Render layout of bxintersect

.gitignore

@@ -1,7 +1,2 @@
-db/
-tests/*testdb/
 .coverage
 *.pyc
-design.html
-timeit*out
-

Makefile

@@ -8,14 +8,11 @@ tool:
 lint:
 	pylint -f parseable nilmdb
 
-%.html: %.md
-	pandoc -s $< > $@
-
 test:
-	python runtests.py
+	nosetests
 
 profile:
-	python runtests.py --with-profile
+	nosetests --with-profile 
 
 clean::
 	find . -name '*pyc' | xargs rm -f

README.txt

@@ -1,3 +1,2 @@
-sudo apt-get install python2.7 python-cherrypy3 python-decorator python-nose python-coverage
+sudo apt-get install python-nose python-coverage
-sudo apt-get install cython # 0.17.1-1 or newer
+sudo apt-get install python-tables cython python-cherrypy3
-

TODO

@@ -1,5 +1,5 @@
--- Clean up error responses.  Specifically I'd like to be able to add
+- Merge adjacent intervals on insert (maybe with client help?)
-   json-formatted data to OverflowError and DB parsing errors.  It
+
-   seems like subclassing cherrypy.HTTPError and overriding
+- Better testing:
-   set_response is the best thing to do -- it would let me get rid
+  - see about getting coverage on layout.pyx
-   of the _be_ie_unfriendly and other hacks in the server.
+  - layout.pyx performance tests, before and after generalization

design.md

@@ -1,12 +1,11 @@
 Structure
 ---------
-nilmdb.nilmdb is the NILM database interface.  A nilmdb.BulkData
+nilmdb.nilmdb is the NILM database interface.  It tracks a PyTables
-interface stores data in flat files, and a SQL database tracks
+database holds actual rows of data, and a SQL database tracks metadata
-metadata and ranges.
+and ranges.
 
 Access to the nilmdb must be single-threaded.  This is handled with
-the nilmdb.serializer class.  In the future this could probably
+the nilmdb.serializer class.
-be turned into a per-path serialization.
 
 nilmdb.server is a HTTP server that provides an interface to talk,
 thorugh the serialization layer, to the nilmdb object.
@@ -19,13 +18,13 @@ 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()
+  1: explicit con.commit()
 
-2. between a series of DML commands and non-DML commands, e.g.
+  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:"
+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.
@@ -48,7 +47,6 @@ transfer?
   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?
@@ -64,7 +62,6 @@ Before timestamps are added:
   - 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.
@@ -141,20 +138,11 @@ Speed
 - 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.
     
-- After all updates, now takes about 8.5 minutes to insert an hour of
-  data, constant after adding 171 hours (4.9 billion data points)
-
-- Data set size: 98 gigs = 20 bytes per data point.
-  6 uint16 data + 1 uint32 timestamp = 16 bytes per point
-  So compression must be off -- will retry with compression forced on.
-
 IntervalSet speed
 -----------------
 - Initial implementation was pretty slow, even with binary search in
@@ -173,18 +161,6 @@ IntervalSet speed
 - 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
 -------
@@ -203,66 +179,3 @@ handlers.  For compatibility:
     "RawData" == "uint16_6"
     "RawNotchedData" == "uint16_9"
     "PrepData" == "float32_8"
-
-
-BulkData design
----------------
-
-BulkData is a custom bulk data storage system that was written to
-replace PyTables.  The general structure is a `data` subdirectory in
-the main NilmDB directory.  Within `data`, paths are created for each
-created stream.  These locations are called tables.  For example,
-tables might be located at
-
-    nilmdb/data/newton/raw/
-    nilmdb/data/newton/prep/
-    nilmdb/data/cottage/raw/
-
-Each table contains:
-
-- An unchanging `_format` file (Python pickle format) that describes
-  parameters of how the data is broken up, like files per directory,
-  rows per file, and the binary data format
-
-- Hex named subdirectories `("%04x", although more than 65536 can exist)`
-
-- Hex named files within those subdirectories, like:
-
-        /nilmdb/data/newton/raw/000b/010a
-
-    The data format of these files is raw binary, interpreted by the
-    Python `struct` module according to the format string in the
-    `_format` file.
-
-- Same as above, with `.removed` suffix, is an optional file (Python
-  pickle format) containing a list of row numbers that have been
-  logically removed from the file.  If this range covers the entire
-  file, the entire file will be removed.
-
-- Note that the `bulkdata.nrows` variable is calculated once in
-  `BulkData.__init__()`, and only ever incremented during use.  Thus,
-  even if all data is removed, `nrows` can remain high.  However, if
-  the server is restarted, the newly calculated `nrows` may be lower
-  than in a previous run due to deleted data.  To be specific, this
-  sequence of events:
-
-    - insert data
-    - remove all data
-    - insert data
-
-    will result in having different row numbers in the database, and
-    differently numbered files on the filesystem, than the sequence:
-
-    - insert data
-    - remove all data
-    - restart server
-    - insert data
-
-    This is okay!  Everything should remain consistent both in the
-    `BulkData` and `NilmDB`.  Not attempting to readjust `nrows` during
-    deletion makes the code quite a bit simpler.
-
-- Similarly, data files are never truncated shorter.  Removing data
-  from the end of the file will not shorten it; it will only be
-  deleted when it has been fully filled and all of the data has been
-  subsequently removed.

nilmdb/__init__.py

@@ -3,10 +3,14 @@
 from .nilmdb import NilmDB
 from .server import Server
 from .client import Client
-
+from .timer import Timer
-import pyximport; pyximport.install()
-import layout
-import interval
 
 import cmdline
 
+import pyximport; pyximport.install()
+import layout
+
+import serializer
+import timestamper
+import interval
+import du

nilmdb/bulkdata.py

@@ -1,460 +0,0 @@
-# Fixed record size bulk data storage
-
-from __future__ import absolute_import
-from __future__ import division
-import nilmdb
-from nilmdb.utils.printf import *
-
-import os
-import sys
-import cPickle as pickle
-import struct
-import fnmatch
-import mmap
-import re
-
-# Up to 256 open file descriptors at any given time.
-# These variables are global so they can be used in the decorator arguments.
-table_cache_size = 16
-fd_cache_size = 16
-
-@nilmdb.utils.must_close(wrap_verify = True)
-class BulkData(object):
-    def __init__(self, basepath, **kwargs):
-        self.basepath = basepath
-        self.root = os.path.join(self.basepath, "data")
-
-        # Tuneables
-        if "file_size" in kwargs:
-            self.file_size = kwargs["file_size"]
-        else:
-            # Default to approximately 128 MiB per file
-            self.file_size = 128 * 1024 * 1024
-
-        if "files_per_dir" in kwargs:
-            self.files_per_dir = kwargs["files_per_dir"]
-        else:
-            # 32768 files per dir should work even on FAT32
-            self.files_per_dir = 32768
-
-        # Make root path
-        if not os.path.isdir(self.root):
-            os.mkdir(self.root)
-
-    def close(self):
-        self.getnode.cache_remove_all()
-
-    def _encode_filename(self, path):
-        # Encode all paths to UTF-8, regardless of sys.getfilesystemencoding(),
-        # because we want to be able to represent all code points and the user
-        # will never be directly exposed to filenames.  We can then do path
-        # manipulations on the UTF-8 directly.
-        if isinstance(path, unicode):
-            return path.encode('utf-8')
-        return path
-
-    def create(self, unicodepath, layout_name):
-        """
-        unicodepath: path to the data (e.g. u'/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'
-        """
-        path = self._encode_filename(unicodepath)
-
-        if path[0] != '/':
-            raise ValueError("paths must start with /")
-        [ group, node ] = path.rsplit("/", 1)
-        if group == '':
-            raise ValueError("invalid path; path must contain at least one "
-                             "folder")
-
-        # Get layout, and build format string for struct module
-        try:
-            layout = nilmdb.layout.get_named(layout_name)
-            struct_fmt = '<d'  # Little endian, double timestamp
-            struct_mapping = {
-                "int8": 'b',
-                "uint8": 'B',
-                "int16": 'h',
-                "uint16": 'H',
-                "int32": 'i',
-                "uint32": 'I',
-                "int64": 'q',
-                "uint64": 'Q',
-                "float32": 'f',
-                "float64": 'd',
-                }
-            for n in range(layout.count):
-                struct_fmt += struct_mapping[layout.datatype]
-        except KeyError:
-            raise ValueError("no such layout, or bad data types")
-
-        # Create the table.  Note that we make a distinction here
-        # between NilmDB paths (always Unix style, split apart
-        # manually) and OS paths (built up with os.path.join)
-
-        # Make directories leading up to this one
-        elements = path.lstrip('/').split('/')
-        for i in range(len(elements)):
-            ospath = os.path.join(self.root, *elements[0:i])
-            if Table.exists(ospath):
-                raise ValueError("path is subdir of existing node")
-            if not os.path.isdir(ospath):
-                os.mkdir(ospath)
-
-        # Make the final dir
-        ospath = os.path.join(self.root, *elements)
-        if os.path.isdir(ospath):
-            raise ValueError("subdirs of this path already exist")
-        os.mkdir(ospath)
-
-        # Write format string to file
-        Table.create(ospath, struct_fmt, self.file_size, self.files_per_dir)
-
-        # Open and cache it
-        self.getnode(unicodepath)
-
-        # Success
-        return
-
-    def destroy(self, unicodepath):
-        """Fully remove all data at a particular path.  No way to undo
-        it!  The group/path structure is removed, too."""
-        path = self._encode_filename(unicodepath)
-
-        # Get OS path
-        elements = path.lstrip('/').split('/')
-        ospath = os.path.join(self.root, *elements)
-
-        # Remove Table object from cache
-        self.getnode.cache_remove(self, unicodepath)
-
-        # Remove the contents of the target directory
-        if not Table.exists(ospath):
-            raise ValueError("nothing at that path")
-        for (root, dirs, files) in os.walk(ospath, topdown = False):
-            for name in files:
-                os.remove(os.path.join(root, name))
-            for name in dirs:
-                os.rmdir(os.path.join(root, name))
-
-        # Remove empty parent directories
-        for i in reversed(range(len(elements))):
-            ospath = os.path.join(self.root, *elements[0:i+1])
-            try:
-                os.rmdir(ospath)
-            except OSError:
-                break
-
-    # Cache open tables
-    @nilmdb.utils.lru_cache(size = table_cache_size,
-                            onremove = lambda x: x.close())
-    def getnode(self, unicodepath):
-        """Return a Table object corresponding to the given database
-        path, which must exist."""
-        path = self._encode_filename(unicodepath)
-        elements = path.lstrip('/').split('/')
-        ospath = os.path.join(self.root, *elements)
-        return Table(ospath)
-
-@nilmdb.utils.must_close(wrap_verify = True)
-class Table(object):
-    """Tools to help access a single table (data at a specific OS path)."""
-    # See design.md for design details
-
-    # Class methods, to help keep format details in this class.
-    @classmethod
-    def exists(cls, root):
-        """Return True if a table appears to exist at this OS path"""
-        return os.path.isfile(os.path.join(root, "_format"))
-
-    @classmethod
-    def create(cls, root, struct_fmt, file_size, files_per_dir):
-        """Initialize a table at the given OS path.
-        'struct_fmt' is a Struct module format description"""
-
-        # Calculate rows per file so that each file is approximately
-        # file_size bytes.
-        packer = struct.Struct(struct_fmt)
-        rows_per_file = max(file_size // packer.size, 1)
-
-        format = { "rows_per_file": rows_per_file,
-                   "files_per_dir": files_per_dir,
-                   "struct_fmt": struct_fmt,
-                   "version": 1 }
-        with open(os.path.join(root, "_format"), "wb") as f:
-            pickle.dump(format, f, 2)
-
-    # Normal methods
-    def __init__(self, root):
-        """'root' is the full OS path to the directory of this table"""
-        self.root = root
-
-        # Load the format and build packer
-        with open(os.path.join(self.root, "_format"), "rb") as f:
-            format = pickle.load(f)
-
-        if format["version"] != 1: # pragma: no cover (just future proofing)
-            raise NotImplementedError("version " + format["version"] +
-                                      " bulk data store not supported")
-
-        self.rows_per_file = format["rows_per_file"]
-        self.files_per_dir = format["files_per_dir"]
-        self.packer = struct.Struct(format["struct_fmt"])
-        self.file_size = self.packer.size * self.rows_per_file
-
-        # Find nrows
-        self.nrows = self._get_nrows()
-
-    def close(self):
-        self.mmap_open.cache_remove_all()
-
-    # Internal helpers
-    def _get_nrows(self):
-        """Find nrows by locating the lexicographically last filename
-        and using its size"""
-        # Note that this just finds a 'nrows' that is guaranteed to be
-        # greater than the row number of any piece of data that
-        # currently exists, not necessarily all data that _ever_
-        # existed.
-        regex = re.compile("^[0-9a-f]{4,}$")
-
-        # Find the last directory.  We sort and loop through all of them,
-        # starting with the numerically greatest, because the dirs could be
-        # empty if something was deleted.
-        subdirs = sorted(filter(regex.search, os.listdir(self.root)),
-                         key = lambda x: int(x, 16), reverse = True)
-
-        for subdir in subdirs:
-            # Now find the last file in that dir
-            path = os.path.join(self.root, subdir)
-            files = filter(regex.search, os.listdir(path))
-            if not files: # pragma: no cover (shouldn't occur)
-                # Empty dir: try the next one
-                continue
-
-            # Find the numerical max
-            filename = max(files, key = lambda x: int(x, 16))
-            offset = os.path.getsize(os.path.join(self.root, subdir, filename))
-
-            # Convert to row number
-            return self._row_from_offset(subdir, filename, offset)
-
-        # No files, so no data
-        return 0
-
-    def _offset_from_row(self, row):
-        """Return a (subdir, filename, offset, count) tuple:
-
-          subdir: subdirectory for the file
-        filename: the filename that contains the specified row
-          offset: byte offset of the specified row within the file
-           count: number of rows (starting at offset) that fit in the file
-        """
-        filenum = row // self.rows_per_file
-        # It's OK if these format specifiers are too short; the filenames
-        # will just get longer but will still sort correctly.
-        dirname = sprintf("%04x", filenum // self.files_per_dir)
-        filename = sprintf("%04x", filenum % self.files_per_dir)
-        offset = (row % self.rows_per_file) * self.packer.size
-        count = self.rows_per_file - (row % self.rows_per_file)
-        return (dirname, filename, offset, count)
-
-    def _row_from_offset(self, subdir, filename, offset):
-        """Return the row number that corresponds to the given
-        'subdir/filename' and byte-offset within that file."""
-        if (offset % self.packer.size) != 0: # pragma: no cover; shouldn't occur
-            raise ValueError("file offset is not a multiple of data size")
-        filenum = int(subdir, 16) * self.files_per_dir + int(filename, 16)
-        row = (filenum * self.rows_per_file) + (offset // self.packer.size)
-        return row
-
-    # Cache open files
-    @nilmdb.utils.lru_cache(size = fd_cache_size,
-                            keys = slice(0,3), # exclude newsize
-                            onremove = lambda x: x.close())
-    def mmap_open(self, subdir, filename, newsize = None):
-        """Open and map a given 'subdir/filename' (relative to self.root).
-        Will be automatically closed when evicted from the cache.
-
-        If 'newsize' is provided, the file is truncated to the given
-        size before the mapping is returned.  (Note that the LRU cache
-        on this function means the truncate will only happen if the
-        object isn't already cached; mmap.resize should be used too.)"""
-        try:
-            os.mkdir(os.path.join(self.root, subdir))
-        except OSError:
-            pass
-        f = open(os.path.join(self.root, subdir, filename), "a+", 0)
-        if newsize is not None:
-            # mmap can't map a zero-length file, so this allows the
-            # caller to set the filesize between file creation and
-            # mmap.
-            f.truncate(newsize)
-        mm = mmap.mmap(f.fileno(), 0)
-        return mm
-
-    def mmap_open_resize(self, subdir, filename, newsize):
-        """Open and map a given 'subdir/filename' (relative to self.root).
-        The file is resized to the given size."""
-        # Pass new size to mmap_open
-        mm = self.mmap_open(subdir, filename, newsize)
-        # In case we got a cached copy, need to call mm.resize too.
-        mm.resize(newsize)
-        return mm
-
-    def append(self, data):
-        """Append the data and flush it to disk.
-        data is a nested Python list [[row],[row],[...]]"""
-        remaining = len(data)
-        dataiter = iter(data)
-        while remaining:
-            # See how many rows we can fit into the current file, and open it
-            (subdir, fname, offset, count) = self._offset_from_row(self.nrows)
-            if count > remaining:
-                count = remaining
-            newsize = offset + count * self.packer.size
-            mm = self.mmap_open_resize(subdir, fname, newsize)
-            mm.seek(offset)
-
-            # Write the data
-            for i in xrange(count):
-                row = dataiter.next()
-                mm.write(self.packer.pack(*row))
-            remaining -= count
-            self.nrows += count
-
-    def __getitem__(self, key):
-        """Extract data and return it.  Supports simple indexing
-        (table[n]) and range slices (table[n:m]).  Returns a nested
-        Python list [[row],[row],[...]]"""
-
-        # Handle simple slices
-        if isinstance(key, slice):
-            # Fall back to brute force if the slice isn't simple
-            if ((key.step is not None and key.step != 1) or
-                key.start is None or
-                key.stop is None or
-                key.start >= key.stop or
-                key.start < 0 or
-                key.stop > self.nrows):
-                return [ self[x] for x in xrange(*key.indices(self.nrows)) ]
-
-            ret = []
-            row = key.start
-            remaining = key.stop - key.start
-            while remaining:
-                (subdir, filename, offset, count) = self._offset_from_row(row)
-                if count > remaining:
-                    count = remaining
-                mm = self.mmap_open(subdir, filename)
-                for i in xrange(count):
-                    ret.append(list(self.packer.unpack_from(mm, offset)))
-                    offset += self.packer.size
-                remaining -= count
-                row += count
-            return ret
-
-        # Handle single points
-        if key < 0 or key >= self.nrows:
-            raise IndexError("Index out of range")
-        (subdir, filename, offset, count) = self._offset_from_row(key)
-        mm = self.mmap_open(subdir, filename)
-        # unpack_from ignores the mmap object's current seek position
-        return list(self.packer.unpack_from(mm, offset))
-
-    def _remove_rows(self, subdir, filename, start, stop):
-        """Helper to mark specific rows as being removed from a
-        file, and potentially removing or truncating the file itself."""
-        # Import an existing list of deleted rows for this file
-        datafile = os.path.join(self.root, subdir, filename)
-        cachefile = datafile + ".removed"
-        try:
-            with open(cachefile, "rb") as f:
-                ranges = pickle.load(f)
-            cachefile_present = True
-        except:
-            ranges = []
-            cachefile_present = False
-
-        # Append our new range and sort
-        ranges.append((start, stop))
-        ranges.sort()
-
-        # Merge adjacent ranges into "out"
-        merged = []
-        prev = None
-        for new in ranges:
-            if prev is None:
-                # No previous range, so remember this one
-                prev = new
-            elif prev[1] == new[0]:
-                # Previous range connected to this new one; extend prev
-                prev = (prev[0], new[1])
-            else:
-                # Not connected; append previous and start again
-                merged.append(prev)
-                prev = new
-        if prev is not None:
-            merged.append(prev)
-
-        # If the range covered the whole file, we can delete it now.
-        # Note that the last file in a table may be only partially
-        # full (smaller than self.rows_per_file).  We purposely leave
-        # those files around rather than deleting them, because the
-        # remainder will be filled on a subsequent append(), and things
-        # are generally easier if we don't have to special-case that.
-        if (len(merged) == 1 and
-            merged[0][0] == 0 and merged[0][1] == self.rows_per_file):
-            # Close potentially open file in mmap_open LRU cache
-            self.mmap_open.cache_remove(self, subdir, filename)
-
-            # Delete files
-            os.remove(datafile)
-            if cachefile_present:
-                os.remove(cachefile)
-
-            # Try deleting subdir, too
-            try:
-                os.rmdir(os.path.join(self.root, subdir))
-            except:
-                pass
-        else:
-            # Update cache.  Try to do it atomically.
-            nilmdb.utils.atomic.replace_file(cachefile,
-                                             pickle.dumps(merged, 2))
-
-    def remove(self, start, stop):
-        """Remove specified rows [start, stop) from this table.
-
-        If a file is left empty, it is fully removed.  Otherwise, a
-        parallel data file is used to remember which rows have been
-        removed, and the file is otherwise untouched."""
-        if start < 0 or start > stop or stop > self.nrows:
-            raise IndexError("Index out of range")
-
-        row = start
-        remaining = stop - start
-        while remaining:
-            # Loop through each file that we need to touch
-            (subdir, filename, offset, count) = self._offset_from_row(row)
-            if count > remaining:
-                count = remaining
-            row_offset = offset // self.packer.size
-            # Mark the rows as being removed
-            self._remove_rows(subdir, filename, row_offset, row_offset + count)
-            remaining -= count
-            row += count
-
-class TimestampOnlyTable(object):
-    """Helper that lets us pass a Tables object into bisect, by
-    returning only the timestamp when a particular row is requested."""
-    def __init__(self, table):
-        self.table = table
-    def __getitem__(self, index):
-        return self.table[index][0]

