Merge remote-tracking branch 'upstream/dev' into cloud_download_tool

# Conflicts:
#	lib/galaxy/managers/cloud.py
#	lib/galaxy/webapps/galaxy/api/cloud.py

.ci/jenkins/api-py3/run_tests.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --skip_flakey_fails -api "$@"

.ci/jenkins/framework-py3/run_tests.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --framework "$@"

.ci/jenkins/integration-py3/run_tests.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --integration "$@"

.ci/jenkins/main-tools-py3/run_tests.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+./run_tests.sh --dockerize --python3 --db postgres --clean_pyc -main "$@"

.ci/jenkins/main-tools/run_tests.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+./run_tests.sh --dockerize --db postgres --external_tmp --clean_pyc -main "$@"

.ci/jenkins/selenium-py3/run_tests.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+
+# Enable retries on tests to reduce chances of transient failures.
+: ${GALAXY_TEST_SELENIUM_RETRIES:=1}
+: ${GALAXY_TEST_CLIENT_BUILD_IMAGE:='node:9.4.0'}
+
+# If in Jenkins environment, use it for artifacts.
+if [ -n "$BUILD_NUMBER" ];
+then
+    : ${GALAXY_TEST_ERRORS_DIRECTORY:=${BUILD_NUMBER}-test-errors}
+    : ${GALAXY_TEST_SCREENSHOTS_DIRECTORY:=${BUILD_NUMBER}-test-screenshots}
+else
+    : ${GALAXY_TEST_ERRORS_DIRECTORY:=database/test-errors}
+    : ${GALAXY_TEST_SCREENSHOTS_DIRECTORY:=database/test-screenshots}
+fi
+
+mkdir -p "$GALAXY_TEST_ERRORS_DIRECTORY"
+mkdir -p "$GALAXY_TEST_SCREENSHOTS_DIRECTORY"
+
+mkdir -p ~/.jenkins-yarn-cache
+YARN_CACHE_FOLDER=~/.jenkins-yarn-cache
+
+# Set git environment variables to enable Git. https://github.com/galaxyproject/galaxy/issues/5912
+# Setup volume and environment variable to cache this users yarn build.
+docker run -e GIT_COMMITTER_NAME=Jenkins -e GIT_COMMITTER_EMAIL=jenkins@galaxyproject.org \
+           -e YARN_CACHE_FOLDER=$YARN_CACHE_FOLDER -v $YARN_CACHE_FOLDER:$YARN_CACHE_FOLDER:rw \
+           -v `pwd`:`pwd`:rw -w `pwd` -u $UID $GALAXY_TEST_CLIENT_BUILD_IMAGE \
+           /bin/bash -c 'make client-production-maps'
+
+# Start Selenium server in the test Docker container.
+DOCKER_RUN_EXTRA_ARGS="-v $YARN_CACHE_FOLDER:$YARN_CACHE_FOLDER -e YARN_CACHE_FOLDER=$YARN_CACHE_FOLDER -e USE_SELENIUM=1 -e GALAXY_TEST_SELENIUM_RETRIES=${GALAXY_TEST_SELENIUM_RETRIES} -e GALAXY_TEST_ERRORS_DIRECTORY=${GALAXY_TEST_ERRORS_DIRECTORY} -e GALAXY_TEST_SCREENSHOTS_DIRECTORY=${GALAXY_TEST_SCREENSHOTS_DIRECTORY} ${DOCKER_RUN_EXTRA_ARGS}"
+export DOCKER_RUN_EXTRA_ARGS
+
+./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --skip_flakey_fails --selenium "$@"

.ci/jenkins/selenium/run_tests.sh

@@ -28,7 +28,7 @@ docker run -e GIT_COMMITTER_NAME=Jenkins -e GIT_COMMITTER_EMAIL=jenkins@galaxypr
            /bin/bash -c 'make client-production-maps'
 
 # Start Selenium server in the test Docker container.
-DOCKER_RUN_EXTRA_ARGS="-v $YARN_CACHE_FOLDER:$YARN_CACHE_FOLDER -e YARN_CACHE_FOLDER=$YARN_CACHE_FOLDER -e USE_SELENIUM=1 -e GALAXY_TEST_SELENIUM_RETRIES=${GALAXY_TEST_SELENIUM_RETRIES} -e GALAXY_TEST_ERRORS_DIRECTORY=${GALAXY_TEST_ERRORS_DIRECTORY} -e GALAXY_TEST_SCREENSHOTS_DIRECTORY=${GALAXY_TEST_SCREENSHOTS_DIRECTORY} ${DOCKER_RUN_EXTRA_ARGS}"
+DOCKER_RUN_EXTRA_ARGS="--shm-size=2g -v $YARN_CACHE_FOLDER:$YARN_CACHE_FOLDER -e YARN_CACHE_FOLDER=$YARN_CACHE_FOLDER -e USE_SELENIUM=1 -e GALAXY_TEST_SELENIUM_RETRIES=${GALAXY_TEST_SELENIUM_RETRIES} -e GALAXY_TEST_ERRORS_DIRECTORY=${GALAXY_TEST_ERRORS_DIRECTORY} -e GALAXY_TEST_SCREENSHOTS_DIRECTORY=${GALAXY_TEST_SCREENSHOTS_DIRECTORY} ${DOCKER_RUN_EXTRA_ARGS}"
 export DOCKER_RUN_EXTRA_ARGS
 
