--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_tables.py	Wed Feb 02 17:16:15 2022 +0000
@@ -0,0 +1,102 @@
+import argparse
+import json
+import pathlib
+from datetime import datetime
+
+"""
+Parse the configfile generated by the Galaxy tool.
+This file is JSON-formatted and should be converted to a set of tabular files.
+"""
+
+FILE_FORMAT = 'fastq'
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--studies', dest='studies_json_path', required=True)
+parser.add_argument('--out_dir', dest='out_path', required=True)
+parser.add_argument('--action', dest='action', required=True)
+args = parser.parse_args()
+
+with open(args.studies_json_path, 'r') as studies_json_file:
+    studies_dict = json.load(studies_json_file)
+studies_table = open(pathlib.Path(args.out_path) / 'studies.tsv', 'w')
+studies_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'study_type',
+                               'study_abstract', 'pubmed_id', 'submission_date']) + '\n')
+samples_table = open(pathlib.Path(args.out_path) / 'samples.tsv', 'w')
+experiments_table = open(pathlib.Path(args.out_path) / 'experiments.tsv', 'w')
+experiments_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'study_alias',
+                                   'sample_alias', 'design_description', 'library_name',
+                                   'library_strategy', 'library_source', 'library_selection',
+                                   'library_layout', 'insert_size',
+                                   'library_construction_protocol', 'platform', 'instrument_model',
+                                   'submission_date']) + '\n')
+runs_table = open(pathlib.Path(args.out_path) / 'runs.tsv', 'w')
+runs_table.write('\t'.join(['alias', 'status', 'accession', 'experiment_alias', 'file_name',
+                            'file_format', 'file_checksum', 'submission_date']) + '\n')
+
+action = args.action
+
+dt_oobj = datetime.now(tz=None)
+timestamp = dt_oobj.strftime("%Y%m%d_%H:%M:%S")
+for study_index, study in enumerate(studies_dict):
+    study_alias = 'study_' + str(study_index) + '_' + timestamp
+    studies_table.write('\t'.join([study_alias, action, 'ENA_accession', study['title'],
+                                   study['type'], study['abstract'], study['pubmed_id'],
+                                   'ENA_submission_data']))
+    if "geo_location" in study['samples'][0].keys():           # sample belongs to a viral sample
+        samples_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'scientific_name',
+                                       'taxon_id', 'sample_description', 'collection_date',
+                                       'geographic_location', 'host_common_name', 'host_subject_id',
+                                       'host_health_state', 'host_sex', 'host_scientific_name',
+                                       'collector_name', 'collecting_institution', 'isolate',
+                                       'submission_date']) + '\n')
+    else:
+        samples_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'scientific_name',
+                                       'taxon_id', 'sample_description', 'submission_date']) + '\n')
+    for sample_index, sample in enumerate(study['samples']):
+        sample_alias = 'sample_' + str(sample_index) + '_' + timestamp
+        if "geo_location" in sample.keys():  # sample belongs to a viral sample
+            if sample['collector_name'] == '':
+                sample['collector_name'] = 'unknown'
+            samples_table.write('\t'.join([sample_alias, action, 'ena_accession', sample['title'],
+                                           sample['tax_name'], sample['tax_id'],
+                                           sample['description'], sample['collection_date'],
+                                           sample['geo_location'], sample['host_common_name'],
+                                           sample['host_subject_id'], sample['host_health_state'],
+                                           sample['host_sex'], sample['host_scientific_name'],
+                                           sample['collector_name'],
+                                           sample['collecting_institution'], sample['isolate'],
+                                           'ENA_submission_date']) + '\n')
+        else:
+            samples_table.write('\t'.join([sample_alias, action, 'ena_accession', sample['title'],
+                                           sample['tax_name'], sample['tax_id'],
+                                           sample['description'], 'ENA_submission_date']) + '\n')
+        for exp_index, exp in enumerate(sample['experiments']):
+            exp_alias = 'experiment_' + str(exp_index) + '.' + str(sample_index) + '_' + timestamp
+            lib_alias = 'library_' + str(exp_index) + '_' + str(sample_index)
+            experiments_table.write('\t'.join([exp_alias, action, 'accession_ena', exp['title'],
+                                               study_alias, sample_alias, exp['experiment_design'],
+                                               lib_alias, exp['library_strategy'],
+                                               exp['library_source'], exp['library_selection'],
+                                               exp['library_layout'].lower(), exp['insert_size'],
+                                               exp['library_construction_protocol'],
+                                               exp['platform'], exp['instrument_model'],
+                                               'submission_date_ENA']) + '\n')
+            run_index = 0
+            # exp['runs'] is a list of lists
+            for (base_run, run_files) in exp['runs']:
+                run_index += 1
+                if base_run != '':
+                    run_alias = base_run
+                else:
+                    # no alias provided, generated a unique one
+                    run_alias = '_'.join(['run_' + str(run_index), str(exp_index),
+                                          str(sample_index)]) + '_' + timestamp
+                for file_entry in run_files:
+                    runs_table.write('\t'.join([run_alias, action, 'ena_run_accession', exp_alias,
+                                                file_entry, FILE_FORMAT, 'file_checksum',
+                                                'submission_date_ENA']) + '\n')
+
+studies_table.close()
+samples_table.close()
+experiments_table.close()
+runs_table.close()