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

commit/galaxy-central: greg: Another fix needed due to the elimination of the get_webapp() method in the old base controller.
by Bitbucket 08 Oct '12

08 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/26dfa56403e1/ changeset: 26dfa56403e1 user: greg date: 2012-10-08 15:13:18 summary: Another fix needed due to the elimination of the get_webapp() method in the old base controller. affected #: 1 file diff -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 -r 26dfa56403e1011445854560b3e9818180b3c8c2 lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -711,7 +711,7 @@ tool_dependencies_dict = {} repository_name = elem.get( 'name' ) changeset_revision = elem.get( 'changeset_revision' ) - url = '%s/repository/get_tool_dependencies?name=%s&owner=devteam&changeset_revision=%s&webapp=install_manager' % \ + url = '%s/repository/get_tool_dependencies?name=%s&owner=devteam&changeset_revision=%s&from_install_manager=True' % \ ( tool_shed_url, repository_name, changeset_revision ) response = urllib2.urlopen( url ) text = response.read() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Enable circster to accept a dataset to add to visualization. Also, make visualization creation more flexible and some small refactoring for JS visualization objects.
by Bitbucket 05 Oct '12

05 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/05fc04a70a3b/ changeset: 05fc04a70a3b user: jgoecks date: 2012-10-05 22:01:55 summary: Enable circster to accept a dataset to add to visualization. Also, make visualization creation more flexible and some small refactoring for JS visualization objects. affected #: 6 files diff -r 3b63335f5b1b33a2d6f74c2dfd38b85d97e9eebd -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -335,16 +335,18 @@ viz_types = [ "trackster", "circster" ] - def create_visualization( self, trans, title, slug, type, dbkey, annotation=None, config={} ): + def create_visualization( self, trans, type, title="Untitled Genome Vis", slug=None, dbkey=None, annotation=None, config={}, save=True ): """ Create visualiation and first revision. """ - visualization = self._create_visualization( trans, title, type, dbkey, slug, annotation ) + visualization = self._create_visualization( trans, title, type, dbkey, slug, annotation, save ) # Create and save first visualization revision revision = trans.model.VisualizationRevision( visualization=visualization, title=title, config=config, dbkey=dbkey ) visualization.latest_revision = revision - session = trans.sa_session - session.add( revision ) - session.flush() + + if save: + session = trans.sa_session + session.add( revision ) + session.flush() return visualization @@ -440,7 +442,7 @@ """ Returns a visualization's configuration. Only works for trackster visualizations right now. """ config = None - if visualization.type == 'trackster': + if visualization.type in [ 'trackster', 'genome' ]: # Unpack Trackster config. latest_revision = visualization.latest_revision bookmarks = latest_revision.config.get( 'bookmarks', [] ) @@ -566,7 +568,7 @@ # -- Helper functions -- - def _create_visualization( self, trans, title, type, dbkey, slug=None, annotation=None ): + def _create_visualization( self, trans, title, type, dbkey=None, slug=None, annotation=None, save=True ): """ Create visualization but not first revision. Returns Visualization object. """ user = trans.get_user() @@ -593,9 +595,10 @@ annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) self.add_item_annotation( trans.sa_session, trans.user, visualization, annotation ) - session = trans.sa_session - session.add( visualization ) - session.flush() + if save: + session = trans.sa_session + session.add( visualization ) + session.flush() return visualization diff -r 3b63335f5b1b33a2d6f74c2dfd38b85d97e9eebd -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -741,20 +741,36 @@ return self.save_visualization( trans, config, type, id, title, dbkey, annotation ) @web.expose - def circster( self, trans, id, **kwargs ): + def circster( self, trans, id=None, hda_ldda=None, dataset_id=None, dbkey=None ): """ Display a circster visualization. """ - vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) + + # Get/create vis. + if id: + # Display existing viz. + vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) + else: + # Create new viz. + vis = self.create_visualization( trans, type="genome", dbkey=dbkey, save=False ) + + # Get the vis config and work with it from here on out. Working with the + # config is only possible because the config structure of trackster/genome + # visualizations is well known. viz_config = self.get_visualization_config( trans, vis ) + # Add dataset if specified. + if dataset_id: + dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) + viz_config[ 'tracks' ].append( self.get_new_track_config( trans, dataset ) ) + # Get genome info. dbkey = viz_config[ 'dbkey' ] chroms_info = self.app.genomes.chroms( trans, dbkey=dbkey ) genome = { 'dbkey': dbkey, 'chroms_info': chroms_info } # Add genome-wide summary tree data to each track in viz. - tracks = viz_config[ 'tracks' ] + tracks = viz_config.get( 'tracks', [] ) for track in tracks: # Get dataset and indexed datatype. dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) diff -r 3b63335f5b1b33a2d6f74c2dfd38b85d97e9eebd -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -351,7 +351,6 @@ if (!extra_params) { extra_params = {}; } // Use additional parameters to get more detailed data. - var mode; if (cur_data.dataset_type === 'bigwig') { extra_params.num_samples = cur_data.data.length * detail_multiplier; } @@ -642,21 +641,10 @@ */ var Visualization = Backbone.RelationalModel.extend({ defaults: { - id: '', title: '', - type: '', - dbkey: '', - tracks: null + type: '' }, - relations: [ - { - type: Backbone.HasMany, - key: 'tracks', - relatedModel: BackboneTrack - } - ], - // Use function because visualization_url changes depending on viz. // FIXME: all visualizations should save to the same URL (and hence // this function won't be needed). @@ -682,13 +670,27 @@ }); /** - * A Genome space visualization. + * A visualization of genome data. */ var GenomeVisualization = Visualization.extend({ defaults: _.extend({}, Visualization.prototype.defaults, { + dbkey: '', + tracks: null, bookmarks: null, viewport: null - }) + }), + + relations: [ + { + type: Backbone.HasMany, + key: 'tracks', + relatedModel: BackboneTrack + } + ], + + add_track: function(track) { + this.get('tracks').push(track); + } }); /** @@ -727,6 +729,7 @@ }); return { + BackboneTrack: BackboneTrack, BrowserBookmark: BrowserBookmark, BrowserBookmarkCollection: BrowserBookmarkCollection, Cache: Cache, diff -r 3b63335f5b1b33a2d6f74c2dfd38b85d97e9eebd -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -236,7 +236,10 @@ } return action; }, - params = {dataset_id: dataset_id}; + params = { + dataset_id: dataset_id, + hda_ldda: 'hda' + }; // Add dbkey to params if it exists. if (dbkey) { params['dbkey'] = dbkey; } diff -r 3b63335f5b1b33a2d6f74c2dfd38b85d97e9eebd -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -226,11 +226,7 @@ ## Visualization icon + visualizations. Using anchor attributes is a HACK to encode needed ## information--URL base, dataset id, dbkey, visualizations--in anchor. <% - visualizations = data.get_visualizations() - ## HACK: if there are visualizations, only provide a subset for now - ## since others are not ready. - comment out to see all WIP visualizations - if visualizations: - visualizations = [ vis for vis in visualizations if vis in [ 'trackster', 'phyloviz', 'scatterplot' ] ] + visualizations = data.get_visualizations() %> %if visualizations: <a href="${h.url_for( controller='visualization' )}" diff -r 3b63335f5b1b33a2d6f74c2dfd38b85d97e9eebd -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 templates/visualization/circster.mako --- a/templates/visualization/circster.mako +++ b/templates/visualization/circster.mako @@ -33,7 +33,7 @@ } }); - require( [ "libs/d3", "viz/visualization", "viz/circster" ], function( d3, visualization, circster ) { + require( [ "viz/visualization", "viz/circster" ], function(visualization, circster ) { $(function() { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 05 Oct '12

05 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b5bda7a5c345/ changeset: b5bda7a5c345 user: natefoo date: 2012-10-05 21:49:26 summary: Fix the Compute tool to only allow for execution of a limited set of expressions. affected #: 1 file diff -r e8fc8e57dadc8a1254d994e4e05f40271d7e856b -r b5bda7a5c34535ada63722941f2a2d62524b1faa tools/stats/column_maker.py --- a/tools/stats/column_maker.py +++ b/tools/stats/column_maker.py @@ -46,6 +46,12 @@ for key, value in mapped_str.items(): expr = expr.replace( key, value ) +builtin_and_math_functions = 'abs|all|any|bin|chr|cmp|complex|divmod|float|hex|int|len|long|max|min|oct|ord|pow|range|reversed|round|sorted|str|sum|type|unichr|unicode|log|exp|sqrt|ceil|floor' +string_and_list_methods = [ name for name in dir('') + dir([]) if not name.startswith('_') ] +whitelist = "^([c0-9\+\-\*\/\.\'\"><=,: ]|%s|%s)*$" % (builtin_and_math_functions, '|'.join(string_and_list_methods)) +if not re.compile(whitelist).match(expr): + stop_err("Invalid expression") + # Prepare the column variable names and wrappers for column data types cols, type_casts = [], [] for col in range( 1, in_columns + 1 ): https://bitbucket.org/galaxy/galaxy-central/changeset/3b63335f5b1b/ changeset: 3b63335f5b1b user: natefoo date: 2012-10-05 21:52:50 summary: Merge from galaxy-dist affected #: 1 file diff -r cf93e8aa50f96e4d43d39e817d9754dc41a5886e -r 3b63335f5b1b33a2d6f74c2dfd38b85d97e9eebd tools/stats/column_maker.py --- a/tools/stats/column_maker.py +++ b/tools/stats/column_maker.py @@ -46,6 +46,12 @@ for key, value in mapped_str.items(): expr = expr.replace( key, value ) +builtin_and_math_functions = 'abs|all|any|bin|chr|cmp|complex|divmod|float|hex|int|len|long|max|min|oct|ord|pow|range|reversed|round|sorted|str|sum|type|unichr|unicode|log|exp|sqrt|ceil|floor' +string_and_list_methods = [ name for name in dir('') + dir([]) if not name.startswith('_') ] +whitelist = "^([c0-9\+\-\*\/\.\'\"><=,: ]|%s|%s)*$" % (builtin_and_math_functions, '|'.join(string_and_list_methods)) +if not re.compile(whitelist).match(expr): + stop_err("Invalid expression") + # Prepare the column variable names and wrappers for column data types cols, type_casts = [], [] for col in range( 1, in_columns + 1 ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: When finding applicable visualizations, check to ensure that there are column_types before trying to iterate over them.
