November 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Per James Johnson, handle files with a .tar extension when installing tool dependencies along with a tool shed repository.
by Bitbucket 06 Nov '12

06 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/dd4786c5b4e4/ changeset: dd4786c5b4e4 user: greg date: 2012-11-06 14:38:52 summary: Per James Johnson, handle files with a .tar extension when installing tool dependencies along with a tool shed repository. affected #: 1 file diff -r b996950ffcf2342f1211dc49e6ca75c4dfd7050f -r dd4786c5b4e48db780f6ec5da42dfafec19538f4 lib/galaxy/tool_shed/tool_dependencies/common_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/common_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/common_util.py @@ -93,7 +93,7 @@ def tar_extraction_directory( file_path, file_name ): """Try to return the correct extraction directory.""" file_name = file_name.strip() - extensions = [ '.tar.gz', '.tgz', '.tar.bz2', '.zip' ] + extensions = [ '.tar.gz', '.tgz', '.tar.bz2', '.tar', '.zip' ] for extension in extensions: if file_name.find( extension ) > 0: dir_name = file_name[ :-len( extension ) ] 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: 7 new changesets
by Bitbucket 05 Nov '12

05 Nov '12

7 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/74f946b09dd0/ changeset: 74f946b09dd0 user: carlfeberhard date: 2012-11-05 22:42:16 summary: util/debugging.py: add stack trace formatter affected #: 1 file diff -r 9d6a61f060d359a0289b3163990f6a8ba122d253 -r 74f946b09dd06341a02d009a81c00e25dd5dfb59 lib/galaxy/util/debugging.py --- /dev/null +++ b/lib/galaxy/util/debugging.py @@ -0,0 +1,29 @@ + +import inspect +import pprint + +import logging +log = logging.getLogger( __name__ ) + +def stack_trace_string( max_depth=None, line_format="{index}:{file}:{function}:{line}" ): + """ + Returns a string representation of the current stack. + + :param depth: positive integer to control how many levels of the stack are + returned. max_depth=None returns the entire stack (default). + """ + stack_list = [] + for index, caller in enumerate( inspect.stack() ): + # don't include this function + if index == 0: continue + if max_depth and index > max_depth: break + + caller_data = { + 'index' : str( index ), + 'file' : caller[1], + 'function' : caller[3], + 'line' : caller[2] + } + stack_list.append( line_format.format( **caller_data ) ) + + return '\n'.join( stack_list ) https://bitbucket.org/galaxy/galaxy-central/changeset/472a8f0ef7f5/ changeset: 472a8f0ef7f5 user: carlfeberhard date: 2012-11-05 22:45:10 summary: fix to model/__init__: was importing sys from galaxy.web.form_builder.* affected #: 1 file diff -r 74f946b09dd06341a02d009a81c00e25dd5dfb59 -r 472a8f0ef7f5517d20cecaa8a0a65d952fc7d35e lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -18,7 +18,7 @@ from galaxy.model.item_attrs import UsesAnnotations, APIItem from sqlalchemy.orm import object_session from sqlalchemy.sql.expression import func -import os.path, os, errno, codecs, operator, socket, pexpect, logging, time, shutil +import sys, os.path, os, errno, codecs, operator, socket, pexpect, logging, time, shutil if sys.version_info[:2] < ( 2, 5 ): from sets import Set as set https://bitbucket.org/galaxy/galaxy-central/changeset/613df4d4ca7d/ changeset: 613df4d4ca7d user: carlfeberhard date: 2012-11-05 22:47:14 summary: comments & docs for QuotaAgent.get_percent affected #: 1 file diff -r 472a8f0ef7f5517d20cecaa8a0a65d952fc7d35e -r 613df4d4ca7d41c240311991022148dedb2e620d lib/galaxy/quota/__init__.py --- a/lib/galaxy/quota/__init__.py +++ b/lib/galaxy/quota/__init__.py @@ -122,20 +122,26 @@ dqa = self.model.DefaultQuotaAssociation( default_type, quota ) self.sa_session.add( dqa ) self.sa_session.flush() + def get_percent( self, trans=None, user=False, history=False, usage=False, quota=False ): + """ + Return the percentage of any storage quota applicable to the user/transaction. + """ + # if trans passed, use it to get the user, history (instead of/override vals passed) if trans: user = trans.user history = trans.history + # if quota wasn't passed, attempt to get the quota if quota is False: quota = self.get_quota( user ) + # return none if no applicable quotas or quotas disabled if quota is None: return None + # get the usage, if it wasn't passed if usage is False: usage = self.get_usage( trans, user, history ) - percent = int( float( usage ) / quota * 100 ) - if percent > 100: - percent = 100 - return percent + return min( ( int( float( usage ) / quota * 100 ), 100 ) ) + def set_entity_quota_associations( self, quotas=[], users=[], groups=[], delete_existing_assocs=True ): for quota in quotas: if delete_existing_assocs: https://bitbucket.org/galaxy/galaxy-central/changeset/c57bcb1d78fc/ changeset: c57bcb1d78fc user: carlfeberhard date: 2012-11-05 22:49:58 summary: api/history_contents: allow anon-user to query own, current history; improve doc string affected #: 1 file diff -r 613df4d4ca7d41c240311991022148dedb2e620d -r c57bcb1d78fcb49e8b856a0c4e28d59626e3403f 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 @@ -26,51 +26,100 @@ def index( self, trans, history_id, ids=None, **kwd ): """ GET /api/histories/{encoded_history_id}/contents - Displays a collection (list) of history contents + Displays a collection (list) of history contents (HDAs) + + :param history_id: an encoded id string of the `History` to search + :param ids: (optional) a comma separated list of encoded `HDA` ids + + If Ids is not given, index returns a list of *summary* json objects for + every `HDA` associated with the given `history_id`. + See _summary_hda_dict. + + If ids is given, index returns a *more complete* json object for each + HDA in the ids list. + + Note: Anonymous users are allowed to get their current history contents + (generally useful for browser UI access of the api) """ rval = [] try: - history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True ) + # get the history, if anon user and requesting current history - allow it + if( ( trans.user == None ) + and ( history_id == trans.security.encode_id( trans.history.id ) ) ): + #TODO:?? is secure? + history = trans.history - # 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, ) ) ) + # otherwise, check permissions for the history first + else: + history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True ) - # 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 + # build the return hda data list + if ids: + # 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 + ids = ids.split( ',' ) + for hda in history.datasets: + if trans.security.encode_id( hda.id ) in ids: + rval.append( get_hda_dict( trans, history, hda, for_editing=True ) ) + 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 ) ) + # if no ids passed, return a _SUMMARY_ of _all_ datasets in the history + for hda in history.datasets: + rval.append( self._summary_hda_dict( trans, history_id, hda ) ) except Exception, e: rval = "Error in history API at listing contents" - log.error( rval + ": %s" % str(e) ) + log.error( rval + ": %s, %s" % ( type( e ), str( e ) ) ) trans.response.status = 500 + return rval + def _summary_hda_dict( self, trans, history_id, hda ): + """ + Returns a dictionary based on the HDA in .. _summary form:: + { + 'id' : < the encoded dataset id >, + 'name' : < currently only returns 'file' >, + 'type' : < name of the dataset >, + 'url' : < api url to retrieve this datasets full data >, + } + """ + api_type = "file" + encoded_id = trans.security.encode_id( hda.id ) + return { + 'id' : encoded_id, + 'name' : hda.name, + 'type' : api_type, + 'url' : url_for( 'history_content', history_id=history_id, id=encoded_id, ), + } + @web.expose_api def show( self, trans, id, history_id, **kwd ): """ GET /api/histories/{encoded_history_id}/contents/{encoded_content_id} Displays information about a history content (dataset). + + """ hda_dict = {} try: - 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 ) + # for anon users: + #TODO: check login_required? + #TODO: this isn't actually most_recently_used (as defined in histories) + if( ( trans.user == None ) + and ( history_id == trans.security.encode_id( trans.history.id ) ) ): + history = trans.history + #TODO: dataset/hda by id (from history) OR check_ownership for anon user + hda = self.get_history_dataset_association( trans, history, id, + check_ownership=False, check_accessible=True ) + + else: + 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: @@ -112,7 +161,7 @@ return "Not implemented." -# move these into model?? hell if I know...doesn't seem like the urls should go here +#TODO: move these into model def get_hda_dict( trans, history, hda, for_editing ): hda_dict = hda.get_api_value( view='element' ) @@ -146,13 +195,14 @@ if meta_files: hda_dict[ 'meta_files' ] = meta_files - #hda_dict[ 'display_apps' ] = get_display_apps( trans, hda ) + 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 ): + #TODO: make more straightforward (somehow) display_apps = [] def get_display_app_url( display_app_link, hda, trans ): @@ -165,7 +215,6 @@ 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(): https://bitbucket.org/galaxy/galaxy-central/changeset/7942fb2a20c5/ changeset: 7942fb2a20c5 user: carlfeberhard date: 2012-11-05 22:51:58 summary: api/users.show: added current as viable id to display json for trans.user; show, index: added key 'auota_percent' to json, returns null if no quota on user, percent otherwise affected #: 1 file diff -r c57bcb1d78fcb49e8b856a0c4e28d59626e3403f -r 7942fb2a20c5bd4b66f02e5f58335fc1b74cb040 lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -26,6 +26,7 @@ # only admins can see deleted users if not trans.user_is_admin(): return [] + else: route = 'user' query = query.filter( trans.app.model.User.table.c.deleted == False ) @@ -33,9 +34,13 @@ if not trans.user_is_admin(): item = trans.user.get_api_value( value_mapper={ 'id': trans.security.encode_id } ) item['url'] = url_for( route, id=item['id'] ) + item['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans ) return [item] + for user in query: item = user.get_api_value( value_mapper={ 'id': trans.security.encode_id } ) + #TODO: move into api_values + item['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans ) item['url'] = url_for( route, id=item['id'] ) rval.append( item ) return rval @@ -50,20 +55,36 @@ """ deleted = util.string_as_bool( deleted ) try: + # user is requesting data about themselves if id == "current": - user = trans.user + # ...and is anonymous - return usage and quota (if any) + if not trans.user: + item = self.anon_user_api_value( trans ) + return item + + # ...and is logged in - return full + else: + user = trans.user else: user = self.get_user( trans, id, deleted=deleted ) + + # check that the user is requesting themselves (and they aren't del'd) unless admin if not trans.user_is_admin(): assert trans.user == user assert not user.deleted + except: if trans.user_is_admin(): raise else: raise HTTPBadRequest( detail='Invalid user id ( %s ) specified' % id ) + item = user.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id, 'total_disk_usage': float } ) + #TODO: move into api_values (needs trans, tho - can we do that with api_keys/@property??) + #TODO: works with other users (from admin)?? + item['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans ) + return item @web.expose_api @@ -93,3 +114,16 @@ @web.expose_api def undelete( self, trans, **kwd ): raise HTTPNotImplemented() + + #TODO: move to more basal, common resource than this + def anon_user_api_value( self, trans ): + """ + Returns data for an anonymous user, truncated to only usage and quota_percent + """ + usage = trans.app.quota_agent.get_usage( trans ) + percent = trans.app.quota_agent.get_percent( trans=trans, usage=usage ) + return { + 'total_disk_usage' : int( usage ), + 'nice_total_disk_usage' : util.nice_size( usage ), + 'quota_percent' : percent + } https://bitbucket.org/galaxy/galaxy-central/changeset/24ce9866b5af/ changeset: 24ce9866b5af user: carlfeberhard date: 2012-11-05 22:56:28 summary: added user backbone model; added quota meter view on user model affected #: 5 files diff -r 7942fb2a20c5bd4b66f02e5f58335fc1b74cb040 -r 24ce9866b5af82325d2047b5d6c346ceae64c041 static/scripts/mvc/user/user-model.js --- /dev/null +++ b/static/scripts/mvc/user/user-model.js @@ -0,0 +1,56 @@ +var User = BaseModel.extend( LoggableMixin ).extend({ + //logger : console, + + defaults : { + id : null, + username : "(anonymous user)", + email : "", + total_disk_usage : 0, + nice_total_disk_usage : "0 bytes" + }, + + initialize : function( data ){ + this.log( 'User.initialize:', data ); + + this.on( 'loaded', function( model, resp ){ this.log( this + ' has loaded:', model, resp ); }); + this.on( 'change', function( model, data ){ this.log( this + ' has changed:', model, data.changes ); }); + }, + + urlRoot : 'api/users', + loadFromApi : function( idOrCurrent, options ){ + idOrCurrent = idOrCurrent || User.CURRENT_ID_STR; + options = options || {}; + var model = this, + userFn = options.success; + options.success = function( model, response ){ + model.trigger( 'loaded', model, response ); + if( userFn ){ userFn( model, response ); } + }; + if( idOrCurrent === User.CURRENT_ID_STR ){ + options.url = this.urlRoot + '/' + User.CURRENT_ID_STR; + } + return BaseModel.prototype.fetch.call( this, options ); + }, + + toString : function(){ + var userInfo = [ this.get( 'username' ) ]; + if( this.get( 'id' ) ){ + userInfo.unshift( this.get( 'id' ) ); + userInfo.push( this.get( 'email' ) ); + } + return 'User(' + userInfo.join( ':' ) + ')'; + } +}); +User.CURRENT_ID_STR = 'current'; + +User.getCurrentUserFromApi = function( options ){ + var currentUser = new User(); + currentUser.loadFromApi( User.CURRENT_ID_STR, options ); + return currentUser; +}; + +var UserCollection = Backbone.Collection.extend( LoggableMixin ).extend({ + model : User, + logger : console, + urlRoot : 'api/users' +}); diff -r 7942fb2a20c5bd4b66f02e5f58335fc1b74cb040 -r 24ce9866b5af82325d2047b5d6c346ceae64c041 static/scripts/mvc/user/user-quotameter.js --- /dev/null +++ b/static/scripts/mvc/user/user-quotameter.js @@ -0,0 +1,118 @@ +// strange view that spans two frames: renders to two separate elements based on a User's disk usage: +// a quota/usage bar (curr. masthead), and +// an over-quota message (curr. history panel) + +// for now, keep the view in the history panel (where the message is), but render ALSO to the masthead + +var UserQuotaMeter = BaseView.extend( LoggableMixin ).extend({ + logger : console, + + options : { + warnAtPercent : 85, + errorAtPercent : 100, + + // the quota/usage bar is in the masthead + meterDocument : window.top.document, + containerSelector : '.quota-meter-container', + meterSelector : '#quota-meter', + barSelector : '#quota-meter-bar', + textSelector : '#quota-meter-text', + + // the quota message currently displays in the history panel + msgDocument : ( top.frames.galaxy_history )?( top.frames.galaxy_history.document ) + :( top.document ), + msgSelector : '#quota-message-container', + + warnClass : 'quota-meter-bar-warn', + errorClass : 'quota-meter-bar-error', + usageTemplate : 'Using <%= nice_total_disk_usage %>', + quotaTemplate : 'Using <%= quota_percent %>%', + meterTemplate : '', // see where I'm going? + animationSpeed : 'fast' + }, + + initialize : function( options ){ + this.log( this + '.initialize:', options ); + + _.extend( this.options, options ); + + //this.bind( 'all', function( event, data ){ this.log( this + ' event:', event, data ); }, this ); + this.model.bind( 'change:quota_percent change:total_disk_usage', this.render, this ); + }, + + update : function( options ){ + this.log( this + ' updating user data...', options ); + this.model.loadFromApi( this.model.get( 'id' ), options ); + return this; + }, + + isOverQuota : function(){ + return ( this.model.get( 'quota_percent' ) !== null + && this.model.get( 'quota_percent' ) >= this.options.errorAtPercent ); + }, + + _render_quota : function(){ + var modelJson = this.model.toJSON(), + //prevPercent = this.model.previous( 'quota_percent' ), + percent = modelJson.quota_percent, + meter = $( UserQuotaMeter.templates.quota( modelJson ) ); + //this.log( this + '.rendering quota, percent:', percent, 'meter:', meter ); + + // OVER QUOTA: color the quota bar and show the quota error message + if( this.isOverQuota() ){ + //this.log( '\t over quota' ); + meter.addClass( 'progress-danger' ); + meter.find( '#quota-meter-text' ).css( 'color', 'white' ); + //TODO: only trigger event if state has changed + this.trigger( 'quota:over', modelJson ); + + // APPROACHING QUOTA: color the quota bar + } else if( percent >= this.options.warnAtPercent ){ + //this.log( '\t approaching quota' ); + meter.addClass( 'progress-warning' ); + //TODO: only trigger event if state has changed + this.trigger( 'quota:under quota:under:approaching', modelJson ); + + // otherwise, hide/don't use the msg box + } else { + meter.addClass( 'progress-success' ); + //TODO: only trigger event if state has changed + this.trigger( 'quota:under quota:under:ok', modelJson ); + } + return meter; + }, + + _render_usage : function(){ + var usage = $( UserQuotaMeter.templates.usage( this.model.toJSON() ) ); + this.log( this + '.rendering usage:', usage ); + return usage; + }, + + render : function(){ + //this.log( this + '.rendering' ); + var meterHtml = null; + + // no quota on server ('quota_percent' === null (can be valid at 0)), show usage instead + this.log( this + '.model.quota_percent:', this.model.get( 'quota_percent' ) ); + if( ( this.model.get( 'quota_percent' ) === null ) + || ( this.model.get( 'quota_percent' ) === undefined ) ){ + meterHtml = this._render_usage(); + + // otherwise, render percent of quota (and warning, error) + } else { + meterHtml = this._render_quota(); + } + + this.$el.html( meterHtml ); + //this.log( this + '.$el:', this.$el ); + return this; + }, + + toString : function(){ + return 'UserQuotaMeter(' + this.model + ')'; + } +}); +UserQuotaMeter.templates = { + quota : Handlebars.templates[ 'template-user-quotaMeter-quota' ], + usage : Handlebars.templates[ 'template-user-quotaMeter-usage' ] +}; diff -r 7942fb2a20c5bd4b66f02e5f58335fc1b74cb040 -r 24ce9866b5af82325d2047b5d6c346ceae64c041 static/scripts/templates/compiled/template-user-quotaMeter-quota.js --- /dev/null +++ b/static/scripts/templates/compiled/template-user-quotaMeter-quota.js @@ -0,0 +1,19 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-user-quotaMeter-quota'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression; + + + buffer += "<div id=\"quota-meter\" class=\"quota-meter progress\">\n <div id=\"quota-meter-bar\" class=\"quota-meter-bar bar\" style=\"width: "; + foundHelper = helpers.quota_percent; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.quota_percent; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "%\"></div>\n "; + buffer += "\n <div id=\"quota-meter-text\" class=\"quota-meter-text\"style=\"top: 6px\">\n Using "; + foundHelper = helpers.quota_percent; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.quota_percent; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "%\n </div>\n</div>"; + return buffer;}); +})(); \ No newline at end of file diff -r 7942fb2a20c5bd4b66f02e5f58335fc1b74cb040 -r 24ce9866b5af82325d2047b5d6c346ceae64c041 static/scripts/templates/compiled/template-user-quotaMeter-usage.js --- /dev/null +++ b/static/scripts/templates/compiled/template-user-quotaMeter-usage.js @@ -0,0 +1,14 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-user-quotaMeter-usage'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression; + + + buffer += "\n<div id=\"quota-meter\" class=\"quota-meter\" style=\"background-color: transparent\">\n <div id=\"quota-meter-text\" class=\"quota-meter-text\" style=\"top: 6px; color: white\">\n Using "; + foundHelper = helpers.nice_total_disk_usage; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.nice_total_disk_usage; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\n </div>\n</div>"; + return buffer;}); +})(); \ No newline at end of file diff -r 7942fb2a20c5bd4b66f02e5f58335fc1b74cb040 -r 24ce9866b5af82325d2047b5d6c346ceae64c041 static/scripts/templates/ui-templates.html --- /dev/null +++ b/static/scripts/templates/ui-templates.html @@ -0,0 +1,18 @@ +<script type="text/template" class="template-history" id="template-user-quotaMeter-quota"> +<div id="quota-meter" class="quota-meter progress"> + <div id="quota-meter-bar" class="quota-meter-bar bar" style="width: {{quota_percent}}%"></div> + {{! TODO: remove the hardcoded style }} + <div id="quota-meter-text" class="quota-meter-text"style="top: 6px"> + Using {{ quota_percent }}% + </div> +</div> +</script> + +<script type="text/template" class="template-history" id="template-user-quotaMeter-usage"> +{{! TODO: remove the hardcoded styles }} +<div id="quota-meter" class="quota-meter" style="background-color: transparent"> + <div id="quota-meter-text" class="quota-meter-text" style="top: 6px; color: white"> + Using {{ nice_total_disk_usage }} + </div> +</div> +</script> https://bitbucket.org/galaxy/galaxy-central/changeset/b996950ffcf2/ changeset: b996950ffcf2 user: carlfeberhard date: 2012-11-05 22:59:20 summary: (alt)history: incorporate quota meter; bugifxes affected #: 4 files diff -r 24ce9866b5af82325d2047b5d6c346ceae64c041 -r b996950ffcf2342f1211dc49e6ca75c4dfd7050f static/scripts/mvc/history.js --- a/static/scripts/mvc/history.js +++ b/static/scripts/mvc/history.js @@ -6,19 +6,44 @@ Backbone.js implementation of history panel TODO: + bug: + anon, mako: + tooltips not rendered + anno, tags rendered + title editable + bug: + when over quota history is re-rendered, over quota msg is not displayed + bc the quota:over event isn't fired + bc the user state hasn't changed + + anon user, mako template init: + bug: rename url seems to be wrong url + currently, adding a dataset (via tool execute, etc.) creates a new dataset and refreshes the page - from mako template: + logged in, mako template: + BUG: am able to start upload even if over quota - 'runs' forever + + BUG: from above sit, delete uploading hda - now in state 'discarded'! ...new state to handle + bug: quotaMeter bar rendering square in chrome + BUG: quotaMsg not showing when 100% (on load) + BUG: upload, history size, doesn't change + TODO: on hdas state:final, update ONLY the size...from what? histories.py? in js? 