diff --git a/compact.py b/compact.py index 9993ab7..f5726cb 100644 --- a/compact.py +++ b/compact.py @@ -1,355 +1,362 @@ import io import logging import psycopg2 import sys from configparser import ConfigParser from pathlib import PosixPath from iterator import ( RevisionEntry, ArchiveRevisionIterator, FileRevisionIterator ) from model import ( DirectoryEntry, FileEntry, TreeEntry, Tree ) from swh.model.identifiers import identifier_to_str 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(f'Section {section} not found in the {filename} file') 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, ): logging.info(f'Processing revision {identifier_to_str(revision.swhid)} (timestamp: {revision.timestamp})') # Processed content starting from the revision's root directory directory = Tree(archive, revision.directory).root directory_compute_early_timestamp(cursor, revision, directory, directory.name) # Add current revision to the compact DB cursor.execute('INSERT INTO revision VALUES (%s,%s)', (revision.swhid, revision.timestamp)) def content_find_first( cursor: psycopg2.extensions.cursor, swhid: str ): logging.info(f'Retrieving first ocurrence of content {identifier_to_str(swhid)}') cursor.execute('''SELECT blob, rev, date, path FROM content_early_in_rev JOIN revision ON revision.id=content_early_in_rev.rev WHERE content_early_in_rev.blob=%s ORDER BY date ASC LIMIT 1''', (swhid,)) return cursor.fetchone() def content_find_all( cursor: psycopg2.extensions.cursor, swhid: str ): logging.info(f'Retrieving all ocurrences of content {identifier_to_str(swhid)}') cursor.execute('''(SELECT blob, rev, date, path, 1 AS early FROM content_early_in_rev JOIN revision ON revision.id=content_early_in_rev.rev WHERE content_early_in_rev.blob=%s) UNION (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, early''', (swhid, swhid)) yield from cursor.fetchall() def content_get_known_timestamp( cursor: psycopg2.extensions.cursor, blob: FileEntry ): cursor.execute('SELECT date FROM content WHERE id=%s', (blob.swhid,)) row = cursor.fetchone() return row[0] if row is not None else None def content_compute_early_timestamp( cursor: psycopg2.extensions.cursor, revision: RevisionEntry, blob: FileEntry, path: PosixPath ): # This method computes the early timestamp of a blob based on the given # revision and the information in the database from previously visited ones. # It updates the database if the given revision comes out-of-order. timestamp = content_get_known_timestamp(cursor, blob) if timestamp is None: # This blob has never been seen before. Just add it to 'content' table. timestamp = revision.timestamp + logging.info(f'FIRST occurrence of blob {identifier_to_str(blob.swhid)} (timestamp: {timestamp})') cursor.execute('INSERT INTO content VALUES (%s,%s)', (blob.swhid, timestamp)) elif revision.timestamp < timestamp: # This is an out-of-order early occurrence of the blob. Update its # timestamp in 'content' table. timestamp = revision.timestamp + logging.info(f'EARLIER occurrence of blob {identifier_to_str(blob.swhid)} (timestamp: {timestamp})') cursor.execute('UPDATE content SET date=%s WHERE id=%s', (timestamp, blob.swhid)) + logging.info(f'NEW early occurrence of blob {identifier_to_str(blob.swhid)} (path: {path})') cursor.execute('INSERT INTO content_early_in_rev VALUES (%s,%s,%s)', (blob.swhid, revision.swhid, bytes(path))) return timestamp def directory_get_known_timestamp( cursor: psycopg2.extensions.cursor, directory: DirectoryEntry ): cursor.execute('SELECT date FROM directory WHERE id=%s', (directory.swhid,)) row = cursor.fetchone() return row[0] if row is not None else None def directory_compute_early_timestamp( cursor: psycopg2.extensions.cursor, revision: RevisionEntry, directory: DirectoryEntry, path: PosixPath ): # This method computes the early timestamp of a directory based on the # given revision and the information in the database from previously # visited ones. It updates the database if the given revision comes # out-of-order. dir_timestamp = directory_get_known_timestamp(cursor, directory) if dir_timestamp is not None: # Current directory has already been seen in the isochrone frontier of # an already processed revision. if revision.timestamp < dir_timestamp: # Current revision is out-of-order. All the content of current # directory should be processed again. Removed entry from # 'directory' and try again. + logging.info(f'OUT-OF-ORDER occurrence of directory {identifier_to_str(directory.swhid)} in the isochrone frontier (old timestamp: {dir_timestamp})') cursor.execute('DELETE FROM directory WHERE id=%s', (directory.swhid,)) return directory_compute_early_timestamp( cursor, revision, directory, path) else: # Current directory has already been seen in the isochrone frontier. # Just add an entry to the 'directory_in_rev' relation that # associates the directory with current revision and computed path. + logging.info(f'FURTHER occurrence of directory {identifier_to_str(directory.swhid)} in the isochrone frontier (path: {path})') cursor.execute('INSERT INTO directory_in_rev