# HG changeset patch
# User fabio
# Date 1495741036 14400
# Node ID 7815152f70c664e81bf0d4beacb34ba63667dfd7
# Parent 23de6169957af9e1825f1ad560385c520bfda369
Uploaded 20170525
diff -r 23de6169957a -r 7815152f70c6 ._gdcwebapp.xml
Binary file ._gdcwebapp.xml has changed
diff -r 23de6169957a -r 7815152f70c6 ._json_data_source_mod.py
Binary file ._json_data_source_mod.py has changed
diff -r 23de6169957a -r 7815152f70c6 ._tool_dependencies.xml
Binary file ._tool_dependencies.xml has changed
diff -r 23de6169957a -r 7815152f70c6 gdcwebapp.xml
--- a/gdcwebapp.xml Wed May 24 16:52:08 2017 -0400
+++ b/gdcwebapp.xml Thu May 25 15:37:16 2017 -0400
@@ -3,20 +3,25 @@
an intuitive interface to filter, extract, and convert Genomic Data Commons experiments
python
- galaxy_json_data_source
+
- json_data_source.py --version
- json_data_source.py "${__app__.config.output_size_limit}" --json_param_file "${output1}" --path "."
+
+ json_data_source_mod.py --version
+
+ json_data_source_mod.py "${__app__.config.output_size_limit}" --json_param_file "${output1}" --path "." --appdata "${tool.name}"
Go to GDCWebApp service $GALAXY_URL
+
+
+
diff -r 23de6169957a -r 7815152f70c6 json_data_source_mod.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/json_data_source_mod.py Thu May 25 15:37:16 2017 -0400
@@ -0,0 +1,277 @@
+#!/usr/bin/env python
+import json
+import optparse
+import urllib
+import os.path
+import os
+from operator import itemgetter
+import tarfile
+
+__version__ = "1.0.0"
+CHUNK_SIZE = 2**20 #1mb
+VALID_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ '
+
+
+def splitext(path):
+ for ext in ['.tar.gz', '.tar.bz2']:
+ if path.endswith(ext):
+ path, ext = path[:-len(ext)], path[-len(ext):]
+ break
+ else:
+ path, ext = os.path.splitext(path)
+ return path, ext[1:]
+
+
+def chunk_write( source_stream, target_stream, source_method = "read", target_method="write" ):
+ source_method = getattr( source_stream, source_method )
+ target_method = getattr( target_stream, target_method )
+ while True:
+ chunk = source_method( CHUNK_SIZE )
+ if chunk:
+ target_method( chunk )
+ else:
+ break
+
+
+def deconstruct_multi_filename( multi_filename ):
+ keys = [ 'primary', 'id', 'name', 'visible', 'file_type' ]
+ return ( dict( zip( keys, multi_filename.split('_') ) ) )
+
+
+def construct_multi_filename( id, name, file_type ):
+ """ Implementation of *Number of Output datasets cannot be determined until tool run* from documentation_.
+ .. _documentation: http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
+ """
+ filename = "%s_%s_%s_%s_%s" % ( 'primary', id, name, 'visible', file_type )
+ return filename
+
+
+def download_from_query( query_data, target_output_filename ):
+ """ Download file from the json data and write it to target_output_filename.
+ """
+ query_url = query_data.get( 'url' )
+ query_file_type = query_data.get( 'extension' )
+ query_stream = urllib.urlopen( query_url )
+ output_stream = open( target_output_filename, 'wb' )
+ chunk_write( query_stream, output_stream )
+ query_stream.close()
+ output_stream.close()
+
+def store_file_from_archive( file_object, target_output_filename ):
+ """ Store file after extracting from archive and organize them as a collection using the structure
+ (collection-name)_(file-name).ext as file name
+ """
+ output_stream = open( target_output_filename, 'wb' )
+ chunk_write( file_object.read(), output_stream )
+ output_stream.close()
+
+
+def download_extra_data( query_ext_data, base_path ):
+ """ Download any extra data defined in the JSON.
+ NOTE: the "path" value is a relative path to the file on our
+ file system. This is slightly dangerous and we should make every effort
+ to avoid a malicious absolute path to write the file elsewhere on the
+ filesystem.
