Merge branch 'remove_toolshed_installation_grid' into dev

(post-prettier merge was simple to resolve)

client/galaxy/scripts/apps/panels/admin-panel.js

@@ -99,9 +99,7 @@ var AdminPanel = Backbone.View.extend({
                     },
                     {
                         title: "Monitor installing repositories",
-                        url:
-                            "admin_toolshed/monitor_repository_installation?installing_repository_ids=" +
-                            self.settings.installing_repository_ids,
+                        url: "admin_toolshed/monitor_repository_installation",
                         enabled: self.settings.installing_repository_ids
                     },
                     {

client/galaxy/scripts/mvc/toolshed/repository-queue-view.js

@@ -107,7 +107,7 @@ define(["mvc/toolshed/toolshed-model", "mvc/toolshed/util"], function(
                 var repositories = iri_params.repositories;
                 var new_route = "status/r/" + repositories.join("|");
                 $.post(
-                    Galaxy.root + "admin_toolshed/manage_repositories",
+                    Galaxy.root + "admin_toolshed/install_repositories",
                     iri_params,
                     function(data) {
                         console.log(

client/galaxy/scripts/mvc/toolshed/repository-view.js

@@ -388,7 +388,7 @@ define(
 
             doInstall: function(params) {
                 var controller_url =
-                    Galaxy.root + "admin_toolshed/manage_repositories";
+                    Galaxy.root + "admin_toolshed/install_repositories";
                 var repositories = params.repositories;
                 var new_route = "status/r/" + repositories.join("|");
                 $.post(controller_url, params, function(data) {

lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

@@ -44,8 +44,6 @@ log = logging.getLogger(__name__)
 class AdminToolshed(AdminGalaxy):
 
     installed_repository_grid = admin_toolshed_grids.InstalledRepositoryGrid()
-    repository_installation_grid = admin_toolshed_grids.RepositoryInstallationGrid()
-    tool_dependency_grid = admin_toolshed_grids.ToolDependencyGrid()
 
     @web.expose
     @web.require_admin
@@ -560,72 +558,28 @@ class AdminToolshed(AdminGalaxy):
 
