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

commit/galaxy-central: jgoecks: Enhancements for finding available visualizations: (a) use dataset rather than datatype and (b) only show scatterplot for tabular datasets with >=2 numerical columns.
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/aa0469dd0078/ changeset: aa0469dd0078 user: jgoecks date: 2012-09-18 19:10:04 summary: Enhancements for finding available visualizations: (a) use dataset rather than datatype and (b) only show scatterplot for tabular datasets with >=2 numerical columns. affected #: 4 files diff -r 5cdb0038c89d1396755b2c7e371bde63b221b8df -r aa0469dd0078fd792ff34db8cd8ee36ae0e9c9be lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -545,7 +545,7 @@ raise Exception('Result %s from %s' % (result, cmd)) merge = staticmethod(merge) - def get_visualizations( self ): + def get_visualizations( self, dataset ): """ Returns a list of visualizations for datatype. """ diff -r 5cdb0038c89d1396755b2c7e371bde63b221b8df -r aa0469dd0078fd792ff34db8cd8ee36ae0e9c9be lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -301,11 +301,25 @@ def as_ucsc_display_file( self, dataset, **kwd ): return open( dataset.file_name ) - def get_visualizations( self ): + def get_visualizations( self, dataset ): """ Returns a list of visualizations for datatype. """ - return super( Tabular, self ).get_visualizations() + [ 'scatterplot' ] + + # 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 + + print dataset.name, num_numerical_cols + + vizs = super( Tabular, self ).get_visualizations( dataset ) + if num_numerical_cols >= 2: + vizs.append( 'scatterplot' ) + + return vizs class Taxonomy( Tabular ): def __init__(self, **kwd): diff -r 5cdb0038c89d1396755b2c7e371bde63b221b8df -r aa0469dd0078fd792ff34db8cd8ee36ae0e9c9be lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1245,6 +1245,9 @@ def get_display_applications( self, trans ): return self.datatype.get_display_applications_by_dataset( self, trans ) + def get_visualizations( self ): + return self.datatype.get_visualizations( self ) + class HistoryDatasetAssociation( DatasetInstance ): def __init__( self, hid = None, diff -r 5cdb0038c89d1396755b2c7e371bde63b221b8df -r aa0469dd0078fd792ff34db8cd8ee36ae0e9c9be templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -229,7 +229,7 @@ ## Visualization icon + visualizations. Using anchor attributes is a HACK to encode needed ## information--URL base, dataset id, dbkey, visualizations--in anchor. <% - visualizations = data.datatype.get_visualizations() + visualizations = data.get_visualizations() ## HACK: if there are visualizations, only provide trackster for now since others ## are not ready. if visualizations: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: fix to apply tooltips to running/queued datasets in history panel
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5cdb0038c89d/ changeset: 5cdb0038c89d user: carlfeberhard date: 2012-09-18 18:39:13 summary: fix to apply tooltips to running/queued datasets in history panel affected #: 1 file diff -r 069768b7833ebae78f1c7c7aa97904627540ac3a -r 5cdb0038c89d1396755b2c7e371bde63b221b8df templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -116,6 +116,43 @@ }); }; +// ----------------------------------------------------------------------------- +function applyTooltip( elem ){ + // apply twitter bootstrap tooltip to elem + + //!! 2 line tooltips placed above do not render properly + //TODO: hack (github has an issue on this - see how it's resolved) + var $this = $( elem ); + if( $this.hasClass( 'tooltip' ) ){ + + // remove original tooltip + if( $this.attr( 'data-original-title' ) ){ + // documented method - that doesn't seem to work + //$( this ).tooltip( 'destroy' ); + $this.data( 'tooltip', false ); + + // swap title back + var title = $this.attr( 'data-original-title' ); + $this.attr( 'data-original-title', null ); + $this.attr( 'title', title ); + } + + // (re-)apply tooltip + // place them on the bottom for now + $this.tooltip({ placement : 'bottom' }); + } + return this; +} + +function applyTooltips( elem ){ + // apply twitter bootstrap tooltips to this element and all children + $( $( elem ).find( '.tooltip' ).andSelf() ).each( function(){ + applyTooltip( this ); + }); + return this; +} + +// ----------------------------------------------------------------------------- // Create trackster action function. function create_trackster_action_fn(vis_url, dataset_params, dbkey) { return function() { @@ -327,24 +364,7 @@ tag_handling(this); annotation_handling(this); - - //TODO: hack (github has an issue on this - see how it's resolved) - // fix for two line bootstrap tooltips when placement: above - $( this ).find( '.tooltip' ).each( function(){ - var $this = $( this ); - - // documented method - that doesn't seem to work - //$( this ).tooltip( 'destroy' ); - - $this.data( 'tooltip', false ); - var title = $this.attr( 'data-original-title' ); - $this.attr( 'data-original-title', null ); - $this.attr( 'title', title ); - - // place them on the bottom for now - $this.tooltip({ placement : 'bottom' }); - }); - + applyTooltips( this ); }); _.each( $(".visualize-icon"), function(icon) { @@ -469,8 +489,12 @@ var container = $("#historyItemContainer-" + id); container.html( val.html ); init_history_items( $("div.historyItemWrapper"), "noinit" ); + + // apply ui element behaviors tag_handling(container); annotation_handling(container); + applyTooltips( container ); + var viz_icon = container.find(".visualize-icon")[0]; if (viz_icon) { init_viz_icon(viz_icon); } @@ -674,4 +698,4 @@ </div></body> -</html> +</html> \ 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: natefoo: Add $__user_name__ to job template.
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/069768b7833e/ changeset: 069768b7833e user: natefoo date: 2012-09-18 18:13:02 summary: Add $__user_name__ to job template. affected #: 1 file diff -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a -r 069768b7833ebae78f1c7c7aa97904627540ac3a lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -155,15 +155,18 @@ if special: out_data[ "output_file" ] = FakeDatasetAssociation( dataset=special.dataset ) - # These can be passed on the command line if wanted as $userId $userEmail - if job.history and job.history.user: # check for anonymous user! - userId = '%d' % job.history.user.id - userEmail = str(job.history.user.email) + # These can be passed on the command line if wanted as $__user_*__ + if job.history and job.history.user: + user_id = '%d' % job.history.user.id + user_email = str(job.history.user.email) + user_name = str(job.history.user.username) else: - userId = 'Anonymous' - userEmail = 'Anonymous' - incoming['__user_id__'] = incoming['userId'] = userId - incoming['__user_email__'] = incoming['userEmail'] = userEmail + user_id = 'Anonymous' + user_email = 'Anonymous' + user_name = 'Anonymous' + incoming['__user_id__'] = incoming['userId'] = user_id + incoming['__user_email__'] = incoming['userEmail'] = user_email + incoming['__user_name__'] = user_name # Build params, done before hook so hook can use param_dict = self.tool.build_param_dict( incoming, inp_data, out_data, self.get_output_fnames(), self.working_directory ) # Certain tools require tasks to be completed prior to job execution 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: Viz framework: (a) add generic method to datatypes to get available visualizations and (b) attach available visualizations to dataset visualization icon.
