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October 2012

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commit/galaxy-central: jgoecks: Viz framework: (a) add option to store open file reference in data providers rather than recreating each time and (b) add ticks marks in Circster for chromosome lengths.
by Bitbucket 31 Oct '12

31 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5440f6b3bdec/ changeset: 5440f6b3bdec user: jgoecks date: 2012-10-31 22:51:38 summary: Viz framework: (a) add option to store open file reference in data providers rather than recreating each time and (b) add ticks marks in Circster for chromosome lengths. affected #: 3 files diff -r 8526b10ca125a99de4d944e776e647c1598ffd06 -r 5440f6b3bdecf081493aa31f473470fd11fecceb lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -130,6 +130,11 @@ original_dataset=original_dataset, dependencies=dependencies, error_max_vals=error_max_vals ) + + # File/pointer where data is obtained from. It is useful to set this for repeated + # queries, such as is necessary for genome-wide data. + # TODO: add functions to (a) create data_file and (b) clean up data_file. + self.data_file = None def write_data_to_file( self, regions, filename ): """ @@ -345,17 +350,18 @@ bgzip_fname = self.dependencies['bgzip'].file_name - tabix = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name) + if not self.data_file: + self.data_file = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name) # Get iterator using either naming scheme. iterator = iter( [] ) - if chrom in tabix.contigs: - iterator = tabix.fetch(reference=chrom, start=start, end=end) + if chrom in self.data_file.contigs: + iterator = self.data_file.fetch(reference=chrom, start=start, end=end) else: # Try alternative naming scheme. chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) - if chrom in tabix.contigs: - iterator = tabix.fetch(reference=chrom, start=start, end=end) + if chrom in self.data_file.contigs: + iterator = self.data_file.fetch(reference=chrom, start=start, end=end) return iterator diff -r 8526b10ca125a99de4d944e776e647c1598ffd06 -r 5440f6b3bdecf081493aa31f473470fd11fecceb lib/galaxy/visualization/tracks/summary.py --- a/lib/galaxy/visualization/tracks/summary.py +++ b/lib/galaxy/visualization/tracks/summary.py @@ -110,5 +110,8 @@ cPickle.dump( self, open( filename, 'wb' ), 2 ) def summary_tree_from_file( filename ): - return cPickle.load( open( filename, "rb" ) ) + st_file = open( filename, "rb" ) + st = cPickle.load( st_file ) + st_file.close() + return st diff -r 8526b10ca125a99de4d944e776e647c1598ffd06 -r 5440f6b3bdecf081493aa31f473470fd11fecceb static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -27,13 +27,7 @@ /** * A label track. */ -var CircsterLabelTrack = Backbone.Model.extend({ - defaults: { - prefs: { - color: '#ccc' - } - } -}); +var CircsterLabelTrack = Backbone.Model.extend({}); /** * Renders a full circster visualization. @@ -46,7 +40,7 @@ this.genome = options.genome; this.dataset_arc_height = options.dataset_arc_height; this.track_gap = 5; - this.label_arc_height = 20; + this.label_arc_height = 50; this.scale = 1; this.circular_views = null; this.chords_views = null; @@ -78,7 +72,7 @@ }, /** - * Returns a list of tracks' radius bounds. + * Returns a list of circular tracks' radius bounds. */ get_tracks_bounds: function() { var circular_tracks = this.get_circular_tracks(); @@ -93,7 +87,7 @@ // Compute range of track starting radii. tracks_start_radii = d3.range(radius_start, min_dimension / 2, this.dataset_arc_height + this.track_gap); - // Map from track start to bounds; for label track + // Map from track start to bounds. var self = this; return _.map(tracks_start_radii, function(radius) { return [radius, radius + self.dataset_arc_height]; @@ -180,12 +174,17 @@ return view; }); - // -- Render label tracks. -- + // -- Render label track. -- - // Set radius start = end for track bounds. - var track_bounds = tracks_bounds[circular_tracks.length]; - track_bounds[1] = track_bounds[0]; - this.label_track_view = new CircsterLabelTrackView({ + // Track bounds are: + // (a) outer radius of last circular track; + // (b) + var outermost_radius = this.circular_views[this.circular_views.length-1].radius_bounds[1], + track_bounds = [ + outermost_radius, + outermost_radius + this.label_arc_height + ]; + this.label_track_view = new CircsterChromLabelTrackView({ el: svg.append('g')[0], track: new CircsterLabelTrack(), radius_bounds: track_bounds, @@ -534,36 +533,97 @@ /** * Render chromosome labels. */ -var CircsterLabelTrackView = CircsterTrackView.extend({ +var CircsterChromLabelTrackView = CircsterTrackView.extend({ initialize: function(options) { CircsterTrackView.prototype.initialize.call(this, options); + // Use a single arc for rendering data. + this.innerRadius = this.radius_bounds[0]; + this.radius_bounds[0] = this.radius_bounds[1]; this.bg_stroke = 'fff'; this.bg_fill = 'fff'; + + // Minimum arc distance for labels to be applied. + this.min_arc_len = 0.08; }, /** * Render labels. */ _render_data: function(svg) { - // Add chromosome label where it will fit; an alternative labeling mechanism - // would be nice for small chromosomes. - var chrom_arcs = svg.selectAll('g'); + // -- Add chromosome label where it will fit; an alternative labeling mechanism + // would be nice for small chromosomes. -- + var self = this, + chrom_arcs = svg.selectAll('g'); chrom_arcs.selectAll('path') .attr('id', function(d) { return 'label-' + d.data.chrom; }); chrom_arcs.append("svg:text") .filter(function(d) { - return d.endAngle - d.startAngle > 0.08; + return d.endAngle - d.startAngle > self.min_arc_len; }) .attr('text-anchor', 'middle') .append("svg:textPath") .attr("xlink:href", function(d) { return "#label-" + d.data.chrom; }) .attr('startOffset', '25%') + .attr('font-weight', 'bold') .text(function(d) { return d.data.chrom; }); + + // -- Add ticks to denote chromosome length. -- + + /** Returns an array of tick angles and labels, given a chrom arc. */ + var chromArcTicks = function(d) { + if (d.endAngle - d.startAngle < self.min_arc_len) { return []; } + var k = (d.endAngle - d.startAngle) / d.value, + ticks = d3.range(0, d.value, 25000000).map(function(v, i) { + return { + angle: v * k + d.startAngle, + label: i === 0 ? 0 : (i % 3 ? null : v / 1000000 + "M") + }; + }); + + // If there are fewer that 4 ticks, label last tick so that at least one non-zero tick is labeled. + if (ticks.length < 4) { + ticks[ticks.length-1].label = Math.round( + ( ticks[ticks.length-1].angle - d.startAngle ) / k / 1000000 + ) + "M"; + } + + return ticks; + }; + + var ticks = this.parent_elt.append("g") + .selectAll("g") + .data(this.chroms_layout) + .enter().append("g") + .selectAll("g") + .data(chromArcTicks) + .enter().append("g") + .attr("transform", function(d) { + return "rotate(" + (d.angle * 180 / Math.PI - 90) + ")" + + "translate(" + self.innerRadius + ",0)"; + }); + + ticks.append("line") + .attr("x1", 1) + .attr("y1", 0) + .attr("x2", 4) + .attr("y2", 0) + .style("stroke", "#000"); + + ticks.append("text") + .attr("x", 4) + .attr("dy", ".35em") + .attr("text-anchor", function(d) { + return d.angle > Math.PI ? "end" : null; + }) + .attr("transform", function(d) { + return d.angle > Math.PI ? "rotate(180)translate(-16)" : null; + }) + .text(function(d) { return d.label; }); } }); 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.

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commit/galaxy-central: jgoecks: Fix bug in getting dataset id in 63f3b08
by Bitbucket 31 Oct '12

31 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8526b10ca125/ changeset: 8526b10ca125 user: jgoecks date: 2012-10-31 20:58:28 summary: Fix bug in getting dataset id in 63f3b08 affected #: 1 file diff -r 4ceab232dc02a5a99eca0b24c0038c490d49a392 -r 8526b10ca125a99de4d944e776e647c1598ffd06 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -249,7 +249,7 @@ # DEPRECATION: We still support unencoded ids for backward compatibility try: # encoded id? - dataset_id = trans.security.decode_id + dataset_id = trans.security.decode_id( dataset_id ) except ( AttributeError, TypeError ), err: # unencoded id 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.

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commit/galaxy-central: 2 new changesets
by Bitbucket 30 Oct '12

30 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8d3caff4bd0f/ changeset: 8d3caff4bd0f user: carlfeberhard date: 2012-10-30 21:53:10 summary: api/histories.show: add 'nice_size', 'annotation', 'state_ids' (map of possible hda states : lists of hda ids in those states ), reorder history state from child hda states (running/queued higher priority than error), return error string; affected #: 1 file diff -r 7b807f69906eff1ea1fa3ea367b299c628736d71 -r 8d3caff4bd0fc2e76bfdf47adc27930c538a9c1f lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -10,6 +10,10 @@ import galaxy.datatypes from galaxy.util.bunch import Bunch +import pkg_resources +pkg_resources.require( "Routes" ) +import routes + log = logging.getLogger( __name__ ) class HistoriesController( BaseAPIController, UsesHistoryMixin ): @@ -31,12 +35,14 @@ item = history.get_api_value(value_mapper={'id':trans.security.encode_id}) item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) rval.append( item ) + elif trans.galaxy_session.current_history: #No user, this must be session authentication with an anonymous user. history = trans.galaxy_session.current_history item = history.get_api_value(value_mapper={'id':trans.security.encode_id}) item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) rval.append(item) + except Exception, e: rval = "Error in history API" log.error( rval + ": %s" % str(e) ) @@ -55,52 +61,90 @@ params = util.Params( kwd ) deleted = util.string_as_bool( deleted ) - def traverse( datasets ): - rval = {} - states = trans.app.model.Dataset.states + states = trans.app.model.Dataset.states + + def get_dataset_state_summaries( datasets ): + # cycles through the history's datasets, building counts and id lists for each possible ds state + state_counts = {} + state_ids = {} + + # init counts, ids for each state for key, state in states.items(): - rval[state] = 0 + state_counts[state] = 0 + state_ids[state] = [] + + # cycle through datasets saving each ds' state for dataset in datasets: - item = dataset.get_api_value( view='element' ) - if not item['deleted']: - rval[item['state']] = rval[item['state']] + 1 - return rval + dataset_dict = dataset.get_api_value( view='element' ) + item_state = dataset_dict[ 'state' ] + + if not dataset_dict['deleted']: + state_counts[ item_state ] = state_counts[ item_state ] + 1 + state_ids[ item_state ].append( trans.security.encode_id( dataset_dict[ 'id' ] ) ) + + return ( state_counts, state_ids ) + + # try to load the history, by most_recently_used or the given id try: if history_id == "most_recently_used": - if trans.user and len(trans.user.galaxy_sessions) > 0: + if trans.user and len( trans.user.galaxy_sessions ) > 0: # Most recent active history for user sessions, not deleted history = trans.user.galaxy_sessions[0].histories[-1].history else: - history = None + return None else: - history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=deleted ) - except Exception, e: - return str( e ) - try: - item = history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) - num_sets = len( [hda.id for hda in history.datasets if not hda.deleted] ) - states = trans.app.model.Dataset.states + history = self.get_history( trans, history_id, check_ownership=False, + check_accessible=True, deleted=deleted ) + + history_data = history.get_api_value( view='element', value_mapper={'id':trans.security.encode_id} ) + history_data[ 'nice_size' ] = history.get_disk_size( nice_size=True ) + + #TODO: separate, move to annotation api, fill on the client + history_data[ 'annotation' ] = history.get_item_annotation_str( trans.sa_session, trans.user, history ) + if not history_data[ 'annotation' ]: + history_data[ 'annotation' ] = '' + + # get the history state using the state summaries of it's datasets (default to ERROR) + num_sets = len([ hda.id for hda in history.datasets if not hda.deleted ]) state = states.ERROR + + ( state_counts, state_ids ) = get_dataset_state_summaries( history.datasets ) + if num_sets == 0: state = states.NEW + else: - summary = traverse(history.datasets) - if summary[states.ERROR] > 0 or summary[states.FAILED_METADATA] > 0: + + if( ( state_counts[ states.RUNNING ] > 0 ) + or ( state_counts[ states.SETTING_METADATA ] > 0 ) + or ( state_counts[ states.UPLOAD ] > 0 ) ): + state = states.RUNNING + + elif state_counts[ states.QUEUED ] > 0: + state = states.QUEUED + + elif( ( state_counts[ states.ERROR ] > 0 ) + or ( state_counts[ states.FAILED_METADATA ] > 0 ) ): state = states.ERROR - elif summary[states.RUNNING] > 0 or summary[states.SETTING_METADATA] > 0: - state = states.RUNNING - elif summary[states.QUEUED] > 0: - state = states.QUEUED - elif summary[states.OK] == num_sets: + + elif state_counts[ states.OK ] == num_sets: state = states.OK - item['contents_url'] = url_for( 'history_contents', history_id=history_id ) - item['state_details'] = summary - item['state'] = state + + history_data[ 'state' ] = state + + history_data[ 'state_details' ] = state_counts + history_data[ 'state_ids' ] = state_ids + + history_data[ 'contents_url' ] = url_for( 'history_contents', history_id=history_id ) + + except Exception, e: - item = "Error in history API at showing history detail" - log.error(item + ": %s" % str(e)) + msg = "Error in history API at showing history detail: %s" % ( str( e ) ) + log.error( msg, exc_info=True ) trans.response.status = 500 - return item + return msg + + return history_data @web.expose_api def create( self, trans, payload, **kwd ): https://bitbucket.org/galaxy/galaxy-central/changeset/4ceab232dc02/ changeset: 4ceab232dc02 user: carlfeberhard date: 2012-10-30 21:55:23 summary: api/history_contents: (1) index: if passed ids=<id|csv id list> in query string, provide full data (as history_contents.show) for each id listed (if no 'ids' - use previous summary behaviour), return error string; (2) show: return 'accessible', 'api_type' (consistent with summary style in index), 'display_types', 'display_apps', 'file_ext', 'hid', 'history_id', 'meta_files' (file types of associated files for generating download urls, eg. myBam.meta_files: [{ 'file_type' : 'bam_index' }]), 'visualizations' (list of visualization names appr. for this hda), 'peek' (data.peek as used in the history panel), return error string; affected #: 1 file diff -r 8d3caff4bd0fc2e76bfdf47adc27930c538a9c1f -r 4ceab232dc02a5a99eca0b24c0038c490d49a392 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -2,8 +2,17 @@ API operations on the contents of a history. """ import logging +import urllib +from gettext import gettext + from galaxy import web -from galaxy.web.base.controller import BaseAPIController, url_for, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesLibraryMixin, UsesLibraryMixinItems +from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy.web.base.controller import UsesHistoryDatasetAssociationMixin, UsesHistoryMixin +from galaxy.web.base.controller import UsesLibraryMixin, UsesLibraryMixinItems + +from galaxy.web.framework.helpers import to_unicode +from galaxy.datatypes.display_applications import util +from galaxy.datatypes.metadata import FileParameter import pkg_resources pkg_resources.require( "Routes" ) @@ -11,27 +20,39 @@ log = logging.getLogger( __name__ ) -class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesLibraryMixin, UsesLibraryMixinItems ): - +class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, + UsesLibraryMixin, UsesLibraryMixinItems ): @web.expose_api - def index( self, trans, history_id, **kwd ): + def index( self, trans, history_id, ids=None, **kwd ): """ GET /api/histories/{encoded_history_id}/contents Displays a collection (list) of history contents """ + rval = [] try: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True ) - except Exception, e: - return str( e ) - rval = [] - try: - for dataset in history.datasets: - api_type = "file" - encoded_id = trans.security.encode_id( dataset.id ) - rval.append( dict( id = encoded_id, - type = api_type, - name = dataset.name, - url = url_for( 'history_content', history_id=history_id, id=encoded_id, ) ) ) + + # if no ids passed, return a _SUMMARY_ of _all_ datasets in the history + if not ids: + for dataset in history.datasets: + api_type = "file" + encoded_id = trans.security.encode_id( dataset.id ) + # build the summary + rval.append( dict( id = encoded_id, + type = api_type, + name = dataset.name, + url = url_for( 'history_content', history_id=history_id, id=encoded_id, ) ) ) + + # if ids, return _FULL_ data (as show) for each id passed + #NOTE: this might not be the best form (passing all info), + # but we(I?) need an hda collection with full data somewhere + else: + ids = ids.split( ',' ) + for id in ids: + hda = self.get_history_dataset_association( trans, history, id, + check_ownership=True, check_accessible=True, check_state=False ) + rval.append( get_hda_dict( trans, history, hda, for_editing=True ) ) + except Exception, e: rval = "Error in history API at listing contents" log.error( rval + ": %s" % str(e) ) @@ -44,30 +65,21 @@ GET /api/histories/{encoded_history_id}/contents/{encoded_content_id} Displays information about a history content (dataset). """ - content_id = id + hda_dict = {} try: - # get the history just for the access checks - history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=False ) - content = self.get_history_dataset_association( trans, history, content_id, check_ownership=True, check_accessible=True ) + history = self.get_history( trans, history_id, + check_ownership=True, check_accessible=True, deleted=False ) + hda = self.get_history_dataset_association( trans, history, id, + check_ownership=True, check_accessible=True ) + hda_dict = get_hda_dict( trans, history, hda, for_editing=True ) + except Exception, e: - return str( e ) - try: - item = content.get_api_value( view='element' ) - if trans.user_is_admin() or trans.app.config.expose_dataset_path: - item['file_name'] = content.file_name - if not item['deleted']: - # Problem: Method url_for cannot use the dataset controller - # Get the environment from DefaultWebTransaction and use default webapp mapper instead of webapp API mapper - url = routes.URLGenerator(trans.webapp.mapper, trans.environ) - # http://routes.groovie.org/generating.html - # url_for is being phased out, so new applications should use url - item['download_url'] = url(controller='dataset', action='display', dataset_id=trans.security.encode_id(content.id), to_ext=content.ext) - item = self.encode_all_ids( trans, item ) - except Exception, e: - item = "Error in history API at listing dataset" - log.error( item + ": %s" % str(e) ) + msg = "Error in history API at listing dataset: %s" % ( str(e) ) + log.error( msg, exc_info=True ) trans.response.status = 500 - return item + return msg + + return hda_dict @web.expose_api def create( self, trans, history_id, payload, **kwd ): @@ -99,3 +111,69 @@ trans.response.status = 403 return "Not implemented." + +# move these into model?? hell if I know...doesn't seem like the urls should go here +def get_hda_dict( trans, history, hda, for_editing ): + hda_dict = hda.get_api_value( view='element' ) + + hda_dict[ 'id' ] = trans.security.encode_id( hda.id ) + hda_dict[ 'history_id' ] = trans.security.encode_id( history.id ) + hda_dict[ 'hid' ] = hda.hid + + hda_dict[ 'file_ext' ] = hda.ext + if trans.user_is_admin() or trans.app.config.expose_dataset_path: + hda_dict[ 'file_name' ] = hda.file_name + + if not hda_dict[ 'deleted' ]: + # Problem: Method url_for cannot use the dataset controller + # Get the environment from DefaultWebTransaction + # and use default webapp mapper instead of webapp API mapper + web_url_for = routes.URLGenerator( trans.webapp.mapper, trans.environ ) + # http://routes.groovie.org/generating.html + # url_for is being phased out, so new applications should use url + hda_dict[ 'download_url' ] = web_url_for( controller='dataset', action='display', + dataset_id=trans.security.encode_id( hda.id ), to_ext=hda.ext ) + + can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) + hda_dict[ 'accessible' ] = ( trans.user_is_admin() or can_access_hda ) + hda_dict[ 'api_type' ] = "file" + + if not( hda.purged or hda.deleted or hda.dataset.purged ): + meta_files = [] + for meta_type in hda.metadata.spec.keys(): + if isinstance( hda.metadata.spec[ meta_type ].param, FileParameter ): + meta_files.append( dict( file_type=meta_type ) ) + if meta_files: + hda_dict[ 'meta_files' ] = meta_files + + #hda_dict[ 'display_apps' ] = get_display_apps( trans, hda ) + hda_dict[ 'visualizations' ] = hda.get_visualizations() + hda_dict[ 'peek' ] = to_unicode( hda.display_peek() ) + + return hda_dict + +def get_display_apps( trans, hda ): + display_apps = [] + + def get_display_app_url( display_app_link, hda, trans ): + web_url_for = routes.URLGenerator( trans.webapp.mapper, trans.environ ) + dataset_hash, user_hash = util.encode_dataset_user( trans, hda, None ) + return web_url_for( controller='/dataset', + action="display_application", + dataset_id=dataset_hash, + user_id=user_hash, + app_name=urllib.quote_plus( display_app_link.display_application.id ), + link_name=urllib.quote_plus( display_app_link.id ) ) + + + for display_app in hda.get_display_applications( trans ).itervalues(): + app_links = [] + for display_app_link in display_app.links.itervalues(): + app_links.append({ + 'target' : display_app_link.url.get( 'target_frame', '_blank' ), + 'href' : get_display_app_url( display_app_link, hda, trans ), + 'text' : gettext( display_app_link.name ) + }) + display_apps.append( dict( label=display_app.name, links=app_links ) ) + + return display_apps Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: galaxy/exceptions: add __str__ to MessageException; galaxy/model: add hda.purged to hda.get_api_value
by Bitbucket 30 Oct '12

30 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7b807f69906e/ changeset: 7b807f69906e user: carlfeberhard date: 2012-10-30 21:50:37 summary: galaxy/exceptions: add __str__ to MessageException; galaxy/model: add hda.purged to hda.get_api_value affected #: 2 files diff -r 63f3b0857be8dae339622b23aa8d10b1ff3f3757 -r 7b807f69906eff1ea1fa3ea367b299c628736d71 lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -9,6 +9,8 @@ def __init__( self, err_msg, type="info" ): self.err_msg = err_msg self.type = type + def __str__( self ): + return self.err_msg class ItemDeletionException( MessageException ): pass diff -r 63f3b0857be8dae339622b23aa8d10b1ff3f3757 -r 7b807f69906eff1ea1fa3ea367b299c628736d71 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1484,6 +1484,7 @@ model_class = self.__class__.__name__, name = hda.name, deleted = hda.deleted, + purged = hda.purged, visible = hda.visible, state = hda.state, file_size = int( hda.get_size() ), 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.

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commit/galaxy-central: carlfeberhard: controller/UsesHistoryDatasetAssociation: get_dataset: allow encoded ids; get_dataset, get_history_dataset_association: add check_state param: check hda.state == 'UPLOADING' to allow api fetch on uploading files, (should be backwards compat with existing calls)
by Bitbucket 30 Oct '12

30 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/63f3b0857be8/ changeset: 63f3b0857be8 user: carlfeberhard date: 2012-10-30 21:46:55 summary: controller/UsesHistoryDatasetAssociation: get_dataset: allow encoded ids; get_dataset, get_history_dataset_association: add check_state param: check hda.state == 'UPLOADING' to allow api fetch on uploading files, (should be backwards compat with existing calls) affected #: 1 file diff -r 2e70816299e40fecc4902adda54126bb00316588 -r 63f3b0857be8dae339622b23aa8d10b1ff3f3757 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -244,20 +244,22 @@ class UsesHistoryDatasetAssociationMixin: """ Mixin for controllers that use HistoryDatasetAssociation objects. """ - def get_dataset( self, trans, dataset_id, check_ownership=True, check_accessible=False ): + def get_dataset( self, trans, dataset_id, check_ownership=True, check_accessible=False, check_state=True ): """ Get an HDA object by id. """ # DEPRECATION: We still support unencoded ids for backward compatibility try: - data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) - if data is None: - raise ValueError( 'Invalid reference dataset id: %s.' % dataset_id ) + # encoded id? + dataset_id = trans.security.decode_id + + except ( AttributeError, TypeError ), err: + # unencoded id + dataset_id = int( dataset_id ) + + try: + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( int( dataset_id ) ) except: - try: - data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( int( dataset_id ) ) - except: - data = None - if not data: raise HTTPRequestRangeNotSatisfiable( "Invalid dataset id: %s." % str( dataset_id ) ) + if check_ownership: # Verify ownership. user = trans.get_user() @@ -265,26 +267,30 @@ error( "Must be logged in to manage Galaxy items" ) if data.history.user != user: error( "%s is not owned by current user" % data.__class__.__name__ ) + if check_accessible: current_user_roles = trans.get_current_user_roles() - if trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): - if data.state == trans.model.Dataset.states.UPLOAD: - return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." ) - else: + + if not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): error( "You are not allowed to access this dataset" ) + + if check_state and data.state == trans.model.Dataset.states.UPLOAD: + return trans.show_error_message( "Please wait until this dataset finishes uploading " + + "before attempting to view it." ) return data - def get_history_dataset_association( self, trans, history, dataset_id, check_ownership=True, check_accessible=False ): + def get_history_dataset_association( self, trans, history, dataset_id, + check_ownership=True, check_accessible=False, check_state=False ): """Get a HistoryDatasetAssociation from the database by id, verifying ownership.""" self.security_check( trans, history, check_ownership=check_ownership, check_accessible=check_accessible ) hda = self.get_object( trans, dataset_id, 'HistoryDatasetAssociation', check_ownership=False, check_accessible=False, deleted=False ) if check_accessible: - if trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ): - if hda.state == trans.model.Dataset.states.UPLOAD: + if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ): + error( "You are not allowed to access this dataset" ) + + if check_state and hda.state == trans.model.Dataset.states.UPLOAD: error( "Please wait until this dataset finishes uploading before attempting to view it." ) - else: - error( "You are not allowed to access this dataset" ) return hda def get_data( self, dataset, preview=True ): 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.

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commit/galaxy-central: 2 new changesets
by Bitbucket 30 Oct '12

