diff --git a/swh/indexer/storage/__init__.py b/swh/indexer/storage/__init__.py index cd8c2f5..841c17e 100644 --- a/swh/indexer/storage/__init__.py +++ b/swh/indexer/storage/__init__.py @@ -1,915 +1,917 @@ # Copyright (C) 2015-2018 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 json import psycopg2 from collections import defaultdict from swh.core.api import remote_api_endpoint from swh.storage.common import db_transaction_generator, db_transaction from swh.storage.exc import StorageDBError from .db import Db from . import converters INDEXER_CFG_KEY = 'indexer_storage' MAPPING_NAMES = ['codemeta', 'gemspec', 'maven', 'npm', 'pkg-info'] def get_indexer_storage(cls, args): """Get an indexer storage object of class `storage_class` with arguments `storage_args`. Args: cls (str): storage's class, either 'local' or 'remote' args (dict): dictionary of arguments passed to the storage class constructor Returns: an instance of swh.indexer's storage (either local or remote) Raises: ValueError if passed an unknown storage class. """ if cls == 'remote': from .api.client import RemoteStorage as IndexerStorage elif cls == 'local': from . import IndexerStorage elif cls == 'memory': from .in_memory import IndexerStorage else: raise ValueError('Unknown indexer storage class `%s`' % cls) return IndexerStorage(**args) def _check_id_duplicates(data): """ If any two dictionaries in `data` have the same id, raises a `ValueError`. Values associated to the key must be hashable. Args: data (List[dict]): List of dictionaries to be inserted >>> _check_id_duplicates([ ... {'id': 'foo', 'data': 'spam'}, ... {'id': 'bar', 'data': 'egg'}, ... ]) >>> _check_id_duplicates([ ... {'id': 'foo', 'data': 'spam'}, ... {'id': 'foo', 'data': 'egg'}, ... ]) Traceback (most recent call last): ... ValueError: The same id is present more than once. """ if len({item['id'] for item in data}) < len(data): raise ValueError('The same id is present more than once.') class IndexerStorage: """SWH Indexer Storage """ def __init__(self, db, min_pool_conns=1, max_pool_conns=10): """ Args: db_conn: either a libpq connection string, or a psycopg2 connection """ try: if isinstance(db, psycopg2.extensions.connection): self._pool = None self._db = Db(db) else: self._pool = psycopg2.pool.ThreadedConnectionPool( min_pool_conns, max_pool_conns, db ) self._db = None except psycopg2.OperationalError as e: raise StorageDBError(e) def get_db(self): if self._db: return self._db return Db.from_pool(self._pool) + def put_db(self, db): + if db is not self._db: + db.put_conn() + @remote_api_endpoint('check_config') - def check_config(self, *, check_write): + @db_transaction() + def check_config(self, *, check_write, db=None, cur=None): """Check that the storage is configured and ready to go.""" # Check permissions on one of the tables - with self.get_db().transaction() as cur: - if check_write: - check = 'INSERT' - else: - check = 'SELECT' - - cur.execute( - "select has_table_privilege(current_user, 'content_mimetype', %s)", # noqa - (check,) - ) - return cur.fetchone()[0] + if check_write: + check = 'INSERT' + else: + check = 'SELECT' - return True + cur.execute( + "select has_table_privilege(current_user, 'content_mimetype', %s)", # noqa + (check,) + ) + return cur.fetchone()[0] @remote_api_endpoint('content_mimetype/missing') @db_transaction_generator() def content_mimetype_missing(self, mimetypes, db=None, cur=None): """Generate mimetypes missing from storage. Args: mimetypes (iterable): iterable of dict with keys: - **id** (bytes): sha1 identifier - **indexer_configuration_id** (int): tool used to compute the results Yields: tuple (id, indexer_configuration_id): missing id """ for obj in db.content_mimetype_missing_from_list(mimetypes, cur): yield obj[0] def _content_get_range(self, content_type, start, end, indexer_configuration_id, limit=1000, with_textual_data=False, db=None, cur=None): """Retrieve ids of type content_type within range [start, end] bound by limit. Args: **content_type** (str): content's type (mimetype, language, etc...) **start** (bytes): Starting identifier range (expected smaller than end) **end** (bytes): Ending identifier range (expected