EVA-3221 - Provide the expected parameter to the brokering prep (#161)

* provide the expected parameter to the brokering prep
EBIvariation · Jul 3, 2023 · ea18009 · ea18009
1 parent 9e53ff4
commit ea18009
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Showing 3 changed files with 29 additions and 6 deletions.
diff --git a/eva_submission/eload_brokering.py b/eva_submission/eload_brokering.py
@@ -1,3 +1,4 @@
+import csv
 import os
 import shutil
 import subprocess
@@ -144,10 +145,26 @@ def _get_valid_vcf_files(self):
             valid_vcf_files.extend(files) if files else None
         return valid_vcf_files
 
+    def _generate_csv_mappings(self):
+        vcf_files_mapping_csv = os.path.join(self.eload_dir, 'brokering_vcf_files_mapping.csv')
+        with open(vcf_files_mapping_csv, 'w', newline='') as file:
+            writer = csv.writer(file)
+            writer.writerow(['vcf', 'fasta', 'report', 'assembly_accession'])
+            sub_analyses = self.eload_cfg.query('submission', 'analyses')
+            valid_analyses = self.eload_cfg.query('validation', 'valid', 'analyses')
+            for analysis_alias in valid_analyses:
+                fasta = sub_analyses[analysis_alias]['assembly_fasta']
+                report = sub_analyses[analysis_alias]['assembly_report']
+                assembly_accession = sub_analyses[analysis_alias]['assembly_accession']
+                for vcf_file in valid_analyses[analysis_alias]['vcf_files']:
+                    writer.writerow([vcf_file, fasta, report, assembly_accession])
+        return vcf_files_mapping_csv
+
     def _run_brokering_prep_workflow(self):
         output_dir = self.create_nextflow_temp_output_directory()
+        cfg['executable']['python']['script_path'] = os.path.dirname(os.path.dirname(__file__))
         brokering_config = {
-            'vcf_files': self._get_valid_vcf_files(),
+            'vcf_files_mapping': self._generate_csv_mappings(),
             'output_dir': output_dir,
             'executable': cfg['executable']
         }

diff --git a/eva_submission/eload_validation.py b/eva_submission/eload_validation.py
@@ -229,18 +229,17 @@ def parse_sv_check_log(self, sv_check_log):
         return nb_sv
 
     def _generate_csv_mappings(self):
-        vcf_files_mapping_csv = os.path.join(self.eload_dir, 'vcf_files_mapping.csv')
+        vcf_files_mapping_csv = os.path.join(self.eload_dir, 'validation_vcf_files_mapping.csv')
         with open(vcf_files_mapping_csv, 'w', newline='') as file:
             writer = csv.writer(file)
-            writer.writerow(['vcf', 'fasta', 'report', 'assembly_accession'])
+            writer.writerow(['vcf', 'fasta', 'report'])
             analyses = self.eload_cfg.query('submission', 'analyses')
             for analysis_alias, analysis_data in analyses.items():
                 fasta = analysis_data['assembly_fasta']
                 report = analysis_data['assembly_report']
-                assembly_accession = analysis_data['assembly_accession']
                 if analysis_data['vcf_files']:
                     for vcf_file in analysis_data['vcf_files']:
-                        writer.writerow([vcf_file, fasta, report, assembly_accession])
+                        writer.writerow([vcf_file, fasta, report])
                 else:
                     self.warning(f"VCF files for analysis {analysis_alias} not found")
         return vcf_files_mapping_csv

diff --git a/tests/test_eload_brokering.py b/tests/test_eload_brokering.py
@@ -86,11 +86,18 @@ def test_run_brokering_prep_workflow(self):
         self.eload.eload_cfg.set('validation', 'valid', 'analyses', value={
             'analysis_alias1': {
                 'vcf_files': [os.path.join(self.resources_folder, 'vcf_file.vcf')],
+            },
+        })
+        self.eload.eload_cfg.set('submission', 'analyses', value={
+            'analysis_alias1': {
                 'assembly_fasta': os.path.join(self.resources_folder, 'reference_genome.fa'),
+                'assembly_report': os.path.join(self.resources_folder, 'reference_genome_assembly_report.tx'),
+                'assembly_accession': 'GCA000000.1'
             },
         })
         cfg.content['executable'] = {
-            'nextflow': 'path_to_nextflow'
+            'nextflow': 'path_to_nextflow',
+            'python': {'script_path': 'path_to_script'}
         }
         temp_dir = 'temporary_directory'
         nf_script = os.path.join(NEXTFLOW_DIR, 'prepare_brokering.nf')