30 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e825b868a31f/ changeset: e825b868a31f user: carlfeberhard date: 2012-10-30 21:39:47 summary: history.js: add hda updater, pull model data from common api code (in initial mako render, and on fetch/update), set up url templates for history, hda models affected #: 8 files diff -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c static/scripts/mvc/history.js --- a/static/scripts/mvc/history.js +++ b/static/scripts/mvc/history.js @@ -7,101 +7,182 @@ TODO: currently, adding a dataset (via tool execute, etc.) creates a new dataset and refreshes the page + from mako template: + BUG: imported, shared history with unaccessible dataset errs in historycontents when getting history + (entire history is inaccessible) + BUG: anon user, broken updater (upload) + added check_state to UsesHistoryDatasetAssocMixin + BUG: anon user + BUG: historyItem, error'd ds show display, download? + + from loadFromAPI: + BUG: not showing previous annotations + + fixed: + BUG: history, broken intial hist state (running, updater, etc.) + ??: doesn't seem to happen anymore + BUG: collapse all should remove all expanded from storage + FIXED: hideAllItemBodies now resets storage.expandedItems + BUG: historyItem, shouldn't allow tag, annotate, peek on purged datasets + FIXED: ok state now shows only: info, rerun + BUG: history?, some ids aren't returning encoded... + FIXED:??? + BUG: history, showing deleted ds + FIXED + UGH: historyItems have to be decorated with history_ids (api/histories/:history_id/contents/:id) + FIXED by adding history_id to history_contents.show + BUG: history, if hist has err'd ds, hist has perm state 'error', updater on following ds's doesn't run + FIXED by reordering history state from ds' states here and histories + BUG: history, broken annotation on reload (can't get thru api (sets fine, tho)) + FIXED: get thru api for now + + to relational model? + HDACollection, meta_files, display_apps, etc. + + + break this file up + localize all + ?: render url templates on init or render? + ?: history, annotation won't accept unicode + quota mgr + show_deleted/hidden: + use storage + on/off ui + move histview fadein/out in render to app? + don't draw body until it's first expand event + + hierarchy: + dataset -> hda + history -> historyForEditing, historyForViewing + display_structured? + + btw: get an error'd ds by running fastqc on fastq (when you don't have it installed) meta: + css/html class/id 'item' -> hda + add classes, ids on empty divs + events (local/ui and otherwise) require.js convert function comments to jsDoc style, complete comments move inline styles into base.less watch the magic strings watch your globals - all: - add classes, ids on empty divs - incorporate relations? - events (local/ui and otherwise) - have info bodies prev. opened, redisplay on refresh - transfer history.mako js: - updater, etc. - create viz icon - trackster - scatterplot - phylo-viz - on ready: - delete function - check_transfer_status (running->ok) - quota meter update - - historyItemView: - poly HistoryItemView (and HistoryView?) on: for_editing, display_structured, trans.user - don't draw body until it's first unhide event - HIview state transitions (eg. upload -> ok), curr: build new, delete old, place new (in render) - move visualizations menu - include phyloviz - - History: - renaming broken - tags rendering broken (url?) - annotation (url?) - meta controls : collapse all, rename, annotate, etc. - - collection: - show_deleted, show_hidden (thru js - no refresh) - + features: + lineage + hide button + show permissions in info + show shared/sharing status on ds, history + maintain scroll position on refresh (storage?) + selection, multi-select (and actions common to selected (ugh)) + searching + sorting, re-shuffling ============================================================================= */ -//TODO: use initialize (or validate) to check purged AND deleted -> purged XOR deleted -var HistoryItem = BaseModel.extend( LoggableMixin ).extend({ +var HistoryDatasetAssociation = BaseModel.extend( LoggableMixin ).extend({ // a single HDA model // uncomment this out see log messages //logger : console, defaults : { + // ---these are part of an HDA proper: + + // parent (containing) history + history_id : null, + // often used with tagging + model_class : 'HistoryDatasetAssociation', + // index within history (??) + hid : 0, + // ---whereas these are Dataset related/inherited + id : null, - name : '', - data_type : null, - file_size : 0, - genome_build : null, - metadata_data_lines : 0, - metadata_dbkey : null, - metadata_sequences : 0, + name : '', + // one of HistoryDatasetAssociation.STATES + state : '', + // sniffed datatype (sam, tabular, bed, etc.) + data_type : null, + // size in bytes + file_size : 0, + + // array of associated file types (eg. [ 'bam_index', ... ]) + meta_files : [], misc_blurb : '', - misc_info : '', - model_class : '', - state : '', + misc_info : '', + deleted : false, purged : false, + // aka. !hidden + visible : false, + // based on trans.user (is_admin or security_agent.can_access_dataset( <user_roles>, hda.dataset )) + accessible : false, - // clash with BaseModel here? - visible : true, - - for_editing : true, - // additional urls will be passed and added, if permissions allow their use - - bodyIsShown : false + // this needs to be removed (it is a function of the view type (e.g. HDAForEditingView)) + for_editing : true + }, + + // fetch location of this history in the api + url : function(){ + //TODO: get this via url router + return 'api/histories/' + this.get( 'history_id' ) + '/contents/' + this.get( 'id' ); }, + // (curr) only handles changing state of non-accessible hdas to STATES.NOT_VIEWABLE + //TODO: use initialize (or validate) to check purged AND deleted -> purged XOR deleted initialize : function(){ this.log( this + '.initialize', this.attributes ); this.log( '\tparent history_id: ' + this.get( 'history_id' ) ); - //TODO: accessible is set in alt_hist - // this state is not in trans.app.model.Dataset.states - set it here + //!! this state is not in trans.app.model.Dataset.states - set it here if( !this.get( 'accessible' ) ){ - this.set( 'state', HistoryItem.STATES.NOT_VIEWABLE ); + this.set( 'state', HistoryDatasetAssociation.STATES.NOT_VIEWABLE ); } + + this.on( 'change', function( event, x, y, z ){ + this.log( this + ' has changed:', event, x, y, z ); + }); }, + isDeletedOrPurged : function(){ + return ( this.get( 'deleted' ) || this.get( 'purged' ) ); + }, + + // roughly can_edit from history_common.mako - not deleted or purged = editable isEditable : function(){ - // roughly can_edit from history_common.mako - not deleted or purged = editable return ( //this.get( 'for_editing' ) - //&& !( this.get( 'deleted' ) || this.get( 'purged' ) ) - !( this.get( 'deleted' ) || this.get( 'purged' ) ) + //&& !( this.get( 'deleted' ) || this.get( 'purged' ) )?? + !this.isDeletedOrPurged() ); }, + + // based on show_deleted, show_hidden (gen. from the container control), would this ds show in the list of ds's? + //TODO: too many visibles + isVisible : function( show_deleted, show_hidden ){ + var isVisible = true; + if( ( !show_deleted ) + && ( this.get( 'deleted' ) || this.get( 'purged' ) ) ){ + isVisible = false; + } + if( ( !show_hidden ) + && ( !this.get( 'visible' ) ) ){ + isVisible = false; + } + return isVisible; + }, + // 'final' states are states where no processing (for the ds) is left to do on the server + inFinalState : function(){ + return ( + ( this.get( 'state' ) === HistoryDatasetAssociation.STATES.OK ) + || ( this.get( 'state' ) === HistoryDatasetAssociation.STATES.FAILED_METADATA ) + || ( this.get( 'state' ) === HistoryDatasetAssociation.STATES.EMPTY ) + || ( this.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) + ); + }, + + // convenience fn to match hda.has_data hasData : function(){ //TODO:?? is this equivalent to all possible hda.has_data calls? return ( this.get( 'file_size' ) > 0 ); @@ -112,13 +193,13 @@ if( this.get( 'name' ) ){ nameAndId += ':"' + this.get( 'name' ) + '"'; } - return 'HistoryItem(' + nameAndId + ')'; + return 'HistoryDatasetAssociation(' + nameAndId + ')'; } }); //------------------------------------------------------------------------------ -HistoryItem.STATES = { - NOT_VIEWABLE : 'not_viewable', // not in trans.app.model.Dataset.states +HistoryDatasetAssociation.STATES = { + NOT_VIEWABLE : 'noPermission', // not in trans.app.model.Dataset.states NEW : 'new', UPLOAD : 'upload', QUEUED : 'queued', @@ -131,34 +212,310 @@ FAILED_METADATA : 'failed_metadata' }; +//============================================================================== +var HDACollection = Backbone.Collection.extend( LoggableMixin ).extend({ + model : HistoryDatasetAssociation, + + logger : console, + + // return the ids of every hda in this collection + ids : function(){ + return this.map( function( item ){ return item.id; }); + }, + + // return an HDA collection containing every 'shown' hda based on show_deleted/hidden + getVisible : function( show_deleted, show_hidden ){ + return new HDACollection( + this.filter( function( item ){ return item.isVisible( show_deleted, show_hidden ); }) + ); + }, + + // get a map where <possible hda state> : [ <list of hda ids in that state> ] + getStateLists : function(){ + var stateLists = {}; + _.each( _.values( HistoryDatasetAssociation.STATES ), function( state ){ + stateLists[ state ] = []; + }); + //NOTE: will err on unknown state + this.each( function( item ){ + stateLists[ item.get( 'state' ) ].push( item.get( 'id' ) ); + }); + return stateLists; + }, + + // update (fetch -> render) the hdas with the ids given + update : function( ids ){ + this.log( this + 'update:', ids ); + + if( !( ids && ids.length ) ){ return; } + + var collection = this; + _.each( ids, function( id, index ){ + var historyItem = collection.get( id ); + historyItem.fetch(); + }); + }, + + toString : function(){ + return ( 'HDACollection(' + this.ids().join(',') + ')' ); + } +}); + //============================================================================== -var HistoryItemView = BaseView.extend( LoggableMixin ).extend({ - //??TODO: add alias in initialize this.hda = this.model? - // view for HistoryItem model above +var History = BaseModel.extend( LoggableMixin ).extend({ + //TODO: bind change events from items and collection to this (itemLengths, states) // uncomment this out see log messages //logger : console, + // values from api (may need more) + defaults : { + id : '', + name : '', + state : '', + + //TODO: wire these to items (or this) + show_deleted : false, + show_hidden : false, + + diskSize : 0, + deleted : false, + + tags : [], + annotation : null, + + //TODO: quota msg and message? how to get those over the api? + message : null, + quotaMsg : false + }, + + url : function(){ + // api location of history resource + //TODO: hardcoded + return 'api/histories/' + this.get( 'id' ); + }, + + initialize : function( initialSettings, initialHdas ){ + this.log( this + ".initialize:", initialSettings, initialHdas ); + + this.hdas = new HDACollection(); + + // if we've got hdas passed in the constructor, load them and set up updates if needed + if( initialHdas && initialHdas.length ){ + this.hdas.reset( initialHdas ); + this.checkForUpdates(); + } + + this.on( 'change', function( event, x, y, z ){ + this.log( this + ' has changed:', event, x, y, z ); + }); + }, + + // get data via the api (alternative to sending options,hdas to initialize) + loadFromAPI : function( historyId, callback ){ + var history = this; + + // fetch the history AND the user (mainly to see if they're logged in at this point) + history.attributes.id = historyId; + //TODO:?? really? fetch user here? + jQuery.when( jQuery.ajax( 'api/users/current' ), history.fetch() + + ).then( function( userResponse, historyResponse ){ + //console.warn( 'fetched user, history: ', userResponse, historyResponse ); + history.attributes.user = userResponse[0]; //? meh. + history.log( history ); + + }).then( function(){ + // ...then the hdas (using contents?ids=...) + jQuery.ajax( history.url() + '/contents?' + jQuery.param({ + ids : history.itemIdsFromStateIds().join( ',' ) + + // reset the collection to the hdas returned + })).success( function( hdas ){ + //console.warn( 'fetched hdas' ); + history.hdas.reset( hdas ); + history.checkForUpdates(); + callback(); + }); + }); + }, + + // reduce the state_ids map of hda id lists -> a single list of ids + //...ugh - seems roundabout; necessary because the history doesn't have a straightforward list of ids + // (and history_contents/index curr returns a summary only) + hdaIdsFromStateIds : function(){ + return _.reduce( _.values( this.get( 'state_ids' ) ), function( reduction, currIdList ){ + return reduction.concat( currIdList ); + }); + }, + + // get the history's state from it's cummulative ds states, delay + update if needed + checkForUpdates : function( datasets ){ + // get overall History state from collection, run updater if History has running/queued hdas + this.stateFromStateIds(); + if( ( this.get( 'state' ) === HistoryDatasetAssociation.STATES.RUNNING ) + || ( this.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) ){ + this.stateUpdater(); + } + return this; + }, + + // sets history state based on current hdas' states + // ported from api/histories.traverse (with placement of error state changed) + stateFromStateIds : function(){ + var stateIdLists = this.hdas.getStateLists(); + this.attributes.state_ids = stateIdLists; + + //TODO: make this more concise + if( ( stateIdLists.running.length > 0 ) + || ( stateIdLists.upload.length > 0 ) + || ( stateIdLists.setting_metadata.length > 0 ) ){ + this.set( 'state', HistoryDatasetAssociation.STATES.RUNNING ); + + } else if( stateIdLists.queued.length > 0 ){ + this.set( 'state', HistoryDatasetAssociation.STATES.QUEUED ); + + } else if( ( stateIdLists.error.length > 0 ) + || ( stateIdLists.failed_metadata.length > 0 ) ){ + this.set( 'state', HistoryDatasetAssociation.STATES.ERROR ); + + } else if( stateIdLists.ok.length === this.hdas.length ){ + this.set( 'state', HistoryDatasetAssociation.STATES.OK ); + + } else { + throw( this + '.stateFromStateDetails: unable to determine ' + + 'history state from hda states: ' + this.get( 'state_ids' ) ); + } + return this; + }, + + // update this history, find any hda's running/queued, update ONLY those that have changed states, + // set up to run this again in some interval of time + stateUpdater : function(){ + var history = this, + oldState = this.get( 'state' ), + // state ids is a map of every possible hda state, each containing a list of ids for hdas in that state + oldStateIds = this.get( 'state_ids' ); + + // pull from the history api + //TODO: fetch? + jQuery.ajax( 'api/histories/' + this.get( 'id' ) + + ).success( function( response ){ + //this.log( 'historyApiRequest, response:', response ); + history.set( response ); + history.log( 'current history state:', history.get( 'state' ), '(was)', oldState ); + + // for each state, check for the difference between old dataset states and new + // the goal here is to check ONLY those datasets that have changed states (not all datasets) + var changedIds = []; + _.each( _.keys( response.state_ids ), function( state ){ + var diffIds = _.difference( response.state_ids[ state ], oldStateIds[ state ] ); + // aggregate those changed ids + changedIds = changedIds.concat( diffIds ); + }); + + // send the changed ids (if any) to dataset collection to have them fetch their own model changes + if( changedIds.length ){ + history.hdas.update( changedIds ); + } + + // set up to keep pulling if this history in run/queue state + //TODO: magic number here + if( ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.RUNNING ) + || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) ){ + setTimeout( function(){ + history.stateUpdater(); + }, 4000 ); + } + + }).error( function( xhr, status, error ){ + if( console && console.warn ){ + console.warn( 'Error getting history updates from the server:', xhr, status, error ); + } + alert( 'Error getting history updates from the server.\n' + error ); + }); + }, + + toString : function(){ + var nameString = ( this.get( 'name' ) )? + ( ',' + this.get( 'name' ) ) : ( '' ); + return 'History(' + this.get( 'id' ) + nameString + ')'; + } +}); + +//============================================================================== +var HDAView = BaseView.extend( LoggableMixin ).extend({ + //??TODO: add alias in initialize this.hda = this.model? + // view for HistoryDatasetAssociation model above + + // uncomment this out see log messages + logger : console, + tagName : "div", className : "historyItemContainer", // ................................................................................ SET UP initialize : function( attributes ){ - this.log( this + '.initialize:', this, this.model ); - this.visible = attributes.visible; + this.log( this + '.initialize:', attributes ); + + // render urlTemplates (gen. provided by GalaxyPaths) to urls + if( !attributes.urlTemplates ){ throw( 'HDAView needs urlTemplates on initialize' ); } + this.urls = this.renderUrls( attributes.urlTemplates, this.model.toJSON() ); + + // whether the body of this hda is expanded (shown) + this.expanded = attributes.expanded || false; + + // re-render the entire view on any model change + this.model.bind( 'change', this.render, this ); }, + // urlTemplates is a map (or nested map) of underscore templates (currently, anyhoo) + // use the templates to create the apropo urls for each action this ds could use + renderUrls : function( urlTemplates, modelJson ){ + var hdaView = this, + urls = {}; + _.each( urlTemplates, function( urlTemplateOrObj, urlKey ){ + // object == nested templates: recurse + if( _.isObject( urlTemplateOrObj ) ){ + urls[ urlKey ] = hdaView.renderUrls( urlTemplateOrObj, modelJson ); + + // string == template: + } else { + // meta_down load is a special case (see renderMetaDownloadUrls) + //TODO: should be a better (gen.) way to handle this case + if( urlKey === 'meta_download' ){ + urls[ urlKey ] = hdaView.renderMetaDownloadUrls( urlTemplateOrObj, modelJson ); + } else { + urls[ urlKey ] = _.template( urlTemplateOrObj, modelJson ); + } + } + }); + return urls; + }, + + // there can be more than one meta_file to download, so return a list of url and file_type for each + renderMetaDownloadUrls : function( urlTemplate, modelJson ){ + return _.map( modelJson.meta_files, function( meta_file ){ + return { + url : _.template( urlTemplate, { id: modelJson.id, file_type: meta_file.file_type }), + file_type : meta_file.file_type + }; + }); + }, + // ................................................................................ RENDER MAIN - //??: this style builds an entire, new DOM tree - is that what we want?? render : function(){ - var id = this.model.get( 'id' ), - state = this.model.get( 'state' ); - this.clearReferences(); - + var view = this, + id = this.model.get( 'id' ), + state = this.model.get( 'state' ), + itemWrapper = $( '<div/>' ).attr( 'id', 'historyItem-' + id ); + + this._clearReferences(); this.$el.attr( 'id', 'historyItemContainer-' + id ); - var itemWrapper = $( '<div/>' ).attr( 'id', 'historyItem-' + id ) + itemWrapper .addClass( 'historyItemWrapper' ).addClass( 'historyItem' ) .addClass( 'historyItem-' + state ); @@ -167,33 +524,52 @@ this.body = $( this._render_body() ); itemWrapper.append( this.body ); + //TODO: move to own function: setUpBehaviours + // we can potentially skip this step and call popupmenu directly on the download button + make_popup_menus( itemWrapper ); + // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) itemWrapper.find( '.tooltip' ).tooltip({ placement : 'bottom' }); - // we can potentially skip this step and call popupmenu directly on the download button - make_popup_menus( itemWrapper ); - - //TODO: better transition/method than this... - this.$el.children().remove(); - return this.$el.append( itemWrapper ); + // transition... + this.$el.fadeOut( 'fast', function(){ + view.$el.children().remove(); + view.$el.append( itemWrapper ).fadeIn( 'fast', function(){ + view.log( view + ' rendered:', view.$el ); + view.trigger( 'rendered' ); + }); + }); + return this; }, - clearReferences : function(){ - //??TODO: best way? + //NOTE: button renderers have the side effect of caching their IconButtonViews to this view + // clear out cached sub-views, dom refs, etc. from prev. render + _clearReferences : function(){ + //??TODO: we should reset these in the button logic checks (i.e. if not needed this.button = null; return null) //?? do we really need these - not so far + //TODO: at least move these to a map this.displayButton = null; this.editButton = null; this.deleteButton = null; this.errButton = null; + this.showParamsButton = null; + this.rerunButton = null; + this.visualizationsButton = null; + this.tagButton = null; + this.annotateButton = null; }, // ................................................................................ RENDER WARNINGS + // hda warnings including: is deleted, is purged, is hidden (including links to further actions (undelete, etc.)) _render_warnings : function(){ // jQ errs on building dom with whitespace - if there are no messages, trim -> '' - return $( jQuery.trim( HistoryItemView.templates.messages( this.model.toJSON() ) ) ); + return $( jQuery.trim( HDAView.templates.messages( + _.extend( this.model.toJSON(), { urls: this.urls } ) + ))); }, // ................................................................................ RENDER TITLEBAR + // the part of an hda always shown (whether the body is expanded or not): title link, title buttons _render_titleBar : function(){ var titleBar = $( '<div class="historyItemTitleBar" style="overflow: hidden"></div>' ); titleBar.append( this._render_titleButtons() ); @@ -203,6 +579,8 @@ }, // ................................................................................ display, edit attr, delete + // icon-button group for the common, most easily accessed actions + //NOTE: these are generally displayed for almost every hda state (tho poss. disabled) _render_titleButtons : function(){ // render the display, edit attr and delete icon-buttons var buttonDiv = $( '<div class="historyItemButtons"></div>' ); @@ -212,31 +590,45 @@ return buttonDiv; }, - //TODO: ?? the three title buttons render for err'd datasets: is this normal? + // icon-button to display this hda in the galaxy main iframe _render_displayButton : function(){ - // don't show display while uploading - if( this.model.get( 'state' ) === HistoryItem.STATES.UPLOAD ){ return null; } + // don't show display if not in final state, error'd, or not accessible + if( ( !this.model.inFinalState() ) + || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) + || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + || ( !this.model.get( 'accessible' ) ) ){ + return null; + } + var displayBtnData = { + icon_class : 'display' + }; + // show a disabled display if the data's been purged - displayBtnData = ( this.model.get( 'purged' ) )?({ - title : 'Cannot display datasets removed from disk', - enabled : false, - icon_class : 'display' + if( this.model.get( 'purged' ) ){ + displayBtnData.enabled = false; + displayBtnData.title = 'Cannot display datasets removed from disk'; - // if not, render the display icon-button with href - }):({ - title : 'Display data in browser', - href : this.model.get( 'display_url' ), - target : ( this.model.get( 'for_editing' ) )?( 'galaxy_main' ):( null ), - icon_class : 'display' - }); + } else { + displayBtnData.title = 'Display data in browser'; + displayBtnData.href = this.urls.display; + } + + if( this.model.get( 'for_editing' ) ){ + displayBtnData.target = 'galaxy_main'; + } + this.displayButton = new IconButtonView({ model : new IconButton( displayBtnData ) }); return this.displayButton.render().$el; }, + // icon-button to edit the attributes (format, permissions, etc.) this hda _render_editButton : function(){ // don't show edit while uploading, or if editable - if( ( this.model.get( 'state' ) === HistoryItem.STATES.UPLOAD ) + if( ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.UPLOAD ) + || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) + || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + || ( !this.model.get( 'accessible' ) ) || ( !this.model.get( 'for_editing' ) ) ){ return null; } @@ -245,7 +637,7 @@ deleted = this.model.get( 'deleted' ), editBtnData = { title : 'Edit attributes', - href : this.model.get( 'edit_url' ), + href : this.urls.edit, target : 'galaxy_main', icon_class : 'edit' }; @@ -254,29 +646,33 @@ //TODO: if for_editing if( deleted || purged ){ editBtnData.enabled = false; - } - if( deleted ){ - editBtnData.title = 'Undelete dataset to edit attributes'; - } else if( purged ){ - editBtnData.title = 'Cannot edit attributes of datasets removed from disk'; + if( purged ){ + editBtnData.title = 'Cannot edit attributes of datasets removed from disk'; + } else if( deleted ){ + editBtnData.title = 'Undelete dataset to edit attributes'; + } } this.editButton = new IconButtonView({ model : new IconButton( editBtnData ) }); return this.editButton.render().$el; }, + // icon-button to delete this hda _render_deleteButton : function(){ - // don't show delete if not editable - if( !this.model.get( 'for_editing' ) ){ return null; } + // don't show delete if... + if( ( !this.model.get( 'for_editing' ) ) + || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + || ( !this.model.get( 'accessible' ) ) ){ + return null; + } var deleteBtnData = { title : 'Delete', - href : this.model.get( 'delete_url' ), + href : this.urls[ 'delete' ], id : 'historyItemDeleter-' + this.model.get( 'id' ), icon_class : 'delete' }; - if( ( this.model.get( 'deleted' ) || this.model.get( 'purged' ) ) - && ( !this.model.get( 'delete_url' ) ) ){ + if( this.model.get( 'deleted' ) || this.model.get( 'purged' ) ){ deleteBtnData = { title : 'Dataset is already deleted', icon_class : 'delete', @@ -288,22 +684,27 @@ }, // ................................................................................ titleLink + // render the hid and hda.name as a link (that will expand the body) _render_titleLink : function(){ - return $( jQuery.trim( HistoryItemView.templates.titleLink( this.model.toJSON() ) ) ); + return $( jQuery.trim( HDAView.templates.titleLink( + _.extend( this.model.toJSON(), { urls: this.urls } ) + ))); }, // ................................................................................ RENDER BODY + // render the data/metadata summary (format, size, misc info, etc.) _render_hdaSummary : function(){ - var modelData = this.model.toJSON(); + var modelData = _.extend( this.model.toJSON(), { urls: this.urls } ); // if there's no dbkey and it's editable : pass a flag to the template to render a link to editing in the '?' if( this.model.get( 'metadata_dbkey' ) === '?' && this.model.isEditable() ){ _.extend( modelData, { dbkey_unknown_and_editable : true }); } - return HistoryItemView.templates.hdaSummary( modelData ); + return HDAView.templates.hdaSummary( modelData ); }, // ................................................................................ primary actions + // render the icon-buttons gen. placed underneath the hda summary _render_primaryActionButtons : function( buttonRenderingFuncs ){ var primaryActionButtons = $( '<div/>' ).attr( 'id', 'primary-actions-' + this.model.get( 'id' ) ), view = this; @@ -313,73 +714,124 @@ return primaryActionButtons; }, + // icon-button/popupmenu to down the data (and/or the associated meta files (bai, etc.)) for this hda _render_downloadButton : function(){ // don't show anything if the data's been purged if( this.model.get( 'purged' ) ){ return null; } // return either: a single download icon-button (if there are no meta files) // or a popupmenu with links to download assoc. meta files (if there are meta files) - var downloadLinkHTML = HistoryItemView.templates.downloadLinks( this.model.toJSON() ); + var downloadLinkHTML = HDAView.templates.downloadLinks( + _.extend( this.model.toJSON(), { urls: this.urls } ) + ); //this.log( this + '_render_downloadButton, downloadLinkHTML:', downloadLinkHTML ); return $( downloadLinkHTML ); }, - //NOTE: button renderers have the side effect of caching their IconButtonViews to this view + // icon-button to show the input and output (stdout/err) for the job that created this hda _render_errButton : function(){ - if( ( this.model.get( 'state' ) !== HistoryItem.STATES.ERROR ) + if( ( this.model.get( 'state' ) !== HistoryDatasetAssociation.STATES.ERROR ) || ( !this.model.get( 'for_editing' ) ) ){ return null; } this.errButton = new IconButtonView({ model : new IconButton({ title : 'View or report this error', - href : this.model.get( 'report_error_url' ), + href : this.urls.report_error, target : 'galaxy_main', icon_class : 'bug' })}); return this.errButton.render().$el; }, + // icon-button to show the input and output (stdout/err) for the job that created this hda _render_showParamsButton : function(){ // gen. safe to show in all cases this.showParamsButton = new IconButtonView({ model : new IconButton({ title : 'View details', - href : this.model.get( 'show_params_url' ), + href : this.urls.show_params, target : 'galaxy_main', icon_class : 'information' }) }); return this.showParamsButton.render().$el; }, + // icon-button to re run the job that created this hda _render_rerunButton : function(){ if( !this.model.get( 'for_editing' ) ){ return null; } this.rerunButton = new IconButtonView({ model : new IconButton({ title : 'Run this job again', - href : this.model.get( 'rerun_url' ), + href : this.urls.rerun, target : 'galaxy_main', icon_class : 'arrow-circle' }) }); return this.rerunButton.render().$el; }, - _render_tracksterButton : function(){ - var trackster_urls = this.model.get( 'trackster_urls' ); + // build an icon-button or popupmenu based on the number of applicable visualizations + // also map button/popup clicks to viz setup functions + _render_visualizationsButton : function(){ + var dbkey = this.model.get( 'dbkey' ), + visualizations = this.model.get( 'visualizations' ), + visualization_url = this.urls.visualization, + popup_menu_dict = {}, + params = { + dataset_id: this.model.get( 'id' ), + hda_ldda: 'hda' + }; + if( !( this.model.hasData() ) || !( this.model.get( 'for_editing' ) ) - || !( trackster_urls ) ){ return null; } + || !( visualizations && visualizations.length ) + || !( visualization_url ) ){ + //console.warn( 'NOT rendering visualization icon' ) + return null; + } - this.tracksterButton = new IconButtonView({ model : new IconButton({ - title : 'View in Trackster', + // render the icon from template + this.visualizationsButton = new IconButtonView({ model : new IconButton({ + title : 'Visualize', + href : visualization_url, icon_class : 'chart_curve' })}); - this.errButton.render(); //?? needed? - this.errButton.$el.addClass( 'trackster-add' ).attr({ - 'data-url' : trackster_urls[ 'data-url' ], - 'action-url': trackster_urls[ 'action-url' ], - 'new-url' : trackster_urls[ 'new-url' ] - }); - return this.errButton.$el; + var $icon = this.visualizationsButton.render().$el; + $icon.addClass( 'visualize-icon' ); // needed? + + //TODO: make this more concise + // map a function to each visualization in the icon's attributes + // create a popupmenu from that map + // Add dbkey to params if it exists. + if( dbkey ){ params.dbkey = dbkey; } + + function create_viz_action( visualization ) { + switch( visualization ){ + case 'trackster': + return create_trackster_action_fn( visualization_url, params, dbkey ); + case 'scatterplot': + return create_scatterplot_action_fn( visualization_url, params ); + default: + return function(){ + window.parent.location = visualization_url + '/' + visualization + '?' + $.param( params ); }; + } + } + + // No need for popup menu because there's a single visualization. + if ( visualizations.length === 1 ) { + $icon.attr( 'title', visualizations[0] ); + $icon.click( create_viz_action( visualizations[0] ) ); + + // >1: Populate menu dict with visualization fns, make the popupmenu + } else { + _.each( visualizations, function( visualization ) { + //TODO: move to utils + var titleCaseVisualization = visualization.charAt( 0 ).toUpperCase() + visualization.slice( 1 ); + popup_menu_dict[ titleCaseVisualization ] = create_viz_action( visualization ); + }); + make_popupmenu( $icon, popup_menu_dict ); + } + return $icon; }, // ................................................................................ secondary actions + // secondary actions: currently tagging and annotation (if user is allowed) _render_secondaryActionButtons : function( buttonRenderingFuncs ){ // move to the right (same level as primary) var secondaryActionButtons = $( '<div/>' ), @@ -394,68 +846,82 @@ return secondaryActionButtons; }, + // icon-button to load and display tagging html + //TODO: these should be a sub-MV _render_tagButton : function(){ if( !( this.model.hasData() ) || !( this.model.get( 'for_editing' ) ) - || ( !this.model.get( 'retag_url' ) ) ){ return null; } + || ( !this.urls.tags.get ) ){ return null; } this.tagButton = new IconButtonView({ model : new IconButton({ title : 'Edit dataset tags', target : 'galaxy_main', - href : this.model.get( 'retag_url' ), + href : this.urls.tags.get, icon_class : 'tags' })}); return this.tagButton.render().$el; }, + // icon-button to load and display annotation html + //TODO: these should be a sub-MV _render_annotateButton : function(){ if( !( this.model.hasData() ) || !( this.model.get( 'for_editing' ) ) - || ( !this.model.get( 'annotate_url' ) ) ){ return null; } + || ( !this.urls.annotation.get ) ){ return null; } this.annotateButton = new IconButtonView({ model : new IconButton({ title : 'Edit dataset annotation', target : 'galaxy_main', - href : this.model.get( 'annotate_url' ), icon_class : 'annotate' })}); return this.annotateButton.render().$el; }, // ................................................................................ other elements - _render_tagArea : function(){ - if( !this.model.get( 'retag_url' ) ){ return null; } - //TODO: move to mvc/tags.js - return $( HistoryItemView.templates.tagArea( this.model.toJSON() ) ); - }, - - _render_annotationArea : function(){ - if( !this.model.get( 'annotate_url' ) ){ return null; } - //TODO: move to mvc/annotations.js - return $( HistoryItemView.templates.annotationArea( this.model.toJSON() ) ); - }, - + // render links to external genome display applications (igb, gbrowse, etc.) + //TODO: not a fan of the style on these _render_displayApps : function(){ - // render links to external genome display applications (igb, gbrowse, etc.) if( !this.model.hasData() ){ return null; } var displayAppsDiv = $( '<div/>' ).addClass( 'display-apps' ); if( !_.isEmpty( this.model.get( 'display_types' ) ) ){ - //this.log( this + 'display_types:', this.model.get( 'display_types' ) ); + //this.log( this + 'display_types:', this.model.get( 'urls' ).display_types ); //TODO:?? does this ever get used? displayAppsDiv.append( - HistoryItemView.templates.displayApps({ displayApps : this.model.toJSON().display_types }) + HDAView.templates.displayApps({ displayApps : this.model.get( 'display_types' ) }) ); } if( !_.isEmpty( this.model.get( 'display_apps' ) ) ){ - //this.log( this + 'display_apps:', this.model.get( 'display_apps' ) ); + //this.log( this + 'display_apps:', this.model.get( 'urls' ).display_apps ); displayAppsDiv.append( - HistoryItemView.templates.displayApps({ displayApps : this.model.toJSON().display_apps }) + HDAView.templates.displayApps({ displayApps : this.model.get( 'display_apps' ) }) ); } return displayAppsDiv; }, + //TODO: into sub-MV + // render the area used to load tag display + _render_tagArea : function(){ + if( !this.urls.tags.set ){ return null; } + //TODO: move to mvc/tags.js + return $( HDAView.templates.tagArea( + _.extend( this.model.toJSON(), { urls: this.urls } ) + )); + }, + + //TODO: into sub-MV + // render the area used to load annotation display + _render_annotationArea : function(){ + if( !this.urls.annotation.get ){ return null; } + //TODO: move to mvc/annotations.js + return $( HDAView.templates.annotationArea( + _.extend( this.model.toJSON(), { urls: this.urls } ) + )); + }, + + // render the data peek + //TODO: curr. pre-formatted into table on the server side - may not be ideal/flexible _render_peek : function(){ if( !this.model.get( 'peek' ) ){ return null; } return $( '<div/>' ).append( @@ -468,6 +934,7 @@ // ................................................................................ state body renderers // _render_body fns for the various states + //TODO: only render these on expansion (or already expanded) _render_body_not_viewable : function( parent ){ //TODO: revisit - still showing display, edit, delete (as common) - that CAN'T be right parent.append( $( '<div>You do not have permission to view dataset.</div>' ) ); @@ -532,7 +999,7 @@ _render_body_failed_metadata : function( parent ){ //TODO: the css for this box is broken (unlike the others) // add a message box about the failure at the top of the body... - parent.append( $( HistoryItemView.templates.failedMetadata( this.model.toJSON() ) ) ); + parent.append( $( HDAView.templates.failedMetadata( this.model.toJSON() ) ) ); //...then render the remaining body as STATES.OK (only diff between these states is the box above) this._render_body_ok( parent ); }, @@ -540,12 +1007,25 @@ _render_body_ok : function( parent ){ // most common state renderer and the most complicated parent.append( this._render_hdaSummary() ); + + // return shortened form if del'd + //TODO: is this correct? maybe only on purged + if( this.model.isDeletedOrPurged() ){ + parent.append( this._render_primaryActionButtons([ + this._render_downloadButton, + this._render_showParamsButton, + this._render_rerunButton + ])); + return; + } + //NOTE: change the order here parent.append( this._render_primaryActionButtons([ this._render_downloadButton, this._render_errButton, this._render_showParamsButton, - this._render_rerunButton + this._render_rerunButton, + this._render_visualizationsButton ])); parent.append( this._render_secondaryActionButtons([ this._render_tagButton, @@ -570,7 +1050,6 @@ _render_body : function(){ //this.log( this + '_render_body' ); - var state = this.model.get( 'state' ); //this.log( 'state:', state, 'for_editing', for_editing ); //TODO: incorrect id (encoded - use hid?) @@ -579,48 +1058,45 @@ .addClass( 'historyItemBody' ) .attr( 'style', 'display: block' ); - //TODO: not a fan of this - switch( state ){ - case HistoryItem.STATES.NOT_VIEWABLE : - this._render_body_not_viewable( body ); + //TODO: not a fan of this dispatch + switch( this.model.get( 'state' ) ){ + case HistoryDatasetAssociation.STATES.NOT_VIEWABLE : + this._render_body_not_viewable( body ); break; - case HistoryItem.STATES.UPLOAD : - this._render_body_uploading( body ); + case HistoryDatasetAssociation.STATES.UPLOAD : + this._render_body_uploading( body ); break; - case HistoryItem.STATES.QUEUED : - this._render_body_queued( body ); + case HistoryDatasetAssociation.STATES.QUEUED : + this._render_body_queued( body ); break; - case HistoryItem.STATES.RUNNING : + case HistoryDatasetAssociation.STATES.RUNNING : this._render_body_running( body ); break; - case HistoryItem.STATES.ERROR : - this._render_body_error( body ); + case HistoryDatasetAssociation.STATES.ERROR : + this._render_body_error( body ); break; - case HistoryItem.STATES.DISCARDED : - this._render_body_discarded( body ); + case HistoryDatasetAssociation.STATES.DISCARDED : + this._render_body_discarded( body ); break; - case HistoryItem.STATES.SETTING_METADATA : - this._render_body_setting_metadata( body ); + case HistoryDatasetAssociation.STATES.SETTING_METADATA : + this._render_body_setting_metadata( body ); break; - case HistoryItem.STATES.EMPTY : - this._render_body_empty( body ); + case HistoryDatasetAssociation.STATES.EMPTY : + this._render_body_empty( body ); break; - case HistoryItem.STATES.FAILED_METADATA : - this._render_body_failed_metadata( body ); + case HistoryDatasetAssociation.STATES.FAILED_METADATA : + this._render_body_failed_metadata( body ); break; - case HistoryItem.STATES.OK : - this._render_body_ok( body ); + case HistoryDatasetAssociation.STATES.OK : + this._render_body_ok( body ); break; default: //??: no body? body.append( $( '<div>Error: unknown dataset state "' + state + '".</div>' ) ); } + body.append( '<div style="clear: both"></div>' ); - body.append( '<div style="clear: both"></div>' ); - if( this.model.get( 'bodyIsShown' ) === false ){ - body.hide(); - } - if( this.visible ){ + if( this.expanded ){ body.show(); } else { body.hide(); @@ -636,6 +1112,8 @@ }, // ................................................................................ STATE CHANGES / MANIPULATION + // find the tag area and, if initial: (via ajax) load the html for displaying them; otherwise, unhide/hide + //TODO: into sub-MV loadAndDisplayTags : function( event ){ //BUG: broken with latest //TODO: this is a drop in from history.mako - should use MV as well @@ -649,7 +1127,7 @@ // Need to fill tag element. $.ajax({ //TODO: the html from this breaks a couple of times - url: this.model.get( 'ajax_get_tag_url' ), + url: this.urls.tags.get, error: function() { alert( "Tagging failed" ); }, success: function(tag_elt_html) { tagElt.html(tag_elt_html); @@ -661,7 +1139,6 @@ // Tag element is filled; show. tagArea.slideDown("fast"); } - } else { // Hide. tagArea.slideUp("fast"); @@ -669,20 +1146,21 @@ return false; }, + // find the annotation area and, if initial: (via ajax) load the html for displaying it; otherwise, unhide/hide + //TODO: into sub-MV loadAndDisplayAnnotation : function( event ){ - //BUG: broken with latest //TODO: this is a drop in from history.mako - should use MV as well this.log( this + '.loadAndDisplayAnnotation', event ); var annotationArea = this.$el.find( '.annotation-area' ), annotationElem = annotationArea.find( '.annotation-elt' ), - setAnnotationUrl = this.model.get( 'ajax_set_annotation_url' ); + setAnnotationUrl = this.urls.annotation.set; // Show or hide annotation area; if showing annotation area and it's empty, fill it. if ( annotationArea.is( ":hidden" ) ){ if( !jQuery.trim( annotationElem.html() ) ){ // Need to fill annotation element. $.ajax({ - url: this.model.get( 'ajax_get_annotation_url' ), + url: this.urls.annotation.get, error: function(){ alert( "Annotations failed" ); }, success: function( htmlFromAjax ){ if( htmlFromAjax === "" ){ @@ -710,253 +1188,264 @@ return false; }, - toggleBodyVisibility : function( visible ){ + // expand/collapse body + //side effect: trigger event + toggleBodyVisibility : function( event, expanded ){ var $body = this.$el.find( '.historyItemBody' ); - if( visible === undefined ){ - $body.toggle(); - } else if( visible ){ - $body.show(); + expanded = ( expanded === undefined )?( !$body.is( ':visible' ) ):( expanded ); + //this.log( 'toggleBodyVisibility, expanded:', expanded, '$body:', $body ); + + if( expanded ){ + $body.slideDown( 'fast' ); } else { - $body.hide(); + $body.slideUp( 'fast' ); } - this.trigger( 'toggleBodyVisibility', this.model.get( 'id' ), $body.is( ':visible' ) ); + this.trigger( 'toggleBodyVisibility', this.model.get( 'id' ), expanded ); }, // ................................................................................ UTILTIY toString : function(){ var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); - return 'HistoryItemView(' + modelString + ')'; + return 'HDAView(' + modelString + ')'; } }); //------------------------------------------------------------------------------ -HistoryItemView.templates = { - warningMsg : Handlebars.templates[ 'template-warningmessagesmall' ], +HDAView.templates = { + warningMsg : Handlebars.templates[ 'template-warningmessagesmall' ], - messages : Handlebars.templates[ 'template-history-warning-messages' ], - titleLink : Handlebars.templates[ 'template-history-titleLink' ], - hdaSummary : Handlebars.templates[ 'template-history-hdaSummary' ], - downloadLinks : Handlebars.templates[ 'template-history-downloadLinks' ], - failedMetadata : Handlebars.templates[ 'template-history-failedMetaData' ], - tagArea : Handlebars.templates[ 'template-history-tagArea' ], - annotationArea : Handlebars.templates[ 'template-history-annotationArea' ], - displayApps : Handlebars.templates[ 'template-history-displayApps' ] + messages : Handlebars.templates[ 'template-history-warning-messages' ], + titleLink : Handlebars.templates[ 'template-history-titleLink' ], + hdaSummary : Handlebars.templates[ 'template-history-hdaSummary' ], + downloadLinks : Handlebars.templates[ 'template-history-downloadLinks' ], + failedMetadata : Handlebars.templates[ 'template-history-failedMetaData' ], + tagArea : Handlebars.templates[ 'template-history-tagArea' ], + annotationArea : Handlebars.templates[ 'template-history-annotationArea' ], + displayApps : Handlebars.templates[ 'template-history-displayApps' ] }; //============================================================================== -var HistoryCollection = Backbone.Collection.extend({ - model : HistoryItem, - - toString : function(){ - return ( 'HistoryCollection()' ); - } -}); +//TODO: these belong somewhere else + +//TODO: should be imported from scatterplot.js +//TODO: OR abstracted to 'load this in the galaxy_main frame' +function create_scatterplot_action_fn( url, params ){ + action = function() { + var galaxy_main = $( window.parent.document ).find( 'iframe#galaxy_main' ), + final_url = url + '/scatterplot?' + $.param(params); + galaxy_main.attr( 'src', final_url ); + //TODO: this needs to go away + $( 'div.popmenu-wrapper' ).remove(); + return false; + }; + return action; +} + +// ----------------------------------------------------------------------------- +// Create trackster action function. +//TODO: should be imported from trackster.js +function create_trackster_action_fn(vis_url, dataset_params, dbkey) { + return function() { + var params = {}; + if (dbkey) { params.dbkey = dbkey; } + $.ajax({ + url: vis_url + '/list_tracks?f-' + $.param(params), + dataType: "html", + error: function() { alert( "Could not add this dataset to browser." ); }, + success: function(table_html) { + var parent = window.parent; + + parent.show_modal("View Data in a New or Saved Visualization", "", { + "Cancel": function() { + parent.hide_modal(); + }, + "View in saved visualization": function() { + // Show new modal with saved visualizations. + parent.show_modal("Add Data to Saved Visualization", table_html, { + "Cancel": function() { + parent.hide_modal(); + }, + "Add to visualization": function() { + $(parent.document).find('input[name=id]:checked').each(function() { + var vis_id = $(this).val(); + dataset_params.id = vis_id; + parent.location = vis_url + "/trackster?" + $.param(dataset_params); + }); + } + }); + }, + "View in new visualization": function() { + parent.location = vis_url + "/trackster?" + $.param(dataset_params); + } + }); + } + }); + return false; + }; +} //============================================================================== -var History = BaseModel.extend( LoggableMixin ).extend({ - //TODO: bind change events from items and collection to this (itemLengths, states) - - // uncomment this out see log messages - //logger : console, - - // values from api (may need more) - defaults : { - id : '', - name : '', - state : '', - //TODO:?? change these to a list of encoded ids? - state_details : { - discarded : 0, - empty : 0, - error : 0, - failed_metadata : 0, - ok : 0, - queued : 0, - running : 0, - setting_metadata: 0, - upload : 0 - }, - - // maybe security issues... - userIsAdmin : false, - userRoles : [], - //TODO: hardcoded - - //TODO: wire this to items - itemsLength : 0, - showDeleted : false, - showHidden : false, - - diskSize : 0, - deleted : false, - - // tagging_common.mako: render_individual_tagging_element(user=trans.get_user(), - // tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20") - tags : [], - annotation : null, - message : null, - quotaMsg : false, - - baseURL : null, - hideDeletedURL : null, - hideHiddenURL : null, - tagURL : null, - annotateURL : null - }, - - initialize : function( data, history_datasets ){ - //this.log( this + '.initialize', data, history_datasets ); - this.items = new HistoryCollection(); - }, - - toJSON : function(){ - // unfortunately, bb doesn't call 'get' to form the JSON meaning computed vals from get aren't used, so... - // a simple example of override and super call - var json = Backbone.Model.prototype.toJSON.call( this ); - json.itemsLength = this.items.length; - //this.log( this + '.json:', json ); - return json; - }, - - loadDatasetsAsHistoryItems : function( datasets ){ - //TODO: add via ajax - multiple datasets at once - // adds the given dataset/Item data to historyItems - // and updates this.state based on their states - //pre: datasets is a list of objs - //this.log( this + '.loadDatasets', datasets ); - var self = this, - selfID = this.get( 'id' ), - stateDetails = this.get( 'state_details' ); - - _.each( datasets, function( dataset, index ){ - //self.log( 'loading dataset: ', dataset, index ); - - // create an item sending along the history_id as well - var historyItem = new HistoryItem( - _.extend( dataset, { history_id: selfID } ) ); - //self.log( 'as History:', historyItem ); - self.items.add( historyItem ); - - // add item's state to running totals in stateDetails - var itemState = dataset.state; - stateDetails[ itemState ] += 1; - }); - - // get overall History state from totals - this.set( 'state_details', stateDetails ); - this._stateFromStateDetails(); - return this; - }, - - _stateFromStateDetails : function(){ - // sets this.state based on current historyItems' states - // ported from api/histories.traverse - //pre: state_details is current counts of dataset/item states - this.set( 'state', '' ); - var stateDetails = this.get( 'state_details' ); - - //TODO: make this more concise - if( ( stateDetails.error > 0 ) - || ( stateDetails.failed_metadata > 0 ) ){ - this.set( 'state', HistoryItem.STATES.ERROR ); - - } else if( ( stateDetails.running > 0 ) - || ( stateDetails.setting_metadata > 0 ) ){ - this.set( 'state', HistoryItem.STATES.RUNNING ); - - } else if( stateDetails.queued > 0 ){ - this.set( 'state', HistoryItem.STATES.QUEUED ); - - } else if( stateDetails.ok === this.items.length ){ - this.set( 'state', HistoryItem.STATES.OK ); - - } else { - throw( '_stateFromStateDetails: unable to determine ' - + 'history state from state details: ' + this.state_details ); - } - return this; - }, - - toString : function(){ - var nameString = ( this.get( 'name' ) )? - ( ',' + this.get( 'name' ) ) : ( '' ); - return 'History(' + this.get( 'id' ) + nameString + ')'; - } -}); - -//------------------------------------------------------------------------------ -// view for the HistoryCollection (as per current right hand panel) +// view for the HDACollection (as per current right hand panel) var HistoryView = BaseView.extend( LoggableMixin ).extend({ // uncomment this out see log messages - //logger : console, + logger : console, // direct attachment to existing element el : 'body.historyPage', - //TODO: add id? - initialize : function(){ - this.log( this + '.initialize:', this ); + // init with the model, urlTemplates, set up storage, bind HDACollection events + //NOTE: this will create or load PersistantStorage keyed under 'HistoryView.<id>' + //pre: you'll need to pass in the urlTemplates (urlTemplates : { history : {...}, hda : {...} }) + initialize : function( attributes ){ + this.log( this + '.initialize:', attributes ); + + // set up url templates + //TODO: prob. better to put this in class scope (as the handlebars templates), but... + // they're added to GalaxyPaths on page load (after this file is loaded) + if( !attributes.urlTemplates ){ throw( 'HDAView needs urlTemplates on initialize' ); } + if( !attributes.urlTemplates.history ){ throw( 'HDAView needs urlTemplates.history on initialize' ); } + if( !attributes.urlTemplates.hda ){ throw( 'HDAView needs urlTemplates.hda on initialize' ); } + this.urlTemplates = attributes.urlTemplates.history; + this.hdaUrlTemplates = attributes.urlTemplates.hda; + // data that needs to be persistant over page refreshes + // (note the key function which uses the history id as well) this.storage = new PersistantStorage( 'HistoryView.' + this.model.get( 'id' ), - { visibleItems : {} } + { expandedHdas : {} } ); - // set up the individual history items/datasets - this.initializeItems(); + //this.model.bind( 'change', this.render, this ); + + // bind events from the model's hda collection + this.model.hdas.bind( 'add', this.add, this ); + this.model.hdas.bind( 'reset', this.addAll, this ); + this.model.hdas.bind( 'all', this.all, this ); + + // set up instance vars + this.hdaViews = {}; + this.urls = {}; }, - initializeItems : function(){ - this.itemViews = {}; - var historyPanel = this; - - // set up a view for each item, init with model and listeners, cache to map ( model.id : view ) - this.model.items.each( function( item ){ - var itemId = item.get( 'id' ), - visible = historyPanel.storage.get( 'visibleItems' ).get( itemId ), - itemView = new HistoryItemView({ - model: item, - visible: visible + add : function( hda ){ + //console.debug( 'add.' + this, hda ); + //TODO + }, + + addAll : function(){ + //console.debug( 'addAll.' + this ); + // re render when all hdas are reset + this.render(); + }, + + all : function( event ){ + //console.debug( 'allItemEvents.' + this, event ); + //...for which to do the debuggings + }, + + // render the urls for this view using urlTemplates and the model data + renderUrls : function( modelJson ){ + var historyView = this; + + historyView.urls = {}; + _.each( this.urlTemplates, function( urlTemplate, urlKey ){ + historyView.urls[ urlKey ] = _.template( urlTemplate, modelJson ); + }); + return historyView.urls; + }, + + // render urls, historyView body, and hdas (if any are shown), fade out, swap, fade in, set up behaviours + render : function(){ + var historyView = this, + setUpQueueName = historyView.toString() + '.set-up', + newRender = $( '<div/>' ), + modelJson = this.model.toJSON(); + + // render the urls and add them to the model json + modelJson.urls = this.renderUrls( modelJson ); + + // render the main template, tooltips + //NOTE: this is done before the items, since item views should handle theirs themselves + newRender.append( HistoryView.templates.historyPanel( modelJson ) ); + historyView.$el.find( '.tooltip' ).tooltip(); + + // render hda views (if any) + if( !this.model.hdas.length + || !this.renderItems( newRender.find( '#' + this.model.get( 'id' ) + '-datasets' ) ) ){ + // if history is empty or no hdas would be rendered, show the empty message + newRender.find( '#emptyHistoryMessage' ).show(); + } + + // fade out existing, swap with the new, fade in, set up behaviours + $( historyView ).queue( setUpQueueName, function( next ){ + historyView.$el.fadeOut( 'fast', function(){ next(); }); + }); + $( historyView ).queue( setUpQueueName, function( next ){ + // swap over from temp div newRender + historyView.$el.html( '' ); + historyView.$el.append( newRender.children() ); + + historyView.$el.fadeIn( 'fast', function(){ next(); }); + }); + $( historyView ).queue( setUpQueueName, function( next ){ + this.log( historyView + ' rendered:', historyView.$el ); + + //TODO: ideally, these would be set up before the fade in (can't because of async save text) + historyView.setUpBehaviours(); + historyView.trigger( 'rendered' ); + next(); + }); + $( historyView ).dequeue( setUpQueueName ); + return this; + }, + + // set up a view for each item to be shown, init with model and listeners, cache to map ( model.id : view ) + renderItems : function( $whereTo ){ + this.hdaViews = {}; + var historyView = this, + show_deleted = this.model.get( 'show_deleted' ), + show_hidden = this.model.get( 'show_hidden' ), + visibleHdas = this.model.hdas.getVisible( show_deleted, show_hidden ); + + // only render the shown hdas + visibleHdas.each( function( hda ){ + var hdaId = hda.get( 'id' ), + expanded = historyView.storage.get( 'expandedHdas' ).get( hdaId ); + historyView.hdaViews[ hdaId ] = new HDAView({ + model : hda, + expanded : expanded, + urlTemplates : historyView.hdaUrlTemplates }); - historyPanel.setUpItemListeners( itemView ); - historyPanel.itemViews[ itemId ] = itemView; + historyView.setUpHdaListeners( historyView.hdaViews[ hdaId ] ); + // render it (NOTE: reverse order, newest on top (prepend)) + //TODO: by default send a reverse order list (although this may be more efficient - it's more confusing) + $whereTo.prepend( historyView.hdaViews[ hdaId ].render().$el ); + }); + return visibleHdas.length; + }, + + // set up HistoryView->HDAView listeners + setUpHdaListeners : function( hdaView ){ + var history = this; + + // use storage to maintain a list of hdas whose bodies are expanded + hdaView.bind( 'toggleBodyVisibility', function( id, visible ){ + if( visible ){ + history.storage.get( 'expandedHdas' ).set( id, true ); + } else { + history.storage.get( 'expandedHdas' ).deleteKey( id ); + } }); }, - setUpItemListeners : function( itemView ){ - var HistoryPanel = this; - - // use storage to maintain a list of items whose bodies are visible - itemView.bind( 'toggleBodyVisibility', function( id, visible ){ - if( visible ){ - HistoryPanel.storage.get( 'visibleItems' ).set( id, true ); - } else { - HistoryPanel.storage.get( 'visibleItems' ).deleteKey( id ); - } - }); - }, - - render : function(){ - this.$el.append( HistoryView.templates.historyPanel( this.model.toJSON() ) ); - this.log( this + ' rendered from template:', this.$el ); - - // set up aliases - this.itemsDiv = this.$el.find( '#' + this.model.get( 'id' ) + '-datasets' ); - - //TODO: set up widgets, tooltips, etc. - async_save_text( - "history-name-container", - "history-name", - this.model.get( 'renameURL' ), - "new_name", - 18 - ); - this.$el.find( '.tooltip' ).tooltip(); - - var historyAnnotationArea = this.$el.find( '#history-annotation-area' ); - $( '#history-annotate' ).click( function() { + // set up js/widget behaviours: tooltips, + //TODO: these should be either sub-MVs, or handled by events + setUpBehaviours : function(){ + // annotation slide down + var historyAnnotationArea = this.$( '#history-annotation-area' ); + this.$( '#history-annotate' ).click( function() { if ( historyAnnotationArea.is( ":hidden" ) ) { historyAnnotationArea.slideDown( "fast" ); } else { @@ -964,77 +1453,60 @@ } return false; }); - async_save_text( - "history-annotation-container", - "history-annotation", - this.model.get( 'annotateURL' ), - "new_annotation", - 18, - true, - 4 - ); - if( this.model.items.length ){ - // render to temp, move all at once, remove temp holder - var tempDiv = this._render_items(); - this.itemsDiv.append( tempDiv.children() ); - tempDiv.remove(); - } - }, + // title and annotation editable text + //NOTE: these use page scoped selectors - so these need to be in the page DOM before they're applicable + async_save_text( "history-name-container", "history-name", + this.urls.rename, "new_name", 18 ); - _render_items : function(){ - var div = $( '<div/>' ), - view = this; - //NOTE!: render in reverse (newest on top) via prepend (instead of append) - _.each( this.itemViews, function( itemView, viewId ){ - view.log( view + '.render_items:', viewId, itemView ); - div.prepend( itemView.render() ); - }); - return div; + async_save_text( "history-annotation-container", "history-annotation", + this.urls.annotate, "new_annotation", 18, true, 4 ); }, events : { - 'click #history-collapse-all' : 'hideAllItemBodies', + 'click #history-collapse-all' : 'hideAllHdaBodies', 'click #history-tag' : 'loadAndDisplayTags' }, - hideAllItemBodies : function(){ + // collapse all hda bodies + hideAllHdaBodies : function(){ _.each( this.itemViews, function( item ){ - item.toggleBodyVisibility( false ); + item.toggleBodyVisibility( null, false ); }); + this.storage.set( 'expandedHdas', {} ); }, + // find the tag area and, if initial: (via ajax) load the html for displaying them; otherwise, unhide/hide + //TODO: into sub-MV loadAndDisplayTags : function( event ){ - //BUG: broken with latest - //TODO: this is a drop in from history.mako - should use MV as well this.log( this + '.loadAndDisplayTags', event ); var tagArea = this.$el.find( '#history-tag-area' ), tagElt = tagArea.find( '.tag-elt' ); this.log( '\t tagArea', tagArea, ' tagElt', tagElt ); - // Show or hide tag area; if showing tag area and it's empty, fill it. + // Show or hide tag area; if showing tag area and it's empty, fill it if( tagArea.is( ":hidden" ) ){ if( !jQuery.trim( tagElt.html() ) ){ var view = this; // Need to fill tag element. $.ajax({ //TODO: the html from this breaks a couple of times - url: this.model.get( 'tagURL' ), + url: view.urls.tag, error: function() { alert( "Tagging failed" ); }, success: function(tag_elt_html) { - view.log( view + ' tag elt html (ajax)', tag_elt_html ); + //view.log( view + ' tag elt html (ajax)', tag_elt_html ); tagElt.html(tag_elt_html); tagElt.find(".tooltip").tooltip(); tagArea.slideDown("fast"); } }); } else { - // Tag element is filled; show. + // Tag element already filled: show tagArea.slideDown("fast"); } } else { - // Hide. + // Currently shown: Hide tagArea.slideUp("fast"); } return false; @@ -1049,12 +1521,10 @@ historyPanel : Handlebars.templates[ 'template-history-historyPanel' ] }; - - //============================================================================== //return { // HistoryItem : HistoryItem, -// HitoryItemView : HistoryItemView, +// HDAView : HDAView, // HistoryCollection : HistoryCollection, // History : History, // HistoryView : HistoryView diff -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c static/scripts/templates/compiled/template-history-downloadLinks.js --- a/static/scripts/templates/compiled/template-history-downloadLinks.js +++ b/static/scripts/templates/compiled/template-history-downloadLinks.js @@ -7,16 +7,18 @@ function program1(depth0,data) { var buffer = "", stack1, foundHelper; + buffer += "\n"; buffer += "\n<div popupmenu=\"dataset-"; foundHelper = helpers.id; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "-popup\">\n <a class=\"action-button\" href=\""; - foundHelper = helpers.download_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.download_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.download; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\">Download Dataset</a>\n <a>Additional Files</a>\n "; - stack1 = depth0.meta_files; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.meta_download; stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n</div>\n<div style=\"float:left;\" class=\"menubutton split popup\" id=\"dataset-"; @@ -24,36 +26,38 @@ if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "-popup\">\n <a href=\""; - foundHelper = helpers.download_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.download_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.download; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\" title=\"Download\" class=\"icon-button disk tooltip\"></a>\n</div>\n"; return buffer;} function program2(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n <a class=\"action-button\" href=\""; - foundHelper = helpers.meta_download_url; + foundHelper = helpers.url; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.meta_download_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + else { stack1 = depth0.url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "\">Download "; - foundHelper = helpers.meta_file_type; + foundHelper = helpers.file_type; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.meta_file_type; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + else { stack1 = depth0.file_type; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "</a>\n "; return buffer;} function program4(depth0,data) { - var buffer = "", stack1, foundHelper; + var buffer = "", stack1; + buffer += "\n"; buffer += "\n<a href=\""; - foundHelper = helpers.download_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.download_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.download; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\" title=\"Download\" class=\"icon-button disk tooltip\"></a>\n"; return buffer;} - stack1 = depth0.meta_files; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.meta_download; stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(4, program4, data),fn:self.program(1, program1, data)}); if(stack1 || stack1 === 0) { return stack1; } else { return ''; }}); diff -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c static/scripts/templates/compiled/template-history-failedMetaData.js --- a/static/scripts/templates/compiled/template-history-failedMetaData.js +++ b/static/scripts/templates/compiled/template-history-failedMetaData.js @@ -6,11 +6,11 @@ function program1(depth0,data) { - var buffer = "", stack1, foundHelper; + var buffer = "", stack1; buffer += "\nAn error occurred setting the metadata for this dataset.\nYou may be able to <a href=\""; - foundHelper = helpers.edit_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.edit_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.edit; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\" target=\"galaxy_main\">set it manually or retry auto-detection</a>.\n"; return buffer;} diff -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c static/scripts/templates/compiled/template-history-hdaSummary.js --- a/static/scripts/templates/compiled/template-history-hdaSummary.js +++ b/static/scripts/templates/compiled/template-history-hdaSummary.js @@ -8,9 +8,9 @@ var buffer = "", stack1, foundHelper; buffer += "\n <a href=\""; - foundHelper = helpers.edit_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.edit_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.edit; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\" target=\"galaxy_main\">"; foundHelper = helpers.metadata_dbkey; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } diff -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c static/scripts/templates/compiled/template-history-historyPanel.js --- a/static/scripts/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/templates/compiled/template-history-historyPanel.js @@ -2,148 +2,130 @@ var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-history-historyPanel'] = template(function (Handlebars,depth0,helpers,partials,data) { helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing, escapeExpression=this.escapeExpression; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; function program1(depth0,data) { + var buffer = "", stack1, foundHelper; + buffer += "\n <div id=\"history-name\" style=\"margin-right: 50px;\" class=\"tooltip editable-text\"\n title=\"Click to rename history\">"; + foundHelper = helpers.name; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n "; + return buffer;} + +function program3(depth0,data) { + return "refresh";} -function program3(depth0,data) { +function program5(depth0,data) { return "collapse all";} -function program5(depth0,data) { +function program7(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n <div style=\"width: 40px; float: right; white-space: nowrap;\">\n <a id=\"history-tag\" title=\""; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; + buffer += "\n <a id=\"history-tag\" title=\""; foundHelper = helpers.local; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n </div>\n "; + buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n "; return buffer;} -function program6(depth0,data) { +function program8(depth0,data) { return "Edit history tags";} -function program8(depth0,data) { +function program10(depth0,data) { return "Edit history annotation";} -function program10(depth0,data) { +function program12(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n<div class=\"historyLinks\">\n <a href=\""; - foundHelper = helpers.hideDeletedURL; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.hideDeletedURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += "\n <a href=\""; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.hide_deleted; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\">"; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</a>\n</div>\n"; + buffer += "</a>\n "; return buffer;} -function program11(depth0,data) { +function program13(depth0,data) { return "hide deleted";} -function program13(depth0,data) { +function program15(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n<div class=\"historyLinks\">\n <a href=\""; - foundHelper = helpers.hideHiddenURL; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.hideHiddenURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += "\n <a href=\""; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.hide_hidden; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\">"; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(16, program16, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(16, program16, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</a>\n</div>\n"; + buffer += "</a>\n "; return buffer;} -function program14(depth0,data) { +function program16(depth0,data) { return "hide hidden";} -function program16(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n "; - buffer += "\n <div id=\"history-size\" style=\"position: absolute; top: 3px; right: 0px;\">"; - foundHelper = helpers.diskSize; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.diskSize; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n <div id=\"history-name\" style=\"margin-right: 50px;\" class=\"tooltip editable-text\" title=\"Click to rename history\">"; - foundHelper = helpers.name; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n \n "; - return buffer;} - function program18(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n <div id=\"history-size\">"; - foundHelper = helpers.diskSize; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.diskSize; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n "; - return buffer;} - -function program20(depth0,data) { - - var buffer = "", stack1, foundHelper; buffer += "\n"; foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(19, program19, data)}); } else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(19, program19, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n"; return buffer;} -function program21(depth0,data) { +function program19(depth0,data) { var stack1, foundHelper; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(22, program22, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(20, program20, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(22, program22, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(20, program20, data)}); } if(stack1 || stack1 === 0) { return stack1; } else { return ''; }} -function program22(depth0,data) { +function program20(depth0,data) { return "You are currently viewing a deleted history!";} -function program24(depth0,data) { +function program22(depth0,data) { var buffer = "", stack1; - buffer += "\n"; - buffer += "\n<div style=\"margin: 0px 5px 10px 5px\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n "; - buffer += "\n "; - buffer += "\n <strong>Tags:</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>Annotation / Notes:</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\" title=\"Click to edit annotation\">\n "; + buffer += "\n <div id=\"history-tag-area\" style=\"display: none\">\n <strong>Tags:</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>Annotation / Notes:</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\" title=\"Click to edit annotation\">\n "; stack1 = depth0.annotation; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(27, program27, data),fn:self.program(25, program25, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(25, program25, data),fn:self.program(23, program23, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n </div>\n </div>\n</div>\n"; + buffer += "\n </div>\n </div>\n </div>\n "; return buffer;} -function program25(depth0,data) { +function program23(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n "; @@ -153,12 +135,12 @@ buffer += escapeExpression(stack1) + "\n "; return buffer;} -function program27(depth0,data) { +function program25(depth0,data) { return "\n <em>Describe or add notes to history</em>\n ";} -function program29(depth0,data) { +function program27(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n<div id=\"message-container\">\n <div class=\""; @@ -172,92 +154,82 @@ buffer += escapeExpression(stack1) + "\n </div><br />\n</div>\n"; return buffer;} -function program31(depth0,data) { +function program29(depth0,data) { return "\n <div id=\"quota-message\" class=\"errormessage\">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n <br/>\n ";} -function program33(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n<div id=\""; - foundHelper = helpers.id; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "-datasets\" class=\"history-datasets-list\">\n "; - buffer += "\n</div>\n\n"; - return buffer;} - -function program35(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n<div class=\"infomessagesmall\" id=\"emptyHistoryMessage\">\n"; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(36, program36, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(36, program36, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</div>\n"; - return buffer;} -function program36(depth0,data) { +function program31(depth0,data) { return "Your history is empty. Click 'Get Data' on the left pane to start";} - buffer += "<div id=\"top-links\" class=\"historyLinks\">\n <a title=\""; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + buffer += "\n<div id=\"history-name-area\" class=\"historyLinks\">\n <div id=\"history-name-container\" style=\"position: relative;\">\n "; + buffer += "\n <div id=\"history-size\" style=\"position: absolute; top: 3px; right: 0px;\">"; + foundHelper = helpers.nice_size; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.nice_size; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n "; + stack1 = depth0.user; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\" class=\"icon-button arrow-circle tooltip\" href=\""; - foundHelper = helpers.baseURL; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.baseURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\"></a>\n <a title='"; + buffer += "\n </div> \n</div>\n<div style=\"clear: both;\"></div>\n\n<div id=\"top-links\" class=\"historyLinks\">\n <a title=\""; foundHelper = helpers.local; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "' id=\"history-collapse-all\"\n class='icon-button toggle tooltip' href='javascript:void(0);'></a>\n "; - stack1 = depth0.userRoles; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); + buffer += "\" class=\"icon-button arrow-circle tooltip\" href=\""; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.base; + stack1 = typeof stack1 === functionType ? stack1() : stack1; + buffer += escapeExpression(stack1) + "\"></a>\n <a title='"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</div>\n<div class=\"clear\"></div>\n\n"; - buffer += "\n"; - stack1 = depth0.showDeleted; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); + buffer += "' id=\"history-collapse-all\"\n class='icon-button toggle tooltip' href='javascript:void(0);'></a>\n <div style=\"width: 40px; float: right; white-space: nowrap;\">\n "; + stack1 = depth0.user; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n"; - stack1 = depth0.showHidden; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); + buffer += "\n </div>\n</div>\n<div style=\"clear: both;\"></div>\n\n"; + buffer += "\n<div class=\"historyLinks\">\n "; + stack1 = depth0.show_deleted; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n"; - buffer += "\n<div id=\"history-name-area\" class=\"historyLinks\">\n <div id=\"history-name-container\" style=\"position: relative;\">\n "; - stack1 = depth0.userRoles; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(18, program18, data),fn:self.program(16, program16, data)}); + buffer += "\n "; + stack1 = depth0.show_hidden; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div> \n</div>\n<div style=\"clear: both;\"></div>\n\n"; + buffer += "\n</div>\n\n"; stack1 = depth0.deleted; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(20, program20, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(18, program18, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n"; buffer += "\n"; - stack1 = depth0.userRoles; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(24, program24, data)}); + buffer += "\n<div style=\"margin: 0px 5px 10px 5px\">\n\n "; + stack1 = depth0.user; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(22, program22, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n"; + buffer += "\n</div>\n\n"; stack1 = depth0.message; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(29, program29, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(27, program27, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n<div id=\"quota-message-container\">\n "; stack1 = depth0.over_quota; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(31, program31, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(29, program29, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</div>\n\n"; - stack1 = depth0.itemsLength; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(35, program35, data),fn:self.program(33, program33, data)}); + buffer += "\n</div>\n\n<div id=\""; + foundHelper = helpers.id; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "-datasets\" class=\"history-datasets-list\"></div>\n\n<div class=\"infomessagesmall\" id=\"emptyHistoryMessage\" style=\"display: none;\">\n "; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(31, program31, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(31, program31, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n</div>"; return buffer;}); })(); \ No newline at end of file diff -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c static/scripts/templates/compiled/template-history-warning-messages.js --- a/static/scripts/templates/compiled/template-history-warning-messages.js +++ b/static/scripts/templates/compiled/template-history-warning-messages.js @@ -6,46 +6,57 @@ function program1(depth0,data) { - var stack1, foundHelper; - foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } - else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } + var stack1; + stack1 = depth0.purged; + stack1 = helpers.unless.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); if(stack1 || stack1 === 0) { return stack1; } else { return ''; }} function program2(depth0,data) { - var buffer = "", stack1; - buffer += "\n This dataset has been deleted.\n "; - stack1 = depth0.undelete_url; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); + var buffer = "", stack1, foundHelper; + buffer += "\n"; + foundHelper = helpers.warningmessagesmall; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } + else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n"; return buffer;} function program3(depth0,data) { + var buffer = "", stack1; + buffer += "\n This dataset has been deleted.\n "; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.undelete; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n"; + return buffer;} +function program4(depth0,data) { + var buffer = "", stack1, foundHelper; buffer += "\n Click <a href=\""; - foundHelper = helpers.undelete_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.undelete_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.undelete; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\" class=\"historyItemUndelete\" id=\"historyItemUndeleter-"; foundHelper = helpers.id; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to undelete it\n "; - stack1 = depth0.purge_url; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.purge; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n "; return buffer;} -function program4(depth0,data) { +function program5(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n or <a href=\""; - foundHelper = helpers.purge_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.purge_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.purge; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\" class=\"historyItemPurge\" id=\"historyItemPurger-"; foundHelper = helpers.id; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } @@ -53,45 +64,46 @@ buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to immediately remove it from disk\n "; return buffer;} -function program6(depth0,data) { +function program7(depth0,data) { var stack1, foundHelper; foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } if(stack1 || stack1 === 0) { return stack1; } else { return ''; }} -function program7(depth0,data) { +function program8(depth0,data) { return "\n This dataset has been deleted and removed from disk.\n";} -function program9(depth0,data) { +function program10(depth0,data) { var stack1, foundHelper; foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } if(stack1 || stack1 === 0) { return stack1; } else { return ''; }} -function program10(depth0,data) { +function program11(depth0,data) { var buffer = "", stack1; buffer += "\n This dataset has been hidden.\n "; - stack1 = depth0.unhide_url; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.unhide; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n"; return buffer;} -function program11(depth0,data) { +function program12(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n Click <a href=\""; - foundHelper = helpers.unhide_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.unhide_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.unhide; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\" class=\"historyItemUnhide\" id=\"historyItemUnhider-"; foundHelper = helpers.id; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } @@ -104,11 +116,11 @@ if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n"; stack1 = depth0.purged; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n"; stack1 = depth0.visible; - stack1 = helpers.unless.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(9, program9, data)}); + stack1 = helpers.unless.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } return buffer;}); })(); \ No newline at end of file diff -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -1,15 +1,17 @@ <script type="text/template" class="template-history" id="template-history-warning-messages"> -{{#if deleted}}{{#warningmessagesmall}} +{{#if deleted}}{{#unless purged}} +{{#warningmessagesmall}} This dataset has been deleted. - {{#if undelete_url}} - Click <a href="{{ undelete_url }}" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" + {{#if urls.undelete}} + Click <a href="{{ urls.undelete }}" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" target="galaxy_history">here</a> to undelete it - {{#if purge_url}} - or <a href="{{ purge_url }}" class="historyItemPurge" id="historyItemPurger-{{ id }}" + {{#if urls.purge}} + or <a href="{{ urls.purge }}" class="historyItemPurge" id="historyItemPurger-{{ id }}" target="galaxy_history">here</a> to immediately remove it from disk {{/if}} {{/if}} -{{/warningmessagesmall}}{{/if}} +{{/warningmessagesmall}} +{{/unless}}{{/if}} {{#if purged}}{{#warningmessagesmall}} This dataset has been deleted and removed from disk. @@ -17,8 +19,8 @@ {{#unless visible}}{{#warningmessagesmall}} This dataset has been hidden. - {{#if unhide_url}} - Click <a href="{{ unhide_url }}" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" + {{#if urls.unhide}} + Click <a href="{{ urls.unhide }}" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" target="galaxy_history">here</a> to unhide it {{/if}} {{/warningmessagesmall}}{{/unless}} @@ -34,7 +36,7 @@ format: <span class="{{ data_type }}">{{ data_type }}</span>, database: {{#if dbkey_unknown_and_editable }} - <a href="{{ edit_url }}" target="galaxy_main">{{ metadata_dbkey }}</a> + <a href="{{ urls.edit }}" target="galaxy_main">{{ metadata_dbkey }}</a> {{else}} <span class="{{ metadata_dbkey }}">{{ metadata_dbkey }}</span> {{/if}} @@ -47,24 +49,26 @@ <script type="text/template" class="template-history" id="template-history-failedMetaData"> {{#warningmessagesmall}} An error occurred setting the metadata for this dataset. -You may be able to <a href="{{ edit_url }}" target="galaxy_main">set it manually or retry auto-detection</a>. +You may be able to <a href="{{ urls.edit }}" target="galaxy_main">set it manually or retry auto-detection</a>. {{/warningmessagesmall}} </script><script type="text/template" class="template-history" id="template-history-downloadLinks"> -{{#if meta_files}} -<div popupmenu="dataset-{{id}}-popup"> - <a class="action-button" href="{{download_url}}">Download Dataset</a> +{{#if urls.meta_download}} +{{! this will be built using a popupmenu }} +<div popupmenu="dataset-{{ id }}-popup"> + <a class="action-button" href="{{ urls.download }}">Download Dataset</a><a>Additional Files</a> - {{#each meta_files}} - <a class="action-button" href="{{meta_download_url}}">Download {{meta_file_type}}</a> + {{#each urls.meta_download}} + <a class="action-button" href="{{ url }}">Download {{ file_type }}</a> {{/each}} </div> -<div style="float:left;" class="menubutton split popup" id="dataset-{{id}}-popup"> - <a href="{{download_url}}" title="Download" class="icon-button disk tooltip"></a> +<div style="float:left;" class="menubutton split popup" id="dataset-{{ id }}-popup"> + <a href="{{ urls.download }}" title="Download" class="icon-button disk tooltip"></a></div> {{else}} -<a href="{{download_url}}" title="Download" class="icon-button disk tooltip"></a> +{{! otherwise a simple icon button }} +<a href="{{ urls.download }}" title="Download" class="icon-button disk tooltip"></a> {{/if}} </script> @@ -101,61 +105,54 @@ History panel/page - the main container for hdas (gen. on the left hand of the glx page) --><script type="text/template" class="template-history" id="template-history-historyPanel"> +{{! history name (if any) }} +<div id="history-name-area" class="historyLinks"> + <div id="history-name-container" style="position: relative;"> + {{! TODO: factor out conditional css }} + <div id="history-size" style="position: absolute; top: 3px; right: 0px;">{{nice_size}}</div> + {{#if user}} + <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text" + title="Click to rename history">{{name}}</div> + {{/if}} + </div> +</div> +<div style="clear: both;"></div> + <div id="top-links" class="historyLinks"> - <a title="{{#local}}refresh{{/local}}" class="icon-button arrow-circle tooltip" href="{{baseURL}}"></a> + <a title="{{#local}}refresh{{/local}}" class="icon-button arrow-circle tooltip" href="{{urls.base}}"></a><a title='{{#local}}collapse all{{/local}}' id="history-collapse-all" class='icon-button toggle tooltip' href='javascript:void(0);'></a> - {{#if userRoles}} <div style="width: 40px; float: right; white-space: nowrap;"> + {{#if user}} <a id="history-tag" title="{{#local}}Edit history tags{{/local}}" class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a><a id="history-annotate" title="{{#local}}Edit history annotation{{/local}}" class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a> + {{/if}} </div> +</div> +<div style="clear: both;"></div> + +{{! TODO: move to js with no reload - use each with historyLinks }} +<div class="historyLinks"> + {{#if show_deleted}} + <a href="{{urls.hide_deleted}}">{{#local}}hide deleted{{/local}}</a> + {{/if}} + {{#if show_hidden}} + <a href="{{urls.hide_hidden}}">{{#local}}hide hidden{{/local}}</a> {{/if}} </div> -<div class="clear"></div> - -{{! TODO: move to js with no reload - use each with historyLinks }} -{{#if showDeleted}} -<div class="historyLinks"> - <a href="{{hideDeletedURL}}">{{#local}}hide deleted{{/local}}</a> -</div> -{{/if}} - -{{#if showHidden}} -<div class="historyLinks"> - <a href="{{hideHiddenURL}}">{{#local}}hide hidden{{/local}}</a> -</div> -{{/if}} - -{{! history name (if any) }} -<div id="history-name-area" class="historyLinks"> - <div id="history-name-container" style="position: relative;"> - {{#if userRoles}} - {{! TODO: factor out conditional css }} - <div id="history-size" style="position: absolute; top: 3px; right: 0px;">{{diskSize}}</div> - <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text" title="Click to rename history">{{name}}</div> - - {{else}} - <div id="history-size">{{diskSize}}</div> - {{/if}} - </div> -</div> -<div style="clear: both;"></div> {{#if deleted}} {{#warningmessagesmall}}{{#local}}You are currently viewing a deleted history!{{/local}}{{/warningmessagesmall}} {{/if}} {{! tags and annotations }} -{{#if userRoles}} {{! TODO: move inline styles out }} <div style="margin: 0px 5px 10px 5px"> + {{#if user}} <div id="history-tag-area" style="display: none"> - {{! load via js render_individual_tagging_element }} - {{! render_individual_tagging_element(user=trans.get_user(), tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20") }} <strong>Tags:</strong><div class="tag-elt"></div></div> @@ -172,8 +169,8 @@ </div></div></div> + {{/if}} </div> -{{/if}} {{#if message}} <div id="message-container"> @@ -192,14 +189,9 @@ {{/if}} </div> -{{#if itemsLength}} -<div id="{{id}}-datasets" class="history-datasets-list"> - {{! NOTE: HistoryItemViews will be appended here }} +<div id="{{id}}-datasets" class="history-datasets-list"></div> + +<div class="infomessagesmall" id="emptyHistoryMessage" style="display: none;"> + {{#local}}Your history is empty. Click 'Get Data' on the left pane to start{{/local}} </div> - -{{else}}{{! no history items }} -<div class="infomessagesmall" id="emptyHistoryMessage"> -{{#local}}Your history is empty. Click 'Get Data' on the left pane to start{{/local}} -</div> -{{/if}} </script> diff -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -1,5 +1,9 @@ <%inherit file="/base.mako"/> +<%def name="title()"> + ${_('Galaxy History')} +</%def> + ## --------------------------------------------------------------------------------------------------------------------- <%def name="create_localization_json( strings_to_localize )"> ## converts strings_to_localize (a list of strings) into a JSON dictionary of { string : localized string } @@ -49,369 +53,233 @@ %></%def> +## --------------------------------------------------------------------------------------------------------------------- +## all the possible history urls (primarily from web controllers at this point) +<%def name="get_history_url_templates()"> +<% + from urllib import unquote_plus + + history_class_name = history.__class__.__name__ + encoded_id_template = '<%= id %>' + + url_dict = { + # TODO:?? next 3 needed? + 'base' : h.url_for( controller="/history" ), + ##TODO: move these into the historyMV + 'hide_deleted' : h.url_for( controller="/history", show_deleted=False ), + 'hide_hidden' : h.url_for( controller="/history", show_hidden=False ), + + ##TODO: into their own MVs + 'rename' : h.url_for( controller="/history", action="rename_async", + id=encoded_id_template ), + 'tag' : h.url_for( controller='tag', action='get_tagging_elt_async', + item_class=history_class_name, item_id=encoded_id_template ), + 'annotate' : h.url_for( controller="/history", action="annotate_async", + id=encoded_id_template ) + } +%> +${ unquote_plus( h.to_json_string( url_dict ) ) } +</%def> ## --------------------------------------------------------------------------------------------------------------------- -<%def name="get_urls_for_hda( hda, encoded_data_id, for_editing )"> +## all the possible hda urls (primarily from web controllers at this point) - whether they should have them or not +##TODO: unify url_for btwn web, api +<%def name="get_hda_url_templates()"><% - from galaxy.datatypes.metadata import FileParameter - #print '\n', hda.name + from urllib import unquote_plus - data_dict = {} - def add_to_data( **kwargs ): - data_dict.update( kwargs ) - - #TODO??: better way to do urls (move into js galaxy_paths (decorate) - _not_ dataset specific) - deleted = hda.deleted - purged = hda.purged - - # ................................................................ link actions - #purged = purged or hda.dataset.purged //?? - # all of these urls are 'datasets/data_id/<action> - if not ( dataset_purged or purged ) and for_editing: - add_to_data( undelete_url=h.url_for( controller='dataset', action='undelete', dataset_id=encoded_data_id ) ) - # trans - if trans.app.config.allow_user_dataset_purge: - add_to_data( purge_url=h.url_for( controller='dataset', action='purge', dataset_id=encoded_data_id ) ) - - if not hda.visible: - add_to_data( unhide_url=h.url_for( controller='dataset', action='unhide', dataset_id=encoded_data_id ) ) - - - # ................................................................ title actions (display, edit, delete) - display_url = '' - if for_editing: - display_url = h.url_for( controller='dataset', action='display', dataset_id=encoded_data_id, preview=True, filename='' ) - else: - # Get URL for display only. - if hda.history.user and hda.history.user.username: - display_url = h.url_for( controller='dataset', action='display_by_username_and_slug', - username=hda.history.user.username, slug=encoded_data_id, filename='' ) - else: - # HACK: revert to for_editing display URL when there is no user/username. This should only happen when - # there's no user/username because dataset is being displayed by history/view after error reported. - # There are no security concerns here because both dataset/display and dataset/display_by_username_and_slug - # check user permissions (to the same degree) before displaying. - display_url = h.url_for( controller='dataset', action='display', dataset_id=encoded_data_id, preview=True, filename='' ) - add_to_data( display_url=display_url ) - - # edit attr button - if for_editing: - if not( hda.deleted or hda.purged ): - edit_url = h.url_for( controller='dataset', action='edit', - dataset_id=encoded_data_id ) - add_to_data( edit_url=edit_url ) - - # delete button - if for_editing and not ( deleted or dataset_purged or purged ): - delete_url = h.url_for( controller='dataset', action='delete', - dataset_id=encoded_data_id, - show_deleted_on_refresh=show_deleted ) - add_to_data( delete_url=delete_url ) - - # ................................................................ primary actions (error, info, download) - # download links (hda and associated meta files) - if not hda.purged: - add_to_data( download_url=h.url_for( controller='/dataset', action='display', - dataset_id=encoded_data_id, to_ext=hda.ext ) ) - - meta_files = [] - for k in hda.metadata.spec.keys(): - if isinstance( hda.metadata.spec[ k ].param, FileParameter ): - file_type = k - download_url = h.url_for( controller='/dataset', action='get_metadata_file', - hda_id=encoded_data_id, metadata_name=file_type ) - meta_files.append( dict( meta_file_type=file_type, meta_download_url=download_url ) ) - - if meta_files: - add_to_data( meta_files=meta_files ) - - # error report - if for_editing: - #NOTE: no state == 'error' check - ##TODO: has to have an _UN_ encoded id - #report_error_url = h.url_for( controller='dataset', action='errors', id=encoded_data_id ) - report_error_url = h.url_for( controller='dataset', action='errors', id=hda.id ) - add_to_data( report_error_url=report_error_url ) - - # info/params - show_params_url = h.url_for( controller='dataset', action='show_params', dataset_id=encoded_data_id ) - add_to_data( show_params_url=show_params_url ) - - # rerun - if for_editing: - ##TODO: has to have an _UN_ encoded id - #rerun_url = h.url_for( controller='tool_runner', action='rerun', id=encoded_data_id ) - rerun_url = h.url_for( controller='tool_runner', action='rerun', id=hda.id ) - add_to_data( rerun_url=rerun_url ) - - # visualizations - if hda.ext in app.datatypes_registry.get_available_tracks(): - # do these need _localized_ dbkeys? - trackster_urls = {} - if hda.dbkey != '?': - data_url = h.url_for( controller='visualization', action='list_tracks', dbkey=hda.dbkey ) - data_url = hda.replace( 'dbkey', 'f-dbkey' ) - else: - data_url = h.url_for( controller='visualization', action='list_tracks' ) - trackster_urls[ 'hda-url' ] = data_url - trackster_urls[ 'action-url' ] = h.url_for( controller='visualization', action='trackster', dataset_id=encoded_data_id ) - trackster_urls[ 'new-url' ] = h.url_for( controller='visualization', action='trackster', dataset_id=encoded_data_id, default_dbkey=hda.dbkey ) - add_to_data( trackster_url=trackster_urls ) - - # display apps (igv, uscs) - display_types = [] - display_apps = [] - if( hda.state in [ 'ok', 'failed_metadata' ] - and hda.has_data() ): - #NOTE: these two data share structures - #TODO: this doesn't seem to get called with the hda I'm using. What would call this? How can I spoof it? - for display_type in hda.datatype.get_display_types(): - display_label = hda.datatype.get_display_label( display_type ) - target_frame, display_links = hda.datatype.get_display_links( hda, display_type, app, request.base ) - if display_links: - display_links = [] - for display_name, display_href in display_links: - display_type_link = dict( - target = target_frame, - href = display_href, - text = display_name - ) - display_links.append( display_type_link ) - - # append the link list to the main map using the display_label - display_types.append( dict( label=display_label, links=display_links ) ) + hda_class_name = 'HistoryDatasetAssociation' + encoded_id_template = '<%= id %>' + username_template = '<%= username %>' + hda_ext_template = '<%= file_ext %>' + meta_type_template = '<%= file_type %>' - for display_app in hda.get_display_applications( trans ).itervalues(): - app_links = [] - for display_app_link in display_app.links.itervalues(): - app_link = dict( - target = display_app_link.url.get( 'target_frame', '_blank' ), - href = display_app_link.get_display_url( hda, trans ), - text = _( display_app_link.name ) - ) - app_links.append( app_link ) - - display_apps.append( dict( label=display_app.name, links=app_links ) ) - - # attach the display types and apps (if any) to the hda obj - #if display_types: print 'display_types:', display_types - #if display_apps: print 'display_apps:', display_apps - add_to_data( display_types=display_types ) - add_to_data( display_apps=display_apps ) + url_dict = { + # ................................................................ warning message links + 'purge' : h.url_for( controller='dataset', action='purge', + dataset_id=encoded_id_template ), + #TODO: hide (via api) + 'unhide' : h.url_for( controller='dataset', action='unhide', + dataset_id=encoded_id_template ), + #TODO: via api + 'undelete' : h.url_for( controller='dataset', action='undelete', + dataset_id=encoded_id_template ), - # ................................................................ secondary actions (tagging, annotation) - if trans.user: - add_to_data( ajax_get_tag_url=( h.url_for( - controller='tag', action='get_tagging_elt_async', - item_class=hda.__class__.__name__, item_id=encoded_data_id ) ) ) - add_to_data( retag_url=( h.url_for( - controller='tag', action='retag', - item_class=hda.__class__.__name__, item_id=encoded_data_id ) ) ) - - add_to_data( annotate_url=( h.url_for( controller='dataset', action='annotate', id=encoded_data_id ) ) ) - add_to_data( ajax_get_annotation_url=( h.url_for( - controller='dataset', action='get_annotation_async', id=encoded_data_id ) ) ) - add_to_data( ajax_set_annotation_url=( h.url_for( - controller='/dataset', action='annotate_async', id=encoded_data_id ) ) ) - - return data_dict + # ................................................................ title actions (display, edit, delete), + 'display' : h.url_for( controller='dataset', action='display', + dataset_id=encoded_id_template, preview=True, filename='' ), + #'user_display_url' : h.url_for( controller='dataset', action='display_by_username_and_slug', + # username=username_template, slug=encoded_id_template, filename='' ), + 'edit' : h.url_for( controller='dataset', action='edit', + dataset_id=encoded_id_template ), + + #TODO: via api + #TODO: show deleted handled by history + 'delete' : h.url_for( controller='dataset', action='delete', + dataset_id=encoded_id_template, show_deleted_on_refresh=show_deleted ), + + # ................................................................ download links (and associated meta files), + 'download' : h.url_for( controller='/dataset', action='display', + dataset_id=encoded_id_template, to_ext=hda_ext_template ), + 'meta_download' : h.url_for( controller='/dataset', action='get_metadata_file', + hda_id=encoded_id_template, metadata_name=meta_type_template ), + + # ................................................................ primary actions (errors, params, rerun), + 'report_error' : h.url_for( controller='dataset', action='errors', + id=encoded_id_template ), + 'show_params' : h.url_for( controller='dataset', action='show_params', + dataset_id=encoded_id_template ), + 'rerun' : h.url_for( controller='tool_runner', action='rerun', + id=encoded_id_template ), + 'visualization' : h.url_for( controller='visualization' ), + + # ................................................................ secondary actions (tagging, annotation), + 'tags' : { + 'get' : h.url_for( controller='tag', action='get_tagging_elt_async', + item_class=hda_class_name, item_id=encoded_id_template ), + 'set' : h.url_for( controller='tag', action='retag', + item_class=hda_class_name, item_id=encoded_id_template ), + }, + 'annotation' : { + #'annotate_url' : h.url_for( controller='dataset', action='annotate', + # id=encoded_id_template ), # doesn't look like this is used (unless graceful degradation) + 'get' : h.url_for( controller='dataset', action='get_annotation_async', + id=encoded_id_template ), + 'set' : h.url_for( controller='/dataset', action='annotate_async', + id=encoded_id_template ), + }, + } +%> +${ unquote_plus( h.to_json_string( url_dict ) ) } +</%def> + +## ----------------------------------------------------------------------------- +## get the history, hda, user data from the api (as opposed to the web controllers/mako) + +## I'd rather do without these (esp. the get_hdas which hits the db twice) +## but we'd need a common map producer (something like get_api_value but more complete) +##TODO: api/web controllers should use common code, and this section should call that code +<%def name="get_history( id )"> +<% + return trans.webapp.api_controllers[ 'histories' ].show( trans, trans.security.encode_id( id ) ) %></%def> -<%def name="prep_hda( data, for_editing )"> +<%def name="get_current_user()"><% - from pprint import pformat - ## 'datasets' passed from root.history are HistoryDatasetAssociations - ## these datas _have_ a Dataset (data.dataset) - #ported mostly from history_common - #post: return dictionary form - #??: move out of templates? - #??: gather data from model? - - DATASET_STATE = trans.app.model.Dataset.states - # {'OK': 'ok', 'FAILED_METADATA': 'failed_metadata', 'UPLOAD': 'upload', - # 'DISCARDED': 'discarded', 'RUNNING': 'running', 'SETTING_METADATA': 'setting_metadata', - # 'ERROR': 'error', 'NEW': 'new', 'QUEUED': 'queued', 'EMPTY': 'empty'} - #TODO: move to Dataset.states? how often are these used? - STATES_INTERPRETED_AS_QUEUED = [ 'no state', '', None ] - - #TODO: clean up magic strings - #TODO: format to 120 - data_dict = data.get_api_value() - - # convert/re-format api values as needed - #TODO: use data_dict.update to add these (instead of localvars) - def add_to_data( **kwargs ): - data_dict.update( kwargs ) - - # trans - add_to_data( hid=data.hid ) - encoded_data_id = trans.security.encode_id( data.id ) - add_to_data( id=encoded_data_id ) - - # localize dbkey - data_dict[ 'metadata_dbkey' ] = _( data_dict[ 'metadata_dbkey' ] ) - - add_to_data( state=data.state ) - if data_state in STATES_INTERPRETED_AS_QUEUED: - #TODO: magic string - add_to_data( state=DATASET_STATE.QUEUED ) - - # trans - current_user_roles = trans.get_current_user_roles() - add_to_data( can_edit=( not ( data.deleted or data.purged ) ) ) - - # considered accessible if user can access or user isn't admin - # trans - accessible = trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ) - accessible = trans.user_is_admin() or accessible - add_to_data( accessible=accessible ) - - url_dict = get_urls_for_hda( data, encoded_data_id, for_editing ) - data_dict.update( url_dict ) - #print 'url_dict:', pformat( url_dict, indent=2 ) - #print 'data_dict:', pformat( data_dict, indent=2 ), "\n" - #print data_dict - - if data.peek != "no peek": - add_to_data( peek=( _( h.to_unicode( data.display_peek() ) ) ) ) - - return data_dict + if not trans.user: + return '{}' + return trans.webapp.api_controllers[ 'users' ].show( + trans, trans.security.encode_id( trans.user.id ) ) %></%def> -##TODO: remove after filling tags.js -<%namespace file="../tagging_common.mako" import="render_individual_tagging_element" /> -<%def name="context_to_js()"> +<%def name="get_hdas( history_id, hdas )"><% - ##print 'context', context, dir( context ) - ##print 'context.kwargs', context.kwargs - ##print 'history:', history - - ##TODO: move to API - - for_editing = True - encoded_history_id = trans.security.encode_id( history.id ) - context_dict = { - 'history' : { - 'id' : encoded_history_id, - 'name' : history.name, - - 'status' : status, - 'showDeleted' : show_deleted, - 'showHidden' : show_hidden, - 'quotaMsg' : over_quota, - 'message' : message, ##'go outside' - - 'deleted' : history.deleted, - 'diskSize' : history.get_disk_size( nice_size=True ), - - ## maybe security issues... - 'userIsAdmin' : trans.user_is_admin(), - 'userRoles' : [ role.get_api_value() for role in trans.get_current_user_roles() ], - - ##tagging_common.mako: render_individual_tagging_element(user=trans.get_user(), - ## tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20") - 'tags' : [], - ##TODO: broken - of course - ##TODO: remove after filling tags.js - ##'tagHTML' : render_individual_tagging_element( - ## user=trans.get_user(), - ## tagged_item=history, - ## elt_context="history.mako", - ## use_toggle_link=False, - ## input_size="20"), - ##TODO:?? h.to_unicode( annotation ) | h - 'annotation' : h.to_unicode( annotation ), - - ##TODO: broken - 'baseURL' : h.url_for( controller="/history", show_deleted=show_deleted ), - 'hideDeletedURL' : h.url_for( controller="/history", show_deleted=False ), - 'hideHiddenURL' : h.url_for( controller="/history", show_hidden=False ), - 'renameURL' : h.url_for( controller="/history", action="rename_async", id=encoded_history_id ), - 'tagURL' : h.url_for( controller='tag', action='get_tagging_elt_async', - item_class=history.__class__.__name__, item_id=encoded_history_id ), - 'annotateURL' : h.url_for( controller="/history", action="annotate_async", id=encoded_history_id ) - }, - 'hdas' : [ prep_hda( hda, for_editing ) for hda in datasets ], - - # some of these may be unneeded when all is said and done... - 'hdaId' : hda_id, - 'forEditing' : for_editing, - } + if not hdas: + return '[]' + # rather just use the history.id (wo the datasets), but... + #BUG: one inaccessible dataset will error entire list + return trans.webapp.api_controllers[ 'history_contents' ].index( + trans, trans.security.encode_id( history_id ), + ids=( ','.join([ trans.security.encode_id( hda.id ) for hda in hdas ]) ) ) %> -${ h.to_json_string( context_dict ) } </%def> +<%def name="print_visualizations( datasets )"> +<% + for dataset in datasets: + print trans.security.encode_id( dataset.id ) + print dataset.get_visualizations() + +%> +</%def> + +## ----------------------------------------------------------------------------- <%def name="javascripts()"> - ${parent.javascripts()} +${parent.javascripts()} + +${h.js( + "libs/jquery/jstorage", + "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", + "libs/json2", + "libs/backbone/backbone-relational", + "mvc/base-mvc", "mvc/ui" +)} + +${h.templates( + "helpers-common-templates", + "template-warningmessagesmall", - ${h.js( - "libs/jquery/jstorage", - "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", - "libs/json2", - "mvc/base-mvc", "mvc/ui" - )} + "template-history-warning-messages", + "template-history-titleLink", + "template-history-failedMetadata", + "template-history-hdaSummary", + "template-history-downloadLinks", + "template-history-tagArea", + "template-history-annotationArea", + "template-history-displayApps", + + "template-history-historyPanel" +)} - ${h.templates( - "helpers-common-templates", - "template-warningmessagesmall", +##TODO: fix: curr hasta be _after_ h.templates - move somehow +${h.js( + "mvc/history" + ##"mvc/tags", "mvc/annotations" +)} + +<script type="text/javascript"> +// set js localizable strings +GalaxyLocalization.setLocalizedString( ${ create_localization_json( get_page_localized_strings() ) } ); + +// add needed controller urls to GalaxyPaths +galaxy_paths.set( 'hda', ${get_hda_url_templates()} ); +galaxy_paths.set( 'history', ${get_history_url_templates()} ); + +$(function(){ + + // ostensibly, this is the App + if( console && console.debug ){ + //if( console.clear ){ console.clear(); } + console.debug( 'using backbone.js in history panel' ); + } + + // Navigate to a dataset. + console.debug( 'getting data' ); + var user = ${ get_current_user() }, + history = ${ get_history( history.id ) }, + hdas = ${ get_hdas( history.id, datasets ) }; + //console.debug( 'user:', user ); + //console.debug( 'history:', history ); + //console.debug( 'hdas:', hdas ); + + // i don't like this, but user authentication changes views/behaviour + history.user = user; + history.show_deleted = ${ 'true' if show_deleted else 'false' }; + history.show_hidden = ${ 'true' if show_hidden else 'false' }; - "template-history-warning-messages", - "template-history-titleLink", - "template-history-failedMetadata", - "template-history-hdaSummary", - "template-history-downloadLinks", - "template-history-tagArea", - "template-history-annotationArea", - "template-history-displayApps", - - "template-history-historyPanel" - )} + //console.debug( 'galaxy_paths:', galaxy_paths ); + var glx_history = new History( history, hdas ); + var glx_history_view = new HistoryView({ model: glx_history, urlTemplates: galaxy_paths.attributes }).render(); + + //var glx_history = new History().setPaths( galaxy_paths ), + // glx_history_view = new HistoryView({ model: glx_history }); + //console.warn( 'fetching' ); + //glx_history.loadFromAPI( pageData.history.id ); - ##TODO: fix: curr hasta be _after_ h.templates - move somehow - ${h.js( - "mvc/history" - ##"mvc/tags", "mvc/annotations" - )} - - <script type="text/javascript"> - GalaxyLocalization.setLocalizedString( ${ create_localization_json( get_page_localized_strings() ) } ); - // add needed controller urls to GalaxyPaths - galaxy_paths.set( 'dataset_path', "${h.url_for( controller='dataset' )}" ) - - // Init. on document load. - var pageData = ${context_to_js()}; - if( console && console.debug ){ - window.pageData = pageData; - - ##_.each( pageData.hdas, function( hda ){ - ## console.debug( hda ); - ##}); - } - - // on ready - USE_CURR_DATA = true; - $(function(){ - if( console && console.debug ){ console.debug( 'using backbone.js in history panel' ); } - - if ( window.USE_CURR_DATA ){ - // Navigate to a dataset. - if( pageData.hdaId ){ - self.location = "#" + pageData.hdaId; - } - var glx_history = new History( pageData.history ).loadDatasetsAsHistoryItems( pageData.hdas ), - glx_history_view = new HistoryView({ model: glx_history }); - glx_history_view.render(); - window.glx_history = glx_history; window.glx_history_view = glx_history_view; - - return; - - } else { - // sandbox - } - }); - </script> + if( console && console.debug ){ + window.user = top.user = user; + window._history = top._history = history; + window.hdas = top.hdas = hdas; + window.glx_history = top.glx_history = glx_history; + window.glx_history_view = top.glx_history_view = glx_history_view; + top.storage = jQuery.jStorage + } + + return; +}); +</script></%def> @@ -453,8 +321,4 @@ </noscript></%def> -<%def name="title()"> - ${_('Galaxy History')} -</%def> - <body class="historyPage"></body> https://bitbucket.org/galaxy/galaxy-central/changeset/2e70816299e4/ changeset: 2e70816299e4 user: carlfeberhard date: 2012-10-30 21:42:11 summary: pack scripts affected #: 6 files diff -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c -r 2e70816299e40fecc4902adda54126bb00316588 static/scripts/packed/mvc/history.js --- a/static/scripts/packed/mvc/history.js +++ b/static/scripts/packed/mvc/history.js @@ -1,1 +1,1 @@ -var HistoryItem=BaseModel.extend(LoggableMixin).extend({defaults:{id:null,name:"",data_type:null,file_size:0,genome_build:null,metadata_data_lines:0,metadata_dbkey:null,metadata_sequences:0,misc_blurb:"",misc_info:"",model_class:"",state:"",deleted:false,purged:false,visible:true,for_editing:true,bodyIsShown:false},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryItem.STATES.NOT_VIEWABLE)}},isEditable:function(){return(!(this.get("deleted")||this.get("purged")))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryItem("+a+")"}});HistoryItem.STATES={NOT_VIEWABLE:"not_viewable",NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HistoryItemView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){this.log(this+".initialize:",this,this.model);this.visible=a.visible},render:function(){var c=this.model.get("id"),b=this.model.get("state");this.clearReferences();this.$el.attr("id","historyItemContainer-"+c);var a=$("<div/>").attr("id","historyItem-"+c).addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+b);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);a.find(".tooltip").tooltip({placement:"bottom"});make_popup_menus(a);this.$el.children().remove();return this.$el.append(a)},clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null},_render_warnings:function(){return $(jQuery.trim(HistoryItemView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if(this.model.get("state")===HistoryItem.STATES.UPLOAD){return null}displayBtnData=(this.model.get("purged"))?({title:"Cannot display datasets removed from disk",enabled:false,icon_class:"display"}):({title:"Display data in browser",href:this.model.get("display_url"),target:(this.model.get("for_editing"))?("galaxy_main"):(null),icon_class:"display"});this.displayButton=new IconButtonView({model:new IconButton(displayBtnData)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryItem.STATES.UPLOAD)||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.model.get("edit_url"),target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false}if(a){b.title="Undelete dataset to edit attributes"}else{if(c){b.title="Cannot edit attributes of datasets removed from disk"}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if(!this.model.get("for_editing")){return null}var a={title:"Delete",href:this.model.get("delete_url"),id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if((this.model.get("deleted")||this.model.get("purged"))&&(!this.model.get("delete_url"))){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HistoryItemView.templates.titleLink(this.model.toJSON())))},_render_hdaSummary:function(){var a=this.model.toJSON();if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HistoryItemView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HistoryItemView.templates.downloadLinks(this.model.toJSON());return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryItem.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.model.get("report_error_url"),target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_tracksterButton:function(){var a=this.model.get("trackster_urls");if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a)){return null}this.tracksterButton=new IconButtonView({model:new IconButton({title:"View in Trackster",icon_class:"chart_curve"})});this.errButton.render();this.errButton.$el.addClass("trackster-add").attr({"data-url":a["data-url"],"action-url":a["action-url"],"new-url":a["new-url"]});return this.errButton.$el},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("retag_url"))){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("annotate_url"))){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotate_url"),icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.model.get("retag_url")){return null}return $(HistoryItemView.templates.tagArea(this.model.toJSON()))},_render_annotationArea:function(){if(!this.model.get("annotate_url")){return null}return $(HistoryItemView.templates.annotationArea(this.model.toJSON()))},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_types}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_apps}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HistoryItemView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var b=this.model.get("state");var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+b+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.model.get("bodyIsShown")===false){a.hide()}if(this.visible){a.show()}else{a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.model.get("ajax_get_tag_url"),error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.model.get("ajax_set_annotation_url");if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.model.get("ajax_get_annotation_url"),error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(b){var a=this.$el.find(".historyItemBody");if(b===undefined){a.toggle()}else{if(b){a.show()}else{a.hide()}}this.trigger("toggleBodyVisibility",this.model.get("id"),a.is(":visible"))},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HistoryItemView("+a+")"}});HistoryItemView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-history-warning-messages"],titleLink:Handlebars.templates["template-history-titleLink"],hdaSummary:Handlebars.templates["template-history-hdaSummary"],downloadLinks:Handlebars.templates["template-history-downloadLinks"],failedMetadata:Handlebars.templates["template-history-failedMetaData"],tagArea:Handlebars.templates["template-history-tagArea"],annotationArea:Handlebars.templates["template-history-annotationArea"],displayApps:Handlebars.templates["template-history-displayApps"]};var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0},userIsAdmin:false,userRoles:[],itemsLength:0,showDeleted:false,showHidden:false,diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false,baseURL:null,hideDeletedURL:null,hideHiddenURL:null,tagURL:null,annotateURL:null},initialize:function(b,a){this.items=new HistoryCollection()},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);a.itemsLength=this.items.length;return a},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){var h=new HistoryItem(_.extend(f,{history_id:b}));a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(){this.log(this+".initialize:",this);this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{visibleItems:{}});this.initializeItems()},initializeItems:function(){this.itemViews={};var a=this;this.model.items.each(function(c){var e=c.get("id"),d=a.storage.get("visibleItems").get(e),b=new HistoryItemView({model:c,visible:d});a.setUpItemListeners(b);a.itemViews[e]=b})},setUpItemListeners:function(b){var a=this;b.bind("toggleBodyVisibility",function(d,c){if(c){a.storage.get("visibleItems").set(d,true)}else{a.storage.get("visibleItems").deleteKey(d)}})},render:function(){this.$el.append(HistoryView.templates.historyPanel(this.model.toJSON()));this.log(this+" rendered from template:",this.$el);this.itemsDiv=this.$el.find("#"+this.model.get("id")+"-datasets");async_save_text("history-name-container","history-name",this.model.get("renameURL"),"new_name",18);this.$el.find(".tooltip").tooltip();var b=this.$el.find("#history-annotation-area");$("#history-annotate").click(function(){if(b.is(":hidden")){b.slideDown("fast")}else{b.slideUp("fast")}return false});async_save_text("history-annotation-container","history-annotation",this.model.get("annotateURL"),"new_annotation",18,true,4);if(this.model.items.length){var a=this._render_items();this.itemsDiv.append(a.children());a.remove()}},_render_items:function(){var b=$("<div/>"),a=this;_.each(this.itemViews,function(d,c){a.log(a+".render_items:",c,d);b.prepend(d.render())});return b},events:{"click #history-collapse-all":"hideAllItemBodies","click #history-tag":"loadAndDisplayTags"},hideAllItemBodies:function(){_.each(this.itemViews,function(a){a.toggleBodyVisibility(false)})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:this.model.get("tagURL"),error:function(){alert("Tagging failed")},success:function(e){a.log(a+" tag elt html (ajax)",e);b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryView.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file +var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"",state:"",data_type:null,file_size:0,meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:false,for_editing:true},url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change",function(b,a,d,c){this.log(this+" has changed:",b,a,d,c)})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isEditable:function(){return(!this.isDeletedOrPurged())},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inFinalState:function(){return((this.get("state")===HistoryDatasetAssociation.STATES.OK)||(this.get("state")===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(this.get("state")===HistoryDatasetAssociation.STATES.EMPTY)||(this.get("state")===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={NOT_VIEWABLE:"noPermission",NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,logger:console,ids:function(){return this.map(function(a){return a.id})},getVisible:function(a,b){return new HDACollection(this.filter(function(c){return c.isVisible(a,b)}))},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return}var b=this;_.each(a,function(e,c){var d=b.get(e);d.fetch()})},toString:function(){return("HDACollection("+this.ids().join(",")+")")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",show_deleted:false,show_hidden:false,diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false},url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}this.on("change",function(d,c,f,e){this.log(this+" has changed:",d,c,f,e)})},loadFromAPI:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.log(b)}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.itemIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();c()})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){this.stateFromStateIds();if((this.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(this.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){this.stateUpdater()}return this},stateFromStateIds:function(){var a=this.hdas.getStateLists();this.attributes.state_ids=a;if((a.running.length>0)||(a.upload.length>0)||(a.setting_metadata.length>0)){this.set("state",HistoryDatasetAssociation.STATES.RUNNING)}else{if(a.queued.length>0){this.set("state",HistoryDatasetAssociation.STATES.QUEUED)}else{if((a.error.length>0)||(a.failed_metadata.length>0)){this.set("state",HistoryDatasetAssociation.STATES.ERROR)}else{if(a.ok.length===this.hdas.length){this.set("state",HistoryDatasetAssociation.STATES.OK)}else{throw (this+".stateFromStateDetails: unable to determine history state from hda states: "+this.get("state_ids"))}}}}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a);var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.hdas.update(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},4000)}}).error(function(f,d,e){if(console&&console.warn){console.warn("Error getting history updates from the server:",f,d,e)}alert("Error getting history updates from the server.\n"+e)})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HDAView=BaseView.extend(LoggableMixin).extend({logger:console,tagName:"div",className:"historyItemContainer",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urls=this.renderUrls(a.urlTemplates,this.model.toJSON());this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b.renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b.renderMetaDownloadUrls(e,a)}else{c[f]=_.template(e,a)}}});return c},renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},render:function(){var b=this,d=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+d);this._clearReferences();this.$el.attr("id","historyItemContainer-"+d);a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"});this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);b.trigger("rendered")})});return this},_clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null;this.showParamsButton=null;this.rerunButton=null;this.visualizationsButton=null;this.tagButton=null;this.annotateButton=null},_render_warnings:function(){return $(jQuery.trim(HDAView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if((!this.model.inFinalState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var a={icon_class:"display"};if(this.model.get("purged")){a.enabled=false;a.title="Cannot display datasets removed from disk"}else{a.title="Display data in browser";a.href=this.urls.display}if(this.model.get("for_editing")){a.target="galaxy_main"}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title="Cannot edit attributes of datasets removed from disk"}else{if(a){b.title="Undelete dataset to edit attributes"}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((!this.model.get("for_editing"))||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var a={title:"Delete",href:this.urls["delete"],id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if(this.model.get("deleted")||this.model.get("purged")){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDAView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDAView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HDAView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a&&a.length)||!(f)){return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:"Visualize",href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");if(c){g.dbkey=c}function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[h]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.urls.tags.get)){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.urls.annotation.get)){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDAView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDAView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HDAView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+state+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.expanded){a.show()}else{a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(b,a){var c=this.$el.find(".historyItemBody");a=(a===undefined)?(!c.is(":visible")):(a);if(a){c.slideDown("fast")}else{c.slideUp("fast")}this.trigger("toggleBodyVisibility",this.model.get("id"),a)},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-history-warning-messages"],titleLink:Handlebars.templates["template-history-titleLink"],hdaSummary:Handlebars.templates["template-history-hdaSummary"],downloadLinks:Handlebars.templates["template-history-downloadLinks"],failedMetadata:Handlebars.templates["template-history-failedMetaData"],tagArea:Handlebars.templates["template-history-tagArea"],annotationArea:Handlebars.templates["template-history-annotationArea"],displayApps:Handlebars.templates["template-history-displayApps"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d.dbkey=b}$.ajax({url:a+"/list_tracks?f-"+$.param(d),dataType:"html",error:function(){alert("Could not add this dataset to browser.")},success:function(e){var f=window.parent;f.show_modal("View Data in a New or Saved Visualization","",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal("Add Data to Saved Visualization",e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}var HistoryView=BaseView.extend(LoggableMixin).extend({logger:console,el:"body.historyPage",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw ("HDAView needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw ("HDAView needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{}});this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("all",this.all,this);this.hdaViews={};this.urls={}},add:function(a){},addAll:function(){this.render()},all:function(a){},renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON();a.urls=this.renderUrls(a);c.append(HistoryView.templates.historyPanel(a));b.$el.find(".tooltip").tooltip();if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(e){b.$el.fadeOut("fast",function(){e()})});$(b).queue(d,function(e){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){e()})});$(b).queue(d,function(e){this.log(b+" rendered:",b.$el);b.setUpBehaviours();b.trigger("rendered");e()});$(b).dequeue(d);return this},renderItems:function(c){this.hdaViews={};var b=this,a=this.model.get("show_deleted"),e=this.model.get("show_hidden"),d=this.model.hdas.getVisible(a,e);d.each(function(h){var g=h.get("id"),f=b.storage.get("expandedHdas").get(g);b.hdaViews[g]=new HDAView({model:h,expanded:f,urlTemplates:b.hdaUrlTemplates});b.setUpHdaListeners(b.hdaViews[g]);c.prepend(b.hdaViews[g].render().$el)});return d.length},setUpHdaListeners:function(a){var b=this;a.bind("toggleBodyVisibility",function(d,c){if(c){b.storage.get("expandedHdas").set(d,true)}else{b.storage.get("expandedHdas").deleteKey(d)}})},setUpBehaviours:function(){var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},events:{"click #history-collapse-all":"hideAllHdaBodies","click #history-tag":"loadAndDisplayTags"},hideAllHdaBodies:function(){_.each(this.itemViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert("Tagging failed")},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryView.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c -r 2e70816299e40fecc4902adda54126bb00316588 static/scripts/packed/templates/compiled/template-history-downloadLinks.js --- a/static/scripts/packed/templates/compiled/template-history-downloadLinks.js +++ b/static/scripts/packed/templates/compiled/template-history-downloadLinks.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-downloadLinks"]=b(function(g,l,f,k,j){f=f||g.helpers;var c,h="function",i=this.escapeExpression,m=this;function e(s,r){var p="",q,o;p+='\n<div popupmenu="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a class="action-button" href="';o=f.download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.download_url;q=typeof q===h?q():q}p+=i(q)+'">Download Dataset</a>\n <a>Additional Files</a>\n ';q=s.meta_files;q=f.each.call(s,q,{hash:{},inverse:m.noop,fn:m.program(2,d,r)});if(q||q===0){p+=q}p+='\n</div>\n<div style="float:left;" class="menubutton split popup" id="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a href="';o=f.download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.download_url;q=typeof q===h?q():q}p+=i(q)+'" title="Download" class="icon-button disk tooltip"></a>\n</div>\n';return p}function d(s,r){var p="",q,o;p+='\n <a class="action-button" href="';o=f.meta_download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.meta_download_url;q=typeof q===h?q():q}p+=i(q)+'">Download ';o=f.meta_file_type;if(o){q=o.call(s,{hash:{}})}else{q=s.meta_file_type;q=typeof q===h?q():q}p+=i(q)+"</a>\n ";return p}function n(s,r){var p="",q,o;p+='\n<a href="';o=f.download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.download_url;q=typeof q===h?q():q}p+=i(q)+'" title="Download" class="icon-button disk tooltip"></a>\n';return p}c=l.meta_files;c=f["if"].call(l,c,{hash:{},inverse:m.program(4,n,j),fn:m.program(1,e,j)});if(c||c===0){return c}else{return""}})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-downloadLinks"]=b(function(g,l,f,k,j){f=f||g.helpers;var c,h="function",i=this.escapeExpression,m=this;function e(s,r){var p="",q,o;p+="\n";p+='\n<div popupmenu="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a class="action-button" href="';q=s.urls;q=q==null||q===false?q:q.download;q=typeof q===h?q():q;p+=i(q)+'">Download Dataset</a>\n <a>Additional Files</a>\n ';q=s.urls;q=q==null||q===false?q:q.meta_download;q=f.each.call(s,q,{hash:{},inverse:m.noop,fn:m.program(2,d,r)});if(q||q===0){p+=q}p+='\n</div>\n<div style="float:left;" class="menubutton split popup" id="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a href="';q=s.urls;q=q==null||q===false?q:q.download;q=typeof q===h?q():q;p+=i(q)+'" title="Download" class="icon-button disk tooltip"></a>\n</div>\n';return p}function d(s,r){var p="",q,o;p+='\n <a class="action-button" href="';o=f.url;if(o){q=o.call(s,{hash:{}})}else{q=s.url;q=typeof q===h?q():q}p+=i(q)+'">Download ';o=f.file_type;if(o){q=o.call(s,{hash:{}})}else{q=s.file_type;q=typeof q===h?q():q}p+=i(q)+"</a>\n ";return p}function n(r,q){var o="",p;o+="\n";o+='\n<a href="';p=r.urls;p=p==null||p===false?p:p.download;p=typeof p===h?p():p;o+=i(p)+'" title="Download" class="icon-button disk tooltip"></a>\n';return o}c=l.urls;c=c==null||c===false?c:c.meta_download;c=f["if"].call(l,c,{hash:{},inverse:m.program(4,n,j),fn:m.program(1,e,j)});if(c||c===0){return c}else{return""}})})(); \ No newline at end of file diff -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c -r 2e70816299e40fecc4902adda54126bb00316588 static/scripts/packed/templates/compiled/template-history-failedMetaData.js --- a/static/scripts/packed/templates/compiled/template-history-failedMetaData.js +++ b/static/scripts/packed/templates/compiled/template-history-failedMetaData.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-failedMetaData"]=b(function(f,l,e,k,j){e=e||f.helpers;var c,h,g="function",i=this.escapeExpression,n=this,m=e.blockHelperMissing;function d(s,r){var p="",q,o;p+='\nAn error occurred setting the metadata for this dataset.\nYou may be able to <a href="';o=e.edit_url;if(o){q=o.call(s,{hash:{}})}else{q=s.edit_url;q=typeof q===g?q():q}p+=i(q)+'" target="galaxy_main">set it manually or retry auto-detection</a>.\n';return p}h=e.warningmessagesmall;if(h){c=h.call(l,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}else{c=l.warningmessagesmall;c=typeof c===g?c():c}if(!e.warningmessagesmall){c=m.call(l,c,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}if(c||c===0){return c}else{return""}})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-failedMetaData"]=b(function(f,l,e,k,j){e=e||f.helpers;var c,h,g="function",i=this.escapeExpression,n=this,m=e.blockHelperMissing;function d(r,q){var o="",p;o+='\nAn error occurred setting the metadata for this dataset.\nYou may be able to <a href="';p=r.urls;p=p==null||p===false?p:p.edit;p=typeof p===g?p():p;o+=i(p)+'" target="galaxy_main">set it manually or retry auto-detection</a>.\n';return o}h=e.warningmessagesmall;if(h){c=h.call(l,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}else{c=l.warningmessagesmall;c=typeof c===g?c():c}if(!e.warningmessagesmall){c=m.call(l,c,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}if(c||c===0){return c}else{return""}})})(); \ No newline at end of file diff -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c -r 2e70816299e40fecc4902adda54126bb00316588 static/scripts/packed/templates/compiled/template-history-hdaSummary.js --- a/static/scripts/packed/templates/compiled/template-history-hdaSummary.js +++ b/static/scripts/packed/templates/compiled/template-history-hdaSummary.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-hdaSummary"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,p=this;function e(u,t){var r="",s,q;r+='\n <a href="';q=f.edit_url;if(q){s=q.call(u,{hash:{}})}else{s=u.edit_url;s=typeof s===h?s():s}r+=k(s)+'" target="galaxy_main">';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+"</a>\n ";return r}function c(u,t){var r="",s,q;r+='\n <span class="';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+'">';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+"</span>\n ";return r}function o(u,t){var r="",s,q;r+='\n<div class="hda-info">';q=f.misc_info;if(q){s=q.call(u,{hash:{}})}else{s=u.misc_info;s=typeof s===h?s():s}r+=k(s)+"</div>\n";return r}j+='<div class="hda-summary">\n ';i=f.misc_blurb;if(i){d=i.call(n,{hash:{}})}else{d=n.misc_blurb;d=typeof d===h?d():d}j+=k(d)+'<br />\n format: <span class="';i=f.data_type;if(i){d=i.call(n,{hash:{}})}else{d=n.data_type;d=typeof d===h?d():d}j+=k(d)+'">';i=f.data_type;if(i){d=i.call(n,{hash:{}})}else{d=n.data_type;d=typeof d===h?d():d}j+=k(d)+"</span>,\n database:\n ";d=n.dbkey_unknown_and_editable;d=f["if"].call(n,d,{hash:{},inverse:p.program(3,c,l),fn:p.program(1,e,l)});if(d||d===0){j+=d}j+="\n</div>\n";d=n.misc_info;d=f["if"].call(n,d,{hash:{},inverse:p.noop,fn:p.program(5,o,l)});if(d||d===0){j+=d}return j})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-hdaSummary"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,p=this;function e(u,t){var r="",s,q;r+='\n <a href="';s=u.urls;s=s==null||s===false?s:s.edit;s=typeof s===h?s():s;r+=k(s)+'" target="galaxy_main">';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+"</a>\n ";return r}function c(u,t){var r="",s,q;r+='\n <span class="';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+'">';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+"</span>\n ";return r}function o(u,t){var r="",s,q;r+='\n<div class="hda-info">';q=f.misc_info;if(q){s=q.call(u,{hash:{}})}else{s=u.misc_info;s=typeof s===h?s():s}r+=k(s)+"</div>\n";return r}j+='<div class="hda-summary">\n ';i=f.misc_blurb;if(i){d=i.call(n,{hash:{}})}else{d=n.misc_blurb;d=typeof d===h?d():d}j+=k(d)+'<br />\n format: <span class="';i=f.data_type;if(i){d=i.call(n,{hash:{}})}else{d=n.data_type;d=typeof d===h?d():d}j+=k(d)+'">';i=f.data_type;if(i){d=i.call(n,{hash:{}})}else{d=n.data_type;d=typeof d===h?d():d}j+=k(d)+"</span>,\n database:\n ";d=n.dbkey_unknown_and_editable;d=f["if"].call(n,d,{hash:{},inverse:p.program(3,c,l),fn:p.program(1,e,l)});if(d||d===0){j+=d}j+="\n</div>\n";d=n.misc_info;d=f["if"].call(n,d,{hash:{},inverse:p.noop,fn:p.program(5,o,l)});if(d||d===0){j+=d}return j})})(); \ No newline at end of file diff -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c -r 2e70816299e40fecc4902adda54126bb00316588 static/scripts/packed/templates/compiled/template-history-historyPanel.js --- a/static/scripts/packed/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/packed/templates/compiled/template-history-historyPanel.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(k,C,A,s,J){A=A||k.helpers;var B="",o,n,y=this,f="function",c=A.blockHelperMissing,e=this.escapeExpression;function u(L,K){return"refresh"}function t(L,K){return"collapse all"}function r(O,N){var L="",M,K;L+='\n <div style="width: 40px; float: right; white-space: nowrap;">\n <a id="history-tag" title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(6,q,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(6,q,N)})}if(M||M===0){L+=M}L+='"\n class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n <a id="history-annotate" title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(8,m,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(8,m,N)})}if(M||M===0){L+=M}L+='"\n class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n </div>\n ';return L}function q(L,K){return"Edit history tags"}function m(L,K){return"Edit history annotation"}function I(O,N){var L="",M,K;L+='\n<div class="historyLinks">\n <a href="';K=A.hideDeletedURL;if(K){M=K.call(O,{hash:{}})}else{M=O.hideDeletedURL;M=typeof M===f?M():M}L+=e(M)+'">';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(11,H,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(11,H,N)})}if(M||M===0){L+=M}L+="</a>\n</div>\n";return L}function H(L,K){return"hide deleted"}function G(O,N){var L="",M,K;L+='\n<div class="historyLinks">\n <a href="';K=A.hideHiddenURL;if(K){M=K.call(O,{hash:{}})}else{M=O.hideHiddenURL;M=typeof M===f?M():M}L+=e(M)+'">';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(14,F,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(14,F,N)})}if(M||M===0){L+=M}L+="</a>\n</div>\n";return L}function F(L,K){return"hide hidden"}function E(O,N){var L="",M,K;L+="\n ";L+='\n <div id="history-size" style="position: absolute; top: 3px; right: 0px;">';K=A.diskSize;if(K){M=K.call(O,{hash:{}})}else{M=O.diskSize;M=typeof M===f?M():M}L+=e(M)+'</div>\n <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text" title="Click to rename history">';K=A.name;if(K){M=K.call(O,{hash:{}})}else{M=O.name;M=typeof M===f?M():M}L+=e(M)+"</div>\n \n ";return L}function D(O,N){var L="",M,K;L+='\n <div id="history-size">';K=A.diskSize;if(K){M=K.call(O,{hash:{}})}else{M=O.diskSize;M=typeof M===f?M():M}L+=e(M)+"</div>\n ";return L}function p(O,N){var L="",M,K;L+="\n";K=A.warningmessagesmall;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(21,l,N)})}else{M=O.warningmessagesmall;M=typeof M===f?M():M}if(!A.warningmessagesmall){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(21,l,N)})}if(M||M===0){L+=M}L+="\n";return L}function l(N,M){var L,K;K=A.local;if(K){L=K.call(N,{hash:{},inverse:y.noop,fn:y.program(22,j,M)})}else{L=N.local;L=typeof L===f?L():L}if(!A.local){L=c.call(N,L,{hash:{},inverse:y.noop,fn:y.program(22,j,M)})}if(L||L===0){return L}else{return""}}function j(L,K){return"You are currently viewing a deleted history!"}function i(N,M){var K="",L;K+="\n";K+='\n<div style="margin: 0px 5px 10px 5px">\n\n <div id="history-tag-area" style="display: none">\n ';K+="\n ";K+='\n <strong>Tags:</strong>\n <div class="tag-elt"></div>\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>Annotation / Notes:</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation">\n ';L=N.annotation;L=A["if"].call(N,L,{hash:{},inverse:y.program(27,g,M),fn:y.program(25,h,M)});if(L||L===0){K+=L}K+="\n </div>\n </div>\n </div>\n</div>\n";return K}function h(O,N){var L="",M,K;L+="\n ";K=A.annotation;if(K){M=K.call(O,{hash:{}})}else{M=O.annotation;M=typeof M===f?M():M}L+=e(M)+"\n ";return L}function g(L,K){return"\n <em>Describe or add notes to history</em>\n "}function d(O,N){var L="",M,K;L+='\n<div id="message-container">\n <div class="';K=A.status;if(K){M=K.call(O,{hash:{}})}else{M=O.status;M=typeof M===f?M():M}L+=e(M)+'message">\n ';K=A.message;if(K){M=K.call(O,{hash:{}})}else{M=O.message;M=typeof M===f?M():M}L+=e(M)+"\n </div><br />\n</div>\n";return L}function z(L,K){return'\n <div id="quota-message" class="errormessage">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n <br/>\n '}function x(O,N){var L="",M,K;L+='\n<div id="';K=A.id;if(K){M=K.call(O,{hash:{}})}else{M=O.id;M=typeof M===f?M():M}L+=e(M)+'-datasets" class="history-datasets-list">\n ';L+="\n</div>\n\n";return L}function w(O,N){var L="",M,K;L+='\n<div class="infomessagesmall" id="emptyHistoryMessage">\n';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(36,v,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(36,v,N)})}if(M||M===0){L+=M}L+="\n</div>\n";return L}function v(L,K){return"Your history is empty. Click 'Get Data' on the left pane to start"}B+='<div id="top-links" class="historyLinks">\n <a title="';n=A.local;if(n){o=n.call(C,{hash:{},inverse:y.noop,fn:y.program(1,u,J)})}else{o=C.local;o=typeof o===f?o():o}if(!A.local){o=c.call(C,o,{hash:{},inverse:y.noop,fn:y.program(1,u,J)})}if(o||o===0){B+=o}B+='" class="icon-button arrow-circle tooltip" href="';n=A.baseURL;if(n){o=n.call(C,{hash:{}})}else{o=C.baseURL;o=typeof o===f?o():o}B+=e(o)+"\"></a>\n <a title='";n=A.local;if(n){o=n.call(C,{hash:{},inverse:y.noop,fn:y.program(3,t,J)})}else{o=C.local;o=typeof o===f?o():o}if(!A.local){o=c.call(C,o,{hash:{},inverse:y.noop,fn:y.program(3,t,J)})}if(o||o===0){B+=o}B+="' id=\"history-collapse-all\"\n class='icon-button toggle tooltip' href='javascript:void(0);'></a>\n ";o=C.userRoles;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(5,r,J)});if(o||o===0){B+=o}B+='\n</div>\n<div class="clear"></div>\n\n';B+="\n";o=C.showDeleted;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(10,I,J)});if(o||o===0){B+=o}B+="\n\n";o=C.showHidden;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(13,G,J)});if(o||o===0){B+=o}B+="\n\n";B+='\n<div id="history-name-area" class="historyLinks">\n <div id="history-name-container" style="position: relative;">\n ';o=C.userRoles;o=A["if"].call(C,o,{hash:{},inverse:y.program(18,D,J),fn:y.program(16,E,J)});if(o||o===0){B+=o}B+='\n </div> \n</div>\n<div style="clear: both;"></div>\n\n';o=C.deleted;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(20,p,J)});if(o||o===0){B+=o}B+="\n\n";B+="\n";o=C.userRoles;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(24,i,J)});if(o||o===0){B+=o}B+="\n\n";o=C.message;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(29,d,J)});if(o||o===0){B+=o}B+='\n\n<div id="quota-message-container">\n ';o=C.over_quota;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(31,z,J)});if(o||o===0){B+=o}B+="\n</div>\n\n";o=C.itemsLength;o=A["if"].call(C,o,{hash:{},inverse:y.program(35,w,J),fn:y.program(33,x,J)});if(o||o===0){B+=o}return B})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(k,y,w,r,G){w=w||k.helpers;var x="",n,m,f="function",e=this.escapeExpression,u=this,c=w.blockHelperMissing;function t(L,K){var I="",J,H;I+='\n <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text"\n title="Click to rename history">';H=w.name;if(H){J=H.call(L,{hash:{}})}else{J=L.name;J=typeof J===f?J():J}I+=e(J)+"</div>\n ";return I}function s(I,H){return"refresh"}function q(I,H){return"collapse all"}function p(L,K){var I="",J,H;I+='\n <a id="history-tag" title="';H=w.local;if(H){J=H.call(L,{hash:{},inverse:u.noop,fn:u.program(8,l,K)})}else{J=L.local;J=typeof J===f?J():J}if(!w.local){J=c.call(L,J,{hash:{},inverse:u.noop,fn:u.program(8,l,K)})}if(J||J===0){I+=J}I+='"\n class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n <a id="history-annotate" title="';H=w.local;if(H){J=H.call(L,{hash:{},inverse:u.noop,fn:u.program(10,F,K)})}else{J=L.local;J=typeof J===f?J():J}if(!w.local){J=c.call(L,J,{hash:{},inverse:u.noop,fn:u.program(10,F,K)})}if(J||J===0){I+=J}I+='"\n class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n ';return I}function l(I,H){return"Edit history tags"}function F(I,H){return"Edit history annotation"}function E(L,K){var I="",J,H;I+='\n <a href="';J=L.urls;J=J==null||J===false?J:J.hide_deleted;J=typeof J===f?J():J;I+=e(J)+'">';H=w.local;if(H){J=H.call(L,{hash:{},inverse:u.noop,fn:u.program(13,D,K)})}else{J=L.local;J=typeof J===f?J():J}if(!w.local){J=c.call(L,J,{hash:{},inverse:u.noop,fn:u.program(13,D,K)})}if(J||J===0){I+=J}I+="</a>\n ";return I}function D(I,H){return"hide deleted"}function C(L,K){var I="",J,H;I+='\n <a href="';J=L.urls;J=J==null||J===false?J:J.hide_hidden;J=typeof J===f?J():J;I+=e(J)+'">';H=w.local;if(H){J=H.call(L,{hash:{},inverse:u.noop,fn:u.program(16,B,K)})}else{J=L.local;J=typeof J===f?J():J}if(!w.local){J=c.call(L,J,{hash:{},inverse:u.noop,fn:u.program(16,B,K)})}if(J||J===0){I+=J}I+="</a>\n ";return I}function B(I,H){return"hide hidden"}function A(L,K){var I="",J,H;I+="\n";H=w.warningmessagesmall;if(H){J=H.call(L,{hash:{},inverse:u.noop,fn:u.program(19,z,K)})}else{J=L.warningmessagesmall;J=typeof J===f?J():J}if(!w.warningmessagesmall){J=c.call(L,J,{hash:{},inverse:u.noop,fn:u.program(19,z,K)})}if(J||J===0){I+=J}I+="\n";return I}function z(K,J){var I,H;H=w.local;if(H){I=H.call(K,{hash:{},inverse:u.noop,fn:u.program(20,o,J)})}else{I=K.local;I=typeof I===f?I():I}if(!w.local){I=c.call(K,I,{hash:{},inverse:u.noop,fn:u.program(20,o,J)})}if(I||I===0){return I}else{return""}}function o(I,H){return"You are currently viewing a deleted history!"}function j(K,J){var H="",I;H+='\n <div id="history-tag-area" style="display: none">\n <strong>Tags:</strong>\n <div class="tag-elt"></div>\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>Annotation / Notes:</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation">\n ';I=K.annotation;I=w["if"].call(K,I,{hash:{},inverse:u.program(25,h,J),fn:u.program(23,i,J)});if(I||I===0){H+=I}H+="\n </div>\n </div>\n </div>\n ";return H}function i(L,K){var I="",J,H;I+="\n ";H=w.annotation;if(H){J=H.call(L,{hash:{}})}else{J=L.annotation;J=typeof J===f?J():J}I+=e(J)+"\n ";return I}function h(I,H){return"\n <em>Describe or add notes to history</em>\n "}function g(L,K){var I="",J,H;I+='\n<div id="message-container">\n <div class="';H=w.status;if(H){J=H.call(L,{hash:{}})}else{J=L.status;J=typeof J===f?J():J}I+=e(J)+'message">\n ';H=w.message;if(H){J=H.call(L,{hash:{}})}else{J=L.message;J=typeof J===f?J():J}I+=e(J)+"\n </div><br />\n</div>\n";return I}function d(I,H){return'\n <div id="quota-message" class="errormessage">\n You are over your disk quota. 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Click 'Get Data' on the left pane to start"}x+='\n<div id="history-name-area" class="historyLinks">\n <div id="history-name-container" style="position: relative;">\n ';x+='\n <div id="history-size" style="position: absolute; top: 3px; right: 0px;">';m=w.nice_size;if(m){n=m.call(y,{hash:{}})}else{n=y.nice_size;n=typeof n===f?n():n}x+=e(n)+"</div>\n ";n=y.user;n=w["if"].call(y,n,{hash:{},inverse:u.noop,fn:u.program(1,t,G)});if(n||n===0){x+=n}x+='\n </div> \n</div>\n<div style="clear: both;"></div>\n\n<div id="top-links" class="historyLinks">\n <a title="';m=w.local;if(m){n=m.call(y,{hash:{},inverse:u.noop,fn:u.program(3,s,G)})}else{n=y.local;n=typeof n===f?n():n}if(!w.local){n=c.call(y,n,{hash:{},inverse:u.noop,fn:u.program(3,s,G)})}if(n||n===0){x+=n}x+='" class="icon-button arrow-circle tooltip" href="';n=y.urls;n=n==null||n===false?n:n.base;n=typeof n===f?n():n;x+=e(n)+"\"></a>\n <a title='";m=w.local;if(m){n=m.call(y,{hash:{},inverse:u.noop,fn:u.program(5,q,G)})}else{n=y.local;n=typeof n===f?n():n}if(!w.local){n=c.call(y,n,{hash:{},inverse:u.noop,fn:u.program(5,q,G)})}if(n||n===0){x+=n}x+="' id=\"history-collapse-all\"\n class='icon-button toggle tooltip' href='javascript:void(0);'></a>\n <div style=\"width: 40px; 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\ No newline at end of file diff -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c -r 2e70816299e40fecc4902adda54126bb00316588 static/scripts/packed/templates/compiled/template-history-warning-messages.js --- a/static/scripts/packed/templates/compiled/template-history-warning-messages.js +++ b/static/scripts/packed/templates/compiled/template-history-warning-messages.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-warning-messages"]=b(function(g,s,q,k,v){q=q||g.helpers;var r="",h,e="function",d=this.escapeExpression,p=this,c=q.blockHelperMissing;function o(z,y){var x,w;w=q.warningmessagesmall;if(w){x=w.call(z,{hash:{},inverse:p.noop,fn:p.program(2,n,y)})}else{x=z.warningmessagesmall;x=typeof x===e?x():x}if(!q.warningmessagesmall){x=c.call(z,x,{hash:{},inverse:p.noop,fn:p.program(2,n,y)})}if(x||x===0){return x}else{return""}}function n(z,y){var w="",x;w+="\n This dataset has been deleted.\n ";x=z.undelete_url;x=q["if"].call(z,x,{hash:{},inverse:p.noop,fn:p.program(3,m,y)});if(x||x===0){w+=x}w+="\n";return w}function m(A,z){var x="",y,w;x+='\n Click <a href="';w=q.undelete_url;if(w){y=w.call(A,{hash:{}})}else{y=A.undelete_url;y=typeof y===e?y():y}x+=d(y)+'" class="historyItemUndelete" id="historyItemUndeleter-';w=q.id;if(w){y=w.call(A,{hash:{}})}else{y=A.id;y=typeof y===e?y():y}x+=d(y)+'"\n target="galaxy_history">here</a> to undelete it\n ';y=A.purge_url;y=q["if"].call(A,y,{hash:{},inverse:p.noop,fn:p.program(4,l,z)});if(y||y===0){x+=y}x+="\n ";return x}function l(A,z){var x="",y,w;x+='\n or <a href="';w=q.purge_url;if(w){y=w.call(A,{hash:{}})}else{y=A.purge_url;y=typeof y===e?y():y}x+=d(y)+'" class="historyItemPurge" id="historyItemPurger-';w=q.id;if(w){y=w.call(A,{hash:{}})}else{y=A.id;y=typeof y===e?y():y}x+=d(y)+'"\n target="galaxy_history">here</a> to immediately remove it from disk\n ';return x}function j(z,y){var x,w;w=q.warningmessagesmall;if(w){x=w.call(z,{hash:{},inverse:p.noop,fn:p.program(7,i,y)})}else{x=z.warningmessagesmall;x=typeof x===e?x():x}if(!q.warningmessagesmall){x=c.call(z,x,{hash:{},inverse:p.noop,fn:p.program(7,i,y)})}if(x||x===0){return x}else{return""}}function i(x,w){return"\n This dataset has been deleted and removed from disk.\n"}function f(z,y){var x,w;w=q.warningmessagesmall;if(w){x=w.call(z,{hash:{},inverse:p.noop,fn:p.program(10,u,y)})}else{x=z.warningmessagesmall;x=typeof x===e?x():x}if(!q.warningmessagesmall){x=c.call(z,x,{hash:{},inverse:p.noop,fn:p.program(10,u,y)})}if(x||x===0){return x}else{return""}}function u(z,y){var w="",x;w+="\n This dataset has been hidden.\n ";x=z.unhide_url;x=q["if"].call(z,x,{hash:{},inverse:p.noop,fn:p.program(11,t,y)});if(x||x===0){w+=x}w+="\n";return w}function t(A,z){var x="",y,w;x+='\n Click <a href="';w=q.unhide_url;if(w){y=w.call(A,{hash:{}})}else{y=A.unhide_url;y=typeof y===e?y():y}x+=d(y)+'" class="historyItemUnhide" id="historyItemUnhider-';w=q.id;if(w){y=w.call(A,{hash:{}})}else{y=A.id;y=typeof y===e?y():y}x+=d(y)+'"\n target="galaxy_history">here</a> to unhide it\n ';return x}h=s.deleted;h=q["if"].call(s,h,{hash:{},inverse:p.noop,fn:p.program(1,o,v)});if(h||h===0){r+=h}r+="\n\n";h=s.purged;h=q["if"].call(s,h,{hash:{},inverse:p.noop,fn:p.program(6,j,v)});if(h||h===0){r+=h}r+="\n\n";h=s.visible;h=q.unless.call(s,h,{hash:{},inverse:p.noop,fn:p.program(9,f,v)});if(h||h===0){r+=h}return r})})(); 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\ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Data providers: (a) add option to report interchromosomal interactions and (b) pass kwargs to get_iterator method for filtering purposes.
by Bitbucket 30 Oct '12

