Added script for retrieving results from Michigan and TOPMed Imputati…

…on Servers

get_imputation_server_results/v1/get_imputation_server_results.py

@@ -0,0 +1,56 @@
+import argparse
+import json
+import os
+
+# Get arguments
+parser = argparse.ArgumentParser()
+parser.add_argument(
+    "--token",
+    help="Authentication token for API",
+    type = str
+)
+parser.add_argument(
+    "--job_id_json",
+    help="File containing job ID",
+    type = str
+)
+parser.add_argument(
+    "--out_dir",
+    help="Output directory",
+    type = str
+)
+parser.add_argument(
+    "--server",
+    help="Server used for imputation",
+    type = str,
+    choices = ["mis", "topmed"]
+)
+args = parser.parse_args()
+
+out_dir = args.out_dir if (args.out_dir[-1] == "/") else (args.out_dir + "/")
+
+with open(args.job_id_json) as f:
+    job_id_json = json.load(f)
+
+# Get job details
+job_details_endpoint = ''
+results_endpoint = ''
+if args.server == 'mis':
+    job_details_endpoint = 'https://imputationserver.sph.umich.edu/api/v2/jobs/' + job_id_json['id']
+    results_endpoint = 'https://imputationserver.sph.umich.edu/share/results/'
+elif args.server == 'topmed':
+    job_details_endpoint = 'https://imputation.biodatacatalyst.nhlbi.nih.gov/api/v2/jobs/' + job_id_json['id']
+    results_endpoint = 'https://imputation.biodatacatalyst.nhlbi.nih.gov/share/results/'
+
+job_details_json = out_dir + 'job_details.json'
+get_job_details_cmd = "curl -H \"X-Auth-Token: {}\" {} > {}".format(args.token, job_details_endpoint, job_details_json)
+os.system(get_job_details_cmd)
+
+# Transfer outputs
+with open(job_details_json) as f:
+    outputs = json.load(f)
+
+for output_category in outputs['outputParams']:
+    for file in output_category['files']:
+        file_download_cmd = "wget -P {} {}{}/{}".format(out_dir, results_endpoint, file['hash'], file['name'])
+        os.system(file_download_cmd)