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/32091cc60876/ changeset: 32091cc60876 user: jgoecks date: 2012-09-18 17:40:57 summary: Viz framework: (a) add generic method to datatypes to get available visualizations and (b) attach available visualizations to dataset visualization icon. affected #: 5 files diff -r 5359d1066d91849fbf075f95f4999613d17a9c45 -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -545,6 +545,15 @@ raise Exception('Result %s from %s' % (result, cmd)) merge = staticmethod(merge) + def get_visualizations( self ): + """ + Returns a list of visualizations for datatype. + """ + + if hasattr( self, 'get_track_type' ): + return [ 'trackster', 'circster' ] + return [] + class Text( Data ): file_ext = 'txt' line_class = 'line' diff -r 5359d1066d91849fbf075f95f4999613d17a9c45 -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -301,6 +301,12 @@ def as_ucsc_display_file( self, dataset, **kwd ): return open( dataset.file_name ) + def get_visualizations( self ): + """ + Returns a list of visualizations for datatype. + """ + return super( Tabular, self ).get_visualizations() + [ 'scatterplot' ] + class Taxonomy( Tabular ): def __init__(self, **kwd): """Initialize taxonomy datatype""" diff -r 5359d1066d91849fbf075f95f4999613d17a9c45 -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -708,9 +708,12 @@ # Get new dataset if specified. new_dataset = kwargs.get("dataset_id", None) + ''' + FIXME: if new_dataset is not None: if trans.security.decode_id(new_dataset) in [ d["dataset_id"] for d in viz_config.get("tracks") ]: new_dataset = None # Already in browser, so don't add + ''' return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=new_dataset ) @web.json diff -r 5359d1066d91849fbf075f95f4999613d17a9c45 -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -116,6 +116,95 @@ }); }; +// Create trackster action function. +function create_trackster_action_fn(vis_url, dataset_params, dbkey) { + return function() { + var params = {}; + if (dbkey) { params['dbkey'] = dbkey; } + $.ajax({ + url: vis_url + '/list_tracks?f-' + $.param(params), + dataType: "html", + error: function() { alert( "Could not add this dataset to browser." ); }, + success: function(table_html) { + var parent = window.parent; + + parent.show_modal("View Data in a New or Saved Visualization", "", { + "Cancel": function() { + parent.hide_modal(); + }, + "View in saved visualization": function() { + // Show new modal with saved visualizations. + parent.show_modal("Add Data to Saved Visualization", table_html, { + "Cancel": function() { + parent.hide_modal(); + }, + "Add to visualization": function() { + $(parent.document).find('input[name=id]:checked').each(function() { + var vis_id = $(this).val(); + dataset_params['id'] = vis_id + parent.location = vis_url + "/trackster?" + $.param(dataset_params); + }); + }, + }); + }, + "View in new visualization": function() { + parent.location = vis_url + "/trackster?" + $.param(dataset_params); + } + }); + } + }); + return false; + }; +}; + +/** + * Create popup menu for visualization icon. + */ +function init_viz_icon(icon) { + var icon = $(icon), + vis_url = icon.attr('href'), + dataset_id = icon.attr('dataset_id'), + visualizations = icon.attr('visualizations').split(','), + dbkey = icon.attr('dbkey'), + popup_menu_dict = {}, + + // Create visualization action. + create_viz_action = function(visualization) { + var action; + if (visualization === 'trackster') { + action = create_trackster_action_fn(vis_url, params, dbkey); + } + else { + action = function() { + window.parent.location = vis_url + '/' + visualization + '?' + + $.param(params); + }; + } + return action; + }, + params = {dataset_id: dataset_id}; + + // Add dbkey to params if it exists. + if (dbkey) { params['dbkey'] = dbkey; } + + // Populate menu dict with visualizations. + _.each(visualizations, function(visualization) { + popup_menu_dict[ + visualization.charAt(0).toUpperCase() + visualization.slice(1) + ] = create_viz_action(visualization); + }); + + // Set up action or menu. + if (visualizations.length === 1) { + // No need for popup menu because there's a single visualization. + icon.click(create_viz_action(visualizations[0])); + } + else { + make_popupmenu(icon, popup_menu_dict); + } +}; + + // Update the message for async operations function render_message(message, status) { $("div#message-container").html( "<div class=\"" + status + "message\">" + message + "</div><br/>" ); @@ -258,96 +347,6 @@ }); - // Trackster links - function init_trackster_links() { - // Add to trackster browser functionality - $(".trackster-add").live("click", function() { - var dataset = this, - dataset_jquery = $(this); - $.ajax({ - url: dataset_jquery.attr("data-url"), - dataType: "html", - error: function() { alert( "Could not add this dataset to browser." ); }, - success: function(table_html) { - var parent = window.parent; - - parent.show_modal("View Data in a New or Saved Visualization", "", { - "Cancel": function() { - parent.hide_modal(); - }, - "View in saved visualization": function() { - // Show new modal with saved visualizations. - parent.show_modal("Add Data to Saved Visualization", table_html, { - "Cancel": function() { - parent.hide_modal(); - }, - "Add to visualization": function() { - $(parent.document).find('input[name=id]:checked').each(function() { - var vis_id = $(this).val(); - parent.location = dataset_jquery.attr("action-url") + "&id=" + vis_id; - }); - }, - }); - }, - "View in new visualization": function() { - parent.location = dataset_jquery.attr("new-url"); - } - }); - } - }); - }); - } - - /** - * Create popup menu for visualization icon. - */ - function init_viz_icon(icon) { - var icon_link = $(icon); - make_popupmenu( icon_link , { - "${_("Trackster")}": function() { - $.ajax({ - url: icon_link.attr("data-url"), - dataType: "html", - error: function() { alert( "Could not add this dataset to browser." ); }, - success: function(table_html) { - var parent = window.parent; - - parent.show_modal("View Data in a New or Saved Visualization", "", { - "Cancel": function() { - parent.hide_modal(); - }, - "View in saved visualization": function() { - // Show new modal with saved visualizations. - parent.hide_modal(); - parent.show_modal("Add Data to Saved Visualization", table_html, { - "Cancel": function() { - parent.hide_modal(); - }, - "Add to visualization": function() { - $(parent.document).find('input[name=id]:checked').each(function() { - var vis_id = $(this).val(); - parent.location = icon_link.attr("action-url") + "&id=" + vis_id; - }); - }, - }); - }, - "View in new visualization": function() { - parent.location = icon_link.attr("new-url"); - } - }); - } - }); - }, - //"${_("Scatterplot")}": function() { - // var data_id = icon_link.parents(".historyItemContainer").attr("id").split("-")[1]; - // parent.galaxy_main.location = - // "${h.url_for( controller='visualization', action='scatterplot', col1=9, col2=13 )}" - // + "&dataset_id=" + data_id; - //} - } ); - return icon; - }; - _.each( $(".visualize-icon"), function(icon) { init_viz_icon(icon); }); @@ -472,6 +471,9 @@ init_history_items( $("div.historyItemWrapper"), "noinit" ); tag_handling(container); annotation_handling(container); + var viz_icon = container.find(".visualize-icon")[0]; + if (viz_icon) { init_viz_icon(viz_icon); } + // If new state is terminal, stop tracking if (TERMINAL_STATES.indexOf(val.state) !== -1) { if ( val.force_history_refresh ){ diff -r 5359d1066d91849fbf075f95f4999613d17a9c45 -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -226,17 +226,24 @@ %if for_editing: <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a> - %if data.ext in app.datatypes_registry.get_available_tracks(): - <% - if data.dbkey != '?': - data_url = h.url_for( controller='visualization', action='list_tracks', dbkey=data.dbkey ) - data_url = data_url.replace( 'dbkey', 'f-dbkey' ) - else: - data_url = h.url_for( controller='visualization', action='list_tracks' ) - %> - <a href="javascript:void(0)" data-url="${data_url}" class="icon-button chart_curve tooltip visualize-icon" - action-url="${h.url_for( controller='tracks', action='browser', dataset_id=dataset_id)}" - new-url="${h.url_for( controller='tracks', action='index', dataset_id=dataset_id, default_dbkey=data.dbkey)}" title="Visualize"></a> + ## Visualization icon + visualizations. Using anchor attributes is a HACK to encode needed + ## information--URL base, dataset id, dbkey, visualizations--in anchor. + <% + visualizations = data.datatype.get_visualizations() + ## HACK: if there are visualizations, only provide trackster for now since others + ## are not ready. + if visualizations: + visualizations = [ 'trackster' ] + %> + %if visualizations: + <a href="${h.url_for( controller='visualization' )}" + class="icon-button chart_curve tooltip visualize-icon" + title="Visualize" + dataset_id="${dataset_id}" + %if data.dbkey != '?': + dbkey="${data.dbkey}" + %endif + visualizations="${','.join(visualizations)}"></a> %endif <% isPhylogenyData = isinstance(data.datatype, (Phyloxml, Nexus, Newick)) 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: Grammar. it's -> its in admin panel (and tests)
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5359d1066d91/ changeset: 5359d1066d91 user: dannon date: 2012-09-18 15:34:51 summary: Grammar. it's -> its in admin panel (and tests) affected #: 2 files diff -r ba64c2178fbee9a83f79580c434ab280d8a0b738 -r 5359d1066d91849fbf075f95f4999613d17a9c45 templates/webapps/galaxy/admin/center.mako --- a/templates/webapps/galaxy/admin/center.mako +++ b/templates/webapps/galaxy/admin/center.mako @@ -51,7 +51,7 @@ then users that have Role2 will be able to access the library, but will not see those contained datasets whose [dataset] "access" permission is associated with only Role1. <p/> - In addition to the "access library" permission, permission to perform the following functions on the data library (and it's contents) can + In addition to the "access library" permission, permission to perform the following functions on the data library (and its contents) can be granted to users (a library item is one of: a data library, a library folder, a library dataset). <p/><ul> diff -r ba64c2178fbee9a83f79580c434ab280d8a0b738 -r 5359d1066d91849fbf075f95f4999613d17a9c45 test/functional/test_library_security.py --- a/test/functional/test_library_security.py +++ b/test/functional/test_library_security.py @@ -93,7 +93,7 @@ permissions_in = [ k for k, v in galaxy.model.Library.permitted_actions.items() ] permissions_out = [] # Role1 members are: admin_user, regular_user1, regular_user3. Each of these users will be permitted for - # LIBRARY_ACCESS, LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE on library1 and it's contents. + # LIBRARY_ACCESS, LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE on library1 and its contents. self.library_permissions( self.security.encode_id( library1.id ), library1.name, str( role1.id ), @@ -163,7 +163,7 @@ # Logged in as admin_user # # LIBRARY_ACCESS = Role1: admin_user, regular_user1, regular_user3. Each of these users will be permitted for - # LIBRARY_ACCESS, LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE on this library and it's contents. + # LIBRARY_ACCESS, LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE on this library and its contents. # # Legitimate roles displayed on the permission form are as follows: # 'Role1' since the LIBRARY_ACCESS permission is associated with Role1. # Role one members are: admin_user, regular_user1, regular_user3. @@ -239,7 +239,7 @@ # groups: group1 # users: test(a)bx.psu.edu, test1(a)bx.psu.edu via group1 # - # We first need to make library1 public, but leave it's contents permissions unchanged + # We first need to make library1 public, but leave its contents permissions unchanged self.make_library_item_public( self.security.encode_id( library1.id ), self.security.encode_id( library1.id ), item_type='library', @@ -433,7 +433,7 @@ permissions_in = [ k for k, v in galaxy.model.Library.permitted_actions.items() ] permissions_out = [] # Only admin_user will be permitted for - # LIBRARY_ACCESS, LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE on library2 and it's contents. + # LIBRARY_ACCESS, LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE on library2 and its contents. self.library_permissions( self.security.encode_id( library1.id ), library1.name, str( admin_user_private_role.id ), @@ -526,7 +526,7 @@ ldda8 = get_latest_ldda_by_name( filename ) assert ldda8 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda8 from the database' def test_090_make_library2_and_contents_public( self ): - """Testing making library2 and all of it's contents public""" + """Testing making library2 and all of its contents public""" self.make_library_item_public( self.security.encode_id( library2.id ), self.security.encode_id( library2.id ), item_type='library', 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: greg: Apply fix from Jim Johnson for rendering tool dependencies defined in a tool shed repository.