     @web.expose
     @web.require_admin
-    def manage_repositories(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        api_installation = util.asbool(kwd.get('api', 'false'))
-        if api_installation:
-            tsr_ids = json.loads(kwd.get('tool_shed_repository_ids', '[]'))
-            kwd['tool_shed_repository_ids'] = tsr_ids
-            tsridslist = common_util.get_tool_shed_repository_ids(**kwd)
-        else:
-            tsridslist = common_util.get_tool_shed_repository_ids(**kwd)
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
-            if not tsridslist:
-                message = 'Select at least 1 tool shed repository to %s.' % operation
-                kwd['message'] = message
-                kwd['status'] = 'error'
-                del kwd['operation']
-                return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
-                                                                action='manage_repositories',
-                                                                **kwd))
-            if operation == 'browse':
-                return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
-                                                                action='browse_repository',
-                                                                **kwd))
-            elif operation == 'uninstall':
-                # TODO: I believe this block should be removed, but make sure..
-                repositories_for_uninstallation = []
-                for repository_id in tsridslist:
-                    repository = trans.install_model.context.query(trans.install_model.ToolShedRepository) \
-                                                            .get(trans.security.decode_id(repository_id))
-                    if repository.status in [trans.install_model.ToolShedRepository.installation_status.INSTALLED,
-                                             trans.install_model.ToolShedRepository.installation_status.ERROR]:
-                        repositories_for_uninstallation.append(repository)
-                if repositories_for_uninstallation:
-                    return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
-                                                                    action='uninstall_repositories',
-                                                                    **kwd))
-                else:
-                    kwd['message'] = 'All selected tool shed repositories are already uninstalled.'
-                    kwd['status'] = 'error'
-            elif operation == "install":
-                irm = install_manager.InstallRepositoryManager(trans.app)
-                reinstalling = util.string_as_bool(kwd.get('reinstalling', False))
-                encoded_kwd = kwd['encoded_kwd']
-                decoded_kwd = encoding_util.tool_shed_decode(encoded_kwd)
-                install_resolver_dependencies = CheckboxField.is_checked(decoded_kwd.get('install_resolver_dependencies', ''))
-                install_tool_dependencies = CheckboxField.is_checked(decoded_kwd.get('install_tool_dependencies', ''))
-                tsr_ids = decoded_kwd['tool_shed_repository_ids']
-                decoded_kwd['install_resolver_dependencies'] = install_resolver_dependencies
-                decoded_kwd['install_tool_dependencies'] = install_tool_dependencies
-                try:
-                    tool_shed_repositories = irm.install_repositories(
-                        tsr_ids=tsr_ids,
-                        decoded_kwd=decoded_kwd,
-                        reinstalling=reinstalling,
-                    )
-                    tsr_ids_for_monitoring = [trans.security.encode_id(tsr.id) for tsr in tool_shed_repositories]
-                    if api_installation:
-                        return json.dumps(tsr_ids_for_monitoring)
-                    else:
-                        trans.response.send_redirect(web.url_for(controller='admin_toolshed',
-                                                                 action='monitor_repository_installation',
-                                                                 tool_shed_repository_ids=tsr_ids_for_monitoring))
-                except install_manager.RepositoriesInstalledException as e:
-                    kwd['message'] = e.message
-                    kwd['status'] = 'error'
-        return self.repository_installation_grid(trans, **kwd)
+    def install_repositories(self, trans, **kwd):
+        reinstalling = util.string_as_bool(kwd.get('reinstalling', False))
+        encoded_kwd = kwd.get('encoded_kwd')
+        decoded_kwd = encoding_util.tool_shed_decode(encoded_kwd) if encoded_kwd else {}
+        install_resolver_dependencies = CheckboxField.is_checked(decoded_kwd.get('install_resolver_dependencies', ''))
+        install_tool_dependencies = CheckboxField.is_checked(decoded_kwd.get('install_tool_dependencies', ''))
+        decoded_kwd['install_resolver_dependencies'] = install_resolver_dependencies
+        decoded_kwd['install_tool_dependencies'] = install_tool_dependencies
+        tsr_ids = decoded_kwd.get('tool_shed_repository_ids')
+        if not tsr_ids:
+            return self.message_exception(trans, 'Repository ids missing.')
+        irm = install_manager.InstallRepositoryManager(trans.app)
+        try:
+            tool_shed_repositories = irm.install_repositories(
+                tsr_ids=tsr_ids,
+                decoded_kwd=decoded_kwd,
+                reinstalling=reinstalling,
+            )
+            tsr_ids_for_monitoring = [trans.security.encode_id(tsr.id) for tsr in tool_shed_repositories]
+            return json.dumps(tsr_ids_for_monitoring)
+        except install_manager.RepositoriesInstalledException as e:
+            return self.message_exception(trans, e.message)
 
     @web.expose
     @web.require_admin
@@ -784,15 +738,6 @@ class AdminToolshed(AdminGalaxy):
         status = kwd.get('status', 'done')
         tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids(as_string=False, **kwd)
         repository_id = kwd.get('repository_id', None)
-        if tool_dependency_ids:
-            # We need a tool_shed_repository, so get it from one of the tool_dependencies.
-            tool_dependency = tool_dependency_util.get_tool_dependency(trans.app, tool_dependency_ids[0])
-            tool_shed_repository = tool_dependency.tool_shed_repository
-        else:
-            # The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a
-            # tool dependency, but they didn't check any of the available tool dependencies on which to perform the action.
-            tool_shed_repository = repository_util.get_tool_shed_repository_by_id(trans.app, repository_id)
-        self.tool_dependency_grid.title = "Tool shed repository '%s' tool dependencies" % escape(tool_shed_repository.name)
         if 'operation' in kwd:
             operation = kwd['operation'].lower()
             if not tool_dependency_ids:
@@ -828,9 +773,6 @@ class AdminToolshed(AdminGalaxy):
                     message += ' and restart your Galaxy server to install tool dependencies.'
                     kwd['message'] = message
                     kwd['status'] = 'error'
-        # Redirect if no tool dependencies are in the process of being installed.
-        if tool_shed_repository.tool_dependencies_being_installed:
-            return self.tool_dependency_grid(trans, **kwd)
         return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
                                                         action='manage_repository_tool_dependencies',
                                                         tool_dependency_ids=tool_dependency_ids,
@@ -841,11 +783,23 @@ class AdminToolshed(AdminGalaxy):
     @web.expose
     @web.require_admin
     def monitor_repository_installation(self, trans, **kwd):
-        tsridslist = common_util.get_tool_shed_repository_ids(**kwd)
-        if not tsridslist:
-            tsridslist = repository_util.get_ids_of_tool_shed_repositories_being_installed(trans.app, as_string=False)
-        kwd['tool_shed_repository_ids'] = tsridslist
-        return self.repository_installation_grid(trans, **kwd)
+        tsr_ids = common_util.get_tool_shed_repository_ids(**kwd)
+        if not tsr_ids:
+            tsr_ids = repository_util.get_ids_of_tool_shed_repositories_being_installed(trans.app, as_string=False)
+        tsr_ids = [trans.security.decode_id(tsr_id) for tsr_id in tsr_ids]
+        tool_shed_repositories = []
+        for tsr_id in tsr_ids:
+            tsr = trans.install_model.context.query(trans.install_model.ToolShedRepository).get(tsr_id)
+            tool_shed_repositories.append(tsr)
+        clause_list = []
+        for tsr_id in tsr_ids:
+            clause_list.append(trans.install_model.ToolShedRepository.table.c.id == tsr_id)
+        query = trans.install_model.context.current.query(trans.install_model.ToolShedRepository).filter(or_(*clause_list))
+        return trans.fill_template('admin/tool_shed_repository/monitor_repository_installation.mako',
+                                   tool_shed_repositories=tool_shed_repositories,
+                                   query=query,
+                                   message=escape(kwd.get('message', '')),
+                                   status=kwd.get('status'))
 
