- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 3490: Update embedded item styles and functionality....
by Greg Von Kuster 09 Mar '10

09 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/97fe4a44b3bf changeset: 3490:97fe4a44b3bf user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Mar 08 11:37:35 2010 -0500 description: Update embedded item styles and functionality. Specific enhancements include: (a) colors for each embedded item; (b) option to make items accessible during embedding; (c) viewing and importing embedded items. To import a dataset, a generic 'dataset copy' was implemented. This functionality was also added to the HDA grid, so users can now copy any dataset they own to their current history. This Fixes #233 diffstat: lib/galaxy/web/base/controller.py | 3 + lib/galaxy/web/controllers/dataset.py | 67 +++++++++++++++++++++++- lib/galaxy/web/controllers/history.py | 4 - lib/galaxy/web/controllers/library_admin.py | 3 - lib/galaxy/web/controllers/page.py | 2 +- lib/galaxy/web/controllers/workflow.py | 1 - static/images/fugue/arrow-045.png | 0 static/images/fugue/plus-circle.png | 0 static/june_2007_style/base.css.tmpl | 8 ++ static/june_2007_style/blue/base.css | 2 + static/june_2007_style/blue/embed_item.css | 6 +- static/june_2007_style/embed_item.css.tmpl | 62 +++++++++++++++++----- templates/dataset/embed.mako | 13 +++- templates/display_base.mako | 4 +- templates/embed_base.mako | 38 +++++++++---- templates/history/embed.mako | 13 ++-- templates/page/display.mako | 75 ++++++++++++++++++--------- templates/page/editor.mako | 56 +++++++++++++------- templates/workflow/embed.mako | 12 ++-- 19 files changed, 265 insertions(+), 104 deletions(-) diffs (675 lines): diff -r 3563fade2c86 -r 97fe4a44b3bf lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py Fri Mar 05 17:21:16 2010 -0500 +++ b/lib/galaxy/web/base/controller.py Mon Mar 08 11:37:35 2010 -0500 @@ -13,6 +13,9 @@ from Cheetah.Template import Template log = logging.getLogger( __name__ ) + +# States for passing messages +SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" class BaseController( object ): """ diff -r 3563fade2c86 -r 97fe4a44b3bf lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Fri Mar 05 17:21:16 2010 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Mon Mar 08 11:37:35 2010 -0500 @@ -85,12 +85,11 @@ columns = [ grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation, # Link name to dataset's history. - link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced" ), + link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced", attach_popup=True ), HistoryColumn( "History", key="history", link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ), grids.IndividualTagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), StatusColumn( "Status", key="deleted", attach_popup=False ), - grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] columns.append( @@ -99,7 +98,9 @@ cols_to_filter=[ columns[0], columns[2] ], key="free-text-search", visible=False, filterable="standard" ) ) - operations = [] + operations = [ + grids.GridOperation( "Copy to current history", condition=( lambda item: not item.deleted ), async_compatible=False ), + ] standard_filters = [] default_filter = dict( name="All", deleted="False", tags="All" ) preserve_state = False @@ -284,11 +285,32 @@ if operation == "switch": hda_ids = [ trans.security.encode_id( hda.id ) for hda in hdas ] trans.template_context[ 'seek_hda_ids' ] = hda_ids + elif operation == "copy to current history": + # Copy a dataset to the current history. + target_histories = [ trans.get_history() ] + status, message = self._copy_datasets( trans, hda_ids, target_histories ) + + # Current history changed, refresh history frame. + trans.template_context['refresh_frames'] = ['history'] # Render the list view return self.stored_list_grid( trans, status=status, message=message, **kwargs ) @web.expose + def imp( self, trans, id=None, **kwd ): + """ Import another user's dataset via a shared URL; dataset is added to user's current history. """ + msg = "" + + # Error checking. + if not id: + return trans.show_error_message( "You must specify an ID for a dataset to import." ) + + # Do import. + cur_history = trans.get_history( create=True ) + status, message = self._copy_datasets( trans, [ id ], [ cur_history ] ) + return trans.show_message( message, type=status ) + + @web.expose @web.json @web.require_login( "use Galaxy datasets" ) def get_name_and_link_async( self, trans, id=None ): @@ -324,7 +346,6 @@ raise web.httpexceptions.HTTPNotFound() @web.expose - @web.require_login("get item content asynchronously") def get_item_content_async( self, trans, id ): """ Returns item content in HTML format. """ @@ -534,4 +555,40 @@ new_history_name = new_history_name, done_msg = done_msg, error_msg = error_msg, - refresh_frames = refresh_frames ) \ No newline at end of file + refresh_frames = refresh_frames ) + + def _copy_datasets( self, trans, dataset_ids, target_histories ): + """ Helper method for copying datasets. """ + user = trans.get_user() + done_msg = error_msg = "" + + invalid_datasets = 0 + if not dataset_ids or not target_histories: + error_msg = "You must provide both source datasets and target histories." + else: + # User must own target histories to copy datasets to them. + for history in target_histories: + if user != history.user: + error_msg = error_msg + "You do not have permission to add datasets to %i requested histories. " % ( len( target_histories ) ) + for dataset_id in dataset_ids: + data = self.get_dataset( trans, dataset_id ) + if data is None: + error_msg = error_msg + "You tried to copy a dataset that does not exist or that you do not have access to. " + invalid_datasets += 1 + else: + for hist in target_histories: + hist.add_dataset( data.copy( copy_children = True ) ) + trans.sa_session.flush() + num_datasets_copied = len( dataset_ids ) - invalid_datasets + done_msg = "%i dataset%s copied to %i histor%s." % \ + ( num_datasets_copied, iff( num_datasets_copied == 1, "", "s"), len( target_histories ), iff( len ( target_histories ) == 1, "y", "ies") ) + trans.sa_session.refresh( history ) + + if error_msg != "": + status = ERROR + message = error_msg + else: + status = SUCCESS + message = done_msg + return status, message + \ No newline at end of file diff -r 3563fade2c86 -r 97fe4a44b3bf lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Fri Mar 05 17:21:16 2010 -0500 +++ b/lib/galaxy/web/controllers/history.py Mon Mar 08 11:37:35 2010 -0500 @@ -13,9 +13,6 @@ log = logging.getLogger( __name__ ) -# States for passing messages -SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" - class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, history ): return history.get_display_name() @@ -475,7 +472,6 @@ return history.slug @web.expose - @web.require_login("get item content asynchronously") def get_item_content_async( self, trans, id ): """ Returns item content in HTML format. """ diff -r 3563fade2c86 -r 97fe4a44b3bf lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Fri Mar 05 17:21:16 2010 -0500 +++ b/lib/galaxy/web/controllers/library_admin.py Mon Mar 08 11:37:35 2010 -0500 @@ -12,9 +12,6 @@ import logging log = logging.getLogger( __name__ ) -# States for passing messages -SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" - class LibraryListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, library ): diff -r 3563fade2c86 -r 97fe4a44b3bf lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Fri Mar 05 17:21:16 2010 -0500 +++ b/lib/galaxy/web/controllers/page.py Mon Mar 08 11:37:35 2010 -0500 @@ -48,7 +48,7 @@ grids.GridOperation( "Edit attributes", allow_multiple=False, url_args=dict( action='edit') ), grids.GridOperation( "Edit content", allow_multiple=False, url_args=dict( action='edit_content') ), grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), - grids.GridOperation( "Delete" ), + grids.GridOperation( "Delete", confirm="Are you sure you want to delete this page?" ), ] def apply_default_filter( self, trans, query, **kwargs ): return query.filter_by( user=trans.user, deleted=False ) diff -r 3563fade2c86 -r 97fe4a44b3bf lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Fri Mar 05 17:21:16 2010 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Mon Mar 08 11:37:35 2010 -0500 @@ -182,7 +182,6 @@ return trans.fill_template_mako( "workflow/display.mako", item=stored_workflow, item_data=stored_workflow.latest_workflow.steps ) @web.expose - @web.require_login("get item content asynchronously") def get_item_content_async( self, trans, id ): """ Returns item content in HTML format. """ diff -r 3563fade2c86 -r 97fe4a44b3bf static/images/fugue/arrow-045.png Binary file static/images/fugue/arrow-045.png has changed diff -r 3563fade2c86 -r 97fe4a44b3bf static/images/fugue/plus-circle.png Binary file static/images/fugue/plus-circle.png has changed diff -r 3563fade2c86 -r 97fe4a44b3bf static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Fri Mar 05 17:21:16 2010 -0500 +++ b/static/june_2007_style/base.css.tmpl Mon Mar 08 11:37:35 2010 -0500 @@ -792,6 +792,14 @@ -sprite-image: fugue/sticky-note-text.png; } +.icon-button.go-to-full-screen { + background: url(/static/images/fugue/arrow-045.png) no-repeat +} + +.icon-button.import { + background:url(/static/images/fugue/plus-circle.png) no-repeat +} + .tipsy { padding: 5px; font-size: 10px; diff -r 3563fade2c86 -r 97fe4a44b3bf static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Fri Mar 05 17:21:16 2010 -0500 +++ b/static/june_2007_style/blue/base.css Mon Mar 08 11:37:35 2010 -0500 @@ -136,6 +136,8 @@ .icon-button.bug{background:url(fugue.png) no-repeat 0px -182px;} .icon-button.disk{background:url(fugue.png) no-repeat 0px -208px;} .icon-button.annotate{background:url(fugue.png) no-repeat 0px -234px;} +.icon-button.go-to-full-screen{background:url(/static/images/fugue/arrow-045.png) no-repeat} +.icon-button.import{background:url(/static/images/fugue/plus-circle.png) no-repeat} .tipsy{padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);} .tipsy-inner{padding:5px 8px 4px 8px;background-color:black;color:white;max-width:200px;text-align:center;} .tipsy-north{background-position:top center;} diff -r 3563fade2c86 -r 97fe4a44b3bf static/june_2007_style/blue/embed_item.css --- a/static/june_2007_style/blue/embed_item.css Fri Mar 05 17:21:16 2010 -0500 +++ b/static/june_2007_style/blue/embed_item.css Mon Mar 08 11:37:35 2010 -0500 @@ -1,5 +1,9 @@ -.embedded-item{background-color:#BBBBBB;margin-left:auto;margin-right:auto;width:90%;max-height:25em;overflow:auto;padding: 0.5em;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;} +.embedded-item{margin-left:auto;margin-right:auto;width:90%;padding: 0.5em;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;} +.embedded-item.history{background-color:#C1C9E5} +.embedded-item.dataset{background-color:#CFC} +.embedded-item.workflow{background-color:#EBD9B2} .embedded-item.placeholder{} +.embedded-item .item-content{max-height:25em;overflow:auto;} .embedded-item .title{vertical-align:top;text-align:center;} .embedded-item.placeholder .content{padding: 1em 1em;font-style:italic;text-align:center;} table.annotated-item{width:100%;border-collapse:collapse;} diff -r 3563fade2c86 -r 97fe4a44b3bf static/june_2007_style/embed_item.css.tmpl --- a/static/june_2007_style/embed_item.css.tmpl Fri Mar 05 17:21:16 2010 -0500 +++ b/static/june_2007_style/embed_item.css.tmpl Mon Mar 08 11:37:35 2010 -0500 @@ -1,24 +1,58 @@ .embedded-item { - background-color: #BBBBBB; - margin-left: auto; - margin-right: auto; - width: 90%; - max-height: 25em; - overflow: auto; + margin-left:auto; + margin-right:auto; + width:90%; padding: 0.5em; - -moz-border-radius: .5em; - -webkit-border-radius: .5em; - border-radius: .5em; + -moz-border-radius:0.5em; + -webkit-border-radius:0.5em; + border-radius:0.5em; } -.embedded-item.placeholder {} + +.embedded-item.history { + background-color:#C1C9E5 +} + +.embedded-item.dataset { + background-color:#CFC +} + +.embedded-item.workflow { + background-color:#EBD9B2 +} + +.embedded-item.placeholder{} + +.embedded-item .item-content { + max-height: 25em; + overflow: auto; +} + .embedded-item .title { - font-weight: bold; - font-size:120%; vertical-align:top; text-align:center; } -.embedded-item.placeholder .content{ + +.embedded-item.placeholder .content { padding: 1em 1em; font-style:italic; text-align:center; - } \ No newline at end of file +} + +table.annotated-item { + width:100%; + border-collapse:collapse; +} + +table.annotated-item td,th { + padding:0; +} + +table.annotated-item .annotation { + padding-left:2em; + width:40%; +} + +table.annotated-item td.annotation { + vertical-align:text-top; + padding-top:1em; +} \ No newline at end of file diff -r 3563fade2c86 -r 97fe4a44b3bf templates/dataset/embed.mako --- a/templates/dataset/embed.mako Fri Mar 05 17:21:16 2010 -0500 +++ b/templates/dataset/embed.mako Mon Mar 08 11:37:35 2010 -0500 @@ -3,8 +3,13 @@ from galaxy.web.framework.helpers import iff %> -<%def name="content( dataset, data )"> - <ul> - <li>Format : ${dataset.extension} - </ul> +<%def name="render_item_specific_title_links( dataset )"> + <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ), to_ext=dataset.ext )}" title="Save dataset" class="icon-button disk tooltip"></a> </%def> + +<%def name="render_summary_content( dataset, data )"> +## <ul> +## <li>Format : ${dataset.extension} +## <pre>${dataset.peek}</pre> +## </ul> +</%def> diff -r 3563fade2c86 -r 97fe4a44b3bf templates/display_base.mako --- a/templates/display_base.mako Fri Mar 05 17:21:16 2010 -0500 +++ b/templates/display_base.mako Mon Mar 08 11:37:35 2010 -0500 @@ -32,7 +32,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "galaxy.base", "jquery", "json2", "jquery.autocomplete", "autocomplete_tagging" )} + ${h.js( "jquery", "jquery.tipsy", "galaxy.base", "json2", "jquery.autocomplete", "jquery.jstore-all", "autocomplete_tagging" )} <script type="text/javascript"> // @@ -102,7 +102,7 @@ <%def name="render_item_header( item )"> <h3>Galaxy ${get_class_display_name( item.__class__ )} '${get_item_name( item )| h}'</h3> %if hasattr( item, "annotation"): - <div class="annotation">Description/Notes: ${item.annotation}</div> + <div class="annotation">Annotation: ${item.annotation}</div> %endif <hr/> </%def> diff -r 3563fade2c86 -r 97fe4a44b3bf templates/embed_base.mako --- a/templates/embed_base.mako Fri Mar 05 17:21:16 2010 -0500 +++ b/templates/embed_base.mako Mon Mar 08 11:37:35 2010 -0500 @@ -6,36 +6,50 @@ <%namespace file="/display_common.mako" import="*" /> ## HTML structure. -<div class='embedded-item'> +<div class='embedded-item ${get_class_display_name( item.__class__ ).lower()}'> <div class='title'> - ${self.title( item )} + ${self.render_title( item )} + <hr/> </div> - <hr/> <div class='summary-content'> - ${self.content( item, item_data )} + ${self.render_summary_content( item, item_data )} </div> <div class='item-content'> </div> </div> -<%def name="title( item )"> - <h4>Galaxy ${get_class_display_name( item.__class__ )} | ${get_item_name( item )}</h4> +## Render item-specific title links. +<%def name="render_item_specific_title_links( item )"> +</%def> + +<%def name="render_title( item )"> <% + item_display_name = get_class_display_name( item.__class__ ).lower() item_controller = "/%s" % get_controller_name( item ) item_user = get_item_user( item ) item_slug = get_item_slug( item ) display_href = h.url_for( controller=item_controller, action='display_by_username_and_slug', username=item_user.username, slug=item_slug ) %> - <a class="display_in_embed icon-button toggle-expand" item_id="${trans.security.encode_id( item.id )}" item_class="$item.__class__.__name__" href="${display_href}"></a> - <a class="toggle-contract icon-button" href="${display_href}"></a> - %if hasattr( item, "annotation"): - <div class="annotation">Description/Notes: ${item.annotation}</div> + <div style="float: left"> + <a class="display_in_embed icon-button toggle-expand tooltip" item_id="${trans.security.encode_id( item.id )}" item_class="$item.__class__.__name__" href="${display_href}" + title="Show ${item_display_name} content"></a> + <a class="toggle-contract icon-button tooltip" href="${display_href}" title="Hide ${item_display_name} content"></a> + </div> + <div style="float: right"> + ${self.render_item_specific_title_links( item )} + ## Links applicable for all items. + <a href="${h.url_for( controller=item_controller, action='imp', id=trans.security.encode_id( item.id ) )}" title="Import ${item_display_name}" class="icon-button import tooltip"></a> + <a class="icon-button go-to-full-screen tooltip" href="${display_href}" title="Go to ${item_display_name}"></a> + </div> + <h4><a class="toggle-embed tooltip" href="${display_href}" title="Show or hide ${item_display_name} content">Galaxy ${get_class_display_name( item.__class__ )} | ${get_item_name( item )}</a></h4> + %if hasattr( item, "annotation") and item.annotation: + <div class="annotation">${item.annotation}</div> %endif ## Use a hidden var to store the ajax URL for getting an item's content. <input type="hidden" name="ajax-item-content-url" value="${h.url_for( controller=item_controller, action='get_item_content_async', id=trans.security.encode_id( item.id ) )}"/> </%def> -## Methods to override to generate content. -<%def name="content( item, item_data )"> +## Methods to override to render summary content. +<%def name="render_summary_content( item, item_data )"> </%def> diff -r 3563fade2c86 -r 97fe4a44b3bf templates/history/embed.mako --- a/templates/history/embed.mako Fri Mar 05 17:21:16 2010 -0500 +++ b/templates/history/embed.mako Mon Mar 08 11:37:35 2010 -0500 @@ -3,10 +3,11 @@ from galaxy.web.framework.helpers import iff %> -<%def name="content( history, datasets )"> - <ul> - <% num_datasets = len ( datasets ) %> - <li>${num_datasets} dataset${iff( num_datasets != 1, "s", "" )} - <li>Operations: ... - </ul> +<%def name="render_summary_content( history, datasets )"> + +## <ul> +## <% num_datasets = len ( datasets ) %> +## <li>${num_datasets} dataset${iff( num_datasets != 1, "s", "" )} +## <li>Operations: ... +## </ul> </%def> diff -r 3563fade2c86 -r 97fe4a44b3bf templates/page/display.mako --- a/templates/page/display.mako Fri Mar 05 17:21:16 2010 -0500 +++ b/templates/page/display.mako Mon Mar 08 11:37:35 2010 -0500 @@ -2,7 +2,6 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "jquery", "json2", "jquery.jstore-all", "jquery.autocomplete", "autocomplete_tagging" )} <script type="text/javascript"> $(function() { // Load jStore for local storage @@ -31,47 +30,68 @@ // (b) ... $('.embedded-item').each( function() { - // Setup toggle expand. var container = $(this); - var toggle_expand = $(this).find('.toggle-expand'); - toggle_expand.click( function() - { + + // Show embedded item. + var show_embedded_item = function() { var ajax_url = container.find("input[type=hidden]").val(); // Only get item content if it's not already there. var item_content = $.trim(container.find(".item-content").text()); if (item_content == "") - $.ajax({ - type: "GET", - url: ajax_url, - error: function() { alert("Getting item content failed."); }, - success: function( item_content ) { - container.find(".summary-content").hide("fast"); - container.find(".item-content").html(item_content).show("fast"); - container.find(".toggle-expand").hide(); - container.find(".toggle-contract").show(); - } - }); + $.ajax({ + type: "GET", + url: ajax_url, + error: function() { alert("Getting item content failed."); }, + success: function( item_content ) { + container.find(".summary-content").hide("fast"); + container.find(".item-content").html(item_content).show("fast"); + container.find(".toggle-expand").hide(); + container.find(".toggle-contract").show(); + } + }); else { - container.find(".summary-content").hide("fast"); - container.find(".item-content").show("fast"); - container.find(".toggle-expand").hide(); - container.find(".toggle-contract").show(); - } + container.find(".summary-content").hide("fast"); + container.find(".item-content").show("fast"); + container.find(".toggle-expand").hide(); + container.find(".toggle-contract").show(); + } + }; + + // Hide embedded item. + var hide_embedded_item = function() { + container.find(".item-content").hide("fast"); + container.find(".summary-content").show("fast"); + container.find(".toggle-contract").hide(); + container.find(".toggle-expand").show(); + }; + + // Setup toggle expand. + var toggle_expand = $(this).find('.toggle-expand'); + toggle_expand.click( function() + { + show_embedded_item(); return false; }); + // Setup toggle contract. var toggle_contract = $(this).find('.toggle-contract'); toggle_contract.click( function() { - container.find(".item-content").hide("fast"); - container.find(".summary-content").show("fast"); - container.find(".toggle-contract").hide(); - container.find(".toggle-expand").show(); + hide_embedded_item(); return false; }); - + // Setup toggle embed. + var toggle_embed = $(this).find('.toggle-embed'); + toggle_embed.click( function() + { + if (container.find(".item-content").is(":visible")) + hide_embedded_item(); + else + show_embedded_item(); + return false; + }); }); }); // Functionized so AJAX'd datasets can call them @@ -199,6 +219,9 @@ <style type="text/css"> .toggle-contract { display: none; } .item-content { overflow: auto; } + .embedded-item h4 { + margin: 0px; + } </style> </%def> diff -r 3563fade2c86 -r 97fe4a44b3bf templates/page/editor.mako --- a/templates/page/editor.mako Fri Mar 05 17:21:16 2010 -0500 +++ b/templates/page/editor.mako Mon Mar 08 11:37:35 2010 -0500 @@ -119,6 +119,19 @@ }; }; + // Make an item importable. + function make_item_importable( item_controller, item_id, item_type ) + { + url_template = "${h.url_for( controller='ITEM_CONTROLLER', action='set_accessible_async' )}"; + ajax_url = url_template.replace( "ITEM_CONTROLLER", item_controller ); + $.ajax({ + type: "POST", + url: ajax_url, + data: { id: item_id, accessible: 'True' }, + error: function() { alert("Making " + item_type + " accessible failed"); } + }); + }; + ## Completely replace WYM's dialog handling WYMeditor.editor.prototype.dialog = function( dialogType, dialogFeatures, bodyHtml ) { @@ -340,7 +353,7 @@ { "Insert": function() { - // Make items accessible (importable) ? + // Make selected items accessible (importable) ? var make_importable = false; if ( $('#make-importable:checked').val() !== null ) make_importable = true; @@ -352,16 +365,7 @@ // Make item importable? if (make_importable) - { - url_template = "${h.url_for( controller='ITEM_CONTROLLER', action='set_accessible_async' )}"; - ajax_url = url_template.replace( "ITEM_CONTROLLER", item_info.controller); - $.ajax({ - type: "POST", - url: ajax_url, - data: { id: item_id, accessible: 'True' }, - error: function() { alert("Making " + item_info.plural.toLowerCase() + " accessible failed"); } - }); - } + make_item_importable(item_info.controller, item_id, item_info.singular); // Insert link(s) to item(s). This is done by getting item info and then manipulating wym. url_template = "${h.url_for( controller='ITEM_CONTROLLER', action='get_name_and_link_async' )}?id=" + item_id; @@ -427,29 +431,43 @@ error: function() { alert( "Failed to list " + item_info.plural.toLowerCase() + " for selection"); }, success: function(list_html) { + // Can make histories, workflows importable; cannot make datasets importable. + if (dialogType == Galaxy.DIALOG_EMBED_HISTORY || dialogType == Galaxy.DIALOG_EMBED_WORKFLOW) + list_html = list_html + "<div><input id='make-importable' type='checkbox' checked/>" + + "Make the selected " + item_info.plural.toLowerCase() + " accessible so that they can viewed by everyone.</div>"; show_modal( "Embed " + item_info.plural, list_html, { "Embed": function() - { - // Embed a Galaxy item. - var item_ids = new Array(); + { + // Make selected items accessible (importable) ? + var make_importable = false; + if ( $('#make-importable:checked').val() != null ) + make_importable = true; + $('input[name=id]:checked').each(function() { // Get item ID and name. var item_id = $(this).val(); // Use ':first' because there are many labels in table; the first one is the item name. var item_name = $("label[for='" + item_id + "']:first").text(); + if (make_importable) + make_item_importable(item_info.controller, item_id, item_info.singular); + // Embedded item HTML; item class is embedded in div container classes; this is necessary because the editor strips // all non-standard attributes when it returns its content (e.g. it will not return an element attribute of the form // item_class='History'). - var item_embed_html = - "<p><div id='" + item_info.iclass + "-" + item_id + "' class='embedded-item placeholder'> \ + var item_embed_html = + "<p> \ + <div id='" + item_info.iclass + "-" + item_id + "' class='embedded-item " + item_info.singular.toLowerCase() + + " placeholder'> \ <div class='title'> Embedded Galaxy " + item_info.singular + " '" + item_name + "'</div> \ - <div class='content'>[Do not edit this block; Galaxy will fill it in with the annotated " + \ - item_info.singular.toLowerCase() + " when it is displayed.]</div> \ - </div></p><p>"; + <div class='content'> \ + [Do not edit this block; Galaxy will fill it in with the annotated " + + item_info.singular.toLowerCase() + " when it is displayed.]</div> \ + </div> \ + </div></p>"; // Insert embedded representation into document. wym.insert(item_embed_html); diff -r 3563fade2c86 -r 97fe4a44b3bf templates/workflow/embed.mako --- a/templates/workflow/embed.mako Fri Mar 05 17:21:16 2010 -0500 +++ b/templates/workflow/embed.mako Mon Mar 08 11:37:35 2010 -0500 @@ -3,10 +3,10 @@ from galaxy.web.framework.helpers import iff %> -<%def name="content( workflow, steps )"> - <ul> - <% num_steps = len ( steps ) %> - <li>${num_steps} step${iff( num_steps != 1, "s", "" )} - <li>Operations: ... - </ul> +<%def name="render_summary_content( workflow, steps )"> +## <ul> +## <% num_steps = len ( steps ) %> +## <li>${num_steps} step${iff( num_steps != 1, "s", "" )} +## <li>Operations: ... +## </ul> </%def>

