From ed992b3b28c7f6d9d637e82e88305b665733a50b Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Thu, 19 Nov 2015 21:03:30 -0500 Subject: [PATCH 01/24] A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name). --- .../mvc/collection/list-collection-creator.js | 6 +++--- .../list-of-pairs-collection-creator.js | 6 +++--- .../mvc/collection/pair-collection-creator.js | 10 +++++----- .../scripts/mvc/dataset/dataset-choice.js | 14 +++++++------- .../scripts/mvc/dataset/dataset-li-edit.js | 14 +++++++------- .../galaxy/scripts/mvc/dataset/dataset-li.js | 2 +- .../scripts/mvc/history/history-panel.js | 4 ++-- .../galaxy/scripts/mvc/history/multi-panel.js | 8 ++++---- client/galaxy/scripts/mvc/job/job-li.js | 18 +++++++++--------- client/galaxy/scripts/mvc/list/list-panel.js | 8 ++++---- .../galaxy/scripts/mvc/ui/ui-select-default.js | 2 +- .../scripts/mvc/groups/group-detail-view.js | 12 ++++++------ .../scripts/mvc/groups/group-listrow-view.js | 2 +- lib/galaxy/webapps/galaxy/controllers/admin.py | 14 +++++++------- .../webapps/galaxy/controllers/dataset.py | 4 ++-- .../galaxy/controllers/external_service.py | 5 ++++- lib/galaxy/webapps/galaxy/controllers/forms.py | 7 +++++-- .../webapps/galaxy/controllers/history.py | 4 ++-- .../webapps/galaxy/controllers/library.py | 4 ++-- .../galaxy/controllers/library_admin.py | 4 ++-- .../webapps/galaxy/controllers/request_type.py | 12 ++++++++---- .../galaxy/controllers/requests_admin.py | 8 +++++--- .../galaxy/controllers/requests_common.py | 7 +++++-- .../galaxy/controllers/visualization.py | 2 +- lib/galaxy/webapps/reports/controllers/jobs.py | 5 ++++- .../reports/controllers/sample_tracking.py | 7 +++++-- .../webapps/reports/controllers/workflows.py | 6 ++++-- lib/tool_shed/grids/admin_grids.py | 13 ++++++++----- lib/tool_shed/grids/repository_grids.py | 6 +++--- lib/tool_shed/grids/repository_review_grids.py | 12 ++++++++---- static/maps/mvc/history/multi-panel.js.map | 2 +- static/maps/mvc/ui/ui-select-default.js.map | 2 +- static/scripts/libs/jquery/jquery.dynatree.js | 2 +- .../mvc/collection/list-collection-creator.js | 2 +- .../list-of-pairs-collection-creator.js | 2 +- .../mvc/collection/pair-collection-creator.js | 2 +- static/scripts/mvc/dataset/dataset-choice.js | 2 +- static/scripts/mvc/dataset/dataset-li-edit.js | 2 +- static/scripts/mvc/dataset/dataset-li.js | 2 +- static/scripts/mvc/history/history-panel.js | 2 +- static/scripts/mvc/history/multi-panel.js | 2 +- static/scripts/mvc/job/job-li.js | 2 +- static/scripts/mvc/list/list-panel.js | 2 +- static/scripts/mvc/ui/ui-select-default.js | 2 +- 44 files changed, 142 insertions(+), 112 deletions(-) diff --git a/client/galaxy/scripts/mvc/collection/list-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-collection-creator.js index 48f849bb83c..f7dfbe6467a 100644 --- a/client/galaxy/scripts/mvc/collection/list-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/list-collection-creator.js @@ -43,7 +43,7 @@ var DatasetCollectionElementView = Backbone.View.extend( BASE_MVC.LoggableMixin //TODO: lots of unused space in the element - possibly load details and display them horiz. template : _.template([ '', - '<%= element.name %>', + '<%- element.name %>', '', '', '', diff --git a/client/galaxy/scripts/mvc/job/job-li.js b/client/galaxy/scripts/mvc/job/job-li.js index 1521c2c6796..3078f8414e5 100644 --- a/client/galaxy/scripts/mvc/job/job-li.js +++ b/client/galaxy/scripts/mvc/job/job-li.js @@ -121,7 +121,7 @@ JobListItemView.prototype.templates = (function(){ var elTemplate = BASE_MVC.wrapTemplate([ '
', - '
<%= model.id %>
', + '
<%- model.id %>
', // errors, messages, etc. '
', @@ -161,7 +161,7 @@ JobListItemView.prototype.templates = (function(){ // ' ', _l( 'Created' ), ': <%= new Date( job.create_time ).toString() %>, ', //'', - // ' (', _l( 'version' ), ': <%= view.tool.version %>)', + // ' (', _l( 'version' ), ': <%- view.tool.version %>)', //'' ], 'job' ); @@ -170,20 +170,20 @@ JobListItemView.prototype.templates = (function(){ '
', //'
', // '', - // '<%= view.tool.version %>', + // '<%- view.tool.version %>', //'
', '
', '<% _.each( view._labelInputMap(), function( input, label ){ %>', - '
', - '', + '
', + '', //TODO: input dataset name - '<%= input.content.name %>', + '<%- input.content.name %>', '
', '<% }) %>', '<% _.each( view._labelParamMap(), function( param, label ){ %>', - '
', - '', - '<%= param %>', + '
', + '', + '<%- param %>', '
', '<% }) %>', '
', diff --git a/client/galaxy/scripts/mvc/list/list-panel.js b/client/galaxy/scripts/mvc/list/list-panel.js index 6741b11d3e0..70dd7b06825 100644 --- a/client/galaxy/scripts/mvc/list/list-panel.js +++ b/client/galaxy/scripts/mvc/list/list-panel.js @@ -801,9 +801,9 @@ ListPanel.prototype.templates = (function(){ var controlsTemplate = BASE_MVC.wrapTemplate([ '
', '
', - '
<%= view.title %>
', + '
<%- view.title %>
', '
', - '
<%= view.subtitle %>
', + '
<%- view.subtitle %>
', // buttons, controls go here '
', // deleted msg, etc. @@ -942,9 +942,9 @@ ModelListPanel.prototype.templates = (function(){ '
', '
', //TODO: this is really the only difference - consider factoring titlebar out - '
<%= model.name %>
', + '
<%- model.name %>
', '
', - '
<%= view.subtitle %>
', + '
<%- view.subtitle %>
', '
', '
', diff --git a/client/galaxy/scripts/mvc/ui/ui-select-default.js b/client/galaxy/scripts/mvc/ui/ui-select-default.js index 61bc233be07..9b7a1c916c4 100644 --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -261,7 +261,7 @@ var View = Backbone.View.extend({ /** Template for select options */ _templateOption: function(options) { - return ''; + return ''; }, /** Template for select view diff --git a/client/toolshed/scripts/mvc/groups/group-detail-view.js b/client/toolshed/scripts/mvc/groups/group-detail-view.js index d0b6bd28b2a..c5825504e2a 100644 --- a/client/toolshed/scripts/mvc/groups/group-detail-view.js +++ b/client/toolshed/scripts/mvc/groups/group-detail-view.js @@ -56,7 +56,7 @@ var GroupDetailView = Backbone.View.extend({ templateRow: function() { return _.template([ '
', - '

<%= group.get("name") %>

', + '

<%= _.escape(group.get("name")) %>

', '

', 'A group of <%= group.get("members").length %> members with <%= group.get("repositories").length %> repositories and a total of <%= group.get("total_downloads") %> combined repository clones.

', @@ -71,10 +71,10 @@ var GroupDetailView = Backbone.View.extend({ '<% _.each(group.get("members"), function(member) { %>', '', '', - '<%= member.username %>', + '<%= _.escape(member.username) %>', '', '', - '<%= member.user_repos_count %>', + '<%= member.user_repos_count %>', '', '', '<%= member.time_created %>', @@ -101,16 +101,16 @@ var GroupDetailView = Backbone.View.extend({ '<% _.each(group.get("repositories"), function(repo) { %>', '', '', - '<%= repo.name %>', + '<%= _.escape(repo.name) %>', '', '', - '<%= repo.description %>', + '<%= _.escape(repo.description) %>', '', '', '<%= repo.times_downloaded %>', '', '', - '<%= repo.owner %>', + '<%= _.escape(repo.owner) %>', '', '', '<% _.each((repo.categories), function(cat) { %>', diff --git a/client/toolshed/scripts/mvc/groups/group-listrow-view.js b/client/toolshed/scripts/mvc/groups/group-listrow-view.js index 59c073907f0..7ffcf7c14d3 100644 --- a/client/toolshed/scripts/mvc/groups/group-listrow-view.js +++ b/client/toolshed/scripts/mvc/groups/group-listrow-view.js @@ -19,7 +19,7 @@ var GroupListRowView = Backbone.View.extend({ templateRow: function() { return _.template([ '">', - '"><%= group.get("name") %>', + '"><%= _.escape(group.get("name")) %>', // 'description', '<%= group.get("total_members") %>', '<%= group.get("total_repos") %>', diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py index 2dca3bf130b..48143bf925e 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -30,12 +30,12 @@ class UserListGrid( grids.Grid ): class EmailColumn( grids.TextColumn ): def get_value( self, trans, grid, user ): - return user.email + return escape(user.email) class UserNameColumn( grids.TextColumn ): def get_value( self, trans, grid, user ): if user.username: - return user.username + return escape(user.username) return 'not set' class StatusColumn( grids.GridColumn ): @@ -149,12 +149,12 @@ class RoleListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, role ): - return role.name + return escape(role.name) class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, role ): if role.description: - return role.description + return escape(role.description) return '' class TypeColumn( grids.TextColumn ): @@ -248,7 +248,7 @@ class GroupListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, group ): - return group.name + return escape(group.name) class StatusColumn( grids.GridColumn ): def get_value( self, trans, grid, group ): @@ -324,12 +324,12 @@ class QuotaListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, quota ): - return quota.name + return escape(quota.name) class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, quota ): if quota.description: - return quota.description + return escape(quota.description) return '' class AmountColumn( grids.TextColumn ): diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py index e41bee9ea68..3018a9fa3b5 100644 --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -29,7 +29,7 @@ class HistoryDatasetAssociationListGrid( grids.Grid ): # Custom columns for grid. class HistoryColumn( grids.GridColumn ): def get_value( self, trans, grid, hda): - return hda.history.name + return escape(hda.history.name) class StatusColumn( grids.GridColumn ): def get_value( self, trans, grid, hda ): @@ -1098,7 +1098,7 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses trans.sa_session.flush() hist_names_str = ", ".join( ['%s' % ( url_for( controller="history", action="switch_to_history", - hist_id=trans.security.encode_id( hist.id ) ), hist.name ) + hist_id=trans.security.encode_id( hist.id ) ), escape(hist.name) ) for hist in target_histories ] ) num_source = len( source_content_ids ) - invalid_contents num_target = len(target_histories) diff --git a/lib/galaxy/webapps/galaxy/controllers/external_service.py b/lib/galaxy/webapps/galaxy/controllers/external_service.py index 83aaf8836d1..c28e53d6476 100644 --- a/lib/galaxy/webapps/galaxy/controllers/external_service.py +++ b/lib/galaxy/webapps/galaxy/controllers/external_service.py @@ -4,6 +4,9 @@ from galaxy.web.base.controller import * from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.model.orm import * from galaxy import model, util +from galaxy import eggs +eggs.require("MarkupSafe") +from markupsafe import escape from galaxy.web.form_builder import * from .requests_common import invalid_id_redirect import logging, os @@ -14,7 +17,7 @@ class ExternalServiceGrid( grids.Grid ): # Custom column types class NameColumn( grids.TextColumn ): def get_value(self, trans, grid, external_service): - return external_service.name + return escape(external_service.name) class ExternalServiceTypeColumn( grids.TextColumn ): def get_value(self, trans, grid, external_service): try: diff --git a/lib/galaxy/webapps/galaxy/controllers/forms.py b/lib/galaxy/webapps/galaxy/controllers/forms.py index f901e42dcde..7f280741310 100644 --- a/lib/galaxy/webapps/galaxy/controllers/forms.py +++ b/lib/galaxy/webapps/galaxy/controllers/forms.py @@ -2,6 +2,9 @@ from galaxy.web.base.controller import * from galaxy.model.orm import * from galaxy.datatypes import sniff from galaxy import model, util +from galaxy import eggs +eggs.require("MarkupSafe") +from markupsafe import escape import logging, os, sys from galaxy.web.form_builder import * from galaxy.tools.parameters.basic import parameter_types @@ -18,10 +21,10 @@ class FormsGrid( grids.Grid ): # Custom column types class NameColumn( grids.TextColumn ): def get_value(self, trans, grid, form): - return form.latest_form.name + return escape(form.latest_form.name) class DescriptionColumn( grids.TextColumn ): def get_value(self, trans, grid, form): - return form.latest_form.desc + return escape(form.latest_form.desc) class TypeColumn( grids.TextColumn ): def get_value(self, trans, grid, form): return form.latest_form.type diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py index 6ce1bfef57a..33151db601c 100644 --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -27,7 +27,7 @@ log = logging.getLogger( __name__ ) class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, history ): - return history.get_display_name() + return escape(history.get_display_name()) class HistoryListGrid( grids.Grid ): @@ -142,7 +142,7 @@ class SharedHistoryListGrid( grids.Grid ): class SharedByColumn( grids.GridColumn ): def get_value( self, trans, grid, history ): - return history.user.email + return escape(history.user.email) # Grid definition title = "Histories shared with you by others" diff --git a/lib/galaxy/webapps/galaxy/controllers/library.py b/lib/galaxy/webapps/galaxy/controllers/library.py index e2dfc1b60eb..94d9c38249d 100644 --- a/lib/galaxy/webapps/galaxy/controllers/library.py +++ b/lib/galaxy/webapps/galaxy/controllers/library.py @@ -14,12 +14,12 @@ class LibraryListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, library ): - return library.name + return escape(library.name) class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, library ): if library.description: - return library.description + return escape(library.description) return '' # Grid definition diff --git a/lib/galaxy/webapps/galaxy/controllers/library_admin.py b/lib/galaxy/webapps/galaxy/controllers/library_admin.py index 8976d07b021..c71c5a6ade9 100644 --- a/lib/galaxy/webapps/galaxy/controllers/library_admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_admin.py @@ -15,11 +15,11 @@ log = logging.getLogger( __name__ ) class LibraryListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, library ): - return library.name + return escape(library.name) class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, library ): if library.description: - return library.description + return escape(library.description) return '' class StatusColumn( grids.GridColumn ): def get_value( self, trans, grid, library ): diff --git a/lib/galaxy/webapps/galaxy/controllers/request_type.py b/lib/galaxy/webapps/galaxy/controllers/request_type.py index 944e44e805c..27ccdd02b11 100644 --- a/lib/galaxy/webapps/galaxy/controllers/request_type.py +++ b/lib/galaxy/webapps/galaxy/controllers/request_type.py @@ -3,27 +3,31 @@ from __future__ import absolute_import from galaxy.web.base.controller import * from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.model.orm import * +from galaxy import eggs +eggs.require("MarkupSafe") +from markupsafe import escape from galaxy import model, util from galaxy.web.form_builder import * from .requests_common import invalid_id_redirect import logging, os + log = logging.getLogger( __name__ ) class RequestTypeGrid( grids.Grid ): # Custom column types class NameColumn( grids.TextColumn ): def get_value(self, trans, grid, request_type): - return request_type.name + return escape(request_type.name) class DescriptionColumn( grids.TextColumn ): def get_value(self, trans, grid, request_type): - return request_type.desc + return escape(request_type.desc) class RequestFormColumn( grids.TextColumn ): def get_value(self, trans, grid, request_type): - return request_type.request_form.name + return escape(request_type.request_form.name) class SampleFormColumn( grids.TextColumn ): def get_value(self, trans, grid, request_type): - return request_type.sample_form.name + return escape(request_type.sample_form.name) class ExternalServiceColumn( grids.IntegerColumn ): def get_value(self, trans, grid, request_type): if request_type.external_services: diff --git a/lib/galaxy/webapps/galaxy/controllers/requests_admin.py b/lib/galaxy/webapps/galaxy/controllers/requests_admin.py index 10665404401..489143b5980 100644 --- a/lib/galaxy/webapps/galaxy/controllers/requests_admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/requests_admin.py @@ -7,6 +7,8 @@ from galaxy import model, util from galaxy.web.form_builder import * from .requests_common import RequestsGrid, invalid_id_redirect from galaxy import eggs +eggs.require( "MarkupSafe" ) +from markupsafe import escape eggs.require("amqp") import amqp import logging, os, pexpect, ConfigParser @@ -16,7 +18,7 @@ log = logging.getLogger( __name__ ) class AdminRequestsGrid( RequestsGrid ): class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, request ): - return request.user.email + return escape(request.user.email) # Grid definition columns = [ col for col in RequestsGrid.columns ] columns.append( UserColumn( "User", @@ -37,7 +39,7 @@ class DataTransferGrid( grids.Grid ): # Custom column types class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, sample_dataset ): - return sample_dataset.name + return escape(sample_dataset.name) class SizeColumn( grids.TextColumn ): def get_value( self, trans, grid, sample_dataset ): return sample_dataset.size @@ -47,7 +49,7 @@ class DataTransferGrid( grids.Grid ): class ExternalServiceColumn( grids.TextColumn ): def get_value( self, trans, grid, sample_dataset ): try: - return sample_dataset.external_service.name + return escape(sample_dataset.external_service.name) except: return 'None' # Grid definition diff --git a/lib/galaxy/webapps/galaxy/controllers/requests_common.py b/lib/galaxy/webapps/galaxy/controllers/requests_common.py index 8a3c3be5682..d6f0301494c 100644 --- a/lib/galaxy/webapps/galaxy/controllers/requests_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/requests_common.py @@ -2,6 +2,9 @@ import csv import logging import re from galaxy import model, util, web +from galaxy import eggs +eggs.require("MarkupSafe") +from markupsafe import escape from galaxy.model.orm import and_, func, select from galaxy.security.validate_user_input import validate_email from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin @@ -14,10 +17,10 @@ class RequestsGrid( grids.Grid ): # Custom column types class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, request ): - return request.name + return escape(request.name) class DescriptionColumn( grids.TextColumn ): def get_value(self, trans, grid, request): - return request.desc + return escape(request.desc) class SamplesColumn( grids.GridColumn ): def get_value(self, trans, grid, request): return str( len( request.samples ) ) diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py index a4a1fc66a8f..e3c7add5d62 100644 --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -33,7 +33,7 @@ log = logging.getLogger( __name__ ) class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, history ): - return history.get_display_name() + return escape(history.get_display_name()) def get_link( self, trans, grid, history ): # Provide link to list all datasets in history that have a given dbkey. # Right now, only dbkey needs to be passed through, but pass through diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index de3edcb1ead..19bca27fa3f 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -7,6 +7,9 @@ from galaxy.web.framework.helpers import grids from galaxy.model.orm import and_, not_, or_ import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) +from galaxy import eggs +eggs.require("MarkupSafe") +from markupsafe import escape import sqlalchemy as sa from galaxy.webapps.reports.controllers.query import ReportQueryBuilder @@ -89,7 +92,7 @@ class SpecifiedDateListGrid( grids.Grid ): def get_value( self, trans, grid, job ): if job.user: - return job.user.email + return escape(job.user.email) return 'anonymous' class EmailColumn( grids.GridColumn ): diff --git a/lib/galaxy/webapps/reports/controllers/sample_tracking.py b/lib/galaxy/webapps/reports/controllers/sample_tracking.py index 8186531e190..577b797f7e9 100644 --- a/lib/galaxy/webapps/reports/controllers/sample_tracking.py +++ b/lib/galaxy/webapps/reports/controllers/sample_tracking.py @@ -6,6 +6,9 @@ from galaxy.web.framework.helpers import grids from galaxy.model.orm import and_ import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) +from galaxy import eggs +eggs.require("MarkupSafe") +from markupsafe import escape import sqlalchemy as sa from galaxy.webapps.reports.controllers.query import ReportQueryBuilder @@ -18,7 +21,7 @@ class SpecifiedDateListGrid( grids.Grid ): class RequestNameColumn( grids.TextColumn ): def get_value( self, trans, grid, request ): - return request.name + return escape(request.name) class CreateTimeColumn( grids.DateTimeColumn ): @@ -29,7 +32,7 @@ class SpecifiedDateListGrid( grids.Grid ): def get_value( self, trans, grid, request ): if request.user: - return request.user.email + return escape(request.user.email) return 'unknown' class EmailColumn( grids.GridColumn ): diff --git a/lib/galaxy/webapps/reports/controllers/workflows.py b/lib/galaxy/webapps/reports/controllers/workflows.py index 562a1a55619..5983988b65c 100644 --- a/lib/galaxy/webapps/reports/controllers/workflows.py +++ b/lib/galaxy/webapps/reports/controllers/workflows.py @@ -6,6 +6,8 @@ from galaxy.model.orm import and_ from galaxy.web.base.controller import BaseUIController, web from galaxy.web.framework.helpers import grids eggs.require( "SQLAlchemy >= 0.4" ) +eggs.require("MarkupSafe") +from markupsafe import escape import sqlalchemy as sa from galaxy.webapps.reports.controllers.query import ReportQueryBuilder from galaxy.webapps.reports.controllers.jobs import sorter @@ -19,7 +21,7 @@ class SpecifiedDateListGrid( grids.Grid ): class WorkflowNameColumn( grids.TextColumn ): def get_value( self, trans, grid, stored_workflow ): - return stored_workflow.name + return escape(stored_workflow.name) class CreateTimeColumn( grids.DateTimeColumn ): @@ -30,7 +32,7 @@ class SpecifiedDateListGrid( grids.Grid ): def get_value( self, trans, grid, stored_workflow ): if stored_workflow.user: - return stored_workflow.user.email + return escape(stored_workflow.user.email) return 'unknown' class EmailColumn( grids.GridColumn ): diff --git a/lib/tool_shed/grids/admin_grids.py b/lib/tool_shed/grids/admin_grids.py index 4489eadacdd..a582e267d88 100644 --- a/lib/tool_shed/grids/admin_grids.py +++ b/lib/tool_shed/grids/admin_grids.py @@ -12,6 +12,9 @@ from tool_shed.grids.repository_grids import RepositoryGrid from galaxy import eggs eggs.require( 'mercurial' ) +eggs.require("MarkupSafe") +from markupsafe import escape + from mercurial import commands from mercurial import hg from mercurial import ui @@ -25,14 +28,14 @@ class UserGrid( grids.Grid ): class UserLoginColumn( grids.TextColumn ): def get_value( self, trans, grid, user ): - return user.email + return escape(user.email) class UserNameColumn( grids.TextColumn ): def get_value( self, trans, grid, user ): if user.username: - return user.username + return escape(user.username) return 'not set' @@ -149,7 +152,7 @@ class RoleGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, role ): - return str( role.name ) + return escape( str( role.name ) ) class DescriptionColumn( grids.TextColumn ): @@ -414,13 +417,13 @@ class RepositoryMetadataGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.repository.name + return escape(repository_metadata.repository.name) class OwnerColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.repository.user.username + return escape(repository_metadata.repository.user.username) class RevisionColumn( grids.TextColumn ): diff --git a/lib/tool_shed/grids/repository_grids.py b/lib/tool_shed/grids/repository_grids.py index d10427d5efe..0180101403b 100644 --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -383,13 +383,13 @@ class MatchedRepositoryGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.repository.name + return escape_html(repository_metadata.repository.name) class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.repository.description + return escape_html(repository_metadata.repository.description) class RevisionColumn( grids.TextColumn ): @@ -402,7 +402,7 @@ class MatchedRepositoryGrid( grids.Grid ): def get_value( self, trans, grid, repository_metadata ): if repository_metadata.repository.user: - return repository_metadata.repository.user.username + return escape_html( repository_metadata.repository.user.username ) return 'no user' # Grid definition diff --git a/lib/tool_shed/grids/repository_review_grids.py b/lib/tool_shed/grids/repository_review_grids.py index 26a4c2b5aba..bd2937e4853 100644 --- a/lib/tool_shed/grids/repository_review_grids.py +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -9,6 +9,10 @@ import tool_shed.util.shed_util_common as suc from tool_shed.util import hg_util from tool_shed.util import metadata_util +from galaxy import eggs +eggs.require("MarkupSafe") +from markupsafe import escape + log = logging.getLogger( __name__ ) @@ -18,13 +22,13 @@ class ComponentGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, component ): - return component.name + return escape(component.name) class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, component ): - return component.description + return escape(component.description) title = "Repository review components" model_class = model.Component @@ -286,13 +290,13 @@ class RepositoryReviewsByUserGrid( grids.Grid ): class RepositoryNameColumn( grids.TextColumn ): def get_value( self, trans, grid, review ): - return review.repository.name + return escape(review.repository.name) class RepositoryDescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, review ): - return review.repository.description + return escape(review.repository.description) class RevisionColumn( grids.TextColumn ): diff --git 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\ No newline at end of file diff --git a/static/maps/mvc/ui/ui-select-default.js.map b/static/maps/mvc/ui/ui-select-default.js.map index 9d1e91c997a..0184d550bbf 100644 --- a/static/maps/mvc/ui/ui-select-default.js.map +++ b/static/maps/mvc/ui/ui-select-default.js.map @@ -1 +1 @@ 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0},a.children||a.initAjax&&a.initAjax.url||a.initId?$(this.divTree).empty():this.divRoot&&$(this.divRoot).remove(),this.tnRoot=new DynaTreeNode(null,this,{title:a.title,key:"root"}),this.tnRoot.data.isFolder=!0,this.tnRoot.render(!1,!1),this.divRoot=this.tnRoot.div,this.divRoot.className=a.classNames.container,this.divTree.appendChild(this.divRoot);var b=this.tnRoot,c=a.persist&&this.persistence.isReloading(),d=!1,e=this.enableUpdate(!1);if(this.logDebug("Dynatree._load(): read tree structure..."),a.children)b.addChild(a.children);else if(a.initAjax&&a.initAjax.url)d=!0,b.data.isLazy=!0,this._reloadAjax();else if(a.initId)this._createFromTag(b,$("#"+a.initId));else{var f=this.$tree.find(">ul").hide();this._createFromTag(b,f),f.remove()}this._checkConsistency(),this.logDebug("Dynatree._load(): render nodes..."),this.enableUpdate(e),this.logDebug("Dynatree._load(): bind events..."),this.$widget.bind(),this.logDebug("Dynatree._load(): postInit..."),this.phase="postInit",a.persist&&this.persistence.write(),this.focusNode&&this.focusNode.isVisible()&&(this.logDebug("Focus on init: %o",this.focusNode),this.focusNode.focus()),!d&&a.onPostInit&&a.onPostInit.call(this,c,!1),this.phase="idle"},_reloadAjax:function(){var a=this.options;if(!a.initAjax||!a.initAjax.url)throw"tree.reload() requires 'initAjax' mode.";var b=this.persistence,c=$.extend({},a.initAjax);if(c.addActiveKey&&(c.data.activeKey=b.activeKey),c.addFocusedKey&&(c.data.focusedKey=b.focusedKey),c.addExpandedKeyList&&(c.data.expandedKeyList=b.expandedKeyList.join(",")),c.addSelectedKeyList&&(c.data.selectedKeyList=b.selectedKeyList.join(",")),a.onPostInit){c.success&&this.logWarning("initAjax: success callback is ignored when onPostInit was specified."),c.error&&this.logWarning("initAjax: error callback is ignored when onPostInit was specified.");var d=b.isReloading();c.success=function(b){a.onPostInit.call(b.tree,d,!1)},c.error=function(b){a.onPostInit.call(b.tree,d,!0)}}this.logDebug("Dynatree._init(): send Ajax request..."),this.tnRoot.appendAjax(c)},toString:function(){return"DynaTree '"+this.options.title+"'"},toDict:function(){return this.tnRoot.toDict(!0)},getPersistData:function(){return this.persistence.toDict()},logDebug:function(){this.options.debugLevel>=2&&(Array.prototype.unshift.apply(arguments,["debug"]),_log.apply(this,arguments))},logInfo:function(){this.options.debugLevel>=1&&(Array.prototype.unshift.apply(arguments,["info"]),_log.apply(this,arguments))},logWarning:function(){Array.prototype.unshift.apply(arguments,["warn"]),_log.apply(this,arguments)},isInitializing:function(){return"init"==this.phase||"postInit"==this.phase},isReloading:function(){return("init"==this.phase||"postInit"==this.phase)&&this.options.persist&&this.persistence.cookiesFound},isUserEvent:function(){return"userEvent"==this.phase},redraw:function(){this.logDebug("dynatree.redraw()..."),this.tnRoot.render(!0,!0),this.logDebug("dynatree.redraw() done.")},reloadAjax:function(){this.logWarning("tree.reloadAjax() is deprecated since v0.5.2 (use reload() instead).")},reload:function(){this._load()},getRoot:function(){return this.tnRoot},getNodeByKey:function(a){var b=document.getElementById(this.options.idPrefix+a);return b&&b.dtnode?b.dtnode:null},getActiveNode:function(){return this.activeNode},reactivate:function(a){var b=this.activeNode;b&&(this.activeNode=null,b.activate(),a&&b.focus())},getSelectedNodes:function(a){var b=[];return this.tnRoot.visit(function(c){return c.bSelected&&(b.push(c),1==a)?!1:void 0}),b},activateKey:function(a){var b=null===a?null:this.getNodeByKey(a);return b?(b.focus(),b.activate(),b):(this.activeNode&&this.activeNode.deactivate(),this.activeNode=null,null)},selectKey:function(a,b){var c=this.getNodeByKey(a);return c?(c.select(b),c):null},enableUpdate:function(a){return this.bEnableUpdate==a?a:(this.bEnableUpdate=a,a&&this.redraw(),!a)},visit:function(a,b,c){return this.tnRoot.visit(a,b,c)},_createFromTag:function(parentTreeNode,$ulParent){var self=this;$ulParent.find(">li").each(function(){var $li=$(this),$liSpan=$li.find(">span:first"),title;if($liSpan.length)title=$liSpan.html();else{title=$li.html();var iPos=title.search(/
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called; consider upgrading to jquery.ui.core.js v1.8 or higher."),this._create()):void _log("debug","ui.dynatree._init() was called; no current default functionality.")},_create:function(){parseFloat($.ui.version)>=1.8&&(this.options=$.extend(!0,{},$[this.namespace][this.widgetName].defaults,this.options)),logMsg("Dynatree._create(): version='%s', debugLevel=%o.",DynaTree.version,this.options.debugLevel);this.options;this.options.event+=".dynatree";this.element.get(0);this.tree=new DynaTree(this),this.tree._load(),this.tree.logDebug("Dynatree._create(): done.")},bind:function(){function a(a){for(var b=5;a&&b--;){if(a.dtnode)return a.dtnode;a=a.parentNode}return null}function b(b){b=arguments[0]=$.event.fix(b||window.event);var c=a(b.target);return c?c.onFocus(b):!1}var c=this.element,d=this.options;this.unbind();var e="click.dynatree dblclick.dynatree";d.keyboard&&(e+=" keypress.dynatree keydown.dynatree"),c.bind(e,function(b){var c=a(b.target);if(!c)return!0;var e=c.tree.phase;c.tree.phase="userEvent";try{switch(c.tree.logDebug("bind(%o): dtnode: %o",b,c),b.type){case"click":return d.onClick&&d.onClick(c,b)===!1?!1:c.onClick(b);case"dblclick":return d.onDblClick&&d.onDblClick(c,b)===!1?!1:c.onDblClick(b);case"keydown":return d.onKeydown&&d.onKeydown(c,b)===!1?!1:c.onKeydown(b);case"keypress":return d.onKeypress&&d.onKeypress(c,b)===!1?!1:c.onKeypress(b)}}catch(f){}finally{c.tree.phase=e}});var f=this.tree.divTree;f.addEventListener?(f.addEventListener("focus",b,!0),f.addEventListener("blur",b,!0)):f.onfocusin=f.onfocusout=b},unbind:function(){this.element.unbind(".dynatree")},enable:function(){this.bind(),$.widget.prototype.enable.apply(this,arguments)},disable:function(){this.unbind(),$.widget.prototype.disable.apply(this,arguments)},getTree:function(){return this.tree},getRoot:function(){return this.tree.getRoot()},getActiveNode:function(){return this.tree.getActiveNode()},getSelectedNodes:function(){return 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function(){this.initialize.apply(this,arguments)}}},DynaTreeNode=Class.create();DynaTreeNode.prototype={initialize:function(a,b,c){this.parent=a,this.tree=b,"string"==typeof c&&(c={title:c}),void 0==c.key&&(c.key="_"+b._nodeCount++),this.data=$.extend({},$.ui.dynatree.nodedatadefaults,c),this.div=null,this.span=null,this.childList=null,this.isLoading=!1,this.hasSubSel=!1},toString:function(){return"dtnode<"+this.data.key+">: '"+this.data.title+"'"},toDict:function(a,b){var c=$.extend({},this.data);if(c.activate=this.tree.activeNode===this,c.focus=this.tree.focusNode===this,c.expand=this.bExpanded,c.select=this.bSelected,b&&b(c),a&&this.childList){c.children=[];for(var d=0;d0||a.minExpandLevel>1,e=a.rootVisible||a.minExpandLevel>0,f="",g=this.parent;g&&(!e||g!=c);)f=(g.isLastSibling()?b.tagEmpty:b.tagVline)+f,g=g.parent;d&&this.parent==c||(f+=this.childList||this.data.isLazy?b.tagExpander:b.tagConnector),a.checkbox&&1!=this.data.hideCheckbox&&!this.data.isStatusNode&&(f+=b.tagCheckbox),this.data.icon?f+="":0==this.data.icon||(f+=b.tagNodeIcon);var h=this.data&&"string"==typeof this.data.tooltip?" title='"+this.data.tooltip+"'":"";return f+=""+this.data.title+""},_fixOrder:function(){var a=this.childList;if(a)for(var b=this.div.firstChild.nextSibling,c=0;c=h&&h+j>=d&&e>=i&&i+k>=e){if(g.className==b.title)return"title";if(g.className==b.expander)return"expander";if(g.className==b.checkbox)return"checkbox";if(g.className==b.nodeIcon)return"icon"}}return"prefix"},getEventTargetType:function(a){var b=a&&a.target?a.target.className:"",c=this.tree.options.classNames;return b==c.title?"title":b==c.expander?"expander":b==c.checkbox?"checkbox":b==c.nodeIcon?"icon":b==c.empty||b==c.vline||b==c.connector?"prefix":b.indexOf(c.folder)>=0||b.indexOf(c.document)>=0?this._getTypeForOuterNodeEvent(a):null},isVisible:function(){for(var a=this._parentList(!0,!1),b=0;ba").focus()}catch(a){}},_activate:function(a,b){this.tree.logDebug("dtnode._activate(%o, fireEvents=%o) - %o",a,b,this);var c=this.tree.options;if(!(this.data.isStatusNode||b&&c.onQueryActivate&&0==c.onQueryActivate.call(this.span,a,this)))if(a){if(this.tree.activeNode){if(this.tree.activeNode===this)return;this.tree.activeNode.deactivate()}c.activeVisible&&this.makeVisible(),this.tree.activeNode=this,c.persist&&$.cookie(c.cookieId+"-active",this.data.key,c.cookie),this.tree.persistence.activeKey=this.data.key,$(this.span).addClass(c.classNames.active),b&&c.onActivate&&c.onActivate.call(this.span,this)}else if(this.tree.activeNode===this){var c=this.tree.options;if(c.onQueryActivate&&0==c.onQueryActivate.call(this.span,!1,this))return;$(this.span).removeClass(c.classNames.active),c.persist&&$.cookie(c.cookieId+"-active","",c.cookie),this.tree.persistence.activeKey=null,this.tree.activeNode=null,b&&c.onDeactivate&&c.onDeactivate.call(this.span,this)}},activate:function(){this._activate(!0,!0)},deactivate:function(){this._activate(!1,!0)},isActive:function(){return this.tree.activeNode===this},_userActivate:function(){var a=!0,b=!1;if(this.data.isFolder)switch(this.tree.options.clickFolderMode){case 2:a=!1,b=!0;break;case 3:a=b=!0}null==this.parent&&this.tree.options.minExpandLevel>0&&(b=!1),b&&(this.toggleExpand(),this.focus()),a&&this.activate()},_setSubSel:function(a){a?(this.hasSubSel=!0,$(this.span).addClass(this.tree.options.classNames.partsel)):(this.hasSubSel=!1,$(this.span).removeClass(this.tree.options.classNames.partsel))},_fixSelectionState:function(){if(this.bSelected){this.visit(function(a){a.parent._setSubSel(!0),a._select(!0,!1,!1)});for(var a=this.parent;a;){a._setSubSel(!0);for(var b=!0,c=0;c0&&!a||this._expand(a))},toggleExpand:function(){this.expand(!this.bExpanded)},collapseSiblings:function(){if(null!=this.parent)for(var a=this.parent.childList,b=0;b=0&&!(c=d[e].nextSibling());e--);c&&c.focus();break;default:b=!1}return!b},onKeypress:function(){},onFocus:function(a){var b=this.tree.options;"blur"==a.type||"focusout"==a.type?(b.onBlur&&b.onBlur.call(this.span,this),this.tree.tnFocused&&$(this.tree.tnFocused.span).removeClass(b.classNames.focused),this.tree.tnFocused=null,b.persist&&$.cookie(b.cookieId+"-focus","",b.cookie)):("focus"==a.type||"focusin"==a.type)&&(this.tree.tnFocused&&this.tree.tnFocused!==this&&(this.tree.logDebug("dtnode.onFocus: out of sync: curFocus: %o",this.tree.tnFocused),$(this.tree.tnFocused.span).removeClass(b.classNames.focused)),this.tree.tnFocused=this,b.onFocus&&b.onFocus.call(this.span,this),$(this.tree.tnFocused.span).addClass(b.classNames.focused),b.persist&&$.cookie(b.cookieId+"-focus",this.data.key,b.cookie))},visit:function(a,b,c){var d=0;if(1==c){if(0==a(this,b))return 1;d++}if(this.childList)for(var e=0;ef)throw" must be a child of ";this.childList.splice(f,0,a)}else this.childList.push(a);var g=c.isInitializing();if(d.persist&&e.cookiesFound&&g?(e.activeKey==a.data.key&&(c.activeNode=a),e.focusedKey==a.data.key&&(c.focusNode=a),a.bExpanded=$.inArray(a.data.key,e.expandedKeyList)>=0,a.bSelected=$.inArray(a.data.key,e.selectedKeyList)>=0):(a.data.activate&&(c.activeNode=a,d.persist&&(e.activeKey=a.data.key)),a.data.focus&&(c.focusNode=a,d.persist&&(e.focusedKey=a.data.key)),a.bExpanded=1==a.data.expand,a.bExpanded&&d.persist&&e.addExpand(a.data.key),a.bSelected=1==a.data.select,a.bSelected&&d.persist&&e.addSelect(a.data.key)),d.minExpandLevel>=a.getLevel()&&(this.bExpanded=!0),a.bSelected&&3==d.selectMode)for(var h=this;h;)h.hasSubSel||h._setSubSel(!0),h=h.parent;return c.bEnableUpdate&&this.render(!0,!0),a},addChild:function(a,b){if(a&&0!=a.length){if(a instanceof DynaTreeNode)return this._addChildNode(a,b);a.length||(a=[a]);for(var c=this.tree.enableUpdate(!1),d=null,e=0;e=0&&(this.expandedKeyList.splice(b,1),$.cookie(this.cookieId+"-expand",this.expandedKeyList.join(","),this.cookieOpts))},addSelect:function(a){this._log("addSelect(%o)",a),$.inArray(a,this.selectedKeyList)<0&&(this.selectedKeyList.push(a),$.cookie(this.cookieId+"-select",this.selectedKeyList.join(","),this.cookieOpts))},clearSelect:function(a){this._log("clearSelect(%o)",a);var b=$.inArray(a,this.selectedKeyList);b>=0&&(this.selectedKeyList.splice(b,1),$.cookie(this.cookieId+"-select",this.selectedKeyList.join(","),this.cookieOpts))},isReloading:function(){return 1==this.cookiesFound},toDict:function(){return{cookiesFound:this.cookiesFound,activeKey:this.activeKey,focusedKey:this.activeKey,expandedKeyList:this.expandedKeyList,selectedKeyList:this.selectedKeyList}},lastentry:void 0};var DynaTree=Class.create();DynaTree.version="$Version: 0.5.4$",DynaTree.prototype={initialize:function(a){this.phase="init",this.$widget=a,this.options=a.options,this.$tree=a.element,this.divTree=this.$tree.get(0)},_load:function(){var a=(this.$widget,this.options);this.bEnableUpdate=!0,this._nodeCount=1,this.activeNode=null,this.focusNode=null,a.classNames!==$.ui.dynatree.defaults.classNames&&(a.classNames=$.extend({},$.ui.dynatree.defaults.classNames,a.classNames)),a.imagePath||$("script").each(function(){return this.src.search(_rexDtLibName)>=0?(a.imagePath=this.src.indexOf("/")>=0?this.src.slice(0,this.src.lastIndexOf("/"))+"/skin/":"skin/",!1):void 0}),this.persistence=new DynaTreeStatus(a.cookieId,a.cookie),a.persist&&($.cookie||_log("warn","Please include jquery.cookie.js to use persistence."),this.persistence.read()),this.logDebug("DynaTree.persistence: %o",this.persistence.toDict()),this.cache={tagEmpty:"",tagVline:"",tagExpander:"",tagConnector:"",tagNodeIcon:"",tagCheckbox:"",lastentry:void 0},a.children||a.initAjax&&a.initAjax.url||a.initId?$(this.divTree).empty():this.divRoot&&$(this.divRoot).remove(),this.tnRoot=new DynaTreeNode(null,this,{title:a.title,key:"root"}),this.tnRoot.data.isFolder=!0,this.tnRoot.render(!1,!1),this.divRoot=this.tnRoot.div,this.divRoot.className=a.classNames.container,this.divTree.appendChild(this.divRoot);var b=this.tnRoot,c=a.persist&&this.persistence.isReloading(),d=!1,e=this.enableUpdate(!1);if(this.logDebug("Dynatree._load(): read tree structure..."),a.children)b.addChild(a.children);else if(a.initAjax&&a.initAjax.url)d=!0,b.data.isLazy=!0,this._reloadAjax();else if(a.initId)this._createFromTag(b,$("#"+a.initId));else{var f=this.$tree.find(">ul").hide();this._createFromTag(b,f),f.remove()}this._checkConsistency(),this.logDebug("Dynatree._load(): render nodes..."),this.enableUpdate(e),this.logDebug("Dynatree._load(): bind events..."),this.$widget.bind(),this.logDebug("Dynatree._load(): postInit..."),this.phase="postInit",a.persist&&this.persistence.write(),this.focusNode&&this.focusNode.isVisible()&&(this.logDebug("Focus on init: %o",this.focusNode),this.focusNode.focus()),!d&&a.onPostInit&&a.onPostInit.call(this,c,!1),this.phase="idle"},_reloadAjax:function(){var a=this.options;if(!a.initAjax||!a.initAjax.url)throw"tree.reload() requires 'initAjax' mode.";var b=this.persistence,c=$.extend({},a.initAjax);if(c.addActiveKey&&(c.data.activeKey=b.activeKey),c.addFocusedKey&&(c.data.focusedKey=b.focusedKey),c.addExpandedKeyList&&(c.data.expandedKeyList=b.expandedKeyList.join(",")),c.addSelectedKeyList&&(c.data.selectedKeyList=b.selectedKeyList.join(",")),a.onPostInit){c.success&&this.logWarning("initAjax: success callback is ignored when onPostInit was specified."),c.error&&this.logWarning("initAjax: error callback is ignored when onPostInit was specified.");var 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      ":": "+d}b._showAlert(content,"alert-danger")},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .reset":"reset","click .clear-selected":"clearSelectedElements","click .collection-elements":"clearSelectedElements","dragover .collection-elements":"_dragoverElements","drop .collection-elements":"_dropElements","collection-element.dragstart .collection-elements":"_elementDragstart","collection-element.dragend .collection-elements":"_elementDragend","change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(){"function"==typeof this.oncancel&&this.oncancel.call(this)},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(a){a.stopPropagation(),this.$(".main-help").addClass("expanded"),this.$(".more-help").hide()},_clickLessHelp:function(a){a.stopPropagation(),this.$(".main-help").removeClass("expanded"),this.$(".more-help").show()},_toggleHelp:function(a){a.stopPropagation(),this.$(".main-help").toggleClass("expanded"),this.$(".more-help").toggle()},_showAlert:function(a,b){b=b||"alert-danger",this.$(".main-help").hide(),this.$(".header .alert").attr("class","alert alert-dismissable").addClass(b).show().find(".alert-message").html(a)},_hideAlert:function(){this.$(".main-help").show(),this.$(".header .alert").hide()},reset:function(){this._instanceSetUp(),this._elementsSetUp(),this.render()},clearSelectedElements:function(){this.$(".collection-elements .collection-element").removeClass("selected"),this.$(".collection-elements-controls > .clear-selected").hide()},_dragoverElements:function(a){a.preventDefault();var b=this.$list();this._checkForAutoscroll(b,a.originalEvent.clientY);var c=this._getNearestElement(a.originalEvent.clientY);this.$(".element-drop-placeholder").remove();var d=$('
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        ","
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      ","