+ """
+ for ext_data in query_ext_data:
+ if not os.path.exists( base_path ):
+ os.mkdir( base_path )
+ query_stream = urllib.urlopen( ext_data.get( 'url' ) )
+ ext_path = ext_data.get( 'path' )
+ os.makedirs( os.path.normpath( '/'.join( [ base_path, os.path.dirname( ext_path ) ] ) ) )
+ output_stream = open( os.path.normpath( '/'.join( [ base_path, ext_path ] ) ), 'wb' )
+ chunk_write( query_stream, output_stream )
+ query_stream.close()
+ output_stream.close()
+
+
+def metadata_to_json_for_archive_entry( dataset_id, extension, metaname, filename, ds_type='dataset', primary=False ):
+ """ Return line separated JSON """
+ meta_dict = dict( type = ds_type,
+ ext = extension,
+ filename = filename,
+ name = metaname,
+ metadata = {} )
+ if primary:
+ meta_dict[ 'base_dataset_id' ] = dataset_id
+ else:
+ meta_dict[ 'dataset_id' ] = dataset_id
+ return "%s\n" % json.dumps( meta_dict )
+
+
+def metadata_to_json( dataset_id, metadata, filename, ds_type='dataset', primary=False):
+ """ Return line separated JSON """
+ meta_dict = dict( type = ds_type,
+ ext = metadata.get( 'extension' ),
+ filename = filename,
+ name = metadata.get( 'name' ),
+ metadata = metadata.get( 'metadata', {} ) )
+ if metadata.get( 'extra_data', None ):
+ meta_dict[ 'extra_files' ] = '_'.join( [ filename, 'files' ] )
+ if primary:
+ meta_dict[ 'base_dataset_id' ] = dataset_id
+ else:
+ meta_dict[ 'dataset_id' ] = dataset_id
+ return "%s\n" % json.dumps( meta_dict )
+
+
+def download_files_and_write_metadata(query_item, json_params, output_base_path, metadata_parameter_file, primary, appdata_path):
+ """ Main work function that operates on the JSON representation of
+ one dataset and its metadata. Returns True.
+ """
+ dataset_url, output_filename, \
+ extra_files_path, file_name, \
+ ext, out_data_name, \
+ hda_id, dataset_id = set_up_config_values(json_params)
+ extension = query_item.get( 'extension' )
+ filename = query_item.get( 'url' )
+ extra_data = query_item.get( 'extra_data', None )
+ if primary:
+ filename = ''.join( c in VALID_CHARS and c or '-' for c in filename )
+ name = construct_multi_filename( hda_id, filename, extension )
+ target_output_filename = os.path.normpath( '/'.join( [ output_base_path, name ] ) )
+ metadata_parameter_file.write( metadata_to_json( dataset_id, query_item,
+ target_output_filename,
+ ds_type='new_primary_dataset',
+ primary=primary) )
+ else:
+ target_output_filename = output_filename
+ metadata_parameter_file.write( metadata_to_json( dataset_id, query_item,
+ target_output_filename,
+ ds_type='dataset',
+ primary=primary) )
+ download_from_query( query_item, target_output_filename )
+ if extra_data:
+ extra_files_path = ''.join( [ target_output_filename, 'files' ] )
+ download_extra_data( extra_data, extra_files_path )
+
+ check_ext = ""
+ if ( fname.endswith( "gz" ) ):
+ check_ext = "r:gz"
+ elif ( fname.endswith( "bz2" ) ):
+ check_ext = "r:bz2"
+ elif ( fname.endswith( "tar" ) ):
+ check_ext = "r:"
+ if ( bool( check_ext and check_ext.strip() ) ):
+ with tarfile.open( target_output_filename, check_ext ) as tf:
+ for entry in tf:
+ fileobj = tf.extractfile( entry )
+ if entry.isfile():
+ """
+ dataset_url, output_filename, \
+ extra_files_path, file_name, \
+ ext, out_data_name, \
+ hda_id, dataset_id = set_up_config_values(json_params)
+ """
+ filename = os.path.basename( entry.name )
+ extension = splitext( filename )
+ extra_data = None
+ #target_output_filename = output_filename
+ """ (?P<archive_name>.*)_(?P<file_name>.*)\..* """
+ filename_with_collection_prefix = query_item.get( 'name' ) + "_" + filename
+ target_output_filename = os.path.join(appdata_path, filename_with_collection_prefix)
+ """
+ metadata_parameter_file.write( metadata_to_json_for_archive_entry( dataset_id, extension,
+ filename, target_output_filename,
+ ds_type='dataset',
+ primary=primary) )
+ """
+ store_file_from_archive( fileobj, target_output_filename )
+
+ return True
+
+
+def set_up_config_values():
+ extra_files_path, file_name, ext, out_data_name, hda_id, dataset_id = \
+ itemgetter('extra_files_path', 'file_name', 'ext', 'out_data_name', 'hda_id', 'dataset_id')(output_data[0])
+
+def set_up_config_values(json_params):
+ """ Parse json_params file and return a tuple of necessary configuration
+ values.
