Tweak cache sizes to account for large numbers of decimated tables

We were still calculating the maximum number of rows correctly,
so the extra data was really extra and would get re-written to the
beginning of the subsequent file.

The only case in which this would lead to database issues is if the
very last file was lengthened incorrectly, and the "nrows" calculation
would therefore be wrong when the database was reopened.  Still, even
in that case, it should just leave a small gap in the data, not cause
any errors.

docs/design.md

@@ -421,3 +421,20 @@ and has all of the same functions.  It adds three new functions:
 It is significantly faster!  It is about 20 times faster to decimate a
 stream with `nilm-decimate` when the filter code is using the new
 binary/numpy interface.
+
+
+WSGI interface & chunked requests
+---------------------------------
+
+mod_wsgi requires "WSGIChunkedRequest On" to handle
+"Transfer-encoding: Chunked" requests.  However, `/stream/insert`
+doesn't handle this correctly right now, because:
+
+- The `cherrpy.request.body.read()` call needs to be fixed for chunked requests
+
+- We don't want to just buffer endlessly in the server, and it will
+  require some thought on how to handle data in chunks (what to do about
+  interval endpoints).
+
+It is probably better to just keep the endpoint management on the client
+side, so leave "WSGIChunkedRequest off" for now.

extras/fix-oversize-files.py

@@ -0,0 +1,50 @@
+#!/usr/bin/python
+
+import os
+import sys
+import cPickle as pickle
+import argparse
+import fcntl
+import re
+from nilmdb.client.numpyclient import layout_to_dtype
+
+parser = argparse.ArgumentParser(
+    description = """
+Fix database corruption where binary writes caused too much data to be
+written to the file.  Truncates files to the correct length.  This was
+fixed by b98ff1331a515ad47fd3203615e835b529b039f9.
+""")
+parser.add_argument("path", action="store", help='Database root path')
+parser.add_argument("-y", "--yes", action="store_true", help='Fix them')
+args = parser.parse_args()
+
+lock = os.path.join(args.path, "data.lock")
+with open(lock, "w") as f:
+    fcntl.flock(f.fileno(), fcntl.LOCK_EX | fcntl.LOCK_NB)
+
+    fix = {}
+
+    for (path, dirs, files) in os.walk(args.path):
+        if "_format" in files:
+            with open(os.path.join(path, "_format")) as format:
+                fmt = pickle.load(format)
+                rowsize = layout_to_dtype(fmt["layout"]).itemsize
+                maxsize = rowsize * fmt["rows_per_file"]
+                fix[path] = maxsize
+                if maxsize < 128000000: # sanity check
+                    raise Exception("bad maxsize " + str(maxsize))
+
+    for fixpath in fix:
+        for (path, dirs, files) in os.walk(fixpath):
+            for fn in files:
+                if not re.match("^[0-9a-f]{4,}$", fn):
+                    continue
+                fn = os.path.join(path, fn)
+                size = os.path.getsize(fn)
+                maxsize = fix[fixpath]
+                if size > maxsize:
+                    diff = size - maxsize
+                    print diff, "too big:", fn
+                    if args.yes:
+                        with open(fn, "a+") as dbfile:
+                            dbfile.truncate(maxsize)

nilmdb/client/client.py

@@ -6,7 +6,6 @@ import nilmdb.utils
 import nilmdb.client.httpclient
 from nilmdb.client.errors import ClientError
 
-import re
 import time
 import simplejson as json
 import contextlib
@@ -66,12 +65,8 @@ class Client(object):
             params["layout"] = layout
         if extended:
             params["extended"] = 1
-        def sort_streams_nicely(x):
+        streams = self.http.get("stream/list", params)
-            """Human-friendly sort (/stream/2 before /stream/10)"""
+        return nilmdb.utils.sort.sort_human(streams, key = lambda s: s[0])
-            num = lambda t: int(t) if t.isdigit() else t
-            key = lambda k: [ num(c) for c in re.split('([0-9]+)', k[0]) ]
-            return sorted(x, key = key)
-        return sort_streams_nicely(self.http.get("stream/list", params))
 
     def stream_get_metadata(self, path, keys = None):
         params = { "path": path }
@@ -122,7 +117,10 @@ class Client(object):
             params["start"] = timestamp_to_string(start)
         if end is not None:
             params["end"] = timestamp_to_string(end)
-        return self.http.post("stream/remove", params)
+        total = 0
+        for count in self.http.post_gen("stream/remove", params):
+            total += int(count)
+        return total
 
