
+            dataline = ' '.join(dataline.split(' ')[1:])
+        print dataline
+        printed = True
+    if not printed:
+        if self.args.annotate:
+            printf("# no data\n")
+        return 2
+
+    return 0

nilmdb/cmdline/info.py

@@ -0,0 +1,21 @@
+from __future__ import absolute_import
+from nilmdb.printf import *
+
+from argparse import ArgumentDefaultsHelpFormatter as def_form
+
+def setup(self, sub):
+    cmd = sub.add_parser("info", help="Server information",
+                         formatter_class = def_form,
+                         description="""
+                         List information about the server, like
+                         version.
+                         """)
+    cmd.set_defaults(handler = cmd_info)
+
+def cmd_info(self):
+    """Print info about the server"""
+    printf("Client library version: %s\n", self.client.client_version)
+    printf("Server version: %s\n", self.client.version())
+    printf("Server URL: %s\n", self.client.geturl())
+    printf("Server database path: %s\n", self.client.dbpath())
+    printf("Server database size: %s\n", self.client.dbsize())

nilmdb/cmdline/insert.py

@@ -0,0 +1,106 @@
+from __future__ import absolute_import
+from nilmdb.printf import *
+import nilmdb.client
+import nilmdb.layout
+import nilmdb.timestamper
+
+import sys
+
+def setup(self, sub):
+    cmd = sub.add_parser("insert", help="Insert data",
+                         description="""
+                         Insert data into a stream.
+                         """)
+    cmd.set_defaults(handler = cmd_insert)
+    cmd.add_argument("-q", "--quiet", action='store_true',
+                     help='suppress unnecessary messages')
+
+    group = cmd.add_argument_group("Timestamping",
+                                   description="""
+                                   If timestamps are already provided in the
+                                   input date, use --none.  Otherwise,
+                                   provide --start, or use --filename to
+                                   try to deduce timestamps from the file.
+
+                                   Set the TZ environment variable to change
+                                   the default timezone.
+                                   """)
+
+    group.add_argument("-r", "--rate", type=float,
+                       help="""
+                       If needed, rate in Hz (required when using --start)
+                       """)
+    exc = group.add_mutually_exclusive_group()
+    exc.add_argument("-s", "--start",
+                     metavar="TIME", type=self.arg_time,
+                     help="Starting timestamp (free-form)")
+    exc.add_argument("-f", "--filename", action="store_true",
+                     help="""
+                     Use filenames to determine start time
+                     (default, if filenames are provided)
+                     """)
+    exc.add_argument("-n", "--none", action="store_true",
+                     help="Timestamp is already present, don't add one")
+
+    group = cmd.add_argument_group("Required parameters")
+    group.add_argument("path",
+                       help="Path of stream, e.g. /foo/bar")
+    group.add_argument("file", nargs="*", default=['-'],
+                       help="File(s) to insert (default: - (stdin))")
+
+def cmd_insert(self):
+    # Find requested stream
+    streams = self.client.stream_list(self.args.path)
+    if len(streams) != 1:
+        self.die("Error getting stream info for path %s", self.args.path)
+
+    layout = streams[0][1]
+
+    if self.args.start and len(self.args.file) != 1:
+        self.die("--start can only be used with one input file, for now")
+
+    for filename in self.args.file:
+        if filename == '-':
+            infile = sys.stdin
+        else:
+            try:
+                infile = open(filename, "r")
+            except IOError:
+                self.die("Error opening input file %s", filename)
+
+        # Build a timestamper for this file
+        if self.args.none:
+            ts = nilmdb.timestamper.TimestamperNull(infile)
+        else:
+            if self.args.start:
+                start = self.args.start
+            else:
+                try:
+                    start = self.parse_time(filename)
+                except ValueError:
+                    self.die("Error extracting time from filename '%s'",
+                             filename)
+
+            if not self.args.rate:
+                self.die("Need to specify --rate")
+            rate = self.args.rate
+
+            ts = nilmdb.timestamper.TimestamperRate(infile, start, rate)
+
+        # Print info
+        if not self.args.quiet:
+            printf("Input file: %s\n", filename)
+            printf("Timestamper: %s\n", str(ts))
+
+        # Insert the data
+        try:
+            result = self.client.stream_insert(self.args.path, ts)
+        except nilmdb.client.Error as e:
+            # TODO: It would be nice to be able to offer better errors
+            # here, particularly in the case of overlap, which just shows
+            # ugly bracketed ranges of 16-digit numbers and a mangled URL.
+            # Need to consider adding something like e.prettyprint()
+            # that is smarter about the contents of the error.
+            self.die("Error inserting data: %s", str(e))
+
+    return

nilmdb/cmdline/list.py

@@ -0,0 +1,54 @@
+from __future__ import absolute_import
+from nilmdb.printf import *
+import nilmdb.client
+
+import fnmatch
+from argparse import ArgumentDefaultsHelpFormatter as def_form
+
+def setup(self, sub):
+    cmd = sub.add_parser("list", help="List streams",
+                         formatter_class = def_form,
+                         description="""
+                         List streams available in the database,
+                         optionally filtering by layout or path.  Wildcards
+                         are accepted.
+                         """)
+    cmd.set_defaults(handler = cmd_list)
+
+    group = cmd.add_argument_group("Stream filtering")
+    group.add_argument("-l", "--layout", default="*",
+                       help="Match only this stream layout")
+    group.add_argument("-p", "--path", default="*",
+                       help="Match only this path")
+
+    group = cmd.add_argument_group("Interval details")
+    group.add_argument("-d", "--detail", action="store_true",
+                       help="Show available data time intervals")
+    group.add_argument("-s", "--start",
+                       metavar="TIME", type=self.arg_time,
+                       help="Starting timestamp (free-form)")
+    group.add_argument("-e", "--end",
+                       metavar="TIME", type=self.arg_time,
+                       help="Ending timestamp (free-form)")
+
+def cmd_list(self):
+    """List available streams"""
+    streams = self.client.stream_list()
+    for (path, layout) in streams:
+        if not (fnmatch.fnmatch(path, self.args.path) and
+                fnmatch.fnmatch(layout, self.args.layout)):
+            continue
+
+        printf("%s %s\n", path, layout)
+        if not self.args.detail:
+            continue
+
+        printed = False
+        for (start, end) in self.client.stream_intervals(path, self.args.start,
+                                                         self.args.end):
+            printf("  [ %s -> %s ]\n",
+                   self.time_string(start),
+                   self.time_string(end))
+            printed = True
+        if not printed:
+            printf("  (no intervals)\n")

nilmdb/cmdline/metadata.py

@@ -0,0 +1,65 @@
+from __future__ import absolute_import
+from nilmdb.printf import *
+import nilmdb.client
+
+def setup(self, sub):
+    cmd = sub.add_parser("metadata", help="Get or set stream metadata",
+                         description="""
+                         Get or set key=value metadata associated with
+                         a stream.
+                         """,
+                         usage="%(prog)s path [-g [key ...] | "
+                         "-s key=value [...] | -u key=value [...]]")
+    cmd.set_defaults(handler = cmd_metadata)
+
+    group = cmd.add_argument_group("Required arguments")
+    group.add_argument("path",
+                       help="Path of stream, e.g. /foo/bar")
+
+    group = cmd.add_argument_group("Actions")
+    exc = group.add_mutually_exclusive_group()
+    exc.add_argument("-g", "--get", nargs="*", metavar="key",
+                     help="Get metadata for specified keys (default all)")
+    exc.add_argument("-s", "--set", nargs="+", metavar="key=value",
+                     help="Replace all metadata with provided "
+                     "key=value pairs")
+    exc.add_argument("-u", "--update", nargs="+", metavar="key=value",
+                     help="Update metadata using provided "
+                     "key=value pairs")
+
+def cmd_metadata(self):
+    """Manipulate metadata"""
+    if self.args.set is not None or self.args.update is not None:
+        # Either set, or update
+        if self.args.set is not None:
+            keyvals = self.args.set
+            handler = self.client.stream_set_metadata
+        else:
+            keyvals = self.args.update
+            handler = self.client.stream_update_metadata
+
+        # Extract key=value pairs
+        data = {}
+        for keyval in keyvals:
+            kv = keyval.split('=')
+            if len(kv) != 2 or kv[0] == "":
+                self.die("Error parsing key=value argument '%s'", keyval)
+            data[kv[0]] = kv[1]
+
+        # Make the call
+        try:
+            handler(self.args.path, data)
+        except nilmdb.client.ClientError as e:
+            self.die("Error setting/updating metadata: %s", str(e))
+    else:
+        # Get (or unspecified)
+        keys = self.args.get or None
+        try:
+            data = self.client.stream_get_metadata(self.args.path, keys)
+        except nilmdb.client.ClientError as e:
+            self.die("Error getting metadata: %s", str(e))
+        for key, value in sorted(data.items()):
+            # Omit nonexistant keys
+            if value is None:
+                value = ""
+            printf("%s=%s\n", key, value)

nilmdb/du.py

@@ -0,0 +1,30 @@
+import nilmdb
+import os
+from math import log
+
+def sizeof_fmt(num):
+    """Human friendly file size"""
+    unit_list = zip(['bytes', 'kiB', 'MiB', 'GiB', 'TiB'], [0, 0, 1, 2, 2])
+    if num > 1:
+        exponent = min(int(log(num, 1024)), len(unit_list) - 1)
+        quotient = float(num) / 1024**exponent
+        unit, num_decimals = unit_list[exponent]
+        format_string = '{:.%sf} {}' % (num_decimals)
+        return format_string.format(quotient, unit)
+    if num == 0: # pragma: no cover
+        return '0 bytes'
+    if num == 1: # pragma: no cover
+        return '1 byte'
+
+def du_bytes(path):
+    """Like du -sb, returns total size of path in bytes."""
+    size = os.path.getsize(path)
+    if os.path.isdir(path):
+        for file in os.listdir(path):
+            filepath = os.path.join(path, file)
+            size += du_bytes(filepath)
+    return size
+
+def du(path):
+    """Like du -sh, returns total size of path as a human-readable string."""
+    return sizeof_fmt(du_bytes(path))

nilmdb/fileinterval.py

@@ -1,37 +0,0 @@
-"""FileInterval
-
-An Interval that is backed with file data storage"""
-
-from nilmdb.interval import Interval, IntervalSet, IntervalError
-from datetime import datetime
-import bisect
-
-class FileInterval(Interval):
-    """Represents an interval of time and its corresponding data"""
-
-    def __init__(self, start, end, 
-                 filename, 
-                 start_offset = None, end_offset = None):
-        self.start = start
-        self.end = end
-        self.filename = filename
-        if start_offset is None:
-            start_offset = 0
-        self.start_offset = start_offset
-        if end_offset is None:
-            f = open(filename, 'rb')
-            f.seek(0, os.SEEK_END)
-            end_offset = f.tell()
-        self.end_offset = end_offset
-
-    def __setattr__(self, name, value):
-        pass
-
-    def subset(self, start, end):
-        """Return a new Interval that is a subset of this one"""
-        # TODO: Any magic regarding file/offset/length mapping for subsets
-        if (start < self.start or end > self.end):
-            raise IntervalError("not a subset")
-        return FileInterval(start, end)            
-
-    

nilmdb/httpclient.py

@@ -0,0 +1,220 @@
+"""HTTP client library"""
+
+from __future__ import absolute_import
+from nilmdb.printf import *
+
+import time
+import sys
+import re
+import os
+import simplejson as json
+import urlparse
+import urllib
+import pycurl
+import cStringIO
+
+import nilmdb.iteratorizer
+
+class Error(Exception):
+    """Base exception for both ClientError and ServerError responses"""
+    def __init__(self,
+                 status = "Unspecified error",
+                 message = None,
+                 url = None,
+                 traceback = None):
+        Exception.__init__(self, status)
+        self.status = status     # e.g. "400 Bad Request"
+        self.message = message   # textual message from the server
+        self.url = url           # URL we were requesting
+        self.traceback = traceback # server traceback, if available
+    def __str__(self):
+        s = sprintf("[%s]", self.status)
+        if self.message:
+            s += sprintf(" %s", self.message)
+        if self.url:
+            s += sprintf(" (%s)", self.url)
+        if self.traceback: # pragma: no cover
+            s += sprintf("\nServer traceback:\n%s", self.traceback)
+        return s
+class ClientError(Error):
+    pass
+class ServerError(Error):
+    pass
+
+class HTTPClient(object):
+    """Class to manage and perform HTTP requests from the client"""
+    def __init__(self, baseurl = ""):
+        """If baseurl is supplied, all other functions that take
+        a URL can be given a relative URL instead."""
+        # Verify / clean up URL
+        reparsed = urlparse.urlparse(baseurl).geturl()
+        if '://' not in reparsed:
+            reparsed = urlparse.urlparse("http://" + baseurl).geturl()
+        self.baseurl = reparsed
+        self.curl = pycurl.Curl()
+        self.curl.setopt(pycurl.SSL_VERIFYHOST, 2)
+        self.curl.setopt(pycurl.FOLLOWLOCATION, 1)
+        self.curl.setopt(pycurl.MAXREDIRS, 5)
+        self._setup_url()
+
+    def _setup_url(self, url = "", params = ""):
+        url = urlparse.urljoin(self.baseurl, url)
+        if params:
+            url = urlparse.urljoin(url, "?" + urllib.urlencode(params, True))
+        self.curl.setopt(pycurl.URL, url)
+        self.url = url
+
+    def _check_error(self, body = None):
+        code = self.curl.getinfo(pycurl.RESPONSE_CODE)
+        if code == 200:
+            return
+        # Default variables for exception
+        args = { "url" : self.url,
+                 "status" : str(code),
+                 "message" : None,
+                 "traceback" : None }
+        try:
+            # Fill with server-provided data if we can
+            jsonerror = json.loads(body)
+            args["status"] = jsonerror["status"]
+            args["message"] = jsonerror["message"]
+            args["traceback"] = jsonerror["traceback"]
+        except Exception: # pragma: no cover
+            pass
+        if code >= 400 and code <= 499:
+            raise ClientError(**args)
+        else: # pragma: no cover
+            if code >= 500 and code <= 599:
+                raise ServerError(**args)
+            else:
+                raise Error(**args)
+
+    def _req_generator(self, url, params):
+        """
+        Like self._req(), but runs the perform in a separate thread.
+        It returns a generator that spits out arbitrary-sized chunks
+        of the resulting data, instead of using the WRITEFUNCTION
+        callback.
+        """
+        self._setup_url(url, params)
+        self._status = None
+        error_body = ""
+        self._headers = ""
+        def header_callback(data):
+            if self._status is None:
+                self._status = int(data.split(" ")[1])
+            self._headers += data
+        self.curl.setopt(pycurl.HEADERFUNCTION, header_callback)
+        def func(callback):
+            self.curl.setopt(pycurl.WRITEFUNCTION, callback)
+            self.curl.perform()
+        try:
+            for i in nilmdb.iteratorizer.Iteratorizer(func):
+                if self._status == 200:
+                    # If we had a 200 response, yield the data to the caller.
+                    yield i
+                else:
+                    # Otherwise, collect it into an error string.
+                    error_body += i
+        except pycurl.error as e:
+            raise ServerError(status = "502 Error",
+                              url = self.url,
+                              message = e[1])
+        # Raise an exception if there was an error
+        self._check_error(error_body)
+
+    def _req(self, url, params):
+        """
+        GET or POST that returns raw data.  Returns the body
+        data as a string, or raises an error if it contained an error.
+        """
+        self._setup_url(url, params)
+        body = cStringIO.StringIO()
+        self.curl.setopt(pycurl.WRITEFUNCTION, body.write)
+        self._headers = ""
+        def header_callback(data):
+            self._headers += data
+        self.curl.setopt(pycurl.HEADERFUNCTION, header_callback)
+        try:
+            self.curl.perform()
+        except pycurl.error as e:
+            raise ServerError(status = "502 Error",
+                              url = self.url,
+                              message = e[1])
+        body_str = body.getvalue()
+        # Raise an exception if there was an error
+        self._check_error(body_str)
+        return body_str
+
+    def close(self):
+        self.curl.close()
+
+    def _iterate_lines(self, it):
+        """
+        Given an iterator that returns arbitrarily-sized chunks
+        of data, return '\n'-delimited lines of text
+        """
+        partial = ""
+        for chunk in it:
+            partial += chunk
+            lines = partial.split("\n")
+            for line in lines[0:-1]:
+                yield line
+            partial = lines[-1]
+        if partial != "":
+            yield partial
+
+    # Non-generator versions
+    def _doreq(self, url, params, retjson):
+        """
+        Perform a request, and return the body.
+
+        url: URL to request (relative to baseurl)
+        params: dictionary of query parameters
+        retjson: expect JSON and return python objects instead of string
+        """
+        out = self._req(url, params)
+        if retjson:
+            return json.loads(out)
+        return out
+
+    def get(self, url, params = None, retjson = True):
+        """Simple GET"""
+        self.curl.setopt(pycurl.UPLOAD, 0)
+        return self._doreq(url, params, retjson)
+
+    def put(self, url, postdata, params = None, retjson = True):
+        """Simple PUT"""
+        self._setup_url(url, params)
+        data = cStringIO.StringIO(postdata)
+        self.curl.setopt(pycurl.UPLOAD, 1)
+        self.curl.setopt(pycurl.READFUNCTION, data.read)
+        return self._doreq(url, params, retjson)
+
+    # Generator versions
+    def _doreq_gen(self, url, params, retjson):
+        """
+        Perform a request, and return lines of the body in a generator.
+
+        url: URL to request (relative to baseurl)
+        params: dictionary of query parameters
+        retjson: expect JSON and yield python objects instead of strings
+        """
+        for line in self._iterate_lines(self._req_generator(url, params)):
+            if retjson:
+                yield json.loads(line)
+            else:
+                yield line
+
+    def get_gen(self, url, params = None, retjson = True):
+        """Simple GET, returning a generator"""
+        self.curl.setopt(pycurl.UPLOAD, 0)
+        return self._doreq_gen(url, params, retjson)
+
+    def put_gen(self, url, postdata, params = None, retjson = True):
+        """Simple PUT, returning a generator"""
+        self._setup_url(url, params)
+        data = cStringIO.StringIO(postdata)
+        self.curl.setopt(pycurl.UPLOAD, 1)
+        self.curl.setopt(pycurl.READFUNCTION, data.read)
+        return self._doreq_gen(url, params, retjson)

nilmdb/interval.py

@@ -1,205 +0,0 @@
-"""Interval and IntervalSet
-
-Represents an interval of time, and a sorted set of such intervals"""
-
-from datetime import datetime
-import bisect
-
-class IntervalError(Exception):
-    """Error due to interval overlap, etc"""
-    pass
-
-class Interval(object):
-    """Represents an interval of time"""
-
-    start = None
-    end = None
-
-    def __init__(self, start, end):
-        self.start = start
-        self.end = end
-
-    def __repr__(self):
-        return "Interval(" + repr(self.start) + ", " + repr(self.end) + ")"
-
-    def __str__(self):
-        return "[" + str(self.start) + " -> " + str(self.end) + "]"
-
-    def __setattr__(self, name, value):
-        """Set attribute"""
-        # TODO: If we need to manipulate file names, offsets, lengths, etc,
-        # based on start and end time changing, maybe this is the right spot?
-        # Or we could just disallow changing it here.
-        if not isinstance(value, datetime):
-            raise IntervalError("Must set datetime values")
-        self.__dict__[name] = value
-        if (type(self.start) is type(self.end)):
-            if (self.start > self.end):
-                raise IntervalError("Interval start must precede interval end")
-
-    def __cmp__(self, other):
-        """Compare two intervals.  If non-equal, order by start then end"""
-        if not isinstance(other, Interval):
-            raise TypeError("Can't compare to non-interval")
-        if (self.start == other.start):
-            if (self.end < other.end):
-                return -1
-            if (self.end > other.end):
-                return 1
-            return 0
-        if (self.start < other.start):
-            return -1
-        return 1
-                
-    def intersects(self, other):
-        """Return True if two Interval objects intersect"""
-        if (not isinstance(other, Interval)):
-            raise TypeError("need Interval for intersection test")
-        if (self.end <= other.start or
-            self.start >= other.end):
-            return False
-        else:
-            return True
-
-    def is_adjacent(self, other):
-        """Return True if two Intervals are adjacent (same end or start)"""
-        if (not isinstance(other, Interval)):
-            raise TypeError("need Interval for adjacency test")
-        if (self.end == other.start or
-            self.start == other.end):
-            return True
-        else:
-            return False
-
-    def subset(self, start, end):
-        """Return a new Interval that is a subset of this one"""
-        # TODO: Any magic regarding file/offset/length mapping for subsets
-        if (start < self.start or end > self.end):
-            raise IntervalError("not a subset")
-        return Interval(start, end)            
-
-class IntervalSet(object):
-    """A non-intersecting set of intervals
-
-    Kept sorted internally"""
-
-    def __init__(self, iterable=None):
-        self.data = []
-        if iterable is not None:
-            if isinstance(iterable, Interval):
-                iterable = [iterable]
-            self._add_intervals(iterable)
-
-    def __iter__(self):
-        return self.data.__iter__()
-
-    def __repr__(self):
-        return "IntervalSet(" + repr(list(self.data)) + ")"
-
-    def __cmp__(self, other):
-        # compare isn't supported, they don't really have an ordering
-        raise TypeError("can't compare IntervalSets with cmp()")
-
-    def __eq__(self, other):
-        """Test equality of two IntervalSets.
-
-        Treats adjacent Intervals as equivalent to one long interval,
-        so this function really tests whether the IntervalSets cover
-        the same spans of time."""
-        if not isinstance(other, IntervalSet):
-            return False
-        i = 0
-        j = 0
-        outside = True
-        try:
-            while True:
-                if (outside):
-                    # To match, we need to be finished this set
-                    if (i >= len(self) and j >= len(other)):
-                        return True
-                    # Or the starts need to match
-                    if (self[i].start != other[j].start):
-                        return False
-                    outside = False
-                else:
-                    # We can move on if the two interval ends match
-                    if (self[i].end == other[j].end):
-                        i += 1
-                        j += 1
-                        outside = True
-                    else:
-                        # Whichever ends first needs to be adjacent to the next
-                        if (self[i].end < other[j].end):
-                            if (not self[i].is_adjacent(self[i+1])):
-                                return False
-                            i += 1
-                        else:
-                            if (not other[j].is_adjacent(other[j+1])):
-                                return False
-                            j += 1
-        except IndexError:
-            return False
-
-    def __ne__(self, other):
-        return not self.__eq__(other)
-
-    def __len__(self):
-        return len(self.data)
-
-    def __getitem__(self, key):
-        return self.data.__getitem__(key)
-
-    def __iadd__(self, other):
-        """Inplace add -- modifies self
-
-        This throws an exception if the regions being added intersect."""
-        if isinstance(other, Interval):
-            other = [other]
-        self._add_intervals(other)
-        return self
-        
-    def __add__(self, other):
-        """Add -- returns a new object
-
-        This throws an exception if the regions being added intersect."""
-        new = IntervalSet(self)
-        new += IntervalSet(other)
-        return new
-
-    def __and__(self, other):
-        """Compute a new IntervalSet from the intersection of two others
-
-        Output intervals are built as subsets of the intervals in the
-        first argument (self)."""
-        # If we were given a set, intersect with each interval in that set
-        if isinstance(other, IntervalSet):
-            out = IntervalSet()
-            for interval in other.data:
-                out += self & interval
-            return out
-
-        if not isinstance(other, Interval):
-            raise TypeError("can't intersect with that type")
-
-        out = IntervalSet()
-        for this in self.data:
-            # If there's any overlap, add the overlapping region
-            if (this.end > other.start and this.start < other.end):
-                out += this.subset(max(this.start, other.start),
-                                   min(this.end, other.end))
-        return out
-    
-    def _add_intervals(self, iterable):
-        """Add each Interval from an interable to this set"""
-        for element in iter(iterable):
-            self._add_single_interval(element)
-
-    def _add_single_interval(self, interval):
-        """Add one Interval to this set"""
-        if (not isinstance(interval, Interval)):
-            raise TypeError("can only add Intervals")
-        for existing in self.data:
-            if existing.intersects(interval):
-                raise IntervalError("Tried to add overlapping interval "
-                                    "to this set")
-        bisect.insort(self.data, interval)

nilmdb/interval.pyx

@@ -0,0 +1,302 @@
+"""Interval, IntervalSet
+
+Represents an interval of time, and a set of such intervals.
+
+Intervals are half-open, ie. they include data points with timestamps
+[start, end)
+"""
+
+# First implementation kept a sorted list of intervals and used
+# biesct() to optimize some operations, but this was too slow.
+
+# Second version was based on the quicksect implementation from
+# python-bx, modified slightly to handle floating point intervals.
+# This didn't support deletion.
+
+# Third version is more similar to the first version, using a rb-tree
+# instead of a simple sorted list to maintain O(log n) operations.
+
+# Fourth version is an optimized rb-tree that stores interval starts
+# and ends directly in the tree, like bxinterval did.
+
+cimport rbtree
+cdef extern from "stdint.h":
+    ctypedef unsigned long long uint64_t
+
+class IntervalError(Exception):
+    """Error due to interval overlap, etc"""
+    pass
+
+cdef class Interval:
+    """Represents an interval of time."""
+
+    cdef public double start, end
+
+    def __init__(self, double start, double end):
+        """
+        'start' and 'end' are arbitrary floats that represent time
+        """
+        if start > end:
+            raise IntervalError("start %s must precede end %s" % (start, end))
+        self.start = float(start)
+        self.end = float(end)
+
+    def __repr__(self):
+        s = repr(self.start) + ", " + repr(self.end)
+        return self.__class__.__name__ + "(" + s + ")"
+
+    def __str__(self):
+        return "[" + repr(self.start) + " -> " + repr(self.end) + ")"
+
+    def __cmp__(self, Interval other):
+        """Compare two intervals.  If non-equal, order by start then end"""
+        if not isinstance(other, Interval):
+            raise TypeError("bad type")
+        if self.start == other.start:
+            if self.end < other.end:
+                return -1
+            if self.end > other.end:
+                return 1
+            return 0
+        if self.start < other.start:
+            return -1
+        return 1
+
+    cpdef intersects(self, Interval other):
+        """Return True if two Interval objects intersect"""
+        if (self.end <= other.start or self.start >= other.end):
+            return False
+        return True
+
+    cpdef subset(self, double start, double end):
+        """Return a new Interval that is a subset of this one"""
+        # A subclass that tracks additional data might override this.
+        if start < self.start or end > self.end:
+            raise IntervalError("not a subset")
+        return Interval(start, end)
+
+cdef class DBInterval(Interval):
+    """
+    Like Interval, but also tracks corresponding start/end times and
+    positions within the database.  These are not currently modified
+    when subsets are taken, but can be used later to help zero in on
+    database positions.
+
+    The actual 'start' and 'end' will always fall within the database
+    start and end, e.g.:
+        db_start = 100, db_startpos = 10000
+        start = 123
+        end = 150
+        db_end = 200, db_endpos = 20000
+    """
+
+    cpdef public double db_start, db_end
+    cpdef public uint64_t db_startpos, db_endpos
+
+    def __init__(self, start, end,
+                 db_start, db_end,
+                 db_startpos, db_endpos):
+        """
+        'db_start' and 'db_end' are arbitrary floats that represent
+        time.  They must be a strict superset of the time interval
+        covered by 'start' and 'end'.  The 'db_startpos' and
+        'db_endpos' are arbitrary database position indicators that
+        correspond to those points.
+        """
+        Interval.__init__(self, start, end)
+        self.db_start = db_start
+        self.db_end = db_end
+        self.db_startpos = db_startpos
+        self.db_endpos = db_endpos
+        if db_start > start or db_end < end:
+            raise IntervalError("database times must span the interval times")
+
+    def __repr__(self):
+        s = repr(self.start) + ", " + repr(self.end)
+        s += ", " + repr(self.db_start) + ", " + repr(self.db_end)
+        s += ", " + repr(self.db_startpos) + ", " + repr(self.db_endpos)
+        return self.__class__.__name__ + "(" + s + ")"
+
+    cpdef subset(self, double start, double end):
+        """
+        Return a new DBInterval that is a subset of this one
+        """
+        if start < self.start or end > self.end:
+            raise IntervalError("not a subset")
+        return DBInterval(start, end,
+                          self.db_start, self.db_end,
+                          self.db_startpos, self.db_endpos)
+
+cdef class IntervalSet:
+    """
+    A non-intersecting set of intervals.
+    """
+
+    cdef public rbtree.RBTree tree
+
+    def __init__(self, source=None):
+        """
+        'source' is an Interval or IntervalSet to add.
+        """
+        self.tree = rbtree.RBTree()
+        if source is not None:
+            self += source
+
+    def __iter__(self):
+        for node in self.tree:
+            if node.obj:
+                yield node.obj
+
+    def __len__(self):
+        return sum(1 for x in self)
+
+    def __repr__(self):
+        descs = [ repr(x) for x in self ]
+        return self.__class__.__name__ + "([" + ", ".join(descs) + "])"
+
+    def __str__(self):
+        descs = [ str(x) for x in self ]
+        return  "[" + ", ".join(descs) + "]"
+
+    def __match__(self, other):
+        # This isn't particularly efficient, but it shouldn't get used in the
+        # general case.
+        """Test equality of two IntervalSets.
+
+        Treats adjacent Intervals as equivalent to one long interval,
+        so this function really tests whether the IntervalSets cover
+        the same spans of time."""
+        i = 0
+        j = 0
+        outside = True
+
+        def is_adjacent(a, b):
+            """Return True if two Intervals are adjacent (same end or start)"""
+            if a.end == b.start or b.end == a.start:
+                return True
+            else:
+                return False
+
+        this = [ x for x in self ]
+        that = [ x for x in other ]
+
+        try:
+            while True:
+                if (outside):
+                    # To match, we need to be finished both sets
+                    if (i >= len(this) and j >= len(that)):
+                        return True
+                    # Or the starts need to match
+                    if (this[i].start != that[j].start):
+                        return False
+                    outside = False
+                else:
+                    # We can move on if the two interval ends match
+                    if (this[i].end == that[j].end):
+                        i += 1
+                        j += 1
+                        outside = True
+                    else:
+                        # Whichever ends first needs to be adjacent to the next
+                        if (this[i].end < that[j].end):
+                            if (not is_adjacent(this[i],this[i+1])):
+                                return False
+                            i += 1
+                        else:
+                            if (not is_adjacent(that[j],that[j+1])):
+                                return False
+                            j += 1
+        except IndexError:
+            return False
+
+    # Use __richcmp__ instead of __eq__, __ne__ for Cython.
+    def __richcmp__(self, other, int op):
+        if op == 2: # ==
+            return self.__match__(other)
+        elif op == 3: # !=
+            return not self.__match__(other)
+        return False
+    #def __eq__(self, other):
+    #    return self.__match__(other)
+    #
+    #def __ne__(self, other):
+    #    return not self.__match__(other)
+
+    def __iadd__(self, object other not None):
+        """Inplace add -- modifies self
+
+        This throws an exception if the regions being added intersect."""
+        if isinstance(other, Interval):
+            if self.intersects(other):
+                raise IntervalError("Tried to add overlapping interval "
+                                    "to this set")
+            self.tree.insert(rbtree.RBNode(other.start, other.end, other))
+        else:
+            for x in other:
+                self.__iadd__(x)
+        return self
+
+    def __isub__(self, Interval other not None):
+        """Inplace subtract -- modifies self
+
+        Removes an interval from the set.  Must exist exactly
+        as provided -- cannot remove a subset of an existing interval."""
+        i = self.tree.find(other.start, other.end)
+        if i is None:
+            raise IntervalError("interval " + str(other) + " not in tree")
+        self.tree.delete(i)
+        return self
+
+    def __add__(self, other not None):
+        """Add -- returns a new object"""
+        new = IntervalSet(self)
+        new += IntervalSet(other)
+        return new
+
+    def __and__(self, other not None):
+        """
+        Compute a new IntervalSet from the intersection of two others
+
+        Output intervals are built as subsets of the intervals in the
+        first argument (self).
+        """
+        out = IntervalSet()
+
+        if not isinstance(other, IntervalSet):
+            for i in self.intersection(other):
+                out.tree.insert(rbtree.RBNode(i.start, i.end, i))
+        else:
+            for x in other:
+                for i in self.intersection(x):
+                    out.tree.insert(rbtree.RBNode(i.start, i.end, i))
+
+        return out
+
+    def intersection(self, Interval interval not None):
+        """
+        Compute a sequence of intervals that correspond to the
+        intersection between `self` and the provided interval.
+        Returns a generator that yields each of these intervals
+        in turn.
+
+        Output intervals are built as subsets of the intervals in the
+        first argument (self).
+        """
+        if not isinstance(interval, Interval):
+            raise TypeError("bad type")
+        for n in self.tree.intersect(interval.start, interval.end):
+            i = n.obj
+            if i:
+                if i.start >= interval.start and i.end <= interval.end:
+                    yield i
+                else:
+                    subset = i.subset(max(i.start, interval.start),
+                                      min(i.end, interval.end))
+                    yield subset
+
+    cpdef intersects(self, Interval other):
+        """Return True if this IntervalSet intersects another interval"""
+        for n in self.tree.intersect(other.start, other.end):
+            if n.obj.intersects(other):
+                return True
+        return False

nilmdb/interval.pyxdep

@@ -0,0 +1 @@
+rbtree.pxd

nilmdb/iteratorizer.py

@@ -0,0 +1,72 @@
+import Queue
+import threading
+import sys
+
+# This file provides a class that will convert a function that
+# takes a callback into a generator that returns an iterator.
+
+# Based partially on http://stackoverflow.com/questions/9968592/
+
+class IteratorizerThread(threading.Thread):
+    def __init__(self, queue, function):
+        """
+        function: function to execute, which takes the
+        callback (provided by this class) as an argument
+        """
+        threading.Thread.__init__(self)
+        self.function = function
+        self.queue = queue
+        self.die = False
+
+    def callback(self, data):
+        if self.die:
+            raise Exception("should die")
+        self.queue.put((1, data))
+
+    def run(self):
+        try:
+            result = self.function(self.callback)
+        except:
+            if sys is not None: # can be None during unclean shutdown
+                self.queue.put((2, sys.exc_info()))
+        else:
+            self.queue.put((0, result))
+
+class Iteratorizer(object):
+    def __init__(self, function):
+        """
+        function: function to execute, which takes the
+        callback (provided by this class) as an argument
+        """
+        self.function = function
+        self.queue = Queue.Queue(maxsize = 1)
+        self.thread = IteratorizerThread(self.queue, self.function)
+        self.thread.daemon = True
+        self.thread.start()
+
+    def __del__(self):
+        # If we get garbage collected, try to get rid of the
+        # thread too by asking it to raise an exception, then
+        # draining the queue until it's gone.
+        self.thread.die = True
+        while self.thread.isAlive():
+            try:
+                self.queue.get(True, 0.01)
+            except: # pragma: no cover
+                pass
+
+    def __iter__(self):
+        return self
+
+    def next(self):
+        (typ, data) = self.queue.get()
+        if typ == 0:
+            # function returned
+            self.retval = data
+            raise StopIteration
+        elif typ == 1:
+            # data available
+            return data
+        else:
+            # exception
+            raise data[0], data[1], data[2]

