EVA-3681 - Allow overwrite and override mode to change existing values on samples

bin/modify_existing_sample.py

@@ -15,6 +15,7 @@
 # limitations under the License.
 
 import argparse
+import logging
 
 from ebi_eva_common_pyutils.logger import logging_config as log_cfg
 
@@ -38,9 +39,12 @@ def main():
                                   '"curate" will create curation object on top of the BioSample. These are not '
                                  'used by ENA. '
                                  '"derive" will create a new BioSample derived from the old one.')
+    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.add_stdout_handler(level=logging.DEBUG)
 
     # Load the config_file from default location
     load_config()

eva_submission/biosample_submission/biosamples_submitters.py

@@ -154,16 +154,16 @@ def convert_sample_data_to_curation_object(self, future_sample):
         return dict(curation=curation_object, sample=future_sample.get('accession'))
 
     @staticmethod
-    def _update_from_array(key, sample_source, sample_dest):
+    def _update_from_array(key, sample_source, sample_dest, allow_overwrite=False):
         """Add the element of an array stored in specified key from source to destination"""
         if key in sample_source:
             if key not in sample_dest:
                 sample_dest[key] = []
             for element in sample_source[key]:
-                if element not in sample_dest[key]:
+                if element not in sample_dest[key] or allow_overwrite:
                     sample_dest[key].append(element)
 
-    def _update_samples_with(self, sample_source, sample_dest):
+    def _update_samples_with(self, sample_source, sample_dest, allow_overwrite=False):
         """Update a BioSample object with the value of another"""
         if 'override' in self.submit_type:
             # Ensure that override only change geographic location and collection date
@@ -173,12 +173,12 @@ def _update_samples_with(self, sample_source, sample_dest):
                     tmp_sample_source['characteristics'][attribute] = sample_source['characteristics'][attribute]
             sample_source = tmp_sample_source
         for attribute in sample_source['characteristics']:
-            if attribute not in sample_dest['characteristics']:
+            if attribute not in sample_dest['characteristics'] or allow_overwrite:
                 sample_dest['characteristics'][attribute] = sample_source['characteristics'][attribute]
-        self._update_from_array('externalReferences', sample_source, sample_dest)
-        self._update_from_array('relationships', sample_source, sample_dest)
-        self._update_from_array('contact', sample_source, sample_dest)
-        self._update_from_array('organization', sample_source, sample_dest)
+        self._update_from_array('externalReferences', sample_source, sample_dest, allow_overwrite)
+        self._update_from_array('relationships', sample_source, sample_dest, allow_overwrite)
+        self._update_from_array('contact', sample_source, sample_dest, allow_overwrite)
+        self._update_from_array('organization', sample_source, sample_dest, allow_overwrite)
         for key in ['taxId', 'accession', 'name', 'release']:
             if key in sample_source and key not in sample_dest:
                 sample_dest[key] = sample_source[key]
@@ -189,7 +189,7 @@ def create_sample_to_overwrite(self, sample):
         if self.can_overwrite(sample) and not self.allow_removal:
             # retrieve the sample without any curation and add the new data on top
             destination_sample = self._get_existing_sample(sample.get('accession'))
-            self._update_samples_with(sample, destination_sample)
+            self._update_samples_with(sample, destination_sample, allow_overwrite=True)
         return destination_sample
 
     def create_derived_sample(self, sample):