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      "),c=a.$list();_.each(this.elementViews,function(b){b.destroy(),a.removeElementView(b)}),a.workingElements.forEach(function(c){var d=a._createElementView(c);b.append(d.$el)}),a._renderClearSelected(),c.empty().append(b.children()),_.invoke(a.elementViews,"render"),c.height()>c.css("max-height")?c.css("border-width","1px 0px 1px 0px"):c.css("border-width","0px")},_createElementView:function(a){var b=new this.elementViewClass({element:a,selected:_.has(this.selectedIds,a.id)});return this.elementViews.push(b),this._listenToElementView(b),b},_listenToElementView:function(a){var b=this;b.listenTo(a,{select:function(a){var c=a.source.element;a.selected?b.selectedIds[c.id]=!0:delete b.selectedIds[c.id],b.trigger("elements:select",a)},discard:function(a){b.trigger("elements:discard",a)}})},addElementView:function(){},removeElementView:function(a){delete this.selectedIds[a.element.id],this._renderClearSelected(),this.elementViews=_.without(this.elementViews,a),this.stopListening(a)},_renderNoElementsLeft:function(){this._disableNameAndCreate(!0),this.$(".collection-elements").append(this.templates.noElementsLeft())},_elementToJSON:function(a){return a},createList:function(a){if(!this.workingElements.length){var b=f("No valid elements for final list")+". ";return b+=''+f("Cancel")+" ",b+=f("or"),b+=' '+f("start over")+".",void this._showAlert(b)}var c=this,d=this.workingElements.map(function(a){return c._elementToJSON(a)});return c.blocking=!0,c.creationFn(d,a).always(function(){c.blocking=!1}).fail(function(a,b){c.trigger("error",{xhr:a,status:b,message:f("An error occurred while creating this collection")})}).done(function(a,b,d){c.trigger("collection:created",a,b,d),c.metric("collection:created",a),"function"==typeof c.oncreate&&c.oncreate.call(this,a,b,d)})},_setUpBehaviors:function(){return this.on("error",this._errorHandler),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.on("elements:select",function(){this._renderClearSelected()}),this.on("elements:discard",function(a){var b=a.source.element;this.removeElementView(a.source),this.workingElements=_.without(this.workingElements,b),this.workingElements.length||this._renderNoElementsLeft()}),this},_errorHandler:function(a){this.error(a);var b=this;if(content=a.message||f("An error occurred"),a.xhr){var c=a.xhr,d=a.message;content+=0===c.readyState&&0===c.status?": "+f("Galaxy could not be reached and may be updating.")+f(" Try again in a few minutes."):c.responseJSON?":
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      ":": "+d}b._showAlert(content,"alert-danger")},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .reset":"reset","click .clear-selected":"clearSelectedElements","click .collection-elements":"clearSelectedElements","dragover .collection-elements":"_dragoverElements","drop .collection-elements":"_dropElements","collection-element.dragstart .collection-elements":"_elementDragstart","collection-element.dragend .collection-elements":"_elementDragend","change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(){"function"==typeof this.oncancel&&this.oncancel.call(this)},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(a){a.stopPropagation(),this.$(".main-help").addClass("expanded"),this.$(".more-help").hide()},_clickLessHelp:function(a){a.stopPropagation(),this.$(".main-help").removeClass("expanded"),this.$(".more-help").show()},_toggleHelp:function(a){a.stopPropagation(),this.$(".main-help").toggleClass("expanded"),this.$(".more-help").toggle()},_showAlert:function(a,b){b=b||"alert-danger",this.$(".main-help").hide(),this.$(".header .alert").attr("class","alert alert-dismissable").addClass(b).show().find(".alert-message").html(a)},_hideAlert:function(){this.$(".main-help").show(),this.$(".header .alert").hide()},reset:function(){this._instanceSetUp(),this._elementsSetUp(),this.render()},clearSelectedElements:function(){this.$(".collection-elements .collection-element").removeClass("selected"),this.$(".collection-elements-controls > .clear-selected").hide()},_dragoverElements:function(a){a.preventDefault();var b=this.$list();this._checkForAutoscroll(b,a.originalEvent.clientY);var c=this._getNearestElement(a.originalEvent.clientY);this.$(".element-drop-placeholder").remove();var d=$('
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      ','
      ','
      '].join("")),header:_.template(['
      ','',f("More help"),"",'
      ','',f("Less"),"","
      ","
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      ','','',"
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      ','',f("Start over"),"",'',f("Clear selected"),"","
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      ','
      ','','
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      ","
      ","
      ",'
      ','
      ','",'
      ','",'","
      ","
      ",'
      ','","
      ","
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      ",f(["Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ","workflows in order to have analyses done on each member of the entire group. This interface allows ","you to create a collection and re-order the final collection."].join("")),"

      ","
        ","
      • ",f(["Rename elements in the list by clicking on ",'the existing name.'].join("")),"
        • ","
      • ",f(["Discard elements from the final created list by clicking on the ",'"Discard" button.'].join("")),"
        • ","
      • ",f(["Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ",'them and you can then move those selected by dragging the ',"entire group. Deselect them by clicking them again or by clicking the ",'the "Clear selected" link.'].join("")),"
        • ","
      • ",f(['Click the "Start over" link to begin again as if you had just opened ',"the interface."].join("")),"
        • ","
      • ",f(['Click the "Cancel" button to exit the interface.'].join("")),"
        • ","

      ","

      ",f(['Once your collection is complete, enter a name and ','click "Create list".'].join("")),"

      "].join("")),invalidElements:_.template([f("The following selections could not be included due to problems:"),"
        <% _.each( problems, function( problem ){ %>","
      • <%- problem.element.name %>: <%- problem.text %>
        • ","<% }); %>
      "].join("")),noElementsLeft:_.template(['
    • ',f("No elements left! "),f("Would you like to "),'',f("start over"),"?","
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      ','
      ','',"<% if( _.size( problems ) ){ %>",f("The following selections could not be included due to problems"),":","
        <% _.each( problems, function( problem ){ %>","
      • <%- problem.element.name %>: <%- problem.text %>
        • ","<% }); %>
      ","<% } else if( _.size( elements ) < 1 ){ %>",f("No datasets were selected"),".","<% } %>","
      ",f("At least one element is needed for the collection"),". ",f("You may need to "),'',f("cancel")," ",f("and reselect new elements"),".","      ","
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a/static/scripts/mvc/collection/list-of-pairs-collection-creator.js +++ b/static/scripts/mvc/collection/list-of-pairs-collection-creator.js @@ -1,2 +1,2 @@ -define(["utils/levenshtein","utils/natural-sort","mvc/collection/list-collection-creator","mvc/base-mvc","utils/localization","ui/hoverhighlight"],function(a,b,c,d,e){function f(a){function b(){return c.length||(c=[new RegExp(this.filters[0]),new RegExp(this.filters[1])]),c}a=a||{},a.createPair=a.createPair||function(a){return this.debug("creating pair:",a.listA[a.indexA].name,a.listB[a.indexB].name),a=a||{},this._pair(a.listA.splice(a.indexA,1)[0],a.listB.splice(a.indexB,1)[0],{silent:!0})};var c=[];return a.preprocessMatch=a.preprocessMatch||function(a){var c=b.call(this);return _.extend(a,{matchTo:a.matchTo.name.replace(c[0],""),possible:a.possible.name.replace(c[1],"")})},function(b){this.debug("autopair _strategy ---------------------------"),b=b||{};var c,d=b.listA,e=b.listB,f=0,g={score:0,index:null},h=[];for(this.debug("starting list lens:",d.length,e.length),this.debug("bestMatch (starting):",JSON.stringify(g,null," "));f=k?(this.debug("creating pair"),h.push(a.createPair.call(this,{listA:d,indexA:f,listB:e,indexB:g.index})),this.debug("list lens now:",d.length,e.length)):f+=1,!d.length||!e.length)return h}return this.debug("paired:",JSON.stringify(h,null," ")),this.debug("autopair _strategy ---------------------------"),h}}function g(a){var b=a.toJSON();return j(b,{historyId:a.historyId})}var h=Backbone.View.extend(d.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(a){this.pair=a.pair||{}},template:_.template(['<%= pair.forward.name %>','','<%= pair.name %>',"",'<%= pair.reverse.name %>'].join("")),render:function(){return this.$el.attr("draggable",!0).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container"),this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(a){a.currentTarget.style.opacity="0.4",a.originalEvent&&(a=a.originalEvent),a.dataTransfer.effectAllowed="move",a.dataTransfer.setData("text/plain",JSON.stringify(this.pair)),this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(a){a.currentTarget.style.opacity="1.0",this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(a){this.$el.parent().trigger(a)},toString:function(){return"PairView("+this.pair.name+")"}}),i=Backbone.View.extend(d.LoggableMixin).extend({className:"list-of-pairs-collection-creator collection-creator 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a.sort(function(a,c){return b(a.name,c.name)}),a},_ensureIds:function(){return this.initialList.forEach(function(a){a.hasOwnProperty("id")||(a.id=_.uniqueId())}),this.initialList},_splitByFilters:function(){function a(a,b){return b.test(a.name)}var b=this.filters.map(function(a){return new RegExp(a)}),c=[[],[]];return this.unpaired.forEach(function(d){b.forEach(function(b,e){a(d,b)&&c[e].push(d)})}),c},_addToUnpaired:function(a){var c=function(d,e){if(d===e)return d;var f=Math.floor((e-d)/2)+d,g=b(a.name,this.unpaired[f].name);if(0>g)return c(d,f);if(g>0)return c(f+1,e);for(;this.unpaired[f]&&this.unpaired[f].name===a.name;)f++;return f}.bind(this);this.unpaired.splice(c(0,this.unpaired.length),0,a)},autoPair:function(a){var b=this._splitByFilters(),c=[];return this.twoPassAutopairing&&(c=this.autopairSimple({listA:b[0],listB:b[1]}),b=this._splitByFilters()),a=a||this.strategy,b=this._splitByFilters(),c=c.concat(this[a].call(this,{listA:b[0],listB:b[1]}))},autopairSimple:f({scoreThreshold:function(){return 1},match:function(a){return a=a||{},a.matchTo===a.possible?{index:a.index,score:1}:a.bestMatch}}),autopairLevenshtein:f({scoreThreshold:function(){return this.matchPercentage},match:function(b){b=b||{};var c=a(b.matchTo,b.possible),d=1-c/Math.max(b.matchTo.length,b.possible.length);return d>b.bestMatch.score?{index:b.index,score:d}:b.bestMatch}}),autopairLCS:f({scoreThreshold:function(){return this.matchPercentage},match:function(a){a=a||{};var b=this._naiveStartingAndEndingLCS(a.matchTo,a.possible).length,c=b/Math.max(a.matchTo.length,a.possible.length);return c>a.bestMatch.score?{index:a.index,score:c}:a.bestMatch}}),_naiveStartingAndEndingLCS:function(a,b){for(var c="",d="",e=0,f=0;e=0&&f>=0&&a[e]===b[f];)d=[a[e],d].join(""),e-=1,f-=1;return c+d},_pair:function(a,b,c){c=c||{};var d=this._createPair(a,b,c.name);return this.paired.push(d),this.unpaired=_.without(this.unpaired,a,b),c.silent||this.trigger("pair:new",d),d},_createPair:function(a,b,c){if(!a||!b||a===b)throw new Error("Bad pairing: "+[JSON.stringify(a),JSON.stringify(b)]);return c=c||this._guessNameForPair(a,b),{forward:a,name:c,reverse:b}},_guessNameForPair:function(a,b,c){c=void 0!==c?c:this.removeExtensions;var d=a.name,e=b.name,f=this._naiveStartingAndEndingLCS(d.replace(this.filters[0],""),e.replace(this.filters[1],""));if(c){var g=f.lastIndexOf(".");if(g>0){var h=f.slice(g,f.length);f=f.replace(h,""),d=d.replace(h,""),e=e.replace(h,"")}}return f||d+" & "+e},_unpair:function(a,b){if(b=b||{},!a)throw new Error("Bad pair: "+JSON.stringify(a));return 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              "].join(""))};var j=function(a,b){var c,d=jQuery.Deferred();if(b=_.defaults(b||{},{datasets:a,oncancel:function(){Galaxy.modal.hide(),d.reject("cancelled")},oncreate:function(a,b){Galaxy.modal.hide(),d.resolve(b)}}),!window.Galaxy||!Galaxy.modal)throw new Error("Galaxy or Galaxy.modal not found");return c=new i(b),Galaxy.modal.show({title:"Create a collection of paired datasets",body:c.$el,width:"80%",height:"800px",closing_events:!0}),c.render(),window.creator=c,d};return{PairedCollectionCreator:i,pairedCollectionCreatorModal:j,createListOfPairsCollection:g}}); +define(["utils/levenshtein","utils/natural-sort","mvc/collection/list-collection-creator","mvc/base-mvc","utils/localization","ui/hoverhighlight"],function(a,b,c,d,e){function f(a){function b(){return c.length||(c=[new RegExp(this.filters[0]),new RegExp(this.filters[1])]),c}a=a||{},a.createPair=a.createPair||function(a){return this.debug("creating 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                      ",e(['Once your collection is complete, enter a name and ','click "Create list". ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"

                      "].join(""))};var j=function(a,b){var c,d=jQuery.Deferred();if(b=_.defaults(b||{},{datasets:a,oncancel:function(){Galaxy.modal.hide(),d.reject("cancelled")},oncreate:function(a,b){Galaxy.modal.hide(),d.resolve(b)}}),!window.Galaxy||!Galaxy.modal)throw new Error("Galaxy or Galaxy.modal not found");return c=new i(b),Galaxy.modal.show({title:"Create a collection of paired datasets",body:c.$el,width:"80%",height:"800px",closing_events:!0}),c.render(),window.creator=c,d};return{PairedCollectionCreator:i,pairedCollectionCreatorModal:j,createListOfPairsCollection:g}}); //# sourceMappingURL=../../../maps/mvc/collection/list-of-pairs-collection-creator.js.map \ No newline at end of file diff --git a/static/scripts/mvc/collection/pair-collection-creator.js b/static/scripts/mvc/collection/pair-collection-creator.js index de301478a2f..63fdb37d920 100644 --- a/static/scripts/mvc/collection/pair-collection-creator.js +++ b/static/scripts/mvc/collection/pair-collection-creator.js @@ -1,2 +1,2 @@ -define(["mvc/collection/list-collection-creator","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(a,b,c,d){function e(a){var b=a.toJSON(),c=i(b,{creationFn:function(b,c){return b=[{name:"forward",src:"hda",id:b[0].id},{name:"reverse",src:"hda",id:b[1].id}],a.createHDCA(b,"paired",c)}});return c}var f=Backbone.View.extend(c.LoggableMixin).extend({tagName:"li",className:"collection-element",initialize:function(a){this.element=a.element||{},this.identifier=a.identifier},render:function(){return this.$el.attr("data-element-id",this.element.id).html(this.template({identifier:this.identifier,element:this.element})),this},template:_.template(['<%= identifier %>','<%= element.name %>'].join("")),destroy:function(){this.off(),this.$el.remove()},toString:function(){return"DatasetCollectionElementView()"}}),g=a.ListCollectionCreator,h=g.extend({elementViewClass:f,collectionClass:b.HistoryPairDatasetCollection,className:"pair-collection-creator collection-creator flex-row-container",_mangleDuplicateNames:function(){},render:function(a,b){return 2===this.workingElements.length?g.prototype.render.call(this,a,b):this._renderInvalid(a,b)},_renderList:function(){var a=this,b=jQuery("
                      "),c=a.$list();_.each(this.elementViews,function(b){b.destroy(),a.removeElementView(b)}),b.append(a._createForwardElementView().$el),b.append(a._createReverseElementView().$el),c.empty().append(b.children()),_.invoke(a.elementViews,"render")},_createForwardElementView:function(){return this._createElementView(this.workingElements[0],{identifier:"forward"})},_createReverseElementView:function(){return this._createElementView(this.workingElements[1],{identifier:"reverse"})},_createElementView:function(a,b){var c=new this.elementViewClass(_.extend(b,{element:a}));return this.elementViews.push(c),c},swap:function(){this.workingElements=[this.workingElements[1],this.workingElements[0]],this._renderList()},events:_.extend(_.clone(g.prototype.events),{"click .swap":"swap"}),templates:_.extend(_.clone(g.prototype.templates),{middle:_.template(['
                      ','',d("Swap"),"","
                      ",'
                      ',"
                      "].join("")),helpContent:_.template(["

                      ",d(["Pair collections are permanent collections containing two datasets: one forward and one reverse. ","Often these are forward and reverse reads. The pair collections can be passed to tools and ","workflows in order to have analyses done on both datasets. This interface allows ","you to create a pair, name it, and swap which is forward and which reverse."].join("")),"

                      ","
                        ","
                      • ",d(['Click the "Swap" link to make your forward dataset the reverse ',"and the reverse dataset forward."].join("")),"
                        • ","
                      • ",d(['Click the "Cancel" button to exit the interface.'].join("")),"
                        • ","

                      ","

                      ",d(['Once your collection is complete, enter a name and ','click "Create list".'].join("")),"

                      "].join("")),invalidInitial:_.template(['
                      ','
                      ','',"<% if( _.size( problems ) ){ %>",d("The following selections could not be included due to problems"),"
                        <% _.each( problems, function( problem ){ %>","
                      • <%= problem.element.name %>: <%= problem.text %>
                        • ","<% }); %>
                      ","<% } else if( _.size( elements ) === 0 ){ %>",d("No datasets were selected"),".","<% } else if( _.size( elements ) === 1 ){ %>",d("Only one dataset was selected"),": <%= elements[0].name %>","<% } else if( _.size( elements ) > 2 ){ %>",d("Too many datasets were selected"),': <%= _.pluck( elements, "name" ).join( ", ") %>',"<% } %>","
                      ",d("Two (and only two) elements are needed for the pair"),". ",d("You may need to "),'',d("cancel")," ",d("and reselect new elements"),".","                      ","
                      ","
                      ",'
                      ','
                      ','
                      ','","
                      ","
                      ","
                      "].join(""))}),toString:function(){return"PairCollectionCreator"}}),i=function(b,c){return c=c||{},c.title=d("Create a collection from a pair of datasets"),a.collectionCreatorModal(b,c,h)};return{PairCollectionCreator:h,pairCollectionCreatorModal:i,createPairCollection:e}}); +define(["mvc/collection/list-collection-creator","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(a,b,c,d){function e(a){var b=a.toJSON(),c=i(b,{creationFn:function(b,c){return b=[{name:"forward",src:"hda",id:b[0].id},{name:"reverse",src:"hda",id:b[1].id}],a.createHDCA(b,"paired",c)}});return c}var f=Backbone.View.extend(c.LoggableMixin).extend({tagName:"li",className:"collection-element",initialize:function(a){this.element=a.element||{},this.identifier=a.identifier},render:function(){return this.$el.attr("data-element-id",this.element.id).html(this.template({identifier:this.identifier,element:this.element})),this},template:_.template(['<%- identifier %>','<%- element.name %>'].join("")),destroy:function(){this.off(),this.$el.remove()},toString:function(){return"DatasetCollectionElementView()"}}),g=a.ListCollectionCreator,h=g.extend({elementViewClass:f,collectionClass:b.HistoryPairDatasetCollection,className:"pair-collection-creator collection-creator flex-row-container",_mangleDuplicateNames:function(){},render:function(a,b){return 2===this.workingElements.length?g.prototype.render.call(this,a,b):this._renderInvalid(a,b)},_renderList:function(){var a=this,b=jQuery("
                      "),c=a.$list();_.each(this.elementViews,function(b){b.destroy(),a.removeElementView(b)}),b.append(a._createForwardElementView().$el),b.append(a._createReverseElementView().$el),c.empty().append(b.children()),_.invoke(a.elementViews,"render")},_createForwardElementView:function(){return this._createElementView(this.workingElements[0],{identifier:"forward"})},_createReverseElementView:function(){return this._createElementView(this.workingElements[1],{identifier:"reverse"})},_createElementView:function(a,b){var c=new this.elementViewClass(_.extend(b,{element:a}));return this.elementViews.push(c),c},swap:function(){this.workingElements=[this.workingElements[1],this.workingElements[0]],this._renderList()},events:_.extend(_.clone(g.prototype.events),{"click .swap":"swap"}),templates:_.extend(_.clone(g.prototype.templates),{middle:_.template(['
                      ','',d("Swap"),"","
                      ",'
                      ',"
                      "].join("")),helpContent:_.template(["

                      ",d(["Pair collections are permanent collections containing two datasets: one forward and one reverse. ","Often these are forward and reverse reads. The pair collections can be passed to tools and ","workflows in order to have analyses done on both datasets. This interface allows ","you to create a pair, name it, and swap which is forward and which reverse."].join("")),"

                      ","
                        ","
                      • ",d(['Click the "Swap" link to make your forward dataset the reverse ',"and the reverse dataset forward."].join("")),"
                        • ","
                      • ",d(['Click the "Cancel" button to exit the interface.'].join("")),"
                        • ","

                      ","

                      ",d(['Once your collection is complete, enter a name and ','click "Create list".'].join("")),"

