From 91aa163620128d6d190d469f5b5f3eea6f1e2141 Mon Sep 17 00:00:00 2001 From: Peter Weber Date: Wed, 20 Dec 2023 20:59:44 +0100 Subject: [PATCH] dependencies: fix security issues * Bumps dependencies. * Better verbose prints. * Cleans code from warnings. Co-Authored-by: Peter Weber --- .../workflows/continuous-integration-test.yml | 4 +- classes.md | 4 +- poetry.lock | 1081 ++++++++--------- pyproject.toml | 42 +- rero_mef/agents/cli.py | 20 +- rero_mef/agents/gnd/tasks.py | 3 +- rero_mef/agents/mef/api.py | 6 +- rero_mef/agents/viaf/api.py | 17 +- rero_mef/api.py | 15 +- rero_mef/config.py | 22 +- rero_mef/jsonschemas/utils.py | 9 +- rero_mef/utils.py | 2 +- scripts/test | 16 +- tests/ui/agents/test_agents_viaf_api.py | 2 +- 14 files changed, 626 insertions(+), 617 deletions(-) diff --git a/.github/workflows/continuous-integration-test.yml b/.github/workflows/continuous-integration-test.yml index f25d5100..5678643b 100644 --- a/.github/workflows/continuous-integration-test.yml +++ b/.github/workflows/continuous-integration-test.yml @@ -16,9 +16,9 @@ jobs: - uses: actions/checkout@v3 - name: Setup node - uses: actions/setup-node@v3 + uses: actions/setup-node@v4 with: - node-version: '14' + node-version: '16' - name: Docker compose up run: docker-compose up -d diff --git a/classes.md b/classes.md index 01827c90..aa48597b 100644 --- a/classes.md +++ b/classes.md @@ -19,8 +19,8 @@ class ReroMefRecord{ dbcommit(self, reindex=False, forceindex=False) reindex(self, forceindex=False) get_record_by_pid(cls, pid, with_deleted=False) - get_pid_by_id(cls, id) - get_persistent_identifier(cls, id) + get_pid_by_id(cls, id_) + get_persistent_identifier(cls, id_) _get_all(cls, with_deleted=False) get_all_pids(cls, with_deleted=False, limit=100000) get_all_ids(cls, with_deleted=False, limit=100000) diff --git a/poetry.lock b/poetry.lock index d18f6c1d..cf62356c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,13 +13,13 @@ files = [ [[package]] name = "alembic" -version = "1.12.1" +version = "1.10.4" description = "A database migration tool for SQLAlchemy." optional = false python-versions = ">=3.7" files = [ - {file = "alembic-1.12.1-py3-none-any.whl", hash = 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(>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"] +socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "uwsgi" @@ -4613,13 +4608,13 @@ watchmedo = ["PyYAML (>=3.10)"] [[package]] name = "wcwidth" -version = "0.2.12" +version = "0.2.13" description = "Measures the displayed width of unicode strings in a terminal" optional = false python-versions = "*" files = [ - {file = "wcwidth-0.2.12-py2.py3-none-any.whl", hash = "sha256:f26ec43d96c8cbfed76a5075dac87680124fa84e0855195a6184da9c187f133c"}, - {file = "wcwidth-0.2.12.tar.gz", hash = "sha256:f01c104efdf57971bcb756f054dd58ddec5204dd15fa31d6503ea57947d97c02"}, + {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"}, + {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"}, ] [[package]] @@ -4761,4 +4756,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">= 3.9, <3.10" -content-hash = "aa9e3748ac8b5db5cc1a84818c269e537c7de2dc423faba32abb4f7d2c04f341" +content-hash = "d7b455af93787f9598da7949430599fb2dc15605564261bf1a6ef897f8c3a4c2" diff --git a/pyproject.toml