diff data_manager/data_manager_ceas_fetch_annotations.py @ 0:f411ce97a351 draft

Uploaded initial version 1.0.2-2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_ceas_fetch_annotations.py	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,153 @@
+#!/usr/bin/env python
+#
+
+import sys
+import os
+import subprocess
+import tempfile
+import optparse
+import urllib2
+import gzip
+import shutil
+
+from galaxy.util.json import from_json_string, to_json_string
+
+# Download file from specified URL and put into local subdir
+
+if __name__ == '__main__':
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    options,args = parser.parse_args()
+    print "options: %s" % options
+    print "args   : %s" % args
+    if len(args) != 2:
+        p.error("Need to supply JSON file name and description text")
+
+    # Read the JSON supplied from the data manager tool
+    # Results from this program will be returned via the
+    # same file
+    jsonfile = args[0]
+    params = from_json_string(open(jsonfile).read() )
+    print "%s" % params
+
+    # Extract the data from the input JSON
+    # See https://wiki.galaxyproject.org/Admin/Tools/DataManagers/HowTo/Define?highlight=%28\bAdmin%2FTools%2FDataManagers\b%29
+    # for example of JSON
+    #
+    # We want the values set in the data manager XML
+    dbkey = params['param_dict']['dbkey']
+    description = args[1].strip()
+    identifier = params['param_dict']['unique_id'].strip()
+    # Where to put the output file
+    # Nb we have to make this ourselves, it doesn't exist by default
+    target_dir = params['output_data'][0]['extra_files_path']
+    os.mkdir(target_dir)
+
+    method = params['param_dict']['reference_source']['reference_source_selector']
+
+    # Dictionary for returning to data manager
+    data_manager_dict = {}
+    data_manager_dict['data_tables'] = dict()
+
+    # Download from URL
+    if method == 'web':
+        url = params['param_dict']['reference_source']['annotation_url']
+        print "Downloading: %s" % url
+        annotation_file_name = os.path.basename(url)
+        annotation_file_path = os.path.join(target_dir,annotation_file_name)
+        print "Annotation file name: %s" % annotation_file_name
+        print "Annotation file path: %s" % annotation_file_path
+        open(annotation_file_path,'wb').write(urllib2.urlopen(url).read())
+        if annotation_file_name.endswith('.gz'):
+            # Uncompress
+            uncompressed_file = annotation_file_path[:-3]
+            open(uncompressed_file,'wb').write(gzip.open(annotation_file_path,'rb').read())
+            # Remove gzipped file
+            os.remove(annotation_file_path)
+            annotation_file_name = os.path.basename(uncompressed_file)
+            annotation_file_path = uncompressed_file
+        # Update the identifier and description
+        if not identifier:
+            identifier = "%s_ceas_web" % dbkey
+        if not description:
+            description = "%s (%s)" % (os.path.splitext(annotation_file_name)[0],dbkey)
+        # Update the output dictionary
+        data_manager_dict['data_tables']['ceas_annotations'] = {
+            'value': identifier,
+            'dbkey': dbkey,
+            'name': description,
+            'path': annotation_file_name,
+        }
+    elif method == 'server':
+        # Pull in a file from the server
+        filename = params['param_dict']['reference_source']['annotation_filename']
+        create_symlink = params['param_dict']['reference_source']['create_symlink']
+        print "Canonical gene list file name: %s" % filename
+        print "Create symlink: %s" % create_symlink
+        target_filename = os.path.join(target_dir,os.path.basename(filename))
+        if create_symlink == 'copy_file':
+            shutil.copyfile(filename,target_filename)
+        else:
+            os.symlink(filename,target_filename)
+        # Update the identifier and description
+        if not identifier:
+            identifier = "%s_%s" % (dbkey,
+                                    os.path.splitext(os.path.basename(filename))[0])
+        if not description:
+            description = "%s: %s" % (dbkey,
+                                      os.path.splitext(os.path.basename(filename))[0])
+        # Update the output dictionary
+        data_manager_dict['data_tables']['ceas_annotations'] = {
+            'value': identifier,
+            'dbkey': dbkey,
+            'name': description,
+            'path': os.path.basename(filename),
+        }
+    elif method == 'from_wig':
+        # Make a reference file from a wig file
+        wig_file = params['param_dict']['reference_source']['wig_file']
+        gene_annotation = params['param_dict']['reference_source']['gene_annotation']
+        target_filename = os.path.join(target_dir,"%s_%s.%s" % (dbkey,
+                                                                os.path.basename(wig_file),
+                                                                gene_annotation))
+        print "Wig file: %s" % wig_file
+        print "Gene annotation: %s" % gene_annotation
+        print "Output file: %s" % os.path.basename(target_filename)
+        # Make a working directory
+        working_dir = tempfile.mkdtemp()
+        # Collect stderr in a file for reporting later
+        stderr_filen = tempfile.NamedTemporaryFile().name
+        # Build the command to run
+        cmd = "build_genomeBG -d %s -g %s -w %s -o %s" % (dbkey,
+                                                          gene_annotation,
+                                                          wig_file,
+                                                          target_filename)
+        print "Running %s" %  cmd
+        proc = subprocess.Popen(args=cmd,shell=True,cwd=working_dir,
+                                stderr=open(stderr_filen,'wb'))
+        proc.wait()
+        # Copy stderr to stdout
+        with open(stderr_filen,'r') as fp:
+            sys.stdout.write(fp.read())
+        # Update identifier and description
+        if not identifier:
+            identifier = "%s_%s_%s" % (dbkey,
+                                       gene_annotation,
+                                       os.path.basename(wig_file))
+        if not description:
+            description = "%s %s from %s" % (dbkey,
+                                             gene_annotation,
+                                             os.path.basename(wig_file))
+        # Update the output dictionary
+        data_manager_dict['data_tables']['ceas_annotations'] = {
+            'value': identifier,
+            'dbkey': dbkey,
+            'name': description,
+            'path': os.path.basename(target_filename),
+        }
+    else:
+        raise NotImplementedError("Method '%s' not implemented" % method)
+
+    #save info to json file
+    open(jsonfile,'wb').write(to_json_string(data_manager_dict))
+