                      "].join("")),invalidInitial:_.template(['
                      ','
                      ','',"<% if( _.size( problems ) ){ %>",d("The following selections could not be included due to problems"),"
                        <% _.each( problems, function( problem ){ %>","
                      • <%- problem.element.name %>: <%- problem.text %>
                        • ","<% }); %>
                      ","<% } else if( _.size( elements ) === 0 ){ %>",d("No datasets were selected"),".","<% } else if( _.size( elements ) === 1 ){ %>",d("Only one dataset was selected"),": <%- elements[0].name %>","<% } else if( _.size( elements ) > 2 ){ %>",d("Too many datasets were selected"),': <%- _.pluck( elements, "name" ).join( ", ") %>',"<% } %>","
                      ",d("Two (and only two) elements are needed for the pair"),". ",d("You may need to "),'',d("cancel")," ",d("and reselect new elements"),".","                      ","
                      ","
                      ",'
                      ','
                      ','
                      ','","
                      ","
                      ","
                      "].join(""))}),toString:function(){return"PairCollectionCreator"}}),i=function(b,c){return c=c||{},c.title=d("Create a collection from a pair of datasets"),a.collectionCreatorModal(b,c,h)};return{PairCollectionCreator:h,pairCollectionCreatorModal:i,createPairCollection:e}}); //# sourceMappingURL=../../../maps/mvc/collection/pair-collection-creator.js.map \ No newline at end of file diff --git a/static/scripts/mvc/dataset/dataset-choice.js b/static/scripts/mvc/dataset/dataset-choice.js index e827a4fa230..3b620ac7e73 100644 --- a/static/scripts/mvc/dataset/dataset-choice.js +++ b/static/scripts/mvc/dataset/dataset-choice.js @@ -1,2 +1,2 @@ -define(["mvc/dataset/dataset-model","mvc/dataset/dataset-list","mvc/ui/ui-modal","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){function f(a,b,c){function d(a,b){for(var c in b)if(b.hasOwnProperty(c)&&a[c]!==b[c])return!1;return!0}return a.filter(function(a){return console.debug(a),!a.deleted&&a.visible&&(!c||void 0===a.collection_type)&&d(a,b)})}var g=function(d,g){function h(){l.resolve(j.getSelectedModels().map(function(a){return a.toJSON()}))}g=_.defaults(g||{},{datasetsOnly:!0,where:{state:"ok"},multiselect:!1,selected:[]}),g.title=g.title||e(g.multiselect?"Choose datasets:":"Choose a dataset:");var i,j,k,l=jQuery.Deferred(),m=g.filter||f;return d=m(d,g.where,g.datasetsOnly),d.length?(g.multiselect&&(k={},k[e("Ok")]=h),i=new c.View({height:"auto",buttons:k,closing_events:!0,closing_callback:function(){l.resolve(null)},body:['
                      '].join("")}),i.$(".modal-header").remove(),i.$(".modal-footer").css("margin-top","0px"),j=new b.DatasetList({title:g.title,subtitle:g.subtitle||e(["Click the checkboxes on the right to select datasets. ","Click the datasets names to see their details. "].join("")),el:i.$body.find(".list-panel"),selecting:!0,selected:g.selected,collection:new a.DatasetAssociationCollection(d)}),j.once("rendered:initial",function(){i.show(),i.$el.addClass("dataset-choice-modal")}),g.multiselect||(j.on("rendered",function(){j.$(".list-actions").hide()}),j.on("view:selected",function(a){l.resolve([a.model.toJSON()])})),j.render(0),l.always(function(){i.hide()})):l.reject("No matches found")},h=Backbone.View.extend(d.LoggableMixin).extend({className:"dataset-choice",initialize:function(a){this.debug(this+"(DatasetChoice).initialize:",a),this.label=void 0!==a.label?e(a.label):"",this.where=a.where,this.datasetsOnly=void 0!==a.datasetsOnly?a.datasetsOnly:!0,this.datasetJSON=a.datasetJSON||[],this.selected=a.selected||[],this._setUpListeners()},_setUpListeners:function(){},render:function(){var a=this.toJSON();return this.$el.html(this._template(a)),this.$(".selected").replaceWith(this._renderSelected(a)),this},_template:function(a){return _.template([""].join(""))(a)},_renderSelected:function(a){return $(a.selected.length?_.template(['
                      ','<%= selected.hid %>: <%= selected.name %>','',"<%= selected.misc_blurb %>","",e("format")+": ","<%= selected.file_ext %>","<%= selected.misc_info %>","","
                      "].join(""),{variable:"selected"})(a.selected[0]):['(',e("click to select a dataset"),")"].join(""))},toJSON:function(){var a=this;return{label:a.label,datasets:a.datasetJSON,selected:_.compact(_.map(a.selected,function(b){return _.findWhere(a.datasetJSON,{id:b})}))}},events:{click:"chooseWithModal"},chooseWithModal:function(){var a=this;return this._createModal().done(function(b){b?(a.selected=_.pluck(b,"id"),a.trigger("selected",a,b),a.render()):a.trigger("cancelled",a)}).fail(function(){a.trigger("error",a,arguments)})},_createModal:function(){return new g(this.datasetJSON,this._getModalOptions())},_getModalOptions:function(){return{title:this.label,multiselect:!1,selected:this.selected,where:this.where,datasetsOnly:this.datasetsOnly}},toString:function(){return"DatasetChoice("+this.selected+")"}}),i=h.extend({className:h.prototype.className+" multi",cells:{hid:e("History #"),name:e("Name"),misc_blurb:e("Summary"),file_ext:e("Format"),genome_build:e("Genome"),tags:e("Tags"),annotation:e("Annotation")},initialize:function(a){this.showHeaders=void 0!==a.showHeaders?a.showHeaders:!0,this.cells=a.cells||this.cells,h.prototype.initialize.call(this,a)},_renderSelected:function(a){return $(a.selected.length?_.template(['',"<% if( json.showHeaders ){ %>","","<% _.map( json.cells, function( val, key ){ %>","","<% }); %>","","<% } %>","","<% _.map( json.selected, function( selected ){ %>","","<% _.map( json.cells, function( val, key ){ %>",'',"<% }) %>","","<% }); %>","","
                      <%= val %>
                      <%= selected[ key ] %>
                      "].join(""),{variable:"json"})(a):['(',e("click to select a dataset"),")"].join(""))},toJSON:function(){return _.extend(h.prototype.toJSON.call(this),{showHeaders:this.showHeaders,cells:this.cells})},_getModalOptions:function(){return _.extend(h.prototype._getModalOptions.call(this),{multiselect:!0})},toString:function(){return"DatasetChoice("+this.selected+")"}});return{DatasetChoiceModal:g,DatasetChoice:h,MultiDatasetChoice:i}}); +define(["mvc/dataset/dataset-model","mvc/dataset/dataset-list","mvc/ui/ui-modal","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){function f(a,b,c){function d(a,b){for(var c in b)if(b.hasOwnProperty(c)&&a[c]!==b[c])return!1;return!0}return a.filter(function(a){return console.debug(a),!a.deleted&&a.visible&&(!c||void 0===a.collection_type)&&d(a,b)})}var g=function(d,g){function h(){l.resolve(j.getSelectedModels().map(function(a){return a.toJSON()}))}g=_.defaults(g||{},{datasetsOnly:!0,where:{state:"ok"},multiselect:!1,selected:[]}),g.title=g.title||e(g.multiselect?"Choose datasets:":"Choose a dataset:");var i,j,k,l=jQuery.Deferred(),m=g.filter||f;return d=m(d,g.where,g.datasetsOnly),d.length?(g.multiselect&&(k={},k[e("Ok")]=h),i=new c.View({height:"auto",buttons:k,closing_events:!0,closing_callback:function(){l.resolve(null)},body:['
                      '].join("")}),i.$(".modal-header").remove(),i.$(".modal-footer").css("margin-top","0px"),j=new b.DatasetList({title:g.title,subtitle:g.subtitle||e(["Click the checkboxes on the right to select datasets. ","Click the datasets names to see their details. "].join("")),el:i.$body.find(".list-panel"),selecting:!0,selected:g.selected,collection:new a.DatasetAssociationCollection(d)}),j.once("rendered:initial",function(){i.show(),i.$el.addClass("dataset-choice-modal")}),g.multiselect||(j.on("rendered",function(){j.$(".list-actions").hide()}),j.on("view:selected",function(a){l.resolve([a.model.toJSON()])})),j.render(0),l.always(function(){i.hide()})):l.reject("No matches found")},h=Backbone.View.extend(d.LoggableMixin).extend({className:"dataset-choice",initialize:function(a){this.debug(this+"(DatasetChoice).initialize:",a),this.label=void 0!==a.label?e(a.label):"",this.where=a.where,this.datasetsOnly=void 0!==a.datasetsOnly?a.datasetsOnly:!0,this.datasetJSON=a.datasetJSON||[],this.selected=a.selected||[],this._setUpListeners()},_setUpListeners:function(){},render:function(){var a=this.toJSON();return this.$el.html(this._template(a)),this.$(".selected").replaceWith(this._renderSelected(a)),this},_template:function(a){return _.template([""].join(""))(a)},_renderSelected:function(a){return $(a.selected.length?_.template(['
                      ','<%- selected.hid %>: <%- selected.name %>','',"<%- selected.misc_blurb %>","",e("format")+": ","<%- selected.file_ext %>","<%- selected.misc_info %>","","
                      "].join(""),{variable:"selected"})(a.selected[0]):['(',e("click to select a dataset"),")"].join(""))},toJSON:function(){var a=this;return{label:a.label,datasets:a.datasetJSON,selected:_.compact(_.map(a.selected,function(b){return _.findWhere(a.datasetJSON,{id:b})}))}},events:{click:"chooseWithModal"},chooseWithModal:function(){var a=this;return this._createModal().done(function(b){b?(a.selected=_.pluck(b,"id"),a.trigger("selected",a,b),a.render()):a.trigger("cancelled",a)}).fail(function(){a.trigger("error",a,arguments)})},_createModal:function(){return new g(this.datasetJSON,this._getModalOptions())},_getModalOptions:function(){return{title:this.label,multiselect:!1,selected:this.selected,where:this.where,datasetsOnly:this.datasetsOnly}},toString:function(){return"DatasetChoice("+this.selected+")"}}),i=h.extend({className:h.prototype.className+" multi",cells:{hid:e("History #"),name:e("Name"),misc_blurb:e("Summary"),file_ext:e("Format"),genome_build:e("Genome"),tags:e("Tags"),annotation:e("Annotation")},initialize:function(a){this.showHeaders=void 0!==a.showHeaders?a.showHeaders:!0,this.cells=a.cells||this.cells,h.prototype.initialize.call(this,a)},_renderSelected:function(a){return $(a.selected.length?_.template(['',"<% if( json.showHeaders ){ %>","","<% _.map( json.cells, function( val, key ){ %>","","<% }); %>","","<% } %>","","<% _.map( json.selected, function( selected ){ %>","","<% _.map( json.cells, function( val, key ){ %>",'',"<% }) %>","","<% }); %>","","
                      <%- val %>
                      <%- selected[ key ] %>
                      "].join(""),{variable:"json"})(a):['(',e("click to select a dataset"),")"].join(""))},toJSON:function(){return _.extend(h.prototype.toJSON.call(this),{showHeaders:this.showHeaders,cells:this.cells})},_getModalOptions:function(){return _.extend(h.prototype._getModalOptions.call(this),{multiselect:!0})},toString:function(){return"DatasetChoice("+this.selected+")"}});return{DatasetChoiceModal:g,DatasetChoice:h,MultiDatasetChoice:i}}); //# sourceMappingURL=../../../maps/mvc/dataset/dataset-choice.js.map \ No newline at end of file diff --git a/static/scripts/mvc/dataset/dataset-li-edit.js b/static/scripts/mvc/dataset/dataset-li-edit.js index c0a3a10b3fd..01431339202 100644 --- a/static/scripts/mvc/dataset/dataset-li-edit.js +++ b/static/scripts/mvc/dataset/dataset-li-edit.js @@ -1,2 +1,2 @@ -define(["mvc/dataset/states","mvc/dataset/dataset-li","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/base-mvc","utils/localization"],function(a,b,c,d,e,f,g){var h=b.DatasetListItemView,i=h.extend({initialize:function(a){h.prototype.initialize.call(this,a),this.hasUser=a.hasUser,this.purgeAllowed=a.purgeAllowed||!1,this.tagsEditorShown=a.tagsEditorShown||!1,this.annotationEditorShown=a.annotationEditorShown||!1},_renderPrimaryActions:function(){var b=h.prototype._renderPrimaryActions.call(this);return this.model.get("state")===a.NOT_VIEWABLE?b:h.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===a.DISCARDED||!this.model.get("accessible"))return null;var b=this.model.get("purged"),c=this.model.get("deleted"),d={title:g("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return c||b?(d.disabled=!0,b?d.title=g("Cannot edit attributes of datasets removed from disk"):c&&(d.title=g("Undelete dataset to edit attributes"))):_.contains([a.UPLOAD,a.NEW],this.model.get("state"))&&(d.disabled=!0,d.title=g("This dataset is not yet editable")),e(d)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var a=this,b=this.model.isDeletedOrPurged();return e({title:g(b?"Dataset is already deleted":"Delete"),disabled:b,faIcon:"fa-times",classes:"delete-btn",onclick:function(){a.$el.find(".icon-btn.delete-btn").trigger("mouseout"),a.model.delete()}})},_renderDetails:function(){var b=h.prototype._renderDetails.call(this),c=this.model.get("state");return!this.model.isDeletedOrPurged()&&_.contains([a.OK,a.FAILED_METADATA],c)&&(this._renderTags(b),this._renderAnnotation(b),this._makeDbkeyEditLink(b)),this._setUpBehaviors(b),b},_renderSecondaryActions:function(){var b=h.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case a.UPLOAD:case a.NEW:case a.NOT_VIEWABLE:return b;case a.ERROR:return b.unshift(this._renderErrButton()),b.concat([this._renderRerunButton()]);case a.OK:case a.FAILED_METADATA:return b.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return b.concat([this._renderRerunButton()])},_renderErrButton:function(){return e({title:g("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){return e({title:g("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_renderVisualizationsButton:function(){var a=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||_.isEmpty(a))return null;if(!_.isObject(a[0]))return this.warn("Visualizations have been switched off"),null;var b=$(this.templates.visualizations(a,this));return b.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(b.find(".visualization-link").addBack(".visualization-link")),b},_addScratchBookFn:function(a){a.click(function(a){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",type:"url",content:$(this).attr("href")}),a.preventDefault(),a.stopPropagation())})},_renderTags:function(a){if(this.hasUser){var b=this;this.tagsEditor=new c.TagsEditor({model:this.model,el:a.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.tagsEditorShown=!0},onhide:function(){b.tagsEditorShown=!1},$activator:e({title:g("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(a.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(a){if(this.hasUser){var b=this;this.annotationEditor=new d.AnnotationEditor({model:this.model,el:a.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.annotationEditorShown=!0},onhide:function(){b.annotationEditorShown=!1},$activator:e({title:g("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(a.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(a){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var b=$('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);a.find(".dbkey .value").replaceWith(b)}},events:_.extend(_.clone(h.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(a){this.trigger("edit",this,a)},"click .delete-btn":function(a){this.trigger("delete",this,a)},"click .rerun-btn":function(a){this.trigger("rerun",this,a)},"click .report-err-btn":function(a){this.trigger("report-err",this,a)},"click .visualization-btn":function(a){this.trigger("visualize",this,a)},"click .dbkey a":function(a){this.trigger("edit",this,a)}}),_clickUndeleteLink:function(){return this.model.undelete(),!1},_clickPurgeLink:function(){return this.model.purge(),!1},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDAEditView("+a+")"}});return i.prototype.templates=function(){var a=_.extend({},h.prototype.templates.warnings,{failed_metadata:f.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
                      ',g("An error occurred setting the metadata for this dataset"),'
                      ',g("Set it manually or retry auto-detection"),"","
                      ","<% } %>"],"dataset"),deleted:f.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
                      ',g("This dataset has been deleted"),'
                      ',g("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
                      ',g("Permanently remove it from disk"),"","<% } %>","
                      ","<% } %>"],"dataset")}),b=f.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
                      ','','',"",'","
                      ","<% } %>"],"visualizations");return _.extend({},h.prototype.templates,{warnings:a,visualizations:b})}(),{DatasetListItemEdit:i}}); +define(["mvc/dataset/states","mvc/dataset/dataset-li","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/base-mvc","utils/localization"],function(a,b,c,d,e,f,g){var h=b.DatasetListItemView,i=h.extend({initialize:function(a){h.prototype.initialize.call(this,a),this.hasUser=a.hasUser,this.purgeAllowed=a.purgeAllowed||!1,this.tagsEditorShown=a.tagsEditorShown||!1,this.annotationEditorShown=a.annotationEditorShown||!1},_renderPrimaryActions:function(){var b=h.prototype._renderPrimaryActions.call(this);return this.model.get("state")===a.NOT_VIEWABLE?b:h.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===a.DISCARDED||!this.model.get("accessible"))return null;var b=this.model.get("purged"),c=this.model.get("deleted"),d={title:g("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return c||b?(d.disabled=!0,b?d.title=g("Cannot edit attributes of datasets removed from disk"):c&&(d.title=g("Undelete dataset to edit attributes"))):_.contains([a.UPLOAD,a.NEW],this.model.get("state"))&&(d.disabled=!0,d.title=g("This dataset is not yet editable")),e(d)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var a=this,b=this.model.isDeletedOrPurged();return e({title:g(b?"Dataset is already deleted":"Delete"),disabled:b,faIcon:"fa-times",classes:"delete-btn",onclick:function(){a.$el.find(".icon-btn.delete-btn").trigger("mouseout"),a.model.delete()}})},_renderDetails:function(){var b=h.prototype._renderDetails.call(this),c=this.model.get("state");return!this.model.isDeletedOrPurged()&&_.contains([a.OK,a.FAILED_METADATA],c)&&(this._renderTags(b),this._renderAnnotation(b),this._makeDbkeyEditLink(b)),this._setUpBehaviors(b),b},_renderSecondaryActions:function(){var b=h.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case a.UPLOAD:case a.NEW:case a.NOT_VIEWABLE:return b;case a.ERROR:return b.unshift(this._renderErrButton()),b.concat([this._renderRerunButton()]);case a.OK:case a.FAILED_METADATA:return b.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return b.concat([this._renderRerunButton()])},_renderErrButton:function(){return e({title:g("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){return e({title:g("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_renderVisualizationsButton:function(){var a=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||_.isEmpty(a))return null;if(!_.isObject(a[0]))return this.warn("Visualizations have been switched off"),null;var b=$(this.templates.visualizations(a,this));return b.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(b.find(".visualization-link").addBack(".visualization-link")),b},_addScratchBookFn:function(a){a.click(function(a){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",type:"url",content:$(this).attr("href")}),a.preventDefault(),a.stopPropagation())})},_renderTags:function(a){if(this.hasUser){var b=this;this.tagsEditor=new c.TagsEditor({model:this.model,el:a.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.tagsEditorShown=!0},onhide:function(){b.tagsEditorShown=!1},$activator:e({title:g("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(a.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(a){if(this.hasUser){var b=this;this.annotationEditor=new d.AnnotationEditor({model:this.model,el:a.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.annotationEditorShown=!0},onhide:function(){b.annotationEditorShown=!1},$activator:e({title:g("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(a.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(a){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var b=$('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);a.find(".dbkey .value").replaceWith(b)}},events:_.extend(_.clone(h.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(a){this.trigger("edit",this,a)},"click .delete-btn":function(a){this.trigger("delete",this,a)},"click .rerun-btn":function(a){this.trigger("rerun",this,a)},"click .report-err-btn":function(a){this.trigger("report-err",this,a)},"click .visualization-btn":function(a){this.trigger("visualize",this,a)},"click .dbkey a":function(a){this.trigger("edit",this,a)}}),_clickUndeleteLink:function(){return this.model.undelete(),!1},_clickPurgeLink:function(){return this.model.purge(),!1},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDAEditView("+a+")"}});return i.prototype.templates=function(){var a=_.extend({},h.prototype.templates.warnings,{failed_metadata:f.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
                      ',g("An error occurred setting the metadata for this dataset"),'
                      ',g("Set it manually or retry auto-detection"),"","
                      ","<% } %>"],"dataset"),deleted:f.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
                      ',g("This dataset has been deleted"),'
                      ',g("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
                      ',g("Permanently remove it from disk"),"","<% } %>","
                      ","<% } %>"],"dataset")}),b=f.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
                      ','','',"",'","
                      ","<% } %>"],"visualizations");return _.extend({},h.prototype.templates,{warnings:a,visualizations:b})}(),{DatasetListItemEdit:i}}); //# sourceMappingURL=../../../maps/mvc/dataset/dataset-li-edit.js.map \ No newline at end of file diff --git a/static/scripts/mvc/dataset/dataset-li.js b/static/scripts/mvc/dataset/dataset-li.js index 65584155f28..ab3119a8b0d 100644 --- a/static/scripts/mvc/dataset/dataset-li.js +++ b/static/scripts/mvc/dataset/dataset-li.js @@ -1,2 +1,2 @@ -define(["mvc/list/list-item","mvc/dataset/states","ui/fa-icon-button","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=a.ListItemView,g=f.extend({className:f.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log(this+".initialize:",a),f.prototype.initialize.call(this,a),this.linkTarget=a.linkTarget||"_blank",this._setUpListeners()},_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(){this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()?this.model.fetch():this.render()},this)},_fetchModelDetails:function(){var a=this;return a.model.inReadyState()&&!a.model.hasDetails()?a.model.fetch({silent:!0}):jQuery.when()},remove:function(a,b){var c=this;a=a||this.fxSpeed,this.$el.fadeOut(a,function(){Backbone.View.prototype.remove.call(c),b&&b.call(c)})},render:function(a){return f.prototype.render.call(this,a)},_swapNewRender:function(a){return f.prototype._swapNewRender.call(this,a),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var a=this.model.get("state");if(a===b.NOT_VIEWABLE||a===b.DISCARDED||!this.model.get("accessible"))return null;var d={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))d.disabled=!0,d.title=e("Cannot display datasets removed from disk");else if(a===b.UPLOAD)d.disabled=!0,d.title=e("This dataset must finish uploading before it can be viewed");else if(a===b.NEW)d.disabled=!0,d.title=e("This dataset is not yet viewable");else{d.title=e("View data"),d.href=this.model.urls.display;var f=this;d.onclick=function(a){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add_dataset(f.model.get("id")),a.preventDefault())}}return d.faIcon="fa-eye",c(d)},_renderDetails:function(){if(this.model.get("state")===b.NOT_VIEWABLE)return $(this.templates.noAccess(this.model.toJSON(),this));var a=f.prototype._renderDetails.call(this);return a.find(".actions .left").empty().append(this._renderSecondaryActions()),a.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),a.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(a),a},_renderSummary:function(){var a=this.model.toJSON(),b=this.templates.summaries[a.state];return(b=b||this.templates.summaries.unknown)(a,this)},_renderDetailMessages:function(){var a=this,b=$('
                      '),c=a.model.toJSON();return _.each(a.templates.detailMessages,function(d){b.append($(d(c,a)))}),b},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case b.NOT_VIEWABLE:return[];case b.OK:case b.FAILED_METADATA:case b.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return c({title:e("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:_.isEmpty(this.model.get("meta_files"))?$(['','',""].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var a=this.model.urls;return $(['
                      ','','',"",'","
                      "].join("\n"))},events:_.extend(_.clone(f.prototype.events),{"click .display-btn":function(a){this.trigger("display",this,a)},"click .params-btn":function(a){this.trigger("params",this,a)},"click .download-btn":function(a){this.trigger("download",this,a)}}),toString:function(){var a=this.model?this.model+"":"(no model)";return"DatasetListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{failed_metadata:d.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','
                      ',e("An error occurred setting the metadata for this dataset"),"
                      ","<% } %>"]),error:d.wrapTemplate(["<% if( model.error ){ %>",'
                      ',e("There was an error getting the data for this dataset"),": <%- model.error %>","
                      ","<% } %>"]),purged:d.wrapTemplate(["<% if( model.purged ){ %>",'
                      ',e("This dataset has been deleted and removed from disk"),"
                      ","<% } %>"]),deleted:d.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
                      ',e("This dataset has been deleted"),"
                      ","<% } %>"])}),c=d.wrapTemplate(['
                      ','
                      ','
                      ','
                      ','
                      ',"
                      ","<% if( !dataset.deleted && !dataset.purged ){ %>",'
                      ','
                      ','
                      ',"<% if( dataset.peek ){ %>",'
                      <%= dataset.peek %>
                      ',"<% } %>","<% } %>","
                      "],"dataset"),g=d.wrapTemplate(['
                      ','
                      ',e("You do not have permission to view this dataset"),"
                      ","
                      "],"dataset"),h={};h[b.OK]=h[b.FAILED_METADATA]=d.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'
                      ','<%- dataset.misc_blurb %>',"
                      ","<% } %>","<% if( dataset.file_ext ){ %>",'
                      ','",'<%- dataset.file_ext %>',"
                      ","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'
                      ','",'',"<%- dataset.metadata_dbkey %>","","
                      ","<% } %>","<% if( dataset.misc_info ){ %>",'
                      ','<%- dataset.misc_info %>',"
                      ","<% } %>"],"dataset"),h[b.NEW]=d.wrapTemplate(["
                      ",e("This is a new dataset and not all of its data are available yet"),"
                      "],"dataset"),h[b.NOT_VIEWABLE]=d.wrapTemplate(["
                      ",e("You do not have permission to view this dataset"),"
                      "],"dataset"),h[b.DISCARDED]=d.wrapTemplate(["
                      ",e("The job creating this dataset was cancelled before completion"),"
                      "],"dataset"),h[b.QUEUED]=d.wrapTemplate(["
                      ",e("This job is waiting to run"),"
                      "],"dataset"),h[b.RUNNING]=d.wrapTemplate(["
                      ",e("This job is currently running"),"
                      "],"dataset"),h[b.UPLOAD]=d.wrapTemplate(["
                      ",e("This dataset is currently uploading"),"
                      "],"dataset"),h[b.SETTING_METADATA]=d.wrapTemplate(["
                      ",e("Metadata is being auto-detected"),"
                      "],"dataset"),h[b.PAUSED]=d.wrapTemplate(["
                      ",e('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"
                      "],"dataset"),h[b.ERROR]=d.wrapTemplate(["<% if( !dataset.purged ){ %>","
                      <%- dataset.misc_blurb %>
                      ","<% } %>",'',e("An error occurred with this dataset"),":",'
                      <%- dataset.misc_info %>
                      '],"dataset"),h[b.EMPTY]=d.wrapTemplate(["
                      ",e("No data"),": <%- dataset.misc_blurb %>
                      "],"dataset"),h.unknown=d.wrapTemplate(['
                      Error: unknown dataset state: "<%- dataset.state %>"
                      '],"dataset");var i={resubmitted:d.wrapTemplate(["<% if( model.resubmitted ){ %>",'
                      ',e("The job creating this dataset has been resubmitted"),"
                      ","<% } %>"])},j=d.wrapTemplate(["<% _.each( apps, function( app ){ %>",'
                      ','<%- app.label %> ','',"<% _.each( app.links, function( link ){ %>",'',"<% print( _l( link.text ) ); %>"," ","<% }); %>","","
                      ","<% }); %>"],"apps");return _.extend({},f.prototype.templates,{warnings:a,details:c,noAccess:g,summaries:h,detailMessages:i,displayApplications:j})}(),{DatasetListItemView:g}}); +define(["mvc/list/list-item","mvc/dataset/states","ui/fa-icon-button","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=a.ListItemView,g=f.extend({className:f.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log(this+".initialize:",a),f.prototype.initialize.call(this,a),this.linkTarget=a.linkTarget||"_blank",this._setUpListeners()},_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(){this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()?this.model.fetch():this.render()},this)},_fetchModelDetails:function(){var a=this;return a.model.inReadyState()&&!a.model.hasDetails()?a.model.fetch({silent:!0}):jQuery.when()},remove:function(a,b){var c=this;a=a||this.fxSpeed,this.$el.fadeOut(a,function(){Backbone.View.prototype.remove.call(c),b&&b.call(c)})},render:function(a){return f.prototype.render.call(this,a)},_swapNewRender:function(a){return f.prototype._swapNewRender.call(this,a),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var a=this.model.get("state");if(a===b.NOT_VIEWABLE||a===b.DISCARDED||!this.model.get("accessible"))return null;var d={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))d.disabled=!0,d.title=e("Cannot display datasets removed from disk");else if(a===b.UPLOAD)d.disabled=!0,d.title=e("This dataset must finish uploading before it can be viewed");else if(a===b.NEW)d.disabled=!0,d.title=e("This dataset is not yet viewable");else{d.title=e("View data"),d.href=this.model.urls.display;var f=this;d.onclick=function(a){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add_dataset(f.model.get("id")),a.preventDefault())}}return d.faIcon="fa-eye",c(d)},_renderDetails:function(){if(this.model.get("state")===b.NOT_VIEWABLE)return $(this.templates.noAccess(this.model.toJSON(),this));var a=f.prototype._renderDetails.call(this);return a.find(".actions .left").empty().append(this._renderSecondaryActions()),a.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),a.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(a),a},_renderSummary:function(){var a=this.model.toJSON(),b=this.templates.summaries[a.state];return(b=b||this.templates.summaries.unknown)(a,this)},_renderDetailMessages:function(){var a=this,b=$('
                      '),c=a.model.toJSON();return _.each(a.templates.detailMessages,function(d){b.append($(d(c,a)))}),b},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case b.NOT_VIEWABLE:return[];case b.OK:case b.FAILED_METADATA:case b.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return c({title:e("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:_.isEmpty(this.model.get("meta_files"))?$(['','',""].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var a=this.model.urls;return $(['
                      ','','',"",'","
                      "].join("\n"))},events:_.extend(_.clone(f.prototype.events),{"click .display-btn":function(a){this.trigger("display",this,a)},"click .params-btn":function(a){this.trigger("params",this,a)},"click .download-btn":function(a){this.trigger("download",this,a)}}),toString:function(){var a=this.model?this.model+"":"(no model)";return"DatasetListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{failed_metadata:d.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','
                      ',e("An error occurred setting the metadata for this dataset"),"
                      ","<% } %>"]),error:d.wrapTemplate(["<% if( model.error ){ %>",'
                      ',e("There was an error getting the data for this dataset"),": <%- model.error %>","
                      ","<% } %>"]),purged:d.wrapTemplate(["<% if( model.purged ){ %>",'
                      ',e("This dataset has been deleted and removed from disk"),"
                      ","<% } %>"]),deleted:d.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
                      ',e("This dataset has been deleted"),"
                      ","<% } %>"])}),c=d.wrapTemplate(['
                      ','
                      ','
                      ','
                      ','
                      ',"
                      ","<% if( !dataset.deleted && !dataset.purged ){ %>",'
                      ','
                      ','
                      ',"<% if( dataset.peek ){ %>",'
                      <%= dataset.peek %>
                      ',"<% } %>","<% } %>","
                      "],"dataset"),g=d.wrapTemplate(['
                      ','
                      ',e("You do not have permission to view this dataset"),"
                      ","
                      "],"dataset"),h={};h[b.OK]=h[b.FAILED_METADATA]=d.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'
                      ','<%- dataset.misc_blurb %>',"
                      ","<% } %>","<% if( dataset.file_ext ){ %>",'
                      ','",'<%- dataset.file_ext %>',"
                      ","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'
                      ','",'',"<%- dataset.metadata_dbkey %>","","
                      ","<% } %>","<% if( dataset.misc_info ){ %>",'
                      ','<%- dataset.misc_info %>',"
                      ","<% } %>"],"dataset"),h[b.NEW]=d.wrapTemplate(["
                      ",e("This is a new dataset and not all of its data are available yet"),"
                      "],"dataset"),h[b.NOT_VIEWABLE]=d.wrapTemplate(["
                      ",e("You do not have permission to view this dataset"),"
                      "],"dataset"),h[b.DISCARDED]=d.wrapTemplate(["
                      ",e("The job creating this dataset was cancelled before completion"),"
                      "],"dataset"),h[b.QUEUED]=d.wrapTemplate(["
                      ",e("This job is waiting to run"),"
                      "],"dataset"),h[b.RUNNING]=d.wrapTemplate(["
                      ",e("This job is currently running"),"
                      "],"dataset"),h[b.UPLOAD]=d.wrapTemplate(["
                      ",e("This dataset is currently uploading"),"
                      "],"dataset"),h[b.SETTING_METADATA]=d.wrapTemplate(["
                      ",e("Metadata is being auto-detected"),"
                      "],"dataset"),h[b.PAUSED]=d.wrapTemplate(["
                      ",e('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"
                      "],"dataset"),h[b.ERROR]=d.wrapTemplate(["<% if( !dataset.purged ){ %>","
                      <%- dataset.misc_blurb %>
                      ","<% } %>",'',e("An error occurred with this dataset"),":",'
                      <%- dataset.misc_info %>
                      '],"dataset"),h[b.EMPTY]=d.wrapTemplate(["
                      ",e("No data"),": <%- dataset.misc_blurb %>
                      "],"dataset"),h.unknown=d.wrapTemplate(['
                      Error: unknown dataset state: "<%- dataset.state %>"
                      '],"dataset");var i={resubmitted:d.wrapTemplate(["<% if( model.resubmitted ){ %>",'
                      ',e("The job creating this dataset has been resubmitted"),"
                      ","<% } %>"])},j=d.wrapTemplate(["<% _.each( apps, function( app ){ %>",'
                      ','<%- app.label %> ','',"<% _.each( app.links, function( link ){ %>",'',"<% print( _l( link.text ) ); %>"," ","<% }); %>","","
                      ","<% }); %>"],"apps");return _.extend({},f.prototype.templates,{warnings:a,details:c,noAccess:g,summaries:h,detailMessages:i,displayApplications:j})}(),{DatasetListItemView:g}}); //# sourceMappingURL=../../../maps/mvc/dataset/dataset-li.js.map \ No newline at end of file diff --git a/static/scripts/mvc/history/history-panel.js b/static/scripts/mvc/history/history-panel.js index 4c009eeb4f1..1a20b8ba9b7 100644 --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -1,2 +1,2 @@ -define(["mvc/list/list-panel","mvc/history/history-model","mvc/history/history-contents","mvc/history/hda-li","mvc/history/hdca-li","mvc/collection/collection-panel","mvc/user/user-model","ui/fa-icon-button","mvc/ui/popup-menu","mvc/base-mvc","utils/localization","ui/search-input"],function(a,b,c,d,e,f,g,h,i,j,k){var l=j.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(a){var b="expandedIds";this.save(b,_.extend(this.get(b),_.object([a.id],[a.get("id")])))},removeExpanded:function(a){var b="expandedIds";this.save(b,_.omit(this.get(b),a.id))},toString:function(){return"HistoryPrefs("+this.id+")"}});l.storageKeyPrefix="history:",l.historyStorageKey=function(a){if(!a)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+a);return l.storageKeyPrefix+a},l.get=function(a){return new l({id:l.historyStorageKey(a)})},l.clearAll=function(){for(var a in sessionStorage)0===a.indexOf(l.storageKeyPrefix)&&sessionStorage.removeItem(a)};var m=a.ModelListPanel,n=m.extend({HDAViewClass:d.HDAListItemView,HDCAViewClass:e.HDCAListItemView,collectionClass:c.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:m.prototype.className+" history-panel",emptyMsg:k("This history is empty"),noneFoundMsg:k("No matching datasets found"),searchPlaceholder:k("search datasets"),initialize:function(a){m.prototype.initialize.call(this,a),this.linkTarget=a.linkTarget||"_blank"},freeModel:function(){return m.prototype.freeModel.call(this),this.model&&this.model.clearUpdateTimeout(),this},_setUpListeners:function(){m.prototype._setUpListeners.call(this),this.on("error",function(a,b,c,d,e){this.errorHandler(a,b,c,d,e)}),this.on("loading-done",function(){this.views.length||this.trigger("empty-history",this)})},loadHistoryWithDetails:function(a,b,c,d){this.info("loadHistoryWithDetails:",a,b,c,d);var e=function(a){return _.values(l.get(a.id).get("expandedIds"))};return this.loadHistory(a,b,c,d,e)},loadHistory:function(a,c,d,e,f){this.info("loadHistory:",a,c,d,e,f);var g=this;c=c||{},g.trigger("loading",g);var h=b.History.getHistoryData(a,{historyFn:d,contentsFn:e,detailIdsFn:c.initiallyExpanded||f});return g._loadHistoryFromXHR(h,c).fail(function(b,d,e){g.trigger("error",g,b,c,k("An error was encountered while "+d),{historyId:a,history:e||{}})}).always(function(){g.trigger("loading-done",g)})},_loadHistoryFromXHR:function(a,b){var c=this;return a.then(function(a,d){c.JSONToModel(a,d,b),c.render()}),a.fail(function(){c.render()}),a},refreshContents:function(a,b){return this.model?this.model.refresh(a,b):$.when()},JSONToModel:function(a,c,d){this.log("JSONToModel:",a,c,d),d=d||{};var e=new b.History(a,c,d);return this.setModel(e),e},setModel:function(a,b){b=b||{},m.prototype.setModel.call(this,a,b),this.model&&this._setUpWebStorage(b.initiallyExpanded,b.show_deleted,b.show_hidden)},_setUpWebStorage:function(a,b,c){return this.storage&&this.stopListening(this.storage),this.storage=new l({id:l.historyStorageKey(this.model.get("id"))}),_.isObject(a)&&this.storage.set("expandedIds",a),_.isBoolean(b)&&this.storage.set("show_deleted",b),_.isBoolean(c)&&this.storage.set("show_hidden",c),this.trigger("new-storage",this.storage,this),this.log(this+" (init'd) storage:",this.storage.get()),this.listenTo(this.storage,{"change:show_deleted":function(a,b){this.showDeleted=b},"change:show_hidden":function(a,b){this.showHidden=b}},this),this.showDeleted=void 0!==b?b:this.storage.get("show_deleted"),this.showHidden=void 0!==c?c:this.storage.get("show_hidden"),this},_buildNewRender:function(){var a=m.prototype._buildNewRender.call(this);return this.multiselectActions().length&&a.find(".controls .actions").prepend(this._renderSelectButton()),a},_renderSelectButton:function(){return h({title:k("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"})},_getItemViewClass:function(a){var b=a.get("history_content_type");switch(b){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+b)},_filterItem:function(a){var b=this;return m.prototype._filterItem.call(b,a)&&(!a.hidden()||b.showHidden)&&(!a.isDeletedOrPurged()||b.showDeleted)},_getItemViewOptions:function(a){var b=m.prototype._getItemViewOptions.call(this,a);return _.extend(b,{linkTarget:this.linkTarget,expanded:!!this.storage.get("expandedIds")[a.id],hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(a){var b=this;return m.prototype._setUpItemViewListeners.call(b,a),a.on("expanded",function(a){b.storage.addExpanded(a.model)}),a.on("collapsed",function(a){b.storage.removeExpanded(a.model)}),this},getSelectedModels:function(){var a=m.prototype.getSelectedModels.call(this);return a.historyId=this.collection.historyId,a},events:_.extend(_.clone(m.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .messages [class$=message]":"clearMessages"}),toggleShowDeleted:function(a,b){return a=void 0!==a?a:!this.showDeleted,b=void 0!==b?b:!0,this.showDeleted=a,b&&this.storage.set("show_deleted",a),this.trigger("show-hidden",a),this.renderItems(),this.showDeleted},toggleShowHidden:function(a,b){return a=void 0!==a?a:!this.showHidden,b=void 0!==b?b:!0,this.showHidden=a,b&&this.storage.set("show_hidden",a),this.trigger("show-hidden",a),this.renderItems(),this.showHidden},_firstSearch:function(a){var b=this,c=".history-search-input";return this.log("onFirstSearch",a),b.model.contents.haveDetails()?void b.searchItems(a):(b.$el.find(c).searchInput("toggle-loading"),void b.model.contents.fetchAllDetails({silent:!0}).always(function(){b.$el.find(c).searchInput("toggle-loading")}).done(function(){b.searchItems(a)}))},errorHandler:function(a,b,c,d,e){if(this.error(a,b,c,d,e),b&&0===b.status&&0===b.readyState);else if(b&&502===b.status);else{var f=this._parseErrorMessage(a,b,c,d,e);this.$messages().is(":visible")?this.displayMessage("error",f.message,f.details):this.once("rendered",function(){this.displayMessage("error",f.message,f.details)})}},_parseErrorMessage:function(a,b,c,d,e){var f=Galaxy.currUser,h={message:this._bePolite(d),details:{message:d,raven:window.Raven&&_.isFunction(Raven.lastEventId)?Raven.lastEventId():void 0,agent:navigator.userAgent,url:window.Galaxy?Galaxy.lastAjax.url:void 0,data:window.Galaxy?Galaxy.lastAjax.data:void 0,options:b?_.omit(c,"xhr"):c,xhr:b,source:_.isFunction(a.toJSON)?a.toJSON():a+"",user:f instanceof g.User?f.toJSON():f+""}};if(_.extend(h.details,e||{}),b&&_.isFunction(b.getAllResponseHeaders)){var i=b.getAllResponseHeaders();i=_.compact(i.split("\n")),i=_.map(i,function(a){return a.split(": ")}),h.details.xhr.responseHeaders=_.object(i)}return h},_bePolite:function(a){return a=a||k("An error occurred while getting updates from the server"),a+". "+k("Please contact a Galaxy administrator if the problem persists")+"."},displayMessage:function(a,b,c){var d=this;this.scrollToTop();var e=this.$messages(),f=$("
                      ").addClass(a+"message").html(b);if(!_.isEmpty(c)){var g=$('Details').click(function(){return Galaxy.modal.show(d._messageToModalOptions(a,b,c)),!1});f.append(" ",g)}return e.append(f)},_messageToModalOptions:function(a,b,c){var d=this,e={title:"Details"};if(_.isObject(c)){c=_.omit(c,_.functions(c));var f=JSON.stringify(c,null," "),g=$("
                      ").text(f);e.body=$("
                      ").append(g)}else e.body=$("
                      ").html(c);return e.buttons={Ok:function(){Galaxy.modal.hide(),d.clearMessages()}},e},clearMessages:function(a){var b=_.isUndefined(a)?this.$messages().children('[class$="message"]'):$(a.currentTarget);return b.fadeOut(this.fxSpeed,function(){$(this).remove()}),this},scrollToHid:function(a){return this.scrollToItem(_.first(this.viewsWhereModel({hid:a})))},toString:function(){return"HistoryPanel("+(this.model?this.model.get("name"):"")+")"}});return n.prototype.templates=function(){var a=j.wrapTemplate(['
                      ','
                      ','
                      <%= history.name %>
                      ',"
                      ",'
                      ','
                      <%= history.nice_size %>
                      ','
                      ','
                      ',"<% if( history.deleted && history.purged ){ %>",'
                      ',k("This history has been purged and deleted"),"
                      ","<% } else if( history.deleted ){ %>",'
                      ',k("This history has been deleted"),"
                      ","<% } else if( history.purged ){ %>",'
                      ',k("This history has been purged"),"
                      ","<% } %>","<% if( history.message ){ %>",'
                      messagesmall">',"<%= history.message.text %>","
                      ","<% } %>","
                      ",'
                      ','
                      ','
                      ','
                      ',"
                      ",'
                      ','
                      ','",'","
                      ",'
                      ',"
                      ","
                      ","
                      "],"history");return _.extend(_.clone(m.prototype.templates),{controls:a})}(),{HistoryPanel:n}});
+define(["mvc/list/list-panel","mvc/history/history-model","mvc/history/history-contents","mvc/history/hda-li","mvc/history/hdca-li","mvc/collection/collection-panel","mvc/user/user-model","ui/fa-icon-button","mvc/ui/popup-menu","mvc/base-mvc","utils/localization","ui/search-input"],function(a,b,c,d,e,f,g,h,i,j,k){var l=j.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(a){var b="expandedIds";this.save(b,_.extend(this.get(b),_.object([a.id],[a.get("id")])))},removeExpanded:function(a){var b="expandedIds";this.save(b,_.omit(this.get(b),a.id))},toString:function(){return"HistoryPrefs("+this.id+")"}});l.storageKeyPrefix="history:",l.historyStorageKey=function(a){if(!a)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+a);return l.storageKeyPrefix+a},l.get=function(a){return new l({id:l.historyStorageKey(a)})},l.clearAll=function(){for(var a in sessionStorage)0===a.indexOf(l.storageKeyPrefix)&&sessionStorage.removeItem(a)};var m=a.ModelListPanel,n=m.extend({HDAViewClass:d.HDAListItemView,HDCAViewClass:e.HDCAListItemView,collectionClass:c.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:m.prototype.className+" history-panel",emptyMsg:k("This history is empty"),noneFoundMsg:k("No matching datasets found"),searchPlaceholder:k("search datasets"),initialize:function(a){m.prototype.initialize.call(this,a),this.linkTarget=a.linkTarget||"_blank"},freeModel:function(){return m.prototype.freeModel.call(this),this.model&&this.model.clearUpdateTimeout(),this},_setUpListeners:function(){m.prototype._setUpListeners.call(this),this.on("error",function(a,b,c,d,e){this.errorHandler(a,b,c,d,e)}),this.on("loading-done",function(){this.views.length||this.trigger("empty-history",this)})},loadHistoryWithDetails:function(a,b,c,d){this.info("loadHistoryWithDetails:",a,b,c,d);var e=function(a){return _.values(l.get(a.id).get("expandedIds"))};return this.loadHistory(a,b,c,d,e)},loadHistory:function(a,c,d,e,f){this.info("loadHistory:",a,c,d,e,f);var g=this;c=c||{},g.trigger("loading",g);var h=b.History.getHistoryData(a,{historyFn:d,contentsFn:e,detailIdsFn:c.initiallyExpanded||f});return g._loadHistoryFromXHR(h,c).fail(function(b,d,e){g.trigger("error",g,b,c,k("An error was encountered while "+d),{historyId:a,history:e||{}})}).always(function(){g.trigger("loading-done",g)})},_loadHistoryFromXHR:function(a,b){var c=this;return a.then(function(a,d){c.JSONToModel(a,d,b),c.render()}),a.fail(function(){c.render()}),a},refreshContents:function(a,b){return this.model?this.model.refresh(a,b):$.when()},JSONToModel:function(a,c,d){this.log("JSONToModel:",a,c,d),d=d||{};var e=new b.History(a,c,d);return this.setModel(e),e},setModel:function(a,b){b=b||{},m.prototype.setModel.call(this,a,b),this.model&&this._setUpWebStorage(b.initiallyExpanded,b.show_deleted,b.show_hidden)},_setUpWebStorage:function(a,b,c){return this.storage&&this.stopListening(this.storage),this.storage=new l({id:l.historyStorageKey(this.model.get("id"))}),_.isObject(a)&&this.storage.set("expandedIds",a),_.isBoolean(b)&&this.storage.set("show_deleted",b),_.isBoolean(c)&&this.storage.set("show_hidden",c),this.trigger("new-storage",this.storage,this),this.log(this+" (init'd) storage:",this.storage.get()),this.listenTo(this.storage,{"change:show_deleted":function(a,b){this.showDeleted=b},"change:show_hidden":function(a,b){this.showHidden=b}},this),this.showDeleted=void 0!==b?b:this.storage.get("show_deleted"),this.showHidden=void 0!==c?c:this.storage.get("show_hidden"),this},_buildNewRender:function(){var a=m.prototype._buildNewRender.call(this);return this.multiselectActions().length&&a.find(".controls .actions").prepend(this._renderSelectButton()),a},_renderSelectButton:function(){return h({title:k("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"})},_getItemViewClass:function(a){var b=a.get("history_content_type");switch(b){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+b)},_filterItem:function(a){var b=this;return m.prototype._filterItem.call(b,a)&&(!a.hidden()||b.showHidden)&&(!a.isDeletedOrPurged()||b.showDeleted)},_getItemViewOptions:function(a){var b=m.prototype._getItemViewOptions.call(this,a);return _.extend(b,{linkTarget:this.linkTarget,expanded:!!this.storage.get("expandedIds")[a.id],hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(a){var b=this;return m.prototype._setUpItemViewListeners.call(b,a),a.on("expanded",function(a){b.storage.addExpanded(a.model)}),a.on("collapsed",function(a){b.storage.removeExpanded(a.model)}),this},getSelectedModels:function(){var a=m.prototype.getSelectedModels.call(this);return a.historyId=this.collection.historyId,a},events:_.extend(_.clone(m.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .messages [class$=message]":"clearMessages"}),toggleShowDeleted:function(a,b){return a=void 0!==a?a:!this.showDeleted,b=void 0!==b?b:!0,this.showDeleted=a,b&&this.storage.set("show_deleted",a),this.trigger("show-hidden",a),this.renderItems(),this.showDeleted},toggleShowHidden:function(a,b){return a=void 0!==a?a:!this.showHidden,b=void 0!==b?b:!0,this.showHidden=a,b&&this.storage.set("show_hidden",a),this.trigger("show-hidden",a),this.renderItems(),this.showHidden},_firstSearch:function(a){var b=this,c=".history-search-input";return this.log("onFirstSearch",a),b.model.contents.haveDetails()?void b.searchItems(a):(b.$el.find(c).searchInput("toggle-loading"),void b.model.contents.fetchAllDetails({silent:!0}).always(function(){b.$el.find(c).searchInput("toggle-loading")}).done(function(){b.searchItems(a)}))},errorHandler:function(a,b,c,d,e){if(this.error(a,b,c,d,e),b&&0===b.status&&0===b.readyState);else if(b&&502===b.status);else{var f=this._parseErrorMessage(a,b,c,d,e);this.$messages().is(":visible")?this.displayMessage("error",f.message,f.details):this.once("rendered",function(){this.displayMessage("error",f.message,f.details)})}},_parseErrorMessage:function(a,b,c,d,e){var f=Galaxy.currUser,h={message:this._bePolite(d),details:{message:d,raven:window.Raven&&_.isFunction(Raven.lastEventId)?Raven.lastEventId():void 0,agent:navigator.userAgent,url:window.Galaxy?Galaxy.lastAjax.url:void 0,data:window.Galaxy?Galaxy.lastAjax.data:void 0,options:b?_.omit(c,"xhr"):c,xhr:b,source:_.isFunction(a.toJSON)?a.toJSON():a+"",user:f instanceof g.User?f.toJSON():f+""}};if(_.extend(h.details,e||{}),b&&_.isFunction(b.getAllResponseHeaders)){var i=b.getAllResponseHeaders();i=_.compact(i.split("\n")),i=_.map(i,function(a){return a.split(": ")}),h.details.xhr.responseHeaders=_.object(i)}return h},_bePolite:function(a){return a=a||k("An error occurred while getting updates from the server"),a+". "+k("Please contact a Galaxy administrator if the problem persists")+"."},displayMessage:function(a,b,c){var d=this;this.scrollToTop();var e=this.$messages(),f=$("
                      ").addClass(a+"message").html(b);if(!_.isEmpty(c)){var g=$('Details').click(function(){return Galaxy.modal.show(d._messageToModalOptions(a,b,c)),!1});f.append(" ",g)}return e.append(f)},_messageToModalOptions:function(a,b,c){var d=this,e={title:"Details"};if(_.isObject(c)){c=_.omit(c,_.functions(c));var f=JSON.stringify(c,null,"  "),g=$("
                      ").text(f);e.body=$("
                      ").append(g)}else e.body=$("
                      ").html(c);return e.buttons={Ok:function(){Galaxy.modal.hide(),d.clearMessages()}},e},clearMessages:function(a){var b=_.isUndefined(a)?this.$messages().children('[class$="message"]'):$(a.currentTarget);return b.fadeOut(this.fxSpeed,function(){$(this).remove()}),this},scrollToHid:function(a){return this.scrollToItem(_.first(this.viewsWhereModel({hid:a})))},toString:function(){return"HistoryPanel("+(this.model?this.model.get("name"):"")+")"}});return n.prototype.templates=function(){var a=j.wrapTemplate(['
                      ','
                      ','
                      <%- history.name %>
                      ',"
                      ",'
                      ','
                      <%- history.nice_size %>
                      ','
                      ','
                      ',"<% if( history.deleted && history.purged ){ %>",'
                      ',k("This history has been purged and deleted"),"
                      ","<% } else if( history.deleted ){ %>",'
                      ',k("This history has been deleted"),"
                      ","<% } else if( history.purged ){ %>",'
                      ',k("This history has been purged"),"
                      ","<% } %>","<% if( history.message ){ %>",'
                      messagesmall">',"<%= history.message.text %>","
                      ","<% } %>","
                      ",'
                      ','
                      ','
                      ','
                      ',"
                      ",'
                      ','
                      ','",'","
                      ",'
                      ',"
                      ","
                      ","
                      "],"history");return _.extend(_.clone(m.prototype.templates),{controls:a})}(),{HistoryPanel:n}});
 //# sourceMappingURL=../../../maps/mvc/history/history-panel.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/history/multi-panel.js b/static/scripts/mvc/history/multi-panel.js
index 0ef96a512c7..0570f52c4a3 100644
--- a/static/scripts/mvc/history/multi-panel.js
+++ b/static/scripts/mvc/history/multi-panel.js
@@ -1,2 +1,2 @@
-define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(a,b,c,d){function e(a,b){function c(a){if(!a){if(!Galaxy.modal.$("#invalid-title").size()){var b=$("
                      ").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(b)}return!1}return a}function d(b){var c=$('
                       Copying history...
                      ').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(c),a.copy(!0,b).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function e(){var a=Galaxy.modal.$("#copy-modal-title").val();c(a)&&d(a)}if(b=b||{},!Galaxy||!Galaxy.modal)return a.copy();var f=a.get("name"),g="Copy of '"+f+"'";Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+f+'"',body:$(['
                      ",''].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:e}},b)),$("#copy-modal-title").focus().select(),$("#copy-modal-title").on("keydown",function(a){13===a.keyCode&&e()})}var f=Backbone.View.extend(c.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function(){return this.model?"history-column-"+this.model.get("id"):""},initialize:function(a){a=a||{},this.purgeAllowed=_.isUndefined(a.purgeAllowed)?!1:a.purgeAllowed,this.panel=a.panel||this.createPanel(a),this.setUpListeners()},createPanel:function(a){a=_.extend({model:this.model,purgeAllowed:this.purgeAllowed,dragItems:!0},a);var c=new b.HistoryPanelEdit(a);return c._renderEmptyMessage=this.__patch_renderEmptyMessage,c},__patch_renderEmptyMessage:function(a){var b=this,c=_.chain(this.model.get("state_ids")).values().flatten().value().length,d=b.$emptyMessage(a);return _.isEmpty(b.hdaViews)?c&&!this.model.contents.length?d.empty().append($(' loading datasets...')).show():b.searchFor?d.text(b.noneFoundMsg).show():d.text(b.emptyMsg).show():d.hide(),d},setUpListeners:function(){var a=this;this.once("rendered",function(){a.trigger("rendered:initial",a)}),this.setUpPanelListeners()},setUpPanelListeners:function(){var a=this;this.listenTo(this.panel,{rendered:function(){a.trigger("rendered",a)}},this)},inView:function(a,b){var c=this.$el.offset().left,d=c+this.$el.width();return a>d?!1:c>b?!1:!0},$panel:function(){return this.$(".history-panel")},render:function(a){a=void 0!==a?a:"fast";var b=this.model?this.model.toJSON():{};return this.$el.html(this.template(b)),this.renderPanel(a),this.setUpBehaviors(),this},setUpBehaviors:function(){},template:function(a){return a=_.extend(a||{},{isCurrentHistory:this.currentHistory}),$(['
