diff --git a/swh/graph/cli.py b/swh/graph/cli.py index 4f654df..cc3e447 100644 --- a/swh/graph/cli.py +++ b/swh/graph/cli.py @@ -1,115 +1,115 @@ # Copyright (C) 2019 The Software Heritage developers # See the AUTHORS file at the top-level directory of this distribution # License: GNU General Public License version 3, or any later version # See top-level LICENSE file for more information import click import sys from swh.core.cli import CONTEXT_SETTINGS, AliasedGroup from swh.graph import client from swh.graph.pid import PidToIntMap, IntToPidMap, PID_BIN_SIZE @click.group(name='graph', context_settings=CONTEXT_SETTINGS, cls=AliasedGroup) @click.pass_context def cli(ctx): """Software Heritage graph tools.""" ctx.ensure_object(dict) @cli.command('api-client') @click.option('--host', default='localhost', help='Graph server host') @click.option('--port', default='5009', help='Graph server port') @click.pass_context def api_client(ctx, host, port): """Client for the Software Heritage Graph REST service """ url = 'http://{}:{}'.format(host, port) app = client.RemoteGraphClient(url) # TODO: run web app print(app.stats()) @cli.group('map') @click.pass_context def map(ctx): """Manage swh-graph on-disk maps""" pass def dump_pid2int(filename): for (pid, int) in PidToIntMap(filename): print('{}\t{}'.format(pid, int)) def dump_int2pid(filename): - for (int, pid) in enumerate(IntToPidMap(filename)): + for (int, pid) in IntToPidMap(filename): print('{}\t{}'.format(int, pid)) def restore_pid2int(filename): """read a textual PID->int map from stdin and write its binary version to filename """ with open(filename, 'wb') as dst: for line in sys.stdin: (str_pid, str_int) = line.split() PidToIntMap.write_record(dst, str_pid, int(str_int)) def restore_int2pid(filename): """read a textual int->PID map from stdin and write its binary version to filename """ with open(filename, 'wb') as dst: for line in sys.stdin: (str_int, str_pid) = line.split() dst.seek(int(str_int) * PID_BIN_SIZE) IntToPidMap.write_record(dst, str_pid) @map.command('dump') @click.option('--type', '-t', 'map_type', required=True, type=click.Choice(['pid2int', 'int2pid']), help='type of map to dump') @click.argument('filename', required=True, type=click.Path(exists=True)) @click.pass_context def dump_map(ctx, map_type, filename): """dump a binary PID<->int map to textual format""" if map_type == 'pid2int': dump_pid2int(filename) elif map_type == 'int2pid': dump_int2pid(filename) else: raise ValueError('invalid map type: ' + map_type) pass @map.command('restore') @click.option('--type', '-t', 'map_type', required=True, type=click.Choice(['pid2int', 'int2pid']), help='type of map to dump') @click.argument('filename', required=True, type=click.Path()) @click.pass_context def restore_map(ctx, map_type, filename): """restore a binary PID<->int map from textual format""" if map_type == 'pid2int': restore_pid2int(filename) elif map_type == 'int2pid': restore_int2pid(filename) else: raise ValueError('invalid map type: ' + map_type) def main(): return cli(auto_envvar_prefix='SWH_GRAPH') if __name__ == '__main__': main() diff --git a/swh/graph/pid.py b/swh/graph/pid.py index 14c8c73..eb44690 100644 --- a/swh/graph/pid.py +++ b/swh/graph/pid.py @@ -1,296 +1,364 @@ # Copyright (C) 2019 The Software Heritage developers # See the AUTHORS file at the top-level directory of this distribution # License: GNU General Public License version 3, or any later version # See top-level LICENSE file for more information import mmap import os import struct -from collections.abc import Mapping, Sequence +from collections.abc import MutableMapping from enum import Enum +from mmap import MAP_SHARED, MAP_PRIVATE from swh.model.identifiers import PersistentId, parse_persistent_identifier PID_BIN_FMT = 'BB20s' # 2 unsigned chars + 20 bytes INT_BIN_FMT = '>q' # big endian, 8-byte integer