30 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0e2eb8ea274a/ changeset: 0e2eb8ea274a user: jgoecks date: 2012-10-30 20:15:11 summary: Data providers: (a) add option to report interchromosomal interactions and (b) pass kwargs to get_iterator method for filtering purposes. affected #: 2 files diff -r c0d8a9c916a50ef3f1fd7d67e987eba8f94e02a8 -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -150,7 +150,7 @@ """ raise Exception( "Unimplemented Function" ) - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): """ Returns an iterator that provides data in the region chrom:start-end """ @@ -172,7 +172,7 @@ dataset_type, data """ start, end = int( low ), int( high ) - iterator = self.get_iterator( chrom, start, end ) + iterator = self.get_iterator( chrom, start, end, **kwargs ) return self.process_data( iterator, start_val, max_vals, **kwargs ) def get_genome_data( self, chroms_info, **kwargs ): @@ -338,7 +338,7 @@ col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): start, end = int(start), int(end) if end >= (2<<29): end = (2<<29 - 1) # Tabix-enforced maximum @@ -387,7 +387,7 @@ Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): raise Exception( "Unimplemented Function" ) def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): @@ -467,7 +467,7 @@ dataset_type = 'interval_index' - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): raise Exception( "Unimplemented Method" ) def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): @@ -562,7 +562,7 @@ for large datasets. """ - def get_iterator( self, chrom=None, start=None, end=None ): + def get_iterator( self, chrom=None, start=None, end=None, **kwargs ): # Read first line in order to match chrom naming format. line = source.readline() dataset_chrom = line.split()[0] @@ -706,7 +706,7 @@ for large datasets. """ - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): # Read first line in order to match chrom naming format. line = source.readline() dataset_chrom = line.split()[0] @@ -864,7 +864,7 @@ new_bamfile.close() bamfile.close() - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): """ Returns an iterator that provides data in the region chrom:start-end """ @@ -1174,7 +1174,7 @@ out.close() - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): """ Returns an array with values: (a) source file and (b) an iterator that provides data in the region chrom:start-end @@ -1233,7 +1233,7 @@ dataset_type = 'interval_index' - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): """ Returns an iterator that provides data in the region chrom:start-end as well as a file offset. @@ -1341,7 +1341,7 @@ Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): raise "Unimplemented Method" def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): @@ -1487,7 +1487,7 @@ return 100000; class ChromatinInteractionsTabixDataProvider( TabixDataProvider, ChromatinInteractionsDataProvider ): - def get_iterator( self, chrom, start=0, end=sys.maxint ): + def get_iterator( self, chrom, start=0, end=sys.maxint, interchromosomal=False, **kwargs ): """ """ # Modify start as needed to get earlier interactions with start region. @@ -1501,9 +1501,12 @@ c = feature[3] s2 = int( feature[4] ) e2 = int( feature[5] ) - #if ( s1 <= filter_end and e1 >= filter_start ) and ( s2 <= filter_end and e2 >= filter_start ) and ( max( s1, s2 ) - min( e1, e2 ) <= span * 2 ): + # Check for intrachromosal interactions. if ( ( s1 + s2 ) / 2 <= end ) and ( ( e1 + e2 ) / 2 >= start ) and ( c == chrom ): yield line + # Check for interchromosal interactions. + if interchromosomal and c != chrom: + yield line return filter( TabixDataProvider.get_iterator( self, chrom, filter_start, end ) ) # diff -r c0d8a9c916a50ef3f1fd7d67e987eba8f94e02a8 -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -630,8 +630,10 @@ data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset=dataset, source=source ) - # HACK: pass in additional params, which are only used for summary tree data, not BBI data. - rval = data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) + # HACK: pass in additional params which are used for only some types of data providers; + # level, cutoffs used for summary tree, and interchromosomal used for chromatin interactions. + rval = data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0, + interchromosomal=True ) return rval Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Tabular Display: left-align 'list' column type.
by Bitbucket 30 Oct '12

30 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c0d8a9c916a5/ changeset: c0d8a9c916a5 user: dannon date: 2012-10-30 20:08:59 summary: Tabular Display: left-align 'list' column type. affected #: 1 file diff -r 172502ced921425b301725949bd8a82ff858bc48 -r c0d8a9c916a50ef3f1fd7d67e987eba8f94e02a8 templates/dataset/tabular_chunked.mako --- a/templates/dataset/tabular_chunked.mako +++ b/templates/dataset/tabular_chunked.mako @@ -18,7 +18,7 @@ if (colspan !== undefined){ return $('<td>').attr('colspan', colspan).addClass('stringalign').text(cell_contents); } - else if (COLUMN_TYPES[index] == 'str'){ + else if (COLUMN_TYPES[index] == 'str' || COLUMN_TYPES[index] == 'list'){ /* Left align all str columns, right align the rest */ return $('<td>').addClass('stringalign').text(cell_contents);; } 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.

