Fix nilmdb-fsck issue caused by 022b50950f

The default bisect module includes a fast C implementation, which
requires that array indices fit within the system "long" type.  For
32-bit systems, that's not acceptable, as the table indices for raw
data can exceed 2^32 very quickly.  A pure python version works fine.

.coveragerc

@@ -7,4 +7,4 @@
 exclude_lines =
 	pragma: no cover
 	if 0:
-omit = nilmdb/utils/datetime_tz*,nilmdb/scripts,nilmdb/_version.py
+omit = nilmdb/utils/datetime_tz*,nilmdb/scripts,nilmdb/_version.py,nilmdb/fsck

README.txt

@@ -8,7 +8,8 @@ Prerequisites:
 
   # Base NilmDB dependencies
   sudo apt-get install python-cherrypy3 python-decorator python-simplejson
-  sudo apt-get install python-requests python-dateutil python-tz python-psutil
+  sudo apt-get install python-requests python-dateutil python-tz
+  sudo apt-get install python-progressbar python-psutil
 
   # Other dependencies (required by some modules)
   sudo apt-get install python-numpy
@@ -26,6 +27,7 @@ Install:
 Usage:
 
   nilmdb-server --help
+  nilmdb-fsck --help
   nilmtool --help
 
 See docs/wsgi.md for info on setting up a WSGI application in Apache.

nilmdb/client/httpclient.py

@@ -9,7 +9,7 @@ import requests
 
 class HTTPClient(object):
     """Class to manage and perform HTTP requests from the client"""
-    def __init__(self, baseurl = "", post_json = False):
+    def __init__(self, baseurl = "", post_json = False, verify_ssl = True):
         """If baseurl is supplied, all other functions that take
         a URL can be given a relative URL instead."""
         # Verify / clean up URL
@@ -18,9 +18,8 @@ class HTTPClient(object):
             reparsed = urlparse.urlparse("http://" + baseurl).geturl()
         self.baseurl = reparsed.rstrip('/') + '/'
 
-        # Build Requests session object, enable SSL verification
-        self.session = requests.Session()
-        self.session.verify = True
+        # Note whether we want SSL verification
+        self.verify_ssl = verify_ssl
 
         # Saved response, so that tests can verify a few things.
         self._last_response = {}
@@ -58,16 +57,34 @@ class HTTPClient(object):
                 raise Error(**args)
 
     def close(self):
-        self.session.close()
+        pass
 
     def _do_req(self, method, url, query_data, body_data, stream, headers):
         url = urlparse.urljoin(self.baseurl, url)
         try:
-            response = self.session.request(method, url,
-                                            params = query_data,
-                                            data = body_data,
-                                            stream = stream,
-                                            headers = headers)
+            # Create a new session, ensure we send "Connection: close",
+            # and explicitly close connection after the transfer.
+            # This is to avoid HTTP/1.1 persistent connections
+            # (keepalive), because they have fundamental race
+            # conditions when there are delays between requests:
+            # a new request may be sent at the same instant that the
+            # server decides to timeout the connection.
+            session = requests.Session()
+            if headers is None:
+                headers = {}
+            headers["Connection"] = "close"
+            response = session.request(method, url,
+                                       params = query_data,
+                                       data = body_data,
+                                       stream = stream,
+                                       headers = headers,
+                                       verify = self.verify_ssl)
+
+            # Close the connection.  If it's a generator (stream =
+            # True), the requests library shouldn't actually close the
+            # HTTP connection until all data has been read from the
+            # response.
+            session.close()
         except requests.RequestException as e:
             raise ServerError(status = "502 Error", url = url,
                               message = str(e.message))

nilmdb/cmdline/cmdline.py

@@ -19,9 +19,8 @@ except ImportError: # pragma: no cover
 
 # Valid subcommands.  Defined in separate files just to break
 # things up -- they're still called with Cmdline as self.
-subcommands = [ "help", "info", "create", "list", "metadata",
-                "insert", "extract", "remove", "destroy",
-                "intervals", "rename" ]
+subcommands = [ "help", "info", "create", "rename", "list", "intervals",
+                "metadata", "insert", "extract", "remove", "destroy" ]
 
 # Import the subcommand modules
 subcmd_mods = {}
@@ -29,6 +28,14 @@ for cmd in subcommands:
     subcmd_mods[cmd] = __import__("nilmdb.cmdline." + cmd, fromlist = [ cmd ])
 
 class JimArgumentParser(argparse.ArgumentParser):
+    def parse_args(self, args=None, namespace=None):
+        # Look for --version anywhere and change it to just "nilmtool
+        # --version".  This makes "nilmtool cmd --version" work, which
+        # is needed by help2man.
+        if "--version" in (args or sys.argv[1:]):
+            args = [ "--version" ]
+        return argparse.ArgumentParser.parse_args(self, args, namespace)
+
     def error(self, message):
         self.print_usage(sys.stderr)
         self.exit(2, sprintf("error: %s\n", message))
@@ -114,7 +121,7 @@ class Cmdline(object):
         group = self.parser.add_argument_group("General options")
         group.add_argument("-h", "--help", action='help',
                            help='show this help message and exit')
-        group.add_argument("-V", "--version", action="version",
+        group.add_argument("-v", "--version", action="version",
                            version = nilmdb.__version__)
 
         group = self.parser.add_argument_group("Server")

nilmdb/cmdline/list.py

@@ -45,6 +45,8 @@ def setup(self, sub):
                        help="Show raw timestamps when printing times")
     group.add_argument("-l", "--layout", action="store_true",
                        help="Show layout type next to path name")
+    group.add_argument("-n", "--no-decim", action="store_true",
+                       help="Skip paths containing \"~decim-\"")
 