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? + ??: still happening? - from loadFromAPI: + from loadFromApi: BUG: not showing previous annotations fixed: + BUG: historyItem, error'd ds show display, download? + FIXED: removed + bug: loading hdas (alt_hist) + FIXED: added anon user api request ( trans.user == None and trans.history.id == requested id ) + bug: quota meter not updating on upload/tool run + FIXED: quotaMeter now listens for 'state:final' from glx_history in alternate_history.mako + bug: use of new HDACollection with event listener in init doesn't die...keeps reporting + FIXED: change getVisible to return an array BUG: history, broken intial hist state (running, updater, etc.) ??: doesn't seem to happen anymore BUG: collapse all should remove all expanded from storage @@ -40,16 +65,16 @@ 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 + localize all + break this file up + ?: render url templates on init or render? + ?: history, annotation won't accept unicode hierarchy: dataset -> hda @@ -62,6 +87,7 @@ css/html class/id 'item' -> hda add classes, ids on empty divs events (local/ui and otherwise) + list in docs as well require.js convert function comments to jsDoc style, complete comments move inline styles into base.less @@ -118,7 +144,7 @@ // based on trans.user (is_admin or security_agent.can_access_dataset( <user_roles>, hda.dataset )) accessible : false, - // this needs to be removed (it is a function of the view type (e.g. HDAForEditingView)) + //TODO: this needs to be removed (it is a function of the view type (e.g. HDAForEditingView)) for_editing : true }, @@ -139,8 +165,14 @@ this.set( 'state', HistoryDatasetAssociation.STATES.NOT_VIEWABLE ); } - this.on( 'change', function( event, x, y, z ){ - this.log( this + ' has changed:', event, x, y, z ); + //this.on( 'change', function( currModel, changedList ){ + // this.log( this + ' has changed:', currModel, changedList ); + //}); + this.on( 'change:state', function( currModel, newState ){ + this.log( this + ' has changed state:', currModel, newState ); + if( this.inFinalState() ){ + this.trigger( 'state:final', currModel, newState, this.previous( 'state' ) ); + } }); }, @@ -148,15 +180,6 @@ return ( this.get( 'deleted' ) || this.get( 'purged' ) ); }, - // roughly can_edit from history_common.mako - not deleted or purged = editable - isEditable : function(){ - return ( - //this.get( 'for_editing' ) - //&& !( 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 ){ @@ -174,11 +197,15 @@ // 'final' states are states where no processing (for the ds) is left to do on the server inFinalState : function(){ + var state = this.get( 'state' ); 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 ) + ( state === HistoryDatasetAssociation.STATES.NEW ) + || ( state === HistoryDatasetAssociation.STATES.OK ) + || ( state === HistoryDatasetAssociation.STATES.EMPTY ) + || ( state === HistoryDatasetAssociation.STATES.FAILED_METADATA ) + || ( state === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + || ( state === HistoryDatasetAssociation.STATES.DISCARDED ) + || ( state === HistoryDatasetAssociation.STATES.ERROR ) ); }, @@ -199,24 +226,32 @@ //------------------------------------------------------------------------------ HistoryDatasetAssociation.STATES = { - NOT_VIEWABLE : 'noPermission', // not in trans.app.model.Dataset.states - NEW : 'new', UPLOAD : 'upload', QUEUED : 'queued', RUNNING : 'running', + SETTING_METADATA : 'setting_metadata', + + NEW : 'new', OK : 'ok', EMPTY : 'empty', - ERROR : 'error', + + FAILED_METADATA : 'failed_metadata', + NOT_VIEWABLE : 'noPermission', // not in trans.app.model.Dataset.states DISCARDED : 'discarded', - SETTING_METADATA : 'setting_metadata', - FAILED_METADATA : 'failed_metadata' + ERROR : 'error' }; //============================================================================== var HDACollection = Backbone.Collection.extend( LoggableMixin ).extend({ model : HistoryDatasetAssociation, - logger : console, + //logger : console, + + initialize : function(){ + //this.bind( 'all', function( x, y, z ){ + // console.info( this + '', x, y, z ); + //}); + }, // return the ids of every hda in this collection ids : function(){ @@ -225,9 +260,7 @@ // 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 ); }) - ); + return 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> ] @@ -243,6 +276,17 @@ return stateLists; }, + // returns the id of every hda still running (not in a final state) + running : function(){ + var idList = []; + this.each( function( item ){ + if( !item.inFinalState() ){ + idList.push( item.get( 'id' ) ); + } + }); + return idList; + }, + // update (fetch -> render) the hdas with the ids given update : function( ids ){ this.log( this + 'update:', ids ); @@ -307,13 +351,13 @@ this.checkForUpdates(); } - this.on( 'change', function( event, x, y, z ){ - this.log( this + ' has changed:', event, x, y, z ); - }); + //this.on( 'change', function( currModel, changedList ){ + // this.log( this + ' has changed:', currModel, changedList ); + //}); }, // get data via the api (alternative to sending options,hdas to initialize) - loadFromAPI : function( historyId, callback ){ + loadFromApi : function( historyId, callback ){ var history = this; // fetch the history AND the user (mainly to see if they're logged in at this point) @@ -353,43 +397,13 @@ // 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 ) ){ + // boiling it down on the client to running/not + if( this.hdas.running().length ){ 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(){ @@ -407,6 +421,7 @@ history.set( response ); history.log( 'current history state:', history.get( 'state' ), '(was)', oldState ); + //TODO: revisit this - seems too elaborate, need something straightforward // 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 = []; @@ -451,7 +466,7 @@ // view for HistoryDatasetAssociation model above // uncomment this out see log messages - logger : console, + //logger : console, tagName : "div", className : "historyItemContainer", @@ -537,6 +552,9 @@ view.$el.append( itemWrapper ).fadeIn( 'fast', function(){ view.log( view + ' rendered:', view.$el ); view.trigger( 'rendered' ); + if( view.model.inFinalState() ){ + view.trigger( 'rendered:final' ); + } }); }); return this; @@ -697,7 +715,7 @@ 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() ){ + && !this.model.isDeletedOrPurged() ){ _.extend( modelData, { dbkey_unknown_and_editable : true }); } return HDAView.templates.hdaSummary( modelData ); @@ -1290,7 +1308,7 @@ var HistoryView = BaseView.extend( LoggableMixin ).extend({ // uncomment this out see log messages - logger : console, + //logger : console, // direct attachment to existing element el : 'body.historyPage', @@ -1369,7 +1387,7 @@ // 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.$el.find( '.tooltip' ).tooltip(); + newRender.find( '.tooltip' ).tooltip(); // render hda views (if any) if( !this.model.hdas.length @@ -1394,6 +1412,7 @@ //TODO: ideally, these would be set up before the fade in (can't because of async save text) historyView.setUpBehaviours(); + historyView.trigger( 'rendered' ); next(); }); @@ -1410,7 +1429,7 @@ visibleHdas = this.model.hdas.getVisible( show_deleted, show_hidden ); // only render the shown hdas - visibleHdas.each( function( hda ){ + _.each( visibleHdas, function( hda ){ var hdaId = hda.get( 'id' ), expanded = historyView.storage.get( 'expandedHdas' ).get( hdaId ); historyView.hdaViews[ hdaId ] = new HDAView({ @@ -1428,21 +1447,28 @@ // set up HistoryView->HDAView listeners setUpHdaListeners : function( hdaView ){ - var history = this; + var historyView = this; // use storage to maintain a list of hdas whose bodies are expanded hdaView.bind( 'toggleBodyVisibility', function( id, visible ){ if( visible ){ - history.storage.get( 'expandedHdas' ).set( id, true ); + historyView.storage.get( 'expandedHdas' ).set( id, true ); } else { - history.storage.get( 'expandedHdas' ).deleteKey( id ); + historyView.storage.get( 'expandedHdas' ).deleteKey( id ); } }); + + // rendering listeners + //hdaView.bind( 'rendered', function(){}); + hdaView.bind( 'rendered:final', function(){ historyView.trigger( 'hda:rendered:final' ); }); }, // set up js/widget behaviours: tooltips, //TODO: these should be either sub-MVs, or handled by events setUpBehaviours : function(){ + // anon users shouldn't have access to any of these + if( !( this.model.get( 'user' ) && this.model.get( 'user' ).email ) ){ return; } + // annotation slide down var historyAnnotationArea = this.$( '#history-annotation-area' ); this.$( '#history-annotate' ).click( function() { @@ -1463,6 +1489,20 @@ this.urls.annotate, "new_annotation", 18, true, 4 ); }, + //TODO: this seems more like a per user message than a history message; IOW, this doesn't belong here + showQuotaMessage : function( userData ){ + var msg = this.$el.find( '#quota-message-container' ); + //this.log( this + ' showing quota message:', msg, userData ); + if( msg.is( ':hidden' ) ){ msg.slideDown( 'fast' ); } + }, + + //TODO: this seems more like a per user message than a history message + hideQuotaMessage : function( userData ){ + var msg = this.$el.find( '#quota-message-container' ); + //this.log( this + ' hiding quota message:', msg, userData ); + if( !msg.is( ':hidden' ) ){ msg.slideUp( 'fast' ); } + }, + events : { 'click #history-collapse-all' : 'hideAllHdaBodies', 'click #history-tag' : 'loadAndDisplayTags' @@ -1470,7 +1510,7 @@ // collapse all hda bodies hideAllHdaBodies : function(){ - _.each( this.itemViews, function( item ){ + _.each( this.hdaViews, function( item ){ item.toggleBodyVisibility( null, false ); }); this.storage.set( 'expandedHdas', {} ); diff -r 24ce9866b5af82325d2047b5d6c346ceae64c041 -r b996950ffcf2342f1211dc49e6ca75c4dfd7050f 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 @@ -16,42 +16,52 @@ function program3(depth0,data) { + var buffer = "", stack1, foundHelper; + buffer += "\n <div id=\"history-name\" style=\"margin-right: 50px;\" class=\"tooltip\"\n title=\"You must be logged in to edit your history name\">"; + 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 program5(depth0,data) { + return "refresh";} -function program5(depth0,data) { +function program7(depth0,data) { return "collapse all";} -function program7(depth0,data) { +function program9(depth0,data) { var buffer = "", stack1, foundHelper; 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 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 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(12, program12, 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(12, program12, 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 program8(depth0,data) { +function program10(depth0,data) { return "Edit history tags";} -function program10(depth0,data) { +function program12(depth0,data) { return "Edit history annotation";} -function program12(depth0,data) { +function program14(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n <a href=\""; @@ -60,18 +70,18 @@ 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(13, program13, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(15, program15, 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(13, program13, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "</a>\n "; return buffer;} -function program13(depth0,data) { +function program15(depth0,data) { return "hide deleted";} -function program15(depth0,data) { +function program17(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n <a href=\""; @@ -80,52 +90,52 @@ 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(16, program16, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(18, program18, 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(16, program16, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(18, program18, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "</a>\n "; return buffer;} -function program16(depth0,data) { +function program18(depth0,data) { return "hide hidden";} -function program18(depth0,data) { +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(19, program19, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(21, program21, 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(19, program19, data)}); } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n"; return buffer;} -function program19(depth0,data) { +function program21(depth0,data) { var stack1, foundHelper; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(20, program20, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(22, program22, 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(20, program20, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(22, program22, data)}); } if(stack1 || stack1 === 0) { return stack1; } else { return ''; }} -function program20(depth0,data) { +function program22(depth0,data) { return "You are currently viewing a deleted history!";} -function program22(depth0,data) { +function program24(depth0,data) { var buffer = "", stack1; 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(25, program25, data),fn:self.program(23, program23, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(27, program27, data),fn:self.program(25, program25, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n </div>\n </div>\n </div>\n "; return buffer;} -function program23(depth0,data) { +function program25(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n "; @@ -135,12 +145,12 @@ buffer += escapeExpression(stack1) + "\n "; return buffer;} -function program25(depth0,data) { +function program27(depth0,data) { return "\n <em>Describe or add notes to history</em>\n ";} -function program27(depth0,data) { +function program29(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n<div id=\"message-container\">\n <div class=\""; @@ -154,11 +164,6 @@ buffer += escapeExpression(stack1) + "\n </div><br />\n</div>\n"; return buffer;} -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 program31(depth0,data) { @@ -171,13 +176,14 @@ 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)}); + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(3, program3, data),fn:self.program(1, program1, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } 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)}); } + 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(3, program3, data)}); } + 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 += "\" class=\"icon-button arrow-circle tooltip\" href=\""; stack1 = depth0.urls; @@ -185,42 +191,40 @@ 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)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(7, program7, 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 (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } 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)}); + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(9, program9, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } 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)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n "; stack1 = depth0.show_hidden; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(17, program17, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n</div>\n\n"; stack1 = depth0.deleted; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(18, program18, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(20, program20, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n"; buffer += "\n"; 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)}); + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(24, program24, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n</div>\n\n"; stack1 = depth0.message; - 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(29, program29, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</div>\n\n<div id=\""; + buffer += "\n\n<div id=\"quota-message-container\" style=\"display: none\">\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</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; } diff -r 24ce9866b5af82325d2047b5d6c346ceae64c041 -r b996950ffcf2342f1211dc49e6ca75c4dfd7050f static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -110,9 +110,12 @@ <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}} + {{#if user.email}} <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text" title="Click to rename history">{{name}}</div> + {{else}} + <div id="history-name" style="margin-right: 50px;" class="tooltip" + title="You must be logged in to edit your history name">{{name}}</div> {{/if}} </div></div> @@ -123,7 +126,7 @@ <a title='{{#local}}collapse all{{/local}}' id="history-collapse-all" class='icon-button toggle tooltip' href='javascript:void(0);'></a><div style="width: 40px; float: right; white-space: nowrap;"> - {{#if user}} + {{#if user.email}} <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}}" @@ -151,7 +154,7 @@ {{! TODO: move inline styles out }} <div style="margin: 0px 5px 10px 5px"> - {{#if user}} + {{#if user.email}} <div id="history-tag-area" style="display: none"><strong>Tags:</strong><div class="tag-elt"></div> @@ -180,13 +183,10 @@ </div> {{/if}} -<div id="quota-message-container"> - {{#if over_quota}} +<div id="quota-message-container" style="display: none"><div id="quota-message" class="errormessage"> You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota. </div> - <br/> - {{/if}} </div><div id="{{id}}-datasets" class="history-datasets-list"></div> diff -r 24ce9866b5af82325d2047b5d6c346ceae64c041 -r b996950ffcf2342f1211dc49e6ca75c4dfd7050f templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -90,10 +90,13 @@ hda_class_name = 'HistoryDatasetAssociation' encoded_id_template = '<%= id %>' - username_template = '<%= username %>' + #username_template = '<%= username %>' hda_ext_template = '<%= file_ext %>' meta_type_template = '<%= file_type %>' + display_app_name_template = '<%= name %>' + display_app_link_template = '<%= link %>' + url_dict = { # ................................................................ warning message links 'purge' : h.url_for( controller='dataset', action='purge', @@ -108,6 +111,7 @@ # ................................................................ title actions (display, edit, delete), 'display' : h.url_for( controller='dataset', action='display', dataset_id=encoded_id_template, preview=True, filename='' ), + #TODO: #'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', @@ -141,8 +145,9 @@ item_class=hda_class_name, item_id=encoded_id_template ), }, 'annotation' : { + #TODO: needed? doesn't look like this is used (unless graceful degradation) #'annotate_url' : h.url_for( controller='dataset', action='annotate', - # id=encoded_id_template ), # doesn't look like this is used (unless graceful degradation) + # id=encoded_id_template ), 'get' : h.url_for( controller='dataset', action='get_annotation_async', id=encoded_id_template ), 'set' : h.url_for( controller='/dataset', action='annotate_async', @@ -167,33 +172,24 @@ <%def name="get_current_user()"><% - if not trans.user: - return '{}' - return trans.webapp.api_controllers[ 'users' ].show( - trans, trans.security.encode_id( trans.user.id ) ) + return trans.webapp.api_controllers[ 'users' ].show( trans, 'current' ) %></%def><%def name="get_hdas( history_id, hdas )"><% + #BUG: one inaccessible dataset will error entire list + 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 ), trans, trans.security.encode_id( history_id ), ids=( ','.join([ trans.security.encode_id( hda.id ) for hda in hdas ]) ) ) %></%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()"> @@ -220,13 +216,17 @@ "template-history-annotationArea", "template-history-displayApps", - "template-history-historyPanel" + "template-history-historyPanel", + + "template-user-quotaMeter-quota", + "template-user-quotaMeter-usage" )} ##TODO: fix: curr hasta be _after_ h.templates - move somehow ${h.js( - "mvc/history" - ##"mvc/tags", "mvc/annotations" + "mvc/history", + ##"mvc/tags", "mvc/annotations", + "mvc/user/user-model", "mvc/user/user-quotameter" )} <script type="text/javascript"> @@ -243,31 +243,65 @@ if( console && console.debug ){ //if( console.clear ){ console.clear(); } console.debug( 'using backbone.js in history panel' ); + console.pretty = function( o ){ $( '<pre/>' ).text( JSON.stringify( o, null, ' ' ) ).appendTo( 'body' ); } } - // Navigate to a dataset. - console.debug( 'getting data' ); + + // load initial data in this page - since we're already sending it... 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 ); + console.debug( 'user:', user ); + console.debug( 'history:', history ); + console.debug( 'hdas:', hdas ); - // i don't like this, but user authentication changes views/behaviour + // i don't like this relationship, 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' }; - + //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(); + glx_history.logger = console; + var glx_history_view = new HistoryView({ + model: glx_history, + urlTemplates: galaxy_paths.attributes, + logger: console + }); + glx_history_view.render(); + + + // ...OR load from the api //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 ); + //glx_history.loadFromApi( pageData.history.id ); + + // quota meter is a cross-frame ui element (meter in masthead, over quota message in history) + // create it and join them here for now (via events) + window.currUser = new User( user ); + //window.currUser.logger = console; + window.quotaMeter = new UserQuotaMeter({ model: currUser, el: $( top.document ).find( '.quota-meter-container' ) }); + window.quotaMeter.render(); + //window.quotaMeter.logger = console; + + // show/hide the 'over quota message' in the history when the meter tells it to + quotaMeter.bind( 'quota:over', glx_history_view.showQuotaMessage, glx_history_view ); + quotaMeter.bind( 'quota:under', glx_history_view.hideQuotaMessage, glx_history_view ); + // having to add this to handle re-render of hview while overquota (the above do not fire) + glx_history_view.on( 'rendered', function(){ + if( window.quotaMeter.isOverQuota() ){ + glx_history_view.showQuotaMessage(); + } + }); + + // update the quota meter when any hda reaches a 'final' state + //NOTE: use an anon function or update will be passed the hda and think it's the options param + glx_history_view.on( 'hda:rendered:final', function(){ window.quotaMeter.update({}) }, window.quotaMeter ) + + if( console && console.debug ){ window.user = top.user = user; window._history = top._history = history; 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: dannon: Cloud Launch: Fix non-keyboard paste detection for cluster lookup step.