nilmdb/bxintersect.pyx

@@ -0,0 +1,502 @@
+# 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 public 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
+
+    # Helper for plots
+    def emptynode( self ):
+        return EmptyNode
+
+    def rootnode( self ):
+        return self.root
+
+    # ---- 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

@@ -1,18 +1,14 @@
-# -*- coding: utf-8 -*-
-
 """Class for performing HTTP client requests via libcurl"""
 
 from __future__ import absolute_import
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
 
 import time
 import sys
 import re
 import os
 import simplejson as json
-import itertools
 
-import nilmdb.utils
 import nilmdb.httpclient
 
 # Other functions expect to see these in the nilmdb.client namespace
@@ -20,10 +16,6 @@ from nilmdb.httpclient import ClientError, ServerError, Error
 
 version = "1.0"
 
-def float_to_string(f):
-    # Use repr to maintain full precision in the string output.
-    return repr(float(f))
-
 class Client(object):
     """Main client interface to the Nilm database."""
 
@@ -92,88 +84,33 @@ class Client(object):
                    "layout" : layout }
         return self.http.get("stream/create", params)
 
-    def stream_destroy(self, path):
+    def stream_insert(self, path, data):
-        """Delete stream and its contents"""
-        params = { "path": path }
-        return self.http.get("stream/destroy", params)
-
-    def stream_remove(self, path, start = None, end = None):
-        """Remove data from the specified time range"""
-        params = {
-            "path": path
-        }
-        if start is not None:
-            params["start"] = float_to_string(start)
-        if end is not None:
-            params["end"] = float_to_string(end)
-        return self.http.get("stream/remove", params)
-
-    def stream_insert(self, path, data, start = None, end = None):
         """Insert data into a stream.  data should be a file-like object
-        that provides ASCII data that matches the database layout for path.
+        that provides ASCII data that matches the database layout for path."""
-
-        start and end are the starting and ending timestamp of this
-        stream; all timestamps t in the data must satisfy 'start <= t
-        < end'.  If left unspecified, 'start' is the timestamp of the
-        first line of data, and 'end' is the timestamp on the last line
-        of data, plus a small delta of 1μs.
-        """
         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
-        end_epsilon = 1e-6
-
-
-        def extract_timestamp(line):
-            return float(line.split()[0])
 
         def sendit():
-            # If we have more data after this, use the timestamp of
+            result = self.http.put("stream/insert", send_data, params)
-            # the next line as the end.  Otherwise, use the given
+            params["old_timestamp"] = result[1]
-            # overall end time, or add end_epsilon to the last data
+            return result
-            # point.
-            if nextline:
-                block_end = extract_timestamp(nextline)
-                if end and block_end > end:
-                    # This is unexpected, but we'll defer to the server
-                    # to return an error in this case.
-                    block_end = end
-            elif end:
-                block_end = end
-            else:
-                block_end = extract_timestamp(line) + end_epsilon
 
-            # Send it
-            params["start"] = float_to_string(block_start)
-            params["end"] = float_to_string(block_end)
-            return self.http.put("stream/insert", block_data, params)
-
-        clock_start = time.time()
-        block_data = ""
-        block_start = start
         result = None
-        for (line, nextline) in nilmdb.utils.misc.pairwise(data):
+        start = time.time()
-            # If we don't have a starting time, extract it from the first line
+        send_data = ""
-            if block_start is None:
+        for line in data:
-                block_start = extract_timestamp(line)
+            elapsed = time.time() - start
+            send_data += line
 
-            clock_elapsed = time.time() - clock_start
+            if (len(send_data) > max_data) or (elapsed > max_time):
-            block_data += line
-
-            # If we have enough data, or enough time has elapsed,
-            # send this block to the server, and empty things out
-            # for the next block.
-            if (len(block_data) > max_data) or (clock_elapsed > max_time):
                 result = sendit()
-                block_start = None
+                send_data = ""
-                block_data = ""
+                start = time.time()
-                clock_start = time.time()
+        if len(send_data):
-
-        # One last block?
-        if len(block_data):
             result = sendit()
 
         # Return the most recent JSON result we got back, or None if
@@ -188,9 +125,9 @@ class Client(object):
             "path": path
         }
         if start is not None:
-            params["start"] = float_to_string(start)
+            params["start"] = repr(start)  # use repr to keep precision
         if end is not None:
-            params["end"] = float_to_string(end)
+            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):
@@ -206,9 +143,9 @@ class Client(object):
             "path": path,
         }
         if start is not None:
-            params["start"] = float_to_string(start)
+            params["start"] = repr(start)  # use repr to keep precision
         if end is not None:
-            params["end"] = float_to_string(end)
+            params["end"] = repr(end)
         if count:
             params["count"] = 1
 

nilmdb/cmdline/cmdline.py

@@ -1,7 +1,7 @@
 """Command line client functionality"""
 
 from __future__ import absolute_import
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
 import nilmdb.client
 
 import datetime_tz
@@ -11,12 +11,11 @@ import re
 import argparse
 from argparse import ArgumentDefaultsHelpFormatter as def_form
 
-version = "1.0"
+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",
+subcommands = [ "info", "create", "list", "metadata", "insert", "extract" ]
-                "remove", "destroy" ]
 
 # Import the subcommand modules.  Equivalent way of doing this would be
 # from . import info as cmd_info
@@ -24,16 +23,10 @@ subcmd_mods = {}
 for cmd in subcommands:
     subcmd_mods[cmd] = __import__("nilmdb.cmdline." + cmd, fromlist = [ cmd ])
 
-class JimArgumentParser(argparse.ArgumentParser):
-    def error(self, message):
-        self.print_usage(sys.stderr)
-        self.exit(2, sprintf("error: %s\n", message))
-
 class Cmdline(object):
 
     def __init__(self, argv):
         self.argv = argv
-        self.client = None
 
     def arg_time(self, toparse):
         """Parse a time string argument"""
@@ -99,7 +92,7 @@ class Cmdline(object):
         version_string = sprintf("nilmtool %s, client library %s",
                                  version, nilmdb.Client.client_version)
 
-        self.parser = JimArgumentParser(add_help = False,
+        self.parser = argparse.ArgumentParser(add_help = False,
                                               formatter_class = def_form)
 
         group = self.parser.add_argument_group("General options")
@@ -125,7 +118,6 @@ class Cmdline(object):
 
     def die(self, formatstr, *args):
         fprintf(sys.stderr, formatstr + "\n", *args)
-        if self.client:
         self.client.close()
         sys.exit(-1)
 
@@ -138,17 +130,13 @@ class Cmdline(object):
         self.parser_setup()
         self.args = self.parser.parse_args(self.argv)
 
-        # Run arg verify handler if there is one
-        if "verify" in self.args:
-            self.args.verify(self)
-
         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))
+            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

nilmdb/cmdline/create.py

@@ -1,5 +1,5 @@
 from __future__ import absolute_import
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
 import nilmdb.client
 
 from argparse import ArgumentDefaultsHelpFormatter as def_form
@@ -24,4 +24,4 @@ def cmd_create(self):
     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))
+        self.die("Error creating stream: %s", str(e))

nilmdb/cmdline/destroy.py

@@ -1,25 +0,0 @@
-from __future__ import absolute_import
-from nilmdb.utils.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 destroying stream: %s", str(e))

nilmdb/cmdline/extract.py

@@ -1,7 +1,7 @@
 from __future__ import absolute_import
-from __future__ import print_function
+from nilmdb.printf import *
-from nilmdb.utils.printf import *
 import nilmdb.client
+import nilmdb.layout
 import sys
 
 def setup(self, sub):
@@ -9,18 +9,17 @@ def setup(self, sub):
                          description="""
                          Extract data from a stream.
                          """)
-    cmd.set_defaults(verify = cmd_extract_verify,
+    cmd.set_defaults(handler = cmd_extract)
-                     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, inclusive)")
+                       help="Starting timestamp (free-form)")
     group.add_argument("-e", "--end", required=True,
                        metavar="TIME", type=self.arg_time,
-                       help="Ending timestamp (free-form, noninclusive)")
+                       help="Ending timestamp (free-form)")
 
     group = cmd.add_argument_group("Output format")
     group.add_argument("-b", "--bare", action="store_true",
@@ -31,15 +30,10 @@ def setup(self, sub):
     group.add_argument("-c", "--count", action="store_true",
                        help="Just output a count of matched data points")
 
-def cmd_extract_verify(self):
-    if self.args.start is not None and self.args.end is not None:
-        if self.args.start > self.args.end:
-            self.parser.error("start is after end")
-
 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)
+        self.die("Error getting stream info for path %s", self.args.path)
     layout = streams[0][1]
 
     if self.args.annotate:
@@ -57,7 +51,7 @@ def cmd_extract(self):
             # Strip timestamp (first element).  Doesn't make sense
             # if we are only returning a count.
             dataline = ' '.join(dataline.split(' ')[1:])
-        print(dataline)
+        print dataline
         printed = True
     if not printed:
         if self.args.annotate:

nilmdb/cmdline/info.py

@@ -1,5 +1,5 @@
 from __future__ import absolute_import
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
 
 from argparse import ArgumentDefaultsHelpFormatter as def_form
 

nilmdb/cmdline/insert.py

@@ -1,6 +1,7 @@
 from __future__ import absolute_import
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
 import nilmdb.client
+import nilmdb.layout
 import nilmdb.timestamper
 
 import sys
@@ -51,12 +52,12 @@ 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)
+        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("error: --start can only be used with one input file")
+        self.die("--start can only be used with one input file, for now")
 
     for filename in self.args.file:
         if filename == '-':
@@ -65,7 +66,7 @@ def cmd_insert(self):
             try:
                 infile = open(filename, "r")
             except IOError:
-                self.die("error opening input file %s", filename)
+                self.die("Error opening input file %s", filename)
 
         # Build a timestamper for this file
         if self.args.none:
@@ -77,11 +78,11 @@ def cmd_insert(self):
                 try:
                     start = self.parse_time(filename)
                 except ValueError:
-                    self.die("error extracting time from filename '%s'",
+                    self.die("Error extracting time from filename '%s'",
                              filename)
 
             if not self.args.rate:
-                self.die("error: --rate is needed, but was not specified")
+                self.die("Need to specify --rate")
             rate = self.args.rate
 
             ts = nilmdb.timestamper.TimestamperRate(infile, start, rate)
@@ -100,6 +101,6 @@ def cmd_insert(self):
             # 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))
+            self.die("Error inserting data: %s", str(e))
 
     return

nilmdb/cmdline/list.py

@@ -1,9 +1,8 @@
 from __future__ import absolute_import
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
 import nilmdb.client
 
 import fnmatch
-import argparse
 from argparse import ArgumentDefaultsHelpFormatter as def_form
 
 def setup(self, sub):
@@ -14,41 +13,23 @@ def setup(self, sub):
                          optionally filtering by layout or path.  Wildcards
                          are accepted.
                          """)
-    cmd.set_defaults(verify = cmd_list_verify,
+    cmd.set_defaults(handler = cmd_list)
-                     handler = cmd_list)
 
     group = cmd.add_argument_group("Stream filtering")
-    group.add_argument("-p", "--path", metavar="PATH", default="*",
-                       help="Match only this path (-p can be omitted)")
-    group.add_argument("path_positional", default="*",
-                       nargs="?", help=argparse.SUPPRESS)
     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, inclusive)")
+                       help="Starting timestamp (free-form)")
     group.add_argument("-e", "--end",
                        metavar="TIME", type=self.arg_time,
-                       help="Ending timestamp (free-form, noninclusive)")
+                       help="Ending timestamp (free-form)")
-
-def cmd_list_verify(self):
-    # A hidden "path_positional" argument lets the user leave off the
-    # "-p" when specifying the path.  Handle it here.
-    got_opt = self.args.path != "*"
-    got_pos = self.args.path_positional != "*"
-    if got_pos:
-        if got_opt:
-            self.parser.error("too many paths specified")
-        else:
-            self.args.path = self.args.path_positional
-
-    if self.args.start is not None and self.args.end is not None:
-        if self.args.start > self.args.end:
-            self.parser.error("start is after end")
 
 def cmd_list(self):
     """List available streams"""

nilmdb/cmdline/metadata.py

@@ -1,5 +1,5 @@
 from __future__ import absolute_import
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
 import nilmdb.client
 
 def setup(self, sub):
@@ -43,21 +43,21 @@ def cmd_metadata(self):
         for keyval in keyvals:
             kv = keyval.split('=')
             if len(kv) != 2 or kv[0] == "":
-                self.die("error parsing key=value argument '%s'", keyval)
+                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))
+            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))
+            self.die("Error getting metadata: %s", str(e))
         for key, value in sorted(data.items()):
             # Omit nonexistant keys
             if value is None:

nilmdb/cmdline/remove.py

@@ -1,45 +0,0 @@
-from __future__ import absolute_import
-from __future__ import print_function
-from nilmdb.utils.printf import *
-import nilmdb.client
-import sys
-
-def setup(self, sub):
-    cmd = sub.add_parser("remove", help="Remove data",
-                         description="""
-                         Remove all data from a specified time range within a
-                         stream.
-                         """)
-    cmd.set_defaults(verify = cmd_remove_verify,
-                     handler = cmd_remove)
-
-    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, inclusive)")
-    group.add_argument("-e", "--end", required=True,
-                       metavar="TIME", type=self.arg_time,
-                       help="Ending timestamp (free-form, noninclusive)")
-
-    group = cmd.add_argument_group("Output format")
-    group.add_argument("-c", "--count", action="store_true",
-                       help="Output number of data points removed")
-
-def cmd_remove_verify(self):
-    if self.args.start is not None and self.args.end is not None:
-        if self.args.start > self.args.end:
-            self.parser.error("start is after end")
-
-def cmd_remove(self):
-    try:
-        count = self.client.stream_remove(self.args.path,
-                                          self.args.start, self.args.end)
-    except nilmdb.client.ClientError as e:
-        self.die("error removing data: %s", str(e))
-
-    if self.args.count:
-        printf("%d\n", count)
-
-    return 0

nilmdb/httpclient.py

@@ -1,8 +1,7 @@
 """HTTP client library"""
 
 from __future__ import absolute_import
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
-import nilmdb.utils
 
 import time
 import sys
@@ -10,9 +9,12 @@ 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,
@@ -26,19 +28,12 @@ class Error(Exception):
         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.traceback: # pragma: no cover
-            s += sprintf("\nServer traceback:\n%s", self.traceback)
-        return s
-    def __repr__(self): # pragma: no cover
         s = sprintf("[%s]", self.status)
         if self.message:
             s += sprintf(" %s", self.message)
         if self.url:
             s += sprintf(" (%s)", self.url)
-        if self.traceback:
+        if self.traceback: # pragma: no cover
             s += sprintf("\nServer traceback:\n%s", self.traceback)
         return s
 class ClientError(Error):
@@ -65,8 +60,7 @@ class HTTPClient(object):
     def _setup_url(self, url = "", params = ""):
         url = urlparse.urljoin(self.baseurl, url)
         if params:
-            url = urlparse.urljoin(
+            url = urlparse.urljoin(url, "?" + urllib.urlencode(params, True))
-                url, "?" + nilmdb.utils.urllib.urlencode(params))
         self.curl.setopt(pycurl.URL, url)
         self.url = url
 