     return cmd
 
@@ -71,6 +73,8 @@ def cmd_list(self):
             (path, layout, int_min, int_max, rows, time) = stream[:6]
             if not fnmatch.fnmatch(path, argpath):
                 continue
+            if self.args.no_decim and "~decim-" in path:
+                continue
 
             if self.args.layout:
                 printf("%s %s\n", path, layout)

nilmdb/fsck/__init__.py

@@ -0,0 +1,5 @@
+"""nilmdb.fsck"""
+
+from __future__ import absolute_import
+
+from nilmdb.fsck.fsck import Fsck

nilmdb/fsck/fsck.py

@@ -0,0 +1,464 @@
+# -*- coding: utf-8 -*-
+
+"""Check database consistency, with some ability to fix problems.
+This should be able to fix cases where a database gets corrupted due
+to unexpected system shutdown, and detect other cases that may cause
+NilmDB to return errors when trying to manipulate the database."""
+
+import nilmdb.utils
+import nilmdb.server
+import nilmdb.client.numpyclient
+from nilmdb.utils.interval import IntervalError
+from nilmdb.server.interval import Interval, IntervalSet
+from nilmdb.utils.printf import *
+from nilmdb.utils.time import timestamp_to_string
+
+from collections import defaultdict
+import sqlite3
+import os
+import sys
+import progressbar
+import re
+import time
+import shutil
+import cPickle as pickle
+import numpy
+
+class FsckError(Exception):
+    def __init__(self, msg = "", *args):
+        if args:
+            msg = sprintf(msg, *args)
+        Exception.__init__(self, msg)
+class FixableFsckError(FsckError):
+    def __init__(self, msg = "", *args):
+        if args:
+            msg = sprintf(msg, *args)
+        FsckError.__init__(self, "%s\nThis may be fixable with \"--fix\".", msg)
+class RetryFsck(FsckError):
+    pass
+
+def log(format, *args):
+    printf(format, *args)
+
+def err(format, *args):
+    fprintf(sys.stderr, format, *args)
+
+# Decorator that retries a function if it returns a specific value
+def retry_if_raised(exc, message = None, max_retries = 100):
+    def f1(func):
+        def f2(*args, **kwargs):
+            for n in range(max_retries):
+                try:
+                    return func(*args, **kwargs)
+                except exc as e:
+                    if message:
+                        log("%s\n\n", message)
+            raise Exception("Max number of retries (%d) exceeded; giving up")
+        return f2
+    return f1
+
+class Progress(object):
+    def __init__(self, maxval):
+        if maxval == 0:
+            maxval = 1
+        self.bar = progressbar.ProgressBar(
+            maxval = maxval,
+            widgets = [ progressbar.Percentage(), ' ',
+                        progressbar.Bar(), ' ',
+                        progressbar.ETA() ])
+        if self.bar.term_width == 0:
+            self.bar.term_width = 75
+    def __enter__(self):
+        self.bar.start()
+        self.last_update = 0
+        return self
+    def __exit__(self, exc_type, exc_value, traceback):
+        if exc_type is None:
+            self.bar.finish()
+        else:
+            printf("\n")
+    def update(self, val):
+        self.bar.update(val)
+
+class Fsck(object):
+
+    def __init__(self, path, fix = False):
+        self.basepath = path
+        self.sqlpath = os.path.join(path, "data.sql")
+        self.bulkpath = os.path.join(path, "data")
+        self.bulklock = os.path.join(path, "data.lock")
+        self.fix = fix
+
+    ### Main checks
+
+    @retry_if_raised(RetryFsck, "Something was fixed: restarting fsck")
+    def check(self, skip_data = False):
+        self.bulk = None
+        self.sql = None
+        try:
+            self.check_paths()
+            self.check_sql()
+            self.check_streams()
+            self.check_intervals()
+            if skip_data:
+                log("skipped data check\n")
+            else:
+                self.check_data()
+        finally:
+            if self.bulk:
+                self.bulk.close()
+            if self.sql:
+                self.sql.commit()
+                self.sql.close()
+        log("ok\n")
+
+    ### Check basic path structure
+
+    def check_paths(self):
+        log("checking paths\n")
+        if self.bulk:
+            self.bulk.close()
+        if not os.path.isfile(self.sqlpath):
+            raise FsckError("SQL database missing (%s)", self.sqlpath)
+        if not os.path.isdir(self.bulkpath):
+            raise FsckError("Bulk data directory missing (%s)", self.bulkpath)
+        with open(self.bulklock, "w") as lockfile:
+            if not nilmdb.utils.lock.exclusive_lock(lockfile):
+                raise FsckError('Database already locked by another process\n'
+                                'Make sure all other processes that might be '
+                                'using the database are stopped.\n'
+                                'Restarting apache will cause it to unlock '
+                                'the db until a request is received.')
+            # unlocked immediately
+        self.bulk = nilmdb.server.bulkdata.BulkData(self.basepath)
+
+    ### Check SQL database health
+
+    def check_sql(self):
+        log("checking sqlite database\n")
+
+        self.sql = sqlite3.connect(self.sqlpath)
+        with self.sql:
+            cur = self.sql.cursor()
+            ver = cur.execute("PRAGMA user_version").fetchone()[0]
+            good = max(nilmdb.server.nilmdb._sql_schema_updates.keys())
+            if ver != good:
+                raise FsckError("database version %d too old, should be %d",
+                                ver, good)
+            self.stream_path = {}
+            self.stream_layout = {}
+            log("  loading paths\n")
+            result = cur.execute("SELECT id, path, layout FROM streams")
+            for r in result:
+                if r[0] in self.stream_path:
+                    raise FsckError("duplicated ID %d in stream IDs", r[0])
+                self.stream_path[r[0]] = r[1]
+                self.stream_layout[r[0]] = r[2]
+
+            log("  loading intervals\n")
+            self.stream_interval = defaultdict(list)
+            result = cur.execute("SELECT stream_id, start_time, end_time, "
+                                 "start_pos, end_pos FROM ranges "
+                                 "ORDER BY start_time")
+            for r in result:
+                if r[0] not in self.stream_path:
+                    raise FsckError("interval ID %d not in streams", k)
+                self.stream_interval[r[0]].append((r[1], r[2], r[3], r[4]))
+
+            log("  loading metadata\n")
+            self.stream_meta = defaultdict(dict)