by Bitbucket 05 Oct '12

05 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/cf93e8aa50f9/ changeset: cf93e8aa50f9 user: jgoecks date: 2012-10-05 15:43:04 summary: When finding applicable visualizations, check to ensure that there are column_types before trying to iterate over them. affected #: 1 file diff -r 210c39f4bf7f2d91c68df84dd9ccecb2ff9f93aa -r cf93e8aa50f96e4d43d39e817d9754dc41a5886e lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -309,9 +309,10 @@ # Can visualize tabular data as scatterplot if there are 2+ numerical # columns. num_numerical_cols = 0 - for col_type in dataset.metadata.column_types: - if col_type in [ 'int', 'float' ]: - num_numerical_cols += 1 + if dataset.metadata.column_types: + for col_type in dataset.metadata.column_types: + if col_type in [ 'int', 'float' ]: + num_numerical_cols += 1 vizs = super( Tabular, self ).get_visualizations( dataset ) if num_numerical_cols >= 2: 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: Moved galaxy.web.controllers references to galaxy.webapps.galaxy.controllers
by Bitbucket 04 Oct '12

04 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/210c39f4bf7f/ changeset: 210c39f4bf7f user: smcmanus date: 2012-10-05 03:43:15 summary: Moved galaxy.web.controllers references to galaxy.webapps.galaxy.controllers affected #: 5 files diff -r 2565580bb7cffd28c237ecafab1fbb46fe6185e9 -r 210c39f4bf7f2d91c68df84dd9ccecb2ff9f93aa templates/admin/requests/rename_datasets.mako --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -1,7 +1,7 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -<% from galaxy.web.controllers.requests_admin import build_rename_datasets_for_sample_select_field %> +<% from galaxy.webapps.galaxy.controllers.requests_admin import build_rename_datasets_for_sample_select_field %><h3>Rename datasets for Sample "${sample.name}"</h3> diff -r 2565580bb7cffd28c237ecafab1fbb46fe6185e9 -r 210c39f4bf7f2d91c68df84dd9ccecb2ff9f93aa templates/library/common/browse_library_opt.mako --- a/templates/library/common/browse_library_opt.mako +++ b/templates/library/common/browse_library_opt.mako @@ -214,7 +214,7 @@ ## 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.web.controllers.library_common import branch_deleted + 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 ) @@ -312,7 +312,7 @@ <%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.web.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 + 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 @@ -472,7 +472,7 @@ <%def name="render_content(simple=False)"><% from galaxy import util - from galaxy.web.controllers.library_common import branch_deleted + from galaxy.webapps.galaxy.controllers.library_common import branch_deleted from time import strftime import logging log = logging.getLogger( __name__ ) diff -r 2565580bb7cffd28c237ecafab1fbb46fe6185e9 -r 210c39f4bf7f2d91c68df84dd9ccecb2ff9f93aa templates/library/common/ldda_info.mako --- a/templates/library/common/ldda_info.mako +++ b/templates/library/common/ldda_info.mako @@ -3,7 +3,7 @@ <%namespace file="/common/template_common.mako" import="render_template_fields" /><% from galaxy import util - from galaxy.web.controllers.library_common import branch_deleted, get_containing_library_from_library_dataset + from galaxy.webapps.galaxy.controllers.library_common import branch_deleted, get_containing_library_from_library_dataset from galaxy.web.framework.helpers import time_ago if ldda == ldda.library_dataset.library_dataset_dataset_association: diff -r 2565580bb7cffd28c237ecafab1fbb46fe6185e9 -r 210c39f4bf7f2d91c68df84dd9ccecb2ff9f93aa templates/library/common/library_dataset_search_results.mako --- a/templates/library/common/library_dataset_search_results.mako +++ b/templates/library/common/library_dataset_search_results.mako @@ -66,8 +66,7 @@ <%def name="render_content()"><% from galaxy import util - from galaxy.web.controllers.library_common import branch_deleted - #from galaxy.webapps.galaxy.controllers.library_common import branch_deleted + from galaxy.webapps.galaxy.controllers.library_common import branch_deleted from time import strftime class RowCounter( object ): diff -r 2565580bb7cffd28c237ecafab1fbb46fe6185e9 -r 210c39f4bf7f2d91c68df84dd9ccecb2ff9f93aa templates/webapps/reports/dataset_info.mako --- a/templates/webapps/reports/dataset_info.mako +++ b/templates/webapps/reports/dataset_info.mako @@ -4,6 +4,7 @@ <% from galaxy.web.framework.helpers import time_ago from galaxy.web.controllers.library_common import get_containing_library_from_library_dataset + from galaxy.webapps.galaxy.controllers.library_common import get_containing_library_from_library_dataset %> %if message: 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: Cleanup: take out traceback and debug
by Bitbucket 04 Oct '12

04 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2565580bb7cf/ changeset: 2565580bb7cf user: smcmanus date: 2012-10-05 02:48:46 summary: Cleanup: take out traceback and debug affected #: 3 files diff -r 029818b7e546a3b6835c49ef4f8694c5ac695dfb -r 2565580bb7cffd28c237ecafab1fbb46fe6185e9 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 @@ -143,8 +143,6 @@ message=message, status=status ) except Exception, e: - import traceback - log.debug( "traceback: %s" % traceback.format_exc() ) message = 'Error attempting to display contents of library (%s): %s.' % ( str( library.name ), str( e ) ) status = 'error' default_action = params.get( 'default_action', None ) diff -r 029818b7e546a3b6835c49ef4f8694c5ac695dfb -r 2565580bb7cffd28c237ecafab1fbb46fe6185e9 lib/galaxy/webapps/galaxy/controllers/requests_admin.py --- a/lib/galaxy/webapps/galaxy/controllers/requests_admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/requests_admin.py @@ -284,7 +284,6 @@ request_id = trans.security.encode_id( sample.request.id ) library_id = trans.security.encode_id( sample.library.id ) self.datatx_grid.title = 'Manage "%s" datasets' % sample.name - log.debug( "!!!!!!!!!!!!!!!!!!!!!!@@@@@@@@@@@@@@@@@@@@@@@##################" ) self.datatx_grid.global_actions = [ grids.GridAction( "Browse target data library", dict( controller='library_common', action='browse_library', diff -r 029818b7e546a3b6835c49ef4f8694c5ac695dfb -r 2565580bb7cffd28c237ecafab1fbb46fe6185e9 templates/library/common/library_dataset_search_results.mako --- a/templates/library/common/library_dataset_search_results.mako +++ b/templates/library/common/library_dataset_search_results.mako @@ -67,6 +67,7 @@ <% from galaxy import util from galaxy.web.controllers.library_common import branch_deleted + #from galaxy.webapps.galaxy.controllers.library_common import branch_deleted from time import strftime class RowCounter( object ): 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 browse_library.mako template referred to galaxy.web.controllers.library_common, which has been updated to galaxy.webapps.galaxy.controllers.library_common. The Data Library browsing should be fixed.