@@ -91,10 +85,6 @@ class HTTPClient(object):
             raise ClientError(**args)
         else: # pragma: no cover
             if code >= 500 and code <= 599:
-                if args["message"] is None:
-                    args["message"] = ("(no message; try disabling " +
-                                       "response.stream option in " +
-                                       "nilmdb.server for better debugging)")
                 raise ServerError(**args)
             else:
                 raise Error(**args)
@@ -119,7 +109,7 @@ class HTTPClient(object):
             self.curl.setopt(pycurl.WRITEFUNCTION, callback)
             self.curl.perform()
         try:
-            for i in nilmdb.utils.Iteratorizer(func):
+            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

nilmdb/interval.py

@@ -1,82 +1,58 @@
-"""Interval, IntervalSet
+"""Interval and IntervalSet
 
 Represents an interval of time, and a set of such intervals.
 
-Intervals are half-open, ie. they include data points with timestamps
+Intervals are closed, ie. they include timestamps [start, end]
-[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
+# This version is based on the quicksect implementation from python-bx,
-# python-bx, modified slightly to handle floating point intervals.
+# 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
+import pyximport
-# instead of a simple sorted list to maintain O(log n) operations.
+pyximport.install()
+import bxintersect
 
-# Fourth version is an optimized rb-tree that stores interval starts
+import bisect
-# 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:
+class Interval(bxintersect.Interval):
     """Represents an interval of time."""
 
-    cdef public double start, end
+    def __init__(self, start, end):
-
-    def __init__(self, double start, double end):
         """
         'start' and 'end' are arbitrary floats that represent time
         """
         if start > end:
-            # Explicitly disallow zero-width intervals (since they're half-open)
             raise IntervalError("start %s must precede end %s" % (start, end))
-        self.start = float(start)
+        bxintersect.Interval.__init__(self, start, end)
-        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) + ")"
+        return "[" + str(self.start) + " -> " + str(self.end) + "]"
 
-    def __cmp__(self, Interval other):
+    def intersects(self, 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):
+    def subset(self, start, 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):
+class DBInterval(Interval):
     """
     Like Interval, but also tracks corresponding start/end times and
     positions within the database.  These are not currently modified
@@ -90,10 +66,6 @@ cdef class DBInterval(Interval):
         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):
@@ -118,7 +90,7 @@ cdef class DBInterval(Interval):
         s += ", " + repr(self.db_startpos) + ", " + repr(self.db_endpos)
         return self.__class__.__name__ + "(" + s + ")"
 
-    cpdef subset(self, double start, double end):
+    def subset(self, start, end):
         """
         Return a new DBInterval that is a subset of this one
         """
@@ -128,25 +100,21 @@ cdef class DBInterval(Interval):
                           self.db_start, self.db_end,
                           self.db_startpos, self.db_endpos)
 
-cdef class IntervalSet:
+class IntervalSet(object):
     """
     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()
+        self.tree = bxintersect.IntervalTree()
         if source is not None:
             self += source
 
     def __iter__(self):
-        for node in self.tree:
+        return self.tree.traverse()
-            if node.obj:
-                yield node.obj
 
     def __len__(self):
         return sum(1 for x in self)
@@ -159,7 +127,7 @@ cdef class IntervalSet:
         descs = [ str(x) for x in self ]
         return  "[" + ", ".join(descs) + "]"
 
-    def __match__(self, other):
+    def __eq__(self, other):
         # This isn't particularly efficient, but it shouldn't get used in the
         # general case.
         """Test equality of two IntervalSets.
@@ -178,8 +146,8 @@ cdef class IntervalSet:
             else:
                 return False
 
-        this = list(self)
+        this = [ x for x in self ]
-        that = list(other)
+        that = [ x for x in other ]
 
         try:
             while True:
@@ -210,20 +178,10 @@ cdef class IntervalSet:
         except IndexError:
             return False
 
-    # Use __richcmp__ instead of __eq__, __ne__ for Cython.
+    def __ne__(self, other):
-    def __richcmp__(self, other, int op):
+        return not self.__eq__(other)
-        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):
+    def __iadd__(self, other):
         """Inplace add -- modifies self
 
         This throws an exception if the regions being added intersect."""
@@ -231,36 +189,19 @@ cdef class IntervalSet:
             if self.intersects(other):
                 raise IntervalError("Tried to add overlapping interval "
                                     "to this set")
-            self.tree.insert(rbtree.RBNode(other.start, other.end, other))
+            self.tree.insert_interval(other)
         else:
             for x in other:
                 self.__iadd__(x)
         return self
 
-    def iadd_nocheck(self, Interval other not None):
+    def __add__(self, other):
-        """Inplace add -- modifies self.
-        'Optimized' version that doesn't check for intersection and
-        only inserts the new interval into the tree."""
-        self.tree.insert(rbtree.RBNode(other.start, other.end, other))
-
-    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):
+    def __and__(self, other):
         """
         Compute a new IntervalSet from the intersection of two others
 
@@ -270,16 +211,15 @@ cdef class IntervalSet:
         out = IntervalSet()
 
         if not isinstance(other, IntervalSet):
-            for i in self.intersection(other):
+            other = [ 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))
+                out.tree.insert_interval(i)
 
         return out
 
-    def intersection(self, Interval interval not None, orig = False):
+    def intersection(self, interval):
         """
         Compute a sequence of intervals that correspond to the
         intersection between `self` and the provided interval.
@@ -288,42 +228,14 @@ cdef class IntervalSet:
 
         Output intervals are built as subsets of the intervals in the
         first argument (self).
-
-        If orig = True, also return the original interval that was
-        (potentially) subsetted to make the one that is being
-        returned.
         """
-        if not isinstance(interval, Interval):
+        for i in self.tree.find(interval.start, interval.end):
-            raise TypeError("bad type")
+            if i.start > interval.start and i.end < interval.end:
-        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:
-                    if orig:
-                        yield (i, i)
-                    else:
                 yield i
             else:
-                    subset = i.subset(max(i.start, interval.start),
+                yield i.subset(max(i.start, interval.start),
                                min(i.end, interval.end))
-                    if orig:
-                        yield (subset, i)
-                    else:
-                        yield subset
 
-    cpdef intersects(self, Interval other):
+    def intersects(self, other):
         """Return True if this IntervalSet intersects another interval"""
-        for n in self.tree.intersect(other.start, other.end):
+        return len(self.tree.find(other.start, other.end)) > 0
-            if n.obj.intersects(other):
-                return True
-        return False
-
-    def find_end(self, double t):
-        """
-        Return an Interval from this tree that ends at time t, or
-        None if it doesn't exist.
-        """
-        n = self.tree.find_left_end(t)
-        if n and n.obj.end == t:
-            return n.obj
-        return None

nilmdb/interval.pyxdep

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

nilmdb/layout.pyx

@@ -1,5 +1,6 @@
 # cython: profile=False
 
+import tables
 import time
 import sys
 import inspect
@@ -121,6 +122,15 @@ class Layout:
             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:

nilmdb/nilmdb.py

@@ -4,16 +4,17 @@
 
 Object that represents a NILM database file.
 
-Manages both the SQL database and the table storage backend.
+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.utils.printf import *
+from nilmdb.printf import *
 
 import sqlite3
+import tables
 import time
 import sys
 import os
@@ -24,8 +25,6 @@ import pyximport
 pyximport.install()
 from nilmdb.interval import Interval, DBInterval, IntervalSet, IntervalError
 
-from . import bulkdata
-
 # Note about performance and transactions:
 #
 # Committing a transaction in the default sync mode (PRAGMA synchronous=FULL)
@@ -80,7 +79,7 @@ _sql_schema_updates = {
 class NilmDBError(Exception):
     """Base exception for NilmDB errors"""
     def __init__(self, message = "Unspecified error"):
-        Exception.__init__(self, message)
+        Exception.__init__(self, self.__class__.__name__ + ": " + message)
 
 class StreamError(NilmDBError):
     pass
@@ -88,14 +87,19 @@ class StreamError(NilmDBError):
 class OverlapError(NilmDBError):
     pass
 
-@nilmdb.utils.must_close()
+# 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,
+    def __init__(self, basepath, sync=True, max_results=None):
-                 bulkdata_args={}):
         # set up path
-        self.basepath = os.path.abspath(basepath)
+        self.basepath = os.path.abspath(basepath.rstrip('/'))
 
         # Create the database path if it doesn't exist
         try:
@@ -104,16 +108,16 @@ class NilmDB(object):
             if e.errno != errno.EEXIST:
                 raise IOError("can't create tree " + self.basepath)
 
-        # Our data goes inside it
+        # Our HD5 file goes inside it
-        self.data = bulkdata.BulkData(self.basepath, **bulkdata_args)
+        h5filename = os.path.abspath(self.basepath + "/data.h5")
+        self.h5file = tables.openFile(h5filename, "a", "NILM Database")
 
         # SQLite database too
-        sqlfilename = os.path.join(self.basepath, "data.sql")
+        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.  Otherwise
+        # database from multiple threads simultaneously.  That requirement
-        # false positives will occur when the database is only opened
+        # may be relaxed later.
-        # in one thread, and only accessed in another.
         self.con = sqlite3.connect(sqlfilename, check_same_thread = False)
         self._sql_schema_update()
 
@@ -130,6 +134,17 @@ class NilmDB(object):
         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
 
@@ -137,7 +152,8 @@ class NilmDB(object):
         if self.con:
             self.con.commit()
             self.con.close()
-        self.data.close()
+        self.h5file.close()
+        del self.opened
 
     def _sql_schema_update(self):
         cur = self.con.cursor()
@@ -154,11 +170,12 @@ class NilmDB(object):
             with self.con:
                 cur.execute("PRAGMA user_version = {v:d}".format(v=version))
 
-    @nilmdb.utils.lru_cache(size = 16)
     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 "
@@ -171,112 +188,42 @@ class NilmDB(object):
                                        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]
 
-        return iset
+    # 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.
 
-    def _sql_interval_insert(self, id, start, end, start_pos, end_pos):
+    # Maybe add a separate optimization step?
-        """Helper that adds interval to the SQL database only"""
+    # Join intervals that have a fairly small gap between them
-        self.con.execute("INSERT INTO ranges "
-                         "(stream_id,start_time,end_time,start_pos,end_pos) "
-                         "VALUES (?,?,?,?,?)",
-                         (id, start, end, start_pos, end_pos))
-
-    def _sql_interval_delete(self, id, start, end, start_pos, end_pos):
-        """Helper that removes interval from the SQL database only"""
-        self.con.execute("DELETE FROM ranges WHERE "
-                         "stream_id=? AND start_time=? AND "
-                         "end_time=? AND start_pos=? AND end_pos=?",
-                         (id, start, end, start_pos, end_pos))
 
     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)
         """
-        # Load this stream's intervals
+        # Ensure this stream's intervals are cached, and add the new
+        # interval to that cache.
         iset = self._get_intervals(stream_id)
-
+        try:
-        # Check for overlap
+            iset += DBInterval(interval.start, interval.end,
-        if iset.intersects(interval): # pragma: no cover (gets caught earlier)
+                               interval.start, interval.end,
+                               start_pos, end_pos)
+        except IntervalError as e: # pragma: no cover
             raise NilmDBError("new interval overlaps existing data")
 
-        # Check for adjacency.  If there's a stream in the database
-        # that ends exactly when this one starts, and the database
-        # rows match up, we can make one interval that covers the
-        # time range [adjacent.start -> interval.end)
-        # and database rows [ adjacent.start_pos -> end_pos ].
-        # Only do this if the resulting interval isn't too large.
-        max_merged_rows = 8000 * 60 * 60 * 1.05 # 1.05 hours at 8 KHz
-        adjacent = iset.find_end(interval.start)
-        if (adjacent is not None and
-            start_pos == adjacent.db_endpos and
-            (end_pos - adjacent.db_startpos) < max_merged_rows):
-            # First delete the old one, both from our iset and the
-            # database
-            iset -= adjacent
-            self._sql_interval_delete(stream_id,
-                                      adjacent.db_start, adjacent.db_end,
-                                      adjacent.db_startpos, adjacent.db_endpos)
-
-            # Now update our interval so the fallthrough add is
-            # correct.
-            interval.start = adjacent.start
-            start_pos = adjacent.db_startpos
-
-        # Add the new interval to the iset
-        iset.iadd_nocheck(DBInterval(interval.start, interval.end,
-                                     interval.start, interval.end,
-                                     start_pos, end_pos))
-
         # Insert into the database
-        self._sql_interval_insert(stream_id, interval.start, interval.end,
+        self.con.execute("INSERT INTO ranges "
-                                  int(start_pos), int(end_pos))
+                         "(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 _remove_interval(self, stream_id, original, remove):
-        """
-        Remove an interval from the internal cache and the database.
-
-        stream_id: id of stream
-         original: original DBInterval; must be already present in DB
-        to_remove: DBInterval to remove; must be subset of 'original'
-        """
-        # Just return if we have nothing to remove
-        if remove.start == remove.end: # pragma: no cover
-            return
-
-        # Load this stream's intervals
-        iset = self._get_intervals(stream_id)
-
-        # Remove existing interval from the cached set and the database
-        iset -= original
-        self._sql_interval_delete(stream_id,
-                                  original.db_start, original.db_end,
-                                  original.db_startpos, original.db_endpos)
-
-        # Add back the intervals that would be left over if the
-        # requested interval is removed.  There may be two of them, if
-        # the removed piece was in the middle.
-        def add(iset, start, end, start_pos, end_pos):
-            iset += DBInterval(start, end, start, end, start_pos, end_pos)
-            self._sql_interval_insert(stream_id, start, end, start_pos, end_pos)
-
-        if original.start != remove.start:
-            # Interval before the removed region
-            add(iset, original.start, remove.start,
-                original.db_startpos, remove.db_startpos)
-
-        if original.end != remove.end:
-            # Interval after the removed region
-            add(iset, remove.end, original.end,
-                remove.db_endpos, original.db_endpos)
-
-        # Commit SQL changes
-        self.con.commit()
-
-        return
-
     def stream_list(self, path = None, layout = None):
         """Return list of [path, layout] lists of all streams
         in the database.
@@ -338,11 +285,38 @@ class NilmDB(object):
 
         layout_name: string for nilmdb.layout.get_named(), e.g. 'float32_8'
         """
-        # Create the bulk storage.  Raises ValueError on error, which we
+        if path[0] != '/':
-        # pass along.
+            raise ValueError("paths must start with /")
-        self.data.create(path, layout_name)
+        [ group, node ] = path.rsplit("/", 1)
+        if group == '':
+            raise ValueError("invalid path")
 