+ """
+ datasource_params = json_params.get( 'param_dict' )
+ dataset_url = datasource_params.get( 'URL' )
+ output_filename = datasource_params.get( 'output1', None )
+ output_data = json_params.get( 'output_data' )
+ extra_files_path, file_name, ext, out_data_name, hda_id, dataset_id = \
+ itemgetter('extra_files_path', 'file_name', 'ext', 'out_data_name', 'hda_id', 'dataset_id')(output_data[0])
+ return (dataset_url, output_filename,
+ extra_files_path, file_name,
+ ext, out_data_name,
+ hda_id, dataset_id)
+
+
+def download_from_json_data( options, args ):
+ """ Parse the returned JSON data and download files. Write metadata
+ to flat JSON file.
+ """
+ output_base_path = options.path
+ appdata_path = options.appdata
+ if not os.path.exists(appdata_path):
+ os.makedirs(appdata_path)
+
+ # read tool job configuration file and parse parameters we need
+ json_params = json.loads( open( options.json_param_file, 'r' ).read() )
+ dataset_url, output_filename, \
+ extra_files_path, file_name, \
+ ext, out_data_name, \
+ hda_id, dataset_id = set_up_config_values(json_params)
+ # line separated JSON file to contain all dataset metadata
+ metadata_parameter_file = open( json_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'wb' )
+
+ # get JSON response from data source
+ # TODO: make sure response is not enormous
+ query_params = json.loads(urllib.urlopen( dataset_url ).read())
+ # download and write files
+ primary = False
+ # query_item, hda_id, output_base_path, dataset_id
+ for query_item in query_params:
+ if isinstance( query_item, list ):
+ # TODO: do something with the nested list as a collection
+ for query_subitem in query_item:
+ primary = download_files_and_write_metadata(query_subitem, json_params, output_base_path,
+ metadata_parameter_file, primary, appdata_path)
+
+ elif isinstance( query_item, dict ):
+ primary = download_files_and_write_metadata(query_item, json_params, output_base_path,
+ metadata_parameter_file, primary, appdata_path)
+ metadata_parameter_file.close()
+
+def __main__():
+ """ Read the JSON return from a data source. Parse each line and request
+ the data, download to "newfilepath", and write metadata.
+
+ Schema
+ ------
+
+ [ {"url":"http://url_of_file",
+ "name":"encode WigData",
+ "extension":"wig",
+ "metadata":{"db_key":"hg19"},
+ "extra_data":[ {"url":"http://url_of_ext_file",
+ "path":"rel/path/to/ext_file"}
+ ]
+ }
+ ]
+
+ """
+ # Parse the command line options
+ usage = "Usage: json_data_source_mod.py max_size --json_param_file filename [options]"
+ parser = optparse.OptionParser(usage = usage)
+ parser.add_option("-j", "--json_param_file", type="string",
+ action="store", dest="json_param_file", help="json schema return data")
+ parser.add_option("-p", "--path", type="string",
+ action="store", dest="path", help="new file path")
+ parser.add_option("-a", "--appdata", type="string",
+ action="store", dest="appdata", help="appdata folder name")
+ parser.add_option("-v", "--version", action="store_true", dest="version",
+ default=False, help="display version and exit")
+
+ (options, args) = parser.parse_args()
+ if options.version:
+ print __version__
+ else:
+ download_from_json_data( options, args )
+
+
+if __name__ == "__main__": __main__()
diff -r 23de6169957a -r 7815152f70c6 tool_dependencies.xml
--- a/tool_dependencies.xml Wed May 24 16:52:08 2017 -0400
+++ b/tool_dependencies.xml Thu May 25 15:37:16 2017 -0400
@@ -3,7 +3,7 @@
-
+