nilmdb/layout.pyx

@@ -0,0 +1,219 @@
+# cython: profile=False
+
+import tables
+import time
+import sys
+import inspect
+import cStringIO
+import numpy as np
+
+cdef enum:
+    max_value_count = 64
+
+cimport cython
+cimport libc.stdlib
+cimport libc.stdio
+cimport libc.string
+
+class ParserError(Exception):
+    def __init__(self, line, message):
+        self.message = "line " + str(line) + ": " + message
+        Exception.__init__(self, self.message)
+
+class FormatterError(Exception):
+    pass
+
+class Layout:
+    """Represents a NILM database layout"""
+
+    def __init__(self, typestring):
+        """Initialize this Layout object to handle the specified
+        type string"""
+        try:
+            [ datatype, count ] = typestring.split("_")
+        except:
+            raise KeyError("invalid layout string")
+
+        try:
+            self.count = int(count)
+        except ValueError:
+            raise KeyError("invalid count")
+        if self.count < 1 or self.count > max_value_count:
+            raise KeyError("invalid count")
+
+        if datatype == 'uint16':
+            self.parse = self.parse_uint16
+            self.format = self.format_uint16
+        elif datatype == 'float32' or datatype == 'float64':
+            self.parse = self.parse_float64
+            self.format = self.format_float64
+        else:
+            raise KeyError("invalid type")
+
+        self.datatype = datatype
+
+    # Parsers
+    def parse_float64(self, char *text):
+        cdef int n
+        cdef double ts
+        # Return doubles even in float32 case, since they're going into
+        # a Python array which would upconvert to double anyway.
+        result = []
+        cdef char *end
+        ts = libc.stdlib.strtod(text, &end)
+        if end == text:
+            raise ValueError("bad timestamp")
+        result.append(ts)
+        for n in range(self.count):
+            text = end
+            result.append(libc.stdlib.strtod(text, &end))
+            if end == text:
+                raise ValueError("wrong number of values")
+        n = 0
+        while end[n] == ' ':
+            n += 1
+        if end[n] != '\n' and end[n] != '#' and end[n] != '\0':
+            raise ValueError("extra data on line")
+        return (ts, result)
+
+    def parse_uint16(self, char *text):
+        cdef int n
+        cdef double ts
+        cdef int v
+        result = []
+        cdef char *end
+        ts = libc.stdlib.strtod(text, &end)
+        if end == text:
+            raise ValueError("bad timestamp")
+        result.append(ts)
+        for n in range(self.count):
+            text = end
+            v = libc.stdlib.strtol(text, &end, 10)
+            if v < 0 or v > 65535:
+                raise ValueError("value out of range")
+            result.append(v)
+            if end == text:
+                raise ValueError("wrong number of values")
+        n = 0
+        while end[n] == ' ':
+            n += 1
+        if end[n] != '\n' and end[n] != '#' and end[n] != '\0':
+            raise ValueError("extra data on line")
+        return (ts, result)
+
+    # Formatters
+    def format_float64(self, d):
+        n = len(d) - 1
+        if n != self.count:
+            raise ValueError("wrong number of values for layout type: "
+                             "got %d, wanted %d" % (n, self.count))
+        s = "%.6f" % d[0]
+        for i in range(n):
+            s += " %f" % d[i+1]
+        return s + "\n"
+
+    def format_uint16(self, d):
+        n = len(d) - 1
+        if n != self.count:
+            raise ValueError("wrong number of values for layout type: "
+                             "got %d, wanted %d" % (n, self.count))
+        s = "%.6f" % d[0]
+        for i in range(n):
+            s += " %d" % d[i+1]
+        return s + "\n"
+
+    # PyTables description
+    def description(self):
+        """Return the PyTables description of this layout"""
+        desc = {}
+        desc['timestamp'] = tables.Col.from_type('float64', pos=0)
+        for n in range(self.count):
+            desc['c' + str(n+1)] = tables.Col.from_type(self.datatype, pos=n+1)
+        return tables.Description(desc)
+
+# Get a layout by name
+def get_named(typestring):
+    try:
+        return Layout(typestring)
+    except KeyError:
+        compat = { "PrepData": "float32_8",
+                   "RawData": "uint16_6",
+                   "RawNotchedData": "uint16_9" }
+        return Layout(compat[typestring])
+
+class Parser(object):
+    """Object that parses and stores ASCII data for inclusion into the
+    database"""
+
+    def __init__(self, layout):
+        if issubclass(layout.__class__, Layout):
+            self.layout = layout
+        else:
+            try:
+                self.layout = get_named(layout)
+            except KeyError:
+                raise TypeError("unknown layout")
+
+        self.data = []
+        self.min_timestamp = None
+        self.max_timestamp = None
+
+    def parse(self, textdata):
+        """
+        Parse the data, provided as lines of text, using the current
+        layout, into an internal data structure suitable for a
+        pytables 'table.append(parser.data)'.
+        """
+        cdef double last_ts = 0, ts
+        cdef int n = 0, i
+        cdef char *line
+
+        indata = cStringIO.StringIO(textdata)
+        # Assume any parsing error is a real error.
+        # In the future we might want to skip completely empty lines,
+        # or partial lines right before EOF?
+        try:
+            self.data = []
+            for pyline in indata:
+                line = pyline
+                n += 1
+                if line[0] == '\#':
+                    continue
+                (ts, row) = self.layout.parse(line)
+                if ts < last_ts:
+                    raise ValueError("timestamp is not "
+                                     "monotonically increasing")
+                last_ts = ts
+                self.data.append(row)
+        except (ValueError, IndexError, TypeError) as e:
+            raise ParserError(n, "error: " + e.message)
+
+        # Mark timestamp ranges
+        if len(self.data):
+            self.min_timestamp = self.data[0][0]
+            self.max_timestamp = self.data[-1][0]
+
+class Formatter(object):
+    """Object that formats database data into ASCII"""
+
+    def __init__(self, layout):
+        if issubclass(layout.__class__, Layout):
+            self.layout = layout
+        else:
+            try:
+                self.layout = get_named(layout)
+            except KeyError:
+                raise TypeError("unknown layout")
+
+    def format(self, data):
+        """
+        Format raw data from the database, using the current layout,
+        as lines of ACSII text.
+        """
+        text = cStringIO.StringIO()
+        try:
+            for row in data:
+                text.write(self.layout.format(row))
+        except (ValueError, IndexError, TypeError) as e:
+            raise FormatterError("formatting error: " + e.message)
+        return text.getvalue()

nilmdb/nilmdb.py

@@ -0,0 +1,518 @@
+# -*- coding: utf-8 -*-
+
+"""NilmDB
+
+Object that represents a NILM database file.
+
+Manages both the SQL database and the PyTables storage backend.
+"""
+
+# Need absolute_import so that "import nilmdb" won't pull in nilmdb.py,
+# but will pull the nilmdb module instead.
+from __future__ import absolute_import
+import nilmdb
+from nilmdb.printf import *
+
+import sqlite3
+import tables
+import time
+import sys
+import os
+import errno
+import bisect
+
+import pyximport
+pyximport.install()
+from nilmdb.interval import Interval, DBInterval, IntervalSet, IntervalError
+
+# Note about performance and transactions:
+#
+# Committing a transaction in the default sync mode (PRAGMA synchronous=FULL)
+# takes about 125msec.  sqlite3 will commit transactions at 3 times:
+# 1: explicit con.commit()
+# 2: between a series of DML commands and non-DML commands, e.g.
+#    after a series of INSERT, SELECT, but before a CREATE TABLE or PRAGMA.
+# 3: at the end of an explicit transaction, e.g. "with self.con as con:"
+#
+# To speed up testing, or if this transaction speed becomes an issue,
+# the sync=False option to NilmDB.__init__ will set PRAGMA synchronous=OFF.
+
+
+# Don't touch old entries -- just add new ones.
+_sql_schema_updates = {
+    0: """
+    -- All streams
+    CREATE TABLE streams(
+    	id INTEGER PRIMARY KEY,		-- stream ID
+        path TEXT UNIQUE NOT NULL,	-- path, e.g. '/newton/prep'
+        layout TEXT NOT NULL		-- layout name, e.g. float32_8
+    );
+
+    -- Individual timestamped ranges in those streams.
+    -- For a given start_time and end_time, this tells us that the
+    -- data is stored between start_pos and end_pos.
+    -- Times are stored as μs since Unix epoch
+    -- Positions are opaque: PyTables rows, file offsets, etc.
+    --
+    -- Note: end_pos points to the row _after_ end_time, so end_pos-1
+    -- is the last valid row.
+    CREATE TABLE ranges(
+        stream_id INTEGER NOT NULL,
+        start_time INTEGER NOT NULL,
+        end_time INTEGER NOT NULL,
+        start_pos INTEGER NOT NULL,
+        end_pos INTEGER NOT NULL
+    );
+    CREATE INDEX _ranges_index ON ranges (stream_id, start_time, end_time);
+    """,
+
+    1: """
+    -- Generic dictionary-type metadata that can be associated with a stream
+    CREATE TABLE metadata(
+    	stream_id INTEGER NOT NULL,
+        key TEXT NOT NULL,
+        value TEXT
+    );
+    """,
+}
+
+class NilmDBError(Exception):
+    """Base exception for NilmDB errors"""
+    def __init__(self, message = "Unspecified error"):
+        Exception.__init__(self, self.__class__.__name__ + ": " + message)
+
+class StreamError(NilmDBError):
+    pass
+
+class OverlapError(NilmDBError):
+    pass
+
+# Helper that lets us pass a Pytables table into bisect
+class BisectableTable(object):
+    def __init__(self, table):
+        self.table = table
+    def __getitem__(self, index):
+        return self.table[index][0]
+
+class NilmDB(object):
+    verbose = 0
+
+    def __init__(self, basepath, sync=True, max_results=None):
+        # set up path
+        self.basepath = os.path.abspath(basepath.rstrip('/'))
+
+        # Create the database path if it doesn't exist
+        try:
+            os.makedirs(self.basepath)
+        except OSError as e:
+            if e.errno != errno.EEXIST:
+                raise IOError("can't create tree " + self.basepath)
+
+        # Our HD5 file goes inside it
+        h5filename = os.path.abspath(self.basepath + "/data.h5")
+        self.h5file = tables.openFile(h5filename, "a", "NILM Database")
+
+        # SQLite database too
+        sqlfilename = os.path.abspath(self.basepath + "/data.sql")
+        # We use check_same_thread = False, assuming that the rest
+        # of the code (e.g. Server) will be smart and not access this
+        # database from multiple threads simultaneously.  That requirement
+        # may be relaxed later.
+        self.con = sqlite3.connect(sqlfilename, check_same_thread = False)
+        self._sql_schema_update()
+
+        # See big comment at top about the performance implications of this
+        if sync:
+            self.con.execute("PRAGMA synchronous=FULL")
+        else:
+            self.con.execute("PRAGMA synchronous=OFF")
+
+        # Approximate largest number of elements that we want to send
+        # in a single reply (for stream_intervals, stream_extract)
+        if max_results:
+            self.max_results = max_results
+        else:
+            self.max_results = 16384
+
+        self.opened = True
+
+        # Cached intervals
+        self._cached_iset = {}
+
+    def __del__(self):
+        if "opened" in self.__dict__: # pragma: no cover
+            fprintf(sys.stderr,
+                    "error: NilmDB.close() wasn't called, path %s",
+                    self.basepath)
+
+    def get_basepath(self):
+        return self.basepath
+
+    def close(self):
+        if self.con:
+            self.con.commit()
+            self.con.close()
+        self.h5file.close()
+        del self.opened
+
+    def _sql_schema_update(self):
+        cur = self.con.cursor()
+        version = cur.execute("PRAGMA user_version").fetchone()[0]
+        oldversion = version
+
+        while version in _sql_schema_updates:
+            cur.executescript(_sql_schema_updates[version])
+            version = version + 1
+            if self.verbose: # pragma: no cover
+                printf("Schema updated to %d\n", version)
+
+        if version != oldversion:
+            with self.con:
+                cur.execute("PRAGMA user_version = {v:d}".format(v=version))
+
+    def _get_intervals(self, stream_id):
+        """
+        Return a mutable IntervalSet corresponding to the given stream ID.
+        """
+        # Load from database if not cached
+        if stream_id not in self._cached_iset:
+            iset = IntervalSet()
+            result = self.con.execute("SELECT start_time, end_time, "
+                                      "start_pos, end_pos "
+                                      "FROM ranges "
+                                      "WHERE stream_id=?", (stream_id,))
+            try:
+                for (start_time, end_time, start_pos, end_pos) in result:
+                    iset += DBInterval(start_time, end_time,
+                                       start_time, end_time,
+                                       start_pos, end_pos)
+            except IntervalError as e: # pragma: no cover
+                raise NilmDBError("unexpected overlap in ranges table!")
+            self._cached_iset[stream_id] = iset
+        # Return cached value
+        return self._cached_iset[stream_id]
+
+    # TODO: Split add_interval into two pieces, one to add
+    # and one to flush to disk?
+    # Need to think about this.  Basic problem is that we can't
+    # mess with intervals once they're in the IntervalSet,
+    # without mucking with bxinterval internals.
+
+    # Maybe add a separate optimization step?
+    # Join intervals that have a fairly small gap between them
+
+    def _add_interval(self, stream_id, interval, start_pos, end_pos):
+        """
+        Add interval to the internal interval cache, and to the database.
+        Note: arguments must be ints (not numpy.int64, etc)
+        """
+        # Ensure this stream's intervals are cached, and add the new
+        # interval to that cache.
+        iset = self._get_intervals(stream_id)
+        try:
+            iset += DBInterval(interval.start, interval.end,
+                               interval.start, interval.end,
+                               start_pos, end_pos)
+        except IntervalError as e: # pragma: no cover
+            raise NilmDBError("new interval overlaps existing data")
+
+        # Insert into the database
+        self.con.execute("INSERT INTO ranges "
+                         "(stream_id,start_time,end_time,start_pos,end_pos) "
+                         "VALUES (?,?,?,?,?)",
+                         (stream_id, interval.start, interval.end,
+                          int(start_pos), int(end_pos)))
+        self.con.commit()
+
+    def stream_list(self, path = None, layout = None):
+        """Return list of [path, layout] lists of all streams
+        in the database.
+
+        If path is specified, include only streams with a path that
+        matches the given string.
+
+        If layout is specified, include only streams with a layout
+        that matches the given string.
+        """
+        where = "WHERE 1=1"
+        params = ()
+        if layout:
+            where += " AND layout=?"
+            params += (layout,)
+        if path:
+            where += " AND path=?"
+            params += (path,)
+        result = self.con.execute("SELECT path, layout "
+                                  "FROM streams " + where, params).fetchall()
+
+        return sorted(list(x) for x in result)
+
+    def stream_intervals(self, path, start = None, end = None):
+        """
+        Returns (intervals, restart) tuple.
+
+        intervals is a list of [start,end] timestamps of all intervals
+        that exist for path, between start and end.
+
+        restart, if nonzero, means that there were too many results to
+        return in a single request.  The data is complete from the
+        starting timestamp to the point at which it was truncated,
+        and a new request with a start time of 'restart' will fetch
+        the next block of data.
+        """
+        stream_id = self._stream_id(path)
+        intervals = self._get_intervals(stream_id)
+        requested = Interval(start or 0, end or 1e12)
+        result = []
+        for n, i in enumerate(intervals.intersection(requested)):
+            if n >= self.max_results:
+                restart = i.start
+                break
+            result.append([i.start, i.end])
+        else:
+            restart = 0
+        return (result, restart)
+
+    def stream_create(self, path, layout_name):
+        """Create a new table in the database.
+
+        path: path to the data (e.g. '/newton/prep').
+        Paths must contain at least two elements, e.g.:
+           /newton/prep
+           /newton/raw
+           /newton/upstairs/prep
+           /newton/upstairs/raw
+
+        layout_name: string for nilmdb.layout.get_named(), e.g. 'float32_8'
+        """
+        if path[0] != '/':
+            raise ValueError("paths must start with /")
+        [ group, node ] = path.rsplit("/", 1)
+        if group == '':
+            raise ValueError("invalid path")
+
+        # Get description
+        try:
+            desc = nilmdb.layout.get_named(layout_name).description()
+        except KeyError:
+            raise ValueError("no such layout")
+
+        # Estimated table size (for PyTables optimization purposes): assume
+        # 3 months worth of data at 8 KHz.  It's OK if this is wrong.
+        exp_rows = 8000 * 60*60*24*30*3
+
+        # Create the table
+        try:
+            table = self.h5file.createTable(group, node,
+                                            description = desc,
+                                            expectedrows = exp_rows,
+                                            createparents = True)
+        except AttributeError:
+            # Trying to create e.g. /foo/bar/baz when /foo/bar is already
+            # a table raises this error.
+            raise ValueError("error creating table at that path")
+
+        # Insert into SQL database once the PyTables is happy
+        with self.con as con:
+            con.execute("INSERT INTO streams (path, layout) VALUES (?,?)",
+                        (path, layout_name))
+
+    def _stream_id(self, path):
+        """Return unique stream ID"""
+        result = self.con.execute("SELECT id FROM streams WHERE path=?",
+                                  (path,)).fetchone()
+        if result is None:
+            raise StreamError("No stream at path " + path)
+        return result[0]
+
+    def stream_set_metadata(self, path, data):
+        """Set stream metadata from a dictionary, e.g.
+           { description = 'Downstairs lighting',
+             v_scaling = 123.45 }
+           This replaces all existing metadata.
+           """
+        stream_id = self._stream_id(path)
+        with self.con as con:
+            con.execute("DELETE FROM metadata WHERE stream_id=?", (stream_id,))
+            for key in data:
+                if data[key] != '':
+                    con.execute("INSERT INTO metadata VALUES (?, ?, ?)",
+                                (stream_id, key, data[key]))
+
+    def stream_get_metadata(self, path):
+        """Return stream metadata as a dictionary."""
+        stream_id = self._stream_id(path)
+        result = self.con.execute("SELECT metadata.key, metadata.value "
+                                  "FROM metadata "
+                                  "WHERE metadata.stream_id=?", (stream_id,))
+        data = {}
+        for (key, value) in result:
+            data[key] = value
+        return data
+
+    def stream_update_metadata(self, path, newdata):
+        """Update stream metadata from a dictionary"""
+        data = self.stream_get_metadata(path)
+        data.update(newdata)
+        self.stream_set_metadata(path, data)
+
+    def stream_destroy(self, path):
+        """Fully remove a table and all of its data from the database.
+        No way to undo it!  The group structure is removed, if there
+        are no other tables in it.  Metadata is removed."""
+        stream_id = self._stream_id(path)
+
+        # Delete the cached interval data
+        if stream_id in self._cached_iset:
+            del self._cached_iset[stream_id]
+
+        # Delete the data node, and all parent nodes (if they have no
+        # remaining children)
+        split_path = path.lstrip('/').split("/")
+        while split_path:
+            name = split_path.pop()
+            where = "/" + "/".join(split_path)
+            try:
+                self.h5file.removeNode(where, name, recursive = False)
+            except tables.NodeError:
+                break
+
+        # Delete metadata, stream, intervals
+        with self.con as con:
+            con.execute("DELETE FROM metadata WHERE stream_id=?", (stream_id,))
+            con.execute("DELETE FROM ranges WHERE stream_id=?", (stream_id,))
+            con.execute("DELETE FROM streams WHERE id=?", (stream_id,))
+
+    def stream_insert(self, path, parser, old_timestamp = None):
+        """Insert new data into the database.
+           path: Path at which to add the data
+           parser: nilmdb.layout.Parser instance full of data to insert
+           """
+        if (not parser.min_timestamp or not parser.max_timestamp or
+            not len(parser.data)):
+            raise StreamError("no data provided")
+
+        # If we were provided with an old timestamp, the expectation
+        # is that the client has a contiguous block of time it is sending,
+        # but it's doing it over multiple calls to stream_insert.
+        # old_timestamp is the max_timestamp of the previous insert.
+        # To make things continuous, use that as our starting timestamp
+        # instead of what the parser found.
+        if old_timestamp:
+            min_timestamp = old_timestamp
+        else:
+            min_timestamp = parser.min_timestamp
+
+        # First check for basic overlap using timestamp info given.
+        stream_id = self._stream_id(path)
+        iset = self._get_intervals(stream_id)
+        interval = Interval(min_timestamp, parser.max_timestamp)
+        if iset.intersects(interval):
+            raise OverlapError("new data overlaps existing data at range: "
+                               + str(iset & interval))
+
+        # Insert the data into pytables
+        table = self.h5file.getNode(path)
+        row_start = table.nrows
+        table.append(parser.data)
+        row_end = table.nrows
+        table.flush()
+
+        # Insert the record into the sql database.
+        # Casts are to convert from numpy.int64.
+        self._add_interval(stream_id, interval, int(row_start), int(row_end))
+
+        # And that's all
+        return "ok"
+
+    def _find_start(self, table, interval):
+        """
+        Given a DBInterval, find the row in the database that
+        corresponds to the start time.  Return the first database
+        position with a timestamp (first element) greater than or
+        equal to 'start'.
+        """
+        # Optimization for the common case where an interval wasn't truncated
+        if interval.start == interval.db_start:
+            return interval.db_startpos
+        return bisect.bisect_left(BisectableTable(table),
+                                  interval.start,
+                                  interval.db_startpos,
+                                  interval.db_endpos)
+
+    def _find_end(self, table, interval):
+        """
+        Given a DBInterval, find the row in the database that follows
+        the end time.  Return the first database position after the
+        row with timestamp (first element) greater than or equal
+        to 'end'.
+        """
+        # Optimization for the common case where an interval wasn't truncated
+        if interval.end == interval.db_end:
+            return interval.db_endpos
+        # Note that we still use bisect_left here, because we don't
+        # want to include the given timestamp in the results.  This is
+        # so a queries like 1:00 -> 2:00 and 2:00 -> 3:00 return
+        # non-overlapping data.
+        return bisect.bisect_left(BisectableTable(table),
+                                  interval.end,
+                                  interval.db_startpos,
+                                  interval.db_endpos)
+
+    def stream_extract(self, path, start = None, end = None, count = False):
+        """
+        Returns (data, restart) tuple.
+
+        data is a list of raw data from the database, suitable for
+        passing to e.g. nilmdb.layout.Formatter to translate into
+        textual form.
+
+        restart, if nonzero, means that there were too many results to
+        return in a single request.  The data is complete from the
+        starting timestamp to the point at which it was truncated,
+        and a new request with a start time of 'restart' will fetch
+        the next block of data.
+
+        count, if true, means to not return raw data, but just the count
+        of rows that would have been returned.  This is much faster
+        than actually fetching the data.  It is not limited by
+        max_results.
+        """
+        table = self.h5file.getNode(path)
+        stream_id = self._stream_id(path)
+        intervals = self._get_intervals(stream_id)
+        requested = Interval(start or 0, end or 1e12)
+        result = []
+        matched = 0
+        remaining = self.max_results
+        restart = 0
+        for interval in intervals.intersection(requested):
+            # Reading single rows from the table is too slow, so
+            # we use two bisections to find both the starting and
+            # ending row for this particular interval, then
+            # read the entire range as one slice.
+            row_start = self._find_start(table, interval)
+            row_end = self._find_end(table, interval)
+
+            if count:
+                matched += row_end - row_start
+                continue
+
+            # Shorten it if we'll hit the maximum number of results
+            row_max = row_start + remaining
+            if row_max < row_end:
+                row_end = row_max
+                restart = table[row_max][0]
+
+            # Gather these results up
+            result.extend(table[row_start:row_end])
+
+            # Count them
+            remaining -= row_end - row_start
+
+            if restart:
+                break
+
+        if count:
+            return matched
+        return (result, restart)

nilmdb/printf.py

@@ -0,0 +1,9 @@
+"""printf, fprintf, sprintf"""
+
+from __future__ import print_function
+def printf(_str, *args):
+    print(_str % args, end='')
+def fprintf(_file, _str, *args):
+    print(_str % args, end='', file=_file)
+def sprintf(_str, *args):
+    return (_str % args)

nilmdb/rbtree.pxd

@@ -0,0 +1,23 @@
+cdef class RBNode:
+    cdef public object obj
+    cdef public double start, end
+    cdef public int red
+    cdef public RBNode left, right, parent
+
+cdef class RBTree:
+    cdef public RBNode nil, root
+
+    cpdef getroot(RBTree self)
+    cdef void __rotate_left(RBTree self, RBNode x)
+    cdef void __rotate_right(RBTree self, RBNode y)
+    cdef RBNode __successor(RBTree self, RBNode x)
+    cpdef RBNode successor(RBTree self, RBNode x)
+    cdef RBNode __predecessor(RBTree self, RBNode x)
+    cpdef RBNode predecessor(RBTree self, RBNode x)
+    cpdef insert(RBTree self, RBNode z)
+    cdef void __insert_fixup(RBTree self, RBNode x)
+    cpdef delete(RBTree self, RBNode z)
+    cdef inline void __delete_fixup(RBTree self, RBNode x)
+    cpdef RBNode find(RBTree self, double start, double end)
+    cpdef RBNode find_left_end(RBTree self, double t)
+    cpdef RBNode find_right_start(RBTree self, double t)

nilmdb/rbtree.pyx

@@ -0,0 +1,377 @@
+# cython: profile=False
+# cython: cdivision=True
+
+"""
+Jim Paris <jim@jtan.com>
+
+Red-black tree, where keys are stored as start/end timestamps.
+This is a basic interval tree that holds half-open intervals:
+  [start, end)
+Intervals must not overlap.  Fixing that would involve making this
+into an augmented interval tree as described in CLRS 14.3.
+
+Code that assumes non-overlapping intervals is marked with the
+string 'non-overlapping'.
+"""
+
+import sys
+cimport rbtree
+
+cdef class RBNode:
+    """One node of the Red/Black tree, containing a key (start, end)
+    and value (obj)"""
+    def __init__(self, double start, double end, object obj = None):
+        self.obj = obj
+        self.start = start
+        self.end = end
+        self.red = False
+        self.left = None
+        self.right = None
+
+    def __str__(self):
+        if self.red:
+            color = "R"
+        else:
+            color = "B"
+        if self.start == sys.float_info.min:
+            return "[node nil]"
+        return ("[node ("
+                + str(self.obj) + ") "
+                + str(self.start) + " -> " + str(self.end) + " "
+                + color + "]")
+
+cdef class RBTree:
+    """Red/Black tree"""
+
+    # Init
+    def __init__(self):
+        self.nil = RBNode(start = sys.float_info.min,
+                          end = sys.float_info.min)
+        self.nil.left = self.nil
+        self.nil.right = self.nil
+        self.nil.parent = self.nil
+
+        self.root = RBNode(start = sys.float_info.max,
+                           end = sys.float_info.max)
+        self.root.left = self.nil
+        self.root.right = self.nil
+        self.root.parent = self.nil
+
+    # We have a dummy root node to simplify operations, so from an
+    # external point of view, its left child is the real root.
+    cpdef getroot(self):
+        return self.root.left
+
+    # Rotations and basic operations
+    cdef void __rotate_left(self, RBNode x):
+        """Rotate left:
+        #   x           y
+        #  / \   -->   / \
+        # z   y       x   w
+        #    / \     / \
+        #   v   w   z   v
+        """
+        cdef RBNode y = x.right
+        x.right = y.left
+        if y.left is not self.nil:
+            y.left.parent = x
+        y.parent = x.parent
+        if x is x.parent.left:
+            x.parent.left = y
+        else:
+            x.parent.right = y
+        y.left = x
+        x.parent = y
+
+    cdef void __rotate_right(self, RBNode y):
+        """Rotate right:
+        #     y           x
+        #    / \   -->   / \
+        #   x   w       z   y
+        #  / \             / \
+        # z   v           v   w
+        """
+        cdef RBNode x = y.left
+        y.left = x.right
+        if x.right is not self.nil:
+            x.right.parent = y
+        x.parent = y.parent
+        if y is y.parent.left:
+            y.parent.left = x
+        else:
+            y.parent.right = x
+        x.right = y
+        y.parent = x
+
+    cdef RBNode __successor(self, RBNode x):
+        """Returns the successor of RBNode x"""
+        cdef RBNode y = x.right
+        if y is not self.nil:
+            while y.left is not self.nil:
+                y = y.left
+        else:
+            y = x.parent
+            while x is y.right:
+                x = y
+                y = y.parent
+            if y is self.root:
+                return self.nil
+        return y
+    cpdef RBNode successor(self, RBNode x):
+        """Returns the successor of RBNode x, or None"""
+        cdef RBNode y = self.__successor(x)
+        return y if y is not self.nil else None
+
+    cdef RBNode __predecessor(self, RBNode x):
+        """Returns the predecessor of RBNode x"""
+        cdef RBNode y = x.left
+        if y is not self.nil:
+            while y.right is not self.nil:
+                y = y.right
+        else:
+            y = x.parent
+            while x is y.left:
+                if y is self.root:
+                    y = self.nil
+                    break
+                x = y
+                y = y.parent
+        return y
+    cpdef RBNode predecessor(self, RBNode x):
+        """Returns the predecessor of RBNode x, or None"""
+        cdef RBNode y = self.__predecessor(x)
+        return y if y is not self.nil else None
+
+    # Insertion
+    cpdef insert(self, RBNode z):
+        """Insert RBNode z into RBTree and rebalance as necessary"""
+        z.left = self.nil
+        z.right = self.nil
+        cdef RBNode y = self.root
+        cdef RBNode x = self.root.left
+        while x is not self.nil:
+            y = x
+            if (x.start > z.start or (x.start == z.start and x.end > z.end)):
+                x = x.left
+            else:
+                x = x.right
+        z.parent = y
+        if (y is self.root or
+            (y.start > z.start or (y.start == z.start and y.end > z.end))):
+            y.left = z
+        else:
+            y.right = z
+        # relabel/rebalance
+        self.__insert_fixup(z)
+
+    cdef void __insert_fixup(self, RBNode x):
+        """Rebalance/fix RBTree after a simple insertion of RBNode x"""
+        x.red = True
+        while x.parent.red:
+            if x.parent is x.parent.parent.left:
+                y = x.parent.parent.right
+                if y.red:
+                    x.parent.red = False
+                    y.red = False
+                    x.parent.parent.red = True
+                    x = x.parent.parent
+                else:
+                    if x is x.parent.right:
+                        x = x.parent
+                        self.__rotate_left(x)
+                    x.parent.red = False
+                    x.parent.parent.red = True
+                    self.__rotate_right(x.parent.parent)
+            else: # same as above, left/right switched
+                y = x.parent.parent.left
+                if y.red:
+                    x.parent.red = False
+                    y.red = False
+                    x.parent.parent.red = True
+                    x = x.parent.parent
+                else:
+                    if x is x.parent.left:
+                        x = x.parent
+                        self.__rotate_right(x)
+                    x.parent.red = False
+                    x.parent.parent.red = True
+                    self.__rotate_left(x.parent.parent)
+        self.root.left.red = False
+
+    # Deletion
+    cpdef delete(self, RBNode z):
+        if z.left is None or z.right is None:
+            raise AttributeError("you can only delete a node object "
+                                 + "from the tree; use find() to get one")
+        cdef RBNode x, y
+        if z.left is self.nil or z.right is self.nil:
+            y = z
+        else:
+            y = self.__successor(z)
+        if y.left is self.nil:
+            x = y.right
+        else:
+            x = y.left
+        x.parent = y.parent
+        if x.parent is self.root:
+            self.root.left = x
+        else:
+            if y is y.parent.left:
+                y.parent.left = x
+            else:
+                y.parent.right = x
+        if y is not z:
+            # y is the node to splice out, x is its child
+            y.left = z.left
+            y.right = z.right
+            y.parent = z.parent
+            z.left.parent = y
+            z.right.parent = y
+            if z is z.parent.left:
+                z.parent.left = y
+            else:
+                z.parent.right = y
+            if not y.red:
+                y.red = z.red
+                self.__delete_fixup(x)
+            else:
+                y.red = z.red
+        else:
+            if not y.red:
+                self.__delete_fixup(x)
+
+    cdef void __delete_fixup(self, RBNode x):
+        """Rebalance/fix RBTree after a deletion.  RBNode x is the
+        child of the spliced out node."""
+        cdef RBNode rootLeft = self.root.left
+        while not x.red and x is not rootLeft:
+            if x is x.parent.left:
+                w = x.parent.right
+                if w.red:
+                    w.red = False
+                    x.parent.red = True
+                    self.__rotate_left(x.parent)
+                    w = x.parent.right
+                if not w.right.red and not w.left.red:
+                    w.red = True
+                    x = x.parent
+                else:
+                    if not w.right.red:
+                        w.left.red = False
+                        w.red = True
+                        self.__rotate_right(w)
+                        w = x.parent.right
+                    w.red = x.parent.red
+                    x.parent.red = False
+                    w.right.red = False
+                    self.__rotate_left(x.parent)
+                    x = rootLeft # exit loop
+            else: # same as above, left/right switched
+                w = x.parent.left
+                if w.red:
+                    w.red = False
+                    x.parent.red = True
+                    self.__rotate_right(x.parent)
+                    w = x.parent.left
+                if not w.left.red and not w.right.red:
+                    w.red = True
+                    x = x.parent
+                else:
+                    if not w.left.red:
+                        w.right.red = False
+                        w.red = True
+                        self.__rotate_left(w)
+                        w = x.parent.left
+                    w.red = x.parent.red
+                    x.parent.red = False
+                    w.left.red = False
+                    self.__rotate_right(x.parent)
+                    x = rootLeft # exit loop
+        x.red = False
+
+    # Walking, searching
+    def __iter__(self):
+        return self.inorder()
+
+    def inorder(self, RBNode x = None):
+        """Generator that performs an inorder walk for the tree
+        rooted at RBNode x"""
+        if x is None:
+            x = self.getroot()
+        while x.left is not self.nil:
+            x = x.left
+        while x is not self.nil:
+            yield x
+            x = self.__successor(x)
+
+    cpdef RBNode find(self, double start, double end):
+        """Return the node with exactly the given start and end."""
+        cdef RBNode x = self.getroot()
+        while x is not self.nil:
+            if start < x.start:
+                x = x.left
+            elif start == x.start:
+                if end == x.end:
+                    break # found it
+                elif end < x.end:
+                    x = x.left
+                else:
+                    x = x.right
+            else:
+                x = x.right
+        return x if x is not self.nil else None
+
+    cpdef RBNode find_left_end(self, double t):
+        """Find the leftmode node with end >= t.  With non-overlapping
+        intervals, this is the first node that might overlap time t.
+
+        Note that this relies on non-overlapping intervals, since
+        it assumes that we can use the endpoints to traverse the
+        tree even though it was created using the start points."""
+        cdef RBNode x = self.getroot()
+        while x is not self.nil:
+            if t < x.end:
+                if x.left is self.nil:
+                    break
+                x = x.left
+            elif t == x.end:
+                break
+            else:
+                if x.right is self.nil:
+                    x = self.__successor(x)
+                    break
+                x = x.right
+        return x if x is not self.nil else None
+
+    cpdef RBNode find_right_start(self, double t):
+        """Find the rightmode node with start <= t.  With non-overlapping
+        intervals, this is the last node that might overlap time t."""
+        cdef RBNode x = self.getroot()
+        while x is not self.nil:
+            if t < x.start:
+                if x.left is self.nil:
+                    x = self.__predecessor(x)
+                    break
+                x = x.left
+            elif t == x.start:
+                break
+            else:
+                if x.right is self.nil:
+                    break
+                x = x.right
+        return x if x is not self.nil else None
+
+    # Intersections
+    def intersect(self, double start, double end):
+        """Generator that returns nodes that overlap the given
+        (start,end) range.  Assumes non-overlapping intervals."""
+        # Start with the leftmode node that ends after start
+        cdef RBNode n = self.find_left_end(start)
+        while n is not None:
+            if n.start >= end:
+                # this node starts after the requested end; we're done
+                break
+            if start < n.end:
+                # this node overlaps our requested area
+                yield n
+            n = self.successor(n)