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commit/galaxy-central: dan: When migrating tools, if install_dependencies is True, but tool_dependency_dir is not set, do not attempt to install, but print informative error message.
by Bitbucket 30 Oct '12

30 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/172502ced921/ changeset: 172502ced921 user: dan date: 2012-10-30 19:46:12 summary: When migrating tools, if install_dependencies is True, but tool_dependency_dir is not set, do not attempt to install, but print informative error message. affected #: 1 file diff -r 394c3bd89926919b3ff861d5bc3daa6c7d10fd12 -r 172502ced921425b301725949bd8a82ff858bc48 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -19,6 +19,10 @@ self.app = app self.toolbox = self.app.toolbox self.migrated_tools_config = migrated_tools_config + # If install_dependencies is True, but tool_dependency_dir is not set, + # do not attempt to install, but print informative error message + if install_dependencies and app.config.tool_dependency_dir is None: + raise Exception( 'You are attempting to install tool dependencies, but do not have a value for "tool_dependency_dir" set in your ini file. Please set this to the path where you would like to install dependencies and rerun the migration script.' ) # Get the local non-shed related tool panel configs (there can be more than one, and the default name is tool_conf.xml). self.proprietary_tool_confs = self.non_shed_tool_panel_configs self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number ) 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.

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commit/galaxy-central: jgoecks: UI framework enhancements: (a) upgrade to jQuery UI 1.9.1; (b) remove version information from jQuery UI file names; (c) add generic jQueryUI search+select combobox widget; (d) use combobox widget for choosing dbkey in Trackster visualizations. Also pack scripts.
by Bitbucket 30 Oct '12