                      ',this.controlsLeftTemplate({history:a,view:this}),this.controlsRightTemplate({history:a,view:this}),"
                      ",'
                      ','
                      ',"
                      "].join(""))},renderPanel:function(a){return a=void 0!==a?a:"fast",this.panel.setElement(this.$panel()).render(a),this.currentHistory&&this.panel.$list().before(this.panel._renderDropTargetHelp()),this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var a=this;this.model._delete().fail(function(a,b,c){alert(_l("Could not delete the history")+":\n"+c)}).done(function(){a.render()})},"click .undelete-history":function(){var a=this;this.model.undelete().fail(function(a,b,c){alert(_l("Could not undelete the history")+":\n"+c)}).done(function(){a.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var a=this;this.model.purge().fail(function(a,b,c){alert(_l("Could not purge the history")+":\n"+c)}).done(function(){a.render()})}},"click .copy-history":"copy"},copy:function(){e(this.model)},controlsLeftTemplate:_.template(['
                      ',"<% if( data.history.isCurrentHistory ){ %>",'',_l("Current History"),"","<% } else { %>",'","<% } %>","
                      "].join(""),{variable:"data"}),controlsRightTemplate:_.template(['
                      ',"<% if( !data.history.purged ){ %>",'
                      ','",'","
                      ","<% } %>","
                      "].join(""),{variable:"data"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}}),g=Backbone.View.extend(c.LoggableMixin).extend({className:"multi-panel-history",initialize:function(a){if(a=a||{},this.log(this+".init",a),this.$el.addClass(this.className),!a.currentHistoryId)throw new Error(this+" requires a currentHistoryId in the options");this.currentHistoryId=a.currentHistoryId,this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20},this.order=a.order||"update",this._initSortOrders(),this.hdaQueue=new d.NamedAjaxQueue([],!1),this.collection=null,this.setCollection(a.histories||[]),this.columnMap={},this.createColumns(a.columnOptions),this.setUpListeners()},_initSortOrders:function(){function a(a,b){return function(c,d,e){return c.id===e?-1:d.id===e?1:(c=a(c),d=a(d),b.asc?c===d?0:c>d?1:-1:c===d?0:c>d?-1:1)}}return this.sortOrders={update:{text:_l("most recent first"),fn:a(function(a){return new Date(a.get("update_time"))},{asc:!1})},name:{text:_l("name, a to z"),fn:a(function(a){return a.get("name")},{asc:!0})},"name-dsc":{text:_l("name, z to a"),fn:a(function(a){return a.get("name")},{asc:!1})},size:{text:_l("size, large to small"),fn:a(function(a){return a.get("size")},{asc:!1})},"size-dsc":{text:_l("size, small to large"),fn:a(function(a){return a.get("size")},{asc:!0})}},this.sortOrders},setUpListeners:function(){},setCollection:function(a){var b=this;return b.stopListening(b.collection),b.collection=a,b.sortCollection(b.order,{silent:!0}),b.setUpCollectionListeners(),b.trigger("new-collection",b),b},setUpCollectionListeners:function(){var a=this,b=a.collection;a.listenTo(b,{add:a.addAsCurrentColumn,"set-as-current":a.setCurrentHistory,"change:deleted change:purged":a.handleDeletedHistory,sort:function(){a.renderColumns(0)}})},setCurrentHistory:function(a){var b=this.columnMap[this.currentHistoryId];b&&(b.currentHistory=!1,b.$el.height("")),this.currentHistoryId=a.id;var c=this.columnMap[this.currentHistoryId];return c.currentHistory=!0,this.sortCollection(),multipanel._recalcFirstColumnHeight(),c},handleDeletedHistory:function(a){if(a.get("deleted")||a.get("purged")){this.log("handleDeletedHistory",this.collection.includeDeleted,a);var b=this;if(column=b.columnMap[a.id],!column)return;column.model.id===this.currentHistoryId||b.collection.includeDeleted||b.removeColumn(column)}},sortCollection:function(a,b){a=_.isUndefined(a)?this.order:a,a in this.sortOrders||(a="update"),this.order=a;var c=this.currentHistoryId,d=this.sortOrders[a];return this.collection.comparator=function(a,b){return d.fn(a,b,c)},this.$(".current-order").text(d.text),this.$(".more-options").is(":visible")&&this.$(".open-more-options.btn").popover("show"),this.collection.sort(b),this.collection},create:function(){return this.collection.create({current:!0})},createColumns:function(a){a=a||{};var b=this;this.columnMap={},b.collection.each(function(c){var d=b.createColumn(c,a);b.columnMap[c.id]=d})},createColumn:function(a,b){b=_.extend({},b,{model:a,purgeAllowed:Galaxy.config.allow_user_dataset_purge});var c=new f(b);return a.id===this.currentHistoryId&&(c.currentHistory=!0),this.setUpColumnListeners(c),c},sortedFilteredColumns:function(a){if(a=a||this.filters,!a||!a.length)return this.sortedColumns();var b=this;return b.sortedColumns().filter(function(b){var c=b.currentHistory||_.every(a.map(function(a){return a.call(b)}));return c})},sortedColumns:function(){var a=this,b=this.collection.map(function(b){return a.columnMap[b.id]});return b},addColumn:function(a,b){b=void 0!==b?b:!0;var c=this.createColumn(a);return this.columnMap[a.id]=c,b&&this.renderColumns(),c},addAsCurrentColumn:function(a){var b=this,c=this.addColumn(a,!1);return this.setCurrentHistory(a),c.once("rendered",function(){b.queueHdaFetch(c)}),c},removeColumn:function(a,b){if(b=void 0!==b?b:!0,this.log("removeColumn",a),a){var c=this,d=this.options.columnWidth+this.options.columnGap;a.$el.fadeOut("fast",function(){b&&($(this).remove(),c.$(".middle").width(c.$(".middle").width()-d),c.checkColumnsInView(),c._recalcFirstColumnHeight()),c.stopListening(a.panel),c.stopListening(a),delete c.columnMap[a.model.id],a.remove()})}},setUpColumnListeners:function(a){var b=this;b.listenTo(a,{"in-view":b.queueHdaFetch}),b.listenTo(a.panel,{"view:draggable:dragstart":function(a){b._dropData=JSON.parse(a.dataTransfer.getData("text")),b.currentColumnDropTargetOn()},"view:draggable:dragend":function(){b._dropData=null,b.currentColumnDropTargetOff()},"droptarget:drop":function(a,c,e){var f=b._dropData.filter(function(a){return e.model.contents.isCopyable(a)});b._dropData=null;var g=new d.NamedAjaxQueue;f.forEach(function(a){g.add({name:"copy-"+a.id,fn:function(){return e.model.contents.copy(a)}})}),g.start(),g.done(function(){e.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function(a){a=void 0!==a?a:this.fxSpeed;var b=this;return b.log(b+".render"),b.$el.html(b.mainTemplate(b)),b.renderColumns(a),b.setUpBehaviors(),b.trigger("rendered",b),b},renderColumns:function(a){a=void 0!==a?a:this.fxSpeed;var b=this,c=b.sortedFilteredColumns();b.$(".middle").width(c.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var d=b.$(".middle");return d.empty(),c.forEach(function(c){c.$el.appendTo(d),c.delegateEvents(),b.renderColumn(c,a)}),this.searchFor&&c.length<=1||(b.checkColumnsInView(),this._recalcFirstColumnHeight()),c},renderColumn:function(a,b){return b=void 0!==b?b:this.fxSpeed,a.render(b)},queueHdaFetch:function(a){if(0===a.model.contents.length&&!a.model.get("empty")){var b={},c=_.values(a.panel.storage.get("expandedIds")).join();c&&(b.dataset_details=c),this.hdaQueue.add({name:a.model.id,fn:function(){var c=a.model.contents.fetch({data:b,silent:!0});return c.done(function(){a.panel.renderItems()})}}),this.hdaQueue.running||this.hdaQueue.start()}},queueHdaFetchDetails:function(a){(0===a.model.contents.length&&!a.model.get("empty")||!a.model.contents.haveDetails())&&(this.hdaQueue.add({name:a.model.id,fn:function(){var b=a.model.contents.fetch({data:{details:"all"},silent:!0});return b.done(function(){a.panel.renderItems()})}}),this.hdaQueue.running||this.hdaQueue.start())},renderInfo:function(a){return this.$(".header .header-info").text(a)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(){var a="/";Galaxy&&Galaxy.options&&Galaxy.options.root?a=Galaxy.options.root:galaxy_config&&galaxy_config.root&&(a=galaxy_config.root),window.location=a},_clickToggleDeletedHistories:function(a){return this.toggleDeletedHistories($(a.currentTarget).is(":checked"))},toggleDeletedHistories:function(a){window.location=a?Galaxy.options.root+"history/view_multiple?include_deleted_histories=True":Galaxy.options.root+"history/view_multiple"},_clickToggleDeletedDatasets:function(a){return this.toggleDeletedDatasets($(a.currentTarget).is(":checked"))},toggleDeletedDatasets:function(a){a=void 0!==a?a:!1;var b=this;b.sortedFilteredColumns().forEach(function(b,c){_.delay(function(){b.panel.toggleShowDeleted(a,!1)},200*c)})},_clickToggleHiddenDatasets:function(a){return this.toggleHiddenDatasets($(a.currentTarget).is(":checked"))},toggleHiddenDatasets:function(a){a=void 0!==a?a:!1;var b=this;b.sortedFilteredColumns().forEach(function(b,c){_.delay(function(){b.panel.toggleShowHidden(a,!1)},200*c)})},_chooseOrder:function(a){var b=$(a.currentTarget).data("order");this.sortCollection(b)},setUpBehaviors:function(){var a=this;a._moreOptionsPopover(),a.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(b){a.searchFor=b,a.filters=[function(){return this.model.matchesAll(a.searchFor)}],a.renderColumns(0)},onclear:function(){a.searchFor=null,a.filters=[],a.renderColumns(0)}}),a.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(b){a.hdaQueue.clear(),a.$("#search-datasets").searchInput("toggle-loading"),a.searchFor=b,a.sortedFilteredColumns().forEach(function(c){c.panel.searchItems(b),a.queueHdaFetchDetails(c)}),a.hdaQueue.progress(function(b){a.renderInfo([_l("searching"),b.curr+1,_l("of"),b.total].join(" "))}),a.hdaQueue.deferred.done(function(){a.renderInfo(""),a.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(b){a.searchFor=b,a.sortedFilteredColumns().forEach(function(a){a.panel.searchItems(b)})},onclear:function(){a.searchFor=null,a.sortedFilteredColumns().forEach(function(a){a.panel.clearSearch()})}}),$(window).resize(function(){a._recalcFirstColumnHeight()});var b=_.debounce(function(){a.checkColumnsInView()},100);this.$(".middle").parent().scroll(b)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:!0,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var a=this.$(".history-column").first(),b=this.$(".middle").height(),c=a.find(".panel-controls").height();a.height(b).find(".inner").height(b-c)},_viewport:function(){var a=this.$(".middle").parent().offset().left;return{left:a,right:a+this.$(".middle").parent().width()}},columnsInView:function(){var a=this._viewport();return this.sortedFilteredColumns().filter(function(b){return b.currentHistory||b.inView(a.left,a.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(a){a.trigger("in-view",a)})},currentColumnDropTargetOn:function(){var a=this.columnMap[this.currentHistoryId];a&&(a.panel.dataDropped=function(){},a.panel.dropTargetOn())},currentColumnDropTargetOff:function(){var a=this.columnMap[this.currentHistoryId];a&&(a.panel.dataDropped=b.HistoryPanelEdit.prototype.dataDrop,a.panel.dropTarget=!1,a.panel.$(".history-drop-target").remove())},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['
                      ','
                      ','",'
                      ','
                      ','','',"","
                      ",'
                      ','
                      ',"
                      ","
                      ",'
                      ',' ","
                      ","
                      ",'
                      ','
                      ',"
                      ",'
                      ',"
                      "].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['
                      ','
                      ','",'","
                      ",'
                      ","
                      ",'
                      ",'
                      ","
                      "].join(""),{variable:"view"})});return{MultiPanelColumns:g}});
+define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(a,b,c,d){function e(a,b){function c(a){if(!a){if(!Galaxy.modal.$("#invalid-title").size()){var b=$("
                      ").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(b)}return!1}return a}function d(b){var c=$('
                       Copying history...
                      ').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(c),a.copy(!0,b).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function e(){var a=Galaxy.modal.$("#copy-modal-title").val();c(a)&&d(a)}if(b=b||{},!Galaxy||!Galaxy.modal)return a.copy();var f=_.escape(a.get("name")),g="Copy of '"+f+"'";Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+f+'"',body:$(['
                      ",''].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:e}},b)),$("#copy-modal-title").focus().select(),$("#copy-modal-title").on("keydown",function(a){13===a.keyCode&&e()})}var f=Backbone.View.extend(c.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function(){return this.model?"history-column-"+this.model.get("id"):""},initialize:function(a){a=a||{},this.purgeAllowed=_.isUndefined(a.purgeAllowed)?!1:a.purgeAllowed,this.panel=a.panel||this.createPanel(a),this.setUpListeners()},createPanel:function(a){a=_.extend({model:this.model,purgeAllowed:this.purgeAllowed,dragItems:!0},a);var c=new b.HistoryPanelEdit(a);return c._renderEmptyMessage=this.__patch_renderEmptyMessage,c},__patch_renderEmptyMessage:function(a){var b=this,c=_.chain(this.model.get("state_ids")).values().flatten().value().length,d=b.$emptyMessage(a);return _.isEmpty(b.hdaViews)?c&&!this.model.contents.length?d.empty().append($(' loading datasets...')).show():b.searchFor?d.text(b.noneFoundMsg).show():d.text(b.emptyMsg).show():d.hide(),d},setUpListeners:function(){var a=this;this.once("rendered",function(){a.trigger("rendered:initial",a)}),this.setUpPanelListeners()},setUpPanelListeners:function(){var a=this;this.listenTo(this.panel,{rendered:function(){a.trigger("rendered",a)}},this)},inView:function(a,b){var c=this.$el.offset().left,d=c+this.$el.width();return a>d?!1:c>b?!1:!0},$panel:function(){return this.$(".history-panel")},render:function(a){a=void 0!==a?a:"fast";var b=this.model?this.model.toJSON():{};return this.$el.html(this.template(b)),this.renderPanel(a),this.setUpBehaviors(),this},setUpBehaviors:function(){},template:function(a){return a=_.extend(a||{},{isCurrentHistory:this.currentHistory}),$(['
                      ',this.controlsLeftTemplate({history:a,view:this}),this.controlsRightTemplate({history:a,view:this}),"
                      ",'
                      ','
                      ',"
                      "].join(""))},renderPanel:function(a){return a=void 0!==a?a:"fast",this.panel.setElement(this.$panel()).render(a),this.currentHistory&&this.panel.$list().before(this.panel._renderDropTargetHelp()),this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var a=this;this.model._delete().fail(function(a,b,c){alert(_l("Could not delete the history")+":\n"+c)}).done(function(){a.render()})},"click .undelete-history":function(){var a=this;this.model.undelete().fail(function(a,b,c){alert(_l("Could not undelete the history")+":\n"+c)}).done(function(){a.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var a=this;this.model.purge().fail(function(a,b,c){alert(_l("Could not purge the history")+":\n"+c)}).done(function(){a.render()})}},"click .copy-history":"copy"},copy:function(){e(this.model)},controlsLeftTemplate:_.template(['
                      ',"<% if( data.history.isCurrentHistory ){ %>",'',_l("Current History"),"","<% } else { %>",'","<% } %>","
                      "].join(""),{variable:"data"}),controlsRightTemplate:_.template(['
                      ',"<% if( !data.history.purged ){ %>",'
                      ','",'","
                      ","<% } %>","
                      "].join(""),{variable:"data"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}}),g=Backbone.View.extend(c.LoggableMixin).extend({className:"multi-panel-history",initialize:function(a){if(a=a||{},this.log(this+".init",a),this.$el.addClass(this.className),!a.currentHistoryId)throw new Error(this+" requires a currentHistoryId in the options");this.currentHistoryId=a.currentHistoryId,this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20},this.order=a.order||"update",this._initSortOrders(),this.hdaQueue=new d.NamedAjaxQueue([],!1),this.collection=null,this.setCollection(a.histories||[]),this.columnMap={},this.createColumns(a.columnOptions),this.setUpListeners()},_initSortOrders:function(){function a(a,b){return function(c,d,e){return c.id===e?-1:d.id===e?1:(c=a(c),d=a(d),b.asc?c===d?0:c>d?1:-1:c===d?0:c>d?-1:1)}}return this.sortOrders={update:{text:_l("most recent first"),fn:a(function(a){return new Date(a.get("update_time"))},{asc:!1})},name:{text:_l("name, a to z"),fn:a(function(a){return a.get("name")},{asc:!0})},"name-dsc":{text:_l("name, z to a"),fn:a(function(a){return a.get("name")},{asc:!1})},size:{text:_l("size, large to small"),fn:a(function(a){return a.get("size")},{asc:!1})},"size-dsc":{text:_l("size, small to large"),fn:a(function(a){return a.get("size")},{asc:!0})}},this.sortOrders},setUpListeners:function(){},setCollection:function(a){var b=this;return b.stopListening(b.collection),b.collection=a,b.sortCollection(b.order,{silent:!0}),b.setUpCollectionListeners(),b.trigger("new-collection",b),b},setUpCollectionListeners:function(){var a=this,b=a.collection;a.listenTo(b,{add:a.addAsCurrentColumn,"set-as-current":a.setCurrentHistory,"change:deleted change:purged":a.handleDeletedHistory,sort:function(){a.renderColumns(0)}})},setCurrentHistory:function(a){var b=this.columnMap[this.currentHistoryId];b&&(b.currentHistory=!1,b.$el.height("")),this.currentHistoryId=a.id;var c=this.columnMap[this.currentHistoryId];return c.currentHistory=!0,this.sortCollection(),multipanel._recalcFirstColumnHeight(),c},handleDeletedHistory:function(a){if(a.get("deleted")||a.get("purged")){this.log("handleDeletedHistory",this.collection.includeDeleted,a);var b=this;if(column=b.columnMap[a.id],!column)return;column.model.id===this.currentHistoryId||b.collection.includeDeleted||b.removeColumn(column)}},sortCollection:function(a,b){a=_.isUndefined(a)?this.order:a,a in this.sortOrders||(a="update"),this.order=a;var c=this.currentHistoryId,d=this.sortOrders[a];return this.collection.comparator=function(a,b){return d.fn(a,b,c)},this.$(".current-order").text(d.text),this.$(".more-options").is(":visible")&&this.$(".open-more-options.btn").popover("show"),this.collection.sort(b),this.collection},create:function(){return this.collection.create({current:!0})},createColumns:function(a){a=a||{};var b=this;this.columnMap={},b.collection.each(function(c){var d=b.createColumn(c,a);b.columnMap[c.id]=d})},createColumn:function(a,b){b=_.extend({},b,{model:a,purgeAllowed:Galaxy.config.allow_user_dataset_purge});var c=new f(b);return a.id===this.currentHistoryId&&(c.currentHistory=!0),this.setUpColumnListeners(c),c},sortedFilteredColumns:function(a){if(a=a||this.filters,!a||!a.length)return this.sortedColumns();var b=this;return b.sortedColumns().filter(function(b){var c=b.currentHistory||_.every(a.map(function(a){return a.call(b)}));return c})},sortedColumns:function(){var a=this,b=this.collection.map(function(b){return a.columnMap[b.id]});return b},addColumn:function(a,b){b=void 0!==b?b:!0;var c=this.createColumn(a);return this.columnMap[a.id]=c,b&&this.renderColumns(),c},addAsCurrentColumn:function(a){var b=this,c=this.addColumn(a,!1);return this.setCurrentHistory(a),c.once("rendered",function(){b.queueHdaFetch(c)}),c},removeColumn:function(a,b){if(b=void 0!==b?b:!0,this.log("removeColumn",a),a){var c=this,d=this.options.columnWidth+this.options.columnGap;a.$el.fadeOut("fast",function(){b&&($(this).remove(),c.$(".middle").width(c.$(".middle").width()-d),c.checkColumnsInView(),c._recalcFirstColumnHeight()),c.stopListening(a.panel),c.stopListening(a),delete c.columnMap[a.model.id],a.remove()})}},setUpColumnListeners:function(a){var b=this;b.listenTo(a,{"in-view":b.queueHdaFetch}),b.listenTo(a.panel,{"view:draggable:dragstart":function(a){b._dropData=JSON.parse(a.dataTransfer.getData("text")),b.currentColumnDropTargetOn()},"view:draggable:dragend":function(){b._dropData=null,b.currentColumnDropTargetOff()},"droptarget:drop":function(a,c,e){var f=b._dropData.filter(function(a){return e.model.contents.isCopyable(a)});b._dropData=null;var g=new d.NamedAjaxQueue;f.forEach(function(a){g.add({name:"copy-"+a.id,fn:function(){return e.model.contents.copy(a)}})}),g.start(),g.done(function(){e.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function(a){a=void 0!==a?a:this.fxSpeed;var b=this;return b.log(b+".render"),b.$el.html(b.mainTemplate(b)),b.renderColumns(a),b.setUpBehaviors(),b.trigger("rendered",b),b},renderColumns:function(a){a=void 0!==a?a:this.fxSpeed;var b=this,c=b.sortedFilteredColumns();b.$(".middle").width(c.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var d=b.$(".middle");return d.empty(),c.forEach(function(c){c.$el.appendTo(d),c.delegateEvents(),b.renderColumn(c,a)}),this.searchFor&&c.length<=1||(b.checkColumnsInView(),this._recalcFirstColumnHeight()),c},renderColumn:function(a,b){return b=void 0!==b?b:this.fxSpeed,a.render(b)},queueHdaFetch:function(a){if(0===a.model.contents.length&&!a.model.get("empty")){var b={},c=_.values(a.panel.storage.get("expandedIds")).join();c&&(b.dataset_details=c),this.hdaQueue.add({name:a.model.id,fn:function(){var c=a.model.contents.fetch({data:b,silent:!0});return c.done(function(){a.panel.renderItems()})}}),this.hdaQueue.running||this.hdaQueue.start()}},queueHdaFetchDetails:function(a){(0===a.model.contents.length&&!a.model.get("empty")||!a.model.contents.haveDetails())&&(this.hdaQueue.add({name:a.model.id,fn:function(){var b=a.model.contents.fetch({data:{details:"all"},silent:!0});return b.done(function(){a.panel.renderItems()})}}),this.hdaQueue.running||this.hdaQueue.start())},renderInfo:function(a){return this.$(".header .header-info").text(a)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(){var a="/";Galaxy&&Galaxy.options&&Galaxy.options.root?a=Galaxy.options.root:galaxy_config&&galaxy_config.root&&(a=galaxy_config.root),window.location=a},_clickToggleDeletedHistories:function(a){return this.toggleDeletedHistories($(a.currentTarget).is(":checked"))},toggleDeletedHistories:function(a){window.location=a?Galaxy.options.root+"history/view_multiple?include_deleted_histories=True":Galaxy.options.root+"history/view_multiple"},_clickToggleDeletedDatasets:function(a){return this.toggleDeletedDatasets($(a.currentTarget).is(":checked"))},toggleDeletedDatasets:function(a){a=void 0!==a?a:!1;var b=this;b.sortedFilteredColumns().forEach(function(b,c){_.delay(function(){b.panel.toggleShowDeleted(a,!1)},200*c)})},_clickToggleHiddenDatasets:function(a){return this.toggleHiddenDatasets($(a.currentTarget).is(":checked"))},toggleHiddenDatasets:function(a){a=void 0!==a?a:!1;var b=this;b.sortedFilteredColumns().forEach(function(b,c){_.delay(function(){b.panel.toggleShowHidden(a,!1)},200*c)})},_chooseOrder:function(a){var b=$(a.currentTarget).data("order");this.sortCollection(b)},setUpBehaviors:function(){var a=this;a._moreOptionsPopover(),a.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(b){a.searchFor=b,a.filters=[function(){return this.model.matchesAll(a.searchFor)}],a.renderColumns(0)},onclear:function(){a.searchFor=null,a.filters=[],a.renderColumns(0)}}),a.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(b){a.hdaQueue.clear(),a.$("#search-datasets").searchInput("toggle-loading"),a.searchFor=b,a.sortedFilteredColumns().forEach(function(c){c.panel.searchItems(b),a.queueHdaFetchDetails(c)}),a.hdaQueue.progress(function(b){a.renderInfo([_l("searching"),b.curr+1,_l("of"),b.total].join(" "))}),a.hdaQueue.deferred.done(function(){a.renderInfo(""),a.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(b){a.searchFor=b,a.sortedFilteredColumns().forEach(function(a){a.panel.searchItems(b)})},onclear:function(){a.searchFor=null,a.sortedFilteredColumns().forEach(function(a){a.panel.clearSearch()})}}),$(window).resize(function(){a._recalcFirstColumnHeight()});var b=_.debounce(function(){a.checkColumnsInView()},100);this.$(".middle").parent().scroll(b)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:!0,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var a=this.$(".history-column").first(),b=this.$(".middle").height(),c=a.find(".panel-controls").height();a.height(b).find(".inner").height(b-c)},_viewport:function(){var a=this.$(".middle").parent().offset().left;return{left:a,right:a+this.$(".middle").parent().width()}},columnsInView:function(){var a=this._viewport();return this.sortedFilteredColumns().filter(function(b){return b.currentHistory||b.inView(a.left,a.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(a){a.trigger("in-view",a)})},currentColumnDropTargetOn:function(){var a=this.columnMap[this.currentHistoryId];a&&(a.panel.dataDropped=function(){},a.panel.dropTargetOn())},currentColumnDropTargetOff:function(){var a=this.columnMap[this.currentHistoryId];a&&(a.panel.dataDropped=b.HistoryPanelEdit.prototype.dataDrop,a.panel.dropTarget=!1,a.panel.$(".history-drop-target").remove())},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['
                      ','
                      ','",'
                      ','
                      ','','',"","
                      ",'
                      ','
                      ',"
                      ","
                      ",'
                      ',' ","
                      ","
                      ",'
                      ','
                      ',"
                      ",'
                      ',"
                      "].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['
                      ','
                      ','",'","
                      ",'
                      ","
                      ",'
                      ",'
                      ","
                      "].join(""),{variable:"view"})});return{MultiPanelColumns:g}});
 //# sourceMappingURL=../../../maps/mvc/history/multi-panel.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/job/job-li.js b/static/scripts/mvc/job/job-li.js
index 28e2173f922..e9657d144ec 100644
--- a/static/scripts/mvc/job/job-li.js
+++ b/static/scripts/mvc/job/job-li.js
@@ -1,2 +1,2 @@
-define(["mvc/list/list-item","mvc/dataset/dataset-list","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=a.FoldoutListItemView,f=e.extend({className:e.prototype.className+" job",id:function(){return["job",this.model.get("id")].join("-")},foldoutPanelClass:b.DatasetList,initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log(this+".initialize:",a),e.prototype.initialize.call(this,a),this.tool=a.tool||{},this.jobData=a.jobData||{},this.linkTarget=a.linkTarget||"_blank"},_swapNewRender:function(a){return e.prototype._swapNewRender.call(this,a),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_getFoldoutPanelOptions:function(){var a=e.prototype._getFoldoutPanelOptions.call(this);return _.extend(a,{collection:this.model.outputCollection,selecting:!1})},_labelParamMap:function(){var a=this.model.get("params"),b={};return _.each(this.tool.inputs,function(c){c.label&&"DataToolParameter"!==c.model_class&&(b[c.label]=a[c.name])}),b},_labelInputMap:function(){var a=this,b={};return _.each(this.jobData.inputs,function(c){var d=a._findToolInput(c.name);d&&(b[d.label]=c)}),b},_findToolInput:function(a){var b=this.tool.inputs,c=_.findWhere(b,{name:a});return c?c:this._findRepeatToolInput(a,b)},_findRepeatToolInput:function(a,b){b=b||this.tool.inputs;var c=_.find(b,function(b){return 0===a.indexOf(b.name)});if(!c)return void 0;var d=_.find(c.inputs,function(b){return-1!==a.indexOf(b.name)});return d},toString:function(){return"JobListItemView("+this.model+")"}});return f.prototype.templates=function(){var a=(c.wrapTemplate(['
                      ','
                      <%= model.id %>
                      ','
                      ','
                      ','',"
                      ",'
                      ','
                      ','
                      ',"
                      "]),c.wrapTemplate(['
                      ','
                      ','<%- view.tool.name %>',"
                      ",'
                      ','<%- view.tool.description %>'," ",d("Created"),": <%= new Date( job.create_time ).toString() %>, ","","
                      "],"job")),b=c.wrapTemplate(['
                      ','<%- view.tool.description %>"],"job"),f=c.wrapTemplate(['
                      ','
                      ',"<% _.each( view._labelInputMap(), function( input, label ){ %>",'
                      ','','<%= input.content.name %>',"
                      ","<% }) %>","<% _.each( view._labelParamMap(), function( param, label ){ %>",'
                      ','','<%= param %>',"
                      ","<% }) %>","
                      ","
                      "],"job");return _.extend({},e.prototype.templates,{titleBar:a,subtitle:b,details:f})}(),{JobListItemView:f}});
+define(["mvc/list/list-item","mvc/dataset/dataset-list","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=a.FoldoutListItemView,f=e.extend({className:e.prototype.className+" job",id:function(){return["job",this.model.get("id")].join("-")},foldoutPanelClass:b.DatasetList,initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log(this+".initialize:",a),e.prototype.initialize.call(this,a),this.tool=a.tool||{},this.jobData=a.jobData||{},this.linkTarget=a.linkTarget||"_blank"},_swapNewRender:function(a){return e.prototype._swapNewRender.call(this,a),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_getFoldoutPanelOptions:function(){var a=e.prototype._getFoldoutPanelOptions.call(this);return _.extend(a,{collection:this.model.outputCollection,selecting:!1})},_labelParamMap:function(){var a=this.model.get("params"),b={};return _.each(this.tool.inputs,function(c){c.label&&"DataToolParameter"!==c.model_class&&(b[c.label]=a[c.name])}),b},_labelInputMap:function(){var a=this,b={};return _.each(this.jobData.inputs,function(c){var d=a._findToolInput(c.name);d&&(b[d.label]=c)}),b},_findToolInput:function(a){var b=this.tool.inputs,c=_.findWhere(b,{name:a});return c?c:this._findRepeatToolInput(a,b)},_findRepeatToolInput:function(a,b){b=b||this.tool.inputs;var c=_.find(b,function(b){return 0===a.indexOf(b.name)});if(!c)return void 0;var d=_.find(c.inputs,function(b){return-1!==a.indexOf(b.name)});return d},toString:function(){return"JobListItemView("+this.model+")"}});return f.prototype.templates=function(){var a=(c.wrapTemplate(['
                      ','
                      <%- model.id %>
                      ','
                      ','
                      ','',"
                      ",'
                      ','
                      ','
                      ',"
                      "]),c.wrapTemplate(['
                      ','
                      ','<%- view.tool.name %>',"
                      ",'
                      ','<%- view.tool.description %>'," ",d("Created"),": <%= new Date( job.create_time ).toString() %>, ","","
                      "],"job")),b=c.wrapTemplate(['
                      ','<%- view.tool.description %>"],"job"),f=c.wrapTemplate(['
                      ','
                      ',"<% _.each( view._labelInputMap(), function( input, label ){ %>",'
                      ','','<%- input.content.name %>',"
                      ","<% }) %>","<% _.each( view._labelParamMap(), function( param, label ){ %>",'
                      ','','<%- param %>',"
                      ","<% }) %>","
                      ","
                      "],"job");return _.extend({},e.prototype.templates,{titleBar:a,subtitle:b,details:f})}(),{JobListItemView:f}});
 //# sourceMappingURL=../../../maps/mvc/job/job-li.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/list/list-panel.js b/static/scripts/mvc/list/list-panel.js
index 46ae3a28b85..5e081e45a78 100644
--- a/static/scripts/mvc/list/list-panel.js
+++ b/static/scripts/mvc/list/list-panel.js
@@ -1,2 +1,2 @@
-define(["mvc/list/list-item","ui/loading-indicator","mvc/base-mvc","utils/localization","ui/search-input"],function(a,b,c,d){var e=Backbone.View.extend(c.LoggableMixin).extend({viewClass:a.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:d("This list is empty"),noneFoundMsg:d("No matching items found"),searchPlaceholder:d("search"),initialize:function(a){a=a||{},a.logger&&(this.logger=a.logger),this.log(this+".initialize:",a),this.fxSpeed=_.has(a,"fxSpeed")?a.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=a.searchFor||"",this.indicator=new b(this.$el),this.selecting=void 0!==a.selecting?a.selecting:!0,this.selected=a.selected||[],this.lastSelected=null,this.dragItems=a.dragItems||!1,this.viewClass=a.viewClass||this.viewClass,this.views=[],this.collection=a.collection||new this.collectionClass([]),this.filters=a.filters||[],this.$scrollContainer=a.$scrollContainer||this.$scrollContainer,this.title=a.title||"",this.subtitle=a.subtitle||"",this._setUpListeners()},freeViews:function(){return _.each(this.views,function(a){a.off()}),this.views=[],this},_setUpListeners:function(){return this.off(),this.on("error",function(a,b,c,d,e){console.error(a,b,c,d,e)},this),this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this),this.on("loading-done",function(){this._hideLoadingIndicator(40)},this),this.once("rendered",function(){this.trigger("rendered:initial",this)},this),this.logger&&this.on("all",function(){this.log(this+"",arguments)},this),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.collection.off(),this.collection.on("error",function(a,b,c,d,e){this.trigger("error",a,b,c,d,e)},this),this.collection.on("reset",function(){this.renderItems()},this),this.collection.on("add",this.addItemView,this),this.collection.on("remove",this.removeItemView,this),this.logger&&this.collection.on("all",function(){this.info(this+"(collection)",arguments)},this),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on("view:selected",function(a,b){if(b&&b.shiftKey&&this.lastSelected){var c=this.viewFromModelId(this.lastSelected);c&&this.selectRange(a,c)}else b&&b.altKey&&!this.selecting&&this.showSelectors();this.selected.push(a.model.id),this.lastSelected=a.model.id},this),this.on("view:de-selected",function(a){this.selected=_.without(this.selected,a.model.id)},this)},render:function(a){this.log(this+".render",a);var b=this._buildNewRender();return this._setUpBehaviors(b),this._queueNewRender(b,a),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var a=$(this.templates.el({},this));return this._renderControls(a),this._renderTitle(a),this._renderSubtitle(a),this._renderSearch(a),this.renderItems(a),a},_renderControls:function(a){this.debug(this+"(ListPanel)._renderControls");var b=$(this.templates.controls({},this));return a.find(".controls").replaceWith(b),b},_renderTitle:function(){},_renderSubtitle:function(){},_queueNewRender:function(a,b){b=void 0===b?this.fxSpeed:b;var c=this;c.log("_queueNewRender:",a,b),$(c).queue("fx",[function(a){this.$el.fadeOut(b,a)},function(b){c._swapNewRender(a),b()},function(a){this.$el.fadeIn(b,a)},function(a){c.trigger("rendered",c),a()}])},_swapNewRender:function(a){return this.$el.empty().attr("class",this.className).append(a.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(a){return a=a||this.$el,a.find(".controls [title]").tooltip({placement:"bottom"}),this._renderMultiselectActionMenu(a),this},_renderMultiselectActionMenu:function(a){a=a||this.$el;var b=a.find(".list-action-menu"),c=this.multiselectActions();if(!c.length)return b.empty();var e=$(['
                      ','",'","
                      "].join("")),f=c.map(function(a){var b=['
                    1. ',a.html,"
                      2. "].join("");return $(b).click(function(b){return b.preventDefault(),a.func(b)})});return e.find("ul").append(f),b.replaceWith(e),e},multiselectActions:function(){return[]},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(a){return(a||this.$el).find("> .list-items")},$messages:function(a){return(a||this.$el).find("> .controls .messages")},$emptyMessage:function(a){return(a||this.$el).find("> .empty-message")},renderItems:function(a){a=a||this.$el;var b=this;b.log(this+".renderItems",a);var c=b.$list(a);return b.views=b._filterCollection().map(function(a){return b._createItemView(a).render(0)}),c.empty(),b.views.length?(b._attachItems(a),b.$emptyMessage(a).hide()):b._renderEmptyMessage(a).show(),b.views},_filterCollection:function(){var a=this;return a.collection.filter(_.bind(a._filterItem,a))},_filterItem:function(a){var b=this;return _.every(b.filters.map(function(b){return b.call(a)}))&&(!b.searchFor||a.matchesAll(b.searchFor))},_createItemView:function(a){var b=this._getItemViewClass(a),c=_.extend(this._getItemViewOptions(a),{model:a}),d=new b(c);return this._setUpItemViewListeners(d),d},_getItemViewClass:function(){return this.viewClass},_getItemViewOptions:function(a){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:_.contains(this.selected,a.id),draggable:this.dragItems}},_setUpItemViewListeners:function(a){var b=this;return a.on("all",function(){var a=Array.prototype.slice.call(arguments,0);a[0]="view:"+a[0],b.trigger.apply(b,a)}),a.on("draggable:dragstart",function(a,b){var c={},d=this.getSelectedModels();c=d.length?d.toJSON():[b.model.toJSON()],a.dataTransfer.setData("text",JSON.stringify(c))},this),b},_attachItems:function(a){return this.$list(a).append(this.views.map(function(a){return a.$el})),this},_renderEmptyMessage:function(a){this.debug("_renderEmptyMessage",a,this.searchFor);var b=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(a).text(b)},expandAll:function(){_.each(this.views,function(a){a.expand()})},collapseAll:function(){_.each(this.views,function(a){a.collapse()})},addItemView:function(a){this.log(this+".addItemView:",a);var b=this;if(!b._filterItem(a))return void 0;var c=b._createItemView(a);return $(c).queue("fx",[function(a){b.$emptyMessage().fadeOut(b.fxSpeed,a)},function(a){b._attachView(c),a()}]),c},_attachView:function(a){var b=this;b.views.push(a),b.$list().append(a.render(0).$el.hide()),b.trigger("view:attached",a),a.$el.slideDown(b.fxSpeed,function(){b.trigger("view:attached:rendered")})},removeItemView:function(a){this.log(this+".removeItemView:",a);var b=this,c=b.viewFromModel(a);return c?(b.views=_.without(b.views,c),b.trigger("view:removed",c),$({}).queue("fx",[function(a){c.$el.fadeOut(b.fxSpeed,a)},function(a){c.remove(),b.trigger("view:removed:rendered"),b.views.length?a():b._renderEmptyMessage().fadeIn(b.fxSpeed,a)}]),c):void 0},viewFromModelId:function(a){for(var b=0;bc?this.views.slice(c,d+1):this.views.slice(d,c+1)},_renderSearch:function(a){return a.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)}),a},_firstSearch:function(a){return this.log("onFirstSearch",a),this.searchItems(a)},searchItems:function(a){return this.searchFor=a,this.trigger("search:searching",a,this),this.renderItems(),this.$("> .controls .search-query").val(a),this},clearSearch:function(){return this.searchFor="",this.trigger("search:clear",this),this.renderItems(),this.$("> .controls .search-query").val(""),this},showSelectors:function(a){a=void 0!==a?a:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(a),_.each(this.views,function(b){b.showSelector(a)})},hideSelectors:function(a){a=void 0!==a?a:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(a),_.each(this.views,function(b){b.hideSelector(a)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(a){_.each(this.views,function(b){b.select(a)})},deselectAll:function(a){this.lastSelected=null,_.each(this.views,function(b){b.deselect(a)})},selectRange:function(a,b){var c=this.viewRange(a,b);return _.each(c,function(a){a.select()}),c},getSelectedViews:function(){return _.filter(this.views,function(a){return a.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(a){return a.model}))},_showLoadingIndicator:function(a,c,d){this.debug("_showLoadingIndicator",this.indicator,a,c,d),c=void 0!==c?c:this.fxSpeed,this.indicator||(this.indicator=new b(this.$el,this.$el.parent()),this.debug("	 created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(c),this.indicator.show(a,c,d)):this.indicator.show(0,d)},_hideLoadingIndicator:function(a,b){this.debug("_hideLoadingIndicator",this.indicator,a,b),a=void 0!==a?a:this.fxSpeed,this.indicator&&this.indicator.hide(a,b)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(a,b){return b=b||0,this.$scrollContainer().animate({scrollTop:a},b),this},scrollToTop:function(a){return this.scrollTo(0,a)},scrollToItem:function(a,b){if(!a)return this;var c=a.$el.position().top;return this.scrollTo(c,b)},scrollToId:function(a,b){return this.scrollToItem(this.viewFromModelId(a),b)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=function(){var a=c.wrapTemplate(["
                      ",'
                      ','
                      ','
                      ',"
                      "]),b=c.wrapTemplate(['
                      ','
                      ','
                      <%= view.title %>
                      ',"
                      ",'
                      <%= view.subtitle %>
                      ','
                      ','
                      ','
                      ','
                      ',"
                      ",'
                      ','
                      ','",'","
                      ",'
                      ',"
                      ","
                      ","
                      "]);return{el:a,controls:b}}();var f=e.extend({modelCollectionKey:"contents",initialize:function(a){e.prototype.initialize.call(this,a),this.selecting=void 0!==a.selecting?a.selecting:!1,this.setModel(this.model,a)},setModel:function(a,b){if(b=b||{},this.debug(this+".setModel:",a,b),this.freeModel(),this.freeViews(),a){var c=this.model?this.model.get("id"):null;this.model=a,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.collection.off(),this.collection=this.model[this.modelCollectionKey]?this.model[this.modelCollectionKey]:b.collection||new this.collectionClass([]),this._setUpCollectionListeners(),c&&a.get("id")!==c&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.model.on("error",function(){var a=Array.prototype.slice.call(arguments,0);a.unshift("error"),this.trigger.apply(this,a)},this),this},_renderControls:function(a){this.debug(this+"(ListPanel)._renderControls");var b=this.model?this.model.toJSON():{},c=$(this.templates.controls(b,this));return a.find(".controls").replaceWith(c),c},toString:function(){return"ModelListPanel("+this.model+")"}});return f.prototype.templates=function(){var a=c.wrapTemplate(['
                      ','
                      ','
                      <%= model.name %>
                      ',"
                      ",'
                      <%= view.subtitle %>
                      ','
                      ','
                      ','
                      ','
                      ',"
                      ",'
                      ','
                      ','",'","
                      ",'
                      ',"
                      ","
                      ","
                      "]);return _.extend(_.clone(e.prototype.templates),{controls:a})}(),{ListPanel:e,ModelListPanel:f}});
+define(["mvc/list/list-item","ui/loading-indicator","mvc/base-mvc","utils/localization","ui/search-input"],function(a,b,c,d){var e=Backbone.View.extend(c.LoggableMixin).extend({viewClass:a.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:d("This list is empty"),noneFoundMsg:d("No matching items found"),searchPlaceholder:d("search"),initialize:function(a){a=a||{},a.logger&&(this.logger=a.logger),this.log(this+".initialize:",a),this.fxSpeed=_.has(a,"fxSpeed")?a.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=a.searchFor||"",this.indicator=new b(this.$el),this.selecting=void 0!==a.selecting?a.selecting:!0,this.selected=a.selected||[],this.lastSelected=null,this.dragItems=a.dragItems||!1,this.viewClass=a.viewClass||this.viewClass,this.views=[],this.collection=a.collection||new this.collectionClass([]),this.filters=a.filters||[],this.$scrollContainer=a.$scrollContainer||this.$scrollContainer,this.title=a.title||"",this.subtitle=a.subtitle||"",this._setUpListeners()},freeViews:function(){return _.each(this.views,function(a){a.off()}),this.views=[],this},_setUpListeners:function(){return this.off(),this.on("error",function(a,b,c,d,e){console.error(a,b,c,d,e)},this),this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this),this.on("loading-done",function(){this._hideLoadingIndicator(40)},this),this.once("rendered",function(){this.trigger("rendered:initial",this)},this),this.logger&&this.on("all",function(){this.log(this+"",arguments)},this),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.collection.off(),this.collection.on("error",function(a,b,c,d,e){this.trigger("error",a,b,c,d,e)},this),this.collection.on("reset",function(){this.renderItems()},this),this.collection.on("add",this.addItemView,this),this.collection.on("remove",this.removeItemView,this),this.logger&&this.collection.on("all",function(){this.info(this+"(collection)",arguments)},this),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on("view:selected",function(a,b){if(b&&b.shiftKey&&this.lastSelected){var c=this.viewFromModelId(this.lastSelected);c&&this.selectRange(a,c)}else b&&b.altKey&&!this.selecting&&this.showSelectors();this.selected.push(a.model.id),this.lastSelected=a.model.id},this),this.on("view:de-selected",function(a){this.selected=_.without(this.selected,a.model.id)},this)},render:function(a){this.log(this+".render",a);var b=this._buildNewRender();return this._setUpBehaviors(b),this._queueNewRender(b,a),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var a=$(this.templates.el({},this));return this._renderControls(a),this._renderTitle(a),this._renderSubtitle(a),this._renderSearch(a),this.renderItems(a),a},_renderControls:function(a){this.debug(this+"(ListPanel)._renderControls");var b=$(this.templates.controls({},this));return a.find(".controls").replaceWith(b),b},_renderTitle:function(){},_renderSubtitle:function(){},_queueNewRender:function(a,b){b=void 0===b?this.fxSpeed:b;var c=this;c.log("_queueNewRender:",a,b),$(c).queue("fx",[function(a){this.$el.fadeOut(b,a)},function(b){c._swapNewRender(a),b()},function(a){this.$el.fadeIn(b,a)},function(a){c.trigger("rendered",c),a()}])},_swapNewRender:function(a){return this.$el.empty().attr("class",this.className).append(a.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(a){return a=a||this.$el,a.find(".controls [title]").tooltip({placement:"bottom"}),this._renderMultiselectActionMenu(a),this},_renderMultiselectActionMenu:function(a){a=a||this.$el;var b=a.find(".list-action-menu"),c=this.multiselectActions();if(!c.length)return b.empty();var e=$(['
                      ','",'","
                      "].join("")),f=c.map(function(a){var b=['
                    2. ',a.html,"
                      3. "].join("");return $(b).click(function(b){return b.preventDefault(),a.func(b)})});return e.find("ul").append(f),b.replaceWith(e),e},multiselectActions:function(){return[]},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(a){return(a||this.$el).find("> .list-items")},$messages:function(a){return(a||this.$el).find("> .controls .messages")},$emptyMessage:function(a){return(a||this.$el).find("> .empty-message")},renderItems:function(a){a=a||this.$el;var b=this;b.log(this+".renderItems",a);var c=b.$list(a);return b.views=b._filterCollection().map(function(a){return b._createItemView(a).render(0)}),c.empty(),b.views.length?(b._attachItems(a),b.$emptyMessage(a).hide()):b._renderEmptyMessage(a).show(),b.views},_filterCollection:function(){var a=this;return a.collection.filter(_.bind(a._filterItem,a))},_filterItem:function(a){var b=this;return _.every(b.filters.map(function(b){return b.call(a)}))&&(!b.searchFor||a.matchesAll(b.searchFor))},_createItemView:function(a){var b=this._getItemViewClass(a),c=_.extend(this._getItemViewOptions(a),{model:a}),d=new b(c);return this._setUpItemViewListeners(d),d},_getItemViewClass:function(){return this.viewClass},_getItemViewOptions:function(a){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:_.contains(this.selected,a.id),draggable:this.dragItems}},_setUpItemViewListeners:function(a){var b=this;return a.on("all",function(){var a=Array.prototype.slice.call(arguments,0);a[0]="view:"+a[0],b.trigger.apply(b,a)}),a.on("draggable:dragstart",function(a,b){var c={},d=this.getSelectedModels();c=d.length?d.toJSON():[b.model.toJSON()],a.dataTransfer.setData("text",JSON.stringify(c))},this),b},_attachItems:function(a){return this.$list(a).append(this.views.map(function(a){return a.$el})),this},_renderEmptyMessage:function(a){this.debug("_renderEmptyMessage",a,this.searchFor);var b=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(a).text(b)},expandAll:function(){_.each(this.views,function(a){a.expand()})},collapseAll:function(){_.each(this.views,function(a){a.collapse()})},addItemView:function(a){this.log(this+".addItemView:",a);var b=this;if(!b._filterItem(a))return void 0;var c=b._createItemView(a);return $(c).queue("fx",[function(a){b.$emptyMessage().fadeOut(b.fxSpeed,a)},function(a){b._attachView(c),a()}]),c},_attachView:function(a){var b=this;b.views.push(a),b.$list().append(a.render(0).$el.hide()),b.trigger("view:attached",a),a.$el.slideDown(b.fxSpeed,function(){b.trigger("view:attached:rendered")})},removeItemView:function(a){this.log(this+".removeItemView:",a);var b=this,c=b.viewFromModel(a);return c?(b.views=_.without(b.views,c),b.trigger("view:removed",c),$({}).queue("fx",[function(a){c.$el.fadeOut(b.fxSpeed,a)},function(a){c.remove(),b.trigger("view:removed:rendered"),b.views.length?a():b._renderEmptyMessage().fadeIn(b.fxSpeed,a)}]),c):void 0},viewFromModelId:function(a){for(var b=0;bc?this.views.slice(c,d+1):this.views.slice(d,c+1)},_renderSearch:function(a){return a.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)}),a},_firstSearch:function(a){return this.log("onFirstSearch",a),this.searchItems(a)},searchItems:function(a){return this.searchFor=a,this.trigger("search:searching",a,this),this.renderItems(),this.$("> .controls .search-query").val(a),this},clearSearch:function(){return this.searchFor="",this.trigger("search:clear",this),this.renderItems(),this.$("> .controls .search-query").val(""),this},showSelectors:function(a){a=void 0!==a?a:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(a),_.each(this.views,function(b){b.showSelector(a)})},hideSelectors:function(a){a=void 0!==a?a:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(a),_.each(this.views,function(b){b.hideSelector(a)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(a){_.each(this.views,function(b){b.select(a)})},deselectAll:function(a){this.lastSelected=null,_.each(this.views,function(b){b.deselect(a)})},selectRange:function(a,b){var c=this.viewRange(a,b);return _.each(c,function(a){a.select()}),c},getSelectedViews:function(){return _.filter(this.views,function(a){return a.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(a){return a.model}))},_showLoadingIndicator:function(a,c,d){this.debug("_showLoadingIndicator",this.indicator,a,c,d),c=void 0!==c?c:this.fxSpeed,this.indicator||(this.indicator=new b(this.$el,this.$el.parent()),this.debug("	 created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(c),this.indicator.show(a,c,d)):this.indicator.show(0,d)},_hideLoadingIndicator:function(a,b){this.debug("_hideLoadingIndicator",this.indicator,a,b),a=void 0!==a?a:this.fxSpeed,this.indicator&&this.indicator.hide(a,b)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(a,b){return b=b||0,this.$scrollContainer().animate({scrollTop:a},b),this},scrollToTop:function(a){return this.scrollTo(0,a)},scrollToItem:function(a,b){if(!a)return this;var c=a.$el.position().top;return this.scrollTo(c,b)},scrollToId:function(a,b){return this.scrollToItem(this.viewFromModelId(a),b)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=function(){var a=c.wrapTemplate(["
                      ",'
                      ','
                      ','
                      ',"
                      "]),b=c.wrapTemplate(['
                      ','
                      ','
                      <%- view.title %>
                      ',"
                      ",'
                      <%- view.subtitle %>
                      ','
                      ','
                      ','
                      ','
                      ',"
                      ",'
                      ','
                      ','",'","
                      ",'
                      ',"
                      ","
                      ","
                      "]);return{el:a,controls:b}}();var f=e.extend({modelCollectionKey:"contents",initialize:function(a){e.prototype.initialize.call(this,a),this.selecting=void 0!==a.selecting?a.selecting:!1,this.setModel(this.model,a)},setModel:function(a,b){if(b=b||{},this.debug(this+".setModel:",a,b),this.freeModel(),this.freeViews(),a){var c=this.model?this.model.get("id"):null;this.model=a,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.collection.off(),this.collection=this.model[this.modelCollectionKey]?this.model[this.modelCollectionKey]:b.collection||new this.collectionClass([]),this._setUpCollectionListeners(),c&&a.get("id")!==c&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.model.on("error",function(){var a=Array.prototype.slice.call(arguments,0);a.unshift("error"),this.trigger.apply(this,a)},this),this},_renderControls:function(a){this.debug(this+"(ListPanel)._renderControls");var b=this.model?this.model.toJSON():{},c=$(this.templates.controls(b,this));return a.find(".controls").replaceWith(c),c},toString:function(){return"ModelListPanel("+this.model+")"}});return f.prototype.templates=function(){var a=c.wrapTemplate(['
                      ','
                      ','
                      <%- model.name %>
                      ',"
                      ",'
                      <%- view.subtitle %>
                      ','
                      ','
                      ','
                      ','
                      ',"
                      ",'
                      ','
                      ','",'","
                      ",'
                      ',"
                      ","
                      ","
                      "]);return _.extend(_.clone(e.prototype.templates),{controls:a})}(),{ListPanel:e,ModelListPanel:f}});
 //# sourceMappingURL=../../../maps/mvc/list/list-panel.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/ui/ui-select-default.js b/static/scripts/mvc/ui/ui-select-default.js
index 5b63052ee10..61e8bb552ab 100644
--- a/static/scripts/mvc/ui/ui-select-default.js
+++ b/static/scripts/mvc/ui/ui-select-default.js
@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-button-check"],function(a,b){var c=Backbone.View.extend({optionsDefault:{id:a.uid(),cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(c){var d=this;this.options=a.merge(c,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon=this.$el.find(".icon"),this.$button=this.$el.find(".button"),this.options.multiple&&(this.options.searchable&&(this.all_button=new b({onclick:function(){var a=[];0!==d.all_button.value()&&(a=d._availableOptions()),d.value(a),d.trigger("change")}}),this.$el.prepend(this.all_button.$el)),this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$button.remove()),this.update(this.options.data),void 0!==this.options.value&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show(),this.$select.on("change",function(){d.trigger("change")}),this.on("change",function(){d.options.onchange&&d.options.onchange(this.value())})},value:function(a){void 0!==a&&(null===a&&(a="__null__"),(this.exists(a)||this.options.multiple)&&(this.$select.val(a),this.$select.select2&&this.$select.select2("val",a)));var b=this._getValue();return this.all_button&&this.all_button.value($.isArray(b)&&b.length||0,this._size()),b},first:function(){var a=this.$select.find("option").first();return a.length>0?a.val():null},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},update:function(a){var b=this._getValue();this.$select.find("option").remove(),!this.options.multiple&&this.options.optional&&this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}));for(var c in a)this.$select.append(this._templateOption(a[c]));0==this._size()?(this.disable(),this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))):this.enable(),this.options.searchable&&(this.$select.select2("destroy"),this.$select.select2(),this.$(".select2-container .select2-search input").off("blur")),this.value(b),null!==this._getValue()||this.options.multiple&&this.options.optional||this.value(this.first())},setOnChange:function(a){this.options.onchange=a},exists:function(a){return this.$select.find('option[value="'+a+'"]').length>0},_getValue:function(){var b=this.$select.val();return a.validate(b)?b:null},_availableOptions:function(){var a=[];return this.$select.find("option").each(function(b,c){a.push($(c).attr("value"))}),a},_size:function(){return this.$select.find("option").length},_templateOption:function(a){return'"},_template:function(a){return'
                      '}});return{View:c}});
 //# sourceMappingURL=../../../maps/mvc/ui/ui-select-default.js.map
\ No newline at end of file

