changeset 6:7815152f70c6 draft

Uploaded 20170525

Binary file ._gdcwebapp.xml has changed

Binary file ._json_data_source_mod.py has changed

Binary file ._tool_dependencies.xml has changed

--- 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 @@
     <description>an intuitive interface to filter, extract, and convert Genomic Data Commons experiments</description>
     <requirements>
         <requirement type="package" version="2.7.10">python</requirement>
-        <requirement type="package" version="1.0.0">galaxy_json_data_source</requirement>
+        <!--<requirement type="package" version="1.0.0">galaxy_json_data_source</requirement>-->
     </requirements>
     <stdio>
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
-    <version_command>json_data_source.py --version</version_command>
-    <command>json_data_source.py "${__app__.config.output_size_limit}" --json_param_file "${output1}" --path "."</command>
+    <!--<version_command>json_data_source.py --version</version_command>-->
+    <version_command>json_data_source_mod.py --version</version_command>
+    <!--<command>json_data_source.py "${__app__.config.output_size_limit}" --json_param_file "${output1}" --path "."</command>-->
+    <command interpreter="python">json_data_source_mod.py "${__app__.config.output_size_limit}" --json_param_file "${output1}" --path "." --appdata "${tool.name}"</command>
     <inputs check_values="False" action="http://bioinf.iasi.cnr.it/gdcwebapp/app.php" >
         <display>Go to GDCWebApp service $GALAXY_URL</display>
         <param name="URL" type="hidden" value="" />
     </inputs>
     <outputs>
         <data name="output1" format="auto" />
+        <collection name="list_output" type="list:list" label="${tool.name} output">
+            <discover_datasets pattern="(?P&lt;archive_name&gt;.*)_(?P&lt;file_name&gt;.*)\..*" ext="auto" visible="True" directory="${tool.name}" />
+        </collection>
     </outputs>
     <options sanitize="False" refresh="True" />
 </tool>

--- /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__()

--- 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 @@
     <package name="python" version="2.7.10">
         <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="galaxy_json_data_source" version="1.0.0">
+    <!--<package name="galaxy_json_data_source" version="1.0.0">
         <repository changeset_revision="5ea54764a6b9" name="package_galaxy_json_data_source" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
+    </package>-->
 </tool_dependency>