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galaxy-dist commit e95e14f5e7a0: Fix for the issue where multiple of the same action on separate outputs of a single tool were being overwritten as one.
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannonbaker(a)me.com> # Date 1282824612 14400 # Node ID e95e14f5e7a0db167a276570495e38f044b17092 # Parent 170229de46ca0b9ca21ea555d5085dd5224dcd79 Fix for the issue where multiple of the same action on separate outputs of a single tool were being overwritten as one. --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -341,16 +341,17 @@ class ActionBox(object): for key, val in incoming.iteritems(): if key.startswith('pja'): sp = key.split('__') + ao_key = sp[2] + sp[1] # flag / output_name / pjatype / desc - if not sp[2] in npd: - npd[sp[2]] = {'action_type' : sp[2], + if not ao_key in npd: + npd[ao_key] = {'action_type' : sp[2], 'output_name' : sp[1], 'action_arguments' : {}} if len(sp) > 3: if sp[3] == 'output_name': - npd[sp[2]]['output_name'] = val + npd[ao_key]['output_name'] = val else: - npd[sp[2]]['action_arguments'][sp[3]] = val + npd[ao_key]['action_arguments'][sp[3]] = val else: # Not pja stuff. pass --- a/static/scripts/galaxy.workflow_editor.canvas.js +++ b/static/scripts/galaxy.workflow_editor.canvas.js @@ -413,8 +413,8 @@ function Workflow( canvas_container ) { output_name : act.output_name, action_arguments : act.action_arguments } - post_job_actions[ act.type + act.output_name ] = null; - post_job_actions[ act.type + act.output_name ] = pja; + post_job_actions[ act.action_type + act.output_name ] = null; + post_job_actions[ act.action_type + act.output_name ] = pja; }); } if (!node.workflow_outputs){

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galaxy-dist commit d36d759bce05: Fix left padding issues on the edit attributes form
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1282674785 14400 # Node ID d36d759bce05d7cd6db99b115ae8ebb549e09ce7 # Parent 5d3e57e28fb7fa524a47d3a9b7e99f73ebca6676 Fix left padding issues on the edit attributes form --- a/templates/dataset/edit_attributes.mako +++ b/templates/dataset/edit_attributes.mako @@ -82,11 +82,13 @@ </form><form name="auto_detect" action="${h.url_for( controller='root', action='edit' )}" method="post"><input type="hidden" name="id" value="${data.id}"/> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="submit" name="detect" value="${_('Auto-detect')}"/> - </div> - <div class="toolParamHelp" style="clear: both;"> - This will inspect the dataset and attempt to correct the above column values if they are not accurate. + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="submit" name="detect" value="${_('Auto-detect')}"/> + </div> + <div class="toolParamHelp" style="clear: both;"> + This will inspect the dataset and attempt to correct the above column values if they are not accurate. + </div></div></form> %if data.missing_meta(): @@ -190,9 +192,9 @@ <form name="copy_hda" action="${h.url_for( controller='dataset', action='copy_datasets', source_dataset_ids=data.id, target_history_ids=data.history_id )}" method="post"><div class="form-row"><input type="submit" name="change" value="Copy history item"/> - </div> - <div class="toolParamHelp" style="clear: both;"> - Make a copy of this history item in your current history or any of your active histories. + <div class="toolParamHelp" style="clear: both;"> + Make a copy of this history item in your current history or any of your active histories. + </div></div></form></div>

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galaxy-dist commit 5d3e57e28fb7: Enhance grid framework to enable custom column sorting. Sort criteria are now mapped to a column, and the column defines the sorting to be done on the grid query. Default sorting behavior has not changed. In addition, column's model_class attribute now defaults to the grid's model_class; this should make column definitions more intuitive and shorter.
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1282595659 14400 # Node ID 5d3e57e28fb7fa524a47d3a9b7e99f73ebca6676 # Parent 60448575467fef8f6a42d83906ee2a622511c541 Enhance grid framework to enable custom column sorting. Sort criteria are now mapped to a column, and the column defines the sorting to be done on the grid query. Default sorting behavior has not changed. In addition, column's model_class attribute now defaults to the grid's model_class; this should make column definitions more intuitive and shorter. Used custom sorting functionality to enable (a) case-insensitive sorting of text fields and (b) case-insensitive sorting of published item by username. --- a/templates/history/list_published.mako +++ b/templates/history/list_published.mako @@ -28,7 +28,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${unicode( grid, 'utf-8' )} + ${h.to_unicode( grid )} </div></div> --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -107,14 +107,14 @@ class HistoryDatasetAssociationListGrid( title = "Saved Datasets" model_class = model.HistoryDatasetAssociation template='/dataset/grid.mako' - default_sort_key = "-create_time" + default_sort_key = "-update_time" columns = [ - grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation, + grids.TextColumn( "Name", key="name", # Link name to dataset's history. - link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced", attach_popup=True ), + 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", key="tags", model_class=model.HistoryDatasetAssociation, model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), StatusColumn( "Status", key="deleted", attach_popup=False ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -38,16 +38,15 @@ class HistoryListGrid( grids.Grid ): title = "Saved Histories" model_class = model.History template='/history/grid.mako' - default_sort_key = "-create_time" + default_sort_key = "-update_time" columns = [ - NameColumn( "Name", key="name", model_class=model.History, + NameColumn( "Name", key="name", link=( lambda