PID_BIN_SIZE = 22 # in bytes INT_BIN_SIZE = 8 # in bytes class PidType(Enum): """types of existing PIDs, used to serialize PID type as a (char) integer note that the order does matter also for driving the binary search in PID-indexed maps """ content = 1 directory = 2 origin = 3 release = 4 revision = 5 snapshot = 6 def str_to_bytes(pid): """Convert a PID to a byte sequence The binary format used to represent PIDs as byte sequences is as follows: - 1 byte for the namespace version represented as a C `unsigned char` - 1 byte for the object type, as the int value of :class:`PidType` enums, represented as a C `unsigned char` - 20 bytes for the SHA1 digest as a byte sequence Args: pid (str): persistent identifier Returns: bytes (bytes): byte sequence representation of pid """ pid = parse_persistent_identifier(pid) return struct.pack(PID_BIN_FMT, pid.scheme_version, PidType[pid.object_type].value, bytes.fromhex(pid.object_id)) def bytes_to_str(bytes): """Inverse function of :func:`str_to_bytes` See :func:`str_to_bytes` for a description of the binary PID format. Args: bytes (bytes): byte sequence representation of pid Returns: pid (str): persistent identifier """ (version, type, bin_digest) = struct.unpack(PID_BIN_FMT, bytes) pid = PersistentId(object_type=PidType(type).name, object_id=bin_digest) return str(pid) class _OnDiskMap(): """mmap-ed on-disk sequence of fixed size records """ - def __init__(self, record_size, fname): + def __init__(self, record_size, fname, mode='rb', length=None): """open an existing on-disk map Args: record_size (int): size of each record in bytes fname (str): path to the on-disk map + mode (str): file open mode, usually either 'rb' for read-only maps, + 'wb' for creating new maps, or 'rb+' for updating existing ones + (default: 'rb') + length (int): map size in number of logical records; used to + initialize writable maps at creation time. Must be given when + mode is 'wb' and the map doesn't exist on disk; ignored + otherwise """ + if mode not in ['rb', 'wb', 'rb+']: + raise ValueError('invalid file open mode: ' + mode) + new_map = (mode == 'wb') + writable_map = mode in ['wb', 'rb+'] + self.record_size = record_size + self.f = open(fname, mode) + if new_map: + if length is None: + raise ValueError('missing length when creating new map') + self.f.truncate(length * self.record_size) + self.size = os.path.getsize(fname) (self.length, remainder) = divmod(self.size, record_size) if remainder: raise ValueError( 'map size {} is not a multiple of the record size {}'.format( self.size, record_size)) - self.f = open(fname, 'rb') - self.mm = mmap.mmap(self.f.fileno(), self.size, mmap.MAP_PRIVATE) + self.mm = mmap.mmap(self.f.fileno(), self.size, + MAP_SHARED if writable_map else MAP_PRIVATE) def close(self): """close the map shuts down both the mmap and the underlying file descriptor """ if not self.mm.closed: self.mm.close() if not self.f.closed: self.f.close() + def __len__(self): + return self.length + + def __delitem__(self, pos): + raise NotImplementedError('cannot delete records from fixed-size map') -class PidToIntMap(_OnDiskMap, Mapping): + +class PidToIntMap(_OnDiskMap, MutableMapping): """memory mapped map from PID (:ref:`persistent-identifiers`) to a continuous range 0..N of (8-byte long) integers This is the converse mapping of :class:`IntToPidMap`. The on-disk serialization format is a sequence of fixed length (30 bytes) records with the following fields: - PID (22 bytes): binary PID representation as per :func:`str_to_bytes` - long (8 bytes): big endian long integer The records are sorted lexicographically by PID type and checksum, where type is the integer value of :class:`PidType`. PID lookup in the map is performed via binary search. Hence a huge map with, say, 11 B entries, will require ~30 disk seeks. + Note that, due to fixed size + ordering, it is not