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a/pyproject.toml b/pyproject.toml index 2c5161a9..2506f135 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 +84,8 @@ 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 = ">=0.2.1" +rero-invenio-base = { git = "https://github.com/rero/rero-invenio-base.git", branch = "master" } 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..63da2ce1 100644 --- a/rero_mef/agents/cli.py +++ b/rero_mef/agents/cli.py @@ -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( 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..ed784e3e 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) @@ -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/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:"