--- a/json_data_source_mod.py	Thu May 25 17:58:23 2017 -0400
+++ b/json_data_source_mod.py	Tue May 30 12:26:32 2017 -0400
@@ -57,12 +57,16 @@
     query_stream.close()
     output_stream.close()
 
-def store_file_from_archive( file_object, target_output_filename ):
+def store_file_from_archive( file_object, target_output_filename, isString=False ):
     """ 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 )
+    #chunk_write( file_object.read(), output_stream )
+    if not isString:
+        output_stream.write(file_object.read())
+    else:
+        output_stream.write(file_object)
     output_stream.close()
 
 
@@ -85,20 +89,6 @@
         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,
@@ -115,7 +105,27 @@
     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):
+def walk_on_archive(target_output_filename, check_ext, archive_name, appdata_path):
+    archive_name = archive_name.replace("_", "-").replace(".", "-")
+    with tarfile.open( target_output_filename, check_ext ) as tf:
+        for entry in tf:
+            if entry.isfile():
+                fileobj = tf.extractfile( entry )
+                # reserve the underscore for the collection searator
+                filename = os.path.basename( entry.name ).replace("_", "-")
+                extension = splitext( filename )[1]
+                # pattern: (?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)
+                if (len(extension) > 0):
+                    filename = (filename[0:len(filename)-(len(extension)+1)]).replace(".", "-") + "." + extension
+                else:
+                    extension = "auto"
+                filename_with_collection_prefix = archive_name + "_" + filename
+                target_entry_output_filename = os.path.join(appdata_path, filename_with_collection_prefix)
+                store_file_from_archive( fileobj, target_entry_output_filename )
+    return True
+
+
+def download_files_and_write_metadata(query_item, json_params, output_base_path, metadata_parameter_file, primary, appdata_path, options, args):
     """ Main work function that operates on the JSON representation of
     one dataset and its metadata. Returns True.
     """
@@ -124,68 +134,48 @@
         ext, out_data_name, \
         hda_id, dataset_id = set_up_config_values(json_params)
     extension = query_item.get( 'extension' )
-    filename = query_item.get( 'url' )
+    #filename = query_item.get( 'url' )
+    filename = query_item.get( 'name' )
+
+    check_ext = ""
+    if ( filename.endswith( "gz" ) ):
+        check_ext = "r:gz"
+    elif ( filename.endswith( "bz2" ) ):
+        check_ext = "r:bz2"
+    elif ( filename.endswith( "tar" ) ):
+        check_ext = "r:"
+    isArchive = bool( check_ext and check_ext.strip() )
+
     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) )
+        if isArchive is False:
+            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) )
+        if isArchive is False:
+            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 )
 
     """ the following code handles archives and decompress them in a collection """
-    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 )
-    
+    if ( isArchive ):
+        walk_on_archive(target_output_filename, check_ext, query_item.get( 'name' ), appdata_path)
+
     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.
@@ -202,7 +192,7 @@
             hda_id, dataset_id)
 
 
-def download_from_json_data( options, args ):
+def download_from_json_data( options, args, json_params=None, json_dataset_url=None ):
     """ Parse the returned JSON data and download files. Write metadata
     to flat JSON file.
     """
@@ -212,7 +202,9 @@
         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() )
+    if json_params is None:
+        json_params = json.loads( open( options.json_param_file, 'r' ).read() )
+    
     dataset_url, output_filename, \
         extra_files_path, file_name, \
         ext, out_data_name, \
@@ -222,7 +214,10 @@
 
     # get JSON response from data source
     # TODO: make sure response is not enormous
-    query_params = json.loads(urllib.urlopen( dataset_url ).read())
+    if json_dataset_url is None:
+        query_params = json.loads(urllib.urlopen( dataset_url ).read())
+    else:
+        query_params = json.loads(urllib.urlopen( json_dataset_url ).read())
     # download and write files
     primary = False
     # query_item, hda_id, output_base_path, dataset_id
@@ -231,11 +226,11 @@
             # 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)
+                                                            metadata_parameter_file, primary, appdata_path, options, args)
 
         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, primary, appdata_path, options, args)
     metadata_parameter_file.close()
 
 def __main__():