by Bitbucket 04 Oct '12

04 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/029818b7e546/ changeset: 029818b7e546 user: smcmanus date: 2012-10-05 02:43:55 summary: The browse_library.mako template referred to galaxy.web.controllers.library_common, which has been updated to galaxy.webapps.galaxy.controllers.library_common. The Data Library browsing should be fixed. affected #: 3 files diff -r f3b183e756f9b209ef0904718ed547e04c74ab7a -r 029818b7e546a3b6835c49ef4f8694c5ac695dfb 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 +131,7 @@ comptypes = get_comptypes( trans ) try: # SM: TODO: Add configuration variable asap. - return trans.fill_template( '/library/common/browse_library.mako', + return trans.fill_template( 'library/common/browse_library.mako', cntrller=cntrller, use_panels=use_panels, library=library, @@ -143,6 +143,8 @@ message=message, status=status ) except Exception, e: + import traceback + log.debug( "traceback: %s" % traceback.format_exc() ) message = 'Error attempting to display contents of library (%s): %s.' % ( str( library.name ), str( e ) ) status = 'error' default_action = params.get( 'default_action', None ) diff -r f3b183e756f9b209ef0904718ed547e04c74ab7a -r 029818b7e546a3b6835c49ef4f8694c5ac695dfb lib/galaxy/webapps/galaxy/controllers/requests_admin.py --- a/lib/galaxy/webapps/galaxy/controllers/requests_admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/requests_admin.py @@ -284,6 +284,7 @@ request_id = trans.security.encode_id( sample.request.id ) library_id = trans.security.encode_id( sample.library.id ) self.datatx_grid.title = 'Manage "%s" datasets' % sample.name + log.debug( "!!!!!!!!!!!!!!!!!!!!!!@@@@@@@@@@@@@@@@@@@@@@@##################" ) self.datatx_grid.global_actions = [ grids.GridAction( "Browse target data library", dict( controller='library_common', action='browse_library', diff -r f3b183e756f9b209ef0904718ed547e04c74ab7a -r 029818b7e546a3b6835c49ef4f8694c5ac695dfb templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako +++ b/templates/library/common/browse_library.mako @@ -213,7 +213,7 @@ ## 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.web.controllers.library_common import branch_deleted + from galaxy.webapps.galaxy.controllers.library_common import branch_deleted is_admin = trans.user_is_admin() and cntrller == 'library_admin' @@ -312,7 +312,7 @@ <%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.web.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, branch_deleted + 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 ) @@ -472,7 +472,7 @@ <%def name="render_content(simple=False)"><% from galaxy import util - from galaxy.web.controllers.library_common import branch_deleted + from galaxy.webapps.galaxy.controllers.library_common import branch_deleted from time import strftime is_admin = trans.user_is_admin() and cntrller == 'library_admin' 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.

1 0

commit/galaxy-central: jgoecks: Pack scripts and add compiled template.
by Bitbucket 04 Oct '12

04 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f3b183e756f9/ changeset: f3b183e756f9 user: jgoecks date: 2012-10-04 18:35:16 summary: Pack scripts and add compiled template. affected #: 3 files diff -r 89c27f6b20f8f261a8e45e33abcc2ed9c1509a71 -r f3b183e756f9b209ef0904718ed547e04c74ab7a static/scripts/packed/templates/compiled/template-visualization-scatterplotControlForm.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-visualization-scatterplotControlForm.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-scatterplotControlForm"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,o=this;function e(t,s){var q="",r,p;q+='\n <option value="';p=f.index;if(p){r=p.call(t,{hash:{}})}else{r=t.index;r=typeof r===h?r():r}q+=k(r)+'">';p=f.name;if(p){r=p.call(t,{hash:{}})}else{r=t.name;r=typeof r===h?r():r}q+=k(r)+"</option>\n ";return q}function c(t,s){var q="",r,p;q+='\n <option value="';p=f.index;if(p){r=p.call(t,{hash:{}})}else{r=t.index;r=typeof r===h?r():r}q+=k(r)+'">';p=f.name;if(p){r=p.call(t,{hash:{}})}else{r=t.name;r=typeof r===h?r():r}q+=k(r)+"</option>\n ";return q}j+='\n<div id="loading-indicator" style="display: none;">\n <img class="loading-img" src="';i=f.loadingIndicatorImagePath;if(i){d=i.call(n,{hash:{}})}else{d=n.loadingIndicatorImagePath;d=typeof d===h?d():d}j+=k(d)+'" />\n <span class="loading-message"></span>\n</div>\n\n';j+='\n<div id="chart-settings">\n\n ';j+='\n <div id="x-column-input">\n <label for="">Data column for X: </label>\n <select name="x-column">\n ';d=n.availableColumns;d=f.each.call(n,d,{hash:{},inverse:o.noop,fn:o.program(1,e,l)});if(d||d===0){j+=d}j+='\n </select>\n </div>\n <div id="y-column-input">\n <label for="">Data column for Y: </label>\n <select name="y-column">\n ';d=n.availableColumns;d=f.each.call(n,d,{hash:{},inverse:o.noop,fn:o.program(3,c,l)});if(d||d===0){j+=d}j+='\n </select>\n </div>\n \n <input id="render-button" type="button" value="Draw" />\n <div class="clear"></div>\n</div>';return j})})(); \ No newline at end of file diff -r 89c27f6b20f8f261a8e45e33abcc2ed9c1509a71 -r f3b183e756f9b209ef0904718ed547e04c74ab7a static/scripts/packed/viz/phyloviz.js --- a/static/scripts/packed/viz/phyloviz.js +++ b/static/scripts/packed/viz/phyloviz.js @@ -1,1 +1,1 @@ -var UserMenuBase=Backbone.View.extend({className:"UserMenuBase",isAcceptableValue:function(e,c,a){var b=this,f=e.val(),g=e.attr("displayLabel")||e.attr("id").replace("phyloViz","");function d(h){return !isNaN(parseFloat(h))&&isFinite(h)}if(!d(f)){alert(g+" is not a number!");return false}if(f>a){alert(g+" is too large.");return false}else{if(f<c){alert(g+" is too small.");return false}}return true},hasIllegalJsonCharacters:function(a){if(a.val().search(/"|'|\\/)!==-1){alert("Named fields cannot contain these illegal characters: double quote(\"), single guote('), or back slash(\\). ");return true}return false}});function PhyloTreeLayout(){var j=this,e=d3.layout.hierarchy().sort(null).value(null),i=360,d="Linear",h=18,f=200,g=0,c=0.5,a=50;j.leafHeight=function(k){if(typeof k==="undefined"){return h}else{h=k;return j}};j.layoutMode=function(k){if(typeof k==="undefined"){return d}else{d=k;return j}};j.layoutAngle=function(k){if(typeof k==="undefined"){return i}if(isNaN(k)||k<0||k>360){return j}else{i=k;return j}};j.separation=function(k){if(typeof k==="undefined"){return f}else{f=k;return j}};j.links=function(k){return d3.layout.tree().links(k)};j.nodes=function(n,l){var m=e.call(j,n,l),k=[],p=0,o=0;m.forEach(function(q){var r=q.data;r.depth=q.depth;p=r.depth>p?r.depth:p;k.push(r)});k.forEach(function(q){if(!q.children){o+=1;q.depth=p}});h=d==="Circular"?i/o:h;g=0;b(k[0],p,h,null);return k};function b(o,q,n,m){var l=o.children,k=0;var p=o.dist||c;p=p>1?1:p;o.dist=p;if(m!==null){o.y0=m.y0+p*f}else{o.y0=a}if(!l){o.x0=g++*n}else{l.forEach(function(r){r.parent=o;k+=b(r,q,n,o)});o.x0=k/l.length}o.x=o.x0;o.y=o.y0;return o.x0}return j}var PhyloTree=Visualization.extend({defaults:{layout:"Linear",separation:250,leafHeight:18,type:"phyloviz",title:"Title",scaleFactor:1,translate:[0,0],fontSize:12,selectedNode:null,nodeAttrChangedTime:0},root:{},toggle:function(a){if(typeof a==="undefined"){return}if(a.children){a._children=a.children;a.children=null}else{a.children=a._children;a._children=null}},toggleAll:function(a){if(a.children&&a.children.length!==0){a.children.forEach(this.toggleAll);toggle(a)}},getData:function(){return this.root},save:function(){var a=this.root;b(a);this.set("root",a);function b(d){delete d.parent;if(d._selected){delete d._selected}d.children?d.children.forEach(b):0;d._children?d._children.forEach(b):0}var c=jQuery.extend(true,{},this.attributes);c.selectedNode=null;show_message("Saving to Galaxy","progress");return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(c)},success:function(d){var e=d.url.split("id=")[1].split("&")[0],f="/phyloviz/visualization?id="+e;window.history.pushState({},"",f+window.location.hash);hide_modal()}})}});var PhylovizLayoutBase=Backbone.View.extend({defaults:{nodeRadius:4.5},stdInit:function(b){var a=this;a.model.on("change:separation change:leafHeight change:fontSize change:nodeAttrChangedTime",a.updateAndRender,a);a.vis=b.vis;a.i=0;a.maxDepth=-1;a.width=b.width;a.height=b.height},updateAndRender:function(c){var b=d3.select(".vis"),a=this;c=c||a.model.root;a.renderNodes(c);a.renderLinks(c);a.addTooltips()},renderLinks:function(a){var j=this;var b=j.diagonal;var c=j.duration;var e=j.layoutMode;var g=j.vis.selectAll("g.completeLink").data(j.tree.links(j.nodes),function(k){return k.target.id});var i=function(k){k.pos0=k.source.y0+" "+k.source.x0;k.pos1=k.source.y0+" "+k.target.x0;k.pos2=k.target.y0+" "+k.target.x0};var h=g.enter().insert("svg:g","g.node").attr("class","completeLink");h.append("svg:path").attr("class","link").attr("d",function(k){i(k);return"M "+k.pos0+" L "+k.pos1});var f=g.transition().duration(500);f.select("path.link").attr("d",function(k){i(k);return"M "+k.pos0+" L "+k.pos1+" L "+k.pos2});var d=g.exit().remove()},selectNode:function(b){var a=this;d3.selectAll("g.node").classed("selectedHighlight",function(c){if(b.id===c.id){if(b._selected){delete b._selected;return false}else{b._selected=true;return true}}return false});a.model.set("selectedNode",b);$("#phyloVizSelectedNodeName").val(b.name);$("#phyloVizSelectedNodeDist").val(b.dist);$("#phyloVizSelectedNodeAnnotation").val(b.annotation||"")},addTooltips:function(){$(".bs-tooltip").remove();$(".node").attr("data-original-title",function(){var b=this.