+            result = cur.execute("SELECT stream_id, key, value FROM metadata")
+            for r in result:
+                if r[0] not in self.stream_path:
+                    raise FsckError("metadata ID %d not in streams", k)
+                if r[1] in self.stream_meta[r[0]]:
+                    raise FsckError("duplicate metadata key '%s' for stream %d",
+                                    r[1], r[0])
+                self.stream_meta[r[0]][r[1]] = r[2]
+
+    ### Check streams and basic interval overlap
+
+    def check_streams(self):
+        ids = self.stream_path.keys()
+        log("checking %s streams\n", "{:,d}".format(len(ids)))
+        with Progress(len(ids)) as pbar:
+            for i, sid in enumerate(ids):
+                pbar.update(i)
+                path = self.stream_path[sid]
+
+                # unique path, valid layout
+                if self.stream_path.values().count(path) != 1:
+                    raise FsckError("duplicated path %s", path)
+                layout = self.stream_layout[sid].split('_')[0]
+                if layout not in ('int8', 'int16', 'int32', 'int64',
+                                  'uint8', 'uint16', 'uint32', 'uint64',
+                                  'float32', 'float64'):
+                    raise FsckError("bad layout %s for %s", layout, path)
+                count = int(self.stream_layout[sid].split('_')[1])
+                if count < 1 or count > 1024:
+                    raise FsckError("bad count %d for %s", count, path)
+
+                # must exist in bulkdata
+                bulk = self.bulkpath + path
+                if not os.path.isdir(bulk):
+                    raise FsckError("%s: missing bulkdata dir", path)
+                if not nilmdb.server.bulkdata.Table.exists(bulk):
+                    raise FsckError("%s: bad bulkdata table", path)
+
+                # intervals don't overlap.  Abuse IntervalSet to check
+                # for intervals in file positions, too.
+                timeiset = IntervalSet()
+                posiset = IntervalSet()
+                for (stime, etime, spos, epos) in self.stream_interval[sid]:
+                    new = Interval(stime, etime)
+                    try:
+                        timeiset += new
+                    except IntervalError:
+                        raise FsckError("%s: overlap in intervals:\n"
+                                        "set: %s\nnew: %s",
+                                        path, str(timeiset), str(new))
+                    if spos != epos:
+                        new = Interval(spos, epos)
+                        try:
+                            posiset += new
+                        except IntervalError:
+                            raise FsckError("%s: overlap in file offsets:\n"
+                                            "set: %s\nnew: %s",
+                                            path, str(posiset), str(new))
+
+                # check bulkdata
+                self.check_bulkdata(sid, path, bulk)
+
+                # Check that we can open bulkdata
+                try:
+                    tab = None
+                    try:
+                        tab = nilmdb.server.bulkdata.Table(bulk)
+                    except Exception as e:
+                        raise FsckError("%s: can't open bulkdata: %s",
+                                        path, str(e))
+                finally:
+                    if tab:
+                        tab.close()
+
+    ### Check that bulkdata is good enough to be opened
+
+    @retry_if_raised(RetryFsck)
+    def check_bulkdata(self, sid, path, bulk):
+        with open(os.path.join(bulk, "_format"), "rb") as f:
+            fmt = pickle.load(f)
+        if fmt["version"] != 3:
+            raise FsckError("%s: bad or unsupported bulkdata version %d",
+                            path, fmt["version"])
+        row_per_file = int(fmt["rows_per_file"])
+        files_per_dir = int(fmt["files_per_dir"])
+        layout = fmt["layout"]
+        if layout != self.stream_layout[sid]:
+            raise FsckError("%s: layout mismatch %s != %s", path,
+                            layout, self.stream_layout[sid])
+
+        # Every file should have a size that's the multiple of the row size
+        rkt = nilmdb.server.rocket.Rocket(layout, None)
+        row_size = rkt.binary_size
+        rkt.close()
+
+        # Find all directories
+        regex = re.compile("^[0-9a-f]{4,}$")
+        subdirs = sorted(filter(regex.search, os.listdir(bulk)),
+                         key = lambda x: int(x, 16), reverse = True)
+        for subdir in subdirs:
+            # Find all files in that dir
+            subpath = os.path.join(bulk, subdir)
+            files = filter(regex.search, os.listdir(subpath))
+            if not files:
+                self.fix_empty_subdir(subpath)
+                raise RetryFsck
+            # Verify that their size is a multiple of the row size
+            for filename in files:
+                filepath = os.path.join(subpath, filename)
+                offset = os.path.getsize(filepath)
+                if offset % row_size:
+                    self.fix_bad_filesize(path, filepath, offset, row_size)
+
+    def fix_empty_subdir(self, subpath):
+        msg = sprintf("bulkdata path %s is missing data files", subpath)
+        if not self.fix:
+            raise FixableFsckError(msg)
+        # Try to fix it by just deleting whatever is present,
+        # as long as it's only ".removed" files.
+        err("\n%s\n", msg)
+        for fn in os.listdir(subpath):
+            if not fn.endswith(".removed"):
+                raise FsckError("can't fix automatically: please manually "
+                                "remove the file %s and try again",
+                                os.path.join(subpath, fn))
+        # Remove the whole thing
+        err("Removing empty subpath\n")
+        shutil.rmtree(subpath)
+        raise RetryFsck
+
+    def fix_bad_filesize(self, path, filepath, offset, row_size):
+        extra = offset % row_size
+        msg = sprintf("%s: size of file %s (%d) is not a multiple" +
+                      " of row size (%d): %d extra bytes present",
+                      path, filepath, offset, row_size, extra)
+        if not self.fix:
+            raise FixableFsckError(msg)
+        # Try to fix it by just truncating the file
+        err("\n%s\n", msg)
+        newsize = offset - extra
+        err("Truncating file to %d bytes and retrying\n", newsize)
+        with open(filepath, "r+b") as f:
+            f.truncate(newsize)
+            raise RetryFsck
+
+    ### Check interval endpoints
+