nilmdb/rbtree.pyxdep

@@ -0,0 +1 @@
+rbtree.pxd

nilmdb/serializer.py

@@ -0,0 +1,69 @@
+import Queue
+import threading
+import sys
+
+# This file provides a class that will wrap an object and serialize
+# all calls to its methods.  All calls to that object will be queued
+# and executed from a single thread, regardless of which thread makes
+# the call.
+
+# Based partially on http://stackoverflow.com/questions/2642515/
+
+class SerializerThread(threading.Thread):
+    """Thread that retrieves call information from the queue, makes the
+    call, and returns the results."""
+    def __init__(self, call_queue):
+        threading.Thread.__init__(self)
+        self.call_queue = call_queue
+
+    def run(self):
+        while True:
+            result_queue, func, args, kwargs = self.call_queue.get()
+            # Terminate if result_queue is None
+            if result_queue is None:
+                return
+            try:
+                result = func(*args, **kwargs) # wrapped
+            except:
+                result_queue.put((sys.exc_info(), None))
+            else:
+                result_queue.put((None, result))
+
+class WrapCall(object):
+    """Wrap a callable using the given queues"""
+
+    def __init__(self, call_queue, result_queue, func):
+        self.call_queue = call_queue
+        self.result_queue = result_queue
+        self.func = func
+
+    def __call__(self, *args, **kwargs):
+        self.call_queue.put((self.result_queue, self.func, args, kwargs))
+        ( exc_info, result ) = self.result_queue.get()
+        if exc_info is None:
+            return result
+        else:
+            raise exc_info[0], exc_info[1], exc_info[2]
+
+class WrapObject(object):
+    """Wrap all calls to methods in a target object with WrapCall"""
+
+    def __init__(self, target):
+        self.__wrap_target = target
+        self.__wrap_call_queue = Queue.Queue()
+        self.__wrap_serializer = SerializerThread(self.__wrap_call_queue)
+        self.__wrap_serializer.daemon = True
+        self.__wrap_serializer.start()
+
+    def __getattr__(self, key):
+        """Wrap methods of self.__wrap_target in a WrapCall instance"""
+        func = getattr(self.__wrap_target, key)
+        if not callable(func):
+            raise TypeError("Can't serialize attribute %r (type: %s)"
+                            % (key, type(func)))
+        result_queue = Queue.Queue()
+        return WrapCall(self.__wrap_call_queue, result_queue, func)
+
+    def __del__(self):
+        self.__wrap_call_queue.put((None, None, None, None))
+        self.__wrap_serializer.join()

nilmdb/server.py

@@ -0,0 +1,414 @@
+"""CherryPy-based server for accessing NILM database via HTTP"""
+
+# Need absolute_import so that "import nilmdb" won't pull in nilmdb.py,
+# but will pull the nilmdb module instead.
+from __future__ import absolute_import
+import nilmdb
+
+from nilmdb.printf import *
+
+import cherrypy
+import sys
+import time
+import os
+import simplejson as json
+
+try:
+    import cherrypy
+    cherrypy.tools.json_out
+except: # pragma: no cover
+    sys.stderr.write("Cherrypy 3.2+ required\n")
+    sys.exit(1)
+
+class NilmApp(object):
+    def __init__(self, db):
+        self.db = db
+
+version = "1.1"
+
+class Root(NilmApp):
+    """Root application for NILM database"""
+
+    def __init__(self, db, version):
+        super(Root, self).__init__(db)
+        self.server_version = version
+
+    # /
+    @cherrypy.expose
+    def index(self):
+        raise cherrypy.NotFound()
+
+    # /favicon.ico
+    @cherrypy.expose
+    def favicon_ico(self):
+        raise cherrypy.NotFound()
+
+    # /version
+    @cherrypy.expose
+    @cherrypy.tools.json_out()
+    def version(self):
+        return self.server_version
+
+    # /dbpath
+    @cherrypy.expose
+    @cherrypy.tools.json_out()
+    def dbpath(self):
+        return self.db.get_basepath()
+
+    # /dbsize
+    @cherrypy.expose
+    @cherrypy.tools.json_out()
+    def dbsize(self):
+        return nilmdb.du.du(self.db.get_basepath())
+
+class Stream(NilmApp):
+    """Stream-specific operations"""
+
+    # /stream/list
+    # /stream/list?layout=PrepData
+    # /stream/list?path=/newton/prep
+    @cherrypy.expose
+    @cherrypy.tools.json_out()
+    def list(self, path = None, layout = None):
+        """List all streams in the database.  With optional path or
+        layout parameter, just list streams that match the given path
+        or layout"""
+        return self.db.stream_list(path, layout)
+
+    # /stream/create?path=/newton/prep&layout=PrepData
+    @cherrypy.expose
+    @cherrypy.tools.json_out()
+    def create(self, path, layout):
+        """Create a new stream in the database.  Provide path
+        and one of the nilmdb.layout.layouts keys.
+        """
+        try:
+            return self.db.stream_create(path, layout)
+        except Exception as e:
+            message = sprintf("%s: %s", type(e).__name__, e.message)
+            raise cherrypy.HTTPError("400 Bad Request", message)
+
+    # /stream/destroy?path=/newton/prep
+    @cherrypy.expose
+    @cherrypy.tools.json_out()
+    def destroy(self, path):
+        """Delete a stream and its associated data."""
+        try:
+            return self.db.stream_destroy(path)
+        except Exception as e:
+            message = sprintf("%s: %s", type(e).__name__, e.message)
+            raise cherrypy.HTTPError("400 Bad Request", message)
+
+    # /stream/get_metadata?path=/newton/prep
+    # /stream/get_metadata?path=/newton/prep&key=foo&key=bar
+    @cherrypy.expose
+    @cherrypy.tools.json_out()
+    def get_metadata(self, path, key=None):
+        """Get metadata for the named stream.  If optional
+        key parameters are specified, only return metadata
+        matching the given keys."""
+        try:
+            data = self.db.stream_get_metadata(path)
+        except nilmdb.nilmdb.StreamError as e:
+            raise cherrypy.HTTPError("404 Not Found", e.message)
+        if key is None:  # If no keys specified, return them all
+            key = data.keys()
+        elif not isinstance(key, list):
+            key = [ key ]
+        result = {}
+        for k in key:
+            if k in data:
+                result[k] = data[k]
+            else: # Return "None" for keys with no matching value
+                result[k] = None
+        return result
+
+    # /stream/set_metadata?path=/newton/prep&data=<json>
+    @cherrypy.expose
+    @cherrypy.tools.json_out()
+    def set_metadata(self, path, data):
+        """Set metadata for the named stream, replacing any
+        existing metadata.  Data should be a json-encoded
+        dictionary"""
+        try:
+            data_dict = json.loads(data)
+            self.db.stream_set_metadata(path, data_dict)
+        except Exception as e:
+            message = sprintf("%s: %s", type(e).__name__, e.message)
+            raise cherrypy.HTTPError("400 Bad Request", message)
+        return "ok"
+
+    # /stream/update_metadata?path=/newton/prep&data=<json>
+    @cherrypy.expose
+    @cherrypy.tools.json_out()
+    def update_metadata(self, path, data):
+        """Update metadata for the named stream.  Data
+        should be a json-encoded dictionary"""
+        try:
+            data_dict = json.loads(data)
+            self.db.stream_update_metadata(path, data_dict)
+        except Exception as e:
+            message = sprintf("%s: %s", type(e).__name__, e.message)
+            raise cherrypy.HTTPError("400 Bad Request", message)
+        return "ok"
+
+    # /stream/insert?path=/newton/prep
+    @cherrypy.expose
+    @cherrypy.tools.json_out()
+    #@cherrypy.tools.disable_prb()
+    def insert(self, path, old_timestamp = None):
+        """
+        Insert new data into the database.  Provide textual data
+        (matching the path's layout) as a HTTP PUT.
+
+        old_timestamp is used when making multiple, split-up insertions
+        for a larger contiguous block of data.  The first insert
+        will return the maximum timestamp that it saw, and the second
+        insert should provide this timestamp as an argument.  This is
+        used to extend the previous database interval rather than
+        start a new one.
+        """
+
+        # Important that we always read the input before throwing any
+        # errors, to keep lengths happy for persistent connections.
+        # However, CherryPy 3.2.2 has a bug where this fails for GET
+        # requests, so catch that. (issue #1134)
+        try:
+            body = cherrypy.request.body.read()
+        except TypeError:
+            raise cherrypy.HTTPError("400 Bad Request", "No request body")
+
+        # Check path and get layout
+        streams = self.db.stream_list(path = path)
+        if len(streams) != 1:
+            raise cherrypy.HTTPError("404 Not Found", "No such stream")
+        layout = streams[0][1]
+
+        # Parse the input data
+        try:
+            parser = nilmdb.layout.Parser(layout)
+            parser.parse(body)
+        except nilmdb.layout.ParserError as e:
+            raise cherrypy.HTTPError("400 Bad Request",
+                                     "Error parsing input data: " +
+                                     e.message)
+
+        # Now do the nilmdb insert, passing it the parser full of data.
+        try:
+            if old_timestamp:
+                old_timestamp = float(old_timestamp)
+            result = self.db.stream_insert(path, parser, old_timestamp)
+        except nilmdb.nilmdb.NilmDBError as e:
+            raise cherrypy.HTTPError("400 Bad Request", e.message)
+
+        # Return the maximum timestamp that we saw.  The client will
+        # return this back to us as the old_timestamp parameter, if
+        # it has more data to send.
+        return ("ok", parser.max_timestamp)
+
+    # /stream/intervals?path=/newton/prep
+    # /stream/intervals?path=/newton/prep&start=1234567890.0&end=1234567899.0
+    @cherrypy.expose
+    def intervals(self, path, start = None, end = None):
+        """
+        Get intervals from backend database.  Streams the resulting
+        intervals as JSON strings separated by newlines.  This may
+        make multiple requests to the nilmdb backend to avoid causing
+        it to block for too long.
+        """
+        if start is not None:
+            start = float(start)
+        if end is not None:
+            end = float(end)
+
+        if start is not None and end is not None:
+            if end < start:
+                raise cherrypy.HTTPError("400 Bad Request",
+                                         "end before start")
+
+        streams = self.db.stream_list(path = path)
+        if len(streams) != 1:
+            raise cherrypy.HTTPError("404 Not Found", "No such stream")
+
+        def content(start, end):
+            # Note: disable response.stream below to get better debug info
+            # from tracebacks in this subfunction.
+            while True:
+                (intervals, restart) = self.db.stream_intervals(path,start,end)
+                response = ''.join([ json.dumps(i) + "\n" for i in intervals ])
+                yield response
+                if restart == 0:
+                    break
+                start = restart
+        return content(start, end)
+    intervals._cp_config = { 'response.stream': True } # chunked HTTP response
+
+    # /stream/extract?path=/newton/prep&start=1234567890.0&end=1234567899.0
+    @cherrypy.expose
+    def extract(self, path, start = None, end = None, count = False):
+        """
+        Extract data from backend database.  Streams the resulting
+        entries as ASCII text lines separated by newlines.  This may
+        make multiple requests to the nilmdb backend to avoid causing
+        it to block for too long.
+
+        Add count=True to return a count rather than actual data.
+        """
+        if start is not None:
+            start = float(start)
+        if end is not None:
+            end = float(end)
+
+        # Check parameters
+        if start is not None and end is not None:
+            if end < start:
+                raise cherrypy.HTTPError("400 Bad Request",
+                                         "end before start")
+
+        # Check path and get layout
+        streams = self.db.stream_list(path = path)
+        if len(streams) != 1:
+            raise cherrypy.HTTPError("404 Not Found", "No such stream")
+        layout = streams[0][1]
+
+        # Get formatter
+        formatter = nilmdb.layout.Formatter(layout)
+
+        def content(start, end, count):
+            # Note: disable response.stream below to get better debug info
+            # from tracebacks in this subfunction.
+            if count:
+                matched = self.db.stream_extract(path, start, end, count)
+                yield sprintf("%d\n", matched)
+                return
+
+            while True:
+                (data, restart) = self.db.stream_extract(path, start, end)
+
+                # Format the data and yield it
+                yield formatter.format(data)
+
+                if restart == 0:
+                    return
+                start = restart
+        return content(start, end, count)
+    extract._cp_config = { 'response.stream': True } # chunked HTTP response
+
+
+class Exiter(object):
+    """App that exits the server, for testing"""
+    @cherrypy.expose
+    def index(self):
+        cherrypy.response.headers['Content-Type'] = 'text/plain'
+        def content():
+            yield 'Exiting by request'
+            raise SystemExit
+        return content()
+    index._cp_config = { 'response.stream': True }
+
+class Server(object):
+    def __init__(self, db, host = '127.0.0.1', port = 8080,
+                 stoppable = False,       # whether /exit URL exists
+                 embedded = True,         # hide diagnostics and output, etc
+                 fast_shutdown = False,   # don't wait for clients to disconn.
+                 force_traceback = False  # include traceback in all errors
+                 ):
+        self.version = version
+
+        # Need to wrap DB object in a serializer because we'll call
+        # into it from separate threads.
+        self.embedded = embedded
+        self.db = nilmdb.serializer.WrapObject(db)
+        cherrypy.config.update({
+            'server.socket_host': host,
+            'server.socket_port': port,
+            'engine.autoreload_on': False,
+            'server.max_request_body_size': 4*1024*1024,
+            'error_page.default': self.json_error_page,
+            })
+        if self.embedded:
+            cherrypy.config.update({ 'environment': 'embedded' })
+
+        # Send tracebacks in error responses.  They're hidden by the
+        # error_page function for client errors (code 400-499).
+        cherrypy.config.update({ 'request.show_tracebacks' : True })
+        self.force_traceback = force_traceback
+
+        cherrypy.tree.apps = {}
+        cherrypy.tree.mount(Root(self.db, self.version), "/")
+        cherrypy.tree.mount(Stream(self.db), "/stream")
+        if stoppable:
+            cherrypy.tree.mount(Exiter(), "/exit")
+
+        # Shutdowns normally wait for clients to disconnect.  To speed
+        # up tests, set fast_shutdown = True
+        if fast_shutdown:
+            # Setting timeout to 0 triggers os._exit(70) at shutdown, grr...
+            cherrypy.server.shutdown_timeout = 0.01
+        else:
+            cherrypy.server.shutdown_timeout = 5
+
+    def json_error_page(self, status, message, traceback, version):
+        """Return a custom error page in JSON so the client can parse it"""
+        errordata = { "status" : status,
+                      "message" : message,
+                      "traceback" : traceback }
+        # Don't send a traceback if the error was 400-499 (client's fault)
+        try:
+            code = int(status.split()[0])
+            if not self.force_traceback:
+                if code >= 400 and code <= 499:
+                    errordata["traceback"] = ""
+        except Exception as e: # pragma: no cover
+            pass
+        # Override the response type, which was previously set to text/html
+        cherrypy.serving.response.headers['Content-Type'] = (
+            "application/json;charset=utf-8" )
+        # Undo the HTML escaping that cherrypy's get_error_page function applies
+        # (cherrypy issue 1135)
+        for k, v in errordata.iteritems():
+            v = v.replace("&lt;","<")
+            v = v.replace("&gt;",">")
+            v = v.replace("&amp;","&")
+            errordata[k] = v
+        return json.dumps(errordata, separators=(',',':'))
+
+    def start(self, blocking = False, event = None):
+
+        if not self.embedded: # pragma: no cover
+            # Handle signals nicely
+            if hasattr(cherrypy.engine, "signal_handler"):
+                cherrypy.engine.signal_handler.subscribe()
+            if hasattr(cherrypy.engine, "console_control_handler"):
+                cherrypy.engine.console_control_handler.subscribe()
+
+        # Cherrypy stupidly calls os._exit(70) when it can't bind the
+        # port.  At least try to print a reasonable error and continue
+        # in this case, rather than just dying silently (as we would
+        # otherwise do in embedded mode)
+        real_exit = os._exit
+        def fake_exit(code): # pragma: no cover
+            if code == os.EX_SOFTWARE:
+                fprintf(sys.stderr, "error: CherryPy called os._exit!\n")
+            else:
+                real_exit(code)
+        os._exit = fake_exit
+        cherrypy.engine.start()
+        os._exit = real_exit
+
+        if event is not None:
+            event.set()
+        if blocking:
+            try:
+                cherrypy.engine.wait(cherrypy.engine.states.EXITING,
+                                     interval = 0.1, channel = 'main')
+            except (KeyboardInterrupt, IOError): # pragma: no cover
+                cherrypy.engine.log('Keyboard Interrupt: shutting down bus')
+                cherrypy.engine.exit()
+            except SystemExit: # pragma: no cover
+                cherrypy.engine.log('SystemExit raised: shutting down bus')
+                cherrypy.engine.exit()
+                raise
+
+    def stop(self):
+        cherrypy.engine.exit()

nilmdb/test_fileinterval.py

@@ -1,46 +0,0 @@
-from nilmdb import Interval, IntervalSet, IntervalError, FileInterval
-from datetime import datetime
-from nose.tools import assert_raises
-
-from test_interval import iset
-
-def fiset(string):
-    """Like iset, but builds with FileIntervals instead of Intervals"""
-    iset = IntervalSet()
-    for i, c in enumerate(string):
-        day = datetime.strptime("{0:04d}".format(i+2000), "%Y")
-        if (c == "["):
-            start = day
-        elif (c == "|"):
-            iset += FileInterval(start, day, "test.dat")
-            start = day
-        elif (c == "]"):
-            iset += FileInterval(start, day, "test.dat")
-            del start
-    return iset
-
-def test_fileinterval_vs_interval():
-    """Test FileInterval/Interval inheritance"""
-
-    i = iset("[--]")
-    f = fiset("[--]")
-
-    # check types
-    assert(isinstance(i[0], Interval))
-    assert(not isinstance(i[0], FileInterval))
-    assert(isinstance(f[0], Interval))
-    assert(isinstance(f[0], FileInterval))
-
-    # when doing an intersection, result should be a subset of the first arg
-    u = (i & f)
-    assert(isinstance(u[0], Interval))
-    assert(not isinstance(u[0], FileInterval))
-    u = (f & i)
-    assert(isinstance(u[0], Interval))
-    assert(isinstance(u[0], FileInterval))
-
-    # they're still the same though
-    assert(i == f == u)
-
-    # just for coverage
-    assert_raises(IntervalError, fiset("[]")[0].subset, f[0].start, f[0].end)

nilmdb/test_interval.py

@@ -1,188 +0,0 @@
-from nilmdb import Interval, IntervalSet, IntervalError
-from datetime import datetime
-from nose.tools import assert_raises
-import itertools 
-
-def test_interval():
-    """Test the Interval class"""
-    d1 = datetime.strptime("19801205","%Y%m%d")
-    d2 = datetime.strptime("19900216","%Y%m%d")
-    d3 = datetime.strptime("20111205","%Y%m%d")
-
-    # basic construction
-    i = Interval(d1, d1)
-    i = Interval(d1, d3)
-    assert(i.start == d1)
-    assert(i.end == d3)
-
-    # assignment should work
-    i.start = d2
-    try:
-        i.end = d1
-        raise Exception("should have died there")
-    except IntervalError:
-        pass
-    i.start = d1
-    i.end = d2
-
-    # end before start
-    assert_raises(IntervalError, Interval, d3, d1)
-
-    # wrong type
-    assert_raises(IntervalError, Interval, 1, 2)
-
-    # compare
-    assert(Interval(d1, d2) == Interval(d1, d2))
-    assert(Interval(d1, d2) < Interval(d1, d3))
-    assert(Interval(d1, d3) > Interval(d1, d2))
-    assert(Interval(d1, d2) < Interval(d2, d3))
-    assert(Interval(d1, d3) < Interval(d2, d3))
-    assert(Interval(d2, d2) > Interval(d1, d3))
-    assert(Interval(d3, d3) == Interval(d3, d3))
-    assert_raises(TypeError, cmp, i, 123)
-
-    # subset
-    assert(Interval(d1, d3).subset(d1, d2) == Interval(d1, d2))
-    assert_raises(IntervalError, Interval(d2, d3).subset, d1, d2)
-
-    # append
-    assert(Interval(d1, d2).is_adjacent(Interval(d2,d3)))
-    assert(Interval(d2, d3).is_adjacent(Interval(d1,d2)))
-    assert(not Interval(d2, d3).is_adjacent(Interval(d1,d3)))
-    assert_raises(TypeError, Interval(d1, d2).is_adjacent, 1)
-
-    # misc
-    assert(repr(i) == repr(eval(repr(i).replace("datetime.",""))))
-    assert(str(i) == "[1980-12-05 00:00:00 -> 1990-02-16 00:00:00]")
-
-def test_interval_intersect():
-    """Test Interval intersections"""
-    dates = [ datetime.strptime(year, "%y") for year in [ "00", "01", "02", "03" ] ]
-    perm = list(itertools.permutations(dates, 2))
-    prod = list(itertools.product(perm, perm))
-    should_intersect = {
-        False: [4, 5, 8, 20, 48, 56, 60, 96, 97, 100],
-        True: [0, 1, 2, 12, 13, 14, 16, 17, 24, 25, 26, 28, 29,
-               32, 49, 50, 52, 53, 61, 62, 64, 65, 68, 98, 101, 104]}
-    for i,((a,b),(c,d)) in enumerate(prod):
-        try:
-            i1 = Interval(a, b)
-            i2 = Interval(c, d)
-            assert(i1.intersects(i2) == i2.intersects(i1))
-            assert(i in should_intersect[i1.intersects(i2)])
-        except IntervalError:
-            assert(i not in should_intersect[True] and
-                   i not in should_intersect[False])
-    assert_raises(TypeError, i1.intersects, 1234)
-
-def test_intervalset_construct():
-    """Test interval set construction"""
-    dates = [ datetime.strptime(year, "%y") for year in [ "00", "01", "02", "03" ]]
-
-    a = Interval(dates[0], dates[1])
-    b = Interval(dates[1], dates[2])
-    c = Interval(dates[0], dates[2])
-    d = Interval(dates[2], dates[3])
-
-    iseta = IntervalSet(a)
-    isetb = IntervalSet([a, b])
-    isetc = IntervalSet([a])
-    assert(iseta != isetb)
-    assert(iseta == isetc)
-    assert(iseta != 3)
-    assert(IntervalSet(a) != IntervalSet(b))
-    
-    assert_raises(TypeError, cmp, iseta, isetb)
-    assert_raises(IntervalError, IntervalSet, [a, b, c])
-    assert_raises(TypeError, IntervalSet, [1, 2])
-
-    iset = IntervalSet(isetb)   # test iterator
-    assert(iset == isetb)
-    assert(len(iset) == 2)
-    assert(len(IntervalSet()) == 0)
-
-    # Test adding
-    iset = IntervalSet(a)
-    iset += IntervalSet(b)
-    assert(iset == IntervalSet([a, b]))
-    iset = IntervalSet(a)
-    iset += b
-    assert(iset == IntervalSet([a, b]))
-    iset = IntervalSet(a) + IntervalSet(b)
-    assert(iset == IntervalSet([a, b]))
-    iset = IntervalSet(b) + a
-    assert(iset == IntervalSet([a, b]))
-
-    # A set consisting of [0-1],[1-2] should match a set consisting of [0-2]
-    assert(IntervalSet([a,b]) == IntervalSet([c]))
-    # Etc
-    assert(IntervalSet([a,d]) != IntervalSet([c]))
-    assert(IntervalSet([c]) != IntervalSet([a,d]))
-    assert(IntervalSet([c,d]) != IntervalSet([b,d]))
-    
-    # misc
-    assert(repr(iset) == repr(eval(repr(iset).replace("datetime.",""))))
-
-def iset(string):
-    """Build an IntervalSet from a string, for testing purposes
-
-    Each character is a year
-    [ = interval start
-    | = interval end + adjacent start
-    ] = interval end
-    anything else is ignored
-    """
-    iset = IntervalSet()
-    for i, c in enumerate(string):
-        day = datetime.strptime("{0:04d}".format(i+2000), "%Y")
-        if (c == "["):
-            start = day
-        elif (c == "|"):
-            iset += Interval(start, day)
-            start = day
-        elif (c == "]"):
-            iset += Interval(start, day)
-            del start
-    return iset
-
-def test_intervalset_iset():
-    """Test basic iset construction"""
-    assert(iset("  [----]   ") ==
-           iset("  [-|--]   "))
-
-    assert(iset("[]  [--]   ") +
-           iset(" []    [--]") ==
-           iset("[|] [-----]"))
-
-def test_intervalset_intsersect():
-    """Test intersection (&)"""
-    assert_raises(TypeError, iset("[--]").__and__, 1234)
-    
-    assert(iset("[---------]") &
-           iset(" [---]     ") ==
-           iset(" [---]     "))
-
-    assert(iset(" [---]     ") &
-           iset("[---------]") ==
-           iset(" [---]     "))
-
-    assert(iset("    [-----]") &
-           iset(" [-----]   ") ==
-           iset("    [--]   "))
-
-    assert(iset("      [---]") &
-           iset(" [--]      ") ==
-           iset("           "))
-
-    assert(iset("    [-|---]") &
-           iset(" [-----|-] ") ==
-           iset("    [----] "))
-
-    assert(iset("    [-|-]  ") &
-           iset(" [-|--|--] ") ==
-           iset("    [---]  "))
-
-    assert(iset(" [----][--]") &
-           iset("[-] [--] []") ==
-           iset(" [] [-]  []"))
-

nilmdb/timer.py

@@ -0,0 +1,21 @@
+# -*- coding: utf-8 -*-
+
+# Simple timer to time a block of code, for optimization debugging
+# use like:
+#   with nilmdb.Timer("flush"):
+#       foo.flush()
+
+import contextlib
+import time
+
+@contextlib.contextmanager
+def Timer(name = None, tosyslog = False):
+    start = time.time()
+    yield
+    elapsed = int((time.time() - start) * 1000)
+    msg = (name or 'elapsed') + ": " + str(elapsed) + " ms"
+    if tosyslog: # pragma: no cover
+        import syslog
+        syslog.syslog(msg)
+    else:
+        print msg

nilmdb/timestamper.py

@@ -0,0 +1,108 @@
+"""File-like objects that add timestamps to the input lines"""
+
+from __future__ import absolute_import
+from nilmdb.printf import *
+
+import time
+import os
+import datetime_tz
+
+class Timestamper(object):
+    """A file-like object that adds timestamps to lines of an input file."""
+    def __init__(self, file, ts_iter):
+        """file: filename, or another file-like object
+           ts_iter: iterator that returns a timestamp string for
+           each line of the file"""
+        if isinstance(file, basestring):
+            self.file = open(file, "r")
+        else:
+            self.file = file
+        self.ts_iter = ts_iter
+
+    def close(self):
+        self.file.close()
+
+    def readline(self, *args):
+        while True:
+            line = self.file.readline(*args)
+            if not line:
+                return ""
+            if line[0] == '#':
+                continue
+            break
+        try:
+            return self.ts_iter.next() + line
+        except StopIteration:
+            return ""
+
+    def readlines(self, size = None):
+        out = ""
+        while True:
+            line = self.readline()
+            out += line
+            if not line or (size and len(out) >= size):
+                break
+        return out
+
+    def __iter__(self):
+        return self
+
+    def next(self):
+        result = self.readline()
+        if not result:
+            raise StopIteration
+        return result
+
+class TimestamperRate(Timestamper):
+    """Timestamper that uses a start time and a fixed rate"""
+    def __init__(self, file, start, rate, end = None):
+        """
+        file: file name or object
+
+        start: Unix timestamp for the first value
+
+        rate: 1/rate is added to the timestamp for each line
+
+        end: If specified, raise StopIteration before outputting a value
+             greater than this."""
+        def iterator(start, rate, end):
+            n = 0
+            rate = float(rate)
+            while True:
+                now = start + n / rate
+                if end and now >= end:
+                    raise StopIteration
+                yield sprintf("%.6f ", start + n / rate)
+                n += 1
+        # Handle case where we're passed a datetime or datetime_tz object
+        if "totimestamp" in dir(start):
+            start = start.totimestamp()
+        Timestamper.__init__(self, file, iterator(start, rate, end))
+        self.start = start
+        self.rate = rate
+    def __str__(self):
+        start = datetime_tz.datetime_tz.fromtimestamp(self.start)
+        start = start.strftime("%a, %d %b %Y %H:%M:%S %Z")
+        return sprintf("TimestamperRate(..., start=\"%s\", rate=%g)",
+                       str(start), self.rate)
+
+class TimestamperNow(Timestamper):
+    """Timestamper that uses current time"""
+    def __init__(self, file):
+        def iterator():
+            while True:
+                now = datetime_tz.datetime_tz.utcnow().totimestamp()
+                yield sprintf("%.6f ", now)
+        Timestamper.__init__(self, file, iterator())
+    def __str__(self):
+        return "TimestamperNow(...)"
+
+class TimestamperNull(Timestamper):
+    """Timestamper that adds nothing to each line"""
+    def __init__(self, file):
+        def iterator():
+            while True:
+                yield ""
+        Timestamper.__init__(self, file, iterator())
+    def __str__(self):
+        return "TimestamperNull(...)"

nilmtool.py

@@ -0,0 +1,6 @@
+#!/usr/bin/python
+
+import nilmdb
+import sys
+
+nilmdb.cmdline.Cmdline(sys.argv[1:]).run()

pytables-test/Makefile

@@ -1,5 +0,0 @@
-all:
-	time python test-indexed-read.py
-
-clean:
-	rm -f *pyc

pytables-test/README.jim

@@ -1,2 +0,0 @@
-New version from:
-  http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=641485#15

pytables-test/TODO.txt

@@ -1,12 +0,0 @@
-- Make CherryPy server that can handle simple GET/POST,
-  and a httplib client that can talk to that server.
-  Steps:
-  - Make server handle GET
-  - Make client send request, get response
-  - Add request streaming to server
-  - Add request streaming to client
-  - Make server handle POST
-  - Make client send request, get response
-  - Add request streaming to server
-  - Add request streaming to client
-  - Integrate into a server process that also keeps database open.