     @web.json
     @web.require_admin
@@ -992,20 +946,19 @@ class AdminToolshed(AdminGalaxy):
                                          tool_panel_section_keys=tool_panel_section_keys,
                                          tool_path=tool_path,
                                          tool_shed_url=tool_shed_url)
-
                 encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \
                     install_repository_manager.initiate_repository_installation(installation_dict)
-                return trans.fill_template('admin/tool_shed_repository/initiate_repository_installation.mako',
+                return trans.fill_template('admin/tool_shed_repository/monitor_repository_installation.mako',
                                            encoded_kwd=encoded_kwd,
                                            query=query,
                                            tool_shed_repositories=tool_shed_repositories,
                                            initiate_repository_installation_ids=encoded_repository_ids,
                                            reinstalling=False)
             else:
-                kwd['message'] = message
+                kwd['message'] = message if message else 'Repository has already been installed.'
                 kwd['status'] = status
                 return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
-                                                                action='manage_repositories',
+                                                                action='monitor_repository_installation',
                                                                 **kwd))
         shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field(trans.app)
         tool_path = suc.get_tool_path_by_shed_tool_conf_filename(trans.app, shed_tool_conf)
@@ -1311,7 +1264,7 @@ class AdminToolshed(AdminGalaxy):
             clause_list.append(trans.install_model.ToolShedRepository.table.c.id == tsr_id)
         query = trans.install_model.context.current.query(trans.install_model.ToolShedRepository) \
                                            .filter(or_(*clause_list))
-        return trans.fill_template('admin/tool_shed_repository/initiate_repository_installation.mako',
+        return trans.fill_template('admin/tool_shed_repository/monitor_repository_installation.mako',
                                    encoded_kwd=encoded_kwd,
                                    query=query,
                                    tool_shed_repositories=tool_shed_repositories,

lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py

@@ -1,12 +1,10 @@
 import logging
 
-from sqlalchemy import false, or_
-
 from galaxy import util
 from galaxy.model import tool_shed_install
 from galaxy.web import url_for
 from galaxy.web.framework.helpers import grids, iff
-from tool_shed.util import repository_util, tool_dependency_util
+from tool_shed.util import repository_util
 
 log = logging.getLogger(__name__)
 