+    def check_intervals(self):
+        total_ints = sum(len(x) for x in self.stream_interval.values())
+        log("checking %s intervals\n", "{:,d}".format(total_ints))
+        done = 0
+        with Progress(total_ints) as pbar:
+            for sid in self.stream_interval:
+                try:
+                    bulk = self.bulkpath + self.stream_path[sid]
+                    tab = nilmdb.server.bulkdata.Table(bulk)
+                    def update(x):
+                        pbar.update(done + x)
+                    ints = self.stream_interval[sid]
+                    done += self.check_table_intervals(sid, ints, tab, update)
+                finally:
+                    tab.close()
+
+    def check_table_intervals(self, sid, ints, tab, update):
+        # look in the table to make sure we can pick out the interval's
+        # endpoints
+        path = self.stream_path[sid]
+        tab.file_open.cache_remove_all()
+        for (i, intv) in enumerate(ints):
+            update(i)
+            (stime, etime, spos, epos) = intv
+            if spos == epos and spos >= 0 and spos <= tab.nrows:
+                continue
+            try:
+                srow = tab[spos]
+                erow = tab[epos-1]
+            except Exception as e:
+                self.fix_bad_interval(sid, intv, tab, str(e))
+                raise RetryFsck
+        return len(ints)
+
+    def fix_bad_interval(self, sid, intv, tab, msg):
+        path = self.stream_path[sid]
+        msg = sprintf("%s: interval %s error accessing rows: %s",
+                      path, str(intv), str(msg))
+        if not self.fix:
+            raise FixableFsckError(msg)
+        err("\n%s\n", msg)
+
+        (stime, etime, spos, epos) = intv
+        # If it's just that the end pos is more than the number of rows
+        # in the table, lower end pos and truncate interval time too.
+        if spos < tab.nrows and epos >= tab.nrows:
+            err("end position is past endrows, but it can be truncated\n")
+            err("old end: time %d, pos %d\n", etime, epos)
+            new_epos = tab.nrows
+            new_etime = tab[new_epos-1] + 1
+            err("new end: time %d, pos %d\n", new_etime, new_epos)
+            if stime < new_etime:
+                # Change it in SQL
+                with self.sql:
+                    cur = self.sql.cursor()
+                    cur.execute("UPDATE ranges SET end_time=?, end_pos=? "
+                                "WHERE stream_id=? AND start_time=? AND "
+                                "end_time=? AND start_pos=? AND end_pos=?",
+                                (new_etime, new_epos, sid, stime, etime,
+                                 spos, epos))
+                    if cur.rowcount != 1:
+                        raise FsckError("failed to fix SQL database")
+                raise RetryFsck
+            err("actually it can't be truncated; times are bad too")
+
+        # Otherwise, the only hope is to delete the interval entirely.
+        err("*** Deleting the entire interval from SQL.\n")
+        err("This may leave stale data on disk.  To fix that, copy all\n")
+        err("data from this stream to a new stream, then remove all data\n")
+        err("from and destroy %s.\n", path)
+        with self.sql:
+            cur = self.sql.cursor()
+            cur.execute("DELETE FROM ranges WHERE "
+                        "stream_id=? AND start_time=? AND "
+                        "end_time=? AND start_pos=? AND end_pos=?",
+                        (sid, stime, etime, spos, epos))
+            if cur.rowcount != 1:
+                raise FsckError("failed to remove interval")
+        raise RetryFsck
+
+    ### Check data in each interval
+
+    def check_data(self):
+        total_rows = sum(sum((y[3] - y[2]) for y in x)
+                         for x in self.stream_interval.values())
+        log("checking %s rows of data\n", "{:,d}".format(total_rows))
+        done = 0
+        with Progress(total_rows) as pbar:
+            for sid in self.stream_interval:
+                try:
+                    bulk = self.bulkpath + self.stream_path[sid]
+                    tab = nilmdb.server.bulkdata.Table(bulk)
+                    def update(x):
+                        pbar.update(done + x)
+                    ints = self.stream_interval[sid]
+                    done += self.check_table_data(sid, ints, tab, update)
+                finally:
+                    tab.close()
+
+    def check_table_data(self, sid, ints, tab, update):
+        # Pull out all of the interval's data and verify that it's
+        # monotonic.
+        maxrows = 100000
+        path = self.stream_path[sid]
+        layout = self.stream_layout[sid]
+        dtype = nilmdb.client.numpyclient.layout_to_dtype(layout)
+        tab.file_open.cache_remove_all()
+        done = 0
+        for intv in ints:
+            last_ts = None
+            (stime, etime, spos, epos) = intv
+
+            # Break interval into maxrows-sized chunks
+            next_start = spos
+            while next_start < epos:
+                start = next_start
+                stop = min(start + maxrows, epos)
+                count = stop - start
+                next_start = stop
+
+                # Get raw data, convert to NumPy arary
+                try:
+                    raw = tab.get_data(start, stop, binary = True)
+                    data = numpy.fromstring(raw, dtype)
+                except Exception as e:
+                    raise FsckError("%s: failed to grab rows %d through %d: %s",
+                                    path, start, stop, repr(e))
+
+                # Verify that timestamps are monotonic
+                if (numpy.diff(data['timestamp']) <= 0).any():
+                    raise FsckError("%s: non-monotonic timestamp(s) in rows "
+                                    "%d through %d", path, start, stop)
+                first_ts = data['timestamp'][0]
+                if last_ts is not None and first_ts <= last_ts:
+                    raise FsckError("%s: first interval timestamp %d is not "
+                                    "greater than the previous last interval "
+                                    "timestamp %d, at row %d",
+                                    path, first_ts, last_ts, start)
+                last_ts = data['timestamp'][-1]
+
+                # These are probably fixable, by removing the offending
+                # intervals.  But I'm not going to bother implementing
+                # that yet.
+
+                # Done
+                done += count
+                update(done)
+        return done