possible to create these + maps by random writing. Hence, __setitem__ can be used only to *update* the + value associated to an existing key, rather than to add a missing item. To + create an entire map from scratch, you should do so *sequentially*, using + static method :meth:`write_record` (or, at your own risk, by hand via the + mmap :attr:`mm`). + """ # record binary format: PID + a big endian 8-byte big endian integer RECORD_BIN_FMT = '>' + PID_BIN_FMT + 'q' RECORD_SIZE = PID_BIN_SIZE + INT_BIN_SIZE - def __init__(self, fname): + def __init__(self, fname, mode='rb', length=None): """open an existing on-disk map Args: fname (str): path to the on-disk map + mode (str): file open mode, usually either 'rb' for read-only maps, + 'wb' for creating new maps, or 'rb+' for updating existing ones + (default: 'rb') + length (int): map size in number of logical records; used to + initialize read-write maps at creation time. Must be given when + mode is 'wb'; ignored otherwise """ - super().__init__(self.RECORD_SIZE, fname) + super().__init__(self.RECORD_SIZE, fname, mode=mode, length=length) def _get_bin_record(self, pos): """seek and return the (binary) record at a given (logical) position see :func:`_get_record` for an equivalent function with additional deserialization Args: pos: 0-based record number Returns: tuple: a pair `(pid, int)`, where pid and int are bytes """ rec_pos = pos * self.RECORD_SIZE int_pos = rec_pos + PID_BIN_SIZE return (self.mm[rec_pos:int_pos], self.mm[int_pos:int_pos+INT_BIN_SIZE]) def _get_record(self, pos): """seek and return the record at a given (logical) position moral equivalent of :func:`_get_bin_record`, with additional deserialization to non-bytes types Args: pos: 0-based record number Returns: tuple: a pair `(pid, int)`, where pid is a string-based PID and int an integer """ (pid_bytes, int_bytes) = self._get_bin_record(pos) return (bytes_to_str(pid_bytes), struct.unpack(INT_BIN_FMT, int_bytes)[0]) @classmethod def write_record(cls, f, pid, int): """write a logical record to a file-like object Args: f: file-like object to write the record to pid (str): textual PID int (int): PID integer identifier """ f.write(str_to_bytes(pid)) f.write(struct.pack(INT_BIN_FMT, int)) - def __getitem__(self, pid_str): - """lookup the integer identifier of a PID + def _find(self, pid_str): + """lookup the integer identifier of a pid and its position Args: - pid (str): the PID as a string + pid (str): the pid as a string Returns: - int: the integer identifier of pid + tuple: a pair `(pid, pos)` with pid integer identifier and its + logical record position in the map """ if not isinstance(pid_str, str): raise TypeError('PID must be a str, not ' + type(pid_str)) try: target = str_to_bytes(pid_str) # desired PID as bytes except ValueError: raise ValueError('invalid PID: "{}"'.format(pid_str)) min = 0 max = self.length - 1 while (min <= max): mid = (min + max) // 2 (pid, int) = self._get_bin_record(mid) if pid < target: min = mid + 1 elif pid > target: max = mid - 1 else: # pid == target - return struct.unpack(INT_BIN_FMT, int)[0] + return (struct.unpack(INT_BIN_FMT, int)[0], mid) raise KeyError(pid_str) + def __getitem__(self, pid_str): + """lookup the integer identifier of a PID + + Args: + pid (str): the PID as a string + + Returns: + int: the integer identifier of pid + + """ + return self._find(pid_str)[0] # return element, ignore position + + def __setitem__(self, pid_str, int): + (_pid, pos) = self._find(pid_str) # might raise KeyError and that's OK + + rec_pos = pos * self.RECORD_SIZE + int_pos = rec_pos + PID_BIN_SIZE + self.mm[rec_pos:int_pos] = str_to_bytes(pid_str) + self.mm[int_pos:int_pos+INT_BIN_SIZE] = struct.pack(INT_BIN_FMT, int) + def __iter__(self): for pos in range(self.length): yield self._get_record(pos) - def __len__(self): - return self.length - -class