1 0

Weird problem with importing datasets
by Chris Cole 09 Mar '10

09 Mar '10

Hi, I've enabled the 'library_import_dir' option in universe_wsgi.ini as: library_import_dir = /homes/www-galaxy/data_import It's contents is: www-galaxy@ge-004: data_import> ls -l total 96 lrwxrwxrwx 1 www-galaxy barton 40 Mar 4 14:40 Dd_inuc_1.txt -> /homes/pschofield/data/TOH/Dd_inuc_1.txt -rw-r--r-- 1 www-galaxy barton 142 Mar 5 13:50 README However, both files fail to import with this error: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line 326, in __main__() File "/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line 318, in __main__ add_file( dataset, error The strangeness comes in if I copy to the Dd_inuc_1.txt file a directory owned by the www-galaxy user and link to it there. Then, the imports works for both files. www-galaxy@ge-004: data_import> ls -l total 96 lrwxrwxrwx 1 www-galaxy barton 20 Mar 5 13:56 Dd_inuc_1.txt -> ../tmp/Dd_inuc_1.txt -rw-r--r-- 1 www-galaxy barton 142 Mar 5 13:50 README The permissions are correct for the file: www-galaxy@ge-004: data_import> ls -l /homes/pschofield/data/TOH/Dd_inuc_1.txt -rw-r--r-- 1 pschofield barton 966480362 Jan 18 16:39 /homes/pschofield/data/TOH/Dd_inuc_1.txt I've no idea why Galaxy cares about who owns the files as it should be able to see them, but something's screwy. Anyone have ideas as to what's going on here? Cheers, Chris -- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris(a)compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096

2 4

Problems with latest update
by Chris Cole 09 Mar '10

09 Mar '10

Hi, I just did an hg pull for the latest version and I've got errors trying to run the 'Fastq Groomer' and 'Fastq Summary Statistics' tools. It looks like they're related. The old Fastq Groomer as found in the 'Deprecated' tools section works fine. Groomer: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/fastq/fastq_groomer.py", line 3, in ? from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator, fastqWriter File "/homes/www-galaxy/galaxy_devel/lib/galaxy_utils/sequence/fastq.py", line 267 class fastqAggregator(): ^ SyntaxError: invalid syntax Summary Stats: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/fastq/fastq_stats.py", line 3, in ? from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator File "/homes/www-galaxy/galaxy_devel/lib/galaxy_utils/sequence/fastq.py", line 267 class fastqAggregator(): ^ SyntaxError: invalid syntax Is this a problem at my end or in Galaxy itself? This is python 2.6, BTW. Cheers, Chris -- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris(a)compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096

3 4

how to specify sge options?
by Edward Kirton 08 Mar '10

08 Mar '10

Hello, Is there a way to pass SGE options to the runner? Specifically, i'd like to tell the scheduler the number of cores required by a tool (-pe). Thanks, Ed Kirton US DOE JGI

2 3

[hg] galaxy 3489: Add the ability for tests to have a lines_diff...
by Greg Von Kuster 08 Mar '10

