diff --git a/compact.py b/compact.py index 2731468..8da27ae 100644 --- a/compact.py +++ b/compact.py @@ -1,243 +1,261 @@ import io import os import psycopg2 import sys from configparser import ConfigParser from pathlib import PosixPath from iterator import ( RevisionEntry, RevisionIterator ) from model import ( DirectoryEntry, FileEntry, TreeEntry, Tree ) from swh.model.identifiers import identifier_to_str from swh.storage.db import Db def config(filename: PosixPath, section: str): # create a parser parser = ConfigParser() # read config file parser.read(filename) # get section, default to postgresql db = {} if parser.has_section(section): params = parser.items(section) for param in params: db[param[0]] = param[1] else: raise Exception('Section {0} not found in the {1} file'.format(section, filename)) return db +def typecast_bytea(value, cur): + if value is not None: + data = psycopg2.BINARY(value, cur) + return data.tobytes() + + +def adapt_conn(conn): + """Makes psycopg2 use 'bytes' to decode bytea instead of + 'memoryview', for this connection.""" + t_bytes = psycopg2.extensions.new_type((17,), "bytea", typecast_bytea) + psycopg2.extensions.register_type(t_bytes, conn) + + t_bytes_array = psycopg2.extensions.new_array_type((1001,), "bytea[]", t_bytes) + psycopg2.extensions.register_type(t_bytes_array, conn) + + def connect(filename: PosixPath, section: str): """ Connect to the PostgreSQL database server """ conn = None try: # read connection parameters params = config(filename, section) # connect to the PostgreSQL server # print('Connecting to the PostgreSQL database...') conn = psycopg2.connect(**params) + adapt_conn(conn) except (Exception, psycopg2.DatabaseError) as error: print(error) return conn def create_tables(conn: psycopg2.extensions.cursor, filename: PosixPath='compact.sql'): with io.open(filename) as file: cur = conn.cursor() cur.execute(file.read()) cur.close() conn.commit() def revision_add( cursor: psycopg2.extensions.cursor, archive: psycopg2.extensions.connection, revision: RevisionEntry, ): # Add current revision to the compact DB and start walking its root directory cursor.execute('INSERT INTO revision VALUES (%s,%s)', (revision.swhid, revision.timestamp)) tree = Tree(archive, revision.directory) walk(cursor, revision, tree.root, tree.root, tree.root.name) def content_find_first( cursor: psycopg2.extensions.cursor, swhid: str ): cursor.execute('SELECT * FROM content WHERE blob=%s ORDER BY date ASC LIMIT 1', (swhid,)) return cursor.fetchone() def content_find_all( cursor: psycopg2.extensions.cursor, swhid: str ): - cursor.execute('''(SELECT blob, rev, date, path FROM content WHERE blob=%s) + cursor.execute('''(SELECT blob, rev, date, path, 1 AS early FROM content WHERE blob=%s) UNION - (SELECT content_in_rev.blob, content_in_rev.rev, revision.date, content_in_rev.path + (SELECT content_in_rev.blob, content_in_rev.rev, revision.date, content_in_rev.path, 2 AS early FROM (SELECT content_in_dir.blob, directory_in_rev.rev, (directory_in_rev.path || '/' || content_in_dir.path)::unix_path AS path FROM content_in_dir JOIN directory_in_rev ON content_in_dir.dir=directory_in_rev.dir WHERE content_in_dir.blob=%s) AS content_in_rev JOIN revision ON revision.id=content_in_rev.rev) - ORDER BY date''', (swhid, swhid)) + ORDER BY date, early''', (swhid, swhid)) yield from cursor.fetchall() def walk( cursor: psycopg2.extensions.cursor, revision: RevisionEntry, directory: DirectoryEntry, relative: DirectoryEntry, prefix: PosixPath, ingraph: bool=True ): # TODO: add logging support! # print("dir: ", identifier_to_str(revision.swhid), revision.timestamp, identifier_to_str(directory.swhid), identifier_to_str(relative.swhid), prefix, ingraph) if ingraph: cursor.execute('SELECT date FROM directory WHERE id=%s', (directory.swhid,)) row = cursor.fetchone() if row is None or row[0] > revision.timestamp: # This directory belongs to the isochrone graph of the revision. # Add directory with the current revision's timestamp as date, and # walk recursively looking for new content. cursor.execute('''INSERT INTO directory VALUES (%s,%s) ON CONFLICT (id) DO UPDATE SET date=%s''', (directory.swhid, revision.timestamp, revision.timestamp)) for child in directory.children: process_child(cursor, revision, child, relative, prefix / child.name) else: # This directory is just beyond the isochrone graph # frontier. Add an entry to the 'directory_in_rev' relation # with the path relative to 'prefix', and continue to walk # recursively looking only for blobs (ie. 