30 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/394c3bd89926/ changeset: 394c3bd89926 user: jgoecks date: 2012-10-30 14:07:29 summary: UI framework enhancements: (a) upgrade to jQuery UI 1.9.1; (b)= remove version information from jQuery UI file names; (c) add generic jQue= ryUI search+select combobox widget; (d) use combobox widget for choosing db= key in Trackster visualizations. Also pack scripts. affected #: 27 files diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/june_2007_style/blue/jquery-ui/smoothness/images/u= i-bg_glass_55_fbf9ee_1x400.png Binary file static/june_2007_style/blue/jquery-ui/smoothness/images/ui-bg_g= lass_55_fbf9ee_1x400.png has changed diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/june_2007_style/blue/jquery-ui/smoothness/images/u= i-icons_2e83ff_256x240.png Binary file static/june_2007_style/blue/jquery-ui/smoothness/images/ui-icon= s_2e83ff_256x240.png has changed diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/june_2007_style/blue/jquery-ui/smoothness/jquery-u= i-1.8.23.custom.css --- a/static/june_2007_style/blue/jquery-ui/smoothness/jquery-ui-1.8.23.cus= tom.css +++ /dev/null @@ -1,363 +0,0 @@ -/*! - * jQuery UI CSS Framework 1.8.23 - * - * Copyright 2012, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI/Theming/API - */ - -/* Layout helpers -----------------------------------*/ -.ui-helper-hidden { display: none; } -.ui-helper-hidden-accessible { position: absolute !important; clip: rect(1= px 1px 1px 1px); clip: rect(1px,1px,1px,1px); } -.ui-helper-reset { margin: 0; padding: 0; border: 0; outline: 0; line-heig= ht: 1.3; text-decoration: none; font-size: 100%; list-style: none; } -.ui-helper-clearfix:before, .ui-helper-clearfix:after { content: ""; displ= ay: table; } -.ui-helper-clearfix:after { clear: both; } -.ui-helper-clearfix { zoom: 1; } -.ui-helper-zfix { width: 100%; height: 100%; top: 0; left: 0; position: ab= solute; opacity: 0; filter:Alpha(Opacity=3D0); } - - -/* Interaction Cues -----------------------------------*/ -.ui-state-disabled { cursor: default !important; } - - -/* Icons -----------------------------------*/ - -/* states and images */ -.ui-icon { display: block; text-indent: -99999px; overflow: hidden; backgr= ound-repeat: no-repeat; } - - -/* Misc visuals -----------------------------------*/ - -/* Overlays */ -.ui-widget-overlay { position: absolute; top: 0; left: 0; width: 100%; hei= ght: 100%; } - - -/*! - * jQuery UI CSS Framework 1.8.23 - * - * Copyright 2012, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI/Theming/API - * - * To view and modify this theme, visit http://jqueryui.com/themeroller/?f= fDefault=3DVerdana,Arial,sans-serif&fwDefault=3Dnormal&fsDefault=3D1.1em&co= rnerRadius=3D4px&bgColorHeader=3Dcccccc&bgTextureHeader=3D03_highlight_soft= .png&bgImgOpacityHeader=3D75&borderColorHeader=3Daaaaaa&fcHeader=3D222222&i= conColorHeader=3D222222&bgColorContent=3Dffffff&bgTextureContent=3D01_flat.= png&bgImgOpacityContent=3D75&borderColorContent=3Daaaaaa&fcContent=3D222222= &iconColorContent=3D222222&bgColorDefault=3De6e6e6&bgTextureDefault=3D02_gl= ass.png&bgImgOpacityDefault=3D75&borderColorDefault=3Dd3d3d3&fcDefault=3D55= 5555&iconColorDefault=3D888888&bgColorHover=3Ddadada&bgTextureHover=3D02_gl= ass.png&bgImgOpacityHover=3D75&borderColorHover=3D999999&fcHover=3D212121&i= conColorHover=3D454545&bgColorActive=3Dffffff&bgTextureActive=3D02_glass.pn= g&bgImgOpacityActive=3D65&borderColorActive=3Daaaaaa&fcActive=3D212121&icon= ColorActive=3D454545&bgColorHighlight=3Dfbf9ee&bgTextureHighlight=3D02_glas= s.png&bgImgOpacityHighlight=3D55&borderColorHighlight=3Dfcefa1&fcHighlight= =3D363636&iconColorHighlight=3D2e83ff&bgColorError=3Dfef1ec&bgTextureError= =3D02_glass.png&bgImgOpacityError=3D95&borderColorError=3Dcd0a0a&fcError=3D= cd0a0a&iconColorError=3Dcd0a0a&bgColorOverlay=3Daaaaaa&bgTextureOverlay=3D0= 1_flat.png&bgImgOpacityOverlay=3D0&opacityOverlay=3D30&bgColorShadow=3Daaaa= aa&bgTextureShadow=3D01_flat.png&bgImgOpacityShadow=3D0&opacityShadow=3D30&= thicknessShadow=3D8px&offsetTopShadow=3D-8px&offsetLeftShadow=3D-8px&corner= RadiusShadow=3D8px - */ - - -/* Component containers -----------------------------------*/ -.ui-widget { font-family: Verdana,Arial,sans-serif; font-size: 1.1em; } -.ui-widget .ui-widget { font-size: 1em; } -.ui-widget input, .ui-widget select, .ui-widget textarea, .ui-widget butto= n { font-family: Verdana,Arial,sans-serif; font-size: 1em; } -.ui-widget-content { border: 1px solid #aaaaaa; background: #ffffff url(im= ages/ui-bg_flat_75_ffffff_40x100.png) 50% 50% repeat-x; color: #222222; } -.ui-widget-content a { color: #222222; } -.ui-widget-header { border: 1px solid #aaaaaa; background: #cccccc url(ima= ges/ui-bg_highlight-soft_75_cccccc_1x100.png) 50% 50% repeat-x; color: #222= 222; font-weight: bold; } -.ui-widget-header a { color: #222222; } - -/* Interaction states -----------------------------------*/ -.ui-state-default, .ui-widget-content .ui-state-default, .ui-widget-header= .ui-state-default { border: 1px solid #d3d3d3; background: #e6e6e6 url(ima= ges/ui-bg_glass_75_e6e6e6_1x400.png) 50% 50% repeat-x; font-weight: normal;= color: #555555; } -.ui-state-default a, .ui-state-default a:link, .ui-state-default a:visited= { color: #555555; text-decoration: none; } -.ui-state-hover, .ui-widget-content .ui-state-hover, .ui-widget-header .ui= -state-hover, .ui-state-focus, .ui-widget-content .ui-state-focus, .ui-widg= et-header .ui-state-focus { border: 1px solid #999999; background: #dadada = url(images/ui-bg_glass_75_dadada_1x400.png) 50% 50% repeat-x; font-weight: = normal; color: #212121; } -.ui-state-hover a, .ui-state-hover a:hover { color: #212121; text-decorati= on: none; } -.ui-state-active, .ui-widget-content .ui-state-active, .ui-widget-header .= ui-state-active { border: 1px solid #aaaaaa; background: #ffffff url(images= /ui-bg_glass_65_ffffff_1x400.png) 50% 50% repeat-x; font-weight: normal; co= lor: #212121; } -.ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited { = color: #212121; text-decoration: none; } -.ui-widget :active { outline: none; } - -/* Interaction Cues -----------------------------------*/ -.ui-state-highlight, .ui-widget-content .ui-state-highlight, .ui-widget-he= ader .ui-state-highlight {border: 1px solid #fcefa1; background: #fbf9ee u= rl(images/ui-bg_glass_55_fbf9ee_1x400.png) 50% 50% repeat-x; color: #363636= ; } -.ui-state-highlight a, .ui-widget-content .ui-state-highlight a,.ui-widget= -header .ui-state-highlight a { color: #363636; } -.ui-state-error, .ui-widget-content .ui-state-error, .ui-widget-header .ui= -state-error {border: 1px solid #cd0a0a; background: #fef1ec url(images/ui-= bg_glass_95_fef1ec_1x400.png) 50% 50% repeat-x; color: #cd0a0a; } -.ui-state-error a, .ui-widget-content .ui-state-error a, .ui-widget-header= .ui-state-error a { color: #cd0a0a; } -.ui-state-error-text, .ui-widget-content .ui-state-error-text, .ui-widget-= header .ui-state-error-text { color: #cd0a0a; } -.ui-priority-primary, .ui-widget-content .ui-priority-primary, .ui-widget-= header .ui-priority-primary { font-weight: bold; } -.ui-priority-secondary, .ui-widget-content .ui-priority-secondary, .ui-wi= dget-header .ui-priority-secondary { opacity: .7; filter:Alpha(Opacity=3D70= ); font-weight: normal; } -.ui-state-disabled, .ui-widget-content .ui-state-disabled, .ui-widget-head= er .ui-state-disabled { opacity: .35; filter:Alpha(Opacity=3D35); backgroun= d-image: none; } - -/* Icons -----------------------------------*/ - -/* states and images */ -.ui-icon { width: 16px; height: 16px; background-image: url(images/ui-icon= s_222222_256x240.png); } -.ui-widget-content .ui-icon {background-image: url(images/ui-icons_222222_= 256x240.png); } -.ui-widget-header .ui-icon {background-image: url(images/ui-icons_222222_2= 56x240.png); } -.ui-state-default .ui-icon { background-image: url(images/ui-icons_888888_= 256x240.png); } -.ui-state-hover .ui-icon, .ui-state-focus .ui-icon {background-image: url(= images/ui-icons_454545_256x240.png); } -.ui-state-active .ui-icon {background-image: url(images/ui-icons_454545_25= 6x240.png); } -.ui-state-highlight .ui-icon {background-image: url(images/ui-icons_2e83ff= _256x240.png); } -.ui-state-error .ui-icon, .ui-state-error-text .ui-icon {background-image:= url(images/ui-icons_cd0a0a_256x240.png); } - -/* positioning */ -.ui-icon-carat-1-n { background-position: 0 0; } -.ui-icon-carat-1-ne { background-position: -16px 0; } -.ui-icon-carat-1-e { background-position: -32px 0; } -.ui-icon-carat-1-se { background-position: -48px 0; } -.ui-icon-carat-1-s { background-position: -64px 0; } -.ui-icon-carat-1-sw { background-position: -80px 0; } -.ui-icon-carat-1-w { background-position: -96px 0; } -.ui-icon-carat-1-nw { background-position: -112px 0; } -.ui-icon-carat-2-n-s { background-position: -128px 0; } -.ui-icon-carat-2-e-w { background-position: -144px 0; } -.ui-icon-triangle-1-n { background-position: 0 -16px; } -.ui-icon-triangle-1-ne { background-position: -16px -16px; } -.ui-icon-triangle-1-e { background-position: -32px -16px; } -.ui-icon-triangle-1-se { background-position: -48px -16px; } -.ui-icon-triangle-1-s { background-position: -64px -16px; } -.ui-icon-triangle-1-sw { background-position: -80px -16px; } -.ui-icon-triangle-1-w { background-position: -96px -16px; } -.ui-icon-triangle-1-nw { background-position: -112px -16px; } -.ui-icon-triangle-2-n-s { background-position: -128px -16px; } -.ui-icon-triangle-2-e-w { background-position: -144px -16px; } -.ui-icon-arrow-1-n { background-position: 0 -32px; } -.ui-icon-arrow-1-ne { background-position: -16px -32px; } -.ui-icon-arrow-1-e { background-position: -32px -32px; } -.ui-icon-arrow-1-se { background-position: -48px -32px; } -.ui-icon-arrow-1-s { background-position: -64px -32px; } -.ui-icon-arrow-1-sw { background-position: -80px -32px; } -.ui-icon-arrow-1-w { background-position: -96px -32px; } -.ui-icon-arrow-1-nw { background-position: -112px -32px; } -.ui-icon-arrow-2-n-s { background-position: -128px -32px; } -.ui-icon-arrow-2-ne-sw { background-position: -144px -32px; } -.ui-icon-arrow-2-e-w { background-position: -160px -32px; } -.ui-icon-arrow-2-se-nw { background-position: -176px -32px; } -.ui-icon-arrowstop-1-n { background-position: -192px -32px; } -.ui-icon-arrowstop-1-e { background-position: -208px -32px; } -.ui-icon-arrowstop-1-s { background-position: -224px -32px; } -.ui-icon-arrowstop-1-w { background-position: -240px -32px; } -.ui-icon-arrowthick-1-n { background-position: 0 -48px; } -.ui-icon-arrowthick-1-ne { background-position: -16px -48px; } -.ui-icon-arrowthick-1-e { background-position: -32px -48px; } -.ui-icon-arrowthick-1-se { background-position: -48px -48px; } -.ui-icon-arrowthick-1-s { background-position: -64px -48px; } -.ui-icon-arrowthick-1-sw { background-position: -80px -48px; } -.ui-icon-arrowthick-1-w { background-position: -96px -48px; } -.ui-icon-arrowthick-1-nw { background-position: -112px -48px; } -.ui-icon-arrowthick-2-n-s { background-position: -128px -48px; } -.ui-icon-arrowthick-2-ne-sw { background-position: -144px -48px; } -.ui-icon-arrowthick-2-e-w { background-position: -160px -48px; } -.ui-icon-arrowthick-2-se-nw { background-position: -176px -48px; } -.ui-icon-arrowthickstop-1-n { background-position: -192px -48px; } -.ui-icon-arrowthickstop-1-e { background-position: -208px -48px; } -.ui-icon-arrowthickstop-1-s { background-position: -224px -48px; } -.ui-icon-arrowthickstop-1-w { background-position: -240px -48px; } -.ui-icon-arrowreturnthick-1-w { background-position: 0 -64px; } -.ui-icon-arrowreturnthick-1-n { background-position: -16px -64px; } -.ui-icon-arrowreturnthick-1-e { background-position: -32px -64px; } -.ui-icon-arrowreturnthick-1-s { background-position: -48px -64px; } -.ui-icon-arrowreturn-1-w { background-position: -64px -64px; } -.ui-icon-arrowreturn-1-n { background-position: -80px -64px; } -.ui-icon-arrowreturn-1-e { background-position: -96px -64px; } -.ui-icon-arrowreturn-1-s { background-position: -112px -64px; } -.ui-icon-arrowrefresh-1-w { background-position: -128px -64px; } -.ui-icon-arrowrefresh-1-n { background-position: -144px -64px; } -.ui-icon-arrowrefresh-1-e { background-position: -160px -64px; } -.ui-icon-arrowrefresh-1-s { background-position: -176px -64px; } -.ui-icon-arrow-4 { background-position: 0 -80px; } -.ui-icon-arrow-4-diag { background-position: -16px -80px; } -.ui-icon-extlink { background-position: -32px -80px; } -.ui-icon-newwin { background-position: -48px -80px; } -.ui-icon-refresh { background-position: -64px -80px; } -.ui-icon-shuffle { background-position: -80px -80px; } -.ui-icon-transfer-e-w { background-position: -96px -80px; } -.ui-icon-transferthick-e-w { background-position: -112px -80px; } -.ui-icon-folder-collapsed { background-position: 0 -96px; } -.ui-icon-folder-open { background-position: -16px -96px; } -.ui-icon-document { background-position: -32px -96px; } -.ui-icon-document-b { background-position: -48px -96px; } -.ui-icon-note { background-position: -64px -96px; } -.ui-icon-mail-closed { background-position: -80px -96px; } -.ui-icon-mail-open { background-position: -96px -96px; } -.ui-icon-suitcase { background-position: -112px -96px; } -.ui-icon-comment { background-position: -128px -96px; } -.ui-icon-person { background-position: -144px -96px; } -.ui-icon-print { background-position: -160px -96px; } -.ui-icon-trash { background-position: -176px -96px; } -.ui-icon-locked { background-position: -192px -96px; } -.ui-icon-unlocked { background-position: -208px -96px; } -.ui-icon-bookmark { background-position: -224px -96px; } -.ui-icon-tag { background-position: -240px -96px; } -.ui-icon-home { background-position: 0 -112px; } -.ui-icon-flag { background-position: -16px -112px; } -.ui-icon-calendar { background-position: -32px -112px; } -.ui-icon-cart { background-position: -48px -112px; } -.ui-icon-pencil { background-position: -64px -112px; } -.ui-icon-clock { background-position: -80px -112px; } -.ui-icon-disk { background-position: -96px -112px; } -.ui-icon-calculator { background-position: -112px -112px; } -.ui-icon-zoomin { background-position: -128px -112px; } -.ui-icon-zoomout { background-position: -144px -112px; } -.ui-icon-search { background-position: -160px -112px; } -.ui-icon-wrench { background-position: -176px -112px; } -.ui-icon-gear { background-position: -192px -112px; } -.ui-icon-heart { background-position: -208px -112px; } -.ui-icon-star { background-position: -224px -112px; } -.ui-icon-link { background-position: -240px -112px; } -.ui-icon-cancel { background-position: 0 -128px; } -.ui-icon-plus { background-position: -16px -128px; } -.ui-icon-plusthick { background-position: -32px -128px; } -.ui-icon-minus { background-position: -48px -128px; } -.ui-icon-minusthick { background-position: -64px -128px; } -.ui-icon-close { background-position: -80px -128px; } -.ui-icon-closethick { background-position: -96px -128px; } -.ui-icon-key { background-position: -112px -128px; } -.ui-icon-lightbulb { background-position: -128px -128px; } -.ui-icon-scissors { background-position: -144px -128px; } -.ui-icon-clipboard { background-position: -160px -128px; } -.ui-icon-copy { background-position: -176px -128px; } -.ui-icon-contact { background-position: -192px -128px; } -.ui-icon-image { background-position: -208px -128px; } -.ui-icon-video { background-position: -224px -128px; } -.ui-icon-script { background-position: -240px -128px; } -.ui-icon-alert { background-position: 0 -144px; } -.ui-icon-info { background-position: -16px -144px; } -.ui-icon-notice { background-position: -32px -144px; } -.ui-icon-help { background-position: -48px -144px; } -.ui-icon-check { background-position: -64px -144px; } -.ui-icon-bullet { background-position: -80px -144px; } -.ui-icon-radio-off { background-position: -96px -144px; } -.ui-icon-radio-on { background-position: -112px -144px; } -.ui-icon-pin-w { background-position: -128px -144px; } -.ui-icon-pin-s { background-position: -144px -144px; } -.ui-icon-play { background-position: 0 -160px; } -.ui-icon-pause { background-position: -16px -160px; } -.ui-icon-seek-next { background-position: -32px -160px; } -.ui-icon-seek-prev { background-position: -48px -160px; } -.ui-icon-seek-end { background-position: -64px -160px; } -.ui-icon-seek-start { background-position: -80px -160px; } -/* ui-icon-seek-first is deprecated, use ui-icon-seek-start instead */ -.ui-icon-seek-first { background-position: -80px -160px; } -.ui-icon-stop { background-position: -96px -160px; } -.ui-icon-eject { background-position: -112px -160px; } -.ui-icon-volume-off { background-position: -128px -160px; } -.ui-icon-volume-on { background-position: -144px -160px; } -.ui-icon-power { background-position: 0 -176px; } -.ui-icon-signal-diag { background-position: -16px -176px; } -.ui-icon-signal { background-position: -32px -176px; } -.ui-icon-battery-0 { background-position: -48px -176px; } -.ui-icon-battery-1 { background-position: -64px -176px; } -.ui-icon-battery-2 { background-position: -80px -176px; } -.ui-icon-battery-3 { background-position: -96px -176px; } -.ui-icon-circle-plus { background-position: 0 -192px; } -.ui-icon-circle-minus { background-position: -16px -192px; } -.ui-icon-circle-close { background-position: -32px -192px; } -.ui-icon-circle-triangle-e { background-position: -48px -192px; } -.ui-icon-circle-triangle-s { background-position: -64px -192px; } -.ui-icon-circle-triangle-w { background-position: -80px -192px; } -.ui-icon-circle-triangle-n { background-position: -96px -192px; } -.ui-icon-circle-arrow-e { background-position: -112px -192px; } -.ui-icon-circle-arrow-s { background-position: -128px -192px; } -.ui-icon-circle-arrow-w { background-position: -144px -192px; } -.ui-icon-circle-arrow-n { background-position: -160px -192px; } -.ui-icon-circle-zoomin { background-position: -176px -192px; } -.ui-icon-circle-zoomout { background-position: -192px -192px; } -.ui-icon-circle-check { background-position: -208px -192px; } -.ui-icon-circlesmall-plus { background-position: 0 -208px; } -.ui-icon-circlesmall-minus { background-position: -16px -208px; } -.ui-icon-circlesmall-close { background-position: -32px -208px; } -.ui-icon-squaresmall-plus { background-position: -48px -208px; } -.ui-icon-squaresmall-minus { background-position: -64px -208px; } -.ui-icon-squaresmall-close { background-position: -80px -208px; } -.ui-icon-grip-dotted-vertical { background-position: 0 -224px; } -.ui-icon-grip-dotted-horizontal { background-position: -16px -224px; } -.ui-icon-grip-solid-vertical { background-position: -32px -224px; } -.ui-icon-grip-solid-horizontal { background-position: -48px -224px; } -.ui-icon-gripsmall-diagonal-se { background-position: -64px -224px; } -.ui-icon-grip-diagonal-se { background-position: -80px -224px; } - - -/* Misc visuals -----------------------------------*/ - -/* Corner radius */ -.ui-corner-all, .ui-corner-top, .ui-corner-left, .ui-corner-tl { -moz-bord= er-radius-topleft: 4px; -webkit-border-top-left-radius: 4px; -khtml-border-= top-left-radius: 4px; border-top-left-radius: 4px; } -.ui-corner-all, .ui-corner-top, .ui-corner-right, .ui-corner-tr { -moz-bor= der-radius-topright: 4px; -webkit-border-top-right-radius: 4px; -khtml-bord= er-top-right-radius: 4px; border-top-right-radius: 4px; } -.ui-corner-all, .ui-corner-bottom, .ui-corner-left, .ui-corner-bl { -moz-b= order-radius-bottomleft: 4px; -webkit-border-bottom-left-radius: 4px; -khtm= l-border-bottom-left-radius: 4px; border-bottom-left-radius: 4px; } -.ui-corner-all, .ui-corner-bottom, .ui-corner-right, .ui-corner-br { -moz-= border-radius-bottomright: 4px; -webkit-border-bottom-right-radius: 4px; -k= html-border-bottom-right-radius: 4px; border-bottom-right-radius: 4px; } - -/* Overlays */ -.ui-widget-overlay { background: #aaaaaa url(images/ui-bg_flat_0_aaaaaa_40= x100.png) 50% 50% repeat-x; opacity: .30;filter:Alpha(Opacity=3D30); } -.ui-widget-shadow { margin: -8px 0 0 -8px; padding: 8px; background: #aaaa= aa url(images/ui-bg_flat_0_aaaaaa_40x100.png) 50% 50% repeat-x; opacity: .3= 0;filter:Alpha(Opacity=3D30); -moz-border-radius: 8px; -khtml-border-radius= : 8px; -webkit-border-radius: 8px; border-radius: 8px; }/*! - * jQuery UI Autocomplete 1.8.23 - * - * Copyright 2012, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI/Autocomplete#theming - */ -.ui-autocomplete { position: absolute; cursor: default; }=09 - -/* workarounds */ -* html .ui-autocomplete { width:1px; } /* without this, the menu expands t= o 100% in IE6 */ - -/* - * jQuery UI Menu 1.8.23 - * - * Copyright 2010, AUTHORS.txt 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selected.text() : "", + wrapper =3D this.wrapper =3D $( "<span>" ) + .addClass( "ui-combobox" ) + .insertAfter( select ); + + function removeIfInvalid(element) { + var value =3D $( element ).val(), + matcher =3D new RegExp( "^" + $.ui.autocomplete.escape= Regex( value ) + "$", "i" ), + valid =3D false; + select.children( "option" ).each(function() { + if ( $( this ).text().match( matcher ) ) { + this.selected =3D valid =3D true; + return false; + } + }); + if ( !valid ) { + // remove invalid value, as it didn't match anything + $( element ) + .val( "" ) + .attr( "title", value + " didn't match any item" ) + .tooltip( "open" ); + select.val( "" ); + setTimeout(function() { + input.tooltip( "close" ).attr( "title", "" ); + }, 2500 ); + input.data( "autocomplete" ).term =3D ""; + return false; + } + } + + var size =3D ( this.options.size ? this.options.size : 20 ); + input =3D $( "<input>" ) + .appendTo( wrapper ) + .val( value ) + .click( function() { + this.select(); + }) + .attr( "title", "" ) + .attr( "size", size ) + .addClass( "ui-state-default ui-combobox-input" ) + .autocomplete({ + appendTo: this.options.appendTo, + delay: 0, + minLength: 0, + source: function( request, response ) { + var matcher =3D new RegExp( $.ui.autocomplete.esca= peRegex(request.term), "i" ); + response( select.children( "option" ).map(function= () { + var text =3D $( this ).text(); + if ( this.value && ( !request.term || matcher.= test(text) ) ) + return { + label: text.replace( + new RegExp( + "(?![^&;]+;)(?!<[^<>]*)(" + + $.ui.autocomplete.escapeRegex(= request.term) + + ")(?![^<>]*>)(?![^&;]+;)", "gi" + ), "<strong>$1</strong>" ), + value: text, + option: this + }; + }) ); + }, + select: function( event, ui ) { + ui.item.option.selected =3D true; + that._trigger( "selected", event, { + item: ui.item.option + }); + }, + change: function( event, ui ) { + if ( !ui.item ) + return removeIfInvalid( this ); + } + }) + .addClass( "ui-widget ui-widget-content ui-corner-left" ); + + input.data( "autocomplete" )._renderItem =3D function( ul, ite= m ) { + return $( "<li>" ) + .data( "item.autocomplete", item ) + .append( "<a>" + item.label + "</a>" ) + .appendTo( ul ); + }; + + $( "<a>" ) + .attr( "tabIndex", -1 ) + .attr( "title", "Show All Items" ) + .tooltip() + .appendTo( wrapper ) + .button({ + icons: { + primary: "ui-icon-triangle-1-s" + }, + text: false + }) + .removeClass( "ui-corner-all" ) + .addClass( "ui-corner-right ui-combobox-toggle" ) + .click(function() { + // close if already visible + if ( input.autocomplete( "widget" ).is( ":visible" ) )= { + input.autocomplete( "close" ); + removeIfInvalid( input ); + return; + } + + // work around a bug (likely same cause as #5265) + $( this ).blur(); + + // pass empty string as value to search for, displayin= g all results + input.autocomplete( "search", "" ); + input.focus(); + }); + + input + .tooltip({ + position: { + of: this.button + }, + tooltipClass: "ui-state-highlight" + }); + }, + + destroy: function() { + this.wrapper.remove(); + this.element.show(); + $.Widget.prototype.destroy.call( this ); + } + }); +})( jQuery ); \ No newline at end of file diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/libs/jquery/jquery-ui.js --- /dev/null +++ b/static/scripts/libs/jquery/jquery-ui.js @@ -0,0 +1,6 @@ +/*! jQuery UI - v1.9.1 - 2012-10-29 +* http://jqueryui.com +* Includes: jquery.ui.core.js, jquery.ui.widget.js, jquery.ui.mouse.js, jq= uery.ui.position.js, jquery.ui.autocomplete.js, jquery.ui.button.js, jquery= .ui.menu.js, jquery.ui.slider.js +* Copyright (c) 2012 jQuery Foundation and other contributors Licensed MIT= */ + +(function(e,t){function i(t,n){var r,i,o,u=3Dt.nodeName.toLowerCase();retu= rn"area"=3D=3D=3Du?(r=3Dt.parentNode,i=3Dr.name,!t.href||!i||r.nodeName.toL= owerCase()!=3D=3D"map"?!1:(o=3De("img[usemap=3D#"+i+"]")[0],!!o&&s(o))):(/i= 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n_click:null,tooltip_config:{},isMenuButton:true,id:null,href:null,target:n= ull,enabled:true,visible:true}});var IconButtonView=3DBackbone.View.extend(= {initialize:function(){this.model.attributes.tooltip_config=3D{placement:"b= ottom"};this.model.bind("change",this.render,this)},render:function(){this.= $el.tooltip("hide");var a=3D$(Handlebars.partials.iconButton(this.model.toJ= SON()));a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a)= ;this.setElement(a);return this},events:{click:"click"},click:function(a){i= f(this.model.attributes.on_click){this.model.attributes.on_click(a);return = false}return true}});IconButtonView.templates=3D{iconButton:Handlebars.part= ials.iconButton};var IconButtonCollection=3DBackbone.Collection.extend({mod= el:IconButton});var IconButtonMenuView=3DBackbone.View.extend({tagName:"div= ",initialize:function(){this.render()},render:function(){var a=3Dthis;this.= collection.each(function(c){var b=3D$("<a/>").attr("href","javascript:void(= 0)").attr("title",c.attributes.title).addClass("icon-button menu-button").a= ddClass(c.attributes.icon_class).appendTo(a.$el).click(c.attributes.on_clic= k);if(c.attributes.tooltip_config){b.tooltip(c.attributes.tooltip_config)}}= );return this}});var create_icon_buttons_menu=3Dfunction(b,a){if(!a){a=3D{}= }var c=3Dnew IconButtonCollection(_.map(b,function(d){return new IconButton= (_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid= =3DBackbone.Collection.extend({});var GridView=3DBackbone.View.extend({});v= ar GalaxyPaths=3DBackbone.Model.extend({defaults:{root_path:"",image_path:"= "}}); \ No newline at end of file +var IconButton=3DBackbone.Model.extend({defaults:{title:"",icon_class:"",o= n_click:null,menu_options:null,tooltip_config:{},isMenuButton:true,id:null,= href:null,target:null,enabled:true,visible:true}});var IconButtonView=3DBac= kbone.View.extend({initialize:function(){this.model.attributes.tooltip_conf= ig=3D{placement:"bottom"};this.model.bind("change",this.render,this)},rende= r:function(){this.$el.tooltip("hide");var a=3D$(Handlebars.partials.iconBut= ton(this.model.toJSON()));a.tooltip(this.model.get("tooltip_config"));this.= $el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},c= lick:function(a){if(this.model.attributes.on_click){this.model.attributes.o= n_click(a);return false}return true}});IconButtonView.templates=3D{iconButt= on:Handlebars.partials.iconButton};var IconButtonCollection=3DBackbone.Coll= ection.extend({model:IconButton});var IconButtonMenuView=3DBackbone.View.ex= tend({tagName:"div",initialize:function(){this.render()},render:function(){= var a=3Dthis;this.collection.each(function(d){var b=3D$("<a/>").attr("href"= ,"javascript:void(0)").attr("title",d.attributes.title).addClass("icon-butt= on menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.= attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes= .tooltip_config)}var c=3Dd.get("options");if(c){make_popupmenu(b,c)}});retu= rn this}});var create_icon_buttons_menu=3Dfunction(b,a){if(!a){a=3D{}}var c= =3Dnew IconButtonCollection(_.map(b,function(d){return new IconButton(_.ext= end(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=3DBack= bone.Collection.extend({});var GridView=3DBackbone.View.extend({});var Gala= xyPaths=3DBackbone.Model.extend({defaults:{root_path:"",image_path:""}}); \ No newline at end of file diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/viz/circster.js --- a/static/scripts/packed/viz/circster.js +++ b/static/scripts/packed/viz/circster.js @@ -1,1 +1,1 @@ -define(["libs/underscore","libs/d3","viz/visualization"],function(g,j,h){v= ar k=3DBackbone.Model.extend({is_visible:function(o,l){var m=3Do.getBoundin= gClientRect(),n=3D$("svg")[0].getBoundingClientRect();if(m.right<0||m.left>= n.right||m.bottom<0||m.top>n.bottom){return false}return true}});var c=3DBa= ckbone.Model.extend({defaults:{prefs:{color:"#ccc"}}});var a=3DBackbone.Vie= w.extend({className:"circster",initialize:function(l){this.total_gap=3Dl.to= tal_gap;this.genome=3Dl.genome;this.dataset_arc_height=3Dl.dataset_arc_heig= ht;this.track_gap=3D5;this.label_arc_height=3D20;this.scale=3D1;this.track_= views=3Dnull;this.model.get("tracks").on("add",this.add_track,this);this.mo= del.get("tracks").on("remove",this.remove_track,this)},get_tracks_bounds:fu= nction(){var n=3Dthis.dataset_arc_height,l=3DMath.min(this.$el.width(),this= .$el.height()),p=3Dl/2-this.model.get("tracks").length*(this.dataset_arc_he= ight+this.track_gap)-(this.label_arc_height+this.track_gap),o=3Dj.range(p,l= /2,this.dataset_arc_height+this.track_gap);var m=3Dthis;return g.map(o,func= tion(q){return[q,q+m.dataset_arc_height]})},render:function(){var o=3Dthis,= q=3Dthis.dataset_arc_height,r=3Do.$el.width(),l=3Do.$el.height(),p=3Dthis.m= odel.get("tracks"),s=3Dthis.get_tracks_bounds(),n=3Dj.select(o.$el[0]).appe= nd("svg").attr("width",r).attr("height",l).attr("pointer-events","all").app= end("svg:g").call(j.behavior.zoom().on("zoom",function(){var t=3Dj.event.sc= ale;n.attr("transform","translate("+j.event.translate+") scale("+t+")");if(= o.scale!=3D=3Dt){if(o.zoom_drag_timeout){clearTimeout(o.zoom_drag_timeout)}= o.zoom_drag_timeout=3DsetTimeout(function(){g.each(o.track_views,function(u= ){u.update_scale(t)})},400)}})).attr("transform","translate("+r/2+","+l/2+"= )").append("svg:g").attr("class","tracks");this.track_views=3Dp.map(functio= n(t,u){track_view_class=3D(t.get("track_type")=3D=3D=3D"LineTrack"?d:e);ret= urn new track_view_class({el:n.append("g")[0],track:t,radius_bounds:s[u],ge= nome:o.genome,total_gap:o.total_gap})});g.each(this.track_views,function(t)= {t.render()});var m=3Ds[p.length];m[1]=3Dm[0];this.label_track_view=3Dnew b= ({el:n.append("g")[0],track:new c(),radius_bounds:m,genome:o.genome,total_g= ap:o.total_gap});this.label_track_view.render()},add_track:function(p){var = o=3Dthis.get_tracks_bounds();g.each(this.track_views,function(r,s){r.update= _radius_bounds(o[s])});var n=3Dthis.track_views.length,q=3D(p.get("track_ty= pe")=3D=3D=3D"LineTrack"?d:e),l=3Dnew q({el:j.select("g.tracks").append("g"= )[0],track:p,radius_bounds:o[n],genome:this.genome,total_gap:this.total_gap= });l.render();this.track_views.push(l);var m=3Do[o.length-1];m[1]=3Dm[0];th= is.label_track_view.update_radius_bounds(m)},remove_track:function(m,o,n){v= ar l=3Dthis.track_views[n.index];this.track_views.splice(n.index,1);l.$el.r= emove();var p=3Dthis.get_tracks_bounds();g.each(this.track_views,function(q= ,r){q.update_radius_bounds(p[r])})}});var i=3DBackbone.View.extend({tagName= :"g",initialize:function(l){this.bg_stroke=3D"ccc";this.loading_bg_fill=3D"= 000";this.bg_fill=3D"ccc";this.total_gap=3Dl.total_gap;this.track=3Dl.track= ;this.radius_bounds=3Dl.radius_bounds;this.genome=3Dl.genome;this.chroms_la= yout=3Dthis._chroms_layout();this.data_bounds=3D[];this.scale=3D1;this.pare= nt_elt=3Dj.select(this.$el[0])},render:function(){var p=3Dthis.parent_elt;i= f(!p){console.log("no parent elt")}var o=3Dthis.chroms_layout,r=3Dj.svg.arc= ().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),l= =3Dp.selectAll("g").data(o).enter().append("svg:g"),n=3Dl.append("path").at= tr("d",r).attr("class","chrom-background").style("stroke",this.bg_stroke).s= tyle("fill",this.loading_bg_fill);n.append("title").text(function(t){return= t.data.chrom});var m=3Dthis,q=3Dm.track.get("data_manager"),s=3D(q?q.data_= is_ready():true);$.when(s).then(function(){$.when(m._render_data(p)).then(f= unction(){n.style("fill",m.bg_fill)})})},update_radius_bounds:function(m){t= his.radius_bounds=3Dm;var l=3Dj.svg.arc().innerRadius(this.radius_bounds[0]= ).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chro= m-background").transition().duration(1000).attr("d",l);this._transition_chr= om_data()},update_scale:function(o){var n=3Dthis.scale;this.scale=3Do;if(o<= =3Dn){return}var m=3Dthis,l=3Dnew k();this.parent_elt.selectAll("path.chrom= -data").filter(function(q,p){return l.is_visible(this)}).each(function(v,r)= {var u=3Dj.select(this),q=3Du.attr("chrom"),t=3Dm.genome.get_chrom_region(q= ),s=3Dm.track.get("data_manager"),p;if(!s.can_get_more_detailed_data(t)){re= turn}p=3Dm.track.get("data_manager").get_more_detailed_data(t,"Coverage",0,= o);$.when(p).then(function(z){u.remove();m._update_data_bounds();var y=3Dg.= find(m.chroms_layout,function(A){return A.data.chrom=3D=3D=3Dq});var w=3Dm.= track.get("prefs"),x=3Dw.block_color;if(!x){x=3Dw.color}m._render_chrom_dat= a(m.parent_elt,y,z).style("stroke",x).style("fill",x)})});return m},_transi= tion_chrom_data:function(){var m=3Dthis.track,o=3Dthis.chroms_layout,l=3Dth= is.parent_elt.selectAll("g>path.chrom-data"),p=3Dl[0].length;if(p>0){var n= =3Dthis;$.when(m.get("data_manager").get_genome_wide_data(this.genome)).the= n(function(r){var q=3Dg.reject(g.map(r,function(s,t){var u=3Dnull,v=3Dn._ge= t_path_function(o[t],s);if(v){u=3Dv(s.data)}return u}),function(s){return s= =3D=3D=3Dnull});l.each(function(t,s){j.select(this).transition().duration(1= 000).attr("d",q[s])})})}},_update_data_bounds:function(){var l=3Dthis.data_= bounds;this.data_bounds=3Dthis.get_data_bounds(this.track.get("data_manager= ").get_genome_wide_data(this.genome));if(this.data_bounds[0]<l[0]||this.dat= a_bounds[1]>l[1]){this._transition_chrom_data()}},_render_data:function(o){= var n=3Dthis,m=3Dthis.chroms_layout,l=3Dthis.track,p=3D$.Deferred();$.when(= l.get("data_manager").get_genome_wide_data(this.genome)).then(function(s){n= .data_bounds=3Dn.get_data_bounds(s);layout_and_data=3Dg.zip(m,s),chroms_dat= a_layout=3Dg.map(layout_and_data,function(t){var u=3Dt[0],v=3Dt[1];return n= ._render_chrom_data(o,u,v)});var q=3Dl.get("config"),r=3Dq.get_value("block= _color");if(!r){r=3Dq.get_value("color")}n.parent_elt.selectAll("path.chrom= -data").style("stroke",r).style("fill",r);p.resolve(o)});return p},_render_= chrom_data:function(l,m,n){},_get_path_function:function(m,l){},_chroms_lay= out:function(){var m=3Dthis.genome.get_chroms_info(),o=3Dj.layout.pie().val= ue(function(q){return q.len}).sort(null),p=3Do(m),l=3Dthis.total_gap/m.leng= th,n=3Dg.map(p,function(s,r){var q=3Ds.endAngle-l;s.endAngle=3D(q>s.startAn= gle?q:s.startAngle);return s});return n}});var b=3Di.extend({initialize:fun= ction(l){i.prototype.initialize.call(this,l);this.bg_stroke=3D"fff";this.bg= _fill=3D"fff"},_render_data:function(m){var l=3Dm.selectAll("g");l.selectAl= l("path").attr("id",function(n){return"label-"+n.data.chrom});l.append("svg= :text").filter(function(n){return n.endAngle-n.startAngle>0.08}).attr("text= -anchor","middle").append("svg:textPath").attr("xlink:href",function(n){ret= urn"#label-"+n.data.chrom}).attr("startOffset","25%").text(function(n){retu= rn n.data.chrom})}});var f=3Di.extend({_render_chrom_data:function(l,o,m){v= ar p=3Dthis._get_path_function(o,m);if(!p){return null}var n=3Dl.datum(m.da= ta),q=3Dn.append("path").attr("class","chrom-data").attr("chrom",o.data.chr= om).attr("d",p);return q},_get_path_function:function(o,n){if(typeof n=3D= =3D=3D"string"||!n.data||n.data.length=3D=3D=3D0){return null}var l=3Dj.sca= le.linear().domain(this.data_bounds).range(this.radius_bounds);var p=3Dj.sc= ale.linear().domain([0,n.data.length]).range([o.startAngle,o.endAngle]);var= m=3Dj.svg.line.radial().interpolate("linear").radius(function(q){return l(= q[1])}).angle(function(r,q){return p(q)});return j.svg.area.radial().interp= olate(m.interpolate()).innerRadius(l(0)).outerRadius(m.radius()).angle(m.an= gle())},get_data_bounds:function(l){}});var e=3Df.extend({get_data_bounds:f= unction(m){var l=3Dg.map(m,function(n){if(typeof n=3D=3D=3D"string"||!n.max= ){return 0}return n.max});return[0,(l&&typeof l!=3D=3D"string"?g.max(l):0)]= }});var d=3Df.extend({get_data_bounds:function(m){var l=3Dg.flatten(g.map(m= ,function(n){if(n){return g.map(n.data,function(o){return o[1]})}else{retur= n 0}}));return[g.min(l),g.max(l)]}});return{CircsterView:a}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/visualization"],function(g,k,h){v= ar l=3DBackbone.Model.extend({is_visible:function(p,m){var n=3Dp.getBoundin= gClientRect(),o=3D$("svg")[0].getBoundingClientRect();if(n.right<0||n.left>= o.right||n.bottom<0||n.top>o.bottom){return false}return true}});var c=3DBa= ckbone.Model.extend({defaults:{prefs:{color:"#ccc"}}});var a=3DBackbone.Vie= w.extend({className:"circster",initialize:function(m){this.total_gap=3Dm.to= tal_gap;this.genome=3Dm.genome;this.dataset_arc_height=3Dm.dataset_arc_heig= ht;this.track_gap=3D5;this.label_arc_height=3D20;this.scale=3D1;this.circul= ar_views=3Dnull;this.chords_views=3Dnull;this.model.get("tracks").on("add",= this.add_track,this);this.model.get("tracks").on("remove",this.remove_track= ,this);this.get_circular_tracks()},get_circular_tracks:function(){return th= is.model.get("tracks").filter(function(m){return m.get("track_type")!=3D=3D= "DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get= ("tracks").filter(function(m){return m.get("track_type")=3D=3D=3D"DiagonalH= eatmapTrack"})},get_tracks_bounds:function(){var n=3Dthis.get_circular_trac= ks();dataset_arc_height=3Dthis.dataset_arc_height,min_dimension=3DMath.min(= this.$el.width(),this.$el.height()),radius_start=3Dmin_dimension/2-n.length= *(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track= _gap),tracks_start_radii=3Dk.range(radius_start,min_dimension/2,this.datase= t_arc_height+this.track_gap);var m=3Dthis;return g.map(tracks_start_radii,f= unction(o){return[o,o+m.dataset_arc_height]})},render:function(){var u=3Dth= is,p=3Dthis.dataset_arc_height,m=3Du.$el.width(),t=3Du.$el.height(),r=3Dthi= s.get_circular_tracks(),o=3Dthis.get_chord_tracks(),q=3Dthis.get_tracks_bou= nds(),n=3Dk.select(u.$el[0]).append("svg").attr("width",m).attr("height",t)= .attr("pointer-events","all").append("svg:g").call(k.behavior.zoom().on("zo= om",function(){var v=3Dk.event.scale;n.attr("transform","translate("+k.even= t.translate+") scale("+v+")");if(u.scale!=3D=3Dv){if(u.zoom_drag_timeout){c= learTimeout(u.zoom_drag_timeout)}u.zoom_drag_timeout=3DsetTimeout(function(= ){g.each(u.circular_views,function(w){w.update_scale(v)})},400)}})).attr("t= ransform","translate("+m/2+","+t/2+")").append("svg:g").attr("class","track= s");this.circular_views=3Dr.map(function(w,x){var y=3D(w.get("track_type")= =3D=3D=3D"LineTrack"?d:e),v=3Dnew y({el:n.append("g")[0],track:w,radius_bou= nds:q[x],genome:u.genome,total_gap:u.total_gap});v.render();return v});this= .chords_views=3Do.map(function(w){var v=3Dnew i({el:n.append("g")[0],track:= w,radius_bounds:q[0],genome:u.genome,total_gap:u.total_gap});v.render();ret= urn v});var s=3Dq[r.length];s[1]=3Ds[0];this.label_track_view=3Dnew b({el:n= .append("g")[0],track:new c(),radius_bounds:s,genome:u.genome,total_gap:u.t= otal_gap});this.label_track_view.render()},add_track:function(s){if(s.get("= track_type")=3D=3D=3D"DiagonalHeatmapTrack"){var o=3Dthis.circular_views[0]= .radius_bounds,r=3Dnew i({el:k.select("g.tracks").append("g")[0],track:s,ra= dius_bounds:o,genome:this.genome,total_gap:this.total_gap});r.render();this= .chords_views.push(r)}else{var q=3Dthis.get_tracks_bounds();g.each(this.cir= cular_views,function(u,v){u.update_radius_bounds(q[v])});g.each(this.chords= _views,function(u){u.update_radius_bounds(q[0])});var p=3Dthis.circular_vie= ws.length,t=3D(s.get("track_type")=3D=3D=3D"LineTrack"?d:e),m=3Dnew t({el:k= .select("g.tracks").append("g")[0],track:s,radius_bounds:q[p],genome:this.g= enome,total_gap:this.total_gap});m.render();this.circular_views.push(m);var= n=3Dq[q.length-1];n[1]=3Dn[0];this.label_track_view.update_radius_bounds(n= )}},remove_track:function(n,p,o){var m=3Dthis.circular_views[o.index];this.= circular_views.splice(o.index,1);m.$el.remove();var q=3Dthis.get_tracks_bou= nds();g.each(this.circular_views,function(r,s){r.update_radius_bounds(q[s])= })}});var j=3DBackbone.View.extend({tagName:"g",initialize:function(m){this= .bg_stroke=3D"ccc";this.loading_bg_fill=3D"000";this.bg_fill=3D"ccc";this.t= otal_gap=3Dm.total_gap;this.track=3Dm.track;this.radius_bounds=3Dm.radius_b= ounds;this.genome=3Dm.genome;this.chroms_layout=3Dthis._chroms_layout();thi= s.data_bounds=3D[];this.scale=3D1;this.parent_elt=3Dk.select(this.$el[0])},= get_fill_color:function(){var m=3Dthis.track.get("config").get_value("block= _color");if(!m){m=3Dthis.track.get("config").get_value("color")}return m},r= ender:function(){var q=3Dthis.parent_elt;if(!q){console.log("no parent elt"= )}var p=3Dthis.chroms_layout,s=3Dk.svg.arc().innerRadius(this.radius_bounds= [0]).outerRadius(this.radius_bounds[1]),m=3Dq.selectAll("g").data(p).enter(= ).append("svg:g"),o=3Dm.append("path").attr("d",s).attr("class","chrom-back= ground").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);= o.append("title").text(function(u){return u.data.chrom});var n=3Dthis,r=3Dn= .track.get("data_manager"),t=3D(r?r.data_is_ready():true);$.when(t).then(fu= nction(){$.when(n._render_data(q)).then(function(){o.style("fill",n.bg_fill= )})})},update_radius_bounds:function(n){this.radius_bounds=3Dn;var m=3Dk.sv= g.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1= ]);this.parent_elt.selectAll("g>path.chrom-background").transition().durati= on(1000).attr("d",m);this._transition_chrom_data()},update_scale:function(p= ){var o=3Dthis.scale;this.scale=3Dp;if(p<=3Do){return}var n=3Dthis,m=3Dnew = l();this.parent_elt.selectAll("path.chrom-data").filter(function(r,q){retur= n m.is_visible(this)}).each(function(w,s){var v=3Dk.select(this),r=3Dv.attr= ("chrom"),u=3Dn.genome.get_chrom_region(r),t=3Dn.track.get("data_manager"),= q;if(!t.can_get_more_detailed_data(u)){return}q=3Dn.track.get("data_manager= ").get_more_detailed_data(u,"Coverage",0,p);$.when(q).then(function(z){v.re= move();n._update_data_bounds();var y=3Dg.find(n.chroms_layout,function(A){r= eturn A.data.chrom=3D=3D=3Dr});var x=3Dn.get_fill_color();n._render_chrom_d= ata(n.parent_elt,y,z).style("stroke",x).style("fill",x)})});return n},_tran= sition_chrom_data:function(){var n=3Dthis.track,p=3Dthis.chroms_layout,m=3D= this.parent_elt.selectAll("g>path.chrom-data"),q=3Dm[0].length;if(q>0){var = o=3Dthis;$.when(n.get("data_manager").get_genome_wide_data(this.genome)).th= en(function(s){var r=3Dg.reject(g.map(s,function(t,u){var v=3Dnull,w=3Do._g= et_path_function(p[u],t);if(w){v=3Dw(t.data)}return v}),function(t){return = t=3D=3D=3Dnull});m.each(function(u,t){k.select(this).transition().duration(= 1000).attr("d",r[t])})})}},_update_data_bounds:function(){var m=3Dthis.data= _bounds;this.data_bounds=3Dthis.get_data_bounds(this.track.get("data_manage= r").get_genome_wide_data(this.genome));if(this.data_bounds[0]<m[0]||this.da= ta_bounds[1]>m[1]){this._transition_chrom_data()}},_render_data:function(p)= {var o=3Dthis,n=3Dthis.chroms_layout,m=3Dthis.track,q=3D$.Deferred();$.when= (m.get("data_manager").get_genome_wide_data(this.genome)).then(function(s){= o.data_bounds=3Do.get_data_bounds(s);layout_and_data=3Dg.zip(n,s),chroms_da= ta_layout=3Dg.map(layout_and_data,function(t){var u=3Dt[0],v=3Dt[1];return = o._render_chrom_data(p,u,v)});var r=3Do.get_fill_color();o.parent_elt.selec= tAll("path.chrom-data").style("stroke",r).style("fill",r);q.resolve(p)});re= turn q},_render_chrom_data:function(m,n,o){},_get_path_function:function(n,= m){},_chroms_layout:function(){var n=3Dthis.genome.get_chroms_info(),p=3Dk.= layout.pie().value(function(r){return r.len}).sort(null),q=3Dp(n),m=3Dthis.= total_gap/n.length,o=3Dg.map(q,function(t,s){var r=3Dt.endAngle-m;t.endAngl= e=3D(r>t.startAngle?r:t.startAngle);return t});return o}});var b=3Dj.extend= ({initialize:function(m){j.prototype.initialize.call(this,m);this.bg_stroke= =3D"fff";this.bg_fill=3D"fff"},_render_data:function(n){var m=3Dn.selectAll= ("g");m.selectAll("path").attr("id",function(o){return"label-"+o.data.chrom= });m.append("svg:text").filter(function(o){return o.endAngle-o.startAngle>0= .08}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href"= ,function(o){return"#label-"+o.data.chrom}).attr("startOffset","25%").text(= function(o){return o.data.chrom})}});var f=3Dj.extend({_render_chrom_data:f= unction(m,p,n){var q=3Dthis._get_path_function(p,n);if(!q){return null}var = o=3Dm.datum(n.data),r=3Do.append("path").attr("class","chrom-data").attr("c= hrom",p.data.chrom).attr("d",q);return r},_get_path_function:function(p,o){= if(typeof o=3D=3D=3D"string"||!o.data||o.data.length=3D=3D=3D0){return null= }var m=3Dk.scale.linear().domain(this.data_bounds).range(this.radius_bounds= );var q=3Dk.scale.linear().domain([0,o.data.length]).range([p.startAngle,p.= endAngle]);var n=3Dk.svg.line.radial().interpolate("linear").radius(functio= n(r){return m(r[1])}).angle(function(s,r){return q(r)});return k.svg.area.r= adial().interpolate(n.interpolate()).innerRadius(m(0)).outerRadius(n.radius= ()).angle(n.angle())},get_data_bounds:function(m){}});var e=3Df.extend({get= _data_bounds:function(n){var m=3Dg.map(n,function(o){if(typeof o=3D=3D=3D"s= tring"||!o.max){return 0}return o.max});return[0,(m&&typeof m!=3D=3D"string= "?g.max(m):0)]}});var d=3Df.extend({get_data_bounds:function(n){var m=3Dg.f= latten(g.map(n,function(o){if(o){return g.map(o.data,function(q){return q[1= ]})}else{return 0}}));return[g.min(m),g.max(m)]}});var i=3Dj.extend({render= :function(){var m=3Dthis;$.when(m.track.get("data_manager").data_is_ready()= ).then(function(){$.when(m.track.get("data_manager").get_genome_wide_data(m= .genome)).then(function(p){var o=3D[],n=3Dm.genome.get_chroms_info();g.each= (p,function(t,s){var q=3Dn[s].chrom;var r=3Dg.map(t.data,function(v){var u= =3Dm._get_region_angle(q,v[1]),w=3Dm._get_region_angle(v[3],v[4]);return{so= 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-define(["../libs/underscore","../mvc/base-mvc","../utils/LazyDataLoader","= ../templates/compiled/template-visualization-scatterplotControlForm","../te= mplates/compiled/template-visualization-statsTable","../templates/compiled/= template-visualization-chartSettings","../libs/d3","../libs/bootstrap","../= libs/jquery/jquery-ui-1.8.23.custom.min"],function(){function a(f){var d=3D= 10,h=3D7,g=3D10,e=3D8,c=3D5;this.log=3Dfunction(){if(this.debugging&&consol= e&&console.debug){var i=3DArray.prototype.slice.call(arguments);i.unshift(t= his.toString());console.debug.apply(console,i)}};this.log("new TwoVarScatte= rplot:",f);this.defaults=3D{id:"TwoVarScatterplot",containerSelector:"body"= ,maxDataPoints:30000,datapointSize:4,animDuration:500,xNumTicks:10,yNumTick= s:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:= 50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:nu= ll,yMax:null,xLabel:"X",yLabel:"Y"};this.config=3D_.extend({},this.defaults= 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X).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transf= orm",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).= text(this.config.yLabel)};this.renderGrid=3Dfunction(){this.vGridLines=3Dth= is.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisF= n.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-lin= e v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).at= tr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().r= emove();this.hGridLines=3Dthis.content.selectAll("line.h-grid-line").data(t= his.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("= svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",= 0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScal= e);this.hGridLines.exit().remove()};this.glyphEnterState=3Dfunction(i){};th= is.glyphFinalState=3Dfunction(i){};this.glyphExitState=3Dfunction(i){};this= 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apiDatasetsURL")}else{this.dataURL=3Dc.apiDatasetsURL+"/"+this.dataset.id+"= ?"}this.log("this.dataURL:",this.dataURL)},initializeChart:function(c){this= .chartConfig=3Dc.chartConfig||{};if(this.logger){this.chartConfig.debugging= =3Dtrue}this.log("initial chartConfig:",this.chartConfig);this.plot=3Dnew a= (this.chartConfig);this.chartConfig=3Dthis.plot.config},initializeDataLoade= r:function(d){var c=3Dthis;this.loader=3Dnew LazyDataLoader({logger:(this.l= ogger)?(this.logger):(null),url:null,start:d.start||0,total:d.total||this.d= ataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,= buildUrl:function(f,e){return this.url+"&"+jQuery.param({start_val:f,max_va= ls:e})}});$(this.loader).bind("error",function(g,e,f){c.log("ERROR:",e,f);a= lert("ERROR fetching data:\n"+e+"\n"+f);c.hideLoadingIndicator()})},render:= function(){var c=3Dthis,d=3D{config:this.chartConfig,allColumns:[],numericC= olumns:[],loadingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this= .loadingIndicatorImage};_.each(this.dataset.metadata_column_types,function(= g,f){var e=3D"column "+(f+1);if(c.dataset.metadata_column_names){e=3Dc.data= set.metadata_column_names[f]}if(g=3D=3D=3D"int"||g=3D=3D=3D"float"){d.numer= icColumns.push({index:f,name:e})}d.allColumns.push({index:f,name:e})});this= .$el.append(b.templates.form(d));this.$dataSettingsPanel=3Dthis.$el.find(".= tab-pane#data-settings");this.$chartSettingsPanel=3Dthis._render_chartSetti= ngs();this.$statsPanel=3Dthis.$el.find(".tab-pane#chart-stats");return this= },_render_chartSettings:function(){var c=3Dthis,d=3Dthis.$el.find(".tab-pan= e#chart-settings"),e=3D{datapointSize:{min:2,max:10,step:1},width:{min:200,= max:800,step:20},height:{min:200,max:800,step:20}};d.append(b.templates.cha= rtSettings(this.chartConfig));d.find(".numeric-slider-input").each(function= (){var h=3D$(this),g=3Dh.find(".slider-output"),i=3Dh.find(".slider"),j=3Dh= .attr("id");function f(){var l=3D$(this),k=3Dl.slider("value");g.text(k)}i.= slider(_.extend(e[j],{value:c.chartConfig[j],change:f,slide:f}))});return d= },events:{"click #include-id-checkbox":"toggleThirdColumnSelector","click #= data-settings #render-button":"renderPlot","click #chart-settings #render-b= utton":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el= .find('select[name=3D"ID"]').parent().toggle()},showLoadingIndicator:functi= on(d,e){d=3Dd||"";var c=3Dthis.$el.find("div#loading-indicator");messageBox= =3Dc.find(".loading-message");if(c.is(":visible")){if(d){messageBox.fadeOut= ("fast",function(){messageBox.text(d);messageBox.fadeIn("fast",e)})}else{e(= )}}else{if(d){messageBox.text(d)}c.fadeIn("fast",e)}},hideLoadingIndicator:= function(c){this.$el.find("div#loading-indicator").fadeOut("fast",c)},rende= rPlot:function(){var c=3Dthis;c.data=3Dnull;c.meta=3Dnull;_.extend(this.cha= rtConfig,this.getGraphSettings());this.log("this.chartConfig:",this.chartCo= nfig);this.plot.updateConfig(this.chartConfig,false);this.loader.url=3Dthis= .dataURL+"&"+jQuery.param(this.getDataSettings());this.log("this.loader, ur= l:",this.loader.url,"total:",this.loader.total);$(this.loader).bind("loaded= .new",function(e,d){c.log(c+" loaded.new",d);c.postProcessDataFetchResponse= (d);c.log("postprocessed data:",c.data,"meta:",c.meta);c.showLoadingIndicat= or("Rendering...",function(){c.$el.find("ul.nav").find('a[href=3D"#chart-st= ats"]').tab("show");c.plot.render(c.data,c.meta);c.renderStats(c.data,c.met= a);c.hideLoadingIndicator()})});$(this.loader).bind("complete",function(d,e= ){c.log("complete",e);$(c.loader).unbind()});c.showLoadingIndicator("Fetchi= ng data...",function(){c.loader.load()})},renderStats:function(){this.$stat= sPanel.html(b.templates.statsTable({stats:[{name:"Count",xval:this.meta[0].= count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.= meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name= :"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.= meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].media= n,yval:this.meta[1].median}]}))},changeChartSettings:function(){var c=3Dthi= s;newGraphSettings=3Dthis.getGraphSettings();this.log("newGraphSettings:",n= ewGraphSettings);_.extend(this.chartConfig,newGraphSettings);this.log("this= .chartConfig:",this.chartConfig);this.plot.updateConfig(this.chartConfig,fa= lse);if(c.data&&c.meta){c.showLoadingIndicator("Rendering...",function(){c.= plot.render(c.data,c.meta);c.hideLoadingIndicator()})}else{this.renderPlot(= )}},postProcessDataFetchResponse:function(c){this.postProcessData(c.data);t= his.postProcessMeta(c.meta)},postProcessData:function(d){var c=3Dthis;if(c.= data){_.each(d,function(f,e){c.data[e]=3Dc.data[e].concat(f)})}else{c.data= =3Dd}},postProcessMeta:function(e){var c=3Dthis,d=3Dthis.dataset.metadata_c= olumn_types;if(c.meta){_.each(e,function(g,f){var k=3Dc.meta[f],i=3Dd[f];c.= log(f+" postprocessing meta:",g);k.count+=3D(g.count)?(g.count):(0);c.log(f= ,"count:",k.count);if((i=3D=3D=3D"int")||(i=3D=3D=3D"float")){k.min=3DMath.= min(g.min,k.min);k.max=3DMath.max(g.max,k.max);k.sum=3Dg.sum+k.sum;k.mean= =3D(k.count)?(k.sum/k.count):(null);var h=3Dc.data[f].slice().sort(),j=3DMa= th.floor(h.length/2);if(h.length%2=3D=3D=3D0){k.median=3D((h[j]+h[(j+1)])/2= )}else{k.median=3Dh[j]}}})}else{c.meta=3De;c.log("initial meta:",c.meta)}},= getDataSettings:function(){var d=3Dthis.getColumnSelections(),c=3D[];this.l= og("columnSelections:",d);c=3D[d.X.colIndex,d.Y.colIndex];if(this.$dataSett= ingsPanel.find("#include-id-checkbox").attr("checked")){c.push(d.ID.colInde= x)}var e=3D{data_type:"raw_data",columns:"["+c+"]"};this.log("params:",e);r= eturn e},getColumnSelections:function(){var c=3D{};this.$dataSettingsPanel.= find("div.column-select select").each(function(){var d=3D$(this),e=3Dd.val(= );c[d.attr("name")]=3D{colIndex:e,colName:d.children('[value=3D"'+e+'"]').t= ext()}});return c},getGraphSettings:function(){var e=3D{},f=3Dthis.getColum= nSelections();e.datapointSize=3Dthis.$chartSettingsPanel.find("#datapointSi= ze.numeric-slider-input").find(".slider").slider("value");e.width=3Dthis.$c= hartSettingsPanel.find("#width.numeric-slider-input").find(".slider").slide= r("value");e.height=3Dthis.$chartSettingsPanel.find("#height.numeric-slider= -input").find(".slider").slider("value");var d=3Dthis.$chartSettingsPanel.f= ind("input#X-axis-label").val(),c=3Dthis.$chartSettingsPanel.find("input#Y-= axis-label").val();e.xLabel=3D(d=3D=3D=3D"X")?(f.X.colName):(d);e.yLabel=3D= (c=3D=3D=3D"Y")?(f.Y.colName):(c);e.animDuration=3D10;if(this.$chartSetting= sPanel.find("#animDuration.checkbox-input").is(":checked")){e.animDuration= =3D500}this.log("graphSettings:",e);return e},toString:function(){return"Sc= atterplotControlForm("+this.dataset.id+")"}});b.templates=3D{form:Handlebar= s.templates["template-visualization-scatterplotControlForm"],statsTable:Han= dlebars.templates["template-visualization-statsTable"],chartSettings:Handle= bars.templates["template-visualization-chartSettings"]};return{LazyDataLoad= er:LazyDataLoader,TwoVarScatterplot:a,ScatterplotControlForm:b}}); \ No newline at end of file +define(["../libs/underscore","../mvc/base-mvc","../utils/LazyDataLoader","= ../templates/compiled/template-visualization-scatterplotControlForm","../te= mplates/compiled/template-visualization-statsTable","../templates/compiled/= template-visualization-chartSettings","../libs/d3","../libs/bootstrap","../= libs/jquery/jquery-ui"],function(){function a(f){var d=3D10,h=3D7,g=3D10,e= =3D8,c=3D5;this.log=3Dfunction(){if(this.debugging&&console&&console.debug)= {var i=3DArray.prototype.slice.call(arguments);i.unshift(this.toString());c= onsole.debug.apply(console,i)}};this.log("new TwoVarScatterplot:",f);this.d= efaults=3D{id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30= 000,datapointSize:4,animDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBu= mpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50= ,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLab= el:"X",yLabel:"Y"};this.config=3D_.extend({},this.defaults,f);this.updateCo= nfig=3Dfunction(i,j){_.extend(this.config,i)};this.toString=3Dfunction(){re= turn this.config.id};this.translateStr=3Dfunction(i,j){return"translate("+i= +","+j+")"};this.rotateStr=3Dfunction(j,i,k){return"rotate("+j+","+i+","+k+= ")"};this.svg=3Dd3.select(this.config.containerSelector).append("svg:svg").= attr("class","chart");this.content=3Dthis.svg.append("svg:g").attr("class",= "content").attr("id",this.config.id);this.xAxis=3Dthis.content.append("g").= attr("class","axis").attr("id","x-axis");this.xAxisLabel=3Dthis.xAxis.appen= d("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis= =3Dthis.content.append("g").attr("class","axis").attr("id","y-axis");this.y= AxisLabel=3Dthis.yAxis.append("text").attr("class","axis-label").attr("id",= "y-axis-label");this.adjustChartDimensions=3Dfunction(l,j,i,k){l=3Dl||0;j= =3Dj||0;i=3Di||0;k=3Dk||0;this.svg.attr("width",this.config.width+(this.con= fig.marginRight+j)+(this.config.marginLeft+k)).attr("height",this.config.he= ight+(this.config.marginTop+l)+(this.config.marginBottom+i)).style("display= ","block");this.content=3Dthis.svg.select("g.content").attr("transform",thi= s.translateStr(this.config.marginLeft+k,this.config.marginTop+l))};this.pre= processData=3Dfunction(k,j,i){return(k.length>this.config.maxDataPoints)?(k= .slice(0,this.config.maxDataPoints)):(k)};this.setUpDomains=3Dfunction(i,k,= j){this.xMin=3Dthis.config.xMin||(j)?(j[0].min):(d3.min(i));this.xMax=3Dthi= s.config.xMax||(j)?(j[0].max):(d3.max(i));this.yMin=3Dthis.config.yMin||(j)= ?(j[1].min):(d3.min(k));this.yMax=3Dthis.config.yMax||(j)?(j[1].max):(d3.ma= x(k))};this.setUpScales=3Dfunction(){this.xScale=3Dd3.scale.linear().domain= ([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=3Dd3.scale= .linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this= .setUpXAxis=3Dfunction(){this.xAxisFn=3Dd3.svg.axis().scale(this.xScale).ti= cks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",thi= s.translateStr(0,this.config.height)).call(this.xAxisFn);this.xLongestLabel= =3Dd3.max(_.map([this.xMin,this.xMax],function(i){return(String(i)).length}= ));if(this.xLongestLabel>=3Dc){this.xAxis.selectAll("g").filter(":nth-child= (odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/= 2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(= this.config.xLabel)};this.setUpYAxis=3Dfunction(){this.yAxisFn=3Dd3.svg.axi= s().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAx= is.call(this.yAxisFn);var i=3Dthis.yAxis.selectAll("text").filter(function(= m,l){return l!=3D=3D0});this.yLongestLabel=3Dd3.max(i[0].map(function(m,l){= return(d3.select(m).text()).length}))||0;var j=3Dd+(this.yLongestLabel*h)+e= +g;this.config.yAxisLabelBumpX=3D-(j-g);if(this.config.marginLeft<j){var k= =3D(j)-this.config.marginLeft;k=3D(k<0)?(0):(k);this.adjustChartDimensions(= 0,0,0,k)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",thi= s.config.height/2).attr("text-anchor","middle").attr("transform",this.rotat= eStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.confi= g.yLabel)};this.renderGrid=3Dfunction(){this.vGridLines=3Dthis.content.sele= ctAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));= this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",= true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xS= cale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hG= ridLines=3Dthis.content.selectAll("line.h-grid-line").data(this.yScale.tick= s(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").clas= sed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",th= is.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLi= nes.exit().remove()};this.glyphEnterState=3Dfunction(i){};this.glyphFinalSt= ate=3Dfunction(i){};this.glyphExitState=3Dfunction(i){};this.renderDatapoin= ts=3Dfunction(i,l,j){this.log(this+".renderDatapoints",arguments);var k=3D0= ;this.datapoints=3Dthis.addDatapoints(i,l,j,".glyph");this.datapoints.exit(= ).each(function(){k+=3D1}).transition().duration(this.config.animDuration).= attr("cy",this.config.height).attr("r",0).remove();this.log(k," glyphs remo= ved")};this.addDatapoints=3Dfunction(m,k,i,l){this.log(this+".addDatapoints= ",arguments);var p=3Dthis,o=3D0,q=3Dfunction(s,r){return p.xScale(m[r])},j= =3Dfunction(s,r){return p.yScale(k[r])};var n=3Dthis.content.selectAll(l);t= his.log("existing datapoints:",n);n=3Dn.data(m);o=3D0;n.enter().append("svg= :circle").each(function(){o+=3D1}).classed("glyph",true).attr("cx",q).attr(= "cy",j).attr("r",0);this.log(o," new glyphs created");o=3D0;n.transition().= duration(this.config.animDuration).each(function(){o+=3D1}).attr("cx",q).at= tr("cy",j).attr("r",p.config.datapointSize);this.log(o," existing glyphs tr= ansitioned");if(i){n.attr("data",function(s,r){return(i[r])})}n.attr("title= ",function(s,r){return((i)?(i[r]+": "):(""))+m[r]+", "+k[r]});n.on("mouseov= er",function(){var r=3Dd3.select(this);r.style("fill","red").style("fill-op= acity",1);p.content.append("line").attr("stroke","red").attr("stroke-width"= ,1).attr("x1",r.attr("cx")).attr("y1",r.attr("cy")).attr("x2",0).attr("y2",= r.attr("cy")).classed("hoverline",true);p.content.append("line").attr("stro= ke","red").attr("stroke-width",1).attr("x1",r.attr("cx")).attr("y1",r.attr(= "cy")).attr("x2",r.attr("cx")).attr("y2",p.config.height).classed("hoverlin= e",true)}).on("mouseout",function(){d3.select(this).style("fill","black").s= tyle("fill-opacity",0.2);d3.selectAll(".hoverline").remove()});return n};th= is.render=3Dfunction(k,l){this.log(this+".render",arguments);var i=3Dk[0],m= =3Dk[1],j=3D(k.length>2)?(k[2]):(undefined);i=3Dthis.preprocessData(i);m=3D= this.preprocessData(m);this.log("xCol len",i.length,"yCol len",m.length);th= is.setUpDomains(i,m,l);this.setUpScales();this.adjustChartDimensions();this= .setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(i,m= ,j)}}var b=3DBaseView.extend(LoggableMixin).extend({className:"scatterplot-= settings-form",dataLoadDelay:500,dataLoadSize:3001,loadingIndicatorImage:"l= oading_large_white_bg.gif",initialize:function(c){if(this.logger){window.fo= rm=3Dthis}this.dataset=3Dnull;this.chartConfig=3Dnull;this.plot=3Dnull;this= .loader=3Dnull;this.$statsPanel=3Dnull;this.$chartSettingsPanel=3Dnull;this= .$dataSettingsPanel=3Dnull;this.dataFetch=3Dnull;this.initializeFromAttribu= tes(c);this.initializeChart(c);this.initializeDataLoader(c)},initializeFrom= Attributes:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires = a dataset")}else{this.dataset=3Dc.dataset}if(jQuery.type(this.dataset.metad= ata_column_types)=3D=3D=3D"string"){this.dataset.metadata_column_types=3Dth= is.dataset.metadata_column_types.split(", ")}this.log("dataset:",this.datas= et);if(!c.