08 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/3563fade2c86 changeset: 3489:3563fade2c86 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Mar 05 17:21:16 2010 -0500 description: Add the ability for tests to have a lines_diff attribute set for standard output datasets that will allow the specified number of lines to vary between test-data and tool run results; a 'change' to a line equates to a difference of 2 lines between files (i.e. 1 line added, 1 line removed). Add the ability for test comparisons to use single or multiline regular expressions, this is accessed by adding the attribute compare= "match_re" or "match_re_multiline" (respectively); the standard diff method can be explicitly declared as "diff", or is used at the default when not specified. diffstat: lib/galaxy/tools/__init__.py | 7 +- lib/galaxy/tools/test.py | 4 +- test/base/twilltestcase.py | 134 ++++++++++++++++++++++++++++----------- test/functional/test_toolbox.py | 4 +- 4 files changed, 106 insertions(+), 43 deletions(-) diffs (225 lines): diff -r 45cfcab6aed7 -r 3563fade2c86 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Fri Mar 05 12:55:51 2010 -0500 +++ b/lib/galaxy/tools/__init__.py Fri Mar 05 17:21:16 2010 -0500 @@ -532,8 +532,11 @@ file = attrib.pop( 'file', None ) if file is None: raise Exception( "Test output does not have a 'file'") - sort = util.string_as_bool( attrib.pop( 'sort', False ) ) - test.add_output( name, file, sort ) + attributes = Bunch() + attributes.compare = attrib.pop( 'compare', 'diff' ).lower() #method of comparison + attributes.lines_diff = int( attrib.pop( 'lines_diff', '0' ) ) # allow a few lines (dates etc) to vary in logs + attributes.sort = util.string_as_bool( attrib.pop( 'sort', False ) ) + test.add_output( name, file, attributes ) except Exception, e: test.error = True test.exception = e diff -r 45cfcab6aed7 -r 3563fade2c86 lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py Fri Mar 05 12:55:51 2010 -0500 +++ b/lib/galaxy/tools/test.py Fri Mar 05 17:21:16 2010 -0500 @@ -37,8 +37,8 @@ except Exception, e: log.debug( "Error in add_param for %s: %s" % ( name, e ) ) self.inputs.append( ( name, value, extra ) ) - def add_output( self, name, file, sort ): - self.outputs.append( ( name, file, sort ) ) + def add_output( self, name, file, extra ): + self.outputs.append( ( name, file, extra ) ) def __expand_grouping_for_data_input( self, name, value, extra, grouping_name, grouping_value ): # Currently handles grouping.Conditional and grouping.Repeat if isinstance( grouping_value, grouping.Conditional ): diff -r 45cfcab6aed7 -r 3563fade2c86 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Fri Mar 05 12:55:51 2010 -0500 +++ b/test/base/twilltestcase.py Fri Mar 05 17:21:16 2010 -0500 @@ -36,14 +36,21 @@ #self.set_history() # Functions associated with files - def files_diff( self, file1, file2, sort=False ): + def files_diff( self, file1, file2, attributes=None ): """Checks the contents of 2 files for differences""" + def get_lines_diff( diff ): + count = 0 + for line in diff: + if ( line.startswith( '+' ) and not line.startswith( '+++' ) ) or ( line.startswith( '-' ) and not line.startswith( '---' ) ): + count += 1 + return count if not filecmp.cmp( file1, file2 ): files_differ = False local_file = open( file1, 'U' ).readlines() history_data = open( file2, 'U' ).readlines() - if sort: + if attributes and attributes.sort: history_data.sort() + ##Why even bother with the check loop below, why not just use the diff output? This seems wasteful. if len( local_file ) == len( history_data ): for i in range( len( history_data ) ): if local_file[i].rstrip( '\r\n' ) != history_data[i].rstrip( '\r\n' ): @@ -52,37 +59,79 @@ else: files_differ = True if files_differ: - diff = difflib.unified_diff( local_file, history_data, "local_file", "history_data" ) - diff_slice = list( islice( diff, 40 ) ) - if file1.endswith( '.pdf' ) or file2.endswith( '.pdf' ): - # PDF files contain creation dates, modification dates, ids and descriptions that change with each - # new file, so we need to handle these differences. As long as the rest of the PDF file does - # not differ we're ok. - valid_diff_strs = [ 'description', 'createdate', 'creationdate', 'moddate', 'id' ] - valid_diff = False - for line in diff_slice: - # Make sure to lower case strings before checking. - line = line.lower() - # Diff lines will always start with a + or - character, but handle special cases: '--- local_file \n', '+++ history_data \n' - if ( line.startswith( '+' ) or line.startswith( '-' ) ) and line.find( 'local_file' ) < 0 and line.find( 'history_data' ) < 0: - for vdf in valid_diff_strs: - if line.find( vdf ) < 0: - valid_diff = False - else: - valid_diff = True - # Stop checking as soon as we know we have a valid difference - break - if not valid_diff: - # Print out diff_slice so we can see what failed - print "###### diff_slice ######" - raise AssertionError( "".join( diff_slice ) ) - break + if attributes and attributes.lines_diff: + allowed_diff_count = attributes.lines_diff else: - for line in diff_slice: - for char in line: - if ord( char ) > 128: - raise AssertionError( "Binary data detected, not displaying diff" ) - raise AssertionError( "".join( diff_slice ) ) + allowed_diff_count = 0 + diff = list( difflib.unified_diff( local_file, history_data, "local_file", "history_data" ) ) + diff_lines = get_lines_diff( diff ) + if diff_lines > allowed_diff_count: + diff_slice = diff[0:40] + #FIXME: This pdf stuff is rather special cased and has not been updated to consider lines_diff + #due to unknown desired behavior when used in conjunction with a non-zero lines_diff + #PDF forgiveness can probably be handled better by not special casing by __extension__ here + #and instead using lines_diff or a regular expression matching + #or by creating and using a specialized pdf comparison function + if file1.endswith( '.pdf' ) or file2.endswith( '.pdf' ): + # PDF files contain creation dates, modification dates, ids and descriptions that change with each + # new file, so we need to handle these differences. As long as the rest of the PDF file does + # not differ we're ok. + valid_diff_strs = [ 'description', 'createdate', 'creationdate', 'moddate', 'id' ] + valid_diff = False + for line in diff_slice: + # Make sure to lower case strings before checking. + line = line.lower() + # Diff lines will always start with a + or - character, but handle special cases: '--- local_file \n', '+++ history_data \n' + if ( line.startswith( '+' ) or line.startswith( '-' ) ) and line.find( 'local_file' ) < 0 and line.find( 'history_data' ) < 0: + for vdf in valid_diff_strs: + if line.find( vdf ) < 0: + valid_diff = False + else: + valid_diff = True + # Stop checking as soon as we know we have a valid difference + break + if not valid_diff: + # Print out diff_slice so we can see what failed + print "###### diff_slice ######" + raise AssertionError( "".join( diff_slice ) ) + else: + for line in diff_slice: + for char in line: + if ord( char ) > 128: + raise AssertionError( "Binary data detected, not displaying diff" ) + raise AssertionError( "".join( diff_slice ) ) + + def files_re_match( self, file1, file2, attributes=None ): + """Checks the contents of 2 files for differences using re.match""" + local_file = open( file1, 'U' ).readlines() #regex file + history_data = open( file2, 'U' ).readlines() + assert len( local_file ) == len( history_data ), 'Data File and Regular Expression File contain a different number of lines (%s != %s)' % ( len( local_file ), len( history_data ) ) + if attributes and attributes.sort: + history_data.sort() + if attributes and attributes.lines_diff: + lines_diff = attributes.lines_diff + else: + lines_diff = 0 + line_diff_count = 0 + diffs = [] + for i in range( len( history_data ) ): + if not re.match( local_file[i].rstrip( '\r\n' ), history_data[i].rstrip( '\r\n' ) ): + line_diff_count += 1 + diffs.append( 'Regular Expression: %s\nData file : %s' % ( local_file[i].rstrip( '\r\n' ), history_data[i].rstrip( '\r\n' ) ) ) + if line_diff_count > lines_diff: + raise AssertionError, "Regular expression did not match data file (allowed variants=%i):\n%s" % ( lines_diff, "".join( diffs ) ) + + def files_re_match_multiline( self, file1, file2, attributes=None ): + """Checks the contents of 2 files for differences using re.match in multiline mode""" + local_file = open( file1, 'U' ).read() #regex file + if attributes and attributes.sort: + history_data = open( file2, 'U' ).readlines() + history_data.sort() + history_data = ''.join( history_data ) + else: + history_data = open( file2, 'U' ).read() + #lines_diff not applicable to multiline matching + assert re.match( local_file, history_data, re.MULTILINE ), "Multiline Regular expression did not match data file" def get_filename( self, filename ): full = os.path.join( self.file_dir, filename) @@ -541,7 +590,7 @@ hid = elem.get('hid') hids.append(hid) return hids - def verify_dataset_correctness( self, filename, hid=None, wait=True, maxseconds=120, sort=False ): + def verify_dataset_correctness( self, filename, hid=None, wait=True, maxseconds=120, attributes=None ): """Verifies that the attributes and contents of a history item meet expectations""" if wait: self.wait( maxseconds=maxseconds ) #wait for job to finish @@ -576,13 +625,24 @@ data = self.last_page() file( temp_name, 'wb' ).write(data) try: - self.files_diff( local_name, temp_name, sort=sort ) + if attributes and 'compare' in attributes: + compare = attributes.compare + else: + compare = 'diff' + if compare == 'diff': + self.files_diff( local_name, temp_name, attributes=attributes ) + elif compare == 're_match': + self.files_re_match( local_name, temp_name, attributes=attributes ) + elif compare == 're_match_multiline': + self.files_re_match_multiline( local_name, temp_name, attributes=attributes ) + else: + raise Exception, 'Unimplemented Compare type: %s' % compare except AssertionError, err: - os.remove(temp_name) - errmsg = 'History item %s different than expected, difference:\n' % hid + errmsg = 'History item %s different than expected, difference (using %s):\n' % ( hid, compare ) errmsg += str( err ) raise AssertionError( errmsg ) - os.remove(temp_name) + finally: + os.remove( temp_name ) def verify_composite_datatype_file_content( self, file_name, hda_id ): local_name = self.get_filename( file_name ) temp_name = self.get_filename( 'temp_%s' % file_name ) diff -r 45cfcab6aed7 -r 3563fade2c86 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Fri Mar 05 12:55:51 2010 -0500 +++ b/test/functional/test_toolbox.py Fri Mar 05 17:21:16 2010 -0500 @@ -66,13 +66,13 @@ self.assertTrue( data_list ) elem_index = 0 - len( testdef.outputs ) for output_tuple in testdef.outputs: - name, file, sort = output_tuple + name, outfile, attributes = output_tuple # Get the correct hid elem = data_list[ elem_index ] self.assertTrue( elem is not None ) elem_hid = elem.get( 'hid' ) elem_index += 1 - self.verify_dataset_correctness( file, hid=elem_hid, maxseconds=testdef.maxseconds, sort=sort ) + self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes ) self.delete_history( id=self.security.encode_id( latest_history.id ) ) def __expand_grouping( self, tool_inputs, declared_inputs, prefix='' ):