-        # Insert into SQL database once the bulk storage is happy
+        # Make the group structure, one element at a time
+        group_path = group.lstrip('/').split("/")
+        for i in range(len(group_path)):
+            parent = "/" + "/".join(group_path[0:i])
+            child = group_path[i]
+            try:
+                self.h5file.createGroup(parent, child)
+            except tables.NodeError:
+                pass
+
+        # 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
+        table = self.h5file.createTable(group, node,
+                                        description = desc,
+                                        expectedrows = exp_rows)
+
+        # 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))
@@ -363,7 +337,8 @@ class NilmDB(object):
            """
         stream_id = self._stream_id(path)
         with self.con as con:
-            con.execute("DELETE FROM metadata WHERE stream_id=?", (stream_id,))
+            con.execute("DELETE FROM metadata "
+                        "WHERE stream_id=?", (stream_id,))
             for key in data:
                 if data[key] != '':
                     con.execute("INSERT INTO metadata VALUES (?, ?, ?)",
@@ -386,52 +361,49 @@ class NilmDB(object):
         data.update(newdata)
         self.stream_set_metadata(path, data)
 
-    def stream_destroy(self, path):
+    def stream_insert(self, path, parser, old_timestamp = None):
-        """Fully remove a table and all of its data from the database.
-        No way to undo it!  Metadata is removed."""
-        stream_id = self._stream_id(path)
-
-        # Delete the cached interval data (if it was cached)
-        self._get_intervals.cache_remove(self, stream_id)
-
-        # Delete the data
-        self.data.destroy(path)
-
-        # 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, start, end, data):
         """Insert new data into the database.
            path: Path at which to add the data
-           start: Starting timestamp
+           parser: nilmdb.layout.Parser instance full of data to insert
-           end: Ending timestamp
-           data: Rows of data, to be passed to PyTable's table.append
-                 method.  E.g. nilmdb.layout.Parser.data
            """
+        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(start, end)
+        interval = Interval(min_timestamp, parser.max_timestamp)
         if iset.intersects(interval):
-            raise OverlapError("new data overlaps existing data at range: "
+            raise OverlapError("new data overlaps existing data: "
                                + str(iset & interval))
 
-        # Insert the data
+        # Insert the data into pytables
-        table = self.data.getnode(path)
+        table = self.h5file.getNode(path)
         row_start = table.nrows
-        table.append(data)
+        table.append(parser.data)
         row_end = table.nrows
+        table.flush()
 
         # Insert the record into the sql database.
-        self._add_interval(stream_id, interval, row_start, row_end)
+        # 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, dbinterval):
+    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
@@ -439,14 +411,14 @@ class NilmDB(object):
         equal to 'start'.
         """
         # Optimization for the common case where an interval wasn't truncated
-        if dbinterval.start == dbinterval.db_start:
+        if interval.start == interval.db_start:
-            return dbinterval.db_startpos
+            return interval.db_startpos
-        return bisect.bisect_left(bulkdata.TimestampOnlyTable(table),
+        return bisect.bisect_left(BisectableTable(table),
-                                  dbinterval.start,
+                                  interval.start,
-                                  dbinterval.db_startpos,
+                                  interval.db_startpos,
-                                  dbinterval.db_endpos)
+                                  interval.db_endpos)
 
-    def _find_end(self, table, dbinterval):
+    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
@@ -454,16 +426,16 @@ class NilmDB(object):
         to 'end'.
         """
         # Optimization for the common case where an interval wasn't truncated
-        if dbinterval.end == dbinterval.db_end:
+        if interval.end == interval.db_end:
-            return dbinterval.db_endpos
+            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(bulkdata.TimestampOnlyTable(table),
+        return bisect.bisect_left(BisectableTable(table),
-                                  dbinterval.end,
+                                  interval.end,
-                                  dbinterval.db_startpos,
+                                  interval.db_startpos,
-                                  dbinterval.db_endpos)
+                                  interval.db_endpos)
 
     def stream_extract(self, path, start = None, end = None, count = False):
         """
@@ -484,8 +456,8 @@ class NilmDB(object):
         than actually fetching the data.  It is not limited by
         max_results.
         """
+        table = self.h5file.getNode(path)
         stream_id = self._stream_id(path)
-        table = self.data.getnode(path)
         intervals = self._get_intervals(stream_id)
         requested = Interval(start or 0, end or 1e12)
         result = []
@@ -522,45 +494,3 @@ class NilmDB(object):
         if count:
             return matched
         return (result, restart)
-
-    def stream_remove(self, path, start = None, end = None):
-        """
-        Remove data from the specified time interval within a stream.
-        Removes all data in the interval [start, end), and intervals
-        are truncated or split appropriately.  Returns the number of
-        data points removed.
-        """
-        stream_id = self._stream_id(path)
-        table = self.data.getnode(path)
-        intervals = self._get_intervals(stream_id)
-        to_remove = Interval(start or 0, end or 1e12)
-        removed = 0
-
-        if start == end:
-            return 0
-
-        # Can't remove intervals from within the iterator, so we need to
-        # remember what's currently in the intersection now.
-        all_candidates = list(intervals.intersection(to_remove, orig = True))
-
-        for (dbint, orig) in all_candidates:
-            # Find row start and end
-            row_start = self._find_start(table, dbint)
-            row_end = self._find_end(table, dbint)
-
-            # Adjust the DBInterval to match the newly found ends
-            dbint.db_start = dbint.start
-            dbint.db_end = dbint.end
-            dbint.db_startpos = row_start
-            dbint.db_endpos = row_end
-
-            # Remove interval from the database
-            self._remove_interval(stream_id, orig, dbint)
-
-            # Remove data from the underlying table storage
-            table.remove(row_start, row_end)
-
-            # Count how many were removed
-            removed += row_end - row_start
-
-        return removed

nilmdb/rbtree.pxd

@@ -1,23 +0,0 @@
-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

@@ -1,377 +0,0 @@
-# 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

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

nilmdb/serializer.py

@@ -67,6 +67,3 @@ class WrapObject(object):
     def __del__(self):
         self.__wrap_call_queue.put((None, None, None, None))
         self.__wrap_serializer.join()
-
-# Just an alias
-Serializer = WrapObject

nilmdb/server.py

@@ -3,18 +3,15 @@
 # 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
-from nilmdb.utils.printf import *
 import nilmdb
 
+from nilmdb.printf import *
+
 import cherrypy
 import sys
 import time
 import os
 import simplejson as json
-import decorator
-import traceback
-
-from nilmdb.nilmdb import NilmDBError
 
 try:
     import cherrypy
@@ -27,53 +24,8 @@ class NilmApp(object):
     def __init__(self, db):
         self.db = db
 
-version = "1.2"
+version = "1.1"
 
-# Decorators
-def chunked_response(func):
-    """Decorator to enable chunked responses."""
-    # Set this to False to get better tracebacks from some requests
-    # (/stream/extract, /stream/intervals).
-    func._cp_config = { 'response.stream': True }
-    return func
-
-@decorator.decorator
-def workaround_cp_bug_1200(func, *args, **kwargs): # pragma: no cover
-    """Decorator to work around CherryPy bug #1200 in a response
-    generator.
-
-    Even if chunked responses are disabled, LookupError or
-    UnicodeError exceptions may still be swallowed by CherryPy due to
-    bug #1200.  This throws them as generic Exceptions instead so that
-    they make it through.
-    """
-    try:
-        for val in func(*args, **kwargs):
-            yield val
-    except (LookupError, UnicodeError) as e:
-        raise Exception("bug workaround; real exception is:\n" +
-                        traceback.format_exc())
-
-def exception_to_httperror(*expected):
-    """Return a decorator-generating function that catches expected
-    errors and throws a HTTPError describing it instead.
-
-        @exception_to_httperror(NilmDBError, ValueError)
-        def foo():
-            pass
-    """
-    def wrapper(func, *args, **kwargs):
-        try:
-            return func(*args, **kwargs)
-        except expected as e:
-            message = sprintf("%s", str(e))
-            raise cherrypy.HTTPError("400 Bad Request", message)
-    # We need to preserve the function's argspecs for CherryPy to
-    # handle argument errors correctly.  Decorator.decorator takes
-    # care of that.
-    return decorator.decorator(wrapper)
-
-# CherryPy apps
 class Root(NilmApp):
     """Root application for NILM database"""
 
@@ -107,7 +59,7 @@ class Root(NilmApp):
     @cherrypy.expose
     @cherrypy.tools.json_out()
     def dbsize(self):
-        return nilmdb.utils.du(self.db.get_basepath())
+        return nilmdb.du.du(self.db.get_basepath())
 
 class Stream(NilmApp):
     """Stream-specific operations"""
@@ -126,20 +78,15 @@ class Stream(NilmApp):
     # /stream/create?path=/newton/prep&layout=PrepData
     @cherrypy.expose
     @cherrypy.tools.json_out()
-    @exception_to_httperror(NilmDBError, ValueError)
     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:
-    # /stream/destroy?path=/newton/prep
+            message = sprintf("%s: %s", type(e).__name__, e.message)
-    @cherrypy.expose
+            raise cherrypy.HTTPError("400 Bad Request", message)
-    @cherrypy.tools.json_out()
-    @exception_to_httperror(NilmDBError)
-    def destroy(self, path):
-        """Delete a stream and its associated data."""
-        return self.db.stream_destroy(path)
 
     # /stream/get_metadata?path=/newton/prep
     # /stream/get_metadata?path=/newton/prep&key=foo&key=bar
@@ -168,35 +115,49 @@ class Stream(NilmApp):
     # /stream/set_metadata?path=/newton/prep&data=<json>
     @cherrypy.expose
     @cherrypy.tools.json_out()
-    @exception_to_httperror(NilmDBError, LookupError, TypeError)
     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()
-    @exception_to_httperror(NilmDBError, LookupError, TypeError)
     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, start, end):
+    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
@@ -218,60 +179,25 @@ class Stream(NilmApp):
             parser.parse(body)
         except nilmdb.layout.ParserError as e:
             raise cherrypy.HTTPError("400 Bad Request",
-                                     "error parsing input data: " +
+                                     "Error parsing input data: " +
                                      e.message)
 
-        if (not parser.min_timestamp or not parser.max_timestamp or
-            not len(parser.data)):
-            raise cherrypy.HTTPError("400 Bad Request",
-                                     "no data provided")
-
-        # Check limits
-        start = float(start)
-        end = float(end)
-        if parser.min_timestamp < start:
-            raise cherrypy.HTTPError("400 Bad Request", "Data timestamp " +
-                                     repr(parser.min_timestamp) +
-                                     " < start time " + repr(start))
-        if parser.max_timestamp >= end:
-            raise cherrypy.HTTPError("400 Bad Request", "Data timestamp " +
-                                     repr(parser.max_timestamp) +
-                                     " >= end time " + repr(end))
-
         # Now do the nilmdb insert, passing it the parser full of data.
         try:
-            result = self.db.stream_insert(path, start, end, parser.data)
+            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)
 
-        # Done
+        # Return the maximum timestamp that we saw.  The client will
-        return "ok"
+        # return this back to us as the old_timestamp parameter, if
-
+        # it has more data to send.
-    # /stream/remove?path=/newton/prep
+        return ("ok", parser.max_timestamp)
-    # /stream/remove?path=/newton/prep&start=1234567890.0&end=1234567899.0
-    @cherrypy.expose
-    @cherrypy.tools.json_out()
-    @exception_to_httperror(NilmDBError)
-    def remove(self, path, start = None, end = None):
-        """
-        Remove data from the backend database.  Removes all data in
-        the interval [start, end).  Returns the number of data points
-        removed.
-        """
-        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")
-        return self.db.stream_remove(path, start, end)
 
     # /stream/intervals?path=/newton/prep
     # /stream/intervals?path=/newton/prep&start=1234567890.0&end=1234567899.0
     @cherrypy.expose
-    @chunked_response
     def intervals(self, path, start = None, end = None):
         """
         Get intervals from backend database.  Streams the resulting
@@ -293,9 +219,9 @@ class Stream(NilmApp):
         if len(streams) != 1:
             raise cherrypy.HTTPError("404 Not Found", "No such stream")
 
-        @workaround_cp_bug_1200
         def content(start, end):
-            # Note: disable chunked responses to see tracebacks from here.
+            # 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 ])
@@ -304,10 +230,10 @@ class Stream(NilmApp):
                     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
-    @chunked_response
     def extract(self, path, start = None, end = None, count = False):
         """
         Extract data from backend database.  Streams the resulting
@@ -337,9 +263,9 @@ class Stream(NilmApp):
         # Get formatter
         formatter = nilmdb.layout.Formatter(layout)
 
-        @workaround_cp_bug_1200
         def content(start, end, count):
-            # Note: disable chunked responses to see tracebacks from here.
+            # 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)
@@ -355,6 +281,8 @@ class Stream(NilmApp):
                     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"""
@@ -379,7 +307,7 @@ class Server(object):
         # Need to wrap DB object in a serializer because we'll call
         # into it from separate threads.
         self.embedded = embedded
-        self.db = nilmdb.utils.Serializer(db)
+        self.db = nilmdb.serializer.WrapObject(db)
         cherrypy.config.update({
             'server.socket_host': host,
             'server.socket_port': port,
@@ -395,11 +323,6 @@ class Server(object):
         cherrypy.config.update({ 'request.show_tracebacks' : True })
         self.force_traceback = force_traceback
 
-        # Patch CherryPy error handler to never pad out error messages.
-        # This isn't necessary, but then again, neither is padding the
-        # error messages.
-        cherrypy._cperror._ie_friendly_error_sizes = {}
-
         cherrypy.tree.apps = {}
         cherrypy.tree.mount(Root(self.db, self.version), "/")
         cherrypy.tree.mount(Stream(self.db), "/stream")

nilmdb/timer.py

@@ -5,7 +5,6 @@
 #   with nilmdb.Timer("flush"):
 #       foo.flush()
 
-from __future__ import print_function
 import contextlib
 import time
 
@@ -19,4 +18,4 @@ def Timer(name = None, tosyslog = False):
         import syslog
         syslog.syslog(msg)
     else:
-        print(msg)
+        print msg

nilmdb/timestamper.py

@@ -1,7 +1,7 @@
 """File-like objects that add timestamps to the input lines"""
 
 from __future__ import absolute_import
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
 
 import time
 import os

nilmdb/utils/__init__.py

@@ -1,11 +0,0 @@
-"""NilmDB utilities"""
-
-from .timer import Timer
-from .iteratorizer import Iteratorizer
-from .serializer import Serializer
-from .lrucache import lru_cache
-from .diskusage import du
-from .mustclose import must_close
-from .urllib import urlencode
-from . import misc
-from . import atomic

nilmdb/utils/atomic.py

@@ -1,26 +0,0 @@
-# Atomic file writing helper.
-
-import os
-
-def replace_file(filename, content):
-    """Attempt to atomically and durably replace the filename with the
-    given contents.  This is intended to be 'pretty good on most
-    OSes', but not necessarily bulletproof."""
-
-    newfilename = filename + ".new"
-
-    # Write to new file, flush it
-    with open(newfilename, "wb") as f:
-        f.write(content)
-        f.flush()
-        os.fsync(f.fileno())
-
-    # Move new file over old one
-    try:
-        os.rename(newfilename, filename)
-    except OSError: # pragma: no cover
-        # Some OSes might not support renaming over an existing file.
-        # This is definitely NOT atomic!
-        os.remove(filename)
-        os.rename(newfilename, filename)
-

nilmdb/utils/lrucache.py

@@ -1,77 +0,0 @@
-# Memoize a function's return value with a least-recently-used cache
-# Based on:
-#   http://code.activestate.com/recipes/498245-lru-and-lfu-cache-decorators/
-# with added 'destructor' functionality.
-
-import collections
-import decorator
-import warnings
-
-def lru_cache(size = 10, onremove = None, keys = slice(None)):
-    """Least-recently-used cache decorator.
-
-    @lru_cache(size = 10, onevict = None)
-    def f(...):
-        pass
-
-    Given a function and arguments, memoize its return value.  Up to
-    'size' elements are cached.  'keys' is a slice object that
-    represents which arguments are used as the cache key.
-
-    When evicting a value from the cache, call the function
-    'onremove' with the value that's being evicted.
-
-    Call f.cache_remove(...) to evict the cache entry with the given
-    arguments.  Call f.cache_remove_all() to evict all entries.
-    f.cache_hits and f.cache_misses give statistics.
-    """
-
-    def decorate(func):
-        cache = collections.OrderedDict()	# order: least- to most-recent
-
-        def evict(value):
-            if onremove:
-                onremove(value)
-
-        def wrapper(orig, *args, **kwargs):
-            if kwargs:
-                raise NotImplementedError("kwargs not supported")
-            key = args[keys]
-            try:
-                value = cache.pop(key)
-                orig.cache_hits += 1
-            except KeyError:
-                value = orig(*args)
-                orig.cache_misses += 1
-                if len(cache) >= size:
-                    evict(cache.popitem(0)[1])	# evict LRU cache entry
-            cache[key] = value              	# (re-)insert this key at end
-            return value
-
-        def cache_remove(*args):
-            """Remove the described key from this cache, if present."""
-            key = args
-            if key in cache:
-                evict(cache.pop(key))
-            else:
-                if len(cache) > 0 and len(args) != len(cache.iterkeys().next()):
-                    raise KeyError("trying to remove from LRU cache, but "
-                                   "number of arguments doesn't match the "
-                                   "cache key length")
-
-        def cache_remove_all():
-            for key in cache:
-                evict(cache.pop(key))
-
-        def cache_info():
-            return (func.cache_hits, func.cache_misses)
-
-        new = decorator.decorator(wrapper, func)
-        func.cache_hits = 0
-        func.cache_misses = 0
-        new.cache_info = cache_info
-        new.cache_remove = cache_remove
-        new.cache_remove_all = cache_remove_all
-        return new
-
-    return decorate