pytables-test/indexing-notes

@@ -1,3 +0,0 @@
-Indexing time64 doesn't seem to work -- needed to do "time >= 1243052015" even though the actual database times
-should be something like 1243052015.847000.  Let's switch to just using a 64-bit integer counting e.g.
-microseconds since 1970-01-01 

pytables-test/sample-query

@@ -1,3 +0,0 @@
-timestamp > 1243052015
-took 394.5 minutes in vitables
-(2340 rows matched)

pytables-test/server.py

@@ -1,53 +0,0 @@
-import sys
-import tables
-import nilmdb
-
-try:
-    import cherrypy
-    cherrypy.tools.json_out
-except:
-    sys.stderr.write("Cherrypy 3.2+ required\n")
-    sys.exit(1)
-
-class NilmApp:
-    def __init__(self, db):
-        self.db = db
-
-class Root(NilmApp):
-    """NILM Database"""
-
-    server_version = "1.0"
-
-    @cherrypy.expose
-    def index(self):
-        raise cherrypy.NotFound()
-
-    @cherrypy.expose
-    def favicon_ico(self):
-        raise cherrypy.NotFound()
-
-    @cherrypy.expose
-    @cherrypy.tools.json_out()
-    def version(self):
-        return self.server_version
-
-class Stream(NilmApp):
-    """Stream operations"""
-
-    @cherrypy.expose
-    @cherrypy.tools.json_out()
-    def list(self):
-        return 
-    
-cherrypy.config.update({
-    'server.socket_host': '127.0.0.1',
-    'server.socket_port': 12380
-    })
-
-db = nilmdb.nilmdb()
-cherrypy.tree.mount(Root(db), "/")
-cherrypy.tree.mount(Stream(db), "/stream")
-
-if __name__ == "__main__":
-    cherrypy.engine.start()
-    cherrypy.engine.block()

pytables-test/speed-pytables.py

@@ -1,16 +0,0 @@
-import tables
-import numpy
-
-class RawSample(tables.IsDescription):
-    timestamp = tables.UInt64Col()
-    voltage   = tables.UInt16Col(shape = 3)
-    current   = tables.UInt16Col(shape = 3)
-
-h5file = tables.openFile("test.h5", mode = "w", title = "Test")
-group = h5file.createGroup("/", "raw", "Raw Data")
-table = h5file.createTable(group, "nilm1", RawSample, "NILM 1")
-
-print repr(h5file)
-
-# write rows
-

pytables-test/test-indexing.py

@@ -1,54 +0,0 @@
-#!/usr/bin/python
-
-from tables import *
-import re
-import time
-
-# A class to describe our data
-class PrepData(IsDescription):
-    timestamp = Int64Col()
-    p1 = Float32Col()
-    q1 = Float32Col()
-    p3 = Float32Col()
-    q3 = Float32Col()
-    p5 = Float32Col()
-    q5 = Float32Col()
-    p7 = Float32Col()
-    q7 = Float32Col()
-
-filename = "test.h5"
-h5file = openFile(filename, mode = "w", title = "NILM Test")
-
-group = h5file.createGroup("/", "newton", "Newton school")
-table = h5file.createTable(group, "prep", PrepData, "Prep Data", expectedrows = 120 * 86400 * 90)
-
-table.cols.timestamp.createIndex()
-
-for i in range(0, 80):
-    # Open file
-    data = open("data/alldata")
-    count = 0
-    oldtime = time.time()
-    prep = table.row
-    for line in data:
-        count = count + 1
-        if count % 1000000 == 0:
-            print str(i) + ": " + str((time.time() - oldtime)) + ", total " + str(count/1000000) + "m lines"
-            oldtime = time.time()
-        v = re.split('\s+', line)
-        prep['timestamp'] = int(v[0]) + 500000000 * i
-        prep['p1'] = v[1]
-        prep['q1'] = v[2]
-        prep['p3'] = v[3]
-        prep['q3'] = v[4]
-        prep['p5'] = v[5]
-        prep['q5'] = v[6]
-        prep['p7'] = v[7]
-        prep['q7'] = v[8]
-        prep.append()
-    data.close()
-
-h5file.close()
-
-
-

pytables-test/test-write.py

@@ -1,54 +0,0 @@
-#!/usr/bin/python
-
-from tables import *
-import re
-import time
-
-# A class to describe our data
-class PrepData(IsDescription):
-    timestamp = Time64Col()
-    p1 = Float32Col()
-    q1 = Float32Col()
-    p3 = Float32Col()
-    q3 = Float32Col()
-    p5 = Float32Col()
-    q5 = Float32Col()
-    p7 = Float32Col()
-    q7 = Float32Col()
-
-filename = "test.h5"
-h5file = openFile(filename, mode = "w", title = "NILM Test")
-
-group = h5file.createGroup("/", "newton", "Newton school")
-table = h5file.createTable(group, "prep", PrepData, "Prep Data")
-
-table.cols.timestamp.createIndex()
-
-for i in range(0, 80):
-    # Open file
-    data = open("data/alldata")
-    count = 0
-    oldtime = time.time()
-    prep = table.row
-    for line in data:
-        count = count + 1
-        if count % 1000000 == 0:
-            print str(i) + ": " + str((time.time() - oldtime)) + ", total " + str(count/1000000) + "m lines"
-            oldtime = time.time()
-        v = re.split('\s+', line)
-        prep['timestamp'] = float(v[0]) / 1000.0 + 500000 * i
-        prep['p1'] = v[1]
-        prep['q1'] = v[2]
-        prep['p3'] = v[3]
-        prep['q3'] = v[4]
-        prep['p5'] = v[5]
-        prep['q5'] = v[6]
-        prep['p7'] = v[7]
-        prep['q7'] = v[8]
-        prep.append()
-    data.close()
-
-h5file.close()
-
-
-

runserver.py

@@ -0,0 +1,32 @@
+#!/usr/bin/python
+
+import nilmdb
+import argparse
+
+parser = argparse.ArgumentParser(description='Run the NILM server')
+parser.add_argument('-p', '--port', help='Port number', type=int, default=12380)
+parser.add_argument('-y', '--yappi', help='Run with yappi profiler',
+                    action='store_true')
+args = parser.parse_args()
+
+# Start web app on a custom port
+db = nilmdb.NilmDB("db")
+server = nilmdb.Server(db, host = "127.0.0.1",
+                       port = args.port,
+                       embedded = False)
+
+
+if args.yappi:
+    print "Running in yappi"
+    try:
+        import yappi
+        yappi.start()
+        server.start(blocking = True)
+    finally:
+        yappi.stop()
+        print "Try: yappi.print_stats(sort_type=yappi.SORTTYPE_TTOT,limit=50)"
+        from IPython import embed
+        embed()
+else:
+    server.start(blocking = True)
+db.close()

setup.cfg

@@ -1,9 +1,26 @@
 [nosetests]
-nocapture=1
-with-coverage=1
-cover-inclusive=1
+# note: the value doesn't matter, that's why they're empty here
+nocapture=
+nologcapture=        # comment to see cherrypy logs on failure
+with-coverage=
+cover-inclusive=
 cover-package=nilmdb
-cover-erase=1
-stop=1
+cover-erase=
+##cover-html=         # this works, puts html output in cover/ dir
+##cover-branches=     # need nose 1.1.3 for this
+stop=
 verbosity=2
-
+#tests=tests/test_cmdline.py
+#tests=tests/test_layout.py
+#tests=tests/test_rbtree.py
+#tests=tests/test_interval.py
+#tests=tests/test_rbtree.py,tests/test_interval.py
+#tests=tests/test_interval.py
+#tests=tests/test_client.py
+#tests=tests/test_timestamper.py
+#tests=tests/test_serializer.py
+#tests=tests/test_iteratorizer.py
+#tests=tests/test_client.py:TestClient.test_client_nilmdb
+#with-profile=
+#profile-sort=time
+##profile-restrict=10  # doesn't work right, treated as string or something

setup.py

@@ -1,9 +0,0 @@
-#!/usr/bin/python
-
-from distutils.core import setup
-
-setup(name = 'nilmdb',
-      version = '1.0',
-      scripts = [ 'bin/nilm-test.py' ],
-      packages = [ 'nilmdb' ],
-      )

test/Makefile

@@ -1,5 +0,0 @@
-all:
-	python speed-readbinary.py
-
-clean:
-	rm -f *pyc

test/printf.py

@@ -1,4 +0,0 @@
-from __future__ import print_function
-def printf(str, *args):
-    print(str % args, end='')
-    

test/speed-readascii.py

@@ -1,60 +0,0 @@
-#!/usr/bin/python
-
-from printf import printf
-import time
-import re
-import numpy as np
-import itertools
-
-class Timer():
-    def __init__(self, arg):
-        self.arg = arg
-    def __enter__(self): self.start = time.time()
-    def __exit__(self, *args): printf("%s: %f lines/sec\n", self.arg, 1e6 / (time.time() - self.start))
-
-def test_split():
-    for n, line in enumerate(open('1m.raw', 'r')):
-        out = [0]*6
-        tmp = [ int(i) for i in line.partition('#')[0].split() ]
-        out[0:len(tmp)] = tmp
-        if (n % 100000 == 0):
-            printf("line %d = %s\n", n, str(out))
-
-def test_split2():
-    for n, line in enumerate(open('1m.raw', 'r')):
-        out = [0]*6
-        tmp = [ int(i,10) for i in line.partition('#')[0].split() ]
-        out[0:len(tmp)] = tmp
-        if (n % 100000 == 0):
-            printf("line %d = %s\n", n, str(out))
-
-def test_regex():
-    for n, line in enumerate(open('1m.raw', 'r')):
-        out = [0]*6
-        tmp = [ int(x) for x in re.findall('(\d+)\s+',line.partition('#')[0]) ]
-        out[0:len(tmp)] = tmp
-        if (n % 100000 == 0):
-            printf("line %d = %s\n", n, str(out))
-
-def test_bigregex():
-    regex = re.compile('^(?:\s*)' + '(?:(\d+)\s+)?' * 6)
-    for n, line in enumerate(open('1m.raw', 'r')):
-        out = [ int(x or 0) for x in re.match(regex, line).groups() ]
-        if (n % 100000 == 0):
-            printf("line %d = %s\n", n, str(out))
-
-with Timer("regex"):
-    test_regex() # 102k/sec
-
-with Timer("split"):
-    test_split() # 175k/sec
-
-with Timer("split2"):
-    test_split2() # 275k/sec
-
-with Timer("bigregex"):
-    test_bigregex() # 110k/sec
-
-# The "int" operation takes quite a while -- int(x,10) is twice as fast
-# Perl does about 500k/sec
-

test/speed-readbinary.py

@@ -1,74 +0,0 @@
-#!/usr/bin/python
-
-from printf import printf
-import time
-import re
-import numpy as np
-import itertools
-import struct
-import array
-import os
-import mmap
-
-class Timer():
-    def __init__(self, arg):
-        self.arg = arg
-    def __enter__(self): self.start = time.time()
-    def __exit__(self, *args): printf("%s: %f klines/sec\n", self.arg, 1e3 / (time.time() - self.start))
-
-def test_struct1():
-    """read with struct.unpack"""
-    f = open('1m.bin', 'rb')
-    f.seek(0,os.SEEK_END)
-    filesize = f.tell()
-    f.seek(0,os.SEEK_SET)
-    packer = struct.Struct('!dHHHHHH')
-    items = filesize / packer.size
-    for n in xrange(items):
-        s = f.read(packer.size)
-        out = packer.unpack(s)
-        if (n % 100000 == 0):
-            printf("line %d = %s\n", n, str(out))
-
-def test_struct2():
-    """read with struct.unpack, convert to string"""
-    f = open('1m.bin', 'rb')
-    f.seek(0,os.SEEK_END)
-    filesize = f.tell()
-    f.seek(0,os.SEEK_SET)
-    packer = struct.Struct('!dHHHHHH')
-    items = filesize / packer.size
-    for n in xrange(items):
-        s = f.read(packer.size)
-        out = packer.unpack(s)
-        x = str(out)
-        if (n % 100000 == 0):
-            printf("line %d = %s\n", n, str(out))
-
-def test_mmap():
-    """struct.unpack with mmap"""
-    with open('1m.bin', 'rb') as f:
-        f.seek(0,os.SEEK_END)
-        filesize = f.tell()
-        f.seek(0,os.SEEK_SET)
-        m = mmap.mmap(f.fileno(), filesize, access=mmap.ACCESS_READ)
-        packer = struct.Struct('!dHHHHHH')
-        items = filesize / packer.size
-        for n in xrange(items):
-            out = packer.unpack(m[packer.size*n : packer.size*(n+1)])
-            if (n % 100000 == 0):
-                printf("line %d = %s\n", n, str(out))
-
-with Timer("mmap"):
-    test_mmap()  # 1600k
-
-with Timer("struct1"):
-    test_struct1()  # 1460k
-
-with Timer("struct2"):
-    test_struct2()  # 210k
-
-# Reading from the file is again much quicker than converting to string
-# Use mmap, it's good
-
-

test/speed-writebinary.py

@@ -1,76 +0,0 @@
-#!/usr/bin/python
-
-from printf import printf
-import time
-import re
-import numpy as np
-import itertools
-import struct
-import array
-
-class Timer():
-    def __init__(self, arg):
-        self.arg = arg
-    def __enter__(self): self.start = time.time()
-    def __exit__(self, *args): printf("%s: %f klines/sec\n", self.arg, 1e3 / (time.time() - self.start))
-
-def read_ascii():
-    for n in xrange(1000000):
-        yield (1234, 2345, 3456, 4576, 5678, 6789)
-#    for n, line in enumerate(open('1m.raw', 'r')):
-#        out = [0]*6
-#        tmp = [ int(i,10) for i in line.partition('#')[0].split() ]
-#        out[0:len(tmp)] = tmp
-#        if (n % 100000 == 0):
-#            printf("line %d = %s\n", n, str(out))
-#        yield out
-
-def test_struct1():
-    """write with struct.pack"""
-    f = open('1m.bin', 'wb')
-    for out in read_ascii():
-        s = struct.pack('!HHHHHH', *out)
-        f.write(s)
-
-def test_struct2():
-    """use constant format string"""
-    f = open('1m.bin', 'wb')
-    packer = struct.Struct('!HHHHHH')
-    for out in read_ascii():
-        f.write(packer.pack(*out))
-    f.close()
-    printf("size was %d\n", packer.size)
-
-def test_struct3():
-    """like struct1, with timestamp"""
-    f = open('1m.bin', 'wb')
-    for out in read_ascii():
-        s = struct.pack('!dHHHHHH', time.time(), *out)
-        f.write(s)
-
-def test_struct4():
-    """like struct2, with timestamp"""
-    f = open('1m.bin', 'wb')
-    packer = struct.Struct('!dHHHHHH')
-    for out in read_ascii():
-        f.write(packer.pack(time.time(), *out))
-    f.close()
-    printf("size was %d\n", packer.size)
-
-#raise Exception('done')
-
-with Timer("struct1"):
-    test_struct1() # 1089k
-
-with Timer("struct2"):
-    test_struct2() # 1249k
-
-with Timer("struct3"):
-    test_struct3() # 845k
-
-with Timer("struct4"):
-    test_struct4() # 922k
-
-# This seems fast enough for writing new data, since it's faster than
-# we read ascii data anyway.  Use e.g. struct4
-

test/test-struct-pack.py

@@ -1,11 +0,0 @@
-#!/usr/bin/python
-
-import struct
-import mmap
-
-f = open("test.dat", "rb+")
-mm = mmap.mmap(f.fileno(),3)
-
-print len(mm)
-print "first 3 bytes: " + mm[0:3];
-

test/test.dat

@@ -1 +0,0 @@
-

















test/todo.md

@@ -1,7 +0,0 @@
-- Have a class representing the file contents
-- Looks like an array
-  - len(), get(), index
-  - some form of bisect search
-  - get_extents = return [0].timestamp, [-1].timestamp
-  - 
-- Can append?  Sure, why not.  Just write to the file, extend mmap accordingly.

tests/aplotter.py

@@ -0,0 +1,419 @@
+
+#-----------------------------------------------
+#aplotter.py - ascii art function plotter
+#Copyright (c) 2006, Imri Goldberg
+#All rights reserved.
+#
+#Redistribution and use in source and binary forms,
+#with or without modification, are permitted provided
+#that the following conditions are met:
+#
+#    * Redistributions of source code must retain the
+#		above copyright notice, this list of conditions
+#		and the following disclaimer.
+#    * Redistributions in binary form must reproduce the
+#		above copyright notice, this list of conditions
+#		and the following disclaimer in the documentation
+#		and/or other materials provided with the distribution.
+#    * Neither the name of the <ORGANIZATION> nor the names of
+#		its contributors may be used to endorse or promote products
+#		derived from this software without specific prior written permission.
+#
+#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+#AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+#IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+#ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+#LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+#DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+#SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+#CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+#OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#-----------------------------------------------
+
+import math
+
+
+EPSILON = 0.000001
+
+def transposed(mat):
+	result = []
+	for i in xrange(len(mat[0])):
+		result.append([x[i] for x in mat])
+	return result
+
+def y_reversed(mat):    
+	result = []
+	for i in range(len(mat)):
+		result.append(list(reversed(mat[i])))
+	return result
+
+def sign(x):
+	if 0<x:
+		return 1
+	if 0 == x:
+		return 0
+	return -1
+
+class Plotter(object):
+
+	class PlotData(object):
+		def __init__(self, x_size, y_size, min_x, max_x, min_y, max_y, x_mod, y_mod):
+			self.x_size = x_size
+			self.y_size = y_size
+			self.min_x = min_x
+			self.max_x = max_x
+			self.min_y = min_y
+			self.max_y = max_y
+			self.x_mod = x_mod
+			self.y_mod = y_mod
+
+			self.x_step = float(max_x - min_x)/float(self.x_size)
+			self.y_step = float(max_y - min_y)/float(self.y_size)
+			self.inv_x_step = 1/self.x_step
+			self.inv_y_step = 1/self.y_step
+
+			self.ratio = self.y_step / self.x_step
+		def __repr__(self):
+			s = "size: %s, bl: %s, tr: %s, step: %s" % ((self.x_size, self.y_size), (self.min_x, self.min_y), (self.max_x, self.max_y),
+														 (self.x_step, self.y_step))
+			return s
+	
+	def __init__(self, **kwargs):
+
+		self.x_size = kwargs.get("x_size", 80)
+		self.y_size = kwargs.get("y_size", 20)
+
+		self.will_draw_axes = kwargs.get("draw_axes", True)
+
+		self.new_line = kwargs.get("newline", "\n")
+
+		self.dot = kwargs.get("dot", "*")
+
+		self.plot_slope = kwargs.get("plot_slope", True)
+
+		self.x_margin = kwargs.get("x_margin", 0.05)
+		self.y_margin = kwargs.get("y_margin", 0.1)
+
+		self.will_plot_labels = kwargs.get("plot_labels", True)
+
+	@staticmethod
+	def get_symbol_by_slope(slope, default_symbol):
+		draw_symbol = default_symbol
+		if slope > math.tan(3*math.pi/8):
+			draw_symbol = "|"
+		elif slope > math.tan(math.pi/8) and slope < math.tan(3*math.pi/8):
+			draw_symbol = "/"
+		elif abs(slope) < math.tan(math.pi/8):
+			draw_symbol = "-"
+		elif slope < math.tan(-math.pi/8) and slope > math.tan(-3*math.pi/8):
+			draw_symbol = "\\"
+		elif slope < math.tan(-3*math.pi/8):
+			draw_symbol = "|"
+		return draw_symbol    
+
+
+	def plot_labels(self, output_buffer, plot_data):
+		if plot_data.y_size < 2:
+			return
+
+		margin_factor = 1
+
+		do_plot_x_label = True
+		do_plot_y_label = True
+
+		x_str = "%+g"
+		if plot_data.x_size < 16:
+			do_plot_x_label = False
+		elif plot_data.x_size < 23:
+			x_str = "%+.2g" 
+
+		y_str = "%+g"    
+		if plot_data.x_size < 8:
+			do_plot_y_label = False
+		elif plot_data.x_size < 11:
+			y_str = "%+.2g"
+			
+		act_min_x = (plot_data.min_x + plot_data.x_mod*margin_factor)
+		act_max_x = (plot_data.max_x - plot_data.x_mod*margin_factor)
+		act_min_y = (plot_data.min_y + plot_data.y_mod*margin_factor)
+		act_max_y = (plot_data.max_y - plot_data.y_mod*margin_factor)
+
+		if abs(act_min_x) < 1:
+			min_x_str = "%+.2g" % act_min_x
+		else:
+			min_x_str = x_str % act_min_x
+
+		if abs(act_max_x) < 1:
+			max_x_str = "%+.2g" % act_max_x
+		else:
+			max_x_str = x_str % act_max_x
+		
+		if abs(act_min_y) < 1:
+			min_y_str = "%+.2g" % act_min_y
+		else:
+			min_y_str = y_str % act_min_y
+
+		if abs(act_max_y) < 1:
+			max_y_str = "%+.2g" % act_max_y
+		else:
+			max_y_str = y_str % act_max_y
+						 
+		min_x_coord = self.get_coord(act_min_x,plot_data.min_x,plot_data.x_step)
+		max_x_coord = self.get_coord(act_max_x,plot_data.min_x,plot_data.x_step)
+		min_y_coord = self.get_coord(act_min_y,plot_data.min_y,plot_data.y_step)
+		max_y_coord = self.get_coord(act_max_y,plot_data.min_y,plot_data.y_step)
+								 
+
+		#print plot_data
+		
+		y_zero_coord = self.get_coord(0, plot_data.min_y, plot_data.y_step)
+
+		#if plot_data.min_x < 0 and plot_data.max_x > 0:
+		x_zero_coord = self.get_coord(0, plot_data.min_x, plot_data.x_step)
+		#else:
+		
+		#pass
+
+		output_buffer[x_zero_coord][min_y_coord] = "+"
+		output_buffer[x_zero_coord][max_y_coord] = "+"
+		output_buffer[min_x_coord][y_zero_coord] = "+"
+		output_buffer[max_x_coord][y_zero_coord] = "+"
+
+		if do_plot_x_label:        
+
+			for i,c in enumerate(min_x_str):
+				output_buffer[min_x_coord+i][y_zero_coord-1] = c
+			for i,c in enumerate(max_x_str):
+				output_buffer[max_x_coord+i-len(max_x_str)][y_zero_coord-1] = c
+
+		if do_plot_y_label:
+
+			for i,c in enumerate(max_y_str):
+				output_buffer[x_zero_coord+i][max_y_coord] = c
+			for i,c in enumerate(min_y_str):
+				output_buffer[x_zero_coord+i][min_y_coord] = c
+			
+
+		
+		
+	
+	def plot_data(self, xy_seq, output_buffer, plot_data):
+		if self.plot_slope:
+			xy_seq = list(xy_seq)
+			#sort according to the x coord
+			xy_seq.sort(key = lambda c: c[0])
+			prev_p = xy_seq[0]
+			e_xy_seq = enumerate(xy_seq)
+			e_xy_seq.next()
+			for i,(x,y) in e_xy_seq:
+				draw_symbol = self.dot
+				line_drawn = self.plot_line(prev_p, (x,y), output_buffer, plot_data)
+				prev_p = (x,y)
+				if not line_drawn:
+					if i > 0 and i < len(xy_seq)-1:
+						px,py = xy_seq[i-1]
+						nx,ny = xy_seq[i+1]
+
+						if abs(nx-px) > EPSILON:
+							slope = (1.0/plot_data.ratio)*(ny-py)/(nx-px)
+							draw_symbol = self.get_symbol_by_slope(slope, draw_symbol)
+					if x < plot_data.min_x or x >= plot_data.max_x or y < plot_data.min_y or y >= plot_data.max_y:
+						continue
+					
+					x_coord = self.get_coord(x, plot_data.min_x, plot_data.x_step)
+					y_coord = self.get_coord(y, plot_data.min_y, plot_data.y_step)            
+					if x_coord >= 0 and x_coord < len(output_buffer) and y_coord >= 0 and y_coord < len(output_buffer[0]):
+						if self.draw_axes:
+							if y_coord == self.get_coord(0, plot_data.min_y, plot_data.y_step) and draw_symbol == "-":
+								draw_symbol = "="
+						output_buffer[x_coord][y_coord] = draw_symbol
+		else:
+			for x,y in xy_seq:
+				if x < plot_data.min_x or x >= plot_data.max_x or y < plot_data.min_y or y >= plot_data.max_y:
+					continue
+				x_coord = self.get_coord(x, plot_data.min_x, plot_data.x_step)
+				y_coord = self.get_coord(y, plot_data.min_y, plot_data.y_step)
+				if x_coord >= 0 and x_coord < len(output_buffer) and y_coord > 0 and y_coord < len(output_buffer[0]):
+					output_buffer[x_coord][y_coord] = self.dot
+
+
+	def plot_line(self, start, end, output_buffer, plot_data):
+
+		start_coord = self.get_coord(start[0], plot_data.min_x, plot_data.x_step), self.get_coord(start[1], plot_data.min_y, plot_data.y_step)
+		end_coord = self.get_coord(end[0], plot_data.min_x, plot_data.x_step), self.get_coord(end[1], plot_data.min_y, plot_data.y_step)
+
+		x0,y0 = start_coord
+		x1,y1 = end_coord
+		if (x0,y0) == (x1,y1):
+			return True    
+		
+		clipped_line = clip_line(start, end, (plot_data.min_x, plot_data.min_y), (plot_data.max_x, plot_data.max_y))
+		if clipped_line != None:
+			start,end = clipped_line
+		else:
+			return False
+		start_coord = self.get_coord(start[0], plot_data.min_x, plot_data.x_step), self.get_coord(start[1], plot_data.min_y, plot_data.y_step)
+		end_coord = self.get_coord(end[0], plot_data.min_x, plot_data.x_step), self.get_coord(end[1], plot_data.min_y, plot_data.y_step)
+
+		x0,y0 = start_coord
+		x1,y1 = end_coord
+		if (x0,y0) == (x1,y1):
+			return True
+		x_zero_coord = self.get_coord(0, plot_data.min_x, plot_data.x_step)
+		y_zero_coord = self.get_coord(0, plot_data.min_y, plot_data.y_step)   
+
+		if start[0]-end[0] == 0:
+			draw_symbol = "|"
+		else:
+			slope = (1.0/plot_data.ratio)*(end[1]-start[1])/(end[0]-start[0])
+			draw_symbol = self.get_symbol_by_slope(slope, self.dot)
+		try:
+
+			delta = x1-x0, y1-y0
+			if abs(delta[0])>abs(delta[1]):
+				s = sign(delta[0])
+				slope = float(delta[1])/delta[0]
+				for i in range(0,abs(int(delta[0]))):
+					cur_draw_symbol = draw_symbol
+					x = i*s
+					cur_y = int(y0+slope*x)
+					if self.draw_axes and cur_y == y_zero_coord and draw_symbol == "-":
+						cur_draw_symbol = "="
+					output_buffer[x0+x][cur_y] = cur_draw_symbol
+				
+				
+			else:
+				s = sign(delta[1])
+				slope = float(delta[0])/delta[1]
+				for i in range(0,abs(int(delta[1]))):
+					y = i*s
+					cur_draw_symbol = draw_symbol
+					cur_y = y0+y
+					if self.draw_axes and cur_y == y_zero_coord and draw_symbol == "-":
+						cur_draw_symbol = "="
+					output_buffer[int(x0+slope*y)][cur_y] = cur_draw_symbol
+		except:
+			print start, end
+			print start_coord, end_coord
+			print plot_data
+			raise
+
+		return False            
+		
+		
+	def plot_single(self, seq, min_x = None, max_x = None, min_y = None, max_y = None):
+		return self.plot_double(range(len(seq)),seq, min_x, max_x, min_y, max_y)
+		
+
+
+
+	def plot_double(self, x_seq, y_seq, min_x = None, max_x = None, min_y = None, max_y = None):
+		if min_x == None:
+			min_x = min(x_seq)
+		if max_x == None:
+			max_x = max(x_seq)
+		if min_y == None:
+			min_y = min(y_seq)
+		if max_y == None:
+			max_y = max(y_seq)
+
+		if max_y == min_y:
+			max_y += 1
+
+		x_mod = (max_x-min_x)*self.x_margin
+		y_mod = (max_y-min_y)*self.y_margin
+		min_x-=x_mod
+		max_x+=x_mod
+		min_y-=y_mod
+		max_y+=y_mod
+
+
+		plot_data = self.PlotData(self.x_size, self.y_size, min_x, max_x, min_y, max_y, x_mod, y_mod)
+
+		output_buffer = [[" "]*self.y_size for i in range(self.x_size)]
+
+		if self.will_draw_axes:
+			self.draw_axes(output_buffer, plot_data)
+
+		self.plot_data(zip(x_seq, y_seq), output_buffer, plot_data)
+
+		if self.will_plot_labels:
+			self.plot_labels(output_buffer, plot_data)
+
+		trans_result = transposed(y_reversed(output_buffer))
+
+		result = self.new_line.join(["".join(row) for row in trans_result])
+		return result
+
+	def draw_axes(self, output_buffer, plot_data):
+		
+		
+		draw_x = False
+		draw_y = False
+
+		if plot_data.min_x <= 0 and plot_data.max_x > 0:
+			draw_y = True
+			zero_x = self.get_coord(0, plot_data.min_x, plot_data.x_step)
+			for y in xrange(plot_data.y_size):
+				output_buffer[zero_x][y] = "|"
+				
+		if plot_data.min_y <= 0 and plot_data.max_y > 0:
+			draw_x = True
+			zero_y = self.get_coord(0, plot_data.min_y, plot_data.y_step)    
+			for x in xrange(plot_data.x_size):
+				output_buffer[x][zero_y] = "-"
+
+		if draw_x and draw_y:
+			output_buffer[zero_x][zero_y] = "+"
+		
+		
+	@staticmethod
+	def get_coord(val, min, step):
+		result = int((val - min)/step)
+		return result
+
+def clip_line(line_pt_1, line_pt_2, rect_bottom_left, rect_top_right):
+	ts = [0.0,1.0]
+	if line_pt_1[0] == line_pt_2[0]:
+		return ((line_pt_1[0], max(min(line_pt_1[1], line_pt_2[1]), rect_bottom_left[1])),
+				(line_pt_1[0], min(max(line_pt_1[1], line_pt_2[1]), rect_top_right[1])))
+	if line_pt_1[1] == line_pt_2[1]:
+		return ((max(min(line_pt_1[0], line_pt_2[0]), rect_bottom_left[0]), line_pt_1[1]),
+				(min(max(line_pt_1[0], line_pt_2[0]), rect_top_right[0]), line_pt_1[1]))
+
+	if ((rect_bottom_left[0] <= line_pt_1[0] and line_pt_1[0] < rect_top_right[0]) and
+		(rect_bottom_left[1] <= line_pt_1[1] and line_pt_1[1] < rect_top_right[1]) and
+		(rect_bottom_left[0] <= line_pt_2[0] and line_pt_2[0] < rect_top_right[0]) and
+		(rect_bottom_left[1] <= line_pt_2[1] and line_pt_2[1] < rect_top_right[1])):
+		return line_pt_1, line_pt_2
+
+	ts.append( float(rect_bottom_left[0]-line_pt_1[0])/(line_pt_2[0]-line_pt_1[0]) )
+	ts.append( float(rect_top_right[0]-line_pt_1[0])/(line_pt_2[0]-line_pt_1[0]) )
+	ts.append( float(rect_bottom_left[1]-line_pt_1[1])/(line_pt_2[1]-line_pt_1[1]) )
+	ts.append( float(rect_top_right[1]-line_pt_1[1])/(line_pt_2[1]-line_pt_1[1]) )
+	
+	ts.sort()
+	if ts[2] < 0 or ts[2] >= 1 or ts[3] < 0 or ts[2]>= 1:
+		return None
+	result = [(pt_1 + t*(pt_2-pt_1)) for t in (ts[2],ts[3]) for (pt_1, pt_2) in zip(line_pt_1, line_pt_2)]
+	return (result[0],result[1]), (result[2], result[3])
+	
+
+
+def plot(*args,**flags):
+	limit_flags_names = set(["min_x","min_y","max_x","max_y"])
+	limit_flags = dict([(n,flags[n]) for n in limit_flags_names & set(flags)])
+	settting_flags = dict([(n,flags[n]) for n in set(flags) - limit_flags_names])
+	
+	if len(args) == 1:
+		p = Plotter(**settting_flags)
+		print p.plot_single(args[0],**limit_flags)
+	elif len(args) == 2:
+		p = Plotter(**settting_flags)
+		print p.plot_double(args[0],args[1],**limit_flags)
+	else:
+		raise NotImplementedError("can't draw multiple graphs yet")
+	
+__all__ = ["Plotter","plot"]
+