1 0

[hg] galaxy 3488: Import some math functions in 'Compute express...
by Greg Von Kuster 08 Mar '10

08 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/45cfcab6aed7 changeset: 3488:45cfcab6aed7 user: gua110 date: Fri Mar 05 12:55:51 2010 -0500 description: Import some math functions in 'Compute expression' tool. diffstat: tools/stats/column_maker.py | 1 + 1 files changed, 1 insertions(+), 0 deletions(-) diffs (11 lines): diff -r b4dc8ea68ac7 -r 45cfcab6aed7 tools/stats/column_maker.py --- a/tools/stats/column_maker.py Fri Mar 05 10:13:36 2010 -0500 +++ b/tools/stats/column_maker.py Fri Mar 05 12:55:51 2010 -0500 @@ -6,6 +6,7 @@ from galaxy import eggs from galaxy.tools import validation from galaxy.datatypes import metadata +from math import log,exp,sqrt,ceil,floor assert sys.version_info[:2] >= ( 2, 4 )

1 0

[hg] galaxy 3487: Make fastqAggregator a new style class.
by Greg Von Kuster 08 Mar '10

08 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b4dc8ea68ac7 changeset: 3487:b4dc8ea68ac7 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Mar 05 10:13:36 2010 -0500 description: Make fastqAggregator a new style class. diffstat: lib/galaxy_utils/sequence/fastq.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 1cd52787c0bb -r b4dc8ea68ac7 lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py Fri Mar 05 09:09:26 2010 -0500 +++ b/lib/galaxy_utils/sequence/fastq.py Fri Mar 05 10:13:36 2010 -0500 @@ -264,7 +264,7 @@ FASTQ_FORMATS[ format.format ] = format -class fastqAggregator(): +class fastqAggregator( object ): VALID_FORMATS = FASTQ_FORMATS.keys() def __init__( self, ): self.ascii_values_used = [] #quick lookup of all ascii chars used

1 0

[hg] galaxy 3486: Handle dialog box overflow gracefully by scrol...
by Greg Von Kuster 08 Mar '10