b/pyproject.toml index 2c5161a9..1f54382f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,12 +21,7 @@ python = ">= 3.9, <3.10" ## foo = ">3.0" # finally will upgrade to 5.0 ## when the python code will be executed a conflict exception will be raised. #------------------------------------------------------------------------------ -# Default from Invenio -lxml = ">=4.9.1" -marshmallow = ">=3.0.0,<4.0.0" -uwsgi = ">=2.0" -uwsgi-tools = ">=1.1.1" -uwsgitop = ">=0.11" + ## Third party inven## Third party invenio modules used by RERO EBOOKS invenio-oaiharvester = { git = "https://github.com/inveniosoftware/invenio-oaiharvester.git", tag = "v1.0.0a4" } invenio-search = {version = ">=2.1.0,<3.0.0", extras = ["elasticsearch7"]} @@ -38,32 +33,41 @@ invenio-cache = ">=1.1.1,<1.2.0" invenio-celery = ">=1.2.4,<1.3.0" invenio-config = ">=1.0.3,<1.1.0" invenio-i18n = ">=2.0.0,<3.0.0" -invenio-db = {version = ">=1.0.14,<1.1.0", extras = ["postgresql"]} +invenio-db = {version = ">=1.1.0,<1.2.0", extras = ["postgresql"]} # Invenio base bundle invenio-admin = ">=1.4.0,<1.5.0" invenio-assets = ">=2.0.0,<3.0.0" -invenio-formatter = ">=1.2.0,<1.3.0" -invenio-logging = {version = ">=1.3.2,<1.4.0", extras = ["sentry-sdk"]} -invenio-mail = ">=1.0.2,<1.1.0" -invenio-rest = ">=1.2.8,<1.3.0" +invenio-formatter = ">=2.0.0,<3.0.0" +invenio-logging = {version = ">=2.0.0,<3.0.0"} +invenio-mail = ">=2.0.0,<3.0.0" +invenio-rest = ">=1.3.0,<1.4.0" invenio-theme = ">=2.0.0,<3.0.0" # Invenio auth bundle -invenio-access = ">=1.4.4,<1.5.0" -invenio-accounts = ">=2.1.0,<2.2.0" -invenio-oauth2server = ">=2.0.0,<2.1.0" -invenio-oauthclient = ">=2.2.0,<3.0.0" -invenio-userprofiles = ">=2.2.0,<2.3.0" +invenio-access = ">=2.0.0,<3.0.0" +invenio-accounts = ">=3.0.0,<4.0.0" +invenio-oauth2server = ">=2.0.0,<3.0.0" +invenio-oauthclient = ">=3.0.0,<4.0.0" +invenio-userprofiles = ">=2.3.0,<3.0.0" # Invenio metadata bundle -invenio-indexer = ">=2.1.0,<2.2.0" +invenio-indexer = ">=2.2.0,<3.0.0" invenio-jsonschemas = ">=1.1.4,<1.2.0" invenio-oaiserver = ">=2.2.0,<2.3.0" invenio-pidstore = ">=1.3.0,<1.4.0" invenio-records-rest = ">=2.2.0,<2.3.0" invenio-records-ui = ">=1.2.0,<1.3.0" -invenio-records = "2.1.0,<2.2.0" +invenio-records = ">=2.1.0,<2.2.0" #invenio-search-ui = ">=2.4.0,<3.0.0" # Pinned due to before_first_request deprecation https://flask.palletsprojects.com/en/2.2.x/api/#flask.Flask.before_first_request + +# Default from Invenio +lxml = ">=4.9.1" +marshmallow = ">=3.0.0,<4.0.0" +uwsgi = ">=2.0" +uwsgi-tools = ">=1.1.1" +uwsgitop = ">=0.11" +# Pinned due to before_first_request deprecation https://flask.palletsprojects.com/en/2.2.x/api/#flask.Flask.before_first_request Flask = ">=2.2.0,<2.3.0" +sentry-sdk = ">=1.0.0" # normaly in invenio-logging = {version = ">=2.0.0,<3.0.0", extras = ["sentry_sdk"]} dojson = ">=1.4.0" # TODO: dojson problem = AttributeError: 'Group' object has no attribute 'resultcallback' click = "<8.1.0" @@ -80,7 +84,7 @@ pydocstyle = ">=6.1.1" ## RERO ILS specific python modules poethepoet = "*" # TODO: solve requires invenio-indexer (<2.0.0) -rero-invenio-base = ">=0.2.1" +rero-invenio-base = ">=0.2.0" sqlitedict = "^2.1.0" werkzeug = "<2.3.0" sqlalchemy-continuum = ">=1.3.12,<1.4.0" diff --git a/rero_mef/agents/cli.py