diff chasm_webservice/chasm_webservice.py @ 7:af0c2fa5bc76 draft

Uploaded

--- a/chasm_webservice/chasm_webservice.py	Tue Apr 15 13:06:25 2014 -0400
+++ b/chasm_webservice/chasm_webservice.py	Wed Jul 16 20:29:51 2014 -0400
@@ -40,7 +40,7 @@
              1: 'Amino_Acid_Level_Analysis.csv', 2: 'Gene_Level_Analysis.csv'}
 
 
-def retry(ExceptionToCheck, tries=4, delay=3, backoff=2, logger=None):
+def retry(ExceptionToCheck, tries=40000, delay=3, backoff=2, logger=None):
     '''Retry calling the decorated function using an exponential backoff.
 
     http://www.saltycrane.com/blog/2009/11/trying-out-retry-decorator-python/
@@ -150,11 +150,13 @@
         else:
             request = requests.post(
                 __URL__, data=stripped_data, files=dict(foo='bar'))
+        print request.text
         job_id = json.loads(request.text)['jobid']
         return job_id
 
     @retry(requests.exceptions.HTTPError)
     def zip_exists(self, job_id):
+        print job_id
         url = 'http://www.cravat.us/results/%s/%s.zip' % (job_id, job_id)
         zip_download_request = requests.request('GET', url)
         if zip_download_request.status_code == 404:
@@ -243,6 +245,9 @@
     parser.add_argument('--amino_acid_level_analysis_out',
                         dest='amino_acid_level_analysis_out',
                         type=str, required=True,)
+    parser.add_argument('--codon_level_analysis_out',
+                        dest='codon_level_analysis_out',
+                        type=str, required=True,)
     parser.add_argument('--error_file', dest='error_file_out',
                         type=str, required=True)
     parser.add_argument('--snv_box_out', dest='snv_box_out',
@@ -266,7 +271,8 @@
                 'Variant_Analysis.Result.tsv': args.variant_analysis_out,
                 'Gene_Level_Analysis.Result.tsv': args.gene_analysis_out,
                 'SnvGet Feature Description.xls': args.snv_features_out,
-                'error.txt': args.error_file_out
+                'error.txt': args.error_file_out,
+                'Codon_Level_Analysis.Result.tsv': args.codon_level_analysis_out,
                 }
     url = chasm_web.zip_exists(job_id)
     download = chasm_web.download_zip(url, job_id)