     @contextlib.contextmanager
     def stream_insert_context(self, path, start = None, end = None):
@@ -146,6 +144,7 @@ class Client(object):
         ctx = StreamInserter(self, path, start, end)
         yield ctx
         ctx.finalize()
+        ctx.destroy()
 
     def stream_insert(self, path, data, start = None, end = None):
         """Insert rows of data into a stream.  data should be a string
@@ -295,6 +294,15 @@ class StreamInserter(object):
         self._block_data = []
         self._block_len = 0
 
+        self.destroyed = False
+
+    def destroy(self):
+        """Ensure this object can't be used again without raising
+        an error"""
+        def error(*args, **kwargs):
+            raise Exception("don't reuse this context object")
+        self._send_block = self.insert = self.finalize = self.send = error
+
     def insert(self, data):
         """Insert a chunk of ASCII formatted data in string form.  The
         overall data must consist of lines terminated by '\\n'."""
@@ -441,7 +449,7 @@ class StreamInserter(object):
             self._interval_start = end_ts
 
         # Double check endpoints
-        if start_ts is None or end_ts is None:
+        if (start_ts is None or end_ts is None) or (start_ts == end_ts):
             # If the block has no non-comment lines, it's OK
             try:
                 self._get_first_noncomment(block)

nilmdb/client/httpclient.py

@@ -137,5 +137,14 @@ class HTTPClient(object):
         """Simple GET (parameters in URL) returning a generator"""
         return self._req_gen("GET", url, params, binary = binary)
 
+    def post_gen(self, url, params = None):
+        """Simple POST (parameters in body) returning a generator"""
+        if self.post_json:
+            return self._req_gen("POST", url, None,
+                                 json.dumps(params),
+                                 { 'Content-type': 'application/json' })
+        else:
+            return self._req_gen("POST", url, None, params)
+
     # Not much use for a POST or PUT generator, since they don't
     # return much data.

nilmdb/client/numpyclient.py

@@ -98,6 +98,7 @@ class NumpyClient(nilmdb.client.client.Client):
         ctx = StreamInserterNumpy(self, path, start, end, dtype)
         yield ctx
         ctx.finalize()
+        ctx.destroy()
 
     def stream_insert_numpy(self, path, data, start = None, end = None,
                             layout = None):
@@ -133,16 +134,8 @@ class StreamInserterNumpy(nilmdb.client.client.StreamInserter):
         contiguous interval and may be None.  'dtype' is the Numpy
         dtype for this stream.
         """
-        self.last_response = None
+        super(StreamInserterNumpy, self).__init__(client, path, start, end)
-
         self._dtype = dtype
-        self._client = client
-        self._path = path
-
-        # Start and end for the overall contiguous interval we're
-        # filling
-        self._interval_start = start
-        self._interval_end = end
 
         # Max rows to send at once
         self._max_rows = self._max_data // self._dtype.itemsize
@@ -250,9 +243,12 @@ class StreamInserterNumpy(nilmdb.client.client.StreamInserter):
             # Next block continues where this one ended
             self._interval_start = end_ts
 
-        # If we have no endpoints, it's because we had no data to send.
+        # If we have no endpoints, or equal endpoints, it's OK as long
-        if start_ts is None or end_ts is None:
+        # as there's no data to send
-            return
+        if (start_ts is None or end_ts is None) or (start_ts == end_ts):
+            if len(array) == 0:
+                return
+            raise ClientError("have data to send, but invalid start/end times")
 
         # Send it
         data = array.tostring()

nilmdb/cmdline/extract.py

@@ -1,6 +1,7 @@
 from __future__ import print_function
 from nilmdb.utils.printf import *
 import nilmdb.client
+import sys
 
 def setup(self, sub):
     cmd = sub.add_parser("extract", help="Extract data",
@@ -24,6 +25,8 @@ def setup(self, sub):
                        ).completer = self.complete.time
 
     group = cmd.add_argument_group("Output format")
+    group.add_argument("-B", "--binary", action="store_true",
+                       help="Raw binary output")
     group.add_argument("-b", "--bare", action="store_true",
                        help="Exclude timestamps from output lines")
     group.add_argument("-a", "--annotate", action="store_true",
@@ -42,6 +45,11 @@ def cmd_extract_verify(self):
         if self.args.start > self.args.end:
             self.parser.error("start is after end")
 