@@ -236,192 +234,3 @@ class InstalledRepositoryGrid(grids.Grid):
         legend_str += '%s&nbsp;&nbsp;This repository contains exported workflows<br/>' % generate_includes_workflows_img_str()
         legend_str += '%s&nbsp;&nbsp;Unable to get information from the Tool Shed<br/>' % generate_unknown_img_str()
         return legend_str
-
-
-class RepositoryInstallationGrid(grids.Grid):
-
-    class NameColumn(grids.TextColumn):
-
-        def get_value(self, trans, grid, tool_shed_repository):
-            return tool_shed_repository.name
-
-    class DescriptionColumn(grids.TextColumn):
-
-        def get_value(self, trans, grid, tool_shed_repository):
-            return tool_shed_repository.description
-
-    class OwnerColumn(grids.TextColumn):
-
-        def get_value(self, trans, grid, tool_shed_repository):
-            return tool_shed_repository.owner
-
-    class RevisionColumn(grids.TextColumn):
-
-        def get_value(self, trans, grid, tool_shed_repository):
-            return tool_shed_repository.changeset_revision
-
-    class StatusColumn(grids.TextColumn):
-
-        def get_value(self, trans, grid, tool_shed_repository):
-            status_label = tool_shed_repository.status
-            if tool_shed_repository.status in [trans.install_model.ToolShedRepository.installation_status.CLONING,
-                                               trans.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS,
-                                               trans.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
-                                               trans.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES]:
-                bgcolor = trans.install_model.ToolShedRepository.states.INSTALLING
-            elif tool_shed_repository.status in [trans.install_model.ToolShedRepository.installation_status.NEW,
-                                                 trans.install_model.ToolShedRepository.installation_status.UNINSTALLED]:
-                bgcolor = trans.install_model.ToolShedRepository.states.UNINSTALLED
-            elif tool_shed_repository.status in [trans.install_model.ToolShedRepository.installation_status.ERROR]:
-                bgcolor = trans.install_model.ToolShedRepository.states.ERROR
-            elif tool_shed_repository.status in [trans.install_model.ToolShedRepository.installation_status.DEACTIVATED]:
-                bgcolor = trans.install_model.ToolShedRepository.states.WARNING
-            elif tool_shed_repository.status in [trans.install_model.ToolShedRepository.installation_status.INSTALLED]:
-                if tool_shed_repository.missing_tool_dependencies or tool_shed_repository.missing_repository_dependencies:
-                    bgcolor = trans.install_model.ToolShedRepository.states.WARNING
-                if tool_shed_repository.missing_tool_dependencies and not tool_shed_repository.missing_repository_dependencies:
-                    status_label = '%s, missing tool dependencies' % status_label
-                if tool_shed_repository.missing_repository_dependencies and not tool_shed_repository.missing_tool_dependencies:
-                    status_label = '%s, missing repository dependencies' % status_label
-                if tool_shed_repository.missing_tool_dependencies and tool_shed_repository.missing_repository_dependencies:
-                    status_label = '%s, missing both tool and repository dependencies' % status_label
-                if not tool_shed_repository.missing_tool_dependencies and not tool_shed_repository.missing_repository_dependencies:
-                    bgcolor = trans.install_model.ToolShedRepository.states.OK
-            else:
-                bgcolor = trans.install_model.ToolShedRepository.states.ERROR
-            rval = '<div class="count-box state-color-%s" id="RepositoryStatus-%s">%s</div>' % \
-                (bgcolor, trans.security.encode_id(tool_shed_repository.id), status_label)
-            return rval
-
-    title = "Monitor installing tool shed repositories"
-    template = "admin/tool_shed_repository/repository_installation_grid.mako"
-    model_class = tool_shed_install.ToolShedRepository
-    default_sort_key = "-create_time"
-    num_rows_per_page = 50
-    preserve_state = True
-    use_paging = False
-    columns = [
-        NameColumn("Name",
-                   link=(lambda item: iff(item.status in
-                                          [tool_shed_install.ToolShedRepository.installation_status.NEW,
-                                           tool_shed_install.ToolShedRepository.installation_status.CLONING,
-                                           tool_shed_install.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS,
-                                           tool_shed_install.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
-                                           tool_shed_install.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
-                                           tool_shed_install.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES,
-                                           tool_shed_install.ToolShedRepository.installation_status.UNINSTALLED],
-                                          None, dict(action="manage_repository", id=item.id))),
-                   filterable="advanced"),
-        DescriptionColumn("Description",
-                    filterable="advanced"),
-        OwnerColumn("Owner",
-                    filterable="advanced"),
-        RevisionColumn("Revision",
-                    filterable="advanced"),
-        StatusColumn("Installation Status",
-                     filterable="advanced",
-                     label_id_prefix="RepositoryStatus-")
-    ]
-    operations = []
-
-    def build_initial_query(self, trans, **kwd):