__data__,a=b.annotation||"None";return b?(b.name?b.name+"<br/>":"")+"Dist: "+b.dist+" <br/>Annotation: "+a:""}).tooltip({placement:"top",trigger:"hover"})}});var PhylovizLinearView=PhylovizLayoutBase.extend({initialize:function(b){var a=this;a.margins=b.margins;a.layoutMode="Linear";a.stdInit(b);a.layout();a.updateAndRender(a.model.root)},layout:function(){var a=this;a.tree=new PhyloTreeLayout().layoutMode("Linear");a.diagonal=d3.svg.diagonal().projection(function(b){return[b.y,b.x]})},renderNodes:function(a){var h=this,i=h.model.get("fontSize")+"px";h.tree.separation(h.model.get("separation")).leafHeight(h.model.get("leafHeight"));var d=500,b=h.tree.separation(h.model.get("separation")).nodes(h.model.root);var c=h.vis.selectAll("g.node").data(b,function(j){return j.name+j.id||(j.id=++h.i)});h.nodes=b;h.duration=d;var e=c.enter().append("svg:g").attr("class","node").on("dblclick",function(){d3.event.stopPropagation()}).on("click",function(j){if(d3.event.altKey){h.selectNode(j)}else{if(j.children&&j.children.length===0){return}h.model.toggle(j);h.updateAndRender(j)}});e.attr("transform",function(j){return"translate("+a.y0+","+a.x0+")"});e.append("svg:circle").attr("r",0.000001).style("fill",function(j){return j._children?"lightsteelblue":"#fff"});e.append("svg:text").attr("class","nodeLabel").attr("x",function(j){return j.children||j._children?-10:10}).attr("dy",".35em").attr("text-anchor",function(j){return j.children||j._children?"end":"start"}).style("fill-opacity",0.000001);var f=c.transition().duration(d);f.attr("transform",function(j){return"translate("+j.y+","+j.x+")"});f.select("circle").attr("r",h.defaults.nodeRadius).style("fill",function(j){return j._children?"lightsteelblue":"#fff"});f.select("text").style("fill-opacity",1).style("font-size",i).text(function(j){return j.name});var g=c.exit().transition().duration(d).remove();g.select("circle").attr("r",0.000001);g.select("text").style("fill-opacity",0.000001);b.forEach(function(j){j.x0=j.x;j.y0=j.y})}});var PhylovizView=Backbone.View.extend({className:"phyloviz",initialize:function(b){var a=this;a.MIN_SCALE=0.05;a.MAX_SCALE=5;a.MAX_DISPLACEMENT=500;a.margins=[10,60,10,80];a.width=$("#PhyloViz").width();a.height=$("#PhyloViz").height();a.radius=a.width;a.data=b.data;$(window).resize(function(){a.width=$("#PhyloViz").width();a.height=$("#PhyloViz").height();a.render()});a.phyloTree=new PhyloTree(b.config);a.phyloTree.root=a.data;a.zoomFunc=d3.behavior.zoom().scaleExtent([a.MIN_SCALE,a.MAX_SCALE]);a.zoomFunc.translate(a.phyloTree.get("translate"));a.zoomFunc.scale(a.phyloTree.get("scaleFactor"));a.navMenu=new HeaderButtons(a);a.settingsMenu=new SettingsMenu({phyloTree:a.phyloTree});a.nodeSelectionView=new NodeSelectionView({phyloTree:a.phyloTree});a.search=new PhyloVizSearch();setTimeout(function(){a.zoomAndPan()},1000)},render:function(){var b=this;$("#PhyloViz").empty();b.mainSVG=d3.select("#PhyloViz").append("svg:svg").attr("width",b.width).attr("height",b.height).attr("pointer-events","all").call(b.zoomFunc.on("zoom",function(){b.zoomAndPan()}));b.boundingRect=b.mainSVG.append("svg:rect").attr("class","boundingRect").attr("width",b.width).attr("height",b.height).attr("stroke","black").attr("fill","white");b.vis=b.mainSVG.append("svg:g").attr("class","vis");b.layoutOptions={model:b.phyloTree,width:b.width,height:b.height,vis:b.vis,margins:b.margins};$("#title").text("Phylogenetic Tree from "+b.phyloTree.get("title")+":");var a=new PhylovizLinearView(b.layoutOptions)},zoomAndPan:function(a){if(typeof a!=="undefined"){var g=a.zoom,c=a.translate}var j=this,e=j.zoomFunc.scale(),i=j.zoomFunc.translate(),f="",h="";switch(g){case"reset":e=1;i=[0,0];break;case"+":e*=1.1;break;case"-":e*=0.9;break;default:if(typeof g==="number"){e=g}else{if(d3.event!==null){e=d3.event.scale}}}if(e<j.MIN_SCALE||e>j.MAX_SCALE){return}j.zoomFunc.scale(e);f="translate("+j.margins[3]+","+j.margins[0]+") scale("+e+")";if(d3.event!==null){h="translate("+d3.event.translate+")"}else{if(typeof c!=="undefined"){var d=c.split(",")[0];var b=c.split(",")[1];if(!isNaN(d)&&!isNaN(b)){i=[i[0]+parseFloat(d),i[1]+parseFloat(b)]}}j.zoomFunc.translate(i);h="translate("+i+")"}j.phyloTree.set("scaleFactor",e);j.phyloTree.set("translate",i);j.vis.attr("transform",h+f)},reloadViz:function(){var b=this,d=$("#phylovizNexSelector :selected").val(),a=b.phyloTree.get("dataset_id"),c="phyloviz/getJsonData?dataset_id="+a+"&treeIndex="+String(d);$.getJSON(c,function(e){window.initPhyloViz(e.data,e.config)})}});var HeaderButtons=Backbone.View.extend({initialize:function(b){var a=this;a.phylovizView=b;$("#panelHeaderRightBtns").empty();$("#phyloVizNavBtns").empty();$("#phylovizNexSelector").off();a.initNavBtns();a.initRightHeaderBtns();$("#phylovizNexSelector").off().on("change",function(){a.phylovizView.reloadViz()})},initRightHeaderBtns:function(){var a=this;rightMenu=create_icon_buttons_menu([{icon_class:"gear",title:"PhyloViz Settings",on_click:function(){$("#SettingsMenu").show();a.settingsMenu.updateUI()}},{icon_class:"disk",title:"Save visualization",on_click:function(){var b=$("#phylovizNexSelector option:selected").text();if(b){a.phylovizView.phyloTree.set("title",b)}a.phylovizView.phyloTree.save()}},{icon_class:"chevron-expand",title:"Search / Edit Nodes",on_click:function(){$("#nodeSelectionView").show()}},{icon_class:"information",title:"Phyloviz 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a=this;a.phyloTree=b.phyloTree;a.el=$("#SettingsMenu");a.inputs={separation:$("#phyloVizTreeSeparation"),leafHeight:$("#phyloVizTreeLeafHeight"),fontSize:$("#phyloVizTreeFontSize")};$("#settingsCloseBtn").off().on("click",function(){a.el.hide()});$("#phylovizResetSettingsBtn").off().on("click",function(){a.resetToDefaults()});$("#phylovizApplySettingsBtn").off().on("click",function(){a.apply()})},apply:function(){var a=this;if(!a.isAcceptableValue(a.inputs.separation,50,2500)||!a.isAcceptableValue(a.inputs.leafHeight,5,30)||!a.isAcceptableValue(a.inputs.fontSize,5,20)){return}$.each(a.inputs,function(b,c){a.phyloTree.set(b,c.val())})},updateUI:function(){var a=this;$.each(a.inputs,function(b,c){c.val(a.phyloTree.get(b))})},resetToDefaults:function(){$(".bs-tooltip").remove();var a=this;$.each(a.phyloTree.defaults,function(b,c){a.phyloTree.set(b,c)});a.updateUI()},render:function(){}});var NodeSelectionView=UserMenuBase.extend({className:"Settings",initialize:function(b){var a=this;a.el=$("#nodeSelectionView");a.phyloTree=b.phyloTree;a.UI={enableEdit:$("#phylovizEditNodesCheck"),saveChanges:$("#phylovizNodeSaveChanges"),cancelChanges:$("#phylovizNodeCancelChanges"),name:$("#phyloVizSelectedNodeName"),dist:$("#phyloVizSelectedNodeDist"),annotation:$("#phyloVizSelectedNodeAnnotation")};a.valuesOfConcern={name:null,dist:null,annotation:null};$("#nodeSelCloseBtn").off().on("click",function(){a.el.hide()});a.UI.saveChanges.off().on("click",function(){a.updateNodes()});a.UI.cancelChanges.off().on("click",function(){a.cancelChanges()});(function(c){c.fn.enable=function(d){return c(this).each(function(){if(d){c(this).removeAttr("disabled")}else{c(this).attr("disabled","disabled")}})}})(jQuery);a.UI.enableEdit.off().on("click",function(){a.toggleUI()})},toggleUI:function(){var a=this,b=a.UI.enableEdit.is(":checked");!b?a.cancelChanges():"";$.each(a.valuesOfConcern,function(c,d){a.UI[c].enable(b)});if(b){a.UI.saveChanges.show();a.UI.cancelChanges.show()}else{a.UI.saveChanges.hide();a.UI.cancelChanges.hide()}},cancelChanges:function(){var a=this,b=a.phyloTree.get("selectedNode");if(b){$.each(a.valuesOfConcern,function(c,d){a.UI[c].val(b[c])})}},updateNodes:function(){var a=this,b=a.phyloTree.get("selectedNode");if(b){if(!a.isAcceptableValue(a.UI.dist,0,1)||a.hasIllegalJsonCharacters(a.UI.name)||a.hasIllegalJsonCharacters(a.UI.annotation)){return}$.each(a.valuesOfConcern,function(c,d){(b[c])=a.UI[c].val()});a.phyloTree.set("nodeAttrChangedTime",new Date())}else{alert("No node selected")}}});var PhyloVizSearch=UserMenuBase.extend({initialize:function(){var a=this;$("#phyloVizSearchBtn").on("click",function(){var c=$("#phyloVizSearchTerm"),d=$("#phyloVizSearchCondition").val().split("-"),b=d[0],e=d[1];a.hasIllegalJsonCharacters(c);if(b==="dist"){a.isAcceptableValue(c,0,1)}a.searchTree(b,e,c.val())})},searchTree:function(a,c,b){d3.selectAll("g.node").classed("searchHighlight",function(f){var e=f[a];if(typeof e!