+    if self.args.binary:
+        if (self.args.bare or self.args.annotate or self.args.markup or
+            self.args.timestamp_raw or self.args.count):
+            self.parser.error("--binary cannot be combined with other options")
+
 def cmd_extract(self):
     streams = self.client.stream_list(self.args.path)
     if len(streams) != 1:
@@ -60,16 +68,23 @@ def cmd_extract(self):
         printf("# end: %s\n", time_string(self.args.end))
 
     printed = False
+    if self.args.binary:
+        printer = sys.stdout.write
+    else:
+        printer = print
+    bare = self.args.bare
+    count = self.args.count
     for dataline in self.client.stream_extract(self.args.path,
                                                self.args.start,
                                                self.args.end,
                                                self.args.count,
-                                               self.args.markup):
+                                               self.args.markup,
-        if self.args.bare and not self.args.count:
+                                               self.args.binary):
+        if bare and not count:
             # Strip timestamp (first element).  Doesn't make sense
             # if we are only returning a count.
             dataline = ' '.join(dataline.split(' ')[1:])
-        print(dataline)
+        printer(dataline)
         printed = True
     if not printed:
         if self.args.annotate:

nilmdb/cmdline/info.py

@@ -21,5 +21,8 @@ def cmd_info(self):
     printf("Server URL: %s\n", self.client.geturl())
     dbinfo = self.client.dbinfo()
     printf("Server database path: %s\n", dbinfo["path"])
-    printf("Server database size: %s\n", human_size(dbinfo["size"]))
+    for (desc, field) in [("used by NilmDB", "size"),
-    printf("Server database free space: %s\n", human_size(dbinfo["free"]))
+                          ("used by other", "other"),
+                          ("reserved", "reserved"),
+                          ("free", "free")]:
+        printf("Server disk space %s: %s\n", desc, human_size(dbinfo[field]))

nilmdb/server/bulkdata.py

@@ -19,8 +19,8 @@ from . import rocket
 
 # 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
+table_cache_size = 32
-fd_cache_size = 16
+fd_cache_size = 8
 
 @nilmdb.utils.must_close(wrap_verify = False)
 class BulkData(object):

nilmdb/server/nilmdb.py

@@ -176,7 +176,7 @@ class NilmDB(object):
             raise NilmDBError("start must precede end")
         return (start, end)
 
-    @nilmdb.utils.lru_cache(size = 16)
+    @nilmdb.utils.lru_cache(size = 64)
     def _get_intervals(self, stream_id):
         """
         Return a mutable IntervalSet corresponding to the given stream ID.
@@ -675,6 +675,7 @@ class NilmDB(object):
 
             # Count how many were removed
             removed += row_end - row_start
+            remaining -= row_end - row_start
 
             if restart is not None:
                 break

nilmdb/server/rocket.c

@@ -28,7 +28,7 @@ const static char __long_ok[1 - 2*!(sizeof(int64_t) ==
 
 /* Somewhat arbitrary, just so we can use fixed sizes for strings
    etc. */
-static const int MAX_LAYOUT_COUNT = 128;
+static const int MAX_LAYOUT_COUNT = 1024;
 
 /* Error object and constants */
 static PyObject *ParseError;
@@ -468,7 +468,7 @@ static PyObject *Rocket_append_binary(Rocket *self, PyObject *args)
         }
 
         /* Write binary data */
-        if (fwrite(data, data_len, 1, self->file) != 1) {
+        if (fwrite(data, self->binary_size, rows, self->file) != rows) {
                 PyErr_SetFromErrno(PyExc_OSError);
                 return NULL;
         }

nilmdb/server/server.py

@@ -167,9 +167,13 @@ class Root(NilmApp):
         """Return a dictionary with the database path,
         size of the database in bytes, and free disk space in bytes"""
         path = self.db.get_basepath()
+        usage = psutil.disk_usage(path)
+        dbsize = nilmdb.utils.du(path)
         return { "path": path,
-                 "size": nilmdb.utils.du(path),
+                 "size": dbsize,
-                 "free": psutil.disk_usage(path).free }
+                 "other": usage.used - dbsize,
+                 "reserved": usage.total - usage.used - usage.free,
+                 "free": usage.free }
 