history: iff( history.deleted, None, dict( operation="Switch", id=history.id ) ) ), attach_popup=True, filterable="advanced" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.History, \ - model_tag_association_class=model.HistoryTagAssociation, \ + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, \ filterable="advanced", grid_name="HistoryListGrid" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. @@ -130,10 +129,10 @@ class HistoryAllPublishedGrid( grids.Gri default_filter = dict( public_url="All", username="All", tags="All" ) use_async = True columns = [ - NameURLColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), - grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.History, model_annotation_association_class=model.HistoryAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.History, model_tag_association_class=model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), + NameURLColumn( "Name", key="name", filterable="advanced" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.HistoryAnnotationAssociation, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -37,8 +37,8 @@ class StoredWorkflowListGrid( grids.Grid default_filter = { "name" : "All", "tags": "All" } default_sort_key = "-update_time" columns = [ - grids.TextColumn( "Name", key="name", model_class=model.StoredWorkflow, attach_popup=True, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="StoredWorkflowListGrid" ), + grids.TextColumn( "Name", key="name", attach_popup=True, filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", "tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="StoredWorkflowListGrid" ), StepsColumn( "Steps" ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), @@ -67,10 +67,10 @@ class StoredWorkflowAllPublishedGrid( gr default_filter = dict( public_url="All", username="All", tags="All" ) use_async = True columns = [ - grids.PublicURLColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), - grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.StoredWorkflow, model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.StoredWorkflow, model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), + grids.PublicURLColumn( "Name", key="name", filterable="advanced" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/templates/visualization/list_published.mako +++ b/templates/visualization/list_published.mako @@ -28,7 +28,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${unicode( grid, 'utf-8' )} + ${h.to_unicode( grid )} </div></div> --- a/templates/workflow/list_published.mako +++ b/templates/workflow/list_published.mako @@ -28,7 +28,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${unicode( grid, 'utf-8' )} + ${h.to_unicode( grid )} </div></div> --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -12,11 +12,11 @@ class VisualizationListGrid( grids.Grid default_sort_key = "-update_time" default_filter = dict( title="All", deleted="False", tags="All", sharing="All" ) columns = [ - grids.TextColumn( "Title", key="title", model_class=model.Visualization, attach_popup=True, + grids.TextColumn( "Title", key="title", attach_popup=True, link=( lambda item: dict( controller="tracks", action="browser", id=item.id ) ) ), - grids.TextColumn( "Dbkey", key="dbkey", model_class=model.Visualization ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Visualization, filterable="advanced", sortable=False ), + grids.TextColumn( "Dbkey", key="dbkey" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] @@ -47,10 +47,10 @@ class VisualizationAllPublishedGrid( gri default_sort_key = "-update_time" default_filter = dict( title="All", username="All" ) columns = [ - grids.PublicURLColumn( "Title", key="title", model_class=model.Visualization, filterable="advanced" ), - grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Visualization, model_annotation_association_class=model.VisualizationAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationAllPublishedGrid" ), + grids.PublicURLColumn( "Title", key="title", filterable="advanced" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.VisualizationAnnotationAssociation, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/templates/page/index.mako +++ b/templates/page/index.mako @@ -15,7 +15,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${grid} + ${h.to_unicode( grid )} <br><br><h2>Pages shared with you by others</h2> --- a/lib/galaxy/web/controllers/page.py +++ b/lib/galaxy/web/controllers/page.py @@ -25,11 +25,11 @@ class PageListGrid( grids.Grid ): default_filter = { "published" : "All", "tags" : "All", "title" : "All", "sharing" : "All" } default_sort_key = "-create_time" columns = [ - grids.TextColumn( "Title", key="title", model_class=model.Page, attach_popup=True, filterable="advanced" ), + grids.TextColumn( "Title", key="title", attach_popup=True, filterable="advanced" ), URLColumn( "Public URL" ), - grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Page, model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] @@ -61,10 +61,10 @@ class PageAllPublishedGrid( grids.Grid ) default_sort_key = "-update_time" default_filter = dict( title="All", username="All" ) columns = [ - grids.PublicURLColumn( "Title", key="title", model_class=model.Page, filterable="advanced" ), - grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Page, model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), + grids.PublicURLColumn( "Title", key="title", filterable="advanced" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( @@ -107,12 +107,12 @@ class HistorySelectionGrid( ItemSelectio title = "Saved Histories" model_class = model.History columns = [ - ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.History, model_tag_association_class=model.HistoryTagAssociation, filterable="advanced"), + ItemSelectionGrid.NameColumn( "Name", key="name", filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -130,12 +130,12 @@ class