larger than start) **indexer_configuration_id** (int): The tool used to index data **limit** (int): Limit result (default to 1000) **with_textual_data** (bool): Deal with only textual content (True) or all content (all contents by defaults, False) Raises: ValueError for; - limit to None - wrong content_type provided Returns: a dict with keys: - **ids** [bytes]: iterable of content ids within the range. - **next** (Optional[bytes]): The next range of sha1 starts at this sha1 if any """ if limit is None: raise ValueError('Development error: limit should not be None') if content_type not in db.content_indexer_names: err = 'Development error: Wrong type. Should be one of [%s]' % ( ','.join(db.content_indexer_names)) raise ValueError(err) ids = [] next_id = None for counter, obj in enumerate(db.content_get_range( content_type, start, end, indexer_configuration_id, limit=limit+1, with_textual_data=with_textual_data, cur=cur)): _id = obj[0] if counter >= limit: next_id = _id break ids.append(_id) return { 'ids': ids, 'next': next_id } @remote_api_endpoint('content_mimetype/range') @db_transaction() def content_mimetype_get_range(self, start, end, indexer_configuration_id, limit=1000, db=None, cur=None): """Retrieve mimetypes within range [start, end] bound by limit. Args: **start** (bytes): Starting identifier range (expected smaller than end) **end** (bytes): Ending identifier range (expected larger than start) **indexer_configuration_id** (int): The tool used to index data **limit** (int): Limit result (default to 1000) Raises: ValueError for limit to None Returns: a dict with keys: - **ids** [bytes]: iterable of content ids within the range. - **next** (Optional[bytes]): The next range of sha1 starts at this sha1 if any """ return self._content_get_range('mimetype', start, end, indexer_configuration_id, limit=limit, db=db, cur=cur) @remote_api_endpoint('content_mimetype/add') @db_transaction() def content_mimetype_add(self, mimetypes, conflict_update=False, db=None, cur=None): """Add mimetypes not present in storage. Args: mimetypes (iterable): dictionaries with keys: - **id** (bytes): sha1 identifier - **mimetype** (bytes): raw content's mimetype - **encoding** (bytes): raw content's encoding - **indexer_configuration_id** (int): tool's id used to compute the results - **conflict_update** (bool): Flag to determine if we want to overwrite (``True``) or skip duplicates (``False``, the default) """ _check_id_duplicates(mimetypes) mimetypes.sort(key=lambda m: m['id']) db.mktemp_content_mimetype(cur) db.copy_to(mimetypes, 'tmp_content_mimetype', ['id', 'mimetype', 'encoding', 'indexer_configuration_id'], cur) db.content_mimetype_add_from_temp(conflict_update, cur) @remote_api_endpoint('content_mimetype') @db_transaction_generator() def content_mimetype_get(self, ids, db=None, cur=None): """Retrieve full content mimetype per ids. Args: ids (iterable): sha1 identifier Yields: mimetypes (iterable): dictionaries with keys: - **id** (bytes): sha1 identifier - **mimetype** (bytes): raw content's mimetype - **encoding** (bytes): raw content's encoding - **tool** (dict): Tool used to compute the language """ for c in db.content_mimetype_get_from_list(ids, cur): yield converters.db_to_mimetype( dict(zip(db.content_mimetype_cols, c))) @remote_api_endpoint('content_language/missing') @db_transaction_generator() def content_language_missing(self, languages, db=None, cur=None): """List languages missing from storage. Args: languages (iterable): dictionaries with keys: - **id** (bytes): sha1 identifier - **indexer_configuration_id** (int): tool used to compute the results Yields: an iterable of missing id for the tuple (id, indexer_configuration_id) """ for obj in db.content_language_missing_from_list(languages, cur): yield obj[0] @remote_api_endpoint('content_language') @db_transaction_generator() def content_language_get(self, ids, db=None, cur=None): """Retrieve full content language per ids. Args: ids (iterable): sha1 identifier Yields: languages (iterable): dictionaries with keys: - **id** (bytes): sha1 identifier - **lang** (bytes): raw content's language - **tool** (dict): Tool used to compute the language """ for c in