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ba64c2178fbe/ changeset: ba64c2178fbe user: greg date: 2012-09-18 15:03:39 summary: Apply fix from Jim Johnson for rendering tool dependencies defined in a tool shed repository. affected #: 1 file diff -r 19345740820fe9fe62fe46e9ae54efbabc1eb019 -r ba64c2178fbee9a83f79580c434ab280d8a0b738 templates/admin/tool_shed_repository/common.mako --- a/templates/admin/tool_shed_repository/common.mako +++ b/templates/admin/tool_shed_repository/common.mako @@ -129,28 +129,30 @@ <% package_header_row_displayed = True %> %endif %for dependency_key, requirements_dict in tool_dependencies.items(): - <% - name = requirements_dict[ 'name' ] - version = requirements_dict[ 'version' ] - type = requirements_dict[ 'type' ] - install_dir = os.path.join( trans.app.config.tool_dependency_dir, - name, - version, - repository_owner, - repository_name, - changeset_revision ) - tool_dependency_readme_text = requirements_dict.get( 'readme', None ) - %> - %if not os.path.exists( install_dir ): - <tr> - <td>${name}</td> - <td>${version}</td> - <td>${type}</td> - <td>${install_dir}</td> - </tr> - %if tool_dependency_readme_text: - <tr><td colspan="4" bgcolor="#FFFFCC">${name} ${version} requirements and installation information</td></tr> - <tr><td colspan="4"><pre>${tool_dependency_readme_text}</pre></td></tr> + %if dependency_key not in [ 'set_environment' ]: + <% + name = requirements_dict[ 'name' ] + version = requirements_dict[ 'version' ] + type = requirements_dict[ 'type' ] + install_dir = os.path.join( trans.app.config.tool_dependency_dir, + name, + version, + repository_owner, + repository_name, + changeset_revision ) + tool_dependency_readme_text = requirements_dict.get( 'readme', None ) + %> + %if not os.path.exists( install_dir ): + <tr> + <td>${name}</td> + <td>${version}</td> + <td>${type}</td> + <td>${install_dir}</td> + </tr> + %if tool_dependency_readme_text: + <tr><td colspan="4" bgcolor="#FFFFCC">${name} ${version} requirements and installation information</td></tr> + <tr><td colspan="4"><pre>${tool_dependency_readme_text}</pre></td></tr> + %endif %endif %endif %endfor Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix bugs when converting BED to FLI and JS module references.
by Bitbucket 17 Sep '12

17 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/19345740820f/ changeset: 19345740820f user: jgoecks date: 2012-09-17 23:36:40 summary: Fix bugs when converting BED to FLI and JS module references. affected #: 2 files diff -r 833f02590bbd11f8ed1bdc024b380c1bb185bfae -r 19345740820fe9fe62fe46e9ae54efbabc1eb019 lib/galaxy/datatypes/converters/interval_to_fli.py --- a/lib/galaxy/datatypes/converters/interval_to_fli.py +++ b/lib/galaxy/datatypes/converters/interval_to_fli.py @@ -53,7 +53,17 @@ else: # BED format. for line in open( in_fname, 'r' ): + # Ignore track lines. + if line.startswith("track"): + continue + fields = line.split() + + # Ignore lines with no feature name. + if len( fields ) < 4: + continue + + # Process line name_loc_dict[ fields[3] ] = { 'contig': fields[0], 'start': int( fields[1] ), diff -r 833f02590bbd11f8ed1bdc024b380c1bb185bfae -r 19345740820fe9fe62fe46e9ae54efbabc1eb019 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -86,17 +86,17 @@ JSON.parse('${ h.to_json_string( config['bookmarks'] ) }'), true ); - ui.init_editor(); + init_editor(); set_up_router({view: view}); %else: var continue_fn = function() { - view = trackster_ui.create_visualization( { + view = ui.create_visualization( { container: $("#browser-container"), name: $("#new-title").val(), dbkey: $("#new-dbkey").val() } ); view.editor = true; - ui.init_editor(); + init_editor(); set_up_router({view: view}); hide_modal(); }; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 17 Sep '12

17 Sep '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5027e0458ef0/ changeset: 5027e0458ef0 user: carlfeberhard date: 2012-09-17 23:12:42 summary: initial, un-wired prototype for scatterplot visualization affected #: 6 files diff -r 65ecf4e0ed28eaa2f3e64495ab800aa7c9779a54 -r 5027e0458ef06686cbf56770c5e02e9d5d1673c1 lib/galaxy/visualization/data_providers/basic.py --- a/lib/galaxy/visualization/data_providers/basic.py +++ b/lib/galaxy/visualization/data_providers/basic.py @@ -90,6 +90,11 @@ break fields = line.split() + #pre: column indeces should be avail in fields + for col_index in cols: + assert col_index < len( fields ), ( + "column index (%d) must be less than fields length: %d" % ( col_index, len( fields ) ) ) + data.append( [ cast_val( fields[c], self.original_dataset.metadata.column_types[c] ) for c in cols ] ) f.close() diff -r 65ecf4e0ed28eaa2f3e64495ab800aa7c9779a54 -r 5027e0458ef06686cbf56770c5e02e9d5d1673c1 lib/galaxy/web/api/datasets.py --- a/lib/galaxy/web/api/datasets.py +++ b/lib/galaxy/web/api/datasets.py @@ -215,8 +215,14 @@ # Return data. data = None data_provider = trans.app.data_provider_registry.get_data_provider( raw=True, original_dataset=dataset ) + if data_provider == ColumnDataProvider: + #pre: should have column kwargs + #print 'kwargs:', kwargs + assert 'cols' in kwargs, ( + "ColumnDataProvider needs a 'cols' parameter in the query string" ) data = data_provider( original_dataset=dataset ).get_data( **kwargs ) + else: # Default to genomic data. # FIXME: need better way to set dataset_type. diff -r 65ecf4e0ed28eaa2f3e64495ab800aa7c9779a54 -r 5027e0458ef06686cbf56770c5e02e9d5d1673c1 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -6,6 +6,7 @@ from galaxy.web.controllers.library import LibraryListGrid from galaxy.visualization.genomes import decode_dbkey from galaxy.visualization.genome.visual_analytics import get_dataset_job +from galaxy.visualization.data_providers.basic import ColumnDataProvider # # -- Grids -- @@ -801,6 +802,28 @@ def get_item( self, trans, id ): return self.get_visualization( trans, id ) + @web.expose + def scatterplot( self, trans, dataset_id, cols ): + # Get HDA. + hda = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) + + # get some metadata for the page + hda_dict = hda.get_api_value() + #title = "Scatter plot of {name}:".format( **hda_dict ) + #subtitle = "{misc_info}".format( **hda_dict ) + + #TODO: add column data + # Read data. + data_provider = ColumnDataProvider( original_dataset=hda ) + data = data_provider.get_data( cols ) + + # Return plot. + return trans.fill_template_mako( "visualization/scatterplot.mako", + title=hda.name, subtitle=hda.info, + hda=hda, + data=data ) + + @web.json def bookmarks_from_dataset( self, trans, hda_id=None, ldda_id=None ): if hda_id: diff -r 65ecf4e0ed28eaa2f3e64495ab800aa7c9779a54 -r 5027e0458ef06686cbf56770c5e02e9d5d1673c1 templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -17,7 +17,16 @@ <meta http-equiv="Pragma" content="no-cache"> ${h.css( "base", "history", "autocomplete_tagging" )} -${h.js( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} +${h.js( + "libs/jquery/jquery", + "libs/bootstrap", + "galaxy.base", + "libs/json2", + "libs/jquery/jstorage", + "libs/jquery/jquery.autocomplete", + "galaxy.autocom_tagging", + "libs/underscore" +)} <script type="text/javascript"> @@ -289,8 +298,61 @@ }); } - init_trackster_links(); + /** + * Create popup menu for visualization icon. + */ + function init_viz_icon(icon) { + var icon_link = $(icon); + make_popupmenu( icon_link , { + "${_("Trackster")}": function() { + $.ajax({ + url: icon_link.attr("data-url"), + dataType: "html", + error: function() { alert( "Could not add this dataset to browser." ); }, + success: function(table_html) { + var parent = window.parent; + parent.show_modal("View Data in a New or Saved Visualization", "", { + "Cancel": function() { + parent.hide_modal(); + }, + "View in saved visualization": function() { + // Show new modal with saved visualizations. + parent.hide_modal(); + parent.show_modal("Add Data to Saved Visualization", table_html, { + "Cancel": function() { + parent.hide_modal(); + }, + "Add to visualization": function() { + $(parent.document).find('input[name=id]:checked').each(function() { + var vis_id = $(this).val(); + parent.location = icon_link.attr("action-url") + "&id=" + vis_id; + }); + }, + }); + }, + "View in new visualization": function() { + parent.location = icon_link.attr("new-url"); + } + }); + } + }); + }, + //"${_("Scatterplot")}": function() { + // var data_id = icon_link.parents(".historyItemContainer").attr("id").split("-")[1]; + // parent.galaxy_main.location = + // "${h.url_for( controller='visualization', action='scatterplot', col1=9, col2=13 )}" + // + "&dataset_id=" + data_id; + //} + } ); + return icon; + }; + + _.each( $(".visualize-icon"), function(icon) { + console.debug( 