nilmdb/scripts/nilmdb_fsck.py

@@ -0,0 +1,26 @@
+#!/usr/bin/python
+
+import nilmdb.fsck
+import argparse
+import os
+import sys
+
+def main():
+    """Main entry point for the 'nilmdb-fsck' command line script"""
+
+    parser = argparse.ArgumentParser(
+        description = 'Check database consistency',
+        formatter_class = argparse.ArgumentDefaultsHelpFormatter,
+        version = nilmdb.__version__)
+    parser.add_argument("-f", "--fix", action="store_true",
+                        default=False, help = 'Fix errors when possible '
+                        '(which may involve removing data)')
+    parser.add_argument("-n", "--no-data", action="store_true",
+                        default=False, help = 'Skip the slow full-data check')
+    parser.add_argument('database', help = 'Database directory')
+    args = parser.parse_args()
+
+    nilmdb.fsck.Fsck(args.database, args.fix).check(skip_data = args.no_data)
+
+if __name__ == "__main__":
+    main()

nilmdb/scripts/nilmdb_server.py

@@ -10,10 +10,8 @@ def main():
 
     parser = argparse.ArgumentParser(
         description = 'Run the NilmDB server',
-        formatter_class = argparse.ArgumentDefaultsHelpFormatter)
-
-    parser.add_argument("-V", "--version", action="version",
-                        version = nilmdb.__version__)
+        formatter_class = argparse.ArgumentDefaultsHelpFormatter,
+        version = nilmdb.__version__)
 
     group = parser.add_argument_group("Standard options")
     group.add_argument('-a', '--address',

nilmdb/server/bulkdata.py

@@ -43,6 +43,12 @@ class BulkData(object):
             # 32768 files per dir should work even on FAT32
             self.files_per_dir = 32768
 
+        if "initial_nrows" in kwargs:
+            self.initial_nrows = kwargs["initial_nrows"]
+        else:
+            # First row is 0
+            self.initial_nrows = 0
+
         # Make root path
         if not os.path.isdir(self.root):
             os.mkdir(self.root)
@@ -194,6 +200,9 @@ class BulkData(object):
         if oldospath == newospath:
             raise ValueError("old and new paths are the same")
 
+        # Remove Table object at old path from cache
+        self.getnode.cache_remove(self, oldunicodepath)
+
         # Move the table to a temporary location
         tmpdir = tempfile.mkdtemp(prefix = "rename-", dir = self.root)
         tmppath = os.path.join(tmpdir, "table")
@@ -251,7 +260,7 @@ class BulkData(object):
         path = self._encode_filename(unicodepath)
         elements = path.lstrip('/').split('/')
         ospath = os.path.join(self.root, *elements)
-        return Table(ospath)
+        return Table(ospath, self.initial_nrows)
 
 @nilmdb.utils.must_close(wrap_verify = False)
 class Table(object):
@@ -288,9 +297,10 @@ class Table(object):
             pickle.dump(fmt, f, 2)
 
     # Normal methods
-    def __init__(self, root):
+    def __init__(self, root, initial_nrows = 0):
         """'root' is the full OS path to the directory of this table"""
         self.root = root
+        self.initial_nrows = initial_nrows
 
         # Load the format
         with open(os.path.join(self.root, "_format"), "rb") as f:
@@ -330,7 +340,8 @@ class Table(object):
 
         # 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.
+        # empty if something was deleted but the directory was unexpectedly
+        # not deleted.
         subdirs = sorted(filter(regex.search, os.listdir(self.root)),
                          key = lambda x: int(x, 16), reverse = True)
 
@@ -349,8 +360,14 @@ class Table(object):
             # Convert to row number
             return self._row_from_offset(subdir, filename, offset)
 
-        # No files, so no data
-        return 0
+        # No files, so no data.  We typically start at row 0 in this
+        # case, although initial_nrows is specified during some tests
+        # to exercise other parts of the code better.  Since we have
+        # no files yet, round initial_nrows up so it points to a row
+        # that would begin a new file.
+        nrows = ((self.initial_nrows + (self.rows_per_file - 1)) //
+                 self.rows_per_file) * self.rows_per_file
+        return nrows
 
     def _offset_from_row(self, row):
         """Return a (subdir, filename, offset, count) tuple:

nilmdb/server/nilmdb.py

@@ -23,7 +23,6 @@ from nilmdb.server.errors import NilmDBError, StreamError, OverlapError
 import sqlite3
 import os
 import errno
-import bisect
 
 # Note about performance and transactions:
 #
@@ -83,8 +82,11 @@ _sql_schema_updates = {
 class NilmDB(object):
     verbose = 0
 
-    def __init__(self, basepath, max_results=None,
-                 max_removals=None, bulkdata_args=None):
+    def __init__(self, basepath,
+                 max_results=None,
+                 max_removals=None,
+                 max_int_removals=None,
+                 bulkdata_args=None):
         """Initialize NilmDB at the given basepath.
         Other arguments are for debugging / testing:
 
@@ -92,7 +94,10 @@ class NilmDB(object):
         stream_intervals or stream_extract response.
 
