diff --git a/compact.py b/compact.py index 86922c8..c89c03e 100644 --- a/compact.py +++ b/compact.py @@ -1,268 +1,264 @@ import io 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 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)) + 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, ): # 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, 1 AS early FROM content WHERE 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 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: + for child in iter(directory): process_child(cursor, revision, child, relative, prefix / child.name) else: # This directory is just beyond the isochrone graph # frontier. Check whether it has already been visited before to # avoid recursively walking its children. - cursor.execute('SELECT dir FROM directory_in_rev WHERE dir=%s', - (directory.swhid,)) + cursor.execute('SELECT dir FROM directory_in_rev WHERE dir=%s', (directory.swhid,)) visited = cursor.fetchone() is not None # Add an entry to the 'directory_in_rev' relation that associates # the directory with current revision and computed prefix. cursor.execute('INSERT INTO directory_in_rev VALUES (%s,%s,%s)', (directory.swhid, revision.swhid, bytes(prefix))) if not visited: # The directory hasn't been visited before. Continue to walk # recursively looking only for blobs (ie. 'ingraph=False'). # From now on path is relative to current directory (ie. # relative=directory) - for child in directory.children: - process_child(cursor, revision, child, directory, PosixPath(child.name), ingraph=False) + for child in iter(directory): + process_child(cursor, revision, child, directory, 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: + for child in iter(directory): 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 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(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() diff --git a/model.py b/model.py index 9eac9ec..8f88fc0 100644 --- a/model.py +++ b/model.py @@ -1,59 +1,58 @@ import operator import psycopg2 from pathlib import PosixPath 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]) + self.root = DirectoryEntry(conn, swhid, PosixPath('.')) 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): + def __init__( + self, + conn: psycopg2.extensions.connection, + swhid: str, + name: PosixPath + ): super().__init__(swhid, name) + self.conn = conn 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 + def __iter__(self): + storage = Db(self.conn) + for child in storage.directory_walk_one(self.swhid): + if child[OTYPE_IDX] == CONTENT: + self.children.append(FileEntry( + child[SWHID_IDX], + PosixPath(child[PATH_IDX].decode('utf-8')) + )) + + elif child[OTYPE_IDX] == DIRECTORY: + self.children.append(DirectoryEntry( + self.conn, + child[SWHID_IDX], + PosixPath(child[PATH_IDX].decode('utf-8')) + )) + + return iter(self.children) class FileEntry(TreeEntry): pass