diff ucsc_xena_download.py @ 0:8bb037f88ed2

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ucsc_xena_download.py	Tue Jan 13 23:37:23 2015 -0500
@@ -0,0 +1,83 @@
+#!/usr/bin/env python
+import socket, urllib, sys, os
+from galaxy import eggs #eggs needs to be imported so that galaxy.util can find docutils egg...
+from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util import get_charset_from_http_headers
+import galaxy.model # need to import model before sniff to resolve a circular import dependency
+from galaxy.datatypes import sniff
+import tarfile
+import re
+
+filemap = [
+        ('genomic', r'genomic(Segment|Matrix)$'),
+        ('clinical', r'clinicalMatrix$'),
+        ]
+
+files = {
+        'genomic': sys.argv[1],
+        'clinical': sys.argv[2]
+        }
+
+max_file_size = sys.argv[3]
+
+def file_type(file):
+    with open(file) as f:
+        return from_json_string(f.read())['type']
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def load_input_parameters( filename, erase_file = True ):
+    datasource_params = {}
+    try:
+        json_params = from_json_string( open( filename, 'r' ).read() )
+        datasource_params = json_params.get( 'param_dict' )
+    except:
+        json_params = None
+        for line in open( filename, 'r' ):
+            try:
+                line = line.strip()
+                fields = line.split( '\t' )
+                datasource_params[ fields[0] ] = fields[1]
+            except:
+                continue
+    if erase_file:
+        open( filename, 'w' ).close() #open file for writing, then close, removes params from file
+    return json_params, datasource_params
+
+def load_file(files):
+    filename = files['genomic']
+    job_params, params = load_input_parameters( filename, False )
+    URL = params.get( 'URL', None ) #using exactly URL indicates that only one dataset is being downloaded
+    URL_method = params.get( 'URL_method', None )
+    socket.setdefaulttimeout( 600 )
+    try:
+        if not URL_method or URL_method == 'get':
+            page = urllib.urlopen( URL )
+        elif URL_method == 'post':
+            page = urllib.urlopen( URL, urllib.urlencode( params ) )
+    except Exception, e:
+        stop_err( 'The remote data source application may be off line, please try again later. Error: %s' % str( e ) )
+    if max_file_size:
+        file_size = int( page.info().get( 'Content-Length', 0 ) )
+        if file_size > max_file_size:
+            stop_err( 'The size of the data (%d bytes) you have requested exceeds the maximum allowed (%d bytes) on this server.' % ( file_size, max_file_size ) )
+    try:
+        cur_filename, is_multi_byte = sniff.stream_to_open_named_file( page, os.open( filename, os.O_WRONLY | os.O_CREAT ), filename, source_encoding=get_charset_from_http_headers( page.headers ) )
+    except Exception, e:
+        stop_err( 'Unable to fetch %s:\n%s' % ( URL, e ) )
+
+load_file(files)
+
+tar = tarfile.open(files['genomic'])
+names = tar.getnames()
+metafiles = [n for n in names if n.endswith('.json')]
+tar.extractall()
+withtype = [(file_type(file), file[0:-len(".json")]) for file in metafiles]
+try:
+    renames = [((n for (t, n) in withtype if re.search(pat, t)).next(), name) for (name, pat) in filemap]
+except StopIteration:
+     stop_err( 'Missing required file type in tarball' )
+for (frm, to) in renames:
+    os.rename(frm, files[to])