VALUES (%s,%s,%s)', (directory.swhid, revision.swhid, bytes(path))) return dir_timestamp else: # Current directory has never been seen before in the isochrone # frontier of a revision. Compute early timestamp for all its childen. children_timestamps = [] for child in iter(directory): if isinstance(child, FileEntry): # Compute early timestamp of current blob. children_timestamps.append( content_compute_early_timestamp( cursor, revision, child, path / child.name) ) else: # Recursively compute the early timestamp. child_timestamp = directory_compute_early_timestamp( cursor, revision, child, path / child.name) # Ignore any sub-tree with empty directories on the leaves. if child_timestamp is not None: children_timestamps.append(child_timestamp) if not children_timestamps: # Current directory does not recursively contain any blob. return None else: dir_timestamp = max(children_timestamps) if revision.timestamp < dir_timestamp: # Current revision is out-of-order. This should not happen # early timestamps for children in this branch of the algorithm # are computed taking current revision into account. - logging.warning("UNEXPECTED SITUATION WITH OUT-OF-ORDER REVISION") + logging.warning(f'UNEXPECTED out-of-order occurrence of directory {identifier_to_str(directory.swhid)} (current timestamp: {revision.timestamp} / directory timestamp: {dir_timestamp})') return revision.timestamp else: # This is the first time that current directory is seen in the # isochrone frontier. Add current directory to 'directory' with # the computed timestamp. + logging.info(f'FIRST occurrence of directory {identifier_to_str(directory.swhid)} in the isochrone frontier (early timestamp: {dir_timestamp} / path: {path})') cursor.execute('INSERT INTO directory VALUES (%s,%s)', (directory.swhid, dir_timestamp)) # Add an entry to the 'directory_in_rev' relation that # associates the directory with current revision and computed # path. cursor.execute('INSERT INTO directory_in_rev VALUES (%s,%s,%s)', (directory.swhid, revision.swhid, bytes(path))) # Recursively find all content within current directory and # add them to 'content_in_dir' with their path relative to # current directory. process_content_in_dir( cursor, directory, directory.swhid, PosixPath('.')) return dir_timestamp def process_content_in_dir( cursor: psycopg2.extensions.cursor, directory: DirectoryEntry, relative: str, prefix: PosixPath ): for child in iter(directory): if isinstance(child, FileEntry): # Add an entry to 'content_in_dir' in dir for the current blob. + logging.info(f'NEW occurrence of content {identifier_to_str(child.swhid)} in directory {identifier_to_str(relative)} (path: {prefix / child.name})') cursor.execute('INSERT INTO content_in_dir VALUES (%s,%s,%s)', (child.swhid, relative, bytes(prefix / child.name))) else: # Recursively walk the child directory. process_content_in_dir(cursor, child, relative, prefix / child.name) if __name__ == "__main__": logging.basicConfig(level=logging.DEBUG) if len(sys.argv) % 2 != 0: print('usage: compact [options] count') print(' -a database database name to retrieve directories/content information') print(' -d database database name to retrieve revisions') print(' -f filename local CSV file to retrieve revisions') print(' -l limit max number of revisions to use') print(' count number of random blobs to query for testing') exit() reset = False limit = None count = int(sys.argv[-1]) archname = None dataname = None filename = None for idx in range(len(sys.argv)): reset = reset or (sys.argv[idx] in ['-d', '-f']) if sys.argv[idx] == '-a': archname = sys.argv[idx+1] if sys.argv[idx] == '-d': dataname = sys.argv[idx+1] if sys.argv[idx] == '-f': filename = sys.argv[idx+1] if sys.argv[idx] == '-l': limit = int(sys.argv[idx+1]) if (dataname is not None or filename is not None) and archname is None: print('Error: -a option is compulsatory when -d or -f options are set') exit() compact = connect('database.conf', 'compact') cursor = compact.cursor() if reset: create_tables(compact) if dataname is not None: print(f'Reconstructing compact model from {dataname} database (limit={limit})') database = connect('database.conf', dataname) revisions = ArchiveRevisionIterator(database, limit=limit) else: print(f'Reconstructing compact model from {filename} CSV file (limit={limit})') revisions = FileRevisionIterator(filename, limit=limit) archive = connect('database.conf', archname) for revision in revisions: revision_add(cursor, archive, revision) compact.commit() archive.close() if dataname is not None: database.close() print(f'========================================') cursor.execute(f'SELECT DISTINCT id FROM content LIMIT {count}') for idx, row in enumerate(cursor.fetchall()): swhid = row[0] print(f'Test blob {idx}: {identifier_to_str(swhid)}') fst = content_find_first(cursor, swhid) 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' {row[4]}, {identifier_to_str(row[0])}, {identifier_to_str(row[1])}, {row[2]}, {row[3].decode("utf-8")}') print(f'========================================') compact.close()