tests/data/extract-1

@@ -0,0 +1,124 @@
+# path: /newton/prep
+# layout: PrepData
+# start: Fri, 23 Mar 2012 10:00:30.000000 +0000
+# end: Fri, 23 Mar 2012 10:00:31.000000 +0000
+1332496830.000000 251774.000000 224241.000000 5688.100098 1915.530029 9329.219727 4183.709961 1212.349976 2641.790039
+1332496830.008333 259567.000000 222698.000000 6207.600098 678.671997 9380.230469 4575.580078 2830.610107 2688.629883
+1332496830.016667 263073.000000 223304.000000 4961.640137 2197.120117 7687.310059 4861.859863 2732.780029 3008.540039
+1332496830.025000 257614.000000 223323.000000 5003.660156 3525.139893 7165.310059 4685.620117 1715.380005 3440.479980
+1332496830.033333 255780.000000 221915.000000 6357.310059 2145.290039 8426.969727 3775.350098 1475.390015 3797.239990
+1332496830.041667 260166.000000 223008.000000 6702.589844 1484.959961 9288.099609 3330.830078 1228.500000 3214.320068
+1332496830.050000 261231.000000 226426.000000 4980.060059 2982.379883 8499.629883 4267.669922 994.088989 2292.889893
+1332496830.058333 255117.000000 226642.000000 4584.410156 4656.439941 7860.149902 5317.310059 1473.599976 2111.689941
+1332496830.066667 253300.000000 223554.000000 6455.089844 3036.649902 8869.750000 4986.310059 2607.360107 2839.590088
+1332496830.075000 261061.000000 221263.000000 6951.979980 1500.239990 9386.099609 3791.679932 2677.010010 3980.629883
+1332496830.083333 266503.000000 223198.000000 5189.609863 2594.560059 8571.530273 3175.000000 919.840027 3792.010010
+1332496830.091667 260692.000000 225184.000000 3782.479980 4642.879883 7662.959961 3917.790039 -251.097000 2907.060059
+1332496830.100000 253963.000000 225081.000000 5123.529785 3839.550049 8669.030273 4877.819824 943.723999 2527.449951
+1332496830.108333 256555.000000 224169.000000 5930.600098 2298.540039 8906.709961 5331.680176 2549.909912 3053.560059
+1332496830.116667 260889.000000 225010.000000 4681.129883 2971.870117 7900.040039 4874.080078 2322.429932 3649.120117
+1332496830.125000 257944.000000 224923.000000 3291.139893 4357.089844 7131.589844 4385.560059 1077.050049 3664.040039
+1332496830.133333 255009.000000 223018.000000 4584.819824 2864.000000 8469.490234 3625.580078 985.557007 3504.229980
+1332496830.141667 260114.000000 221947.000000 5676.189941 1210.339966 9393.780273 3390.239990 1654.020020 3018.699951
+1332496830.150000 264277.000000 224438.000000 4446.620117 2176.719971 8142.089844 4584.879883 2327.830078 2615.800049
+1332496830.158333 259221.000000 226471.000000 2734.439941 4182.759766 6389.549805 5540.520020 1958.880005 2720.120117
+1332496830.166667 252650.000000 224831.000000 4163.640137 2989.989990 7179.200195 5213.060059 1929.550049 3457.659912
+1332496830.175000 257083.000000 222048.000000 5759.040039 702.440979 8566.549805 3552.020020 1832.939941 3956.189941
+1332496830.183333 263130.000000 222967.000000 5141.140137 1166.119995 8666.959961 2720.370117 971.374023 3479.729980
+1332496830.191667 260236.000000 225265.000000 3425.139893 3339.080078 7853.609863 3674.949951 525.908020 2443.310059
+1332496830.200000 253503.000000 224527.000000 4398.129883 2927.429932 8110.279785 4842.470215 1513.869995 2467.100098
+1332496830.208333 256126.000000 222693.000000 6043.529785 656.223999 8797.559570 4832.410156 2832.370117 3426.139893
+1332496830.216667 261677.000000 223608.000000 5830.459961 1033.910034 8123.939941 3980.689941 1927.959961 4092.719971
+1332496830.225000 259457.000000 225536.000000 4015.570068 2995.989990 7135.439941 3713.550049 307.220001 3849.429932
+1332496830.233333 253352.000000 224216.000000 4650.560059 3196.620117 8131.279785 3586.159912 70.832298 3074.179932
+1332496830.241667 256124.000000 221513.000000 6100.479980 821.979980 9757.540039 3474.510010 1647.520020 2559.860107
+1332496830.250000 263024.000000 221559.000000 5789.959961 699.416992 9129.740234 4153.080078 2829.250000 2677.270020
+1332496830.258333 261720.000000 224015.000000 4358.500000 2645.360107 7414.109863 4810.669922 2225.989990 3185.989990
+1332496830.266667 254756.000000 224240.000000 4857.379883 3229.679932 7539.310059 4769.140137 1507.130005 3668.260010
+1332496830.275000 256889.000000 222658.000000 6473.419922 1214.109985 9010.759766 3848.729980 1303.839966 3778.500000
+1332496830.283333 264208.000000 223316.000000 5700.450195 1116.560059 9087.610352 3846.679932 1293.589966 2891.560059
+1332496830.291667 263310.000000 225719.000000 3936.120117 3252.360107 7552.850098 4897.859863 1156.630005 2037.160034
+1332496830.300000 255079.000000 225086.000000 4536.450195 3960.110107 7454.589844 5479.069824 1596.359985 2190.800049
+1332496830.308333 254487.000000 222508.000000 6635.859863 1758.849976 8732.969727 4466.970215 2650.360107 3139.310059
+1332496830.316667 261241.000000 222432.000000 6702.270020 1085.130005 8989.230469 3112.989990 1933.560059 3828.409912
+1332496830.325000 262119.000000 225587.000000 4714.950195 2892.360107 8107.819824 2961.310059 239.977997 3273.719971
+1332496830.333333 254999.000000 226514.000000 4532.089844 4126.899902 8200.129883 3872.590088 56.089001 2370.580078
+1332496830.341667 254289.000000 224033.000000 6538.810059 2251.439941 9419.429688 4564.450195 2077.810059 2508.169922
+1332496830.350000 261890.000000 221960.000000 6846.089844 1475.270020 9125.589844 4598.290039 3299.219971 3475.419922
+1332496830.358333 264502.000000 223085.000000 5066.379883 3270.560059 7933.169922 4173.709961 1908.910034 3867.459961
+1332496830.366667 257889.000000 223656.000000 4201.660156 4473.640137 7688.339844 4161.580078 687.578979 3653.689941
+1332496830.375000 254270.000000 223151.000000 5715.140137 2752.139893 9273.320312 3772.949951 896.403992 3256.060059
+1332496830.383333 258257.000000 224217.000000 6114.310059 1856.859985 9604.320312 4200.490234 1764.380005 2939.219971
+1332496830.391667 260020.000000 226868.000000 4237.529785 3605.879883 8066.220215 5430.250000 2138.580078 2696.709961
+1332496830.400000 255083.000000 225924.000000 3350.310059 4853.069824 7045.819824 5925.200195 1893.609985 2897.340088
+1332496830.408333 254453.000000 222127.000000 5271.330078 2491.500000 8436.679688 5032.080078 2436.050049 3724.590088
+1332496830.416667 262588.000000 219950.000000 5994.620117 789.273987 9029.650391 3515.739990 1953.569946 4014.520020
+1332496830.425000 265610.000000 223333.000000 4391.410156 2400.959961 8146.459961 3536.959961 530.231995 3133.919922
+1332496830.433333 257470.000000 226977.000000 2975.320068 4633.529785 7278.560059 4640.100098 -50.150200 2024.959961
+1332496830.441667 250687.000000 226331.000000 4517.859863 3183.800049 8072.600098 5281.660156 1605.140015 2335.139893
+1332496830.450000 255563.000000 224495.000000 5551.000000 1101.300049 8461.490234 4725.700195 2726.669922 3480.540039
+1332496830.458333 261335.000000 224645.000000 4764.680176 1557.020020 7833.350098 3524.810059 1577.410034 4038.620117
+1332496830.466667 260269.000000 224008.000000 3558.030029 2987.610107 7362.439941 3279.229980 562.442017 3786.550049
+1332496830.475000 257435.000000 221777.000000 4972.600098 2166.879883 8481.440430 3328.719971 1037.130005 3271.370117
+1332496830.483333 261046.000000 221550.000000 5816.180176 590.216980 9120.929688 3895.399902 2382.669922 2824.169922
+1332496830.491667 262766.000000 224473.000000 4835.049805 1785.770020 7880.759766 4745.620117 2443.659912 3229.550049
+1332496830.500000 256509.000000 226413.000000 3758.870117 3461.199951 6743.770020 4928.959961 1536.619995 3546.689941
+1332496830.508333 250793.000000 224372.000000 5218.490234 2865.260010 7803.959961 4351.089844 1333.819946 3680.489990
+1332496830.516667 256319.000000 222066.000000 6403.970215 732.344971 9627.759766 3089.300049 1516.780029 3653.689941
+1332496830.525000 263343.000000 223235.000000 5200.430176 1388.579956 9372.849609 3371.229980 1450.390015 2678.909912
+1332496830.533333 260903.000000 225110.000000 3722.580078 3246.659912 7876.540039 4716.810059 1498.439941 2116.520020
+1332496830.541667 254416.000000 223769.000000 4841.649902 2956.399902 8115.919922 5392.359863 2142.810059 2652.320068
+1332496830.550000 256698.000000 222172.000000 6471.229980 970.395996 8834.980469 4816.839844 2376.629883 3605.860107
+1332496830.558333 261841.000000 223537.000000 5500.740234 1189.660034 8365.730469 4016.469971 1042.270020 3821.199951
+1332496830.566667 259503.000000 225840.000000 3827.929932 3088.840088 7676.140137 3978.310059 -357.006989 3016.419922
+1332496830.575000 253457.000000 224636.000000 4914.609863 3097.449951 8224.900391 4321.439941 171.373993 2412.360107
+1332496830.583333 256029.000000 222221.000000 6841.799805 1028.500000 9252.299805 4387.569824 2418.139893 2510.100098
+1332496830.591667 262840.000000 222550.000000 6210.250000 1410.729980 8538.900391 4152.580078 3009.300049 3219.760010
+1332496830.600000 261633.000000 225065.000000 4284.529785 3357.209961 7282.169922 3823.590088 1402.839966 3644.669922
+1332496830.608333 254591.000000 225109.000000 4693.160156 3647.739990 7745.160156 3686.379883 490.161011 3448.860107
+1332496830.616667 254780.000000 223599.000000 6527.379883 1569.869995 9438.429688 3456.580078 1162.520020 3252.010010
+1332496830.625000 260639.000000 224107.000000 6531.049805 1633.050049 9283.719727 4174.020020 2089.550049 2775.750000
+1332496830.633333 261108.000000 225472.000000 4968.259766 3527.850098 7692.870117 5137.100098 2207.389893 2436.659912
+1332496830.641667 255775.000000 223708.000000 4963.450195 4017.370117 7701.419922 5269.649902 2284.399902 2842.080078
+1332496830.650000 257398.000000 220947.000000 6767.500000 1645.709961 9107.070312 4000.179932 2548.860107 3624.770020
+1332496830.658333 264924.000000 221559.000000 6471.459961 1110.329956 9459.650391 3108.169922 1696.969971 3893.439941
+1332496830.666667 265339.000000 225733.000000 4348.799805 3459.510010 8475.299805 4031.239990 573.346985 2910.270020
+1332496830.675000 256814.000000 226995.000000 3479.540039 4949.790039 7499.910156 5624.709961 751.656006 2347.709961
+1332496830.683333 253316.000000 225161.000000 5147.060059 3218.429932 8460.160156 5869.299805 2336.320068 2987.959961
+1332496830.691667 259360.000000 223101.000000 5549.120117 1869.949951 8740.759766 4668.939941 2457.909912 3758.820068
+1332496830.700000 262012.000000 224016.000000 4173.609863 3004.129883 8157.040039 3704.729980 987.963989 3652.750000
+1332496830.708333 257176.000000 224420.000000 3517.300049 4118.750000 7822.240234 3718.229980 37.264900 2953.679932
+1332496830.716667 255146.000000 223322.000000 4923.979980 2330.679932 9095.910156 3792.399902 1013.070007 2711.239990
+1332496830.725000 260524.000000 223651.000000 5413.629883 1146.209961 8817.169922 4419.649902 2446.649902 2832.050049
+1332496830.733333 262098.000000 225752.000000 4262.979980 2270.969971 7135.479980 5067.120117 2294.679932 3376.620117
+1332496830.741667 256889.000000 225379.000000 3606.459961 3568.189941 6552.649902 4970.270020 1516.380005 3662.570068
+1332496830.750000 253948.000000 222631.000000 5511.700195 2066.300049 7952.660156 4019.909912 1513.140015 3752.629883
+1332496830.758333 259799.000000 222067.000000 5873.500000 608.583984 9253.780273 2870.739990 1348.239990 3344.199951
+1332496830.766667 262547.000000 224901.000000 4346.080078 1928.099976 8590.969727 3455.459961 904.390991 2379.270020
+1332496830.775000 256137.000000 226761.000000 3423.560059 3379.080078 7471.149902 4894.169922 1153.540039 2031.410034
+1332496830.783333 250326.000000 225013.000000 5519.979980 2423.969971 7991.759766 5117.950195 2098.790039 3099.239990
+1332496830.791667 255454.000000 222992.000000 6547.950195 496.496002 8751.339844 3900.560059 2132.290039 4076.810059
+1332496830.800000 261286.000000 223489.000000 5152.850098 1501.510010 8425.610352 2888.030029 776.114014 3786.360107
+1332496830.808333 258969.000000 224069.000000 3832.610107 3001.979980 7979.259766 3182.310059 52.716000 2874.800049
+1332496830.816667 254946.000000 222035.000000 5317.879883 2139.800049 9103.139648 3955.610107 1235.170044 2394.149902
+1332496830.825000 258676.000000 221205.000000 6594.910156 505.343994 9423.360352 4562.470215 2913.739990 2892.350098
+1332496830.833333 262125.000000 223566.000000 5116.750000 1773.599976 8082.200195 4776.370117 2386.389893 3659.729980
+1332496830.841667 257835.000000 225918.000000 3714.300049 3477.080078 7205.370117 4554.609863 711.539001 3878.419922
+1332496830.850000 253660.000000 224371.000000 5022.450195 2592.429932 8277.200195 4119.370117 486.507996 3666.739990
+1332496830.858333 259503.000000 222061.000000 6589.950195 659.935974 9596.919922 3598.100098 1702.489990 3036.600098
+1332496830.866667 265495.000000 222843.000000 5541.850098 1728.430054 8459.959961 4492.000000 2231.969971 2430.620117
+1332496830.875000 260929.000000 224996.000000 4000.949951 3745.989990 6983.790039 5430.859863 1855.260010 2533.379883
+1332496830.883333 252716.000000 224335.000000 5086.560059 3401.149902 7597.970215 5196.120117 1755.719971 3079.760010
+1332496830.891667 254110.000000 223111.000000 6822.189941 1229.079956 9164.339844 3761.229980 1679.390015 3584.879883
+1332496830.900000 259969.000000 224693.000000 6183.950195 1538.500000 9222.080078 3139.169922 949.901978 3180.800049
+1332496830.908333 259078.000000 226913.000000 4388.890137 3694.820068 8195.019531 3933.000000 426.079987 2388.449951
+1332496830.916667 254563.000000 224760.000000 5168.439941 4020.939941 8450.269531 4758.910156 1458.900024 2286.429932
+1332496830.925000 258059.000000 221217.000000 6883.459961 1649.530029 9232.780273 4457.649902 3057.820068 3031.949951
+1332496830.933333 264667.000000 221177.000000 6218.509766 1645.729980 8657.179688 3663.500000 2528.280029 3978.340088
+1332496830.941667 262925.000000 224382.000000 4627.500000 3635.929932 7892.799805 3431.320068 604.508972 3901.370117
+1332496830.950000 254708.000000 225448.000000 4408.250000 4461.040039 8197.169922 3953.750000 -44.534599 3154.870117
+1332496830.958333 253702.000000 224635.000000 5825.770020 2577.050049 9590.049805 4569.250000 1460.270020 2785.169922
+1332496830.966667 260206.000000 224140.000000 5387.979980 1951.160034 8789.509766 5131.660156 2706.379883 2972.479980
+1332496830.975000 261240.000000 224737.000000 3860.810059 3418.310059 7414.529785 5284.520020 2271.379883 3183.149902
+1332496830.983333 256140.000000 223252.000000 3850.010010 3957.139893 7262.649902 4964.640137 1499.510010 3453.129883
+1332496830.991667 256116.000000 221349.000000 5594.479980 2054.399902 8835.129883 3662.010010 1485.510010 3613.010010

tests/data/extract-2

@@ -0,0 +1,119 @@
+1332496830.008333 259567.000000 222698.000000 6207.600098 678.671997 9380.230469 4575.580078 2830.610107 2688.629883
+1332496830.016667 263073.000000 223304.000000 4961.640137 2197.120117 7687.310059 4861.859863 2732.780029 3008.540039
+1332496830.025000 257614.000000 223323.000000 5003.660156 3525.139893 7165.310059 4685.620117 1715.380005 3440.479980
+1332496830.033333 255780.000000 221915.000000 6357.310059 2145.290039 8426.969727 3775.350098 1475.390015 3797.239990
+1332496830.041667 260166.000000 223008.000000 6702.589844 1484.959961 9288.099609 3330.830078 1228.500000 3214.320068
+1332496830.050000 261231.000000 226426.000000 4980.060059 2982.379883 8499.629883 4267.669922 994.088989 2292.889893
+1332496830.058333 255117.000000 226642.000000 4584.410156 4656.439941 7860.149902 5317.310059 1473.599976 2111.689941
+1332496830.066667 253300.000000 223554.000000 6455.089844 3036.649902 8869.750000 4986.310059 2607.360107 2839.590088
+1332496830.075000 261061.000000 221263.000000 6951.979980 1500.239990 9386.099609 3791.679932 2677.010010 3980.629883
+1332496830.083333 266503.000000 223198.000000 5189.609863 2594.560059 8571.530273 3175.000000 919.840027 3792.010010
+1332496830.091667 260692.000000 225184.000000 3782.479980 4642.879883 7662.959961 3917.790039 -251.097000 2907.060059
+1332496830.100000 253963.000000 225081.000000 5123.529785 3839.550049 8669.030273 4877.819824 943.723999 2527.449951
+1332496830.108333 256555.000000 224169.000000 5930.600098 2298.540039 8906.709961 5331.680176 2549.909912 3053.560059
+1332496830.116667 260889.000000 225010.000000 4681.129883 2971.870117 7900.040039 4874.080078 2322.429932 3649.120117
+1332496830.125000 257944.000000 224923.000000 3291.139893 4357.089844 7131.589844 4385.560059 1077.050049 3664.040039
+1332496830.133333 255009.000000 223018.000000 4584.819824 2864.000000 8469.490234 3625.580078 985.557007 3504.229980
+1332496830.141667 260114.000000 221947.000000 5676.189941 1210.339966 9393.780273 3390.239990 1654.020020 3018.699951
+1332496830.150000 264277.000000 224438.000000 4446.620117 2176.719971 8142.089844 4584.879883 2327.830078 2615.800049
+1332496830.158333 259221.000000 226471.000000 2734.439941 4182.759766 6389.549805 5540.520020 1958.880005 2720.120117
+1332496830.166667 252650.000000 224831.000000 4163.640137 2989.989990 7179.200195 5213.060059 1929.550049 3457.659912
+1332496830.175000 257083.000000 222048.000000 5759.040039 702.440979 8566.549805 3552.020020 1832.939941 3956.189941
+1332496830.183333 263130.000000 222967.000000 5141.140137 1166.119995 8666.959961 2720.370117 971.374023 3479.729980
+1332496830.191667 260236.000000 225265.000000 3425.139893 3339.080078 7853.609863 3674.949951 525.908020 2443.310059
+1332496830.200000 253503.000000 224527.000000 4398.129883 2927.429932 8110.279785 4842.470215 1513.869995 2467.100098
+1332496830.208333 256126.000000 222693.000000 6043.529785 656.223999 8797.559570 4832.410156 2832.370117 3426.139893
+1332496830.216667 261677.000000 223608.000000 5830.459961 1033.910034 8123.939941 3980.689941 1927.959961 4092.719971
+1332496830.225000 259457.000000 225536.000000 4015.570068 2995.989990 7135.439941 3713.550049 307.220001 3849.429932
+1332496830.233333 253352.000000 224216.000000 4650.560059 3196.620117 8131.279785 3586.159912 70.832298 3074.179932
+1332496830.241667 256124.000000 221513.000000 6100.479980 821.979980 9757.540039 3474.510010 1647.520020 2559.860107
+1332496830.250000 263024.000000 221559.000000 5789.959961 699.416992 9129.740234 4153.080078 2829.250000 2677.270020
+1332496830.258333 261720.000000 224015.000000 4358.500000 2645.360107 7414.109863 4810.669922 2225.989990 3185.989990
+1332496830.266667 254756.000000 224240.000000 4857.379883 3229.679932 7539.310059 4769.140137 1507.130005 3668.260010
+1332496830.275000 256889.000000 222658.000000 6473.419922 1214.109985 9010.759766 3848.729980 1303.839966 3778.500000
+1332496830.283333 264208.000000 223316.000000 5700.450195 1116.560059 9087.610352 3846.679932 1293.589966 2891.560059
+1332496830.291667 263310.000000 225719.000000 3936.120117 3252.360107 7552.850098 4897.859863 1156.630005 2037.160034
+1332496830.300000 255079.000000 225086.000000 4536.450195 3960.110107 7454.589844 5479.069824 1596.359985 2190.800049
+1332496830.308333 254487.000000 222508.000000 6635.859863 1758.849976 8732.969727 4466.970215 2650.360107 3139.310059
+1332496830.316667 261241.000000 222432.000000 6702.270020 1085.130005 8989.230469 3112.989990 1933.560059 3828.409912
+1332496830.325000 262119.000000 225587.000000 4714.950195 2892.360107 8107.819824 2961.310059 239.977997 3273.719971
+1332496830.333333 254999.000000 226514.000000 4532.089844 4126.899902 8200.129883 3872.590088 56.089001 2370.580078
+1332496830.341667 254289.000000 224033.000000 6538.810059 2251.439941 9419.429688 4564.450195 2077.810059 2508.169922
+1332496830.350000 261890.000000 221960.000000 6846.089844 1475.270020 9125.589844 4598.290039 3299.219971 3475.419922
+1332496830.358333 264502.000000 223085.000000 5066.379883 3270.560059 7933.169922 4173.709961 1908.910034 3867.459961
+1332496830.366667 257889.000000 223656.000000 4201.660156 4473.640137 7688.339844 4161.580078 687.578979 3653.689941
+1332496830.375000 254270.000000 223151.000000 5715.140137 2752.139893 9273.320312 3772.949951 896.403992 3256.060059
+1332496830.383333 258257.000000 224217.000000 6114.310059 1856.859985 9604.320312 4200.490234 1764.380005 2939.219971
+1332496830.391667 260020.000000 226868.000000 4237.529785 3605.879883 8066.220215 5430.250000 2138.580078 2696.709961
+1332496830.400000 255083.000000 225924.000000 3350.310059 4853.069824 7045.819824 5925.200195 1893.609985 2897.340088
+1332496830.408333 254453.000000 222127.000000 5271.330078 2491.500000 8436.679688 5032.080078 2436.050049 3724.590088
+1332496830.416667 262588.000000 219950.000000 5994.620117 789.273987 9029.650391 3515.739990 1953.569946 4014.520020
+1332496830.425000 265610.000000 223333.000000 4391.410156 2400.959961 8146.459961 3536.959961 530.231995 3133.919922
+1332496830.433333 257470.000000 226977.000000 2975.320068 4633.529785 7278.560059 4640.100098 -50.150200 2024.959961
+1332496830.441667 250687.000000 226331.000000 4517.859863 3183.800049 8072.600098 5281.660156 1605.140015 2335.139893
+1332496830.450000 255563.000000 224495.000000 5551.000000 1101.300049 8461.490234 4725.700195 2726.669922 3480.540039
+1332496830.458333 261335.000000 224645.000000 4764.680176 1557.020020 7833.350098 3524.810059 1577.410034 4038.620117
+1332496830.466667 260269.000000 224008.000000 3558.030029 2987.610107 7362.439941 3279.229980 562.442017 3786.550049
+1332496830.475000 257435.000000 221777.000000 4972.600098 2166.879883 8481.440430 3328.719971 1037.130005 3271.370117
+1332496830.483333 261046.000000 221550.000000 5816.180176 590.216980 9120.929688 3895.399902 2382.669922 2824.169922
+1332496830.491667 262766.000000 224473.000000 4835.049805 1785.770020 7880.759766 4745.620117 2443.659912 3229.550049
+1332496830.500000 256509.000000 226413.000000 3758.870117 3461.199951 6743.770020 4928.959961 1536.619995 3546.689941
+1332496830.508333 250793.000000 224372.000000 5218.490234 2865.260010 7803.959961 4351.089844 1333.819946 3680.489990
+1332496830.516667 256319.000000 222066.000000 6403.970215 732.344971 9627.759766 3089.300049 1516.780029 3653.689941
+1332496830.525000 263343.000000 223235.000000 5200.430176 1388.579956 9372.849609 3371.229980 1450.390015 2678.909912
+1332496830.533333 260903.000000 225110.000000 3722.580078 3246.659912 7876.540039 4716.810059 1498.439941 2116.520020
+1332496830.541667 254416.000000 223769.000000 4841.649902 2956.399902 8115.919922 5392.359863 2142.810059 2652.320068
+1332496830.550000 256698.000000 222172.000000 6471.229980 970.395996 8834.980469 4816.839844 2376.629883 3605.860107
+1332496830.558333 261841.000000 223537.000000 5500.740234 1189.660034 8365.730469 4016.469971 1042.270020 3821.199951
+1332496830.566667 259503.000000 225840.000000 3827.929932 3088.840088 7676.140137 3978.310059 -357.006989 3016.419922
+1332496830.575000 253457.000000 224636.000000 4914.609863 3097.449951 8224.900391 4321.439941 171.373993 2412.360107
+1332496830.583333 256029.000000 222221.000000 6841.799805 1028.500000 9252.299805 4387.569824 2418.139893 2510.100098
+1332496830.591667 262840.000000 222550.000000 6210.250000 1410.729980 8538.900391 4152.580078 3009.300049 3219.760010
+1332496830.600000 261633.000000 225065.000000 4284.529785 3357.209961 7282.169922 3823.590088 1402.839966 3644.669922
+1332496830.608333 254591.000000 225109.000000 4693.160156 3647.739990 7745.160156 3686.379883 490.161011 3448.860107
+1332496830.616667 254780.000000 223599.000000 6527.379883 1569.869995 9438.429688 3456.580078 1162.520020 3252.010010
+1332496830.625000 260639.000000 224107.000000 6531.049805 1633.050049 9283.719727 4174.020020 2089.550049 2775.750000
+1332496830.633333 261108.000000 225472.000000 4968.259766 3527.850098 7692.870117 5137.100098 2207.389893 2436.659912
+1332496830.641667 255775.000000 223708.000000 4963.450195 4017.370117 7701.419922 5269.649902 2284.399902 2842.080078
+1332496830.650000 257398.000000 220947.000000 6767.500000 1645.709961 9107.070312 4000.179932 2548.860107 3624.770020
+1332496830.658333 264924.000000 221559.000000 6471.459961 1110.329956 9459.650391 3108.169922 1696.969971 3893.439941
+1332496830.666667 265339.000000 225733.000000 4348.799805 3459.510010 8475.299805 4031.239990 573.346985 2910.270020
+1332496830.675000 256814.000000 226995.000000 3479.540039 4949.790039 7499.910156 5624.709961 751.656006 2347.709961
+1332496830.683333 253316.000000 225161.000000 5147.060059 3218.429932 8460.160156 5869.299805 2336.320068 2987.959961
+1332496830.691667 259360.000000 223101.000000 5549.120117 1869.949951 8740.759766 4668.939941 2457.909912 3758.820068
+1332496830.700000 262012.000000 224016.000000 4173.609863 3004.129883 8157.040039 3704.729980 987.963989 3652.750000
+1332496830.708333 257176.000000 224420.000000 3517.300049 4118.750000 7822.240234 3718.229980 37.264900 2953.679932
+1332496830.716667 255146.000000 223322.000000 4923.979980 2330.679932 9095.910156 3792.399902 1013.070007 2711.239990
+1332496830.725000 260524.000000 223651.000000 5413.629883 1146.209961 8817.169922 4419.649902 2446.649902 2832.050049
+1332496830.733333 262098.000000 225752.000000 4262.979980 2270.969971 7135.479980 5067.120117 2294.679932 3376.620117
+1332496830.741667 256889.000000 225379.000000 3606.459961 3568.189941 6552.649902 4970.270020 1516.380005 3662.570068
+1332496830.750000 253948.000000 222631.000000 5511.700195 2066.300049 7952.660156 4019.909912 1513.140015 3752.629883
+1332496830.758333 259799.000000 222067.000000 5873.500000 608.583984 9253.780273 2870.739990 1348.239990 3344.199951
+1332496830.766667 262547.000000 224901.000000 4346.080078 1928.099976 8590.969727 3455.459961 904.390991 2379.270020
+1332496830.775000 256137.000000 226761.000000 3423.560059 3379.080078 7471.149902 4894.169922 1153.540039 2031.410034
+1332496830.783333 250326.000000 225013.000000 5519.979980 2423.969971 7991.759766 5117.950195 2098.790039 3099.239990
+1332496830.791667 255454.000000 222992.000000 6547.950195 496.496002 8751.339844 3900.560059 2132.290039 4076.810059
+1332496830.800000 261286.000000 223489.000000 5152.850098 1501.510010 8425.610352 2888.030029 776.114014 3786.360107
+1332496830.808333 258969.000000 224069.000000 3832.610107 3001.979980 7979.259766 3182.310059 52.716000 2874.800049
+1332496830.816667 254946.000000 222035.000000 5317.879883 2139.800049 9103.139648 3955.610107 1235.170044 2394.149902
+1332496830.825000 258676.000000 221205.000000 6594.910156 505.343994 9423.360352 4562.470215 2913.739990 2892.350098
+1332496830.833333 262125.000000 223566.000000 5116.750000 1773.599976 8082.200195 4776.370117 2386.389893 3659.729980
+1332496830.841667 257835.000000 225918.000000 3714.300049 3477.080078 7205.370117 4554.609863 711.539001 3878.419922
+1332496830.850000 253660.000000 224371.000000 5022.450195 2592.429932 8277.200195 4119.370117 486.507996 3666.739990
+1332496830.858333 259503.000000 222061.000000 6589.950195 659.935974 9596.919922 3598.100098 1702.489990 3036.600098
+1332496830.866667 265495.000000 222843.000000 5541.850098 1728.430054 8459.959961 4492.000000 2231.969971 2430.620117
+1332496830.875000 260929.000000 224996.000000 4000.949951 3745.989990 6983.790039 5430.859863 1855.260010 2533.379883
+1332496830.883333 252716.000000 224335.000000 5086.560059 3401.149902 7597.970215 5196.120117 1755.719971 3079.760010
+1332496830.891667 254110.000000 223111.000000 6822.189941 1229.079956 9164.339844 3761.229980 1679.390015 3584.879883
+1332496830.900000 259969.000000 224693.000000 6183.950195 1538.500000 9222.080078 3139.169922 949.901978 3180.800049
+1332496830.908333 259078.000000 226913.000000 4388.890137 3694.820068 8195.019531 3933.000000 426.079987 2388.449951
+1332496830.916667 254563.000000 224760.000000 5168.439941 4020.939941 8450.269531 4758.910156 1458.900024 2286.429932
+1332496830.925000 258059.000000 221217.000000 6883.459961 1649.530029 9232.780273 4457.649902 3057.820068 3031.949951
+1332496830.933333 264667.000000 221177.000000 6218.509766 1645.729980 8657.179688 3663.500000 2528.280029 3978.340088
+1332496830.941667 262925.000000 224382.000000 4627.500000 3635.929932 7892.799805 3431.320068 604.508972 3901.370117
+1332496830.950000 254708.000000 225448.000000 4408.250000 4461.040039 8197.169922 3953.750000 -44.534599 3154.870117
+1332496830.958333 253702.000000 224635.000000 5825.770020 2577.050049 9590.049805 4569.250000 1460.270020 2785.169922
+1332496830.966667 260206.000000 224140.000000 5387.979980 1951.160034 8789.509766 5131.660156 2706.379883 2972.479980
+1332496830.975000 261240.000000 224737.000000 3860.810059 3418.310059 7414.529785 5284.520020 2271.379883 3183.149902
+1332496830.983333 256140.000000 223252.000000 3850.010010 3957.139893 7262.649902 4964.640137 1499.510010 3453.129883
+1332496830.991667 256116.000000 221349.000000 5594.479980 2054.399902 8835.129883 3662.010010 1485.510010 3613.010010

tests/data/extract-3

@@ -0,0 +1 @@
+1332496830.008333 259567.000000 222698.000000 6207.600098 678.671997 9380.230469 4575.580078 2830.610107 2688.629883

tests/data/extract-4

@@ -0,0 +1,2 @@
+1332496830.008333 259567.000000 222698.000000 6207.600098 678.671997 9380.230469 4575.580078 2830.610107 2688.629883
+1332496830.016667 263073.000000 223304.000000 4961.640137 2197.120117 7687.310059 4861.859863 2732.780029 3008.540039