'ingraph=False'). cursor.execute('INSERT INTO directory_in_rev VALUES (%s,%s,%s)', (directory.swhid, revision.swhid, bytes(prefix))) for child in directory.children: # From now on path is relative to current directory (ie. relative=directory) process_child(cursor, revision, child, directory, PosixPath('.') / child.name, ingraph=False) else: # This directory is completely outside the isochrone graph (far # from the frontier). We are just looking for blobs here. for child in directory.children: process_child(cursor, revision, child, relative, prefix / child.name, ingraph=False) def process_child( cursor: psycopg2.extensions.cursor, revision: RevisionEntry, entry: TreeEntry, relative: DirectoryEntry, prefix: PosixPath, ingraph: bool=True ): if isinstance(entry, DirectoryEntry): walk(cursor, revision, entry, relative, prefix, ingraph) else: process_file(cursor, revision, relative, entry, prefix) def process_file( cursor: psycopg2.extensions.cursor, revision: RevisionEntry, directory: DirectoryEntry, blob: FileEntry, path: PosixPath ): # TODO: add logging support! # print("blob:", identifier_to_str(revision.swhid), revision.timestamp, identifier_to_str(directory), identifier_to_str(blob), path) cursor.execute('SELECT date FROM content WHERE blob=%s ORDER BY date ASC LIMIT 1', (blob.swhid,)) # cursor.execute('SELECT MIN(date) FROM content WHERE blob=%s', (blob.swhid,)) row = cursor.fetchone() if row is None or row[0] > revision.timestamp: # This is an earlier occurrence of the blob. Add it with the current # revision's timestamp as date. cursor.execute('''INSERT INTO content VALUES (%s,%s,%s,%s)''', # cursor.execute('''INSERT INTO content VALUES (%s,%s,%s,%s) # ON CONFLICT (blob, rev) DO UPDATE # SET date=%s, path=%s''', (blob.swhid, revision.swhid, revision.timestamp, bytes(path))) else: # This blob was seen before but this occurrence is older. Add # an entry to the 'content_in_dir' relation with the path # relative to the parent directory in the isochrone graph # frontier. cursor.execute('''INSERT INTO content_in_dir VALUES (%s,%s,%s) ON CONFLICT DO NOTHING''', (blob.swhid, directory.swhid, bytes(path))) # WARNING: There seem to be duplicated directories within the same # revision. Hence, their blobs may appear many times with the # same directory ID and 'relative' path. That's why we need # the 'ON CONFLICT DO NOTHING' statement. if __name__ == "__main__": if len(sys.argv) != 4: print('usage: compact ') - print(' : bool reconstruct compact model database') - print(' : int number of revision to add') - print(' : int number of blobs to query') + print(' : bool reconstruct compact model database') + print(' : int number of revision to use') + print(' : int number of blobs to query for testing') + exit() reset = sys.argv[1].lower() == 'true' limit = int(sys.argv[2]) count = int(sys.argv[3]) compact = connect('database.conf', 'compact') cursor = compact.cursor() if reset: print(f'Reconstructing compact model database with {limit} revisions') archive = connect('database.conf', 'archive') create_tables(compact) revisions = RevisionIterator(archive, limit=limit) for idx, revision in enumerate(revisions): # TODO: add logging support! print(f'{idx} - id: {identifier_to_str(revision.swhid)} - date: {revision.timestamp} - dir: {identifier_to_str(revision.directory)}') revision_add(cursor, archive, revision) compact.commit() archive.close() print(f'========================================') cursor.execute(f'SELECT DISTINCT blob FROM content LIMIT {count}') for idx, row in enumerate(cursor.fetchall()): swhid = row[0] - print(f'Test blob {idx}: {identifier_to_str(bytes(swhid))}') + print(f'Test blob {idx}: {identifier_to_str(swhid)}') fst = content_find_first(cursor, swhid) - print(f' First occurrence:\n {identifier_to_str(bytes(fst[0]))}, {identifier_to_str(bytes(fst[1]))}, {fst[2]}, {bytes(fst[3]).decode("utf-8")}') + print(f' First occurrence:\n {identifier_to_str(fst[0])}, {identifier_to_str(fst[1])}, {fst[2]}, {fst[3].decode("utf-8")}') print(f' All occurrences:') for row in content_find_all(cursor, swhid): - print(f' {identifier_to_str(bytes(row[0]))}, {identifier_to_str(bytes(row[1]))}, {row[2]}, {bytes(row[3]).decode("utf-8")}') + print(f' {row[4]}, {identifier_to_str(row[0])}, {identifier_to_str(row[1])}, {row[2]}, {row[3].decode("utf-8")}') print(f'========================================') compact.close() diff --git a/iterator.py b/iterator.py index 89a9982..3e9a407 100644 --- a/iterator.py +++ b/iterator.py @@ -1,77 +1,61 @@ import psycopg2 from swh.model.identifiers import identifier_to_str -def typecast_bytea(value, cur): - if value is not None: - data = psycopg2.BINARY(value, cur) - return data.tobytes() - - class RevisionIterator: """Iterator over revisions present in the given database.""" - def adapt_conn(self, conn): - """Makes psycopg2 use 'bytes' to decode bytea instead of - 'memoryview', for this connection.""" - t_bytes = psycopg2.extensions.new_type((17,), "bytea", typecast_bytea) - psycopg2.extensions.register_type(t_bytes, conn) - - t_bytes_array = psycopg2.extensions.new_array_type((1001,), "bytea[]", t_bytes) - psycopg2.extensions.register_type(t_bytes_array, conn) - def __init__(self, conn, limit=None, chunksize=100): - self.adapt_conn(conn) self.cur = conn.cursor() self.chunksize = chunksize self.limit = limit self.records = [] def __del__(self): self.cur.close() def __iter__(self): self.records.clear() if self.limit is None: self.cur.execute('''SELECT id, date, committer_date, directory FROM revision''') else: self.cur.execute('''SELECT id, date, committer_date, directory FROM revision LIMIT %s''', (self.limit,)) for row in self.cur.fetchmany(self.chunksize): record = self.make_record(row) if record is not None: self.records.append(record) return self def __next__(self): if not self.records: self.records.clear() for row in self.cur.fetchmany(self.chunksize): record = self.make_record(row) if record is not None: self.records.append(record) if self.records: revision, *self.records = self.records return revision else: raise StopIteration def make_record(self, row): # Only revision with author or commiter date are considered if row[1] is not None: # If the revision has author date, it takes precedence return RevisionEntry(row[0], row[1], row[3]) elif row[2] is not None: # If not, we use the commiter date return RevisionEntry(row[0], row[2], row[3]) class RevisionEntry: def __init__(self, swhid, timestamp, directory): self.swhid = swhid self.timestamp = timestamp self.directory = directory diff --git a/model.py b/model.py index 27b99c4..ab3bff8 100644 --- a/model.py +++ b/model.py @@ -1,60 +1,61 @@ import operator import psycopg2 from pathlib import PosixPath from typing import List from swh.model.identifiers import DIRECTORY, CONTENT from swh.storage.db import Db CONTENT = "file" DIRECTORY = "dir" OTYPE_IDX = 1 PATH_IDX = 3 SWHID_IDX = 2 class Tree: + def __init__(self, conn: psycopg2.extensions.connection, swhid: str): self.root = DirectoryEntry(swhid, PosixPath('.')) storage = Db(conn) entries = list(map( lambda x: (x[SWHID_IDX], x[PATH_IDX].decode('utf-8'), x[OTYPE_IDX]), storage.directory_walk(swhid) )) entries.sort(key=operator.itemgetter(1)) for entry in entries: self.root.addChild(entry[0], PosixPath(entry[1]), entry[2]) class TreeEntry: def __init__(self, swhid: str, name: PosixPath): self.swhid = swhid self.name = name class DirectoryEntry(TreeEntry): def __init__(self, swhid: str, name: PosixPath): super().__init__(swhid, name) self.children = [] def addChild(self, swhid: str, path: PosixPath, otype: str): if path.parent == PosixPath('.'): if otype == CONTENT: self.children.append(FileEntry(swhid, path.name)) elif otype == DIRECTORY: self.children.append(DirectoryEntry(swhid, path.name)) else: for child in filter(lambda x: isinstance(x, DirectoryEntry), self.children): if path.parts[0] == child.name: child.addChild(swhid, PosixPath(*path.parts[1:]), otype) break class FileEntry(TreeEntry): pass