From 6c9a82e142c5bf70ae4612f094b8d0c89e3fd2f3 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg 
Date: Thu, 3 Dec 2015 12:27:01 -0500
Subject: [PATCH 02/24] Fix for Section upgrade messages.

---
 lib/galaxy/tools/__init__.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 912d35042b4..651a3cc033e 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2003,7 +2003,7 @@ class Tool( object, Dictifiable ):
                 if isinstance( input, Conditional ):
                     cond_messages = {}
                     if not input.is_job_resource_conditional:
-                        cond_messages = { input.test_param.name: "No value found for '%s%s', used default" % ( prefix, input.label ) }
+                        cond_messages = { input.test_param.name: "No value found for '%s%s', used default" % ( prefix, input.label() ) }
                         messages[ input.name ] = cond_messages
                     test_value = input.test_param.get_initial_value( trans, context )
                     current_case = input.get_current_case( test_value, trans )
@@ -2017,7 +2017,7 @@ class Tool( object, Dictifiable ):
                             messages[ input.name ].append( rep_dict )
                             self.check_and_update_param_values_helper( input.inputs, {}, trans, rep_dict, context, rep_prefix, allow_workflow_parameters=allow_workflow_parameters )
                 elif isinstance( input, Section ):
-                    messages[ input.name ] = { input.name: "No value found for '%s%s', used default" % ( prefix, input.label ) }
+                    messages[ input.name ] = {}
                     self.check_and_update_param_values_helper( input.inputs, {}, trans, messages[ input.name ], context, prefix, allow_workflow_parameters=allow_workflow_parameters )
                 else:
                     messages[ input.name ] = "No value found for '%s%s', used default" % ( prefix, input.label )
@@ -2047,8 +2047,8 @@ class Tool( object, Dictifiable ):
                         current = group_values["__current_case__"]
                         self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix, allow_workflow_parameters=allow_workflow_parameters )
                 elif isinstance( input, Section ):
-                    messages[ input.name ] = "No value found for '%s%s', used default" % ( prefix, input.label )
-                    self.check_and_update_param_values_helper( input.inputs, values[ input.name ], trans, messages, context, prefix, allow_workflow_parameters=allow_workflow_parameters )
+                    messages[ input.name ] = {}
+                    self.check_and_update_param_values_helper( input.inputs, values[ input.name ], trans, messages[ input.name ], context, prefix, allow_workflow_parameters=allow_workflow_parameters )
                 else:
                     # Regular tool parameter, no recursion needed
                     try:

From 2c0ad432f8485cb40719adfa8ecbbf1a342afd03 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg 
Date: Thu, 3 Dec 2015 12:30:34 -0500
Subject: [PATCH 03/24] Use test param label instead of param label in
 conditional upgrade missing message.

---
 lib/galaxy/tools/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 651a3cc033e..d075ade97c9 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2003,7 +2003,7 @@ class Tool( object, Dictifiable ):
                 if isinstance( input, Conditional ):
                     cond_messages = {}
                     if not input.is_job_resource_conditional:
-                        cond_messages = { input.test_param.name: "No value found for '%s%s', used default" % ( prefix, input.label() ) }
+                        cond_messages = { input.test_param.name: "No value found for '%s%s', used default" % ( prefix, input.test_param.label ) }
                         messages[ input.name ] = cond_messages
                     test_value = input.test_param.get_initial_value( trans, context )
                     current_case = input.get_current_case( test_value, trans )

From 8334593de11e915389b1da58c3b5db26121c7bef Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg 
Date: Thu, 3 Dec 2015 17:00:54 -0500
Subject: [PATCH 04/24] Fixes for dataset 'cleanup'/association linking when
 extracting workflows from a history.

---
 lib/galaxy/workflow/extract.py | 22 ++++++++++++++--------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py
index 39c2e57fc2e..2725ae1546a 100644
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -14,7 +14,8 @@ from galaxy.tools.parameters.basic import (
 from galaxy.tools import ToolOutputCollectionPart
 from galaxy.tools.parameters.grouping import (
     Conditional,
-    Repeat
+    Repeat,
+    Section
 )
 from .steps import (
     attach_ordered_steps,
@@ -340,10 +341,11 @@ def __cleanup_param_values( inputs, values ):
                     if k.startswith( key ):
                         del root_values[k]
             elif isinstance( input, Repeat ):
-                group_values = values[key]
-                for i, rep_values in enumerate( group_values ):
-                    rep_index = rep_values['__index__']
-                    cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] )
+                if key in values:
+                    group_values = values[key]
+                    for i, rep_values in enumerate( group_values ):
+                        rep_index = rep_values['__index__']
+                        cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] )
             elif isinstance( input, Conditional ):
                 # Scrub dynamic resource related parameters from workflows,
                 # they cause problems and the workflow probably should include
@@ -352,9 +354,13 @@ def __cleanup_param_values( inputs, values ):
                     if input.name in values:
                         del values[input.name]
                     return
-                group_values = values[input.name]
-                current_case = group_values['__current_case__']
-                cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values )
+                if input.name in values:
+                    group_values = values[input.name]
+                    current_case = group_values['__current_case__']
+                    cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values )
+            elif isinstance( input, Section ):
+                if input.name in values:
+                    cleanup( "%s%s|" % ( prefix, key ), input.inputs, values[input.name] )
     cleanup( "", inputs, values )
     return associations
 

From 7923360dcec48b2e98d7c2a5bcae5f47187d6bf6 Mon Sep 17 00:00:00 2001
From: John Chilton 
Date: Fri, 4 Dec 2015 13:13:22 +0000
Subject: [PATCH 05/24] "Fix" collection outputs to hide the HDAs in the
 history.

Long term this is just not a solution, but it is the strategy we use for mapped over output HDAs also.

Rebased and fixed based on comments from @nsoranzo indicating the previous attempt did absolutely nothing to fix the problem.

xref https://github.com/galaxyproject/tools-iuc/pull/412/files
---
 lib/galaxy/tools/actions/__init__.py | 11 ++++++++---
 test/api/test_tools.py               |  4 ++--
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 7bd281aa703..c6d77991942 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -224,7 +224,7 @@ class DefaultToolAction( object ):
         child_dataset_names = set()
         object_store_populator = ObjectStorePopulator( trans.app )
 
-        def handle_output( name, output ):
+        def handle_output( name, output, hidden=None ):
             if output.parent:
                 parent_to_child_pairs.append( ( output.parent, name ) )
                 child_dataset_names.add( name )
@@ -240,7 +240,9 @@ class DefaultToolAction( object ):
             else:
                 ext = determine_output_format( output, wrapped_params.params, inp_data, input_ext )
                 data = trans.app.model.HistoryDatasetAssociation( extension=ext, create_dataset=True, sa_session=trans.sa_session )
-                if output.hidden:
+                if hidden is None:
+                    hidden = output.hidden
+                if hidden:
                     data.visible = False
                 # Commit the dataset immediately so it gets database assigned unique id
                 trans.sa_session.add( data )
@@ -318,7 +320,10 @@ class DefaultToolAction( object ):
                             current_element_identifiers = current_element_identifiers[ index ][ "element_identifiers" ]
 
                         effective_output_name = output_part_def.effective_output_name
-                        element = handle_output( effective_output_name, output_part_def.output_def )
+                        element = handle_output( effective_output_name, output_part_def.output_def, hidden=True )
+                        # TODO: this shouldn't exist in the top-level of the history at all
+                        # but for now we are still working around that by hiding the contents
+                        # there.
                         # Following hack causes dataset to no be added to history...
                         child_dataset_names.add( effective_output_name )
 
diff --git a/test/api/test_tools.py b/test/api/test_tools.py
index 8e71ef14cec..ec880a669e0 100644
--- a/test/api/test_tools.py
+++ b/test/api/test_tools.py
@@ -296,8 +296,8 @@ class ToolsTestCase( api.ApiTestCase ):
         output_collection = self._assert_one_job_one_collection_run( create )
         element0, element1 = self._assert_elements_are( output_collection, "forward", "reverse" )
         self.dataset_populator.wait_for_history( history_id, assert_ok=True )
-        self._verify_element( history_id, element0, contents="123\n789\n", file_ext="txt" )
-        self._verify_element( history_id, element1, contents="456\n0ab\n", file_ext="txt" )
+        self._verify_element( history_id, element0, contents="123\n789\n", file_ext="txt", visible=False )
+        self._verify_element( history_id, element1, contents="456\n0ab\n", file_ext="txt", visible=False )
 
     @skip_without_tool( "collection_creates_list" )
     def test_list_collection_output( self ):

From 41a56ead749bd25c6bc46107201b0e62bb65af9a Mon Sep 17 00:00:00 2001
From: carlfeberhard 
Date: Mon, 7 Dec 2015 15:55:17 -0500
Subject: [PATCH 06/24] Fix list collection creator being cutoff by restoring
 height: 100%

---
 client/galaxy/scripts/mvc/collection/list-collection-creator.js | 2 +-
 static/maps/mvc/collection/list-collection-creator.js.map       | 2 +-
 static/scripts/mvc/collection/list-collection-creator.js        | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/mvc/collection/list-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-collection-creator.js
index f7dfbe6467a..f587a1202d9 100644
--- a/client/galaxy/scripts/mvc/collection/list-collection-creator.js
+++ b/client/galaxy/scripts/mvc/collection/list-collection-creator.js
@@ -1003,7 +1003,7 @@ var collectionCreatorModal = function _collectionCreatorModal( elements, options
         title   : options.title || _l( 'Create a collection' ),
         body    : creator.$el,
         width   : '80%',
-        height  : 'min-content',
+        height  : '100%',
         closing_events: true
     });
     creator.render();
diff --git a/static/maps/mvc/collection/list-collection-creator.js.map b/static/maps/mvc/collection/list-collection-creator.js.map
index 1a85bfe38a3..29d941306b7 100644
--- a/static/maps/mvc/collection/list-collection-creator.js.map
+++ b/static/maps/mvc/collection/list-collection-creator.js.map
@@ -1 +1 @@
-{"version":3,"file":"list-collection-creator.js","sources":["../../../src/mvc/collection/list-collection-creator.js"],"names":["define","HDCA","STATES","BASE_MVC","UI_MODAL","naturalSort","_l","createListCollection","contents","elements","toJSON","promise","listCollectionCreatorModal","creationFn","name","map","element","id","src","history_content_type","createHDCA","DatasetCollectionElementView","Backbone","View","extend","LoggableMixin","tagName","className","initialize","attributes","this","selected","render","$el","attr","html","template","addClass","_","join","select","toggle","toggleClass","trigger","source","hasClass","discard","view","parentWidth","parent","width","animate","margin-right","destroy","off","remove","events","click","click .name","click .discard","dragstart","dragend","dragover","drop","_click","ev","stopPropagation","_clickName","preventDefault","response","prompt","_clickDiscard","_dragstart","originalEvent","dataTransfer","effectAllowed","setData","JSON","stringify","_dragend","removeClass","_sendToParent","toString","ListCollectionCreator","elementViewClass","collectionClass","HistoryListDatasetCollection","minElements","defaultAttributes","TypeError","oncreate","oncancel","autoscrollDist","highlightClr","metric","creator","each","value","key","initialElements","_instanceSetUp","_elementsSetUp","_setUpBehaviors","selectedIds","$dragging","blocking","invalidElements","workingElements","elementViews","slice","_ensureElementIds","_validateElements","_mangleDuplicateNames","_sortElements","forEach","hasOwnProperty","uniqueId","filter","problem","_isElementInvalid","push","text","state","OK","contains","NOT_READY_STATES","deleted","purged","SAFETY","counter","existingNames","currName","Error","speed","callback","length","_renderInvalid","empty","templates","main","_renderHeader","_renderMiddle","_renderFooter","_addPluginComponents","$","focus","invalidInitial","problems","show","$header","header","find","prepend","helpContent","_invalidElementsAlert","$middle","middle","_renderList","$footer","footer","hoverhighlight","_showAlert","_validationWarning","what","clear","VALIDATION_CLASS","add","_disableNameAndCreate","disable","isUndefined","prop","$list","_renderClearSelected","size","hide","$tmp","jQuery","removeElementView","elementView","_createElementView","append","children","invoke","height","css","has","_listenToElementView","listenTo","data","addElementView","without","stopListening","_renderNoElementsLeft","noElementsLeft","_elementToJSON","createList","message","always","fail","xhr","status","done","call","on","_errorHandler","once","error","content","readyState","responseJSON","click 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\ No newline at end of file
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\ No newline at end of file
diff --git a/static/scripts/mvc/collection/list-collection-creator.js b/static/scripts/mvc/collection/list-collection-creator.js
index b73a39d7cac..754ca884cfa 100644
--- a/static/scripts/mvc/collection/list-collection-creator.js
+++ b/static/scripts/mvc/collection/list-collection-creator.js
@@ -1,2 +1,2 @@
-define(["mvc/history/hdca-model","mvc/dataset/states","mvc/base-mvc","mvc/ui/ui-modal","utils/natural-sort","utils/localization","ui/hoverhighlight"],function(a,b,c,d,e,f){function g(a){var b=a.toJSON(),c=k(b,{creationFn:function(b,c){return b=b.map(function(a){return{id:a.id,name:a.name,src:"dataset"===a.history_content_type?"hda":"hdca"}}),a.createHDCA(b,"list",c)}});return c}var h=Backbone.View.extend(c.LoggableMixin).extend({tagName:"li",className:"collection-element",initialize:function(a){this.element=a.element||{},this.selected=a.selected||!1},render:function(){return this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})),this.selected&&this.$el.addClass("selected"),this},template:_.template(['',"<%- element.name %>","",'"].join("")),select:function(a){this.$el.toggleClass("selected",a),this.trigger("select",{source:this,selected:this.$el.hasClass("selected")})},discard:function(){var a=this,b=this.$el.parent().width();this.$el.animate({"margin-right":b},"fast",function(){a.trigger("discard",{source:a}),a.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click .discard":"_clickDiscard",dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(a){a.stopPropagation(),this.select(a)},_clickName:function(a){a.stopPropagation(),a.preventDefault();var b=([f("Enter a new name for the element"),":\n(",f("Note that changing the name here will not rename the dataset"),")"].join(""),prompt(f("Enter a new name for the element")+":",this.element.name));b&&(this.element.name=b,this.render())},_clickDiscard:function(a){a.stopPropagation(),this.discard()},_dragstart:function(a){a.originalEvent&&(a=a.originalEvent),a.dataTransfer.effectAllowed="move",a.dataTransfer.setData("text/plain",JSON.stringify(this.element)),this.$el.addClass("dragging"),this.$el.parent().trigger("collection-element.dragstart",[this])},_dragend:function(){this.$el.removeClass("dragging"),this.$el.parent().trigger("collection-element.dragend",[this])},_sendToParent:function(a){this.$el.parent().trigger(a)},toString:function(){return"DatasetCollectionElementView()"}}),i=Backbone.View.extend(c.LoggableMixin).extend({elementViewClass:h,collectionClass:a.HistoryListDatasetCollection,className:"list-collection-creator collection-creator flex-row-container",minElements:1,defaultAttributes:{creationFn:function(){throw new TypeError("no creation fn for creator")},oncreate:function(){},oncancel:function(){},autoscrollDist:24,highlightClr:"rgba( 64, 255, 255, 1.0 )"},initialize:function(a){this.metric("ListCollectionCreator.initialize",a);var b=this;_.each(this.defaultAttributes,function(c,d){c=a[d]||c,b[d]=c}),b.initialElements=a.elements||[],this._instanceSetUp(),this._elementsSetUp(),this._setUpBehaviors()},_instanceSetUp:function(){this.selectedIds={},this.$dragging=null,this.blocking=!1},_elementsSetUp:function(){this.invalidElements=[],this.workingElements=[],this.elementViews=[],this.workingElements=this.initialElements.slice(0),this._ensureElementIds(),this._validateElements(),this._mangleDuplicateNames(),this._sortElements()},_ensureElementIds:function(){return this.workingElements.forEach(function(a){a.hasOwnProperty("id")||(a.id=_.uniqueId())}),this.workingElements},_validateElements:function(){var a=this;return a.invalidElements=[],this.workingElements=this.workingElements.filter(function(b){var c=a._isElementInvalid(b);return c&&a.invalidElements.push({element:b,text:c}),!c}),this.workingElements},_isElementInvalid:function(a){return"dataset"!==a.history_content_type?f("is not a dataset"):a.state!==b.OK?f(_.contains(b.NOT_READY_STATES,a.state)?"hasn't finished running yet":"has errored, is paused, or is not accessible"):a.deleted||a.purged?f("has been deleted or purged"):null},_mangleDuplicateNames:function(){var a=900,b=1,c={};this.workingElements.forEach(function(d){for(var e=d.name;c.hasOwnProperty(e);)if(e=d.name+" ("+b+")",b+=1,b>=a)throw new Error("Safety hit in while loop - thats impressive");d.name=e,c[d.name]=!0})},_sortElements:function(){},render:function(a,b){return this.workingElements.length .clear-selected").show():this.$(".collection-elements-controls > .clear-selected").hide()},_renderList:function(){var a=this,b=jQuery("
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                      ":": "+d}b._showAlert(content,"alert-danger")},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .reset":"reset","click .clear-selected":"clearSelectedElements","click .collection-elements":"clearSelectedElements","dragover .collection-elements":"_dragoverElements","drop .collection-elements":"_dropElements","collection-element.dragstart .collection-elements":"_elementDragstart","collection-element.dragend   .collection-elements":"_elementDragend","change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(){"function"==typeof this.oncancel&&this.oncancel.call(this)},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(a){a.stopPropagation(),this.$(".main-help").addClass("expanded"),this.$(".more-help").hide()},_clickLessHelp:function(a){a.stopPropagation(),this.$(".main-help").removeClass("expanded"),this.$(".more-help").show()},_toggleHelp:function(a){a.stopPropagation(),this.$(".main-help").toggleClass("expanded"),this.$(".more-help").toggle()},_showAlert:function(a,b){b=b||"alert-danger",this.$(".main-help").hide(),this.$(".header .alert").attr("class","alert alert-dismissable").addClass(b).show().find(".alert-message").html(a)},_hideAlert:function(){this.$(".main-help").show(),this.$(".header .alert").hide()},reset:function(){this._instanceSetUp(),this._elementsSetUp(),this.render()},clearSelectedElements:function(){this.$(".collection-elements .collection-element").removeClass("selected"),this.$(".collection-elements-controls > .clear-selected").hide()},_dragoverElements:function(a){a.preventDefault();var b=this.$list();this._checkForAutoscroll(b,a.originalEvent.clientY);var c=this._getNearestElement(a.originalEvent.clientY);this.$(".element-drop-placeholder").remove();var d=$('
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                      • ",f(['Click the "Start over" link to begin again as if you had just opened ',"the interface."].join("")),"
                        • ","
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                        • ","

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                      ",f(['Once your collection is complete, enter a name and ','click "Create list".'].join("")),"
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+define(["mvc/history/hdca-model","mvc/dataset/states","mvc/base-mvc","mvc/ui/ui-modal","utils/natural-sort","utils/localization","ui/hoverhighlight"],function(a,b,c,d,e,f){function g(a){var b=a.toJSON(),c=k(b,{creationFn:function(b,c){return b=b.map(function(a){return{id:a.id,name:a.name,src:"dataset"===a.history_content_type?"hda":"hdca"}}),a.createHDCA(b,"list",c)}});return c}var h=Backbone.View.extend(c.LoggableMixin).extend({tagName:"li",className:"collection-element",initialize:function(a){this.element=a.element||{},this.selected=a.selected||!1},render:function(){return this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})),this.selected&&this.$el.addClass("selected"),this},template:_.template(['',"<%- element.name %>","",'"].join("")),select:function(a){this.$el.toggleClass("selected",a),this.trigger("select",{source:this,selected:this.$el.hasClass("selected")})},discard:function(){var a=this,b=this.$el.parent().width();this.$el.animate({"margin-right":b},"fast",function(){a.trigger("discard",{source:a}),a.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click .discard":"_clickDiscard",dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(a){a.stopPropagation(),this.select(a)},_clickName:function(a){a.stopPropagation(),a.preventDefault();var b=([f("Enter a new name for the element"),":\n(",f("Note that changing the name here will not rename the dataset"),")"].join(""),prompt(f("Enter a new name for the element")+":",this.element.name));b&&(this.element.name=b,this.render())},_clickDiscard:function(a){a.stopPropagation(),this.discard()},_dragstart:function(a){a.originalEvent&&(a=a.originalEvent),a.dataTransfer.effectAllowed="move",a.dataTransfer.setData("text/plain",JSON.stringify(this.element)),this.$el.addClass("dragging"),this.$el.parent().trigger("collection-element.dragstart",[this])},_dragend:function(){this.$el.removeClass("dragging"),this.$el.parent().trigger("collection-element.dragend",[this])},_sendToParent:function(a){this.$el.parent().trigger(a)},toString:function(){return"DatasetCollectionElementView()"}}),i=Backbone.View.extend(c.LoggableMixin).extend({elementViewClass:h,collectionClass:a.HistoryListDatasetCollection,className:"list-collection-creator collection-creator flex-row-container",minElements:1,defaultAttributes:{creationFn:function(){throw new TypeError("no creation fn for creator")},oncreate:function(){},oncancel:function(){},autoscrollDist:24,highlightClr:"rgba( 64, 255, 255, 1.0 )"},initialize:function(a){this.metric("ListCollectionCreator.initialize",a);var b=this;_.each(this.defaultAttributes,function(c,d){c=a[d]||c,b[d]=c}),b.initialElements=a.elements||[],this._instanceSetUp(),this._elementsSetUp(),this._setUpBehaviors()},_instanceSetUp:function(){this.selectedIds={},this.$dragging=null,this.blocking=!1},_elementsSetUp:function(){this.invalidElements=[],this.workingElements=[],this.elementViews=[],this.workingElements=this.initialElements.slice(0),this._ensureElementIds(),this._validateElements(),this._mangleDuplicateNames(),this._sortElements()},_ensureElementIds:function(){return this.workingElements.forEach(function(a){a.hasOwnProperty("id")||(a.id=_.uniqueId())}),this.workingElements},_validateElements:function(){var a=this;return a.invalidElements=[],this.workingElements=this.workingElements.filter(function(b){var c=a._isElementInvalid(b);return c&&a.invalidElements.push({element:b,text:c}),!c}),this.workingElements},_isElementInvalid:function(a){return"dataset"!==a.history_content_type?f("is not a dataset"):a.state!==b.OK?f(_.contains(b.NOT_READY_STATES,a.state)?"hasn't finished running yet":"has errored, is paused, or is not accessible"):a.deleted||a.purged?f("has been deleted or purged"):null},_mangleDuplicateNames:function(){var a=900,b=1,c={};this.workingElements.forEach(function(d){for(var e=d.name;c.hasOwnProperty(e);)if(e=d.name+" ("+b+")",b+=1,b>=a)throw new Error("Safety hit in while loop - thats impressive");d.name=e,c[d.name]=!0})},_sortElements:function(){},render:function(a,b){return this.workingElements.length .clear-selected").show():this.$(".collection-elements-controls > .clear-selected").hide()},_renderList:function(){var a=this,b=jQuery("
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                      ":": "+d}b._showAlert(content,"alert-danger")},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .reset":"reset","click .clear-selected":"clearSelectedElements","click .collection-elements":"clearSelectedElements","dragover .collection-elements":"_dragoverElements","drop .collection-elements":"_dropElements","collection-element.dragstart .collection-elements":"_elementDragstart","collection-element.dragend   .collection-elements":"_elementDragend","change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(){"function"==typeof this.oncancel&&this.oncancel.call(this)},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(a){a.stopPropagation(),this.$(".main-help").addClass("expanded"),this.$(".more-help").hide()},_clickLessHelp:function(a){a.stopPropagation(),this.$(".main-help").removeClass("expanded"),this.$(".more-help").show()},_toggleHelp:function(a){a.stopPropagation(),this.$(".main-help").toggleClass("expanded"),this.$(".more-help").toggle()},_showAlert:function(a,b){b=b||"alert-danger",this.$(".main-help").hide(),this.$(".header .alert").attr("class","alert alert-dismissable").addClass(b).show().find(".alert-message").html(a)},_hideAlert:function(){this.$(".main-help").show(),this.$(".header .alert").hide()},reset:function(){this._instanceSetUp(),this._elementsSetUp(),this.render()},clearSelectedElements:function(){this.$(".collection-elements .collection-element").removeClass("selected"),this.$(".collection-elements-controls > .clear-selected").hide()},_dragoverElements:function(a){a.preventDefault();var b=this.$list();this._checkForAutoscroll(b,a.originalEvent.clientY);var c=this._getNearestElement(a.originalEvent.clientY);this.$(".element-drop-placeholder").remove();var d=$('
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                      "].join("")),invalidElements:_.template([f("The following selections could not be included due to problems:"),"
                        <% _.each( problems, function( problem ){ %>","
                      • <%- problem.element.name %>: <%- problem.text %>
                        • ","<% }); %>
                      "].join("")),noElementsLeft:_.template(['
                    4. ',f("No elements left! "),f("Would you like to "),'',f("start over"),"?","
                      5. "].join("")),invalidInitial:_.template(['
                      ','
                      ','',"<% if( _.size( problems ) ){ %>",f("The following selections could not be included due to problems"),":","
                        <% _.each( problems, function( problem ){ %>","
                      • <%- problem.element.name %>: <%- problem.text %>
                        • ","<% }); %>
                      ","<% } else if( _.size( elements ) < 1 ){ %>",f("No datasets were selected"),".","<% } %>","
                      ",f("At least one element is needed for the collection"),". ",f("You may need to "),'',f("cancel")," ",f("and reselect new elements"),".","                      ","
                      ","
                      ",'
                      ','
                      ','
                      ','","
                      ","
                      ","
                      "].join(""))},toString:function(){return"ListCollectionCreator"}}),j=function(a,b,c){var e,g=jQuery.Deferred(),h=Galaxy.modal||new d.View;return b=_.defaults(b||{},{elements:a,oncancel:function(){h.hide(),g.reject("cancelled")},oncreate:function(a,b){h.hide(),g.resolve(b)}}),e=new c(b),h.show({title:b.title||f("Create a collection"),body:e.$el,width:"80%",height:"100%",closing_events:!0}),e.render(),window._collectionCreator=e,g},k=function(a,b){return b=b||{},b.title=f("Create a collection from a list of datasets"),j(a,b,i)};return{DatasetCollectionElementView:h,ListCollectionCreator:i,collectionCreatorModal:j,listCollectionCreatorModal:k,createListCollection:g}});
 //# sourceMappingURL=../../../maps/mvc/collection/list-collection-creator.js.map
\ No newline at end of file

From 3924a5a0e3d2c7d787e81fabc4e2908f30ff0168 Mon Sep 17 00:00:00 2001
From: Mark Iskander 
Date: Mon, 7 Dec 2015 15:44:13 -0600
Subject: [PATCH 07/24] Fixed indentation errors

---
 .../webapps/reports/jobs_errors_per_tool.mako | 88 +++---------------
 .../webapps/reports/jobs_per_month_all.mako   | 69 ++------------
 .../reports/jobs_per_month_in_error.mako      | 69 ++------------
 templates/webapps/reports/jobs_per_tool.mako  | 90 +++----------------
 templates/webapps/reports/jobs_per_user.mako  | 73 ++-------------
 .../reports/jobs_specified_month_all.mako     | 69 ++------------
 .../jobs_specified_month_in_error.mako        | 69 ++------------
 .../webapps/reports/jobs_tool_per_month.mako  | 44 ++-------
 .../webapps/reports/jobs_user_per_month.mako  | 36 ++------
 .../reports/registered_users_per_month.mako   | 20 +----
 .../reports/requests_user_per_month.mako      | 22 +----
 .../reports/users_last_access_date.mako       | 28 ++----
 .../reports/users_user_disk_usage.mako        | 24 +----
 .../reports/workflows_per_month_all.mako      | 56 ++----------
 .../webapps/reports/workflows_per_user.mako   | 75 +++-------------
 .../reports/workflows_per_workflow.mako       | 90 +++----------------
 .../reports/workflows_user_per_month.mako     | 32 +------
 17 files changed, 119 insertions(+), 835 deletions(-)

diff --git a/templates/webapps/reports/jobs_errors_per_tool.mako b/templates/webapps/reports/jobs_errors_per_tool.mako
index ad7e69b8847..7f4b82261e9 100644
--- a/templates/webapps/reports/jobs_errors_per_tool.mako
+++ b/templates/webapps/reports/jobs_errors_per_tool.mako
@@ -25,13 +25,7 @@ ${get_css()}
         
                      
             
                      
                 
-                    ${
-                        get_pages( sort_id, order, 
-                                   page_specs,
-                                   'jobs',
-                                   'errors_per_tool',
-                                   spark_time=time_period )
-                    }
+                    ${get_pages(sort_id, order, page_specs, 'jobs', 'errors_per_tool', spark_time=time_period)}
                 
                 
                     
                      Jobs In Error Per Tool
                      
@@ -41,30 +35,12 @@ ${get_css()}
                             Click error number to view job details.
                         