         'max_removals' is the max rows to delete at once
-        in stream_move.
+        in stream_remove.
+
+        'max_int_removals' is the max intervals to delete
+        at once in stream_remove.
 
         'bulkdata_args' is kwargs for the bulkdata module.
         """
@@ -134,6 +139,9 @@ class NilmDB(object):
         # Remove up to this many rows per call to stream_remove.
         self.max_removals = max_removals or 1048576
 
+        # Remove up to this many intervals per call to stream_remove.
+        self.max_int_removals = max_int_removals or 4096
+
     def get_basepath(self):
         return self.basepath
 
@@ -507,6 +515,17 @@ class NilmDB(object):
         # And that's all
         return
 
+    def _bisect_left(self, a, x, lo, hi):
+        # Like bisect.bisect_left, but doesn't choke on large indices on
+        # 32-bit systems, like bisect's fast C implementation does.
+        while lo < hi:
+            mid = (lo + hi) / 2
+            if a[mid] < x:
+                lo = mid + 1
+            else:
+                hi = mid
+        return lo
+
     def _find_start(self, table, dbinterval):
         """
         Given a DBInterval, find the row in the database that
@@ -517,10 +536,10 @@ class NilmDB(object):
         # Optimization for the common case where an interval wasn't truncated
         if dbinterval.start == dbinterval.db_start:
             return dbinterval.db_startpos
-        return bisect.bisect_left(table,
-                                  dbinterval.start,
-                                  dbinterval.db_startpos,
-                                  dbinterval.db_endpos)
+        return self._bisect_left(table,
+                                 dbinterval.start,
+                                 dbinterval.db_startpos,
+                                 dbinterval.db_endpos)
 
     def _find_end(self, table, dbinterval):
         """
@@ -536,10 +555,10 @@ class NilmDB(object):
         # 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(table,
-                                  dbinterval.end,
-                                  dbinterval.db_startpos,
-                                  dbinterval.db_endpos)
+        return self._bisect_left(table,
+                                 dbinterval.end,
+                                 dbinterval.db_startpos,
+                                 dbinterval.db_endpos)
 
     def stream_extract(self, path, start = None, end = None,
                        count = False, markup = False, binary = False):
@@ -643,13 +662,22 @@ class NilmDB(object):
         to_remove = Interval(start, end)
         removed = 0
         remaining = self.max_removals
+        int_remaining = self.max_int_removals
         restart = None
 
         # 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))
 
+        remove_start = None
+        remove_end = None
+
         for (dbint, orig) in all_candidates:
+            # Stop if we've hit the max number of interval removals
+            if int_remaining <= 0:
+                restart = dbint.start
+                break
+
             # Find row start and end
             row_start = self._find_start(table, dbint)
             row_end = self._find_end(table, dbint)
@@ -670,14 +698,29 @@ class NilmDB(object):
             # 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)
+            # Remove data from the underlying table storage,
+            # coalescing adjacent removals to reduce the number of calls
+            # to table.remove.
+            if remove_end == row_start:
+                # Extend our coalesced region
+                remove_end = row_end
+            else:
+                # Perform previous removal, then save this one
+                if remove_end is not None:
+                    table.remove(remove_start, remove_end)
+                remove_start = row_start
+                remove_end = row_end
 
             # Count how many were removed
             removed += row_end - row_start
             remaining -= row_end - row_start
+            int_remaining -= 1
 
             if restart is not None:
                 break
 
+        # Perform any final coalesced removal
+        if remove_end is not None:
+            table.remove(remove_start, remove_end)
+
         return (removed, restart)

nilmdb/server/server.py

@@ -74,8 +74,8 @@ class Root(NilmApp):
         dbsize = nilmdb.utils.du(path)
         return { "path": path,
                  "size": dbsize,
-                 "other": usage.used - dbsize,
-                 "reserved": usage.total - usage.used - usage.free,
+                 "other": max(usage.used - dbsize, 0),
+                 "reserved": max(usage.total - usage.used - usage.free, 0),
                  "free": usage.free }
 
 class Stream(NilmApp):
@@ -84,10 +84,18 @@ class Stream(NilmApp):
     # Helpers
     def _get_times(self, start_param, end_param):
         (start, end) = (None, None)
-        if start_param is not None:
-            start = string_to_timestamp(start_param)
-        if end_param is not None:
-            end = string_to_timestamp(end_param)
+        try:
+            if start_param is not None:
+                start = string_to_timestamp(start_param)
+        except Exception:
+            raise cherrypy.HTTPError("400 Bad Request", sprintf(
+                "invalid start (%s): must be a numeric timestamp", start_param))
+        try:
+            if end_param is not None:
+                end = string_to_timestamp(end_param)
+        except Exception:
+            raise cherrypy.HTTPError("400 Bad Request", sprintf(
+                "invalid end (%s): must be a numeric timestamp", end_param))
         if start is not None and end is not None:
             if start >= end:
                 raise cherrypy.HTTPError(
@@ -421,7 +429,7 @@ class Server(object):
         cherrypy.config.update({
             'server.socket_host': host,
             'server.socket_port': port,
-            'engine.autoreload_on': False,
+            'engine.autoreload.on': False,
             'server.max_request_body_size': 8*1024*1024,
             })
         if self.embedded:

nilmdb/utils/diskusage.py

@@ -21,7 +21,8 @@ def du(path):
     errors that might occur if we encounter broken symlinks or
     files in the process of being removed."""
     try:
-        size = os.path.getsize(path)
+        st = os.stat(path)
+        size = st.st_blocks * 512
         if os.path.isdir(path):
             for thisfile in os.listdir(path):
                 filepath = os.path.join(path, thisfile)

nilmdb/utils/mustclose.py

@@ -28,10 +28,13 @@ def must_close(errorfile = sys.stderr, wrap_verify = False):
 