=="undefined"&&e!==null){if(a==="dist"){switch(c){case"greaterEqual":return e>=+b;case"lesserEqual":return e<=+b;default:return}}else{if(a==="name"||a==="annotation"){return e.toLowerCase().indexOf(b.toLowerCase())!==-1}}}})}}); \ No newline at end of file +define(["libs/d3","viz/visualization"],function(l,f){var k=Backbone.View.extend({className:"UserMenuBase",isAcceptableValue:function(q,o,m){var n=this,r=q.val(),s=q.attr("displayLabel")||q.attr("id").replace("phyloViz","");function p(t){return !isNaN(parseFloat(t))&&isFinite(t)}if(!p(r)){alert(s+" is not a number!");return false}if(r>m){alert(s+" is too large.");return false}else{if(r<o){alert(s+" is too small.");return false}}return true},hasIllegalJsonCharacters:function(m){if(m.val().search(/"|'|\\/)!==-1){alert("Named fields cannot contain these illegal characters: double quote(\"), single guote('), or back slash(\\). ");return true}return false}});function g(){var v=this,q=l.layout.hierarchy().sort(null).value(null),u=360,p="Linear",t=18,r=200,s=0,o=0.5,m=50;v.leafHeight=function(w){if(typeof w==="undefined"){return t}else{t=w;return v}};v.layoutMode=function(w){if(typeof w==="undefined"){return p}else{p=w;return v}};v.layoutAngle=function(w){if(typeof w==="undefined"){return u}if(isNaN(w)||w<0||w>360){return v}else{u=w;return v}};v.separation=function(w){if(typeof w==="undefined"){return r}else{r=w;return v}};v.links=function(w){return l.layout.tree().links(w)};v.nodes=function(z,x){var y=q.call(v,z,x),w=[],B=0,A=0;y.forEach(function(C){var D=C.data;D.depth=C.depth;B=D.depth>B?D.depth:B;w.push(D)});w.forEach(function(C){if(!C.children){A+=1;C.depth=B}});t=p==="Circular"?u/A:t;s=0;n(w[0],B,t,null);return w};function n(A,C,z,y){var x=A.children,w=0;var B=A.dist||o;B=B>1?1:B;A.dist=B;if(y!==null){A.y0=y.y0+B*r}else{A.y0=m}if(!x){A.x0=s++*z}else{x.forEach(function(D){D.parent=A;w+=n(D,C,z,A)});A.x0=w/x.length}A.x=A.x0;A.y=A.y0;return A.x0}return v}var b=f.Visualization.extend({defaults:{layout:"Linear",separation:250,leafHeight:18,type:"phyloviz",title:"Title",scaleFactor:1,translate:[0,0],fontSize:12,selectedNode:null,nodeAttrChangedTime:0},root:{},toggle:function(m){if(typeof m==="undefined"){return}if(m.children){m._children=m.children;m.children=null}else{m.children=m._children;m._children=null}},toggleAll:function(m){if(m.children&&m.children.length!==0){m.children.forEach(this.toggleAll);toggle(m)}},getData:function(){return this.root},save:function(){var m=this.root;n(m);this.set("root",m);function n(p){delete p.parent;if(p._selected){delete p._selected}if(p.children){p.children.forEach(n)}if(p._children){p._children.forEach(n)}}var o=jQuery.extend(true,{},this.attributes);o.selectedNode=null;show_message("Saving to Galaxy","progress");return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(o)},success:function(p){var q=p.url.split("id=")[1].split("&")[0],r="/phyloviz/visualization?id="+q;window.history.pushState({},"",r+window.location.hash);hide_modal()}})}});var d=Backbone.View.extend({defaults:{nodeRadius:4.5},stdInit:function(n){var m=this;m.model.on("change:separation change:leafHeight change:fontSize change:nodeAttrChangedTime",m.updateAndRender,m);m.vis=n.vis;m.i=0;m.maxDepth=-1;m.width=n.width;m.height=n.height},updateAndRender:function(o){var n=l.select(".vis"),m=this;o=o||m.model.root;m.renderNodes(o);m.renderLinks(o);m.addTooltips()},renderLinks:function(m){var v=this;var n=v.diagonal;var o=v.duration;var q=v.layoutMode;var s=v.vis.selectAll("g.completeLink").data(v.tree.links(v.nodes),function(w){return w.target.id});var u=function(w){w.pos0=w.source.y0+" "+w.source.x0;w.pos1=w.source.y0+" "+w.target.x0;w.pos2=w.target.y0+" "+w.target.x0};var t=s.enter().insert("svg:g","g.node").attr("class","completeLink");t.append("svg:path").attr("class","link").attr("d",function(w){u(w);return"M "+w.pos0+" L "+w.pos1});var r=s.transition().duration(500);r.select("path.link").attr("d",function(w){u(w);return"M "+w.pos0+" L "+w.pos1+" L "+w.pos2});var p=s.exit().remove()},selectNode:function(n){var m=this;l.selectAll("g.node").classed("selectedHighlight",function(o){if(n.id===o.id){if(n._selected){delete n._selected;return false}else{n._selected=true;return true}}return false});m.model.set("selectedNode",n);$("#phyloVizSelectedNodeName").val(n.name);$("#phyloVizSelectedNodeDist").val(n.dist);$("#phyloVizSelectedNodeAnnotation").val(n.annotation||"")},addTooltips:function(){$(".bs-tooltip").remove();$(".node").attr("data-original-title",function(){var n=this.__data__,m=n.annotation||"None";return n?(n.name?n.name+"<br/>":"")+"Dist: "+n.dist+" <br/>Annotation: "+m:""}).tooltip({placement:"top",trigger:"hover"})}});var a=d.extend({initialize:function(n){var m=this;m.margins=n.margins;m.layoutMode="Linear";m.stdInit(n);m.layout();m.updateAndRender(m.model.root)},layout:function(){var m=this;m.tree=new g().layoutMode("Linear");m.diagonal=l.svg.diagonal().projection(function(n){return[n.y,n.x]})},renderNodes:function(m){var t=this,u=t.model.get("fontSize")+"px";t.tree.separation(t.model.get("separation")).leafHeight(t.model.get("leafHeight"));var p=500,n=t.tree.separation(t.model.get("separation")).nodes(t.model.root);var o=t.vis.selectAll("g.node").data(n,function(v){return v.name+v.id||(v.id=++t.i)});t.nodes=n;t.duration=p;var q=o.enter().append("svg:g").attr("class","node").on("dblclick",function(){l.event.stopPropagation()}).on("click",function(v){if(l.event.altKey){t.selectNode(v)}else{if(v.children&&v.children.length===0){return}t.model.toggle(v);t.updateAndRender(v)}});q.attr("transform",function(v){return"translate("+m.y0+","+m.x0+")"});q.append("svg:circle").attr("r",0.000001).style("fill",function(v){return v._children?"lightsteelblue":"#fff"});q.append("svg:text").attr("class","nodeLabel").attr("x",function(v){return v.children||v._children?-10:10}).attr("dy",".35em").attr("text-anchor",function(v){return v.children||v._children?"end":"start"}).style("fill-opacity",0.000001);var r=o.transition().duration(p);r.attr("transform",function(v){return"translate("+v.y+","+v.x+")"});r.select("circle").attr("r",t.defaults.nodeRadius).style("fill",function(v){return v._children?"lightsteelblue":"#fff"});r.select("text").style("fill-opacity",1).style("font-size",u).text(function(v){return v.name});var s=o.exit().transition().duration(p).remove();s.select("circle").attr("r",0.000001);s.select("text").style("fill-opacity",0.000001);n.forEach(function(v){v.x0=v.x;v.y0=v.y})}});var i=Backbone.View.extend({className:"phyloviz",initialize:function(n){var m=this;m.MIN_SCALE=0.05;m.MAX_SCALE=5;m.MAX_DISPLACEMENT=500;m.margins=[10,60,10,80];m.width=$("#PhyloViz").width();m.height=$("#PhyloViz").height();m.radius=m.width;m.data=n.data;$(window).resize(function(){m.width=$("#PhyloViz").width();m.height=$("#PhyloViz").height();m.render()});m.phyloTree=new b(n.config);m.phyloTree.root=m.data;m.zoomFunc=l.behavior.zoom().scaleExtent([m.MIN_SCALE,m.MAX_SCALE]);m.zoomFunc.translate(m.phyloTree.get("translate"));m.zoomFunc.scale(m.phyloTree.get("scaleFactor"));m.navMenu=new c(m);m.settingsMenu=new h({phyloTree:m.phyloTree});m.nodeSelectionView=new e({phyloTree:m.phyloTree});m.search=new j();setTimeout(function(){m.zoomAndPan()},1000)},render:function(){var n=this;$("#PhyloViz").empty();n.mainSVG=l.select("#PhyloViz").append("svg:svg").attr("width",n.width).attr("height",n.height).attr("pointer-events","all").call(n.zoomFunc.on("zoom",function(){n.zoomAndPan()}));n.boundingRect=n.mainSVG.append("svg:rect").attr("class","boundingRect").attr("width",n.width).attr("height",n.height).attr("stroke","black").attr("fill","white");n.vis=n.mainSVG.append("svg:g").attr("class","vis");n.layoutOptions={model:n.phyloTree,width:n.width,height:n.height,vis:n.vis,margins:n.margins};$("#title").text("Phylogenetic Tree from "+n.phyloTree.get("title")+":");var m=new a(n.layoutOptions)},zoomAndPan:function(m){var s,o;if(typeof m!