-        clause_list = []
-        tool_shed_repository_ids = util.listify(kwd.get('tool_shed_repository_ids', None))
-        if tool_shed_repository_ids:
-            for tool_shed_repository_id in tool_shed_repository_ids:
-                clause_list.append(self.model_class.table.c.id == trans.security.decode_id(tool_shed_repository_id))
-            if clause_list:
-                return trans.install_model.context.query(self.model_class) \
-                                                  .filter(or_(*clause_list))
-        for tool_shed_repository in trans.install_model.context.query(self.model_class) \
-                                                               .filter(self.model_class.table.c.deleted == false()):
-            if tool_shed_repository.status in [trans.install_model.ToolShedRepository.installation_status.NEW,
-                                               trans.install_model.ToolShedRepository.installation_status.CLONING,
-                                               trans.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS,
-                                               trans.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
-                                               trans.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES]:
-                clause_list.append(self.model_class.table.c.id == tool_shed_repository.id)
-        if clause_list:
-            return trans.install_model.context.query(self.model_class) \
-                                              .filter(or_(*clause_list))
-        return trans.install_model.context.query(self.model_class) \
-                                          .filter(self.model_class.table.c.status == trans.install_model.ToolShedRepository.installation_status.NEW)
-
-    def apply_query_filter(self, trans, query, **kwd):
-        tool_shed_repository_id = kwd.get('tool_shed_repository_id', None)
-        if tool_shed_repository_id:
-            return query.filter_by(tool_shed_repository_id=trans.security.decode_id(tool_shed_repository_id))
-        return query
-
-
-class ToolDependencyGrid(grids.Grid):
-
-    class NameColumn(grids.TextColumn):
-
-        def get_value(self, trans, grid, tool_dependency):
-            return tool_dependency.name
-
-    class VersionColumn(grids.TextColumn):
-
-        def get_value(self, trans, grid, tool_dependency):
-            return tool_dependency.version
-
-    class TypeColumn(grids.TextColumn):
-
-        def get_value(self, trans, grid, tool_dependency):
-            return tool_dependency.type
-
-    class StatusColumn(grids.TextColumn):
-
-        def get_value(self, trans, grid, tool_dependency):
-            if tool_dependency.status in [trans.install_model.ToolDependency.installation_status.INSTALLING]:
-                bgcolor = trans.install_model.ToolDependency.states.INSTALLING
-            elif tool_dependency.status in [trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
-                                            trans.install_model.ToolDependency.installation_status.UNINSTALLED]:
-                bgcolor = trans.install_model.ToolDependency.states.UNINSTALLED
-            elif tool_dependency.status in [trans.install_model.ToolDependency.installation_status.ERROR]:
-                bgcolor = trans.install_model.ToolDependency.states.ERROR
-            elif tool_dependency.status in [trans.install_model.ToolDependency.installation_status.INSTALLED]:
-                bgcolor = trans.install_model.ToolDependency.states.OK
-            rval = '<div class="count-box state-color-%s" id="ToolDependencyStatus-%s">%s</div>' % \
-                (bgcolor, trans.security.encode_id(tool_dependency.id), tool_dependency.status)
-            return rval
-
-    title = "Tool Dependencies"
-    template = "admin/tool_shed_repository/tool_dependencies_grid.mako"
-    model_class = tool_shed_install.ToolDependency
-    default_sort_key = "-create_time"
-    num_rows_per_page = 50
-    preserve_state = True
-    use_paging = False
-    columns = [
-        NameColumn("Name",
-                   link=(lambda item: iff(item.status in [tool_shed_install.ToolDependency.installation_status.NEVER_INSTALLED,
-                                                          tool_shed_install.ToolDependency.installation_status.INSTALLING,
-                                                          tool_shed_install.ToolDependency.installation_status.UNINSTALLED],
-                                          None,
-                                          dict(action="manage_tool_dependencies", operation='browse', id=item.id))),
-                   filterable="advanced"),
-        VersionColumn("Version",
-                      filterable="advanced"),
-        TypeColumn("Type",
-                   filterable="advanced"),
-        StatusColumn("Installation Status",
-                     filterable="advanced"),
-    ]
-
-    def build_initial_query(self, trans, **kwd):
-        tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids(as_string=False, **kwd)
-        if tool_dependency_ids:
-            clause_list = []
-            for tool_dependency_id in tool_dependency_ids:
-                clause_list.append(self.model_class.table.c.id == trans.security.decode_id(tool_dependency_id))
-            return trans.install_model.context.query(self.model_class) \
-                                              .filter(or_(*clause_list))
-        return trans.install_model.context.query(self.model_class)
-
-    def apply_query_filter(self, trans, query, **kwd):
-        tool_dependency_id = kwd.get('tool_dependency_id', None)
-        if tool_dependency_id:
-            return query.filter_by(tool_dependency_id=trans.security.decode_id(tool_dependency_id))
-        return query