nilmdb/utils/misc.py

@@ -1,8 +0,0 @@
-import itertools
-
-def pairwise(iterable):
-    "s -> (s0,s1), (s1,s2), ..., (sn,None)"
-    a, b = itertools.tee(iterable)
-    next(b, None)
-    return itertools.izip_longest(a, b)
-

nilmdb/utils/mustclose.py

@@ -1,63 +0,0 @@
-from nilmdb.utils.printf import *
-import sys
-import inspect
-import decorator
-
-def must_close(errorfile = sys.stderr, wrap_verify = False):
-    """Class decorator that warns on 'errorfile' at deletion time if
-    the class's close() member wasn't called.
-
-    If 'wrap_verify' is True, every class method is wrapped with a
-    verifier that will raise AssertionError if the .close() method has
-    already been called."""
-    def class_decorator(cls):
-
-        # Helper to replace a class method with a wrapper function,
-        # while maintaining argument specs etc.
-        def wrap_class_method(wrapper_func):
-            method = wrapper_func.__name__
-            if method in cls.__dict__:
-                orig = getattr(cls, method).im_func
-            else:
-                orig = lambda self: None
-            setattr(cls, method, decorator.decorator(wrapper_func, orig))
-
-        @wrap_class_method
-        def __init__(orig, self, *args, **kwargs):
-            ret = orig(self, *args, **kwargs)
-            self.__dict__["_must_close"] = True
-            self.__dict__["_must_close_initialized"] = True
-            return ret
-
-        @wrap_class_method
-        def __del__(orig, self, *args, **kwargs):
-            if "_must_close" in self.__dict__:
-                fprintf(errorfile, "error: %s.close() wasn't called!\n",
-                        self.__class__.__name__)
-            return orig(self, *args, **kwargs)
-
-        @wrap_class_method
-        def close(orig, self, *args, **kwargs):
-            del self._must_close
-            return orig(self, *args, **kwargs)
-
-        # Optionally wrap all other functions
-        def verifier(orig, self, *args, **kwargs):
-            if ("_must_close" not in self.__dict__ and
-                "_must_close_initialized" in self.__dict__):
-                raise AssertionError("called " + str(orig) + " after close")
-            return orig(self, *args, **kwargs)
-        if wrap_verify:
-            for (name, method) in inspect.getmembers(cls, inspect.ismethod):
-                # Skip class methods
-                if method.__self__ is not None:
-                    continue
-                # Skip some methods
-                if name in [ "__del__", "__init__" ]:
-                    continue
-                # Set up wrapper
-                setattr(cls, name, decorator.decorator(verifier,
-                                                       method.im_func))
-
-        return cls
-    return class_decorator

nilmdb/utils/urllib.py

@@ -1,40 +0,0 @@
-from __future__ import absolute_import
-from urllib import quote_plus, _is_unicode
-
-# urllib.urlencode insists on encoding Unicode as ASCII.  This is based
-# on that function, except we always encode it as UTF-8 instead.
-
-def urlencode(query):
-    """Encode a dictionary into a URL query string.
-
-    If any values in the query arg are sequences, each sequence
-    element is converted to a separate parameter.
-    """
-
-    query = query.items()
-
-    l = []
-    for k, v in query:
-        k = quote_plus(str(k))
-        if isinstance(v, str):
-            v = quote_plus(v)
-            l.append(k + '=' + v)
-        elif _is_unicode(v):
-            # is there a reasonable way to convert to ASCII?
-            # encode generates a string, but "replace" or "ignore"
-            # lose information and "strict" can raise UnicodeError
-            v = quote_plus(v.encode("utf-8","strict"))
-            l.append(k + '=' + v)
-        else:
-            try:
-                # is this a sufficient test for sequence-ness?
-                len(v)
-            except TypeError:
-                # not a sequence
-                v = quote_plus(str(v))
-                l.append(k + '=' + v)
-            else:
-                # loop over the sequence
-                for elt in v:
-                    l.append(k + '=' + quote_plus(str(elt)))
-    return '&'.join(l)

runserver.py

@@ -3,17 +3,14 @@
 import nilmdb
 import argparse
 
-formatter = argparse.ArgumentDefaultsHelpFormatter
+parser = argparse.ArgumentParser(description='Run the NILM server')
-parser = argparse.ArgumentParser(description='Run the NILM server',
-                                 formatter_class = formatter)
 parser.add_argument('-p', '--port', help='Port number', type=int, default=12380)
-parser.add_argument('-d', '--database', help='Database directory', default="db")
 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(args.database)
+db = nilmdb.NilmDB("db")
 server = nilmdb.Server(db, host = "127.0.0.1",
                        port = args.port,
                        embedded = False)

runtests.py

@@ -1,46 +0,0 @@
-#!/usr/bin/python
-
-import nose
-import os
-import sys
-import glob
-from collections import OrderedDict
-
-class JimOrderPlugin(nose.plugins.Plugin):
-    """When searching for tests and encountering a directory that
-    contains a 'test.order' file, run tests listed in that file, in the
-    order that they're listed.  Globs are OK in that file and duplicates
-    are removed."""
-    name = 'jimorder'
-    score = 10000
-
-    def prepareTestLoader(self, loader):
-        def wrap(func):
-            def wrapper(name, *args, **kwargs):
-                addr = nose.selector.TestAddress(
-                    name, workingDir=loader.workingDir)
-                try:
-                    order = os.path.join(addr.filename, "test.order")
-                except:
-                    order = None
-                if order and os.path.exists(order):
-                    files = []
-                    for line in open(order):
-                        line = line.split('#')[0].strip()
-                        if not line:
-                            continue
-                        fn = os.path.join(addr.filename, line.strip())
-                        files.extend(sorted(glob.glob(fn)) or [fn])
-                    files = list(OrderedDict.fromkeys(files))
-                    tests = [ wrapper(fn, *args, **kwargs) for fn in files ]
-                    return loader.suiteClass(tests)
-                return func(name, *args, **kwargs)
-            return wrapper
-        loader.loadTestsFromName = wrap(loader.loadTestsFromName)
-        return loader
-
-# Use setup.cfg for most of the test configuration.  Adding
-# --with-jimorder here means that a normal "nosetests" run will
-# still work, it just won't support test.order.
-nose.main(addplugins = [ JimOrderPlugin() ],
-          argv = sys.argv + ["--with-jimorder"])

setup.cfg

@@ -8,26 +8,16 @@ cover-package=nilmdb
 cover-erase=
 ##cover-html=         # this works, puts html output in cover/ dir
 ##cover-branches=     # need nose 1.1.3 for this
-#debug=nose
-#debug-log=nose.log
 stop=
 verbosity=2
-tests=tests
-#tests=tests/test_bulkdata.py
-#tests=tests/test_mustclose.py
-#tests=tests/test_lrucache.py
 #tests=tests/test_cmdline.py
 #tests=tests/test_layout.py
-#tests=tests/test_rbtree.py
+tests=tests/test_interval.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
-#tests=tests/test_nilmdb.py
 #with-profile=
 #profile-sort=time
 ##profile-restrict=10  # doesn't work right, treated as string or something

tests/data/prep-20120323T1002-first19lines

@@ -1,19 +0,0 @@
-2.56437e+05  2.24430e+05  4.01161e+03  3.47534e+03  7.49589e+03  3.38894e+03  2.61397e+02  3.73126e+03  
-2.53963e+05  2.24167e+05  5.62107e+03  1.54801e+03  9.16517e+03  3.52293e+03  1.05893e+03  2.99696e+03  
-2.58508e+05  2.24930e+05  6.01140e+03  8.18866e+02  9.03995e+03  4.48244e+03  2.49039e+03  2.67934e+03  
-2.59627e+05  2.26022e+05  4.47450e+03  2.42302e+03  7.41419e+03  5.07197e+03  2.43938e+03  2.96296e+03  
-2.55187e+05  2.24632e+05  4.73857e+03  3.39804e+03  7.39512e+03  4.72645e+03  1.83903e+03  3.39353e+03  
-2.57102e+05  2.21623e+05  6.14413e+03  1.44109e+03  8.75648e+03  3.49532e+03  1.86994e+03  3.75253e+03  
-2.63653e+05  2.21770e+05  6.22177e+03  7.38962e+02  9.54760e+03  2.66682e+03  1.46266e+03  3.33257e+03  
-2.63613e+05  2.25256e+05  4.47712e+03  2.43745e+03  8.51021e+03  3.85563e+03  9.59442e+02  2.38718e+03  
-2.55350e+05  2.26264e+05  4.28372e+03  3.92394e+03  7.91247e+03  5.46652e+03  1.28499e+03  2.09372e+03  
-2.52727e+05  2.24609e+05  5.85193e+03  2.49198e+03  8.54063e+03  5.62305e+03  2.33978e+03  3.00714e+03  
-2.58475e+05  2.23578e+05  5.92487e+03  1.39448e+03  8.77962e+03  4.54418e+03  2.13203e+03  3.84976e+03  
-2.61563e+05  2.24609e+05  4.33614e+03  2.45575e+03  8.05538e+03  3.46911e+03  6.27873e+02  3.66420e+03  
-2.56401e+05  2.24441e+05  4.18715e+03  3.45717e+03  7.90669e+03  3.53355e+03  -5.84482e+00  2.96687e+03  
-2.54745e+05  2.22644e+05  6.02005e+03  1.94721e+03  9.28939e+03  3.80020e+03  1.34820e+03  2.37785e+03  
-2.60723e+05  2.22660e+05  6.69719e+03  1.03048e+03  9.26124e+03  4.34917e+03  2.84530e+03  2.73619e+03  
-2.63089e+05  2.25711e+05  4.77887e+03  2.60417e+03  7.39660e+03  4.59811e+03  2.17472e+03  3.40729e+03  
-2.55843e+05  2.27128e+05  4.02413e+03  4.39323e+03  6.79336e+03  4.62535e+03  7.52009e+02  3.44647e+03  
-2.51904e+05  2.24868e+05  5.82289e+03  3.02127e+03  8.46160e+03  3.80298e+03  8.07212e+02  3.53468e+03  
-2.57670e+05  2.22974e+05  6.73436e+03  1.60956e+03  9.92960e+03  2.98028e+03  1.44168e+03  3.05351e+03  

tests/renderdot.py

@@ -13,7 +13,7 @@ class Renderer(object):
 
     # Rendering
     def __render_dot_node(self, node, max_depth = 20):
-        from nilmdb.utils.printf import sprintf
+        from nilmdb.printf import sprintf
         """Render a single node and its children into a dot graph fragment"""
         if max_depth == 0:
             return ""
@@ -71,20 +71,3 @@ class Renderer(object):
                 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.order

@@ -1,18 +0,0 @@
-test_printf.py
-test_lrucache.py
-test_mustclose.py
-
-test_serializer.py
-test_iteratorizer.py
-
-test_timestamper.py
-test_layout.py
-test_rbtree.py
-test_interval.py
-
-test_bulkdata.py
-test_nilmdb.py
-test_client.py
-test_cmdline.py
-
-test_*.py

tests/test_bulkdata.py

@@ -1,103 +0,0 @@
-# -*- coding: utf-8 -*-
-
-import nilmdb
-from nilmdb.utils.printf import *
-import nilmdb.bulkdata
-
-from nose.tools import *
-from nose.tools import assert_raises
-import itertools
-
-from testutil.helpers import *
-
-testdb = "tests/bulkdata-testdb"
-
-from nilmdb.bulkdata import BulkData
-
-class TestBulkData(object):
-
-    def test_bulkdata(self):
-        for (size, files, db) in [ ( 0, 0, testdb ),
-                                       ( 25, 1000, testdb ),
-                                       ( 1000, 3, testdb.decode("utf-8") ) ]:
-            recursive_unlink(db)
-            os.mkdir(db)
-            self.do_basic(db, size, files)
-
-    def do_basic(self, db, size, files):
-        """Do the basic test with variable file_size and files_per_dir"""
-        if not size or not files:
-            data = BulkData(db)
-        else:
-            data = BulkData(db, file_size = size, files_per_dir = files)
-
-        # create empty
-        with assert_raises(ValueError):
-            data.create("/foo", "uint16_8")
-        with assert_raises(ValueError):
-            data.create("foo/bar", "uint16_8")
-        with assert_raises(ValueError):
-            data.create("/foo/bar", "uint8_8")
-        data.create("/foo/bar", "uint16_8")
-        data.create(u"/foo/baz/quux", "float64_16")
-        with assert_raises(ValueError):
-            data.create("/foo/bar/baz", "uint16_8")
-        with assert_raises(ValueError):
-            data.create("/foo/baz", "float64_16")
-
-        # get node -- see if caching works
-        nodes = []
-        for i in range(5000):
-            nodes.append(data.getnode("/foo/bar"))
-            nodes.append(data.getnode("/foo/baz/quux"))
-        del nodes
-
-        # Test node
-        node = data.getnode("/foo/bar")
-        with assert_raises(IndexError):
-            x = node[0]
-        raw = []
-        for i in range(1000):
-            raw.append([10000+i, 1, 2, 3, 4, 5, 6, 7, 8 ])
-        node.append(raw[0:1])
-        node.append(raw[1:100])
-        node.append(raw[100:])
-
-        misc_slices = [ 0, 100, slice(None), slice(0), slice(10),
-                        slice(5,10), slice(3,None), slice(3,-3),
-                        slice(20,10), slice(200,100,-1), slice(None,0,-1),
-                        slice(100,500,5) ]
-        # Extract slices
-        for s in misc_slices:
-            eq_(node[s], raw[s])
-
-        # Get some coverage of remove; remove is more fully tested
-        # in cmdline
-        with assert_raises(IndexError):
-            node.remove(9999,9998)
-
-        # close, reopen
-        # reopen
-        data.close()
-        if not size or not files:
-            data = BulkData(db)
-        else:
-            data = BulkData(db, file_size = size, files_per_dir = files)
-        node = data.getnode("/foo/bar")
-
-        # Extract slices
-        for s in misc_slices:
-            eq_(node[s], raw[s])
-
-        # destroy
-        with assert_raises(ValueError):
-            data.destroy("/foo")
-        with assert_raises(ValueError):
-            data.destroy("/foo/baz")
-        with assert_raises(ValueError):
-            data.destroy("/foo/qwerty")
-        data.destroy("/foo/baz/quux")
-        data.destroy("/foo/bar")
-
-        # close
-        data.close()

tests/test_client.py

@@ -1,7 +1,5 @@
-# -*- coding: utf-8 -*-
-
 import nilmdb
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
 from nilmdb.client import ClientError, ServerError
 
 import datetime_tz
@@ -17,9 +15,8 @@ import cStringIO
 import simplejson as json
 import unittest
 import warnings
-import resource
 
-from testutil.helpers import *
+from test_helpers import *
 
 testdb = "tests/client-testdb"
 
@@ -70,11 +67,7 @@ class TestClient(object):
         eq_(distutils.version.StrictVersion(version),
             distutils.version.StrictVersion(test_server.version))
 
-        # Bad URLs should give 404, not 500
+    def test_client_2_nilmdb(self):
-        with assert_raises(ClientError):
-            client.http.get("/stream/create")
-
-    def test_client_2_createlist(self):
         # Basic stream tests, like those in test_nilmdb:test_stream
         client = nilmdb.Client(url = "http://localhost:12380/")
 
@@ -89,8 +82,6 @@ class TestClient(object):
         # Bad layout type
         with assert_raises(ClientError):
             client.stream_create("/newton/prep", "NoSuchLayout")
-
-        # Create three streams
         client.stream_create("/newton/prep", "PrepData")
         client.stream_create("/newton/raw", "RawData")
         client.stream_create("/newton/zzz/rawnotch", "RawNotchedData")
@@ -104,20 +95,6 @@ class TestClient(object):
         eq_(client.stream_list(layout="RawData"), [ ["/newton/raw", "RawData"] ])
         eq_(client.stream_list(path="/newton/raw"), [ ["/newton/raw", "RawData"] ])
 
-        # Try messing with resource limits to trigger errors and get
-        # more coverage.  Here, make it so we can only create files 1
-        # byte in size, which will trigger an IOError in the server when
-        # we create a table.
-        limit = resource.getrlimit(resource.RLIMIT_FSIZE)
-        resource.setrlimit(resource.RLIMIT_FSIZE, (1, limit[1]))
-        with assert_raises(ServerError) as e:
-            client.stream_create("/newton/hello", "RawData")
-        resource.setrlimit(resource.RLIMIT_FSIZE, limit)
-
-
-    def test_client_3_metadata(self):
-        client = nilmdb.Client(url = "http://localhost:12380/")
-
         # Set / get metadata
         eq_(client.stream_get_metadata("/newton/prep"), {})
         eq_(client.stream_get_metadata("/newton/raw"), {})
@@ -147,14 +124,13 @@ class TestClient(object):
         with assert_raises(ClientError):
             client.stream_update_metadata("/newton/prep", [1,2,3])
 