                      
 
-                        Graph goes from present to past for 
-                        ${
-                            make_spark_settings( 
-                                "jobs",
-                                "errors_per_tool",
-                                spark_limit,
-                                sort_id,
-                                order,
-                                time_period,
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        Graph goes from present to past for
+                        ${make_spark_settings("jobs", "errors_per_tool", spark_limit, sort_id, order, time_period, page=page, offset=offset, entries=entries)}
                     
                                       		
                 
-                    ${
-                        get_entry_selector(
-                            "jobs",
-                            "errors_per_tool",
-                            page_specs.entries,
-                            sort_id,
-                            order)
-                    }
+                    ${get_entry_selector("jobs", "errors_per_tool", page_specs.entries, sort_id, order)}
                 
             
                      
         
                      
@@ -78,59 +54,23 @@ ${get_css()}
             %else:
                 
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'tool_id',
-                                'jobs',
-                                'errors_per_tool',
-                                'Tool ID',
-                                spark_time=time_period,
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        ${get_sort_url(sort_id, order, 'tool_id', 'jobs', 'errors_per_tool', 'Tool ID', spark_time=time_period, page=page, offset=offset, entries=entries)}
                         ${arrow}
                     
                     %if is_user_jobs_only:
     					
-                            ${
-                                get_sort_url(
-                                    sort_id,
-                                    order,
-                                    'total_jobs',
-                                    'jobs',
-                                    'errors_per_tool',
-                                    'User Jobs in Error',
-                                    spark_time=time_period,
-                                    page=page,
-                                    offset=offset,
-                                    entries=entries)
-                            }
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'errors_per_tool', 'User Jobs in Error', spark_time=time_period, page=page, offset=offset, entries=entries)}
                             ${arrow}
                         
 					%else:
 	                    
-                            ${
-                                get_sort_url(
-                                    sort_id,
-                                    order,
-                                    'total_jobs',
-                                    'jobs',
-                                    'errors_per_tool',
-                                    'User and Monitor Jobs in Error',
-                                    spark_time=time_period,
-                                    page=page,
-                                    offset=offset,
-                                    entries=entries)
-                            }
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'errors_per_tool', 'User and Monitor Jobs in Error', spark_time=time_period, page=page, offset=offset, entries=entries)}
                             ${arrow}
                         
 	                %endif
                     
                 
-                <% 
+                <%
                    ctr = 0
                    entries = 1
                 %>
@@ -158,18 +98,12 @@ ${get_css()}
                             
                         
                         %try:
-                            ${
-                                make_sparkline(
-                                    key,
-                                    trends[key],
-                                    "bar",
-                                    "/ " + time_period[:-1])
-                            }
+                            ${make_sparkline(key, trends[key], "bar", "/ " + time_period[:-1])}
                         %except KeyError:
                         %endtry
                         
                     
-                    <% 
+                    <%
                        ctr += 1
                        entries += 1
                     %>
@@ -178,4 +112,4 @@ ${get_css()}
         
     
                      
 
                      
-
\ No newline at end of file
+
diff --git a/templates/webapps/reports/jobs_per_month_all.mako b/templates/webapps/reports/jobs_per_month_all.mako
index 9498d1a4f87..33165df257d 100644
--- a/templates/webapps/reports/jobs_per_month_all.mako
+++ b/templates/webapps/reports/jobs_per_month_all.mako
@@ -22,14 +22,7 @@ ${get_css()}
         
                      
             
                      
                 
-                    ${
-                        get_pages(
-                            sort_id,
-                            order,
-                            page_specs,
-                            'jobs',
-                            'per_month_all')
-                    }
+                    ${get_pages(sort_id, order, page_specs, 'jobs', 'per_month_all')}
                 
                 
                     
                      Jobs Per Month
                      
@@ -39,68 +32,28 @@ ${get_css()}
                     
                                       		
                 
-                    ${
-                        get_entry_selector(
-                            "jobs",
-                            "per_month_all",
-                            page_specs.entries,
-                            sort_id,
-                            order)
-                    }
+                    ${get_entry_selector("jobs", "per_month_all", page_specs.entries, sort_id, order)}
                 
             
                      
         
                      
-        
+
         
             %if len( jobs ) == 0:
                 
             %else:
                 
                     %if is_user_jobs_only:
     					
 					%else:
 	                    
 	                %endif
@@ -129,16 +82,10 @@ ${get_css()}
                             
-                        ${
-                            make_sparkline(
-                                key,
-                                trends[key],
-                                "bar",
-                                "/ day")
-                        }
+                        ${make_sparkline(key, trends[key], "bar", "/ day")}
                         
-                    <% 
+                    <%
                        ctr += 1
                        entries += 1
                     %>
diff --git a/templates/webapps/reports/jobs_per_month_in_error.mako b/templates/webapps/reports/jobs_per_month_in_error.mako
index b6b738e2a91..d805733da8c 100644
--- a/templates/webapps/reports/jobs_per_month_in_error.mako
+++ b/templates/webapps/reports/jobs_per_month_in_error.mako
@@ -22,28 +22,14 @@ ${get_css()}
         
                      There are no jobs.
                      
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'date',
-                                'jobs',
-                                'per_month_all',
-                                'Month',
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        ${get_sort_url(sort_id, order, 'date', 'jobs', 'per_month_all', 'Month', page=page, offset=offset, entries=entries)}
                         ${arrow}
                     
-                            ${
-                                get_sort_url(
-                                    sort_id,
-                                    order,
-                                    'total_jobs',
-                                    'jobs',
-                                    'per_month_all',
-                                    'User Jobs',
-                                    page=page,
-                                    offset=offset,
-                                    entries=entries)
-                            }
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_month_all', 'User Jobs', page=page, offset=offset, entries=entries)}
                             ${arrow}
                         
-                            ${
-                                get_sort_url(
-                                    sort_id,
-                                    order,
-                                    'total_jobs',
-                                    'jobs',
-                                    'per_month_all',
-                                    'User and Monitor Jobs',
-                                    page=page,
-                                    offset=offset,
-                                    entries=entries)
-                            }
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_month_all', 'User and Monitor Jobs', page=page, offset=offset, entries=entries)}
                             ${arrow}
                         
                         
                         ${job[1]}
                     
                      
             
                      
                 
-                    ${
-                        get_pages(
-                            sort_id,
-                            order,
-                            page_specs,
-                            'jobs',
-                            'per_month_in_error')
-                    }
+                    ${get_pages(sort_id, order, page_specs, 'jobs', 'per_month_in_error')}
                 
                 
                     
                      Jobs In Error Per Month
                      
                     
                      Click Month to view details.
                      
                                       		
                 
-                    ${
-                        get_entry_selector(
-                            "jobs",
-                            "per_month_in_error",
-                            page_specs.entries,
-                            sort_id,
-                            order)
-                    }
+                    ${get_entry_selector("jobs", "per_month_in_error", page_specs.entries, sort_id, order)}
                 
             
                      
         
                      
@@ -57,56 +43,23 @@ ${get_css()}
             %else:
                 
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'date',
-                                'jobs',
-                                'per_month_in_error',
-                                'Month',
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        ${get_sort_url(sort_id, order, 'date', 'jobs', 'per_month_in_error', 'Month', page=page, offset=offset, entries=entries)}
                         ${arrow}
                     
                     %if is_user_jobs_only:
     					
-                            ${
-                                get_sort_url(
-                                    sort_id,
-                                    order,
-                                    'total_jobs',
-                                    'jobs',
-                                    'per_month_in_error',
-                                    'User Jobs',
-                                    page=page,
-                                    offset=offset,
-                                    entries=entries)
-                            }
+                            ${get_sort_url( sort_id, order, 'total_jobs', 'jobs', 'per_month_in_error', 'User Jobs', page=page, offset=offset, entries=entries)}
                             ${arrow}
                         
 					%else:
 	                    
-                            ${
-                                get_sort_url(
-                                    sort_id,
-                                    order,
-                                    'total_jobs',
-                                    'jobs',
-                                    'per_month_in_error',
-                                    'User and Monitor Jobs',
-                                    page=page,
-                                    offset=offset,
-                                    entries=entries)
-                            }
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_month_in_error', 'User and Monitor Jobs', page=page, offset=offset, entries=entries)}
                             ${arrow}
                         
 	                %endif
                     
                 
-                <% 
+                <%
                    ctr = 0
                    entries = 1
                 %>
@@ -125,16 +78,10 @@ ${get_css()}
 
                         ${job[2]} ${job[3]}
                         ${job[1]}
-                        ${
-                            make_sparkline(
-                                key,
-                                trends[key],
-                                "bar",
-                                "/ day")
-                        }
+                        ${make_sparkline(key, trends[key], "bar", "/ day")}
                         
                     
-                    <% 
+                    <%
                        ctr += 1
                        entries += 1
                     %>
diff --git a/templates/webapps/reports/jobs_per_tool.mako b/templates/webapps/reports/jobs_per_tool.mako
index 12b1dea3ac7..723013f5fc8 100644
--- a/templates/webapps/reports/jobs_per_tool.mako
+++ b/templates/webapps/reports/jobs_per_tool.mako
@@ -25,44 +25,18 @@ ${get_css()}
         
                      
             
                      
                 
-                    ${
-                        get_pages(
-                            sort_id,
-                            order,
-                            page_specs,
-                            'jobs',
-                            'per_tool',
-                            spark_time=time_period)
-                    }
+                    ${get_pages(sort_id, order, page_specs, 'jobs', 'per_tool', spark_time=time_period)}
                 
                 
                     
                      Jobs Per Tool
                      
                     
                      
-                        Click Tool ID to view details. 
-                        Graph goes from present to past 
-                        ${
-                            make_spark_settings(
-                                "jobs",
-                                "per_tool",
-                                spark_limit,
-                                sort_id,
-                                order,
-                                time_period,
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        Click Tool ID to view details.
+                        Graph goes from present to past
+                        ${make_spark_settings("jobs", "per_tool", spark_limit, sort_id, order, time_period, page=page, offset=offset, entries=entries)}
                     
                      
                                       		
                 
-                    ${
-                        get_entry_selector(
-                            "jobs",
-                            "per_tool",
-                            page_specs.entries,
-                            sort_id,
-                            order)
-                    }
+                    ${get_entry_selector("jobs", "per_tool", page_specs.entries, sort_id, order)}
                 
             
                      
         
                      
@@ -72,59 +46,23 @@ ${get_css()}
             %else:
                 
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'tool_id',
-                                'jobs',
-                                'per_tool',
-                                'Tool ID',
-                                spark_time=time_period,
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        ${get_sort_url(sort_id, order, 'tool_id', 'jobs', 'per_tool', 'Tool ID', spark_time=time_period, page=page, offset=offset, entries=entries)}
                         ${arrow}
                     
                     %if is_user_jobs_only:
                         
-                            ${
-                                get_sort_url(
-                                    sort_id,
-                                    order,
-                                    'total_jobs',
-                                    'jobs',
-                                    'per_tool',
-                                    'User Jobs',
-                                    spark_time=time_period,
-                                    page=page,
-                                    offset=offset,
-                                    entries=entries)
-                            }
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_tool', 'User Jobs', spark_time=time_period, page=page, offset=offset, entries=entries)}
                             ${arrow}
                         
 					%else:
                         
-                            ${
-                                get_sort_url(
-                                    sort_id,
-                                    order,
-                                    'total_jobs',
-                                    'jobs',
-                                    'per_tool',
-                                    'User and Monitor Jobs',
-                                    spark_time=time_period,
-                                    page=page,
-                                    offset=offset,
-                                    entries=entries)
-                            }
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_tool', 'User and Monitor Jobs', spark_time=time_period, page=page, offset=offset, entries=entries)}
                             ${arrow}
                         
 	                %endif
                     
                 
-                <% 
+                <%
                    ctr = 0
                    entries = 1
                 %>
@@ -148,18 +86,12 @@ ${get_css()}
                         
                         ${job[1]}
                         %try:
-                            ${
-                                make_sparkline(
-                                    key,
-                                    trends[key],
-                                    "bar",
-                                    "/ " + time_period[:-1])
-                            }
+                            ${make_sparkline(key, trends[key], "bar", "/ " + time_period[:-1])}
                         %except KeyError:
                         %endtry
                         
                     
-                    <% 
+                    <%
                        ctr += 1
                        entries += 1
                     %>
diff --git a/templates/webapps/reports/jobs_per_user.mako b/templates/webapps/reports/jobs_per_user.mako
index 1a316855c60..c928f797397 100644
--- a/templates/webapps/reports/jobs_per_user.mako
+++ b/templates/webapps/reports/jobs_per_user.mako
@@ -26,44 +26,18 @@ ${q1time}, ${q2time}, ${ttime}
         
                      
             
                      
                 
-                    ${
-                        get_pages(
-                            sort_id,
-                            order,
-                            page_specs,
-                            'jobs',
-                            'per_user',
-                            spark_time=time_period)
-                    }
+                  ${get_pages(sort_id, order, page_specs, 'jobs', 'per_user', spark_time=time_period)}
                 
                 
                     
                      Jobs Per User
                      
                     
                      
                         Click User to view details.
                         Graph goes from present to past
-                        ${
-                            make_spark_settings(
-                                "jobs",
-                                "per_user",
-                                spark_limit,
-                                sort_id,
-                                order,
-                                time_period,
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        ${make_spark_settings("jobs", "per_user", spark_limit, sort_id, order, time_period, page=page, offset=offset, entries=entries)}
                     
                      
                                       		
                 
-                    ${
-                        get_entry_selector(
-                            "jobs",
-                            "per_user",
-                            page_specs.entries,
-                            sort_id,
-                            order)
-                    }
+                  ${get_entry_selector("jobs", "per_user", page_specs.entries, sort_id, order)}
                 
             
                      
         
                      
@@ -73,40 +47,16 @@ ${q1time}, ${q2time}, ${ttime}
             %else:
                 
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'user_email',
-                                'jobs',
-                                'per_user',
-                                'User',
-                                spark_time=time_period,
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        ${get_sort_url(sort_id, order, 'user_email', 'jobs', 'per_user', 'User', spark_time=time_period, page=page, offset=offset, entries=entries)}
                         ${arrow}
                     
                     
-                        ${
-                            get_sort_url(
-                            sort_id,
-                            order,
-                            'total_jobs',
-                            'jobs',
-                            'per_user',
-                            'Total Jobs',
-                            spark_time=time_period,
-                            page=page,
-                            offset=offset,
-                            entries=entries)
-                        }
+                        ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_user', 'Total Jobs', spark_time=time_period, page=page, offset=offset, entries=entries)}
                         ${arrow}
                     
                     
                 
-                <% 
+                <%
                    ctr = 0
                    entries = 1
                 %>
@@ -130,18 +80,12 @@ ${q1time}, ${q2time}, ${ttime}
                         
                         ${job[1]}
                         %try:
-                            ${
-                                make_sparkline(
-                                    key,
-                                    trends[key],
-                                    "bar",
-                                    "/ " + time_period[:-1])
-                            }
+                            ${make_sparkline(key, trends[key], "bar", "/ " + time_period[:-1])}
                         %except KeyError:
                         %endtry
                         
                     
-                    <% 
+                    <%
                        ctr += 1
                        entries += 1
                     %>
@@ -151,4 +95,3 @@ ${q1time}, ${q2time}, ${ttime}
     
                      
 
                      
 
-        
\ No newline at end of file
diff --git a/templates/webapps/reports/jobs_specified_month_all.mako b/templates/webapps/reports/jobs_specified_month_all.mako
index 8877af47860..b9c5edcbea1 100644
--- a/templates/webapps/reports/jobs_specified_month_all.mako
+++ b/templates/webapps/reports/jobs_specified_month_all.mako
@@ -22,14 +22,7 @@ ${get_css()}
         
                      
             
                      
                 
-                    ${
-                        get_pages(
-                            sort_id,
-                            order,
-                            page_specs,
-                            'jobs',
-                            'specified_month_all')
-                    }
+                    ${get_pages(sort_id, order, page_specs, 'jobs', 'specified_month_all')}
                 
                 
                     
                      
@@ -43,14 +36,7 @@ ${get_css()}
                     
                      
                                       		
                 
-                    ${
-                        get_entry_selector(
-                            "jobs",
-                            "specified_month_all",
-                            page_specs.entries,
-                            sort_id,
-                            order)
-                    }
+                    ${get_entry_selector("jobs", "specified_month_all", page_specs.entries, sort_id, order)}
                 
             
                      
         
                      
@@ -65,56 +51,23 @@ ${get_css()}
                 
                     Day
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'date',
-                                'jobs',
-                                'specified_month_all',
-                                'Date',
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        ${get_sort_url(sort_id, order, 'date', 'jobs', 'specified_month_all', 'Date', page=page, offset=offset, entries=entries)}
                         ${arrow}
                     
                     %if is_user_jobs_only:
     					
-                            ${
-                                get_sort_url(
-                                    sort_id,
-                                    order,
-                                    'total_jobs',
-                                    'jobs',
-                                    'specified_month_all',
-                                    'User Jobs',
-                                    page=page,
-                                    offset=offset,
-                                    entries=entries)
-                            }
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'specified_month_all', 'User Jobs', page=page, offset=offset, entries=entries)}
                             ${arrow}
                         
 					%else:
 	                    
-                            ${
-                                get_sort_url(
-                                    sort_id,
-                                    order,
-                                    'total_jobs',
-                                    'jobs',
-                                    'specified_month_all',
-                                    'User and Monitor Jobs',
-                                    page=page,
-                                    offset=offset,
-                                    entries=entries)
-                            }
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'specified_month_all', 'User and Monitor Jobs', page=page, offset=offset, entries=entries)}
                             ${arrow}
                         
 	                %endif
                     
                 
-                <% 
+                <%
                    ctr = 0
                    entries = 1
                 %>
@@ -138,16 +91,10 @@ ${get_css()}
                                 ${job[2]}
                             
                         
-                        ${
-                            make_sparkline(
-                                key,
-                                trends[key],
-                                "bar",
-                                "/ hour")
-                        }
+                        ${make_sparkline(key, trends[key], "bar", "/ hour")}
                         
                     
-                    <% 
+                    <%
                        ctr += 1
                        entries += 1
                     %>
diff --git a/templates/webapps/reports/jobs_specified_month_in_error.mako b/templates/webapps/reports/jobs_specified_month_in_error.mako
index eafbaadab5d..e24464c963c 100644
--- a/templates/webapps/reports/jobs_specified_month_in_error.mako
+++ b/templates/webapps/reports/jobs_specified_month_in_error.mako
@@ -21,14 +21,7 @@ ${get_css()}
         
                      
             
                      
                 
-                    ${
-                        get_pages(
-                            sort_id,
-                            order,
-                            page_specs,
-                            'jobs',
-                            'specified_month_in_error')
-                    }
+                    ${get_pages(sort_id, order, page_specs, 'jobs', 'specified_month_in_error')}
                 
                 
                     
                      
@@ -39,14 +32,7 @@ ${get_css()}
                     
                      
                                       		
                 
-                    ${
-                        get_entry_selector(
-                            "jobs",
-                            "specified_month_in_error",
-                            page_specs.entries,
-                            sort_id,
-                            order)
-                    }
+                    ${get_entry_selector("jobs", "specified_month_in_error", page_specs.entries, sort_id, order)}
                 
             
                      
         
                      
@@ -62,56 +48,23 @@ ${get_css()}
                 
                     Day
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'date',
-                                'jobs',
-                                'specified_month_in_error',
-                                'Date',
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        ${get_sort_url(sort_id, order, 'date', 'jobs', 'specified_month_in_error', 'Date', page=page, offset=offset, entries=entries)}
                         ${arrow}
                     
                     %if is_user_jobs_only:
     					
-                            ${
-                                get_sort_url(
-                                    sort_id,
-                                    order,
-                                    'total_jobs',
-                                    'jobs',
-                                    'specified_month_in_error',
-                                    'User Jobs in Error',
-                                    page=page,
-                                    offset=offset,
-                                    entries=entries)
-                            }
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'specified_month_in_error', 'User Jobs in Error', page=page, offset=offset, entries=entries)}
                             ${arrow}
                         
 					%else:
 	                    
-                            ${
-                                get_sort_url(
-                                    sort_id,
-                                    order,
-                                    'total_jobs',
-                                    'jobs',
-                                    'specified_month_in_error',
-                                    'User and Monitor Jobs in Error',
-                                    page=page,
-                                    offset=offset,
-                                    entries=entries)
-                            }
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'specified_month_in_error', 'User and Monitor Jobs in Error', page=page, offset=offset, entries=entries)}
                             ${arrow}
                         
 	                %endif
                     
                 
-                <% 
+                <%
                     ctr = 0
                     entries = 1
                 %>
@@ -137,16 +90,10 @@ ${get_css()}
                                 ${job[2]}
                             
                         
-                        ${
-                            make_sparkline(
-                                key,
-                                trends[key],
-                                "bar",
-                                "/ hour")
-                        }
+                        ${make_sparkline(key, trends[key], "bar", "/ hour")}
                         
                     
-                    <% 
+                    <%
                         ctr += 1
                         entries += 1
                     %>
diff --git a/templates/webapps/reports/jobs_tool_per_month.mako b/templates/webapps/reports/jobs_tool_per_month.mako
index 032e6061544..e14dfca7ec8 100644
--- a/templates/webapps/reports/jobs_tool_per_month.mako
+++ b/templates/webapps/reports/jobs_tool_per_month.mako
@@ -7,7 +7,7 @@
     ${render_msg( message, 'done' )}
 %endif
 
-${get_css()}   
+${get_css()}
 
 
 
@@ -28,44 +28,17 @@ ${get_css()}
             %else:
                 
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'date',
-                                'jobs',
-                                'tool_per_month',
-                                'Month',
-                                tool_id=tool_id)
-                        }
+                        ${get_sort_url(sort_id, order, 'date', 'jobs', 'tool_per_month', 'Month', tool_id=tool_id)}
                         ${arrow}
                     
                     %if is_user_jobs_only:
     					
-                            ${
-                                get_sort_url(
-                                    sort_id,
-                                    order,
-                                    'total_jobs',
-                                    'jobs',
-                                    'tool_per_month',
-                                    'User Jobs',
-                                    tool_id=tool_id)
-                            }
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'tool_per_month', 'User Jobs', tool_id=tool_id)}
                             ${arrow}
                         
 					%else:
 	                    
-                            ${
-                                get_sort_url(
-                                    sort_id,
-                                    order,
-                                    'total_jobs',
-                                    'jobs',
-                                    'tool_per_month',
-                                    'User and Monitor Jobs',
-                                    tool_id=tool_id)
-                            }
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'tool_per_month', 'User and Monitor Jobs', tool_id=tool_id)}
                             ${arrow}
                         
 	                %endif
@@ -81,13 +54,7 @@ ${get_css()}
                     %endif
                         ${job[2]} ${job[3]}
                         ${job[1]}
-                        ${
-                            make_sparkline(
-                                key,
-                                trends[key],
-                                "bar",
-                                "/ day")
-                        }
+                        ${make_sparkline(key, trends[key], "bar", "/ day")}
                         
                     
                     <% ctr += 1 %>
@@ -97,4 +64,3 @@ ${get_css()}
     
                      
 
                      
 
-        
\ No newline at end of file
diff --git a/templates/webapps/reports/jobs_user_per_month.mako b/templates/webapps/reports/jobs_user_per_month.mako
index 6f930c812f9..5e32179e193 100644
--- a/templates/webapps/reports/jobs_user_per_month.mako
+++ b/templates/webapps/reports/jobs_user_per_month.mako
@@ -3,8 +3,8 @@
 <%namespace file="/spark_base.mako" import="make_sparkline" />
 <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" />
 
-<% 
-   from galaxy import util 
+<%
+   from galaxy import util
 %>
 
 %if message:
@@ -16,7 +16,7 @@ ${get_css()}
 <%
    _email = util.restore_text( email )
 %>
-    
+
 
 
                      
     
                      
@@ -35,29 +35,11 @@ ${get_css()}
             %else:
                 
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'date',
-                                'jobs',
-                                'user_per_month',
-                                'Month',
-                                email=email)
-                        }
+                        ${get_sort_url(sort_id, order, 'date', 'jobs', 'user_per_month', 'Month', email=email)}
                         ${arrow}
                     
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'total_jobs',
-                                'jobs',
-                                'user_per_month',
-                                'Total Jobs',
-                                email=email)
-                        }
+                        ${get_sort_url( sort_id, order, 'total_jobs', 'jobs', 'user_per_month', 'Total Jobs', email=email)}
                         ${arrow}
                     
                     
@@ -76,13 +58,7 @@ ${get_css()}
                                 ${job[1]}
                             
                         
-                        ${
-                            make_sparkline(
-                                key,
-                                trends[key],
-                                "bar",
-                                "/ day")
-                        }
+                        ${make_sparkline(key, trends[key], "bar", "/ day")}
                         
                     
                     <% ctr += 1 %>
diff --git a/templates/webapps/reports/registered_users_per_month.mako b/templates/webapps/reports/registered_users_per_month.mako
index 56b9d6497fe..0e212dd5383 100644
--- a/templates/webapps/reports/registered_users_per_month.mako
+++ b/templates/webapps/reports/registered_users_per_month.mako
@@ -21,27 +21,11 @@ ${get_css()}
             %else:
                 
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'date',
-                                'users',
-                                'registered_users_per_month',
-                                'Month')
-                        }
+                        ${get_sort_url(sort_id, order, 'date', 'users', 'registered_users_per_month', 'Month')}
                         ${arrow}
                     
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'num_users',
-                                'users',
-                                'registered_users_per_month',
-                                'Number of Registrations')
-                        }
+                        ${get_sort_url(sort_id, order, 'num_users', 'users', 'registered_users_per_month', 'Number of Registrations')}
                         ${arrow}
                     
                 
diff --git a/templates/webapps/reports/requests_user_per_month.mako b/templates/webapps/reports/requests_user_per_month.mako
index 70dc5294550..a1e5c2fc29d 100644
--- a/templates/webapps/reports/requests_user_per_month.mako
+++ b/templates/webapps/reports/requests_user_per_month.mako
@@ -9,7 +9,7 @@
 %if message:
     ${render_msg( message, 'done' )}
 %endif
-    
+
 ${get_css()}
 
 
                      
@@ -29,27 +29,11 @@ ${get_css()}
             %else:
                 
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'date',
-                                'users',
-                                'requests_users_per_month',
-                                'Month')
-                        }
+                        ${get_sort_url(sort_id, order, 'date', 'users', 'requests_users_per_month', 'Month')}
                         ${arrow}
                     
                     Total
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'num_users',
-                                'users',
-                                'requests_users_per_month',
-                                'Month')
-                        }
+                        ${get_sort_url(sort_id, order, 'num_users', 'users', 'requests_users_per_month', 'Month')}
                         ${arrow}
                     
                 
diff --git a/templates/webapps/reports/users_last_access_date.mako b/templates/webapps/reports/users_last_access_date.mako
index bda17dd7d39..d4ef0a94cb7 100644
--- a/templates/webapps/reports/users_last_access_date.mako
+++ b/templates/webapps/reports/users_last_access_date.mako
@@ -24,9 +24,9 @@ ${get_css()}
                             ${len( users ) }
                         %else:
                             0
-                        %endif 
-                         users have not logged in to Galaxy for 
-                        
@@ -46,29 +46,11 @@ ${get_css()}
         %if users:
             
                 
-                    ${
-                        get_sort_url(
-                            sort_id,
-                            order,
-                            'zero',
-                            'users',
-                            'last_access_date',
-                            'Email',
-                            days_not_logged_in=days_not_logged_in)
-                    }
+                    ${get_sort_url(sort_id, order, 'zero', 'users', 'last_access_date', 'Email', days_not_logged_in=days_not_logged_in)}
                     ${arrow}
                 
                 
-                    ${
-                        get_sort_url(
-                            sort_id,
-                            order,
-                            'one',
-                            'users',
-                            'last_access_date',
-                            'Date of last Login',
-                            days_not_logged_in=days_not_logged_in)
-                    }
+                    ${get_sort_url(sort_id, order, 'one', 'users', 'last_access_date', 'Date of last Login', days_not_logged_in=days_not_logged_in)}
                     ${arrow}
                 
             
diff --git a/templates/webapps/reports/users_user_disk_usage.mako b/templates/webapps/reports/users_user_disk_usage.mako
index bdd512ada54..37dbd8cc2b3 100644
--- a/templates/webapps/reports/users_user_disk_usage.mako
+++ b/templates/webapps/reports/users_user_disk_usage.mako
@@ -15,11 +15,11 @@ ${get_css()}
     
diff --git a/templates/webapps/reports/workflows_per_month_all.mako b/templates/webapps/reports/workflows_per_month_all.mako
index 73984c3ea47..11aa976fddd 100644
--- a/templates/webapps/reports/workflows_per_month_all.mako
+++ b/templates/webapps/reports/workflows_per_month_all.mako
@@ -21,27 +21,13 @@ ${get_css()}
         
                      
         
                      
             
-                
                      
                     
                      
-                        Top 
@@ -36,27 +36,11 @@ ${get_css()}
         %if users:
             
                      
                 
-                    ${
-                        get_sort_url(
-                            sort_id,
-                            order,
-                            'email',
-                            'users',
-                            'user_disk_usage',
-                            'Email')
-                    }
+                    ${get_sort_url(sort_id, order, 'email', 'users', 'user_disk_usage', 'Email')}
                     
                 
                 
-                    ${
-                        get_sort_url(
-                            sort_id,
-                            order,
-                            'disk_usage',
-                            'users',
-                            'user_disk_usage',
-                            'Disk Usage')
-                    }
+                    ${get_sort_url(sort_id, order, 'disk_usage', 'users', 'user_disk_usage', 'Disk Usage')}
                     ${arrow}
                 
             
                      
             
                      
                 
-                    ${
-                        get_pages(
-                            sort_id,
-                            order,
-                            page_specs,
-                            'workflows',
-                            'per_month_all')
-                    }
+                    ${get_pages(sort_id, order, page_specs, 'workflows', 'per_month_all')}
                 
                 
                     
                      Workflows Per Month
                      
                                       		
                 
-                    ${
-                        get_entry_selector(
-                            "workflows",
-                            "per_month_all",
-                            page_specs.entries,
-                            sort_id,
-                            order)
-                    }
+                    ${get_entry_selector("workflows", "per_month_all", page_specs.entries, sort_id, order)}
                 
             
                      
         
                      
@@ -52,33 +38,11 @@ ${get_css()}
             %else:
                 
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'date',
-                                'workflows',
-                                'per_month_all',
-                                'Month',
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        ${get_sort_url(sort_id, order, 'date', 'workflows', 'per_month_all', 'Month', page=page, offset=offset, entries=entries)}
                         ${arrow}
                     
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'total_workflows',
-                                'workflows',
-                                'per_month_all',
-                                'Total',
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        ${get_sort_url(sort_id, order, 'total_workflows', 'workflows', 'per_month_all', 'Total', page=page, offset=offset, entries=entries)}
                         ${arrow}
                     
                     
@@ -104,22 +68,16 @@ ${get_css()}
                     %else:
                         
                     %endif
-                    
+
                         ${month}
                         ${total}
                         %try:
-                            ${
-                                make_sparkline(
-                                    key,
-                                    trends[key],
-                                    "bar",
-                                    "/ day")
-                            }
+                            ${make_sparkline(key, trends[key], "bar", "/ day")}
                         %except KeyError:
                         %endtry
                         
                     
-                    <% 
+                    <%
                        ctr += 1
                        entries += 1
                     %>
diff --git a/templates/webapps/reports/workflows_per_user.mako b/templates/webapps/reports/workflows_per_user.mako
index 9871f0bde84..2f35c4657f6 100644
--- a/templates/webapps/reports/workflows_per_user.mako
+++ b/templates/webapps/reports/workflows_per_user.mako
@@ -26,86 +26,37 @@ ${get_css()}
         
                      
             
                      
                 
-                    ${
-                        get_pages(
-                            sort_id,
-                            order,
-                            page_specs,
-                            'workflows',
-                            'per_user',
-                            spark_time=time_period)
-                    }
+                    ${get_pages(sort_id, order, page_specs, 'workflows', 'per_user', spark_time=time_period)}
                 
                 
                     
                      Workflows Per User
                      
                     
                      
-                        Graph goes from present to past 
-                        ${
-                            make_spark_settings(
-                                "jobs",
-                                "per_user",
-                                spark_limit,
-                                sort_id, order,
-                                time_period,
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        Graph goes from present to past
+                        ${make_spark_settings("jobs", "per_user", spark_limit, sort_id, order, time_period, page=page, offset=offset, entries=entries)}
                     
                      
                                       		
                 
-                    ${
-                        get_entry_selector(
-                            "workflows",
-                            "per_user",
-                            page_specs.entries,
-                            sort_id,
-                            order)
-                    }
+                    ${get_entry_selector("workflows", "per_user", page_specs.entries, sort_id, order)}
                 
             
                      
         
                      
-        
+
         
             %if len( workflows ) == 0:
                 
             %else:
                 
-                <% 
+                <%
                    ctr = 0
                    entries = 1
                 %>
@@ -136,18 +87,12 @@ ${get_css()}
                         
                         %try:
-                            ${
-                                make_sparkline(
-                                    key,
-                                    trends[key],
-                                    "bar",
-                                    "/ " + time_period[:-1])
-                            }
+                            ${make_sparkline(key, trends[key], "bar", "/ " + time_period[:-1])}
                         %except KeyError:
                         %endtry
                         
-                    <% 
+                    <%
                        ctr += 1
                        entries += 1
                     %>
diff --git a/templates/webapps/reports/workflows_per_workflow.mako b/templates/webapps/reports/workflows_per_workflow.mako
index 394b7befa56..0426ae62c40 100644
--- a/templates/webapps/reports/workflows_per_workflow.mako
+++ b/templates/webapps/reports/workflows_per_workflow.mako
@@ -25,103 +25,41 @@ ${get_css()}
         
                      There are no workflows
                      
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'user_email',
-                                'workflows',
-                                'per_user',
-                                'User',
-                                spark_time=time_period,
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        ${get_sort_url(sort_id, order, 'user_email', 'workflows', 'per_user', 'User', spark_time=time_period, page=page, offset=offset, entries=entries)}
                         ${arrow}
                     
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'total_workflows',
-                                'workflows',
-                                'per_user',
-                                'Total Workflows',
-                                spark_time=time_period,
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        ${get_sort_url(sort_id, order, 'total_workflows', 'workflows', 'per_user', 'Total Workflows', spark_time=time_period, page=page, offset=offset, entries=entries)}
                         ${arrow}
                     
                     
                 
                      
                         
                      ${total}
                     
                      
             
                      
                 
-                    ${
-                        get_pages(
-                            sort_id,
-                            order,
-                            page_specs,
-                            'workflows',
-                            'per_workflow',
-                            spark_time=time_period)
-                    }
+                    ${get_pages(sort_id, order, page_specs, 'workflows', 'per_workflow', spark_time=time_period)}
                 
                 
                     
                      Runs per Workflow
                      
                     
                      
-                        Graph goes from present to past 
-                        ${
-                            make_spark_settings(
-                                'workflows',
-                                'per_workflow',
-                                spark_limit,
-                                sort_id,
-                                order,
-                                time_period,
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        Graph goes from present to past
+                        ${make_spark_settings('workflows', 'per_workflow', spark_limit, sort_id, order, time_period, page=page, offset=offset, entries=entries)}
                     
                      
                                       		
                 
-                    ${
-                        get_entry_selector(
-                            "workflows",
-                            "per_workflow",
-                            page_specs.entries,
-                            sort_id,
-                            order)
-                    }
+                    ${get_entry_selector("workflows", "per_workflow", page_specs.entries, sort_id, order)}
                 
             
                      
         
                      
-        
+
         
             %if len( runs ) == 0:
                 
             %else:
                 
-                <% 
+                <%
                    ctr = 0
                    entries = 1
                 %>
@@ -142,18 +80,12 @@ ${get_css()}
                         
                         %try:
-                            ${
-                                make_sparkline(
-                                    key,
-                                    trends[key],
-                                    "bar",
-                                    "/ " + time_period[:-1])
-                            }
+                            ${make_sparkline(key, trends[key], "bar", "/ " + time_period[:-1])}
                         %except KeyError:
                         %endtry
                         
-                    <% 
+                    <%
                        ctr += 1
                        entries += 1
                     %>
diff --git a/templates/webapps/reports/workflows_user_per_month.mako b/templates/webapps/reports/workflows_user_per_month.mako
index b13014d2bc5..a35ae30c1d2 100644
--- a/templates/webapps/reports/workflows_user_per_month.mako
+++ b/templates/webapps/reports/workflows_user_per_month.mako
@@ -12,7 +12,7 @@
 %endif
 
 ${get_css()}
-    
+
 <%
    _email = util.restore_text( email )
 %>
@@ -33,29 +33,11 @@ ${get_css()}
             %else:
                 
@@ -74,13 +56,7 @@ ${get_css()}
                     %endif
                         
-                        ${
-                            make_sparkline(
-                                key,
-                                trends[key],
-                                "bar",
-                                "/ day")
-                        }
+                        ${make_sparkline(key, trends[key], "bar", "/ day")}
                         
                     <% ctr += 1 %>

From 0d98cf8ab76a374362302547b5699fa024d5ce21 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo 
Date: Wed, 9 Dec 2015 17:51:37 +0000
Subject: [PATCH 08/24] Log a warning for missing tool whitelist file only if
 explicitly defined.

Also fix the log message.
---
 lib/galaxy/config.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index 4ccc6beaa8c..45a3ca1fc65 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -253,7 +253,7 @@ class Configuration( object ):
         self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) )
         self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) )
         self.sanitize_whitelist_file = resolve_path( kwargs.get( 'sanitize_whitelist_file', "config/sanitize_whitelist.txt" ), self.root )
-        self.reload_sanitize_whitelist()
+        self.reload_sanitize_whitelist(kwargs.get('sanitize_whitelist_file', None) is not None)
         self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) )
         self.trust_ipython_notebook_conversion = string_as_bool( kwargs.get( 'trust_ipython_notebook_conversion', False ) )
         self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) )
@@ -466,7 +466,7 @@ class Configuration( object ):
         else:
             return None
 
-    def reload_sanitize_whitelist( self ):
+    def reload_sanitize_whitelist( self, whitelist_file_explicitly_defined ):
         self.sanitize_whitelist = []
         try:
             with open(self.sanitize_whitelist_file, 'rt') as f:
@@ -474,7 +474,8 @@ class Configuration( object ):
                     if not line.startswith("#"):
                         self.sanitize_whitelist.append(line.strip())
         except IOError:
-            log.warning("Sanitize log file %s does not exist, continuing with no tools whitelisted.")
+            if whitelist_file_explicitly_defined:
+                log.warning("Sanitize log file %s does not exist, continuing with no tools whitelisted.", self.sanitize_whitelist_file)
 
     def __parse_config_file_options( self, kwargs ):
         """

From a9034b5df3f3c80144727ebc161caa38b64ba7a1 Mon Sep 17 00:00:00 2001
From: Nate Coraor 
Date: Wed, 9 Dec 2015 15:54:55 -0500
Subject: [PATCH 09/24] Update Kombu and AMQP eggs to fix problems with El
 Capitan's System Integrity Protection.

---
 eggs.ini | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/eggs.ini b/eggs.ini
index 12a9f88f3e9..0daf2317e64 100644
--- a/eggs.ini
+++ b/eggs.ini
@@ -30,7 +30,7 @@ SQLAlchemy = 1.0.8
 ; msgpack_python = 0.2.4
 
 [eggs:noplatform]
-amqp = 1.4.6
+amqp = 1.4.8
 anyjson = 0.3.3
 Beaker = 1.4
 bioblend = 0.5.2
@@ -40,7 +40,7 @@ docutils = 0.7
 drmaa = 0.7.6
 Fabric = 1.7.0
 importlib = 1.0.3
-kombu = 3.0.24
+kombu = 3.0.30
 lrucache = 0.2
 Mako = 0.4.1
 mock = 1.0.1

From b6e7b9a33b5dec7fdad2ad2f863bbf88980626ec Mon Sep 17 00:00:00 2001
From: Dannon Baker 
Date: Thu, 10 Dec 2015 14:50:37 -0500
Subject: [PATCH 10/24] Adjustments to sanitize_whitelist reloading.