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL= ")}else{this.dataURL=3Dc.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("t= his.dataURL:",this.dataURL)},initializeChart:function(c){this.chartConfig= =3Dc.chartConfig||{};if(this.logger){this.chartConfig.debugging=3Dtrue}this= .log("initial chartConfig:",this.chartConfig);this.plot=3Dnew a(this.chartC= onfig);this.chartConfig=3Dthis.plot.config},initializeDataLoader:function(d= ){var c=3Dthis;this.loader=3Dnew LazyDataLoader({logger:(this.logger)?(this= .logger):(null),url:null,start:d.start||0,total:d.total||this.dataset.metad= ata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:fun= ction(f,e){return this.url+"&"+jQuery.param({start_val:f,max_vals:e})}});$(= this.loader).bind("error",function(g,e,f){c.log("ERROR:",e,f);alert("ERROR = fetching data:\n"+e+"\n"+f);c.hideLoadingIndicator()})},render:function(){v= ar c=3Dthis,d=3D{config:this.chartConfig,allColumns:[],numericColumns:[],lo= adingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this.loadingIndi= catorImage};_.each(this.dataset.metadata_column_types,function(g,f){var e= =3D"column "+(f+1);if(c.dataset.metadata_column_names){e=3Dc.dataset.metada= ta_column_names[f]}if(g=3D=3D=3D"int"||g=3D=3D=3D"float"){d.numericColumns.= push({index:f,name:e})}d.allColumns.push({index:f,name:e})});this.$el.appen= d(b.templates.form(d));this.$dataSettingsPanel=3Dthis.$el.find(".tab-pane#d= ata-settings");this.$chartSettingsPanel=3Dthis._render_chartSettings();this= .$statsPanel=3Dthis.$el.find(".tab-pane#chart-stats");return this},_render_= chartSettings:function(){var c=3Dthis,d=3Dthis.$el.find(".tab-pane#chart-se= ttings"),e=3D{datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,st= ep:20},height:{min:200,max:800,step:20}};d.append(b.templates.chartSettings= (this.chartConfig));d.find(".numeric-slider-input").each(function(){var h= =3D$(this),g=3Dh.find(".slider-output"),i=3Dh.find(".slider"),j=3Dh.attr("i= d");function f(){var l=3D$(this),k=3Dl.slider("value");g.text(k)}i.slider(_= .extend(e[j],{value:c.chartConfig[j],change:f,slide:f}))});return d},events= :{"click #include-id-checkbox":"toggleThirdColumnSelector","click #data-set= tings #render-button":"renderPlot","click #chart-settings #render-button":"= changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('s= elect[name=3D"ID"]').parent().toggle()},showLoadingIndicator:function(d,e){= d=3Dd||"";var c=3Dthis.$el.find("div#loading-indicator");messageBox=3Dc.fin= d(".loading-message");if(c.is(":visible")){if(d){messageBox.fadeOut("fast",= function(){messageBox.text(d);messageBox.fadeIn("fast",e)})}else{e()}}else{= if(d){messageBox.text(d)}c.fadeIn("fast",e)}},hideLoadingIndicator:function= (c){this.$el.find("div#loading-indicator").fadeOut("fast",c)},renderPlot:fu= nction(){var c=3Dthis;c.data=3Dnull;c.meta=3Dnull;_.extend(this.chartConfig= ,this.getGraphSettings());this.log("this.chartConfig:",this.chartConfig);th= is.plot.updateConfig(this.chartConfig,false);this.loader.url=3Dthis.dataURL= +"&"+jQuery.param(this.getDataSettings());this.log("this.loader, url:",this= .loader.url,"total:",this.loader.total);$(this.loader).bind("loaded.new",fu= nction(e,d){c.log(c+" loaded.new",d);c.postProcessDataFetchResponse(d);c.lo= g("postprocessed data:",c.data,"meta:",c.meta);c.showLoadingIndicator("Rend= ering...",function(){c.$el.find("ul.nav").find('a[href=3D"#chart-stats"]').= tab("show");c.plot.render(c.data,c.meta);c.renderStats(c.data,c.meta);c.hid= eLoadingIndicator()})});$(this.loader).bind("complete",function(d,e){c.log(= "complete",e);$(c.loader).unbind()});c.showLoadingIndicator("Fetching data.= ..",function(){c.loader.load()})},renderStats:function(){this.$statsPanel.h= tml(b.templates.statsTable({stats:[{name:"Count",xval:this.meta[0].count,yv= al:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].= min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",x= val:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].= mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:t= his.meta[1].median}]}))},changeChartSettings:function(){var c=3Dthis;newGra= phSettings=3Dthis.getGraphSettings();this.log("newGraphSettings:",newGraphS= ettings);_.extend(this.chartConfig,newGraphSettings);this.log("this.chartCo= nfig:",this.chartConfig);this.plot.updateConfig(this.chartConfig,false);if(= c.data&&c.meta){c.showLoadingIndicator("Rendering...",function(){c.plot.ren= der(c.data,c.meta);c.hideLoadingIndicator()})}else{this.renderPlot()}},post= ProcessDataFetchResponse:function(c){this.postProcessData(c.data);this.post= ProcessMeta(c.meta)},postProcessData:function(d){var c=3Dthis;if(c.data){_.= each(d,function(f,e){c.data[e]=3Dc.data[e].concat(f)})}else{c.data=3Dd}},po= stProcessMeta:function(e){var c=3Dthis,d=3Dthis.dataset.metadata_column_typ= es;if(c.meta){_.each(e,function(g,f){var k=3Dc.meta[f],i=3Dd[f];c.log(f+" p= ostprocessing meta:",g);k.count+=3D(g.count)?(g.count):(0);c.log(f,"count:"= ,k.count);if((i=3D=3D=3D"int")||(i=3D=3D=3D"float")){k.min=3DMath.min(g.min= ,k.min);k.max=3DMath.max(g.max,k.max);k.sum=3Dg.sum+k.sum;k.mean=3D(k.count= )?(k.sum/k.count):(null);var h=3Dc.data[f].slice().sort(),j=3DMath.floor(h.= length/2);if(h.length%2=3D=3D=3D0){k.median=3D((h[j]+h[(j+1)])/2)}else{k.me= dian=3Dh[j]}}})}else{c.meta=3De;c.log("initial meta:",c.meta)}},getDataSett= ings:function(){var d=3Dthis.getColumnSelections(),c=3D[];this.log("columnS= elections:",d);c=3D[d.X.colIndex,d.Y.colIndex];if(this.$dataSettingsPanel.f= ind("#include-id-checkbox").attr("checked")){c.push(d.ID.colIndex)}var e=3D= {data_type:"raw_data",columns:"["+c+"]"};this.log("params:",e);return e},ge= tColumnSelections:function(){var c=3D{};this.$dataSettingsPanel.find("div.c= olumn-select select").each(function(){var d=3D$(this),e=3Dd.val();c[d.attr(= "name")]=3D{colIndex:e,colName:d.children('[value=3D"'+e+'"]').text()}});re= turn c},getGraphSettings:function(){var e=3D{},f=3Dthis.getColumnSelections= ();e.datapointSize=3Dthis.$chartSettingsPanel.find("#datapointSize.numeric-= slider-input").find(".slider").slider("value");e.width=3Dthis.$chartSetting= sPanel.find("#width.numeric-slider-input").find(".slider").slider("value");= e.height=3Dthis.$chartSettingsPanel.find("#height.numeric-slider-input").fi= nd(".slider").slider("value");var d=3Dthis.$chartSettingsPanel.find("input#= X-axis-label").val(),c=3Dthis.$chartSettingsPanel.find("input#Y-axis-label"= ).val();e.xLabel=3D(d=3D=3D=3D"X")?(f.X.colName):(d);e.yLabel=3D(c=3D=3D=3D= "Y")?(f.Y.colName):(c);e.animDuration=3D10;if(this.$chartSettingsPanel.find= ("#animDuration.checkbox-input").is(":checked")){e.animDuration=3D500}this.= log("graphSettings:",e);return e},toString:function(){return"ScatterplotCon= trolForm("+this.dataset.id+")"}});b.templates=3D{form:Handlebars.templates[= "template-visualization-scatterplotControlForm"],statsTable:Handlebars.temp= lates["template-visualization-statsTable"],chartSettings:Handlebars.templat= es["template-visualization-chartSettings"]};return{LazyDataLoader:LazyDataL= oader,TwoVarScatterplot:a,ScatterplotControlForm:b}}); \ No newline at end of file diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/viz/trackster/painters.js --- a/static/scripts/packed/viz/trackster/painters.js +++ b/static/scripts/packed/viz/trackster/painters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(_){var extend=3D_.extend;var BEFORE=3D= 1001,CONTAINS=3D1002,OVERLAP_START=3D1003,OVERLAP_END=3D1004,CONTAINED_BY= =3D1005,AFTER=3D1006;var compute_overlap=3Dfunction(first_region,second_reg= ion){var first_start=3Dfirst_region[0],first_end=3Dfirst_region[1],second_s= tart=3Dsecond_region[0],second_end=3Dsecond_region[1],overlap;if(first_star= t<second_start){if(first_end<second_start){overlap=3DBEFORE}else{if(first_e= nd<=3Dsecond_end){overlap=3DOVERLAP_START}else{overlap=3DCONTAINS}}}else{if= (first_start>second_end){overlap=3DAFTER}else{if(first_end<=3Dsecond_end){o= verlap=3DCONTAINED_BY}else{overlap=3DOVERLAP_END}}}return overlap};var is_o= verlap=3Dfunction(first_region,second_region){var overlap=3Dcompute_overlap= (first_region,second_region);return(overlap!=3D=3DBEFORE&&overlap!=3D=3DAFT= ER)};var dashedLine=3Dfunction(ctx,x1,y1,x2,y2,dashLen){if(dashLen=3D=3D=3D= undefined){dashLen=3D4}var dX=3Dx2-x1;var dY=3Dy2-y1;var dashes=3DMath.floo= r(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=3DdX/dashes;var dashY=3DdY/dash= es;var q;for(q=3D0;q<dashes;q++,x1+=3DdashX,y1+=3DdashY){if(q%2!=3D=3D0){co= ntinue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle= =3Dfunction(ctx,down_vertex_x,down_vertex_y,side_len){var x1=3Ddown_vertex_= x-side_len/2,x2=3Ddown_vertex_x+side_len/2,y=3Ddown_vertex_y-Math.sqrt(side= _len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down= _vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=3Dthis.fillStyle;= ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=3Dfunction(default_val)= {this.default_val=3D(default_val?default_val:1)};Scaler.prototype.gen_val= =3Dfunction(input){return this.default_val};var Painter=3Dfunction(data,vie= w_start,view_end,prefs,mode){this.data=3Ddata;this.view_start=3Dview_start;= this.view_end=3Dview_end;this.prefs=3Dextend({},this.default_prefs,prefs);t= his.mode=3Dmode};Painter.prototype.default_prefs=3D{};Painter.prototype.dra= w=3Dfunction(ctx,width,height,w_scale){};var SummaryTreePainter=3Dfunction(= data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view= _end,prefs,mode)};SummaryTreePainter.prototype.default_prefs=3D{show_counts= :false};SummaryTreePainter.prototype.draw=3Dfunction(ctx,width,height,w_sca= le){var view_start=3Dthis.view_start,points=3Dthis.data.data,max=3D(this.pr= efs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=3Dheight;d= elta_x_px=3DMath.ceil(this.data.delta*w_scale);ctx.save();for(var i=3D0,len= =3Dpoints.length;i<len;i++){var x=3DMath.floor((points[i][0]-view_start)*w_= scale);var y=3Dpoints[i][1];if(!y){continue}var y_px=3Dy/max*height;if(y!= =3D=3D0&&y_px<1){y_px=3D1}ctx.fillStyle=3Dthis.prefs.block_color;ctx.fillRe= ct(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=3D4;if(this.prefs.= show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.= fillStyle=3Dthis.prefs.label_color;ctx.textAlign=3D"center";ctx.fillText(y,= x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=3Dfunction(data,view_s= tart,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,= mode);var i,len;if(this.prefs.min_value=3D=3D=3Dundefined){var min_value=3D= Infinity;for(i=3D0,len=3Dthis.data.length;i<len;i++){min_value=3DMath.min(m= in_value,this.data[i][1])}this.prefs.min_value=3Dmin_value}if(this.prefs.ma= x_value=3D=3D=3Dundefined){var max_value=3D-Infinity;for(i=3D0,len=3Dthis.d= ata.length;i<len;i++){max_value=3DMath.max(max_value,this.data[i][1])}this.= prefs.max_value=3Dmax_value}};LinePainter.prototype.default_prefs=3D{min_va= lue:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_co= lor:"#F66"};LinePainter.prototype.draw=3Dfunction(ctx,width,height,w_scale)= {var in_path=3Dfalse,min_value=3Dthis.prefs.min_value,max_value=3Dthis.pref= s.max_value,vertical_range=3Dmax_value-min_value,height_px=3Dheight,view_st= art=3Dthis.view_start,mode=3Dthis.mode,data=3Dthis.data;ctx.save();var y_ze= ro=3DMath.round(height+min_value/vertical_range*height);if(mode!=3D=3D"Inte= nsity"){ctx.fillStyle=3D"#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath= ();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=3DMath.ceil((data= [1][0]-data[0][0])*w_scale)}else{delta_x_px=3D10}var pref_color=3DparseInt(= this.prefs.color.slice(1),16),pref_r=3D(pref_color&16711680)>>16,pref_g=3D(= pref_color&65280)>>8,pref_b=3Dpref_color&255;for(var i=3D0,len=3Ddata.lengt= h;i<len;i++){ctx.fillStyle=3Dctx.strokeStyle=3Dthis.prefs.color;x_scaled=3D= Math.round((data[i][0]-view_start-1)*w_scale);y=3Ddata[i][1];var top_overfl= ow=3Dfalse,bot_overflow=3Dfalse;if(y=3D=3D=3Dnull){if(in_path&&mode=3D=3D= =3D"Filled"){ctx.lineTo(x_scaled,height_px)}in_path=3Dfalse;continue}if(y<m= in_value){bot_overflow=3Dtrue;y=3Dmin_value}else{if(y>max_value){top_overfl= ow=3Dtrue;y=3Dmax_value}}if(mode=3D=3D=3D"Histogram"){y=3DMath.round(y/vert= ical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(m= ode=3D=3D=3D"Intensity"){var saturation=3D(y-min_value)/vertical_range,new_= r=3DMath.round(pref_r+(255-pref_r)*(1-saturation)),new_g=3DMath.round(pref_= g+(255-pref_g)*(1-saturation)),new_b=3DMath.round(pref_b+(255-pref_b)*(1-sa= turation));ctx.fillStyle=3D"rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRec= t(x_scaled,0,delta_x_px,height_px)}else{y=3DMath.round(height_px-(y-min_val= ue)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_pa= th=3Dtrue;if(mode=3D=3D=3D"Filled"){ctx.moveTo(x_scaled,height_px);ctx.line= To(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=3Dthis.prefs.ov= erflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode=3D=3D=3D= "Histogram"||mode=3D=3D=3D"Intensity"){overflow_x=3Ddelta_x_px}else{x_scale= d-=3D2;overflow_x=3D4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3= )}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fil= lStyle=3Dthis.prefs.color}if(mode=3D=3D=3D"Filled"){if(in_path){ctx.lineTo(= x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.rest= ore()};var FeaturePositionMapper=3Dfunction(slot_height){this.feature_posit= ions=3D{};this.slot_height=3Dslot_height;this.translation=3D0;this.y_transl= ation=3D0};FeaturePositionMapper.prototype.map_feature_data=3Dfunction(feat= ure_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature= _positions[slot]=3D[]}this.feature_positions[slot].push({data:feature_data,= x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_= data=3Dfunction(x,y){var slot=3DMath.floor((y-this.y_translation)/this.slot= _height),feature_dict;if(!this.feature_positions[slot]){return null}x+=3Dth= is.translation;for(var i=3D0;i<this.feature_positions[slot].length;i++){fea= ture_dict=3Dthis.feature_positions[slot][i];if(x>=3Dfeature_dict.x_start&&x= <=3Dfeature_dict.x_end){return feature_dict.data}}};var FeaturePainter=3Dfu= nction(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Pain= ter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=3D(alp= ha_scaler?alpha_scaler:new Scaler());this.height_scaler=3D(height_scaler?he= ight_scaler:new Scaler())};FeaturePainter.prototype.default_prefs=3D{block_= color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_r= equired_height:function(rows_required,width){var required_height=3Dthis.get= _row_height(),y_scale=3Drequired_height,mode=3Dthis.mode;if(mode=3D=3D=3D"n= o_detail"||mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Pack"){required_height=3Dro= ws_required*y_scale}return required_height+this.get_top_padding(width)+this= .get_bottom_padding(width)},get_top_padding:function(width){return 0},get_b= ottom_padding:function(width){return Math.max(Math.round(this.get_row_heigh= t()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=3Dthis.da= ta,view_start=3Dthis.view_start,view_end=3Dthis.view_end;ctx.save();ctx.fil= lStyle=3Dthis.prefs.block_color;ctx.textAlign=3D"right";var y_scale=3Dthis.= get_row_height(),feature_mapper=3Dnew FeaturePositionMapper(y_scale),x_draw= _coords;for(var i=3D0,len=3Ddata.length;i<len;i++){var feature=3Ddata[i],fe= ature_uid=3Dfeature[0],feature_start=3Dfeature[1],feature_end=3Dfeature[2],= slot=3D(slots&&slots[feature_uid]!=3D=3Dundefined?slots[feature_uid]:null);= if((feature_start<view_end&&feature_end>view_start)&&(this.mode=3D=3D=3D"De= nse"||slot!=3D=3Dnull)){x_draw_coords=3Dthis.draw_element(ctx,this.mode,fea= ture,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_fea= ture_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();fe= ature_mapper.y_translation=3Dthis.get_top_padding(width);return feature_map= per},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale= ,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]= }});var DENSE_TRACK_HEIGHT=3D10,NO_DETAIL_TRACK_HEIGHT=3D3,SQUISH_TRACK_HEI= GHT=3D5,PACK_TRACK_HEIGHT=3D10,NO_DETAIL_FEATURE_HEIGHT=3D1,DENSE_FEATURE_H= EIGHT=3D9,SQUISH_FEATURE_HEIGHT=3D3,PACK_FEATURE_HEIGHT=3D9,LABEL_SPACING= =3D2,CONNECTOR_COLOR=3D"#ccc";var LinkedFeaturePainter=3Dfunction(data,view= _start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(= this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.d= raw_background_connector=3Dtrue;this.draw_individual_connectors=3Dfalse};ex= tend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_heigh= t:function(){var mode=3Dthis.mode,height;if(mode=3D=3D=3D"Dense"){height=3D= DENSE_TRACK_HEIGHT}else{if(mode=3D=3D=3D"no_detail"){height=3DNO_DETAIL_TRA= CK_HEIGHT}else{if(mode=3D=3D=3D"Squish"){height=3DSQUISH_TRACK_HEIGHT}else{= height=3DPACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,= feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=3Dfe= ature[0],feature_start=3Dfeature[1],feature_end=3Dfeature[2]-1,feature_name= =3Dfeature[3],feature_strand=3Dfeature[4],f_start=3DMath.floor(Math.max(0,(= feature_start-tile_low)*w_scale)),f_end=3DMath.ceil(Math.min(width,Math.max= (0,(feature_end-tile_low)*w_scale))),draw_start=3Df_start,draw_end=3Df_end,= y_center=3D(mode=3D=3D=3D"Dense"?0:(0+slot))*y_scale+this.get_top_padding(w= idth),thickness,y_start,thick_start=3Dnull,thick_end=3Dnull,block_color=3D(= !feature_strand||feature_strand=3D=3D=3D"+"||feature_strand=3D=3D=3D"."?thi= s.prefs.block_color:this.prefs.reverse_strand_color);label_color=3Dthis.pre= fs.label_color;ctx.globalAlpha=3Dthis.alpha_scaler.gen_val(feature);if(mode= =3D=3D=3D"Dense"){slot=3D1}if(mode=3D=3D=3D"no_detail"){ctx.fillStyle=3Dblo= ck_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HE= IGHT)}else{var feature_ts=3Dfeature[5],feature_te=3Dfeature[6],feature_bloc= ks=3Dfeature[7],full_height=3Dtrue;if(feature_ts&&feature_te){thick_start= =3DMath.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=3DMath.c= eil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_hei= ght,thick_height;if(mode=3D=3D=3D"Squish"){thin_height=3D1;thick_height=3DS= QUISH_FEATURE_HEIGHT;full_height=3Dfalse}else{if(mode=3D=3D=3D"Dense"){thin= _height=3D5;thick_height=3DDENSE_FEATURE_HEIGHT}else{thin_height=3D5;thick_= height=3DPACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=3Dblock_col= or;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_s= trand&&full_height){if(feature_strand=3D=3D=3D"+"){ctx.fillStyle=3Dctx.canv= as.manager.get_pattern("right_strand_inv")}else{if(feature_strand=3D=3D=3D"= -"){ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.= fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_cen= ter,cur_height;if(mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Dense"){cur_y_center= =3Dy_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=3D1}else{if(fe= ature_strand){cur_y_center=3Dy_center;cur_height=3Dthick_height}else{cur_y_= center+=3D(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=3D1}}if(this.draw_backgrou= nd_connector){if(mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Dense"){ctx.fillStyle= =3DCONNECTOR_COLOR}else{if(feature_strand){if(feature_strand=3D=3D=3D"+"){c= tx.fillStyle=3Dctx.canvas.manager.get_pattern("right_strand")}else{if(featu= re_strand=3D=3D=3D"-"){ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left= _strand")}}}else{ctx.fillStyle=3DCONNECTOR_COLOR}}ctx.fillRect(f_start,cur_= y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=3D0,k_len= =3Dfeature_blocks.length;k<k_len;k++){var block=3Dfeature_blocks[k],block_s= tart=3DMath.floor(Math.max(0,(block[0]-tile_low)*w_scale)),block_end=3DMath= .ceil(Math.min(width,Math.max((block[1]-1-tile_low)*w_scale))),last_block_s= tart,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=3Dbloc= k_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,bl= ock_end-block_start,thin_height);if(thick_start!=3D=3Dundefined&&feature_te= >feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thi= ck_start=3DMath.max(block_start,thick_start),block_thick_end=3DMath.min(blo= ck_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end= -block_thick_start,thick_height);if(feature_blocks.length=3D=3D=3D1&&mode= =3D=3D=3D"Pack"){if(feature_strand=3D=3D=3D"+"){ctx.fillStyle=3Dctx.canvas.= manager.get_pattern("right_strand_inv")}else{if(feature_strand=3D=3D=3D"-")= {ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left_strand_inv")}}if(bloc= k_thick_start+14<block_thick_end){block_thick_start+=3D2;block_thick_end-= =3D2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_= start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){= this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_e= nd,y_center)}last_block_start=3Dblock_start;last_block_end=3Dblock_end}if(m= ode=3D=3D=3D"Pack"){ctx.globalAlpha=3D1;ctx.fillStyle=3D"white";var hscale_= factor=3Dthis.height_scaler.gen_val(feature),new_height=3DMath.ceil(thick_h= eight*hscale_factor),ws_height=3DMath.round((thick_height-new_height)/2);if= (hscale_factor!=3D=3D1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,w= s_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-= f_start,ws_height)}}}ctx.globalAlpha=3D1;if(feature_name&&mode=3D=3D=3D"Pac= k"&&feature_start>tile_low){ctx.fillStyle=3Dlabel_color;if(tile_low=3D=3D= =3D0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign=3D"left"= ;ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=3Dctx.= measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign=3D"right";= ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=3Dc= tx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=3D1;retu= rn[draw_start,draw_end]}});var ReadPainter=3Dfunction(data,view_start,view_= end,prefs,mode,alpha_scaler,height_scaler,ref_seq){FeaturePainter.call(this= ,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_s= eq=3D(ref_seq?ref_seq.data:null)};extend(ReadPainter.prototype,FeaturePaint= er.prototype,{get_row_height:function(){var height,mode=3Dthis.mode;if(mode= =3D=3D=3D"Dense"){height=3DDENSE_TRACK_HEIGHT}else{if(mode=3D=3D=3D"Squish"= ){height=3DSQUISH_TRACK_HEIGHT}else{height=3DPACK_TRACK_HEIGHT;if(this.pref= s.show_insertions){height*=3D2}}}return height},draw_read:function(ctx,mode= ,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,ref_seq){ct= x.textAlign=3D"center";var tile_region=3D[tile_low,tile_high],base_offset= =3D0,seq_offset=3D0,gap=3D0,char_width_px=3Dctx.canvas.manager.char_width_p= x,block_color=3D(strand=3D=3D=3D"+"?this.prefs.block_color:this.prefs.rever= se_strand_color);var draw_last=3D[];if((mode=3D=3D=3D"Pack"||this.mode=3D= =3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w_scale>char_width_px){gap=3DMath.r= ound(w_scale/2)}if(!cigar){cigar=3D[[0,ref_seq.length]]}for(var cig_id=3D0,= len=3Dcigar.length;cig_id<len;cig_id++){var cig=3Dcigar[cig_id],cig_op=3D"M= IDNSHP=3DX"[cig[0]],cig_len=3Dcig[1];if(cig_op=3D=3D=3D"H"||cig_op=3D=3D=3D= "S"){base_offset-=3Dcig_len}var seq_start=3D(feature_start-1)+base_offset,s= _start=3DMath.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=3DMath.= floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start=3D=3D=3D= s_end){s_end+=3D1}switch(cig_op){case"H":break;case"S":case"M":case"=3D":if= (is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=3Dref_seq.s= lice(seq_offset-1,seq_offset+cig_len);if(gap>0){ctx.fillStyle=3Dblock_color= ;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=3DCONNE= CTOR_COLOR;for(var c=3D0,str_len=3Dseq.length;c<str_len;c++){if(this.prefs.= show_differences){if(this.ref_seq){var ref_char=3Dthis.ref_seq[seq_start-ti= le_low+c];if(!ref_char||ref_char.toLowerCase()=3D=3D=3Dseq[c].toLowerCase()= ){continue}}else{continue}}if(seq_start+c>=3Dtile_low&&seq_start+c<=3Dtile_= high){var c_start=3DMath.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));= ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=3Dblock_color;= ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_o= ffset+=3Dcig_len;base_offset+=3Dcig_len;break;case"N":ctx.fillStyle=3DCONNE= CTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset= +=3Dcig_len;break;case"D":ctx.fillStyle=3D"red";ctx.fillRect(s_start-gap,y_= center+4,s_end-s_start,3);base_offset+=3Dcig_len;break;case"P":break;case"I= ":var insert_x_coord=3Ds_start-gap;if(is_overlap([seq_start,seq_start+cig_l= en],tile_region)){var seq=3Dref_seq.slice(seq_offset-1,seq_offset+cig_len);= if(this.prefs.show_insertions){var x_center=3Ds_start-(s_end-s_start)/2;if(= (mode=3D=3D=3D"Pack"||this.mode=3D=3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w= _scale>char_width_px){ctx.fillStyle=3D"yellow";ctx.fillRect(x_center-gap,y_= center-9,s_end-s_start,9);draw_last[draw_last.length]=3D{type:"triangle",da= ta:[insert_x_coord,y_center+4,5]};ctx.fillStyle=3DCONNECTOR_COLOR;switch(co= mpute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_STA= RT):seq=3Dseq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=3Dseq.= slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS= ):seq=3Dseq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c= =3D0,str_len=3Dseq.length;c<str_len;c++){var c_start=3DMath.floor(Math.max(= 0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_sta= rt)/2,y_center)}}else{ctx.fillStyle=3D"yellow";ctx.fillRect(x_center,y_cent= er+(this.mode!=3D=3D"Dense"?2:5),s_end-s_start,(mode!=3D=3D"Dense"?SQUISH_F= EATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode=3D=3D=3D"Pack"||this.mo= de=3D=3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w_scale>char_width_px){draw_la= st.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}= seq_offset+=3Dcig_len;break;case"X":seq_offset+=3Dcig_len;break}}ctx.fillSt= yle=3D"yellow";var item,type,data;for(var i=3D0;i<draw_last.length;i++){ite= m=3Ddraw_last[i];type=3Ditem.type;data=3Ditem.data;if(type=3D=3D=3D"text"){= ctx.save();ctx.font=3D"bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]= );ctx.restore()}else{if(type=3D=3D=3D"triangle"){drawDownwardEquilateralTri= angle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,featu= re,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=3Dfeature= [0],feature_start=3Dfeature[1],feature_end=3Dfeature[2],feature_name=3Dfeat= ure[3],f_start=3DMath.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f= _end=3DMath.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))= ),y_center=3D(mode=3D=3D=3D"Dense"?0:(0+slot))*y_scale,label_color=3Dthis.p= refs.label_color,gap=3D0;if((mode=3D=3D=3D"Pack"||this.mode=3D=3D=3D"Auto")= &&w_scale>ctx.canvas.manager.char_width_px){var gap=3DMath.round(w_scale/2)= }if(feature[5] instanceof Array){var b1_start=3DMath.floor(Math.max(0,(feat= ure[4][0]-tile_low)*w_scale)),b1_end=3DMath.ceil(Math.min(width,Math.max(0,= (feature[4][1]-tile_low)*w_scale))),b2_start=3DMath.floor(Math.max(0,(featu= re[5][0]-tile_low)*w_scale)),b2_end=3DMath.ceil(Math.min(width,Math.max(0,(= feature[5][1]-tile_low)*w_scale))),connector=3Dtrue;if(feature[4][1]>=3Dtil= e_low&&feature[4][0]<=3Dtile_high&&feature[4][2]){this.draw_read(ctx,mode,w= _scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3= ],feature[4][4])}else{connector=3Dfalse}if(feature[5][1]>=3Dtile_low&&featu= re[5][0]<=3Dtile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_cen= ter,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5]= [4])}else{connector=3Dfalse}if(connector&&b2_start>b1_end){ctx.fillStyle=3D= CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+= 5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,featur= e_start,feature[4],feature[5],feature[6])}if(mode=3D=3D=3D"Pack"&&feature_s= tart>tile_low&&feature_name!=3D=3D"."){ctx.fillStyle=3Dthis.prefs.label_col= or;var tile_index=3D1;if(tile_index=3D=3D=3D0&&f_start-ctx.measureText(feat= ure_name).width<0){ctx.textAlign=3D"left";ctx.fillText(feature_name,f_end+L= ABEL_SPACING-gap,y_center+8)}else{ctx.textAlign=3D"right";ctx.fillText(feat= ure_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});var ArcLinke= dFeaturePainter=3Dfunction(data,view_start,view_end,prefs,mode,alpha_scaler= ,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,pre= fs,mode,alpha_scaler,height_scaler);this.longest_feature_length=3Dthis.calc= ulate_longest_feature_length();this.draw_background_connector=3Dfalse;this.= draw_individual_connectors=3Dtrue};extend(ArcLinkedFeaturePainter.prototype= ,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest= _feature_length:function(){var longest_feature_length=3D0;for(var i=3D0,len= =3Dthis.data.length;i<len;i++){var feature=3Dthis.data[i],feature_start=3Df= eature[1],feature_end=3Dfeature[2];longest_feature_length=3DMath.max(longes= t_feature_length,feature_end-feature_start)}return longest_feature_length},= get_top_padding:function(width){var view_range=3Dthis.view_end-this.view_st= art,w_scale=3Dwidth/view_range;return Math.min(128,Math.ceil((this.longest_= feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block= 1_end,block2_start,block2_end,y_center){var x_center=3D(block1_end+block2_s= tart)/2,radius=3Dblock2_start-x_center;var angle1=3DMath.PI,angle2=3D0;if(r= adius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Ma= th.PI,0);ctx.stroke()}}});var Color=3Dfunction(rgb,a){if(Array.isArray(rgb)= ){this.rgb=3Drgb}else{if(rgb.length=3D=3D6){this.rgb=3Drgb.match(/.{2}/g).m= ap(function(c){return parseInt(c,16)})}else{this.rgb=3Drgb.split("").map(fu= nction(c){return parseInt(c+c,16)})}}this.alpha=3Dtypeof(a)=3D=3D=3D"number= "?a:1};Color.prototype=3D{eval:function(){return this},toCSS:function(){if(= this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)})= .concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){= i=3DMath.round(i);i=3D(i>255?255:(i<0?0:i)).toString(16);return i.length=3D= =3D=3D1?"0"+i:i}).join("")}},toHSL:function(){var r=3Dthis.rgb[0]/255,g=3Dt= his.rgb[1]/255,b=3Dthis.rgb[2]/255,a=3Dthis.alpha;var max=3DMath.max(r,g,b)= ,min=3DMath.min(r,g,b);var h,s,l=3D(max+min)/2,d=3Dmax-min;if(max=3D=3D=3Dm= in){h=3Ds=3D0}else{s=3Dl>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h= =3D(g-b)/d+(g<b?6:0);break;case g:h=3D(b-r)/d+2;break;case b:h=3D(r-g)/d+4;= break}h/=3D6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=3D[Mat= h.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i= =3DMath.round(i);i=3D(i>255?255:(i<0?0:i)).toString(16);return i.length=3D= =3D=3D1?"0"+i:i}).join("")},mix:function(color2,weight){color1=3Dthis;var p= =3Dweight;var w=3Dp*2-1;var a=3Dcolor1.toHSL().a-color2.toHSL().a;var w1=3D= (((w*a=3D=3D-1)?w:(w+a)/(1+w*a))+1)/2;var w2=3D1-w1;var rgb=3D[color1.rgb[0= ]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+co= lor2.rgb[2]*w2];var alpha=3Dcolor1.alpha*p+color2.alpha*(1-p);return new Co= lor(rgb,alpha)}};var LinearRamp=3Dfunction(start_color,end_color,start_valu= e,end_value){this.start_color=3Dnew Color(start_color);this.end_color=3Dnew= Color(end_color);this.start_value=3Dstart_value;this.end_value=3Dend_value= ;this.value_range=3Dend_value-start_value};LinearRamp.prototype.map_value= =3Dfunction(value){value=3DMath.max(value,this.start_value);value=3DMath.mi= n(value,this.end_value);value=3D(value-this.start_value)/this.value_range;r= eturn this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp= =3Dfunction(start_color,middle_color,end_color,start_value,end_value){this.= positive_ramp=3Dnew LinearRamp(middle_color,end_color,0,end_value);this.neg= ative_ramp=3Dnew LinearRamp(middle_color,start_color,0,-start_value);this.s= tart_value=3Dstart_value;this.end_value=3Dend_value};SplitRamp.prototype.ma= p_value=3Dfunction(value){value=3DMath.max(value,this.start_value);value=3D= Math.min(value,this.end_value);if(value>=3D0){return this.positive_ramp.map= _value(value)}else{return this.negative_ramp.map_value(-value)}};var Diagon= alHeatmapPainter=3Dfunction(data,view_start,view_end,prefs,mode){Painter.ca= ll(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_va= lue=3D=3D=3Dundefined){var min_value=3DInfinity;for(i=3D0,len=3Dthis.data.l= ength;i<len;i++){min_value=3DMath.min(min_value,this.data[i][5])}this.prefs= .min_value=3Dmin_value}if(this.prefs.max_value=3D=3D=3Dundefined){var max_v= alue=3D-Infinity;for(i=3D0,len=3Dthis.data.length;i<len;i++){max_value=3DMa= th.max(max_value,this.data[i][5])}this.prefs.max_value=3Dmax_value}};Diagon= alHeatmapPainter.prototype.default_prefs=3D{min_value:undefined,max_value:u= ndefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHe= atmapPainter.prototype.draw=3Dfunction(ctx,width,height,w_scale){var min_va= lue=3Dthis.prefs.min_value,max_value=3Dthis.prefs.max_value,value_range=3Dm= ax_value-min_value,height_px=3Dheight,view_start=3Dthis.view_start,mode=3Dt= his.mode,data=3Dthis.data,invsqrt2=3D1/Math.sqrt(2);var ramp=3D(new SplitRa= mp(this.prefs.neg_color,"FFFFFF",this.prefs.pos_color,min_value,max_value))= ;var d,s1,e1,s2,e2,value;var scale=3Dfunction(p){return(p-view_start)*w_sca= le};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for= (var i=3D0,len=3Ddata.length;i<len;i++){d=3Ddata[i];s1=3Dscale(d[1]);e1=3Ds= cale(d[2]);s2=3Dscale(d[4]);e2=3Dscale(d[5]);value=3Dd[6];ctx.fillStyle=3D(= ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};r= eturn{Scaler:Scaler,SummaryTreePainter:SummaryTreePainter,LinePainter:LineP= ainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,Ar= cLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:Diagon= alHeatmapPainter}}); \ No newline at end of file +define(["libs/underscore"],function(_){var extend=3D_.extend;var BEFORE=3D= 1001,CONTAINS=3D1002,OVERLAP_START=3D1003,OVERLAP_END=3D1004,CONTAINED_BY= =3D1005,AFTER=3D1006;var compute_overlap=3Dfunction(first_region,second_reg= ion){var first_start=3Dfirst_region[0],first_end=3Dfirst_region[1],second_s= tart=3Dsecond_region[0],second_end=3Dsecond_region[1],overlap;if(first_star= t<second_start){if(first_end<second_start){overlap=3DBEFORE}else{if(first_e= nd<=3Dsecond_end){overlap=3DOVERLAP_START}else{overlap=3DCONTAINS}}}else{if= (first_start>second_end){overlap=3DAFTER}else{if(first_end<=3Dsecond_end){o= verlap=3DCONTAINED_BY}else{overlap=3DOVERLAP_END}}}return overlap};var is_o= verlap=3Dfunction(first_region,second_region){var overlap=3Dcompute_overlap= (first_region,second_region);return(overlap!=3D=3DBEFORE&&overlap!=3D=3DAFT= ER)};var dashedLine=3Dfunction(ctx,x1,y1,x2,y2,dashLen){if(dashLen=3D=3D=3D= undefined){dashLen=3D4}var dX=3Dx2-x1;var dY=3Dy2-y1;var dashes=3DMath.floo= r(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=3DdX/dashes;var dashY=3DdY/dash= es;var q;for(q=3D0;q<dashes;q++,x1+=3DdashX,y1+=3DdashY){if(q%2!=3D=3D0){co= ntinue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle= =3Dfunction(ctx,down_vertex_x,down_vertex_y,side_len){var x1=3Ddown_vertex_= x-side_len/2,x2=3Ddown_vertex_x+side_len/2,y=3Ddown_vertex_y-Math.sqrt(side= _len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down= _vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=3Dthis.fillStyle;= ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=3Dfunction(default_val)= {this.default_val=3D(default_val?default_val:1)};Scaler.prototype.gen_val= =3Dfunction(input){return this.default_val};var Painter=3Dfunction(data,vie= w_start,view_end,prefs,mode){this.data=3Ddata;this.view_start=3Dview_start;= this.view_end=3Dview_end;this.prefs=3Dextend({},this.default_prefs,prefs);t= his.mode=3Dmode};Painter.prototype.default_prefs=3D{};Painter.prototype.dra= w=3Dfunction(ctx,width,height,w_scale){};var SummaryTreePainter=3Dfunction(= data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view= _end,prefs,mode)};SummaryTreePainter.prototype.default_prefs=3D{show_counts= :false};SummaryTreePainter.prototype.draw=3Dfunction(ctx,width,height,w_sca= le){var view_start=3Dthis.view_start,points=3Dthis.data.data,max=3D(this.pr= efs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=3Dheight;d= elta_x_px=3DMath.ceil(this.data.delta*w_scale);ctx.save();for(var i=3D0,len= =3Dpoints.length;i<len;i++){var x=3DMath.floor((points[i][0]-view_start)*w_= scale);var y=3Dpoints[i][1];if(!y){continue}var y_px=3Dy/max*height;if(y!= =3D=3D0&&y_px<1){y_px=3D1}ctx.fillStyle=3Dthis.prefs.block_color;ctx.fillRe= ct(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=3D4;if(this.prefs.= show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.= fillStyle=3Dthis.prefs.label_color;ctx.textAlign=3D"center";ctx.fillText(y,= x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=3Dfunction(data,view_s= tart,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,= mode);var i,len;if(this.prefs.min_value=3D=3D=3Dundefined){var min_value=3D= Infinity;for(i=3D0,len=3Dthis.data.length;i<len;i++){min_value=3DMath.min(m= in_value,this.data[i][1])}this.prefs.min_value=3Dmin_value}if(this.prefs.ma= x_value=3D=3D=3Dundefined){var max_value=3D-Infinity;for(i=3D0,len=3Dthis.d= ata.length;i<len;i++){max_value=3DMath.max(max_value,this.data[i][1])}this.= prefs.max_value=3Dmax_value}};LinePainter.prototype.default_prefs=3D{min_va= lue:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_co= lor:"#F66"};LinePainter.prototype.draw=3Dfunction(ctx,width,height,w_scale)= {var in_path=3Dfalse,min_value=3Dthis.prefs.min_value,max_value=3Dthis.pref= s.max_value,vertical_range=3Dmax_value-min_value,height_px=3Dheight,view_st= art=3Dthis.view_start,mode=3Dthis.mode,data=3Dthis.data;ctx.save();var y_ze= ro=3DMath.round(height+min_value/vertical_range*height);if(mode!=3D=3D"Inte= nsity"){ctx.fillStyle=3D"#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath= ();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=3DMath.ceil((data= [1][0]-data[0][0])*w_scale)}else{delta_x_px=3D10}var pref_color=3DparseInt(= this.prefs.color.slice(1),16),pref_r=3D(pref_color&16711680)>>16,pref_g=3D(= pref_color&65280)>>8,pref_b=3Dpref_color&255;for(var i=3D0,len=3Ddata.lengt= h;i<len;i++){ctx.fillStyle=3Dctx.strokeStyle=3Dthis.prefs.color;x_scaled=3D= Math.round((data[i][0]-view_start-1)*w_scale);y=3Ddata[i][1];var top_overfl= ow=3Dfalse,bot_overflow=3Dfalse;if(y=3D=3D=3Dnull){if(in_path&&mode=3D=3D= =3D"Filled"){ctx.lineTo(x_scaled,height_px)}in_path=3Dfalse;continue}if(y<m= in_value){bot_overflow=3Dtrue;y=3Dmin_value}else{if(y>max_value){top_overfl= ow=3Dtrue;y=3Dmax_value}}if(mode=3D=3D=3D"Histogram"){y=3DMath.round(y/vert= ical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(m= ode=3D=3D=3D"Intensity"){var saturation=3D(y-min_value)/vertical_range,new_= r=3DMath.round(pref_r+(255-pref_r)*(1-saturation)),new_g=3DMath.round(pref_= g+(255-pref_g)*(1-saturation)),new_b=3DMath.round(pref_b+(255-pref_b)*(1-sa= turation));ctx.fillStyle=3D"rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRec= t(x_scaled,0,delta_x_px,height_px)}else{y=3DMath.round(height_px-(y-min_val= ue)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_pa= th=3Dtrue;if(mode=3D=3D=3D"Filled"){ctx.moveTo(x_scaled,height_px);ctx.line= To(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=3Dthis.prefs.ov= erflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode=3D=3D=3D= "Histogram"||mode=3D=3D=3D"Intensity"){overflow_x=3Ddelta_x_px}else{x_scale= d-=3D2;overflow_x=3D4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3= )}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fil= lStyle=3Dthis.prefs.color}if(mode=3D=3D=3D"Filled"){if(in_path){ctx.lineTo(= x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.rest= ore()};var FeaturePositionMapper=3Dfunction(slot_height){this.feature_posit= ions=3D{};this.slot_height=3Dslot_height;this.translation=3D0;this.y_transl= ation=3D0};FeaturePositionMapper.prototype.map_feature_data=3Dfunction(feat= ure_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature= _positions[slot]=3D[]}this.feature_positions[slot].push({data:feature_data,= x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_= data=3Dfunction(x,y){var slot=3DMath.floor((y-this.y_translation)/this.slot= _height),feature_dict;if(!this.feature_positions[slot]){return null}x+=3Dth= is.translation;for(var i=3D0;i<this.feature_positions[slot].length;i++){fea= ture_dict=3Dthis.feature_positions[slot][i];if(x>=3Dfeature_dict.x_start&&x= <=3Dfeature_dict.x_end){return feature_dict.data}}};var FeaturePainter=3Dfu= nction(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Pain= ter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=3D(alp= ha_scaler?alpha_scaler:new Scaler());this.height_scaler=3D(height_scaler?he= ight_scaler:new Scaler())};FeaturePainter.prototype.default_prefs=3D{block_= color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_r= equired_height:function(rows_required,width){var required_height=3Dthis.get= _row_height(),y_scale=3Drequired_height,mode=3Dthis.mode;if(mode=3D=3D=3D"n= o_detail"||mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Pack"){required_height=3Dro= ws_required*y_scale}return required_height+this.get_top_padding(width)+this= .get_bottom_padding(width)},get_top_padding:function(width){return 0},get_b= ottom_padding:function(width){return Math.max(Math.round(this.get_row_heigh= t()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=3Dthis.da= ta,view_start=3Dthis.view_start,view_end=3Dthis.view_end;ctx.save();ctx.fil= lStyle=3Dthis.prefs.block_color;ctx.textAlign=3D"right";var y_scale=3Dthis.= get_row_height(),feature_mapper=3Dnew FeaturePositionMapper(y_scale),x_draw= _coords;for(var i=3D0,len=3Ddata.length;i<len;i++){var feature=3Ddata[i],fe= ature_uid=3Dfeature[0],feature_start=3Dfeature[1],feature_end=3Dfeature[2],= slot=3D(slots&&slots[feature_uid]!=3D=3Dundefined?slots[feature_uid]:null);= if((feature_start<view_end&&feature_end>view_start)&&(this.mode=3D=3D=3D"De= nse"||slot!=3D=3Dnull)){x_draw_coords=3Dthis.draw_element(ctx,this.mode,fea= ture,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_fea= ture_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();fe= ature_mapper.y_translation=3Dthis.get_top_padding(width);return feature_map= per},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale= ,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]= }});var DENSE_TRACK_HEIGHT=3D10,NO_DETAIL_TRACK_HEIGHT=3D3,SQUISH_TRACK_HEI= GHT=3D5,PACK_TRACK_HEIGHT=3D10,NO_DETAIL_FEATURE_HEIGHT=3D1,DENSE_FEATURE_H= EIGHT=3D9,SQUISH_FEATURE_HEIGHT=3D3,PACK_FEATURE_HEIGHT=3D9,LABEL_SPACING= =3D2,CONNECTOR_COLOR=3D"#ccc";var LinkedFeaturePainter=3Dfunction(data,view= _start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(= this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.d= raw_background_connector=3Dtrue;this.draw_individual_connectors=3Dfalse};ex= tend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_heigh= t:function(){var mode=3Dthis.mode,height;if(mode=3D=3D=3D"Dense"){height=3D= DENSE_TRACK_HEIGHT}else{if(mode=3D=3D=3D"no_detail"){height=3DNO_DETAIL_TRA= CK_HEIGHT}else{if(mode=3D=3D=3D"Squish"){height=3DSQUISH_TRACK_HEIGHT}else{= height=3DPACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,= feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=3Dfe= ature[0],feature_start=3Dfeature[1],feature_end=3Dfeature[2]-1,feature_name= =3Dfeature[3],feature_strand=3Dfeature[4],f_start=3DMath.floor(Math.max(0,(= feature_start-tile_low)*w_scale)),f_end=3DMath.ceil(Math.min(width,Math.max= (0,(feature_end-tile_low)*w_scale))),draw_start=3Df_start,draw_end=3Df_end,= y_center=3D(mode=3D=3D=3D"Dense"?0:(0+slot))*y_scale+this.get_top_padding(w= idth),thickness,y_start,thick_start=3Dnull,thick_end=3Dnull,block_color=3D(= !feature_strand||feature_strand=3D=3D=3D"+"||feature_strand=3D=3D=3D"."?thi= s.prefs.block_color:this.prefs.reverse_strand_color);label_color=3Dthis.pre= fs.label_color;ctx.globalAlpha=3Dthis.alpha_scaler.gen_val(feature);if(mode= =3D=3D=3D"Dense"){slot=3D1}if(mode=3D=3D=3D"no_detail"){ctx.fillStyle=3Dblo= ck_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HE= IGHT)}else{var feature_ts=3Dfeature[5],feature_te=3Dfeature[6],feature_bloc= ks=3Dfeature[7],full_height=3Dtrue;if(feature_ts&&feature_te){thick_start= =3DMath.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=3DMath.c= eil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_hei= ght,thick_height;if(mode=3D=3D=3D"Squish"){thin_height=3D1;thick_height=3DS= QUISH_FEATURE_HEIGHT;full_height=3Dfalse}else{if(mode=3D=3D=3D"Dense"){thin= _height=3D5;thick_height=3DDENSE_FEATURE_HEIGHT}else{thin_height=3D5;thick_= height=3DPACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=3Dblock_col= or;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_s= trand&&full_height){if(feature_strand=3D=3D=3D"+"){ctx.fillStyle=3Dctx.canv= as.manager.get_pattern("right_strand_inv")}else{if(feature_strand=3D=3D=3D"= -"){ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.= fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_cen= ter,cur_height;if(mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Dense"){cur_y_center= =3Dy_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=3D1}else{if(fe= ature_strand){cur_y_center=3Dy_center;cur_height=3Dthick_height}else{cur_y_= center+=3D(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=3D1}}if(this.draw_backgrou= nd_connector){if(mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Dense"){ctx.fillStyle= =3DCONNECTOR_COLOR}else{if(feature_strand){if(feature_strand=3D=3D=3D"+"){c= tx.fillStyle=3Dctx.canvas.manager.get_pattern("right_strand")}else{if(featu= re_strand=3D=3D=3D"-"){ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left= _strand")}}}else{ctx.fillStyle=3DCONNECTOR_COLOR}}ctx.fillRect(f_start,cur_= y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=3D0,k_len= =3Dfeature_blocks.length;k<k_len;k++){var block=3Dfeature_blocks[k],block_s= tart=3DMath.floor(Math.max(0,(block[0]-tile_low)*w_scale)),block_end=3DMath= .ceil(Math.min(width,Math.max((block[1]-1-tile_low)*w_scale))),last_block_s= tart,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=3Dbloc= k_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,bl= ock_end-block_start,thin_height);if(thick_start!=3D=3Dundefined&&feature_te= >feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thi= ck_start=3DMath.max(block_start,thick_start),block_thick_end=3DMath.min(blo= ck_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end= -block_thick_start,thick_height);if(feature_blocks.length=3D=3D=3D1&&mode= =3D=3D=3D"Pack"){if(feature_strand=3D=3D=3D"+"){ctx.fillStyle=3Dctx.canvas.= manager.get_pattern("right_strand_inv")}else{if(feature_strand=3D=3D=3D"-")= {ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left_strand_inv")}}if(bloc= k_thick_start+14<block_thick_end){block_thick_start+=3D2;block_thick_end-= =3D2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_= start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){= this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_e= nd,y_center)}last_block_start=3Dblock_start;last_block_end=3Dblock_end}if(m= ode=3D=3D=3D"Pack"){ctx.globalAlpha=3D1;ctx.fillStyle=3D"white";var hscale_= factor=3Dthis.height_scaler.gen_val(feature),new_height=3DMath.ceil(thick_h= eight*hscale_factor),ws_height=3DMath.round((thick_height-new_height)/2);if= (hscale_factor!=3D=3D1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,w= s_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-= f_start,ws_height)}}}ctx.globalAlpha=3D1;if(feature_name&&mode=3D=3D=3D"Pac= k"&&feature_start>tile_low){ctx.fillStyle=3Dlabel_color;if(tile_low=3D=3D= =3D0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign=3D"left"= ;ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=3Dctx.= measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign=3D"right";= ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=3Dc= tx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=3D1;retu= rn[draw_start,draw_end]}});var ReadPainter=3Dfunction(data,view_start,view_= end,prefs,mode,alpha_scaler,height_scaler,ref_seq){FeaturePainter.call(this= ,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_s= eq=3D(ref_seq?ref_seq.data:null)};extend(ReadPainter.prototype,FeaturePaint= er.prototype,{get_row_height:function(){var height,mode=3Dthis.mode;if(mode= =3D=3D=3D"Dense"){height=3DDENSE_TRACK_HEIGHT}else{if(mode=3D=3D=3D"Squish"= ){height=3DSQUISH_TRACK_HEIGHT}else{height=3DPACK_TRACK_HEIGHT;if(this.pref= s.show_insertions){height*=3D2}}}return height},draw_read:function(ctx,mode= ,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,ref_seq){ct= x.textAlign=3D"center";var tile_region=3D[tile_low,tile_high],base_offset= =3D0,seq_offset=3D0,gap=3D0,char_width_px=3Dctx.canvas.manager.char_width_p= x,block_color=3D(strand=3D=3D=3D"+"?this.prefs.block_color:this.prefs.rever= se_strand_color);var draw_last=3D[];if((mode=3D=3D=3D"Pack"||this.mode=3D= =3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w_scale>char_width_px){gap=3DMath.r= ound(w_scale/2)}if(!cigar){cigar=3D[[0,ref_seq.length]]}for(var cig_id=3D0,= len=3Dcigar.length;cig_id<len;cig_id++){var cig=3Dcigar[cig_id],cig_op=3D"M= IDNSHP=3DX"[cig[0]],cig_len=3Dcig[1];if(cig_op=3D=3D=3D"H"||cig_op=3D=3D=3D= "S"){base_offset-=3Dcig_len}var seq_start=3D(feature_start-1)+base_offset,s= _start=3DMath.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=3DMath.= floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start=3D=3D=3D= s_end){s_end+=3D1}switch(cig_op){case"H":break;case"S":case"M":case"=3D":if= (is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=3Dref_seq.s= lice(seq_offset-1,seq_offset+cig_len);if(gap>0){ctx.fillStyle=3Dblock_color= ;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=3DCONNE= CTOR_COLOR;for(var c=3D0,str_len=3Dseq.length;c<str_len;c++){if(this.prefs.= show_differences){if(this.ref_seq){var ref_char=3Dthis.ref_seq[seq_start-ti= le_low+c];if(!ref_char||ref_char.toLowerCase()=3D=3D=3Dseq[c].toLowerCase()= ){continue}}else{continue}}if(seq_start+c>=3Dtile_low&&seq_start+c<=3Dtile_= high){var c_start=3DMath.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));= ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=3Dblock_color;= ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_o= ffset+=3Dcig_len;base_offset+=3Dcig_len;break;case"N":ctx.fillStyle=3DCONNE= CTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset= +=3Dcig_len;break;case"D":ctx.fillStyle=3D"red";ctx.fillRect(s_start-gap,y_= center+4,s_end-s_start,3);base_offset+=3Dcig_len;break;case"P":break;case"I= ":var insert_x_coord=3Ds_start-gap;if(is_overlap([seq_start,seq_start+cig_l= en],tile_region)){var seq=3Dref_seq.slice(seq_offset-1,seq_offset+cig_len);= if(this.prefs.show_insertions){var x_center=3Ds_start-(s_end-s_start)/2;if(= (mode=3D=3D=3D"Pack"||this.mode=3D=3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w= _scale>char_width_px){ctx.fillStyle=3D"yellow";ctx.fillRect(x_center-gap,y_= center-9,s_end-s_start,9);draw_last[draw_last.length]=3D{type:"triangle",da= ta:[insert_x_coord,y_center+4,5]};ctx.fillStyle=3DCONNECTOR_COLOR;switch(co= mpute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_STA= RT):seq=3Dseq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=3Dseq.= slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS= ):seq=3Dseq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c= =3D0,str_len=3Dseq.length;c<str_len;c++){var c_start=3DMath.floor(Math.max(= 0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_sta= rt)/2,y_center)}}else{ctx.fillStyle=3D"yellow";ctx.fillRect(x_center,y_cent= er+(this.mode!=3D=3D"Dense"?2:5),s_end-s_start,(mode!=3D=3D"Dense"?SQUISH_F= EATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode=3D=3D=3D"Pack"||this.mo= de=3D=3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w_scale>char_width_px){draw_la= st.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}= seq_offset+=3Dcig_len;break;case"X":seq_offset+=3Dcig_len;break}}ctx.fillSt= yle=3D"yellow";var item,type,data;for(var i=3D0;i<draw_last.length;i++){ite= m=3Ddraw_last[i];type=3Ditem.type;data=3Ditem.data;if(type=3D=3D=3D"text"){= ctx.save();ctx.font=3D"bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]= );ctx.restore()}else{if(type=3D=3D=3D"triangle"){drawDownwardEquilateralTri= angle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,featu= re,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=3Dfeature= [0],feature_start=3Dfeature[1],feature_end=3Dfeature[2],feature_name=3Dfeat= ure[3],f_start=3DMath.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f= _end=3DMath.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))= ),y_center=3D(mode=3D=3D=3D"Dense"?0:(0+slot))*y_scale,label_color=3Dthis.p= refs.label_color,gap=3D0;if((mode=3D=3D=3D"Pack"||this.mode=3D=3D=3D"Auto")= &&w_scale>ctx.canvas.manager.char_width_px){var gap=3DMath.round(w_scale/2)= }if(feature[5] instanceof Array){var b1_start=3DMath.floor(Math.max(0,(feat= ure[4][0]-tile_low)*w_scale)),b1_end=3DMath.ceil(Math.min(width,Math.max(0,= (feature[4][1]-tile_low)*w_scale))),b2_start=3DMath.floor(Math.max(0,(featu= re[5][0]-tile_low)*w_scale)),b2_end=3DMath.ceil(Math.min(width,Math.max(0,(= feature[5][1]-tile_low)*w_scale))),connector=3Dtrue;if(feature[4][1]>=3Dtil= e_low&&feature[4][0]<=3Dtile_high&&feature[4][2]){this.draw_read(ctx,mode,w= _scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3= ],feature[4][4])}else{connector=3Dfalse}if(feature[5][1]>=3Dtile_low&&featu= re[5][0]<=3Dtile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_cen= ter,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5]= [4])}else{connector=3Dfalse}if(connector&&b2_start>b1_end){ctx.fillStyle=3D= CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+= 5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,featur= e_start,feature[4],feature[5],feature[6])}if(mode=3D=3D=3D"Pack"&&feature_s= tart>tile_low&&feature_name!=3D=3D"."){ctx.fillStyle=3Dthis.prefs.label_col= or;var tile_index=3D1;if(tile_index=3D=3D=3D0&&f_start-ctx.measureText(feat= ure_name).width<0){ctx.textAlign=3D"left";ctx.fillText(feature_name,f_end+L= ABEL_SPACING-gap,y_center+8)}else{ctx.textAlign=3D"right";ctx.fillText(feat= ure_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});var ArcLinke= dFeaturePainter=3Dfunction(data,view_start,view_end,prefs,mode,alpha_scaler= ,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,pre= fs,mode,alpha_scaler,height_scaler);this.longest_feature_length=3Dthis.calc= ulate_longest_feature_length();this.draw_background_connector=3Dfalse;this.= draw_individual_connectors=3Dtrue};extend(ArcLinkedFeaturePainter.prototype= ,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest= _feature_length:function(){var longest_feature_length=3D0;for(var i=3D0,len= =3Dthis.data.length;i<len;i++){var feature=3Dthis.data[i],feature_start=3Df= eature[1],feature_end=3Dfeature[2];longest_feature_length=3DMath.max(longes= t_feature_length,feature_end-feature_start)}return longest_feature_length},= get_top_padding:function(width){var view_range=3Dthis.view_end-this.view_st= art,w_scale=3Dwidth/view_range;return Math.min(128,Math.ceil((this.longest_= feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block= 1_end,block2_start,block2_end,y_center){var x_center=3D(block1_end+block2_s= tart)/2,radius=3Dblock2_start-x_center;var angle1=3DMath.PI,angle2=3D0;if(r= adius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Ma= th.PI,0);ctx.stroke()}}});var Color=3Dfunction(rgb,a){if(Array.isArray(rgb)= ){this.rgb=3Drgb}else{if(rgb.length=3D=3D6){this.rgb=3Drgb.match(/.{2}/g).m= ap(function(c){return parseInt(c,16)})}else{if(rgb.length=3D=3D7){this.rgb= =3Drgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)}= )}else{this.rgb=3Drgb.split("").map(function(c){return parseInt(c+c,16)})}}= }this.alpha=3Dtypeof(a)=3D=3D=3D"number"?a:1};Color.prototype=3D{eval:funct= ion(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb= .map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}e= lse{return"#"+this.rgb.map(function(i){i=3DMath.round(i);i=3D(i>255?255:(i<= 0?0:i)).toString(16);return i.length=3D=3D=3D1?"0"+i:i}).join("")}},toHSL:f= unction(){var r=3Dthis.rgb[0]/255,g=3Dthis.rgb[1]/255,b=3Dthis.rgb[2]/255,a= =3Dthis.alpha;var max=3DMath.max(r,g,b),min=3DMath.min(r,g,b);var h,s,l=3D(= max+min)/2,d=3Dmax-min;if(max=3D=3D=3Dmin){h=3Ds=3D0}else{s=3Dl>0.5?d/(2-ma= x-min):d/(max+min);switch(max){case r:h=3D(g-b)/d+(g<b?6:0);break;case g:h= =3D(b-r)/d+2;break;case b:h=3D(r-g)/d+4;break}h/=3D6}return{h:h*360,s:s,l:l= ,a:a}},toARGB:function(){var argb=3D[Math.round(this.alpha*255)].concat(thi= s.rgb);return"#"+argb.map(function(i){i=3DMath.round(i);i=3D(i>255?255:(i<0= ?0:i)).toString(16);return i.length=3D=3D=3D1?"0"+i:i}).join("")},mix:funct= ion(color2,weight){color1=3Dthis;var p=3Dweight;var w=3Dp*2-1;var a=3Dcolor= 1.toHSL().a-color2.toHSL().a;var w1=3D(((w*a=3D=3D-1)?w:(w+a)/(1+w*a))+1)/2= ;var w2=3D1-w1;var rgb=3D[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w= 1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=3Dcolor1.al= pha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=3Dfun= ction(start_color,end_color,start_value,end_value){this.start_color=3Dnew C= olor(start_color);this.end_color=3Dnew Color(end_color);this.start_value=3D= start_value;this.end_value=3Dend_value;this.value_range=3Dend_value-start_v= alue};LinearRamp.prototype.map_value=3Dfunction(value){value=3DMath.max(val= ue,this.start_value);value=3DMath.min(value,this.end_value);value=3D(value-= this.start_value)/this.value_range;return this.start_color.mix(this.end_col= or,1-value).toCSS()};var SplitRamp=3Dfunction(start_color,middle_color,end_= color,start_value,end_value){this.positive_ramp=3Dnew LinearRamp(middle_col= or,end_color,0,end_value);this.negative_ramp=3Dnew LinearRamp(middle_color,= start_color,0,-start_value);this.start_value=3Dstart_value;this.end_value= =3Dend_value};SplitRamp.prototype.map_value=3Dfunction(value){value=3DMath.= max(value,this.start_value);value=3DMath.min(value,this.end_value);if(value= >=3D0){return this.positive_ramp.map_value(value)}else{return this.negative= _ramp.map_value(-value)}};var DiagonalHeatmapPainter=3Dfunction(data,view_s= tart,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,= mode);var i,len;if(this.prefs.min_value=3D=3D=3Dundefined){var min_value=3D= Infinity;for(i=3D0,len=3Dthis.data.length;i<len;i++){min_value=3DMath.min(m= in_value,this.data[i][5])}this.prefs.min_value=3Dmin_value}if(this.prefs.ma= x_value=3D=3D=3Dundefined){var max_value=3D-Infinity;for(i=3D0,len=3Dthis.d= ata.length;i<len;i++){max_value=3DMath.max(max_value,this.data[i][5])}this.= prefs.max_value=3Dmax_value}};DiagonalHeatmapPainter.prototype.default_pref= s=3D{min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8= C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=3Dfunction(= ctx,width,height,w_scale){var min_value=3Dthis.prefs.min_value,max_value=3D= this.prefs.max_value,value_range=3Dmax_value-min_value,height_px=3Dheight,v= iew_start=3Dthis.view_start,mode=3Dthis.mode,data=3Dthis.data,invsqrt2=3D1/= Math.sqrt(2);var ramp=3D(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.= prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=3Df= unction(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/= 180);ctx.scale(invsqrt2,invsqrt2);for(var i=3D0,len=3Ddata.length;i<len;i++= ){d=3Ddata[i];s1=3Dscale(d[1]);e1=3Dscale(d[2]);s2=3Dscale(d[4]);e2=3Dscale= (d[5]);value=3Dd[6];ctx.fillStyle=3D(ramp.map_value(value));ctx.fillRect(s1= ,s2,(e1-s1),(e2-s2))}ctx.restore()};return{Scaler:Scaler,SummaryTreePainter= :SummaryTreePainter,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeat= urePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeature= Painter,DiagonalHeatmapPainter:DiagonalHeatmapPainter}}); \ No newline at end of file diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/tr= ackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filter= s"],function(ab,x,l,u,L,Z,i){var q=3Dab.extend;var V=3Dfunction(ac){return(= "isResolved" in ac)};var n=3D{};var k=3Dfunction(ac,ad){n[ac.attr("id")]=3D= ad};var m=3Dfunction(ac,ae,ag,af){ag=3D".group";var ad=3D{};n[ac.attr("id")= ]=3Daf;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an= =3D$(this),at=3D$(this).parent(),ak=3Dat.children(),am=3Dn[$(this).attr("id= ")],aj,ai,aq,ah,al;ai=3D$(this).parents(ag);if(ai.length!=3D=3D0){aq=3Dai.p= osition().top;ah=3Daq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefo= re(ai);var ar=3Dn[ai.attr("id")];ar.remove_drawable(am);ar.container.add_dr= awable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);= var ar=3Dn[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(= am);return}}}ai=3Dnull;for(al=3D0;al<ak.length;al++){aj=3D$(ak.get(al));aq= =3Daj.position().top;ah=3Daq+aj.outerHeight();if(aj.is(ag)&&this!=3D=3Daj.g= et(0)&&ap.offsetY>=3Daq&&ap.offsetY<=3Dah){if(ap.offsetY-aq<ah-ap.offsetY){= aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(t= his)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add= _drawable(am);return}}for(al=3D0;al<ak.length;al++){aj=3D$(ak.get(al));if(a= p.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass(= "intro"))){break}}if(al=3D=3D=3Dak.length){if(this!=3D=3Dak.get(al-1)){at.a= ppend(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!=3D=3Dak.ge= t(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(= ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=3Dac= .css("border-top");ad["border-bottom"]=3Dac.css("border-bottom");$(this).cs= s({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind(= "dragend",function(){$(this).css(ad)})};exports.moveable=3Dm;var aa=3D16,G= =3D9,D=3D20,A=3D100,I=3D12000,S=3D400,K=3D5000,w=3D100,o=3D"There was an er= ror in indexing this dataset. ",J=3D"A converter for this dataset is not in= stalled. Please check your datatypes_conf.xml file.",E=3D"No data for this = chrom/contig.",v=3D"Preparing data. This can take a while for a large datas= et. If the visualization is saved and closed, preparation will continue in = the background.",y=3D"Tool cannot be rerun: ",a=3D"Loading data...",U=3D"Re= ady for display",Q=3D10,H=3D20;function W(ad,ac){if(!ac){ac=3D0}var ae=3DMa= th.pow(10,ac);return Math.round(ad*ae)/ae}var r=3Dfunction(ad,ac,af){if(!r.= id_counter){r.id_counter=3D0}this.id=3Dr.id_counter++;this.name=3Daf.name;t= his.view=3Dad;this.container=3Dac;this.config=3Dnew F({track:this,params:[{= key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:= af.prefs,onchange:function(){this.track.set_name(this.track.config.values.n= ame)}});this.prefs=3Dthis.config.values;this.drag_handle_class=3Daf.drag_ha= ndle_class;this.is_overview=3Dfalse;this.action_icons=3D{};this.content_vis= ible=3Dtrue;this.container_div=3Dthis.build_container_div();this.header_div= =3Dthis.build_header_div();if(this.header_div){this.container_div.append(th= is.header_div);this.icons_div=3D$("<div/>").css("float","left").hide().appe= ndTo(this.header_div);this.build_action_icons(this.action_icons_def);this.h= eader_div.append($("<div style=3D'clear: both'/>"));this.header_div.dblclic= k(function(ag){ag.stopPropagation()});var ae=3Dthis;this.container_div.hove= r(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div = style=3D'clear: both'/>").appendTo(this.container_div)}};r.prototype.action= _icons_def=3D[{name:"toggle_icon",title:"Hide/show content",css_class:"togg= le",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_= icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.