 class Stream(NilmApp):
     """Stream-specific operations"""
@@ -347,24 +351,34 @@ class Stream(NilmApp):
     # /stream/remove?path=/newton/prep&start=1234567890.0&end=1234567899.0
     @cherrypy.expose
     @cherrypy.tools.json_in()
-    @cherrypy.tools.json_out()
-    @exception_to_httperror(NilmDBError)
     @cherrypy.tools.CORS_allow(methods = ["POST"])
+    @chunked_response
+    @response_type("application/x-json-stream")
     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
+        the interval [start, end).
-        removed.
+
+        Returns the number of data points removed.  Since this is a potentially
+        long-running operation, multiple numbers may be returned as the
+        data gets removed from the backend database.  The total number of
+        points removed is the sum of all of these numbers.
         """
         (start, end) = self._get_times(start, end)
-        total_removed = 0
+
-        while True:
+        if len(self.db.stream_list(path = path)) != 1:
-            (removed, restart) = self.db.stream_remove(path, start, end)
+            raise cherrypy.HTTPError("404", "No such stream: " + path)
-            total_removed += removed
+
-            if restart is None:
+        @workaround_cp_bug_1200
-                break
+        def content(start, end):
-            start = restart
+            # Note: disable chunked responses to see tracebacks from here.
-        return total_removed
+            while True:
+                (removed, restart) = self.db.stream_remove(path, start, end)
+                yield json.dumps(removed) + "\r\n"
+                if restart is None:
+                    break
+                start = restart
+        return content(start, end)
 
     # /stream/intervals?path=/newton/prep
     # /stream/intervals?path=/newton/prep&start=1234567890.0&end=1234567899.0

nilmdb/utils/__init__.py

@@ -13,3 +13,4 @@ import nilmdb.utils.time
 import nilmdb.utils.iterator
 import nilmdb.utils.interval
 import nilmdb.utils.lock
+import nilmdb.utils.sort

nilmdb/utils/diskusage.py

@@ -1,4 +1,5 @@
 import os
+import errno
 from math import log
 
 def human_size(num):
@@ -16,10 +17,17 @@ def human_size(num):
         return '1 byte'
 
 def du(path):
-    """Like du -sb, returns total size of path in bytes."""
+    """Like du -sb, returns total size of path in bytes.  Ignore
-    size = os.path.getsize(path)
+    errors that might occur if we encounter broken symlinks or
-    if os.path.isdir(path):
+    files in the process of being removed."""
-        for thisfile in os.listdir(path):
+    try:
-            filepath = os.path.join(path, thisfile)
+        size = os.path.getsize(path)
-            size += du(filepath)
+        if os.path.isdir(path):
-    return size
+            for thisfile in os.listdir(path):
+                filepath = os.path.join(path, thisfile)
+                size += du(filepath)
+        return size
+    except OSError as e: # pragma: no cover
+        if e.errno != errno.ENOENT:
+            raise
+        return 0

nilmdb/utils/sort.py

@@ -0,0 +1,18 @@
+import re
+
+def sort_human(items, key = None):
+    """Human-friendly sort (/stream/2 before /stream/10)"""
+    def to_num(val):
+        try:
+            return int(val)
+        except Exception:
+            return val
+
+    def human_key(text):
+        if key:
+            text = key(text)
+        # Break into character and numeric chunks.
+        chunks = re.split(r'([0-9]+)', text)
+        return [ to_num(c) for c in chunks ]
+
+    return sorted(items, key = human_key)

tests/test_client.py

@@ -105,16 +105,19 @@ class TestClient(object):
                 client.http.post("/stream/list")
         client = nilmdb.client.Client(url = testurl)
 
-        # Create three streams
+        # Create four streams
         client.stream_create("/newton/prep", "float32_8")
         client.stream_create("/newton/raw", "uint16_6")
-        client.stream_create("/newton/zzz/rawnotch", "uint16_9")
+        client.stream_create("/newton/zzz/rawnotch2", "uint16_9")
+        client.stream_create("/newton/zzz/rawnotch11", "uint16_9")
 
-        # Verify we got 3 streams
+        # Verify we got 4 streams in the right order
         eq_(client.stream_list(), [ ["/newton/prep", "float32_8"],
                                     ["/newton/raw", "uint16_6"],
-                                    ["/newton/zzz/rawnotch", "uint16_9"]
+                                    ["/newton/zzz/rawnotch2", "uint16_9"],
+                                    ["/newton/zzz/rawnotch11", "uint16_9"]
                                     ])
+
         # Match just one type or one path
         eq_(client.stream_list(layout="uint16_6"),
             [ ["/newton/raw", "uint16_6"] ])
@@ -327,6 +330,10 @@ class TestClient(object):
                      2525.169921875, 8350.83984375, 3724.699951171875,
                      1355.3399658203125, 2039.0))
 