 ./run_tests.sh --dockerize --db postgres --external_tmp --clean_pyc --skip_flakey_fails --selenium "$@"

.coveragerc

@@ -1,3 +1,4 @@
 [run]
 branch = True
 include = lib/galaxy/*
+disable_warnings = include-ignored

.gitignore

@@ -99,9 +99,13 @@ tool-data/toolshed.g2.bx.psu.edu/
 tool-data/**/*.fa
 
 # Test output
+.pytest_cache/
+assets/
 test-data-cache
 run_framework_tests.html
 run_functional_tests.html
+run_integration_tests.html
+run_selenium_tests.html
 run_toolshed_tests.html
 run_api_tests.html
 test/tool_shed/tmp/*

.travis.yml

@@ -10,7 +10,6 @@ env:
   - TOX_ENV=qunit
   - TOX_ENV=py27-first_startup
   - TOX_ENV=py27-lint_docstring_include_list
-  - TOX_ENV=check_python_dependencies
 
 matrix:
   include:
@@ -33,9 +32,6 @@ matrix:
             - ack-grep
     - env: TOX_ENV=py34-unit
       addons: *py3_addons
-  allow_failures:
-    - env: TOX_ENV=check_python_dependencies
-
 
 install:
   - set -e

client/galaxy/docs/bootstrap.md

@@ -135,8 +135,8 @@ Disabled
 
 ```
 <div>
-  <span class="badge badge-default">Default</span>
   <span class="badge badge-primary">Primary</span>
+  <span class="badge badge-secondary">Secondary</span>
   <span class="badge badge-success">Success</span>
   <span class="badge badge-warning">Warning</span>
   <span class="badge badge-danger">Danger</span>

client/galaxy/scripts/admin.toolshed.js

@@ -1,10 +1,14 @@
+import * as Backbone from "backbone";
 import mod_shed_list_view from "mvc/toolshed/shed-list-view";
 import mod_categories_view from "mvc/toolshed/categories-view";
 import mod_repositories_view from "mvc/toolshed/repositories-view";
 import mod_repository_view from "mvc/toolshed/repository-view";
 import mod_repoqueue_view from "mvc/toolshed/repository-queue-view";
 import mod_repo_status_view from "mvc/toolshed/repo-status-view";
 import mod_workflows_view from "mvc/toolshed/workflows-view";
+
+/* global Galaxy */
+
 var AdminToolshedRouter = Backbone.Router.extend({
     initialize: function() {
         this.routesHit = 0;
@@ -48,81 +52,43 @@ var AdminToolshedRouter = Backbone.Router.extend({
 
 var GalaxyAdminToolshedApp = Backbone.View.extend({
     app_config: {
-        known_views: ["toolsheds", "queue", "status", "categories", "repositories", "repoository"]
+        known_views: ["toolsheds", "queue", "status", "categories", "repositories", "repository"]
     },
 
     initialize: function() {
         Galaxy.admintoolshedapp = this;
         this.admin_toolshed_router = new AdminToolshedRouter();
 
         this.admin_toolshed_router.on("route:queue", () => {
-            if (Galaxy.admintoolshedapp.adminRepoQueueView) {
-                Galaxy.admintoolshedapp.adminRepoQueueView.reDraw();
-            } else {
-                Galaxy.admintoolshedapp.adminRepoQueueView = new mod_repoqueue_view.RepoQueueView();
-            }
+            Galaxy.admintoolshedapp.adminRepoQueueView = new mod_repoqueue_view.RepoQueueView();
         });
         this.admin_toolshed_router.on("route:toolsheds", () => {
-            if (Galaxy.admintoolshedapp.adminShedListView) {
-                Galaxy.admintoolshedapp.adminShedListView.reDraw();
-            } else {
-                Galaxy.admintoolshedapp.adminShedListView = new mod_shed_list_view.ShedListView();
-            }
+            Galaxy.admintoolshedapp.adminShedListView = new mod_shed_list_view.ShedListView();
         });
         this.admin_toolshed_router.on("route:categories", tool_shed => {
-            if (Galaxy.admintoolshedapp.adminShedCategoriesView) {
-                Galaxy.admintoolshedapp.adminShedCategoriesView.reDraw({
-                    tool_shed: tool_shed.replace(/\//g, "%2f")
-                });
-            } else {
-                Galaxy.admintoolshedapp.adminShedCategoriesView = new mod_categories_view.CategoryView({
-                    tool_shed: tool_shed.replace(/\//g, "%2f")
-                });
-            }
+            Galaxy.admintoolshedapp.adminShedCategoriesView = new mod_categories_view.CategoryView({
+                tool_shed: tool_shed.replace(/\//g, "%2f")
+            });
         });
         this.admin_toolshed_router.on("route:repositories", (tool_shed, category_id) => {
-            if (Galaxy.admintoolshedapp.adminShedCategoryView) {
-                Galaxy.admintoolshedapp.adminShedCategoryView.reDraw({
-                    tool_shed: tool_shed.replace(/\//g, "%2f"),
-                    category_id: category_id
