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Merge with -central

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This commit is contained in:
Dannon Baker
2013-04-10 14:04:50 -04:00
parent 3c046de0aa a6b0cdcfc4
commit ef73a7b7bf
3 changed files with 57 additions and 56 deletions
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lib/galaxy/visualization/genomes.py
+23 -6
View File
@@ -31,21 +31,38 @@ class GenomeRegion( object ):
A genomic region on an individual chromosome.
"""
def __init__( self, chrom=None, start=None, end=None ):
def __init__( self, chrom = None, start = 0, end = 0 ):
self.chrom = chrom
self.start = int( start )
self.end = int( end )
def __str__( self ):
return self.chrom + ":" + str( self.start ) + "-" + str( self.end )
@staticmethod
def from_dict( obj_dict ):
return GenomeRegion( chrom=obj_dict[ 'chrom' ],
start=obj_dict[ 'start' ],
end=obj_dict[ 'end' ] )
return GenomeRegion( chrom = obj_dict[ 'chrom' ],
start = obj_dict[ 'start' ],
end = obj_dict[ 'end' ] )
@staticmethod
def from_str( obj_str ):
# check for gene region
gene_region = obj_str.split(':')
# split gene region into components
if (len(gene_region) == 2):
gene_interval = gene_region[1].split('-')
# check length
if (len(gene_interval) == 2):
return GenomeRegion(chrom = gene_region[0],
start = gene_interval[0],
end = gene_interval[1])
# return genome region instance
return GenomeRegion()
class Genome( object ):
"""
Encapsulates information about a known genome/dbkey.
lib/galaxy/webapps/galaxy/controllers/visualization.py
+10 -21
View File
@@ -12,6 +12,7 @@ from galaxy.util.sanitize_html import sanitize_html
from galaxy.visualization.genomes import decode_dbkey
from galaxy.visualization.genome.visual_analytics import get_dataset_job
from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider
from galaxy.visualization.genomes import GenomeRegion
from .library import LibraryListGrid
@@ -697,22 +698,8 @@ class VisualizationController( BaseUIController, SharableMixin, UsesAnnotations,
# Get dataset to add.
new_dataset_id = kwargs.get( "dataset_id", None )
# viewport configuration
gene_region_config = {"chrom" : None, "start" : 0, "end" : 0}
# Check for gene region
gene_region = kwargs.get("gene_region", "").split(':')
# Split gene region into components
if (len(gene_region) == 2):
gene_chrom = gene_region[0];
gene_interval = gene_region[1].split('-')
# Check length
if (len(gene_interval) == 2):
gene_region_config['chrom'] = gene_chrom
gene_region_config['start'] = int(gene_interval[0])
gene_region_config['end'] = int(gene_interval[1])
gene_region = GenomeRegion.from_str(kwargs.get("gene_region", ""))
# Set up new browser if no id provided.
if not id:
@@ -722,18 +709,19 @@ class VisualizationController( BaseUIController, SharableMixin, UsesAnnotations,
dbkey = self.get_dataset( trans, new_dataset_id ).dbkey
if dbkey == '?':
dbkey = kwargs.get( "dbkey", None )
return trans.fill_template( "tracks/browser.mako", viewport_config=gene_region_config, add_dataset=new_dataset_id, default_dbkey=dbkey )
# fill template
return trans.fill_template( "tracks/browser.mako", viewport_config=gene_region.__dict__, add_dataset=new_dataset_id, default_dbkey=dbkey )
# Display saved visualization.
vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True )
viz_config = self.get_visualization_config( trans, vis )
# Update gene region of saved visualization if user parses a new gene region in the url
if gene_region_config['chrom'] is not None:
viz_config['viewport']['chrom'] = gene_region_config['chrom']
viz_config['viewport']['start'] = gene_region_config['start']
viz_config['viewport']['end'] = gene_region_config['end']
if gene_region.chrom is not None:
viz_config['viewport']['chrom'] = gene_region.chrom
viz_config['viewport']['start'] = gene_region.start
viz_config['viewport']['end'] = gene_region.end
'''
FIXME:
@@ -741,6 +729,7 @@ class VisualizationController( BaseUIController, SharableMixin, UsesAnnotations,
if trans.security.decode_id(new_dataset) in [ d["dataset_id"] for d in viz_config.get("tracks") ]:
new_dataset = None # Already in browser, so don't add
'''
# fill template
return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=new_dataset_id )
@web.expose
static/scripts/mvc/data.js
+24 -29
View File
@@ -109,7 +109,11 @@ var DatasetCollection = Backbone.Collection.extend({
*/
var TabularDatasetChunkedView = Backbone.View.extend({
initialize: function(options) {},
initialize: function(options)
{
// load trackster button
(new TabularButtonTrackster(options)).render();
},
render: function()
{
@@ -221,13 +225,8 @@ var TabularDatasetChunkedView = Backbone.View.extend({
}
});
/**
* Provides table-based, dynamic view of a bed dataset.
