changeset 0:78cf37bd389d draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ucsc_cancer_download.py	Fri Jun 21 13:27:39 2013 -0400
@@ -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])

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ucsc_cancerbrowser.xml	Fri Jun 21 13:27:39 2013 -0400
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<!--
+    If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
+    the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
+    initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
+-->
+<tool name="UCSC Cancer Genomics Browser" id="ucsc_cancer_browser1" tool_type="data_source">
+    <description>server</description>
+    <command interpreter="python">ucsc_cancer_download.py $genomic $clinical $__app__.config.output_size_limit</command>
+    <inputs action="https://genome-cancer.ucsc.edu/proj/site/hgHeatmap" check_values="false" method="get">
+        <display>go to UCSC Cancer Browser $GALAXY_URL</display>
+        <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
+        <param name="tool_id" type="hidden" value="ucsc_cancer_browser1" />
+    </inputs>
+    <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
+        <request_param galaxy_name="URL" remote_name="URL" missing="" />
+    </request_param_translation>
+    <uihints minwidth="800"/>
+    <outputs>
+        <data name="genomic" format="tabular" label="#echo $URL.rsplit('/',1)[1].rsplit('.',1)[0]+' genomic'" />
+        <data name="clinical" format="tabular" label="#echo $URL.rsplit('/',1)[1].rsplit('.',1)[0]+' clinical'"/>
+    </outputs>
+    <options sanitize="False" refresh="True"/>
+</tool>