by Bitbucket 05 Nov '12

05 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9d6a61f060d3/ changeset: 9d6a61f060d3 user: dannon date: 2012-11-05 21:30:44 summary: Cloud Launch: Fix non-keyboard paste detection for cluster lookup step. affected #: 1 file diff -r 4d0bfc13fd582083eb2caec31029a3b4664da4ce -r 9d6a61f060d359a0289b3163990f6a8ba122d253 templates/cloud/index.mako --- a/templates/cloud/index.mako +++ b/templates/cloud/index.mako @@ -76,7 +76,7 @@ } }); //When id_secret and id_key are complete, submit to get_account_info - $("#id_secret, #id_key_id").bind("change paste keyup", function(){ + $("#id_secret, #id_key_id").bind("change paste keyup input propertychange", function(){ secret_el = $("#id_secret"); key_el = $("#id_key_id"); if (secret_el.val().length === 40 && key_el.val().length === 20){ 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: dannon: Security: Prevent potential reflected XSS via MessageException (possible in the case of invalid/malicious id lookups, for instance). Cleanup imports.
by Bitbucket 05 Nov '12

05 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4d0bfc13fd58/ changeset: 4d0bfc13fd58 user: dannon date: 2012-11-05 21:21:05 summary: Security: Prevent potential reflected XSS via MessageException (possible in the case of invalid/malicious id lookups, for instance). Cleanup imports. affected #: 1 file diff -r 873dba0459da52335fab1dab38de88a92d44a264 -r 4d0bfc13fd582083eb2caec31029a3b4664da4ce lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -4,19 +4,19 @@ import pkg_resources -import os, sys, time, socket, random, string +import os, time, socket, random, string import inspect from Cookie import CookieError pkg_resources.require( "Cheetah" ) from Cheetah.Template import Template import base -import pickle from functools import wraps from galaxy import util from galaxy.exceptions import MessageException from galaxy.util.json import to_json_string, from_json_string from galaxy.util.backports.importlib import import_module +from galaxy.util.sanitize_html import sanitize_html pkg_resources.require( "simplejson" ) import simplejson @@ -240,11 +240,11 @@ output_encoding = 'utf-8' ) def handle_controller_exception( self, e, trans, **kwargs ): + if isinstance( e, MessageException ): + #In the case of a controller exception, sanitize to make sure unsafe html input isn't reflected back to the user + return trans.show_message( sanitize_html(e.err_msg), e.type ) - if isinstance( e, MessageException ): - return trans.show_message( e.err_msg, e.type ) def make_body_iterable( self, trans, body ): - if isinstance( body, FormBuilder ): body = trans.show_form( body ) return base.WebApplication.make_body_iterable( self, trans, body ) 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: Add a message about tools that will not be enabled during migration due to not being in the tool_conf.xml.
by Bitbucket 05 Nov '12

05 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/873dba0459da/ changeset: 873dba0459da user: dan date: 2012-11-05 17:09:50 summary: Add a message about tools that will not be enabled during migration due to not being in the tool_conf.xml. affected #: 1 file diff -r 8afb981f46c11886a6106fa317936e709c311791 -r 873dba0459da52335fab1dab38de88a92d44a264 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -143,6 +143,8 @@ tool_panel_dict_for_tool_config = generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) for k, v in tool_panel_dict_for_tool_config.items(): tool_panel_dict_for_display[ k ] = v + else: + print 'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).' % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) ) metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=self.app, repository=tool_shed_repository, repository_clone_url=repository_clone_url, 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: 4 new changesets
by Bitbucket 04 Nov '12

04 Nov '12

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a1a547faab1e/ changeset: a1a547faab1e user: jgoecks date: 2012-11-04 17:04:55 summary: Unordered GTF parsing enhancements: (a) make more lenient by default so that transcript_ids are local to chromosomes, as is the case for some popular data sources and (b) add 'strict' mode for strict parsing. affected #: 1 file diff -r b3585fb0c98639a57d8934f09f4553a3ad69e80b -r a1a547faab1e43c09fa53c6bb8470bd11deaef7d lib/galaxy/datatypes/util/gff_util.py --- a/lib/galaxy/datatypes/util/gff_util.py +++ b/lib/galaxy/datatypes/util/gff_util.py @@ -359,23 +359,35 @@ attrs_strs.append( format_string % ( name, value ) ) return " ; ".join( attrs_strs ) -def read_unordered_gtf( iterator ): +def read_unordered_gtf( iterator, strict=False ): """ Returns GTF features found in an iterator. GTF lines need not be ordered or clustered for reader to work. Reader returns GFFFeature objects sorted by transcript_id, chrom, and start position. """ + + # -- Get function that generates line/feature key. -- + + get_transcript_id = lambda fields: parse_gff_attributes( fields[8] )[ 'transcript_id' ] + if strict: + # Strict GTF parsing uses transcript_id only to group lines into feature. + key_fn = get_transcript_id + else: + # Use lenient parsing where chromosome + transcript_id is the key. This allows + # transcripts with same ID on different chromosomes; this occurs in some popular + # datasources, such as RefGenes in UCSC. + key_fn = lambda fields: fields[0] + '_' + get_transcript_id( fields ) + # Aggregate intervals by transcript_id. feature_intervals = odict() for count, line in enumerate( iterator ): - line_attrs = parse_gff_attributes( line.split('\t')[8] ) - transcript_id = line_attrs[ 'transcript_id' ] - if transcript_id in feature_intervals: - feature = feature_intervals[ transcript_id ] + line_key = key_fn( line.split('\t') ) + if line_key in feature_intervals: + feature = feature_intervals[ line_key ] else: feature = [] - feature_intervals[ transcript_id ] = feature + feature_intervals[ line_key ] = feature feature.append( GFFInterval( None, line.split( '\t' ) ) ) # Create features. https://bitbucket.org/galaxy/galaxy-central/changeset/b49bf5d522ee/ changeset: b49bf5d522ee user: jgoecks date: 2012-11-04 20:49:46 summary: Transition track labels when adding/removing tracks. affected #: 1 file diff -r a1a547faab1e43c09fa53c6bb8470bd11deaef7d -r b49bf5d522eef420b1dff41690aa09abb6492202 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -40,6 +40,7 @@ .selectAll("g") .data(dataHandler) .enter().append("g") + .attr("class", "tick") .attr("transform", function(d) { return "rotate(" + (d.angle * 180 / Math.PI - 90) + ")" + "translate(" + d.radius + ",0)"; @@ -214,9 +215,14 @@ } self.zoom_drag_timeout = setTimeout(function() { // Render more detail in tracks' visible elements. + // FIXME: do not do this right now; it is not fully implemented--e.g. data bounds + // are not updated when new data is fetched--and fetching more detailed quantitative + // data is not that useful. + /* _.each(self.circular_views, function(view) { view.update_scale(scale); }); + */ }, 400); } })) @@ -452,6 +458,8 @@ this.parent_elt.selectAll('g>path.chrom-background').transition().duration(1000).attr('d', new_d); this._transition_chrom_data(); + + this._transition_labels(); }, /** @@ -547,6 +555,11 @@ }, /** + * Transition labels to new values (e.g new radius or data bounds). + */ + _transition_labels: function() {}, + + /** * Update data bounds. */ _update_data_bounds: function() { @@ -669,7 +682,6 @@ /** 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 { @@ -694,7 +706,10 @@ return d.angle > Math.PI ? "rotate(180)translate(-16)" : null; }; - this.drawTicks(this.parent_elt, this.chroms_layout, chromArcTicks, textTransform); + // Filter chroms for only those large enough for display. + var visibleChroms = _.filter(this.chroms_layout, function(c) { return c.endAngle - c.startAngle > self.min_arc_len; }); + + this.drawTicks(this.parent_elt, visibleChroms, chromArcTicks, textTransform); } }); _.extend(CircsterChromLabelTrackView.prototype, UsesTicks); @@ -755,37 +770,67 @@ .angle(line.angle()); }, + /** + * Render track min, max using ticks. + */ render_labels: function() { - // -- Render min and max using ticks. -- var self = this, // Keep counter of visible chroms. - visibleChroms = 0, - dataBoundsTicks = function(d) { - // Do not add ticks to small chroms. - if (d.endAngle - d.startAngle < 0.08) { return []; } - - // Only show bounds on every 3rd chromosome; also update visibleChroms count. - if (visibleChroms++ % 3 !== 0) { return []; } - - // Set up data to display min, max ticks. - return [ - { - radius: self.radius_bounds[0], - angle: d.startAngle, - label: self.formatNum(self.data_bounds[0]) - }, - { - radius: self.radius_bounds[1], - angle: d.startAngle, - label: self.formatNum(self.data_bounds[1]) - } - ]; - }, textTransform = function() { return "rotate(90)"; }; - this.drawTicks(this.parent_elt, this.chroms_layout, dataBoundsTicks, textTransform, true); + // Filter for visible chroms, then for every third chrom so that labels attached to only every + // third chrom. + var visibleChroms = _.filter(this.chroms_layout, function(c) { return c.endAngle - c.startAngle > 0.08; }), + labeledChroms = _.filter(visibleChroms, function(c, i) { return i % 3 === 0; }); + this.drawTicks(this.parent_elt, labeledChroms, this._data_bounds_ticks_fn(), textTransform, true); + }, + + /** + * Transition labels to new values (e.g new radius or data bounds). + */ + _transition_labels: function() { + // FIXME: (a) pull out function for getting labeled chroms? and (b) function used in transition below + // is copied from UseTicks mixin, so pull out and make generally available. + + // Transition labels to new radius bounds. + var self = this, + visibleChroms = _.filter(this.chroms_layout, function(c) { return c.endAngle - c.startAngle > 0.08; }), + labeledChroms = _.filter(visibleChroms, function(c, i) { return i % 3 === 0; }), + new_data = _.flatten( _.map(labeledChroms, function(c) { + return self._data_bounds_ticks_fn()(c); + })); + this.parent_elt.selectAll('g.tick').data(new_data).transition().attr("transform", function(d) { + return "rotate(" + (d.angle * 180 / Math.PI - 90) + ")" + + "translate(" + d.radius + ",0)"; + }); + }, + + /** + * Get function for locating data bounds ticks. + */ + _data_bounds_ticks_fn: function() { + // Closure vars. + var self = this; + visibleChroms = 0; + + // Return function for locating ticks based on chrom arc data. + return function(d) { + // Set up data to display min, max ticks. + return [ + { + radius: self.radius_bounds[0], + angle: d.startAngle, + label: self.formatNum(self.data_bounds[0]) + }, + { + radius: self.radius_bounds[1], + angle: d.startAngle, + label: self.formatNum(self.data_bounds[1]) + } + ]; + }; }, /** https://bitbucket.org/galaxy/galaxy-central/changeset/54ed06c15085/ changeset: 54ed06c15085 user: jgoecks date: 2012-11-05 01:26:33 summary: When running tools in Trackster, use Region object. affected #: 1 file diff -r b49bf5d522eef420b1dff41690aa09abb6492202 -r 54ed06c150857fb4e3d9a96b2f5d177208bad8cf static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1695,22 +1695,24 @@ // // Create track for tool's output immediately to provide user feedback. // - var + var region = new visualization.GenomeRegion({ + chrom: this.track.view.chrom, + start: this.track.view.low, + end: this.track.view.high + }), url_params = { target_dataset_id: this.track.original_dataset_id, action: 'rerun', tool_id: this.name, - regions: [{ - chrom: this.track.view.chrom, - start: this.track.view.low, - end: this.track.view.high - }] + regions: [ + region.toJSON() + ] }, current_track = this.track, // Set name of track to include tool name, parameters, and region used. track_name = url_params.tool_id + - current_track.tool_region_and_parameters_str(url_params.chrom, url_params.low, url_params.high), + current_track.tool_region_and_parameters_str(region), container; // If track not in a group, create a group for it and add new track to group. If track @@ -3040,13 +3042,10 @@ /** * Utility function that creates a label string describing the region and parameters of a track's tool. */ - tool_region_and_parameters_str: function(chrom, low, high) { - // Region is chrom:low-high or 'all.' - var - track = this, - region = (chrom !== undefined && low !== undefined && high !== undefined ? - chrom + ":" + low + "-" + high : "all"); - return " - region=[" + region + "], parameters=[" + track.tool.get_param_values().join(", ") + "]"; + tool_region_and_parameters_str: function(region) { + var track = this, + region_str = (region !== undefined ? region.toString() : "all"); + return " - region=[" + region_str + "], parameters=[" + track.tool.get_param_values().join(", ") + "]"; }, /** * Returns true if data is compatible with a given mode. Defaults to true because, for many tracks, https://bitbucket.org/galaxy/galaxy-central/changeset/8afb981f46c1/ changeset: 8afb981f46c1 user: jgoecks date: 2012-11-05 03:44:29 summary: Pack scripts. affected #: 2 files diff -r 54ed06c150857fb4e3d9a96b2f5d177208bad8cf -r 8afb981f46c11886a6106fa317936e709c311791 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,k,h){var l=Backbone.Model.extend({is_visible:function(p,m){var n=p.getBoundingClientRect(),o=$("svg")[0].getBoundingClientRect();if(n.right<0||n.left>o.right||n.bottom<0||n.top>o.bottom){return false}return true}});var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(m){this.total_gap=m.total_gap;this.genome=m.genome;this.dataset_arc_height=m.dataset_arc_height;this.track_gap=5;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("tracks").on("add",this.add_track,this);this.model.get("tracks").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("tracks").filter(function(m){return m.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("tracks").filter(function(m){return m.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var n=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-n.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=k.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var m=this;return g.map(tracks_start_radii,function(o){return[o,o+m.dataset_arc_height]})},render:function(){var v=this,p=this.dataset_arc_height,m=v.$el.width(),u=v.$el.height(),r=this.get_circular_tracks(),o=this.get_chord_tracks(),q=this.get_tracks_bounds(),n=k.select(v.$el[0]).append("svg").attr("width",m).attr("height",u).attr("pointer-events","all").append("svg:g").call(k.behavior.zoom().on("zoom",function(){var w=k.event.scale;n.attr("transform","translate("+k.event.translate+") scale("+w+")");if(v.scale!==w){if(v.zoom_drag_timeout){clearTimeout(v.zoom_drag_timeout)}v.zoom_drag_timeout=setTimeout(function(){g.each(v.circular_views,function(x){x.update_scale(w)})},400)}})).attr("transform","translate("+m/2+","+u/2+")").append("svg:g").attr("class","tracks");this.circular_views=r.map(function(x,y){var z=(x.get("track_type")==="LineTrack"?d:e),w=new z({el:n.append("g")[0],track:x,radius_bounds:q[y],genome:v.genome,total_gap:v.total_gap});w.render();return w});this.chords_views=o.map(function(x){var w=new i({el:n.append("g")[0],track:x,radius_bounds:q[0],genome:v.genome,total_gap:v.total_gap});w.render();return w});var t=this.circular_views[this.circular_views.length-1].radius_bounds[1],s=[t,t+this.label_arc_height];this.label_track_view=new b({el:n.append("g")[0],track:new c(),radius_bounds:s,genome:v.genome,total_gap:v.total_gap});this.label_track_view.render()},add_track:function(s){if(s.get("track_type")==="DiagonalHeatmapTrack"){var o=this.circular_views[0].radius_bounds,r=new i({el:k.select("g.tracks").append("g")[0],track:s,radius_bounds:o,genome:this.genome,total_gap:this.total_gap});r.render();this.chords_views.push(r)}else{var q=this.get_tracks_bounds();g.each(this.circular_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=this.circular_views.length,t=(s.get("track_type")==="LineTrack"?d:e),m=new t({el:k.select("g.tracks").append("g")[0],track:s,radius_bounds:q[p],genome:this.genome,total_gap:this.total_gap});m.render();this.circular_views.push(m);var n=q[q.length-1];n[1]=n[0];this.label_track_view.update_radius_bounds(n)}},remove_track:function(n,p,o){var m=this.circular_views[o.index];this.circular_views.splice(o.index,1);m.$el.remove();var q=this.get_tracks_bounds();g.each(this.circular_views,function(r,s){r.update_radius_bounds(q[s])})}});var j=Backbone.View.extend({tagName:"g",initialize:function(m){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=m.total_gap;this.track=m.track;this.radius_bounds=m.radius_bounds;this.genome=m.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=k.select(this.$el[0])},get_fill_color:function(){var m=this.track.get("config").get_value("block_color");if(!m){m=this.track.get("config").get_value("color")}return m},render:function(){var q=this.parent_elt;if(!q){console.log("no parent elt")}var p=this.chroms_layout,s=k.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),m=q.selectAll("g").data(p).enter().append("svg:g"),o=m.append("path").attr("d",s).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);o.append("title").text(function(u){return u.data.chrom});var n=this,r=n.track.get("data_manager"),t=(r?r.data_is_ready():true);$.when(t).then(function(){$.when(n._render_data(q)).then(function(){o.style("fill",n.bg_fill)})})},update_radius_bounds:function(n){this.radius_bounds=n;var m=k.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",m);this._transition_chrom_data()},update_scale:function(p){var o=this.scale;this.scale=p;if(p<=o){return}var n=this,m=new l();this.parent_elt.selectAll("path.chrom-data").filter(function(r,q){return m.is_visible(this)}).each(function(w,s){var v=k.select(this),r=v.attr("chrom"),u=n.genome.get_chrom_region(r),t=n.track.get("data_manager"),q;if(!t.can_get_more_detailed_data(u)){return}q=n.track.get("data_manager").get_more_detailed_data(u,"Coverage",0,p);$.when(q).then(function(z){v.remove();n._update_data_bounds();var y=g.find(n.chroms_layout,function(A){return A.data.chrom===r});var x=n.get_fill_color();n._render_chrom_data(n.parent_elt,y,z).style("stroke",x).style("fill",x)})});return n},_transition_chrom_data:function(){var n=this.track,p=this.chroms_layout,m=this.parent_elt.selectAll("g>path.chrom-data"),q=m[0].length;if(q>0){var o=this;$.when(n.get("data_manager").get_genome_wide_data(this.genome)).then(function(s){var r=g.reject(g.map(s,function(t,u){var v=null,w=o._get_path_function(p[u],t);if(w){v=w(t.data)}return v}),function(t){return t===null});m.each(function(u,t){k.select(this).transition().duration(1000).attr("d",r[t])})})}},_update_data_bounds:function(){var m=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<m[0]||this.data_bounds[1]>m[1]){this._transition_chrom_data()}},_render_data:function(p){var o=this,n=this.chroms_layout,m=this.track,q=$.Deferred();$.when(m.get("data_manager").get_genome_wide_data(this.genome)).then(function(s){o.data_bounds=o.get_data_bounds(s);layout_and_data=g.zip(n,s),chroms_data_layout=g.map(layout_and_data,function(t){var u=t[0],v=t[1];return o._render_chrom_data(p,u,v)});var r=o.get_fill_color();o.parent_elt.selectAll("path.chrom-data").style("stroke",r).style("fill",r);q.resolve(p)});return q},_render_chrom_data:function(m,n,o){},_get_path_function:function(n,m){},_chroms_layout:function(){var n=this.genome.get_chroms_info(),p=k.layout.pie().value(function(r){return r.len}).sort(null),q=p(n),m=this.total_gap/n.length,o=g.map(q,function(t,s){var r=t.endAngle-m;t.endAngle=(r>t.startAngle?r:t.startAngle);return t});return o}});var b=j.extend({initialize:function(m){j.prototype.initialize.call(this,m);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.08},_render_data:function(o){var n=this,m=o.selectAll("g");m.selectAll("path").attr("id",function(r){return"label-"+r.data.chrom});m.append("svg:text").filter(function(r){return r.endAngle-r.startAngle>n.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(r){return"#label-"+r.data.chrom}).attr("startOffset","25%").attr("font-weight","bold").text(function(r){return r.data.chrom});var q=function(t){if(t.endAngle-t.startAngle<n.min_arc_len){return[]}var r=(t.endAngle-t.startAngle)/t.value,s=k.range(0,t.value,25000000).map(function(u,w){return{angle:u*r+t.startAngle,label:w===0?0:(w%3?null:u/1000000+"M")}});if(s.length<4){s[s.length-1].label=Math.round((s[s.length-1].angle-t.startAngle)/r/1000000)+"M"}return s};var p=this.parent_elt.append("g").selectAll("g").data(this.chroms_layout).enter().append("g").selectAll("g").data(q).enter().append("g").attr("transform",function(r){return"rotate("+(r.angle*180/Math.PI-90)+")translate("+n.innerRadius+",0)"});p.append("line").attr("x1",1).attr("y1",0).attr("x2",4).attr("y2",0).style("stroke","#000");p.append("text").attr("x",4).attr("dy",".35em").attr("text-anchor",function(r){return r.angle>Math.PI?"end":null}).attr("transform",function(r){return r.angle>Math.PI?"rotate(180)translate(-16)":null}).text(function(r){return r.label})}});var f=j.extend({_render_chrom_data:function(m,p,n){var q=this._get_path_function(p,n);if(!q){return null}var o=m.datum(n.data),r=o.append("path").attr("class","chrom-data").attr("chrom",p.data.chrom).attr("d",q);return r},_get_path_function:function(p,o){if(typeof o==="string"||!o.data||o.data.length===0){return null}var m=k.scale.linear().domain(this.data_bounds).range(this.radius_bounds);var q=k.scale.linear().domain([0,o.data.length]).range([p.startAngle,p.endAngle]);var n=k.svg.line.radial().interpolate("linear").radius(function(r){return m(r[1])}).angle(function(s,r){return q(r)});return k.svg.area.radial().interpolate(n.interpolate()).innerRadius(m(0)).outerRadius(n.radius()).angle(n.angle())},get_data_bounds:function(m){}});var e=f.extend({get_data_bounds:function(n){var m=g.map(n,function(o){if(typeof o==="string"||!o.max){return 0}return o.max});return[0,(m&&typeof m!=="string"?g.max(m):0)]}});var d=f.extend({get_data_bounds:function(n){var m=g.flatten(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=j.extend({render:function(){var m=this;$.when(m.track.get("data_manager").data_is_ready()).then(function(){$.when(m.track.get("data_manager").get_genome_wide_data(m.genome)).then(function(p){var o=[],n=m.genome.get_chroms_info();g.each(p,function(t,s){var q=n[s].chrom;var r=g.map(t.data,function(v){var u=m._get_region_angle(q,v[1]),w=m._get_region_angle(v[3],v[4]);return{source:{startAngle:u,endAngle:u+0.01},target:{startAngle:w,endAngle:w+0.01}}});o=o.concat(r)});m.parent_elt.append("g").attr("class","chord").selectAll("path").data(o).enter().append("path").style("fill",m.get_fill_color()).attr("d",k.svg.chord().radius(m.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(m){this.radius_bounds=m;this.parent_elt.selectAll("path").transition().attr("d",k.