-    def test_client_4_insert(self):
+    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")
-        start = start.totimestamp()
         rate = 120
 
         # First try a nonexistent path
@@ -179,60 +155,30 @@ class TestClient(object):
 
         # Try forcing a server request with empty data
         with assert_raises(ClientError) as e:
-            client.http.put("stream/insert", "", { "path": "/newton/prep",
+            client.http.put("stream/insert", "", { "path": "/newton/prep" })
-                                                   "start": 0, "end": 0 })
         in_("400 Bad Request", str(e.exception))
         in_("no data provided", str(e.exception))
 
-        # Specify start/end (starts too late)
-        data = nilmdb.timestamper.TimestamperRate(testfile, start, 120)
-        with assert_raises(ClientError) as e:
-            result = client.stream_insert("/newton/prep", data,
-                                          start + 5, start + 120)
-        in_("400 Bad Request", str(e.exception))
-        in_("Data timestamp 1332511200.0 < start time 1332511205.0",
-            str(e.exception))
-
-        # Specify start/end (ends too early)
-        data = nilmdb.timestamper.TimestamperRate(testfile, start, 120)
-        with assert_raises(ClientError) as e:
-            result = client.stream_insert("/newton/prep", data,
-                                          start, start + 1)
-        in_("400 Bad Request", str(e.exception))
-        # Client chunks the input, so the exact timestamp here might change
-        # if the chunk positions change.
-        in_("Data timestamp 1332511271.016667 >= end time 1332511201.0",
-            str(e.exception))
-
         # Now do the real load
         data = nilmdb.timestamper.TimestamperRate(testfile, start, 120)
-        result = client.stream_insert("/newton/prep", data,
+        result = client.stream_insert("/newton/prep", data)
-                                      start, start + 119.999777)
+        eq_(result[0], "ok")
-        eq_(result, "ok")
-
-        # Verify the intervals.  Should be just one, even if the data
-        # was inserted in chunks, due to nilmdb interval concatenation.
-        intervals = list(client.stream_intervals("/newton/prep"))
-        eq_(intervals, [[start, start + 119.999777]])
 
         # 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_("verlap", str(e.exception))
+        in_("OverlapError", str(e.exception))
 
-    def test_client_5_extractremove(self):
+    def test_client_4_extract(self):
-        # Misc tests for extract and remove.  Most of them are in test_cmdline.
+        # 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")
 
-        with assert_raises(ClientError) as e:
+    def test_client_5_generators(self):
-            client.stream_remove("/newton/prep", 123, 120)
-
-    def test_client_6_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/")
@@ -269,8 +215,7 @@ class TestClient(object):
         # Check PUT with generator out
         with assert_raises(ClientError) as e:
             client.http.put_gen("stream/insert", "",
-                                { "path": "/newton/prep",
+                                { "path": "/newton/prep" }).next()
-                                  "start": 0, "end": 0 }).next()
         in_("400 Bad Request", str(e.exception))
         in_("no data provided", str(e.exception))
 
@@ -281,7 +226,7 @@ class TestClient(object):
             in_("404 Not Found", str(e.exception))
             in_("No such stream", str(e.exception))
 
-    def test_client_7_chunked(self):
+    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
@@ -293,7 +238,7 @@ class TestClient(object):
         # still disable chunked responses for debugging.
         x = client.http.get("stream/intervals", { "path": "/newton/prep" },
                             retjson=False)
-        lines_(x, 1)
+        eq_(x.count('\n'), 2)
         if "transfer-encoding: chunked" not in client.http._headers.lower():
             warnings.warn("Non-chunked HTTP response for /stream/intervals")
 
@@ -303,40 +248,3 @@ class TestClient(object):
                               "end": "123" }, retjson=False)
         if "transfer-encoding: chunked" not in client.http._headers.lower():
             warnings.warn("Non-chunked HTTP response for /stream/extract")
-
-    def test_client_8_unicode(self):
-        # Basic Unicode tests
-        client = nilmdb.Client(url = "http://localhost:12380/")
-
-        # Delete streams that exist
-        for stream in client.stream_list():
-            client.stream_destroy(stream[0])
-
-        # Database is empty
-        eq_(client.stream_list(), [])
-
-        # Create Unicode stream, match it
-        raw = [ u"/düsseldorf/raw", u"uint16_6" ]
-        prep = [ u"/düsseldorf/prep", u"uint16_6" ]
-        client.stream_create(*raw)
-        eq_(client.stream_list(), [raw])
-        eq_(client.stream_list(layout=raw[1]), [raw])
-        eq_(client.stream_list(path=raw[0]), [raw])
-        client.stream_create(*prep)
-        eq_(client.stream_list(), [prep, raw])
-
-        # Set / get metadata with Unicode keys and values
-        eq_(client.stream_get_metadata(raw[0]), {})
-        eq_(client.stream_get_metadata(prep[0]), {})
-        meta1 = { u"alpha": u"α",
-                  u"β": u"beta" }
-        meta2 = { u"alpha": u"α" }
-        meta3 = { u"β": u"beta" }
-        client.stream_set_metadata(prep[0], meta1)
-        client.stream_update_metadata(prep[0], {})
-        client.stream_update_metadata(raw[0], meta2)
-        client.stream_update_metadata(raw[0], meta3)
-        eq_(client.stream_get_metadata(prep[0]), meta1)
-        eq_(client.stream_get_metadata(raw[0]), meta1)
-        eq_(client.stream_get_metadata(raw[0], [ "alpha" ]), meta2)
-        eq_(client.stream_get_metadata(raw[0], [ "alpha", "β" ]), meta1)

tests/test_cmdline.py

@@ -1,35 +1,29 @@
-# -*- coding: utf-8 -*-
-
 import nilmdb
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
 import nilmdb.cmdline
 
-import unittest
 from nose.tools import *
 from nose.tools import assert_raises
 import itertools
 import datetime_tz
 import os
-import re
 import shutil
 import sys
 import threading
 import urllib2
 from urllib2 import urlopen, HTTPError
 import Queue
-import StringIO
+import cStringIO
 import shlex
 
-from testutil.helpers import *
+from test_helpers import *
 
 testdb = "tests/cmdline-testdb"
 
-def server_start(max_results = None, bulkdata_args = {}):
+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,
+    test_db = nilmdb.NilmDB(testdb, sync = False, max_results = max_results)
-                            max_results = max_results,
-                            bulkdata_args = bulkdata_args)
     test_server = nilmdb.Server(test_db, host = "127.0.0.1",
                                 port = 12380, stoppable = False,
                                 fast_shutdown = True,
@@ -51,18 +45,12 @@ def setup_module():
 def teardown_module():
     server_stop()
 
-# Add an encoding property to StringIO so Python will convert Unicode
-# properly when writing or reading.
-class UTF8StringIO(StringIO.StringIO):
-    encoding = 'utf-8'
-
 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"""
-        # printf("TZ=UTC ./nilmtool.py %s\n", arg_string)
         class stdio_wrapper:
             def __init__(self, stdin, stdout, stderr):
                 self.io = (stdin, stdout, stderr)
@@ -73,18 +61,15 @@ class TestCmdline(object):
                 ( sys.stdin, sys.stdout, sys.stderr ) = self.saved
         # Empty input if none provided
         if infile is None:
-            infile = UTF8StringIO("")
+            infile = cStringIO.StringIO("")
         # Capture stderr
-        errfile = UTF8StringIO()
+        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:
-                # shlex doesn't support Unicode very well.  Encode the
+                nilmdb.cmdline.Cmdline(shlex.split(arg_string)).run()
-                # string as UTF-8 explicitly before splitting.
-                args = shlex.split(arg_string.encode('utf-8'))
-                nilmdb.cmdline.Cmdline(args).run()
                 sys.exit(0)
             except SystemExit as e:
                 exitcode = e.code
@@ -98,24 +83,14 @@ class TestCmdline(object):
             self.dump()
             eq_(self.exitcode, 0)
 
-    def fail(self, arg_string, infile = None,
+    def fail(self, arg_string, infile = None, exitcode = None):
-             exitcode = None, require_error = True):
         self.run(arg_string, infile)
         if exitcode is not None and self.exitcode != exitcode:
-            # Wrong exit code
             self.dump()
             eq_(self.exitcode, exitcode)
         if self.exitcode == 0:
-            # Success, when we wanted failure
             self.dump()
             ne_(self.exitcode, 0)
-        # Make sure the output contains the word "error" at the
-        # beginning of a line, but only if an exitcode wasn't
-        # specified.
-        if require_error and not re.search("^error",
-                                           self.captured, re.MULTILINE):
-            raise AssertionError("command failed, but output doesn't "
-                                 "contain the string 'error'")
 
     def contain(self, checkstring):
         in_(checkstring, self.captured)
@@ -145,7 +120,7 @@ class TestCmdline(object):
     def dump(self):
         printf("-----dump start-----\n%s-----dump end-----\n", self.captured)
 
-    def test_01_basic(self):
+    def test_cmdline_01_basic(self):
 
         # help
         self.ok("--help")
@@ -191,14 +166,14 @@ class TestCmdline(object):
             self.fail("extract --start 2000-01-01 --start 2001-01-02")
             self.contain("duplicated argument")
 
-    def test_02_info(self):
+    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_03_createlist(self):
+    def test_cmdline_03_createlist(self):
         # Basic stream tests, like those in test_client.
 
         # No streams
@@ -215,44 +190,22 @@ class TestCmdline(object):
         # Bad layout type
         self.fail("create /newton/prep NoSuchLayout")
         self.contain("no such layout")
-        self.fail("create /newton/prep float32_0")
-        self.contain("no such layout")
-        self.fail("create /newton/prep float33_1")
-        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")
+        self.ok("create /newton/zzz/rawnotch RawNotchedData")
 
-        # Should not be able to create a stream with another stream as
+        # Verify we got those 3 streams
-        # its parent
-        self.fail("create /newton/prep/blah PrepData")
-        self.contain("path is subdir of existing node")
-
-        # Should not be able to create a stream at a location that
-        # has other nodes as children
-        self.fail("create /newton/zzz PrepData")
-        self.contain("subdirs of this path already exist")
-
-        # 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.  Also check
+        # Match just one type or one path
-        # that --path is optional
         self.ok("list --path /newton/raw")
         self.match("/newton/raw RawData\n")
 
-        self.ok("list /newton/raw")
-        self.match("/newton/raw RawData\n")
-
-        self.fail("list -p /newton/raw /newton/raw")
-        self.contain("too many paths")
-
         self.ok("list --layout RawData")
         self.match("/newton/raw RawData\n")
 
@@ -264,17 +217,10 @@ class TestCmdline(object):
         self.ok("list --path *zzz* --layout Raw*")
         self.match("/newton/zzz/rawnotch RawNotchedData\n")
 
-        self.ok("list *zzz* --layout Raw*")
-        self.match("/newton/zzz/rawnotch RawNotchedData\n")
-
         self.ok("list --path *zzz* --layout Prep*")
         self.match("")
 
-        # reversed range
+    def test_cmdline_04_metadata(self):
-        self.fail("list /newton/prep --start 2020-01-01 --end 2000-01-01")
-        self.contain("start is after end")
-
-    def test_04_metadata(self):
         # Set / get metadata
         self.fail("metadata")
         self.fail("metadata --get")
@@ -331,7 +277,7 @@ class TestCmdline(object):
         self.fail("metadata /newton/nosuchpath")
         self.contain("No stream at path /newton/nosuchpath")
 
-    def test_05_parsetime(self):
+    def test_cmdline_05_parsetime(self):
         os.environ['TZ'] = "America/New_York"
         cmd = nilmdb.cmdline.Cmdline(None)
         test = datetime_tz.datetime_tz.now()
@@ -340,23 +286,30 @@ class TestCmdline(object):
         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)
-        for badtime in [ "20120405 1400-9999", "hello", "-", "", "14:00" ]:
         with assert_raises(ValueError):
-                x = cmd.parse_time(badtime)
+            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_06_insert(self):
+    def test_cmdline_06_insert(self):
         self.ok("insert --help")
 
         self.fail("insert /foo/bar baz qwer")
-        self.contain("error getting stream info")
+        self.contain("Error getting stream info")
 
         self.fail("insert /newton/prep baz qwer")
-        self.match("error opening input file baz\n")
+        self.match("Error opening input file baz\n")
 
         self.fail("insert /newton/prep")
-        self.contain("error extracting time")
+        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")
@@ -397,7 +350,7 @@ class TestCmdline(object):
         os.environ['TZ'] = "UTC"
         self.fail("insert --rate 120 /newton/raw "
                   "tests/data/prep-20120323T1004")
-        self.contain("error parsing input data")
+        self.contain("Error parsing input data")
 
         # empty data does nothing
         self.ok("insert --rate 120 --start '03/23/2012 06:05:00' /newton/prep "
@@ -406,64 +359,57 @@ class TestCmdline(object):
         # bad start time
         self.fail("insert --rate 120 --start 'whatever' /newton/prep /dev/null")
 
-    def test_07_detail(self):
+    def test_cmdline_07_detail(self):
         # Just count the number of lines, it's probably fine
         self.ok("list --detail")
-        lines_(self.captured, 8)
+        eq_(self.captured.count('\n'), 11)
 
         self.ok("list --detail --path *prep")
-        lines_(self.captured, 4)
+        eq_(self.captured.count('\n'), 7)
 
         self.ok("list --detail --path *prep --start='23 Mar 2012 10:02'")
-        lines_(self.captured, 3)
+        eq_(self.captured.count('\n'), 5)
 
         self.ok("list --detail --path *prep --start='23 Mar 2012 10:05'")
-        lines_(self.captured, 2)
+        eq_(self.captured.count('\n'), 3)
 
         self.ok("list --detail --path *prep --start='23 Mar 2012 10:05:15'")
-        lines_(self.captured, 2)
+        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'")
-        lines_(self.captured, 2)
+        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'")
-        lines_(self.captured, 2)
+        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'")
-        lines_(self.captured, 2)
+        eq_(self.captured.count('\n'), 2)
         self.contain("10:05:15.500")
 
         self.ok("list --detail")
-        lines_(self.captured, 8)
+        eq_(self.captured.count('\n'), 11)
 
-    def test_08_extract(self):
+    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")
+        self.contain("Error getting stream info")
 
-        # reversed range
+        # empty ranges return an error
-        self.fail("extract -a /newton/prep --start 2020-01-01 --end 2000-01-01")
-        self.contain("start is after end")
-
-        # empty ranges return error 2
         self.fail("extract -a /newton/prep " +
                   "--start '23 Mar 2012 10:00:30' " +
-                  "--end '23 Mar 2012 10:00:30'",
+                  "--end '23 Mar 2012 10:00:30'", exitcode = 2)
-                  exitcode = 2, require_error = False)
         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'",
+                  "--end '23 Mar 2012 10:00:30.000001'", exitcode = 2)
-                  exitcode = 2, require_error = False)
         self.contain("no data")
         self.fail("extract -a /newton/prep " +
                   "--start '23 Mar 2022 10:00:30' " +
-                  "--end '23 Mar 2022 10:00:30'",
+                  "--end '23 Mar 2022 10:00:30'", exitcode = 2)
-                  exitcode = 2, require_error = False)
         self.contain("no data")
 