+        # Just get some coverage
+        with assert_raises(ClientError) as e:
+            client.http.post("/stream/remove", { "path": "/none" })
+
         client.close()
 
     def test_client_06_generators(self):
@@ -613,8 +620,12 @@ class TestClient(object):
         with client.stream_insert_context("/empty/test", end = 950):
             pass
 
+        # Equal start and end is OK as long as there's no data
+        with client.stream_insert_context("/empty/test", start=9, end=9):
+            pass
+
         # Try various things that might cause problems
-        with client.stream_insert_context("/empty/test", 1000, 1050):
+        with client.stream_insert_context("/empty/test", 1000, 1050) as ctx:
             ctx.finalize() # inserts [1000, 1050]
             ctx.finalize() # nothing
             ctx.finalize() # nothing

tests/test_cmdline.py

@@ -245,8 +245,10 @@ class TestCmdline(object):
         self.contain("Client version: " + nilmdb.__version__)
         self.contain("Server version: " + test_server.version)
         self.contain("Server database path")
-        self.contain("Server database size")
+        self.contain("Server disk space used by NilmDB")
-        self.contain("Server database free space")
+        self.contain("Server disk space used by other")
+        self.contain("Server disk space reserved")
+        self.contain("Server disk space free")
 
     def test_04_createlist(self):
         # Basic stream tests, like those in test_client.
@@ -601,6 +603,14 @@ class TestCmdline(object):
         self.ok("extract -c /newton/prep --start 2000-01-01 --end 2020-01-01")
         self.match("43200\n")
 
+        # test binary mode
+        self.fail("extract -c -B /newton/prep -s min -e max")
+        self.contain("binary cannot be combined")
+        self.fail("extract -m -B /newton/prep -s min -e max")
+        self.contain("binary cannot be combined")
+        self.ok("extract -B /newton/prep -s min -e max")
+        eq_(len(self.captured), 43200 * (8 + 8*4))
+
         # markup for 3 intervals, plus extra markup lines whenever we had
         # a "restart" from the nilmdb.stream_extract function
         self.ok("extract -m /newton/prep --start 2000-01-01 --end 2020-01-01")

tests/test_numpyclient.py

@@ -28,7 +28,10 @@ def setup_module():
     recursive_unlink(testdb)
 
     # Start web app on a custom port
-    test_db = nilmdb.utils.serializer_proxy(nilmdb.server.NilmDB)(testdb)
+    test_db = nilmdb.utils.serializer_proxy(nilmdb.server.NilmDB)(
+        testdb, bulkdata_args = { "file_size" : 16384,
+                                  "files_per_dir" : 3 } )
+
     test_server = nilmdb.server.Server(test_db, host = "127.0.0.1",
                                        port = 32180, stoppable = False,
                                        fast_shutdown = True,
@@ -179,6 +182,17 @@ class TestNumpyClient(object):
         assert(np.array_equal(a,b))
         assert(np.array_equal(a,c))
 
+        # Make sure none of the files are greater than 16384 bytes as
+        # we configured with the bulkdata_args above.
+        datapath = os.path.join(testdb, "data")
+        for (dirpath, dirnames, filenames) in os.walk(datapath):
+            for f in filenames:
+                fn = os.path.join(dirpath, f)
+                size = os.path.getsize(fn)
+                if size > 16384:
+                    raise AssertionError(sprintf("%s is too big: %d > %d\n",
+                                                 fn, size, 16384))
+
         nilmdb.client.numpyclient.StreamInserterNumpy._max_data = old_max_data
         client.close()
 
@@ -295,8 +309,25 @@ class TestNumpyClient(object):
         with client.stream_insert_numpy_context("/empty/test", end = 950):
             pass
 
+        # Equal start and end is OK as long as there's no data
+        with assert_raises(ClientError) as e:
+            with client.stream_insert_numpy_context("/empty/test",
+                                                    start=9, end=9) as ctx:
+                ctx.insert([[9, 9]])
+                ctx.finalize()
+        in_("have data to send, but invalid start/end times", str(e.exception))
+
+        with client.stream_insert_numpy_context("/empty/test",
+                                                start=9, end=9) as ctx:
+            pass
+
+        # reusing a context object is bad
+        with assert_raises(Exception) as e:
+            ctx.insert([[9, 9]])
+
         # Try various things that might cause problems
-        with client.stream_insert_numpy_context("/empty/test", 1000, 1050):
+        with client.stream_insert_numpy_context("/empty/test",
+                                                1000, 1050) as ctx:
             ctx.finalize() # inserts [1000, 1050]
             ctx.finalize() # nothing
             ctx.finalize() # nothing