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Remove unneeded vis_id parameter from tracks/chroms method.

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This commit is contained in:
Jeremy Goecks
2011-12-03 17:06:33 -05:00
parent 4ea357be73
commit 74799ec699
2 changed files with 15 additions and 27 deletions
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lib/galaxy/web/controllers/tracks.py
+13 -26
View File
@@ -293,7 +293,7 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
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 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
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 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
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 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
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
static/scripts/trackster.js
+2 -1
View File
@@ -1195,7 +1195,8 @@ extend( View.prototype, DrawableCollection.prototype, {
*/
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();