HistoryDatasetAssociationSelection title = "Saved Datasets" model_class = model.HistoryDatasetAssociation columns = [ - ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.HistoryDatasetAssociation, model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), + ItemSelectionGrid.NameColumn( "Name", key="name", filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.HistoryDatasetAssociation, filterable="advanced", sortable=False, visible=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -155,12 +155,12 @@ class WorkflowSelectionGrid( ItemSelecti title = "Saved Workflows" model_class = model.StoredWorkflow columns = [ - ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.StoredWorkflow, model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced"), + ItemSelectionGrid.NameColumn( "Name", key="name", filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.StoredWorkflow, filterable="advanced", sortable=False, visible=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -175,12 +175,12 @@ class PageSelectionGrid( ItemSelectionGr title = "Saved Pages" model_class = model.Page columns = [ - grids.TextColumn( "Title", key="title", model_class=model.Page, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced"), + grids.TextColumn( "Title", key="title", filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False, visible=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -195,10 +195,10 @@ class VisualizationSelectionGrid( ItemSe title = "Saved Visualizations" model_class = model.Visualization columns = [ - grids.TextColumn( "Title", key="title", model_class=model.Visualization, filterable="advanced" ), - grids.TextColumn( "Type", key="type", model_class=model.Visualization ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Visualization, filterable="advanced", sortable=False ), + grids.TextColumn( "Title", key="title", filterable="advanced" ), + grids.TextColumn( "Type", key="type" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] columns.append( @@ -299,8 +299,8 @@ class PageController( BaseController, Sh return self.sharing( trans, **kwargs ) session.flush() - # Build grid HTML and make sure to encode in utf-8 to support unicode characters. - grid = unicode( self._page_list( trans, *args, **kwargs ), 'utf-8' ) + # Build grid HTML. + grid = self._page_list( trans, *args, **kwargs ) # Build list of pages shared with user. shared_by_others = trans.sa_session \ @@ -316,7 +316,7 @@ class PageController( BaseController, Sh @web.expose def list_published( self, trans, *args, **kwargs ): - grid = unicode( self._all_published_list( trans, *args, **kwargs ), 'utf-8' ) + grid = self._all_published_list( trans, *args, **kwargs ) if 'async' in kwargs: return grid else: --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -4,6 +4,7 @@ from galaxy.web.framework.helpers import from galaxy.web import url_for from galaxy.util.json import from_json_string, to_json_string from galaxy.util.odict import odict +from galaxy.web.framework.helpers import to_unicode import sys, logging, math @@ -41,12 +42,25 @@ class Grid( object ): if operation.allow_multiple: self.has_multiple_item_operations = True break + + # If a column does not have a model class, set the column's model class + # to be the grid's model class. + for column in self.columns: + if not column.model_class: + column.model_class = self.model_class + def __call__( self, trans, **kwargs ): + # + # Get basics. + # webapp = kwargs.get( 'webapp', 'galaxy' ) status = kwargs.get( 'status', None ) message = kwargs.get( 'message', None ) + + # # Build a base filter and sort key that is the combination of the saved state and defaults. # Saved state takes preference over defaults. + # base_filter = {} if self.default_filter: # default_filter is a dictionary that provides a default set of filters based on the grid's columns. @@ -70,8 +84,11 @@ class Grid( object ): use_default_filter = False if use_default_filter_str: use_default_filter = ( use_default_filter_str.lower() == 'true' ) + + # # Process filtering arguments to (a) build a query that represents the filter and (b) builds a - # dictionary that denotes the current filter. + # dictionary that denotes the current filter. + # cur_filter_dict = {} for column in self.columns: if column.key: @@ -134,23 +151,39 @@ class Grid( object ): if not isinstance( column_filter, basestring ): column_filter = unicode(column_filter) extra_url_args[ "f-" + column.key ] = column_filter.encode("utf-8") + + # # Process sort arguments. + # sort_key = None if 'sort' in kwargs: sort_key = kwargs['sort'] elif base_sort_key: sort_key = base_sort_key - if sort_key: + + if sort_key: if sort_key.startswith( "-" ): - # Can't use lower() on timestamp or integer objects, so func.lower() is not used here... - query = query.order_by( self.model_class.table.c.get( sort_key[1:] ).desc() ) + ascending = False + column_key = sort_key[1:] else: - # See reason for not using lower() to do case-insensitive sorting. - query = query.order_by( self.model_class.table.c.get( sort_key ).asc() ) - extra_url_args['sort'] = sort_key + ascending = True + column_key = sort_key + + # Sort key is a column key. + for column in self.columns: + if column.key == column_key: + query = column.sort( query, ascending ) + break + extra_url_args['sort'] = sort_key + + # # There might be a current row + # current_item = self.get_current_item( trans, **kwargs ) + + # # Process page number. + # if self.use_paging: if 'page' in kwargs: if kwargs['page'] == 'all': @@ -175,7 +208,10 @@ class Grid( object ): # Defaults. page_num = 1 num_pages = 1 + + # # Preserve grid state: save current filter and sort key. + # if self.preserve_state: pref_name = unicode( self.__class__.