1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/7e5b7ae22a29/ changeset: 7e5b7ae22a29 user: jgoecks date: 2011-12-03 23:06:33 summary: Remove unneeded vis_id parameter from tracks/chroms method. affected #: 2 files
diff -r 866567627a0f78ee78fe443c65a43a86229802b4 -r 7e5b7ae22a29ec69cbcfb28c8820e70b6d2ca89c lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -293,7 +293,7 @@ return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=new_dataset )
@web.json - def chroms( self, trans, vis_id=None, dbkey=None, num=None, chrom=None, low=None ): + def chroms( self, trans, dbkey=None, num=None, chrom=None, low=None ): """ Returns a naturally sorted list of chroms/contigs for either a given visualization or a given dbkey. Use either chrom or low to specify the starting chrom in the return list. @@ -322,25 +322,12 @@ else: low = 0
- # - # Get viz, dbkey. - # - - # Must specify either vis_id or dbkey. - if not vis_id and not dbkey: - return trans.show_error_message("No visualization id or dbkey specified.") - - # Need to get user and dbkey in order to get chroms data. - if vis_id: - # Use user, dbkey from viz. - visualization = self.get_visualization( trans, vis_id, check_ownership=False, check_accessible=True ) - visualization.config = self.get_visualization_config( trans, visualization ) - vis_user = visualization.user - vis_dbkey = visualization.dbkey + # If there is no dbkey owner, default to current user. + dbkey_owner, dbkey = self._decode_dbkey( dbkey ) + if dbkey_owner: + dbkey_user = trans.sa_session.query( trans.app.model.User ).filter_by( username=dbkey_owner ).first() else: - # No vis_id, so visualization is new. User is current user, dbkey must be given. - vis_user = trans.user - vis_dbkey = dbkey + dbkey_user = trans.user
# # Get len file. @@ -348,21 +335,21 @@ len_file = None len_ds = None user_keys = {} - if 'dbkeys' in vis_user.preferences: - user_keys = from_json_string( vis_user.preferences['dbkeys'] ) - if vis_dbkey in user_keys: - dbkey_attributes = user_keys[ vis_dbkey ] + if 'dbkeys' in dbkey_user.preferences: + user_keys = from_json_string( dbkey_user.preferences['dbkeys'] ) + if dbkey in user_keys: + dbkey_attributes = user_keys[ dbkey ] if 'fasta' in dbkey_attributes: build_fasta = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dbkey_attributes[ 'fasta' ] ) len_file = build_fasta.get_converted_dataset( trans, 'len' ).file_name # Backwards compatibility: look for len file directly. elif 'len' in dbkey_attributes: - len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[ vis_dbkey ][ 'len' ] ).file_name + len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[ dbkey ][ 'len' ] ).file_name
if not len_file: len_ds = trans.db_dataset_for( dbkey ) if not len_ds: - len_file = os.path.join( trans.app.config.len_file_path, "%s.len" % vis_dbkey ) + len_file = os.path.join( trans.app.config.len_file_path, "%s.len" % dbkey ) else: len_file = len_ds.file_name
@@ -432,7 +419,7 @@
to_sort = [{ 'chrom': chrom, 'len': length } for chrom, length in chroms.iteritems()] to_sort.sort(lambda a,b: cmp( split_by_number(a['chrom']), split_by_number(b['chrom']) )) - return { 'reference': self._has_reference_data( trans, vis_dbkey, vis_user ), 'chrom_info': to_sort, + return { 'reference': self._has_reference_data( trans, dbkey, dbkey_user ), 'chrom_info': to_sort, 'prev_chroms' : prev_chroms, 'next_chroms' : next_chroms, 'start_index' : start_index }
@web.json
diff -r 866567627a0f78ee78fe443c65a43a86229802b4 -r 7e5b7ae22a29ec69cbcfb28c8820e70b6d2ca89c static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -1195,7 +1195,8 @@ */ load_chroms: function(url_parms) { url_parms['num'] = MAX_CHROMS_SELECTABLE; - $.extend( url_parms, (this.vis_id !== undefined ? { vis_id: this.vis_id } : { dbkey: this.dbkey } ) ); + url_parms['dbkey'] = this.dbkey; + var view = this, chrom_data = $.Deferred();
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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