         # but are ok if we're just counting results
@@ -498,325 +444,15 @@ class TestCmdline(object):
 
         # all data put in by tests
         self.ok("extract -a /newton/prep --start 2000-01-01 --end 2020-01-01")
-        lines_(self.captured, 43204)
+        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_09_truncated(self):
+    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")
-        lines_(self.captured, 8)
+        eq_(self.captured.count('\n'), 11)
         server_stop()
         server_start()
-
-    def test_10_remove(self):
-        # Removing data
-
-        # Try nonexistent stream
-        self.fail("remove /no/such/foo --start 2000-01-01 --end 2020-01-01")
-        self.contain("No stream at path")
-
-        self.fail("remove /newton/prep --start 2020-01-01 --end 2000-01-01")
-        self.contain("start is after end")
-
-        # empty ranges return success, backwards ranges return error
-        self.ok("remove /newton/prep " +
-                "--start '23 Mar 2012 10:00:30' " +
-                "--end '23 Mar 2012 10:00:30'")
-        self.match("")
-        self.ok("remove /newton/prep " +
-                "--start '23 Mar 2012 10:00:30.000001' " +
-                "--end '23 Mar 2012 10:00:30.000001'")
-        self.match("")
-        self.ok("remove /newton/prep " +
-                "--start '23 Mar 2022 10:00:30' " +
-                "--end '23 Mar 2022 10:00:30'")
-        self.match("")
-
-        # Verbose
-        self.ok("remove -c /newton/prep " +
-                "--start '23 Mar 2012 10:00:30' " +
-                "--end '23 Mar 2012 10:00:30'")
-        self.match("0\n")
-        self.ok("remove --count /newton/prep " +
-                "--start '23 Mar 2012 10:00:30' " +
-                "--end '23 Mar 2012 10:00:30'")
-        self.match("0\n")
-
-        # Make sure we have the data we expect
-        self.ok("list --detail /newton/prep")
-        self.match("/newton/prep PrepData\n" +
-                   "  [ Fri, 23 Mar 2012 10:00:00.000000 +0000"
-                   " -> Fri, 23 Mar 2012 10:01:59.991668 +0000 ]\n"
-                   "  [ Fri, 23 Mar 2012 10:02:00.000000 +0000"
-                   " -> Fri, 23 Mar 2012 10:03:59.991668 +0000 ]\n"
-                   "  [ Fri, 23 Mar 2012 10:04:00.000000 +0000"
-                   " -> Fri, 23 Mar 2012 10:05:59.991668 +0000 ]\n")
-
-        # Remove various chunks of prep data and make sure
-        # they're gone.
-        self.ok("remove -c /newton/prep " +
-                "--start '23 Mar 2012 10:00:30' " +
-                "--end '23 Mar 2012 10:00:40'")
-        self.match("1200\n")
-
-        self.ok("remove -c /newton/prep " +
-                "--start '23 Mar 2012 10:00:10' " +
-                "--end '23 Mar 2012 10:00:20'")
-        self.match("1200\n")
-
-        self.ok("remove -c /newton/prep " +
-                "--start '23 Mar 2012 10:00:05' " +
-                "--end '23 Mar 2012 10:00:25'")
-        self.match("1200\n")
-
-        self.ok("remove -c /newton/prep " +
-                "--start '23 Mar 2012 10:03:50' " +
-                "--end '23 Mar 2012 10:06:50'")
-        self.match("15600\n")
-
-        self.ok("extract -c /newton/prep --start 2000-01-01 --end 2020-01-01")
-        self.match("24000\n")
-
-        # See the missing chunks in list output
-        self.ok("list --detail /newton/prep")
-        self.match("/newton/prep PrepData\n" +
-                   "  [ Fri, 23 Mar 2012 10:00:00.000000 +0000"
-                   " -> Fri, 23 Mar 2012 10:00:05.000000 +0000 ]\n"
-                   "  [ Fri, 23 Mar 2012 10:00:25.000000 +0000"
-                   " -> Fri, 23 Mar 2012 10:00:30.000000 +0000 ]\n"
-                   "  [ Fri, 23 Mar 2012 10:00:40.000000 +0000"
-                   " -> Fri, 23 Mar 2012 10:01:59.991668 +0000 ]\n"
-                   "  [ Fri, 23 Mar 2012 10:02:00.000000 +0000"
-                   " -> Fri, 23 Mar 2012 10:03:50.000000 +0000 ]\n")
-
-        # Remove all data, verify it's missing
-        self.ok("remove /newton/prep --start 2000-01-01 --end 2020-01-01")
-        self.match("")  # no count requested this time
-        self.ok("list --detail /newton/prep")
-        self.match("/newton/prep PrepData\n" +
-                   "  (no intervals)\n")
-
-        # Reinsert some data, to verify that no overlaps with deleted
-        # data are reported
-        os.environ['TZ'] = "UTC"
-        self.ok("insert --rate 120 /newton/prep "
-                "tests/data/prep-20120323T1000 "
-                "tests/data/prep-20120323T1002")
-
-    def test_11_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")
-        lines_(self.captured, 7)
-
-        # 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)")
-
-    def test_12_unicode(self):
-        # Unicode paths.
-        self.ok("destroy /newton/asdf/qwer")
-        self.ok("destroy /newton/prep")
-        self.ok("destroy /newton/raw")
-        self.ok("destroy /newton/zzz")
-
-        self.ok(u"create /düsseldorf/raw uint16_6")
-        self.ok("list --detail")
-        self.contain(u"/düsseldorf/raw uint16_6")
-        self.contain("(no intervals)")
-
-        # Unicode metadata
-        self.ok(u"metadata /düsseldorf/raw --set α=beta 'γ=δ'")
-        self.ok(u"metadata /düsseldorf/raw --update 'α=β ε τ α'")
-        self.ok(u"metadata /düsseldorf/raw")
-        self.match(u"α=β ε τ α\nγ=δ\n")
-
-        self.ok(u"destroy /düsseldorf/raw")
-
-    def test_13_files(self):
-        # Test BulkData's ability to split into multiple files,
-        # by forcing the file size to be really small.
-        server_stop()
-        server_start(bulkdata_args = { "file_size" : 920, # 23 rows per file
-                                       "files_per_dir" : 3 })
-
-        # Fill data
-        self.ok("create /newton/prep float32_8")
-        os.environ['TZ'] = "UTC"
-        with open("tests/data/prep-20120323T1004-timestamped") as input:
-            self.ok("insert --none /newton/prep", input)
-
-        # Extract it
-        self.ok("extract /newton/prep --start '2000-01-01' " +
-                "--end '2012-03-23 10:04:01'")
-        lines_(self.captured, 120)
-        self.ok("extract /newton/prep --start '2000-01-01' " +
-                "--end '2022-03-23 10:04:01'")
-        lines_(self.captured, 14400)
-
-        # Make sure there were lots of files generated in the database
-        # dir
-        nfiles = 0
-        for (dirpath, dirnames, filenames) in os.walk(testdb):
-            nfiles += len(filenames)
-        assert(nfiles > 500)
-
-        # Make sure we can restart the server with a different file
-        # size and have it still work
-        server_stop()
-        server_start()
-        self.ok("extract /newton/prep --start '2000-01-01' " +
-                "--end '2022-03-23 10:04:01'")
-        lines_(self.captured, 14400)
-
-        # Now recreate the data one more time and make sure there are
-        # fewer files.
-        self.ok("destroy /newton/prep")
-        self.fail("destroy /newton/prep") # already destroyed
-        self.ok("create /newton/prep float32_8")
-        os.environ['TZ'] = "UTC"
-        with open("tests/data/prep-20120323T1004-timestamped") as input:
-            self.ok("insert --none /newton/prep", input)
-        nfiles = 0
-        for (dirpath, dirnames, filenames) in os.walk(testdb):
-            nfiles += len(filenames)
-        lt_(nfiles, 50)
-        self.ok("destroy /newton/prep") # destroy again
-
-    def test_14_remove_files(self):
-        # Test BulkData's ability to remove when data is split into
-        # multiple files.  Should be a fairly comprehensive test of
-        # remove functionality.
-        server_stop()
-        server_start(bulkdata_args = { "file_size" : 920, # 23 rows per file
-                                       "files_per_dir" : 3 })
-
-        # Insert data.  Just for fun, insert out of order
-        self.ok("create /newton/prep PrepData")
-        os.environ['TZ'] = "UTC"
-        self.ok("insert --rate 120 /newton/prep "
-                "tests/data/prep-20120323T1002 "
-                "tests/data/prep-20120323T1000")
-
-        # Should take up about 2.8 MB here (including directory entries)
-        du_before = nilmdb.utils.diskusage.du_bytes(testdb)
-
-        # Make sure we have the data we expect
-        self.ok("list --detail")
-        self.match("/newton/prep PrepData\n" +
-                   "  [ Fri, 23 Mar 2012 10:00:00.000000 +0000"
-                   " -> Fri, 23 Mar 2012 10:01:59.991668 +0000 ]\n"
-                   "  [ Fri, 23 Mar 2012 10:02:00.000000 +0000"
-                   " -> Fri, 23 Mar 2012 10:03:59.991668 +0000 ]\n")
-
-        # Remove various chunks of prep data and make sure
-        # they're gone.
-        self.ok("extract -c /newton/prep --start 2000-01-01 --end 2020-01-01")
-        self.match("28800\n")
-
-        self.ok("remove -c /newton/prep " +
-                "--start '23 Mar 2012 10:00:30' " +
-                "--end '23 Mar 2012 10:03:30'")
-        self.match("21600\n")
-
-        self.ok("remove -c /newton/prep " +
-                "--start '23 Mar 2012 10:00:10' " +
-                "--end '23 Mar 2012 10:00:20'")
-        self.match("1200\n")
-
-        self.ok("remove -c /newton/prep " +
-                "--start '23 Mar 2012 10:00:05' " +
-                "--end '23 Mar 2012 10:00:25'")
-        self.match("1200\n")
-
-        self.ok("remove -c /newton/prep " +
-                "--start '23 Mar 2012 10:03:50' " +
-                "--end '23 Mar 2012 10:06:50'")
-        self.match("1200\n")
-
-        self.ok("extract -c /newton/prep --start 2000-01-01 --end 2020-01-01")
-        self.match("3600\n")
-
-        # See the missing chunks in list output
-        self.ok("list --detail")
-        self.match("/newton/prep PrepData\n" +
-                   "  [ Fri, 23 Mar 2012 10:00:00.000000 +0000"
-                   " -> Fri, 23 Mar 2012 10:00:05.000000 +0000 ]\n"
-                   "  [ Fri, 23 Mar 2012 10:00:25.000000 +0000"
-                   " -> Fri, 23 Mar 2012 10:00:30.000000 +0000 ]\n"
-                   "  [ Fri, 23 Mar 2012 10:03:30.000000 +0000"
-                   " -> Fri, 23 Mar 2012 10:03:50.000000 +0000 ]\n")
-
-        # We have 1/8 of the data that we had before, so the file size
-        # should have dropped below 1/4 of what it used to be
-        du_after = nilmdb.utils.diskusage.du_bytes(testdb)
-        lt_(du_after, (du_before / 4))
-
-        # Remove anything that came from the 10:02 data file
-        self.ok("remove /newton/prep " +
-                "--start '23 Mar 2012 10:02:00' --end '2020-01-01'")
-
-        # Re-insert 19 lines from that file, then remove them again.
-        # With the specific file_size above, this will cause the last
-        # file in the bulk data storage to be exactly file_size large,
-        # so removing the data should also remove that last file.
-        self.ok("insert --rate 120 /newton/prep " +
-                "tests/data/prep-20120323T1002-first19lines")
-        self.ok("remove /newton/prep " +
-                "--start '23 Mar 2012 10:02:00' --end '2020-01-01'")
-
-        # Shut down and restart server, to force nrows to get refreshed.
-        server_stop()
-        server_start()
-
-        # Re-add the full 10:02 data file.  This tests adding new data once
-        # we removed data near the end.
-        self.ok("insert --rate 120 /newton/prep tests/data/prep-20120323T1002")
-
-        # See if we can extract it all
-        self.ok("extract /newton/prep --start 2000-01-01 --end 2020-01-01")
-        lines_(self.captured, 15600)

tests/test_helpers.py

@@ -12,10 +12,6 @@ def eq_(a, b):
     if not a == b:
         raise AssertionError("%s != %s" % (myrepr(a), myrepr(b)))
 
-def lt_(a, b):
-    if not a < b:
-        raise AssertionError("%s is not less than %s" % (myrepr(a), myrepr(b)))
-
 def in_(a, b):
     if a not in b:
         raise AssertionError("%s not in %s" % (myrepr(a), myrepr(b)))
@@ -24,14 +20,6 @@ def ne_(a, b):
     if not a != b:
         raise AssertionError("unexpected %s == %s" % (myrepr(a), myrepr(b)))
 
-def lines_(a, n):
-    l = a.count('\n')
-    if not l == n:
-        if len(a) > 5000:
-            a = a[0:5000] + " ... truncated"
-        raise AssertionError("wanted %d lines, got %d in output: '%s'"
-                             % (n, l, a))
-
 def recursive_unlink(path):
     try:
         shutil.rmtree(path)

tests/test_interval.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 
 import nilmdb
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
 import datetime_tz
 
 from nose.tools import *
@@ -10,24 +10,16 @@ import itertools
 
 from nilmdb.interval import Interval, DBInterval, IntervalSet, IntervalError
 
-from testutil.helpers import *
+from test_helpers import *
 import unittest
 
-# set to False to skip live renders
-do_live_renders = False
-def render(iset, description = "", live = True):
-    import testutil.renderdot as 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 + adjacent start
     ] = interval end
-    . = zero-width interval (identical start and end)
     anything else is ignored
     """
     iset = IntervalSet()
@@ -38,11 +30,9 @@ def makeset(string):
         elif (c == "|"):
             iset += Interval(start, day)
             start = day
-        elif (c == ")"):
+        elif (c == "]"):
             iset += Interval(start, day)
             del start
-        elif (c == "."):
-            iset += Interval(day, day)
     return iset
 
 class TestInterval:
@@ -78,24 +68,24 @@ class TestInterval:
         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
+        with assert_raises(AttributeError):
-        #    x = (i == 123)
+            x = (i == 123)
 
         # subset
-        eq_(Interval(d1, d3).subset(d1, d2), Interval(d1, d2))
+        assert(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)")
+        eq_(str(x), "[5000111222.0 -> 6000111222.0]")
         x = Interval(123.45, 234.56)
-        eq_(str(x), "[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)")
+        eq_(str(i), "[1332561600.0 -> 1332648000.0]")
 
     def test_interval_intersect(self):
         # Test Interval intersections
@@ -116,7 +106,7 @@ class TestInterval:
             except IntervalError:
                 assert(i not in should_intersect[True] and
                        i not in should_intersect[False])
-        with assert_raises(TypeError):
+        with assert_raises(AttributeError):
             x = i1.intersects(1234)
 
     def test_intervalset_construct(self):
@@ -137,15 +127,6 @@ class TestInterval:
             x = iseta != 3
         ne_(IntervalSet(a), IntervalSet(b))
 
-        # Note that assignment makes a new reference (not a copy)
-        isetd = IntervalSet(isetb)
-        isete = isetd
-        eq_(isetd, isetb)
-        eq_(isetd, isete)
-        isetd -= a
-        ne_(isetd, isetb)
-        eq_(isetd, isete)
-
         # test iterator
         for interval in iseta:
             pass
@@ -167,18 +148,11 @@ class TestInterval:
         iset = IntervalSet(a)
         iset += IntervalSet(b)
         eq_(iset, IntervalSet([a, b]))
-
         iset = IntervalSet(a)
         iset += b
         eq_(iset, IntervalSet([a, b]))
-
-        iset = IntervalSet(a)
-        iset.iadd_nocheck(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]))
 
@@ -191,81 +165,54 @@ class TestInterval:
 
         # misc
         eq_(repr(iset), repr(eval(repr(iset))))
-        eq_(str(iset), "[[100.0 -> 200.0), [200.0 -> 300.0)]")
+        eq_(str(iset), "[[100.0 -> 200.0], [200.0 -> 300.0]]")
 
     def test_intervalset_geniset(self):
         # Test basic iset construction
-        eq_(makeset("  [----)   "),
+        assert(makeset("  [----]   ") ==
-            makeset("  [-|--)   "))
+               makeset("  [-|--]   "))
 
-        eq_(makeset("[)  [--)   ") +
+        assert(makeset("[]  [--]   ") +
-            makeset(" [)    [--)"),
+               makeset(" []    [--]") ==
-            makeset("[|) [-----)"))
+               makeset("[|] [-----]"))
 
-        eq_(makeset("  [-------)"),
+        assert(makeset("  [-------]") ==
                makeset("  [-|-----|"))
 
 
     def test_intervalset_intersect(self):
         # Test intersection (&)
-        with assert_raises(TypeError): # was AttributeError
+        with assert_raises(AttributeError):
-            x = makeset("[--)") & 1234
+            x = makeset("[--]") & 1234
 
-        # Intersection with interval
+        assert(makeset("[---------]") &
-        eq_(makeset("[---|---)[)") &
+               makeset(" [---]     ") ==
-            list(makeset("  [------) "))[0],
+               makeset(" [---]     "))
-            makeset("  [-----)  "))
 
-        # Intersection with sets
+        assert(makeset(" [---]     ") &
-        eq_(makeset("[---------)") &
+               makeset("[---------]") ==
-            makeset(" [---)     "),
+               makeset(" [---]     "))
-            makeset(" [---)     "))
 
-        eq_(makeset(" [---)     ") &
+        assert(makeset("    [-----]") &
-            makeset("[---------)"),
+               makeset(" [-----]   ") ==
-            makeset(" [---)     "))
+               makeset("    [--]   "))
 
-        eq_(makeset("    [-----)") &
+        assert(makeset("      [---]") &
-            makeset(" [-----)   "),
+               makeset(" [--]      ") ==
-            makeset("    [--)   "))
-
-        eq_(makeset(" [--)  [--)") &
-            makeset("  [------) "),
-            makeset("  [-)  [-) "))
-
-        eq_(makeset("      [---)") &
-            makeset(" [--)      "),
                makeset("           "))
 
-        eq_(makeset("    [-|---)") &
+        assert(makeset("    [-|---]") &
-            makeset(" [-----|-) "),
+               makeset(" [-----|-] ") ==
-            makeset("    [----) "))
+               makeset("    [----] "))
 