'Init visualization icons, icon:', icon ); + init_viz_icon(icon); + }); + function init_phyloviz_links() { // PhyloViz links // Add to trackster browser functionality diff -r 65ecf4e0ed28eaa2f3e64495ab800aa7c9779a54 -r 5027e0458ef06686cbf56770c5e02e9d5d1673c1 templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -234,9 +234,12 @@ else: data_url = h.url_for( controller='visualization', action='list_tracks' ) %> - <a href="javascript:void(0)" data-url="${data_url}" class="icon-button chart_curve tooltip trackster-add" - action-url="${h.url_for( controller='visualization', action='trackster', dataset_id=dataset_id)}" - new-url="${h.url_for( controller='visualization', action='trackster', dataset_id=dataset_id, default_dbkey=data.dbkey)}" title="View in Trackster"></a> +  +  +  + <a href="javascript:void(0)" data-url="${data_url}" class="icon-button chart_curve tooltip visualize-icon" + action-url="${h.url_for( controller='tracks', action='browser', dataset_id=dataset_id)}" + new-url="${h.url_for( controller='tracks', action='index', dataset_id=dataset_id, default_dbkey=data.dbkey)}" title="Visualize"></a> %endif <% isPhylogenyData = isinstance(data.datatype, (Phyloxml, Nexus, Newick)) diff -r 65ecf4e0ed28eaa2f3e64495ab800aa7c9779a54 -r 5027e0458ef06686cbf56770c5e02e9d5d1673c1 templates/visualization/scatterplot.mako --- /dev/null +++ b/templates/visualization/scatterplot.mako @@ -0,0 +1,205 @@ +<%inherit file="/base.mako"/> + +<%def name="stylesheets()"> +${parent.stylesheets()} +${h.css( "history", "autocomplete_tagging", "trackster", "overcast/jquery-ui-1.8.5.custom", "library" )} + +<style type="text/css"> +* { margin: 0px, padding: 0px; } + +.subtitle { + margin-left: 1em; + margin-top: -1em; + color: grey; + font-size: small; +} + +.chart { + /*shape-rendering: crispEdges;*/ +} + +.grid-line { + fill: none; + stroke: lightgrey; + stroke-opacity: 0.5; + shape-rendering: crispEdges; + stroke-dasharray: 3, 3; +} + +.axis path, .axis line { + fill: none; + stroke: black; + shape-rendering: crispEdges; +} +.axis text { + font-family: sans-serif; + font-size: 12px; +} + + +circle.bubble { + stroke: none; + fill: black; + fill-opacity: 0.2; +} + +</style> + +</%def> + +<%def name="javascripts()"> +${parent.javascripts()} +${h.js( "libs/d3" )} + +<script type="text/javascript"> +/* ============================================================================= +todo: + validate columns (here or server) + send: type, column title/name in JSON + + + move to obj, possibly view? + fetch (new?) data + config changes to the graph + download svg (png?) + +============================================================================= */ +function translateStr( x, y ){ + return 'translate(' + x + ',' + y + ')'; +} +function rotateStr( d, x, y ){ + return 'rotate(' + d + ',' + x + ',' + y + ')'; +} + +$(function() { + // Constants + var data = ${data}, + MAX_DATA_POINTS = 30000, + BUBBLE_RADIUS = 5, + ENTRY_ANIM_DURATION = 500, + X_TICKS = 10, Y_TICKS = 10, + X_AXIS_LABEL_BUMP_Y = 40, + Y_AXIS_LABEL_BUMP_X = -35, + WIDTH = 300, + HEIGHT = 300, + MARGIN= 50, + xLabel = "Magnitude", + yLabel = "Depth"; + + // set a cap on the data, limit to first n points + data = data.slice( 0, MAX_DATA_POINTS ); + + // split the data into columns + //TODO: compute min, max on server. + var col1_data = data.map( function(e) { return e[0] }), + col2_data = data.map( function(e) { return e[1] }), + xMin = d3.min( col1_data ), + xMax = d3.max( col1_data ), + yMin = d3.min( col2_data ), + yMax = d3.max( col2_data ); + console.log( 'col1_data:', col1_data ); + console.log( 'col2_data:', col2_data ); + console.log( 'xMin, xMax, yMin, yMax:', xMin, xMax, yMin, yMax ); + + // Set up. + d3.select( "body" ).append( "svg:svg" ) + .attr( "width", WIDTH + ( MARGIN * 2 ) ) + .attr( "height", HEIGHT + ( MARGIN * 2 ) ) + .attr( "class", "chart" ); + + // Scale for x, y based on data domains + // origin: bottom, left + var x_scale = d3.scale.linear() + .domain([ xMin, xMax ]) + .range([ 0, WIDTH ]), + y_scale = d3.scale.linear() + .domain([ yMin, yMax ]) + .range([ HEIGHT, 0 ]); + + // Selection of SVG, append group (will group our entire chart), give attributes + // apply a group and transform all coords away from margins + var chart = d3.select( ".chart" ).append( "svg:g" ) + .attr( "class", "content" ) + .attr( "transform", translateStr( MARGIN, MARGIN ) ); + + // axes + var xAxisFn = d3.svg.axis() + .scale( x_scale ) + .ticks( X_TICKS ) + .orient( 'bottom' ); + var xAxis = chart.append( 'g' ).attr( 'class', 'axis' ).attr( 'id', 'x-axis' ) + .attr( 'transform', translateStr( 0, HEIGHT ) ) + .call( xAxisFn ) + console.debug( 'xAxis:', xAxis ); window.xAxis = xAxis, window.xAxisFn = xAxisFn; + + var xAxisLabel = xAxis.append( 'text' ).attr( 'class', 'axis-label' ).attr( 'id', 'x-axis-label' ) + .attr( 'x', WIDTH / 2 ) + .attr( 'y', X_AXIS_LABEL_BUMP_Y ) + .attr( 'text-anchor', 'middle' ) + .text( xLabel ); + console.debug( 'xAxisLabel:', xAxisLabel ); window.xAxisLabel = xAxisLabel; + + var yAxisFn = d3.svg.axis() + .scale( y_scale ) + .ticks( Y_TICKS ) + .orient( 'left' ); + var yAxis = chart.append( 'g' ).attr( 'class', 'axis' ).attr( 'id', 'y-axis' ) + .call( yAxisFn ); + console.debug( 'yAxis:', yAxis ); window.yAxis = yAxis, window.yAxisFn = yAxisFn; + + var yAxisLabel = yAxis.append( 'text' ).attr( 'class', 'axis-label' ).attr( 'id', 'y-axis-label' ) + .attr( 'x', Y_AXIS_LABEL_BUMP_X ) + .attr( 'y', HEIGHT / 2 ) + .attr( 'text-anchor', 'middle' ) + .attr( 'transform', rotateStr( -90, Y_AXIS_LABEL_BUMP_X, HEIGHT / 2 ) ) + .text( yLabel ); + console.debug( 'yAxisLabel:', yAxisLabel ); window.yAxisLabel = yAxisLabel; + + // grid lines + var hGridLines = chart.selectAll( '.h-grid-line' ) + .data( x_scale.ticks( xAxisFn.ticks()[0] ) ) + .enter().append( 'svg:line' ) + .classed( 'grid-line h-grid-line', true ) + .attr( 'x1', x_scale ).attr( 'y1', 0 ) + .attr( 'x2', x_scale ).attr( 'y2', HEIGHT ) + console.debug( 'hGridLines:', hGridLines ); window.hGridLines = hGridLines; + + var vGridLines = chart.selectAll( '.v-grid-line' ) + .data( y_scale.ticks( yAxisFn.ticks()[0] ) ) + .enter().append( 'svg:line' ) + .classed( 'grid-line v-grid-line', true ) + .attr( 'x1', 0 ) .attr( 'y1', y_scale ) + .attr( 'x2', WIDTH ).attr( 'y2', y_scale ) + console.debug( 'vGridLines:', vGridLines ); window.vGridLines = vGridLines; + + // Functions used to render plot. + var xPosFn = function( d, i ){ + return x_scale( col1_data[ i ] ); + }; + var yPosFn = function( d, i ){ + return y_scale( col2_data[ i ] ); + }; + + // Create bubbles for each data point. + chart.selectAll( "circle.bubble" ) + .data(data).enter() + .append( "svg:circle" ).attr( "class", "bubble" ) + // start all bubbles at corner... + .attr( "r", 0 ) + .attr( "fill", "white" ) + // ...animate to final position + .transition().duration( ENTRY_ANIM_DURATION ) + .attr("cx", xPosFn ) + .attr("cy", yPosFn ) + .attr("r", BUBBLE_RADIUS); + + //TODO: on hover red line to axes, display values +}); +</script> +</%def> + +<%def name="body()"> + <h1 class="title">Scatterplot of '${title}':</h1> + <h2 class="subtitle">${subtitle}</h2> + +</%def> https://bitbucket.org/galaxy/galaxy-central/changeset/833f02590bbd/ changeset: 833f02590bbd user: carlfeberhard date: 2012-09-17 23:19:53 summary: scatterplot.mako: some cleanup affected #: 4 files diff -r 5027e0458ef06686cbf56770c5e02e9d5d1673c1 -r 833f02590bbd11f8ed1bdc024b380c1bb185bfae lib/galaxy/web/api/datasets.py --- a/lib/galaxy/web/api/datasets.py +++ b/lib/galaxy/web/api/datasets.py @@ -219,6 +219,7 @@ if data_provider == ColumnDataProvider: #pre: should have column kwargs #print 'kwargs:', kwargs + #TODO??: could default to first two here assert 'cols' in kwargs, ( "ColumnDataProvider needs a 'cols' parameter in the query string" ) data = data_provider( original_dataset=dataset ).get_data( **kwargs ) diff -r 5027e0458ef06686cbf56770c5e02e9d5d1673c1 -r 833f02590bbd11f8ed1bdc024b380c1bb185bfae templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -349,7 +349,6 @@ }; _.each( $(".visualize-icon"), function(icon) { - console.debug( 'Init visualization icons, icon:', icon ); init_viz_icon(icon); }); diff -r 5027e0458ef06686cbf56770c5e02e9d5d1673c1 -r 833f02590bbd11f8ed1bdc024b380c1bb185bfae templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -234,9 +234,6 @@ else: data_url = h.url_for( controller='visualization', action='list_tracks' ) %> -  -  - <a href="javascript:void(0)" data-url="${data_url}" class="icon-button chart_curve tooltip