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(o,m){var n=g.find(this.chroms_layout,function(p){return p.data.chrom===o});return n.endAngle-((n.endAngle-n.startAngle)*(n.data.len-m)/n.data.len)}});return{CircsterView:a}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/visualization"],function(g,l,i){var m=Backbone.Model.extend({is_visible:function(q,n){var o=q.getBoundingClientRect(),p=$("svg")[0].getBoundingClientRect();if(o.right<0||o.left>p.right||o.bottom<0||o.top>p.bottom){return false}return true}});var h={drawTicks:function(r,q,v,p,n){var u=r.append("g").selectAll("g").data(q).enter().append("g").selectAll("g").data(v).enter().append("g").attr("class","tick").attr("transform",function(w){return"rotate("+(w.angle*180/Math.PI-90)+")translate("+w.radius+",0)"});var t=[],s=[],o=function(w){return w.angle>Math.PI?"end":null};if(n){t=[0,0,0,-4];s=[4,0,"",".35em"];o=null}else{t=[1,0,4,0];s=[0,4,".35em",""]}u.append("line").attr("x1",t[0]).attr("y1",t[1]).attr("x2",t[2]).attr("y1",t[3]).style("stroke","#000");u.append("text").attr("x",s[0]).attr("y",s[1]).attr("dx",s[2]).attr("dy",s[3]).attr("text-anchor",o).attr("transform",p).text(function(w){return w.label})},formatNum:function(o,n){var q=null;if(o<1){q=o.toPrecision(n)}else{var p=Math.round(o.toPrecision(n));if(o<1000){q=p}else{if(o<1000000){q=Math.round((p/1000).toPrecision(3)).toFixed(0)+"K"}else{if(o<1000000000){q=Math.round((p/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return q}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(n){this.total_gap=n.total_gap;this.genome=n.genome;this.dataset_arc_height=n.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("tracks").on("add",this.add_track,this);this.model.get("tracks").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var o=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-o.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=l.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var n=this;return g.map(tracks_start_radii,function(p){return[p,p+n.dataset_arc_height]})},render:function(){var w=this,q=this.dataset_arc_height,n=w.$el.width(),v=w.$el.height(),s=this.get_circular_tracks(),p=this.get_chord_tracks(),r=this.get_tracks_bounds(),o=l.select(w.$el[0]).append("svg").attr("width",n).attr("height",v).attr("pointer-events","all").append("svg:g").call(l.behavior.zoom().on("zoom",function(){var x=l.event.scale;o.attr("transform","translate("+l.event.translate+") scale("+x+")");if(w.scale!==x){if(w.zoom_drag_timeout){clearTimeout(w.zoom_drag_timeout)}w.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+n/2+","+v/2+")").append("svg:g").attr("class","tracks");this.circular_views=s.map(function(y,z){var A=(y.get("track_type")==="LineTrack"?d:e),x=new A({el:o.append("g")[0],track:y,radius_bounds:r[z],genome:w.genome,total_gap:w.total_gap});x.render();return x});this.chords_views=p.map(function(y){var x=new j({el:o.append("g")[0],track:y,radius_bounds:r[0],genome:w.genome,total_gap:w.total_gap});x.render();return x});var u=this.circular_views[this.circular_views.length-1].radius_bounds[1],t=[u,u+this.label_arc_height];this.label_track_view=new b({el:o.append("g")[0],track:new c(),radius_bounds:t,genome:w.genome,total_gap:w.total_gap});this.label_track_view.render()},add_track:function(t){if(t.get("track_type")==="DiagonalHeatmapTrack"){var p=this.circular_views[0].radius_bounds,s=new j({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:p,genome:this.genome,total_gap:this.total_gap});s.render();this.chords_views.push(s)}else{var r=this.get_tracks_bounds();g.each(this.circular_views,function(v,w){v.update_radius_bounds(r[w])});g.each(this.chords_views,function(v){v.update_radius_bounds(r[0])});var q=this.circular_views.length,u=(t.get("track_type")==="LineTrack"?d:e),n=new u({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:r[q],genome:this.genome,total_gap:this.total_gap});n.render();this.circular_views.push(n);var o=r[r.length-1];o[1]=o[0];this.label_track_view.update_radius_bounds(o)}},remove_track:function(o,q,p){var n=this.circular_views[p.index];this.circular_views.splice(p.index,1);n.$el.remove();var r=this.get_tracks_bounds();g.each(this.circular_views,function(s,t){s.update_radius_bounds(r[t])})}});var k=Backbone.View.extend({tagName:"g",initialize:function(n){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=n.total_gap;this.track=n.track;this.radius_bounds=n.radius_bounds;this.genome=n.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=l.select(this.$el[0])},get_fill_color:function(){var n=this.track.get("config").get_value("block_color");if(!n){n=this.track.get("config").get_value("color")}return n},render:function(){var r=this.parent_elt;if(!r){console.log("no parent elt")}var q=this.chroms_layout,t=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),n=r.selectAll("g").data(q).enter().append("svg:g"),p=n.append("path").attr("d",t).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);p.append("title").text(function(v){return v.data.chrom});var o=this,s=o.track.get("data_manager"),u=(s?s.data_is_ready():true);$.when(u).then(function(){$.when(o._render_data(r)).then(function(){p.style("fill",o.bg_fill);o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(o){this.radius_bounds=o;var n=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",n);this._transition_chrom_data();this._transition_labels()},update_scale:function(q){var p=this.scale;this.scale=q;if(q<=p){return}var o=this,n=new m();this.parent_elt.selectAll("path.chrom-data").filter(function(s,r){return n.is_visible(this)}).each(function(x,t){var w=l.select(this),s=w.attr("chrom"),v=o.genome.get_chrom_region(s),u=o.track.get("data_manager"),r;if(!u.can_get_more_detailed_data(v)){return}r=o.track.get("data_manager").get_more_detailed_data(v,"Coverage",0,q);$.when(r).then(function(A){w.remove();o._update_data_bounds();var z=g.find(o.chroms_layout,function(B){return B.data.chrom===s});var y=o.get_fill_color();o._render_chrom_data(o.parent_elt,z,A).style("stroke",y).style("fill",y)})});return o},_transition_chrom_data:function(){var o=this.track,q=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data"),r=n[0].length;if(r>0){var p=this;$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){var s=g.reject(g.map(t,function(u,v){var w=null,x=p._get_path_function(q[v],u);if(x){w=x(u.data)}return w}),function(u){return u===null});n.each(function(v,u){l.select(this).transition().duration(1000).attr("d",s[u])})})}},_transition_labels:function(){},_update_data_bounds:function(){var n=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<n[0]||this.data_bounds[1]>n[1]){this._transition_chrom_data()}},_render_data:function(q){var p=this,o=this.chroms_layout,n=this.track,r=$.Deferred();$.when(n.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){p.data_bounds=p.get_data_bounds(t);layout_and_data=g.zip(o,t),chroms_data_layout=g.map(layout_and_data,function(u){var v=u[0],w=u[1];return p._render_chrom_data(q,v,w)});var s=p.get_fill_color();p.parent_elt.selectAll("path.chrom-data").style("stroke",s).style("fill",s);r.resolve(q)});return r},_render_chrom_data:function(n,o,p){},_get_path_function:function(o,n){},_chroms_layout:function(){var o=this.genome.get_chroms_info(),q=l.layout.pie().value(function(s){return s.len}).sort(null),r=q(o),n=this.total_gap/o.length,p=g.map(r,function(u,t){var s=u.endAngle-n;u.endAngle=(s>u.startAngle?s:u.startAngle);return u});return p}});var b=k.extend({initialize:function(n){k.prototype.initialize.call(this,n);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.08},_render_data:function(p){var o=this,n=p.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom});n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>o.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").attr("font-weight","bold").text(function(t){return t.data.chrom});var q=function(v){var t=(v.endAngle-v.startAngle)/v.value,u=l.range(0,v.value,25000000).map(function(w,x){return{radius:o.innerRadius,angle:w*t+v.startAngle,label:x===0?0:(x%3?null:o.formatNum(w))}});if(u.length<4){u[u.length-1].label=o.formatNum(Math.round((u[u.length-1].angle-v.startAngle)/t))}return u};var s=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null};var r=g.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>o.min_arc_len});this.drawTicks(this.parent_elt,r,q,s)}});g.extend(b.prototype,h);var f=k.extend({_render_chrom_data:function(n,q,o){var r=this._get_path_function(q,o);if(!r){return null}var p=n.datum(o.data),s=p.append("path").attr("class","chrom-data").attr("chrom",q.data.chrom).attr("d",r);return s},_get_path_function:function(q,p){if(typeof p==="string"||!p.data||p.data.length===0){return null}var n=l.scale.linear().domain(this.data_bounds).range(this.radius_bounds);var r=l.scale.linear().domain([0,p.data.length]).range([q.startAngle,q.endAngle]);var o=l.svg.line.radial().interpolate("linear").radius(function(s){return n(s[1])}).angle(function(t,s){return r(s)});return l.svg.area.radial().interpolate(o.interpolate()).innerRadius(n(0)).outerRadius(o.radius()).angle(o.angle())},render_labels:function(){var n=this,q=function(){return"rotate(90)"};var p=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),o=g.filter(p,function(s,r){return r%3===0});this.drawTicks(this.parent_elt,o,this._data_bounds_ticks_fn(),q,true)},_transition_labels:function(){var o=this,q=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),p=g.filter(q,function(s,r){return r%3===0}),n=g.flatten(g.map(p,function(r){return o._data_bounds_ticks_fn()(r)}));this.parent_elt.selectAll("g.tick").data(n).transition().attr("transform",function(r){return"rotate("+(r.angle*180/Math.PI-90)+")translate("+r.radius+",0)"})},_data_bounds_ticks_fn:function(){var n=this;visibleChroms=0;return function(o){return[{radius:n.radius_bounds[0],angle:o.startAngle,label:n.formatNum(n.data_bounds[0])},{radius:n.radius_bounds[1],angle:o.startAngle,label:n.formatNum(n.data_bounds[1])}]}},get_data_bounds:function(n){}});g.extend(f.prototype,h);var e=f.extend({get_data_bounds:function(o){var n=g.map(o,function(p){if(typeof p==="string"||!p.max){return 0}return p.max});return[0,(n&&typeof n!=="string"?g.max(n):0)]}});var d=f.extend({get_data_bounds:function(o){var n=g.flatten(g.map(o,function(p){if(p){return g.map(p.data,function(q){return q[1]})}else{return 0}}));return[g.min(n),g.max(n)]}});var j=k.extend({render:function(){var n=this;$.when(n.track.get("data_manager").data_is_ready()).then(function(){$.when(n.track.get("data_manager").get_genome_wide_data(n.genome)).then(function(q){var p=[],o=n.genome.get_chroms_info();g.each(q,function(u,t){var r=o[t].chrom;var s=g.map(u.data,function(w){var v=n._get_region_angle(r,w[1]),x=n._get_region_angle(w[3],w[4]);return{source:{startAngle:v,endAngle:v+0.01},target:{startAngle:x,endAngle:x+0.01}}});p=p.concat(s)});n.parent_elt.append("g").attr("class","chord").selectAll("path").data(p).enter().append("path").style("fill",n.get_fill_color()).attr("d",l.svg.chord().radius(n.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(n){this.radius_bounds=n;this.parent_elt.selectAll("path").transition().attr("d",l.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(p,n){var o=g.find(this.chroms_layout,function(q){return q.data.chrom===p});return o.endAngle-((o.endAngle-o.startAngle)*(o.data.len-n)/o.data.len)}});return{CircsterView:a}}); \ No newline at end of file diff -r 54ed06c150857fb4e3d9a96b2f5d177208bad8cf -r 8afb981f46c11886a6106fa317936e709c311791 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/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,x,l,u,L,Y,i){var q=ab.extend;var V=function(ac){return("isResolved" in ac)};var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,A=100,I=12000,S=400,K=5000,w=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",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=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[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:function(){},get_drawables:function(){}});var z=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(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_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.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=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.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=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new f(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){z.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});z.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new x.CanvasManager(this.container.get(0).ownerDocument);this.reset()},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){x.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_drawables(),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new X(this,{content_div:this.top_labeltrack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")}});q(Z.prototype,z.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=w;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+w+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+w+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-w});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+w});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw();var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,al){var ai=this,ah=(al?[al]:ai.drawables),ae;var ad;for(var ag=0;ag<ah.length;ag++){ad=ah[ag];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ag][1]=ac;ai.tracks_to_be_redrawn[ag][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.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_highlight.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(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=null}});var s=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="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=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=ae});return ac},get_param_values:function(){var ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new P(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.tiles_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.set_dataset(new Y.Dataset(aj));ai.tiles_div.text("Running job.");ai.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(y+ag.message)}else{af(ag)}}})}});var N=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){N.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};q(F.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(l.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ac,ah,ae,ad,af,ag){b.call(this,ac,ah,ae,ad,af);this.max_val=ag};q(j.prototype,b.prototype);var O=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new x.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=new Y.Dataset({id:ae.dataset_id,hda_ldda:ae.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new x.GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new x.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset_id,hda_ldda:ac.hda_ldda,regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter 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function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred(),af={hda_ldda:ad.hda_ldda,data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(v);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=new x.Cache(Q);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").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_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. 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ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_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(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*S)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*S*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(ae,af,ah,ac){var ag=false;for(var ad=0;ad<ae.length;ad++){if(ae[ad].has_icons){ag=true;break}}if(ag){for(var ad=0;ad<ae.length;ad++){tile=ae[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar);if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get_elt(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(af,an.mode,ar,an.data_url_extra_params);if(V(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params);if(V(aj)){al=false}}if(al){q(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),av=af.get("start"),ad=af.get("end"),ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,af,ai,aj);if(aw!==undefined){an.tile_cache.set_elt(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,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.")},show_tile:function(ae,ah,ai){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ag-=this.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=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+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:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new l.ServerStateDeferred({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!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var X=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){M.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ac){M.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();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=this,aD=this._gen_tile_cache_key(at,am,az),ah=this._get_tile_bounds(az,aw);if(!au){au={}}var aC=(ad?undefined:ar.tile_cache.get_elt(aD));if(aC){ar.show_tile(aC,ak,am);return aC}var al=[],ar,ap=true,ax,an;for(var ay=0;ay<this.drawables.length;ay++){ar=this.drawables[ay];ax=ar.data_manager.get_data(ah,ar.mode,aw,ar.data_url_extra_params);if(V(ax)){ap=false}al.push(ax);an=null;if(view.reference_track&&am>view.canvas_manager.char_width_px){an=view.reference_track.data_manager.get_data(ah,ar.mode,aw,view.reference_track.data_url_extra_params);if(V(an)){ap=false}}al.push(an)}if(ap){q(ax,au.more_tile_data);this.tile_predraw_init();var ag=ar.view.canvas_manager.new_canvas(),ai=ar._get_tile_bounds(az,aw),aA=ah.get("start"),ae=ah.get("end"),aB=0,at=Math.ceil((ae-aA)*am)+this.left_offset,aq=0,af=[],ay;var ac=0;for(ay=0;ay<this.drawables.length;ay++,aB+=2){ar=this.drawables[ay];ax=al[aB];var ao=ar.mode;if(ao==="Auto"){ao=ar.get_mode(ax);ar.update_auto_mode(ao)}af.push(ao);ac=ar.get_canvas_height(ax,ao,am,at);if(ac>aq){aq=ac}}ag.width=at;ag.height=(au.height?au.height:aq);aB=0;var av=ag.getContext("2d");av.translate(this.left_offset,0);av.globalAlpha=0.5;av.globalCompositeOperation="source-over";for(ay=0;ay<this.drawables.length;ay++,aB+=2){ar=this.drawables[ay];ax=al[aB];an=al[aB+1];aC=ar.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=$.Deferred(),ar=this;$.when.apply($,al).then(function(){view.request_redraw(false,false,false,ar);aj.resolve()});return aj},show_group:function(){var af=new P(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof h){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var B=function(ac){M.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},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_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=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){this.hide_contents();return}var ad=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ah=0,aj=ak.length;ah<aj;ah++){var ac=Math.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=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new 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:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.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=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min,ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=aj.canvas,af=ag.get("start"),ai=ag.get("end"),ah=new 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=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_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=ac.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=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_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=ac;this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;this.tile_cache.clear();this.request_draw()},draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,af,ae,ah);var ag=l.get_random_color(),ac=l.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{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_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],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=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=ah.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ac){this.dataset_id=ac.get("id");this.hda_ldda=ac.get("hda_ldda");this.dataset=ac;this.data_manager.set("dataset",ac)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ar,am,ah,ag){M.prototype.postdraw_actions.call(this,ar,ag);var al=this,ao;if(al.mode==="Coverage"){var ad=-1;for(ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){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=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof j){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".bs-tooltip").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.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=true;for(ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;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==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,A,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Coverage"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(ao==="summary_tree"||ao==="Coverage"){var aA=new L.SummaryTreePainter(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=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null);var aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae);var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-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==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="summary_tree"}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message||ac.extra_info==="no_detail"){return false}return true}});var R=function(ad,ac,ae){c.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"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",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(R.prototype,r.prototype,M.prototype,c.prototype);var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=l.get_random_color(),ac=l.get_random_color([af,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_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 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:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(T.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,DiagonalHeatmapTrack:t,CompositeTrack:f,DrawableGroup:P};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,x,l,u,L,Y,i){var q=ab.extend;var V=function(ac){return("isResolved" in ac)};var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,A=100,I=12000,S=400,K=5000,w=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new 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.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[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:function(){},get_drawables:function(){}});var z=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".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.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.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=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.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=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new f(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){z.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});z.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new x.CanvasManager(this.container.get(0).ownerDocument);this.reset()},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){x.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.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=[],ah=$.map(ac.get_drawables(),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).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=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new X(this,{content_div:this.top_labeltrack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")}});q(Z.prototype,z.