Mercurial > repos > eric-rasche > gsaf_downloader

changeset 4:a90d7b00d727 draft default tip

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Removed testing code
author eric-rasche
date Fri, 05 Dec 2014 14:38:00 -0500
parents ba70ea57cef9
children
files gsaf_download.py
diffstat 1 files changed, 9 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/gsaf_download.py	Fri Dec 05 14:34:49 2014 -0500
+++ b/gsaf_download.py	Fri Dec 05 14:38:00 2014 -0500
@@ -40,14 +40,14 @@
     data = json.loads(gsafjson)
     log.info("Fetching %s" % data['filename'])
     file_path = os.path.join('output', data['filename'])
-    #urllib.urlretrieve(data['url'], file_path)
+    urllib.urlretrieve(data['url'], file_path)
     log.info("Hashing file")
-    #file_md5 = hashlib.md5(open(file_path).read()).hexdigest()
-    #log.debug("Hashed to %s" % file_md5)
+    file_md5 = hashlib.md5(open(file_path).read()).hexdigest()
+    log.debug("Hashed to %s" % file_md5)
 
     stderr = ''
-    #if file_md5 != data['md5']:
-        #stderr = 'md5sum mismatch: %s != %s' % (file_md5, data['md5'])
+    if file_md5 != data['md5']:
+        stderr = 'md5sum mismatch: %s != %s' % (file_md5, data['md5'])
 
     # Galaxy.json
     # {"name": "lambda.fa", "stdout": "uploaded fasta file", "line_count": 811, "ext": "fasta", "dataset_id": 16220, "type": "dataset"}
@@ -65,10 +65,10 @@
         'type': 'dataset'
     }
 
-    #try:
-        #subprocess.check_call(['gunzip', file_path])
-    #except:
-        #log.error("Couldn't extract %s" % data['filename'])
+    try:
+        subprocess.check_call(['gunzip', file_path])
+    except:
+        log.error("Couldn't extract %s" % data['filename'])
 
     gx_json.write(json.dumps(galaxy_json) + "\n")