--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gsaf_download.py	Fri Dec 05 14:24:41 2014 -0500
@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+import urllib, urllib2
+import sys
+import subprocess
+import json
+import hashlib
+import os
+import logging
+logging.basicConfig(level=logging.DEBUG)
+log = logging.getLogger()
+
+try:
+    os.makedirs("output")
+except:
+    #TODO
+    pass
+
+URL = sys.argv[1]
+DATASET_ID = sys.argv[2]
+
+#req = urllib2.urlopen(URL)
+#page = req.read()
+with open('file.html', 'r') as handle:
+    page = handle.read()
+comments = [x.strip() for x in page.split('\n') if x.strip().startswith('<!--')]
+
+gx_json = open('galaxy.json', 'w')
+
+prefix = '<!--gsafjson'
+suffix = '-->'
+for gsafjson in [x[len(prefix): -len(suffix)].strip() for x in comments if 'gsafjson' in x]:
+    #{"file_type":"fastq.gz",
+    # "JA":"****",
+    # "sample_name":"Sample10",
+    # "user_data":{"description":{} } ,
+    # "md5":"2ea00f4eef8f6a2344b80fbe12ab2eb7",
+    # "url":"http://gsaf.s3.amazonaws.com/****",
+    # "size_in_mb":45,
+    # "filename":"Sample10_S8_L001_R1_001.fastq.gz",
+    # "reads":["Sample10_S8_L001_R1_001.fastq.gz","Sample10_S8_L001_R2_001.fastq.gz"],
+    # "SA":"***"}
+    data = json.loads(gsafjson)
+    log.info("Fetching %s" % data['filename'])
+    file_path = os.path.join('output', data['filename'])
+    #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)
+
+    stderr = ''
+    #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"}
+    line_count = subprocess.check_output(['wc', '-l', file_path]).strip()
+    line_count = line_count[0:line_count.index(' ')]
+
+    galaxy_json = {
+        'name': data['filename'].strip(data['file_type']),
+        'stdout': None,
+        'stderr': stderr,
+        'line_count': int(line_count),
+        # TODO, check that data is really .gz
+        'ext': data['file_type'].strip('.gz'),
+        'dataset_id': DATASET_ID,
+        'type': 'dataset'
+    }
+
+    #try:
+        #subprocess.check_call(['gunzip', file_path])
+    #except:
+        #log.error("Couldn't extract %s" % data['filename'])
+
+    gx_json.write(json.dumps(galaxy_json) + "\n")
+