visualize-icon" action-url="${h.url_for( controller='tracks', action='browser', dataset_id=dataset_id)}" new-url="${h.url_for( controller='tracks', action='index', dataset_id=dataset_id, default_dbkey=data.dbkey)}" title="Visualize"></a> diff -r 5027e0458ef06686cbf56770c5e02e9d5d1673c1 -r 833f02590bbd11f8ed1bdc024b380c1bb185bfae templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -56,7 +56,6 @@ todo: validate columns (here or server) send: type, column title/name in JSON - move to obj, possibly view? fetch (new?) data @@ -97,9 +96,9 @@ xMax = d3.max( col1_data ), yMin = d3.min( col2_data ), yMax = d3.max( col2_data ); - console.log( 'col1_data:', col1_data ); - console.log( 'col2_data:', col2_data ); - console.log( 'xMin, xMax, yMin, yMax:', xMin, xMax, yMin, yMax ); + //console.log( 'col1_data:', col1_data ); + //console.log( 'col2_data:', col2_data ); + //console.log( 'xMin, xMax, yMin, yMax:', xMin, xMax, yMin, yMax ); // Set up. d3.select( "body" ).append( "svg:svg" ) @@ -130,14 +129,14 @@ var xAxis = chart.append( 'g' ).attr( 'class', 'axis' ).attr( 'id', 'x-axis' ) .attr( 'transform', translateStr( 0, HEIGHT ) ) .call( xAxisFn ) - console.debug( 'xAxis:', xAxis ); window.xAxis = xAxis, window.xAxisFn = xAxisFn; + //console.debug( 'xAxis:', xAxis ); window.xAxis = xAxis, window.xAxisFn = xAxisFn; var xAxisLabel = xAxis.append( 'text' ).attr( 'class', 'axis-label' ).attr( 'id', 'x-axis-label' ) .attr( 'x', WIDTH / 2 ) .attr( 'y', X_AXIS_LABEL_BUMP_Y ) .attr( 'text-anchor', 'middle' ) .text( xLabel ); - console.debug( 'xAxisLabel:', xAxisLabel ); window.xAxisLabel = xAxisLabel; + //console.debug( 'xAxisLabel:', xAxisLabel ); window.xAxisLabel = xAxisLabel; var yAxisFn = d3.svg.axis() .scale( y_scale ) @@ -145,7 +144,7 @@ .orient( 'left' ); var yAxis = chart.append( 'g' ).attr( 'class', 'axis' ).attr( 'id', 'y-axis' ) .call( yAxisFn ); - console.debug( 'yAxis:', yAxis ); window.yAxis = yAxis, window.yAxisFn = yAxisFn; + //console.debug( 'yAxis:', yAxis ); window.yAxis = yAxis, window.yAxisFn = yAxisFn; var yAxisLabel = yAxis.append( 'text' ).attr( 'class', 'axis-label' ).attr( 'id', 'y-axis-label' ) .attr( 'x', Y_AXIS_LABEL_BUMP_X ) @@ -153,7 +152,7 @@ .attr( 'text-anchor', 'middle' ) .attr( 'transform', rotateStr( -90, Y_AXIS_LABEL_BUMP_X, HEIGHT / 2 ) ) .text( yLabel ); - console.debug( 'yAxisLabel:', yAxisLabel ); window.yAxisLabel = yAxisLabel; + //console.debug( 'yAxisLabel:', yAxisLabel ); window.yAxisLabel = yAxisLabel; // grid lines var hGridLines = chart.selectAll( '.h-grid-line' ) @@ -162,7 +161,7 @@ .classed( 'grid-line h-grid-line', true ) .attr( 'x1', x_scale ).attr( 'y1', 0 ) .attr( 'x2', x_scale ).attr( 'y2', HEIGHT ) - console.debug( 'hGridLines:', hGridLines ); window.hGridLines = hGridLines; + //console.debug( 'hGridLines:', hGridLines ); window.hGridLines = hGridLines; var vGridLines = chart.selectAll( '.v-grid-line' ) .data( y_scale.ticks( yAxisFn.ticks()[0] ) ) @@ -170,7 +169,7 @@ .classed( 'grid-line v-grid-line', true ) .attr( 'x1', 0 ) .attr( 'y1', y_scale ) .attr( 'x2', WIDTH ).attr( 'y2', y_scale ) - console.debug( 'vGridLines:', vGridLines ); window.vGridLines = vGridLines; + //console.debug( 'vGridLines:', vGridLines ); window.vGridLines = vGridLines; // Functions used to render plot. var xPosFn = function( d, i ){ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 17 Sep '12

17 Sep '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5a61f5123386/ changeset: 5a61f5123386 user: james_taylor date: 2012-09-17 22:24:13 summary: trackster: moving more stuff out of mako into javascript affected #: 2 files diff -r 6c0bb542d2e0cbda209e473db9d77a7076614f0d -r 5a61f51233861c6f7f4be41c5fd2de94d468ea61 static/scripts/viz/trackster_ui.js --- a/static/scripts/viz/trackster_ui.js +++ b/static/scripts/viz/trackster_ui.js @@ -12,6 +12,90 @@ this.baseURL = baseURL; }, + + /** + * Create button menu + */ + createButtonMenu: function() { + var menu = create_icon_buttons_menu([ + { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { + add_datasets(add_datasets_url, add_track_async_url, function(tracks) { + _.each(tracks, function(track) { + view.add_drawable( trackster_ui.object_from_template(track, view, view) ); + }); + }); + } }, + { icon_class: 'block--plus', title: 'Add group', on_click: function() { + view.add_drawable( new tracks.DrawableGroup(view, view, { name: "New Group" }) ); + } }, + { icon_class: 'bookmarks', title: 'Bookmarks', on_click: function() { + // HACK -- use style to determine if panel is hidden and hide/show accordingly. + parent.force_right_panel(($("div#right").css("right") == "0px" ? "hide" : "show")); + } }, + { + icon_class: 'globe', + title: 'Circster', + on_click: function() { + // Add viz id dynamically so that newly saved visualizations work as well. + window.location = "${h.url_for( controller='visualization', action='circster' )}?id=" + view.vis_id; + } + }, + { icon_class: 'disk--arrow', title: 'Save', on_click: function() { + // Show saving dialog box + show_modal("Saving...", "progress"); + + // Save bookmarks. + var bookmarks = []; + $(".bookmark").each(function() { + bookmarks.push({ + position: $(this).children(".position").text(), + annotation: $(this).children(".annotation").text() + }); + }); + + // FIXME: give unique IDs to Drawables and save overview as ID. + var overview_track_name = (view.overview_drawable ? view.overview_drawable.name : null), + viz_config = { + 'id': view.vis_id, + 'title': view.name, + 'dbkey': view.dbkey, + 'type': 'trackster', + 'datasets': view.to_dict(), + 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name }, + 'bookmarks': bookmarks + }; + + $.ajax({ + url: galaxy_paths.get("visualization_url"), + type: "POST", + dataType: "json", + data: { + vis_json: JSON.stringify(viz_config) + } + }).success(function(vis_info) { + hide_modal(); + view.vis_id = vis_info.vis_id; + view.has_changes = false; + + // Needed to set URL when first saving a visualization. + window.history.pushState({}, "", vis_info.url + window.location.hash); + }) + .error(function() { + show_modal( "Could Not Save", "Could not save visualization. Please try again later.", + { "Close" : hide_modal } ); + }); + } }, + { icon_class: 'cross-circle', title: 'Close', on_click: function() { + window.location = "${h.url_for( controller='visualization', action='list' )}"; + } } + ], + { + tooltip_config: { placement: 'bottom' } + }); + this.buttonMenu = menu; + return menu; + }, + /** * Use a popup to select a dataset of create bookmarks from */ diff -r 6c0bb542d2e0cbda209e473db9d77a7076614f0d -r 5a61f51233861c6f7f4be41c5fd2de94d468ea61 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -61,85 +61,12 @@ var browser_router; $(function() { - // Create and initialize menu. - var menu = create_icon_buttons_menu([ - { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { - add_datasets(add_datasets_url, add_track_async_url, function(tracks) { - _.each(tracks, function(track) { - view.add_drawable( trackster_ui.object_from_template(track, view, view) ); - }); - }); - } }, - { icon_class: 'block--plus', title: 'Add group', on_click: function() { - view.add_drawable( new tracks.DrawableGroup(view, view, { name: "New Group" }) ); - } }, - { icon_class: 'bookmarks', title: 'Bookmarks', on_click: function() { - // HACK -- use style to determine if panel is hidden and hide/show accordingly. - parent.force_right_panel(($("div#right").css("right") == "0px" ? "hide" : "show")); - } }, - { - icon_class: 'globe', - title: 'Circster', - on_click: function() { - // Add viz id dynamically so that newly saved visualizations work as well. - window.location = "${h.url_for( controller='visualization', action='circster' )}?id=" + view.vis_id; - } - }, - { icon_class: 'disk--arrow', title: 'Save', on_click: function() { - // Show saving dialog box - show_modal("Saving...", "progress"); - - // Save bookmarks. - var bookmarks = []; - $(".bookmark").each(function() { - bookmarks.push({ - position: $(this).children(".position").text(), - annotation: $(this).children(".annotation").text() - }); - }); - // FIXME: give unique IDs to Drawables and save overview as ID. - var overview_track_name = (view.overview_drawable ? view.overview_drawable.name : null), - viz_config = { - 'id': view.vis_id, - 'title': view.name, - 'dbkey': view.dbkey, - 'type': 'trackster', - 'datasets': view.to_dict(), - 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name }, - 'bookmarks': bookmarks - }; + ui.createButtonMenu(); - $.ajax({ - url: galaxy_paths.get("visualization_url"), - type: "POST", - dataType: "json", - data: { - vis_json: JSON.stringify(viz_config) - } - }).success(function(vis_info) { - hide_modal(); - view.vis_id = vis_info.vis_id; - view.has_changes = false; - - // Needed to set URL when first saving a visualization. - window.history.pushState({}, "", vis_info.url + window.location.hash); - }) - .error(function() { - show_modal( "Could Not Save", "Could not save visualization. Please try again later.", - { "Close" : hide_modal } ); - }); - } }, - { icon_class: 'cross-circle', title: 'Close', on_click: function() { - window.location = "${h.url_for( controller='visualization', action='list' )}"; - } } - ], - { - tooltip_config: { placement: 'bottom' } - }); - - menu.