=="undefined"){s=m.zoom;o=m.translate}var v=this,q=v.zoomFunc.scale(),u=v.zoomFunc.translate(),r="",t="";switch(s){case"reset":q=1;u=[0,0];break;case"+":q*=1.1;break;case"-":q*=0.9;break;default:if(typeof s==="number"){q=s}else{if(l.event!==null){q=l.event.scale}}}if(q<v.MIN_SCALE||q>v.MAX_SCALE){return}v.zoomFunc.scale(q);r="translate("+v.margins[3]+","+v.margins[0]+") scale("+q+")";if(l.event!==null){t="translate("+l.event.translate+")"}else{if(typeof o!=="undefined"){var p=o.split(",")[0];var n=o.split(",")[1];if(!isNaN(p)&&!isNaN(n)){u=[u[0]+parseFloat(p),u[1]+parseFloat(n)]}}v.zoomFunc.translate(u);t="translate("+u+")"}v.phyloTree.set("scaleFactor",q);v.phyloTree.set("translate",u);v.vis.attr("transform",t+r)},reloadViz:function(){var n=this,p=$("#phylovizNexSelector :selected").val(),m=n.phyloTree.get("dataset_id"),o="phyloviz/getJsonData?dataset_id="+m+"&treeIndex="+String(p);$.getJSON(o,function(q){window.initPhyloViz(q.data,q.config)})}});var c=Backbone.View.extend({initialize:function(n){var m=this;m.phylovizView=n;$("#panelHeaderRightBtns").empty();$("#phyloVizNavBtns").empty();$("#phylovizNexSelector").off();m.initNavBtns();m.initRightHeaderBtns();$("#phylovizNexSelector").off().on("change",function(){m.phylovizView.reloadViz()})},initRightHeaderBtns:function(){var m=this;rightMenu=create_icon_buttons_menu([{icon_class:"gear",title:"PhyloViz Settings",on_click:function(){$("#SettingsMenu").show();m.settingsMenu.updateUI()}},{icon_class:"disk",title:"Save visualization",on_click:function(){var n=$("#phylovizNexSelector option:selected").text();if(n){m.phylovizView.phyloTree.set("title",n)}m.phylovizView.phyloTree.save()}},{icon_class:"chevron-expand",title:"Search / Edit Nodes",on_click:function(){$("#nodeSelectionView").show()}},{icon_class:"information",title:"Phyloviz Help",on_click:function(){window.open("http://wiki.g2.bx.psu.edu/Learn/Visualization/PhylogeneticTree")}}],{tooltip_config:{placement:"bottom"}});$("#panelHeaderRightBtns").append(rightMenu.$el)},initNavBtns:function(){var m=this,n=create_icon_buttons_menu([{icon_class:"zoom-in",title:"Zoom in",on_click:function(){m.phylovizView.zoomAndPan({zoom:"+"})}},{icon_class:"zoom-out",title:"Zoom out",on_click:function(){m.phylovizView.zoomAndPan({zoom:"-"})}},{icon_class:"arrow-circle",title:"Reset Zoom/Pan",on_click:function(){m.phylovizView.zoomAndPan({zoom:"reset"})}}],{tooltip_config:{placement:"bottom"}});$("#phyloVizNavBtns").append(n.$el)}});var h=k.extend({className:"Settings",initialize:function(n){var m=this;m.phyloTree=n.phyloTree;m.el=$("#SettingsMenu");m.inputs={separation:$("#phyloVizTreeSeparation"),leafHeight:$("#phyloVizTreeLeafHeight"),fontSize:$("#phyloVizTreeFontSize")};$("#settingsCloseBtn").off().on("click",function(){m.el.hide()});$("#phylovizResetSettingsBtn").off().on("click",function(){m.resetToDefaults()});$("#phylovizApplySettingsBtn").off().on("click",function(){m.apply()})},apply:function(){var m=this;if(!m.isAcceptableValue(m.inputs.separation,50,2500)||!m.isAcceptableValue(m.inputs.leafHeight,5,30)||!m.isAcceptableValue(m.inputs.fontSize,5,20)){return}$.each(m.inputs,function(n,o){m.phyloTree.set(n,o.val())})},updateUI:function(){var m=this;$.each(m.inputs,function(n,o){o.val(m.phyloTree.get(n))})},resetToDefaults:function(){$(".bs-tooltip").remove();var m=this;$.each(m.phyloTree.defaults,function(n,o){m.phyloTree.set(n,o)});m.updateUI()},render:function(){}});var e=k.extend({className:"Settings",initialize:function(n){var m=this;m.el=$("#nodeSelectionView");m.phyloTree=n.phyloTree;m.UI={enableEdit:$("#phylovizEditNodesCheck"),saveChanges:$("#phylovizNodeSaveChanges"),cancelChanges:$("#phylovizNodeCancelChanges"),name:$("#phyloVizSelectedNodeName"),dist:$("#phyloVizSelectedNodeDist"),annotation:$("#phyloVizSelectedNodeAnnotation")};m.valuesOfConcern={name:null,dist:null,annotation:null};$("#nodeSelCloseBtn").off().on("click",function(){m.el.hide()});m.UI.saveChanges.off().on("click",function(){m.updateNodes()});m.UI.cancelChanges.off().on("click",function(){m.cancelChanges()});(function(o){o.fn.enable=function(p){return o(this).each(function(){if(p){o(this).removeAttr("disabled")}else{o(this).attr("disabled","disabled")}})}})(jQuery);m.UI.enableEdit.off().on("click",function(){m.toggleUI()})},toggleUI:function(){var m=this,n=m.UI.enableEdit.is(":checked");if(!n){m.cancelChanges()}$.each(m.valuesOfConcern,function(o,p){m.UI[o].enable(n)});if(n){m.UI.saveChanges.show();m.UI.cancelChanges.show()}else{m.UI.saveChanges.hide();m.UI.cancelChanges.hide()}},cancelChanges:function(){var m=this,n=m.phyloTree.get("selectedNode");if(n){$.each(m.valuesOfConcern,function(o,p){m.UI[o].val(n[o])})}},updateNodes:function(){var m=this,n=m.phyloTree.get("selectedNode");if(n){if(!m.isAcceptableValue(m.UI.dist,0,1)||m.hasIllegalJsonCharacters(m.UI.name)||m.hasIllegalJsonCharacters(m.UI.annotation)){return}$.each(m.valuesOfConcern,function(o,p){(n[o])=m.UI[o].val()});m.phyloTree.set("nodeAttrChangedTime",new Date())}else{alert("No node selected")}}});var j=k.extend({initialize:function(){var m=this;$("#phyloVizSearchBtn").on("click",function(){var o=$("#phyloVizSearchTerm"),p=$("#phyloVizSearchCondition").val().split("-"),n=p[0],q=p[1];m.hasIllegalJsonCharacters(o);if(n==="dist"){m.isAcceptableValue(o,0,1)}m.searchTree(n,q,o.val())})},searchTree:function(m,o,n){l.selectAll("g.node").classed("searchHighlight",function(q){var p=q[m];if(typeof p!=="undefined"&&p!==null){if(m==="dist"){switch(o){case"greaterEqual":return p>=+n;case"lesserEqual":return p<=+n;default:return}}else{if(m==="name"||m==="annotation"){return p.toLowerCase().indexOf(n.toLowerCase())!==-1}}}})}});return{PhylovizView:i}}); \ No newline at end of file diff -r 89c27f6b20f8f261a8e45e33abcc2ed9c1509a71 -r f3b183e756f9b209ef0904718ed547e04c74ab7a static/scripts/packed/viz/scatterplot.js --- a/static/scripts/packed/viz/scatterplot.js +++ b/static/scripts/packed/viz/scatterplot.js @@ -1,1 +1,1 @@ -define(["../libs/underscore","../libs/d3","../mvc/base-mvc"],function(){function b(f){var i=this,d=10,h=7,g=10,e=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var j=Array.prototype.slice.call(arguments);j.unshift(this.toString());console.debug.apply(null,j)}};this.log("new TwoVarScatterplot:",f);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,bubbleRadius:4,entryAnimDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,f);this.updateConfig=function(j){_.extend(this.config,j)};this.toString=function(){return this.config.id};this.translateStr=function(j,k){return"translate("+j+","+k+")"};this.rotateStr=function(k,j,l){return"rotate("+k+","+j+","+l+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart").style("display","none");this.content=this.svg.append("svg:g").attr("class","content");this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.log("built svg:",d3.selectAll("svg"));this.adjustChartDimensions=function(m,k,j,l){m=m||0;k=k||0;j=j||0;l=l||0;this.svg.attr("width",this.config.width+(this.config.marginRight+k)+(this.config.marginLeft+l)).attr("height",this.config.height+(this.config.marginTop+m)+(this.config.marginBottom+j)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft+l,this.config.marginTop+m))};this.preprocessData=function(j){return(j.length>this.config.maxDataPoints)?(j.slice(0,this.config.maxDataPoints)):(j)};this.setUpDomains=function(j,l,k){this.log("setUpDomains");this.xMin=this.config.xMin||(k)?(k[0].min):(d3.min(j));this.xMax=this.config.xMax||(k)?(k[0].max):(d3.max(j));this.yMin=this.config.yMin||(k)?(k[1].min):(d3.min(l));this.yMax=this.config.yMax||(k)?(k[1].max):(d3.max(l))};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(j){return(String(j)).length}));if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);this.log("yAxis:",this.yAxis);var j=this.yAxis.selectAll("text").filter(function(n,m){return m!==0});this.yLongestLabel=d3.max(j[0].map(function(n,m){return(d3.select(n).text()).length}))||0;var k=d+(this.yLongestLabel*h)+e+g;this.config.yAxisLabelBumpX=-(k-g);if(this.config.marginLeft<k){var l=(k)-this.config.marginLeft;l=(l<0)?