tests/data/extract-5

@@ -0,0 +1,124 @@
+# path: /newton/prep
+# layout: PrepData
+# start: Fri, 23 Mar 2012 10:00:30.000000 +0000
+# end: Fri, 23 Mar 2012 10:00:31.000000 +0000
+251774.000000 224241.000000 5688.100098 1915.530029 9329.219727 4183.709961 1212.349976 2641.790039
+259567.000000 222698.000000 6207.600098 678.671997 9380.230469 4575.580078 2830.610107 2688.629883
+263073.000000 223304.000000 4961.640137 2197.120117 7687.310059 4861.859863 2732.780029 3008.540039
+257614.000000 223323.000000 5003.660156 3525.139893 7165.310059 4685.620117 1715.380005 3440.479980
+255780.000000 221915.000000 6357.310059 2145.290039 8426.969727 3775.350098 1475.390015 3797.239990
+260166.000000 223008.000000 6702.589844 1484.959961 9288.099609 3330.830078 1228.500000 3214.320068
+261231.000000 226426.000000 4980.060059 2982.379883 8499.629883 4267.669922 994.088989 2292.889893
+255117.000000 226642.000000 4584.410156 4656.439941 7860.149902 5317.310059 1473.599976 2111.689941
+253300.000000 223554.000000 6455.089844 3036.649902 8869.750000 4986.310059 2607.360107 2839.590088
+261061.000000 221263.000000 6951.979980 1500.239990 9386.099609 3791.679932 2677.010010 3980.629883
+266503.000000 223198.000000 5189.609863 2594.560059 8571.530273 3175.000000 919.840027 3792.010010
+260692.000000 225184.000000 3782.479980 4642.879883 7662.959961 3917.790039 -251.097000 2907.060059
+253963.000000 225081.000000 5123.529785 3839.550049 8669.030273 4877.819824 943.723999 2527.449951
+256555.000000 224169.000000 5930.600098 2298.540039 8906.709961 5331.680176 2549.909912 3053.560059
+260889.000000 225010.000000 4681.129883 2971.870117 7900.040039 4874.080078 2322.429932 3649.120117
+257944.000000 224923.000000 3291.139893 4357.089844 7131.589844 4385.560059 1077.050049 3664.040039
+255009.000000 223018.000000 4584.819824 2864.000000 8469.490234 3625.580078 985.557007 3504.229980
+260114.000000 221947.000000 5676.189941 1210.339966 9393.780273 3390.239990 1654.020020 3018.699951
+264277.000000 224438.000000 4446.620117 2176.719971 8142.089844 4584.879883 2327.830078 2615.800049
+259221.000000 226471.000000 2734.439941 4182.759766 6389.549805 5540.520020 1958.880005 2720.120117
+252650.000000 224831.000000 4163.640137 2989.989990 7179.200195 5213.060059 1929.550049 3457.659912
+257083.000000 222048.000000 5759.040039 702.440979 8566.549805 3552.020020 1832.939941 3956.189941
+263130.000000 222967.000000 5141.140137 1166.119995 8666.959961 2720.370117 971.374023 3479.729980
+260236.000000 225265.000000 3425.139893 3339.080078 7853.609863 3674.949951 525.908020 2443.310059
+253503.000000 224527.000000 4398.129883 2927.429932 8110.279785 4842.470215 1513.869995 2467.100098
+256126.000000 222693.000000 6043.529785 656.223999 8797.559570 4832.410156 2832.370117 3426.139893
+261677.000000 223608.000000 5830.459961 1033.910034 8123.939941 3980.689941 1927.959961 4092.719971
+259457.000000 225536.000000 4015.570068 2995.989990 7135.439941 3713.550049 307.220001 3849.429932
+253352.000000 224216.000000 4650.560059 3196.620117 8131.279785 3586.159912 70.832298 3074.179932
+256124.000000 221513.000000 6100.479980 821.979980 9757.540039 3474.510010 1647.520020 2559.860107
+263024.000000 221559.000000 5789.959961 699.416992 9129.740234 4153.080078 2829.250000 2677.270020
+261720.000000 224015.000000 4358.500000 2645.360107 7414.109863 4810.669922 2225.989990 3185.989990
+254756.000000 224240.000000 4857.379883 3229.679932 7539.310059 4769.140137 1507.130005 3668.260010
+256889.000000 222658.000000 6473.419922 1214.109985 9010.759766 3848.729980 1303.839966 3778.500000
+264208.000000 223316.000000 5700.450195 1116.560059 9087.610352 3846.679932 1293.589966 2891.560059
+263310.000000 225719.000000 3936.120117 3252.360107 7552.850098 4897.859863 1156.630005 2037.160034
+255079.000000 225086.000000 4536.450195 3960.110107 7454.589844 5479.069824 1596.359985 2190.800049
+254487.000000 222508.000000 6635.859863 1758.849976 8732.969727 4466.970215 2650.360107 3139.310059
+261241.000000 222432.000000 6702.270020 1085.130005 8989.230469 3112.989990 1933.560059 3828.409912
+262119.000000 225587.000000 4714.950195 2892.360107 8107.819824 2961.310059 239.977997 3273.719971
+254999.000000 226514.000000 4532.089844 4126.899902 8200.129883 3872.590088 56.089001 2370.580078
+254289.000000 224033.000000 6538.810059 2251.439941 9419.429688 4564.450195 2077.810059 2508.169922
+261890.000000 221960.000000 6846.089844 1475.270020 9125.589844 4598.290039 3299.219971 3475.419922
+264502.000000 223085.000000 5066.379883 3270.560059 7933.169922 4173.709961 1908.910034 3867.459961
+257889.000000 223656.000000 4201.660156 4473.640137 7688.339844 4161.580078 687.578979 3653.689941
+254270.000000 223151.000000 5715.140137 2752.139893 9273.320312 3772.949951 896.403992 3256.060059
+258257.000000 224217.000000 6114.310059 1856.859985 9604.320312 4200.490234 1764.380005 2939.219971
+260020.000000 226868.000000 4237.529785 3605.879883 8066.220215 5430.250000 2138.580078 2696.709961
+255083.000000 225924.000000 3350.310059 4853.069824 7045.819824 5925.200195 1893.609985 2897.340088
+254453.000000 222127.000000 5271.330078 2491.500000 8436.679688 5032.080078 2436.050049 3724.590088
+262588.000000 219950.000000 5994.620117 789.273987 9029.650391 3515.739990 1953.569946 4014.520020
+265610.000000 223333.000000 4391.410156 2400.959961 8146.459961 3536.959961 530.231995 3133.919922
+257470.000000 226977.000000 2975.320068 4633.529785 7278.560059 4640.100098 -50.150200 2024.959961
+250687.000000 226331.000000 4517.859863 3183.800049 8072.600098 5281.660156 1605.140015 2335.139893
+255563.000000 224495.000000 5551.000000 1101.300049 8461.490234 4725.700195 2726.669922 3480.540039
+261335.000000 224645.000000 4764.680176 1557.020020 7833.350098 3524.810059 1577.410034 4038.620117
+260269.000000 224008.000000 3558.030029 2987.610107 7362.439941 3279.229980 562.442017 3786.550049
+257435.000000 221777.000000 4972.600098 2166.879883 8481.440430 3328.719971 1037.130005 3271.370117
+261046.000000 221550.000000 5816.180176 590.216980 9120.929688 3895.399902 2382.669922 2824.169922
+262766.000000 224473.000000 4835.049805 1785.770020 7880.759766 4745.620117 2443.659912 3229.550049
+256509.000000 226413.000000 3758.870117 3461.199951 6743.770020 4928.959961 1536.619995 3546.689941
+250793.000000 224372.000000 5218.490234 2865.260010 7803.959961 4351.089844 1333.819946 3680.489990
+256319.000000 222066.000000 6403.970215 732.344971 9627.759766 3089.300049 1516.780029 3653.689941
+263343.000000 223235.000000 5200.430176 1388.579956 9372.849609 3371.229980 1450.390015 2678.909912
+260903.000000 225110.000000 3722.580078 3246.659912 7876.540039 4716.810059 1498.439941 2116.520020
+254416.000000 223769.000000 4841.649902 2956.399902 8115.919922 5392.359863 2142.810059 2652.320068
+256698.000000 222172.000000 6471.229980 970.395996 8834.980469 4816.839844 2376.629883 3605.860107
+261841.000000 223537.000000 5500.740234 1189.660034 8365.730469 4016.469971 1042.270020 3821.199951
+259503.000000 225840.000000 3827.929932 3088.840088 7676.140137 3978.310059 -357.006989 3016.419922
+253457.000000 224636.000000 4914.609863 3097.449951 8224.900391 4321.439941 171.373993 2412.360107
+256029.000000 222221.000000 6841.799805 1028.500000 9252.299805 4387.569824 2418.139893 2510.100098
+262840.000000 222550.000000 6210.250000 1410.729980 8538.900391 4152.580078 3009.300049 3219.760010
+261633.000000 225065.000000 4284.529785 3357.209961 7282.169922 3823.590088 1402.839966 3644.669922
+254591.000000 225109.000000 4693.160156 3647.739990 7745.160156 3686.379883 490.161011 3448.860107
+254780.000000 223599.000000 6527.379883 1569.869995 9438.429688 3456.580078 1162.520020 3252.010010
+260639.000000 224107.000000 6531.049805 1633.050049 9283.719727 4174.020020 2089.550049 2775.750000
+261108.000000 225472.000000 4968.259766 3527.850098 7692.870117 5137.100098 2207.389893 2436.659912
+255775.000000 223708.000000 4963.450195 4017.370117 7701.419922 5269.649902 2284.399902 2842.080078
+257398.000000 220947.000000 6767.500000 1645.709961 9107.070312 4000.179932 2548.860107 3624.770020
+264924.000000 221559.000000 6471.459961 1110.329956 9459.650391 3108.169922 1696.969971 3893.439941
+265339.000000 225733.000000 4348.799805 3459.510010 8475.299805 4031.239990 573.346985 2910.270020
+256814.000000 226995.000000 3479.540039 4949.790039 7499.910156 5624.709961 751.656006 2347.709961
+253316.000000 225161.000000 5147.060059 3218.429932 8460.160156 5869.299805 2336.320068 2987.959961
+259360.000000 223101.000000 5549.120117 1869.949951 8740.759766 4668.939941 2457.909912 3758.820068
+262012.000000 224016.000000 4173.609863 3004.129883 8157.040039 3704.729980 987.963989 3652.750000
+257176.000000 224420.000000 3517.300049 4118.750000 7822.240234 3718.229980 37.264900 2953.679932
+255146.000000 223322.000000 4923.979980 2330.679932 9095.910156 3792.399902 1013.070007 2711.239990
+260524.000000 223651.000000 5413.629883 1146.209961 8817.169922 4419.649902 2446.649902 2832.050049
+262098.000000 225752.000000 4262.979980 2270.969971 7135.479980 5067.120117 2294.679932 3376.620117
+256889.000000 225379.000000 3606.459961 3568.189941 6552.649902 4970.270020 1516.380005 3662.570068
+253948.000000 222631.000000 5511.700195 2066.300049 7952.660156 4019.909912 1513.140015 3752.629883
+259799.000000 222067.000000 5873.500000 608.583984 9253.780273 2870.739990 1348.239990 3344.199951
+262547.000000 224901.000000 4346.080078 1928.099976 8590.969727 3455.459961 904.390991 2379.270020
+256137.000000 226761.000000 3423.560059 3379.080078 7471.149902 4894.169922 1153.540039 2031.410034
+250326.000000 225013.000000 5519.979980 2423.969971 7991.759766 5117.950195 2098.790039 3099.239990
+255454.000000 222992.000000 6547.950195 496.496002 8751.339844 3900.560059 2132.290039 4076.810059
+261286.000000 223489.000000 5152.850098 1501.510010 8425.610352 2888.030029 776.114014 3786.360107
+258969.000000 224069.000000 3832.610107 3001.979980 7979.259766 3182.310059 52.716000 2874.800049
+254946.000000 222035.000000 5317.879883 2139.800049 9103.139648 3955.610107 1235.170044 2394.149902
+258676.000000 221205.000000 6594.910156 505.343994 9423.360352 4562.470215 2913.739990 2892.350098
+262125.000000 223566.000000 5116.750000 1773.599976 8082.200195 4776.370117 2386.389893 3659.729980
+257835.000000 225918.000000 3714.300049 3477.080078 7205.370117 4554.609863 711.539001 3878.419922
+253660.000000 224371.000000 5022.450195 2592.429932 8277.200195 4119.370117 486.507996 3666.739990
+259503.000000 222061.000000 6589.950195 659.935974 9596.919922 3598.100098 1702.489990 3036.600098
+265495.000000 222843.000000 5541.850098 1728.430054 8459.959961 4492.000000 2231.969971 2430.620117
+260929.000000 224996.000000 4000.949951 3745.989990 6983.790039 5430.859863 1855.260010 2533.379883
+252716.000000 224335.000000 5086.560059 3401.149902 7597.970215 5196.120117 1755.719971 3079.760010
+254110.000000 223111.000000 6822.189941 1229.079956 9164.339844 3761.229980 1679.390015 3584.879883
+259969.000000 224693.000000 6183.950195 1538.500000 9222.080078 3139.169922 949.901978 3180.800049
+259078.000000 226913.000000 4388.890137 3694.820068 8195.019531 3933.000000 426.079987 2388.449951
+254563.000000 224760.000000 5168.439941 4020.939941 8450.269531 4758.910156 1458.900024 2286.429932
+258059.000000 221217.000000 6883.459961 1649.530029 9232.780273 4457.649902 3057.820068 3031.949951
+264667.000000 221177.000000 6218.509766 1645.729980 8657.179688 3663.500000 2528.280029 3978.340088
+262925.000000 224382.000000 4627.500000 3635.929932 7892.799805 3431.320068 604.508972 3901.370117
+254708.000000 225448.000000 4408.250000 4461.040039 8197.169922 3953.750000 -44.534599 3154.870117
+253702.000000 224635.000000 5825.770020 2577.050049 9590.049805 4569.250000 1460.270020 2785.169922
+260206.000000 224140.000000 5387.979980 1951.160034 8789.509766 5131.660156 2706.379883 2972.479980
+261240.000000 224737.000000 3860.810059 3418.310059 7414.529785 5284.520020 2271.379883 3183.149902
+256140.000000 223252.000000 3850.010010 3957.139893 7262.649902 4964.640137 1499.510010 3453.129883
+256116.000000 221349.000000 5594.479980 2054.399902 8835.129883 3662.010010 1485.510010 3613.010010

tests/data/extract-6

@@ -0,0 +1,120 @@
+251774.000000 224241.000000 5688.100098 1915.530029 9329.219727 4183.709961 1212.349976 2641.790039
+259567.000000 222698.000000 6207.600098 678.671997 9380.230469 4575.580078 2830.610107 2688.629883
+263073.000000 223304.000000 4961.640137 2197.120117 7687.310059 4861.859863 2732.780029 3008.540039
+257614.000000 223323.000000 5003.660156 3525.139893 7165.310059 4685.620117 1715.380005 3440.479980
+255780.000000 221915.000000 6357.310059 2145.290039 8426.969727 3775.350098 1475.390015 3797.239990
+260166.000000 223008.000000 6702.589844 1484.959961 9288.099609 3330.830078 1228.500000 3214.320068
+261231.000000 226426.000000 4980.060059 2982.379883 8499.629883 4267.669922 994.088989 2292.889893
+255117.000000 226642.000000 4584.410156 4656.439941 7860.149902 5317.310059 1473.599976 2111.689941
+253300.000000 223554.000000 6455.089844 3036.649902 8869.750000 4986.310059 2607.360107 2839.590088
+261061.000000 221263.000000 6951.979980 1500.239990 9386.099609 3791.679932 2677.010010 3980.629883
+266503.000000 223198.000000 5189.609863 2594.560059 8571.530273 3175.000000 919.840027 3792.010010
+260692.000000 225184.000000 3782.479980 4642.879883 7662.959961 3917.790039 -251.097000 2907.060059
+253963.000000 225081.000000 5123.529785 3839.550049 8669.030273 4877.819824 943.723999 2527.449951
+256555.000000 224169.000000 5930.600098 2298.540039 8906.709961 5331.680176 2549.909912 3053.560059
+260889.000000 225010.000000 4681.129883 2971.870117 7900.040039 4874.080078 2322.429932 3649.120117
+257944.000000 224923.000000 3291.139893 4357.089844 7131.589844 4385.560059 1077.050049 3664.040039
+255009.000000 223018.000000 4584.819824 2864.000000 8469.490234 3625.580078 985.557007 3504.229980
+260114.000000 221947.000000 5676.189941 1210.339966 9393.780273 3390.239990 1654.020020 3018.699951
+264277.000000 224438.000000 4446.620117 2176.719971 8142.089844 4584.879883 2327.830078 2615.800049
+259221.000000 226471.000000 2734.439941 4182.759766 6389.549805 5540.520020 1958.880005 2720.120117
+252650.000000 224831.000000 4163.640137 2989.989990 7179.200195 5213.060059 1929.550049 3457.659912
+257083.000000 222048.000000 5759.040039 702.440979 8566.549805 3552.020020 1832.939941 3956.189941
+263130.000000 222967.000000 5141.140137 1166.119995 8666.959961 2720.370117 971.374023 3479.729980
+260236.000000 225265.000000 3425.139893 3339.080078 7853.609863 3674.949951 525.908020 2443.310059
+253503.000000 224527.000000 4398.129883 2927.429932 8110.279785 4842.470215 1513.869995 2467.100098
+256126.000000 222693.000000 6043.529785 656.223999 8797.559570 4832.410156 2832.370117 3426.139893
+261677.000000 223608.000000 5830.459961 1033.910034 8123.939941 3980.689941 1927.959961 4092.719971
+259457.000000 225536.000000 4015.570068 2995.989990 7135.439941 3713.550049 307.220001 3849.429932
+253352.000000 224216.000000 4650.560059 3196.620117 8131.279785 3586.159912 70.832298 3074.179932
+256124.000000 221513.000000 6100.479980 821.979980 9757.540039 3474.510010 1647.520020 2559.860107
+263024.000000 221559.000000 5789.959961 699.416992 9129.740234 4153.080078 2829.250000 2677.270020
+261720.000000 224015.000000 4358.500000 2645.360107 7414.109863 4810.669922 2225.989990 3185.989990
+254756.000000 224240.000000 4857.379883 3229.679932 7539.310059 4769.140137 1507.130005 3668.260010
+256889.000000 222658.000000 6473.419922 1214.109985 9010.759766 3848.729980 1303.839966 3778.500000
+264208.000000 223316.000000 5700.450195 1116.560059 9087.610352 3846.679932 1293.589966 2891.560059
+263310.000000 225719.000000 3936.120117 3252.360107 7552.850098 4897.859863 1156.630005 2037.160034
+255079.000000 225086.000000 4536.450195 3960.110107 7454.589844 5479.069824 1596.359985 2190.800049
+254487.000000 222508.000000 6635.859863 1758.849976 8732.969727 4466.970215 2650.360107 3139.310059
+261241.000000 222432.000000 6702.270020 1085.130005 8989.230469 3112.989990 1933.560059 3828.409912
+262119.000000 225587.000000 4714.950195 2892.360107 8107.819824 2961.310059 239.977997 3273.719971
+254999.000000 226514.000000 4532.089844 4126.899902 8200.129883 3872.590088 56.089001 2370.580078
+254289.000000 224033.000000 6538.810059 2251.439941 9419.429688 4564.450195 2077.810059 2508.169922
+261890.000000 221960.000000 6846.089844 1475.270020 9125.589844 4598.290039 3299.219971 3475.419922
+264502.000000 223085.000000 5066.379883 3270.560059 7933.169922 4173.709961 1908.910034 3867.459961
+257889.000000 223656.000000 4201.660156 4473.640137 7688.339844 4161.580078 687.578979 3653.689941
+254270.000000 223151.000000 5715.140137 2752.139893 9273.320312 3772.949951 896.403992 3256.060059
+258257.000000 224217.000000 6114.310059 1856.859985 9604.320312 4200.490234 1764.380005 2939.219971
+260020.000000 226868.000000 4237.529785 3605.879883 8066.220215 5430.250000 2138.580078 2696.709961
+255083.000000 225924.000000 3350.310059 4853.069824 7045.819824 5925.200195 1893.609985 2897.340088
+254453.000000 222127.000000 5271.330078 2491.500000 8436.679688 5032.080078 2436.050049 3724.590088
+262588.000000 219950.000000 5994.620117 789.273987 9029.650391 3515.739990 1953.569946 4014.520020
+265610.000000 223333.000000 4391.410156 2400.959961 8146.459961 3536.959961 530.231995 3133.919922
+257470.000000 226977.000000 2975.320068 4633.529785 7278.560059 4640.100098 -50.150200 2024.959961
+250687.000000 226331.000000 4517.859863 3183.800049 8072.600098 5281.660156 1605.140015 2335.139893
+255563.000000 224495.000000 5551.000000 1101.300049 8461.490234 4725.700195 2726.669922 3480.540039
+261335.000000 224645.000000 4764.680176 1557.020020 7833.350098 3524.810059 1577.410034 4038.620117
+260269.000000 224008.000000 3558.030029 2987.610107 7362.439941 3279.229980 562.442017 3786.550049
+257435.000000 221777.000000 4972.600098 2166.879883 8481.440430 3328.719971 1037.130005 3271.370117
+261046.000000 221550.000000 5816.180176 590.216980 9120.929688 3895.399902 2382.669922 2824.169922
+262766.000000 224473.000000 4835.049805 1785.770020 7880.759766 4745.620117 2443.659912 3229.550049
+256509.000000 226413.000000 3758.870117 3461.199951 6743.770020 4928.959961 1536.619995 3546.689941
+250793.000000 224372.000000 5218.490234 2865.260010 7803.959961 4351.089844 1333.819946 3680.489990
+256319.000000 222066.000000 6403.970215 732.344971 9627.759766 3089.300049 1516.780029 3653.689941
+263343.000000 223235.000000 5200.430176 1388.579956 9372.849609 3371.229980 1450.390015 2678.909912
+260903.000000 225110.000000 3722.580078 3246.659912 7876.540039 4716.810059 1498.439941 2116.520020
+254416.000000 223769.000000 4841.649902 2956.399902 8115.919922 5392.359863 2142.810059 2652.320068
+256698.000000 222172.000000 6471.229980 970.395996 8834.980469 4816.839844 2376.629883 3605.860107
+261841.000000 223537.000000 5500.740234 1189.660034 8365.730469 4016.469971 1042.270020 3821.199951
+259503.000000 225840.000000 3827.929932 3088.840088 7676.140137 3978.310059 -357.006989 3016.419922
+253457.000000 224636.000000 4914.609863 3097.449951 8224.900391 4321.439941 171.373993 2412.360107
+256029.000000 222221.000000 6841.799805 1028.500000 9252.299805 4387.569824 2418.139893 2510.100098
+262840.000000 222550.000000 6210.250000 1410.729980 8538.900391 4152.580078 3009.300049 3219.760010
+261633.000000 225065.000000 4284.529785 3357.209961 7282.169922 3823.590088 1402.839966 3644.669922
+254591.000000 225109.000000 4693.160156 3647.739990 7745.160156 3686.379883 490.161011 3448.860107
+254780.000000 223599.000000 6527.379883 1569.869995 9438.429688 3456.580078 1162.520020 3252.010010
+260639.000000 224107.000000 6531.049805 1633.050049 9283.719727 4174.020020 2089.550049 2775.750000
+261108.000000 225472.000000 4968.259766 3527.850098 7692.870117 5137.100098 2207.389893 2436.659912
+255775.000000 223708.000000 4963.450195 4017.370117 7701.419922 5269.649902 2284.399902 2842.080078
+257398.000000 220947.000000 6767.500000 1645.709961 9107.070312 4000.179932 2548.860107 3624.770020
+264924.000000 221559.000000 6471.459961 1110.329956 9459.650391 3108.169922 1696.969971 3893.439941
+265339.000000 225733.000000 4348.799805 3459.510010 8475.299805 4031.239990 573.346985 2910.270020
+256814.000000 226995.000000 3479.540039 4949.790039 7499.910156 5624.709961 751.656006 2347.709961
+253316.000000 225161.000000 5147.060059 3218.429932 8460.160156 5869.299805 2336.320068 2987.959961
+259360.000000 223101.000000 5549.120117 1869.949951 8740.759766 4668.939941 2457.909912 3758.820068
+262012.000000 224016.000000 4173.609863 3004.129883 8157.040039 3704.729980 987.963989 3652.750000
+257176.000000 224420.000000 3517.300049 4118.750000 7822.240234 3718.229980 37.264900 2953.679932
+255146.000000 223322.000000 4923.979980 2330.679932 9095.910156 3792.399902 1013.070007 2711.239990
+260524.000000 223651.000000 5413.629883 1146.209961 8817.169922 4419.649902 2446.649902 2832.050049
+262098.000000 225752.000000 4262.979980 2270.969971 7135.479980 5067.120117 2294.679932 3376.620117
+256889.000000 225379.000000 3606.459961 3568.189941 6552.649902 4970.270020 1516.380005 3662.570068
+253948.000000 222631.000000 5511.700195 2066.300049 7952.660156 4019.909912 1513.140015 3752.629883
+259799.000000 222067.000000 5873.500000 608.583984 9253.780273 2870.739990 1348.239990 3344.199951
+262547.000000 224901.000000 4346.080078 1928.099976 8590.969727 3455.459961 904.390991 2379.270020
+256137.000000 226761.000000 3423.560059 3379.080078 7471.149902 4894.169922 1153.540039 2031.410034
+250326.000000 225013.000000 5519.979980 2423.969971 7991.759766 5117.950195 2098.790039 3099.239990
+255454.000000 222992.000000 6547.950195 496.496002 8751.339844 3900.560059 2132.290039 4076.810059
+261286.000000 223489.000000 5152.850098 1501.510010 8425.610352 2888.030029 776.114014 3786.360107
+258969.000000 224069.000000 3832.610107 3001.979980 7979.259766 3182.310059 52.716000 2874.800049
+254946.000000 222035.000000 5317.879883 2139.800049 9103.139648 3955.610107 1235.170044 2394.149902
+258676.000000 221205.000000 6594.910156 505.343994 9423.360352 4562.470215 2913.739990 2892.350098
+262125.000000 223566.000000 5116.750000 1773.599976 8082.200195 4776.370117 2386.389893 3659.729980
+257835.000000 225918.000000 3714.300049 3477.080078 7205.370117 4554.609863 711.539001 3878.419922
+253660.000000 224371.000000 5022.450195 2592.429932 8277.200195 4119.370117 486.507996 3666.739990
+259503.000000 222061.000000 6589.950195 659.935974 9596.919922 3598.100098 1702.489990 3036.600098
+265495.000000 222843.000000 5541.850098 1728.430054 8459.959961 4492.000000 2231.969971 2430.620117
+260929.000000 224996.000000 4000.949951 3745.989990 6983.790039 5430.859863 1855.260010 2533.379883
+252716.000000 224335.000000 5086.560059 3401.149902 7597.970215 5196.120117 1755.719971 3079.760010
+254110.000000 223111.000000 6822.189941 1229.079956 9164.339844 3761.229980 1679.390015 3584.879883
+259969.000000 224693.000000 6183.950195 1538.500000 9222.080078 3139.169922 949.901978 3180.800049
+259078.000000 226913.000000 4388.890137 3694.820068 8195.019531 3933.000000 426.079987 2388.449951
+254563.000000 224760.000000 5168.439941 4020.939941 8450.269531 4758.910156 1458.900024 2286.429932
+258059.000000 221217.000000 6883.459961 1649.530029 9232.780273 4457.649902 3057.820068 3031.949951
+264667.000000 221177.000000 6218.509766 1645.729980 8657.179688 3663.500000 2528.280029 3978.340088
+262925.000000 224382.000000 4627.500000 3635.929932 7892.799805 3431.320068 604.508972 3901.370117
+254708.000000 225448.000000 4408.250000 4461.040039 8197.169922 3953.750000 -44.534599 3154.870117
+253702.000000 224635.000000 5825.770020 2577.050049 9590.049805 4569.250000 1460.270020 2785.169922
+260206.000000 224140.000000 5387.979980 1951.160034 8789.509766 5131.660156 2706.379883 2972.479980
+261240.000000 224737.000000 3860.810059 3418.310059 7414.529785 5284.520020 2271.379883 3183.149902
+256140.000000 223252.000000 3850.010010 3957.139893 7262.649902 4964.640137 1499.510010 3453.129883
+256116.000000 221349.000000 5594.479980 2054.399902 8835.129883 3662.010010 1485.510010 3613.010010

tests/renderdot.py

@@ -0,0 +1,90 @@
+import sys
+
+class Renderer(object):
+
+    def __init__(self, getleft, getright,
+                 getred, getstart, getend, nil):
+        self.getleft = getleft
+        self.getright = getright
+        self.getred = getred
+        self.getstart = getstart
+        self.getend = getend
+        self.nil = nil
+
+    # Rendering
+    def __render_dot_node(self, node, max_depth = 20):
+        from nilmdb.printf import sprintf
+        """Render a single node and its children into a dot graph fragment"""
+        if max_depth == 0:
+            return ""
+        if node is self.nil:
+            return ""
+        def c(red):
+            if red:
+                return 'color="#ff0000", style=filled, fillcolor="#ffc0c0"'
+            else:
+                return 'color="#000000", style=filled, fillcolor="#c0c0c0"'
+        s = sprintf("%d [label=\"%g\\n%g\", %s];\n",
+                    id(node),
+                    self.getstart(node), self.getend(node),
+                    c(self.getred(node)))
+
+        if self.getleft(node) is self.nil:
+            s += sprintf("L%d [label=\"-\", %s];\n", id(node), c(False))
+            s += sprintf("%d -> L%d [label=L];\n", id(node), id(node))
+        else:
+            s += sprintf("%d -> %d [label=L];\n",
+                         id(node),id(self.getleft(node)))
+        if self.getright(node) is self.nil:
+            s += sprintf("R%d [label=\"-\", %s];\n", id(node), c(False))
+            s += sprintf("%d -> R%d [label=R];\n", id(node), id(node))
+        else:
+            s += sprintf("%d -> %d [label=R];\n",
+                         id(node), id(self.getright(node)))
+        s += self.__render_dot_node(self.getleft(node), max_depth-1)
+        s += self.__render_dot_node(self.getright(node), max_depth-1)
+        return s
+
+    def render_dot(self, rootnode, title = "Tree"):
+        """Render the entire tree as a dot graph"""
+        return ("digraph rbtree {\n"
+                + self.__render_dot_node(rootnode)
+                + "}\n");
+
+    def render_dot_live(self, rootnode, title = "Tree"):
+        """Render the entiretree as a dot graph, live GTK view"""
+        import gtk
+        import gtk.gdk
+        sys.path.append("/usr/share/xdot")
+        import xdot
+        xdot.Pen.highlighted = lambda pen: pen
+        s = ("digraph rbtree {\n"
+             + self.__render_dot_node(rootnode)
+             + "}\n");
+        window = xdot.DotWindow()
+        window.set_dotcode(s)
+        window.set_title(title + " - any key to close")
+        window.connect('destroy', gtk.main_quit)
+        def quit(widget, event):
+            if not event.is_modifier:
+                window.destroy()
+                gtk.main_quit()
+        window.widget.connect('key-press-event', quit)
+        gtk.main()
+
+class RBTreeRenderer(Renderer):
+    def __init__(self, tree):
+        Renderer.__init__(self,
+                          lambda node: node.left,
+                          lambda node: node.right,
+                          lambda node: node.red,
+                          lambda node: node.start,
+                          lambda node: node.end,
+                          tree.nil)
+        self.tree = tree
+
+    def render(self, title = "RBTree", live = True):
+        if live:
+            return Renderer.render_dot_live(self, self.tree.getroot(), title)
+        else:
+            return Renderer.render_dot(self, self.tree.getroot(), title)

tests/test_client.py

@@ -0,0 +1,250 @@
+import nilmdb
+from nilmdb.printf import *
+from nilmdb.client import ClientError, ServerError
+
+import datetime_tz
+
+from nose.tools import *
+from nose.tools import assert_raises
+import itertools
+import distutils.version
+import os
+import sys
+import threading
+import cStringIO
+import simplejson as json
+import unittest
+import warnings
+
+from test_helpers import *
+
+testdb = "tests/client-testdb"
+
+def setup_module():
+    global test_server, test_db
+    # Clear out DB
+    recursive_unlink(testdb)
+
+    # Start web app on a custom port
+    test_db = nilmdb.NilmDB(testdb, sync = False)
+    test_server = nilmdb.Server(test_db, host = "127.0.0.1",
+                                port = 12380, stoppable = False,
+                                fast_shutdown = True,
+                                force_traceback = False)
+    test_server.start(blocking = False)
+
+def teardown_module():
+    global test_server, test_db
+    # Close web app
+    test_server.stop()
+    test_db.close()
+
+class TestClient(object):
+
+    def test_client_1_basic(self):
+        # Test a fake host
+        client = nilmdb.Client(url = "http://localhost:1/")
+        with assert_raises(nilmdb.client.ServerError):
+            client.version()
+
+        # Trigger same error with a PUT request
+        client = nilmdb.Client(url = "http://localhost:1/")
+        with assert_raises(nilmdb.client.ServerError):
+            client.version()
+
+        # Then a fake URL on a real host
+        client = nilmdb.Client(url = "http://localhost:12380/fake/")
+        with assert_raises(nilmdb.client.ClientError):
+            client.version()
+
+        # Now a real URL with no http:// prefix
+        client = nilmdb.Client(url = "localhost:12380")
+        version = client.version()
+
+        # Now use the real URL
+        client = nilmdb.Client(url = "http://localhost:12380/")
+        version = client.version()
+        eq_(distutils.version.StrictVersion(version),
+            distutils.version.StrictVersion(test_server.version))
+
+    def test_client_2_nilmdb(self):
+        # Basic stream tests, like those in test_nilmdb:test_stream
+        client = nilmdb.Client(url = "http://localhost:12380/")
+
+        # Database starts empty
+        eq_(client.stream_list(), [])
+
+        # Bad path
+        with assert_raises(ClientError):
+            client.stream_create("foo/bar/baz", "PrepData")
+        with assert_raises(ClientError):
+            client.stream_create("/foo", "PrepData")
+        # Bad layout type
+        with assert_raises(ClientError):
+            client.stream_create("/newton/prep", "NoSuchLayout")
+        client.stream_create("/newton/prep", "PrepData")
+        client.stream_create("/newton/raw", "RawData")
+        client.stream_create("/newton/zzz/rawnotch", "RawNotchedData")
+
+        # Verify we got 3 streams
+        eq_(client.stream_list(), [ ["/newton/prep", "PrepData"],
+                                    ["/newton/raw", "RawData"],
+                                    ["/newton/zzz/rawnotch", "RawNotchedData"]
+                                    ])
+        # Match just one type or one path
+        eq_(client.stream_list(layout="RawData"), [ ["/newton/raw", "RawData"] ])
+        eq_(client.stream_list(path="/newton/raw"), [ ["/newton/raw", "RawData"] ])
+
+        # Set / get metadata
+        eq_(client.stream_get_metadata("/newton/prep"), {})
+        eq_(client.stream_get_metadata("/newton/raw"), {})
+        meta1 = { "description": "The Data",
+                  "v_scale": "1.234" }
+        meta2 = { "description": "The Data" }
+        meta3 = { "v_scale": "1.234" }
+        client.stream_set_metadata("/newton/prep", meta1)
+        client.stream_update_metadata("/newton/prep", {})
+        client.stream_update_metadata("/newton/raw", meta2)
+        client.stream_update_metadata("/newton/raw", meta3)
+        eq_(client.stream_get_metadata("/newton/prep"), meta1)
+        eq_(client.stream_get_metadata("/newton/raw"), meta1)
+        eq_(client.stream_get_metadata("/newton/raw", [ "description" ] ), meta2)
+        eq_(client.stream_get_metadata("/newton/raw", [ "description",
+                                                        "v_scale" ] ), meta1)
+
+        # missing key
+        eq_(client.stream_get_metadata("/newton/raw", "descr"),
+            { "descr": None })
+        eq_(client.stream_get_metadata("/newton/raw", [ "descr" ]),
+            { "descr": None })
+
+        # test wrong types (list instead of dict)
+        with assert_raises(ClientError):
+            client.stream_set_metadata("/newton/prep", [1,2,3])
+        with assert_raises(ClientError):
+            client.stream_update_metadata("/newton/prep", [1,2,3])
+
+    def test_client_3_insert(self):
+        client = nilmdb.Client(url = "http://localhost:12380/")
+
+        datetime_tz.localtz_set("America/New_York")
+
+        testfile = "tests/data/prep-20120323T1000"
+        start = datetime_tz.datetime_tz.smartparse("20120323T1000")
+        rate = 120
+
+        # First try a nonexistent path
+        data = nilmdb.timestamper.TimestamperRate(testfile, start, 120)
+        with assert_raises(ClientError) as e:
+            result = client.stream_insert("/newton/no-such-path", data)
+        in_("404 Not Found", str(e.exception))
+
+        # Now try reversed timestamps
+        data = nilmdb.timestamper.TimestamperRate(testfile, start, 120)
+        data = reversed(list(data))
+        with assert_raises(ClientError) as e:
+            result = client.stream_insert("/newton/prep", data)
+        in_("400 Bad Request", str(e.exception))
+        in_("timestamp is not monotonically increasing", str(e.exception))
+
+        # Now try empty data (no server request made)
+        empty = cStringIO.StringIO("")
+        data = nilmdb.timestamper.TimestamperRate(empty, start, 120)
+        result = client.stream_insert("/newton/prep", data)
+        eq_(result, None)
+
+        # Try forcing a server request with empty data
+        with assert_raises(ClientError) as e:
+            client.http.put("stream/insert", "", { "path": "/newton/prep" })
+        in_("400 Bad Request", str(e.exception))
+        in_("no data provided", str(e.exception))
+
+        # Now do the real load
+        data = nilmdb.timestamper.TimestamperRate(testfile, start, 120)
+        result = client.stream_insert("/newton/prep", data)
+        eq_(result[0], "ok")
+
+        # Try some overlapping data -- just insert it again
+        data = nilmdb.timestamper.TimestamperRate(testfile, start, 120)
+        with assert_raises(ClientError) as e:
+            result = client.stream_insert("/newton/prep", data)
+        in_("400 Bad Request", str(e.exception))
+        in_("OverlapError", str(e.exception))
+
+    def test_client_4_extract(self):
+        # Misc tests for extract.  Most of them are in test_cmdline.
+        client = nilmdb.Client(url = "http://localhost:12380/")
+
+        for x in client.stream_extract("/newton/prep", 123, 123):
+            raise Exception("shouldn't be any data for this request")
+
+    def test_client_5_generators(self):
+        # A lot of the client functionality is already tested by test_cmdline,
+        # but this gets a bit more coverage that cmdline misses.
+        client = nilmdb.Client(url = "http://localhost:12380/")
+
+        # Trigger a client error in generator
+        start = datetime_tz.datetime_tz.smartparse("20120323T2000")
+        end = datetime_tz.datetime_tz.smartparse("20120323T1000")
+        for function in [ client.stream_intervals, client.stream_extract ]:
+            with assert_raises(ClientError) as e:
+                function("/newton/prep",
+                         start.totimestamp(),
+                         end.totimestamp()).next()
+            in_("400 Bad Request", str(e.exception))
+            in_("end before start", str(e.exception))
+
+        # Trigger a curl error in generator
+        with assert_raises(ServerError) as e:
+            client.http.get_gen("http://nosuchurl/").next()
+
+        # Trigger a curl error in generator
+        with assert_raises(ServerError) as e:
+            client.http.get_gen("http://nosuchurl/").next()
+
+        # Check non-json version of string output
+        eq_(json.loads(client.http.get("/stream/list",retjson=False)),
+            client.http.get("/stream/list",retjson=True))
+
+        # Check non-json version of generator output
+        for (a, b) in itertools.izip(
+            client.http.get_gen("/stream/list",retjson=False),
+            client.http.get_gen("/stream/list",retjson=True)):
+            eq_(json.loads(a), b)
+
+        # Check PUT with generator out
+        with assert_raises(ClientError) as e:
+            client.http.put_gen("stream/insert", "",
+                                { "path": "/newton/prep" }).next()
+        in_("400 Bad Request", str(e.exception))
+        in_("no data provided", str(e.exception))
+
+        # Check 404 for missing streams
+        for function in [ client.stream_intervals, client.stream_extract ]:
+            with assert_raises(ClientError) as e:
+                function("/no/such/stream").next()
+            in_("404 Not Found", str(e.exception))
+            in_("No such stream", str(e.exception))
+
+    def test_client_6_chunked(self):
+        # Make sure that /stream/intervals and /stream/extract
+        # properly return streaming, chunked response.  Pokes around
+        # in client.http internals a bit to look at the response
+        # headers.
+
+        client = nilmdb.Client(url = "http://localhost:12380/")
+
+        # Use a warning rather than returning a test failure, so that we can
+        # still disable chunked responses for debugging.
+        x = client.http.get("stream/intervals", { "path": "/newton/prep" },
+                            retjson=False)
+        eq_(x.count('\n'), 2)
+        if "transfer-encoding: chunked" not in client.http._headers.lower():
+            warnings.warn("Non-chunked HTTP response for /stream/intervals")
+
+        x = client.http.get("stream/extract",
+                            { "path": "/newton/prep",
+                              "start": "123",
+                              "end": "123" }, retjson=False)
+        if "transfer-encoding: chunked" not in client.http._headers.lower():
+            warnings.warn("Non-chunked HTTP response for /stream/extract")