__name__ + self.cur_filter_pref_name ) trans.get_user().preferences[pref_name] = unicode( to_json_string( cur_filter_dict ) ) @@ -191,7 +227,10 @@ class Grid( object ): params['async'] = ( 'async' in kwargs ) params['webapp'] = webapp trans.log_action( trans.get_user(), unicode( "grid.view" ), context, params ) + + # # Render grid. + # def url( *args, **kwargs ): # Only include sort/filter arguments if not linking to another # page. This is a bit of a hack. @@ -211,9 +250,14 @@ class Grid( object ): else: new_kwargs[ 'id' ] = trans.security.encode_id( id ) return url_for( **new_kwargs ) - use_panels = ( 'use_panels' in kwargs ) and ( kwargs['use_panels'] in [ True, 'True', 'true' ] ) - async_request = ( ( self.use_async ) and ( 'async' in kwargs ) and ( kwargs['async'] in [ True, 'True', 'true'] ) ) - return trans.fill_template( iff( async_request, self.async_template, self.template), + use_panels = ( kwargs.get( 'use_panels', False ) in [ True, 'True', 'true' ] ) + async_request = ( ( self.use_async ) and ( kwargs.get( 'async', False ) in [ True, 'True', 'true'] ) ) + # Currently, filling the template returns a str object; this requires decoding the string into a + # unicode object within mako templates. What probably should be done is to return the template as + # utf-8 unicode; however, this would require encoding the object as utf-8 before returning the grid + # results via a controller method, which is require substantial changes. Hence, for now, return grid + # as str. + return trans.fill_template( iff( async_request, self.async_template, self.template ), grid=self, query=query, cur_page_num = page_num, @@ -258,11 +302,14 @@ class Grid( object ): return query class GridColumn( object ): - def __init__( self, label, grid=None, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, ncells=1, - # Valid values for filterable are ['standard', 'advanced', None] - filterable=None, sortable=True ): + def __init__( self, label, key=None, model_class=None, method=None, format=None, \ + link=None, attach_popup=False, visible=True, ncells=1, \ + # Valid values for filterable are ['standard', 'advanced', None] + filterable=None, sortable=True ): + """ + Create a grid column. + """ self.label = label - self.grid = grid self.key = key self.model_class = model_class self.method = method @@ -272,12 +319,9 @@ class GridColumn( object ): self.visible = visible self.ncells = ncells self.filterable = filterable - # Currently can only sort of columns that have a database - # representation, not purely derived. - if self.key and sortable: - self.sortable = True - else: - self.sortable = False + # Column must have a key to be sortable. + self.sortable = ( self.key is not None and sortable ) + def get_value( self, trans, grid, item ): if self.method: value = getattr( grid, self.method )( trans, item ) @@ -288,10 +332,12 @@ class GridColumn( object ): if self.format: value = self.format( value ) return value + def get_link( self, trans, grid, item ): if self.link and self.link( item ): return self.link( item ) return None + def filter( self, trans, user, query, column_filter ): """ Modify query to reflect the column filter. """ if column_filter == "All": @@ -301,6 +347,7 @@ class GridColumn( object ): elif column_filter == "False": query = query.filter_by( **{ self.key: False } ) return query + def get_accepted_filters( self ): """ Returns a list of accepted filters for this column. """ accepted_filters_vals = [ "False", "True", "All" ] @@ -309,6 +356,15 @@ class GridColumn( object ): args = { self.key: val } accepted_filters.append( GridColumnFilter( val, args) ) return accepted_filters + + def sort( self, query, ascending ): + """ Sort query using this column. """ + if ascending: + query = query.order_by( self.model_class.table.c.get( self.key ).asc() ) + else: + query = query.order_by( self.model_class.table.c.get( self.key ).desc() ) + return query + class TextColumn( GridColumn ): """ Generic column that employs freetext and, hence, supports freetext, case-independent filtering. """ @@ -332,6 +388,14 @@ class TextColumn( GridColumn ): """ Returns a SQLAlchemy criterion derived for a single filter. Single filter is the most basic filter--usually a string--and cannot be a list. """ model_class_key_field = getattr( self.model_class, self.key ) return func.lower( model_class_key_field ).like( "%" + a_filter.lower() + "%" ) + + def sort( self, query, ascending ): + """ Sort column using case-insensitive alphabetical sorting. """ + if ascending: + query = query.order_by( func.lower ( self.model_class.table.c.get( self.key ) ).asc() ) + else: + query = query.order_by( func.lower( self.model_class.table.c.get( self.key ) ).desc() ) + return query class IntegerColumn( TextColumn ): """ @@ -357,7 +421,7 @@ class IntegerColumn( TextColumn ): class OwnerAnnotationColumn( TextColumn, UsesAnnotations ): """ Column that displays and filters item owner's annotations. """ - def __init__( self, col_name, key, model_class, model_annotation_association_class, filterable ): + def __init__( self, col_name, key, model_class=None, model_annotation_association_class=None, filterable=None ): GridColumn.__init__( self, col_name, key=key, model_class=model_class, filterable=filterable ) self.sortable = False self.model_annotation_association_class = model_annotation_association_class @@ -375,11 +439,9 @@ class OwnerAnnotationColumn( TextColumn, class CommunityTagsColumn( TextColumn ): """ Column that supports community tags. """ - def __init__( self, col_name, key, model_class, model_tag_association_class, filterable, grid_name=None ): - GridColumn.__init__( self, col_name, key=key, model_class=model_class, filterable=filterable ) + def __init__( self, col_name, key, model_class=None, model_tag_association_class=None, filterable=None, grid_name=None ): + GridColumn.