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=w;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+w+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+w+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-w});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+w});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw();var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,al){var ai=this,ah=(al?[al]:ai.drawables),ae;var ad;for(var ag=0;ag<ah.length;ag++){ad=ah[ag];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ag][1]=ac;ai.tracks_to_be_redrawn[ag][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.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_highlight.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(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=null}});var s=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="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=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=ae});return ac},get_param_values:function(){var ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai=new x.GenomeRegion({chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}),ad={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[ai.toJSON()]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ag=new P(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var aj=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});aj.init_for_tool_data();aj.change_mode(ah.mode);aj.set_filters_manager(ah.filters_manager.copy(aj));aj.update_icons();ac.add_drawable(aj);aj.tiles_div.text("Starting job.");this.update_params();this.run(ad,aj,function(ak){aj.set_dataset(new Y.Dataset(ak));aj.tiles_div.text("Running job.");aj.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(y+ag.message)}else{af(ag)}}})}});var N=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){N.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};q(F.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(l.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ac,ah,ae,ad,af,ag){b.call(this,ac,ah,ae,ad,af);this.max_val=ag};q(j.prototype,b.prototype);var O=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new x.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=new Y.Dataset({id:ae.dataset_id,hda_ldda:ae.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new x.GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new x.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset_id,hda_ldda:ac.hda_ldda,regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ae,{No:ah,Yes:ad})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred(),af={hda_ldda:ad.hda_ldda,data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(v);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=new x.Cache(Q);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").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_icons_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.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_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(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*S)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*S*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(ae,af,ah,ac){var ag=false;for(var ad=0;ad<ae.length;ad++){if(ae[ad].has_icons){ag=true;break}}if(ag){for(var ad=0;ad<ae.length;ad++){tile=ae[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar);if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get_elt(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(af,an.mode,ar,an.data_url_extra_params);if(V(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params);if(V(aj)){al=false}}if(al){q(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),av=af.get("start"),ad=af.get("end"),ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,af,ai,aj);if(aw!==undefined){an.tile_cache.set_elt(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah,ai){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append(ac)}ae.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae){var ac=this,ad=(ae!==undefined?ae.toString():"all");return" - region=["+ad+"], parameters=["+ac.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new l.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var X=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){M.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ac){M.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(ad,at,az,aw,ak,am,au){var ar=this,aD=this._gen_tile_cache_key(at,am,az),ah=this._get_tile_bounds(az,aw);if(!au){au={}}var aC=(ad?undefined:ar.tile_cache.get_elt(aD));if(aC){ar.show_tile(aC,ak,am);return aC}var al=[],ar,ap=true,ax,an;for(var ay=0;ay<this.drawables.length;ay++){ar=this.drawables[ay];ax=ar.data_manager.get_data(ah,ar.mode,aw,ar.data_url_extra_params);if(V(ax)){ap=false}al.push(ax);an=null;if(view.reference_track&&am>view.canvas_manager.char_width_px){an=view.reference_track.data_manager.get_data(ah,ar.mode,aw,view.reference_track.data_url_extra_params);if(V(an)){ap=false}}al.push(an)}if(ap){q(ax,au.more_tile_data);this.tile_predraw_init();var ag=ar.view.canvas_manager.new_canvas(),ai=ar._get_tile_bounds(az,aw),aA=ah.get("start"),ae=ah.get("end"),aB=0,at=Math.ceil((ae-aA)*am)+this.left_offset,aq=0,af=[],ay;var ac=0;for(ay=0;ay<this.drawables.length;ay++,aB+=2){ar=this.drawables[ay];ax=al[aB];var ao=ar.mode;if(ao==="Auto"){ao=ar.get_mode(ax);ar.update_auto_mode(ao)}af.push(ao);ac=ar.get_canvas_height(ax,ao,am,at);if(ac>aq){aq=ac}}ag.width=at;ag.height=(au.height?au.height:aq);aB=0;var av=ag.getContext("2d");av.translate(this.left_offset,0);av.globalAlpha=0.5;av.globalCompositeOperation="source-over";for(ay=0;ay<this.drawables.length;ay++,aB+=2){ar=this.drawables[ay];ax=al[aB];an=al[aB+1];aC=ar.draw_tile(ax,av,af[ay],aw,ah,am,an)}this.tile_cache.set_elt(aD,aC);this.show_tile(aC,ak,am);return aC}var aj=$.Deferred(),ar=this;$.when.apply($,al).then(function(){view.request_redraw(false,false,false,ar);aj.resolve()});return aj},show_group:function(){var af=new P(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof h){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var B=function(ac){M.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},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_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=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){this.hide_contents();return}var ad=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ah=0,aj=ak.length;ah<aj;ah++){var ac=Math.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=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new 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:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.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=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min,ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=aj.canvas,af=ag.get("start"),ai=ag.get("end"),ah=new 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=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_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=ac.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=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_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=ac;this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;this.tile_cache.clear();this.request_draw()},draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,af,ae,ah);var ag=l.get_random_color(),ac=l.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{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_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],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=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=ah.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ac){this.dataset_id=ac.get("id");this.hda_ldda=ac.get("hda_ldda");this.dataset=ac;this.data_manager.set("dataset",ac)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ar,am,ah,ag){M.prototype.postdraw_actions.call(this,ar,ag);var al=this,ao;if(al.mode==="Coverage"){var ad=-1;for(ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){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=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof j){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".bs-tooltip").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.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=true;for(ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;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==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,A,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Coverage"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(ao==="summary_tree"||ao==="Coverage"){var aA=new L.SummaryTreePainter(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=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null);var aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae);var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-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==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="summary_tree"}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message||ac.extra_info==="no_detail"){return false}return true}});var R=function(ad,ac,ae){c.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"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",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(R.prototype,r.prototype,M.prototype,c.prototype);var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=l.get_random_color(),ac=l.get_random_color([af,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_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 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:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(T.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,DiagonalHeatmapTrack:t,CompositeTrack:f,DrawableGroup:P};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file 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: smcmanus: The input datatype for display changed from LibraryDataset to Dataset, causing permission-checking issues. They've been fixed.
by Bitbucket 04 Nov '12

04 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b3585fb0c986/ changeset: b3585fb0c986 user: smcmanus date: 2012-11-04 07:49:43 summary: The input datatype for display changed from LibraryDataset to Dataset, causing permission-checking issues. They've been fixed. affected #: 2 files diff -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef -r b3585fb0c98639a57d8934f09f4553a3ad69e80b lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -275,11 +275,12 @@ # then the returned permissions will not carry an entry for the dataset. ret_permissions = {} if ( len( permission_items ) > 0 ): + # SM: NB: LibraryDatasets became Datasets for some odd reason. if ( isinstance( permission_items[0], trans.model.LibraryDataset ) ): ids = [ item.library_dataset_id for item in permission_items ] permissions = trans.sa_session.query( trans.model.LibraryDatasetPermissions ) \ .filter( and_( trans.model.LibraryDatasetPermissions.library_dataset_id.in_( ids ), - trans.model.LibraryDatasetPermissions.action == action ) ) \ + trans.model.LibraryDatasetPermissions.action == action.action ) ) \ .all() # Massage the return data. We will return a list of permissions @@ -292,6 +293,23 @@ ret_permissions[ item.library_dataset_id ] = [] for permission in permissions: ret_permissions[ permission.library_dataset_id ].append( permission ) + elif ( isinstance( permission_items[0], trans.model.Dataset ) ): + ids = [ item.id for item in permission_items ] + permissions = trans.sa_session.query( trans.model.DatasetPermissions ) \ + .filter( and_( trans.model.DatasetPermissions.dataset_id.in_( ids ), + trans.model.DatasetPermissions.action == action.action ) ) \ + .all() + + # Massage the return data. We will return a list of permissions + # for each library dataset. So we initialize the return list to + # have an empty list for each dataset. Then each permission is + # appended to the right lib dataset. + # TODO: Consider eliminating the initialization and just return + # empty values for each library dataset id. + for item in permission_items: + ret_permissions[ item.id ] = [] + for permission in permissions: + ret_permissions[ permission.dataset_id ].append( permission ) # Test that we get the same response from get_item_actions each item: test_code = False @@ -333,14 +351,13 @@ LDDAs. """ all_items_actions = self.get_actions_for_items( trans, action, items ) + ret_allow_action = {} - ret_allow_action = {} # Change item to lib_dataset or vice-versa. for item in items: if all_items_actions.has_key( item.id ): item_actions = all_items_actions[ item.id ] - # For access, all of the dataset's if self.permitted_actions.DATASET_ACCESS == action: ret_allow_action[ item.id ] = True for item_action in item_actions: diff -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef -r b3585fb0c98639a57d8934f09f4553a3ad69e80b lib/galaxy/webapps/galaxy/controllers/library_common.py --- a/lib/galaxy/webapps/galaxy/controllers/library_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py @@ -131,7 +131,17 @@ comptypes = get_comptypes( trans ) try: if self.app.config.new_lib_browse: - pass + return trans.fill_template( 'library/common/browse_library_opt.mako', + cntrller=cntrller, + use_panels=use_panels, + library=library, + created_ldda_ids=created_ldda_ids, + hidden_folder_ids=hidden_folder_ids, + show_deleted=show_deleted, + comptypes=comptypes, + current_user_roles=current_user_roles, + message=message, + status=status ) else: return trans.fill_template( 'library/common/browse_library.mako', cntrller=cntrller, 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: clem...@galaxyproject.org: Bringing Sphinx RST files up to date; changing generated doc so all modules are documented, not just galaxy.*
by Bitbucket 02 Nov '12

02 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c0f9edeb7ab1/ changeset: c0f9edeb7ab1 user: clem...(a)galaxyproject.org date: 2012-10-31 23:41:13 summary: Bringing Sphinx RST files up to date; changing generated doc so all modules are documented, not just galaxy.* affected #: 27 files diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/index.rst --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -3,22 +3,19 @@ Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. - - Accessible: Users without programming experience can easily specify - parameters and run tools and workflows. - - Reproducible: Galaxy captures information so that any user can repeat and - understand a complete computational analysis. - - Transparent: Users share and publish analyses via the web and create - Pages, interactive, web-based documents that describe a complete - analysis. + +- Accessible: Users without programming experience can easily specify parameters and run tools and workflows. +- Reproducible: Galaxy captures information so that any user can repeat and understand a complete computational analysis. +- Transparent: Users share and publish analyses via the web and create Pages, interactive, web-based documents that describe a complete analysis. Contents ======== .. toctree:: - :maxdepth: 4 + :maxdepth: 5 - API Documentation <lib/galaxy.web.api> + API Documentation <lib/galaxy.webapps.galaxy.api> - Application Documentation <lib/galaxy> + Application Documentation <lib/modules> Indices and tables ================== diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.datatypes.converters.rst --- a/doc/source/lib/galaxy.datatypes.converters.rst +++ b/doc/source/lib/galaxy.datatypes.converters.rst @@ -113,6 +113,14 @@ :undoc-members: :show-inheritance: +:mod:`interval_to_fli` Module +----------------------------- + +.. automodule:: galaxy.datatypes.converters.interval_to_fli + :members: + :undoc-members: + :show-inheritance: + :mod:`interval_to_interval_index_converter` Module -------------------------------------------------- diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.jobs.deferred.rst --- a/doc/source/lib/galaxy.jobs.deferred.rst +++ b/doc/source/lib/galaxy.jobs.deferred.rst @@ -17,6 +17,14 @@ :undoc-members: :show-inheritance: +:mod:`genome_index` Module +-------------------------- + +.. automodule:: galaxy.jobs.deferred.genome_index + :members: + :undoc-members: + :show-inheritance: + :mod:`genome_transfer` Module ----------------------------- diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.jobs.rst --- a/doc/source/lib/galaxy.jobs.rst +++ b/doc/source/lib/galaxy.jobs.rst @@ -25,6 +25,14 @@ :undoc-members: :show-inheritance: +:mod:`mapper` Module +-------------------- + +.. automodule:: galaxy.jobs.mapper + :members: + :undoc-members: + :show-inheritance: + :mod:`transfer_manager` Module ------------------------------ @@ -40,6 +48,7 @@ galaxy.jobs.actions galaxy.jobs.deferred + galaxy.jobs.rules galaxy.jobs.runners galaxy.jobs.splitters diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.jobs.runners.cli_job.rst --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.cli_job.rst @@ -0,0 +1,19 @@ +cli_job Package +=============== + +:mod:`cli_job` Package +---------------------- + +.. automodule:: galaxy.jobs.runners.cli_job + :members: + :undoc-members: + :show-inheritance: + +:mod:`torque` Module +-------------------- + +.. automodule:: galaxy.jobs.runners.cli_job.torque + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.jobs.runners.cli_shell.rst --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.cli_shell.rst @@ -0,0 +1,19 @@ +cli_shell Package +================= + +:mod:`cli_shell` Package +------------------------ + +.. automodule:: galaxy.jobs.runners.cli_shell + :members: + :undoc-members: + :show-inheritance: + +:mod:`rsh` Module +----------------- + +.. automodule:: galaxy.jobs.runners.cli_shell.rsh + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.jobs.runners.rst --- a/doc/source/lib/galaxy.jobs.runners.rst +++ b/doc/source/lib/galaxy.jobs.runners.rst @@ -9,6 +9,22 @@ :undoc-members: :show-inheritance: +:mod:`cli` Module +----------------- + +.. automodule:: galaxy.jobs.runners.cli + :members: + :undoc-members: + :show-inheritance: + +:mod:`condor` Module +-------------------- + +.. automodule:: galaxy.jobs.runners.condor + :members: + :undoc-members: + :show-inheritance: + :mod:`drmaa` Module ------------------- @@ -57,3 +73,11 @@ :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + + galaxy.jobs.runners.cli_job + galaxy.jobs.runners.cli_shell + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.util.backports.importlib.rst --- /dev/null +++ b/doc/source/lib/galaxy.util.backports.importlib.rst @@ -0,0 +1,11 @@ +importlib Package +================= + +:mod:`importlib` Package +------------------------ + +.. automodule:: galaxy.util.backports.importlib + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.util.backports.rst --- /dev/null +++ b/doc/source/lib/galaxy.util.backports.rst @@ -0,0 +1,18 @@ +backports Package +================= + +:mod:`backports` Package +------------------------ + +.. automodule:: galaxy.util.backports + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.util.backports.importlib + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.util.rst --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -137,3 +137,10 @@ :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + + galaxy.util.backports + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst --- /dev/null +++ b/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst @@ -0,0 +1,43 @@ +phyloviz Package +================ + +:mod:`phyloviz` Package +----------------------- + +.. automodule:: galaxy.visualization.data_providers.phyloviz + :members: + :undoc-members: + :show-inheritance: + +:mod:`baseparser` Module +------------------------ + +.. automodule:: galaxy.visualization.data_providers.phyloviz.baseparser + :members: + :undoc-members: + :show-inheritance: + +:mod:`newickparser` Module +-------------------------- + +.. automodule:: galaxy.visualization.data_providers.phyloviz.newickparser + :members: + :undoc-members: + :show-inheritance: + +:mod:`nexusparser` Module +------------------------- + +.. automodule:: galaxy.visualization.data_providers.phyloviz.nexusparser + :members: + :undoc-members: + :show-inheritance: + +:mod:`phyloxmlparser` Module +---------------------------- + +.. automodule:: galaxy.visualization.data_providers.phyloviz.phyloxmlparser + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.visualization.data_providers.rst --- /dev/null +++ b/doc/source/lib/galaxy.visualization.data_providers.rst @@ -0,0 +1,42 @@ +data_providers Package +====================== + +:mod:`data_providers` Package +----------------------------- + +.. automodule:: galaxy.visualization.data_providers + :members: + :undoc-members: + :show-inheritance: + +:mod:`basic` Module +------------------- + +.. automodule:: galaxy.visualization.data_providers.basic + :members: + :undoc-members: + :show-inheritance: + +:mod:`genome` Module +-------------------- + +.. automodule:: galaxy.visualization.data_providers.genome + :members: + :undoc-members: + :show-inheritance: + +:mod:`registry` Module +---------------------- + +.. automodule:: galaxy.visualization.data_providers.registry + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.visualization.data_providers.phyloviz + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.visualization.genome.rst --- /dev/null +++ b/doc/source/lib/galaxy.visualization.genome.rst @@ -0,0 +1,19 @@ +genome Package +============== + +:mod:`genome` Package +--------------------- + +.. automodule:: galaxy.visualization.genome + :members: + :undoc-members: + :show-inheritance: + +:mod:`visual_analytics` Module +------------------------------ + +.. automodule:: galaxy.visualization.genome.visual_analytics + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.visualization.rst --- a/doc/source/lib/galaxy.visualization.rst +++ b/doc/source/lib/galaxy.visualization.rst @@ -22,5 +22,7 @@ .. toctree:: + galaxy.visualization.data_providers + galaxy.visualization.genome galaxy.visualization.tracks diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.visualization.tracks.rst --- a/doc/source/lib/galaxy.visualization.tracks.rst +++ b/doc/source/lib/galaxy.visualization.tracks.rst @@ -9,14 +9,6 @@ :undoc-members: :show-inheritance: -:mod:`data_providers` Module ----------------------------- - -.. automodule:: galaxy.visualization.tracks.data_providers - :members: - :undoc-members: - :show-inheritance: - :mod:`summary` Module --------------------- @@ -25,11 +17,3 @@ :undoc-members: :show-inheritance: -:mod:`visual_analytics` Module ------------------------------- - -.. automodule:: galaxy.visualization.tracks.visual_analytics - :members: - :undoc-members: - :show-inheritance: - diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.web.api.rst --- a/doc/source/lib/galaxy.web.api.rst +++ /dev/null @@ -1,352 +0,0 @@ -Galaxy API Documentation -************************ - -Background -========== -In addition to being accessible through a web interface, Galaxy can now also be -accessed programmatically, through shell scripts and other programs. The web -interface is appropriate for things like exploratory analysis, visualization, -construction of workflows, and