tests/test_cmdline.py

@@ -0,0 +1,515 @@
+import nilmdb
+from nilmdb.printf import *
+import nilmdb.cmdline
+
+from nose.tools import *
+from nose.tools import assert_raises
+import itertools
+import datetime_tz
+import os
+import shutil
+import sys
+import threading
+import urllib2
+from urllib2 import urlopen, HTTPError
+import Queue
+import cStringIO
+import shlex
+
+from test_helpers import *
+
+testdb = "tests/cmdline-testdb"
+
+def server_start(max_results = None):
+    global test_server, test_db
+    # Start web app on a custom port
+    test_db = nilmdb.NilmDB(testdb, sync = False, max_results = max_results)
+    test_server = nilmdb.Server(test_db, host = "127.0.0.1",
+                                port = 12380, stoppable = False,
+                                fast_shutdown = True,
+                                force_traceback = False)
+    test_server.start(blocking = False)
+
+def server_stop():
+    global test_server, test_db
+    # Close web app
+    test_server.stop()
+    test_db.close()
+
+def setup_module():
+    global test_server, test_db
+    # Clear out DB
+    recursive_unlink(testdb)
+    server_start()
+
+def teardown_module():
+    server_stop()
+
+class TestCmdline(object):
+
+    def run(self, arg_string, infile=None, outfile=None):
+        """Run a cmdline client with the specified argument string,
+        passing the given input.  Returns a tuple with the output and
+        exit code"""
+        class stdio_wrapper:
+            def __init__(self, stdin, stdout, stderr):
+                self.io = (stdin, stdout, stderr)
+            def __enter__(self):
+                self.saved = ( sys.stdin, sys.stdout, sys.stderr )
+                ( sys.stdin, sys.stdout, sys.stderr ) = self.io
+            def __exit__(self, type, value, traceback):
+                ( sys.stdin, sys.stdout, sys.stderr ) = self.saved
+        # Empty input if none provided
+        if infile is None:
+            infile = cStringIO.StringIO("")
+        # Capture stderr
+        errfile = cStringIO.StringIO()
+        if outfile is None:
+            # If no output file, capture stdout with stderr
+            outfile = errfile
+        with stdio_wrapper(infile, outfile, errfile) as s:
+            try:
+                nilmdb.cmdline.Cmdline(shlex.split(arg_string)).run()
+                sys.exit(0)
+            except SystemExit as e:
+                exitcode = e.code
+        captured = outfile.getvalue()
+        self.captured = captured
+        self.exitcode = exitcode
+
+    def ok(self, arg_string, infile = None):
+        self.run(arg_string, infile)
+        if self.exitcode != 0:
+            self.dump()
+            eq_(self.exitcode, 0)
+
+    def fail(self, arg_string, infile = None, exitcode = None):
+        self.run(arg_string, infile)
+        if exitcode is not None and self.exitcode != exitcode:
+            self.dump()
+            eq_(self.exitcode, exitcode)
+        if self.exitcode == 0:
+            self.dump()
+            ne_(self.exitcode, 0)
+
+    def contain(self, checkstring):
+        in_(checkstring, self.captured)
+
+    def match(self, checkstring):
+        eq_(checkstring, self.captured)
+
+    def matchfile(self, file):
+        # Captured data should match file contents exactly
+        with open(file) as f:
+            contents = f.read()
+            if contents != self.captured:
+                #print contents[1:1000] + "\n"
+                #print self.captured[1:1000] + "\n"
+                raise AssertionError("captured data doesn't match " + file)
+
+    def matchfilecount(self, file):
+        # Last line of captured data should match the number of
+        # non-commented lines in file
+        count = 0
+        with open(file) as f:
+            for line in f:
+                if line[0] != '#':
+                    count += 1
+        eq_(self.captured.splitlines()[-1], sprintf("%d", count))
+
+    def dump(self):
+        printf("-----dump start-----\n%s-----dump end-----\n", self.captured)
+
+    def test_cmdline_01_basic(self):
+
+        # help
+        self.ok("--help")
+        self.contain("usage:")
+
+        # fail for no args
+        self.fail("")
+
+        # fail for no such option
+        self.fail("--nosuchoption")
+
+        # fail for bad command
+        self.fail("badcommand")
+
+        # try some URL constructions
+        self.fail("--url http://nosuchurl/ info")
+        self.contain("Couldn't resolve host 'nosuchurl'")
+
+        self.fail("--url nosuchurl info")
+        self.contain("Couldn't resolve host 'nosuchurl'")
+
+        self.fail("-u nosuchurl/foo info")
+        self.contain("Couldn't resolve host 'nosuchurl'")
+
+        self.fail("-u localhost:0 info")
+        self.contain("couldn't connect to host")
+
+        self.ok("-u localhost:12380 info")
+        self.ok("info")
+
+        # Duplicated arguments should fail, but this isn't implemented
+        # due to it being kind of a pain with argparse.
+        if 0:
+            self.fail("-u url1 -u url2 info")
+            self.contain("duplicated argument")
+
+            self.fail("list --detail --detail")
+            self.contain("duplicated argument")
+
+            self.fail("list --detail --path path1 --path path2")
+            self.contain("duplicated argument")
+
+            self.fail("extract --start 2000-01-01 --start 2001-01-02")
+            self.contain("duplicated argument")
+
+    def test_cmdline_02_info(self):
+        self.ok("info")
+        self.contain("Server URL: http://localhost:12380/")
+        self.contain("Server version: " + test_server.version)
+        self.contain("Server database path")
+        self.contain("Server database size")
+
+    def test_cmdline_03_createlist(self):
+        # Basic stream tests, like those in test_client.
+
+        # No streams
+        self.ok("list")
+        self.match("")
+
+        # Bad paths
+        self.fail("create foo/bar/baz PrepData")
+        self.contain("paths must start with /")
+
+        self.fail("create /foo PrepData")
+        self.contain("invalid path")
+
+        # Bad layout type
+        self.fail("create /newton/prep NoSuchLayout")
+        self.contain("no such layout")
+
+        # Create a few streams
+        self.ok("create /newton/zzz/rawnotch RawNotchedData")
+        self.ok("create /newton/prep PrepData")
+        self.ok("create /newton/raw RawData")
+
+        # Should not be able to create a stream with another stream as
+        # its parent
+        self.fail("create /newton/prep/blah PrepData")
+        self.contain("error creating table at that path")
+
+        # Verify we got those 3 streams and they're returned in
+        # alphabetical order.
+        self.ok("list")
+        self.match("/newton/prep PrepData\n"
+                   "/newton/raw RawData\n"
+                   "/newton/zzz/rawnotch RawNotchedData\n")
+
+        # Match just one type or one path
+        self.ok("list --path /newton/raw")
+        self.match("/newton/raw RawData\n")
+
+        self.ok("list --layout RawData")
+        self.match("/newton/raw RawData\n")
+
+        # Wildcard matches
+        self.ok("list --layout Raw*")
+        self.match("/newton/raw RawData\n"
+                   "/newton/zzz/rawnotch RawNotchedData\n")
+
+        self.ok("list --path *zzz* --layout Raw*")
+        self.match("/newton/zzz/rawnotch RawNotchedData\n")
+
+        self.ok("list --path *zzz* --layout Prep*")
+        self.match("")
+
+    def test_cmdline_04_metadata(self):
+        # Set / get metadata
+        self.fail("metadata")
+        self.fail("metadata --get")
+
+        self.ok("metadata /newton/prep")
+        self.match("")
+
+        self.ok("metadata /newton/raw --get")
+        self.match("")
+
+        self.ok("metadata /newton/prep --set "
+                "'description=The Data' "
+                "v_scale=1.234")
+        self.ok("metadata /newton/raw --update "
+                "'description=The Data'")
+        self.ok("metadata /newton/raw --update "
+                "v_scale=1.234")
+
+        # various parsing tests
+        self.ok("metadata /newton/raw --update foo=")
+        self.fail("metadata /newton/raw --update =bar")
+        self.fail("metadata /newton/raw --update foo==bar")
+        self.fail("metadata /newton/raw --update foo;bar")
+
+        # errors
+        self.fail("metadata /newton/nosuchstream foo=bar")
+        self.contain("unrecognized arguments")
+        self.fail("metadata /newton/nosuchstream")
+        self.contain("No stream at path")
+        self.fail("metadata /newton/nosuchstream --set foo=bar")
+        self.contain("No stream at path")
+
+        self.ok("metadata /newton/prep")
+        self.match("description=The Data\nv_scale=1.234\n")
+
+        self.ok("metadata /newton/prep --get")
+        self.match("description=The Data\nv_scale=1.234\n")
+
+        self.ok("metadata /newton/prep --get descr")
+        self.match("descr=\n")
+
+        self.ok("metadata /newton/prep --get description")
+        self.match("description=The Data\n")
+
+        self.ok("metadata /newton/prep --get description v_scale")
+        self.match("description=The Data\nv_scale=1.234\n")
+
+        self.ok("metadata /newton/prep --set "
+                "'description=The Data'")
+
+        self.ok("metadata /newton/prep --get")
+        self.match("description=The Data\n")
+
+        self.fail("metadata /newton/nosuchpath")
+        self.contain("No stream at path /newton/nosuchpath")
+
+    def test_cmdline_05_parsetime(self):
+        os.environ['TZ'] = "America/New_York"
+        cmd = nilmdb.cmdline.Cmdline(None)
+        test = datetime_tz.datetime_tz.now()
+        eq_(cmd.parse_time(str(test)), test)
+        test = datetime_tz.datetime_tz.smartparse("20120405 1400-0400")
+        eq_(cmd.parse_time("hi there 20120405 1400-0400 testing! 123"), test)
+        eq_(cmd.parse_time("20120405 1800 UTC"), test)
+        eq_(cmd.parse_time("20120405 1400-0400 UTC"), test)
+        with assert_raises(ValueError):
+            print cmd.parse_time("20120405 1400-9999")
+        with assert_raises(ValueError):
+            print cmd.parse_time("hello")
+        with assert_raises(ValueError):
+            print cmd.parse_time("-")
+        with assert_raises(ValueError):
+            print cmd.parse_time("")
+        with assert_raises(ValueError):
+            print cmd.parse_time("14:00")
+        eq_(cmd.parse_time("snapshot-20120405-140000.raw.gz"), test)
+        eq_(cmd.parse_time("prep-20120405T1400"), test)
+
+    def test_cmdline_06_insert(self):
+        self.ok("insert --help")
+
+        self.fail("insert /foo/bar baz qwer")
+        self.contain("Error getting stream info")
+
+        self.fail("insert /newton/prep baz qwer")
+        self.match("Error opening input file baz\n")
+
+        self.fail("insert /newton/prep")
+        self.contain("Error extracting time")
+
+        self.fail("insert --start 19801205 /newton/prep 1 2 3 4")
+        self.contain("--start can only be used with one input file")
+
+        self.fail("insert /newton/prep "
+                  "tests/data/prep-20120323T1000")
+
+        # insert pre-timestamped data, from stdin
+        os.environ['TZ'] = "UTC"
+        with open("tests/data/prep-20120323T1004-timestamped") as input:
+            self.ok("insert --none /newton/prep", input)
+
+        # insert data with normal timestamper from filename
+        os.environ['TZ'] = "UTC"
+        self.ok("insert --rate 120 /newton/prep "
+                "tests/data/prep-20120323T1000 "
+                "tests/data/prep-20120323T1002")
+
+        # overlap
+        os.environ['TZ'] = "UTC"
+        self.fail("insert --rate 120 /newton/prep "
+                  "tests/data/prep-20120323T1004")
+        self.contain("overlap")
+
+        # Just to help test more situations -- stop and restart
+        # the server now.  This tests nilmdb's interval caching,
+        # at the very least.
+        server_stop()
+        server_start()
+
+        # still an overlap if we specify a different start
+        os.environ['TZ'] = "America/New_York"
+        self.fail("insert --rate 120 --start '03/23/2012 06:05:00' /newton/prep"
+                  " tests/data/prep-20120323T1004")
+        self.contain("overlap")
+
+        # wrong format
+        os.environ['TZ'] = "UTC"
+        self.fail("insert --rate 120 /newton/raw "
+                  "tests/data/prep-20120323T1004")
+        self.contain("Error parsing input data")
+
+        # empty data does nothing
+        self.ok("insert --rate 120 --start '03/23/2012 06:05:00' /newton/prep "
+                "/dev/null")
+
+        # bad start time
+        self.fail("insert --rate 120 --start 'whatever' /newton/prep /dev/null")
+
+    def test_cmdline_07_detail(self):
+        # Just count the number of lines, it's probably fine
+        self.ok("list --detail")
+        eq_(self.captured.count('\n'), 11)
+
+        self.ok("list --detail --path *prep")
+        eq_(self.captured.count('\n'), 7)
+
+        self.ok("list --detail --path *prep --start='23 Mar 2012 10:02'")
+        eq_(self.captured.count('\n'), 5)
+
+        self.ok("list --detail --path *prep --start='23 Mar 2012 10:05'")
+        eq_(self.captured.count('\n'), 3)
+
+        self.ok("list --detail --path *prep --start='23 Mar 2012 10:05:15'")
+        eq_(self.captured.count('\n'), 2)
+        self.contain("10:05:15.000")
+
+        self.ok("list --detail --path *prep --start='23 Mar 2012 10:05:15.50'")
+        eq_(self.captured.count('\n'), 2)
+        self.contain("10:05:15.500")
+
+        self.ok("list --detail --path *prep --start='23 Mar 2012 19:05:15.50'")
+        eq_(self.captured.count('\n'), 2)
+        self.contain("no intervals")
+
+        self.ok("list --detail --path *prep --start='23 Mar 2012 10:05:15.50'"
+                + " --end='23 Mar 2012 10:05:15.50'")
+        eq_(self.captured.count('\n'), 2)
+        self.contain("10:05:15.500")
+
+        self.ok("list --detail")
+        eq_(self.captured.count('\n'), 11)
+
+    def test_cmdline_08_extract(self):
+        # nonexistent stream
+        self.fail("extract /no/such/foo --start 2000-01-01 --end 2020-01-01")
+        self.contain("Error getting stream info")
+
+        # empty ranges return an error
+        self.fail("extract -a /newton/prep " +
+                  "--start '23 Mar 2012 10:00:30' " +
+                  "--end '23 Mar 2012 10:00:30'", exitcode = 2)
+        self.contain("no data")
+        self.fail("extract -a /newton/prep " +
+                  "--start '23 Mar 2012 10:00:30.000001' " +
+                  "--end '23 Mar 2012 10:00:30.000001'", exitcode = 2)
+        self.contain("no data")
+        self.fail("extract -a /newton/prep " +
+                  "--start '23 Mar 2022 10:00:30' " +
+                  "--end '23 Mar 2022 10:00:30'", exitcode = 2)
+        self.contain("no data")
+
+        # but are ok if we're just counting results
+        self.ok("extract --count /newton/prep " +
+                "--start '23 Mar 2012 10:00:30' " +
+                "--end '23 Mar 2012 10:00:30'")
+        self.match("0\n")
+        self.ok("extract -c /newton/prep " +
+                "--start '23 Mar 2012 10:00:30.000001' " +
+                "--end '23 Mar 2012 10:00:30.000001'")
+        self.match("0\n")
+
+        # Check various dumps against stored copies of how they should appear
+        def test(file, start, end, extra=""):
+            self.ok("extract " + extra + " /newton/prep " +
+                    "--start '23 Mar 2012 " + start + "' " +
+                    "--end '23 Mar 2012 " + end + "'")
+            self.matchfile("tests/data/extract-" + str(file))
+            self.ok("extract --count " + extra + " /newton/prep " +
+                    "--start '23 Mar 2012 " + start + "' " +
+                    "--end '23 Mar 2012 " + end + "'")
+            self.matchfilecount("tests/data/extract-" + str(file))
+        test(1, "10:00:30", "10:00:31", extra="-a")
+        test(1, "10:00:30.000000", "10:00:31", extra="-a")
+        test(2, "10:00:30.000001", "10:00:31")
+        test(2, "10:00:30.008333", "10:00:31")
+        test(3, "10:00:30.008333", "10:00:30.008334")
+        test(3, "10:00:30.008333", "10:00:30.016667")
+        test(4, "10:00:30.008333", "10:00:30.025")
+        test(5, "10:00:30", "10:00:31", extra="--annotate --bare")
+        test(6, "10:00:30", "10:00:31", extra="-b")
+
+        # all data put in by tests
+        self.ok("extract -a /newton/prep --start 2000-01-01 --end 2020-01-01")
+        eq_(self.captured.count('\n'), 43204)
+        self.ok("extract -c /newton/prep --start 2000-01-01 --end 2020-01-01")
+        self.match("43200\n")
+
+    def test_cmdline_09_truncated(self):
+        # Test truncated responses by overriding the nilmdb max_results
+        server_stop()
+        server_start(max_results = 2)
+        self.ok("list --detail")
+        eq_(self.captured.count('\n'), 11)
+        server_stop()
+        server_start()
+
+    def test_cmdline_10_destroy(self):
+        # Delete records
+        self.ok("destroy --help")
+
+        self.fail("destroy")
+        self.contain("too few arguments")
+
+        self.fail("destroy /no/such/stream")
+        self.contain("No stream at path")
+
+        self.fail("destroy asdfasdf")
+        self.contain("No stream at path")
+
+        # From previous tests, we have:
+        self.ok("list")
+        self.match("/newton/prep PrepData\n"
+                   "/newton/raw RawData\n"
+                   "/newton/zzz/rawnotch RawNotchedData\n")
+
+        # Notice how they're not empty
+        self.ok("list --detail")
+        eq_(self.captured.count('\n'), 11)
+
+        # Delete some
+        self.ok("destroy /newton/prep")
+        self.ok("list")
+        self.match("/newton/raw RawData\n"
+                   "/newton/zzz/rawnotch RawNotchedData\n")
+
+        self.ok("destroy /newton/zzz/rawnotch")
+        self.ok("list")
+        self.match("/newton/raw RawData\n")
+
+        self.ok("destroy /newton/raw")
+        self.ok("create /newton/raw RawData")
+        self.ok("destroy /newton/raw")
+        self.ok("list")
+        self.match("")
+
+        # Re-create a previously deleted location, and some new ones
+        rebuild = [ "/newton/prep", "/newton/zzz",
+                    "/newton/raw", "/newton/asdf/qwer" ]
+        for path in rebuild:
+            # Create the path
+            self.ok("create " + path + " PrepData")
+            self.ok("list")
+            self.contain(path)
+            # Make sure it was created empty
+            self.ok("list --detail --path " + path)
+            self.contain("(no intervals)")

tests/test_helpers.py

@@ -0,0 +1,32 @@
+# Just some helpers for test functions
+
+import shutil, os
+
+def myrepr(x):
+    if isinstance(x, basestring):
+        return '"' + x + '"'
+    else:
+        return repr(x)
+
+def eq_(a, b):
+    if not a == b:
+        raise AssertionError("%s != %s" % (myrepr(a), myrepr(b)))
+
+def in_(a, b):
+    if a not in b:
+        raise AssertionError("%s not in %s" % (myrepr(a), myrepr(b)))
+
+def ne_(a, b):
+    if not a != b:
+        raise AssertionError("unexpected %s == %s" % (myrepr(a), myrepr(b)))
+
+def recursive_unlink(path):
+    try:
+        shutil.rmtree(path)
+    except OSError:
+        pass
+    try:
+        os.unlink(path)
+    except OSError:
+        pass
+

tests/test_interval.py

@@ -0,0 +1,355 @@
+# -*- coding: utf-8 -*-
+
+import nilmdb
+from nilmdb.printf import *
+import datetime_tz
+
+from nose.tools import *
+from nose.tools import assert_raises
+import itertools
+
+from nilmdb.interval import Interval, DBInterval, IntervalSet, IntervalError
+
+from test_helpers import *
+import unittest
+
+# set to False to skip live renders
+do_live_renders = False
+def render(iset, description = "", live = True):
+    import renderdot
+    r = renderdot.RBTreeRenderer(iset.tree)
+    return r.render(description, live and do_live_renders)
+
+def makeset(string):
+    """Build an IntervalSet from a string, for testing purposes
+
+    Each character is 1 second
+    [ = interval start
+    | = interval end + next start
+    ] = interval end
+    . = zero-width interval (identical start and end)
+    anything else is ignored
+    """
+    iset = IntervalSet()
+    for i, c in enumerate(string):
+        day = i + 10000
+        if (c == "["):
+            start = day
+        elif (c == "|"):
+            iset += Interval(start, day)
+            start = day
+        elif (c == ")"):
+            iset += Interval(start, day)
+            del start
+        elif (c == "."):
+            iset += Interval(day, day)
+    return iset
+
+class TestInterval:
+    def test_interval(self):
+        # Test Interval class
+        os.environ['TZ'] = "America/New_York"
+        datetime_tz._localtz = None
+        (d1, d2, d3) = [ datetime_tz.datetime_tz.smartparse(x).totimestamp()
+                         for x in [ "03/24/2012", "03/25/2012", "03/26/2012" ] ]
+
+        # basic construction
+        i = Interval(d1, d1)
+        i = Interval(d1, d3)
+        eq_(i.start, d1)
+        eq_(i.end, d3)
+
+        # assignment is allowed, but not verified
+        i.start = d2
+        #with assert_raises(IntervalError):
+        #    i.end = d1
+        i.start = d1
+        i.end = d2
+
+        # end before start
+        with assert_raises(IntervalError):
+            i = Interval(d3, d1)
+
+        # compare
+        assert(Interval(d1, d2) == Interval(d1, d2))
+        assert(Interval(d1, d2) < Interval(d1, d3))
+        assert(Interval(d1, d3) > Interval(d1, d2))
+        assert(Interval(d1, d2) < Interval(d2, d3))
+        assert(Interval(d1, d3) < Interval(d2, d3))
+        assert(Interval(d2, d2) > Interval(d1, d3))
+        assert(Interval(d3, d3) == Interval(d3, d3))
+        #with assert_raises(TypeError): # was AttributeError, that's wrong
+        #    x = (i == 123)
+
+        # subset
+        eq_(Interval(d1, d3).subset(d1, d2), Interval(d1, d2))
+        with assert_raises(IntervalError):
+            x = Interval(d2, d3).subset(d1, d2)
+
+        # big integers and floats
+        x = Interval(5000111222, 6000111222)
+        eq_(str(x), "[5000111222.0 -> 6000111222.0)")
+        x = Interval(123.45, 234.56)
+        eq_(str(x), "[123.45 -> 234.56)")
+
+        # misc
+        i = Interval(d1, d2)
+        eq_(repr(i), repr(eval(repr(i))))
+        eq_(str(i), "[1332561600.0 -> 1332648000.0)")
+
+    def test_interval_intersect(self):
+        # Test Interval intersections
+        dates = [ 100, 200, 300, 400 ]
+        perm = list(itertools.permutations(dates, 2))
+        prod = list(itertools.product(perm, perm))
+        should_intersect = {
+            False: [4, 5, 8, 20, 48, 56, 60, 96, 97, 100],
+            True: [0, 1, 2, 12, 13, 14, 16, 17, 24, 25, 26, 28, 29,
+                   32, 49, 50, 52, 53, 61, 62, 64, 65, 68, 98, 101, 104]
+            }
+        for i,((a,b),(c,d)) in enumerate(prod):
+            try:
+                i1 = Interval(a, b)
+                i2 = Interval(c, d)
+                eq_(i1.intersects(i2), i2.intersects(i1))
+                in_(i, should_intersect[i1.intersects(i2)])
+            except IntervalError:
+                assert(i not in should_intersect[True] and
+                       i not in should_intersect[False])
+        with assert_raises(TypeError):
+            x = i1.intersects(1234)
+
+    def test_intervalset_construct(self):
+        # Test IntervalSet construction
+        dates = [ 100, 200, 300, 400 ]
+
+        a = Interval(dates[0], dates[1])
+        b = Interval(dates[1], dates[2])
+        c = Interval(dates[0], dates[2])
+        d = Interval(dates[2], dates[3])
+
+        iseta = IntervalSet(a)
+        isetb = IntervalSet([a, b])
+        isetc = IntervalSet([a])
+        ne_(iseta, isetb)
+        eq_(iseta, isetc)
+        with assert_raises(TypeError):
+            x = iseta != 3
+        ne_(IntervalSet(a), IntervalSet(b))
+
+        # test iterator
+        for interval in iseta:
+            pass
+
+        # overlap
+        with assert_raises(IntervalError):
+            x = IntervalSet([a, b, c])
+
+        # bad types
+        with assert_raises(Exception):
+            x = IntervalSet([1, 2])
+
+        iset = IntervalSet(isetb)   # test iterator
+        eq_(iset, isetb)
+        eq_(len(iset), 2)
+        eq_(len(IntervalSet()), 0)
+
+        # Test adding
+        iset = IntervalSet(a)
+        iset += IntervalSet(b)
+        eq_(iset, IntervalSet([a, b]))
+        iset = IntervalSet(a)
+        iset += b
+        eq_(iset, IntervalSet([a, b]))
+        iset = IntervalSet(a) + IntervalSet(b)
+        eq_(iset, IntervalSet([a, b]))
+        iset = IntervalSet(b) + a
+        eq_(iset, IntervalSet([a, b]))
+
+        # A set consisting of [0-1],[1-2] should match a set consisting of [0-2]
+        eq_(IntervalSet([a,b]), IntervalSet([c]))
+        # Etc
+        ne_(IntervalSet([a,d]), IntervalSet([c]))
+        ne_(IntervalSet([c]), IntervalSet([a,d]))
+        ne_(IntervalSet([c,d]), IntervalSet([b,d]))
+
+        # misc
+        eq_(repr(iset), repr(eval(repr(iset))))
+        eq_(str(iset), "[[100.0 -> 200.0), [200.0 -> 300.0)]")
+
+    def test_intervalset_geniset(self):
+        # Test basic iset construction
+        eq_(makeset("  [----)   "),
+            makeset("  [-|--)   "))
+
+        eq_(makeset("[)  [--)   ") +
+            makeset(" [)    [--)"),
+            makeset("[|) [-----)"))
+
+        eq_(makeset("  [-------)"),
+            makeset("  [-|-----|"))
+
+
+    def test_intervalset_intersect(self):
+        # Test intersection (&)
+        with assert_raises(TypeError): # was AttributeError
+            x = makeset("[--)") & 1234
+
+        # Intersection with interval
+        eq_(makeset("[---|---)[)") &
+            list(makeset("  [------) "))[0],
+            makeset("  [-----)  "))
+
+        # Intersection with sets
+        eq_(makeset("[---------)") &
+            makeset(" [---)     "),
+            makeset(" [---)     "))
+
+        eq_(makeset(" [---)     ") &
+            makeset("[---------)"),
+            makeset(" [---)     "))
+
+        eq_(makeset("    [-----)") &
+            makeset(" [-----)   "),
+            makeset("    [--)   "))
+
+        eq_(makeset(" [--)  [--)") &
+            makeset("  [------) "),
+            makeset("  [-)  [-) "))
+
+        eq_(makeset("      [---)") &
+            makeset(" [--)      "),
+            makeset("           "))
+
+        eq_(makeset("    [-|---)") &
+            makeset(" [-----|-) "),
+            makeset("    [----) "))
+
+        eq_(makeset("    [-|-)  ") &
+            makeset(" [-|--|--) "),
+            makeset("    [---)  "))
+
+        # Border cases -- will give different results if intervals are
+        # half open or fully closed.  Right now, they are half open,
+        # although that's a little messy since the database intervals
+        # often contain a data point at the endpoint.
+        half_open = True
+        if half_open:
+            eq_(makeset("      [---)") &
+                makeset(" [----)    "),
+                makeset("           "))
+            eq_(makeset(" [----)[--)") &
+                makeset("[-) [--) [)"),
+                makeset(" [) [-)  [)"))
+        else:
+            eq_(makeset("      [---)") &
+                makeset(" [----)    "),
+                makeset("      .    "))
+            eq_(makeset(" [----)[--)") &
+                makeset("[-) [--) [)"),
+                makeset(" [) [-). [)"))
+
+class TestIntervalDB:
+    def test_dbinterval(self):
+        # Test DBInterval class
+        i = DBInterval(100, 200, 100, 200, 10000, 20000)
+        eq_(i.start, 100)
+        eq_(i.end, 200)
+        eq_(i.db_start, 100)
+        eq_(i.db_end, 200)
+        eq_(i.db_startpos, 10000)
+        eq_(i.db_endpos, 20000)
+        eq_(repr(i), repr(eval(repr(i))))
+
+        # end before start
+        with assert_raises(IntervalError):
+            i = DBInterval(200, 100, 100, 200, 10000, 20000)
+
+        # db_start too late
+        with assert_raises(IntervalError):
+            i = DBInterval(100, 200, 150, 200, 10000, 20000)
+
+        # db_end too soon
+        with assert_raises(IntervalError):
+            i = DBInterval(100, 200, 100, 150, 10000, 20000)
+
+        # actual start, end can be a subset
+        a = DBInterval(150, 200, 100, 200, 10000, 20000)
+        b = DBInterval(100, 150, 100, 200, 10000, 20000)
+        c = DBInterval(150, 150, 100, 200, 10000, 20000)
+
+        # Make a set of DBIntervals
+        iseta = IntervalSet([a, b])
+        isetc = IntervalSet(c)
+        assert(iseta.intersects(a))
+        assert(iseta.intersects(b))
+
+        # Test subset
+        with assert_raises(IntervalError):
+            x = a.subset(150, 250)
+
+        # Subset of those IntervalSets should still contain DBIntervals
+        for i in IntervalSet(iseta.intersection(Interval(125,250))):
+            assert(isinstance(i, DBInterval))
+
+class TestIntervalTree:
+
+    def test_interval_tree(self):
+        import random
+        random.seed(1234)
+
+        # make a set of 100 intervals
+        iset = IntervalSet()
+        j = 100
+        for i in random.sample(xrange(j),j):
+            interval = Interval(i, i+1)
+            iset += interval
+        render(iset, "Random Insertion")
+
+        # remove about half of them
+        for i in random.sample(xrange(j),j):
+            if random.randint(0,1):
+                iset -= Interval(i, i+1)
+
+        # try removing an interval that doesn't exist
+        with assert_raises(IntervalError):
+            iset -= Interval(1234,5678)
+        render(iset, "Random Insertion, deletion")
+
+        # make a set of 100 intervals, inserted in order
+        iset = IntervalSet()
+        j = 100
+        for i in xrange(j):
+            interval = Interval(i, i+1)
+            iset += interval
+        render(iset, "In-order insertion")
+
+class TestIntervalSpeed:
+    @unittest.skip("this is slow")
+    def test_interval_speed(self):
+        import yappi
+        import time
+        import aplotter
+        import random
+        import math
+
+        print
+        yappi.start()
+        speeds = {}
+        for j in [ 2**x for x in range(5,20) ]:
+            start = time.time()
+            iset = IntervalSet()
+            for i in random.sample(xrange(j),j):
+                interval = Interval(i, i+1)
+                iset += interval
+            speed = (time.time() - start) * 1000000.0
+            printf("%d: %g μs (%g μs each, O(n log n) ratio %g)\n",
+                   j,
+                   speed,
+                   speed/j,
+                   speed / (j*math.log(j))) # should be constant
+            speeds[j] = speed
+        aplotter.plot(speeds.keys(), speeds.values(), plot_slope=True)
+        yappi.stop()
+        yappi.print_stats(sort_type=yappi.SORTTYPE_TTOT, limit=10)
+