         @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)
+            try:
+                if "_must_close" in self.__dict__:
+                    fprintf(errorfile, "error: %s.close() wasn't called!\n",
+                            self.__class__.__name__)
+                return orig(self, *args, **kwargs)
+            except: # pragma: no cover
+                pass
 
         @wrap_class_method
         def close(orig, self, *args, **kwargs):

nilmdb/utils/serializer.py

@@ -117,7 +117,10 @@ def serializer_proxy(obj_or_type):
             return ret
 
         def __del__(self):
-            self.__call_queue.put((None, None, None, None))
-            self.__thread.join()
+            try:
+                self.__call_queue.put((None, None, None, None))
+                self.__thread.join()
+            except: # pragma: no cover
+                pass
 
     return SerializerObjectProxy(obj_or_type)

nilmdb/utils/time.py

@@ -87,7 +87,7 @@ def parse_time(toparse):
     try:
         return unix_to_timestamp(datetime_tz.datetime_tz.
                                  smartparse(toparse).totimestamp())
-    except (ValueError, OverflowError):
+    except (ValueError, OverflowError, TypeError):
         pass
 
     # If it's parseable as a float, treat it as a Unix or NILM

setup.py

@@ -6,15 +6,6 @@
 # Then just package it up:
 #   python setup.py sdist
 
-# This is supposed to be using Distribute:
-#
-#   distutils provides a "setup" method.
-#   setuptools is a set of monkeypatches on top of that.
-#   distribute is a particular version/implementation of setuptools.
-#
-# So we don't really know if this is using the old setuptools or the
-# Distribute-provided version of setuptools.
-
 import traceback
 import sys
 import os
@@ -109,7 +100,7 @@ setup(name='nilmdb',
                         'coverage',
                         'numpy',
                         ],
-      setup_requires = [ 'distribute',
+      setup_requires = [ 'setuptools',
                          ],
       install_requires = [ 'decorator',
                            'cherrypy >= 3.2',
@@ -117,7 +108,8 @@ setup(name='nilmdb',
                            'python-dateutil',
                            'pytz',
                            'psutil >= 0.3.0',
-                           'requests >= 1.1.0, < 2.0.0',
+                           'requests >= 1.1.0',
+                           'progressbar >= 2.2',
                            ],
       packages = [ 'nilmdb',
                    'nilmdb.utils',
@@ -126,11 +118,13 @@ setup(name='nilmdb',
                    'nilmdb.client',
                    'nilmdb.cmdline',
                    'nilmdb.scripts',
+                   'nilmdb.fsck',
                    ],
       entry_points = {
           'console_scripts': [
               'nilmtool = nilmdb.scripts.nilmtool:main',
               'nilmdb-server = nilmdb.scripts.nilmdb_server:main',
+              'nilmdb-fsck = nilmdb.scripts.nilmdb_fsck:main',
               ],
           },
       ext_modules = ext_modules,

tests/test_client.py

@@ -242,6 +242,19 @@ class TestClient(object):
         in_("400 Bad Request", str(e.exception))
         in_("start must precede end", str(e.exception))
 
+        # Invalid times in HTTP request
+        with assert_raises(ClientError) as e:
+            client.http.put("stream/insert", "", { "path": "/newton/prep",
+                                                   "start": "asdf", "end": 0 })
+        in_("400 Bad Request", str(e.exception))
+        in_("invalid start", str(e.exception))
+
+        with assert_raises(ClientError) as e:
+            client.http.put("stream/insert", "", { "path": "/newton/prep",
+                                                   "start": 0, "end": "asdf" })
+        in_("400 Bad Request", str(e.exception))
+        in_("invalid end", str(e.exception))
+
         # Good content type
         with assert_raises(ClientError) as e:
             client.http.put("stream/insert", "",
@@ -677,40 +690,15 @@ class TestClient(object):
         client.close()
 
     def test_client_12_persistent(self):
-        # Check that connections are persistent when they should be.
-        # This is pretty hard to test; we have to poke deep into
-        # the Requests library.
+        # Check that connections are NOT persistent.  Rather than trying
+        # to verify this at the TCP level, just make sure that the response
+        # contained a "Connection: close" header.
         with nilmdb.client.Client(url = testurl) as c:
-            def connections():
-                try:
-                    poolmanager = c.http._last_response.connection.poolmanager
-                    pool = poolmanager.pools[('http','localhost',32180)]
-                    return (pool.num_connections, pool.num_requests)
-                except Exception:
-                    raise SkipTest("can't get connection info")
-
-            # First request makes a connection
             c.stream_create("/persist/test", "uint16_1")
-            eq_(connections(), (1, 1))
+            eq_(c.http._last_response.headers["Connection"], "close")
 
