# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu&gt; # Date 1277733095 14400 # Node ID 89fbba1fc87e5dc59e449bab7a38addd24493337 # Parent 71b1a5920fc12514a9e151770eaf250d6fc6da46 Include annotations and tags when exporting histories to and importing histories from file. --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -476,12 +476,24 @@ class HistoryController( BaseController, history_attrs = from_json_string( history_attr_str ) # Create history. - # TODO: set tags, annotations. - new_history = model.History( name='imported: %s' % history_attrs['name'].encode( 'utf-8' ), user=trans.user ) + new_history = model.History( name='imported from archive: %s' % history_attrs['name'].encode( 'utf-8' ), user=trans.user ) trans.sa_session.add( new_history ) - trans.sa_session.flush() - # TODO: Ignore hid_counter for now since it just artificially increases the hid for all the history's HDAs. - #new_history.hid_counter = history_attrs['hid_counter'] + + # Builds a tag string for a tag, value pair. + def get_tag_str( tag, value ): + if not value: + return tag + else: + return tag + ":" + value + + # Add annotation, tags. + if trans.user: + self.add_item_annotation( trans, new_history, history_attrs[ 'annotation' ] ) + for tag, value in history_attrs[ 'tags' ].items(): + trans.app.tag_handler.apply_item_tags( trans, trans.user, new_history, get_tag_str( tag, value ) ) + + # Ignore hid_counter since it artificially increases the hid for all HDAs? + # new_history.hid_counter = history_attrs['hid_counter'] new_history.genome_build = history_attrs['genome_build'] trans.sa_session.flush() @@ -515,7 +527,7 @@ class HistoryController( BaseController, metadata = metadata, history = new_history, create_dataset = True, - sa_session = trans.sa_session ) + sa_session = trans.sa_session ) hda.state = hda.states.OK trans.sa_session.add( hda ) trans.sa_session.flush() @@ -528,7 +540,12 @@ class HistoryController( BaseController, temp_dataset_name = '%s/datasets/%s' % ( temp_output_dir, dataset_attrs['file_name'] ) shutil.copyfile( temp_dataset_name, hda.file_name ) - # TODO: set tags, annotations. + # Set tags, annotations. + if trans.user: + self.add_item_annotation( trans, hda, dataset_attrs[ 'annotation' ] ) + for tag, value in dataset_attrs[ 'tags' ].items(): + trans.app.tag_handler.apply_item_tags( trans, trans.user, hda, get_tag_str( tag, value ) ) + trans.sa_session.flush() # Cleanup. if os.path.exists( temp_output_dir ): @@ -537,7 +554,7 @@ class HistoryController( BaseController, return trans.show_ok_message( message="History '%s' has been imported. " % history_attrs['name'] ) except Exception, e: return trans.show_error_message( 'Error importing history archive. ' + str( e ) ) - + return trans.show_form( web.FormBuilder( web.url_for(), "Import a History from an Archive", submit_text="Submit" ) @@ -567,7 +584,7 @@ class HistoryController( BaseController, # Create archive and stream back to client. - # Simple method to convert strings to unicode in utf-8 format. Method should be used for all user input. + # Convert strings to unicode in utf-8 format. Method should be used for all user input. def unicode_wrangler( a_string ): a_string_type = type ( a_string ) if a_string_type is str: @@ -575,18 +592,28 @@ class HistoryController( BaseController, elif a_string_type is unicode: return a_string.encode( 'utf-8' ) + # Create dictionary of an item's tags. + def get_item_tag_dict( item ): + tags = {} + for tag in item.tags: + tag_user_tname = unicode_wrangler( tag.user_tname ) + tag_user_value = unicode_wrangler( tag.user_value ) + tags[ tag_user_tname ] = tag_user_value + return tags + try: # Use temporary directory for temp output files. temp_output_dir = tempfile.mkdtemp() # Write history attributes to file. - # TODO: include tags, annotations. history_attrs = { "create_time" : history.create_time.__str__(), "update_time" : history.update_time.__str__(), "name" : unicode_wrangler( history.name ), "hid_counter" : history.hid_counter, - "genome_build" : history.genome_build + "genome_build" : history.genome_build, + "annotation" : unicode_wrangler( self.get_item_annotation_str( trans, history.user, history ) ), + "tags" : get_item_tag_dict( history ) } history_attrs_file_name = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name history_attrs_out = open( history_attrs_file_name, 'w' ) @@ -597,7 +624,6 @@ class HistoryController( BaseController, history_attrs_file_name = new_name # Write datasets' attributes to file. - # TODO: include tags, annotations. datasets = self.get_history_datasets( trans, history ) datasets_attrs = [] for dataset in datasets: @@ -615,7 +641,9 @@ class HistoryController( BaseController, "designation" : dataset.designation, "deleted" : dataset.deleted, "visible" : dataset.visible, - "file_name" : dataset.file_name.split('/')[-1] + "file_name" : dataset.file_name.split('/')[-1], + "annotation" : unicode_wrangler( self.get_item_annotation_str( trans, history.user, dataset ) ), + "tags" : get_item_tag_dict( dataset ) } datasets_attrs.append( attribute_dict ) datasets_attrs_file_name = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name