rerunning workflows on new datasets. - -The web interface is less suitable for things like - - Connecting a Galaxy instance directly to your sequencer and running - workflows whenever data is ready - - Running a workflow against multiple datasets (which can be done with the - web interface, but is tedious) - - When the analysis involves complex control, such as looping and - branching. - -The Galaxy API addresses these and other situations by exposing Galaxy -internals through an additional interface, known as an Application Programming -Interface, or API. - -Quickstart -========== - -Set the following option in universe_wsgi.ini and start the server:: - - enable_api = True - -Log in as your user, navigate to the API Keys page in the User menu, and -generate a new API key. Make a note of the API key, and then pull up a -terminal. Now we'll use the display.py script in your galaxy/scripts/api -directory for a short example:: - - % ./display.py my_key http://localhost:4096/api/histories - Collection Members - ------------------ - #1: /api/histories/8c49be448cfe29bc - name: Unnamed history - id: 8c49be448cfe29bc - #2: /api/histories/33b43b4e7093c91f - name: output test - id: 33b43b4e7093c91f - -The result is a Collection of the histories of the user specified by the API -key (you). To look at the details of a particular history, say #1 above, do -the following:: - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc - Member Information - ------------------ - state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0} - state: ok - contents_url: /api/histories/8c49be448cfe29bc/contents - id: 8c49be448cfe29bc - name: Unnamed history - -This gives detailed information about the specific member in question, in this -case the History. To view history contents, do the following:: - - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents - Collection Members - ------------------ - #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a - name: Pasted Entry - type: file - id: 6f91353f3eb0fa4a - -What we have here is another Collection of items containing all of the datasets -in this particular history. Finally, to view details of a particular dataset -in this collection, execute the following:: - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0f… - Member Information - ------------------ - misc_blurb: 1 line - name: Pasted Entry - data_type: txt - deleted: False - file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat - state: ok - download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt - visible: True - genome_build: ? - model_class: HistoryDatasetAssociation - file_size: 17 - metadata_data_lines: 1 - id: 6f91353f3eb0fa4a - misc_info: uploaded txt file - metadata_dbkey: ? - -And now you've successfully used the API to request and select a history, -browse the contents of that history, and then look at detailed information -about a particular dataset. - -For a more comprehensive Data Library example, set the following option in your -universe_wsgi.ini as well, and restart galaxy again:: - - admin_users = you(a)example.org - library_import_dir = /path/to/some/directory - -In the directory you specified for 'library_import_dir', create some -subdirectories, and put (or symlink) files to import into Galaxy into those -subdirectories. - -In Galaxy, create an account that matches the address you put in 'admin_users', -then browse to that user's preferences and generate a new API Key. Copy the -key to your clipboard and then use these scripts:: - - % ./display.py my_key http://localhost:4096/api/libraries - Collection Members - ------------------ - - 0 elements in collection - - % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library' - Response - -------- - /api/libraries/f3f73e481f432006 - name: api_test - id: f3f73e481f432006 - - % ./display.py my_key http://localhost:4096/api/libraries - Collection Members - ------------------ - /api/libraries/f3f73e481f432006 - name: api_test - id: f3f73e481f432006 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006 - Member Information - ------------------ - synopsis: None - contents_url: /api/libraries/f3f73e481f432006/contents - description: API Test Library - name: api_test - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents - Collection Members - ------------------ - /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 - name: / - type: folder - id: 28202595c0d2591f61ddda595d2c3670 - - % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1' - Response - -------- - /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 - name: api_test_folder1 - id: 28202595c0d2591fa4f9089d2303fd89 - - % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19 - Response - -------- - /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b - name: 2.bed - id: e9ef7fdb2db87d7b - /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 - name: 3.bed - id: 3b7f6a31f80a5018 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents - Collection Members - ------------------ - /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 - name: / - type: folder - id: 28202595c0d2591f61ddda595d2c3670 - /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 - name: /api_test_folder1 - type: folder - id: 28202595c0d2591fa4f9089d2303fd89 - /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b - name: /api_test_folder1/2.bed - type: file - id: e9ef7fdb2db87d7b - /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 - name: /api_test_folder1/3.bed - type: file - id: 3b7f6a31f80a5018 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87… - Member Information - ------------------ - misc_blurb: 68 regions - metadata_endCol: 3 - data_type: bed - metadata_columns: 6 - metadata_nameCol: 4 - uploaded_by: nate@... - metadata_strandCol: 6 - name: 2.bed - genome_build: hg19 - metadata_comment_lines: None - metadata_startCol: 2 - metadata_chromCol: 1 - file_size: 4272 - metadata_data_lines: 68 - message: - metadata_dbkey: hg19 - misc_info: uploaded bed file - date_uploaded: 2010-06-22T17:01:51.266119 - metadata_column_types: str, int, int, str, int, str - -Other parameters are valid when uploading, they are the same parameters as are -used in the web form, like 'link_data_only' and etc. - -The request and response format should be considered alpha and are subject to change. - - -API Controllers -=============== - -:mod:`datasets` Module ----------------------- - -.. automodule:: galaxy.web.api.datasets - :members: - :undoc-members: - :show-inheritance: - -:mod:`forms` Module -------------------- - -.. automodule:: galaxy.web.api.forms - :members: - :undoc-members: - :show-inheritance: - -:mod:`genomes` Module ---------------------- - -.. automodule:: galaxy.web.api.genomes - :members: - :undoc-members: - :show-inheritance: - -:mod:`histories` Module ------------------------ - -.. automodule:: galaxy.web.api.histories - :members: - :undoc-members: - :show-inheritance: - -:mod:`history_contents` Module ------------------------------- - -.. automodule:: galaxy.web.api.history_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`libraries` Module ------------------------ - -.. automodule:: galaxy.web.api.libraries - :members: - :undoc-members: - :show-inheritance: - -:mod:`library_contents` Module ------------------------------- - -.. automodule:: galaxy.web.api.library_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`permissions` Module -------------------------- - -.. automodule:: galaxy.web.api.permissions - :members: - :undoc-members: - :show-inheritance: - -:mod:`quotas` Module --------------------- - -.. automodule:: galaxy.web.api.quotas - :members: - :undoc-members: - :show-inheritance: - -:mod:`request_types` Module ---------------------------- - -.. automodule:: galaxy.web.api.request_types - :members: - :undoc-members: - :show-inheritance: - -:mod:`requests` Module ----------------------- - -.. automodule:: galaxy.web.api.requests - :members: - :undoc-members: - :show-inheritance: - -:mod:`roles` Module -------------------- - -.. automodule:: galaxy.web.api.roles - :members: - :undoc-members: - :show-inheritance: - -:mod:`samples` Module ---------------------- - -.. automodule:: galaxy.web.api.samples - :members: - :undoc-members: - :show-inheritance: - -:mod:`tools` Module -------------------- - -.. automodule:: galaxy.web.api.tools - :members: - :undoc-members: - :show-inheritance: - -:mod:`users` Module -------------------- - -.. automodule:: galaxy.web.api.users - :members: - :undoc-members: - :show-inheritance: - -:mod:`visualizations` Module ----------------------------- - -.. automodule:: galaxy.web.api.visualizations - :members: - :undoc-members: - :show-inheritance: - -:mod:`workflows` Module ------------------------ - -.. automodule:: galaxy.web.api.workflows - :members: - :undoc-members: - :show-inheritance: - - diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.web.base.controllers.rst --- /dev/null +++ b/doc/source/lib/galaxy.web.base.controllers.rst @@ -0,0 +1,11 @@ +controllers Package +=================== + +:mod:`admin` Module +------------------- + +.. automodule:: galaxy.web.base.controllers.admin + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.web.base.rst --- a/doc/source/lib/galaxy.web.base.rst +++ b/doc/source/lib/galaxy.web.base.rst @@ -9,3 +9,10 @@ :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + + galaxy.web.base.controllers + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.web.controllers.rst --- a/doc/source/lib/galaxy.web.controllers.rst +++ /dev/null @@ -1,235 +0,0 @@ -controllers Package -=================== - -:mod:`controllers` Package --------------------------- - -.. automodule:: galaxy.web.controllers - :members: - :undoc-members: - :show-inheritance: - -:mod:`admin` Module -------------------- - -.. automodule:: galaxy.web.controllers.admin - :members: - :undoc-members: - :show-inheritance: - -:mod:`admin_toolshed` Module ----------------------------- - -.. automodule:: galaxy.web.controllers.admin_toolshed - :members: - :undoc-members: - :show-inheritance: - -:mod:`async` Module -------------------- - -.. automodule:: galaxy.web.controllers.async - :members: - :undoc-members: - :show-inheritance: - -:mod:`cloud` Module -------------------- - -.. automodule:: galaxy.web.controllers.cloud - :members: - :undoc-members: - :show-inheritance: - -:mod:`data_admin` Module ------------------------- - -.. automodule:: galaxy.web.controllers.data_admin - :members: - :undoc-members: - :show-inheritance: - -:mod:`dataset` Module ---------------------- - -.. automodule:: galaxy.web.controllers.dataset - :members: - :undoc-members: - :show-inheritance: - -:mod:`error` Module -------------------- - -.. automodule:: galaxy.web.controllers.error - :members: - :undoc-members: - :show-inheritance: - -:mod:`external_service` Module ------------------------------- - -.. automodule:: galaxy.web.controllers.external_service - :members: - :undoc-members: - :show-inheritance: - -:mod:`external_services` Module -------------------------------- - -.. automodule:: galaxy.web.controllers.external_services - :members: - :undoc-members: - :show-inheritance: - -:mod:`forms` Module -------------------- - -.. automodule:: galaxy.web.controllers.forms - :members: - :undoc-members: - :show-inheritance: - -:mod:`history` Module ---------------------- - -.. automodule:: galaxy.web.controllers.history - :members: - :undoc-members: - :show-inheritance: - -:mod:`library` Module ---------------------- - -.. automodule:: galaxy.web.controllers.library - :members: - :undoc-members: - :show-inheritance: - -:mod:`library_admin` Module ---------------------------- - -.. automodule:: galaxy.web.controllers.library_admin - :members: - :undoc-members: - :show-inheritance: - -:mod:`library_common` Module ----------------------------- - -.. automodule:: galaxy.web.controllers.library_common - :members: - :undoc-members: - :show-inheritance: - -:mod:`mobile` Module --------------------- - -.. automodule:: galaxy.web.controllers.mobile - :members: - :undoc-members: - :show-inheritance: - -:mod:`page` Module ------------------- - -.. automodule:: galaxy.web.controllers.page - :members: - :undoc-members: - :show-inheritance: - -:mod:`request_type` Module --------------------------- - -.. automodule:: galaxy.web.controllers.request_type - :members: - :undoc-members: - :show-inheritance: - -:mod:`requests` Module ----------------------- - -.. automodule:: galaxy.web.controllers.requests - :members: - :undoc-members: - :show-inheritance: - -:mod:`requests_admin` Module ----------------------------- - -.. automodule:: galaxy.web.controllers.requests_admin - :members: - :undoc-members: - :show-inheritance: - -:mod:`requests_common` Module ------------------------------ - -.. automodule:: galaxy.web.controllers.requests_common - :members: - :undoc-members: - :show-inheritance: - -:mod:`root` Module ------------------- - -.. automodule:: galaxy.web.controllers.root - :members: - :undoc-members: - :show-inheritance: - -:mod:`tag` Module ------------------ - -.. automodule:: galaxy.web.controllers.tag - :members: - :undoc-members: - :show-inheritance: - -:mod:`tool_runner` Module -------------------------- - -.. automodule:: galaxy.web.controllers.tool_runner - :members: - :undoc-members: - :show-inheritance: - -:mod:`tracks` Module --------------------- - -.. automodule:: galaxy.web.controllers.tracks - :members: - :undoc-members: - :show-inheritance: - -:mod:`ucsc_proxy` Module ------------------------- - -.. automodule:: galaxy.web.controllers.ucsc_proxy - :members: - :undoc-members: - :show-inheritance: - -:mod:`user` Module ------------------- - -.. automodule:: galaxy.web.controllers.user - :members: - :undoc-members: - :show-inheritance: - -:mod:`visualization` Module ---------------------------- - -.. automodule:: galaxy.web.controllers.visualization - :members: - :undoc-members: - :show-inheritance: - -:mod:`workflow` Module ----------------------- - -.. automodule:: galaxy.web.controllers.workflow - :members: - :undoc-members: - :show-inheritance: - diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.web.rst --- a/doc/source/lib/galaxy.web.rst +++ b/doc/source/lib/galaxy.web.rst @@ -38,9 +38,7 @@ .. toctree:: - galaxy.web.api galaxy.web.base - galaxy.web.controllers galaxy.web.framework galaxy.web.security diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.community.controllers.rst --- a/doc/source/lib/galaxy.webapps.community.controllers.rst +++ b/doc/source/lib/galaxy.webapps.community.controllers.rst @@ -41,6 +41,14 @@ :undoc-members: :show-inheritance: +:mod:`repository_review` Module +------------------------------- + +.. automodule:: galaxy.webapps.community.controllers.repository_review + :members: + :undoc-members: + :show-inheritance: + :mod:`upload` Module -------------------- @@ -49,6 +57,14 @@ :undoc-members: :show-inheritance: +:mod:`user` Module +------------------ + +.. automodule:: galaxy.webapps.community.controllers.user + :members: + :undoc-members: + :show-inheritance: + :mod:`workflow` Module ---------------------- diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.community.framework.middleware.rst --- a/doc/source/lib/galaxy.webapps.community.framework.middleware.rst +++ b/doc/source/lib/galaxy.webapps.community.framework.middleware.rst @@ -17,3 +17,11 @@ :undoc-members: :show-inheritance: +:mod:`remoteuser` Module +------------------------ + +.. automodule:: galaxy.webapps.community.framework.middleware.remoteuser + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.galaxy.api.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -0,0 +1,391 @@ +Galaxy API Documentation +************************ + +Background +========== +In addition to being accessible through a web interface, Galaxy can now also be +accessed programmatically, through shell scripts and other programs. The web +interface is appropriate for things like exploratory analysis, visualization, +construction of workflows, and rerunning workflows on new datasets. + +The web interface is less suitable for things like + - Connecting a Galaxy instance directly to your sequencer and running + workflows whenever data is ready + - Running a workflow against multiple datasets (which can be done with the + web interface, but is tedious) + - When the analysis involves complex control, such as looping and + branching. + +The Galaxy API addresses these and other situations by exposing Galaxy +internals through an additional interface, known as an Application Programming +Interface, or API. + +Quickstart +========== + +Set the following option in universe_wsgi.ini and start the server:: + + enable_api = True + +Log in as your user, navigate to the API Keys page in the User menu, and +generate a new API key. Make a note of the API key, and then pull up a +terminal. Now we'll use the display.py script in your galaxy/scripts/api +directory for a short example:: + + % ./display.py my_key http://localhost:4096/api/histories + Collection Members + ------------------ + #1: /api/histories/8c49be448cfe29bc + name: Unnamed history + id: 8c49be448cfe29bc + #2: /api/histories/33b43b4e7093c91f + name: output test + id: 33b43b4e7093c91f + +The result is a Collection of the histories of the user specified by the API +key (you). To look at the details of a particular history, say #1 above, do +the following:: + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc + Member Information + ------------------ + state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0} + state: ok + contents_url: /api/histories/8c49be448cfe29bc/contents + id: 8c49be448cfe29bc + name: Unnamed history + +This gives detailed information about the specific member in question, in this +case the History. To view history contents, do the following:: + + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents + Collection Members + ------------------ + #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a + name: Pasted Entry + type: file + id: 6f91353f3eb0fa4a + +What we have here is another Collection of items containing all of the datasets +in this particular history. Finally, to view details of a particular dataset +in this collection, execute the following:: + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0f… + Member Information + ------------------ + misc_blurb: 1 line + name: Pasted Entry + data_type: txt + deleted: False + file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat + state: ok + download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt + visible: True + genome_build: ? + model_class: HistoryDatasetAssociation + file_size: 17 + metadata_data_lines: 1 + id: 6f91353f3eb0fa4a + misc_info: uploaded txt file + metadata_dbkey: ? + +And now you've successfully used the API to request and select a history, +browse the contents of that history, and then look at detailed information +about a particular dataset. + +For a more comprehensive Data Library example, set the following option in your +universe_wsgi.ini as well, and restart galaxy again:: + + admin_users = you(a)example.org + library_import_dir = /path/to/some/directory + +In the directory you specified for 'library_import_dir', create some +subdirectories, and put (or symlink) files to import into Galaxy into those +subdirectories. + +In Galaxy, create an account that matches the address you put in 'admin_users', +then browse to that user's preferences and generate a new API Key. Copy the +key to your clipboard and then use these scripts:: + + % ./display.py my_key http://localhost:4096/api/libraries + Collection Members + ------------------ + + 0 elements in collection + + % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library' + Response + -------- + /api/libraries/f3f73e481f432006 + name: api_test + id: f3f73e481f432006 + + % ./display.py my_key http://localhost:4096/api/libraries + Collection Members + ------------------ + /api/libraries/f3f73e481f432006 + name: api_test + id: f3f73e481f432006 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006 + Member Information + ------------------ + synopsis: None + contents_url: /api/libraries/f3f73e481f432006/contents + description: API Test Library + name: api_test + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents + Collection Members + ------------------ + /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 + name: / + type: folder + id: 28202595c0d2591f61ddda595d2c3670 + + % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1' + Response + -------- + /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 + name: api_test_folder1 + id: 28202595c0d2591fa4f9089d2303fd89 + + % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19 + Response + -------- + /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + name: 2.bed + id: e9ef7fdb2db87d7b + /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 + name: 3.bed + id: 3b7f6a31f80a5018 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents + Collection Members + ------------------ + /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 + name: / + type: folder + id: 28202595c0d2591f61ddda595d2c3670 + /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 + name: /api_test_folder1 + type: folder + id: 28202595c0d2591fa4f9089d2303fd89 + /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + name: /api_test_folder1/2.bed + type: file + id: e9ef7fdb2db87d7b + /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 + name: /api_test_folder1/3.bed + type: file + id: 3b7f6a31f80a5018 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87… + Member Information + ------------------ + misc_blurb: 68 regions + metadata_endCol: 3 + data_type: bed + metadata_columns: 6 + metadata_nameCol: 4 + uploaded_by: nate@... + metadata_strandCol: 6 + name: 2.bed + genome_build: hg19 + metadata_comment_lines: None + metadata_startCol: 2 + metadata_chromCol: 1 + file_size: 4272 + metadata_data_lines: 68 + message: + metadata_dbkey: hg19 + misc_info: uploaded bed file + date_uploaded: 2010-06-22T17:01:51.266119 + metadata_column_types: str, int, int, str, int, str + +Other parameters are valid when uploading, they are the same parameters as are +used in the web form, like 'link_data_only' and etc. + +The request and response format should be considered alpha and are subject to change. + + +API Controllers +=============== + +:mod:`datasets` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.datasets + :members: + :undoc-members: + :show-inheritance: + +:mod:`folder_contents` Module +----------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.folder_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`folders` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.folders + :members: + :undoc-members: + :show-inheritance: + +:mod:`forms` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.forms + :members: + :undoc-members: + :show-inheritance: + +:mod:`genomes` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.genomes + :members: + :undoc-members: + :show-inheritance: + +:mod:`group_roles` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.group_roles + :members: + :undoc-members: + :show-inheritance: + +:mod:`group_users` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.group_users + :members: + :undoc-members: + :show-inheritance: + +:mod:`groups` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.api.groups + :members: + :undoc-members: + :show-inheritance: + +:mod:`histories` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.histories + :members: + :undoc-members: + :show-inheritance: + +:mod:`history_contents` Module +------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.history_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`libraries` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.libraries + :members: + :undoc-members: + :show-inheritance: + +:mod:`library_contents` Module +------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.library_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`permissions` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.permissions + :members: + :undoc-members: + :show-inheritance: + +:mod:`quotas` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.api.quotas + :members: + :undoc-members: + :show-inheritance: + +:mod:`request_types` Module +--------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.request_types + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.requests + :members: + :undoc-members: + :show-inheritance: + +:mod:`roles` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.roles + :members: + :undoc-members: + :show-inheritance: + +:mod:`samples` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.samples + :members: + :undoc-members: + :show-inheritance: + +:mod:`tools` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.tools + :members: + :undoc-members: + :show-inheritance: + +:mod:`users` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.users + :members: + :undoc-members: + :show-inheritance: + +:mod:`visualizations` Module +---------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.visualizations + :members: + :undoc-members: + :show-inheritance: + +:mod:`workflows` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.workflows + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.galaxy.api.rst~ --- /dev/null +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst~ @@ -0,0 +1,179 @@ +api Package +=========== + +:mod:`datasets` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.datasets + :members: + :undoc-members: + :show-inheritance: + +:mod:`folder_contents` Module +----------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.folder_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`folders` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.folders + :members: + :undoc-members: + :show-inheritance: + +:mod:`forms` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.forms + :members: + :undoc-members: + :show-inheritance: + +:mod:`genomes` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.genomes + :members: + :undoc-members: + :show-inheritance: + +:mod:`group_roles` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.group_roles + :members: + :undoc-members: + :show-inheritance: + +:mod:`group_users` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.group_users + :members: + :undoc-members: + :show-inheritance: + +:mod:`groups` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.api.groups + :members: + :undoc-members: + :show-inheritance: + +:mod:`histories` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.histories + :members: + :undoc-members: + :show-inheritance: + +:mod:`history_contents` Module +------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.history_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`libraries` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.libraries + :members: + :undoc-members: + :show-inheritance: + +:mod:`library_contents` Module +------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.library_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`permissions` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.permissions + :members: + :undoc-members: + :show-inheritance: + +:mod:`quotas` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.api.quotas + :members: + :undoc-members: + :show-inheritance: + +:mod:`request_types` Module +--------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.request_types + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.requests + :members: + :undoc-members: + :show-inheritance: + +:mod:`roles` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.roles + :members: + :undoc-members: + :show-inheritance: + +:mod:`samples` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.samples + :members: + :undoc-members: + :show-inheritance: + +:mod:`tools` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.tools + :members: + :undoc-members: + :show-inheritance: + +:mod:`users` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.users + :members: + :undoc-members: + :show-inheritance: + +:mod:`visualizations` Module +---------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.visualizations + :members: + :undoc-members: + :show-inheritance: + +:mod:`workflows` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.workflows + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.galaxy.controllers.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst @@ -0,0 +1,227 @@ +controllers Package +=================== + +:mod:`controllers` Package +-------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers + :members: + :undoc-members: + :show-inheritance: + +:mod:`admin` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`admin_toolshed` Module +---------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.admin_toolshed + :members: + :undoc-members: + :show-inheritance: + +:mod:`async` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.async + :members: + :undoc-members: + :show-inheritance: + +:mod:`cloudlaunch` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.cloudlaunch + :members: + :undoc-members: + :show-inheritance: + +:mod:`data_admin` Module +------------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.data_admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`dataset` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.dataset + :members: + :undoc-members: + :show-inheritance: + +:mod:`error` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.error + :members: + :undoc-members: + :show-inheritance: + +:mod:`external_service` Module +------------------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.external_service + :members: + :undoc-members: + :show-inheritance: + +:mod:`external_services` Module +------------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.external_services + :members: + :undoc-members: + :show-inheritance: + +:mod:`forms` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.forms + :members: + :undoc-members: + :show-inheritance: + +:mod:`history` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.history + :members: + :undoc-members: + :show-inheritance: + +:mod:`library` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.library + :members: + :undoc-members: + :show-inheritance: + +:mod:`library_admin` Module +--------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.library_admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`library_common` Module +---------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.library_common + :members: + :undoc-members: + :show-inheritance: + +:mod:`mobile` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.mobile + :members: + :undoc-members: + :show-inheritance: + +:mod:`page` Module +------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.page + :members: + :undoc-members: + :show-inheritance: + +:mod:`request_type` Module +-------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.request_type + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.requests + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests_admin` Module +---------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.requests_admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests_common` Module +----------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.requests_common + :members: + :undoc-members: + :show-inheritance: + +:mod:`root` Module +------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.root + :members: + :undoc-members: + :show-inheritance: + +:mod:`tag` Module +----------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.tag + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_runner` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.tool_runner + :members: + :undoc-members: + :show-inheritance: + +:mod:`ucsc_proxy` Module +------------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.ucsc_proxy + :members: + :undoc-members: + :show-inheritance: + +:mod:`user` Module +------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.user + :members: + :undoc-members: + :show-inheritance: + +:mod:`visualization` Module +--------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.visualization + :members: + :undoc-members: + :show-inheritance: + +:mod:`workflow` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.workflow + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.galaxy.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.galaxy.rst @@ -0,0 +1,19 @@ +galaxy Package +============== + +:mod:`buildapp` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.buildapp + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.webapps.galaxy.api + galaxy.webapps.galaxy.controllers + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.rst --- a/doc/source/lib/galaxy.webapps.rst +++ b/doc/source/lib/galaxy.webapps.rst @@ -16,5 +16,6 @@ galaxy.webapps.community galaxy.webapps.demo_sequencer + galaxy.webapps.galaxy galaxy.webapps.reports Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Circster: (a) create mixin for drawing tick labels and (b) use ticks for denoting chromosome length and track min/max.
by Bitbucket 02 Nov '12

02 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/86f05ee5dedb/ changeset: 86f05ee5dedb user: jgoecks date: 2012-11-02 21:15:15 summary: Circster: (a) create mixin for drawing tick labels and (b) use ticks for denoting chromosome length and track min/max. affected #: 1 file diff -r 154cda53407f8360ab00b54ec563c1985157c9a5 -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -1,5 +1,9 @@ define(["libs/underscore", "libs/d3", "viz/visualization"], function(_, d3, visualization) { +/** + * Utility class for working with SVG. + */ +// TODO: make into a mixin. var SVGUtils = Backbone.Model.extend({ /** @@ -21,8 +25,89 @@ } return true; } +}); -}); +/** + * Mixin for using ticks. + */ +var UsesTicks = { + drawTicks: function(parent_elt, data, dataHandler, textTransform, horizontal) { + // Set up group elements for chroms and for each tick. + var ticks = parent_elt.append("g") + .selectAll("g") + .data(data) + .enter().append("g") + .selectAll("g") + .data(dataHandler) + .enter().append("g") + .attr("transform", function(d) { + return "rotate(" + (d.angle * 180 / Math.PI - 90) + ")" + + "translate(" + d.radius + ",0)"; + }); + + // Add line + text for ticks. + var tick_coords = [], + text_coords = [], + text_anchor = function(d) { + return d.angle > Math.PI ? "end" : null; + }; + if (horizontal) { + tick_coords = [0, 0, 0, -4]; + text_coords = [4, 0, "", ".35em"]; + text_anchor = null; + } + else { + tick_coords = [1, 0, 4, 0]; + text_coords = [0, 4, ".35em", ""]; + + } + + ticks.append("line") + .attr("x1", tick_coords[0]) + .attr("y1", tick_coords[1]) + .attr("x2", tick_coords[2]) + .attr("y1", tick_coords[3]) + .style("stroke", "#000"); + + ticks.append("text") + .attr("x", text_coords[0]) + .attr("y", text_coords[1]) + .attr("dx", text_coords[2]) + .attr("dy", text_coords[3]) + .attr("text-anchor", text_anchor) + .attr("transform", textTransform) + .text(function(d) { return d.label; }); + }, + + /** + * Format number for display at a tick. + */ + formatNum: function(num, sigDigits) { + var rval = null; + if (num < 1) { + rval = num.toPrecision(sigDigits); + } + else { + // Use round to turn string from toPrecision() back into a number. + var roundedNum = Math.round(num.toPrecision(sigDigits)); + + // Use abbreviations. + if (num < 1000) { + rval = roundedNum; + } + else if (num < 1000000) { + // Use K. + rval = Math.round((roundedNum/1000).toPrecision(3)).toFixed(0) + 'K'; + } + else if (num < 1000000000) { + // Use M. + rval = Math.round((roundedNum/1000000).toPrecision(3)).toFixed(0) + 'M'; + } + } + + return rval; + } +}; /** * A label track. @@ -39,7 +124,7 @@ this.total_gap = options.total_gap; this.genome = options.genome; this.dataset_arc_height = options.dataset_arc_height; - this.track_gap = 5; + this.track_gap = 10; this.label_arc_height = 50; this.scale = 1; this.circular_views = null; @@ -340,11 +425,19 @@ $.when(data_ready_deferred).then(function() { $.when(self._render_data(track_parent_elt)).then(function() { chroms_paths.style("fill", self.bg_fill); + + // Render labels after data is available so that data attributes are available. + self.render_labels(); }); }); }, /** + * Render track labels. + */ + render_labels: function() {}, + + /** * Update radius bounds. */ update_radius_bounds: function(radius_bounds) { @@ -580,52 +673,31 @@ var k = (d.endAngle - d.startAngle) / d.value, ticks = d3.range(0, d.value, 25000000).map(function(v, i) { return { + radius: self.innerRadius, angle: v * k + d.startAngle, - label: i === 0 ? 0 : (i % 3 ? null : v / 1000000 + "M") + label: i === 0 ? 0 : (i % 3 ? null : self.formatNum(v)) }; }); // 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"; + ticks[ticks.length-1].label = self.formatNum( + Math.round( ( ticks[ticks.length-1].angle - d.startAngle ) / k ) + ); } 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)"; - }); + /** Rotate and move text as needed. */ + var textTransform = function(d) { + return d.angle > Math.PI ? "rotate(180)translate(-16)" : null; + }; - 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; }); + this.drawTicks(this.parent_elt, this.chroms_layout, chromArcTicks, textTransform); } }); +_.extend(CircsterChromLabelTrackView.prototype, UsesTicks); /** * View for quantitative track in Circster. @@ -683,6 +755,39 @@ .angle(line.angle()); }, + render_labels: function() { + // -- Render min and max using ticks. -- + var self = this, + // Keep counter of visible chroms. + visibleChroms = 0, + dataBoundsTicks = function(d) { + // Do not add ticks to small chroms. + if (d.endAngle - d.startAngle < 0.08) { return []; } + + // Only show bounds on every 3rd chromosome; also update visibleChroms count. + if (visibleChroms++ % 3 !== 0) { return []; } + + // Set up data to display min, max ticks. + return [ + { + radius: self.radius_bounds[0], + angle: d.startAngle, + label: self.formatNum(self.data_bounds[0]) + }, + { + radius: self.radius_bounds[1], + angle: d.startAngle, + label: self.formatNum(self.data_bounds[1]) + } + ]; + }, + textTransform = function() { + return "rotate(90)"; + }; + + this.drawTicks(this.parent_elt, this.chroms_layout, dataBoundsTicks, textTransform, true); + }, + /** * Returns an array with two values denoting the minimum and maximum * values for the track. @@ -690,6 +795,8 @@ get_data_bounds: function(data) {} }); +_.extend(CircsterQuantitativeTrackView.prototype, UsesTicks); + /** * Layout for summary tree data in a circster visualization. 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: smcmanus: Temporarily reverted library browsing.
by Bitbucket 02 Nov '12

02 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/154cda53407f/ changeset: 154cda53407f user: smcmanus date: 2012-11-02 20:38:54 summary: Temporarily reverted library browsing. affected #: 2 files diff -r 59a35ec1e2e7ce608d2ae566c7c1e201760c53a1 -r 154cda53407f8360ab00b54ec563c1985157c9a5 templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako +++ b/templates/library/common/browse_library.mako @@ -48,7 +48,6 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js("libs/json2")} ${h.js("libs/jquery/jstorage")} ${common_javascripts()} ${self.grid_javascripts()} @@ -207,7 +206,7 @@ </script></%def> -<%def name="render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False, simple=False )"> +<%def name="render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False, simple=False )"><% ## The received ldda must always be a LibraryDatasetDatasetAssociation object. The object id passed to methods ## from the drop down menu should be the ldda id to prevent id collision ( which could happen when displaying @@ -215,14 +214,22 @@ ## library_dataset, so we display the attributes from the ldda. from galaxy.webapps.galaxy.controllers.library_common import branch_deleted - + is_admin = trans.user_is_admin() and cntrller == 'library_admin' - current_version = ( ldda == library_dataset.library_dataset_dataset_association ) + + if ldda == library_dataset.library_dataset_dataset_association: + current_version = True + if is_admin: + can_modify = can_manage = True + elif cntrller in [ 'library', 'requests' ]: + can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, library_dataset ) + can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, library_dataset ) + else: + can_modify = can_manage = False + else: + current_version = False if current_version and ldda.state not in ( 'ok', 'error', 'empty', 'deleted', 'discarded' ): tracked_datasets[ldda.id] = ldda.state - # SM: This causes a query to be emitted, but it quickly goes down a - # rabbit hole of many possible inheritable cases. It may not be - # possible to easily eliminate the extra query from this call. info_association, inherited = ldda.get_info_association( restrict=True ) form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE %> @@ -303,21 +310,9 @@ %endif </%def> -<%def name="format_delta( tdelta )"> - <% - from datetime import datetime - return "%d.%.6d" % ( tdelta.seconds, tdelta.microseconds ) - %> -</%def> - <%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False, simple=False )"><% - from galaxy.webapps.galaxy.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, map_library_datasets_to_lddas, branch_deleted, datasets_for_lddas - - # SM: DELETEME - from datetime import datetime, timedelta - import logging - log = logging.getLogger( __name__ ) + from galaxy.webapps.galaxy.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, branch_deleted is_admin = trans.user_is_admin() and cntrller == 'library_admin' has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False ) @@ -330,9 +325,6 @@ pad = folder_pad + 20 expander = h.url_for("/static/images/silk/resultset_next.png") folder_img = h.url_for("/static/images/silk/folder.png") - # SM: If this is a comma-delimited list of LDDAs, then split them up - # into a list. For anything else, turn created_ldda_ids into a single - # item list. if created_ldda_ids: created_ldda_ids = util.listify( created_ldda_ids ) if str( folder.id ) in hidden_folder_ids: @@ -434,39 +426,47 @@ %> %endif <% - # TODO: If show_deleted is set to True, then nothing is displayed. Why? This wasn't the case - # in the past. if show_deleted: sub_folders, library_datasets = activatable_folders_and_library_datasets( trans, folder ) else: sub_folders, library_datasets = active_folders_and_library_datasets( trans, folder ) - # Render all the subfolders: - # TODO: Check permissions first. - for sub_folder in sub_folders: - render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False ) - - # Map LibraryDatasets to LDDAs, then map LDDAs to Datasets. - # Then determine which Datasets are accessible and which are not. - # For every LibraryDataset, if there's an LDDA for it and it's - # accessible then display it. - if ( len( library_datasets ) > 0 ): - lib_dataset_ldda_map = map_library_datasets_to_lddas( trans, library_datasets ) - dataset_list = datasets_for_lddas( trans, lib_dataset_ldda_map.values() ) - #can_access_datasets = trans.app.security_agent.dataset_access_mapping( trans, current_user_roles, dataset_list ) - can_access_datasets = trans.app.security_agent.dataset_permission_map_for_access( trans, current_user_roles, dataset_list ) - can_modify_datasets = trans.app.security_agent.item_permission_map_for_modify( trans, current_user_roles, dataset_list ) - can_manage_datasets = trans.app.security_agent.item_permission_map_for_manage( trans, current_user_roles, dataset_list ) - for library_dataset in library_datasets: - ldda = lib_dataset_ldda_map[ library_dataset.id ] - if ldda: - # SMTODO: Fix awkard modify/manage permission checks. - can_access = is_admin or can_access_datasets[ ldda.dataset_id ] - can_modify = is_admin or ( cntrller in ['library', 'requests'] and can_modify_datasets[ ldda.dataset_id ]) - can_manage = is_admin or ( cntrller in ['library', 'requests'] and can_manage_datasets[ ldda.dataset_id ]) + %> + %if is_admin: + %for sub_folder in sub_folders: + ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )} + %endfor + %for library_dataset in library_datasets: + <% + ldda = library_dataset.library_dataset_dataset_association + if ldda: + # There should always be an ldda, but some users running their own instances have reported that + # some of their LibraryDatasets have no associated lddas selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids - if can_access: - render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted ) - %> + %> + %if ldda: + ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )} + %endif + %endfor + %else: + %for sub_folder in sub_folders: + ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False, simple=simple )} + %endfor + %for library_dataset in library_datasets: + <% + ldda = library_dataset.library_dataset_dataset_association + if ldda: + # There should always be an ldda, but some users running their own instances have reported that + # some of their LibraryDatasets have no associated lddas + can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ldda.dataset ) + selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids + else: + can_access = False + %> + %if can_access: + ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted, simple=simple )} + %endif + %endfor + %endif </%def><%def name="render_content(simple=False)"> @@ -474,8 +474,6 @@ from galaxy import util from galaxy.webapps.galaxy.controllers.library_common import branch_deleted from time import strftime - import logging - log = logging.getLogger( __name__ ) is_admin = trans.user_is_admin() and cntrller == 'library_admin' @@ -491,8 +489,6 @@ info_association, inherited = library.get_info_association() form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE - # SM: These are mostly display-specific; ignore them for now. - # The has_accessible_folders determines if anything can be shown - use it. self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles ) root_folder_has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False ) has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles ) @@ -585,16 +581,13 @@ </tr></thead><% row_counter = RowCounter() %> - ## SM: Here is where we render the libraries based on admin/non-admin privileges: %if cntrller in [ 'library', 'requests' ]: ${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True, simple=simple )} - ## SM: TODO: WTF? %if not library.deleted and self.has_accessible_datasets and not simple: ${render_actions_on_multiple_items()} %endif %elif ( trans.user_is_admin() and cntrller in [ 'library_admin', 'requests_admin' ] ): ${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} - ## SM: TODO: WTF? %if not library.deleted and not show_deleted and self.has_accessible_datasets: ${render_actions_on_multiple_items()} %endif diff -r 59a35ec1e2e7ce608d2ae566c7c1e201760c53a1 -r 154cda53407f8360ab00b54ec563c1985157c9a5 templates/library/common/browse_library_opt.mako --- /dev/null +++ b/templates/library/common/browse_library_opt.mako @@ -0,0 +1,622 @@ +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/library/common/library_item_info.mako" import="render_library_item_info" /> +<%namespace file="/library/common/common.mako" import="render_actions_on_multiple_items" /> +<%namespace file="/library/common/common.mako" import="render_compression_types_help" /> +<%namespace file="/library/common/common.mako" import="common_javascripts" /> + +<%! + def inherit(context): + if context.get('use_panels'): + return '/webapps/galaxy/base_panels.mako' + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.message_box_visible=False + self.active_view="user" + self.overlay_visible=False + self.has_accessible_datasets = False +%> +</%def> + +## +## Override methods from base.mako and base_panels.mako +## +<%def name="center_panel()"> + <div style="overflow: auto; height: 100%;"> + <div class="page-container" style="padding: 10px;"> + ${render_content()} + </div> + </div> +</%def> + +## Render the grid's basic elements. Each of these elements can be subclassed. +<%def name="body()"> + ${render_content()} +</%def> + +<%def name="title()">Browse data library</%def> +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "library" )} +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js("libs/json2")} + ${h.js("libs/jquery/jstorage")} + ${common_javascripts()} + ${self.grid_javascripts()} +</%def> + +<%def name="grid_javascripts()"> + <script type="text/javascript"> + var init_libraries = function() { + var storage_id = "library-expand-state-${trans.security.encode_id(library.id)}"; + + var restore_folder_state = function() { + var state = $.jStorage.get(storage_id); + if (state) { + for (var id in state) { + if (state[id] === true) { + var row = $("#" + id), + index = row.parent().children().index(row); + row.addClass("expanded").show(); + row.siblings().filter("tr[parent='" + index + "']").show(); + } + } + } + }; + + var save_folder_state = function() { + var state = {}; + $("tr.folderRow").each( function() { + var folder = $(this); + state[folder.attr("id")] = folder.hasClass("expanded"); + }); + $.jStorage.set(storage_id, state); + }; + + $("#library-grid").each(function() { + var child_of_parent_cache = {}; + // Recursively fill in children and descendents of each row + var process_row = function(q, parents) { + // Find my index + var parent = q.parent(), + this_level = child_of_parent_cache[parent] || (child_of_parent_cache[parent] = parent.children()); + + var index = this_level.index(q); + // Find my immediate children + var children = $(par_child_dict[index]); + // Recursively handle them + var descendents = children; + children.each( function() { + child_descendents = process_row( $(this), parents.add(q) ); + descendents = descendents.add(child_descendents); + }); + // Set up expand / hide link + var expand_fn = function() { + if ( q.hasClass("expanded") ) { + descendents.hide(); + descendents.removeClass("expanded"); + q.removeClass("expanded"); + } else { + children.show(); + q.addClass("expanded"); + } + save_folder_state(); + }; + $("." + q.attr("id") + "-click").click(expand_fn); + // Check/uncheck boxes in subfolders. + q.children("td").children("input[type=checkbox]").click( function() { + if ( $(this).is(":checked") ) { + descendents.find("input[type=checkbox]").attr("checked", true); + } else { + descendents.find("input[type=checkbox]").attr("checked", false); + // If you uncheck a lower level checkbox, uncheck the boxes above it + // (since deselecting a child means the parent is not fully selected any more). + parents.children("td").children("input[type=checkbox]").attr("checked", false); + } + }); + // return descendents for use by parent + return descendents; + } + + // Initialize dict[parent_id] = rows_which_have_that_parent_id_as_parent_attr + var par_child_dict = {}, + no_parent = []; + + $(this).find("tbody tr").each( function() { + if ( $(this).attr("parent")) { + var parent = $(this).attr("parent"); + if (par_child_dict[parent] !== undefined) { + par_child_dict[parent].push(this); + } else { + par_child_dict[parent] = [this]; + } + } else { + no_parent.push(this); + } + }); + + $(no_parent).each( function() { + descendents = process_row( $(this), $([]) ); + descendents.hide(); + }); + }); + + restore_folder_state(); + }; + $(function() { + init_libraries(); + }); + + // Looks for changes in dataset state using an async request. Keeps + // calling itself (via setTimeout) until all datasets are in a terminal + // state. + var updater = function ( tracked_datasets ) { + // Check if there are any items left to track + var empty = true; + for ( i in tracked_datasets ) { + empty = false; + break; + } + if ( ! empty ) { + setTimeout( function() { updater_callback( tracked_datasets ) }, 3000 ); + } + }; + var updater_callback = function ( tracked_datasets ) { + // Build request data + var ids = [] + var states = [] + $.each( tracked_datasets, function ( id, state ) { + ids.push( id ); + states.push( state ); + }); + // Make ajax call + $.ajax( { + type: "POST", + url: "${h.url_for( controller='library_common', action='library_item_updates' )}", + dataType: "json", + data: { ids: ids.join( "," ), states: states.join( "," ) }, + success : function ( data ) { + $.each( data, function( id, val ) { + // Replace HTML + var cell = $("#libraryItem-" + id).find("#libraryItemInfo"); + cell.html( val.html ); + // If new state was terminal, stop tracking + if (( val.state == "ok") || ( val.state == "error") || ( val.state == "empty") || ( val.state == "deleted" ) || ( val.state == "discarded" )) { + delete tracked_datasets[ parseInt(id) ]; + } else { + tracked_datasets[ parseInt(id) ] = val.state; + } + }); + updater( tracked_datasets ); + }, + error: function() { + // Just retry, like the old method, should try to be smarter + updater( tracked_datasets ); + } + }); + }; + </script> +</%def> + +<%def name="render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False, simple=False )"> + <% + ## The received ldda must always be a LibraryDatasetDatasetAssociation object. The object id passed to methods + ## from the drop down menu should be the ldda id to prevent id collision ( which could happen when displaying + ## children, which are always lddas ). We also need to make sure we're displaying the latest version of this + ## library_dataset, so we display the attributes from the ldda. + + from galaxy.webapps.galaxy.controllers.library_common import branch_deleted + + is_admin = trans.user_is_admin() and cntrller == 'library_admin' + current_version = ( ldda == library_dataset.library_dataset_dataset_association ) + if current_version and ldda.state not in ( 'ok', 'error', 'empty', 'deleted', 'discarded' ): + tracked_datasets[ldda.id] = ldda.state + # SM: This causes a query to be emitted, but it quickly goes down a + # rabbit hole of many possible inheritable cases. It may not be + # possible to easily eliminate the extra query from this call. + info_association, inherited = ldda.get_info_association( restrict=True ) + form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE + %> + %if current_version and ( not ldda.library_dataset.deleted or show_deleted ): + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-${ldda.id}"> + <td style="padding-left: ${pad+20}px;"> + <input style="float: left;" type="checkbox" name="ldda_ids" id="${trans.security.encode_id( ldda.id )}" value="${trans.security.encode_id( ldda.id )}" + %if selected: + checked="checked" + %endif + /> + %if simple: + <label for="${trans.security.encode_id( ldda.id )}">${ util.unicodify( ldda.name )}</label> + %else: + <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="dataset-${ldda.id}-popup"> + <a class="view-info" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}"> + %if ldda.library_dataset.deleted: + <div class="libraryItem-error">${util.unicodify( ldda.name )}</div> + %else: + ${util.unicodify( ldda.name )} + %endif + </a> + </div> + %if not library.deleted: + <div popupmenu="dataset-${ldda.id}-popup"> + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify: + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='move_library_item', cntrller=cntrller, item_type='ldda', item_id=trans.security.encode_id( ldda.id ), source_library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Move this dataset</a> + %else: + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and not info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='ldda', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Use template</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='ldda', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Unuse template</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_manage: + %if not trans.app.security_agent.dataset_is_public( ldda.dataset ): + <a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='ldda', id=trans.security.encode_id( ldda.dataset.id ), use_panels=use_panels, show_deleted=show_deleted )}">Make public</a> + %endif + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify: + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), replace_id=trans.security.encode_id( library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data: + <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into selected histories</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a> + %endif + %if can_modify: + %if not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.deleted: + <a class="action-button" confirm="Click OK to delete dataset '${util.unicodify( ldda.name )}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Delete this dataset</a> + %elif not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.purged and ldda.library_dataset.deleted: + <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Undelete this dataset</a> + %endif + %endif + </div> + %endif + %endif + </td> + % if not simple: + <td id="libraryItemInfo">${render_library_item_info( ldda )}</td> + <td>${ldda.extension}</td> + % endif + <td>${ldda.create_time.strftime( "%Y-%m-%d" )}</td> + <td>${ldda.get_size( nice_size=True )}</td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> + %endif +</%def> + +<%def name="format_delta( tdelta )"> + <% + from datetime import datetime + return "%d.%.6d" % ( tdelta.seconds, tdelta.microseconds ) + %> +</%def> + +<%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False, simple=False )"> + <% + from galaxy.webapps.galaxy.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, map_library_datasets_to_lddas, branch_deleted, datasets_for_lddas + + # SM: DELETEME + from datetime import datetime, timedelta + import logging + log = logging.getLogger( __name__ ) + + is_admin = trans.user_is_admin() and cntrller == 'library_admin' + has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False ) + + if root_folder: + pad = folder_pad + expander = h.url_for("/static/images/silk/resultset_bottom.png") + folder_img = h.url_for("/static/images/silk/folder_page.png") + else: + pad = folder_pad + 20 + expander = h.url_for("/static/images/silk/resultset_next.png") + folder_img = h.url_for("/static/images/silk/folder.png") + # SM: If this is a comma-delimited list of LDDAs, then split them up + # into a list. For anything else, turn created_ldda_ids into a single + # item list. + if created_ldda_ids: + created_ldda_ids = util.listify( created_ldda_ids ) + if str( folder.id ) in hidden_folder_ids: + return "" + my_row = None + if is_admin: + can_add = can_modify = can_manage = True + elif cntrller in [ 'library' ]: + can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, folder ) + if not can_access: + can_show, folder_ids = \ + trans.app.security_agent.show_library_item( trans.user, + current_user_roles, + folder, + [ trans.app.security_agent.permitted_actions.LIBRARY_ADD, + trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, + trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ] ) + if not can_show: + return "" + can_add = trans.app.security_agent.can_add_library_item( current_user_roles, folder ) + can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, folder ) + can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, folder ) + else: + can_add = can_modify = can_manage = False + + form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE + info_association, inherited = folder.get_info_association( restrict=True ) + %> + %if not root_folder and ( not folder.deleted or show_deleted ): + <% encoded_id = trans.security.encode_id( folder.id ) %> + <tr id="folder-${encoded_id}" class="folderRow libraryOrFolderRow" + %if parent is not None: + parent="${parent}" + style="display: none;" + %endif + > + <td style="padding-left: ${folder_pad}px;"> + <input type="checkbox" class="folderCheckbox"/> + <span class="expandLink folder-${encoded_id}-click"> + <div style="float: left; margin-left: 2px;" class="menubutton split popup" id="folder_img-${folder.id}-popup"> + <a class="folder-${encoded_id}-click" href="javascript:void(0);"> + <span class="rowIcon"></span> + %if folder.deleted: + <div class="libraryItem-error">${folder.name}</div> + %else: + ${folder.name} + %endif + </a> + </div> + </span> + %if not library.deleted: + <div popupmenu="folder_img-${folder.id}-popup"> + %if not branch_deleted( folder ) and can_add: + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add sub-folder</a> + %endif + %if not branch_deleted( folder ): + %if has_accessible_library_datasets: + <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a> + %endif + %if can_modify: + <a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='move_library_item', cntrller=cntrller, item_type='folder', item_id=trans.security.encode_id( folder.id ), source_library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Move this folder</a> + %else: + <a class="action-button" class="view-info" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> + %endif + %endif + %if not branch_deleted( folder ) and can_modify and not info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='folder', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Use template</a> + %endif + %if not branch_deleted( folder ) and can_modify and info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='folder', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='folder', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Unuse template</a> + %endif + %if not branch_deleted( folder ) and can_manage: + %if not trans.app.security_agent.folder_is_public( folder ): + <a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='folder', id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Make public</a> + %endif + <a class="action-button" href="${h.url_for( controller='library_common', action='folder_permissions', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> + %endif + %if can_modify: + %if not library.deleted and not folder.deleted: + <a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Delete this folder</a> + %elif not library.deleted and folder.deleted and not folder.purged: + <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Undelete this folder</a> + %endif + %endif + </div> + %endif + <td> + %if folder.description: + ${folder.description} + %endif + <td colspan="3"></td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> + %endif + <% + # TODO: If show_deleted is set to True, then nothing is displayed. Why? This wasn't the case + # in the past. + if show_deleted: + sub_folders, library_datasets = activatable_folders_and_library_datasets( trans, folder ) + else: + sub_folders, library_datasets = active_folders_and_library_datasets( trans, folder ) + # Render all the subfolders: + # TODO: Check permissions first. + for sub_folder in sub_folders: + render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False ) + + # Map LibraryDatasets to LDDAs, then map LDDAs to Datasets. + # Then determine which Datasets are accessible and which are not. + # For every LibraryDataset, if there's an LDDA for it and it's + # accessible then display it. + if ( len( library_datasets ) > 0 ): + lib_dataset_ldda_map = map_library_datasets_to_lddas( trans, library_datasets ) + dataset_list = datasets_for_lddas( trans, lib_dataset_ldda_map.values() ) + #can_access_datasets = trans.app.security_agent.dataset_access_mapping( trans, current_user_roles, dataset_list ) + can_access_datasets = trans.app.security_agent.dataset_permission_map_for_access( trans, current_user_roles, dataset_list ) + can_modify_datasets = trans.app.security_agent.item_permission_map_for_modify( trans, current_user_roles, dataset_list ) + can_manage_datasets = trans.app.security_agent.item_permission_map_for_manage( trans, current_user_roles, dataset_list ) + for library_dataset in library_datasets: + ldda = lib_dataset_ldda_map[ library_dataset.id ] + if ldda: + # SMTODO: Fix awkard modify/manage permission checks. + can_access = is_admin or can_access_datasets[ ldda.dataset_id ] + can_modify = is_admin or ( cntrller in ['library', 'requests'] and can_modify_datasets[ ldda.dataset_id ]) + can_manage = is_admin or ( cntrller in ['library', 'requests'] and can_manage_datasets[ ldda.dataset_id ]) + selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids + if can_access: + render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted ) + %> +</%def> + +<%def name="render_content(simple=False)"> + <% + from galaxy import util + from galaxy.webapps.galaxy.controllers.library_common import branch_deleted + from time import strftime + import logging + log = logging.getLogger( __name__ ) + + is_admin = trans.user_is_admin() and cntrller == 'library_admin' + + if is_admin: + can_add = can_modify = can_manage = True + elif cntrller in [ 'library', 'requests' ]: + can_add = trans.app.security_agent.can_add_library_item( current_user_roles, library ) + can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, library ) + can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, library ) + else: + can_add = can_modify = can_manage = False + + info_association, inherited = library.get_info_association() + form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE + + # SM: These are mostly display-specific; ignore them for now. + # The has_accessible_folders determines if anything can be shown - use it. + self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles ) + root_folder_has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False ) + has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles ) + + tracked_datasets = {} + + class RowCounter( object ): + def __init__( self ): + self.count = 0 + def increment( self ): + self.count += 1 + def __str__( self ): + return str( self.count ) + %> + + <h2>Data Library “${library.name}”</h2> + + <ul class="manage-table-actions"> + %if not library.deleted and ( is_admin or can_add ): + <li><a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a></li> + <li><a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( library.root_folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add folder</a></li> + %endif + %if ( ( not library.deleted ) and ( can_modify or can_manage ) ) or ( can_modify and not library.purged ) or ( library.purged ): + <li><a class="action-button" id="library-${library.id}-popup" class="menubutton">Library Actions</a></li> + <div popupmenu="library-${library.id}-popup"> + %if not library.deleted: + %if can_modify: + <a class="action-button" href="${h.url_for( controller='library_common', action='library_info', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> + <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library' )}">Delete this data library</a> + %if show_deleted: + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=False )}">Hide deleted items</a> + %else: + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=True )}">Show deleted items</a> + %endif + %endif + %if can_modify and not library.info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='library', form_type=form_type, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Use template</a> + %endif + %if can_modify and info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='library', form_type=form_type, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='library', form_type=form_type, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Unuse template</a> + %endif + %if can_manage: + %if not trans.app.security_agent.library_is_public( library, contents=True ): + <a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='library', id=trans.security.encode_id( library.id ), contents=True, use_panels=use_panels, show_deleted=show_deleted )}">Make public</a> + %endif + <a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> + %endif + %if root_folder_has_accessible_library_datasets: + <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a> + %endif + %elif can_modify and not library.purged: + <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library', use_panels=use_panels )}">Undelete this data library</a> + %elif library.purged: + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">This data library has been purged</a> + %endif + </div> + %endif + </ul> + + %if message: + ${render_msg( message, status )} + %endif + + %if library.synopsis not in [ '', 'None', None ]: + <div class="libraryItemBody"> + ${library.synopsis} + </div> + %endif + + %if self.has_accessible_datasets: + <form name="act_on_multiple_datasets" action="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}" onSubmit="javascript:return checkForm();" method="post"> + %endif + %if has_accessible_folders: + <table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid"> + <thead> + <tr class="libraryTitle"> + <th> + %if self.has_accessible_datasets: + <input type="checkbox" id="checkAll" name=select_all_datasets_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_datasets_checkbox value="true"/> + %endif + Name + </th> + % if not simple: + <th>Message</th> + <th>Data type</th> + % endif + <th>Date uploaded</th> + <th>File size</th> + </tr> + </thead> + <% row_counter = RowCounter() %> + ## SM: Here is where we render the libraries based on admin/non-admin privileges: + %if cntrller in [ 'library', 'requests' ]: + ${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True, simple=simple )} + ## SM: TODO: WTF? + %if not library.deleted and self.has_accessible_datasets and not simple: + ${render_actions_on_multiple_items()} + %endif + %elif ( trans.user_is_admin() and cntrller in [ 'library_admin', 'requests_admin' ] ): + ${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} + ## SM: TODO: WTF? + %if not library.deleted and not show_deleted and self.has_accessible_datasets: + ${render_actions_on_multiple_items()} + %endif + %endif + </table> + %endif + %if self.has_accessible_datasets: + </form> + %endif + + %if tracked_datasets: + <script type="text/javascript"> + // Updater + updater({${ ",".join( [ '"%s" : "%s"' % ( k, v ) for k, v in tracked_datasets.iteritems() ] ) }}); + </script> +  + %endif + + %if self.has_accessible_datasets and not simple: + ${render_compression_types_help( comptypes )} + %endif + %if not has_accessible_folders: + The data library '${library.name}' does not contain any datasets that you can access. + %endif +</%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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