= content_visible=3Dfalse}else{ac.action_icons.toggle_icon.addClass("toggle")= .removeClass("toggle-expand");ac.content_visible=3Dtrue;ac.show_contents()}= }},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on= _click_fn:function(ad){var af=3Dfunction(){hide_modal();$(window).unbind("k= eypress.check_enter_esc")},ac=3Dfunction(){ad.config.update_from_form($(".d= ialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae= =3Dfunction(ag){if((ag.keyCode||ag.which)=3D=3D=3D27){af()}else{if((ag.keyC= ode||ag.which)=3D=3D=3D13){ac()}}};$(window).bind("keypress.check_enter_esc= ",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{n= ame:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:functi= on(ac){$(".bs-tooltip").remove();ac.remove()}}];q(r.prototype,{init:functio= n(){},changed:function(){this.view.changed()},can_draw:function(){if(this.e= nabled&&this.content_visible){return true}return false},request_draw:functi= on(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.o= ld_name=3Dthis.name;this.name=3Dac;this.name_div.text(this.name)},revert_na= me:function(){if(this.old_name){this.name=3Dthis.old_name;this.name_div.tex= t(this.name)}},remove:function(){this.changed();this.container.remove_drawa= ble(this);var ac=3Dthis.view;this.container_div.hide(0,function(){$(this).r= emove();ac.update_intro_div()})},build_container_div:function(){},build_hea= der_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=3Dt= his;this.action_icons[ad]=3D$("<a/>").attr("href","javascript:void(0);").at= tr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(functio= n(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}}= ,build_action_icons:function(ac){var ae;for(var ad=3D0;ad<ac.length;ad++){a= e=3Dac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_f= n,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){= },show_contents:function(){},get_drawables:function(){}});var z=3Dfunction(= ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=3Dae.obj_type;this.drawables= =3D[]};q(z.prototype,r.prototype,{unpack_drawables:function(ae){this.drawab= les=3D[];var ad;for(var ac=3D0;ac<ae.length;ac++){ad=3Dp(ae[ac],this.view,t= his);this.add_drawable(ad)}},init:function(){for(var ac=3D0;ac<this.drawabl= es.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=3D0= ;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:functi= on(){var ad=3D[];for(var ac=3D0;ac<this.drawables.length;ac++){ad.push(this= .drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:t= his.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(a= c);ac.container=3Dthis;this.changed()},add_drawable_before:function(ae,ac){= this.changed();var ad=3Dthis.drawables.indexOf(ac);if(ad!=3D=3D-1){this.dra= wables.splice(ad,0,ae);return true}return false},replace_drawable:function(= ae,ac,ad){var af=3Dthis.drawables.indexOf(ae);if(af!=3D=3D-1){this.drawable= s[af]=3Dac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.chang= ed()}return af},remove_drawable:function(ad){var ac=3Dthis.drawables.indexO= f(ad);if(ac!=3D=3D-1){this.drawables.splice(ac,1);ad.container=3Dnull;this.= changed();return true}return false},move_drawable:function(ad,ae){var ac=3D= this.drawables.indexOf(ad);if(ac!=3D=3D-1){this.drawables.splice(ac,1);this= .drawables.splice(ae,0,ad);this.changed();return true}return false},get_dra= wables:function(){return this.drawables}});var P=3Dfunction(ad,ac,af){q(af,= {obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,ad= ,ac,af);this.content_div=3D$("<div/>").addClass("content-div").attr("id","g= roup_"+this.id+"_content_div").appendTo(this.container_div);k(this.containe= r_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_= class,".group",this);this.filters_manager=3Dnew i.FiltersManager(this);this= .header_div.after(this.filters_manager.parent_div);this.saved_filters_manag= ers=3D[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filt= ers" in af){var ae=3Dthis.filters_manager;this.filters_manager=3Dnew i.Filt= ersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.= parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P= .prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_ic= ons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Sh= ow composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".b= s-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title= :"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_= manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_ma= nagers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filt= ers_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div= :function(){var ac=3D$("<div/>").addClass("group").attr("id","group_"+this.= id);if(this.container){this.container.content_div.append(ac)}return ac},bui= ld_header_div:function(){var ac=3D$("<div/>").addClass("track-header");ac.a= ppend($("<div/>").addClass(this.drag_handle_class));this.name_div=3D$("<div= />").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_co= ntents:function(){this.tiles_div.hide()},show_contents:function(){this.tile= s_div.show();this.request_draw()},update_icons:function(){var ae=3Dthis.dra= wables.length;if(ae=3D=3D=3D0){this.action_icons.composite_icon.hide();this= .action_icons.filters_icon.hide()}else{if(ae=3D=3D=3D1){if(this.drawables[0= ] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.f= ilters_icon.hide()}else{var al,ak,ai,ao=3Dtrue,ag=3Dthis.drawables[0].get_t= ype(),ac=3D0;for(al=3D0;al<ae;al++){ai=3Dthis.drawables[al];if(ai.get_type(= )!=3D=3Dag){can_composite=3Dfalse;break}if(ai instanceof c){ac++}}if(ao||ac= =3D=3D=3D1){this.action_icons.composite_icon.show()}else{this.action_icons.= composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac=3D=3D=3Dthis.dr= awables.length){var ap=3D{},ad;ai=3Dthis.drawables[0];for(ak=3D0;ak<ai.filt= ers_manager.filters.length;ak++){ad=3Dai.filters_manager.filters[ak];ap[ad.= name]=3D[ad]}for(al=3D1;al<this.drawables.length;al++){ai=3Dthis.drawables[= al];for(ak=3D0;ak<ai.filters_manager.filters.length;ak++){ad=3Dai.filters_m= anager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_ma= nager.remove_all();var af,ah,aj,am;for(var an in ap){af=3Dap[an];if(af.leng= th=3D=3D=3Dac){ah=3Dnew i.NumberFilter({name:af[0].name,index:af[0].index})= ;this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.lengt= h>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_i= con.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_= managers:function(){for(var ac=3D0;ac<this.drawables.length;ac++){this.draw= ables[ac].filters_manager=3Dthis.saved_filters_managers[ac]}this.saved_filt= ers_managers=3D[]},setup_multitrack_filtering:function(){if(this.filters_ma= nager.filters.length>0){this.saved_filters_managers=3D[];for(var ac=3D0;ac<= this.drawables.length;ac++){drawable=3Dthis.drawables[ac];this.saved_filter= s_managers.push(drawable.filters_manager);drawable.filters_manager=3Dthis.f= ilters_manager}}this.filters_manager.init_filters()},show_composite_track:f= unction(){var ag=3D[];for(var ad=3D0;ad<this.drawables.length;ad++){ag.push= (this.drawables[ad].name)}var ae=3D"Composite Track of "+this.drawables.len= gth+" tracks ("+ag.join(", ")+")";var af=3Dnew f(this.view,this.view,{name:= ae,drawables:this.drawables});var ac=3Dthis.container.replace_drawable(this= ,af,true);af.request_draw()},add_drawable:function(ac){z.prototype.add_draw= able.call(this,ac);this.update_icons()},remove_drawable:function(ac){z.prot= otype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function()= {if(this.filters_manager.visible()){this._restore_filter_managers()}var ac= =3Dq(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()= });if(this.filters_manager.visible()){this.setup_multitrack_filtering()}ret= urn ac},request_draw:function(ac,ae){for(var ad=3D0;ad<this.drawables.lengt= h;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Y=3Dfunction(ac){q(a= c,{obj_type:"View"});z.call(this,"View",ac.container,ac);this.chrom=3Dnull;= this.vis_id=3Dac.vis_id;this.dbkey=3Dac.dbkey;this.label_tracks=3D[];this.t= racks_to_be_redrawn=3D[];this.max_low=3D0;this.max_high=3D0;this.zoom_facto= r=3D3;this.min_separation=3D30;this.has_changes=3Dfalse;this.load_chroms_de= ferred=3Dnull;this.init();this.canvas_manager=3Dnew x.CanvasManager(this.co= ntainer.get(0).ownerDocument);this.reset()};ab.extend(Y.prototype,Backbone.= Events);q(Y.prototype,z.prototype,{init:function(){this.requested_redraw=3D= false;var ae=3Dthis.container,ac=3Dthis;this.top_container=3D$("<div/>").ad= dClass("top-container").appendTo(ae);this.browser_content_div=3D$("<div/>")= .addClass("content").css("position","relative").appendTo(ae);this.bottom_co= ntainer=3D$("<div/>").addClass("bottom-container").appendTo(ae);this.top_la= beltrack=3D$("<div/>").addClass("top-labeltrack").appendTo(this.top_contain= er);this.viewport_container=3D$("<div/>").addClass("viewport-container").at= tr("id","viewport-container").appendTo(this.browser_content_div);this.conte= nt_div=3Dthis.viewport_container;k(this.viewport_container,ac);this.intro_d= iv=3D$("<div/>").addClass("intro").appendTo(this.viewport_container).hide()= ;var af=3D$("<div/>").text("Add Datasets to Visualization").addClass("actio= n-button").appendTo(this.intro_div).click(function(){x.select_datasets(sele= ct_datasets_url,add_track_async_url,ac.dbkey,function(ag){ab.each(ag,functi= on(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=3D$("<div/>")= .addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_contai= ner=3D$("<div/>").addClass("trackster-nav-container").prependTo(this.top_co= ntainer);this.nav=3D$("<div/>").addClass("trackster-nav").appendTo(this.nav= _container);this.overview=3D$("<div/>").addClass("overview").appendTo(this.= bottom_container);this.overview_viewport=3D$("<div/>").addClass("overview-v= iewport").appendTo(this.overview);this.overview_close=3D$("<a/>").attr("hre= f","javascript:void(0);").attr("title","Close overview").addClass("icon-but= ton overview-close tooltip").hide().appendTo(this.overview_viewport);this.o= verview_highlight=3D$("<div/>").addClass("overview-highlight").hide().appen= dTo(this.overview_viewport);this.overview_box_background=3D$("<div/>").addC= lass("overview-boxback").appendTo(this.overview_viewport);this.overview_box= =3D$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);th= is.default_overview_height=3Dthis.overview_box.height();this.nav_controls= =3D$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_selec= t=3D$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option= value=3D''>Loading</option>").appendTo(this.nav_controls);var ad=3Dfunctio= n(ag){if(ag.type=3D=3D=3D"focusout"||(ag.keyCode||ag.which)=3D=3D=3D13||(ag= .keyCode||ag.which)=3D=3D=3D27){if((ag.keyCode||ag.which)!=3D=3D27){ac.go_t= o($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.= chrom_select.show()}};this.nav_input=3D$("<input/>").addClass("nav-input").= hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_= span=3D$("<span/>").addClass("location").attr("original-title","Click to ch= ange location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);t= his.location_span.click(function(){ac.location_span.hide();ac.chrom_select.= hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("= display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_= input.autocomplete({source:function(ai,ag){var aj=3D[],ah=3D$.map(ac.get_dr= awables(),function(ak){return ak.data_manager.search_features(ai.term).succ= ess(function(al){aj=3Daj.concat(al)})});$.when.apply($,ah).done(function(){= ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.= vis_id!=3D=3Dundefined){this.hidden_input=3D$("<input/>").attr("type","hidd= en").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=3D$("<a/>").= attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}= ).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_co= ntrols);this.zi_link=3D$("<a/>").attr("id","zoom-in").attr("title","Zoom in= ").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_r= edraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=3Dthis.load= _chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom= (ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(thi= s).find("input").trigger("blur")});this.browser_content_div.bind("dblclick"= ,function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_= box.bind("dragstart",function(ag,ah){this.current_x=3Dah.offsetX}).bind("dr= ag",function(ag,ai){var aj=3Dai.offsetX-this.current_x;this.current_x=3Dai.= offsetX;var ah=3DMath.round(aj/ac.viewport_container.width()*(ac.max_high-a= c.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.re= set_overview()});this.viewport_container.bind("draginit",function(ag,ah){if= (ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragsta= rt",function(ag,ah){ah.original_low=3Dac.low;ah.current_height=3Dag.clientY= ;ah.current_x=3Dah.offsetX}).bind("drag",function(ai,ak){var ag=3D$(this);v= ar al=3Dak.offsetX-ak.current_x;var ah=3Dag.scrollTop()-(ai.clientY-ak.curr= ent_height);ag.scrollTop(ah);ak.current_height=3Dai.clientY;ak.current_x=3D= ak.offsetX;var aj=3DMath.round(al/ac.viewport_container.width()*(ac.high-ac= .low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){a= h*=3D50;var aj=3DMath.round(-ah/ac.viewport_container.width()*(ac.high-ac.l= ow));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,= ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_= labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolu= te","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this)= )}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.= startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var= ah=3DMath.min(ak.pageX,al.startX)-ac.container.offset().left,ag=3DMath.max= (ak.pageX,al.startX)-ac.container.offset().left,aj=3D(ac.high-ac.low),ai=3D= ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.lo= w,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=3DMa= th.min(al.pageX,am.startX),ag=3DMath.max(al.pageX,am.startX),aj=3D(ac.high-= ac.low),ai=3Dac.viewport_container.width(),ak=3Dac.low;ac.low=3DMath.round(= ah/ai*aj)+ak;ac.high=3DMath.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.requ= est_redraw()});this.add_label_track(new X(this,{content_div:this.top_labelt= rack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}))= ;$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this= .resize_timer)}this.resize_timer=3DsetTimeout(function(){ac.resize_window()= },500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(= window).trigger("resize")},changed:function(){this.has_changes=3Dtrue},upda= te_intro_div:function(){if(this.drawables.length=3D=3D=3D0){this.intro_div.= show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){= if(this.timer){clearTimeout(this.timer)}if(ag){var ae=3Dthis;this.timer=3Ds= etTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{vie= w.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){th= is.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val= (this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=3Dview.chrom_select= .val();if(ad!=3D=3D""){this.trigger_navigate(ad,view.low,view.high,true)}},= load_chroms:function(ae){ae.num=3Dw;var ac=3Dthis,ad=3D$.Deferred();$.ajax(= {url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){= if(ag.chrom_info.length=3D=3D=3D0){return}if(ag.reference){ac.add_label_tra= ck(new B(ac))}ac.chrom_data=3Dag.chrom_info;var aj=3D'<option value=3D"">Se= lect Chrom/Contig</option>';for(var ai=3D0,af=3Dac.chrom_data.length;ai<af;= ai++){var ah=3Dac.chrom_data[ai].chrom;aj+=3D'<option value=3D"'+ah+'">'+ah= +"</option>"}if(ag.prev_chroms){aj+=3D'<option value=3D"previous">Previous = '+w+"</option>"}if(ag.next_chroms){aj+=3D'<option value=3D"next">Next '+w+"= </option>"}ac.chrom_select.html(aj);ac.chrom_start_index=3Dag.start_index;a= d.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey= :",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=3Dthis;if= (!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah= ,ad,aj)});return}if(!ah||ah=3D=3D=3D"None"){return}if(ah=3D=3D=3D"previous"= ){ae.load_chroms({low:this.chrom_start_index-w});return}if(ah=3D=3D=3D"next= "){ae.load_chroms({low:this.chrom_start_index+w});return}var ai=3D$.grep(ae= .chrom_data,function(ak,al){return ak.chrom=3D=3D=3Dah})[0];if(ai=3D=3D=3Du= ndefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});= return}else{if(ah!=3D=3Dae.chrom){ae.chrom=3Dah;ae.chrom_select.val(ae.chro= m);ae.max_high=3Dai.len-1;ae.reset();ae.request_redraw(true);for(var ag=3D0= ,ac=3Dae.drawables.length;ag<ac;ag++){var af=3Dae.drawables[ag];if(af.init)= {af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!=3D=3Du= ndefined&&aj!=3D=3Dundefined){ae.low=3DMath.max(ad,0);ae.high=3DMath.min(aj= ,ae.max_high)}else{ae.low=3D0;ae.high=3Dae.max_high}ae.reset_overview();ae.= request_redraw()}},go_to:function(ag){ag=3Dag.replace(/ |,/g,"");var ak=3Dt= his,ac,af,ad=3Dag.split(":"),ai=3Dad[0],aj=3Dad[1];if(aj!=3D=3Dundefined){t= ry{var ah=3Daj.split("-");ac=3DparseInt(ah[0],10);af=3DparseInt(ah[1],10)}c= atch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae= ){var ac=3Dthis;var ad=3Dac.high-ac.low;this.move_delta(ae*ad)},move_delta:= function(af){var ac=3Dthis;var ae=3Dac.high-ac.low;if(ac.low-af<ac.max_low)= {ac.low=3Dac.max_low;ac.high=3Dac.max_low+ae}else{if(ac.high-af>ac.max_high= ){ac.high=3Dac.max_high;ac.low=3Dac.max_high-ae}else{ac.high-=3Daf;ac.low-= =3Daf}}ac.request_redraw();var ad=3Dac.chrom_select.val();this.trigger_navi= gate(ad,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_dra= wable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_l= abel_track:function(ac){ac.view=3Dthis;ac.init();this.label_tracks.push(ac)= },remove_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae)= ;if(ad){var ac=3Dthis;ae.container_div.hide(0,function(){$(this).remove();a= c.update_intro_div()})}},reset:function(){this.low=3Dthis.max_low;this.high= =3Dthis.max_high;this.viewport_container.find(".yaxislabel").remove()},requ= est_redraw:function(ak,ac,aj,al){var ai=3Dthis,ah=3D(al?[al]:ai.drawables),= ae;var ad;for(var ag=3D0;ag<ah.length;ag++){ad=3Dah[ag];ae=3D-1;for(var af= =3D0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af]= [0]=3D=3D=3Dad){ae=3Daf;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac= ,aj])}else{ai.tracks_to_be_redrawn[ag][1]=3Dac;ai.tracks_to_be_redrawn[ag][= 2]=3Daj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._re= draw(ak)});this.requested_redraw=3Dtrue}},_redraw:function(am){this.request= ed_redraw=3Dfalse;var aj=3Dthis.low,af=3Dthis.high;if(aj<this.max_low){aj= =3Dthis.max_low}if(af>this.max_high){af=3Dthis.max_high}var al=3Dthis.high-= this.low;if(this.high!=3D=3D0&&al<this.min_separation){af=3Daj+this.min_sep= aration}this.low=3DMath.floor(aj);this.high=3DMath.ceil(af);this.update_loc= ation(this.low,this.high);this.resolution_b_px=3D(this.high-this.low)/this.= viewport_container.width();this.resolution_px_b=3Dthis.viewport_container.w= idth()/(this.high-this.low);var ac=3D(this.low/(this.max_high-this.max_low)= *this.overview_viewport.width())||0;var ai=3D((this.high-this.low)/(this.ma= x_high-this.max_low)*this.overview_viewport.width())||0;var an=3D13;this.ov= erview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overv= iew_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_= highlight.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=3D0,ah=3D= this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=3Dthis.tracks_to_be_redrawn= [ag][0];ad=3Dthis.tracks_to_be_redrawn[ag][1];ak=3Dthis.tracks_to_be_redraw= n[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=3D[];for(ag=3D0,= ah=3Dthis.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},= zoom_in:function(ad,ae){if(this.max_high=3D=3D=3D0||this.high-this.low<=3Dt= his.min_separation){return}var af=3Dthis.high-this.low,ag=3Daf/2+this.low,a= c=3D(af/this.zoom_factor)/2;if(ad){ag=3Dad/this.viewport_container.width()*= (this.high-this.low)+this.low}this.low=3DMath.round(ag-ac);this.high=3DMath= .round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(= this.max_high=3D=3D=3D0){return}var ad=3Dthis.high-this.low,ae=3Dad/2+this.= low,ac=3D(ad*this.zoom_factor)/2;this.low=3DMath.round(ae-ac);this.high=3DM= ath.round(ae+ac);this.changed();this.request_redraw()},resize_window:functi= on(){this.viewport_container.height(this.container.height()-this.top_contai= ner.height()-this.bottom_container.height());this.request_redraw()},set_ove= rview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dat= aset_id=3D=3D=3Dae.dataset_id){return}this.overview_viewport.find(".track")= .remove()}var ad=3Dae.copy({content_div:this.overview_viewport}),ac=3Dthis;= ad.header_div.hide();ad.is_overview=3Dtrue;ac.overview_drawable=3Dad;this.o= verview_drawable.postdraw_actions=3Dfunction(){ac.overview_highlight.show()= .height(ac.overview_drawable.content_div.height());ac.overview_viewport.hei= ght(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight()= );ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request= _draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove()= ;this.overview_viewport.find(".track-tile").remove();this.overview_viewport= .height(this.default_overview_height);this.overview_box.height(this.default= _overview_height);this.overview_close.hide();this.overview_highlight.hide()= ;view.resize_window();view.overview_drawable=3Dnull}});var s=3Dfunction(ae,= aj,af){this.track=3Dae;this.name=3Daj.name;this.params=3D[];var aq=3Daj.par= ams;for(var ag=3D0;ag<aq.length;ag++){var al=3Daq[ag],ad=3Dal.name,ap=3Dal.= label,ah=3Dunescape(al.html),ar=3Dal.value,an=3Dal.type;if(an=3D=3D=3D"numb= er"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}e= lse{if(an=3D=3D=3D"select"){this.params.push(new N(ad,ap,ah,(ad in af?af[ad= ]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an= )}}}this.parent_div=3D$("<div/>").addClass("dynamic-tool").hide();this.pare= nt_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){a= u.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});v= ar ao=3D$("<div class=3D'tool-name'>").appendTo(this.parent_div).text(this.= name);var am=3Dthis.params;var ak=3Dthis;$.each(this.params,function(av,ay)= {var ax=3D$("<div>").addClass("param-row").appendTo(ak.parent_div);var au= =3D$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=3D= $("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":in= put").val(ay.value);$("<div style=3D'clear: both;'/>").appendTo(ax)});this.= parent_div.find("input").click(function(){$(this).select()});var at=3D$("<d= iv>").addClass("param-row").appendTo(this.parent_div);var ai=3D$("<input ty= pe=3D'submit'>").attr("value","Run on complete dataset").appendTo(at);var a= c=3D$("<input type=3D'submit'>").attr("value","Run on visible region").css(= "margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});= ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){t= his.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ac= =3D0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dic= t:function(){var ad=3D{};for(var ac=3D0;ac<this.params.length;ac++){ad[this= .params[ac].name]=3Dthis.params[ac].value}ad.visible=3Dthis.parent_div.is("= :visible");return ad},get_param_values_dict:function(){var ac=3D{};this.par= ent_div.find(":input").each(function(){var ad=3D$(this).attr("name"),ae=3D$= (this).val();ac[ad]=3Dae});return ac},get_param_values:function(){var ac=3D= [];this.parent_div.find(":input").each(function(){var ad=3D$(this).attr("na= me"),ae=3D$(this).val();if(ad){ac[ac.length]=3Dae}});return ac},run_on_data= set:function(){var ac=3Dthis;ac.run({target_dataset_id:this.track.original_= dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Runni= ng",ac.name+" is running on the complete dataset. 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Z.Dataset(aj));ai.tiles_div.text("Running job."= );ai.init()})},run:function(ac,ae,af){ac.inputs=3Dthis.get_param_values_dic= t();var ad=3Dnew l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get= ("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"applicati= on/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=3D= =3D"pending"}});$.when(ad.go()).then(function(ag){if(ag=3D=3D=3D"no convert= er"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.e= rror){ae.container_div.addClass("error");ae.content_div.text(y+ag.message)}= else{af(ag)}}})}});var N=3Dfunction(ad,ac,ae,af){this.name=3Dad;this.label= =3Dac;this.html=3D$(ae);this.value=3Daf};q(N.prototype,{update_value:functi= on(){this.value=3D$(this.html).val()}});var e=3Dfunction(ae,ad,ag,ah,af,ac)= {N.call(this,ae,ad,ag,ah);this.min=3Daf;this.max=3Dac};q(e.prototype,N.prot= otype,{update_value:function(){N.prototype.update_value.call(this);this.val= 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m({dataset_id:ac.dataset_id,hda_ldda:ac.hda_ldda,regions:JSON.stringify(new= Backbone.Collection(al).toJSON())})},ag=3Dfunction(ai){if((ai.keyCode||ai.= which)=3D=3D=3D27){ah()}else{if((ai.keyCode||ai.which)=3D=3D=3D13){ad()}}};= show_modal("Visualize tool parameter space and output from different parame= ter settings?",ae,{No:ah,Yes:ad})}},r.prototype.action_icons_def[2]],can_dr= aw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return t= rue}return false},build_container_div:function(){return $("<div/>").addClas= s("track").attr("id","track_"+this.id).css("position","relative")},build_he= ader_div:function(){var ac=3D$("<div class=3D'track-header'/>");if(this.vie= w.editor){this.drag_div=3D$("<div/>").addClass(this.drag_handle_class).appe= ndTo(ac)}this.name_div=3D$("<div/>").addClass("track-name").appendTo(ac).te= xt(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\= -]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle= 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ac=3Dthis;if(ac.filters_availabl= e){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hi= de()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_sp= ace_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.= param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return= ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(fa= lse,ad,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.ca= n_draw()){return}var al=3Dthis.view.low,ah=3Dthis.view.high,aj=3Dah-al,ae= =3Dthis.view.container.width(),ap=3Dthis.view.resolution_px_b,ag=3Dthis.vie= w.resolution_b_px;if(this.is_overview){al=3Dthis.view.max_low;ah=3Dthis.vie= w.max_high;ag=3D(view.max_high-view.max_low)/ae;ap=3D1/ag}this.before_draw(= );this.tiles_div.children().addClass("remove");var ac=3DMath.floor(al/(ag*S= )),ak=3Dtrue,ao=3D[],ai=3Dfunction(aq){return(aq&&"track" in aq)};while((ac= *S*ag)<ah){var am=3Dthis.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(a= m)){ao.push(am)}else{ak=3Dfalse}ac+=3D1}if(!an){this.tiles_div.children(".r= emove").removeClass("remove").remove()}var af=3Dthis;if(ak){this.tiles_div.= children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_ac= tions:function(ae,af,ah,ac){var ag=3Dfalse;for(var ad=3D0;ad<ae.length;ad++= ){if(ae[ad].has_icons){ag=3Dtrue;break}}if(ag){for(var ad=3D0;ad<ae.length;= ad++){tile=3Dae[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}= }}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=3Dthis,ax=3Dthis._gen= _tile_cache_key(ao,ai,au),af=3Dthis._get_tile_bounds(au,ar);if(!ap){ap=3D{}= }var aw=3D(ac?undefined:an.tile_cache.get_elt(ax));if(aw){an.show_tile(aw,a= h,ai);return aw}var al=3Dtrue;var at=3Dan.data_manager.get_data(af,an.mode,= ar,an.data_url_extra_params);if(V(at)){al=3Dfalse}var aj;if(view.reference_= track&&ai>view.canvas_manager.char_width_px){aj=3Dview.reference_track.data= _manager.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params)= ;if(V(aj)){al=3Dfalse}}if(al){q(at,ap.more_tile_data);var ak=3Dan.mode;if(a= k=3D=3D=3D"Auto"){ak=3Dan.get_mode(at);an.update_auto_mode(ak)}var ae=3Dan.= view.canvas_manager.new_canvas(),av=3Daf.get("start"),ad=3Daf.get("end"),ao= =3DMath.ceil((ad-av)*ai)+an.left_offset,am=3Dan.get_canvas_height(at,ak,ai,= ao);ae.width=3Dao;ae.height=3Dam;var aq=3Dae.getContext("2d");aq.translate(= this.left_offset,0);var aw=3Dan.draw_tile(at,aq,ak,ar,af,ai,aj);if(aw!=3D= =3Dundefined){an.tile_cache.set_elt(ax,aw);an.show_tile(aw,ah,ai)}return aw= }var ag=3D$.Deferred();$.when(at,aj).then(function(){view.request_redraw(fa= lse,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac= ,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag= ,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},sh= ow_tile:function(ae,ah,ai){var ad=3Dthis,ac=3Dae.html_elt;ae.predisplay_act= ions();var ag=3D(ae.low-(this.is_overview?this.view.max_low:this.view.low))= *ai;if(this.left_offset){ag-=3Dthis.left_offset}ac.css({position:"absolute"= ,top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah= .append(ac)}ae.html_elt.height("auto");this.max_height_px=3DMath.max(this.m= ax_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("hei= ght",this.max_height_px+"px");var af=3Dthis.max_height_px;if(this.visible_h= eight_px!=3D=3D0){af=3DMath.min(this.max_height_px,this.visible_height_px)}= this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var = af=3DMath.floor(ac*S*ad),ag=3DMath.ceil(S*ad),ae=3D(af+ag<=3Dthis.view.max_= high?af+ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.c= hrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae,ac,af){v= ar ad=3Dthis,ag=3D(ae!=3D=3Dundefined&&ac!=3D=3Dundefined&&af!=3D=3Dundefin= ed?ae+":"+ac+"-"+af:"all");return" - region=3D["+ag+"], parameters=3D["+ad.= tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(a= c,ad){return true},can_subset:function(ac){return false},init_for_tool_data= :function(){this.data_manager.set("data_type","raw_data");this.data_query_w= ait=3D1000;this.dataset_check_type=3D"state";this.normal_postdraw_actions= =3Dthis.postdraw_actions;this.postdraw_actions=3Dfunction(ae,af,ah,ac){var = ad=3Dthis;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type=3D"= converted_datasets_state";ad.data_query_wait=3DK;var ag=3Dnew l.ServerState= Deferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda= _ldda:ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){retu= rn ai!=3D=3D"pending"}});$.when(ag.go()).then(function(){ad.data_manager.se= t("data_type","data")});ad.postdraw_actions=3Dad.normal_postdraw_actions}}}= );var X=3Dfunction(ad,ac){var ae=3D{resize:false};g.call(this,ad,ac,ae);thi= s.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_h= eader_div:function(){},init:function(){this.enabled=3Dtrue},_draw:function(= ){var ae=3Dthis.view,af=3Dae.high-ae.low,ai=3DMath.floor(Math.pow(10,Math.f= loor(Math.log(af)/Math.log(10)))),ac=3DMath.floor(ae.low/ai)*ai,ag=3Dthis.v= iew.container.width(),ad=3D$("<div style=3D'position: relative; height: 1.3= em;'></div>");while(ac<ae.high){var ah=3D(ac-ae.low)/af*ag;ad.append($("<di= v class=3D'label'>"+commatize(ac)+"</div>").css({position:"absolute",left:a= h-1}));ac+=3Dai}this.content_div.children(":first").remove();this.content_d= iv.append(ad)}});var f=3Dfunction(ad,ac,ag){M.call(this,ad,ac,ag);this.draw= ables=3D[];this.left_offset=3D0;if("drawables" in ag){var af;for(var ae=3D0= ;ae<ag.drawables.length;ae++){af=3Dag.drawables[ae];this.drawables[ae]=3Dp(= af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=3Daf.left_= offset}}this.enabled=3Dtrue}if(this.drawables.length!=3D=3D0){this.set_disp= lay_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.upda= te_icons();this.obj_type=3D"CompositeTrack"};q(f.prototype,M.prototype,{act= ion_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_cl= ass:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.sh= ow_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_d= ict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpa= ck_drawables,change_mode:function(ac){M.prototype.change_mode.call(this,ac)= ;for(var ad=3D0;ad<this.drawables.length;ad++){this.drawables[ad].change_mo= de(ac)}},init:function(){var ae=3D[];for(var ad=3D0;ad<this.drawables.lengt= h;ad++){ae.push(this.drawables[ad].init())}var ac=3Dthis;$.when.apply($,ae)= .then(function(){ac.enabled=3Dtrue;ac.request_draw()})},update_icons:functi= on(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hid= e();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can= _draw,draw_helper:function(ad,at,az,aw,ak,am,au){var ar=3Dthis,aD=3Dthis._g= en_tile_cache_key(at,am,az),ah=3Dthis._get_tile_bounds(az,aw);if(!au){au=3D= {}}var aC=3D(ad?undefined:ar.tile_cache.get_elt(aD));if(aC){ar.show_tile(aC= ,ak,am);return aC}var al=3D[],ar,ap=3Dtrue,ax,an;for(var ay=3D0;ay<this.dra= wables.length;ay++){ar=3Dthis.drawables[ay];ax=3Dar.data_manager.get_data(a= h,ar.mode,aw,ar.data_url_extra_params);if(V(ax)){ap=3Dfalse}al.push(ax);an= =3Dnull;if(view.reference_track&&am>view.canvas_manager.char_width_px){an= =3Dview.reference_track.data_manager.get_data(ah,ar.mode,aw,view.reference_= track.data_url_extra_params);if(V(an)){ap=3Dfalse}}al.push(an)}if(ap){q(ax,= au.more_tile_data);this.tile_predraw_init();var ag=3Dar.view.canvas_manager= .new_canvas(),ai=3Dar._get_tile_bounds(az,aw),aA=3Dah.get("start"),ae=3Dah.= get("end"),aB=3D0,at=3DMath.ceil((ae-aA)*am)+this.left_offset,aq=3D0,af=3D[= ],ay;var ac=3D0;for(ay=3D0;ay<this.drawables.length;ay++,aB+=3D2){ar=3Dthis= .drawables[ay];ax=3Dal[aB];var ao=3Dar.mode;if(ao=3D=3D=3D"Auto"){ao=3Dar.g= et_mode(ax);ar.update_auto_mode(ao)}af.push(ao);ac=3Dar.get_canvas_height(a= x,ao,am,at);if(ac>aq){aq=3Dac}}ag.width=3Dat;ag.height=3D(au.height?au.heig= ht:aq);aB=3D0;var av=3Dag.getContext("2d");av.translate(this.left_offset,0)= ;av.globalAlpha=3D0.5;av.globalCompositeOperation=3D"source-over";for(ay=3D= 0;ay<this.drawables.length;ay++,aB+=3D2){ar=3Dthis.drawables[ay];ax=3Dal[aB= ];an=3Dal[aB+1];aC=3Dar.draw_tile(ax,av,af[ay],aw,ah,am,an)}this.tile_cache= .set_elt(aD,aC);this.show_tile(aC,ak,am);return aC}var aj=3D$.Deferred(),ar= =3Dthis;$.when.apply($,al).then(function(){view.request_redraw(false,false,= false,ar);aj.resolve()});return aj},show_group:function(){var af=3Dnew P(th= is.view,this.container,{name:this.name}),ac;for(var ae=3D0;ae<this.drawable= s.length;ae++){ac=3Dthis.drawables[ae];ac.update_icons();af.add_drawable(ac= );ac.container=3Daf;af.content_div.append(ac.container_div)}var ad=3Dthis.c= ontainer.replace_drawable(this,af,true);af.request_draw()},tile_predraw_ini= t:function(){var af=3DNumber.MAX_VALUE,ac=3D-af,ad;for(var ae=3D0;ae<this.d= rawables.length;ae++){ad=3Dthis.drawables[ae];if(ad instanceof h){if(ad.pre= fs.min_value<af){af=3Dad.prefs.min_value}if(ad.prefs.max_value>ac){ac=3Dad.= prefs.max_value}}}for(var ae=3D0;ae<this.drawables.length;ae++){ad=3Dthis.d= rawables[ae];ad.prefs.min_value=3Daf;ad.prefs.max_value=3Dac}},postdraw_act= ions:function(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,= ad);var ag=3D-1;for(var af=3D0;af<ae.length;af++){var ac=3Dae[af].html_elt.= find("canvas").height();if(ac>ag){ag=3Dac}}for(var af=3D0;af<ae.length;af++= ){var ai=3Dae[af];if(ai.html_elt.find("canvas").height()!=3D=3Dag){this.dra= w_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag}= );ai.html_elt.remove()}}}});var B=3Dfunction(ac){M.call(this,ac,{content_di= v:ac.top_labeltrack},{resize:false});ac.reference_track=3Dthis;this.left_of= fset=3D200;this.visible_height_px=3D12;this.container_div.addClass("referen= ce-track");this.content_div.css("background","none");this.content_div.css("= min-height","0px");this.content_div.css("border","none");this.data_url=3Dre= ference_url+"/"+this.view.dbkey;this.data_url_extra_params=3D{reference:tru= e};this.data_manager=3Dnew x.ReferenceTrackDataManager({data_url:this.data_= url});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_he= ader_div:function(){},init:function(){this.data_manager.clear();this.enable= d=3Dtrue},can_draw:r.prototype.can_draw,draw_helper:function(ag,ae,ac,ad,ah= ,ai,af){if(ai>this.view.canvas_manager.char_width_px){return M.prototype.dr= aw_helper.call(this,ag,ae,ac,ad,ah,ai,af)}else{this.hide_contents();return = null}},draw_tile:function(ak,al,ag,af,ai,am){var ae=3Dthis;if(am>this.view.= canvas_manager.char_width_px){if(ak.data=3D=3D=3Dnull){this.hide_contents()= ;return}var ad=3Dal.canvas;al.font=3Dal.canvas.manager.default_font;al.text= Align=3D"center";ak=3Dak.data;for(var ah=3D0,aj=3Dak.length;ah<aj;ah++){var= ac=3DMath.floor(ah*am);al.fillText(ak[ah],ac,10)}this.show_contents();retu= rn new b(ae,ai,af,ad,ak)}this.hide_contents()}});var h=3Dfunction(ae,ad,af)= {var ac=3Dthis;this.display_modes=3D["Histogram","Line","Filled","Intensity= "];this.mode=3D"Histogram";M.call(this,ae,ad,af);this.hda_ldda=3Daf.hda_ldd= a;this.dataset_id=3Daf.dataset_id;this.original_dataset_id=3Dthis.dataset_i= d;this.left_offset=3D0;this.config=3Dnew F({track:this,params:[{key:"name",= label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color= ",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"= Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Ma= x Value",type:"float",default_value:undefined},{key:"mode",type:"string",de= fault_value:this.mode,hidden:true},{key:"height",type:"int",default_value:3= 2,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.pr= efs.name);ac.vertical_range=3Dac.prefs.max_value-ac.prefs.min_value;ac.set_= min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.= prefs=3Dthis.config.values;this.visible_height_px=3Dthis.config.values.heig= ht;this.vertical_range=3Dthis.config.values.max_value-this.config.values.mi= n_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.r= equest_draw(true)},set_min_value:function(ac){this.prefs.min_value=3Dac;$("= #linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.til= e_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.= max_value=3Dac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.m= ax_value);this.tile_cache.clear();this.request_draw()},predraw_init:functio= n(){var ac=3Dthis;ac.vertical_range=3Dundefined;return $.getJSON(ac.dataset= .url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.= max_high,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line= -track");var ag=3Dad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(p= arseFloat(ac.prefs.max_value))){var ae=3Dag.min,ai=3Dag.max;ae=3DMath.floor= (Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=3DMath.ceil(Math.max(0,Math.m= in(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=3Dae;ac.prefs.max_value=3Dai;$(= "#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.d= ataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=3Dac.prefs.m= ax_value-ac.prefs.min_value;ac.total_frequency=3Dag.total_frequency;ac.cont= ainer_div.find(".yaxislabel").remove();var ah=3D$("<div/>").text(W(ac.prefs= .min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs= -tooltip").remove();var aj=3DparseFloat(aj);if(!isNaN(aj)){ac.set_min_value= (aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id",= "linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=3D$("<= div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_fin= ish:function(aj){$(".bs-tooltip").remove();var aj=3DparseFloat(aj);if(!isNa= N(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxisla= bel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.cont= ainer_div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=3Daj.canvas,af= =3Dag.get("start"),ai=3Dag.get("end"),ah=3Dnew L.LinePainter(al.data,af,ai,= this.prefs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac= ,al.data)},can_subset:function(ac){return false}});var t=3Dfunction(ae,ad,a= f){var ac=3Dthis;this.display_modes=3D["Heatmap"];this.mode=3D"Heatmap";M.c= all(this,ae,ad,af);this.hda_ldda=3Daf.hda_ldda;this.dataset_id=3Daf.dataset= _id;this.original_dataset_id=3Dthis.dataset_id;this.left_offset=3D0;this.co= nfig=3Dnew F({track:this,params:[{key:"name",label:"Name",type:"text",defau= lt_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",de= fault_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color"= ,default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",d= efault_value:0},{key:"max_value",label:"Max Value",type:"float",default_val= ue:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"= height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,on= change:function(){ac.set_name(ac.prefs.name);ac.vertical_range=3Dac.prefs.m= ax_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max= _value(ac.prefs.max_value)}});this.prefs=3Dthis.config.values;this.visible_= height_px=3Dthis.config.values.height;this.vertical_range=3Dthis.config.val= ues.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.pro= totype,{on_resize:function(){this.request_draw(true)},set_min_value:functio= n(ac){this.prefs.min_value=3Dac;this.tile_cache.clear();this.request_draw()= },set_max_value:function(ac){this.prefs.max_value=3Dac;this.tile_cache.clea= r();this.request_draw()},draw_tile:function(am,ak,ah,af,ad,al){var ae=3Dak.= canvas,ac=3Dthis._get_tile_bounds(ad,af),ag=3Dac[0],aj=3Dac[1],ai=3Dnew L.D= iagonalHeatmapPainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.h= eight,al);return new b(this,ad,af,ae,am.data)}});var c=3Dfunction(af,ae,ah)= {var ad=3Dthis;this.display_modes=3D["Auto","Coverage","Dense","Squish","Pa= ck"];M.call(this,af,ae,ah);var ag=3Dl.get_random_color(),ac=3Dl.get_random_= color([ag,"#ffffff"]);this.config=3Dnew F({track:this,params:[{key:"name",l= abel:"Name",type:"text",default_value:this.name},{key:"block_color",label:"= Block color",type:"color",default_value:ag},{key:"reverse_strand_color",lab= el:"Antisense strand color",type:"color",default_value:ac},{key:"label_colo= r",label:"Label color",type:"color",default_value:"black"},{key:"show_count= s",label:"Show summary counts",type:"bool",default_value:true,help:"Show th= e number of items in each bin when drawing summary histogram"},{key:"histog= ram_max",label:"Histogram maximum",type:"float",default_value:null,help:"cl= ear value to set automatically"},{key:"connector_style",label:"Connector st= yle",type:"select",default_value:"fishbones",options:[{label:"Line with arr= ows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"stri= ng",default_value:this.mode,hidden:true},{key:"height",type:"int",default_v= alue:this.visible_height_px,hidden:true}],saved_values:ah.prefs,onchange:fu= nction(){ad.set_name(ad.prefs.name);ad.tile_cache.clear();ad.set_painter_fr= om_config();ad.request_draw()}});this.prefs=3Dthis.config.values;this.visib= le_height_px=3Dthis.config.values.height;this.container_div.addClass("featu= re-track");this.hda_ldda=3Dah.hda_ldda;this.dataset_id=3Dah.dataset_id;this= .original_dataset_id=3Dah.dataset_id;this.show_labels_scale=3D0.001;this.sh= owing_details=3Dfalse;this.summary_draw_height=3D30;this.slotters=3D{};this= .start_end_dct=3D{};this.left_offset=3D200;this.set_painter_from_config()};= q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ac){this.datase= t_id=3Dac.get("id");this.hda_ldda=3Dac.get("hda_ldda");this.dataset=3Dac;th= is.data_manager.set("dataset",ac)},set_painter_from_config:function(){if(th= is.config.values.connector_style=3D=3D=3D"arcs"){this.painter=3DL.ArcLinked= FeaturePainter}else{this.painter=3DL.LinkedFeaturePainter}},before_draw:fun= ction(){this.max_height_px=3D0},postdraw_actions:function(ar,am,ah,ag){M.pr= ototype.postdraw_actions.call(this,ar,ag);var al=3Dthis,ao;if(al.mode=3D=3D= =3D"Coverage"){var ad=3D-1;for(ao=3D0;ao<ar.length;ao++){var an=3Dar[ao].ma= x_val;if(an>ad){ad=3Dan}}for(ao=3D0;ao<ar.length;ao++){var au=3Dar[ao];if(a= u.max_val!=3D=3Dad){au.html_elt.remove();al.draw_helper(true,am,au.index,au= .resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filt= ers_manager){var ai=3Dal.filters_manager.filters;for(var aq=3D0;aq<ai.lengt= h;aq++){ai[aq].update_ui_elt()}var at=3Dfalse,ac,aj;for(ao=3D0;ao<ar.length= ;ao++){if(ar[ao].data.length){ac=3Dar[ao].data[0];for(var aq=3D0;aq<ai.leng= th;aq++){aj=3Dai[aq];if(aj.applies_to(ac)&&aj.min!=3D=3Daj.max){at=3Dtrue;b= reak}}}}if(al.filters_available!=3D=3Dat){al.filters_available=3Dat;if(!al.= filters_available){al.filters_manager.hide()}al.update_icons()}}this.contai= ner_div.find(".yaxislabel").remove();var af=3Dar[0];if(af instanceof j){var= ak=3D(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=3D$= ("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){= $(".bs-tooltip").remove();var av=3DparseFloat(av);al.prefs.histogram_max=3D= (!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Se= t max value; leave blank to use default"}).addClass("yaxislabel top").css("= color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanc= eof O){var ap=3Dtrue;for(ao=3D0;ao<ar.length;ao++){if(!ar[ao].all_slotted){= ap=3Dfalse;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else= {this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_= more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode= =3D=3D=3D"Auto"){if(ac=3D=3D=3D"no_detail"){ac=3D"feature spans"}else{if(ac= =3D=3D=3D"summary_tree"){ac=3D"coverage histogram"}}this.action_icons.mode_= icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slot= s:function(ag,ac,af){var ad=3Dthis.view.canvas_manager.dummy_context,ae=3Dt= his.slotters[ag];if(!ae||(ae.mode!=3D=3Daf)){ae=3Dnew (u.FeatureSlotter)(ag= ,af,A,function(ah){return ad.measureText(ah)});this.slotters[ag]=3Dae}retur= n ae.slot_features(ac)},get_mode:function(ac){if(ac.dataset_type=3D=3D=3D"s= ummary_tree"){mode=3D"summary_tree"}else{if(ac.extra_info=3D=3D=3D"no_detai= l"||this.is_overview){mode=3D"no_detail"}else{if(this.view.high-this.view.l= ow>I){mode=3D"Squish"}else{mode=3D"Pack"}}}return mode},get_canvas_height:f= unction(ac,ag,ah,ad){if(ag=3D=3D=3D"summary_tree"||ag=3D=3D=3D"Coverage"){r= eturn this.summary_draw_height}else{var af=3Dthis.incremental_slots(ah,ac.d= ata,ag);var ae=3Dnew (this.painter)(null,null,null,this.prefs,ag);return Ma= th.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,a= f,aj,ae){var ap=3Dthis,ad=3Daq.canvas,ay=3Daf.get("start"),ac=3Daf.get("end= "),ag=3Dthis.left_offset;if(ao=3D=3D=3D"summary_tree"||ao=3D=3D=3D"Coverage= "){var aA=3Dnew L.SummaryTreePainter(am,ay,ac,this.prefs);aA.draw(aq,ad.wid= th,ad.height,aj);return new j(ap,af,ar,ad,am.data,am.max)}var ai=3D[],an=3D= this.slotters[aj].slots;all_slotted=3Dtrue;if(am.data){var ak=3Dthis.filter= s_manager.filters;for(var at=3D0,av=3Dam.data.length;at<av;at++){var ah=3Da= m.data[at];var au=3Dfalse;var al;for(var ax=3D0,aC=3Dak.length;ax<aC;ax++){= al=3Dak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=3Dtrue;break}}if(!au){a= i.push(ah);if(!(ah[0] in an)){all_slotted=3Dfalse}}}}var aB=3D(this.filters= _manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var az= =3D(this.filters_manager.height_filter?new C(this.filters_manager.height_fi= lter):null);var aA=3Dnew (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae);va= r aw=3Dnull;aq.fillStyle=3Dthis.prefs.block_color;aq.font=3Daq.canvas.manag= er.default_font;aq.textAlign=3D"right";if(am.data){aw=3DaA.draw(aq,ad.width= ,ad.height,aj,an);aw.translation=3D-ag}return new O(ap,af,ar,ad,am.data,aj,= ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(= ad=3D=3D=3D"Auto"){return true}else{if(ad=3D=3D=3D"Coverage"){return ac.dat= aset_type=3D=3D=3D"summary_tree"}else{if(ac.extra_info=3D=3D=3D"no_detail"|= |ac.dataset_type=3D=3D=3D"summary_tree"){return false}else{return true}}}},= can_subset:function(ac){if(ac.dataset_type=3D=3D=3D"summary_tree"||ac.messa= ge||ac.extra_info=3D=3D=3D"no_detail"){return false}return true}});var R=3D= function(ad,ac,ae){c.call(this,ad,ac,ae);this.config=3Dnew F({track:this,pa= rams:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"b= lock_color",label:"Block color",type:"color",default_value:l.get_random_col= or()},{key:"label_color",label:"Label color",type:"color",default_value:"bl= ack"},{key:"show_insertions",label:"Show insertions",type:"bool",default_va= lue:false},{key:"show_counts",label:"Show summary counts",type:"bool",defau= lt_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:tru= e}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.trac= k.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});th= is.prefs=3Dthis.config.values;this.painter=3DL.ReadPainter};q(R.prototype,r= .prototype,M.prototype,c.prototype);var T=3Dfunction(ae,ad,ag){c.call(this,= ae,ad,ag);var af=3Dl.get_random_color(),ac=3Dl.get_random_color([af,"#fffff= f"]);this.config=3Dnew F({track:this,params:[{key:"name",label:"Name",type:= "text",default_value:this.name},{key:"block_color",label:"Block and sense s= trand color",type:"color",default_value:af},{key:"reverse_strand_color",lab= el:"Antisense strand color",type:"color",default_value:ac},{key:"label_colo= r",label:"Label color",type:"color",default_value:"black"},{key:"show_inser= tions",label:"Show insertions",type:"bool",default_value:false},{key:"show_= differences",label:"Show differences only",type:"bool",default_value:true},= {key:"show_counts",label:"Show summary counts",type:"bool",default_value:tr= ue},{key:"histogram_max",label:"Histogram maximum",type:"float",default_val= ue:null,help:"Clear value to set automatically"},{key:"mode",type:"string",= default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:functi= on(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear= ();this.track.request_draw()}});this.prefs=3Dthis.config.values;this.painte= r=3DL.ReadPainter;this.update_icons()};q(T.prototype,r.prototype,M.prototyp= e,c.prototype);var d=3D{LineTrack:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,C= ompositeTrack:f,DrawableGroup:P};var p=3Dfunction(ae,ad,ac){if("copy" in ae= ){return ae.copy(ac)}else{var af=3Dae.obj_type;if(!af){af=3Dae.track_type}r= eturn new d[af](ad,ac,ae)}};return{View:Y,DrawableGroup:P,LineTrack:h,Featu= reTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:f,ob= ject_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/tr= ackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filter= s"],function(ab,x,l,u,L,Y,i){var q=3Dab.extend;var V=3Dfunction(ac){return(= "isResolved" in ac)};var n=3D{};var k=3Dfunction(ac,ad){n[ac.attr("id")]=3D= ad};var m=3Dfunction(ac,ae,ag,af){ag=3D".group";var ad=3D{};n[ac.attr("id")= ]=3Daf;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an= =3D$(this),at=3D$(this).parent(),ak=3Dat.children(),am=3Dn[$(this).attr("id= ")],aj,ai,aq,ah,al;ai=3D$(this).parents(ag);if(ai.length!=3D=3D0){aq=3Dai.p= osition().top;ah=3Daq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefo= re(ai);var ar=3Dn[ai.attr("id")];ar.remove_drawable(am);ar.container.add_dr= awable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);= var ar=3Dn[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(= am);return}}}ai=3Dnull;for(al=3D0;al<ak.length;al++){aj=3D$(ak.get(al));aq= =3Daj.position().top;ah=3Daq+aj.outerHeight();if(aj.is(ag)&&this!=3D=3Daj.g= et(0)&&ap.offsetY>=3Daq&&ap.offsetY<=3Dah){if(ap.offsetY-aq<ah-ap.offsetY){= aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(t= his)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add= _drawable(am);return}}for(al=3D0;al<ak.length;al++){aj=3D$(ak.get(al));if(a= p.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass(= "intro"))){break}}if(al=3D=3D=3Dak.length){if(this!=3D=3Dak.get(al-1)){at.a= ppend(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!=3D=3Dak.ge= t(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(= ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=3Dac= .css("border-top");ad["border-bottom"]=3Dac.css("border-bottom");$(this).cs= s({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind(= "dragend",function(){$(this).css(ad)})};var aa=3D16,G=3D9,D=3D20,A=3D100,I= =3D12000,S=3D400,K=3D5000,w=3D100,o=3D"There was an error in indexing this = dataset. ",J=3D"A converter for this dataset is not installed. Please check= your datatypes_conf.xml file.",E=3D"No data for this chrom/contig.",v=3D"P= reparing data. This can take a while for a large dataset. If the visualizat= ion is saved and closed, preparation will continue in the background.",y=3D= "Tool cannot be rerun: ",a=3D"Loading data...",U=3D"Ready for display",Q=3D= 10,H=3D20;function W(ad,ac){if(!ac){ac=3D0}var ae=3DMath.pow(10,ac);return = Math.round(ad*ae)/ae}var r=3Dfunction(ad,ac,af){if(!r.id_counter){r.id_coun= ter=3D0}this.id=3Dr.id_counter++;this.name=3Daf.name;this.view=3Dad;this.co= ntainer=3Dac;this.config=3Dnew F({track:this,params:[{key:"name",label:"Nam= e",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:fun= ction(){this.track.set_name(this.track.config.values.name)}});this.prefs=3D= this.config.values;this.drag_handle_class=3Daf.drag_handle_class;this.is_ov= erview=3Dfalse;this.action_icons=3D{};this.content_visible=3Dtrue;this.cont= ainer_div=3Dthis.build_container_div();this.header_div=3Dthis.build_header_= div();if(this.header_div){this.container_div.append(this.header_div);this.i= cons_div=3D$("<div/>").css("float","left").hide().appendTo(this.header_div)= ;this.build_action_icons(this.action_icons_def);this.header_div.append($("<= div style=3D'clear: both'/>"));this.header_div.dblclick(function(ag){ag.sto= pPropagation()});var ae=3Dthis;this.container_div.hover(function(){ae.icons= _div.show()},function(){ae.icons_div.hide()});$("<div style=3D'clear: both'= />").appendTo(this.container_div)}};r.prototype.action_icons_def=3D[{name:"= toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:funct= ion(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle= -expand").removeClass("toggle");ac.hide_contents();ac.content_visible=3Dfal= se}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-= expand");ac.content_visible=3Dtrue;ac.show_contents()}}},{name:"settings_ic= on",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad= ){var af=3Dfunction(){hide_modal();$(window).unbind("keypress.check_enter_e= sc")},ac=3Dfunction(){ad.config.update_from_form($(".dialog-box"));hide_mod= al();$(window).unbind("keypress.check_enter_esc")},ae=3Dfunction(ag){if((ag= .keyCode||ag.which)=3D=3D=3D27){af()}else{if((ag.keyCode||ag.which)=3D=3D= =3D13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Co= nfigure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",ti= tle:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-toolti= p").remove();ac.remove()}}];q(r.prototype,{init:function(){},changed:functi= on(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content= _visible){return true}return false},request_draw:function(){},_draw:functio= n(){},to_dict:function(){},set_name:function(ac){this.old_name=3Dthis.name;= this.name=3Dac;this.name_div.text(this.name)},revert_name:function(){if(thi= s.old_name){this.name=3Dthis.old_name;this.name_div.text(this.name)}},remov= e:function(){this.changed();this.container.remove_drawable(this);var ac=3Dt= his.view;this.container_div.hide(0,function(){$(this).remove();ac.update_in= tro_div()})},build_container_div:function(){},build_header_div:function(){}= ,add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=3Dthis;this.action_icon= s[ad]=3D$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addCl= ass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendT= o(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:= function(ac){var ae;for(var ad=3D0;ad<ac.length;ad++){ae=3Dac[ad];this.add_= action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide= )}},update_icons:function(){},hide_contents:function(){},show_contents:func= tion(){},get_drawables:function(){}});var z=3Dfunction(ad,ac,ae){r.call(thi= s,ad,ac,ae);this.obj_type=3Dae.obj_type;this.drawables=3D[]};q(z.prototype,= r.prototype,{unpack_drawables:function(ae){this.drawables=3D[];var ad;for(v= ar ac=3D0;ac<ae.length;ac++){ad=3Dp(ae[ac],this.view,this);this.add_drawabl= e(ad)}},init:function(){for(var ac=3D0;ac<this.drawables.length;ac++){this.= drawables[ac].init()}},_draw:function(){for(var ac=3D0;ac<this.drawables.le= ngth;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=3D[];for(= var ac=3D0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dic= t())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawable= s:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=3Dthi= s;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad= =3Dthis.drawables.indexOf(ac);if(ad!=3D=3D-1){this.drawables.splice(ad,0,ae= );return true}return false},replace_drawable:function(ae,ac,ad){var af=3Dth= is.drawables.indexOf(ae);if(af!=3D=3D-1){this.drawables[af]=3Dac;if(ad){ae.= container_div.replaceWith(ac.container_div)}this.changed()}return af},remov= e_drawable:function(ad){var ac=3Dthis.drawables.indexOf(ad);if(ac!=3D=3D-1)= {this.drawables.splice(ac,1);ad.container=3Dnull;this.changed();return true= }return false},move_drawable:function(ad,ae){var ac=3Dthis.drawables.indexO= f(ad);if(ac!=3D=3D-1){this.drawables.splice(ac,1);this.drawables.splice(ae,= 0,ad);this.changed();return true}return false},get_drawables:function(){ret= urn this.drawables}});var P=3Dfunction(ad,ac,af){q(af,{obj_type:"DrawableGr= oup",drag_handle_class:"group-handle"});z.call(this,ad,ac,af);this.content_= div=3D$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_cont= ent_div").appendTo(this.container_div);k(this.container_div,this);k(this.co= ntent_div,this);m(this.container_div,this.drag_handle_class,".group",this);= this.filters_manager=3Dnew i.FiltersManager(this);this.header_div.after(thi= s.filters_manager.parent_div);this.saved_filters_managers=3D[];if("drawable= s" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=3D= this.filters_manager;this.filters_manager=3Dnew i.FiltersManager(this,af.fi= lters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.fil= ters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototyp= e,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototyp= e.action_icons_def[1],{name:"composite_icon",title:"Show composite track",c= ss_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();= ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:= "filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac= .filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setu= p_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}= },r.prototype.action_icons_def[2]],build_container_div:function(){var ac=3D= $("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container= ){this.container.content_div.append(ac)}return ac},build_header_div:functio= n(){var ac=3D$("<div/>").addClass("track-header");ac.append($("<div/>").add= Class(this.drag_handle_class));this.name_div=3D$("<div/>").addClass("track-= name").text(this.name).appendTo(ac);return ac},hide_contents:function(){thi= s.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.req= uest_draw()},update_icons:function(){var ae=3Dthis.drawables.length;if(ae= =3D=3D=3D0){this.action_icons.composite_icon.hide();this.action_icons.filte= rs_icon.hide()}else{if(ae=3D=3D=3D1){if(this.drawables[0] instanceof f){thi= s.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}= else{var al,ak,ai,ao=3Dtrue,ag=3Dthis.drawables[0].get_type(),ac=3D0;for(al= =3D0;al<ae;al++){ai=3Dthis.drawables[al];if(ai.get_type()!=3D=3Dag){can_com= posite=3Dfalse;break}if(ai instanceof c){ac++}}if(ao||ac=3D=3D=3D1){this.ac= tion_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide= ();$(".bs-tooltip").remove()}if(ac>1&&ac=3D=3D=3Dthis.drawables.length){var= ap=3D{},ad;ai=3Dthis.drawables[0];for(ak=3D0;ak<ai.filters_manager.filters= .length;ak++){ad=3Dai.filters_manager.filters[ak];ap[ad.name]=3D[ad]}for(al= =3D1;al<this.drawables.length;al++){ai=3Dthis.drawables[al];for(ak=3D0;ak<a= i.filters_manager.filters.length;ak++){ad=3Dai.filters_manager.filters[ak];= if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();= var af,ah,aj,am;for(var an in ap){af=3Dap[an];if(af.length=3D=3D=3Dac){ah= =3Dnew i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_man= ager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_= icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{= this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function= (){for(var ac=3D0;ac<this.drawables.length;ac++){this.drawables[ac].filters= _manager=3Dthis.saved_filters_managers[ac]}this.saved_filters_managers=3D[]= },setup_multitrack_filtering:function(){if(this.filters_manager.filters.len= gth>0){this.saved_filters_managers=3D[];for(var ac=3D0;ac<this.drawables.le= ngth;ac++){drawable=3Dthis.drawables[ac];this.saved_filters_managers.push(d= 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s.overview_close.click(function(){ac.reset_overview()});this.viewport_conta= iner.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.wi= dth()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low= =3Dac.low;ah.current_height=3Dag.clientY;ah.current_x=3Dah.offsetX}).bind("= drag",function(ai,ak){var ag=3D$(this);var al=3Dak.offsetX-ak.current_x;var= ah=3Dag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.cur= rent_height=3Dai.clientY;ak.current_x=3Dak.offsetX;var aj=3DMath.round(al/a= c.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mo= usewheel",function(ai,ak,ah,ag){if(ah){ah*=3D50;var aj=3DMath.round(-ah/ac.= viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_= labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height= :ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltra= ck.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opaci= 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on(af){var ac=3Dthis;var ae=3Dac.high-ac.low;if(ac.low-af<ac.max_low){ac.lo= w=3Dac.max_low;ac.high=3Dac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.h= igh=3Dac.max_high;ac.low=3Dac.max_high-ae}else{ac.high-=3Daf;ac.low-=3Daf}}= ac.request_redraw();var ad=3Dac.chrom_select.val();this.trigger_navigate(ad= ,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_drawable.c= all(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_tr= ack:function(ac){ac.view=3Dthis;ac.init();this.label_tracks.push(ac)},remov= e_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae);if(ad)= {var ac=3Dthis;ae.container_div.hide(0,function(){$(this).remove();ac.updat= e_intro_div()})}},reset:function(){this.low=3Dthis.max_low;this.high=3Dthis= .max_high;this.viewport_container.find(".yaxislabel").remove()},request_red= raw:function(ak,ac,aj,al){var ai=3Dthis,ah=3D(al?[al]:ai.drawables),ae;var = ad;for(var ag=3D0;ag<ah.length;ag++){ad=3Dah[ag];ae=3D-1;for(var af=3D0;af<= ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]=3D= =3D=3Dad){ae=3Daf;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}= else{ai.tracks_to_be_redrawn[ag][1]=3Dac;ai.tracks_to_be_redrawn[ag][2]=3Da= j}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(a= k)});this.requested_redraw=3Dtrue}},_redraw:function(am){this.requested_red= raw=3Dfalse;var aj=3Dthis.low,af=3Dthis.high;if(aj<this.max_low){aj=3Dthis.= max_low}if(af>this.max_high){af=3Dthis.max_high}var al=3Dthis.high-this.low= ;if(this.high!