jpayne@0: #! /usr/bin/env python3
jpayne@0: 
jpayne@0: "Grab SRR numbers from BioProjects via the EMBL-ENA REST API's."
jpayne@0: 
jpayne@0: import requests
jpayne@0: import sys
jpayne@0: 
jpayne@0: sra_exp_query = "http://www.ebi.ac.uk/ebisearch/ws/rest/sra-experiment?query={bioproject}"
jpayne@0: 
jpayne@0: sample = """{
jpayne@0:     "hitCount": 2,
jpayne@0:     "entries": [
jpayne@0:         {
jpayne@0:             "id": "SRX377510",
jpayne@0:             "source": "sra-experiment"
jpayne@0:         },
jpayne@0:         {
jpayne@0:             "id": "SRX583279",
jpayne@0:             "source": "sra-experiment"
jpayne@0:         }
jpayne@0:     ],
jpayne@0:     "facets": []
jpayne@0: }"""
jpayne@0: 
jpayne@0: sra_run_query = "http://www.ebi.ac.uk/ebisearch/ws/rest/sra-run?query={experiment}"
jpayne@0: 
jpayne@0: sample = """{
jpayne@0:     "hitCount": 1,
jpayne@0:     "entries": [
jpayne@0:         {
jpayne@0:             "id": "SRR1029665",
jpayne@0:             "source": "sra-run"
jpayne@0:         }
jpayne@0:     ],
jpayne@0:     "facets": []
jpayne@0: }"""
jpayne@0: 
jpayne@0: if __name__ == "__main__":
jpayne@0: 	try:
jpayne@0: 		bioproject = sys.argv[1]
jpayne@0: 		b_result = requests.get(sra_exp_query.format(bioproject=bioproject), headers=dict(Accept="application/json"))
jpayne@0: 		b_result.raise_for_status()
jpayne@0: 		if b_result.json()['entries']:
jpayne@0: 			for experiment in [d['id'] for d in b_result.json()['entries']]:
jpayne@0: 				r_result = requests.get(sra_run_query.format(experiment=experiment), headers=dict(Accept="application/json"))
jpayne@0: 				r_result.raise_for_status()
jpayne@0: 				for run in [d['id'] for d in r_result.json()['entries']]:
jpayne@0: 					print(run)
jpayne@0: 		else:
jpayne@0: 			print(f"No results found for '{bioproject}'.", file=sys.stderr)
jpayne@0: 			quit(1)
jpayne@0: 	except IndexError:
jpayne@0: 		raise ValueError("Please provide an NCBI BioProject, NCBI BioSample, EMBL Project, or EMBL Study accession.")
jpayne@0: 	except KeyError as e:
jpayne@0: 		raise ValueError() from e
jpayne@0: 
jpayne@0: 
jpayne@0: