Delete Curation

bin/delete_existing_curation.py

@@ -0,0 +1,105 @@
+#!/usr/bin/env python
+
+# Copyright 2023 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
+
+from ebi_eva_common_pyutils.config import cfg
+from ebi_eva_common_pyutils.logger import logging_config as log_cfg
+
+from eva_submission.biosample_submission.biosamples_communicators import WebinHALCommunicator, AAPHALCommunicator
+from eva_submission.biosample_submission.biosamples_submitters import BioSamplesSubmitter
+from eva_submission.submission_config import load_config
+
+logger = log_cfg.get_logger(__name__)
+
+
+class LastSampleCurationDeleter(BioSamplesSubmitter):
+
+    def __init__(self, communicators=None):
+        if not communicators:
+            communicators = LastSampleCurationDeleter.get_config_communicators()
+        super().__init__(communicators, submit_type=('curate',), allow_removal=True)
+
+
+    @staticmethod
+    def get_config_communicators():
+        communicators = []
+        # If the config has the credential for using webin with BioSamples use webin first
+        if cfg.query('biosamples', 'webin_url') and cfg.query('biosamples', 'webin_username') and \
+                cfg.query('biosamples', 'webin_password'):
+            communicators.append(WebinHALCommunicator(
+                cfg.query('biosamples', 'webin_url'), cfg.query('biosamples', 'bsd_url'),
+                cfg.query('biosamples', 'webin_username'), cfg.query('biosamples', 'webin_password')
+            ))
+        communicators.append(AAPHALCommunicator(
+            cfg.query('biosamples', 'aap_url'), cfg.query('biosamples', 'bsd_url'),
+            cfg.query('biosamples', 'username'), cfg.query('biosamples', 'password'),
+            cfg.query('biosamples', 'domain')
+        ))
+        return communicators
+
+    def delete_last_curation_of(self, accession, delete=False):
+        sample_data = self.default_communicator.follows_link('samples', method='GET', join_url=accession)
+        curation_data = self.default_communicator.follows_link('curationLinks', json_obj=sample_data, all_pages=True)
+        curation_links = curation_data.get('_embedded').get('curationLinks')
+        curation_object = curation_links[-1]
+
+        communicator = None
+        # Check if we own the curation
+        for c in self.communicators:
+            if c.communicator_attributes.items() <= curation_object.items():
+                communicator = c
+        if not communicator:
+            self.warning(f'Curation object {curation_object["hash"]} is not owned by you: '
+                         f'Webin: {curation_object["webinSubmissionAccountId"]} - '
+                         f'Domain: {curation_object["domain"]}')
+        else:
+            if curation_object:
+                logger.info(
+                    f'About to delete BioSamples curation {curation_object["hash"]} for accession {accession} which changed\n '
+                    f'- attributes with {curation_object["curation"]["attributesPre"]} to {curation_object["curation"]["attributesPost"]}\n'
+                    f'- External Ref with {curation_object["curation"]["externalReferencesPre"]} to {curation_object["curation"]["externalReferencesPost"]}\n'
+                    f'- Relationship with {curation_object["curation"]["relationshipsPre"]} to {curation_object["curation"]["relationshipsPost"]}'
+                )
+                if delete:
+                    self.default_communicator.follows_link('self', json_obj=curation_object, method='DELETE')
+                pass
+
+
+def main():
+    arg_parser = argparse.ArgumentParser(
+        description='query Biosamples accessions from a file')
+    arg_parser.add_argument('--accession_file', required=True,
+                            help='file containing the list of accession to query')
+    arg_parser.add_argument('--set_delete', action='store_true', default=False, help='Actually does the deletion')
+    # Load the config_file from default location
+    load_config()
+
+    args = arg_parser.parse_args()
+
+    log_cfg.add_stdout_handler()
+
+    # Load the config_file from default location
+    load_config()
+    last_sample_curation_deleter = LastSampleCurationDeleter()
+    with open(args.accession_file) as open_file:
+        for line in open_file:
+            accession = line.strip()
+            last_sample_curation_deleter.delete_last_curation_of(accession, args.set_delete)
+
+
+if __name__ == "__main__":
+    main()

eva_submission/biosample_submission/biosamples_communicators.py

@@ -14,6 +14,7 @@
 # limitations under the License.
 
 import re
+from json import JSONDecodeError
 
 import requests
 from cached_property import cached_property
@@ -29,7 +30,7 @@ class HALCommunicator(AppLogger):
     """
     This class helps navigate through REST API that uses the HAL standard.
     """
-    acceptable_code = [200, 201]
+    acceptable_code = [200, 201, 204]
 
     def __init__(self, auth_url, bsd_url, username, password):
         self.auth_url = auth_url
@@ -102,7 +103,12 @@ def follows(self, query, json_obj=None, method='GET', url_template_values=None,
         if join_url:
             url += '/' + join_url
         # Now query the url
-        json_response = self._req(method, url, **kwargs).json()
+        response = self._req(method, url, **kwargs)
+        try:
+            json_response = response.json()
+        except JSONDecodeError:
+            self.debug(f'No response available for request {method} to {url}')
+            return {}
 
         # Depaginate the call if requested
         if all_pages is True:

tests/test_biosamples_submission.py

@@ -5,13 +5,12 @@
 
 import yaml
 
+from eva_submission.biosample_submission.biosamples_communicators import HALCommunicator
 from eva_submission import ROOT_DIR
 from eva_submission.biosample_submission import biosamples_submitters
-from eva_submission.biosample_submission.biosamples_communicators import HALCommunicator, WebinHALCommunicator, \
-    AAPHALCommunicator
 from eva_submission.biosample_submission.biosamples_submitters import BioSamplesSubmitter, SampleMetadataSubmitter, \
-    SampleReferenceSubmitter
-import eva_submission.biosample_submission.biosamples_submitters
+    SampleReferenceSubmitter, AAPHALCommunicator, WebinHALCommunicator
+
 
 class BSDTestCase(TestCase):