db.content_language_get_from_list(ids, cur): yield converters.db_to_language( dict(zip(db.content_language_cols, c))) @remote_api_endpoint('content_language/add') @db_transaction() def content_language_add(self, languages, conflict_update=False, db=None, cur=None): """Add languages not present in storage. Args: languages (iterable): dictionaries with keys: - **id** (bytes): sha1 - **lang** (bytes): language detected conflict_update (bool): Flag to determine if we want to overwrite (true) or skip duplicates (false, the default) """ _check_id_duplicates(languages) languages.sort(key=lambda m: m['id']) db.mktemp_content_language(cur) # empty language is mapped to 'unknown' db.copy_to( ({ 'id': l['id'], 'lang': 'unknown' if not l['lang'] else l['lang'], 'indexer_configuration_id': l['indexer_configuration_id'], } for l in languages), 'tmp_content_language', ['id', 'lang', 'indexer_configuration_id'], cur) db.content_language_add_from_temp(conflict_update, cur) @remote_api_endpoint('content/ctags/missing') @db_transaction_generator() def content_ctags_missing(self, ctags, db=None, cur=None): """List ctags missing from storage. Args: ctags (iterable): dicts with keys: - **id** (bytes): sha1 identifier - **indexer_configuration_id** (int): tool used to compute the results Yields: an iterable of missing id for the tuple (id, indexer_configuration_id) """ for obj in db.content_ctags_missing_from_list(ctags, cur): yield obj[0] @remote_api_endpoint('content/ctags') @db_transaction_generator() def content_ctags_get(self, ids, db=None, cur=None): """Retrieve ctags per id. Args: ids (iterable): sha1 checksums Yields: Dictionaries with keys: - **id** (bytes): content's identifier - **name** (str): symbol's name - **kind** (str): symbol's kind - **lang** (str): language for that content - **tool** (dict): tool used to compute the ctags' info """ for c in db.content_ctags_get_from_list(ids, cur): yield converters.db_to_ctags(dict(zip(db.content_ctags_cols, c))) @remote_api_endpoint('content/ctags/add') @db_transaction() def content_ctags_add(self, ctags, conflict_update=False, db=None, cur=None): """Add ctags not present in storage Args: ctags (iterable): dictionaries with keys: - **id** (bytes): sha1 - **ctags** ([list): List of dictionary with keys: name, kind, line, lang """ _check_id_duplicates(ctags) ctags.sort(key=lambda m: m['id']) def _convert_ctags(__ctags): """Convert ctags dict to list of ctags. """ for ctags in __ctags: yield from converters.ctags_to_db(ctags) db.mktemp_content_ctags(cur) db.copy_to(list(_convert_ctags(ctags)), tblname='tmp_content_ctags', columns=['id', 'name', 'kind', 'line', 'lang', 'indexer_configuration_id'], cur=cur) db.content_ctags_add_from_temp(conflict_update, cur) @remote_api_endpoint('content/ctags/search') @db_transaction_generator() def content_ctags_search(self, expression, limit=10, last_sha1=None, db=None, cur=None): """Search through content's raw ctags symbols. Args: expression (str): Expression to search for limit (int): Number of rows to return (default to 10). last_sha1 (str): Offset from which retrieving data (default to ''). Yields: rows of ctags including id, name, lang, kind, line, etc... """ for obj in db.content_ctags_search(expression, last_sha1, limit, cur=cur): yield converters.db_to_ctags(dict(zip(db.content_ctags_cols, obj))) @remote_api_endpoint('content/fossology_license') @db_transaction_generator() def content_fossology_license_get(self, ids, db=None, cur=None): """Retrieve licenses per id. Args: ids (iterable): sha1 checksums Yields: dict: ``{id: facts}`` where ``facts`` is a dict with the following keys: - **licenses** ([str]): associated licenses for that content - **tool** (dict): Tool used to compute the license """ d = defaultdict(list) for c in db.content_fossology_license_get_from_list(ids, cur): license = dict(zip(db.content_fossology_license_cols, c)) id_ = license['id'] d[id_].append(converters.db_to_fossology_license(license)) for id_, facts in d.items(): yield {id_: facts} @remote_api_endpoint('content/fossology_license/add') @db_transaction() def content_fossology_license_add(self, licenses, conflict_update=False, db=None, cur=None): """Add