(0):(l);this.log("adjusting:",l);this.adjustChartDimensions(0,0,0,l)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove()};this.glyphEnterState=function(j){};this.glyphFinalState=function(j){};this.glyphExitState=function(j){};this.renderDatapoints=function(j,m){var l=function(o,n){return i.xScale(j[n])};var k=function(o,n){return i.yScale(m[n])};this.datapoints=this.content.selectAll(".glyph").data(j);this.datapoints.enter().append("svg:circle").attr("class","glyph").attr("cx",l).attr("cy",0).attr("r",0);this.datapoints.transition().duration(this.config.entryAnimDuration).attr("cx",l).attr("cy",k).attr("r",this.config.bubbleRadius);this.datapoints.exit().transition().duration(this.config.entryAnimDuration).attr("cy",this.config.height).attr("r",0).style("fill-opacity",0).remove()};this.render=function(k,l){var j=k[0],m=k[1];this.log("renderScatterplot",j.length,m.length,this.config);j=this.preprocessData(j);m=this.preprocessData(m);this.setUpDomains(j,m,l);this.log("xMin, xMax, yMin, yMax:",this.xMin,this.xMax,this.yMin,this.yMax);this.setUpScales();this.adjustChartDimensions();this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(j,m)}}var a=BaseView.extend(LoggableMixin).extend({tagName:"form",className:"scatterplot-settings-form",loadingIndicatorImagePath:(galaxy_paths.get("image_path")+"/loading_large_white_bg.gif"),events:{"click #render-button":"renderScatterplot"},initialize:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}this.apiDatasetsURL=c.apiDatasetsURL;this.chartConfig=c.chartConfig||{};this.log("this.chartConfig:",this.chartConfig);this.plot=new b(this.chartConfig)},render:function(){var c=this,e="",d="";this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ");_.each(this.dataset.metadata_column_types,function(h,g){if(h==="int"||h==="float"){var f="column "+g;if(c.dataset.metadata_column_names){f=c.dataset.metadata_column_names[g]}d+='<option value="'+g+'">'+f+"</option>"}});e+='<div id="loading-indicator" style="display: none;">';e+='<img class="loading-img" src='+this.loadingIndicatorImagePath+" />";e+='<span class="loading-message"></span>';e+="</div>";e+='<div id="x-column-input">';e+='<label for="">Data column for X: </label><select name="x-column">'+d+"</select>";e+="</div>";e+='<div id="y-column-input">';e+='<label for="">Data column for Y: </label><select name="y-column">'+d+"</select>";e+="</div>";e+='<input id="render-button" type="button" value="Draw" />';e+='<div class="clear"></div>';this.$el.append(e);this.$el.find("#render-button");return this},showLoadingIndicator:function(c){c=c||"";this.$el.find("div#loading-indicator").children(".loading-message").text(c);this.$el.find("div#loading-indicator").show("fast")},hideLoadingIndicator:function(){this.$el.find("div#loading-indicator").hide("fast")},renderScatterplot:function(){var d=this,e=this.apiDatasetsURL+"/"+this.dataset.id+"?data_type=raw_data&",i=this.$el.find('[name="x-column"]'),j=i.val(),g=i.children('[value="'+j+'"]').text(),h=this.$el.find('[name="y-column"]'),f=h.val(),c=h.children('[value="'+f+'"]').text();this.log(g,c);this.chartConfig.xLabel=g;this.chartConfig.yLabel=c;d.plot.updateConfig(this.chartConfig);e+=jQuery.param({columns:"["+[j,f]+"]"});this.log("url:",e);this.showLoadingIndicator("Fetching data...");jQuery.ajax({url:e,dataType:"json",success:function(k){d.showLoadingIndicator("Rendering...");d.endpoint=k.endpoint;d.plot.render(k.data,k.meta);d.hideLoadingIndicator()},error:function(m,k,l){d.hideLoadingIndicator();alert("ERROR:"+k+"\n"+l)}})}});return{ScatterplotView:a}}); \ No newline at end of file +define(["../libs/underscore","../libs/d3","../mvc/base-mvc","../templates/compiled/template-visualization-scatterplotControlForm"],function(){function a(f){var i=this,d=10,h=7,g=10,e=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var j=Array.prototype.slice.call(arguments);j.unshift(this.toString());console.debug.apply(null,j)}};this.log("new TwoVarScatterplot:",f);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,bubbleRadius:4,entryAnimDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,f);this.updateConfig=function(j){_.extend(this.config,j)};this.toString=function(){return this.config.id};this.translateStr=function(j,k){return"translate("+j+","+k+")"};this.rotateStr=function(k,j,l){return"rotate("+k+","+j+","+l+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart").style("display","none");this.content=this.svg.append("svg:g").attr("class","content");this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.log("built svg:",d3.selectAll("svg"));this.adjustChartDimensions=function(m,k,j,l){m=m||0;k=k||0;j=j||0;l=l||0;this.svg.attr("width",this.config.width+(this.config.marginRight+k)+(this.config.marginLeft+l)).attr("height",this.config.height+(this.config.marginTop+m)+(this.config.marginBottom+j)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft+l,this.config.marginTop+m))};this.preprocessData=function(j){return(j.length>this.config.maxDataPoints)?(j.slice(0,this.config.maxDataPoints)):(j)};this.setUpDomains=function(j,l,k){this.log("setUpDomains");this.xMin=this.config.xMin||(k)?(k[0].min):(d3.min(j));this.xMax=this.config.xMax||(k)?(k[0].max):(d3.max(j));this.yMin=this.config.yMin||(k)?(k[1].min):(d3.min(l));this.yMax=this.config.yMax||(k)?(k[1].max):(d3.max(l))};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(j){return(String(j)).length}));if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);this.log("yAxis:",this.yAxis);var j=this.yAxis.selectAll("text").filter(function(n,m){return m!==0});this.yLongestLabel=d3.max(j[0].map(function(n,m){return(d3.select(n).text()).length}))||0;var k=d+(this.yLongestLabel*h)+e+g;this.config.yAxisLabelBumpX=-(k-g);if(this.config.marginLeft<k){var l=(k)-this.config.marginLeft;l=(l<0)?(0):(l);this.log("adjusting:",l);this.adjustChartDimensions(0,0,0,l)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove()};this.glyphEnterState=function(j){};this.glyphFinalState=function(j){};this.glyphExitState=function(j){};this.renderDatapoints=function(j,m){var l=function(o,n){return i.xScale(j[n])};var k=function(o,n){return i.yScale(m[n])};this.datapoints=this.content.selectAll(".glyph").data(j);this.datapoints.enter().append("svg:circle").attr("class","glyph").attr("cx",l).attr("cy",0).attr("r",0);this.datapoints.transition().duration(this.config.entryAnimDuration).attr("cx",l).attr("cy",k).attr("r",this.config.bubbleRadius);this.datapoints.exit().transition().duration(this.config.entryAnimDuration).attr("cy",this.config.height).attr("r",0).style("fill-opacity",0).remove()};this.render=function(k,l){var j=k[0],m=k[1];this.log("renderScatterplot",j.length,m.length,this.config);j=this.preprocessData(j);m=this.preprocessData(m);this.setUpDomains(j,m,l);this.log("xMin, xMax, yMin, yMax:",this.xMin,this.xMax,this.yMin,this.yMax);this.setUpScales();this.adjustChartDimensions();this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(j,m)}}var b=BaseView.extend(LoggableMixin).extend({tagName:"form",className:"scatterplot-settings-form",loadingIndicatorImagePath:(galaxy_paths.get("image_path")+"/loading_large_white_bg.gif"),events:{"click #render-button":"renderScatterplot"},initialize:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}this.apiDatasetsURL=c.apiDatasetsURL;this.chartConfig=c.chartConfig||{};this.log("this.chartConfig:",this.chartConfig);this.plot=new a(this.chartConfig)},render:function(){var c=this,d="";var e={loadingIndicatorImagePath:this.loadingIndicatorImagePath,config:this.chartConfig,availableColumns:[]};_.each(this.dataset.metadata_column_types.split(", "),function(h,g){if(h==="int"||h==="float"){var f="column "+g;if(c.dataset.metadata_column_names){f=c.dataset.metadata_column_names[g]}e.availableColumns.push({index:g,name:f})}});d=b.templates.form(e);this.$el.append(d);return this},showLoadingIndicator:function(c){c=c||"";this.$el.find("div#loading-indicator").children(".loading-message").text(c);this.$el.find("div#loading-indicator").show("fast")},hideLoadingIndicator:function(){this.$el.find("div#loading-indicator").hide("fast")},renderScatterplot:function(){var d=this,e=this.apiDatasetsURL+"/"+this.dataset.id+"?data_type=raw_data&",i=this.$el.find('[name="x-column"]'),j=i.val(),g=i.children('[value="'+j+'"]').text(),h=this.$el.find('[name="y-column"]'),f=h.val(),c=h.children('[value="'+f+'"]').text();this.log(g,c);this.chartConfig.xLabel=g;this.chartConfig.yLabel=c;d.plot.updateConfig(this.chartConfig);e+=jQuery.param({columns:"["+[j,f]+"]"});this.log("url:",e);this.showLoadingIndicator("Fetching data...");jQuery.ajax({url:e,dataType:"json",success:function(k){d.endpoint=k.endpoint;d.showLoadingIndicator("Rendering...");d.plot.render(k.data,k.meta);d.hideLoadingIndicator()},error:function(m,k,l){d.hideLoadingIndicator();alert("ERROR:"+k+"\n"+l)}})}});b.templates=CompiledTemplateLoader.getTemplates({"visualization-templates.html":{form:"template-visualization-scatterplotControlForm"}});return{TwoVarScatterplot:a,ScatterplotControlForm:b}}); \ 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: jgoecks: (a) JSLint cleanup for phyloviz.js and (b) make phyloviz, scatterplot available.