__init__( self, col_name, key=key, model_class=model_class, filterable=filterable, sortable=False ) self.model_tag_association_class = model_tag_association_class - # Tags cannot be sorted. - self.sortable = False # Column-specific attributes. self.grid_name = grid_name def get_value( self, trans, grid, item ): @@ -464,6 +526,15 @@ class OwnerColumn( TextColumn ): """ Column that lists item's owner. """ def get_value( self, trans, grid, item ): return item.user.username + + def sort( self, query, ascending ): + """ Sort column using case-insensitive alphabetical sorting on item's username. """ + if ascending: + query = query.order_by( func.lower ( self.model_class.username ).asc() ) + else: + query = query.order_by( func.lower( self.model_class.username ).desc() ) + return query + class PublicURLColumn( TextColumn ): """ Column displays item's public URL based on username and slug. """ @@ -474,7 +545,7 @@ class PublicURLColumn( TextColumn ): # TODO: provide link to set username. return None elif not item.user.slug: - # TODO: provide link to set slg + # TODO: provide link to set slug. return None class DeletedColumn( GridColumn ): --- a/templates/page/list_published.mako +++ b/templates/page/list_published.mako @@ -28,6 +28,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${grid} - + ${h.to_unicode( grid )} + </div> + </div></%def> --- a/templates/visualization/list.mako +++ b/templates/visualization/list.mako @@ -13,7 +13,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${grid} + ${h.to_unicode( grid )} <br><br><h2>Visualizations shared with you by others</h2>

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galaxy-dist commit 7fa394981ef6: Bug fixes and basic zoom feature for mutation viz tool
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1282769259 14400 # Node ID 7fa394981ef6f8d079cd8dd776cba349baca958f # Parent 95915784818931029539fd058c328e45470d34c2 Bug fixes and basic zoom feature for mutation viz tool --- a/tools/mutation/visualize.py +++ b/tools/mutation/visualize.py @@ -85,8 +85,6 @@ def mainsvg(opts): total = int(row[start_col+4]) diff = int(row[start_col+5]) imp = int(row[start_col+6]) - - #print 'sample_index', sample_index, total if total: x = 16+(sample_index*(WIDTH+GAP)) y = 30+(count*(HEIGHT+GAP))

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galaxy-dist commit b1a970038273: added svg datatype
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1282753644 14400 # Node ID b1a9700382738ba805c20047f40541b06d33b04b # Parent d36d759bce05d7cd6db99b115ae8ebb549e09ce7 added svg datatype --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -105,6 +105,7 @@ <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/><datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/><datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/><datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/><datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/><datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>

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galaxy-dist commit 959157848189: (no commit message)
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1282769169 14400 # Node ID 95915784818931029539fd058c328e45470d34c2 # Parent b1a9700382738ba805c20047f40541b06d33b04b (no commit message) --- a/tools/mutation/visualize.xml +++ b/tools/mutation/visualize.xml @@ -1,9 +1,16 @@ <tool id="mutation_visualize" name="Mutation Visualization" version="1.0.0"><description></description> - <command interpreter="python">visualize.py --input-file=$input --output-file=$out_file1 $header_row</command> + <command interpreter="python">visualize.py --input-file=$input --output-file=$out_file1 --zoom=$zoom_value $header_row</command><inputs><param format="tabular" name="input" type="data" label="Compare sequences in"></param><param name="header_row" type="boolean" label="Header in dataset?" checked="yes" truevalue="" falsevalue="--noheaders"/> + <param name="zoom_value" type="select" label="Zoom"> + <option value="1">1x</option> + <option value="2">2x</option> + <option value="3">3x</option> + <option value="4">4x</option> + <option value="5">5x</option> + </param></inputs><outputs><data format="svg" name="out_file1" /> --- a/tools/mutation/visualize.py +++ b/tools/mutation/visualize.py @@ -17,21 +17,21 @@ import svgfig as svg COLS_PER_SAMPLE = 7 HEADER_COLS = 4 -SPACE_PAIRS = 0.8 -SPACE_SAMPLES = 1 +HEIGHT = 6 +WIDTH = 12 +BAR_WIDTH = 1.5 +GAP = 2 -HEIGHT = 4 -WIDTH = 8 colors = {'A':'blue', 'C':'green', 'G':'orange', 'T':'red'} bases = ['A', 'C', 'G', 'T' ] def mainsvg(opts): - s = svg.SVG('g') + s = svg.SVG('g', transform="translate(20,0)") # display legend - for i, b in enumerate(bases): + for i, b in enumerate( bases ): bt = svg.SVG("tspan", b, style="font-family:Verdana;font-size:3") s.append(svg.SVG("text", bt, x=12+(i*10), y=8, stroke="none", fill="black")) s.append(svg.SVG("rect", x=13+(i*10), y=5, width=4, height=3, @@ -71,10 +71,10 @@ def mainsvg(opts): #print 'position', position, ref, count # display positions - bt = svg.SVG("tspan", str(position), style="font-family:Verdana;font-size:3") - s.append(svg.SVG("text", bt, x=9, y=33+(count*5), stroke="none", fill="black")) - s.append(svg.SVG("rect", x=4, y=30+(count*5), width=10, height=4, - stroke='none', fill=colors[ref.upper()], fill_opacity=0.3)) + bt = svg.SVG("tspan", str(position), style="font-family:Verdana;font-size:4") + s.append(svg.SVG("text", bt, x=7, y=34+(count*(HEIGHT+GAP)), stroke="none", fill="black")) + s.append(svg.SVG("rect", x=0, y=30+(count*(HEIGHT+GAP)), width=14, height=HEIGHT, + stroke='none', fill=colors[ref.upper()], fill_opacity=0.2)) for sample_index in range(int((len(row)-HEADER_COLS)/COLS_PER_SAMPLE)): start_col = HEADER_COLS+(COLS_PER_SAMPLE*sample_index) @@ -88,10 +88,10 @@ def mainsvg(opts): #print 'sample_index', sample_index, total if total: - x = 16+(sample_index*10) - y = 30+(count*5) + x = 16+(sample_index*(WIDTH+GAP)) + y = 30+(count*(HEIGHT+GAP)) width = WIDTH - height = 4 + height = HEIGHT if imp == 1: fill_opacity = 0.1 @@ -104,18 +104,21 @@ def mainsvg(opts): stroke='none', fill='grey', fill_opacity=fill_opacity)) for base, value in enumerate([n_a, n_c, n_g, n_t]): width = int(math.ceil(value / total * WIDTH)) - s.append(svg.SVG("rect", x=x, y=y, width=width, height=1, + s.append(svg.SVG("rect", x=x, y=y, width=width, height=BAR_WIDTH, stroke='none', fill=colors[bases[base]], fill_opacity=0.6)) - y = y + 1 + y = y + BAR_WIDTH #print base, value, total, x, y, width count=count+1 - - w = str(int(700)) + "px" - h = str(int(1000)) + "px" - canv = svg.canvas(s, width=w, height=h, viewBox="0 0 200 300") + + #print x, y + + zoom = int(opts.zoom) + w = "%ipx" % (x*(10+zoom)) + h = "%ipx" % (y*(2+zoom)) + canv = svg.canvas(s, width=w, height=h, viewBox="0 0 %i %i" %(x+100, y+100)) canv.save(opts.output_file) @@ -123,6 +126,7 @@ if __name__ == '__main__': parser = optparse.OptionParser() parser.add_option('-i', '--input-file', dest='input_file', action='store') parser.add_option('-o', '--output-file', dest='output_file', action='store') + parser.add_option('-z', '--zoom', dest='zoom', action='store', default='1') parser.add_option('-n', '--noheaders', dest='header_row', action='store_false', default=True) (opts, args) = parser.parse_args() mainsvg(opts)

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galaxy-dist commit 7242f2dffed3: Fixed another bug in column join so it will handle filling empty columns properly
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1282338256 14400 # Node ID 7242f2dffed302ad6d0d727e43ede1ed65c39463 # Parent 8a3d3fba037061a818b4417978542ae7b71f2e1a Fixed another bug in column join so it will handle filling empty columns properly --- a/tools/new_operations/column_join.py +++ b/tools/new_operations/column_join.py @@ -241,10 +241,14 @@ def __main__(): new_split_line = split_line[:] split_line = [] for i, item in enumerate( new_split_line ): - if item: + col = i + 1 + if not item: + try: + split_line.append( fill_empty[ i + 1 ] ) + except KeyError: + split_line.append( item ) + else: split_line.append( item ) - else: - split_line.append( fill_empty[ i + 1 ] ) # add actual data to be output below if ''.join( split_line ): for col in cols: @@ -265,9 +269,11 @@ def __main__(): fout.write( '%s%s' % ( delimiter, delimiter.join( current_data ) ) ) elif current_data: fout.write( '%s%s%s' % ( current, delimiter, delimiter.join( current_data ) ) ) + last_lines = ''.join( current_lines ) + else: + last_lines = None last_loc = loc old_current = current - last_lines = ''.join( current_lines ) first_line = False # fill trailing empty columns for final line if last_loc < len( inputs ) - 1:

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galaxy-dist commit 9bcd722236bd: Refactoring of grid framework in preparation for enhancing sorting. Removed unused keyword 'encoded_sort_key' and made all GridColumn constructor keyword parameters explicit.
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1282492757 14400 # Node ID 9bcd722236bd7d74784d7317bbe53fa3f050d101 # Parent 3ab68d0ba173ea4b21317c79fdea907bd91f5a81 Refactoring of grid framework in preparation for enhancing sorting. Removed unused keyword 'encoded_sort_key' and made all GridColumn constructor keyword parameters explicit. --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -114,7 +114,7 @@ class HistoryDatasetAssociationListGrid( 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" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.HistoryDatasetAssociation, model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), StatusColumn( "Status", key="deleted", attach_popup=False ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -44,7 +44,9 @@ class HistoryListGrid( grids.Grid ): link=( lambda history: iff( history.deleted, None, dict( operation="Switch", id=history.id ) ) ), attach_popup=True, filterable="advanced" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), - grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="HistoryListGrid" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.History, \ + model_tag_association_class=model.HistoryTagAssociation, \ + filterable="advanced", grid_name="HistoryListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), @@ -131,7 +133,7 @@ class HistoryAllPublishedGrid( grids.Gri NameURLColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.History, model_annotation_association_class=model.HistoryAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.History, model_tag_association_class=model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -70,7 +70,7 @@ class StoredWorkflowAllPublishedGrid( gr grids.PublicURLColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.StoredWorkflow, model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.StoredWorkflow, model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -15,7 +15,7 @@ class VisualizationListGrid( grids.Grid grids.TextColumn( "Title", key="title", model_class=model.Visualization, attach_popup=True, link=( lambda item: dict( controller="tracks", action="browser", id=item.id ) ) ), grids.TextColumn( "Dbkey", key="dbkey", model_class=model.Visualization ), - grids.IndividualTagsColumn( "Tags", "tags", model.Visualization, model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Visualization, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), @@ -50,7 +50,7 @@ class VisualizationAllPublishedGrid( gri grids.PublicURLColumn( "Title", key="title", model_class=model.Visualization, filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Visualization, model_annotation_association_class=model.VisualizationAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", "tags", model.Visualization, model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationAllPublishedGrid" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/lib/galaxy/web/controllers/page.py +++ b/lib/galaxy/web/controllers/page.py @@ -27,7 +27,8 @@ class PageListGrid( grids.Grid ): columns = [ grids.TextColumn( "Title", key="title", model_class=model.Page, attach_popup=True, filterable="advanced" ), URLColumn( "Public URL" ), - grids.IndividualTagsColumn( "Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Page, model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), @@ -63,7 +64,7 @@ class PageAllPublishedGrid( grids.Grid ) grids.PublicURLColumn( "Title", key="title", model_class=model.Page, filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Page, model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( @@ -107,7 +108,7 @@ class HistorySelectionGrid( ItemSelectio model_class = model.History columns = [ ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.History, model_tag_association_class=model.HistoryTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), @@ -130,7 +131,7 @@ class HistoryDatasetAssociationSelection model_class = model.HistoryDatasetAssociation columns = [ ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.HistoryDatasetAssociation, model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), @@ -155,7 +156,7 @@ class WorkflowSelectionGrid( ItemSelecti model_class = model.StoredWorkflow columns = [ ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced"), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.StoredWorkflow, model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), @@ -175,7 +176,7 @@ class PageSelectionGrid( ItemSelectionGr model_class = model.Page columns = [ grids.TextColumn( "Title", key="title", model_class=model.Page, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced"), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), @@ -196,7 +197,7 @@ class VisualizationSelectionGrid( ItemSe columns = [ grids.TextColumn( "Title", key="title", model_class=model.Visualization, filterable="advanced" ), grids.TextColumn( "Type", key="type", model_class=model.Visualization ), - grids.IndividualTagsColumn( "Tags", "tags", model.Visualization, model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Visualization, filterable="advanced", sortable=False ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -140,15 +140,14 @@ class Grid( object ): sort_key = kwargs['sort'] elif base_sort_key: sort_key = base_sort_key - encoded_sort_key = sort_key if sort_key: if sort_key.startswith( "-" ): # Can't use lower() on timestamp or integer objects, so func.lower() is not used here... query = query.order_by( self.model_class.table.c.get( sort_key[1:] ).desc() ) else: - # See reason for not using lower() to do case-insensitive search. + # See reason for not using lower() to do case-insensitive sorting. query = query.order_by( self.model_class.table.c.get( sort_key ).asc() ) - extra_url_args['sort'] = encoded_sort_key + extra_url_args['sort'] = sort_key # There might be a current row current_item = self.get_current_item( trans, **kwargs ) # Process page number. @@ -222,7 +221,6 @@ class Grid( object ): default_filter_dict=self.default_filter, cur_filter_dict=cur_filter_dict, sort_key=sort_key, - encoded_sort_key=encoded_sort_key, current_item=current_item, ids = kwargs.get( 'id', [] ), url = url, @@ -260,10 +258,11 @@ class Grid( object ): return query class GridColumn( object ): - def __init__( self, label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, ncells=1, + def __init__( self, label, grid=None, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, ncells=1, # Valid values for filterable are ['standard', 'advanced', None] filterable=None, sortable=True ): self.label = label + self.grid = grid self.key = key self.model_class = model_class self.method = method --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -255,7 +255,7 @@ } // Add sort argument to URL args. - url_args['sort'] = "${encoded_sort_key}"; + url_args['sort'] = "${sort_key}"; // Add async keyword to URL args. url_args['async'] = true;

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galaxy-dist commit 26a0b620490d: Quick fix to hide outputs until they're nicer.
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannonbaker(a)me.com> # Date 1282572262 14400 # Node ID 26a0b620490dd8698deb907ecaa540e7fa19a6ee # Parent d9e099daa8279880d5e054680ab28e8fc3064f77 Quick fix to hide outputs until they're nicer. --- a/templates/workflow/list.mako +++ b/templates/workflow/list.mako @@ -58,7 +58,6 @@ <td><div popupmenu="wf-${i}-popup"><a class="action-button" href="${h.url_for( action='editor', id=trans.security.encode_id(workflow.id) )}" target="_parent">Edit</a> - <a class="action-button" href="${h.url_for( action='tag_outputs', id=trans.security.encode_id(workflow.id) )}">Tag Outputs</a><a class="action-button" href="${h.url_for( controller='root', action='index', workflow_id=trans.security.encode_id(workflow.id) )}" target="_parent">Run</a><a class="action-button" href="${h.url_for( action='sharing', id=trans.security.encode_id(workflow.id) )}">Share or Publish</a><a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(workflow.id) )}">Clone</a> --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -132,7 +132,7 @@ make_popupmenu( $("#workflow-options-button"), { ##"Create New" : create_new_workflow_dialog, "Edit Attributes" : edit_workflow_attributes, - "Edit Workflow Outputs": edit_workflow_outputs, + ##"Edit Workflow Outputs": edit_workflow_outputs, "Layout": layout_editor, "Save" : save_current_workflow, ##"Load a Workflow" : load_workflow, @@ -399,7 +399,7 @@ } function show_form_for_tool( text, node ) { - $("#edit-attributes").hide(); + $('.right-content').hide(); $("#right-content").show().html( text ); // Add metadata form to tool. if (node) { --- a/templates/workflow/tag_outputs.mako +++ /dev/null @@ -1,161 +0,0 @@ -<%inherit file="/base.mako"/> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "jquery.autocomplete" )} - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - $( "#tool_form" ).submit(); - }); - }); - </script> -</%def> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "autocomplete_tagging" )} - <style type="text/css"> - div.toolForm{ - margin-top: 10px; - margin-bottom: 10px; - } - </style> -</%def> - -<% -from galaxy.tools.parameters import DataToolParameter, RuntimeValue -from galaxy.jobs.actions.post import ActionBox -%> - -<%def