---
 lib/galaxy/config.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index 45a3ca1fc65..43d6b1a73a7 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -253,7 +253,9 @@ class Configuration( object ):
         self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) )
         self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) )
         self.sanitize_whitelist_file = resolve_path( kwargs.get( 'sanitize_whitelist_file', "config/sanitize_whitelist.txt" ), self.root )
-        self.reload_sanitize_whitelist(kwargs.get('sanitize_whitelist_file', None) is not None)
+        self.sanitize_whitelist = []
+        if kwargs.get('sanitize_whitelist_file', None) is not None:
+            self.reload_sanitize_whitelist()
         self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) )
         self.trust_ipython_notebook_conversion = string_as_bool( kwargs.get( 'trust_ipython_notebook_conversion', False ) )
         self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) )
@@ -466,7 +468,7 @@ class Configuration( object ):
         else:
             return None
 
-    def reload_sanitize_whitelist( self, whitelist_file_explicitly_defined ):
+    def reload_sanitize_whitelist( self ):
         self.sanitize_whitelist = []
         try:
             with open(self.sanitize_whitelist_file, 'rt') as f:
@@ -474,8 +476,7 @@ class Configuration( object ):
                     if not line.startswith("#"):
                         self.sanitize_whitelist.append(line.strip())
         except IOError:
-            if whitelist_file_explicitly_defined:
-                log.warning("Sanitize log file %s does not exist, continuing with no tools whitelisted.", self.sanitize_whitelist_file)
+            log.warning("Sanitize log file %s does not exist, continuing with no tools whitelisted.", self.sanitize_whitelist_file)
 
     def __parse_config_file_options( self, kwargs ):
         """

From 760c2b56bee664f2f874e2cc26d2129858da1bb1 Mon Sep 17 00:00:00 2001
From: guerler 
Date: Fri, 11 Dec 2015 14:57:59 -0500
Subject: [PATCH 11/24] Properly show and label hidden datasets on rerurn

---
 lib/galaxy/tools/parameters/basic.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 51cda184de6..0fd0b8560d4 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2166,14 +2166,15 @@ class DataToolParameter( BaseDataToolParameter ):
         multiple = self.multiple
 
         # add datasets
+        visible_hda = other_values.get( self.name )
         for hda in history.active_datasets_children_and_roles:
-            match = dataset_matcher.hda_match( hda )
+            match = dataset_matcher.hda_match( hda, ensure_visible=visible_hda != hda )
             if match:
                 m = match.hda
                 d['options']['hda'].append({
                     'id'            : trans.security.encode_id( m.id ),
                     'hid'           : m.hid,
-                    'name'          : m.name,
+                    'name'          : m.name if m.visible else '(hidden) %s' % m.name,
                     'src'           : 'hda'
                 })
 

From 9b30b134d6ab93c2a84a856352f32a6713dd49cd Mon Sep 17 00:00:00 2001
From: Nicola Soranzo 
Date: Mon, 14 Dec 2015 12:03:57 +0000
Subject: [PATCH 12/24] Reduce code duplication by reusing
 get_installed_repository() function.

---
 lib/galaxy/tools/toolbox/base.py | 23 ++++++-----------------
 1 file changed, 6 insertions(+), 17 deletions(-)

diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index 22c393af709..08110e20327 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -6,8 +6,6 @@ import tarfile
 import tempfile
 
 from galaxy import eggs
-eggs.require( "SQLAlchemy >= 0.4" )
-from sqlalchemy import and_
 eggs.require( "MarkupSafe" )
 from markupsafe import escape
 
@@ -19,7 +17,7 @@ from galaxy.util import parse_xml
 from galaxy.util import string_as_bool
 from galaxy.util.bunch import Bunch
 
-from tool_shed.util import common_util
+from tool_shed.util import shed_util_common
 
 from .panel import ToolPanelElements
 from .panel import ToolSectionLabel
@@ -449,16 +447,6 @@ class AbstractToolBox( object, Dictifiable, ManagesIntegratedToolPanelMixin ):
     def tools( self ):
         return self._tools_by_id.iteritems()
 
-    def __get_tool_shed_repository( self, tool_shed, name, owner, installed_changeset_revision ):
-        # We store only the port, if one exists, in the database.
-        tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
-        return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \
-            .filter( and_( self.app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed,
-                           self.app.install_model.ToolShedRepository.table.c.name == name,
-                           self.app.install_model.ToolShedRepository.table.c.owner == owner,
-                           self.app.install_model.ToolShedRepository.table.c.installed_changeset_revision == installed_changeset_revision ) ) \
-            .first()
-
     def get_tool_components( self, tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=False ):
         """
         Retrieve all loaded versions of a tool from the toolbox and return a select list enabling
@@ -588,10 +576,11 @@ class AbstractToolBox( object, Dictifiable, ManagesIntegratedToolPanelMixin ):
                     # Backward compatibility issue - the tag used to be named 'changeset_revision'.
                     installed_changeset_revision_elem = elem.find( "changeset_revision" )
                 installed_changeset_revision = installed_changeset_revision_elem.text
-                tool_shed_repository = self.__get_tool_shed_repository( tool_shed,
-                                                                        repository_name,
-                                                                        repository_owner,
-                                                                        installed_changeset_revision )
+                tool_shed_repository = shed_util_common.get_installed_repository(self.app,
+                                                                                 tool_shed=tool_shed,
+                                                                                 name=repository_name,
+                                                                                 owner=repository_owner,
+                                                                                 installed_changeset_revision=installed_changeset_revision)
 
                 if tool_shed_repository:
                     # Only load tools if the repository is not deactivated or uninstalled.

From 11eca70db129173ea20aac0040c9645049af189c Mon Sep 17 00:00:00 2001
From: Nicola Soranzo 
Date: Mon, 14 Dec 2015 17:56:44 +0000
Subject: [PATCH 13/24] When loading a tool from Tool Shed, check that the
  element matches the tool path.

Workaround for issue #1283, which causes the loaded tool to have a
StockLineage instead of a ToolShedLineage, thus creating multiple entries
for the tool in the panel.
---
 lib/galaxy/tools/toolbox/base.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index 08110e20327..527d8bba8fd 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -576,6 +576,20 @@ class AbstractToolBox( object, Dictifiable, ManagesIntegratedToolPanelMixin ):
                     # Backward compatibility issue - the tag used to be named 'changeset_revision'.
                     installed_changeset_revision_elem = elem.find( "changeset_revision" )
                 installed_changeset_revision = installed_changeset_revision_elem.text
+                try:
+                    splitted_path = path.split('/')
+                    assert splitted_path[0] == tool_shed
+                    assert splitted_path[2] == repository_owner
+                    assert splitted_path[3] == repository_name
+                    if splitted_path[4] != installed_changeset_revision:
+                        # This can happen if the Tool Shed repository has been
+                        # updated to a new revision and the installed_changeset_revision
+                        # element in shed_tool_conf.xml file has been updated too
+                        log.debug("The installed_changeset_revision for tool %s is %s, using %s instead", path, installed_changeset_revision, splitted_path[4])
+                        installed_changeset_revision = splitted_path[4]
+                except Exception as e:
+                    log.debug("Error while loading tool %s : %s", path, e)
+                    pass
                 tool_shed_repository = shed_util_common.get_installed_repository(self.app,
                                                                                  tool_shed=tool_shed,
                                                                                  name=repository_name,

From f953005f72310279fe69a0deb0b9adef973bf6da Mon Sep 17 00:00:00 2001
From: Nicola Soranzo 
Date: Tue, 15 Dec 2015 14:50:46 +0000
Subject: [PATCH 14/24] Fix typo causing the option "Link files instead of
 copying" to be ignored.

When uploading folders with the new data library interface.
---
 lib/galaxy/webapps/galaxy/api/lda_datasets.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/lda_datasets.py b/lib/galaxy/webapps/galaxy/api/lda_datasets.py
index 439d404d5c0..bd4abf3b5d0 100644
--- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py
@@ -413,7 +413,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
 
         :param  encoded_folder_id:      the encoded id of the folder to import dataset(s) to
         :type   encoded_folder_id:      an encoded id string
-        :param  source:                 source the datasets should be loaded form
+        :param  source:                 source the datasets should be loaded from
         :type   source:                 str
         :param  link_data:              flag whether to link the dataset to data or copy it to Galaxy, defaults to copy
                                         while linking is set to True all symlinks will be resolved _once_
@@ -434,7 +434,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
         kwd[ 'to_posix_lines' ] = 'True'
         kwd[ 'dbkey' ] = kwd.get( 'dbkey', '?' )
         kwd[ 'file_type' ] = kwd.get( 'file_type', 'auto' )
-        kwd[' link_data_only' ] = 'link_to_files' if util.string_as_bool( kwd.get( 'link_data', False ) ) else 'copy_files'
+        kwd['link_data_only'] = 'link_to_files' if util.string_as_bool( kwd.get( 'link_data', False ) ) else 'copy_files'
         encoded_folder_id = kwd.get( 'encoded_folder_id', None )
         if encoded_folder_id is not None:
             folder_id = self.folder_manager.cut_and_decode( trans, encoded_folder_id )

From 31f174a4254e5cc4c85747a76c3908b0170cf358 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster 
Date: Sat, 28 Nov 2015 13:58:56 -0500
Subject: [PATCH 15/24] Add enhancements to the Galaxy repository install
 process

to cleanly handle the case described here:
https://github.com/galaxyproject/galaxy/issues/667.  Specifically, the
following scenario is now cleanly handled:

Example use case: In a toolshed I have a repository of a tool, say

package_new_gene_db_1_2_3, and in revision 1 it depends on
package_sqlite_1_0_0:

package_new_gene_db_1_2_3
package_sqlite_1_0_0

At some point in time I discover that postgres is a better solution for
my gene database, and I upload revision 2:

package_new_gene_db_1_2_3
package_postgres__2_0_0

And I remove the dependecy of sqlite.  If I go to my galaxy instance and
I remove revision 1 and install revision 2, the installation is cleanly
handled with theis PR.

It should be noted that this enhancement could adversely impact
reproducibility if best practices are not followed with regard to
defining package dependencies.  Since it is now cleanly possible to
eliminate dependencies over time, best practices must be followed to
ensure that elimination of a dependency does not affect the output of a
tool that uses the underlying hierarchy of packages.
---
 .../galaxy/controllers/admin_toolshed.py      | 15 ++++
 .../tool_shed/controllers/repository.py       | 24 ++++++
 lib/tool_shed/util/shed_util_common.py        | 78 +++++++++++++++++++
 3 files changed, 117 insertions(+)

diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index e13d0979985..cc947b569c3 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1296,6 +1296,21 @@ class AdminToolshed( AdminGalaxy ):
                 # Just in case the tool_section.id differs from tool_panel_section_id, which it shouldn't...
                 tool_panel_section_id = str( tool_section.id )
         if tool_shed_repository.status == trans.install_model.ToolShedRepository.installation_status.UNINSTALLED:
+            repository_type = suc.get_repository_type_from_tool_shed(trans.app,
+                                                                     tool_shed_url,
+                                                                     tool_shed_repository.name,
+                                                                     tool_shed_repository.owner)
+            if repository_type == rt_util.TOOL_DEPENDENCY_DEFINITION:
+                # Repositories of type tool_dependency_definition must get the latest
+                # metadata from the Tool Shed since they have only a single installable
+                # revision.
+                raw_text = suc.get_tool_dependency_definition_metadata_from_tool_shed(trans.app,
+                                                                                      tool_shed_url,
+                                                                                      tool_shed_repository.name,
+                                                                                      tool_shed_repository.owner)
+                new_meta = json.loads(raw_text)
+                # Clean up old repository dependency and tool dependency relationships.
+                suc.clean_dependency_relationships(trans, new_meta, tool_shed_repository, tool_shed_url)
             # The repository's status must be updated from 'Uninstalled' to 'New' when initiating reinstall
             # so the repository_installation_updater will function.
             tool_shed_repository = suc.create_or_update_tool_shed_repository( trans.app,
diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py
index 89268ce899b..411f420ff7a 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -1684,6 +1684,14 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                      includes_tool_dependencies=includes_tool_dependencies,
                      repo_info_dicts=repo_info_dicts )
 
+    @web.expose
+    def get_repository_type( self, trans, **kwd ):
+        """Given a repository name and owner, return the type."""
+        repository_name = kwd[ 'name' ]
+        repository_owner = kwd[ 'owner' ]
+        repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
+        return str( repository.type )
+
     @web.json
     def get_required_repo_info_dict( self, trans, encoded_str=None ):
         """
@@ -1751,6 +1759,22 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
             return contents
         return ''
 
+    @web.json
+    def get_tool_dependency_definition_metadata( self, trans, **kwd ):
+        """
+        Given a repository name and ownerof a repository whose type is
+        tool_dependency_definition, return the current metadata.
+        """
+        repository_name = kwd[ 'name' ]
+        repository_owner = kwd[ 'owner' ]
+        repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
+        encoded_id = trans.app.security.encode_id( repository.id )
+        repository_tip = repository.tip( trans.app )
+        repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app,
+                                                                                 encoded_id,
+                                                                                 repository_tip )
+        return repository_metadata.metadata
+
     @web.expose
     def get_tool_versions( self, trans, **kwd ):
         """
diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index 09028cdae8d..7c6f1d8b2a3 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -83,6 +83,59 @@ This message was sent from the Galaxy Tool Shed instance hosted on the server
 """
 
 
+def can_eliminate_repository_dependency(metadata_dict, tool_shed_url, name, owner):
+    """
+    Determine if the relationship between a repository_dependency record
+    associated with a tool_shed_repository record on the Galaxy side
+    can be eliminated.
+    """
+    rd_dict = metadata_dict.get('repository_dependencies', {})
+    rd_tups = rd_dict.get( 'repository_dependencies', [] )
+    for rd_tup in rd_tups:
+        tsu, n, o, none1, none2, none3 = common_util.parse_repository_dependency_tuple(rd_tup)
+        if tsu == tool_shed_url and n == name and o == owner:
+            # The repository dependency is current, so keep it.
+            return False
+    return True
+
+
+def can_eliminate_tool_dependency(metadata_dict, name, type, version):
+    """
+    Determine if the relationship between a tool_dependency record
+    associated with a tool_shed_repository record on the Galaxy side
+    can be eliminated.
+    """
+    td_dict = metadata_dict.get('tool_dependencies', {})
+    for td_key, td_val in td_dict.items():
+        n = td_val.get('name', None)
+        t = td_val.get('type', None)
+        v = td_val.get('version', None)
+        if n == name and t == type and v == version:
+            # The tool dependency is current, so keep it.
+            return False
+    return True
+
+
+def clean_dependency_relationships(trans, metadata_dict, tool_shed_repository, tool_shed_url):
+    """
+    Repositories of type tool_dependency_definition allow for defining a
+    package dependency at some point in the change log and then removing the
+    dependency later in the change log.  This function keeps the dependency
+    relationships on the Galaxy side current by deleting database records
+    that defined the now-broken relationships.
+    """
+    for rrda in tool_shed_repository.required_repositories:
+        rd = rrda.repository_dependency
+        r = rd.repository
+        if can_eliminate_repository_dependency(metadata_dict, tool_shed_url, r.name, r.owner):
+            trans.install_model.context.delete(rrda)
+            trans.install_model.context.flush()
+    for td in tool_shed_repository.tool_dependencies:
+        if can_eliminate_tool_dependency(metadata_dict, td.name, td.type, td.version):
+            trans.install_model.context.delete(td)
+            trans.install_model.context.flush()
+
+
 def create_or_update_tool_shed_repository( app, name, description, installed_changeset_revision, ctx_rev, repository_clone_url,
                                            metadata_dict, status, current_changeset_revision=None, owner='', dist_to_shed=False ):
     """
@@ -300,6 +353,19 @@ def get_latest_downloadable_changeset_revision( app, repository, repo ):
     return hg_util.INITIAL_CHANGELOG_HASH
 
 
+def get_tool_dependency_definition_metadata_from_tool_shed( app, tool_shed_url, name, owner ):
+    """
+    Send a request to the tool shed to retrieve the current metadata for a
+    repository of type tool_dependency_definition defined by the combination
+    of a name and owner.
+    """
+    tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
+    params = dict( name=name, owner=owner )
+    pathspec = [ 'repository', 'get_tool_dependency_definition_metadata' ]
+    metadata = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+    return metadata
+
+
 def get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision ):
     """
     Return the installable changeset_revision in the repository changelog after the changeset to which
@@ -713,6 +779,18 @@ def get_repository_query( app ):
     return query
 
 
+def get_repository_type_from_tool_shed( app, tool_shed_url, name, owner ):
+    """
+    Send a request to the tool shed to retrieve the type for a repository defined by the
+    combination of a name and owner.
+    """
+    tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
+    params = dict( name=name, owner=owner )
+    pathspec = [ 'repository', 'get_repository_type' ]
+    repository_type = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+    return repository_type
+
+
 def get_tool_panel_config_tool_path_install_dir( app, repository ):
     """
     Return shed-related tool panel config, the tool_path configured in it, and the relative path to

From b0deead9c3260598f83d1ab2ec74b3c3e8974456 Mon Sep 17 00:00:00 2001
From: guerler 
Date: Thu, 17 Dec 2015 11:40:25 -0500
Subject: [PATCH 16/24] Fix change handler association

---
 client/galaxy/scripts/utils/uploadbox.js | 4 ++--
 static/maps/utils/uploadbox.js.map       | 2 +-
 static/scripts/utils/uploadbox.js        | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/client/galaxy/scripts/utils/uploadbox.js b/client/galaxy/scripts/utils/uploadbox.js
index d80c8f0465d..5395a84fbb9 100755
--- a/client/galaxy/scripts/utils/uploadbox.js
+++ b/client/galaxy/scripts/utils/uploadbox.js
@@ -117,10 +117,10 @@
 
         // append hidden upload field
         var $input = $('');
-        el.append($input).change(function (e) {
+        el.append($input.change(function (e) {
             opts.onchange(e.target.files);
             $(this).val('');
-        });
+        }));
 
         // drag/drop events
         el.on('drop', function (e) {
diff --git a/static/maps/utils/uploadbox.js.map b/static/maps/utils/uploadbox.js.map
index d3cda5640d0..1ae608e9d1c 100644
--- a/static/maps/utils/uploadbox.js.map
+++ b/static/maps/utils/uploadbox.js.map
@@ -1 +1 @@
-{"version":3,"file":"uploadbox.js","sources":["../../src/utils/uploadbox.js"],"names":["$","jQuery","event","props","push","uploadpost","config","cnf","extend","data","success","error","progress","url","maxfilesize","error_filesize","error_default","error_server","error_login","error_message","form","FormData","key","payload","append","sizes","files","d","name","file","size","xhr","XMLHttpRequest","open","setRequestHeader","onreadystatechange","readyState","DONE","response","responseText","parseJSON","e","status","text","statusText","upload","addEventListener","lengthComputable","Math","round","loaded","total","console","debug","send","fn","uploadinput","options","el","this","opts","ondragover","ondragleave","onchange","multiple","$input","change","target","val","on","dataTransfer","preventDefault","stopPropagation","dialog","trigger","uploadbox","add","length","queue_running","current_index","queue_index","i","index","String","queue","announce","queue_length","remove","process","queue_stop","complete","initialize","message","percentage","select","reset","start","stop","configure","compatible","window","File","FileList","dragover","dragleave","m","alert"],"mappings":"CAGC,SAAUA,GAEPC,OAAOC,MAAMC,MAAMC,KAAK,gBAKxBJ,EAAEK,WAAa,SAAUC,GAErB,GAAIC,GAAMP,EAAEQ,WACRC,QACAC,QAAkB,aAClBC,MAAkB,aAClBC,SAAkB,aAClBC,IAAkB,KAClBC,YAAkB,KAClBC,eAAkB,8CAClBC,cAAkB,0CAClBC,aAAkB,yBAClBC,YAAkB,kCACnBZ,GAGCG,EAAOF,EAAIE,IAGf,IAAIA,EAAKU,cAEL,WADAZ,GAAII,MAAMF,EAAKU,cAKnB,IAAIC,GAAO,GAAIC,SACf,KAAK,GAAIC,KAAOb,GAAKc,QACjBH,EAAKI,OAAOF,EAAKb,EAAKc,QAAQD,GAIlC,IAAIG,GAAQ,CACZ,KAAK,GAAIH,KAAOb,GAAKiB,MAAO,CACxB,GAAIC,GAAIlB,EAAKiB,MAAMJ,EACnBF,GAAKI,OAAOG,EAAEC,KAAMD,EAAEE,KAAMF,EAAEE,KAAKD,MACnCH,GAASE,EAAEE,KAAKC,KAIpB,MAAIL,GAAQ,QAAUlB,EAAIO,gBACtBP,GAAII,MAAMJ,EAAIQ,iBAKlBgB,IAAM,GAAIC,gBACVD,IAAIE,KAAK,OAAQ1B,EAAIM,KAAK,GAC1BkB,IAAIG,iBAAiB,SAAU,oBAC/BH,IAAIG,iBAAiB,gBAAiB,YACtCH,IAAIG,iBAAiB,mBAAoB,kBAGzCH,IAAII,mBAAqB,WAErB,GAAIJ,IAAIK,YAAcL,IAAIM,KAAM,CAE5B,GAAIC,GAAW,IACf,IAAIP,IAAIQ,aACJ,IACID,EAAWrC,OAAOuC,UAAUT,IAAIQ,cAClC,MAAOE,GACLH,EAAWP,IAAIQ,aAIvB,GAAIR,IAAIW,OAAS,KAAOX,IAAIW,OAAS,IAAK,CACtC,GAAIC,GAAOZ,IAAIa,UACG,MAAdb,IAAIW,OACJC,EAAOpC,EAAIW,YACU,GAAda,IAAIW,OACXC,EAAOpC,EAAIU,aACH0B,IACRA,EAAOpC,EAAIS,eAEfT,EAAII,MAAMgC,EAAO,KAAOZ,IAAIW,OAAS,SAErCnC,GAAIG,QAAQ4B,KAMxBP,IAAIc,OAAOC,iBAAiB,WAAY,SAASL,GACzCA,EAAEM,kBACFxC,EAAIK,SAASoC,KAAKC,MAAkB,IAAXR,EAAES,OAAgBT,EAAEU,UAElD,GAGHC,QAAQC,MAAM,qDACdD,QAAQC,MAAM9C,OACdwB,KAAIuB,KAAKlC,KAMbpB,EAAEuD,GAAGC,YAAc,SAASC,GAExB,GAAIC,GAAKC,KACLC,EAAO5D,EAAEQ,WACTqD,WAAc,aACdC,YAAc,aACdC,SAAc,aACdC,UAAc,GACfP,GAGCQ,EAASjE,EAAE,6CAA+C4D,EAAKI,UAAY,YAAc,IAAM,KAwBnG,OAvBAN,GAAGlC,OAAOyC,GAAQC,OAAO,SAAUzB,GAC/BmB,EAAKG,SAAStB,EAAE0B,OAAOzC,OACvB1B,EAAE2D,MAAMS,IAAI,MAIhBV,EAAGW,GAAG,OAAQ,SAAU5B,GACpBmB,EAAKE,YAAYrB,GACdA,EAAE6B,eACDV,EAAKG,SAAStB,EAAE6B,aAAa5C,OAC7Be,EAAE8B,oBAGVb,EAAGW,GAAG,WAAa,SAAU5B,GACzBA,EAAE8B,iBACFX,EAAKC,WAAWpB,KAEpBiB,EAAGW,GAAG,YAAa,SAAU5B,GACzBA,EAAE+B,kBACFZ,EAAKE,YAAYrB,MAKjBgC,OAAQ,WACJR,EAAOS,QAAQ,YAQ3B1E,EAAEuD,GAAGoB,UAAY,SAASlB,GAiCtB,QAASmB,GAAIlD,GACT,GAAIA,GAASA,EAAMmD,SAAWC,EAAe,CAEzC,IAAK,GADDC,GAAgBC,EACXC,EAAI,EAAGA,EAAIvD,EAAMmD,OAAQI,IAAK,CACnC,GAAIC,GAAQC,OAAOH,IACnBI,GAAMF,GAASxD,EAAMuD,GACrBrB,EAAKyB,SAASH,EAAOE,EAAMF,IAC3BI,IAEJ,MAAOP,IAKf,QAASQ,GAAOL,GACRE,EAAMF,WACCE,GAAMF,GACbI,KAKR,QAASE,KAEL,GAAoB,GAAhBF,GAAqBG,EAIrB,MAHAA,IAAa,EACbX,GAAgB,MAChBlB,GAAK8B,UAGLZ,IAAgB,CAIpB,IAAII,GAAQ,EACZ,KAAK,GAAI5D,KAAO8D,GAAO,CACnBF,EAAQ5D,CACR,OAIO8D,EAAMF,EAGjBK,GAAOL,GAGPlF,EAAEK,YACEQ,IAAW+C,EAAK/C,IAChBJ,KAAWmD,EAAK+B,WAAWT,GAC3BxE,QAAW,SAASkF,GAAWhC,EAAKlD,QAAQwE,EAAOU,GAAUJ,KAC7D7E,MAAW,SAASiF,GAAWhC,EAAKjD,MAAMuE,EAAOU,GAAUJ,KAC3D5E,SAAW,SAASiF,GAAcjC,EAAKhD,SAASsE,EAAOW,MAS/D,QAASC,KACLtC,EAAYiB,SAIhB,QAASsB,GAAMb,GACX,IAAKA,IAASE,GACVG,EAAOL,GAKf,QAASc,KACAlB,IACDA,GAAgB,EAChBU,KAKR,QAASS,KACLR,GAAa,EAIjB,QAASS,GAAUzC,GAEf,MADAG,GAAO5D,EAAEQ,UAAWoD,EAAMH,GAK9B,QAAS0C,KACL,MAAOC,QAAOC,MAAQD,OAAO/E,UAAY+E,OAAOpE,gBAAkBoE,OAAOE,SA5H7E,GAAI1C,GAAO5D,EAAEQ,WACT+F,SAAkB,aAClBC,UAAkB,aAClBnB,SAAkB,aAClBM,WAAkB,aAClB/E,SAAkB,aAClBF,QAAkB,aAClBC,MAAkB,SAASgB,EAAG8E,GAAKC,MAAMD,IACzCf,SAAkB,cACnBjC,GAGC2B,KAGAJ,EAAc,EACdM,EAAe,EAGfR,GAAgB,EAChBW,GAAa,EAGbjC,EAAcxD,EAAE2D,MAAMH,aACtBQ,UAAc,EACdD,SAAc,SAASrC,GAASkD,EAAIlD,IACpCmC,WAAcJ,EAAQI,WACtBC,YAAcL,EAAQK,aAqG1B,QACIgC,OAAkBA,EAClBlB,IAAkBA,EAClBW,OAAkBA,EAClBS,MAAkBA,EAClBC,KAAkBA,EAClBF,MAAkBA,EAClBG,UAAkBA,EAClBC,WAAkBA,KAG3BlG"}
\ No newline at end of file
+{"version":3,"file":"uploadbox.js","sources":["../../src/utils/uploadbox.js"],"names":["$","jQuery","event","props","push","uploadpost","config","cnf","extend","data","success","error","progress","url","maxfilesize","error_filesize","error_default","error_server","error_login","error_message","form","FormData","key","payload","append","sizes","files","d","name","file","size","xhr","XMLHttpRequest","open","setRequestHeader","onreadystatechange","readyState","DONE","response","responseText","parseJSON","e","status","text","statusText","upload","addEventListener","lengthComputable","Math","round","loaded","total","console","debug","send","fn","uploadinput","options","el","this","opts","ondragover","ondragleave","onchange","multiple","$input","change","target","val","on","dataTransfer","preventDefault","stopPropagation","dialog","trigger","uploadbox","add","length","queue_running","current_index","queue_index","i","index","String","queue","announce","queue_length","remove","process","queue_stop","complete","initialize","message","percentage","select","reset","start","stop","configure","compatible","window","File","FileList","dragover","dragleave","m","alert"],"mappings":"CAGC,SAAUA,GAEPC,OAAOC,MAAMC,MAAMC,KAAK,gBAKxBJ,EAAEK,WAAa,SAAUC,GAErB,GAAIC,GAAMP,EAAEQ,WACRC,QACAC,QAAkB,aAClBC,MAAkB,aAClBC,SAAkB,aAClBC,IAAkB,KAClBC,YAAkB,KAClBC,eAAkB,8CAClBC,cAAkB,0CAClBC,aAAkB,yBAClBC,YAAkB,kCACnBZ,GAGCG,EAAOF,EAAIE,IAGf,IAAIA,EAAKU,cAEL,WADAZ,GAAII,MAAMF,EAAKU,cAKnB,IAAIC,GAAO,GAAIC,SACf,KAAK,GAAIC,KAAOb,GAAKc,QACjBH,EAAKI,OAAOF,EAAKb,EAAKc,QAAQD,GAIlC,IAAIG,GAAQ,CACZ,KAAK,GAAIH,KAAOb,GAAKiB,MAAO,CACxB,GAAIC,GAAIlB,EAAKiB,MAAMJ,EACnBF,GAAKI,OAAOG,EAAEC,KAAMD,EAAEE,KAAMF,EAAEE,KAAKD,MACnCH,GAASE,EAAEE,KAAKC,KAIpB,MAAIL,GAAQ,QAAUlB,EAAIO,gBACtBP,GAAII,MAAMJ,EAAIQ,iBAKlBgB,IAAM,GAAIC,gBACVD,IAAIE,KAAK,OAAQ1B,EAAIM,KAAK,GAC1BkB,IAAIG,iBAAiB,SAAU,oBAC/BH,IAAIG,iBAAiB,gBAAiB,YACtCH,IAAIG,iBAAiB,mBAAoB,kBAGzCH,IAAII,mBAAqB,WAErB,GAAIJ,IAAIK,YAAcL,IAAIM,KAAM,CAE5B,GAAIC,GAAW,IACf,IAAIP,IAAIQ,aACJ,IACID,EAAWrC,OAAOuC,UAAUT,IAAIQ,cAClC,MAAOE,GACLH,EAAWP,IAAIQ,aAIvB,GAAIR,IAAIW,OAAS,KAAOX,IAAIW,OAAS,IAAK,CACtC,GAAIC,GAAOZ,IAAIa,UACG,MAAdb,IAAIW,OACJC,EAAOpC,EAAIW,YACU,GAAda,IAAIW,OACXC,EAAOpC,EAAIU,aACH0B,IACRA,EAAOpC,EAAIS,eAEfT,EAAII,MAAMgC,EAAO,KAAOZ,IAAIW,OAAS,SAErCnC,GAAIG,QAAQ4B,KAMxBP,IAAIc,OAAOC,iBAAiB,WAAY,SAASL,GACzCA,EAAEM,kBACFxC,EAAIK,SAASoC,KAAKC,MAAkB,IAAXR,EAAES,OAAgBT,EAAEU,UAElD,GAGHC,QAAQC,MAAM,qDACdD,QAAQC,MAAM9C,OACdwB,KAAIuB,KAAKlC,KAMbpB,EAAEuD,GAAGC,YAAc,SAASC,GAExB,GAAIC,GAAKC,KACLC,EAAO5D,EAAEQ,WACTqD,WAAc,aACdC,YAAc,aACdC,SAAc,aACdC,UAAc,GACfP,GAGCQ,EAASjE,EAAE,6CAA+C4D,EAAKI,UAAY,YAAc,IAAM,KAwBnG,OAvBAN,GAAGlC,OAAOyC,EAAOC,OAAO,SAAUzB,GAC9BmB,EAAKG,SAAStB,EAAE0B,OAAOzC,OACvB1B,EAAE2D,MAAMS,IAAI,OAIhBV,EAAGW,GAAG,OAAQ,SAAU5B,GACpBmB,EAAKE,YAAYrB,GACdA,EAAE6B,eACDV,EAAKG,SAAStB,EAAE6B,aAAa5C,OAC7Be,EAAE8B,oBAGVb,EAAGW,GAAG,WAAa,SAAU5B,GACzBA,EAAE8B,iBACFX,EAAKC,WAAWpB,KAEpBiB,EAAGW,GAAG,YAAa,SAAU5B,GACzBA,EAAE+B,kBACFZ,EAAKE,YAAYrB,MAKjBgC,OAAQ,WACJR,EAAOS,QAAQ,YAQ3B1E,EAAEuD,GAAGoB,UAAY,SAASlB,GAiCtB,QAASmB,GAAIlD,GACT,GAAIA,GAASA,EAAMmD,SAAWC,EAAe,CAEzC,IAAK,GADDC,GAAgBC,EACXC,EAAI,EAAGA,EAAIvD,EAAMmD,OAAQI,IAAK,CACnC,GAAIC,GAAQC,OAAOH,IACnBI,GAAMF,GAASxD,EAAMuD,GACrBrB,EAAKyB,SAASH,EAAOE,EAAMF,IAC3BI,IAEJ,MAAOP,IAKf,QAASQ,GAAOL,GACRE,EAAMF,WACCE,GAAMF,GACbI,KAKR,QAASE,KAEL,GAAoB,GAAhBF,GAAqBG,EAIrB,MAHAA,IAAa,EACbX,GAAgB,MAChBlB,GAAK8B,UAGLZ,IAAgB,CAIpB,IAAII,GAAQ,EACZ,KAAK,GAAI5D,KAAO8D,GAAO,CACnBF,EAAQ5D,CACR,OAIO8D,EAAMF,EAGjBK,GAAOL,GAGPlF,EAAEK,YACEQ,IAAW+C,EAAK/C,IAChBJ,KAAWmD,EAAK+B,WAAWT,GAC3BxE,QAAW,SAASkF,GAAWhC,EAAKlD,QAAQwE,EAAOU,GAAUJ,KAC7D7E,MAAW,SAASiF,GAAWhC,EAAKjD,MAAMuE,EAAOU,GAAUJ,KAC3D5E,SAAW,SAASiF,GAAcjC,EAAKhD,SAASsE,EAAOW,MAS/D,QAASC,KACLtC,EAAYiB,SAIhB,QAASsB,GAAMb,GACX,IAAKA,IAASE,GACVG,EAAOL,GAKf,QAASc,KACAlB,IACDA,GAAgB,EAChBU,KAKR,QAASS,KACLR,GAAa,EAIjB,QAASS,GAAUzC,GAEf,MADAG,GAAO5D,EAAEQ,UAAWoD,EAAMH,GAK9B,QAAS0C,KACL,MAAOC,QAAOC,MAAQD,OAAO/E,UAAY+E,OAAOpE,gBAAkBoE,OAAOE,SA5H7E,GAAI1C,GAAO5D,EAAEQ,WACT+F,SAAkB,aAClBC,UAAkB,aAClBnB,SAAkB,aAClBM,WAAkB,aAClB/E,SAAkB,aAClBF,QAAkB,aAClBC,MAAkB,SAASgB,EAAG8E,GAAKC,MAAMD,IACzCf,SAAkB,cACnBjC,GAGC2B,KAGAJ,EAAc,EACdM,EAAe,EAGfR,GAAgB,EAChBW,GAAa,EAGbjC,EAAcxD,EAAE2D,MAAMH,aACtBQ,UAAc,EACdD,SAAc,SAASrC,GAASkD,EAAIlD,IACpCmC,WAAcJ,EAAQI,WACtBC,YAAcL,EAAQK,aAqG1B,QACIgC,OAAkBA,EAClBlB,IAAkBA,EAClBW,OAAkBA,EAClBS,MAAkBA,EAClBC,KAAkBA,EAClBF,MAAkBA,EAClBG,UAAkBA,EAClBC,WAAkBA,KAG3BlG"}
\ No newline at end of file
diff --git a/static/scripts/utils/uploadbox.js b/static/scripts/utils/uploadbox.js
index 4efe383038e..be4f0c7dd89 100755
--- a/static/scripts/utils/uploadbox.js
+++ b/static/scripts/utils/uploadbox.js
@@ -1,2 +1,2 @@
-!function(a){jQuery.event.props.push("dataTransfer"),a.uploadpost=function(b){var c=a.extend({},{data:{},success:function(){},error:function(){},progress:function(){},url:null,maxfilesize:2048,error_filesize:"File exceeds 2GB. Please use an FTP client.",error_default:"Please make sure the file is available.",error_server:"Upload request failed.",error_login:"Uploads require you to log in."},b),d=c.data;if(d.error_message)return void c.error(d.error_message);var e=new FormData;for(var f in d.payload)e.append(f,d.payload[f]);var g=0;for(var f in d.files){var h=d.files[f];e.append(h.name,h.file,h.file.name),g+=h.file.size}return g>1048576*c.maxfilesize?void c.error(c.error_filesize):(xhr=new XMLHttpRequest,xhr.open("POST",c.url,!0),xhr.setRequestHeader("Accept","application/json"),xhr.setRequestHeader("Cache-Control","no-cache"),xhr.setRequestHeader("X-Requested-With","XMLHttpRequest"),xhr.onreadystatechange=function(){if(xhr.readyState==xhr.DONE){var a=null;if(xhr.responseText)try{a=jQuery.parseJSON(xhr.responseText)}catch(b){a=xhr.responseText}if(xhr.status<200||xhr.status>299){var d=xhr.statusText;403==xhr.status?d=c.error_login:0==xhr.status?d=c.error_server:d||(d=c.error_default),c.error(d+" ("+xhr.status+")")}else c.success(a)}},xhr.upload.addEventListener("progress",function(a){a.lengthComputable&&c.progress(Math.round(100*a.loaded/a.total))},!1),console.debug("uploadbox::uploadpost() - Posting following data:"),console.debug(c),void xhr.send(e))},a.fn.uploadinput=function(b){var c=this,d=a.extend({},{ondragover:function(){},ondragleave:function(){},onchange:function(){},multiple:!1},b),e=a('");return c.append(e).change(function(b){d.onchange(b.target.files),a(this).val("")}),c.on("drop",function(a){d.ondragleave(a),a.dataTransfer&&(d.onchange(a.dataTransfer.files),a.preventDefault())}),c.on("dragover",function(a){a.preventDefault(),d.ondragover(a)}),c.on("dragleave",function(a){a.stopPropagation(),d.ondragleave(a)}),{dialog:function(){e.trigger("click")}}},a.fn.uploadbox=function(b){function c(a){if(a&&a.length&&!p){for(var b=n,c=0;c1048576*c.maxfilesize?void c.error(c.error_filesize):(xhr=new XMLHttpRequest,xhr.open("POST",c.url,!0),xhr.setRequestHeader("Accept","application/json"),xhr.setRequestHeader("Cache-Control","no-cache"),xhr.setRequestHeader("X-Requested-With","XMLHttpRequest"),xhr.onreadystatechange=function(){if(xhr.readyState==xhr.DONE){var a=null;if(xhr.responseText)try{a=jQuery.parseJSON(xhr.responseText)}catch(b){a=xhr.responseText}if(xhr.status<200||xhr.status>299){var d=xhr.statusText;403==xhr.status?d=c.error_login:0==xhr.status?d=c.error_server:d||(d=c.error_default),c.error(d+" ("+xhr.status+")")}else c.success(a)}},xhr.upload.addEventListener("progress",function(a){a.lengthComputable&&c.progress(Math.round(100*a.loaded/a.total))},!1),console.debug("uploadbox::uploadpost() - Posting following data:"),console.debug(c),void xhr.send(e))},a.fn.uploadinput=function(b){var c=this,d=a.extend({},{ondragover:function(){},ondragleave:function(){},onchange:function(){},multiple:!1},b),e=a('");return c.append(e.change(function(b){d.onchange(b.target.files),a(this).val("")})),c.on("drop",function(a){d.ondragleave(a),a.dataTransfer&&(d.onchange(a.dataTransfer.files),a.preventDefault())}),c.on("dragover",function(a){a.preventDefault(),d.ondragover(a)}),c.on("dragleave",function(a){a.stopPropagation(),d.ondragleave(a)}),{dialog:function(){e.trigger("click")}}},a.fn.uploadbox=function(b){function c(a){if(a&&a.length&&!p){for(var b=n,c=0;c
Date: Thu, 17 Dec 2015 12:40:09 -0500
Subject: [PATCH 17/24] raise and show specific exception and warning when no
 files detected

