EVA-3641 Specify the analysis only option correctly

eva_submission/eload_brokering.py

@@ -106,7 +106,7 @@ def upload_to_bioSamples(self, force=False):
             sample_name_to_accession = sample_metadata_submitter.already_submitted_sample_names_to_accessions()
             self.eload_cfg.set('brokering', 'Biosamples', 'Samples', value=sample_name_to_accession)
         elif (
-            self.eload_cfg.query('brokering', 'Biosamples', 'Samples')
+                self.eload_cfg.query('brokering', 'Biosamples', 'Samples')
             and self.eload_cfg.query('brokering', 'Biosamples', 'pass')
         ):
             self.info('BioSamples brokering is already done, Skip!')
@@ -124,7 +124,9 @@ def upload_to_bioSamples(self, force=False):
             if not passed:
                 raise ValueError(f'Not all samples were successfully brokered to BioSamples! '
                                  f'Found {len(sample_name_to_accession)} and expected '
-                                 f'{len(sample_metadata_submitter.all_sample_names())}')
+                                 f'{len(sample_metadata_submitter.all_sample_names())}. '
+                                 f'Missing samples are '
+                                 f'{[sample_name for sample_name in sample_metadata_submitter.all_sample_names() if sample_name not in sample_name_to_accession]}')
 
     def update_biosamples_with_study(self, force=False):
         if not self.eload_cfg.query('brokering', 'Biosamples', 'backlinks') or force:

eva_submission/eload_ingestion.py

@@ -226,7 +226,7 @@ def load_from_ena_from_project_or_analysis(self, analysis_accession=None):
         command = (f"perl {cfg['executable']['load_from_ena']} -p {self.project_accession} -c submitted -v 1 "
                    f"-l {self._get_dir('scratch')} -e {str(self.eload_num)}")
         if analysis_accession:
-            command += f' -A -a {analysis_accession}'
+            command += f' -A 1 -a {analysis_accession}'
         try:
             command_utils.run_command_with_output('Load metadata from ENA to EVAPRO', command)
             self.eload_cfg.set(self.config_section, 'ena_load', value='success')
@@ -555,7 +555,7 @@ def update_files_with_ftp_path(self):
                 execute_query(conn, ftp_update)
 
     def update_loaded_assembly_in_browsable_files(self):
-        # find assembly associated with each browseable file and copy it to the browsable file table
+        # find assembly associated with each browsable file and copy it to the browsable file table
         query = ('select bf.file_id, a.vcf_reference_accession '
                  'from analysis a '
                  'join analysis_file af on a.analysis_accession=af.analysis_accession '
@@ -564,7 +564,8 @@ def update_loaded_assembly_in_browsable_files(self):
         with self.metadata_connection_handle as conn:
             rows = get_all_results_for_query(conn, query)
             if len(rows) == 0:
-                raise ValueError('Something went wrong with loading from ENA')
+                raise ValueError(f'No files found associated with project {self.project_accession}. '
+                                 f'Something went wrong with loading from ENA')
 
             # Update each file with its associated assembly accession
             for file_id, assembly_accession in rows:

tests/test_eload_ingestion.py

@@ -202,7 +202,7 @@ def test_load_from_ena_from_analysis(self):
             analysis_accession = 'ERZ2499196'
             self.eload.load_from_ena_from_project_or_analysis(analysis_accession)
             command = ('perl /path/to/load_from_ena_script -p PRJEB12345 -c submitted -v 1 -l '
-                       f'{self.eload._get_dir("scratch")} -e 33 -A -a ERZ2499196')
+                       f'{self.eload._get_dir("scratch")} -e 33 -A 1 -a ERZ2499196')
             mockrun.assert_called_once_with('Load metadata from ENA to EVAPRO', command)
 
     def test_ingest_accession(self):