EVA-3426 - Insert a publication in EVAPRO (#180)

Script to add external reference to EVAPRO

bin/add_ext_reference.py

@@ -0,0 +1,126 @@
+#!/usr/bin/env python
+
+# Copyright 2020 EMBL - European Bioinformatics Institute
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import argparse
+import logging
+import sys
+
+import requests
+from ebi_eva_common_pyutils.config import cfg
+from ebi_eva_common_pyutils.logger import logging_config as log_cfg
+from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle
+from ebi_eva_internal_pyutils.pg_utils import get_all_results_for_query, execute_query
+from retry import retry
+
+from eva_submission.eload_utils import check_project_exists_in_evapro, check_existing_project_in_ena
+from eva_submission.submission_config import load_config
+
+logger = log_cfg.get_logger(__name__)
+
+
+def add_external_reference_to_ena(project_accession, source_database, identifier):
+    logger.warning('This script does not support uploading the external reference to ENA. Please do this manually')
+
+
+class EvaproExtReference:
+
+    @property
+    def metadata_connection_handle(self):
+        return get_metadata_connection_handle(cfg['maven']['environment'], cfg['maven']['settings_file'])
+
+    def _get_dbxref_id(self, source_database, identifier):
+        # get the dbxref_id that was autogenerated in the row that we just inserted in dbxref
+        with self.metadata_connection_handle as conn:
+            query = f"SELECT dbxref_id FROM evapro.dbxref WHERE db='{source_database}' and id='{identifier}'"
+            res = list(get_all_results_for_query(conn, query))
+            if res:
+                return res[0][0]
+
+    def _get_project_dbxref_id(self, project_accession, dbxref_id):
+        with self.metadata_connection_handle as conn:
+            query = f"SELECT dbxref_id FROM evapro.project_dbxref " \
+                    f"WHERE project_accession='{project_accession}' and dbxref_id='{dbxref_id}'"
+            res = list(get_all_results_for_query(conn, query))
+            if res:
+                return res[0]
+
+    def add_external_reference_to_evapro(self, project_accession, source_database, identifier):
+        dbxref_id = self._get_dbxref_id(source_database, identifier)
+        if not dbxref_id:
+            query = f"INSERT into evapro.dbxref (db, id, link_type, source_object) " \
+                    f"VALUES ('{source_database}', '{identifier}', 'publication', 'project')"
+            with self.metadata_connection_handle as conn:
+                execute_query(conn, query)
+            dbxref_id = self._get_dbxref_id(source_database, identifier)
+        assert dbxref_id, f"Failed to create the entry for {source_database}:{identifier}"
+        if not self._get_project_dbxref_id(project_accession, dbxref_id):
+            query = f"INSERT into project_dbxref (project_accession, dbxref_id) " \
+                    f"VALUES ('{project_accession}', '{dbxref_id}')"
+            with self.metadata_connection_handle as conn:
+                execute_query(conn, query)
+
+
+@retry(tries=3, delay=2, backoff=1.2, jitter=(1, 3))
+def _curie_exist(curie):
+    response = requests.get('https://resolver.api.identifiers.org/' + curie)
+    json_data = response.json()
+    resources = json_data["payload"]["resolvedResources"]
+    for resource in resources:
+        response = requests.head(resource['compactIdentifierResolvedUrl'])
+        if response.ok:
+            return True
+        else:
+            logger.warning(f'Cannot resolve {curie} in {resource["description"]}')
+    return False
+
+
+def main():
+    arg_parser = argparse.ArgumentParser(description='Add an external reference to the project specified')
+    arg_parser.add_argument('--project_accession', type=str, required=True,
+                            help='The project associated with the external reference.')
+    arg_parser.add_argument('--source_database', required=True, default='PubMed',
+                            help='The database the external reference relates to')
+
+    arg_parser.add_argument('--identifier', required=True, help='The identifier of the external reference')
+    arg_parser.add_argument('--debug', action='store_true', default=False,
+                            help='Set the script to output logging information at debug level')
+    args = arg_parser.parse_args()
+
+    log_cfg.add_stdout_handler()
+
+    if args.debug:
+        log_cfg.set_log_level(logging.DEBUG)
+
+    # Load the config_file from default location
+    load_config()
+
+    if not check_project_exists_in_evapro(args.project_accession):
+        logger.error(f'{args.project_accession} does not exist in EVAPRO')
+        return 1
+    if not check_existing_project_in_ena(args.project_accession):
+        logger.error(f'{args.project_accession} does not exist or is not public in ENA')
+        return 1
+    if _curie_exist(args.source_database + ":" + args.identifier):
+        add_external_reference_to_ena(args.project_accession, args.source_database, args.identifier)
+        EvaproExtReference().add_external_reference_to_evapro(args.project_accession, args.source_database, args.identifier)
+    else:
+        logger.error(f'Cannot resolve {args.source_database}:{args.identifier} in identifiers.org')
+
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())