diff --git a/.gitignore b/.gitignore index abfcd17..4e58291 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,5 @@ -*.txt *.csv +*.log +*.txt __pycache__ PKG-INFO diff --git a/compact.py b/compact.py index 18e0d83..d69cbba 100644 --- a/compact.py +++ b/compact.py @@ -1,307 +1,334 @@ import click import io import logging import psycopg2 import sys +import time import utils from datetime import datetime 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 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 revision_process_directory(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 occurrence 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, rev, path ASC LIMIT 1''', (swhid,)) return cursor.fetchone() def content_find_all( cursor: psycopg2.extensions.cursor, swhid: str ): logging.info(f'Retrieving all occurrences 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) UNION (SELECT content_in_rev.blob, content_in_rev.rev, revision.date, content_in_rev.path FROM (SELECT content_in_dir.blob, directory_in_rev.rev, CASE directory_in_rev.path WHEN '.' THEN content_in_dir.path ELSE (directory_in_rev.path || '/' || content_in_dir.path)::unix_path END 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, rev, path''', (swhid, swhid)) yield from cursor.fetchall() ################################################################################ ################################################################################ ################################################################################ def normalize(path: PosixPath) -> PosixPath: spath = str(path) if spath.startswith('./'): return PosixPath(spath[2:]) return path def content_get_early_timestamp( cursor: psycopg2.extensions.cursor, - blob: FileEntry + blob: FileEntry, + depth: int ): + logging.debug(f'{" "*depth}Getting content {identifier_to_str(blob.swhid)} early timestamp') + start = time.perf_counter_ns() cursor.execute('SELECT date FROM content WHERE id=%s', (blob.swhid,)) row = cursor.fetchone() + stop = time.perf_counter_ns() + logging.debug(f'{" "*depth} Time elapsed: {stop-start}ns') return row[0] if row is not None else None def content_set_early_timestamp( cursor: psycopg2.extensions.cursor, blob: FileEntry, timestamp: datetime, depth: int ): logging.debug(f'{" "*depth}EARLY occurrence of blob {identifier_to_str(blob.swhid)} (timestamp: {timestamp})') + start = time.perf_counter_ns() cursor.execute('''INSERT INTO content VALUES (%s,%s) ON CONFLICT (id) DO UPDATE SET date=%s''', (blob.swhid, timestamp, timestamp)) + stop = time.perf_counter_ns() + logging.debug(f'{" "*depth} Time elapsed: {stop-start}ns') def content_add_to_directory( cursor: psycopg2.extensions.cursor, directory: DirectoryEntry, blob: FileEntry, prefix: PosixPath, depth: int ): logging.debug(f'{" "*depth}NEW occurrence of content {identifier_to_str(blob.swhid)} in directory {identifier_to_str(directory.swhid)} (path: {prefix / blob.name})') + start = time.perf_counter_ns() cursor.execute('INSERT INTO content_in_dir VALUES (%s,%s,%s)', (blob.swhid, directory.swhid, bytes(normalize(prefix / blob.name)))) + stop = time.perf_counter_ns() + logging.debug(f'{" "*depth} Time elapsed: {stop-start}ns') def content_add_to_revision( cursor: psycopg2.extensions.cursor, revision: RevisionEntry, blob: FileEntry, prefix: PosixPath, depth: int ): logging.debug(f'{" "*depth}EARLY occurrence of blob {identifier_to_str(blob.swhid)} in revision {identifier_to_str(revision.swhid)} (path: {prefix / blob.name})') + start = time.perf_counter_ns() cursor.execute('INSERT INTO content_early_in_rev VALUES (%s,%s,%s)', (blob.swhid, revision.swhid, bytes(normalize(prefix / blob.name)))) + stop = time.perf_counter_ns() + logging.debug(f'{" "*depth} Time elapsed: {stop-start}ns') def directory_get_early_timestamp( cursor: psycopg2.extensions.cursor, - directory: DirectoryEntry + directory: DirectoryEntry, + depth: int ): + logging.debug(f'{" "*depth}Getting directory {identifier_to_str(directory.swhid)} early timestamp') + start = time.perf_counter_ns() cursor.execute('SELECT date FROM directory WHERE id=%s', (directory.swhid,)) row = cursor.fetchone() + stop = time.perf_counter_ns() + logging.debug(f'{" "*depth} Time elapsed: {stop-start}ns') return row[0] if row is not None else None def directory_set_early_timestamp( cursor: psycopg2.extensions.cursor, directory: DirectoryEntry, timestamp: datetime, depth: int ): logging.debug(f'{" "*depth}EARLY occurrence of directory {identifier_to_str(directory.swhid)} on the ISOCHRONE FRONTIER (timestamp: {timestamp})') + start = time.perf_counter_ns() cursor.execute('''INSERT INTO directory VALUES (%s,%s) ON CONFLICT (id) DO UPDATE SET date=%s''', (directory.swhid, timestamp, timestamp)) + stop = time.perf_counter_ns() + logging.debug(f'{" "*depth} Time elapsed: {stop-start}ns') def directory_add_to_revision( cursor: psycopg2.extensions.cursor, revision: RevisionEntry, directory: DirectoryEntry, path: PosixPath, depth: int ): logging.debug(f'{" "*depth}NEW occurrence of directory {identifier_to_str(directory.swhid)} on the ISOCHRONE FRONTIER of revision {identifier_to_str(revision.swhid)} (path: {path})') + start = time.perf_counter_ns() cursor.execute('INSERT INTO directory_in_rev VALUES (%s,%s,%s)', (directory.swhid, revision.swhid, bytes(normalize(path)))) + stop = time.perf_counter_ns() + logging.debug(f'{" "*depth} Time elapsed: {stop-start}ns') def directory_process_content( cursor: psycopg2.extensions.cursor, directory: DirectoryEntry, relative: DirectoryEntry, prefix: PosixPath, depth: int ): for child in iter(directory): if isinstance(child, FileEntry): # Add content to the relative directory with the computed prefix. content_add_to_directory(cursor, relative, child, prefix, depth) - else: # Recursively walk the child directory. directory_process_content(cursor, child, relative, prefix / child.name, depth) +def revision_process_content( + cursor: psycopg2.extensions.cursor, + revision: RevisionEntry, + directory: DirectoryEntry, + path: PosixPath, + depth: int +): + for child in iter(directory): + if isinstance(child, FileEntry): + timestamp = content_get_early_timestamp(cursor, child, depth) + if timestamp is None or revision.timestamp < timestamp: + content_set_early_timestamp(cursor, child, revision.timestamp, depth) + content_add_to_revision(cursor, revision, child, path, depth) + else: + revision_process_directory(cursor, revision, child, path / child.name, depth + 1) + + def revision_process_directory( cursor: psycopg2.extensions.cursor, revision: RevisionEntry, directory: DirectoryEntry, path: PosixPath, depth: int=0 ): - timestamp = directory_get_early_timestamp(cursor, directory) + timestamp = directory_get_early_timestamp(cursor, directory, depth) if timestamp is None: # The directory has never been seen on the isochrone graph of a # revision. Its children should be checked. timestamps = [] for child in iter(directory): if isinstance(child, FileEntry): - timestamps.append(content_get_early_timestamp(cursor, child)) + timestamps.append(content_get_early_timestamp(cursor, child, depth)) else: - timestamps.append(directory_get_early_timestamp(cursor, child)) + timestamps.append(directory_get_early_timestamp(cursor, child, depth)) if timestamps != [] and None not in timestamps and max(timestamps) <= revision.timestamp: # The directory belongs to the isochrone frontier of the current # revision, and this is the first time it appears as such. directory_set_early_timestamp(cursor, directory, max(timestamps), depth) directory_add_to_revision(cursor, revision, directory, path, depth) directory_process_content(cursor, directory, directory, PosixPath('.'), depth) - else: # The directory is not on the isochrone frontier of the current # revision. Its child nodes should be analyzed. - for child in iter(directory): - if isinstance(child, FileEntry): - ts = content_get_early_timestamp(cursor, child) - if ts is None or ts <= revision.timestamp: - content_set_early_timestamp(cursor, child, revision.timestamp, depth) - content_add_to_revision(cursor, revision, child, path, depth) - - else: - revision_process_directory(cursor, revision, child, path / child.name, depth=depth+1) + revision_process_content(cursor, revision, directory, path, depth) elif revision.timestamp < timestamp: # The directory has already been seen on the isochrone frontier of a # revision, but current revision is earlier. Its children should be # updated. - for child in iter(directory): - if isinstance(child, FileEntry): - ts = content_get_early_timestamp(cursor, child) - if ts is None or ts <= revision.timestamp: - content_set_early_timestamp(cursor, child, revision.timestamp, depth) - content_add_to_revision(cursor, revision, child, path, depth) - - else: - revision_process_directory(cursor, revision, child, path / child.name, depth=depth+1) + revision_process_content(cursor, revision, directory, path, depth) + directory_set_early_timestamp(cursor, directory, revision.timestamp, depth) else: # The directory has already been seen on the isochrone frontier of an # earlier revision. Just add it to the current revision. directory_add_to_revision(cursor, revision, directory, path, depth) ################################################################################ ################################################################################ ################################################################################ @click.command() @click.argument('count', type=int) @click.option('-c', '--compact', nargs=2, required=True) @click.option('-a', '--archive', nargs=2) @click.option('-d', '--database', nargs=2) @click.option('-f', '--filename') @click.option('-l', '--limit', type=int) def cli(count, compact, archive, database, filename, limit): """Compact model utility.""" logging.basicConfig(level=logging.INFO) + # logging.basicConfig(filename='compact.log', level=logging.DEBUG) click.echo(f'{count} {compact} {archive} {database} {filename} {limit}') if not database: database = None reset = database is not None or filename is not None if reset and archive is None: logging.error('Error: -a option is compulsatory when -d or -f options are set') exit() comp_conn = utils.connect(compact[0], compact[1]) cursor = comp_conn.cursor() if reset: create_tables(comp_conn) if database is not None: logging.info(f'Reconstructing compact model from {database} database (limit={limit})') data_conn = utils.connect(database[0], database[1]) revisions = ArchiveRevisionIterator(data_conn, limit=limit) else: logging.info(f'Reconstructing compact model from {filename} CSV file (limit={limit})') revisions = FileRevisionIterator(filename, limit=limit) arch_conn = utils.connect(archive[0], archive[1]) for revision in revisions: revision_add(cursor, arch_conn, revision) comp_conn.commit() arch_conn.close() if database is not None: data_conn.close() cursor.execute(f'SELECT DISTINCT id FROM content ORDER BY id 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:') print(f' {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(row[0])}, {identifier_to_str(row[1])}, {row[2]}, {row[3].decode("utf-8")}') print(f'========================================') comp_conn.close() diff --git a/model.py b/model.py index 6a6a54a..115ff33 100644 --- a/model.py +++ b/model.py @@ -1,60 +1,61 @@ import operator +import os 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(conn, swhid, PosixPath('.')) class TreeEntry: def __init__(self, swhid: str, name: PosixPath): self.swhid = swhid self.name = name class DirectoryEntry(TreeEntry): def __init__( self, conn: psycopg2.extensions.connection, swhid: str, name: PosixPath ): super().__init__(swhid, name) self.conn = conn self.children = None def __iter__(self): if self.children is None: self.children = [] 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')) + PosixPath(os.fsdecode(child[PATH_IDX])) )) elif child[OTYPE_IDX] == DIRECTORY: self.children.append(DirectoryEntry( self.conn, child[SWHID_IDX], - PosixPath(child[PATH_IDX].decode('utf-8')) + PosixPath(os.fsdecode(child[PATH_IDX])) )) return iter(self.children) class FileEntry(TreeEntry): pass