name="do_inputs( inputs, values, errors, prefix, step, other_values = None )"> - %if other_values is None: - <% other_values = values %> - %endif - %for input_index, input in enumerate( inputs.itervalues() ): - %if input.type == "repeat": - <div class="repeat-group"> - <div class="form-title-row"><b>${input.title_plural}</b></div> - <% repeat_values = values[input.name] %> - %for i in range( len( repeat_values ) ): - %if input.name in errors: - <% rep_errors = errors[input.name][i] %> - %else: - <% rep_errors = dict() %> - %endif - <div class="repeat-group-item"> - <% index = repeat_values[i]['__index__'] %> - <div class="form-title-row"><b>${input.title} ${i + 1}</b></div> - ${do_inputs( input.inputs, repeat_values[ i ], rep_errors, prefix + input.name + "_" + str(index) + "|", step, other_values )} - ## <div class="form-row"><input type="submit" name="${step.id}|${prefix}${input.name}_${i}_remove" value="Remove ${input.title} ${i+1}" /></div> - </div> - %endfor - ## <div class="form-row"><input type="submit" name="${step.id}|${prefix}${input.name}_add" value="Add new ${input.title}" /></div> - </div> - %elif input.type == "conditional": - <% group_values = values[input.name] %> - <% current_case = group_values['__current_case__'] %> - <% new_prefix = prefix + input.name + "|" %> - <% group_errors = errors.get( input.name, {} ) %> - ${row_for_param( input.test_param, group_values[ input.test_param.name ], other_values, group_errors, prefix, step )} - ${do_inputs( input.cases[ current_case ].inputs, group_values, group_errors, new_prefix, step, other_values )} - %else: - ${row_for_param( input, values[ input.name ], other_values, errors, prefix, step )} - %endif - %endfor -</%def> - -<%def name="row_for_param( param, value, other_values, error_dict, prefix, step )"> - ## -- ${param.name} -- ${step.state.inputs} -- - %if error_dict.has_key( param.name ): - <% cls = "form-row form-row-error" %> - %else: - <% cls = "form-row" %> - %endif - <div class="${cls}"> - <label>${param.get_label()}</label> - <div> - %if isinstance( param, DataToolParameter ): - %if ( prefix + param.name ) in step.input_connections_by_name: - <% - conn = step.input_connections_by_name[ prefix + param.name ] - %> - Output dataset '${conn.output_name}' from step ${int(conn.output_step.order_index)+1} - %else: - ## FIXME: Initialize in the controller - <% - if value is None: - value = other_values[ param.name ] = param.get_initial_value( t, other_values ) - %> - ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )} - <input type="hidden" name="${step.id}|__force_update__${prefix}${param.name}" value="true" /> - %endif - %elif isinstance( value, RuntimeValue ) or ( str(step.id) + '|__runtime__' + prefix + param.name ) in incoming: - ## On the first load we may see a RuntimeValue, so we write - ## an input field using the initial value for the param. - ## Subsequents posts will no longer have the runtime value - ## (since an actualy value will be posted) so we add a hidden - ## field so we know to continue drawing form for this param. - ## FIXME: This logic shouldn't be in the template. The - ## controller should go through the inputs on the first - ## load, fill in initial values where needed, and mark - ## all that are runtime modifiable in some way. - <% value = other_values[ param.name ] = param.get_initial_value( t, other_values ) %> - ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )} - <input type="hidden" name="${step.id}|__runtime__${prefix}${param.name}" value="true" /> - %else: - ${param.value_to_display_text( value, app )} - %endif - </div> - %if step.upgrade_messages and param.name in step.upgrade_messages: - <div class="warningmark">${step.upgrade_messages[param.name]}</div> - %endif - %if error_dict.has_key( param.name ): - <div style="color: red; font-weight: bold; padding-top: 1px; padding-bottom: 3px;"> - <div style="width: 300px;"><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${error_dict[param.name]}</span></div> - </div> - %endif - <div style="clear: both"></div> - </div> -</%def> - -<h2>Set outputs for workflow "${workflow.name}"</h2> -<p>Select the checkboxes for step outputs you would like to mark as whole-workflow outputs.</p> -%if has_upgrade_messages: -<div class="warningmessage"> - Problems were encourered when loading this workflow, likely due to tool - version changes. Missing parameter values have been replaced with default. - Please review the parameter values below. -</div> -%endif - -<form id="tool_form" name="tool_form" method="POST"> -## <input type="hidden" name="workflow_name" value="${workflow.name | h}" /> -%for i, step in enumerate( steps ): - %if step.type == 'tool': - <% tool = app.toolbox.tools_by_id[step.tool_id] %> - <input type="hidden" name="${step.id}|tool_state" value="${step.state.encode( tool, app )}"> - <div class="toolForm"> - <div class="toolFormTitle">Step ${int(step.order_index)+1}: ${tool.name}</div> - <div class="toolFormBody"> - % for output in tool.outputs: - <div class='form-row'> - %if step.workflow_outputs and output in [wf_output.output_name for wf_output in step.workflow_outputs]: - <p>${output} <input type="checkbox" name="${step.id}|otag|${output}" checked /></p> - %else: - <p>${output} <input type="checkbox" name="${step.id}|otag|${output}"/></p> - %endif - </div> - % endfor - % if step.annotations: - <hr/> - <div class='form-row'> - <label>Annotation:</label> ${step.annotations[0].annotation} - </div> - % endif - </div> - </div> - %endif -%endfor -<input type="submit" name="save_outputs" value="Save output settings" /> -</form>

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galaxy-dist commit 60448575467f: Merge.
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannonbaker(a)me.com> # Date 1282572917 14400 # Node ID 60448575467fef8f6a42d83906ee2a622511c541 # Parent 26a0b620490dd8698deb907ecaa540e7fa19a6ee # Parent 9bcd722236bd7d74784d7317bbe53fa3f050d101 Merge.

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