-                });
-            } else {
-                Galaxy.admintoolshedapp.adminShedCategoryView = new mod_repositories_view.Category({
-                    tool_shed: tool_shed.replace(/\//g, "%2f"),
-                    category_id: category_id
-                });
-            }
+            Galaxy.admintoolshedapp.adminShedCategoryView = new mod_repositories_view.Category({
+                tool_shed: tool_shed.replace(/\//g, "%2f"),
+                category_id: category_id
+            });
         });
         this.admin_toolshed_router.on("route:repository", (tool_shed, repository_id) => {
-            if (Galaxy.admintoolshedapp.adminRepositoryView) {
-                Galaxy.admintoolshedapp.adminRepositoryView.reDraw({
-                    tool_shed: tool_shed.replace(/\//g, "%2f"),
-                    repository_id: repository_id
-                });
-            } else {
-                Galaxy.admintoolshedapp.adminRepositoryView = new mod_repository_view.RepoDetails({
-                    tool_shed: tool_shed.replace(/\//g, "%2f"),
-                    repository_id: repository_id
-                });
-            }
+            Galaxy.admintoolshedapp.adminRepositoryView = new mod_repository_view.RepoDetails({
+                tool_shed: tool_shed.replace(/\//g, "%2f"),
+                repository_id: repository_id
+            });
         });
         this.admin_toolshed_router.on("route:status", repositories => {
-            if (Galaxy.admintoolshedapp.adminRepoStatusView) {
-                Galaxy.admintoolshedapp.adminRepoStatusView.reDraw({
-                    repositories: repositories.split("|")
-                });
-            } else {
-                Galaxy.admintoolshedapp.adminRepoStatusView = new mod_repo_status_view.RepoStatus({
-                    repositories: repositories.split("|")
-                });
-            }
+            Galaxy.admintoolshedapp.adminRepoStatusView = new mod_repo_status_view.RepoStatus({
+                repositories: repositories.split("|")
+            });
         });
         this.admin_toolshed_router.on("route:workflows", () => {
-            if (Galaxy.admintoolshedapp.adminWorkflowsView) {
-                Galaxy.admintoolshedapp.adminWorkflowsView.reDraw();
-            } else {
-                Galaxy.admintoolshedapp.adminWorkflowsView = new mod_workflows_view.Workflows();
-            }
+            Galaxy.admintoolshedapp.adminWorkflowsView = new mod_workflows_view.Workflows();
         });
 
         Backbone.history.start({ pushState: false });

client/galaxy/scripts/apps/admin.js

@@ -1,3 +1,5 @@
+import * as Backbone from "backbone";
+import * as _ from "underscore";
 import _l from "utils/localization";
 import jQuery from "jquery";
 var $ = jQuery;
@@ -13,13 +15,16 @@ import DataTables from "components/admin/DataTables.vue";
 import DataTypes from "components/admin/DataTypes.vue";
 import Vue from "vue";
 
+/* global Galaxy */
+
 window.app = function app(options, bootstrapped) {
     window.Galaxy = new GalaxyApp.GalaxyApp(options, bootstrapped);
     Galaxy.debug("admin app");
 
     /** Routes */
     var AdminRouter = Router.extend({
         routes: {
+            "(/)admin(/)": "home",
             "(/)admin(/)users": "show_users",
             "(/)admin(/)roles": "show_roles",
             "(/)admin(/)groups": "show_groups",
@@ -29,13 +34,24 @@ window.app = function app(options, bootstrapped) {
             "(/)admin(/)forms": "show_forms",
             "(/)admin(/)form(/)(:form_id)": "show_form",
             "(/)admin/data_tables": "show_data_tables",
-            "(/)admin/data_types": "show_data_types"
+            "(/)admin/data_types": "show_data_types",
+            "*notFound": "not_found"
         },
 
         authenticate: function() {
             return Galaxy.user && Galaxy.user.id && Galaxy.user.get("is_admin");
         },
 
+        not_found: function() {
+            window.location.href = window.location.href;
+        },
+
+        home: function() {
+            this.page
+                .$("#galaxy_main")
+                .prop("src", `${Galaxy.root}admin/center?message=${options.message}&status=${options.status}`);
+        },
+
         show_users: function() {
             this.page.display(
                 new GridView({

client/galaxy/scripts/apps/analysis.js

@@ -1,6 +1,7 @@
 import $ from "jquery";
 import "bootstrap";