licenses not present in storage. Args: licenses (iterable): dictionaries with keys: - **id**: sha1 - **licenses** ([bytes]): List of licenses associated to sha1 - **tool** (str): nomossa conflict_update: Flag to determine if we want to overwrite (true) or skip duplicates (false, the default) Returns: list: content_license entries which failed due to unknown licenses """ _check_id_duplicates(licenses) licenses.sort(key=lambda m: m['id']) db.mktemp_content_fossology_license(cur) db.copy_to( ({ 'id': sha1['id'], 'indexer_configuration_id': sha1['indexer_configuration_id'], 'license': license, } for sha1 in licenses for license in sha1['licenses']), tblname='tmp_content_fossology_license', columns=['id', 'license', 'indexer_configuration_id'], cur=cur) db.content_fossology_license_add_from_temp(conflict_update, cur) @remote_api_endpoint('content/fossology_license/range') @db_transaction() def content_fossology_license_get_range( self, start, end, indexer_configuration_id, limit=1000, db=None, cur=None): """Retrieve licenses within range [start, end] bound by limit. Args: **start** (bytes): Starting identifier range (expected smaller than end) **end** (bytes): Ending identifier range (expected larger than start) **indexer_configuration_id** (int): The tool used to index data **limit** (int): Limit result (default to 1000) Raises: ValueError for limit to None Returns: a dict with keys: - **ids** [bytes]: iterable of content ids within the range. - **next** (Optional[bytes]): The next range of sha1 starts at this sha1 if any """ return self._content_get_range('fossology_license', start, end, indexer_configuration_id, limit=limit, with_textual_data=True, db=db, cur=cur) @remote_api_endpoint('content_metadata/missing') @db_transaction_generator() def content_metadata_missing(self, metadata, db=None, cur=None): """List metadata missing from storage. Args: metadata (iterable): dictionaries with keys: - **id** (bytes): sha1 identifier - **indexer_configuration_id** (int): tool used to compute the results Yields: missing sha1s """ for obj in db.content_metadata_missing_from_list(metadata, cur): yield obj[0] @remote_api_endpoint('content_metadata') @db_transaction_generator() def content_metadata_get(self, ids, db=None, cur=None): """Retrieve metadata per id. Args: ids (iterable): sha1 checksums Yields: dictionaries with the following keys: id (bytes) metadata (str): associated metadata tool (dict): tool used to compute metadata """ for c in db.content_metadata_get_from_list(ids, cur): yield converters.db_to_metadata( dict(zip(db.content_metadata_cols, c))) @remote_api_endpoint('content_metadata/add') @db_transaction() def content_metadata_add(self, metadata, conflict_update=False, db=None, cur=None): """Add metadata not present in storage. Args: metadata (iterable): dictionaries with keys: - **id**: sha1 - **metadata**: arbitrary dict conflict_update: Flag to determine if we want to overwrite (true) or skip duplicates (false, the default) """ _check_id_duplicates(metadata) metadata.sort(key=lambda m: m['id']) db.mktemp_content_metadata(cur) db.copy_to(metadata, 'tmp_content_metadata', ['id', 'metadata', 'indexer_configuration_id'], cur) db.content_metadata_add_from_temp(conflict_update, cur) @remote_api_endpoint('revision_intrinsic_metadata/missing') @db_transaction_generator() def revision_intrinsic_metadata_missing(self, metadata, db=None, cur=None): """List metadata missing from storage. Args: metadata (iterable): dictionaries with keys: - **id** (bytes): sha1_git revision identifier - **indexer_configuration_id** (int): tool used to compute the results Yields: missing ids """ for obj in db.revision_intrinsic_metadata_missing_from_list( metadata, cur): yield obj[0] @remote_api_endpoint('revision_intrinsic_metadata') @db_transaction_generator() def revision_intrinsic_metadata_get(self, ids, db=None, cur=None): """Retrieve revision metadata per id. Args: ids (iterable): sha1 checksums Yields: dictionaries with the following keys: - **id** (bytes) - **metadata** (str): associated metadata - **tool** (dict): tool used to compute metadata - **mappings** (List[str]): list of mappings used to translate these metadata """ for c in db.revision_intrinsic_metadata_get_from_list(ids, cur): yield converters.db_to_metadata( dict(zip(db.revision_intrinsic_metadata_cols, c))) @remote_api_endpoint('revision_intrinsic_metadata/add') @db_transaction() def revision_intrinsic_metadata_add(self, metadata, conflict_update=False, db=None, cur=None): """Add metadata not present in storage. Args: metadata (iterable): dictionaries with keys: - **id**: sha1_git of revision - **metadata**: arbitrary dict - **indexer_configuration_id**: tool used to compute metadata - **mappings** (List[str]): list of mappings used to translate these metadata conflict_update: Flag to determine if we want to overwrite (true) or skip duplicates (false, the default) """ _check_id_duplicates(metadata) metadata.sort(key=lambda m: m['id']) db.mktemp_revision_intrinsic_metadata(cur) db.copy_to(metadata, 'tmp_revision_intrinsic_metadata', ['id', 'metadata', 'mappings', 'indexer_configuration_id'], cur) db.revision_intrinsic_metadata_add_from_temp(conflict_update, cur) @remote_api_endpoint('revision_intrinsic_metadata/delete') @db_transaction() def revision_intrinsic_metadata_delete(self, entries, db=None, cur=None): """Remove revision metadata from the storage. Args: entries (dict): dictionaries with the following keys: - **id** (bytes): revision identifier - **indexer_configuration_id** (int): tool used to compute metadata """ db.revision_intrinsic_metadata_delete(entries, cur) @remote_api_endpoint('origin_intrinsic_metadata') @db_transaction_generator() def origin_intrinsic_metadata_get(self, ids, db=None, cur=None): """Retrieve origin metadata per id. Args: ids (iterable): origin identifiers Yields: list: dictionaries with the following keys: - **id** (int) - **metadata** (str): associated metadata - **tool** (dict): tool used to compute metadata - **mappings** (List[str]): list of mappings used to translate these metadata """ for c in db.origin_intrinsic_metadata_get_from_list(ids, cur): yield converters.db_to_metadata( dict(zip(db.origin_intrinsic_metadata_cols, c))) @remote_api_endpoint('origin_intrinsic_metadata/add') @db_transaction() def origin_intrinsic_metadata_add(self, metadata, conflict_update=False, db=None, cur=None): """Add origin metadata not present in storage. Args: metadata (iterable): dictionaries with keys: - **id**: origin identifier - **from_revision**: sha1 id of the revision used to generate these metadata. - **metadata**: arbitrary dict - **indexer_configuration_id**: tool used to compute metadata - **mappings** (List[str]): list of mappings used to translate these metadata conflict_update: Flag to determine if we want to overwrite (true) or skip duplicates (false, the default) """ _check_id_duplicates(metadata) metadata.sort(key=lambda m: m['id']) db.mktemp_origin_intrinsic_metadata(cur) db.copy_to(metadata, 'tmp_origin_intrinsic_metadata', ['id', 'metadata', 'indexer_configuration_id', 'from_revision', 'mappings'], cur) db.origin_intrinsic_metadata_add_from_temp(conflict_update, cur) @remote_api_endpoint('origin_intrinsic_metadata/delete') @db_transaction() def origin_intrinsic_metadata_delete( self, entries, db=None, cur=None): """Remove origin metadata from the storage. Args: entries (dict): dictionaries with the following keys: - **id** (int): origin identifier - **indexer_configuration_id** (int): tool used to compute metadata """ db.origin_intrinsic_metadata_delete(entries, cur) @remote_api_endpoint('origin_intrinsic_metadata/search/fulltext') @db_transaction_generator() def origin_intrinsic_metadata_search_fulltext( self, conjunction, limit=100, db=None, cur=None): """Returns the list of origins whose metadata contain all the terms. Args: conjunction (List[str]): List of terms to be searched for. limit (int): The maximum number of results to return Yields: list: dictionaries with the following keys: - **id** (int) - **metadata** (str): associated metadata - **tool** (dict): tool used to compute metadata - **mappings** (List[str]): list of mappings used to translate these metadata """ for c in db.origin_intrinsic_metadata_search_fulltext( conjunction, limit=limit, cur=cur): yield