---
 .../scripts/mvc/library/library-foldertoolbar-view.js       | 6 +++++-
 lib/galaxy/webapps/galaxy/api/remote_files.py               | 4 ++++
 static/maps/mvc/library/library-foldertoolbar-view.js.map   | 2 +-
 static/scripts/mvc/library/library-foldertoolbar-view.js    | 2 +-
 4 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
index 785b2410233..937325b954f 100644
--- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
@@ -550,7 +550,11 @@ var FolderToolbarView = Backbone.View.extend({
       },
       error: function(model, response){
         if (typeof response.responseJSON !== "undefined"){
-          mod_toastr.error(response.responseJSON.err_msg);
+          if (response.responseJSON.err_code === 404001){
+            mod_toastr.warning(response.responseJSON.err_msg);
+          } else{
+            mod_toastr.error(response.responseJSON.err_msg);
+          }
         } else {
           mod_toastr.error('An error ocurred.');
         }
diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py
index 912d1590ac5..e60e82c5b16 100644
--- a/lib/galaxy/webapps/galaxy/api/remote_files.py
+++ b/lib/galaxy/webapps/galaxy/api/remote_files.py
@@ -42,6 +42,8 @@ class RemoteFilesAPIController( BaseAPIController ):
             if user_base_dir is None:
                 raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow upload from user directories.' )
             full_import_dir = os.path.join( user_base_dir, user_login )
+            if not os.path.exists(full_import_dir):
+                raise exceptions.ObjectNotFound('You do not have any files in your user directory. Use FTP to upload there.')
             if full_import_dir is not None:
                 if format == 'jstree':
                     disable = kwd.get( 'disable', 'folders')
@@ -51,6 +53,8 @@ class RemoteFilesAPIController( BaseAPIController ):
                     except Exception, exception:
                         log.debug( str( exception ) )
                         raise exceptions.InternalServerError( 'Could not create tree representation of the given folder: ' + str( full_import_dir ) )
+                    if not response:
+                        raise exceptions.ObjectNotFound('You do not have any files in your user directory. Use FTP to upload there.')
                 elif format == 'ajax':
                     raise exceptions.NotImplemented( 'Not implemented yet. Sorry.' )
                 else:
diff --git a/static/maps/mvc/library/library-foldertoolbar-view.js.map b/static/maps/mvc/library/library-foldertoolbar-view.js.map
index f9585700300..9568fea05dc 100644
--- a/static/maps/mvc/library/library-foldertoolbar-view.js.map
+++ b/static/maps/mvc/library/library-foldertoolbar-view.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/static/scripts/mvc/library/library-foldertoolbar-view.js b/static/scripts/mvc/library/library-foldertoolbar-view.js
index 08d586c46eb..3a175ef29b1 100644
--- a/static/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/static/scripts/mvc/library/library-foldertoolbar-view.js
@@ -1,3 +1,3 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(a,b,c,d,e){var f=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets","click #page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file_or_folder:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(a){this.options=_.defaults(a||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(a){this.options=_.extend(this.options,a);var b=this.templateToolBar(),c={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.currUser&&(c.is_admin=Galaxy.currUser.isAdmin(),c.is_anonym=Galaxy.currUser.isAnonymous(),(null!==Galaxy.config.user_library_import_dir||Galaxy.config.allow_library_path_paste!==!1||null!==Galaxy.config.library_import_dir)&&(c.mutiple_add_dataset_options=!0)),this.$el.html(b(c))},renderPaginator:function(a){this.options=_.extend(this.options,a);var b=this.templatePaginator();this.$el.find("#folder_paginator").html(b({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown}))},configureElements:function(a){this.options=_.extend(this.options,a),this.options.can_add_library_item===!0?$(".add-library-items").show():$(".add-library-items").hide(),this.options.contains_file_or_folder===!0&&Galaxy.currUser?Galaxy.currUser.isAnonymous()?($(".dataset-manipulation").show(),$(".logged-dataset-manipulation").hide()):($(".logged-dataset-manipulation").show(),$(".dataset-manipulation").show()):($(".logged-dataset-manipulation").hide(),$(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(a){a.preventDefault(),a.stopPropagation();var b=this,c=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:c(),buttons:{Create:function(){b.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var a=this.serialize_new_folder();if(this.validate_new_folder(a)){var b=new d.FolderAsModel;url_items=Backbone.history.fragment.split("/"),current_folder_id=url_items[url_items.length-1],b.url=b.urlRoot+current_folder_id,b.save(a,{success:function(a){Galaxy.modal.hide(),c.success("Folder created."),a.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(a)},error:function(a,b){Galaxy.modal.hide(),c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})}else c.error("Folder's name is missing.");return!1},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(a){return""!==a.name},modalBulkImport:function(){var a=$("#folder_table").find(":checked");0===a.length?c.info("You must select some datasets first."):this.refreshUserHistoriesList(function(a){var b=a.templateBulkImportInModal();a.modal=Galaxy.modal,a.modal.show({closing_events:!0,title:"Import into History",body:b({histories:a.histories.models}),buttons:{Import:function(){a.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(a){var b=this;this.histories=new d.GalaxyHistories,this.histories.fetch({success:function(){a(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var a=$("select[name=dataset_import_bulk] option:selected").val(),b=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=a;var c=[],e=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("dataset_row")?c.push(this.parentElement.parentElement.id):""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("folder_row")&&e.push(this.parentElement.parentElement.id)});for(var f=[],g=c.length-1;g>=0;g--){var h=c[g],i=new d.HistoryItem;i.url=i.urlRoot+a+"/contents",i.content=h,i.source="library",f.push(i)}for(var g=e.length-1;g>=0;g--){var j=e[g],i=new d.HistoryItem;i.url=i.urlRoot+a+"/contents",i.content=j,i.source="library_folder",f.push(i)}this.initChainCallControl({length:f.length,action:"to_history",history_name:b}),jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+a),this.chainCallImportingIntoHistory(f,b)},updateProgress:function(){this.progress+=this.progressStep,$(".progress-bar-import").width(Math.round(this.progress)+"%"),txt_representation=Math.round(this.progress)+"% Complete",$(".completion_span").text(txt_representation)},download:function(a,b){var c=[],d=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("dataset_row")?c.push(this.parentElement.parentElement.id):""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("folder_row")&&d.push(this.parentElement.parentElement.id)});var e=(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/download/"+b,f={ld_ids:c,folder_ids:d};this.processDownload(e,f,"get")},processDownload:function(a,b,d){if(a&&b){b="string"==typeof b?b:$.param(b);var e="";$.each(b.split("&"),function(){var a=this.split("=");e+=''}),$(''+e+"").appendTo("body").submit().remove(),c.info("Your download will begin soon.")}else c.error("An error occurred.")},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(a){a.modal=Galaxy.modal;var b=a.templateAddFilesFromHistory(),d=a.options.full_path[a.options.full_path.length-1][1];a.modal.show({closing_events:!0,title:"Adding datasets from your history to folder "+d,body:b({histories:a.histories.models}),buttons:{Add:function(){a.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}}),a.histories.models.length>0?(a.fetchAndDisplayHistoryContents(a.histories.models[0].id),$("#dataset_add_bulk").change(function(b){a.fetchAndDisplayHistoryContents(b.target.value)})):c.error("An error ocurred.")})},importFilesFromPathModal:function(){var a=this;this.modal=Galaxy.modal;var b=this.templateImportPathModal();this.modal.show({closing_events:!0,title:"Please enter paths to import",body:b({}),buttons:{Import:function(){a.importFromPathsClicked(a)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+a.id,{trigger:!0})}}),this.renderSelectBoxes()},fetchExtAndGenomes:function(){var a=this;b.get({url:(window.galaxy_config?galaxy_config.root:"/")+"api/datatypes?extension_only=False",success:function(b){for(key in b)a.list_extensions.push({id:b[key].extension,text:b[key].extension,description:b[key].description,description_url:b[key].description_url});a.list_extensions.sort(function(a,b){return a.id>b.id?1:a.idb.id?1:a.id=0;h--)trimmed=f[h].trim(),0!==trimmed.length&&g.push(trimmed);this.initChainCallControl({length:g.length,action:"adding_datasets"}),this.chainCallImportingFolders({paths:g,preserve_dirs:a,link_data:b,source:"admin_path",file_type:d,dbkey:e})}else c.info("Please enter a path relative to Galaxy root.")},initChainCallControl:function(a){var b;switch(a.action){case"adding_datasets":b=this.templateAddingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(b({folder_name:this.options.folder_name}));break;case"deleting_datasets":b=this.templateDeletingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(b());break;case"to_history":b=this.templateImportIntoHistoryProgressBar(),this.modal.$el.find(".modal-body").html(b({history_name:a.history_name}));break;default:console.error("Wrong action specified.")}this.progress=0,this.progressStep=100/a.length,this.options.chain_call_control.total_number=a.length,this.options.chain_call_control.failed_number=0},importFromJstreePath:function(a,b){var d=$("#jstree_browser").jstree().get_selected(!0),e=this.modal.$el.find(".preserve-checkbox").is(":checked"),f=this.modal.$el.find(".link-checkbox").is(":checked"),g=this.select_extension.value(),h=this.select_genome.value(),i=d[0].type,j=[];if(d.length<1)c.info("Please select some items first.");else{this.modal.disableButton("Import");for(var k=d.length-1;k>=0;k--)void 0!==d[k].li_attr.full_path&&j.push(d[k].li_attr.full_path);if(this.initChainCallControl({length:j.length,action:"adding_datasets"}),"folder"===i){var l=b.source+"_folder";this.chainCallImportingFolders({paths:j,preserve_dirs:e,link_data:f,source:l,file_type:g,dbkey:h})}else if("file"===i){var l=b.source+"_file";this.chainCallImportingUserdirFiles({paths:j,file_type:g,dbkey:h,source:l})}}},fetchAndDisplayHistoryContents:function(a){var b=new d.HistoryContents({id:a}),e=this;b.fetch({success:function(b){var c=e.templateHistoryContents();e.histories.get(a).set({contents:b}),e.modal.$el.find("#selected_history_content").html(c({history_contents:b.models.reverse()}))},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},addAllDatasetsFromHistory:function(){var a=this.modal.$el.find("#selected_history_content").find(":checked"),b=[],e=[];if(a.length<1)c.info("You must select some datasets first.");else{this.modal.disableButton("Add"),a.each(function(){var a=$(this.parentElement).data("id");a&&b.push(a)});for(var f=b.length-1;f>=0;f--){history_dataset_id=b[f];var g=new d.Item;g.url=(window.galaxy_config?galaxy_config.root:"/")+"api/folders/"+this.options.id+"/contents",g.set({from_hda_id:history_dataset_id}),e.push(g)}this.initChainCallControl({length:e.length,action:"adding_datasets"}),this.chainCallAddingHdas(e)}},chainCallImportingIntoHistory:function(a,b){var d=this,e=a.pop();if("undefined"==typeof e)return 0===this.options.chain_call_control.failed_number?c.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}}):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.error("There was an error and no datasets were imported into history."):this.options.chain_call_control.failed_number=0;i--){var j=new d.Item({id:e[i]});h.push(j)}for(var i=f.length-1;i>=0;i--){var k=new d.FolderAsModel({id:f[i]});h.push(k)}this.options.chain_call_control.total_number=g.length,this.chainCallDeletingItems(h)}},showLibInfo:function(){var a=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id,b=null,e=this;null!==Galaxy.libraries.libraryListView?(b=Galaxy.libraries.libraryListView.collection.get(a),this.showLibInfoModal(b)):(b=new d.Library({id:a}),b.fetch({success:function(){e.showLibInfoModal(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}}))},showLibInfoModal:function(a){var b=this.templateLibInfoInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Library Information",body:b({library:a}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(a){switch(a.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back(),c.error("Invalid import source.")}},showPageSizePrompt:function(){var a=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));null!=a&&a==parseInt(a)&&(Galaxy.libraries.preferences.set({folder_page_size:parseInt(a)}),Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1}))},templateToolBar:function(){return tmpl_array=[],tmpl_array.push('
                      '),tmpl_array.push(' 
                      '),tmpl_array.push('
                      '),tmpl_array.push("   DATA LIBRARIES"),tmpl_array.push('          '),tmpl_array.push("          "),tmpl_array.push('"),tmpl_array.push('   '),tmpl_array.push("<% if(mutiple_add_dataset_options) { %>"),tmpl_array.push('   "),tmpl_array.push("<% } else { %>"),tmpl_array.push(' '),tmpl_array.push("<% } %>"),tmpl_array.push('  '),tmpl_array.push('   "),tmpl_array.push('   '),tmpl_array.push('   '),tmpl_array.push('   '),tmpl_array.push(" 
                      "),tmpl_array.push(""),tmpl_array.push(' 
                      '),tmpl_array.push(" 
                      "),tmpl_array.push("
                      "),_.template(tmpl_array.join(""))},templateLibInfoInModal:function(){return tmpl_array=[],tmpl_array.push('
                      '),tmpl_array.push("
                      Library name:
                      "),tmpl_array.push('
                      <%- library.get("name") %>
                      '),tmpl_array.push("
                      Library description:
                      "),tmpl_array.push('
                      <%- library.get("description") %>
                      '),tmpl_array.push("
                      Library synopsis:
                      "),tmpl_array.push('
                      <%- library.get("synopsis") %>
                      '),tmpl_array.push('
                      ">created <%- library.get("create_time_pretty") %>
                      '),tmpl_array.push("
                      "),_.template(tmpl_array.join(""))},templateNewFolderInModal:function(){return tmpl_array=[],tmpl_array.push('
                      '),tmpl_array.push("
                      "),tmpl_array.push(''),tmpl_array.push(''),tmpl_array.push(""),tmpl_array.push("
                      "),_.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var a=[];return a.push(''),a.push("Select history: "),a.push('"),a.push(""),_.template(a.join(""))},templateImportIntoHistoryProgressBar:function(){var a=[];return a.push('
                      '),a.push("Importing selected datasets to history <%= _.escape(history_name) %>"),a.push("
                      "),a.push('
                      '),a.push('   
                      '),a.push('       0% Complete'),a.push("   
                      "),a.push("
                      "),a.push(""),_.template(a.join(""))},templateAddingDatasetsProgressBar:function(){var a=[];return a.push('
                      '),a.push("Adding selected datasets to library folder <%= _.escape(folder_name) %>"),a.push("
                      "),a.push('
                      '),a.push('   
                      '),a.push('       0% Complete'),a.push("   
                      "),a.push("
                      "),a.push(""),_.template(a.join(""))},templateDeletingDatasetsProgressBar:function(){var a=[];return a.push('
                      '),a.push("
                      "),a.push('
                      '),a.push('   
                      '),a.push('       0% Complete'),a.push("   
                      "),a.push("
                      "),a.push(""),_.template(a.join(""))},templateBrowserModal:function(){var a=[];return a.push('
                      '),a.push('
                      All files you select will be imported into the current folder.
                      '),a.push(''),a.push('
                      '),a.push('"),a.push('"),a.push("
                      "),a.push('
                      '),a.push('"),a.push('"),a.push("
                      "),a.push('
                      '),a.push("
                      "),a.push("
                      "),a.push("
                      You can set extension type and genome for all imported datasets at once:
                      "),a.push("
                      "),a.push('Type: '),a.push('  Genome: '),a.push("
                      "),a.push("
                      "),_.template(a.join(""))},templateImportPathModal:function(){var a=[];return a.push('
                      '),a.push('
                      All files within the given folders and their subfolders will be imported into the current folder.
                      '),a.push('
                      '),a.push('"),a.push('"),a.push("
                      "),a.push(''),a.push("
                      "),a.push("
                      You can set extension type and genome for all imported datasets at once:
                      "),a.push("
                      "),a.push('Type: '),a.push('  Genome: '),a.push("
                      "),a.push("
                      "),_.template(a.join(""))},templateAddFilesFromHistory:function(){var a=[];return a.push('
                      '),a.push('
                      '),a.push("Select history:  "),a.push(''}),$('
                      '+e+"").appendTo("body").submit().remove(),c.info("Your download will begin soon.")}else c.error("An error occurred.")},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(a){a.modal=Galaxy.modal;var b=a.templateAddFilesFromHistory(),d=a.options.full_path[a.options.full_path.length-1][1];a.modal.show({closing_events:!0,title:"Adding datasets from your history to folder "+d,body:b({histories:a.histories.models}),buttons:{Add:function(){a.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}}),a.histories.models.length>0?(a.fetchAndDisplayHistoryContents(a.histories.models[0].id),$("#dataset_add_bulk").change(function(b){a.fetchAndDisplayHistoryContents(b.target.value)})):c.error("An error ocurred.")})},importFilesFromPathModal:function(){var a=this;this.modal=Galaxy.modal;var b=this.templateImportPathModal();this.modal.show({closing_events:!0,title:"Please enter paths to import",body:b({}),buttons:{Import:function(){a.importFromPathsClicked(a)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+a.id,{trigger:!0})}}),this.renderSelectBoxes()},fetchExtAndGenomes:function(){var a=this;b.get({url:(window.galaxy_config?galaxy_config.root:"/")+"api/datatypes?extension_only=False",success:function(b){for(key in b)a.list_extensions.push({id:b[key].extension,text:b[key].extension,description:b[key].description,description_url:b[key].description_url});a.list_extensions.sort(function(a,b){return a.id>b.id?1:a.idb.id?1:a.id=0;h--)trimmed=f[h].trim(),0!==trimmed.length&&g.push(trimmed);this.initChainCallControl({length:g.length,action:"adding_datasets"}),this.chainCallImportingFolders({paths:g,preserve_dirs:a,link_data:b,source:"admin_path",file_type:d,dbkey:e})}else c.info("Please enter a path relative to Galaxy root.")},initChainCallControl:function(a){var b;switch(a.action){case"adding_datasets":b=this.templateAddingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(b({folder_name:this.options.folder_name}));break;case"deleting_datasets":b=this.templateDeletingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(b());break;case"to_history":b=this.templateImportIntoHistoryProgressBar(),this.modal.$el.find(".modal-body").html(b({history_name:a.history_name}));break;default:console.error("Wrong action specified.")}this.progress=0,this.progressStep=100/a.length,this.options.chain_call_control.total_number=a.length,this.options.chain_call_control.failed_number=0},importFromJstreePath:function(a,b){var d=$("#jstree_browser").jstree().get_selected(!0),e=this.modal.$el.find(".preserve-checkbox").is(":checked"),f=this.modal.$el.find(".link-checkbox").is(":checked"),g=this.select_extension.value(),h=this.select_genome.value(),i=d[0].type,j=[];if(d.length<1)c.info("Please select some items first.");else{this.modal.disableButton("Import");for(var k=d.length-1;k>=0;k--)void 0!==d[k].li_attr.full_path&&j.push(d[k].li_attr.full_path);if(this.initChainCallControl({length:j.length,action:"adding_datasets"}),"folder"===i){var l=b.source+"_folder";this.chainCallImportingFolders({paths:j,preserve_dirs:e,link_data:f,source:l,file_type:g,dbkey:h})}else if("file"===i){var l=b.source+"_file";this.chainCallImportingUserdirFiles({paths:j,file_type:g,dbkey:h,source:l})}}},fetchAndDisplayHistoryContents:function(a){var b=new d.HistoryContents({id:a}),e=this;b.fetch({success:function(b){var c=e.templateHistoryContents();e.histories.get(a).set({contents:b}),e.modal.$el.find("#selected_history_content").html(c({history_contents:b.models.reverse()}))},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},addAllDatasetsFromHistory:function(){var a=this.modal.$el.find("#selected_history_content").find(":checked"),b=[],e=[];if(a.length<1)c.info("You must select some datasets first.");else{this.modal.disableButton("Add"),a.each(function(){var a=$(this.parentElement).data("id");a&&b.push(a)});for(var f=b.length-1;f>=0;f--){history_dataset_id=b[f];var g=new d.Item;g.url=(window.galaxy_config?galaxy_config.root:"/")+"api/folders/"+this.options.id+"/contents",g.set({from_hda_id:history_dataset_id}),e.push(g)}this.initChainCallControl({length:e.length,action:"adding_datasets"}),this.chainCallAddingHdas(e)}},chainCallImportingIntoHistory:function(a,b){var d=this,e=a.pop();if("undefined"==typeof e)return 0===this.options.chain_call_control.failed_number?c.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}}):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.error("There was an error and no datasets were imported into history."):this.options.chain_call_control.failed_number=0;i--){var j=new d.Item({id:e[i]});h.push(j)}for(var i=f.length-1;i>=0;i--){var k=new d.FolderAsModel({id:f[i]});h.push(k)}this.options.chain_call_control.total_number=g.length,this.chainCallDeletingItems(h)}},showLibInfo:function(){var a=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id,b=null,e=this;null!==Galaxy.libraries.libraryListView?(b=Galaxy.libraries.libraryListView.collection.get(a),this.showLibInfoModal(b)):(b=new d.Library({id:a}),b.fetch({success:function(){e.showLibInfoModal(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}}))},showLibInfoModal:function(a){var b=this.templateLibInfoInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Library Information",body:b({library:a}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(a){switch(a.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back(),c.error("Invalid import source.")}},showPageSizePrompt:function(){var a=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));null!=a&&a==parseInt(a)&&(Galaxy.libraries.preferences.set({folder_page_size:parseInt(a)}),Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1}))},templateToolBar:function(){return tmpl_array=[],tmpl_array.push('
                      '),tmpl_array.push(' 
                      '),tmpl_array.push('
                      '),tmpl_array.push("   DATA LIBRARIES"),tmpl_array.push('          '),tmpl_array.push("          "),tmpl_array.push('"),tmpl_array.push('   '),tmpl_array.push("<% if(mutiple_add_dataset_options) { %>"),tmpl_array.push('   "),tmpl_array.push("<% } else { %>"),tmpl_array.push(' '),tmpl_array.push("<% } %>"),tmpl_array.push('  '),tmpl_array.push('   "),tmpl_array.push('   '),tmpl_array.push('   '),tmpl_array.push('   '),tmpl_array.push(" 
                      "),tmpl_array.push(""),tmpl_array.push(' 
                      '),tmpl_array.push(" 
                      "),tmpl_array.push("
                      "),_.template(tmpl_array.join(""))},templateLibInfoInModal:function(){return tmpl_array=[],tmpl_array.push('
                      '),tmpl_array.push("
                      Library name:
                      "),tmpl_array.push('
                      <%- library.get("name") %>
                      '),tmpl_array.push("
                      Library description:
                      "),tmpl_array.push('
                      <%- library.get("description") %>
                      '),tmpl_array.push("
                      Library synopsis:
                      "),tmpl_array.push('
                      <%- library.get("synopsis") %>
                      '),tmpl_array.push('
                      ">created <%- library.get("create_time_pretty") %>
                      '),tmpl_array.push("
                      "),_.template(tmpl_array.join(""))},templateNewFolderInModal:function(){return tmpl_array=[],tmpl_array.push('
                      '),tmpl_array.push("
                      "),tmpl_array.push(''),tmpl_array.push(''),tmpl_array.push(""),tmpl_array.push("
                      "),_.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var a=[];return a.push(''),a.push("Select history: "),a.push('"),a.push(""),_.template(a.join(""))},templateImportIntoHistoryProgressBar:function(){var a=[];return a.push('
                      '),a.push("Importing selected datasets to history <%= _.escape(history_name) %>"),a.push("
                      "),a.push('
                      '),a.push('   
                      '),a.push('       0% Complete'),a.push("   
                      "),a.push("
                      "),a.push(""),_.template(a.join(""))},templateAddingDatasetsProgressBar:function(){var a=[];return a.push('
                      '),a.push("Adding selected datasets to library folder <%= _.escape(folder_name) %>"),a.push("
                      "),a.push('
                      '),a.push('   
                      '),a.push('       0% Complete'),a.push("   
                      "),a.push("
                      "),a.push(""),_.template(a.join(""))},templateDeletingDatasetsProgressBar:function(){var a=[];return a.push('
                      '),a.push("
                      "),a.push('
                      '),a.push('   
                      '),a.push('       0% Complete'),a.push("   
                      "),a.push("
                      "),a.push(""),_.template(a.join(""))},templateBrowserModal:function(){var a=[];return a.push('
                      '),a.push('
                      All files you select will be imported into the current folder.
                      '),a.push(''),a.push('
                      '),a.push('"),a.push('"),a.push("
                      "),a.push('
                      '),a.push('"),a.push('"),a.push("
                      "),a.push('
                      '),a.push("
                      "),a.push("
                      "),a.push("
                      You can set extension type and genome for all imported datasets at once:
                      "),a.push("
                      "),a.push('Type: '),a.push('  Genome: '),a.push("
                      "),a.push("
                      "),_.template(a.join(""))},templateImportPathModal:function(){var a=[];return a.push('
                      '),a.push('
                      All files within the given folders and their subfolders will be imported into the current folder.
                      '),a.push('
                      '),a.push('"),a.push('"),a.push("
                      "),a.push(''),a.push("
                      "),a.push("
                      You can set extension type and genome for all imported datasets at once:
                      "),a.push("
                      "),a.push('Type: '),a.push('  Genome: '),a.push("
                      "),a.push("
                      "),_.template(a.join(""))},templateAddFilesFromHistory:function(){var a=[];return a.push('
                      '),a.push('
                      '),a.push("Select history:  "),a.push('"),a.push("
                      "),a.push("
                      "),a.push('
                      '),a.push("
                      "),a.push("
                      "),_.template(a.join(""))},templateHistoryContents:function(){var a=[];return a.push("Choose the datasets to import:"),a.push("
                        "),a.push(" <% _.each(history_contents, function(history_item) { %>"),a.push(' 
                      • ">'),a.push('    <%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>'),a.push(" 
                        • "),a.push(" <% }); %>"),a.push("
                      "),_.template(a.join(""))},templatePaginator:function(){return tmpl_array=[],tmpl_array.push('   
                        '),tmpl_array.push("       <% if ( ( show_page - 1 ) > 0 ) { %>"),tmpl_array.push("           <% if ( ( show_page - 1 ) > page_count ) { %>"),tmpl_array.push('               
                        • '),tmpl_array.push('               
                      • <% print( show_page - 1 ) %>
                        • '),tmpl_array.push("           <% } else { %>"),tmpl_array.push('               
                        • '),tmpl_array.push('               
                      • <% print( show_page - 1 ) %>
                        • '),tmpl_array.push("           <% } %>"),tmpl_array.push("       <% } else { %>"),tmpl_array.push('           
                        • '),tmpl_array.push('           
                      • <% print( show_page - 1 ) %>
                        • '),tmpl_array.push("       <% } %>"),tmpl_array.push('       
                      • '),tmpl_array.push('       <% print( show_page ) %>'),tmpl_array.push("       
                        • "),tmpl_array.push("       <% if ( ( show_page ) < page_count ) { %>"),tmpl_array.push('           
                      • <% print( show_page + 1 ) %>
                        • '),tmpl_array.push('           
                        • '),tmpl_array.push("       <% } else { %>"),tmpl_array.push('           
                      • <% print( show_page + 1 ) %>
                        • '),tmpl_array.push('           
                        • '),tmpl_array.push("       <% } %>"),tmpl_array.push("   
                      "),tmpl_array.push("   "),tmpl_array.push('       showing <%- items_shown %> of <%- total_items_count %> items'),tmpl_array.push("   "),_.template(tmpl_array.join(""))}});return{FolderToolbarView:f}});
 //# sourceMappingURL=../../../maps/mvc/library/library-foldertoolbar-view.js.map
\ No newline at end of file

From f042fe8548ec4a0f2f29b72d0c34736e2ff524f9 Mon Sep 17 00:00:00 2001
From: John Chilton 
Date: Tue, 6 Oct 2015 14:44:50 +0100
Subject: [PATCH 18/24] Attempt to fix transiently failing API tests.

 - Fix default timeout of wait_on_state api helper. Had the wrong default specified and might fix this failure: https://jenkins.galaxyproject.org/job/docker-api/229/testReport/junit/api.test_libraries/LibrariesApiTestCase/test_create_dataset/
 - Modify job search test case to allow a little more time between the history being "ok" and the job, in case there is a timing condition if the HDA is committed first and then job. Also improve the test output in case this isn't the problem.
---
 test/api/test_jobs.py | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/test/api/test_jobs.py b/test/api/test_jobs.py
index cd8ad52ccd6..cba31d68b6f 100644
--- a/test/api/test_jobs.py
+++ b/test/api/test_jobs.py
@@ -137,17 +137,27 @@ class JobsApiTestCase( api.ApiTestCase, TestsDatasets ):
 
         empty_search_response = self._post( "jobs/search", data=search_payload )
         self._assert_status_code_is( empty_search_response, 200 )
-        assert len( empty_search_response.json() ) == 0
+        self.assertEquals( len( empty_search_response.json() ), 0 )
 
         self.__run_cat_tool( history_id, dataset_id )
         self._wait_for_history( history_id, assert_ok=True )
 
-        self.__assert_one_search_result( search_payload )
+        search_count = -1
+        # in case job and history aren't updated at exactly the same
+        # time give time to wait
+        for i in range(5):
+            search_count = self._search_count(search_payload)
+            if search_count == 1:
+                break
+            time.sleep(.1)
 
-    def __assert_one_search_result( self, search_payload ):
+        self.assertEquals( search_count, 1 )
+
+    def _search_count( self, search_payload ):
         search_response = self._post( "jobs/search", data=search_payload )
         self._assert_status_code_is( search_response, 200 )
-        assert len( search_response.json() ) == 1, search_response.json()
+        search_json = search_response.json()
+        return len(search_json)
 
     def __run_cat_tool( self, history_id, dataset_id ):
         # Code duplication with test_jobs.py, eliminate

From 93c6d0542124c220e36c1e90d62e3e2aef607e9a Mon Sep 17 00:00:00 2001
From: John Chilton 
Date: Wed, 18 Nov 2015 11:17:09 +0000
Subject: [PATCH 19/24] Revise and fix waiting for tool tests.

- maxseconds on test tag stopped being respected at some point, fix that.
- maxseconds on test tag stopped being parsed at some later point, fix that.
- Revise default behavior so it can be overridden with yet another testing environment variable GALAXY_TEST_DEFAULT_WAIT.
- Add test case to ensure there is no future regression of these behaviors.
---
 lib/galaxy/tools/parser/xml.py              |  1 +
 lib/galaxy/tools/test.py                    |  6 ++++--
 test/base/twilltestcase.py                  |  9 ++++++---
 test/functional/tools/maxseconds.xml        | 16 ++++++++++++++++
 test/functional/tools/samples_tool_conf.xml |  1 +
 5 files changed, 28 insertions(+), 5 deletions(-)
 create mode 100644 test/functional/tools/maxseconds.xml

diff --git a/lib/galaxy/tools/parser/xml.py b/lib/galaxy/tools/parser/xml.py
index 216469613a8..8434a9bafc2 100644
--- a/lib/galaxy/tools/parser/xml.py
+++ b/lib/galaxy/tools/parser/xml.py
@@ -306,6 +306,7 @@ def _test_elem_to_dict(test_elem, i):
         stderr=__parse_assert_list_from_elem( test_elem.find("assert_stderr") ),
         expect_exit_code=test_elem.get("expect_exit_code"),
         expect_failure=string_as_bool(test_elem.get("expect_failure", False)),
+        maxseconds=test_elem.get("maxseconds", None),
     )
     _copy_to_dict_if_present(test_elem, rval, ["interactor", "num_outputs"])
     return rval
diff --git a/lib/galaxy/tools/test.py b/lib/galaxy/tools/test.py
index e98527c1d0e..201a5fed707 100644
--- a/lib/galaxy/tools/test.py
+++ b/lib/galaxy/tools/test.py
@@ -14,7 +14,7 @@ log = logging.getLogger( __name__ )
 DEFAULT_FTYPE = 'auto'
 DEFAULT_DBKEY = 'hg17'
 DEFAULT_INTERACTOR = "api"  # Default mechanism test code uses for interacting with Galaxy instance.
-DEFAULT_MAX_SECS = 120
+DEFAULT_MAX_SECS = None
 
 
 @nottest
@@ -42,7 +42,9 @@ class ToolTestBuilder( object ):
 
     def __init__( self, tool, test_dict, i, default_interactor ):
         name = test_dict.get( 'name', 'Test-%d' % (i + 1) )
-        maxseconds = int( test_dict.get( 'maxseconds', DEFAULT_MAX_SECS ) )
+        maxseconds = test_dict.get( 'maxseconds', DEFAULT_MAX_SECS )
+        if maxseconds is not None:
+            maxseconds = int( maxseconds )
 
         self.tool = tool
         self.name = name
diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py
index fa956559081..126c0b90a98 100644
--- a/test/base/twilltestcase.py
+++ b/test/base/twilltestcase.py
@@ -40,6 +40,8 @@ tc.config( 'use_tidy', 0 )
 logging.getLogger( "ClientCookie.cookies" ).setLevel( logging.WARNING )
 log = logging.getLogger( __name__ )
 
+DEFAULT_TOOL_TEST_WAIT = os.environ.get("GALAXY_TEST_DEFAULT_WAIT", 86400)
+
 
 class TwillTestCase( unittest.TestCase ):
 
@@ -2443,15 +2445,16 @@ class TwillTestCase( unittest.TestCase ):
     def wait_for( self, func, **kwd ):
         sleep_amount = 0.2
         slept = 0
-        walltime_exceeded = 86400
+        walltime_exceeded = kwd.get("maxseconds", None)
+        if walltime_exceeded is None:
+            walltime_exceeded = DEFAULT_TOOL_TEST_WAIT
+        log.info("walltime_exceeded is %s" % walltime_exceeded)
         while slept <= walltime_exceeded:
             result = func()
             if result:
                 time.sleep( sleep_amount )
                 slept += sleep_amount
                 sleep_amount *= 2
-                if slept + sleep_amount > walltime_exceeded:
-                    sleep_amount = walltime_exceeded - slept  # don't overshoot maxseconds
             else:
                 break
         assert slept < walltime_exceeded, 'Tool run exceeded reasonable walltime of 24 hours, terminating.'
diff --git a/test/functional/tools/maxseconds.xml b/test/functional/tools/maxseconds.xml
new file mode 100644
index 00000000000..a36c3da09db
--- /dev/null
+++ b/test/functional/tools/maxseconds.xml
@@ -0,0 +1,16 @@
+
+    
+        sleep 100
+    
+    
+    
+    
+        
+    
+    
+        
+        
+    
+    
+    
+
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 2ad67eff206..457f5050ced 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -23,6 +23,7 @@
   
   
   
+  
   
   
   

From ffb973477b02c4bc1cbfa95c7a6247f1d7949fdd Mon Sep 17 00:00:00 2001
From: John Chilton 
Date: Wed, 25 Nov 2015 15:14:22 +0000
Subject: [PATCH 20/24] Do not check for tool migrations when running tests.

This is an inappropriate time for the check and causes slow down when running tests.
---
 scripts/functional_tests.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py
index e25a885ddbd..e5102f98b7b 100644
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -336,6 +336,7 @@ def main():
                        user_library_import_dir=user_library_import_dir,
                        master_api_key=master_api_key,
                        use_tasked_jobs=True,
+                       check_migrate_tools=False,
                        cleanup_job='onsuccess',
                        enable_beta_tool_formats=True,
                        auto_configure_logging=logging_config_file is None,

From 641b275aa424421591833f6a3bce3ebd8b358017 Mon Sep 17 00:00:00 2001
From: John Chilton 
Date: Thu, 3 Dec 2015 16:33:45 +0000
Subject: [PATCH 21/24] Wait on jobs and history in certain API test cases.

This strategy proved to work around certain race conditions in tool testing so hopefully it will solve the transiently failing job searching and filtering test cases.
---
 test/api/helpers.py   | 10 +++++++---
 test/api/test_jobs.py |  4 ++--
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/test/api/helpers.py b/test/api/helpers.py
index 98087760950..799c790ee9b 100644
--- a/test/api/helpers.py
+++ b/test/api/helpers.py
@@ -70,10 +70,14 @@ class BaseDatasetPopulator( object ):
     Galaxy - implementations must implement _get and _post.
     """
 
-    def new_dataset( self, history_id, content='TestData123', **kwds ):
+    def new_dataset( self, history_id, content='TestData123', wait=False, **kwds ):
         payload = self.upload_payload( history_id, content, **kwds )
-        run_response = self._post( "tools", data=payload )
-        return run_response.json()["outputs"][0]
+        run_response = self._post( "tools", data=payload ).json()
+        if wait:
+            job = run_response["jobs"][0]
+            self.wait_for_job(job["id"])
+            self.wait_for_history(history_id)
+        return run_response["outputs"][0]
 
     def wait_for_history( self, history_id, assert_ok=False, timeout=DEFAULT_TIMEOUT ):
         try:
diff --git a/test/api/test_jobs.py b/test/api/test_jobs.py
index cba31d68b6f..18c850f65bc 100644
--- a/test/api/test_jobs.py
+++ b/test/api/test_jobs.py
@@ -200,8 +200,8 @@ class JobsApiTestCase( api.ApiTestCase, TestsDatasets ):
         return history_id, dataset_id
 
     def __history_with_ok_dataset( self ):
-        history_id, dataset_id = self.__history_with_new_dataset()
-        self._wait_for_history( history_id, assert_ok=True )
+        history_id = self._new_history()
+        dataset_id = self._new_dataset( history_id, wait=True )[ "id" ]
         return history_id, dataset_id
 
     def __jobs_index( self, **kwds ):

From 57a76065a54f63a47874158c121f002308648025 Mon Sep 17 00:00:00 2001
From: John Chilton 
Date: Fri, 4 Dec 2015 12:42:49 +0000
Subject: [PATCH 22/24] Fix missing assertion pointed out @nsoranzo.

Lots of other tests would fail if simple uploads aren't working, but it is better to be direct and very explicit about why this particular test is failing.
---
 test/api/helpers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/api/helpers.py b/test/api/helpers.py
index 799c790ee9b..dfc8a8036c0 100644
--- a/test/api/helpers.py
+++ b/test/api/helpers.py
@@ -76,7 +76,7 @@ class BaseDatasetPopulator( object ):
         if wait:
             job = run_response["jobs"][0]
             self.wait_for_job(job["id"])
-            self.wait_for_history(history_id)
+            self.wait_for_history(history_id, assert_ok=True)
         return run_response["outputs"][0]
 
     def wait_for_history( self, history_id, assert_ok=False, timeout=DEFAULT_TIMEOUT ):

From 2817eabf95a980a250e272c3917e5dcfc24743b2 Mon Sep 17 00:00:00 2001
From: John Chilton 
Date: Sat, 5 Dec 2015 18:12:18 +0000
Subject: [PATCH 23/24] Fail maxseconds test tool if sleep is interrupted.

---
 test/functional/tools/maxseconds.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/functional/tools/maxseconds.xml b/test/functional/tools/maxseconds.xml
index a36c3da09db..9c2ec0e714c 100644
--- a/test/functional/tools/maxseconds.xml
+++ b/test/functional/tools/maxseconds.xml
@@ -1,5 +1,5 @@
 
-    
+    
         sleep 100
     
     

From c3580da7b826b42de631017d4d2baf7e6ac3cfdf Mon Sep 17 00:00:00 2001
From: Marius van den Beek 
Date: Fri, 18 Dec 2015 12:00:41 +0100
Subject: [PATCH 24/24] Allow installation of different repositories with the
 same name in a single install transaction.

---
 .../repository_dependency_manager.py            | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py b/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
index 6aa8abe7342..6cf00f42d70 100644
--- a/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
+++ b/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
@@ -414,6 +414,23 @@ class RepositoryDependencyInstallManager( object ):
                                     all_repo_info_dicts_keys = [ d.keys()[ 0 ] for d in all_repo_info_dicts ]
                                     if required_repo_info_dict_key not in all_repo_info_dicts_keys:
                                         all_repo_info_dicts.append( required_repo_info_dict )
+                                    else:
+                                        # required_repo_info_dict_key corresponds to the repo name.
+                                        # A single install transaction might require the installation of 2 or more repos
+                                        # with the same repo name but different owners or versions.
+                                        # Therefore, if required_repo_info_dict_key is already in all_repo_info_dicts,
+                                        # check that the tool id is already present. If it is not, we are dealing with the same repo name,
+                                        # but a different owner/changeset revision or version and we add the repo to the list of repos to be installed.
+                                        tool_id = required_repo_info_dict[ required_repo_info_dict_key ][ 1 ]
+                                        is_present = False
+                                        for repo_info_dict in all_repo_info_dicts:
+                                            for k, v in repo_info_dict.items():
+                                                if required_repo_info_dict_key == k:
+                                                    if tool_id == v[1]:
+                                                        is_present = True
+                                                        break
+                                        if not is_present:
+                                            all_repo_info_dicts.append( required_repo_info_dict )
                         all_required_repo_info_dict[ 'all_repo_info_dicts' ] = all_repo_info_dicts
         return all_required_repo_info_dict
 

                      There are no runs.
                      
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'workflow_id',
-                                'workflows',
-                                'per_workflow',
-                                'Workflow ID',
-                                spark_time=time_period,
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        ${get_sort_url(sort_id, order, 'workflow_id', 'workflows', 'per_workflow', 'Workflow ID', spark_time=time_period, page=page, offset=offset, entries=entries)}
                         ${arrow}
                     
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'workflow_name',
-                                'workflows',
-                                'per_workflow',
-                                'Workflow Name',
-                                spark_time=time_period,
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        ${get_sort_url(sort_id, order, 'workflow_name', 'workflows', 'per_workflow', 'Workflow Name', spark_time=time_period, page=page, offset=offset, entries=entries)}
                         ${arrow}
                     
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'total_runs',
-                                'workflows',
-                                'per_workflow',
-                                'Workflow Runs',
-                                spark_time=time_period,
-                                page=page,
-                                offset=offset,
-                                entries=entries)
-                        }
+                        ${get_sort_url(sort_id, order, 'total_runs', 'workflows', 'per_workflow', 'Workflow Runs', spark_time=time_period, page=page, offset=offset, entries=entries)}
                         ${arrow}
                     
                     
                 
                      ${run[0]}
                         ${run[1]}
                     
                      
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'date',
-                                'workflows',
-                                'user_per_month',
-                                'Month',
-                                email=util.sanitize_text( email ))
-                        }
+                        ${get_sort_url(sort_id, order, 'date', 'workflows', 'user_per_month', 'Month', email=util.sanitize_text( email ))}
                         ${arrow}
                     
                     
-                        ${
-                            get_sort_url(
-                                sort_id,
-                                order,
-                                'total_workflows',
-                                'workflows',
-                                'user_per_month',
-                                'Total',
-                                email=util.sanitize_text( email ))
-                        }
+                        ${get_sort_url(sort_id, order, 'total_workflows', 'workflows', 'user_per_month', 'Total', email=util.sanitize_text( email ))}
                         ${arrow}
                     
                     ${month}
                         ${total}