 import * as _ from "underscore";
+import decodeUriComponent from "decode-uri-component";
 import GalaxyApp from "galaxy";
 import Router from "layout/router";
 import ToolPanel from "./panels/tool-panel";
@@ -357,7 +358,12 @@ window.app = function app(options, bootstrapped) {
         /** load the center panel with a tool form described by the given params obj */
         _loadToolForm: function(params) {
             //TODO: load tool form code async
-            params.id = decodeURIComponent(params.tool_id);
+            if (params.tool_id) {
+                params.id = decodeUriComponent(params.tool_id);
+            }
+            if (params.version) {
+                params.version = decodeUriComponent(params.version);
+            }
             this.page.display(new ToolForm.View(params));
         },
 

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

@@ -1,14 +1,18 @@
+import * as Backbone from "backbone";
+import * as _ from "underscore";
+
 import _l from "utils/localization";
 
+/* global Galaxy */
+/* global $ */
+
 var AdminPanel = Backbone.View.extend({
     initialize: function(page, options) {
         var self = this;
         this.page = page;
         this.root = options.root;
         this.config = options.config;
         this.settings = options.settings;
-        this.message = options.message;
-        this.status = options.status;
         this.model = new Backbone.Model({
             title: `Galaxy version ${Galaxy.config.version_major}`
         });
@@ -77,12 +81,6 @@ var AdminPanel = Backbone.View.extend({
                         title: _l("Forms"),
                         url: "admin/forms",
                         target: "__use_router__"
-                    },
-                    {
-                        title: _l("API keys"),
-                        url: "admin/api_keys",
-                        target: "__use_router__",
-                        id: "admin-link-api-keys"
                     }
                 ]
             },
@@ -147,7 +145,7 @@ var AdminPanel = Backbone.View.extend({
         this.$el.empty();
         this.categories.each(category => {
             var $section = $(self._templateSection(category.attributes));
-            var $entries = $section.find(".ui-side-section-body");
+            var $entries = $section.find(".toolSectionBody");
             _.each(category.get("items"), item => {
                 if (item.enabled === undefined || item.enabled) {
                     var $link = $("<a/>")
@@ -166,29 +164,24 @@ var AdminPanel = Backbone.View.extend({
                     }
                     $entries.append(
                         $("<div/>")
-                            .addClass("ui-side-section-body-title")
+                            .addClass("toolTitle")
                             .append($link)
                     );
                 }
             });
             self.$el.append($section);
         });
-        this.page
-            .$("#galaxy_main")
-            .prop("src", `${this.root}admin/center?message=${this.message}&status=${this.status}`);
     },
 
     _templateSection: function(options) {
-        return [
-            "<div>",
-            `<div class="ui-side-section-title">${_l(options.title)}</div>`,
-            '<div class="ui-side-section-body"/>',
-            "</div>"
-        ].join("");
+        return `<div class="toolSectionWrapper">
+                    <div class="toolSectionTitle">${_l(options.title)}</div>
+                    <div class="toolSectionBody"/>
+                </div>`;
     },
 
     _template: function() {
-        return '<div class="ui-side-panel"/>';
+        return '<div class="toolMenuContainer"/>';
     },
 
     toString: function() {

client/galaxy/scripts/components/Citations.vue

@@ -2,7 +2,7 @@
     <b-card>
         <h4 slot="header" class="mb-0">
             Citations
-            <b-button v-if="viewRender" @click="toggleViewRender" title="Show all in BibTeX format.">
+            <b-button v-if="viewRender" @click="toggleViewRender" title="Show all in BibTeX format." class="citations-to-bibtex">
                 <i class="fa fa-pencil-square-o"></i>
                 Show BibTeX
             </b-button>
@@ -20,7 +20,7 @@
             </p>
         </span>
         <pre v-else>
-            <code>
+            <code class="citations-bibtex">
                 {{ content }}
             </code>
         </pre>