static/scripts/mvc/toolshed/repository-queue-view.js

@@ -1,2 +1,2 @@
-"use strict";define(["mvc/toolshed/toolshed-model","mvc/toolshed/util"],function(e,t){return{RepoQueueView:Backbone.View.extend({el:"#center",defaults:[{}],initialize:function(t){var o=this;this.model=new e.RepoQueue,this.listenTo(this.model,"sync",this.render),this.model.fetch(),o.render()},render:function(e){var o=this,i=o.templateRepoQueue,r=o.model.models;o.$el.html(i({title:"Repository Installation Queue",repositories:r,queue:t.queueLength()})),$("#center").css("overflow","auto"),o.bindEvents()},bindEvents:function(){var e=this;$(".install_one").on("click",function(){var t=e.loadFromQueue($(this).attr("data-repokey"));e.installFromQueue(t,$(this).attr("data-repokey"))}),$(".remove_one").on("click",function(){var e=$(this).attr("data-repokey"),t=JSON.parse(localStorage.repositories);if(t.hasOwnProperty(e)){var o=t[e].repository.id;delete t[e],$("#queued_repository_"+o).remove()}localStorage.repositories=JSON.stringify(t)}),$("#clear_queue").on("click",function(){localStorage.repositories="{}"}),$("#from_workflow").on("click",function(){Backbone.history.navigate("workflows",{trigger:!0,replace:!0})})},installFromQueue:function(e,o){var i=Object();i.install_tool_dependencies=e.install_tool_dependencies,i.install_repository_dependencies=e.install_repository_dependencies,i.install_resolver_dependencies=e.install_resolver_dependencies,i.tool_panel_section=e.tool_panel_section,i.shed_tool_conf=e.shed_tool_conf,i.repositories=JSON.stringify([[e.repository.id,e.changeset_revision]]),i.tool_shed_repository_ids=JSON.stringify([e.repository.id]),i.tool_shed_url=o.split("|")[0],i.changeset=e.changeset_revision;var r=Galaxy.root+"api/tool_shed_repositories/install?async=True";if($("#queued_repository_"+e.repository.id).remove(),localStorage.repositories){void 0===o&&(o=t.queueKey(e));var s=JSON.parse(localStorage.repositories);s.hasOwnProperty(o)&&(delete s[o],localStorage.repositories=JSON.stringify(s))}$.post(r,i,function(e){var t=JSON.parse(e),o="status/r/"+t.repositories.join("|");$.post(Galaxy.root+"admin_toolshed/manage_repositories",t,function(e){console.log("Initializing repository installation succeeded")}),Backbone.history.navigate(o,{trigger:!0,replace:!0})})},loadFromQueue:function(e){var t=JSON.parse(localStorage.repositories);if(t.hasOwnProperty(e))return t[e]},reDraw:function(e){this.$el.empty(),this.initialize(e),this.model.fetch(),this.render(e)},templateRepoQueue:_.template(['<div class="unified-panel-header" id="panel_header" unselectable="on">','<div class="unified-panel-header-inner"><%= title %></div>','<div class="unified-panel-header-inner" style="position: absolute; right: 5px; top: 0px;"><a href="#/queue">Repository Queue (<%= queue %>)</a></div>',"</div>",'<div class="tab-pane" id="panel_header" id="repository_queue">','<table id="queued_repositories" class="grid" border="0" cellpadding="2" cellspacing="2" width="100%">','<thead id="grid-table-header">',"<tr>",'<th class="datasetRow">Name</th>','<th class="datasetRow">Owner</th>','<th class="datasetRow">Revision</th>','<th class="datasetRow">ToolShed</th>','<th class="datasetRow">Install</th>','<th class="datasetRow"><input class="btn btn-primary" type="submit" id="clear_queue" name="clear_queue" value="Clear queue" /></th>',"</tr>","</thead>","<tbody>","<% _.each(repositories, function(repository) { %>",'<tr id="queued_repository_<%= repository.get("id") %>">','<td class="datasetRow"><%= repository.get("repository").name %></td>','<td class="datasetRow"><%= repository.get("repository").owner %></td>','<td class="datasetRow"><%= repository.get("changeset_revision") %></td>','<td class="datasetRow"><%= repository.get("tool_shed_url") %></td>','<td class="datasetRow">','<input class="btn btn-primary install_one" data-repokey="<%= repository.get("queue_key") %>" type="submit" id="install_repository_<%= repository.get("id") %>" name="install_repository" value="Install now" />',"</td>",'<td class="datasetRow">','<input class="btn btn-primary remove_one" data-repokey="<%= repository.get("queue_key") %>" type="submit" id="unqueue_repository_<%= repository.get("id") %>" name="unqueue_repository" value="Remove from queue" />',"</td>","</tr>","<% }); %>","</tbody>","</table>",'<input type="button" class="btn btn-primary" id="from_workflow" value="Add from workflow" />',"</div>"].join(""))})}});