b/rero_mef/agents/cli.py index 2d546a92..fb028025 100644 --- a/rero_mef/agents/cli.py +++ b/rero_mef/agents/cli.py @@ -55,7 +55,7 @@ def create_from_viaf(enqueue, online, verbose, online_verbose, """Create MEF and agents from viaf.""" def get_pids_from_json(json_file): """Get all pids from JSON file.""" - for record in read_json_record(viaf_file): + for record in read_json_record(json_file): yield record['pid'] click.secho( @@ -69,26 +69,28 @@ def get_pids_from_json(json_file): if missing: missing_pids, non_existing_pids = AgentMefRecord. \ - get_all_missing_viaf_pids( - verbose=progress or verbose - ) + get_all_missing_viaf_pids(verbose=(progress or verbose)) progress_bar = progressbar( items=missing_pids, length=len(missing_pids), - verbose=progress + verbose=progress, + label='VIAF missing' ) elif viaf_file: progress_bar = progressbar( items=get_pids_from_json(viaf_file), length=number_records_in_file(viaf_file.name, 'json'), - verbose=progress + verbose=progress, + label='VIAF file' ) else: progress_bar = progressbar( items=AgentViafRecord.get_all_pids(), length=counts['viaf']['old'], - verbose=progress + verbose=progress, + label='VIAF all' ) + click.echo('Create MEF and agents from VIAF') for pid in progress_bar: if enqueue: task = task_create_mef_and_agents_from_viaf.delay( @@ -111,7 +113,7 @@ def get_pids_from_json(json_file): if non_existing_pids: click.echo( f'Clean VIAF pids from MEF records: {len(non_existing_pids)}') - for pid, viaf_pid in non_existing_pids.items(): + for pid, _ in non_existing_pids.items(): # TODO: clean MEF records with non existing VIAF pids: pass @@ -185,7 +187,7 @@ def create_csv_mef(viaf_metadata_file, output_directory, verbose): click.secho( f' VIAF input file: {viaf_metadata_file}', err=True) - message = f' CSV output files: {pidstore}, {metadata}' + # message = f' CSV output files: {pidstore}, {metadata}' count = create_mef_files( viaf_metadata_file_name=viaf_metadata_file, diff --git a/rero_mef/agents/gnd/tasks.py b/rero_mef/agents/gnd/tasks.py index b772fd37..12060bb8 100644 --- a/rero_mef/agents/gnd/tasks.py +++ b/rero_mef/agents/gnd/tasks.py @@ -109,7 +109,7 @@ def gnd_get_record(id_, debug=False): if records := parse_xml_to_array(BytesIO(response.content)): trans_record = Transformation(records[0]).json pid = trans_record.get('pid') - if id_ != trans_record.get('pid'): + if id_ != pid: msg = f'{msg} | PID changed: {id_} -> {pid}' trans_record = None else: @@ -119,6 +119,7 @@ def gnd_get_record(id_, debug=False): else: msg = f'{msg} | HTTP Error: {status_code}' except Exception as err: + trans_record = None msg = f'{msg} | Error: {err}' if debug: raise diff --git a/rero_mef/agents/mef/api.py b/rero_mef/agents/mef/api.py index 34c0afa0..0c108d85 100644 --- a/rero_mef/agents/mef/api.py +++ b/rero_mef/agents/mef/api.py @@ -83,7 +83,8 @@ def get_all_missing_viaf_pids(cls, verbose=False): progress = progressbar( items=AgentViafRecord.get_all_pids(), length=AgentViafRecord.count(), - verbose=verbose + verbose=verbose, + label='VIAF all' ) missing_pids = {pid: 1 for pid in progress} if verbose: @@ -92,7 +93,8 @@ def get_all_missing_viaf_pids(cls, verbose=False): progress = progressbar( items=query.source(['pid', 'viaf_pid']).scan(), length=query.count(), - verbose=True + verbose=verbose, + label='VIAF from MEF' ) non_existing_pids = {hit.pid: hit.viaf_pid for hit in progress if not missing_pids.pop(hit.viaf_pid, None)} diff --git a/rero_mef/agents/viaf/api.py b/rero_mef/agents/viaf/api.py index 2b57ce56..6275f1b7 100644 --- a/rero_mef/agents/viaf/api.py +++ b/rero_mef/agents/viaf/api.py @@ -32,8 +32,6 @@ from .. import AgentGndRecord, AgentIdrefRecord, AgentMefRecord, \ AgentReroRecord from ..api import Action, ReroIndexer, ReroMefRecord -from ..mef.api import AgentMefRecord -from ..utils import get_entity_class from ...filter import exists_filter from ...utils import add_md5, get_entity_class, progressbar, \ requests_retry_session @@ -209,7 +207,7 @@ def update_online(agent_class, pid, online): if agent_class.provider.pid_type in online: data, msg = agent_class.get_online_record(id_=pid) if online_verbose: - click.echo(msg) + click.echo(f'\n{msg}') if data and not data.get('NO TRANSFORMATION'): agent_record, action = agent_class.create_or_update( data=data, dbcommit=dbcommit, reindex=reindex) @@ -320,7 +318,7 @@ def reindex(self, forceindex=False): return result @classmethod - def get_online_record(cls, viaf_source_code, pid, format=None): + def get_online_record(cls, viaf_source_code, pid, rec_format=None): """Get VIAF record. Get's the VIAF record from: @@ -328,14 +326,14 @@ def get_online_record(cls, viaf_source_code, pid, format=None): :param viaf_source_code: agent source code :param pid: pid for agent source code - :param format: raw = get the not transformed VIAF record + :param rec_format: raw = get the not transformed VIAF record link = get the VIAF link record :returns: VIAF record as json """ viaf_format = '/viaf.json' - if format == 'link': + if rec_format == 'link': viaf_format = '/justlinks.json' - format = 'raw' + rec_format = 'raw' viaf_url = current_app.config.get('RERO_MEF_VIAF_BASE_URL') url = f'{viaf_url}/viaf' if viaf_source_code.upper() == 'VIAF': @@ -346,7 +344,7 @@ def get_online_record(cls, viaf_source_code, pid, format=None): result = {} if response.status_code == requests.codes.ok: msg = f'VIAF get: {pid:<15} {url} | OK' - if format == 'raw': + if rec_format == 'raw': return response.json(), msg data_json = response.json() result['pid'] = data_json.get('viafID') @@ -394,7 +392,6 @@ def update_online(self, dbcommit=False, reindex=False): :param reindex: Reindex record. :returns: record and actions message. """ - from rero_mef.api import Action online_data, _ = self.get_online_record( viaf_source_code='VIAF', pid=self.pid @@ -491,7 +488,7 @@ def delete(self, force=True, dbcommit=False, delindex=False): AgentMefRecord.flush_indexes() # recreate MEF records for agents for agent_record in old_agent_records.values(): - mef, test = agent_record.create_or_update_mef( + mef, _ = agent_record.create_or_update_mef( dbcommit=True, reindex=True ) diff --git a/rero_mef/api.py b/rero_mef/api.py index 152e7edf..4e5d1e47 100644 --- a/rero_mef/api.py +++ b/rero_mef/api.py @@ -236,13 +236,12 @@ def replace(self, data, commit=False, dbcommit=False, reindex=False): if self.get('md5'): new_data = add_md5(new_data) self.clear() - self = self.update( + return self.update( data=new_data, commit=commit, dbcommit=dbcommit, reindex=reindex ) - return self def