* NOTE: view's el must be in DOM already and provided when
* creating the view so that scrolling event can be attached
* to the correct container.
*/
var TabularDatasetChunkedViewWithButton = TabularDatasetChunkedView.extend(
// button for trackster visualization
var TabularButtonTrackster = Backbone.View.extend(
{
// gene region columns
col: {
@@ -245,17 +244,13 @@ var TabularDatasetChunkedViewWithButton = TabularDatasetChunkedView.extend(
// database key
genome_build: null,
get_type : function(obj) {
return ({}).toString.call(obj).match(/\s([a-zA-Z]+)/)[1].toLowerCase()
},
// backbone initialize
initialize: function (options)
{
// verify that metadata exists
var metadata = options.model.attributes.metadata.attributes;
if (typeof metadata.chromCol === "undefined" || typeof metadata.startCol === "undefined" || typeof metadata.endCol === "undefined")
console.log("TabularDatasetChunkedViewWithButton : Metadata for column identification is missing.");
console.log("TabularButtonTrackster : Metadata for column identification is missing.");
else
{
// read in columns
@@ -270,13 +265,13 @@ var TabularDatasetChunkedViewWithButton = TabularDatasetChunkedView.extend(
// get dataset id
if (typeof options.model.attributes.id === "undefined")
console.log("TabularDatasetChunkedViewWithButton : Dataset identification is missing.");
console.log("TabularButtonTrackster : Dataset identification is missing.");
else
this.dataset_id = options.model.attributes.id;
// get url
if (typeof options.model.attributes.url_viz === "undefined")
console.log("TabularDatasetChunkedViewWithButton : Url for visualization controller is missing.");
console.log("TabularButtonTrackster : Url for visualization controller is missing.");
else
this.url_viz = options.model.attributes.url_viz;
@@ -301,20 +296,23 @@ var TabularDatasetChunkedViewWithButton = TabularDatasetChunkedView.extend(
// get selected data line
var row = $(e.target).parent();
// get target gene region
var btn_viz_pars = {
dataset_id : this.dataset_id,
gene_region : row.children().eq(this.col.chrom).html() + ":" + row.children().eq(this.col.start).html() + "-" + row.children().eq(this.col.end).html()
};
// verify that location has been found
if (row.children().eq(this.col.chrom).html() != "")
var chrom = row.children().eq(this.col.chrom).html();
var start = row.children().eq(this.col.start).html();
var end = row.children().eq(this.col.end).html();
if (chrom != "" && start != "" && end != "")
{
// get target gene region
var btn_viz_pars = {
dataset_id : this.dataset_id,
gene_region : chrom + ":" + start + "-" + end
};
// get button position
var offset = row.offset();
var left = offset.left - 10;
var top = offset.top;
var offset = row.offset();
var left = offset.left - 10;
var top = offset.top;
// update css
$('#btn_viz').css({'position': 'fixed', 'top': top + 'px', 'left': left + 'px'});
@@ -401,9 +399,6 @@ var TabularDatasetChunkedViewWithButton = TabularDatasetChunkedView.extend(
// hide the button
$('#btn_viz').hide();
// call parent render
TabularDatasetChunkedView.prototype.render.call(this);
}
});
@@ -436,7 +431,7 @@ var createTabularDatasetChunkedView = function(dataset_config, parent_elt) {
var view_div = $('<div/>').appendTo(parent_elt);
// default viewer
return new TabularDatasetChunkedViewWithButton({
return new TabularDatasetChunkedView({
el: view_div,
model: new TabularDataset(dataset_config)
}).render();