+"use strict";define(["mvc/toolshed/toolshed-model","mvc/toolshed/util"],function(e,t){return{RepoQueueView:Backbone.View.extend({el:"#center",defaults:[{}],initialize:function(t){var o=this;this.model=new e.RepoQueue,this.listenTo(this.model,"sync",this.render),this.model.fetch(),o.render()},render:function(e){var o=this,i=o.templateRepoQueue,s=o.model.models;o.$el.html(i({title:"Repository Installation Queue",repositories:s,queue:t.queueLength()})),$("#center").css("overflow","auto"),o.bindEvents()},bindEvents:function(){var e=this;$(".install_one").on("click",function(){var t=e.loadFromQueue($(this).attr("data-repokey"));e.installFromQueue(t,$(this).attr("data-repokey"))}),$(".remove_one").on("click",function(){var e=$(this).attr("data-repokey"),t=JSON.parse(localStorage.repositories);if(t.hasOwnProperty(e)){var o=t[e].repository.id;delete t[e],$("#queued_repository_"+o).remove()}localStorage.repositories=JSON.stringify(t)}),$("#clear_queue").on("click",function(){localStorage.repositories="{}"}),$("#from_workflow").on("click",function(){Backbone.history.navigate("workflows",{trigger:!0,replace:!0})})},installFromQueue:function(e,o){var i=Object();i.install_tool_dependencies=e.install_tool_dependencies,i.install_repository_dependencies=e.install_repository_dependencies,i.install_resolver_dependencies=e.install_resolver_dependencies,i.tool_panel_section=e.tool_panel_section,i.shed_tool_conf=e.shed_tool_conf,i.repositories=JSON.stringify([[e.repository.id,e.changeset_revision]]),i.tool_shed_repository_ids=JSON.stringify([e.repository.id]),i.tool_shed_url=o.split("|")[0],i.changeset=e.changeset_revision;var s=Galaxy.root+"api/tool_shed_repositories/install?async=True";if($("#queued_repository_"+e.repository.id).remove(),localStorage.repositories){void 0===o&&(o=t.queueKey(e));var r=JSON.parse(localStorage.repositories);r.hasOwnProperty(o)&&(delete r[o],localStorage.repositories=JSON.stringify(r))}$.post(s,i,function(e){var t=JSON.parse(e),o="status/r/"+t.repositories.join("|");$.post(Galaxy.root+"admin_toolshed/install_repositories",t,function(e){console.log("Initializing repository installation succeeded")}),Backbone.history.navigate(o,{trigger:!0,replace:!0})})},loadFromQueue:function(e){var t=JSON.parse(localStorage.repositories);if(t.hasOwnProperty(e))return t[e]},reDraw:function(e){this.$el.empty(),this.initialize(e),this.model.fetch(),this.render(e)},templateRepoQueue:_.template(['<div class="unified-panel-header" id="panel_header" unselectable="on">','<div class="unified-panel-header-inner"><%= title %></div>','<div class="unified-panel-header-inner" style="position: absolute; right: 5px; top: 0px;"><a href="#/queue">Repository Queue (<%= queue %>)</a></div>',"</div>",'<div class="tab-pane" id="panel_header" id="repository_queue">','<table id="queued_repositories" class="grid" border="0" cellpadding="2" cellspacing="2" width="100%">','<thead id="grid-table-header">',"<tr>",'<th class="datasetRow">Name</th>','<th class="datasetRow">Owner</th>','<th class="datasetRow">Revision</th>','<th class="datasetRow">ToolShed</th>','<th class="datasetRow">Install</th>','<th class="datasetRow"><input class="btn btn-primary" type="submit" id="clear_queue" name="clear_queue" value="Clear queue" /></th>',"</tr>","</thead>","<tbody>","<% _.each(repositories, function(repository) { %>",'<tr id="queued_repository_<%= repository.get("id") %>">','<td class="datasetRow"><%= repository.get("repository").name %></td>','<td class="datasetRow"><%= repository.get("repository").owner %></td>','<td class="datasetRow"><%= repository.get("changeset_revision") %></td>','<td class="datasetRow"><%= repository.get("tool_shed_url") %></td>','<td class="datasetRow">','<input class="btn btn-primary install_one" data-repokey="<%= repository.get("queue_key") %>" type="submit" id="install_repository_<%= repository.get("id") %>" name="install_repository" value="Install now" />',"</td>",'<td class="datasetRow">','<input class="btn btn-primary remove_one" data-repokey="<%= repository.get("queue_key") %>" type="submit" id="unqueue_repository_<%= repository.get("id") %>" name="unqueue_repository" value="Remove from queue" />',"</td>","</tr>","<% }); %>","</tbody>","</table>",'<input type="button" class="btn btn-primary" id="from_workflow" value="Add from workflow" />',"</div>"].join(""))})}});
 //# sourceMappingURL=../../../maps/mvc/toolshed/repository-queue-view.js.map