dbcommit(self, reindex=False, forceindex=False): """Commit changes to db.""" @@ -285,18 +284,18 @@ def get_record_by_pid(cls, pid, with_deleted=False): db.session.rollback() @classmethod - def get_pid_by_id(cls, id): + def get_pid_by_id(cls, id_): """Get pid by uuid.""" - persistent_identifier = cls.get_persistent_identifier(id) + persistent_identifier = cls.get_persistent_identifier(id_) return str(persistent_identifier.pid_value) @classmethod - def get_persistent_identifier(cls, id): + def get_persistent_identifier(cls, id_): """Get Persistent Identifier.""" return PersistentIdentifier.get_by_object( cls.provider.pid_type, cls.object_type, - id + id_ ) @classmethod @@ -374,8 +373,8 @@ def get_all_ids(cls, with_deleted=False, limit=100000, date=None): @classmethod def get_all_records(cls, with_deleted=False, limit=100000): """Get all records. Return a generator iterator.""" - for id in cls.get_all_ids(with_deleted=with_deleted, limit=limit): - yield cls.get_record(id) + for id_ in cls.get_all_ids(with_deleted=with_deleted, limit=limit): + yield cls.get_record(id_) @classmethod def count(cls, with_deleted=False): diff --git a/rero_mef/config.py b/rero_mef/config.py index 784d4a2a..566c3803 100644 --- a/rero_mef/config.py +++ b/rero_mef/config.py @@ -229,7 +229,7 @@ '&recordSchema=MARC21-xml' SEARCH_CLIENT_CONFIG = dict( - timeout=30, + timeout=60, max_retries=5, ) @@ -259,7 +259,7 @@ '"rero_mef.agents.mef.api:AgentMefRecord"):pid_value>'), default_media_type='application/json', max_result_window=MAX_RESULT_WINDOW, - error_handlers=dict(), + error_handlers={}, ), viaf=dict( pid_type='viaf', @@ -283,7 +283,7 @@ '"rero_mef.agents.viaf.api:AgentViafRecord"):pid_value>'), default_media_type='application/json', max_result_window=MAX_RESULT_WINDOW, - error_handlers=dict(), + error_handlers={}, ), aggnd=dict( pid_type='aggnd', @@ -307,7 +307,7 @@ '"rero_mef.agents.gnd.api:AgentGndRecord"):pid_value>'), default_media_type='application/json', max_result_window=MAX_RESULT_WINDOW, - error_handlers=dict() + error_handlers={} ), aidref=dict( pid_type='aidref', @@ -332,7 +332,7 @@ '"rero_mef.agents.idref.api:AgentIdrefRecord"):pid_value>'), default_media_type='application/json', max_result_window=MAX_RESULT_WINDOW, - error_handlers=dict() + error_handlers={} ), agrero=dict( pid_type='agrero', @@ -356,7 +356,7 @@ '"rero_mef.agents.rero.api:AgentReroRecord"):pid_value>'), default_media_type='application/json', max_result_window=MAX_RESULT_WINDOW, - error_handlers=dict(), + error_handlers={}, ), comef=dict( pid_type='comef', @@ -381,7 +381,7 @@ ':pid_value>'), default_media_type='application/json', max_result_window=MAX_RESULT_WINDOW, - error_handlers=dict(), + error_handlers={}, ), corero=dict( pid_type='corero', @@ -406,7 +406,7 @@ '"rero_mef.concepts.rero.api:ConceptReroRecord"):pid_value>'), default_media_type='application/json', max_result_window=MAX_RESULT_WINDOW, - error_handlers=dict(), + error_handlers={}, ), cidref=dict( pid_type='cidref', @@ -431,7 +431,7 @@ '"rero_mef.concepts.idref.api:ConceptIdrefRecord"):pid_value>'), default_media_type='application/json', max_result_window=MAX_RESULT_WINDOW, - error_handlers=dict(), + error_handlers={}, ), plmef=dict( pid_type='plmef', @@ -456,7 +456,7 @@ ':pid_value>'), default_media_type='application/json', max_result_window=MAX_RESULT_WINDOW, - error_handlers=dict(), + error_handlers={}, ), pidref=dict( pid_type='pidref', @@ -481,7 +481,7 @@ '"rero_mef.places.idref.api:PlaceIdrefRecord"):pid_value>'), default_media_type='application/json', max_result_window=MAX_RESULT_WINDOW, - error_handlers=dict(), + error_handlers={}, ) ) diff --git a/rero_mef/jsonschemas/utils.py b/rero_mef/jsonschemas/utils.py index 0c8d8a10..a0c0271d 100644 --- a/rero_mef/jsonschemas/utils.py +++ b/rero_mef/jsonschemas/utils.py @@ -54,11 +54,10 @@ def __call__(self, uri, **kwargs): """ if uri in self.store: return self.store[uri] - else: - result = self.get_remote_json(uri, **kwargs) - if self.cache_results: - self.store[uri] = result - return result + result = self.get_remote_json(uri, **kwargs) + if self.cache_results: + self.store[uri] = result + return result @lru_cache(maxsize=1000) def get_remote_json(self, uri, **kwargs): diff --git a/rero_mef/utils.py b/rero_mef/utils.py index e6a89740..6f9e7b1d 100644 --- a/rero_mef/utils.py +++ b/rero_mef/utils.py @@ -190,7 +190,7 @@ def _next_response(self): while count < 5: try: self.oai_response = self.sickle.harvest(**params) - xml = self.oai_response.xml + self.oai_response.xml # try to get xml count = 5 except Exception as err: count += 1 diff --git a/scripts/test b/scripts/test index f491c7de..90ac2940 100755 --- a/scripts/test +++ b/scripts/test @@ -69,16 +69,26 @@ set -e # Vulnerability ID: 45183 # -> Vulnerability found in flask-security version 3.0.0 # Vulnerability ID: 44501 -# -> Vulnerability found in sqlalchemy version 1.4.48 +# CVE-2021-23385, an open redirect vulnerability: When using the... +# -> Vulnerability found in sqlalchemy version 1.4.50 # Vulnerability ID: 51668 # -> Vulnerability found in sqlalchemy-utils version 0.38.3 # Vulnerability ID: 42194 # -> Vulnerability found in wtforms version 2.3.3 # Vulnerability ID: 42852 +# -> Vulnerability found in werkzeug version 2.2.3 +# Vulnerability ID: 62019 +# -> Vulnerability found in pip version 23.2.1 +# Vulnerability ID: 62044 # -> Vulnerability found in py version 1.11.0 # Vulnerability ID: 51457 -info_msg "Test safety:" -safety check -o bare -i 40459 -i 45183 -i 44501 -i 51668 -i 42194 -i 42852 -i 51457 +info_msg "Check vulnerabilities:" +safety_exceptions="-i 40459 -i 45183 -i 44501 -i 51668 -i 42194 -i 42852 -i 62019 -i 62044 -i 51457" +msg=$(safety check -o text ${safety_exceptions}) || { + echo "Safety vulnerabilites found for packages:" $(safety check -o bare ${safety_exceptions}) + echo "Run:" "safety check -o screen ${safety_exceptions} | grep -i vulnerability" "for more details" + exit 1 +} info_msg "Test pydocstyle:" pydocstyle rero_mef tests docs info_msg "Test isort:" diff --git a/tests/ui/agents/test_agents_viaf_api.py b/tests/ui/agents/test_agents_viaf_api.py index a7ae6f3e..79f938c9 100644 --- a/tests/ui/agents/test_agents_viaf_api.py +++ b/tests/ui/agents/test_agents_viaf_api.py @@ -83,7 +83,7 @@ def test_get_online(mock_get, app, agent_viaf_online_response): json_data=agent_viaf_online_response ) data, msg = AgentViafRecord.get_online_record( - 'SUDOC', '076515788', format='raw') + 'SUDOC', '076515788', rec_format='raw') assert data == agent_viaf_online_response assert msg == ( 'VIAF get: 076515788 '