tests/test_iteratorizer.py

@@ -0,0 +1,54 @@
+import nilmdb
+from nilmdb.printf import *
+
+import nose
+from nose.tools import *
+from nose.tools import assert_raises
+import threading
+import time
+
+from test_helpers import *
+
+import nilmdb.iteratorizer
+
+def func_with_callback(a, b, callback):
+    callback(a)
+    callback(b)
+    callback(a+b)
+
+class TestIteratorizer(object):
+    def test(self):
+
+        # First try it with a normal callback
+        self.result = ""
+        def cb(x):
+            self.result += str(x)
+        func_with_callback(1, 2, cb)
+        eq_(self.result, "123")
+
+        # Now make it an iterator
+        it = nilmdb.iteratorizer.Iteratorizer(lambda x:
+                                              func_with_callback(1, 2, x))
+        result = ""
+        for i in it:
+            result += str(i)
+        eq_(result, "123")
+
+        # Make sure things work when an exception occurs
+        it = nilmdb.iteratorizer.Iteratorizer(lambda x:
+                                              func_with_callback(1, "a", x))
+        result = ""
+        with assert_raises(TypeError) as e:
+            for i in it:
+                result += str(i)
+        eq_(result, "1a")
+
+        # Now try to trigger the case where we stop iterating
+        # mid-generator, and expect the iteratorizer to clean up after
+        # itself.  This doesn't have a particular result in the test,
+        # but gains coverage.
+        def foo():
+            it = nilmdb.iteratorizer.Iteratorizer(lambda x:
+                                                  func_with_callback(1, 2, x))
+            it.next()
+        foo()

tests/test_layout.py

@@ -0,0 +1,250 @@
+# -*- coding: utf-8 -*-
+
+import nilmdb
+
+from nilmdb.printf import *
+
+from nose.tools import *
+from nose.tools import assert_raises
+import distutils.version
+import itertools
+import os
+import shutil
+import sys
+import cherrypy
+import threading
+import urllib2
+from urllib2 import urlopen, HTTPError
+import Queue
+import cStringIO
+import random
+import unittest
+
+from test_helpers import *
+
+from nilmdb.layout import *
+
+class TestLayouts(object):
+    # Some nilmdb.layout tests.  Not complete, just fills in missing
+    # coverage.
+    def test_layouts(self):
+        x = nilmdb.layout.get_named("PrepData").description()
+        y = nilmdb.layout.get_named("float32_8").description()
+        eq_(repr(x), repr(y))
+
+    def test_parsing(self):
+        self.real_t_parsing("PrepData", "RawData", "RawNotchedData")
+        self.real_t_parsing("float32_8", "uint16_6", "uint16_9")
+    def real_t_parsing(self, name_prep, name_raw, name_rawnotch):
+        # invalid layouts
+        with assert_raises(TypeError) as e:
+            parser = Parser("NoSuchLayout")
+        with assert_raises(TypeError) as e:
+            parser = Parser("float32")
+
+        # too little data
+        parser = Parser(name_prep)
+        data = ( "1234567890.000000 1.1 2.2 3.3 4.4 5.5\n" +
+                 "1234567890.100000 1.1 2.2 3.3 4.4 5.5\n")
+        with assert_raises(ParserError) as e:
+            parser.parse(data)
+        in_("error", str(e.exception))
+
+        # too much data
+        parser = Parser(name_prep)
+        data = ( "1234567890.000000 1.1 2.2 3.3 4.4 5.5 6.6 7.7 8.8 9.9\n" +
+                 "1234567890.100000 1.1 2.2 3.3 4.4 5.5 6.6 7.7 8.8 9.9\n")
+        with assert_raises(ParserError) as e:
+            parser.parse(data)
+        in_("error", str(e.exception))
+
+        # just right
+        parser = Parser(name_prep)
+        data = ( "1234567890.000000 1.1 2.2 3.3 4.4 5.5 6.6 7.7 8.8\n" +
+                 "1234567890.100000 1.1 2.2 3.3 4.4 5.5 6.6 7.7 8.8\n")
+        parser.parse(data)
+        eq_(parser.min_timestamp, 1234567890.0)
+        eq_(parser.max_timestamp, 1234567890.1)
+        eq_(parser.data, [[1234567890.0,1.1,2.2,3.3,4.4,5.5,6.6,7.7,8.8],
+                          [1234567890.1,1.1,2.2,3.3,4.4,5.5,6.6,7.7,8.8]])
+
+        # try RawData too, with clamping
+        parser = Parser(name_raw)
+        data = ( "1234567890.000000 1 2 3 4 5 6\n" +
+                 "1234567890.100000 1 2 3 4 5 6\n" )
+        parser.parse(data)
+        eq_(parser.data, [[1234567890.0,1,2,3,4,5,6],
+                          [1234567890.1,1,2,3,4,5,6]])
+
+        # pass an instantiated class
+        parser = Parser(get_named(name_rawnotch))
+        data = ( "1234567890.000000 1 2 3 4 5 6 7 8 9\n" +
+                 "1234567890.100000 1 2 3 4 5 6 7 8 9\n" )
+        parser.parse(data)
+
+        # non-monotonic
+        parser = Parser(name_raw)
+        data = ( "1234567890.100000 1 2 3 4 5 6\n" +
+                 "1234567890.000000 1 2 3 4 5 6\n" )
+        with assert_raises(ParserError) as e:
+            parser.parse(data)
+        in_("not monotonically increasing", str(e.exception))
+
+        # RawData with values out of bounds
+        parser = Parser(name_raw)
+        data = ( "1234567890.000000 1 2 3 4 500000 6\n" +
+                 "1234567890.100000 1 2 3 4 5 6\n" )
+        with assert_raises(ParserError) as e:
+            parser.parse(data)
+        in_("value out of range", str(e.exception))
+
+        # Empty data should work but is useless
+        parser = Parser(name_raw)
+        data = ""
+        parser.parse(data)
+        assert(parser.min_timestamp is None)
+        assert(parser.max_timestamp is None)
+
+    def test_formatting(self):
+        self.real_t_formatting("PrepData", "RawData", "RawNotchedData")
+        self.real_t_formatting("float32_8", "uint16_6", "uint16_9")
+    def real_t_formatting(self, name_prep, name_raw, name_rawnotch):
+        # invalid layout
+        with assert_raises(TypeError) as e:
+            formatter = Formatter("NoSuchLayout")
+
+        # too little data
+        formatter = Formatter(name_prep)
+        data = [ [ 1234567890.000000, 1.1, 2.2, 3.3, 4.4, 5.5 ],
+                 [ 1234567890.100000, 1.1, 2.2, 3.3, 4.4, 5.5 ] ]
+        with assert_raises(FormatterError) as e:
+            formatter.format(data)
+        in_("error", str(e.exception))
+
+        # too much data
+        formatter = Formatter(name_prep)
+        data = [ [ 1234567890.000000, 1, 2, 3, 4, 5, 6, 7, 8, 9 ],
+                 [ 1234567890.100000, 1, 2, 3, 4, 5, 6, 7, 8, 9 ] ]
+        with assert_raises(FormatterError) as e:
+            formatter.format(data)
+        in_("error", str(e.exception))
+
+        # just right
+        formatter = Formatter(name_prep)
+        data = [ [ 1234567890.000000, 1.1, 2.2, 3.3, 4.4, 5.5, 6.6, 7.7, 8.8 ],
+                 [ 1234567890.100000, 1.1, 2.2, 3.3, 4.4, 5.5, 6.6, 7.7, 8.8 ] ]
+        text = formatter.format(data)
+        eq_(text,
+            "1234567890.000000 1.100000 2.200000 3.300000 4.400000 " +
+            "5.500000 6.600000 7.700000 8.800000\n" +
+            "1234567890.100000 1.100000 2.200000 3.300000 4.400000 " +
+            "5.500000 6.600000 7.700000 8.800000\n")
+
+        # try RawData too
+        formatter = Formatter(name_raw)
+        data = [ [ 1234567890.000000, 1, 2, 3, 4, 5, 6 ],
+                 [ 1234567890.100000, 1, 2, 3, 4, 5, 6 ] ]
+        text = formatter.format(data)
+        eq_(text,
+            "1234567890.000000 1 2 3 4 5 6\n" +
+            "1234567890.100000 1 2 3 4 5 6\n")
+
+        # pass an instantiated class
+        formatter = Formatter(get_named(name_rawnotch))
+        data = [ [ 1234567890.000000, 1, 2, 3, 4, 5, 6, 7, 8, 9 ],
+                 [ 1234567890.100000, 1, 2, 3, 4, 5, 6, 7, 8, 9 ] ]
+        text = formatter.format(data)
+        eq_(text,
+            "1234567890.000000 1 2 3 4 5 6 7 8 9\n" +
+            "1234567890.100000 1 2 3 4 5 6 7 8 9\n")
+
+        # Empty data should work but is useless
+        formatter = Formatter(name_raw)
+        data = []
+        text = formatter.format(data)
+        eq_(text, "")
+
+    def test_roundtrip(self):
+        self.real_t_roundtrip("PrepData", "RawData", "RawNotchedData")
+        self.real_t_roundtrip("float32_8", "uint16_6", "uint16_9")
+    def real_t_roundtrip(self, name_prep, name_raw, name_rawnotch):
+        # Verify that textual data passed into the Parser, and then
+        # back through the Formatter, then back into the Parser,
+        # gives identical parsed representations
+        random.seed(12345)
+
+        def do_roundtrip(layout, datagen):
+            for i in range(100):
+                rows = random.randint(1,100)
+                data = ""
+                ts = 1234567890
+                for r in range(rows):
+                    ts += random.uniform(0,1)
+                    row = sprintf("%f", ts) + " "
+                    row += " ".join(datagen())
+                    row += "\n"
+                    data += row
+                parser1 = Parser(layout)
+                formatter = Formatter(layout)
+                parser2 = Parser(layout)
+                parser1.parse(data)
+                parser2.parse(formatter.format(parser1.data))
+                eq_(parser1.data, parser2.data)
+
+        def datagen():
+            return [ sprintf("%f", random.uniform(-1000,1000))
+                     for x in range(8) ]
+        do_roundtrip(name_prep, datagen)
+
+        def datagen():
+            return [ sprintf("%d", random.randint(0,65535))
+                     for x in range(6) ]
+        do_roundtrip(name_raw, datagen)
+
+        def datagen():
+            return [ sprintf("%d", random.randint(0,65535))
+                     for x in range(9) ]
+        do_roundtrip(name_rawnotch, datagen)
+
+class TestLayoutSpeed:
+    @unittest.skip("this is slow")
+    def test_layout_speed(self):
+        import time
+
+        random.seed(54321)
+
+        def do_speedtest(layout, datagen, rows = 5000, times = 100):
+            # Build data once
+            data = ""
+            ts = 1234567890
+            for r in range(rows):
+                ts += random.uniform(0,1)
+                row = sprintf("%f", ts) + " "
+                row += " ".join(datagen())
+                row += "\n"
+                data += row
+
+            # Do lots of roundtrips
+            start = time.time()
+            for i in range(times):
+                parser = Parser(layout)
+                formatter = Formatter(layout)
+                parser.parse(data)
+                data = formatter.format(parser.data)
+            elapsed = time.time() - start
+            printf("roundtrip %s: %d ms, %.1f μs/row, %d rows/sec\n",
+                   layout,
+                   elapsed * 1e3,
+                   (elapsed * 1e6) / (rows * times),
+                   (rows * times) / elapsed)
+
+        print ""
+        def datagen():
+            return [ sprintf("%f", random.uniform(-1000,1000))
+                     for x in range(10) ]
+        do_speedtest("float32_10", datagen)
+
+        def datagen():
+            return [ sprintf("%d", random.randint(0,65535))
+                     for x in range(10) ]
+        do_speedtest("uint16_10", datagen)

tests/test_nilmdb.py

@@ -0,0 +1,201 @@
+import nilmdb
+
+from nose.tools import *
+from nose.tools import assert_raises
+import distutils.version
+import simplejson as json
+import itertools
+import os
+import shutil
+import sys
+import cherrypy
+import threading
+import urllib2
+from urllib2 import urlopen, HTTPError
+import Queue
+import cStringIO
+
+testdb = "tests/testdb"
+
+#@atexit.register
+#def cleanup():
+#    os.unlink(testdb)
+
+from test_helpers import *
+
+class Test00Nilmdb(object):  # named 00 so it runs first
+    def test_NilmDB(self):
+        recursive_unlink(testdb)
+
+        with assert_raises(IOError):
+            nilmdb.NilmDB("/nonexistant-db/foo")
+
+        db = nilmdb.NilmDB(testdb)
+        db.close()
+        db = nilmdb.NilmDB(testdb, sync=False)
+        db.close()
+
+        # test timer, just to get coverage
+        capture = cStringIO.StringIO()
+        old = sys.stdout
+        sys.stdout = capture
+        with nilmdb.Timer("test"):
+            nilmdb.timer.time.sleep(0.01)
+        sys.stdout = old
+        in_("test: ", capture.getvalue())
+
+    def test_stream(self):
+        db = nilmdb.NilmDB(testdb, sync=False)
+        eq_(db.stream_list(), [])
+
+        # Bad path
+        with assert_raises(ValueError):
+            db.stream_create("foo/bar/baz", "PrepData")
+        with assert_raises(ValueError):
+            db.stream_create("/foo", "PrepData")
+        # Bad layout type
+        with assert_raises(ValueError):
+            db.stream_create("/newton/prep", "NoSuchLayout")
+        db.stream_create("/newton/prep", "PrepData")
+        db.stream_create("/newton/raw", "RawData")
+        db.stream_create("/newton/zzz/rawnotch", "RawNotchedData")
+
+        # Verify we got 3 streams
+        eq_(db.stream_list(), [ ["/newton/prep", "PrepData"],
+                                ["/newton/raw", "RawData"],
+                                ["/newton/zzz/rawnotch", "RawNotchedData"]
+                                ])
+        # Match just one type or one path
+        eq_(db.stream_list(layout="RawData"), [ ["/newton/raw", "RawData"] ])
+        eq_(db.stream_list(path="/newton/raw"), [ ["/newton/raw", "RawData"] ])
+
+        # Verify that columns were made right
+        eq_(len(db.h5file.getNode("/newton/prep").cols), 9)
+        eq_(len(db.h5file.getNode("/newton/raw").cols), 7)
+        eq_(len(db.h5file.getNode("/newton/zzz/rawnotch").cols), 10)
+        assert(not db.h5file.getNode("/newton/prep").colindexed["timestamp"])
+        assert(not db.h5file.getNode("/newton/prep").colindexed["c1"])
+
+        # Set / get metadata
+        eq_(db.stream_get_metadata("/newton/prep"), {})
+        eq_(db.stream_get_metadata("/newton/raw"), {})
+        meta1 = { "description": "The Data",
+                  "v_scale": "1.234" }
+        meta2 = { "description": "The Data" }
+        meta3 = { "v_scale": "1.234" }
+        db.stream_set_metadata("/newton/prep", meta1)
+        db.stream_update_metadata("/newton/prep", {})
+        db.stream_update_metadata("/newton/raw", meta2)
+        db.stream_update_metadata("/newton/raw", meta3)
+        eq_(db.stream_get_metadata("/newton/prep"), meta1)
+        eq_(db.stream_get_metadata("/newton/raw"), meta1)
+
+        db.close()
+
+class TestBlockingServer(object):
+    def setUp(self):
+        self.db = nilmdb.NilmDB(testdb, sync=False)
+
+    def tearDown(self):
+        self.db.close()
+
+    def test_blocking_server(self):
+        # Start web app on a custom port
+        self.server = nilmdb.Server(self.db, host = "127.0.0.1",
+                                    port = 12380, stoppable = True)
+
+        # Run it
+        event = threading.Event()
+        def run_server():
+            self.server.start(blocking = True, event = event)
+        thread = threading.Thread(target = run_server)
+        thread.start()
+        event.wait(timeout = 2)
+
+        # Send request to exit.
+        req = urlopen("http://127.0.0.1:12380/exit/", timeout = 1)
+
+        # Wait for it
+        thread.join()
+
+def geturl(path):
+    req = urlopen("http://127.0.0.1:12380" + path, timeout = 10)
+    return req.read()
+
+def getjson(path):
+    return json.loads(geturl(path))
+
+class TestServer(object):
+
+    def setUp(self):
+        # Start web app on a custom port
+        self.db = nilmdb.NilmDB(testdb, sync=False)
+        self.server = nilmdb.Server(self.db, host = "127.0.0.1",
+                                    port = 12380, stoppable = False)
+        self.server.start(blocking = False)
+
+    def tearDown(self):
+        # Close web app
+        self.server.stop()
+        self.db.close()
+
+    def test_server(self):
+        # Make sure we can't force an exit, and test other 404 errors
+        for url in [ "/exit", "/", "/favicon.ico" ]:
+            with assert_raises(HTTPError) as e:
+                geturl(url)
+            eq_(e.exception.code, 404)
+
+        # Check version
+        eq_(distutils.version.StrictVersion(getjson("/version")),
+            distutils.version.StrictVersion(self.server.version))
+
+    def test_stream_list(self):
+        # Known streams that got populated by an earlier test (test_nilmdb)
+        streams = getjson("/stream/list")
+
+        eq_(streams, [
+            ['/newton/prep', 'PrepData'],
+            ['/newton/raw', 'RawData'],
+            ['/newton/zzz/rawnotch', 'RawNotchedData'],
+            ])
+
+        streams = getjson("/stream/list?layout=RawData")
+        eq_(streams, [['/newton/raw', 'RawData']])
+
+        streams = getjson("/stream/list?layout=NoSuchLayout")
+        eq_(streams, [])
+
+
+    def test_stream_metadata(self):
+        with assert_raises(HTTPError) as e:
+            getjson("/stream/get_metadata?path=foo")
+        eq_(e.exception.code, 404)
+
+        data = getjson("/stream/get_metadata?path=/newton/prep")
+        eq_(data, {'description': 'The Data', 'v_scale': '1.234'})
+
+        data = getjson("/stream/get_metadata?path=/newton/prep"
+                       "&key=v_scale")
+        eq_(data, {'v_scale': '1.234'})
+
+        data = getjson("/stream/get_metadata?path=/newton/prep"
+                       "&key=v_scale&key=description")
+        eq_(data, {'description': 'The Data', 'v_scale': '1.234'})
+
+        data = getjson("/stream/get_metadata?path=/newton/prep"
+                       "&key=v_scale&key=foo")
+        eq_(data, {'foo': None, 'v_scale': '1.234'})
+
+        data = getjson("/stream/get_metadata?path=/newton/prep"
+                       "&key=foo")
+        eq_(data, {'foo': None})
+
+
+    def test_insert(self):
+        # GET instead of POST (no body)
+        # (actual POST test is done by client code)
+        with assert_raises(HTTPError) as e:
+            getjson("/stream/insert?path=/newton/prep")
+        eq_(e.exception.code, 400)
+

tests/test_printf.py

@@ -0,0 +1,27 @@
+import nilmdb
+from nilmdb.printf import *
+
+from nose.tools import *
+from nose.tools import assert_raises
+from cStringIO import StringIO
+import sys
+
+from test_helpers import *
+
+class TestPrintf(object):
+    def test_printf(self):
+        old_stdout = sys.stdout
+        sys.stdout = test1 = StringIO()
+        test2 = StringIO()
+        test3 = ""
+        try:
+            printf("hello, world: %d", 123)
+            fprintf(test2, "hello too: %d", 123)
+            test3 = sprintf("hello three: %d", 123)
+        except:
+            sys.stdout = old_stdout
+            raise
+        sys.stdout = old_stdout
+        eq_(test1.getvalue(), "hello, world: 123")
+        eq_(test2.getvalue(), "hello too: 123")
+        eq_(test3, "hello three: 123")

tests/test_rbtree.py

@@ -0,0 +1,159 @@
+# -*- coding: utf-8 -*-
+
+import nilmdb
+from nilmdb.printf import *
+
+from nose.tools import *
+from nose.tools import assert_raises
+
+from nilmdb.rbtree import RBTree, RBNode
+
+from test_helpers import *
+import unittest
+
+# set to False to skip live renders
+do_live_renders = False
+def render(tree, description = "", live = True):
+    import renderdot
+    r = renderdot.RBTreeRenderer(tree)
+    return r.render(description, live and do_live_renders)
+
+class TestRBTree:
+    def test_rbtree(self):
+        rb = RBTree()
+        rb.insert(RBNode(10000, 10001))
+        rb.insert(RBNode(10004, 10007))
+        rb.insert(RBNode(10001, 10002))
+        # There was a typo that gave the RBTree a loop in this case.
+        # Verify that the dot isn't too big.
+        s = render(rb, live = False)
+        assert(len(s.splitlines()) < 30)
+
+    def test_rbtree_big(self):
+        import random
+        random.seed(1234)
+
+        # make a set of 100 intervals, inserted in order
+        rb = RBTree()
+        j = 100
+        for i in xrange(j):
+            rb.insert(RBNode(i, i+1))
+        render(rb, "in-order insert")
+
+        # remove about half of them
+        for i in random.sample(xrange(j),j):
+            if random.randint(0,1):
+                rb.delete(rb.find(i, i+1))
+        render(rb, "in-order insert, random delete")
+
+        # make a set of 100 intervals, inserted at random
+        rb = RBTree()
+        j = 100
+        for i in random.sample(xrange(j),j):
+            rb.insert(RBNode(i, i+1))
+        render(rb, "random insert")
+
+        # remove about half of them
+        for i in random.sample(xrange(j),j):
+            if random.randint(0,1):
+                rb.delete(rb.find(i, i+1))
+        render(rb, "random insert, random delete")
+
+        # in-order insert of 50 more
+        for i in xrange(50):
+            rb.insert(RBNode(i+500, i+501))
+        render(rb, "random insert, random delete, in-order insert")
+
+    def test_rbtree_basics(self):
+        rb = RBTree()
+        vals = [ 7, 14, 1, 2, 8, 11, 5, 15, 4]
+        for n in vals:
+            rb.insert(RBNode(n, n))
+
+        # stringify
+        s = ""
+        for node in rb:
+            s += str(node)
+        in_("[node (None) 1", s)
+        eq_(str(rb.nil), "[node nil]")
+
+        # inorder traversal, successor and predecessor
+        last = 0
+        for node in rb:
+            assert(node.start > last)
+            last = node.start
+            successor = rb.successor(node)
+            if successor:
+                assert(rb.predecessor(successor) is node)
+            predecessor = rb.predecessor(node)
+            if predecessor:
+                assert(rb.successor(predecessor) is node)
+
+        # Delete node not in the tree
+        with assert_raises(AttributeError):
+            rb.delete(RBNode(1,2))
+
+        # Delete all nodes!
+        for node in rb:
+            rb.delete(node)
+
+        # Build it up again, make sure it matches
+        for n in vals:
+            rb.insert(RBNode(n, n))
+        s2 = ""
+        for node in rb:
+            s2 += str(node)
+        assert(s == s2)
+
+    def test_rbtree_find(self):
+        # Get a little bit of coverage for some overlapping cases,
+        # even though the class doesn't fully support it.
+        rb = RBTree()
+        nodes = [ RBNode(1, 5), RBNode(1, 10), RBNode(1, 15) ]
+        for n in nodes:
+            rb.insert(n)
+        assert(rb.find(1, 5) is nodes[0])
+        assert(rb.find(1, 10) is nodes[1])
+        assert(rb.find(1, 15) is nodes[2])
+
+    def test_rbtree_find_leftright(self):
+        # Now let's get some ranges in there
+        rb = RBTree()
+        vals = [ 7, 14, 1, 2, 8, 11, 5, 15, 4]
+        for n in vals:
+            rb.insert(RBNode(n*10, n*10+5))
+
+        # Check find_end_left, find_right_start
+        for i in range(160):
+            left = rb.find_left_end(i)
+            right = rb.find_right_start(i)
+            if left:
+                # endpoint should be more than i
+                assert(left.end >= i)
+                # all earlier nodes should have a lower endpoint
+                for node in rb:
+                    if node is left:
+                        break
+                    assert(node.end < i)
+            if right:
+                # startpoint should be less than i
+                assert(right.start <= i)
+                # all later nodes should have a higher startpoint
+                for node in reversed(list(rb)):
+                    if node is right:
+                        break
+                    assert(node.start > i)
+
+    def test_rbtree_intersect(self):
+        # Fill with some ranges
+        rb = RBTree()
+        rb.insert(RBNode(10,20))
+        rb.insert(RBNode(20,25))
+        rb.insert(RBNode(30,40))
+        # Just a quick test; test_interval will do better.
+        eq_(len(list(rb.intersect(1,100))), 3)
+        eq_(len(list(rb.intersect(10,20))), 1)
+        eq_(len(list(rb.intersect(5,15))), 1)
+        eq_(len(list(rb.intersect(15,15))), 1)
+        eq_(len(list(rb.intersect(20,21))), 1)
+        eq_(len(list(rb.intersect(19,21))), 2)

tests/test_serializer.py

@@ -0,0 +1,72 @@
+import nilmdb
+from nilmdb.printf import *
+
+import nose
+from nose.tools import *
+from nose.tools import assert_raises
+import threading
+import time
+
+from test_helpers import *
+
+#raise nose.exc.SkipTest("Skip these")
+
+class Foo(object):
+    val = 0
+
+    def fail(self):
+        raise Exception("you asked me to do this")
+
+    def test(self, debug = False):
+        # purposely not thread-safe
+        oldval = self.val
+        newval = oldval + 1
+        time.sleep(0.05)
+        self.val = newval
+        if debug:
+            printf("[%s] value changed: %d -> %d\n",
+                   threading.current_thread().name, oldval, newval)
+
+class Base(object):
+
+    def test_wrapping(self):
+        self.foo.test()
+        with assert_raises(Exception):
+            self.foo.fail()
+
+    def test_threaded(self):
+        def func(foo):
+            foo.test()
+        threads = []
+        for i in xrange(20):
+            threads.append(threading.Thread(target = func, args = (self.foo,)))
+        for t in threads:
+            t.start()
+        for t in threads:
+            t.join()
+        self.verify_result()
+
+class TestUnserialized(Base):
+    def setUp(self):
+        self.foo = Foo()
+
+    def verify_result(self):
+        # This should have failed to increment properly
+        assert(self.foo.val != 20)
+
+class TestSerialized(Base):
+    def setUp(self):
+        self.realfoo = Foo()
+        self.foo = nilmdb.serializer.WrapObject(self.realfoo)
+
+    def tearDown(self):
+        del self.foo
+
+    def verify_result(self):
+        # This should have worked
+        eq_(self.realfoo.val, 20)
+
+    def test_attribute(self):
+        # Can't wrap attributes yet
+        with assert_raises(TypeError):
+            self.foo.val

tests/test_timestamper.py

@@ -0,0 +1,91 @@
+import nilmdb
+from nilmdb.printf import *
+
+import datetime_tz
+
+from nose.tools import *
+from nose.tools import assert_raises
+import os
+import sys
+import cStringIO
+
+from test_helpers import *
+
+class TestTimestamper(object):
+
+    # Not a very comprehensive test, but it's good enough.
+
+    def test_timestamper(self):
+        def join(list):
+            return "\n".join(list) + "\n"
+
+        start = datetime_tz.datetime_tz.smartparse("03/24/2012").totimestamp()
+        lines_in  = [ "hello", "world", "hello world", "# commented out" ]
+        lines_out = [ "1332561600.000000 hello",
+                      "1332561600.000125 world",
+                      "1332561600.000250 hello world" ]
+
+        # full
+        input = cStringIO.StringIO(join(lines_in))
+        ts = nilmdb.timestamper.TimestamperRate(input, start, 8000)
+        foo = ts.readlines()
+        eq_(foo, join(lines_out))
+        in_("TimestamperRate(..., start=", str(ts))
+
+        # first 30 or so bytes means the first 2 lines
+        input = cStringIO.StringIO(join(lines_in))
+        ts = nilmdb.timestamper.TimestamperRate(input, start, 8000)
+        foo = ts.readlines(30)
+        eq_(foo, join(lines_out[0:2]))
+
+        # stop iteration early
+        input = cStringIO.StringIO(join(lines_in))
+        ts = nilmdb.timestamper.TimestamperRate(input, start, 8000,
+                                                1332561600.000200)
+        foo = ""
+        for line in ts:
+            foo += line
+        eq_(foo, join(lines_out[0:2]))
+
+        # stop iteration early (readlines)
+        input = cStringIO.StringIO(join(lines_in))
+        ts = nilmdb.timestamper.TimestamperRate(input, start, 8000,
+                                                1332561600.000200)
+        foo = ts.readlines()
+        eq_(foo, join(lines_out[0:2]))
+
+        # stop iteration really early
+        input = cStringIO.StringIO(join(lines_in))
+        ts = nilmdb.timestamper.TimestamperRate(input, start, 8000,
+                                                1332561600.000000)
+        foo = ts.readlines()
+        eq_(foo, "")
+
+        # use iterator
+        input = cStringIO.StringIO(join(lines_in))
+        ts = nilmdb.timestamper.TimestamperRate(input, start, 8000)
+        foo = ""
+        for line in ts:
+            foo += line
+        eq_(foo, join(lines_out))
+
+        # check that TimestamperNow gives similar result
+        input = cStringIO.StringIO(join(lines_in))
+        ts = nilmdb.timestamper.TimestamperNow(input)
+        foo = ts.readlines()
+        ne_(foo, join(lines_out))
+        eq_(len(foo), len(join(lines_out)))
+        eq_(str(ts), "TimestamperNow(...)")
+
+        # Test passing a file (should be empty)
+        ts = nilmdb.timestamper.TimestamperNow("/dev/null")
+        for line in ts:
+            raise AssertionError
+        ts.close()
+
+        # Test the null timestamper
+        input = cStringIO.StringIO(join(lines_out))  # note: lines_out
+        ts = nilmdb.timestamper.TimestamperNull(input)
+        foo = ts.readlines()
+        eq_(foo, join(lines_out))
+        eq_(str(ts), "TimestamperNull(...)")

time-bxintersect

@@ -0,0 +1,54 @@
+nosetests
+
+32: 386 μs (12.0625 μs each)
+64: 672.102 μs (10.5016 μs each)
+128: 1510.86 μs (11.8036 μs each)
+256: 2782.11 μs (10.8676 μs each)
+512: 5591.87 μs (10.9216 μs each)
+1024: 12812.1 μs (12.5119 μs each)
+2048: 21835.1 μs (10.6617 μs each)
+4096: 46059.1 μs (11.2449 μs each)
+8192: 114127 μs (13.9315 μs each)
+16384: 181217 μs (11.0606 μs each)
+32768: 419649 μs (12.8067 μs each)
+65536: 804320 μs (12.2729 μs each)
+131072: 1.73534e+06 μs (13.2396 μs each)
+262144: 3.74451e+06 μs (14.2842 μs each)
+524288: 8.8694e+06 μs (16.917 μs each)
+1048576: 1.69993e+07 μs (16.2118 μs each)
+2097152: 3.29387e+07 μs (15.7064 μs each)
+   |                                                                            
+   +3.29387e+07                                                             *   
+   |                                                                    ----    
+   |                                                               -----        
+   |                                                           ----             
+   |                                                      -----                 
+   |                                                 -----                      
+   |                                             ----                           
+   |                                        -----                               
+   |                                   -----                                    
+   |                               ----                                         
+   |                          -----                                             
+   |                      ----                                                  
+   |                 -----                                                      
+   |              ---                                                           
+   |           ---                                                              
+   |        ---                                                                 
+   | -------                                                                    
+---+386---------------------------------------------------------------------+---
+   +32                                                          +2.09715e+06    
+
+name                                 #n            tsub      ttot      tavg
+..vl/lees/bucket/nilm/nilmdb/nilmdb/interval.py.__iadd__:184  4194272          10.025323     30.262723     0.000007    
+..evl/lees/bucket/nilm/nilmdb/nilmdb/interval.py.__init__:27  4194272          24.715377     24.715377     0.000006    
+../lees/bucket/nilm/nilmdb/nilmdb/interval.py.intersects:239  4194272          6.705053      12.577620     0.000003    
+..im/devl/lees/bucket/nilm/nilmdb/tests/aplotter.py.plot:404  1                0.000048      0.001412      0.001412    
+../lees/bucket/nilm/nilmdb/tests/aplotter.py.plot_double:311  1                0.000106      0.001346      0.001346    
+..vl/lees/bucket/nilm/nilmdb/tests/aplotter.py.plot_data:201  1                0.000098      0.000672      0.000672    
+..vl/lees/bucket/nilm/nilmdb/tests/aplotter.py.plot_line:241  16               0.000298      0.000496      0.000031    
+..jim/devl/lees/bucket/nilm/nilmdb/nilmdb/printf.py.printf:4  17               0.000252      0.000334      0.000020    
+..vl/lees/bucket/nilm/nilmdb/tests/aplotter.py.transposed:39  1                0.000229      0.000235      0.000235    
+..vl/lees/bucket/nilm/nilmdb/tests/aplotter.py.y_reversed:45  1                0.000151      0.000174      0.000174    
+
+name           tid              fname                      ttot      scnt
+_MainThread           47269783682784        ..b/python2.7/threading.py.setprofile:88  64.746000     1              

timeit.sh

@@ -0,0 +1,21 @@
+./nilmtool.py destroy /bpnilm/2/raw
+./nilmtool.py create /bpnilm/2/raw RawData
+
+if true; then
+    time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s 20110513-110000 -r 8000 /bpnilm/2/raw
+    time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s 20110513-120001 -r 8000 /bpnilm/2/raw
+else
+    for i in $(seq 2000 2050); do
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-010001 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-020002 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-030003 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-040004 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-050005 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-060006 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-070007 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-080008 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-090009 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-100010 /bpnilm/2/raw
+    done
+fi
+

todo.txt

@@ -1,7 +0,0 @@
-- test performance of binary storage
-  - write
-  - read
-  - seek to timestamp?
-
-- implement binary storage classes
-  - fileinterval, binaryfileinterval, etc?