templates/admin/tool_shed_repository/monitor_repository_installation.mako

@@ -1,4 +1,5 @@
 <%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
 <%namespace file="/admin/tool_shed_repository/common.mako" import="*" />
 
 <%def name="javascripts()">
@@ -10,24 +11,30 @@
 
 <%def name="repository_installation_javascripts()">
     <script type="text/javascript">
-        $(document).ready(function( ){
-            initiate_repository_installation( "${initiate_repository_installation_ids}", "${encoded_kwd}", "${reinstalling}" );
-        });
+        %if context.get("initiate_repository_installation_ids"):
+            $(document).ready(function( ){
+                initiate_repository_installation( "${initiate_repository_installation_ids}", "${encoded_kwd}", "${reinstalling}" );
+            });
+        %endif
         var initiate_repository_installation = function ( iri_ids, encoded_kwd, reinstalling ) {
             // Make ajax call
             $.ajax( {
                 type: "POST",
-                url: "${h.url_for( controller='admin_toolshed', action='manage_repositories' )}",
+                url: "${h.url_for( controller='admin_toolshed', action='install_repositories' )}",
                 dataType: "html",
-                data: { operation: "install", tool_shed_repository_ids: iri_ids, encoded_kwd: encoded_kwd, reinstalling: reinstalling },
+                data: { tool_shed_repository_ids: iri_ids, encoded_kwd: encoded_kwd, reinstalling: reinstalling },
                 success : function ( data ) {
                     console.log( "Initializing repository installation succeeded" );
-                },
+                }
             });
         };
     </script>
 </%def>
 
+%if context.get("message"):
+    ${render_msg( message, status )}
+%endif
+
 %if tool_shed_repositories:
     <div class="toolForm">
         <div class="toolFormTitle">Monitor installing tool shed repositories</div>
@@ -68,4 +75,6 @@
             <br clear="left"/>
         </div>
     </div>
+%else:
+    ${render_msg("There is no repository being installed.", "info")}
 %endif

templates/admin/tool_shed_repository/repository_installation_grid.mako

@@ -1,8 +0,0 @@
-<%inherit file="/grid_base.mako"/>
-<%namespace file="/admin/tool_shed_repository/common.mako" import="*" />
-
-<%def name="javascripts()">
-   ${parent.javascripts()}
-   ${repository_installation_status_updater()}
-   ${repository_installation_updater()}
-</%def>

templates/admin/tool_shed_repository/tool_dependencies_grid.mako

@@ -1,8 +0,0 @@
-<%inherit file="/grid_base.mako"/>
-<%namespace file="/admin/tool_shed_repository/common.mako" import="*" />
-
-<%def name="javascripts()">
-   ${parent.javascripts()}
-   ${dependency_status_updater()}
-   ${tool_dependency_installation_updater()}
-</%def>

test/shed_functional/base/twilltestcase.py

@@ -921,7 +921,7 @@ class ShedTwillTestCase(TwillTestCase):
             repository_ids = re.sub('[^a-fA-F0-9,]+', '', repository_ids)
             encoded_kwd = install_parameters.group(2)
             reinstalling = install_parameters.group(3)
-            url = '/admin_toolshed/manage_repositories?operation=install&tool_shed_repository_ids=%s&encoded_kwd=%s&reinstalling=%s' % \
+            url = '/admin_toolshed/install_repositories?tool_shed_repository_ids=%s&encoded_kwd=%s&reinstalling=%s' % \
                 (','.join(galaxy.util.listify(repository_ids)), encoded_kwd, reinstalling)
             self.visit_galaxy_url(url)
             return galaxy.util.listify(repository_ids)