$el.attr("style", "float: right"); - $("#center .unified-panel-header-inner").append(menu.$el); + // Attach the button menu to the panel header and float it left + ui.buttonMenu.$el.attr("style", "float: right"); + $("#center .unified-panel-header-inner").append(ui.buttonMenu.$el); // Hide bookmarks by default right now. parent.force_right_panel("hide"); @@ -159,7 +86,7 @@ JSON.parse('${ h.to_json_string( config['bookmarks'] ) }'), true ); - init_editor(); + ui.init_editor(); set_up_router({view: view}); %else: var continue_fn = function() { @@ -169,7 +96,7 @@ dbkey: $("#new-dbkey").val() } ); view.editor = true; - init_editor(); + ui.init_editor(); set_up_router({view: view}); hide_modal(); }; https://bitbucket.org/galaxy/galaxy-central/changeset/65ecf4e0ed28/ changeset: 65ecf4e0ed28 user: james_taylor date: 2012-09-17 22:24:27 summary: pack affected #: 1 file diff -r 5a61f51233861c6f7f4be41c5fd2de94d468ea61 -r 65ecf4e0ed28eaa2f3e64495ab800aa7c9779a54 static/scripts/packed/viz/trackster_ui.js --- a/static/scripts/packed/viz/trackster_ui.js +++ b/static/scripts/packed/viz/trackster_ui.js @@ -1,1 +1,1 @@ -define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks"],function(f,c,g,d,b){var a=b.object_from_template;var e=f.Base.extend({initialize:function(h){this.baseURL=h},add_bookmarks:function(){var h=this.baseURL;show_modal("Select dataset for new bookmarks","progress");$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(j){show_modal("Select dataset for new bookmarks",j,{Cancel:function(){hide_modal()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var k,l=$(this).val();if($(this).attr("name")==="id"){k={hda_id:l}}else{k={ldda_id:l}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:k,dataType:"json",}).then(function(m){for(i=0;i<m.data.length;i++){var n=m.data[i];add_bookmark(n[0],n[1])}})});hide_modal()}})}})},add_bookmark:function(m,k,h){var o=$("#bookmarks-container"),q=$("<div/>").addClass("bookmark").appendTo(o);var r=$("<div/>").addClass("position").appendTo(q),n=$("<a href=''/>").text(m).appendTo(r).click(function(){view.go_to(m);return false}),l=$("<div/>").text(k).appendTo(q);if(h){var p=$("<div/>").addClass("delete-icon-container").prependTo(q).click(function(){q.slideUp("fast");q.remove();view.has_changes=true;return false}),j=$("<a href=''/>").addClass("icon-button delete").appendTo(p);l.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return q},create_visualization:function(l,h,k,m,j){view=new b.View(l);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(h){var v=h.chrom,n=h.start,s=h.end,p=h.overview;if(v&&(n!==undefined)&&s){view.change_chrom(v,n,s)}}if(k){var q,o,r;for(var t=0;t<k.length;t++){view.add_drawable(a(k[t],view,view))}}view.update_intro_div();var w;for(var t=0;t<view.drawables.length;t++){if(view.drawables[t].name===p){view.set_overview(view.drawables[t]);break}}if(m){var u;for(var t=0;t<m.length;t++){u=m[t];add_bookmark(u.position,u.annotation,j)}}view.has_changes=false});return view},init_keyboard_nav:function(h){$(document).keydown(function(j){if($(j.srcElement).is(":input")){return}switch(j.which){case 37:h.move_fraction(0.25);break;case 38:var k=Math.round(h.viewport_container.height()/15);h.viewport_container.scrollTop(h.viewport_container.scrollTop()-20);break;case 39:h.move_fraction(-0.25);break;case 40:var k=Math.round(h.viewport_container.height()/15);h.viewport_container.scrollTop(h.viewport_container.scrollTop()+20);break}})}});return{object_from_template:a,TracksterUI:e}}); \ No newline at end of file +define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks"],function(f,c,g,d,b){var a=b.object_from_template;var e=f.Base.extend({initialize:function(h){this.baseURL=h},createButtonMenu:function(){var h=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){add_datasets(add_datasets_url,add_track_async_url,function(j){c.each(j,function(k){view.add_drawable(trackster_ui.object_from_template(k,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new b.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){parent.force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location="${h.url_for( controller='visualization', action='circster' )}?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){show_modal("Saving...","progress");var j=[];$(".bookmark").each(function(){j.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var k=(view.overview_drawable?view.overview_drawable.name:null),l={id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",datasets:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:k},bookmarks:j};$.ajax({url:galaxy_paths.get("visualization_url"),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(l)}}).success(function(m){hide_modal();view.vis_id=m.vis_id;view.has_changes=false;window.history.pushState({},"",m.url+window.location.hash)}).error(function(){show_modal("Could Not Save","Could not save visualization. Please try again later.",{Close:hide_modal})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=h;return h},add_bookmarks:function(){var h=this.baseURL;show_modal("Select dataset for new bookmarks","progress");$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(j){show_modal("Select dataset for new bookmarks",j,{Cancel:function(){hide_modal()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var k,l=$(this).val();if($(this).attr("name")==="id"){k={hda_id:l}}else{k={ldda_id:l}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:k,dataType:"json",}).then(function(m){for(i=0;i<m.data.length;i++){var n=m.data[i];add_bookmark(n[0],n[1])}})});hide_modal()}})}})},add_bookmark:function(m,k,h){var o=$("#bookmarks-container"),q=$("<div/>").addClass("bookmark").appendTo(o);var r=$("<div/>").addClass("position").appendTo(q),n=$("<a href=''/>").text(m).appendTo(r).click(function(){view.go_to(m);return false}),l=$("<div/>").text(k).appendTo(q);if(h){var p=$("<div/>").addClass("delete-icon-container").prependTo(q).click(function(){q.slideUp("fast");q.remove();view.has_changes=true;return false}),j=$("<a href=''/>").addClass("icon-button delete").appendTo(p);l.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return q},create_visualization:function(l,h,k,m,j){view=new b.View(l);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(h){var v=h.chrom,n=h.start,s=h.end,p=h.overview;if(v&&(n!==undefined)&&s){view.change_chrom(v,n,s)}}if(k){var q,o,r;for(var t=0;t<k.length;t++){view.add_drawable(a(k[t],view,view))}}view.update_intro_div();var w;for(var t=0;t<view.drawables.length;t++){if(view.drawables[t].name===p){view.set_overview(view.drawables[t]);break}}if(m){var u;for(var t=0;t<m.length;t++){u=m[t];add_bookmark(u.position,u.annotation,j)}}view.has_changes=false});return view},init_keyboard_nav:function(h){$(document).keydown(function(j){if($(j.srcElement).is(":input")){return}switch(j.which){case 37:h.move_fraction(0.25);break;case 38:var k=Math.round(h.viewport_container.height()/15);h.viewport_container.scrollTop(h.viewport_container.scrollTop()-20);break;case 39:h.move_fraction(-0.25);break;case 40:var k=Math.round(h.viewport_container.height()/15);h.viewport_container.scrollTop(h.viewport_container.scrollTop()+20);break}})}});return{object_from_template:a,TracksterUI:e}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 17 Sep '12