08 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/1cd52787c0bb changeset: 3486:1cd52787c0bb user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Mar 05 09:09:26 2010 -0500 description: Handle dialog box overflow gracefully by scrolling body; this fix makes it possible to place item selection grids in dialog boxes without poor overflow. Also fixed msg when displaying an empty history. diffstat: static/june_2007_style/blue/panel_layout.css | 3 ++- static/june_2007_style/panel_layout.css.tmpl | 8 +++++++- templates/base_panels.mako | 2 +- templates/history/display.mako | 2 +- 4 files changed, 11 insertions(+), 4 deletions(-) diffs (56 lines): diff -r ef90fbe0eda1 -r 1cd52787c0bb static/june_2007_style/blue/panel_layout.css --- a/static/june_2007_style/blue/panel_layout.css Thu Mar 04 18:33:11 2010 -0500 +++ b/static/june_2007_style/blue/panel_layout.css Fri Mar 05 09:09:26 2010 -0500 @@ -27,7 +27,8 @@ .dialog-box-container{position:relative;margin-top:80px;margin-right:auto;margin-left:auto;} .dialog-box-wrapper{position:relative;padding:1em;background-color:rgba(0,0,0,0.5);-moz-border-radius:1em;-webkit-border-radius:1em;} .dialog-box{border:solid #999 1px;background:white;z-index:80000;} -.dialog-box .body,.dialog-box .buttons{padding:5px;} +.dialog-box .body{padding:5px;overflow:auto;max-height:500px;} +.dialog-box .buttons{padding:5px;} .panel-error-message,.panel-warning-message,.panel-done-message,.panel-info-message{height:24px;line-height:24px;color:#303030;padding:0px;padding-left:26px;background-color:#FFCCCC;background-image:url(error_small.png);background-repeat:no-repeat;background-position:6px 50%;} .panel-warning-message{background-image:url(warn_small.png);background-color:#FFFFCC;} .panel-done-message{background-image:url(done_small.png);background-color:#CCFFCC;} diff -r ef90fbe0eda1 -r 1cd52787c0bb static/june_2007_style/panel_layout.css.tmpl --- a/static/june_2007_style/panel_layout.css.tmpl Thu Mar 04 18:33:11 2010 -0500 +++ b/static/june_2007_style/panel_layout.css.tmpl Fri Mar 05 09:09:26 2010 -0500 @@ -190,7 +190,13 @@ z-index: 80000; } -.dialog-box .body, .dialog-box .buttons { +.dialog-box .body { + padding: 5px; + overflow: auto; + max-height: 500px; +} + +.dialog-box .buttons { padding: 5px; } diff -r ef90fbe0eda1 -r 1cd52787c0bb templates/base_panels.mako --- a/templates/base_panels.mako Thu Mar 04 18:33:11 2010 -0500 +++ b/templates/base_panels.mako Fri Mar 05 09:09:26 2010 -0500 @@ -314,7 +314,7 @@ <div class="unified-panel-header"> <div class="unified-panel-header-inner"><span class='title'>${title}</span></div> </div> - <div class="body" style="max-height: 600px;">${content}</div> + <div class="body">${content}</div> <div> <div class="buttons" style="display: none; float: right;"></div> <div class="extra_buttons" style="display: none; padding: 5px;"></div> diff -r ef90fbe0eda1 -r 1cd52787c0bb templates/history/display.mako --- a/templates/history/display.mako Thu Mar 04 18:33:11 2010 -0500 +++ b/templates/history/display.mako Fri Mar 05 09:09:26 2010 -0500 @@ -277,7 +277,7 @@ </table> <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> %endif - ${_("Your history is empty. Click 'Get Data' on the left pane to start")} + ${_("This history is empty.")} </div> </%def> \ No newline at end of file

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[hg] galaxy 3485: Add boxplot tool to tool_conf.xml.main
by Greg Von Kuster 08 Mar '10

08 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ef90fbe0eda1 changeset: 3485:ef90fbe0eda1 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Mar 04 18:33:11 2010 -0500 description: Add boxplot tool to tool_conf.xml.main diffstat: tool_conf.xml.main | 1 + 1 files changed, 1 insertions(+), 0 deletions(-) diffs (11 lines): diff -r d1900a25eb45 -r ef90fbe0eda1 tool_conf.xml.main --- a/tool_conf.xml.main Thu Mar 04 16:16:42 2010 -0500 +++ b/tool_conf.xml.main Thu Mar 04 18:33:11 2010 -0500 @@ -119,6 +119,7 @@ <tool file="plotting/histogram2.xml" /> <tool file="plotting/scatterplot.xml" /> <tool file="plotting/xy_plot.xml" /> + <tool file="plotting/boxplot.xml" /> <tool file="visualization/GMAJ.xml" /> <tool file="visualization/build_ucsc_custom_track.xml" /> </section>

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[hg] galaxy 3484: Better handling of workflow step annotations.
by Greg Von Kuster 08 Mar '10

08 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/d1900a25eb45 changeset: 3484:d1900a25eb45 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Mar 04 16:16:42 2010 -0500 description: Better handling of workflow step annotations. diffstat: static/scripts/galaxy.workflow_editor.canvas.js | 8 +++++++- templates/workflow/editor.mako | 7 +++---- 2 files changed, 10 insertions(+), 5 deletions(-) diffs (43 lines): diff -r c349f517ffb8 -r d1900a25eb45 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Thu Mar 04 13:55:21 2010 -0500 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Thu Mar 04 16:16:42 2010 -0500 @@ -308,6 +308,7 @@ this.tool_state = data.tool_state; this.form_html = data.form_html; this.tool_errors = data.tool_errors; + this.annotation = data['annotation']; if ( this.tool_errors ) { el.addClass( "tool-node-error" ); } else { @@ -447,7 +448,12 @@ // If active form has changed, save it if (this.active_form_has_changes) { this.has_changes = true; - $("#right-content").find("form").submit(); + // Get annotation and add to form. + var annotation = $("textarea[name=annotation]").val(); + var tool_form = $("#right-content").find("form"); + tool_form.append( "<input type='hidden' name='annotation' value='"+annotation+"' />" ); + // Submit form. + tool_form.submit(); this.active_form_has_changes = false; } }, diff -r c349f517ffb8 -r d1900a25eb45 templates/workflow/editor.mako --- a/templates/workflow/editor.mako Thu Mar 04 13:55:21 2010 -0500 +++ b/templates/workflow/editor.mako Thu Mar 04 16:16:42 2010 -0500 @@ -367,11 +367,10 @@ </div> \ </div> \ </div>"); - // When metadata is changed, update node and set workflow changes flag. + // See above comment: this is necessary to handle autosaving. var textarea = $(metadata_div).find("textarea"); - textarea.change( function () { - node.annotation = $(this).val(); - workflow.has_changes = true; + textarea.focus( function () { + workflow.active_form_has_changes = true; }); $("#right-content").find(".toolForm").after( metadata_div ); }

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