Try to figure out where UCSC is hosting our submitted files

[htsworkflow.git] / htsworkflow / submission / ucsc.py

diff --git a/htsworkflow/submission/ucsc.py b/htsworkflow/submission/ucsc.py
index f80629a9cda462ac6ce8e45f58949b4ffb9037f9..9181830e34983724e586a906a7194d96fc9507eb 100644 (file)
--- a/htsworkflow/submission/ucsc.py
+++ b/htsworkflow/submission/ucsc.py
@@ -1,7 +1,11 @@
+"""Utilities for extracting information from the ENCODE DCC
+"""
 import urlparse
+import urllib2
 
 UCSCEncodePipeline = "http://encodesubmit.ucsc.edu/pipeline/"
 
+
 def ddf_download_url(submission_id):
     """Return url to download a DDF for a submission
 
@@ -11,6 +15,7 @@ def ddf_download_url(submission_id):
     fragment = 'download_ddf/%s' % (submission_id,)
     return urlparse.urljoin(UCSCEncodePipeline, fragment)
 
+
 def daf_download_url(submission_id):
     """Return url to download a DAF for a submission
 
@@ -20,6 +25,7 @@ def daf_download_url(submission_id):
     fragment = 'download_daf/%s' % (submission_id,)
     return urlparse.urljoin(UCSCEncodePipeline, fragment)
 
+
 def submission_view_url(submission_id):
     """Return url to download a DAF for a submission
 
@@ -28,3 +34,27 @@ def submission_view_url(submission_id):
     """
     fragment = 'show/%s' % (submission_id,)
     return urlparse.urljoin(UCSCEncodePipeline, fragment)
+
+
+def get_ucsc_file_index(base_url):
+    """Get index of files for a ENCODE collection
+    """
+    if base_url[-1] != '/': base_url += '/'
+    request = urllib2.urlopen(base_url + 'files.txt')
+    file_index = parse_ucsc_file_index(request)
+    return file_index
+
+
+def parse_ucsc_file_index(stream):
+    """Turn a UCSC DCC files.txt index into a dictionary of name-value pairs
+    """
+    file_index = {}
+    for line in stream:
+        filename, attribute_line = line.split('\t')
+        attributes = {}
+        for assignment in  attribute_line.split(';'):
+            name, value = assignment.split('=')
+            attributes[name.strip()] = value.strip()
+
+        file_index[filename] = attributes
+    return file_index