-        eq_(makeset("    [-|-)  ") &
+        assert(makeset("    [-|-]  ") &
-            makeset(" [-|--|--) "),
+               makeset(" [-|--|--] ") ==
-            makeset("    [---)  "))
+               makeset("    [---]  "))
 
-        # Border cases -- will give different results if intervals are
+        assert(makeset(" [----][--]") &
-        # half open or fully closed.  Right now, they are half open,
+               makeset("[-] [--] []") ==
-        # although that's a little messy since the database intervals
+               makeset(" [] [-]  []"))
-        # 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)
@@ -308,65 +255,66 @@ class TestIntervalDB:
         for i in IntervalSet(iseta.intersection(Interval(125,250))):
             assert(isinstance(i, DBInterval))
 
-class TestIntervalTree:
+class TestIntervalShape:
-
+    def test_interval_shape(self):
-    def test_interval_tree(self):
         import random
         random.seed(1234)
 
-        # make a set of 100 intervals
+        # make a set of 500 intervals
         iset = IntervalSet()
-        j = 100
+        j = 500
         for i in random.sample(xrange(j),j):
             interval = Interval(i, i+1)
             iset += interval
-        render(iset, "Random Insertion")
 
-        # remove about half of them
+        # Plot it
-        for i in random.sample(xrange(j),j):
+        import renderdot
-            if random.randint(0,1):
+        r = renderdot.Renderer(lambda node: node.cleft,
-                iset -= Interval(i, i+1)
+                               lambda node: node.cright,
+                               lambda node: False,
+                               lambda node: node.start,
+                               lambda node: node.end,
+                               iset.tree.emptynode())
+        r.render_dot_live(iset.tree.rootnode(), "Random")
 
-        # try removing an interval that doesn't exist
+        # make a set of 500 intervals, inserted in order
-        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
+        j = 500
         for i in xrange(j):
             interval = Interval(i, i+1)
             iset += interval
-        render(iset, "In-order insertion")
+
+        # Plot it
+        import renderdot
+        r = renderdot.Renderer(lambda node: node.cleft,
+                               lambda node: node.cright,
+                               lambda node: False,
+                               lambda node: node.start,
+                               lambda node: node.end,
+                               iset.tree.emptynode())
+        r.render_dot_live(iset.tree.rootnode(), "In-order")
+
+        assert(False)
 
 class TestIntervalSpeed:
-    @unittest.skip("this is slow")
+    #@unittest.skip("this is slow")
     def test_interval_speed(self):
         import yappi
         import time
-        import testutil.aplotter as aplotter
+        import aplotter
-        import random
-        import math
 
         print
         yappi.start()
         speeds = {}
-        limit = 10 # was 20
+        for j in [ 2**x for x in range(5,22) ]:
-        for j in [ 2**x for x in range(5,limit) ]:
             start = time.time()
             iset = IntervalSet()
-            for i in random.sample(xrange(j),j):
+            for i in xrange(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",
+            printf("%d: %g μs (%g μs each)\n", j, speed, speed/j)
-                   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

@@ -1,5 +1,5 @@
 import nilmdb
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
 
 import nose
 from nose.tools import *
@@ -7,7 +7,9 @@ from nose.tools import assert_raises
 import threading
 import time
 
-from testutil.helpers import *
+from test_helpers import *
+
+import nilmdb.iteratorizer
 
 def func_with_callback(a, b, callback):
     callback(a)
@@ -25,8 +27,7 @@ class TestIteratorizer(object):
         eq_(self.result, "123")
 
         # Now make it an iterator
-        it = nilmdb.utils.Iteratorizer(
+        it = nilmdb.iteratorizer.Iteratorizer(lambda x:
-            lambda x:
                                               func_with_callback(1, 2, x))
         result = ""
         for i in it:
@@ -34,8 +35,7 @@ class TestIteratorizer(object):
         eq_(result, "123")
 
         # Make sure things work when an exception occurs
-        it = nilmdb.utils.Iteratorizer(
+        it = nilmdb.iteratorizer.Iteratorizer(lambda x:
-            lambda x:
                                               func_with_callback(1, "a", x))
         result = ""
         with assert_raises(TypeError) as e:
@@ -48,8 +48,7 @@ class TestIteratorizer(object):
         # itself.  This doesn't have a particular result in the test,
         # but gains coverage.
         def foo():
-            it = nilmdb.utils.Iteratorizer(
+            it = nilmdb.iteratorizer.Iteratorizer(lambda x:
-                lambda x:
                                                   func_with_callback(1, 2, x))
             it.next()
         foo()

tests/test_layout.py

@@ -2,7 +2,7 @@
 
 import nilmdb
 
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
 
 from nose.tools import *
 from nose.tools import assert_raises
@@ -20,7 +20,7 @@ import cStringIO
 import random
 import unittest
 
-from testutil.helpers import *
+from test_helpers import *
 
 from nilmdb.layout import *
 
@@ -28,13 +28,9 @@ class TestLayouts(object):
     # Some nilmdb.layout tests.  Not complete, just fills in missing
     # coverage.
     def test_layouts(self):
-        x = nilmdb.layout.get_named("PrepData")
+        x = nilmdb.layout.get_named("PrepData").description()
-        y = nilmdb.layout.get_named("float32_8")
+        y = nilmdb.layout.get_named("float32_8").description()
-        eq_(x.count, y.count)
+        eq_(repr(x), repr(y))
-        eq_(x.datatype, y.datatype)
-        y = nilmdb.layout.get_named("float32_7")
-        ne_(x.count, y.count)
-        eq_(x.datatype, y.datatype)
 
     def test_parsing(self):
         self.real_t_parsing("PrepData", "RawData", "RawNotchedData")

tests/test_lrucache.py

@@ -1,83 +0,0 @@
-import nilmdb
-from nilmdb.utils.printf import *
-
-import nose
-from nose.tools import *
-from nose.tools import assert_raises
-import threading
-import time
-import inspect
-
-from testutil.helpers import *
-
-@nilmdb.utils.lru_cache(size = 3)
-def foo1(n):
-    return n
-
-@nilmdb.utils.lru_cache(size = 5)
-def foo2(n):
-    return n
-
-def foo3d(n):
-    foo3d.destructed.append(n)
-foo3d.destructed = []
-@nilmdb.utils.lru_cache(size = 3, onremove = foo3d)
-def foo3(n):
-    return n
-
-class Foo:
-    def __init__(self):
-        self.calls = 0
-    @nilmdb.utils.lru_cache(size = 3, keys = slice(1, 2))
-    def foo(self, n, **kwargs):
-        self.calls += 1
-
-class TestLRUCache(object):
-    def test(self):
-
-        [ foo1(n) for n in [ 1, 2, 3, 1, 2, 3, 1, 2, 3 ] ]
-        eq_(foo1.cache_info(), (6, 3))
-        [ foo1(n) for n in [ 1, 2, 3, 1, 2, 3, 1, 2, 3 ] ]
-        eq_(foo1.cache_info(), (15, 3))
-        [ foo1(n) for n in [ 4, 2, 1, 1, 4 ] ]
-        eq_(foo1.cache_info(), (18, 5))
-
-        [ foo2(n) for n in [ 1, 2, 3, 1, 2, 3, 1, 2, 3 ] ]
-        eq_(foo2.cache_info(), (6, 3))
-        [ foo2(n) for n in [ 1, 2, 3, 1, 2, 3, 1, 2, 3 ] ]
-        eq_(foo2.cache_info(), (15, 3))
-        [ foo2(n) for n in [ 4, 2, 1, 1, 4 ] ]
-        eq_(foo2.cache_info(), (19, 4))
-
-        [ foo3(n) for n in [ 1, 2, 3, 1, 2, 3, 1, 2, 3 ] ]
-        eq_(foo3.cache_info(), (6, 3))
-        [ foo3(n) for n in [ 1, 2, 3, 1, 2, 3, 1, 2, 3 ] ]
-        eq_(foo3.cache_info(), (15, 3))
-        [ foo3(n) for n in [ 4, 2, 1, 1, 4 ] ]
-        eq_(foo3.cache_info(), (18, 5))
-        eq_(foo3d.destructed, [1, 3])
-        with assert_raises(KeyError):
-            foo3.cache_remove(1,2,3)
-        foo3.cache_remove(1)
-        eq_(foo3d.destructed, [1, 3, 1])
-        foo3.cache_remove_all()
-        eq_(foo3d.destructed, [1, 3, 1, 2, 4 ])
-
-        foo = Foo()
-        foo.foo(5)
-        foo.foo(6)
-        foo.foo(7)
-        foo.foo(5)
-        eq_(foo.calls, 3)
-
-        # Can't handle keyword arguments right now
-        with assert_raises(NotImplementedError):
-            foo.foo(3, asdf = 7)
-
-        # Verify that argspecs were maintained
-        eq_(inspect.getargspec(foo1),
-            inspect.ArgSpec(args=['n'],
-                            varargs=None, keywords=None, defaults=None))
-        eq_(inspect.getargspec(foo.foo),
-            inspect.ArgSpec(args=['self', 'n'],
-                            varargs=None, keywords="kwargs", defaults=None))

tests/test_mustclose.py

@@ -1,110 +0,0 @@
-import nilmdb
-from nilmdb.utils.printf import *
-
-import nose
-from nose.tools import *
-from nose.tools import assert_raises
-
-from testutil.helpers import *
-
-import sys
-import cStringIO
-import gc
-
-import inspect
-
-err = cStringIO.StringIO()
-
-@nilmdb.utils.must_close(errorfile = err)
-class Foo:
-    def __init__(self, arg):
-        fprintf(err, "Init %s\n", arg)
-
-    def __del__(self):
-        fprintf(err, "Deleting\n")
-
-    def close(self):
-        fprintf(err, "Closing\n")
-
-@nilmdb.utils.must_close(errorfile = err, wrap_verify = True)
-class Bar:
-    def __init__(self):
-        fprintf(err, "Init\n")
-
-    def __del__(self):
-        fprintf(err, "Deleting\n")
-
-    def close(self):
-        fprintf(err, "Closing\n")
-
-    def blah(self, arg):
-        fprintf(err, "Blah %s\n", arg)
-
-@nilmdb.utils.must_close(errorfile = err)
-class Baz:
-    pass
-
-class TestMustClose(object):
-    def test(self):
-
-        # Note: this test might fail if the Python interpreter doesn't
-        # garbage collect the object (and call its __del__ function)
-        # right after a "del x".
-
-        # Trigger error
-        err.truncate()
-        x = Foo("hi")
-        # Verify that the arg spec was maintained
-        eq_(inspect.getargspec(x.__init__),
-            inspect.ArgSpec(args = ['self', 'arg'],
-                            varargs = None, keywords = None, defaults = None))
-        del x
-        gc.collect()
-        eq_(err.getvalue(),
-            "Init hi\n"
-            "error: Foo.close() wasn't called!\n"
-            "Deleting\n")
-
-        # No error
-        err.truncate(0)
-        y = Foo("bye")
-        y.close()
-        del y
-        gc.collect()
-        eq_(err.getvalue(),
-            "Init bye\n"
-            "Closing\n"
-            "Deleting\n")
-
-        # Verify function calls when wrap_verify is True
-        err.truncate(0)
-        z = Bar()
-        eq_(inspect.getargspec(z.blah),
-            inspect.ArgSpec(args = ['self', 'arg'],
-                            varargs = None, keywords = None, defaults = None))
-        z.blah("boo")
-        z.close()
-        with assert_raises(AssertionError) as e:
-            z.blah("hello")
-        in_("called <function blah at 0x", str(e.exception))
-        in_("> after close", str(e.exception))
-        # Since the most recent assertion references 'z',
-        # we need to raise another assertion here so that
-        # 'z' will get properly deleted.
-        with assert_raises(AssertionError):
-            raise AssertionError()
-        del z
-        gc.collect()
-        eq_(err.getvalue(),
-            "Init\n"
-            "Blah boo\n"
-            "Closing\n"
-            "Deleting\n")
-
-        # Class with missing methods
-        err.truncate(0)
-        w = Baz()
-        w.close()
-        del w
-        eq_(err.getvalue(), "")
-

tests/test_nilmdb.py

@@ -14,7 +14,6 @@ import urllib2
 from urllib2 import urlopen, HTTPError
 import Queue
 import cStringIO
-import time
 
 testdb = "tests/testdb"
 
@@ -22,7 +21,7 @@ testdb = "tests/testdb"
 #def cleanup():
 #    os.unlink(testdb)
 
-from testutil.helpers import *
+from test_helpers import *
 
 class Test00Nilmdb(object):  # named 00 so it runs first
     def test_NilmDB(self):
@@ -40,8 +39,8 @@ class Test00Nilmdb(object):  # named 00 so it runs first
         capture = cStringIO.StringIO()
         old = sys.stdout
         sys.stdout = capture
-        with nilmdb.utils.Timer("test"):
+        with nilmdb.Timer("test"):
-            time.sleep(0.01)
+            nilmdb.timer.time.sleep(0.01)
         sys.stdout = old
         in_("test: ", capture.getvalue())
 
@@ -70,14 +69,12 @@ class Test00Nilmdb(object):  # named 00 so it runs first
         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 (pytables specific)
+        # Verify that columns were made right
-        if "h5file" in db.data.__dict__:
+        eq_(len(db.h5file.getNode("/newton/prep").cols), 9)
-            h5file = db.data.h5file
+        eq_(len(db.h5file.getNode("/newton/raw").cols), 7)
-            eq_(len(h5file.getNode("/newton/prep").cols), 9)
+        eq_(len(db.h5file.getNode("/newton/zzz/rawnotch").cols), 10)
-            eq_(len(h5file.getNode("/newton/raw").cols), 7)
+        assert(not db.h5file.getNode("/newton/prep").colindexed["timestamp"])
-            eq_(len(h5file.getNode("/newton/zzz/rawnotch").cols), 10)
+        assert(not db.h5file.getNode("/newton/prep").colindexed["c1"])
-            assert(not h5file.getNode("/newton/prep").colindexed["timestamp"])
-            assert(not h5file.getNode("/newton/prep").colindexed["c1"])
 
         # Set / get metadata
         eq_(db.stream_get_metadata("/newton/prep"), {})
@@ -199,6 +196,6 @@ class TestServer(object):
         # 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&start=0&end=0")
+            getjson("/stream/insert?path=/newton/prep")
         eq_(e.exception.code, 400)
 

tests/test_printf.py

@@ -1,12 +1,12 @@
 import nilmdb
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
 
 from nose.tools import *
 from nose.tools import assert_raises
 from cStringIO import StringIO
 import sys
 
-from testutil.helpers import *
+from test_helpers import *
 
 class TestPrintf(object):
     def test_printf(self):

tests/test_rbtree.py

@@ -1,159 +0,0 @@
-# -*- coding: utf-8 -*-
-
-import nilmdb
-from nilmdb.utils.printf import *
-
-from nose.tools import *
-from nose.tools import assert_raises
-
-from nilmdb.rbtree import RBTree, RBNode
-
-from testutil.helpers import *
-import unittest
-
-# set to False to skip live renders
-do_live_renders = False
-def render(tree, description = "", live = True):
-    import testutil.renderdot as 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

@@ -1,5 +1,5 @@
 import nilmdb
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
 
 import nose
 from nose.tools import *
@@ -7,7 +7,7 @@ from nose.tools import assert_raises
 import threading
 import time
 
-from testutil.helpers import *
+from test_helpers import *
 
 #raise nose.exc.SkipTest("Skip these")
 
@@ -57,7 +57,7 @@ class TestUnserialized(Base):
 class TestSerialized(Base):
     def setUp(self):
         self.realfoo = Foo()
-        self.foo = nilmdb.utils.Serializer(self.realfoo)
+        self.foo = nilmdb.serializer.WrapObject(self.realfoo)
 
     def tearDown(self):
         del self.foo

tests/test_timestamper.py

@@ -1,5 +1,5 @@
 import nilmdb
-from nilmdb.utils.printf import *
+from nilmdb.printf import *
 
 import datetime_tz
 
@@ -9,7 +9,7 @@ import os
 import sys
 import cStringIO
 
-from testutil.helpers import *
+from test_helpers import *
 
 class TestTimestamper(object):
 

tests/testutil/__init__.py

@@ -1 +0,0 @@
-# empty

time-bxintersect

@@ -1,54 +0,0 @@
-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

@@ -1,22 +1,20 @@
-./nilmtool.py destroy /bpnilm/2/raw
 ./nilmtool.py create /bpnilm/2/raw RawData
 
-if false; then
+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 20110513-110000 /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
+    time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s 20110513-120001 /bpnilm/2/raw
 else
-    # 170 hours, about 98 gigs uncompressed:
+    for i in $(seq 2000 2050); do
-    for i in $(seq 2000 2016); 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}0101-010001 -r 8000 /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}0101-020002 -r 8000 /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}0101-030003 -r 8000 /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}0101-040004 -r 8000 /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}0101-050005 -r 8000 /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}0101-060006 -r 8000 /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}0101-070007 -r 8000 /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}0101-080008 -r 8000 /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}0101-090009 -r 8000 /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
-	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-100010 -r 8000 /bpnilm/2/raw
     done
 fi