IntToPidMap(_OnDiskMap, Sequence): +class IntToPidMap(_OnDiskMap, MutableMapping): """memory mapped map from a continuous range of 0..N (8-byte long) integers to PIDs (:ref:`persistent-identifiers`) This is the converse mapping of :class:`PidToIntMap`. The on-disk serialization format is a sequence of fixed length (22 bytes), where each record is the binary representation of PID as per :func:`str_to_bytes`. The records are sorted by long integer, so that integer lookup is possible via fixed-offset seek. """ RECORD_BIN_FMT = PID_BIN_FMT RECORD_SIZE = PID_BIN_SIZE - def __init__(self, fname): + def __init__(self, fname, mode='rb', length=None): """open an existing on-disk map Args: fname (str): path to the on-disk map + mode (str): file open mode, usually either 'rb' for read-only maps, + 'wb' for creating new maps, or 'rb+' for updating existing ones + (default: 'rb') + size (int): map size in number of logical records; used to + initialize read-write maps at creation time. Must be given when + mode is 'wb'; ignored otherwise """ - super().__init__(self.RECORD_SIZE, fname) + + super().__init__(self.RECORD_SIZE, fname, mode=mode, length=length) def _get_bin_record(self, pos): """seek and return the (binary) PID at a given (logical) position Args: pos: 0-based record number Returns: bytes: PID as a byte sequence """ rec_pos = pos * self.RECORD_SIZE return self.mm[rec_pos:rec_pos+self.RECORD_SIZE] @classmethod def write_record(cls, f, pid): """write a PID to a file-like object Args: f: file-like object to write the record to pid (str): textual PID """ f.write(str_to_bytes(pid)) def __getitem__(self, pos): orig_pos = pos if pos < 0: pos = len(self) + pos if not (0 <= pos < len(self)): raise IndexError(orig_pos) return bytes_to_str(self._get_bin_record(pos)) - def __len__(self): - return self.length + def __setitem__(self, pos, pid): + rec_pos = pos * self.RECORD_SIZE + self.mm[rec_pos:rec_pos+self.RECORD_SIZE] = str_to_bytes(pid) + + def __iter__(self): + for pos in range(self.length): + yield (pos, self[pos]) diff --git a/swh/graph/tests/test_pid.py b/swh/graph/tests/test_pid.py index 83a8000..ba1f583 100644 --- a/swh/graph/tests/test_pid.py +++ b/swh/graph/tests/test_pid.py @@ -1,159 +1,183 @@ # Copyright (C) 2019 The Software Heritage developers # See the AUTHORS file at the top-level directory of this distribution # License: GNU General Public License version 3, or any later version # See top-level LICENSE file for more information import os import shutil import tempfile import unittest +from itertools import islice + from swh.graph.pid import str_to_bytes, bytes_to_str from swh.graph.pid import PidToIntMap, IntToPidMap class TestPidSerialization(unittest.TestCase): pairs = [ ('swh:1:cnt:94a9ed024d3859793618152ea559a168bbcbb5e2', bytes.fromhex('01' + '01' + '94a9ed024d3859793618152ea559a168bbcbb5e2')), ('swh:1:dir:d198bc9d7a6bcf6db04f476d29314f157507d505', bytes.fromhex('01' + '02' + 'd198bc9d7a6bcf6db04f476d29314f157507d505')), ('swh:1:ori:b63a575fe3faab7692c9f38fb09d4bb45651bb0f', bytes.fromhex('01' + '03' + 'b63a575fe3faab7692c9f38fb09d4bb45651bb0f')), ('swh:1:rel:22ece559cc7cc2364edc5e5593d63ae8bd229f9f', bytes.fromhex('01' + '04' + '22ece559cc7cc2364edc5e5593d63ae8bd229f9f')), ('swh:1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d', bytes.fromhex('01' + '05' + '309cf2674ee7a0749978cf8265ab91a60aea0f7d')), ('swh:1:snp:c7c108084bc0bf3d81436bf980b46e98bd338453', bytes.fromhex('01' + '06' + 'c7c108084bc0bf3d81436bf980b46e98bd338453')), ] def test_str_to_bytes(self): for (pid_str, pid_bytes) in self.pairs: self.assertEqual(str_to_bytes(pid_str), pid_bytes) def test_bytes_to_str(self): for (pid_str, pid_bytes) in self.pairs: self.assertEqual(bytes_to_str(pid_bytes), pid_str) def test_round_trip(self): for (pid_str, pid_bytes) in self.pairs: self.assertEqual(pid_str, bytes_to_str(str_to_bytes(pid_str))) self.assertEqual(pid_bytes, str_to_bytes(bytes_to_str(pid_bytes))) -def gen_records(types=['ori', 'snp', 'rev', 'rel', 'dir', 'cnt'], +def gen_records(types=['cnt', 'dir', 'rel', 'rev', 'ori', 'snp'], length=10000): """generate sequential PID/int records, suitable for filling int<->pid maps for testing swh-graph on-disk binary databases Args: types (list): list of PID types to be generated, specified as the corresponding 3-letter component in PIDs length (int): number of PIDs to generate *per type* Yields: pairs (pid, int) where pid is a textual PID and int its sequential integer identifier """ pos = 0 for t in sorted(types): for i in range(0, length): seq = format(pos, 'x') # current position as hex string pid = 'swh:1:{}:{}{}'.format(t, '0' * (40 - len(seq)), seq) yield (pid, pos) pos += 1 # pairs PID/position in the sequence generated by :func:`gen_records` above MAP_PAIRS = [ ('swh:1:cnt:0000000000000000000000000000000000000000', 0), ('swh:1:cnt:000000000000000000000000000000000000002a', 42), ('swh:1:dir:0000000000000000000000000000000000002afc', 11004), ('swh:1:ori:00000000000000000000000000000000000056ce', 22222), ('swh:1:rel:0000000000000000000000000000000000008235', 33333), ('swh:1:rev:000000000000000000000000000000000000ad9c', 44444), ('swh:1:snp:000000000000000000000000000000000000ea5f', 59999), ] class TestPidToIntMap(unittest.TestCase): @classmethod def setUpClass(cls): """create reasonably sized (~2 MB) PID->int map to test on-disk DB """ cls.tmpdir = tempfile.mkdtemp(prefix='swh.graph.test.') cls.fname = os.path.join(cls.tmpdir, 'pid2int.bin') with open(cls.fname, 'wb') as f: for (pid, i) in gen_records(length=10000): PidToIntMap.write_record(f, pid, i) @classmethod def tearDownClass(cls): shutil.rmtree(cls.tmpdir) def setUp(self): self.map = PidToIntMap(self.fname) def tearDown(self): self.map.close() def test_lookup(self): for (pid, pos) in MAP_PAIRS: self.assertEqual(self.map[pid], pos) def test_missing(self): with self.assertRaises(KeyError): self.map['swh:1:ori:0101010100000000000000000000000000000000'], with self.assertRaises(KeyError): self.map['swh:1:cnt:0101010100000000000000000000000000000000'], def test_type_error(self): with self.assertRaises(TypeError): self.map[42] with self.assertRaises(TypeError): self.map[1.2] + def test_update(self): + fname2 = self.fname + '.update' + shutil.copy(self.fname, fname2) # fresh map copy + map2 = PidToIntMap(fname2, mode='rb+') + for (pid, int) in islice(map2, 11): # update the first N items + new_int = int + 42 + map2[pid] = new_int + self.assertEqual(map2[pid], new_int) # check updated value + + os.unlink(fname2) # tmpdir will be cleaned even if we don't reach this + class TestIntToPidMap(unittest.TestCase): @classmethod def setUpClass(cls): """create reasonably sized (~1 MB) int->PID map to test on-disk DB """ cls.tmpdir = tempfile.mkdtemp(prefix='swh.graph.test.') cls.fname = os.path.join(cls.tmpdir, 'int2pid.bin') with open(cls.fname, 'wb') as f: for (pid, _i) in gen_records(length=10000): IntToPidMap.write_record(f, pid) @classmethod def tearDownClass(cls): shutil.rmtree(cls.tmpdir) def setUp(self): self.map = IntToPidMap(self.fname) def tearDown(self): self.map.close() def test_lookup(self): for (pid, pos) in MAP_PAIRS: self.assertEqual(self.map[pos], pid) def test_out_of_bounds(self): with self.assertRaises(IndexError): self.map[1000000] with self.assertRaises(IndexError): self.map[-1000000] + + def test_update(self): + fname2 = self.fname + '.update' + shutil.copy(self.fname, fname2) # fresh map copy + map2 = IntToPidMap(fname2, mode='rb+') + for (int, pid) in islice(map2, 11): # update the first N items + new_pid = pid.replace(':0', ':f') # mangle first hex digit + map2[int] = new_pid + self.assertEqual(map2[int], new_pid) # check updated value + + os.unlink(fname2) # tmpdir will be cleaned even if we don't reach this