2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4e5ab1d17d7d/ Changeset: 4e5ab1d17d7d User: jgoecks Date: 2013-04-17 16:24:43 Summary: Add sample names to VCF metadata. Affected #: 1 file diff -r 57b64ceac4b5eaef10eb0f6c3cf94a87646901c2 -r 4e5ab1d17d7d00e34b12b61fa8b846d1d612b132 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -543,7 +543,8 @@ MetadataElement( name="columns", default=10, desc="Number of columns", readonly=True, visible=False ) MetadataElement( name="column_types", default=['str','int','str','str','str','int','str','list','str','str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) - MetadataElement( name="viz_filter_cols", desc="Score column for visualization", default=[5], param=metadata.ColumnParameter, multiple=True ) + MetadataElement( name="viz_filter_cols", desc="Score column for visualization", default=[5], param=metadata.ColumnParameter, multiple=True, visible=False ) + MetadataElement( name="sample_names", default=[], desc="Sample names", readonly=True, visible=False, optional=True, no_value=[] ) def sniff( self, filename ): headers = get_headers( filename, '\n', count=1 ) @@ -553,6 +554,21 @@ """Returns formated html of peek""" return Tabular.make_html_table( self, dataset, column_names=self.column_names ) + def set_meta( self, dataset, **kwd ): + Tabular.set_meta( self, dataset, **kwd ) + source = open( dataset.file_name ) + + # Skip comments. + line = None + for line in source: + if not line.startswith( '##' ): + break + + if line and line.startswith( '#' ): + # Found header line, get sample names. + dataset.metadata.sample_names = line.split()[ 9: ] + + class Eland( Tabular ): """Support for the export.txt.gz file used by Illumina's ELANDv2e aligner""" file_ext = '_export.txt.gz' https://bitbucket.org/galaxy/galaxy-central/commits/df9c639133ff/ Changeset: df9c639133ff User: jgoecks Date: 2013-04-17 16:25:36 Summary: Use full HDA/LDDA dict to get data into Trackster. Affected #: 3 files diff -r 4e5ab1d17d7d00e34b12b61fa8b846d1d612b132 -r df9c639133ff04b39a9da8cdb1083d899cb4e19d lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -595,9 +595,8 @@ source='data' ) return { "track_type": dataset.datatype.track_type, + "dataset": trans.security.encode_dict_ids( dataset.get_api_value() ), "name": track_dict['name'], - "hda_ldda": track_dict.get("hda_ldda", "hda"), - "dataset_id": trans.security.encode_id( dataset.id ), "prefs": prefs, "mode": track_dict.get( 'mode', 'Auto' ), "filters": track_dict.get( 'filters', { 'filters' : track_data_provider.get_filters() } ), @@ -676,8 +675,7 @@ return { "track_type": dataset.datatype.track_type, "name": dataset.name, - "hda_ldda": hda_ldda, - "dataset_id": trans.security.encode_id( dataset.id ), + "dataset": trans.security.encode_dict_ids( dataset.get_api_value() ), "prefs": {}, "filters": { 'filters' : track_data_provider.get_filters() }, "tool": get_tool_def( trans, dataset ), diff -r 4e5ab1d17d7d00e34b12b61fa8b846d1d612b132 -r df9c639133ff04b39a9da8cdb1083d899cb4e19d static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2248,10 +2248,7 @@ // // Attribute init. // - this.dataset = new data.Dataset({ - id: obj_dict.dataset_id, - hda_ldda: obj_dict.hda_ldda - }); + this.dataset = new data.Dataset(obj_dict.dataset); this.dataset_id = this.dataset.get('id'); this.hda_ldda = this.dataset.get('hda_ldda'); this.dataset_check_type = 'converted_datasets_state'; diff -r 4e5ab1d17d7d00e34b12b61fa8b846d1d612b132 -r df9c639133ff04b39a9da8cdb1083d899cb4e19d templates/webapps/galaxy/tracks/browser.mako --- a/templates/webapps/galaxy/tracks/browser.mako +++ b/templates/webapps/galaxy/tracks/browser.mako @@ -76,9 +76,9 @@ vis_id: "${config.get('vis_id')}", dbkey: "${config.get('dbkey')}" }, - JSON.parse('${ h.to_json_string( config.get( 'viewport', dict() ) ) }'), - JSON.parse('${ h.to_json_string( config['tracks'] ).replace("'", "\\'") }'), - JSON.parse('${ h.to_json_string( config['bookmarks'] ) }'), + ${ h.to_json_string( config.get( 'viewport', dict() ) ) }, + ${ h.to_json_string( config['tracks'] ) }, + ${ h.to_json_string( config['bookmarks'] ) }, true ); init_editor(); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.