by Bitbucket 04 Oct '12

04 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/89c27f6b20f8/ changeset: 89c27f6b20f8 user: jgoecks date: 2012-10-04 17:07:29 summary: (a) JSLint cleanup for phyloviz.js and (b) make phyloviz, scatterplot available. affected #: 2 files diff -r d7eba083859770e676f173b75f2053f575305113 -r 89c27f6b20f8f261a8e45e33abcc2ed9c1509a71 static/scripts/viz/phyloviz.js --- a/static/scripts/viz/phyloviz.js +++ b/static/scripts/viz/phyloviz.js @@ -233,12 +233,16 @@ // removing unnecessary attributes if (node._selected){ delete node._selected;} - node.children ? node.children.forEach(cleanTree) : 0; - node._children ? node._children.forEach(cleanTree) : 0; + if (node.children) { + node.children.forEach(cleanTree); + } + if (node._children) { + node._children.forEach(cleanTree); + } } var config = jQuery.extend(true, {}, this.attributes); - config["selectedNode"] = null; + config.selectedNode = null; show_message("Saving to Galaxy", "progress"); @@ -598,9 +602,11 @@ * Function to zoom and pan the svg element which the entire tree is contained within * Uses d3.zoom events, and extend them to allow manual updates and keeping states in model */ + var zoomParams, + translateParams; if (typeof event !== "undefined") { - var zoomParams = event.zoom, - translateParams = event.translate; + zoomParams = event.zoom; + translateParams = event.translate; } var self = this, @@ -761,9 +767,9 @@ * Applying user values to phylotree model. */ var self = this; - if (!self.isAcceptableValue(self.inputs["separation"], 50, 2500) || - !self.isAcceptableValue(self.inputs["leafHeight"], 5, 30) || - !self.isAcceptableValue(self.inputs["fontSize"], 5, 20)){ + if (!self.isAcceptableValue(self.inputs.separation, 50, 2500) || + !self.isAcceptableValue(self.inputs.leafHeight, 5, 30) || + !self.isAcceptableValue(self.inputs.fontSize, 5, 20)){ return; } $.each(self.inputs, function(key, $input){ @@ -854,7 +860,7 @@ var self = this, checked = self.UI.enableEdit.is(':checked'); - !checked ? self.cancelChanges() : ""; + if (!checked) { self.cancelChanges(); } $.each(self.valuesOfConcern, function(key, value) { self.UI[key].enable(checked); diff -r d7eba083859770e676f173b75f2053f575305113 -r 89c27f6b20f8f261a8e45e33abcc2ed9c1509a71 templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -227,10 +227,10 @@ ## information--URL base, dataset id, dbkey, visualizations--in anchor. <% visualizations = data.get_visualizations() - ## HACK: if there are visualizations, only provide trackster for now + ## HACK: if there are visualizations, only provide a subset for now ## since others are not ready. - comment out to see all WIP visualizations - #if visualizations: - # visualizations = [ vis for vis in visualizations if vis in [ 'trackster' ] ] + if visualizations: + visualizations = [ vis for vis in visualizations if vis in [ 'trackster', 'phyloviz', 'scatterplot' ] ] %> %if visualizations: <a href="${h.url_for( controller='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: jgoecks: Make Phyloviz into an AMD module and use requireJS for Phyloviz.
by Bitbucket 04 Oct '12

04 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d7eba0838597/ changeset: d7eba0838597 user: jgoecks date: 2012-10-04 16:51:10 summary: Make Phyloviz into an AMD module and use requireJS for Phyloviz. affected #: 2 files diff -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 -r d7eba083859770e676f173b75f2053f575305113 static/scripts/viz/phyloviz.js --- a/static/scripts/viz/phyloviz.js +++ b/static/scripts/viz/phyloviz.js @@ -1,3 +1,5 @@ +define(['libs/d3', 'viz/visualization'], function(d3, visualization_mod) { + var UserMenuBase = Backbone.View.extend({ /** * Base class of any menus that takes in user interaction. Contains checking methods. @@ -165,7 +167,7 @@ /** * -- PhyloTree Model -- */ -var PhyloTree = Visualization.extend({ +var PhyloTree = visualization_mod.Visualization.extend({ defaults : { layout: "Linear", separation : 250, // px dist between nodes of different depth to represent 1 evolutionary until @@ -588,7 +590,7 @@ $("#title").text("Phylogenetic Tree from " + self.phyloTree.get("title") + ":"); // -- Create Linear view instance -- - var linearView = new PhylovizLinearView(self.layoutOptions) + var linearView = new PhylovizLinearView(self.layoutOptions); }, zoomAndPan : function(event){ @@ -952,4 +954,10 @@ } }); } +}); + +return { + PhylovizView: PhylovizView +}; + }); \ No newline at end of file diff -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 -r d7eba083859770e676f173b75f2053f575305113 templates/visualization/phyloviz.mako --- a/templates/visualization/phyloviz.mako +++ b/templates/visualization/phyloviz.mako @@ -138,7 +138,43 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "galaxy.panels", "libs/d3", "mvc/data", "viz/visualization", "viz/phyloviz")} + ${h.js( "libs/require" )} + + <script type="text/javascript"> + + require.config({ + baseUrl: "${h.url_for('/static/scripts')}", + shim: { + "libs/underscore": { exports: "_" }, + "libs/d3": { exports: "d3" } + } + }); + + require(["viz/phyloviz"], function(phyloviz_mod) { + + function initPhyloViz(data, config) { + var phyloviz; + + // -- Initialization code |--> + phyloviz = new phyloviz_mod.PhylovizView({ + data: data, + layout : "Linear", + config : config + }); + + // -- Render viz. -- + phyloviz.render(); + + } + + $(function firstVizLoad(){ // calls when viz is loaded for the first time + var config = JSON.parse( '${ h.to_json_string( config )}'); + var data = JSON.parse('${h.to_json_string(data)}'); + initPhyloViz(data, config); + }); + }); + + </script></%def> @@ -290,31 +326,6 @@ <div id="PhyloViz" ></div> - <script type="text/javascript"> - - function initPhyloViz(data, config) { - var phyloviz; - - // -- Initialization code |--> - phyloviz = new PhylovizView({ - data: data, - layout : "Linear", - config : config - }); - - // -- Render viz. -- - phyloviz.render(); - - } - - $(function firstVizLoad(){ // calls when viz is loaded for the first time - var config = JSON.parse( '${ h.to_json_string( config )}'); - var data = JSON.parse('${h.to_json_string(data)}'); - initPhyloViz(data, config); - }); - - </script> - </%def> 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.

1 0