17 Sep '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/67c3ec05a121/ changeset: 67c3ec05a121 user: james_taylor date: 2012-09-17 22:14:52 summary: trackster: misc fixes and reorganization affected #: 3 files diff -r 9deeb2fec6612253de699cc7207ffba09775c88b -r 67c3ec05a12195d30a3fc0ce5247cbc4545027e3 static/scripts/base.js --- a/static/scripts/base.js +++ b/static/scripts/base.js @@ -1,15 +1,15 @@ -define( "libs/backbone", function( backbone ) { +define( ["libs/backbone/backbone"], function( Backbone ) { var Base = function() { if( this.initialize ) { this.initialize.apply(this, arguments); } }; - Base.extend = backbone.Backbone.Model.extend; + Base.extend = Backbone.Model.extend; return { Base: Base, - Backbone: backbone.Backbone + Backbone: Backbone }; }); \ No newline at end of file diff -r 9deeb2fec6612253de699cc7207ffba09775c88b -r 67c3ec05a12195d30a3fc0ce5247cbc4545027e3 static/scripts/viz/trackster_ui.js --- a/static/scripts/viz/trackster_ui.js +++ b/static/scripts/viz/trackster_ui.js @@ -1,4 +1,4 @@ -define( ["libs/underscore","viz/trackster/slotting", "viz/trackster/painters","viz/trackster/tracks"], function( _, slotting, painters, tracks ) { +define( ["base","libs/underscore","viz/trackster/slotting", "viz/trackster/painters","viz/trackster/tracks"], function( base, _, slotting, painters, tracks ) { /************************************************************************ * Functions used for creating and managing the Trackster user interface. @@ -6,139 +6,191 @@ var object_from_template = tracks.object_from_template; -/** - * Add bookmark. - */ -var add_bookmark = function(position, annotation, editable) { - // Create HTML. - var bookmarks_container = $("#bookmarks-container"), - new_bookmark = $("<div/>").addClass("bookmark").appendTo(bookmarks_container); +var TracksterUI = base.Base.extend({ - var position_div = $("<div/>").addClass("position").appendTo(new_bookmark), - position_link = $("<a href=''/>").text(position).appendTo(position_div).click(function() { - view.go_to(position); - return false; - }), - annotation_div = $("<div/>").text(annotation).appendTo(new_bookmark); + initialize: function( baseURL ) { + this.baseURL = baseURL; + }, - // If editable, enable bookmark deletion and annotation editing. - if (editable) { - var delete_icon_container = $("<div/>").addClass("delete-icon-container").prependTo(new_bookmark).click(function (){ - // Remove bookmark. - new_bookmark.slideUp("fast"); - new_bookmark.remove(); - view.has_changes = true; + /** + * Use a popup to select a dataset of create bookmarks from + */ + add_bookmarks: function() { + var baseURL = this.baseURL; + show_modal( "Select dataset for new bookmarks", "progress" ); + $.ajax({ + url: this.baseURL + "/visualization/list_histories", + data: { "f-dbkey": view.dbkey }, + error: function() { alert( "Grid failed" ); }, + success: function(table_html) { + show_modal( + "Select dataset for new bookmarks", + table_html, { + "Cancel": function() { + hide_modal(); + }, + "Insert": function() { + // Just use the first selected + $('input[name=id]:checked,input[name=ldda_ids]:checked').first().each(function(){ + var data, id = $(this).val(); + if ($(this).attr("name") === "id") { + data = { hda_id: id }; + } else { + data = { ldda_id: id}; + } + + $.ajax({ + url: this.baseURL + "/visualization/bookmarks_from_dataset", + data: data, + dataType: "json", + }).then( function(data) { + for( i = 0; i < data.data.length; i++ ) { + var row = data.data[i]; + add_bookmark( row[0], row[1] ); + } + }); + }); + hide_modal(); + } + } + ); + } + }); + }, + + /** + * Add bookmark. + */ + add_bookmark: function(position, annotation, editable) { + // Create HTML. + var bookmarks_container = $("#bookmarks-container"), + new_bookmark = $("<div/>").addClass("bookmark").appendTo(bookmarks_container); + + var position_div = $("<div/>").addClass("position").appendTo(new_bookmark), + position_link = $("<a href=''/>").text(position).appendTo(position_div).click(function() { + view.go_to(position); return false; }), - delete_icon = $("<a href=''/>").addClass("icon-button delete").appendTo(delete_icon_container); - annotation_div.make_text_editable({ - num_rows: 3, - use_textarea: true, - help_text: "Edit bookmark note" - }).addClass("annotation"); + annotation_div = $("<div/>").text(annotation).appendTo(new_bookmark); + + // If editable, enable bookmark deletion and annotation editing. + if (editable) { + var delete_icon_container = $("<div/>").addClass("delete-icon-container").prependTo(new_bookmark).click(function (){ + // Remove bookmark. + new_bookmark.slideUp("fast"); + new_bookmark.remove(); + view.has_changes = true; + return false; + }), + delete_icon = $("<a href=''/>").addClass("icon-button delete").appendTo(delete_icon_container); + annotation_div.make_text_editable({ + num_rows: 3, + use_textarea: true, + help_text: "Edit bookmark note" + }).addClass("annotation"); + } + + view.has_changes = true; + return new_bookmark; + }, + + /** + * Create a complete Trackster visualization. Returns view. + */ + create_visualization: function(view_config, viewport_config, drawables_config, bookmarks_config, editable) { + + // Create view. + view = new tracks.View(view_config); + view.editor = true; + $.when( view.load_chroms_deferred ).then(function() { + // Viewport config. + if (viewport_config) { + var + chrom = viewport_config.chrom, + start = viewport_config.start, + end = viewport_config.end, + overview_drawable_name = viewport_config.overview; + + if (chrom && (start !== undefined) && end) { + view.change_chrom(chrom, start, end); + } + } + + // Add drawables to view. + if (drawables_config) { + // FIXME: can from_dict() be used to create view and add drawables? + var drawable_config, + drawable_type, + drawable; + for (var i = 0; i < drawables_config.length; i++) { + view.add_drawable( object_from_template( drawables_config[i], view, view ) ); + } + } + + // Need to update intro div after drawables have been added. + view.update_intro_div(); + + // Set overview. + var overview_drawable; + for (var i = 0; i < view.drawables.length; i++) { + if (view.drawables[i].name === overview_drawable_name) { + view.set_overview(view.drawables[i]); + break; + } + } + + // Load bookmarks. + if (bookmarks_config) { + var bookmark; + for (var i = 0; i < bookmarks_config.length; i++) { + bookmark = bookmarks_config[i]; + add_bookmark(bookmark['position'], bookmark['annotation'], editable); + } + } + + // View has no changes as of yet. + view.has_changes = false; + }); + + return view; + }, + + /** + * Set up keyboard navigation for a visualization. + */ + init_keyboard_nav: function(view) { + // Keyboard navigation. Scroll ~7% of height when scrolling up/down. + $(document).keydown(function(e) { + // Do not navigate if arrow keys used in input element. + if ($(e.srcElement).is(':input')) { + return; + } + + // Key codes: left == 37, up == 38, right == 39, down == 40 + switch(e.which) { + case 37: + view.move_fraction(0.25); + break + case 38: + var change = Math.round(view.viewport_container.height()/15.0); + view.viewport_container.scrollTop( view.viewport_container.scrollTop() - 20); + break; + case 39: + view.move_fraction(-0.25); + break; + case 40: + var change = Math.round(view.viewport_container.height()/15.0); + view.viewport_container.scrollTop( view.viewport_container.scrollTop() + 20); + break; + } + }); } - view.has_changes = true; - return new_bookmark; -}; - -/** - * Create a complete Trackster visualization. Returns view. - */ -var create_visualization = function(view_config, viewport_config, drawables_config, bookmarks_config, editable) { - - // Create view. - view = new tracks.View(view_config); - view.editor = true; - $.when( view.load_chroms_deferred ).then(function() { - // Viewport config. - if (viewport_config) { - var - chrom = viewport_config.chrom, - start = viewport_config.start, - end = viewport_config.end, - overview_drawable_name = viewport_config.overview; - - if (chrom && (start !== undefined) && end) { - view.change_chrom(chrom, start, end); - } - } - - // Add drawables to view. - if (drawables_config) { - // FIXME: can from_dict() be used to create view and add drawables? - var drawable_config, - drawable_type, - drawable; - for (var i = 0; i < drawables_config.length; i++) { - view.add_drawable( object_from_template( drawables_config[i], view, view ) ); - } - } - - // Need to update intro div after drawables have been added. - view.update_intro_div(); - - // Set overview. - var overview_drawable; - for (var i = 0; i < view.drawables.length; i++) { - if (view.drawables[i].name === overview_drawable_name) { - view.set_overview(view.drawables[i]); - break; - } - } - - // Load bookmarks. - if (bookmarks_config) { - var bookmark; - for (var i = 0; i < bookmarks_config.length; i++) { - bookmark = bookmarks_config[i]; - add_bookmark(bookmark['position'], bookmark['annotation'], editable); - } - } - - // View has no changes as of yet. - view.has_changes = false; - }); - - return view; -}; - -/** - * Set up keyboard navigation for a visualization. - */ - var init_keyboard_nav = function(view) { - // Keyboard navigation. Scroll ~7% of height when scrolling up/down. - $(document).keydown(function(e) { - // Do not navigate if arrow keys used in input element. - if ($(e.srcElement).is(':input')) { - return; - } - - // Key codes: left == 37, up == 38, right == 39, down == 40 - switch(e.which) { - case 37: - view.move_fraction(0.25); - break - case 38: - var