converters.db_to_metadata( dict(zip(db.origin_intrinsic_metadata_cols, c))) @remote_api_endpoint('origin_intrinsic_metadata/search/by_producer') @db_transaction_generator() def origin_intrinsic_metadata_search_by_producer( self, start=0, end=None, limit=100, ids_only=False, mappings=None, tool_ids=None, db=None, cur=None): """Returns the list of origins whose metadata contain all the terms. Args: start (int): The minimum origin id to return end (int): The maximum origin id to return limit (int): The maximum number of results to return ids_only (bool): Determines whether only origin ids are returned or the content as well mappings (List[str]): Returns origins whose intrinsic metadata were generated using at least one of these mappings. Yields: list: list of origin ids (int) if `ids_only=True`, else dictionaries with the following keys: - **id** (int) - **metadata** (str): associated metadata - **tool** (dict): tool used to compute metadata - **mappings** (List[str]): list of mappings used to translate these metadata """ res = db.origin_intrinsic_metadata_search_by_producer( start, end, limit, ids_only, mappings, tool_ids, cur) if ids_only: for (origin_id,) in res: yield origin_id else: for c in res: yield converters.db_to_metadata( dict(zip(db.origin_intrinsic_metadata_cols, c))) @remote_api_endpoint('origin_intrinsic_metadata/stats') @db_transaction() def origin_intrinsic_metadata_stats( self, db=None, cur=None): """Returns counts of indexed metadata per origins, broken down into metadata types. Returns: dict: dictionary with keys: - total (int): total number of origins that were indexed (possibly yielding an empty metadata dictionary) - non_empty (int): total number of origins that we extracted a non-empty metadata dictionary from - per_mapping (dict): a dictionary with mapping names as keys and number of origins whose indexing used this mapping. Note that indexing a given origin may use 0, 1, or many mappings. """ mapping_names = [m for m in MAPPING_NAMES] select_parts = [] # Count rows for each mapping for mapping_name in mapping_names: select_parts.append(( "sum(case when (mappings @> ARRAY['%s']) " " then 1 else 0 end)" ) % mapping_name) # Total select_parts.append("sum(1)") # Rows whose metadata has at least one key that is not '@context' select_parts.append( "sum(case when ('{}'::jsonb @> (metadata - '@context')) " " then 0 else 1 end)") cur.execute('select ' + ', '.join(select_parts) + ' from origin_intrinsic_metadata') results = dict(zip(mapping_names + ['total', 'non_empty'], cur.fetchone())) return { 'total': results.pop('total'), 'non_empty': results.pop('non_empty'), 'per_mapping': results, } @remote_api_endpoint('indexer_configuration/add') @db_transaction_generator() def indexer_configuration_add(self, tools, db=None, cur=None): """Add new tools to the storage. Args: tools ([dict]): List of dictionary representing tool to insert in the db. Dictionary with the following keys: - **tool_name** (str): tool's name - **tool_version** (str): tool's version - **tool_configuration** (dict): tool's configuration (free form dict) Returns: List of dict inserted in the db (holding the id key as well). The order of the list is not guaranteed to match the order of the initial list. """ db.mktemp_indexer_configuration(cur) db.copy_to(tools, 'tmp_indexer_configuration', ['tool_name', 'tool_version', 'tool_configuration'], cur) tools = db.indexer_configuration_add_from_temp(cur) for line in tools: yield dict(zip(db.indexer_configuration_cols, line)) @remote_api_endpoint('indexer_configuration/data') @db_transaction() def indexer_configuration_get(self, tool, db=None, cur=None): """Retrieve tool information. Args: tool (dict): Dictionary representing a tool with the following keys: - **tool_name** (str): tool's name - **tool_version** (str): tool's version - **tool_configuration** (dict): tool's configuration (free form dict) Returns: The same dictionary with an `id` key, None otherwise. """ tool_conf = tool['tool_configuration'] if isinstance(tool_conf, dict): tool_conf = json.dumps(tool_conf) idx = db.indexer_configuration_get(tool['tool_name'], tool['tool_version'], tool_conf) if not idx: return None return dict(zip(db.indexer_configuration_cols, idx))