=3D=3D0&&al<this.min_separation){af=3Daj+this.min_separation}= this.low=3DMath.floor(aj);this.high=3DMath.ceil(af);this.update_location(th= is.low,this.high);this.resolution_b_px=3D(this.high-this.low)/this.viewport= _container.width();this.resolution_px_b=3Dthis.viewport_container.width()/(= this.high-this.low);var ac=3D(this.low/(this.max_high-this.max_low)*this.ov= erview_viewport.width())||0;var ai=3D((this.high-this.low)/(this.max_high-t= his.max_low)*this.overview_viewport.width())||0;var an=3D13;this.overview_b= ox.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.= css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highligh= t.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=3D0,ah=3Dthis.tra= cks_to_be_redrawn.length;ag<ah;ag++){ae=3Dthis.tracks_to_be_redrawn[ag][0];= ad=3Dthis.tracks_to_be_redrawn[ag][1];ak=3Dthis.tracks_to_be_redrawn[ag][2]= ;if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=3D[];for(ag=3D0,ah=3Dthi= s.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:= function(ad,ae){if(this.max_high=3D=3D=3D0||this.high-this.low<=3Dthis.min_= separation){return}var af=3Dthis.high-this.low,ag=3Daf/2+this.low,ac=3D(af/= this.zoom_factor)/2;if(ad){ag=3Dad/this.viewport_container.width()*(this.hi= gh-this.low)+this.low}this.low=3DMath.round(ag-ac);this.high=3DMath.round(a= g+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max= _high=3D=3D=3D0){return}var ad=3Dthis.high-this.low,ae=3Dad/2+this.low,ac= =3D(ad*this.zoom_factor)/2;this.low=3DMath.round(ae-ac);this.high=3DMath.ro= und(ae+ac);this.changed();this.request_redraw()},resize_window:function(){t= his.viewport_container.height(this.container.height()-this.top_container.he= ight()-this.bottom_container.height());this.request_redraw()},set_overview:= function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_i= d=3D=3D=3Dae.dataset_id){return}this.overview_viewport.find(".track").remov= e()}var ad=3Dae.copy({content_div:this.overview_viewport}),ac=3Dthis;ad.hea= der_div.hide();ad.is_overview=3Dtrue;ac.overview_drawable=3Dad;this.overvie= w_drawable.postdraw_actions=3Dfunction(){ac.overview_highlight.show().heigh= t(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac= .overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.o= verview_close.show();ac.resize_window()};ac.overview_drawable.request_draw(= 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s.filters_manager);this.filters_available=3Dfalse;this.tool=3D("tool" in af= &&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=3Dnew x.C= ache(Q);if(this.header_div){this.set_filters_manager(this.filters_manager);= if(this.tool){this.dynamic_tool_div=3Dthis.tool.parent_div;this.header_div.= after(this.dynamic_tool_div)}}this.tiles_div=3D$("<div/>").addClass("tiles"= ).appendTo(this.content_div);this.overlay_div=3D$("<div/>").addClass("overl= ay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};q(M= .prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_ico= ns_def.concat([{name:"show_more_rows_icon",title:"To minimize track height,= not all feature rows are displayed. Click to display more rows.",css_class= :"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotte= rs[ac.view.resolution_px_b].max_rows*=3D2;ac.request_draw(true)},hide:true}= ]),copy:function(ac){var ad=3Dthis.to_dict();q(ad,{data_manager:this.data_m= anager});var ae=3Dnew this.constructor(this.view,ac,ad);ae.change_mode(this= .mode);ae.enabled=3Dthis.enabled;return ae},set_filters_manager:function(ac= ){this.filters_manager=3Dac;this.header_div.after(this.filters_manager.pare= nt_div)},to_dict:function(){return{track_type:this.get_type(),name:this.nam= e,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:t= his.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.= tool.state_dict():{})}},change_mode:function(ad){var ac=3Dthis;ac.mode=3Dad= ;ac.config.values.mode=3Dad;ac.tile_cache.clear();ac.request_draw();this.ac= tion_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");re= turn ac},update_icons:function(){var ac=3Dthis;if(ac.filters_available){ac.= action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}i= f(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_vi= z_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_= space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_= "+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad= ,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.can_draw= ()){return}var al=3Dthis.view.low,ah=3Dthis.view.high,aj=3Dah-al,ae=3Dthis.= view.container.width(),ap=3Dthis.view.resolution_px_b,ag=3Dthis.view.resolu= tion_b_px;if(this.is_overview){al=3Dthis.view.max_low;ah=3Dthis.view.max_hi= gh;ag=3D(view.max_high-view.max_low)/ae;ap=3D1/ag}this.before_draw();this.t= iles_div.children().addClass("remove");var ac=3DMath.floor(al/(ag*S)),ak=3D= true,ao=3D[],ai=3Dfunction(aq){return(aq&&"track" in aq)};while((ac*S*ag)<a= h){var am=3Dthis.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(am)){ao.p= ush(am)}else{ak=3Dfalse}ac+=3D1}if(!an){this.tiles_div.children(".remove").= removeClass("remove").remove()}var af=3Dthis;if(ak){this.tiles_div.children= (".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:fu= nction(ae,af,ah,ac){var ag=3Dfalse;for(var ad=3D0;ad<ae.length;ad++){if(ae[= ad].has_icons){ag=3Dtrue;break}}if(ag){for(var ad=3D0;ad<ae.length;ad++){ti= le=3Dae[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}}}},draw= _helper:function(ac,ao,au,ar,ah,ai,ap){var an=3Dthis,ax=3Dthis._gen_tile_ca= che_key(ao,ai,au),af=3Dthis._get_tile_bounds(au,ar);if(!ap){ap=3D{}}var aw= =3D(ac?undefined:an.tile_cache.get_elt(ax));if(aw){an.show_tile(aw,ah,ai);r= eturn aw}var al=3Dtrue;var at=3Dan.data_manager.get_data(af,an.mode,ar,an.d= ata_url_extra_params);if(V(at)){al=3Dfalse}var aj;if(view.reference_track&&= ai>view.canvas_manager.char_width_px){aj=3Dview.reference_track.data_manage= r.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params);if(V(a= j)){al=3Dfalse}}if(al){q(at,ap.more_tile_data);var ak=3Dan.mode;if(ak=3D=3D= =3D"Auto"){ak=3Dan.get_mode(at);an.update_auto_mode(ak)}var ae=3Dan.view.ca= nvas_manager.new_canvas(),av=3Daf.get("start"),ad=3Daf.get("end"),ao=3DMath= .ceil((ad-av)*ai)+an.left_offset,am=3Dan.get_canvas_height(at,ak,ai,ao);ae.= width=3Dao;ae.height=3Dam;var aq=3Dae.getContext("2d");aq.translate(this.le= ft_offset,0);var aw=3Dan.draw_tile(at,aq,ak,ar,af,ai,aj);if(aw!=3D=3Dundefi= ned){an.tile_cache.set_elt(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag= =3D$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,fal= se,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,= ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag,ai,ae)= {console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile= :function(ae,ah,ai){var ad=3Dthis,ac=3Dae.html_elt;ae.predisplay_actions();= var ag=3D(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(= this.left_offset){ag-=3Dthis.left_offset}ac.css({position:"absolute",top:0,= left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append= (ac)}ae.html_elt.height("auto");this.max_height_px=3DMath.max(this.max_heig= ht_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",th= is.max_height_px+"px");var af=3Dthis.max_height_px;if(this.visible_height_p= x!=3D=3D0){af=3DMath.min(this.max_height_px,this.visible_height_px)}this.ti= les_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=3DMa= th.floor(ac*S*ad),ag=3DMath.ceil(S*ad),ae=3D(af+ag<=3Dthis.view.max_high?af= +ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,st= art:af,end:ae})},tool_region_and_parameters_str:function(ae,ac,af){var ad= =3Dthis,ag=3D(ae!=3D=3Dundefined&&ac!=3D=3Dundefined&&af!=3D=3Dundefined?ae= +":"+ac+"-"+af:"all");return" - region=3D["+ag+"], parameters=3D["+ad.tool.= get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad)= {return true},can_subset:function(ac){return false},init_for_tool_data:func= tion(){this.data_manager.set("data_type","raw_data");this.data_query_wait= =3D1000;this.dataset_check_type=3D"state";this.normal_postdraw_actions=3Dth= is.postdraw_actions;this.postdraw_actions=3Dfunction(ae,af,ah,ac){var ad=3D= this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type=3D"conve= rted_datasets_state";ad.data_query_wait=3DK;var ag=3Dnew l.ServerStateDefer= red({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda_ldda= :ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){return ai= !=3D=3D"pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("da= ta_type","data")});ad.postdraw_actions=3Dad.normal_postdraw_actions}}});var= X=3Dfunction(ad,ac){var ae=3D{resize:false};g.call(this,ad,ac,ae);this.con= tainer_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header= _div:function(){},init:function(){this.enabled=3Dtrue},_draw:function(){var= ae=3Dthis.view,af=3Dae.high-ae.low,ai=3DMath.floor(Math.pow(10,Math.floor(= Math.log(af)/Math.log(10)))),ac=3DMath.floor(ae.low/ai)*ai,ag=3Dthis.view.c= ontainer.width(),ad=3D$("<div style=3D'position: relative; height: 1.3em;'>= </div>");while(ac<ae.high){var ah=3D(ac-ae.low)/af*ag;ad.append($("<div cla= ss=3D'label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1})= );ac+=3Dai}this.content_div.children(":first").remove();this.content_div.ap= pend(ad)}});var f=3Dfunction(ad,ac,ag){M.call(this,ad,ac,ag);this.drawables= =3D[];this.left_offset=3D0;if("drawables" in ag){var af;for(var ae=3D0;ae<a= g.drawables.length;ae++){af=3Dag.drawables[ae];this.drawables[ae]=3Dp(af,ad= ,null);if(af.left_offset>this.left_offset){this.left_offset=3Daf.left_offse= t}}this.enabled=3Dtrue}if(this.drawables.length!=3D=3D0){this.set_display_m= odes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_ic= ons();this.obj_type=3D"CompositeTrack"};q(f.prototype,M.prototype,{action_i= cons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"= layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_gr= oup()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,a= dd_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_dr= awables,change_mode:function(ac){M.prototype.change_mode.call(this,ac);for(= var ad=3D0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac= )}},init:function(){var ae=3D[];for(var ad=3D0;ad<this.drawables.length;ad+= +){ae.push(this.drawables[ad].init())}var ac=3Dthis;$.when.apply($,ae).then= (function(){ac.enabled=3Dtrue;ac.request_draw()})},update_icons:function(){= this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();t= his.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw= ,draw_helper:function(ad,at,az,aw,ak,am,au){var ar=3Dthis,aD=3Dthis._gen_ti= le_cache_key(at,am,az),ah=3Dthis._get_tile_bounds(az,aw);if(!au){au=3D{}}va= r aC=3D(ad?undefined:ar.tile_cache.get_elt(aD));if(aC){ar.show_tile(aC,ak,a= m);return aC}var al=3D[],ar,ap=3Dtrue,ax,an;for(var ay=3D0;ay<this.drawable= s.length;ay++){ar=3Dthis.drawables[ay];ax=3Dar.data_manager.get_data(ah,ar.= mode,aw,ar.data_url_extra_params);if(V(ax)){ap=3Dfalse}al.push(ax);an=3Dnul= l;if(view.reference_track&&am>view.canvas_manager.char_width_px){an=3Dview.= reference_track.data_manager.get_data(ah,ar.mode,aw,view.reference_track.da= ta_url_extra_params);if(V(an)){ap=3Dfalse}}al.push(an)}if(ap){q(ax,au.more_= tile_data);this.tile_predraw_init();var ag=3Dar.view.canvas_manager.new_can= vas(),ai=3Dar._get_tile_bounds(az,aw),aA=3Dah.get("start"),ae=3Dah.get("end= "),aB=3D0,at=3DMath.ceil((ae-aA)*am)+this.left_offset,aq=3D0,af=3D[],ay;var= ac=3D0;for(ay=3D0;ay<this.drawables.length;ay++,aB+=3D2){ar=3Dthis.drawabl= es[ay];ax=3Dal[aB];var ao=3Dar.mode;if(ao=3D=3D=3D"Auto"){ao=3Dar.get_mode(= ax);ar.update_auto_mode(ao)}af.push(ao);ac=3Dar.get_canvas_height(ax,ao,am,= at);if(ac>aq){aq=3Dac}}ag.width=3Dat;ag.height=3D(au.height?au.height:aq);a= B=3D0;var av=3Dag.getContext("2d");av.translate(this.left_offset,0);av.glob= alAlpha=3D0.5;av.globalCompositeOperation=3D"source-over";for(ay=3D0;ay<thi= s.drawables.length;ay++,aB+=3D2){ar=3Dthis.drawables[ay];ax=3Dal[aB];an=3Da= l[aB+1];aC=3Dar.draw_tile(ax,av,af[ay],aw,ah,am,an)}this.tile_cache.set_elt= (aD,aC);this.show_tile(aC,ak,am);return aC}var aj=3D$.Deferred(),ar=3Dthis;= $.when.apply($,al).then(function(){view.request_redraw(false,false,false,ar= );aj.resolve()});return aj},show_group:function(){var af=3Dnew P(this.view,= this.container,{name:this.name}),ac;for(var ae=3D0;ae<this.drawables.length= ;ae++){ac=3Dthis.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.con= tainer=3Daf;af.content_div.append(ac.container_div)}var ad=3Dthis.container= .replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:functi= on(){var af=3DNumber.MAX_VALUE,ac=3D-af,ad;for(var ae=3D0;ae<this.drawables= .length;ae++){ad=3Dthis.drawables[ae];if(ad instanceof h){if(ad.prefs.min_v= alue<af){af=3Dad.prefs.min_value}if(ad.prefs.max_value>ac){ac=3Dad.prefs.ma= x_value}}}for(var ae=3D0;ae<this.drawables.length;ae++){ad=3Dthis.drawables= [ae];ad.prefs.min_value=3Daf;ad.prefs.max_value=3Dac}},postdraw_actions:fun= ction(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var = ag=3D-1;for(var af=3D0;af<ae.length;af++){var ac=3Dae[af].html_elt.find("ca= nvas").height();if(ac>ag){ag=3Dac}}for(var af=3D0;af<ae.length;af++){var ai= =3Dae[af];if(ai.html_elt.find("canvas").height()!=3D=3Dag){this.draw_helper= (true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.htm= l_elt.remove()}}}});var B=3Dfunction(ac){M.call(this,ac,{content_div:ac.top= _labeltrack},{resize:false});ac.reference_track=3Dthis;this.left_offset=3D2= 00;this.visible_height_px=3D12;this.container_div.addClass("reference-track= ");this.content_div.css("background","none");this.content_div.css("min-heig= ht","0px");this.content_div.css("border","none");this.data_url=3Dreference_= url+"/"+this.view.dbkey;this.data_url_extra_params=3D{reference:true};this.= data_manager=3Dnew x.ReferenceTrackDataManager({data_url:this.data_url});th= is.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div= :function(){},init:function(){this.data_manager.clear();this.enabled=3Dtrue= },can_draw:r.prototype.can_draw,draw_helper:function(ag,ae,ac,ad,ah,ai,af){= if(ai>this.view.canvas_manager.char_width_px){return M.prototype.draw_helpe= r.call(this,ag,ae,ac,ad,ah,ai,af)}else{this.hide_contents();return null}},d= raw_tile:function(ak,al,ag,af,ai,am){var ae=3Dthis;if(am>this.view.canvas_m= anager.char_width_px){if(ak.data=3D=3D=3Dnull){this.hide_contents();return}= var ad=3Dal.canvas;al.font=3Dal.canvas.manager.default_font;al.textAlign=3D= "center";ak=3Dak.data;for(var ah=3D0,aj=3Dak.length;ah<aj;ah++){var ac=3DMa= th.floor(ah*am);al.fillText(ak[ah],ac,10)}this.show_contents();return new b= (ae,ai,af,ad,ak)}this.hide_contents()}});var h=3Dfunction(ae,ad,af){var ac= =3Dthis;this.display_modes=3D["Histogram","Line","Filled","Intensity"];this= .mode=3D"Histogram";M.call(this,ae,ad,af);this.hda_ldda=3Daf.hda_ldda;this.= dataset_id=3Daf.dataset_id;this.original_dataset_id=3Dthis.dataset_id;this.= left_offset=3D0;this.config=3Dnew F({track:this,params:[{key:"name",label:"= Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:= "color",default_value:l.get_random_color()},{key:"min_value",label:"Min Val= ue",type:"float",default_value:undefined},{key:"max_value",label:"Max Value= ",type:"float",default_value:undefined},{key:"mode",type:"string",default_v= alue:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidde= n:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.nam= e);ac.vertical_range=3Dac.prefs.max_value-ac.prefs.min_value;ac.set_min_val= ue(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs= =3Dthis.config.values;this.visible_height_px=3Dthis.config.values.height;th= is.vertical_range=3Dthis.config.values.max_value-this.config.values.min_val= ue};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.reques= t_draw(true)},set_min_value:function(ac){this.prefs.min_value=3Dac;$("#line= track_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cac= he.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_v= alue=3Dac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_va= lue);this.tile_cache.clear();this.request_draw()},predraw_init:function(){v= ar ac=3Dthis;ac.vertical_range=3Dundefined;return $.getJSON(ac.dataset.url(= ),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_h= igh,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line-trac= k");var ag=3Dad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseF= loat(ac.prefs.max_value))){var ae=3Dag.min,ai=3Dag.max;ae=3DMath.floor(Math= .min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=3DMath.ceil(Math.max(0,Math.min(ai= ,ag.mean+2*ag.sd)));ac.prefs.min_value=3Dae;ac.prefs.max_value=3Dai;$("#tra= ck_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.datase= t_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=3Dac.prefs.max_va= lue-ac.prefs.min_value;ac.total_frequency=3Dag.total_frequency;ac.container= _div.find(".yaxislabel").remove();var ah=3D$("<div/>").text(W(ac.prefs.min_= value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tool= tip").remove();var aj=3DparseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}= },help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","line= track_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=3D$("<div/>= ").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:f= unction(aj){$(".bs-tooltip").remove();var aj=3DparseFloat(aj);if(!isNaN(aj)= ){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel t= op").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container= _div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=3Daj.canvas,af=3Dag.g= et("start"),ai=3Dag.get("end"),ah=3Dnew L.LinePainter(al.data,af,ai,this.pr= efs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac,al.dat= a)},can_subset:function(ac){return false}});var t=3Dfunction(ae,ad,af){var = ac=3Dthis;this.display_modes=3D["Heatmap"];this.mode=3D"Heatmap";M.call(thi= s,ae,ad,af);this.hda_ldda=3Daf.hda_ldda;this.dataset_id=3Daf.dataset_id;thi= s.original_dataset_id=3Dthis.dataset_id;this.left_offset=3D0;this.config=3D= new F({track:this,params:[{key:"name",label:"Name",type:"text",default_valu= e:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_v= alue:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",defaul= t_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_= value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},= {key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height= ",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange= :function(){ac.set_name(ac.prefs.name);ac.vertical_range=3Dac.prefs.max_val= ue-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value= (ac.prefs.max_value)}});this.prefs=3Dthis.config.values;this.visible_height= _px=3Dthis.config.values.height;this.vertical_range=3Dthis.config.values.ma= x_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype= ,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){= this.prefs.min_value=3Dac;this.tile_cache.clear();this.request_draw()},set_= max_value:function(ac){this.prefs.max_value=3Dac;this.tile_cache.clear();th= is.request_draw()},draw_tile:function(ac,ae,ai,ag,ah,aj){var af=3Dae.canvas= ,ad=3Dnew L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),th= is.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,a= c.data)}});var c=3Dfunction(af,ae,ah){var ad=3Dthis;this.display_modes=3D["= Auto","Coverage","Dense","Squish","Pack"];M.call(this,af,ae,ah);var ag=3Dl.= get_random_color(),ac=3Dl.get_random_color([ag,"#FFFFFF"]);this.config=3Dne= w F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:= this.name},{key:"block_color",label:"Block color",type:"color",default_valu= e:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"colo= r",default_value:ac},{key:"label_color",label:"Label color",type:"color",de= fault_value:"black"},{key:"show_counts",label:"Show summary counts",type:"b= ool",default_value:true,help:"Show the number of items in each bin when dra= wing summary histogram"},{key:"histogram_max",label:"Histogram maximum",typ= e:"float",default_value:null,help:"clear value to set automatically"},{key:= "connector_style",label:"Connector style",type:"select",default_value:"fish= bones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",v= alue:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:tru= e},{key:"height",type:"int",default_value:this.visible_height_px,hidden:tru= e}],saved_values:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad= .tile_cache.clear();ad.set_painter_from_config();ad.request_draw()}});this.= prefs=3Dthis.config.values;this.visible_height_px=3Dthis.config.values.heig= ht;this.container_div.addClass("feature-track");this.hda_ldda=3Dah.hda_ldda= ;this.dataset_id=3Dah.dataset_id;this.original_dataset_id=3Dah.dataset_id;t= his.show_labels_scale=3D0.001;this.showing_details=3Dfalse;this.summary_dra= w_height=3D30;this.slotters=3D{};this.start_end_dct=3D{};this.left_offset= =3D200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototyp= e,{set_dataset:function(ac){this.dataset_id=3Dac.get("id");this.hda_ldda=3D= ac.get("hda_ldda");this.dataset=3Dac;this.data_manager.set("dataset",ac)},s= et_painter_from_config:function(){if(this.config.values.connector_style=3D= =3D=3D"arcs"){this.painter=3DL.ArcLinkedFeaturePainter}else{this.painter=3D= L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=3D0},pos= tdraw_actions:function(ar,am,ah,ag){M.prototype.postdraw_actions.call(this,= ar,ag);var al=3Dthis,ao;if(al.mode=3D=3D=3D"Coverage"){var ad=3D-1;for(ao= =3D0;ao<ar.length;ao++){var an=3Dar[ao].max_val;if(an>ad){ad=3Dan}}for(ao= =3D0;ao<ar.length;ao++){var au=3Dar[ao];if(au.max_val!=3D=3Dad){au.html_elt= .remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(= ),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=3Dal.filter= s_manager.filters;for(var aq=3D0;aq<ai.length;aq++){ai[aq].update_ui_elt()}= var at=3Dfalse,ac,aj;for(ao=3D0;ao<ar.length;ao++){if(ar[ao].data.length){a= c=3Dar[ao].data[0];for(var aq=3D0;aq<ai.length;aq++){aj=3Dai[aq];if(aj.appl= ies_to(ac)&&aj.min!=3D=3Daj.max){at=3Dtrue;break}}}}if(al.filters_available= !=3D=3Dat){al.filters_available=3Dat;if(!al.filters_available){al.filters_m= anager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").rem= ove();var af=3Dar[0];if(af instanceof j){var ak=3D(this.prefs.histogram_max= ?this.prefs.histogram_max:af.max_val),ae=3D$("<div/>").text(ak).make_text_e= ditable({num_cols:12,on_finish:function(av){$(".bs-tooltip").remove();var a= v=3DparseFloat(av);al.prefs.histogram_max=3D(!isNaN(av)?av:null);al.tile_ca= che.clear();al.request_draw()},help_text:"Set max value; leave blank to use= default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);= this.container_div.prepend(ae)}if(af instanceof O){var ap=3Dtrue;for(ao=3D0= ;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=3Dfalse;break}}if(!ap){this.= action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_ro= ws_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_= auto_mode:function(ac){var ac;if(this.mode=3D=3D=3D"Auto"){if(ac=3D=3D=3D"n= o_detail"){ac=3D"feature spans"}else{if(ac=3D=3D=3D"summary_tree"){ac=3D"co= verage histogram"}}this.action_icons.mode_icon.attr("title","Set display mo= de (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=3Dthi= s.view.canvas_manager.dummy_context,ae=3Dthis.slotters[ag];if(!ae||(ae.mode= !=3D=3Daf)){ae=3Dnew (u.FeatureSlotter)(ag,af,A,function(ah){return ad.meas= ureText(ah)});this.slotters[ag]=3Dae}return ae.slot_features(ac)},get_mode:= function(ac){if(ac.dataset_type=3D=3D=3D"summary_tree"){mode=3D"summary_tre= e"}else{if(ac.extra_info=3D=3D=3D"no_detail"||this.is_overview){mode=3D"no_= detail"}else{if(this.view.high-this.view.low>I){mode=3D"Squish"}else{mode= =3D"Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag=3D= =3D=3D"summary_tree"||ag=3D=3D=3D"Coverage"){return this.summary_draw_heigh= t}else{var af=3Dthis.incremental_slots(ah,ac.data,ag);var ae=3Dnew (this.pa= inter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_hei= ght(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=3Dthis,ad=3Da= q.canvas,ay=3Daf.get("start"),ac=3Daf.get("end"),ag=3Dthis.left_offset;if(a= o=3D=3D=3D"summary_tree"||ao=3D=3D=3D"Coverage"){var aA=3Dnew L.SummaryTree= Painter(am,ay,ac,this.prefs);aA.draw(aq,ad.width,ad.height,aj);return new j= (ap,af,ar,ad,am.data,am.max)}var ai=3D[],an=3Dthis.slotters[aj].slots;all_s= lotted=3Dtrue;if(am.data){var ak=3Dthis.filters_manager.filters;for(var at= =3D0,av=3Dam.data.length;at<av;at++){var ah=3Dam.data[at];var au=3Dfalse;va= r al;for(var ax=3D0,aC=3Dak.length;ax<aC;ax++){al=3Dak[ax];al.update_attrs(= ah);if(!al.keep(ah)){au=3Dtrue;break}}if(!au){ai.push(ah);if(!(ah[0] in an)= ){all_slotted=3Dfalse}}}}var aB=3D(this.filters_manager.alpha_filter?new C(= this.filters_manager.alpha_filter):null);var az=3D(this.filters_manager.hei= ght_filter?new C(this.filters_manager.height_filter):null);var aA=3Dnew (th= is.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae);var aw=3Dnull;aq.fillStyle=3Dt= his.prefs.block_color;aq.font=3Daq.canvas.manager.default_font;aq.textAlign= =3D"right";if(am.data){aw=3DaA.draw(aq,ad.width,ad.height,aj,an);aw.transla= tion=3D-ag}return new O(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw= )},data_and_mode_compatible:function(ac,ad){if(ad=3D=3D=3D"Auto"){return tr= ue}else{if(ad=3D=3D=3D"Coverage"){return ac.dataset_type=3D=3D=3D"summary_t= ree"}else{if(ac.extra_info=3D=3D=3D"no_detail"||ac.dataset_type=3D=3D=3D"su= mmary_tree"){return false}else{return true}}}},can_subset:function(ac){if(a= c.dataset_type=3D=3D=3D"summary_tree"||ac.message||ac.extra_info=3D=3D=3D"n= o_detail"){return false}return true}});var R=3Dfunction(ad,ac,ae){c.call(th= is,ad,ac,ae);this.config=3Dnew F({track:this,params:[{key:"name",label:"Nam= e",type:"text",default_value:this.name},{key:"block_color",label:"Block col= or",type:"color",default_value:l.get_random_color()},{key:"label_color",lab= el:"Label color",type:"color",default_value:"black"},{key:"show_insertions"= ,label:"Show insertions",type:"bool",default_value:false},{key:"show_counts= ",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",t= ype:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,on= change:function(){this.track.set_name(this.track.prefs.name);this.track.til= e_cache.clear();this.track.request_draw()}});this.prefs=3Dthis.config.value= s;this.painter=3DL.ReadPainter};q(R.prototype,r.prototype,M.prototype,c.pro= totype);var T=3Dfunction(ae,ad,ag){c.call(this,ae,ad,ag);var af=3Dl.get_ran= dom_color(),ac=3Dl.get_random_color([af,"#ffffff"]);this.config=3Dnew F({tr= ack:this,params:[{key:"name",label:"Name",type:"text",default_value:this.na= me},{key:"block_color",label:"Block and sense strand color",type:"color",de= fault_value:af},{key:"reverse_strand_color",label:"Antisense strand color",= type:"color",default_value:ac},{key:"label_color",label:"Label color",type:= "color",default_value:"black"},{key:"show_insertions",label:"Show insertion= s",type:"bool",default_value:false},{key:"show_differences",label:"Show dif= ferences only",type:"bool",default_value:true},{key:"show_counts",label:"Sh= ow summary counts",type:"bool",default_value:true},{key:"histogram_max",lab= el:"Histogram maximum",type:"float",default_value:null,help:"Clear value to= set automatically"},{key:"mode",type:"string",default_value:this.mode,hidd= en:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(thi= s.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()= }});this.prefs=3Dthis.config.values;this.painter=3DL.ReadPainter;this.updat= e_icons()};q(T.prototype,r.prototype,M.prototype,c.prototype);var d=3D{Line= Track:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,DiagonalHeatmapTrack:t,Compos= iteTrack:f,DrawableGroup:P};var p=3Dfunction(ae,ad,ac){if("copy" in ae){ret= urn ae.copy(ac)}else{var af=3Dae.obj_type;if(!af){af=3Dae.track_type}return= new d[af](ad,ac,ae)}};return{TracksterView:Z,DrawableGroup:P,LineTrack:h,F= eatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:= f,object_from_template:p}}); \ No newline at end of file diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/viz/trackster_ui.js --- a/static/scripts/packed/viz/trackster_ui.js +++ b/static/scripts/packed/viz/trackster_ui.js @@ -1,1 +1,1 @@ -define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/p= ainters","viz/trackster/tracks","viz/visualization"],function(g,c,h,e,b,d){= var a=3Db.object_from_template;var f=3Dg.Base.extend({initialize:function(j= ){this.baseURL=3Dj},createButtonMenu:function(){var j=3Dthis,k=3Dcreate_ico= n_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:funct= ion(){d.select_datasets(select_datasets_url,add_track_async_url,view.dbkey,= function(l){c.each(l,function(m){view.add_drawable(a(m,view,view))})})}},{i= con_class:"block--plus",title:"Add group",on_click:function(){view.add_draw= able(new b.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"book= marks",title:"Bookmarks",on_click:function(){parent.force_right_panel(($("d= iv#right").css("right")=3D=3D"0px"?"hide":"show"))}},{icon_class:"globe",ti= tle:"Circster",on_click:function(){window.location=3Dj.baseURL+"visualizati= on/circster?id=3D"+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_= click:function(){show_modal("Saving...","progress");var l=3D[];$(".bookmark= ").each(function(){l.push({position:$(this).children(".position").text(),an= notation:$(this).children(".annotation").text()})});var m=3D(view.overview_= drawable?view.overview_drawable.name:null),n=3D{view:view.to_dict(),viewpor= t:{chrom:view.chrom,start:view.low,end:view.high,overview:m},bookmarks:l};$= .ajax({url:galaxy_paths.get("visualization_url"),type:"POST",dataType:"json= ",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",vi= s_json:JSON.stringify(n)}}).success(function(o){hide_modal();view.vis_id=3D= o.vis_id;view.has_changes=3Dfalse;window.history.pushState({},"",o.url+wind= ow.location.hash)}).error(function(){show_modal("Could Not Save","Could not= save visualization. Please try again later.",{Close:hide_modal})})}},{icon= _class:"cross-circle",title:"Close",on_click:function(){window.location=3Dj= .baseURL+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});thi= s.buttonMenu=3Dk;return k},add_bookmarks:function(){var j=3Dthis,k=3Dthis.b= aseURL;show_modal("Select dataset for new bookmarks","progress");$.ajax({ur= l:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},= error:function(){alert("Grid failed")},success:function(l){show_modal("Sele= ct dataset for new bookmarks",l,{Cancel:function(){hide_modal()},Insert:fun= ction(){$("input[name=3Did]:checked,input[name=3Dldda_ids]:checked").first(= ).each(function(){var m,n=3D$(this).val();if($(this).attr("name")=3D=3D=3D"= id"){m=3D{hda_id:n}}else{m=3D{ldda_id:n}}$.ajax({url:this.baseURL+"/visuali= zation/bookmarks_from_dataset",data:m,dataType:"json"}).then(function(o){fo= r(i=3D0;i<o.data.length;i++){var p=3Do.data[i];j.add_bookmark(p[0],p[1])}})= });hide_modal()}})}})},add_bookmark:function(n,l,j){var p=3D$("#bookmarks-c= ontainer"),r=3D$("<div/>").addClass("bookmark").appendTo(p);var s=3D$("<div= />").addClass("position").appendTo(r),o=3D$("<a href=3D''/>").text(n).appen= dTo(s).click(function(){view.go_to(n);return false}),m=3D$("<div/>").text(l= ).appendTo(r);if(j){var q=3D$("<div/>").addClass("delete-icon-container").p= rependTo(r).click(function(){r.slideUp("fast");r.remove();view.has_changes= =3Dtrue;return false}),k=3D$("<a href=3D''/>").addClass("icon-button delete= ").appendTo(q);m.make_text_editable({num_rows:3,use_textarea:true,help_text= :"Edit bookmark note"}).addClass("annotation")}view.has_changes=3Dtrue;retu= rn r},create_visualization:function(o,j,n,p,m){var l=3Dthis,k=3Dnew b.View(= o);k.editor=3Dtrue;$.when(k.load_chroms_deferred).then(function(){if(j){var= y=3Dj.chrom,q=3Dj.start,v=3Dj.end,s=3Dj.overview;if(y&&(q!=3D=3Dundefined)= &&v){k.change_chrom(y,q,v)}}if(n){var t,r,u;for(var w=3D0;w<n.length;w++){k= .add_drawable(a(n[w],k,k))}}k.update_intro_div();var z;for(var w=3D0;w<k.dr= awables.length;w++){if(k.drawables[w].name=3D=3D=3Ds){k.set_overview(k.draw= ables[w]);break}}if(p){var x;for(var w=3D0;w<p.length;w++){x=3Dp[w];l.add_b= ookmark(x.position,x.annotation,m)}}k.has_changes=3Dfalse});return k},init_= keyboard_nav:function(j){$(document).keydown(function(k){if($(k.srcElement)= .is(":input")){return}switch(k.which){case 37:j.move_fraction(0.25);break;c= ase 38:var l=3DMath.round(j.viewport_container.height()/15);j.viewport_cont= ainer.scrollTop(j.viewport_container.scrollTop()-20);break;case 39:j.move_f= raction(-0.25);break;case 40:var l=3DMath.round(j.viewport_container.height= ()/15);j.viewport_container.scrollTop(j.viewport_container.scrollTop()+20);= break}})}});return{object_from_template:a,TracksterUI:f}}); \ No newline at end of file +define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/p= ainters","viz/trackster/tracks","viz/visualization"],function(g,c,h,e,b,d){= var a=3Db.object_from_template;var f=3Dg.Base.extend({initialize:function(j= ){this.baseURL=3Dj},createButtonMenu:function(){var j=3Dthis,k=3Dcreate_ico= n_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:funct= ion(){d.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":= view.dbkey},function(l){c.each(l,function(m){view.add_drawable(a(m,view,vie= w))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){v= iew.add_drawable(new b.DrawableGroup(view,view,{name:"New Group"}))}},{icon= _class:"bookmarks",title:"Bookmarks",on_click:function(){parent.force_right= _panel(($("div#right").css("right")=3D=3D"0px"?"hide":"show"))}},{icon_clas= s:"globe",title:"Circster",on_click:function(){window.location=3Dj.baseURL+= "visualization/circster?id=3D"+view.vis_id}},{icon_class:"disk--arrow",titl= e:"Save",on_click:function(){show_modal("Saving...","progress");var l=3D[];= $(".bookmark").each(function(){l.push({position:$(this).children(".position= ").text(),annotation:$(this).children(".annotation").text()})});var m=3D(vi= ew.overview_drawable?view.overview_drawable.name:null),n=3D{view:view.to_di= ct(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:m},bo= okmarks:l};$.ajax({url:galaxy_paths.get("visualization_url"),type:"POST",da= taType:"json",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"t= rackster",vis_json:JSON.stringify(n)}}).success(function(o){hide_modal();vi= ew.vis_id=3Do.vis_id;view.has_changes=3Dfalse;window.history.pushState({},"= ",o.url+window.location.hash)}).error(function(){show_modal("Could Not Save= ","Could not save visualization. Please try again later.",{Close:hide_modal= })})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.= location=3Dj.baseURL+"visualization/list"}}],{tooltip_config:{placement:"bo= ttom"}});this.buttonMenu=3Dk;return k},add_bookmarks:function(){var j=3Dthi= s,k=3Dthis.baseURL;show_modal("Select dataset for new bookmarks","progress"= );$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":= view.dbkey},error:function(){alert("Grid failed")},success:function(l){show= _modal("Select dataset for new bookmarks",l,{Cancel:function(){hide_modal()= },Insert:function(){$("input[name=3Did]:checked,input[name=3Dldda_ids]:chec= ked").first().each(function(){var m,n=3D$(this).val();if($(this).attr("name= ")=3D=3D=3D"id"){m=3D{hda_id:n}}else{m=3D{ldda_id:n}}$.ajax({url:this.baseU= RL+"/visualization/bookmarks_from_dataset",data:m,dataType:"json"}).then(fu= nction(o){for(i=3D0;i<o.data.length;i++){var p=3Do.data[i];j.add_bookmark(p= [0],p[1])}})});hide_modal()}})}})},add_bookmark:function(n,l,j){var p=3D$("= #bookmarks-container"),r=3D$("<div/>").addClass("bookmark").appendTo(p);var= s=3D$("<div/>").addClass("position").appendTo(r),o=3D$("<a href=3D''/>").t= ext(n).appendTo(s).click(function(){view.go_to(n);return false}),m=3D$("<di= v/>").text(l).appendTo(r);if(j){var q=3D$("<div/>").addClass("delete-icon-c= ontainer").prependTo(r).click(function(){r.slideUp("fast");r.remove();view.= has_changes=3Dtrue;return false}),k=3D$("<a href=3D''/>").addClass("icon-bu= tton delete").appendTo(q);m.make_text_editable({num_rows:3,use_textarea:tru= e,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes= =3Dtrue;return r},create_visualization:function(o,j,n,p,m){var l=3Dthis,k= =3Dnew b.TracksterView(o);k.editor=3Dtrue;$.when(k.load_chroms_deferred).th= en(function(){if(j){var y=3Dj.chrom,q=3Dj.start,v=3Dj.end,s=3Dj.overview;if= (y&&(q!=3D=3Dundefined)&&v){k.change_chrom(y,q,v)}}if(n){var t,r,u;for(var = w=3D0;w<n.length;w++){k.add_drawable(a(n[w],k,k))}}k.update_intro_div();var= z;for(var w=3D0;w<k.drawables.length;w++){if(k.drawables[w].name=3D=3D=3Ds= ){k.set_overview(k.drawables[w]);break}}if(p){var x;for(var w=3D0;w<p.lengt= h;w++){x=3Dp[w];l.add_bookmark(x.position,x.annotation,m)}}k.has_changes=3D= false});return k},init_keyboard_nav:function(j){$(document).keydown(functio= n(k){if($(k.srcElement).is(":input")){return}switch(k.which){case 37:j.move= _fraction(0.25);break;case 38:var l=3DMath.round(j.viewport_container.heigh= t()/15);j.viewport_container.scrollTop(j.viewport_container.scrollTop()-20)= ;break;case 39:j.move_fraction(-0.25);break;case 40:var l=3DMath.round(j.vi= ewport_container.height()/15);j.viewport_container.scrollTop(j.viewport_con= tainer.scrollTop()+20);break}})}});return{object_from_template:a,TracksterU= I:f}}); \ No newline at end of file diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],= function(s,i,l,p){var a=3Dfunction(u,x,v,w){$.ajax({url:u,data:(v?{"f-dbkey= ":v}:{}),error:function(){alert("Grid failed")},success:function(y){show_mo= dal("Select datasets for new tracks",y,{Cancel:function(){hide_modal()},Add= :function(){var z=3D[];$("input[name=3Did]:checked,input[name=3Dldda_ids]:c= hecked").each(function(){var A=3D{data_type:"track_config",hda_ldda:"hda"},= B=3D$(this).val();if($(this).attr("name")!=3D=3D"id"){A.hda_ldda=3D"ldda"}z= [z.length]=3D$.ajax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,= z).then(function(){var A=3D(arguments[0] instanceof Array?$.map(arguments,f= unction(B){return B[0]}):[arguments[0]]);w(A)});hide_modal()}})}})};var j= =3Dfunction(u){return("isResolved" in u)};var f=3Dfunction(u){this.default_= font=3Du!=3D=3Dundefined?u:"9px Monaco, Lucida Console, monospace";this.dum= my_canvas=3Dthis.new_canvas();this.dummy_context=3Dthis.dummy_canvas.getCon= text("2d");this.dummy_context.font=3Dthis.default_font;this.char_width_px= =3Dthis.dummy_context.measureText("A").width;this.patterns=3D{};this.load_p= attern("right_strand","/visualization/strand_right.png");this.load_pattern(= "left_strand","/visualization/strand_left.png");this.load_pattern("right_st= rand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_st= rand_inv","/visualization/strand_left_inv.png")};s.extend(f.prototype,{load= _pattern:function(u,y){var v=3Dthis.patterns,w=3Dthis.dummy_context,x=3Dnew= Image();x.src=3Dgalaxy_paths.attributes.image_path+y;x.onload=3Dfunction()= {v[u]=3Dw.createPattern(x,"repeat")}},get_pattern:function(u){return this.p= atterns[u]},new_canvas:function(){var u=3D$("<canvas/>")[0];if(window.G_vml= CanvasManager){G_vmlCanvasManager.initElement(u)}u.manager=3Dthis;return u}= });var q=3DBackbone.Model.extend({defaults:{num_elements:20,obj_cache:null,= key_ary:null},initialize:function(u){this.clear()},get_elt:function(v){var = w=3Dthis.attributes.obj_cache,x=3Dthis.attributes.key_ary,u=3Dx.indexOf(v);= if(u!=3D=3D-1){if(w[v].stale){x.splice(u,1);delete w[v]}else{this.move_key_= to_end(v,u)}}return w[v]},set_elt:function(v,x){var y=3Dthis.attributes.obj= _cache,z=3Dthis.attributes.key_ary,w=3Dthis.attributes.num_elements;if(!y[v= ]){if(z.length>=3Dw){var u=3Dz.shift();delete y[u]}z.push(v)}y[v]=3Dx;retur= n x},move_key_to_end:function(v,u){this.attributes.key_ary.splice(u,1);this= .attributes.key_ary.push(v)},clear:function(){this.attributes.obj_cache=3D{= };this.attributes.key_ary=3D[]},size:function(){return this.attributes.key_= ary.length}});var d=3Dq.extend({defaults:s.extend({},q.prototype.defaults,{= dataset:null,init_data:null,filters_manager:null,data_type:"data",data_mode= _compatible:function(u,v){return true},can_subset:function(u){return false}= }),initialize:function(u){q.prototype.initialize.call(this);var v=3Dthis.ge= t("init_data");if(v){this.add_data(v)}},add_data:function(u){if(this.get("n= um_elements")<u.length){this.set("num_elements",u.length)}var v=3Dthis;s.ea= ch(u,function(w){v.set_data(w.region,w)})},data_is_ready:function(){var x= =3Dthis.get("dataset"),w=3D$.Deferred(),u=3D(this.get("data_type")=3D=3D"ra= w_data"?"state":this.get("data_type")=3D=3D"data"?"converted_datasets_state= ":"error"),v=3Dnew l.ServerStateDeferred({ajax_settings:{url:this.get("data= set").url(),data:{hda_ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},= interval:5000,success_fn:function(y){return y!=3D=3D"pending"}});$.when(v.g= o()).then(function(y){w.resolve(y=3D=3D=3D"ok"||y=3D=3D=3D"data")});return = w},search_features:function(u){var v=3Dthis.get("dataset"),w=3D{query:u,hda= _ldda:v.get("hda_ldda"),data_type:"features"};return $.getJSON(v.url(),w)},= load_data:function(C,B,v,A){var y=3Dthis.get("dataset"),x=3D{data_type:this= .get("data_type"),chrom:C.get("chrom"),low:C.get("start"),high:C.get("end")= ,mode:B,resolution:v,hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=3Dthis= .get("filters_manager");if(E){var F=3D[];var u=3DE.filters;for(var z=3D0;z<= u.length;z++){F.push(u[z].name)}x.filter_cols=3DJSON.stringify(F)}var w=3Dt= his,D=3D$.getJSON(y.url(),x,function(G){w.set_data(C,G)});this.set_data(C,D= );return D},get_data:function(A,z,w,y){var B=3Dthis.get_elt(A);if(B&&(j(B)|= |this.get("data_mode_compatible")(B,z))){return B}var C=3Dthis.get("key_ary= "),v=3Dthis.get("obj_cache"),D,u;for(var x=3D0;x<C.length;x++){D=3DC[x];u= =3Dnew g({from_str:D});if(u.contains(A)){B=3Dv[D];if(j(B)||(this.get("data_= mode_compatible")(B,z)&&this.get("can_subset")(B))){this.move_key_to_end(D,= x);return B}}}return this.load_data(A,z,w,y)},set_data:function(v,u){this.s= et_elt(v,u)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:fu= nction(C,B,x,A,y){var E=3Dthis._mark_stale(C);if(!(E&&this.get("data_mode_c= ompatible")(E,B))){console.log("ERROR: problem with getting more data: curr= ent data is not compatible");return}var w=3DC.get("start");if(y=3D=3D=3Dthi= s.DEEP_DATA_REQ){$.extend(A,{start_val:E.data.length+1})}else{if(y=3D=3D=3D= this.BROAD_DATA_REQ){w=3D(E.max_high?E.max_high:E.data[E.data.length-1][2])= +1}}var D=3DC.copy().set("start",w);var v=3Dthis,z=3Dthis.load_data(D,B,x,A= ),u=3D$.Deferred();this.set_data(C,u);$.when(z).then(function(F){if(F.data)= {F.data=3DE.data.concat(F.data);if(F.max_low){F.max_low=3DE.max_low}if(F.me= ssage){F.message=3DF.message.replace(/[0-9]+/,F.data.length)}}v.set_data(C,= F);u.resolve(F)});return u},can_get_more_detailed_data:function(v){var u=3D= this.get_elt(v);return(u.dataset_type=3D=3D=3D"bigwig"&&u.data.length<8000)= },get_more_detailed_data:function(x,z,v,y,w){var u=3Dthis._mark_stale(x);if= (!u){console.log("ERROR getting more detailed data: no current data");retur= n}if(!w){w=3D{}}if(u.dataset_type=3D=3D=3D"bigwig"){w.num_samples=3D1000*y}= else{if(u.dataset_type=3D=3D=3D"summary_tree"){w.level=3DMath.min(u.level-1= ,2)}}return this.load_data(x,z,v,w)},_mark_stale:function(v){var u=3Dthis.g= et_elt(v);if(!u){console.log("ERROR: no data to mark as stale: ",this.get("= dataset"),v.toString())}u.stale=3Dtrue;return u},get_genome_wide_data:funct= ion(u){var w=3Dthis,y=3Dtrue,x=3Ds.map(u.get("chroms_info").chrom_info,func= tion(A){var z=3Dw.get_elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){= y=3Dfalse}return z});if(y){return x}var v=3D$.Deferred();$.getJSON(this.get= ("dataset").url(),{data_type:"genome_data"},function(z){w.add_data(z.data);= v.resolve(z.data)});return v},get_elt:function(u){return q.prototype.get_el= t.call(this,u.toString())},set_elt:function(v,u){return q.prototype.set_elt= .call(this,v.toString(),u)}});var n=3Dd.extend({initialize:function(u){var = v=3Dnew Backbone.Model();v.urlRoot=3Du.data_url;this.set("dataset",v)},load= _data:function(w,x,u,v){if(u>1){return{data:null}}return d.prototype.load_d= ata.call(this,w,x,u,v)}});var c=3DBackbone.Model.extend({defaults:{name:nul= l,key:null,chroms_info:null},initialize:function(u){this.id=3Du.dbkey},get_= chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_c= hrom_region:function(u){var v=3Ds.find(this.get_chroms_info(),function(w){r= eturn w.chrom=3D=3Du});return new g({chrom:v.chrom,end:v.len})}});var g=3DB= ackbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHRO= MS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTA= INED_BY:1005,AFTER:1006},initialize:function(v){if(v.from_str){var x=3Dv.fr= om_str.split(":"),w=3Dx[0],u=3Dx[1].split("-");this.set({chrom:w,start:pars= eInt(u[0],10),end:parseInt(u[1],10)})}},copy:function(){return new g({chrom= :this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:fu= nction(){return this.get("end")-this.get("start")},toString:function(){retu= rn this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:func= tion(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get(= "end")}},compute_overlap:function(B){var v=3Dthis.get("chrom"),A=3DB.get("c= hrom"),z=3Dthis.get("start"),x=3DB.get("start"),y=3Dthis.get("end"),w=3DB.g= et("end"),u;if(v&&A&&v!=3D=3DA){return this.get("DIF_CHROMS")}if(z<x){if(y<= x){u=3Dthis.get("BEFORE")}else{if(y<=3Dw){u=3Dthis.get("OVERLAP_START")}els= e{u=3Dthis.get("CONTAINS")}}}else{if(z>w){u=3Dthis.get("AFTER")}else{if(y<= =3Dw){u=3Dthis.get("CONTAINED_BY")}else{u=3Dthis.get("OVERLAP_END")}}}retur= n u},contains:function(u){return this.compute_overlap(u)=3D=3D=3Dthis.get("= CONTAINS")},overlaps:function(u){return s.intersection([this.compute_overla= p(u)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length= =3D=3D=3D0}});var m=3DBackbone.Collection.extend({model:g});var e=3DBackbon= e.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:B= ackbone.HasOne,key:"region",relatedModel:g}]});var r=3DBackbone.Collection.= extend({model:e});var t=3Di.Dataset.extend({initialize:function(u){this.set= ("id",u.dataset_id);this.set("config",p.ConfigSettingCollection.from_config= _dict(u.prefs));this.get("config").add([{key:"name",value:this.get("name")}= ,{key:"color"}]);var v=3Dthis.get("preloaded_data");if(v){v=3Dv.data}else{v= =3D[]}this.set("data_manager",new d({dataset:this,init_data:v}))}});var o= =3DBackbone.RelationalModel.extend({defaults:{title:"",type:""},url:galaxy_= paths.get("visualization_url"),save:function(){return $.ajax({url:this.url(= ),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var= k=3Do.extend({defaults:s.extend({},o.prototype.defaults,{dbkey:"",tracks:n= ull,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"t= racks",relatedModel:t}],add_tracks:function(u){this.get("tracks").add(u)}})= ;var b=3DBackbone.Model.extend({});var h=3DBackbone.Router.extend({initiali= ze:function(v){this.view=3Dv.view;this.route(/([\w]+)$/,"change_location");= this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var u=3Dthis;u.view= .on("navigate",function(w){u.navigate(w)})},change_location:function(u){thi= s.view.go_to(u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmark= Collection:r,Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeReg= ion:g,GenomeRegionCollection:m,GenomeVisualization:k,ReferenceTrackDataMana= ger:n,TrackBrowserRouter:h,TrackConfig:b,Visualization:o,select_datasets:a}= }); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],= function(s,i,l,p){var a=3Dfunction(u,x,w,v){$.ajax({url:u,data:w,error:func= tion(){alert("Grid failed")},success:function(y){show_modal("Select dataset= s for new tracks",y,{Cancel:function(){hide_modal()},Add:function(){var z= =3D[];$("input[name=3Did]:checked,input[name=3Dldda_ids]:checked").each(fun= ction(){var A=3D{data_type:"track_config",hda_ldda:"hda"},B=3D$(this).val()= ;if($(this).attr("name")!=3D=3D"id"){A.hda_ldda=3D"ldda"}z[z.length]=3D$.aj= ax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,z).then(function(= ){var A=3D(arguments[0] instanceof Array?$.map(arguments,function(B){return= B[0]}):[arguments[0]]);v(A)});hide_modal()}})}})};var j=3Dfunction(u){retu= rn("isResolved" in u)};var f=3Dfunction(u){this.default_font=3Du!=3D=3Dunde= fined?u:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=3Dthis.ne= w_canvas();this.dummy_context=3Dthis.dummy_canvas.getContext("2d");this.dum= my_context.font=3Dthis.default_font;this.char_width_px=3Dthis.dummy_context= .measureText("A").width;this.patterns=3D{};this.load_pattern("right_strand"= ,"/visualization/strand_right.png");this.load_pattern("left_strand","/visua= lization/strand_left.png");this.load_pattern("right_strand_inv","/visualiza= tion/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualiza= tion/strand_left_inv.png")};s.extend(f.prototype,{load_pattern:function(u,y= ){var v=3Dthis.patterns,w=3Dthis.dummy_context,x=3Dnew Image();x.src=3Dgala= xy_paths.attributes.image_path+y;x.onload=3Dfunction(){v[u]=3Dw.createPatte= rn(x,"repeat")}},get_pattern:function(u){return this.patterns[u]},new_canva= s:function(){var u=3D$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlC= anvasManager.initElement(u)}u.manager=3Dthis;return u}});var q=3DBackbone.M= odel.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initial= ize:function(u){this.clear()},get_elt:function(v){var w=3Dthis.attributes.o= bj_cache,x=3Dthis.attributes.key_ary,u=3Dx.indexOf(v);if(u!=3D=3D-1){if(w[v= ].stale){x.splice(u,1);delete w[v]}else{this.move_key_to_end(v,u)}}return w= [v]},set_elt:function(v,x){var y=3Dthis.attributes.obj_cache,z=3Dthis.attri= butes.key_ary,w=3Dthis.attributes.num_elements;if(!y[v]){if(z.length>=3Dw){= var u=3Dz.shift();delete y[u]}z.push(v)}y[v]=3Dx;return x},move_key_to_end:= function(v,u){this.attributes.key_ary.splice(u,1);this.attributes.key_ary.p= ush(v)},clear:function(){this.attributes.obj_cache=3D{};this.attributes.key= _ary=3D[]},size:function(){return this.attributes.key_ary.length}});var d= =3Dq.extend({defaults:s.extend({},q.prototype.defaults,{dataset:null,init_d= ata:null,filters_manager:null,data_type:"data",data_mode_compatible:functio= n(u,v){return true},can_subset:function(u){return false}}),initialize:funct= ion(u){q.prototype.initialize.call(this);var v=3Dthis.get("init_data");if(v= ){this.add_data(v)}},add_data:function(u){if(this.get("num_elements")<u.len= gth){this.set("num_elements",u.length)}var v=3Dthis;s.each(u,function(w){v.= set_data(w.region,w)})},data_is_ready:function(){var x=3Dthis.get("dataset"= ),w=3D$.Deferred(),u=3D(this.get("data_type")=3D=3D"raw_data"?"state":this.= get("data_type")=3D=3D"data"?"converted_datasets_state":"error"),v=3Dnew l.= ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda= _ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},interval:5000,success= _fn:function(y){return y!=3D=3D"pending"}});$.when(v.go()).then(function(y)= {w.resolve(y=3D=3D=3D"ok"||y=3D=3D=3D"data")});return w},search_features:fu= nction(u){var v=3Dthis.get("dataset"),w=3D{query:u,hda_ldda:v.get("hda_ldda= "),data_type:"features"};return $.getJSON(v.url(),w)},load_data:function(C,= B,v,A){var y=3Dthis.get("dataset"),x=3D{data_type:this.get("data_type"),chr= om:C.get("chrom"),low:C.get("start"),high:C.get("end"),mode:B,resolution:v,= hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=3Dthis.get("filters_manager= ");if(E){var F=3D[];var u=3DE.filters;for(var z=3D0;z<u.length;z++){F.push(= u[z].name)}x.filter_cols=3DJSON.stringify(F)}var w=3Dthis,D=3D$.getJSON(y.u= rl(),x,function(G){w.set_data(C,G)});this.set_data(C,D);return D},get_data:= function(A,z,w,y){var B=3Dthis.get_elt(A);if(B&&(j(B)||this.get("data_mode_= compatible")(B,z))){return B}var C=3Dthis.get("key_ary"),v=3Dthis.get("obj_= cache"),D,u;for(var x=3D0;x<C.length;x++){D=3DC[x];u=3Dnew g({from_str:D});= if(u.contains(A)){B=3Dv[D];if(j(B)||(this.get("data_mode_compatible")(B,z)&= &this.get("can_subset")(B))){this.move_key_to_end(D,x);return B}}}return th= is.load_data(A,z,w,y)},set_data:function(v,u){this.set_elt(v,u)},DEEP_DATA_= REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(C,B,x,A,y){var E= =3Dthis._mark_stale(C);if(!(E&&this.get("data_mode_compatible")(E,B))){cons= ole.log("ERROR: problem with getting more data: current data is not compati= ble");return}var w=3DC.get("start");if(y=3D=3D=3Dthis.DEEP_DATA_REQ){$.exte= nd(A,{start_val:E.data.length+1})}else{if(y=3D=3D=3Dthis.BROAD_DATA_REQ){w= =3D(E.max_high?E.max_high:E.data[E.data.length-1][2])+1}}var D=3DC.copy().s= et("start",w);var v=3Dthis,z=3Dthis.load_data(D,B,x,A),u=3D$.Deferred();thi= s.set_data(C,u);$.when(z).then(function(F){if(F.data){F.data=3DE.data.conca= t(F.data);if(F.max_low){F.max_low=3DE.max_low}if(F.message){F.message=3DF.m= essage.replace(/[0-9]+/,F.data.length)}}v.set_data(C,F);u.resolve(F)});retu= rn u},can_get_more_detailed_data:function(v){var u=3Dthis.get_elt(v);return= (u.dataset_type=3D=3D=3D"bigwig"&&u.data.length<8000)},get_more_detailed_da= ta:function(x,z,v,y,w){var u=3Dthis._mark_stale(x);if(!u){console.log("ERRO= R getting more detailed data: no current data");return}if(!w){w=3D{}}if(u.d= ataset_type=3D=3D=3D"bigwig"){w.num_samples=3D1000*y}else{if(u.dataset_type= =3D=3D=3D"summary_tree"){w.level=3DMath.min(u.level-1,2)}}return this.load_= data(x,z,v,w)},_mark_stale:function(v){var u=3Dthis.get_elt(v);if(!u){conso= le.log("ERROR: no data to mark as stale: ",this.get("dataset"),v.toString()= )}u.stale=3Dtrue;return u},get_genome_wide_data:function(u){var w=3Dthis,y= =3Dtrue,x=3Ds.map(u.get("chroms_info").chrom_info,function(A){var z=3Dw.get= _elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){y=3Dfalse}return z});= if(y){return x}var v=3D$.Deferred();$.getJSON(this.get("dataset").url(),{da= ta_type:"genome_data"},function(z){w.add_data(z.data);v.resolve(z.data)});r= eturn v},get_elt:function(u){return q.prototype.get_elt.call(this,u.toStrin= g())},set_elt:function(v,u){return q.prototype.set_elt.call(this,v.toString= (),u)}});var n=3Dd.extend({initialize:function(u){var v=3Dnew Backbone.Mode= l();v.urlRoot=3Du.data_url;this.set("dataset",v)},load_data:function(w,x,u,= v){if(u>1){return{data:null}}return d.prototype.load_data.call(this,w,x,u,v= )}});var c=3DBackbone.Model.extend({defaults:{name:null,key:null,chroms_inf= o:null},initialize:function(u){this.id=3Du.dbkey},get_chroms_info:function(= ){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(= u){var v=3Ds.find(this.get_chroms_info(),function(w){return w.chrom=3D=3Du}= );return new g({chrom:v.chrom,end:v.len})}});var g=3DBackbone.RelationalMod= el.extend({defaults:{chrom:null,start:0,end:0},initialize:function(v){if(v.= from_str){var x=3Dv.from_str.split(":"),w=3Dx[0],u=3Dx[1].split("-");this.s= et({chrom:w,start:parseInt(u[0],10),end:parseInt(u[1],10)})}},copy:function= (){return new g({chrom:this.get("chrom"),start:this.get("start"),end:this.g= et("end")})},length:function(){return this.get("end")-this.get("start")},to= String:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.g= et("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get(= "start"),end:this.get("end")}},compute_overlap:function(B){var v=3Dthis.get= ("chrom"),A=3DB.get("chrom"),z=3Dthis.get("start"),x=3DB.get("start"),y=3Dt= his.get("end"),w=3DB.get("end"),u;if(v&&A&&v!=3D=3DA){return g.overlap_resu= lts.DIF_CHROMS}if(z<x){if(y<x){u=3Dg.overlap_results.BEFORE}else{if(y<=3Dw)= {u=3Dg.overlap_results.OVERLAP_START}else{u=3Dg.overlap_results.CONTAINS}}}= else{if(z>w){u=3Dg.overlap_results.AFTER}else{if(y<=3Dw){u=3Dg.overlap_resu= lts.CONTAINED_BY}else{u=3Dg.overlap_results.OVERLAP_END}}}return u},contain= s:function(u){return this.compute_overlap(u)=3D=3D=3Dg.overlap_results.CONT= AINS},overlaps:function(u){return s.intersection([this.compute_overlap(u)],= [g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AF= TER]).length=3D=3D=3D0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONT= AINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}= });var m=3DBackbone.Collection.extend({model:g});var e=3DBackbone.Relationa= lModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.Has= One,key:"region",relatedModel:g}]});var r=3DBackbone.Collection.extend({mod= el:e});var t=3Di.Dataset.extend({initialize:function(u){this.set("id",u.dat= aset_id);this.set("config",p.ConfigSettingCollection.from_config_dict(u.pre= fs));this.get("config").add([{key:"name",value:this.get("name")},{key:"colo= r"}]);var v=3Dthis.get("preloaded_data");if(v){v=3Dv.data}else{v=3D[]}this.= set("data_manager",new d({dataset:this,init_data:v}))}});var o=3DBackbone.R= elationalModel.extend({defaults:{title:"",type:""},url:galaxy_paths.get("vi= sualization_url"),save:function(){return $.ajax({url:this.url(),type:"POST"= ,dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=3Do.extend= ({defaults:s.extend({},o.prototype.defaults,{dbkey:"",tracks:null,bookmarks= :null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relate= dModel:t}],add_tracks:function(u){this.get("tracks").add(u)}});var b=3DBack= bone.Model.extend({});var h=3DBackbone.Router.extend({initialize:function(v= ){this.view=3Dv.view;this.route(/([\w]+)$/,"change_location");this.route(/(= [\w]+\:[\d,]+-[\d,]+)$/,"change_location");var u=3Dthis;u.view.on("navigate= ",function(w){u.navigate(w)})},change_location:function(u){this.view.go_to(= u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmarkCollection:r,= Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeR= egionCollection:m,GenomeVisualization:k,ReferenceTrackDataManager:n,TrackBr= owserRouter:h,TrackConfig:b,Visualization:o,select_datasets:a}}); \ No newline at end of file diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -10,7 +10,7 @@ "../libs/d3", =20 "../libs/bootstrap", - "../libs/jquery/jquery-ui-1.8.23.custom.min" + "../libs/jquery/jquery-ui" ], function(){ =20 /* =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/admin/requests/select_datasets_to_transfer.mako --- a/templates/admin/requests/select_datasets_to_transfer.mako +++ b/templates/admin/requests/select_datasets_to_transfer.mako @@ -8,7 +8,7 @@ ${common_javascripts()} </%def> =20 -${h.js( "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery.coo= kie", "libs/jquery/jquery.dynatree" )} +${h.js( "libs/jquery/jquery-ui", "libs/jquery/jquery.cookie", "libs/jquery= /jquery.dynatree" )} ${h.css( "dynatree_skin/ui.dynatree" )} =20 <script type=3D"text/javascript"> diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/admin/tool_shed_repository/browse_repository.ma= ko --- a/templates/admin/tool_shed_repository/browse_repository.mako +++ b/templates/admin/tool_shed_repository/browse_repository.mako @@ -9,7 +9,7 @@ =20 <%def name=3D"javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery= .dynatree" )} + ${h.js( "libs/jquery/jquery-ui", "libs/jquery/jquery.dynatree" )} ${browse_files(repository.name, repository.repo_files_directory(trans.= app))} </%def> =20 diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/admin/tool_shed_repository/browse_tool_dependen= cy.mako --- a/templates/admin/tool_shed_repository/browse_tool_dependency.mako +++ b/templates/admin/tool_shed_repository/browse_tool_dependency.mako @@ -9,7 +9,7 @@ =20 <%def name=3D"javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery= .dynatree" )} + ${h.js( "libs/jquery/jquery-ui", "libs/jquery/jquery.dynatree" )} ${browse_files(tool_dependency.name, tool_dependency.installation_dire= ctory( trans.app ))} </%def> =20 diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -23,8 +23,6 @@ <![endif]--> =20 ${render_trackster_js_files()} -${h.js( "libs/jquery/jquery.autocomplete" )} - =20 <script type=3D"text/javascript"> =20 @@ -107,7 +105,12 @@ "Create": function() { $(document).trigger("conver= t_to_values"); continue_fn(); } }); $("#new-title").focus(); - replace_big_select_inputs(); + $("select[name=3D'dbkey']").combobox({ + appendTo: $("#overlay"), + size: 40 + }); + // To support the large number of options for dbkey, e= nable scrolling in overlay. + $("#overlay").css("overflow", "auto"); } }); %endif diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -5,7 +5,7 @@ ${h.css( "base", "autocomplete_tagging", - "jquery-ui/smoothness/jquery-ui-1.8.23.custom" + "jquery-ui/smoothness/jquery-ui" )} =20 <style type=3D"text/css"> diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/visualization/sweepster.mako --- a/templates/visualization/sweepster.mako +++ b/templates/visualization/sweepster.mako @@ -107,7 +107,7 @@ ${parent.javascripts()} =20 ${h.templates( "tool_link", "panel_section", "tool_search", "tool_form= " )} - ${h.js( "libs/require", "libs/jquery/jquery-ui-1.8.23.custom.min" )} + ${h.js( "libs/require", "libs/jquery/jquery-ui" )} =20 <script type=3D"text/javascript"> require.config({=20 diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/visualization/trackster_common.mako --- a/templates/visualization/trackster_common.mako +++ b/templates/visualization/trackster_common.mako @@ -5,13 +5,14 @@ ## Render needed CSS files. <%def name=3D"render_trackster_css_files()"> ${h.css( "history", "autocomplete_tagging", "trackster", "library",=20 - "jquery-ui/smoothness/jquery-ui-1.8.23.custom" )} + "jquery-ui/smoothness/jquery-ui" )} </%def> =20 =20 ## Render needed JavaScript files. <%def name=3D"render_trackster_js_files()"> - ${h.js( "galaxy.panels", "libs/jquery/jstorage", "libs/jquery/jquery.e= vent.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel= ", "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/require", "libs/farbtas= tic" )} + ${h.js( "galaxy.panels", "libs/jquery/jstorage", "libs/jquery/jquery.e= vent.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel= ", "libs/jquery/jquery-ui", "libs/jquery/jquery-ui-combobox", + "libs/require", "libs/farbtastic" )} </%def> =20 ## Render a block of JavaScript that contains all necessary variables for = Trackster. diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/webapps/community/repository/browse_repository.= mako --- a/templates/webapps/community/repository/browse_repository.mako +++ b/templates/webapps/community/repository/browse_repository.mako @@ -58,7 +58,7 @@ =20 <%def name=3D"javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery.rating", "libs/jquery/jquery-ui-1.8.23.cus= tom.min", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} + ${h.js( "libs/jquery/jquery.rating", "libs/jquery/jquery-ui", "libs/jq= uery/jquery.cookie", "libs/jquery/jquery.dynatree" )} ${common_javascripts(repository)} </%def> =20 diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/webapps/community/repository/upload.mako --- a/templates/webapps/community/repository/upload.mako +++ b/templates/webapps/community/repository/upload.mako @@ -28,7 +28,7 @@ =20 <%def name=3D"javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery= .cookie", "libs/jquery/jquery.dynatree" )} + ${h.js( "libs/jquery/jquery-ui", "libs/jquery/jquery.cookie", "libs/jq= uery/jquery.dynatree" )} ${common_javascripts(repository)} <script type=3D"text/javascript"> $( function() { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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