-            # Non-generator
-            c.stream_list("/persist/test")
-            eq_(connections(), (1, 2))
-            c.stream_list("/persist/test")
-            eq_(connections(), (1, 3))
-
-            # Generators
-            for x in c.stream_intervals("/persist/test"):
-                pass
-            eq_(connections(), (1, 4))
-            for x in c.stream_intervals("/persist/test"):
-                pass
-            eq_(connections(), (1, 5))
-
-            # Clean up
-            c.stream_remove("/persist/test")
             c.stream_destroy("/persist/test")
-            eq_(connections(), (1, 7))
+            eq_(c.http._last_response.headers["Connection"], "close")
 
     def test_client_13_timestamp_rounding(self):
         # Test potentially bad timestamps (due to floating point

tests/test_cmdline.py

@@ -21,13 +21,17 @@ from testutil.helpers import *
 
 testdb = "tests/cmdline-testdb"
 
-def server_start(max_results = None, max_removals = None, bulkdata_args = {}):
+def server_start(max_results = None,
+                 max_removals = None,
+                 max_int_removals = None,
+                 bulkdata_args = {}):
     global test_server, test_db
     # Start web app on a custom port
     test_db = nilmdb.utils.serializer_proxy(nilmdb.server.NilmDB)(
         testdb,
         max_results = max_results,
         max_removals = max_removals,
+        max_int_removals = max_int_removals,
         bulkdata_args = bulkdata_args)
     test_server = nilmdb.server.Server(test_db, host = "127.0.0.1",
                                        port = 32180, stoppable = False,
@@ -59,8 +63,7 @@ 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"""
+        passing the given input.  Save the output and exit code."""
         # printf("TZ=UTC ./nilmtool.py %s\n", arg_string)
         os.environ['NILMDB_URL'] = "http://localhost:32180/"
         class stdio_wrapper:
@@ -160,6 +163,12 @@ class TestCmdline(object):
         self.ok("--help")
         self.contain("usage:")
 
+        # help
+        self.ok("--version")
+        ver = self.captured
+        self.ok("list --version")
+        eq_(self.captured, ver)
+
         # fail for no args
         self.fail("")
 
@@ -285,6 +294,7 @@ class TestCmdline(object):
         self.ok("create /newton/zzz/rawnotch uint16_9")
         self.ok("create /newton/prep float32_8")
         self.ok("create /newton/raw uint16_6")
+        self.ok("create /newton/raw~decim-1234 uint16_6")
 
         # Create a stream that already exists
         self.fail("create /newton/raw uint16_6")
@@ -300,13 +310,23 @@ class TestCmdline(object):
         self.fail("create /newton/zzz float32_8")
         self.contain("subdirs of this path already exist")
 
-        # Verify we got those 3 streams and they're returned in
+        # Verify we got those 4 streams and they're returned in
         # alphabetical order.
         self.ok("list -l")
         self.match("/newton/prep float32_8\n"
                    "/newton/raw uint16_6\n"
+                   "/newton/raw~decim-1234 uint16_6\n"
                    "/newton/zzz/rawnotch uint16_9\n")
 
+        # No decimated streams if -n specified
+        self.ok("list -n -l")
+        self.match("/newton/prep float32_8\n"
+                   "/newton/raw uint16_6\n"
+                   "/newton/zzz/rawnotch uint16_9\n")
+
+        # Delete that decimated stream
+        self.ok("destroy /newton/raw~decim-1234")
+
         # Match just one type or one path.  Also check
         # that --path is optional
         self.ok("list --layout /newton/raw")
@@ -814,9 +834,12 @@ class TestCmdline(object):
     def test_13_files(self):
         # Test BulkData's ability to split into multiple files,
         # by forcing the file size to be really small.
+        # Also increase the initial nrows, so that start/end positions
+        # in the database are very large (> 32 bit)
         server_stop()
         server_start(bulkdata_args = { "file_size" : 920, # 23 rows per file
-                                       "files_per_dir" : 3 })
+                                       "files_per_dir" : 3,
+                                       "initial_nrows" : 2**40 })
 
         # Fill data
         self.ok("create /newton/prep float32_8")
@@ -864,14 +887,28 @@ class TestCmdline(object):
         self.ok("destroy -R /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.
-        # Also limit max_removals, to cover more functionality.
+        # Limit max_removals, to cover more functionality.
         server_stop()
         server_start(max_removals = 4321,
                      bulkdata_args = { "file_size" : 920, # 23 rows per file
-                                       "files_per_dir" : 3 })
+                                       "files_per_dir" : 3,
+                                       "initial_nrows" : 2**40 })
+        self.do_remove_files()
+        self.ok("destroy -R /newton/prep") # destroy again
+
+    def test_14b_remove_files_maxint(self):
+        # Limit max_int_removals, to cover more functionality.
+        server_stop()
+        server_start(max_int_removals = 1,
+                     bulkdata_args = { "file_size" : 920, # 23 rows per file
+                                       "files_per_dir" : 3,
+                                       "initial_nrows" : 2**40 })
+        self.do_remove_files()
+
+    def do_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.
 
         # Insert data.  Just for fun, insert out of order
         self.ok("create /newton/prep float32_8")

tests/test_timestamper.py

@@ -1,5 +1,6 @@
 import nilmdb
 from nilmdb.utils.printf import *
+from nilmdb.utils import datetime_tz
 
 from nose.tools import *
 from nose.tools import assert_raises
@@ -19,6 +20,8 @@ class TestTimestamper(object):
         def join(list):
             return "\n".join(list) + "\n"
 
+        datetime_tz.localtz_set("America/New_York")
+
         start = nilmdb.utils.time.parse_time("03/24/2012")
         lines_in  = [ "hello", "world", "hello world", "# commented out" ]
         lines_out = [ "1332561600000000 hello",