change = Math.round(view.viewport_container.height()/15.0); - view.viewport_container.scrollTop( view.viewport_container.scrollTop() - 20); - break; - case 39: - view.move_fraction(-0.25); - break; - case 40: - var change = Math.round(view.viewport_container.height()/15.0); - view.viewport_container.scrollTop( view.viewport_container.scrollTop() + 20); - break; - } - }); -}; +}); return { - add_bookmark: add_bookmark, object_from_template: object_from_template, - create_visualization: create_visualization, - init_keyboard_nav: init_keyboard_nav + TracksterUI: TracksterUI }; }); diff -r 9deeb2fec6612253de699cc7207ffba09775c88b -r 67c3ec05a12195d30a3fc0ce5247cbc4545027e3 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -31,12 +31,11 @@ require.config({ baseUrl: "${h.url_for('/static/scripts') }", shim: { - "libs/underscore": { exports: "_" } + "libs/underscore": { exports: "_" }, + "libs/backbone/backbone": { exports: "Backbone" } } }); - require( ["viz/trackster_ui","viz/trackster/util","viz/trackster/tracks"], function( trackster_ui, util, tracks ) { - - var add_bookmark = trackster_ui.add_bookmark + require( ["base", "viz/trackster_ui","viz/trackster/util","viz/trackster/tracks"], function( base, trackster_ui, util, tracks ) { // // Place URLs here so that url_for can be used to generate them. @@ -48,8 +47,9 @@ ${render_trackster_js_vars()} var view, - browser_router; - + browser_router, + ui = new (trackster_ui.TracksterUI)( "${h.url_for('/')}" ); + /** * Set up router. */ @@ -58,51 +58,7 @@ Backbone.history.start(); }; - /** - * Use a popup grid to bookmarks from a dataset. - */ - var add_bookmarks = function() { - show_modal( "Select dataset for new bookmarks", "progress" ); - $.ajax({ - url: "${h.url_for( controller='visualization', action='list_histories' )}", - data: { "f-dbkey": view.dbkey }, - error: function() { alert( "Grid failed" ); }, - success: function(table_html) { - show_modal( - "Select dataset for new bookmarks", - table_html, { - "Cancel": function() { - hide_modal(); - }, - "Insert": function() { - // Just use the first selected - $('input[name=id]:checked,input[name=ldda_ids]:checked').first().each(function(){ - var data, id = $(this).val(); - if ($(this).attr("name") === "id") { - data = { hda_id: id }; - } else { - data = { ldda_id: id}; - } - $.ajax({ - url: "${h.url_for( action='bookmarks_from_dataset' )}", - data: data, - dataType: "json", - }).then( function(data) { - for( i = 0; i < data.data.length; i++ ) { - var row = data.data[i]; - add_bookmark( row[0], row[1] ); - } - }); - }); - hide_modal(); - } - } - ); - } - }); - }; - var browser_router; $(function() { // Create and initialize menu. @@ -192,7 +148,7 @@ $("#right-border").click(function() { view.resize_window(); }); %if config: - view = trackster_ui.create_visualization( { + view = ui.create_visualization( { container: $("#browser-container"), name: "${config.get('title') | h}", vis_id: "${config.get('vis_id')}", @@ -262,7 +218,7 @@ // Add new bookmark. var position = view.chrom + ":" + view.low + "-" + view.high, annotation = "Bookmark description"; - return add_bookmark(position, annotation, true); + return ui.add_bookmark(position, annotation, true); }); // make_popupmenu( $("#bookmarks-more-button"), { @@ -271,7 +227,7 @@ // } // }); - trackster_ui.init_keyboard_nav(view); + ui.init_keyboard_nav(view); }; }); https://bitbucket.org/galaxy/galaxy-central/changeset/6c0bb542d2e0/ changeset: 6c0bb542d2e0 user: james_taylor date: 2012-09-17 22:15:09 summary: pack scripts affected #: 2 files diff -r 67c3ec05a12195d30a3fc0ce5247cbc4545027e3 -r 6c0bb542d2e0cbda209e473db9d77a7076614f0d static/scripts/packed/base.js --- a/static/scripts/packed/base.js +++ b/static/scripts/packed/base.js @@ -1,1 +1,1 @@ -define("libs/backbone",function(b){var a=function(){if(this.initialize){this.initialize.apply(this,arguments)}};a.extend=b.Backbone.Model.extend;return{Base:a,Backbone:b.Backbone}}); \ No newline at end of file +define(["libs/backbone/backbone"],function(b){var a=function(){if(this.initialize){this.initialize.apply(this,arguments)}};a.extend=b.Model.extend;return{Base:a,Backbone:b}}); \ No newline at end of file diff -r 67c3ec05a12195d30a3fc0ce5247cbc4545027e3 -r 6c0bb542d2e0cbda209e473db9d77a7076614f0d static/scripts/packed/viz/trackster_ui.js --- a/static/scripts/packed/viz/trackster_ui.js +++ b/static/scripts/packed/viz/trackster_ui.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks"],function(d,h,g,c){var a=c.object_from_template;var f=function(m,k,i){var o=$("#bookmarks-container"),q=$("<div/>").addClass("bookmark").appendTo(o);var r=$("<div/>").addClass("position").appendTo(q),n=$("<a href=''/>").text(m).appendTo(r).click(function(){view.go_to(m);return false}),l=$("<div/>").text(k).appendTo(q);if(i){var p=$("<div/>").addClass("delete-icon-container").prependTo(q).click(function(){q.slideUp("fast");q.remove();view.has_changes=true;return false}),j=$("<a href=''/>").addClass("icon-button delete").appendTo(p);l.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return q};var b=function(l,i,k,m,j){view=new c.View(l);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(i){var v=i.chrom,n=i.start,s=i.end,p=i.overview;if(v&&(n!==undefined)&&s){view.change_chrom(v,n,s)}}if(k){var q,o,r;for(var t=0;t<k.length;t++){view.add_drawable(a(k[t],view,view))}}view.update_intro_div();var w;for(var t=0;t<view.drawables.length;t++){if(view.drawables[t].name===p){view.set_overview(view.drawables[t]);break}}if(m){var u;for(var t=0;t<m.length;t++){u=m[t];f(u.position,u.annotation,j)}}view.has_changes=false});return view};var e=function(i){$(document).keydown(function(j){if($(j.srcElement).is(":input")){return}switch(j.which){case 37:i.move_fraction(0.25);break;case 38:var k=Math.round(i.viewport_container.height()/15);i.viewport_container.scrollTop(i.viewport_container.scrollTop()-20);break;case 39:i.move_fraction(-0.25);break;case 40:var k=Math.round(i.viewport_container.height()/15);i.viewport_container.scrollTop(i.viewport_container.scrollTop()+20);break}})};return{add_bookmark:f,object_from_template:a,create_visualization:b,init_keyboard_nav:e}}); \ No newline at end of file +define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks"],function(f,c,g,d,b){var a=b.object_from_template;var e=f.Base.extend({initialize:function(h){this.baseURL=h},add_bookmarks:function(){var h=this.baseURL;show_modal("Select dataset for new bookmarks","progress");$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(j){show_modal("Select dataset for new bookmarks",j,{Cancel:function(){hide_modal()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var k,l=$(this).val();if($(this).attr("name")==="id"){k={hda_id:l}}else{k={ldda_id:l}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:k,dataType:"json",}).then(function(m){for(i=0;i<m.data.length;i++){var n=m.data[i];add_bookmark(n[0],n[1])}})});hide_modal()}})}})},add_bookmark:function(m,k,h){var o=$("#bookmarks-container"),q=$("<div/>").addClass("bookmark").appendTo(o);var r=$("<div/>").addClass("position").appendTo(q),n=$("<a href=''/>").text(m).appendTo(r).click(function(){view.go_to(m);return false}),l=$("<div/>").text(k).appendTo(q);if(h){var p=$("<div/>").addClass("delete-icon-container").prependTo(q).click(function(){q.slideUp("fast");q.remove();view.has_changes=true;return false}),j=$("<a href=''/>").addClass("icon-button delete").appendTo(p);l.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return q},create_visualization:function(l,h,k,m,j){view=new b.View(l);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(h){var v=h.chrom,n=h.start,s=h.end,p=h.overview;if(v&&(n!==undefined)&&s){view.change_chrom(v,n,s)}}if(k){var q,o,r;for(var t=0;t<k.length;t++){view.add_drawable(a(k[t],view,view))}}view.update_intro_div();var w;for(var t=0;t<view.drawables.length;t++){if(view.drawables[t].name===p){view.set_overview(view.drawables[t]);break}}if(m){var u;for(var t=0;t<m.length;t++){u=m[t];add_bookmark(u.position,u.annotation,j)}}view.has_changes=false});return view},init_keyboard_nav:function(h){$(document).keydown(function(j){if($(j.srcElement).is(":input")){return}switch(j.which){case 37:h.move_fraction(0.25);break;case 38:var k=Math.round(h.viewport_container.height()/15);h.viewport_container.scrollTop(h.viewport_container.scrollTop()-20);break;case 39:h.move_fraction(-0.25);break;case 40:var k=Math.round(h.viewport_container.height()/15);h.viewport_container.scrollTop(h.viewport_container.scrollTop()+20);break}})}});return{object_from_template:a,TracksterUI:e}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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