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

client/galaxy/scripts/apps/analysis.js

@@ -76,7 +76,7 @@ window.app = function app(options, bootstrapped) {
 
         show_tours: function(tour_id) {
             if (tour_id) {
-                Tours.giveTour(tour_id);
+                Tours.giveTourById(tour_id);
             } else {
                 this.page.display(new Tours.ToursView());
             }

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

@@ -59,7 +59,7 @@ var ToolPanel = Backbone.View.extend({
         self.$("#internal-workflows").append(
             self._templateAllWorkflow({
                 title: _l("All workflows"),
-                href: "workflow"
+                href: "workflows/list"
             })
         );
         _.each(this.stored_workflow_menu_entries, menu_entry => {

client/galaxy/scripts/mvc/tours.js

@@ -4,7 +4,10 @@ import _l from "utils/localization";
  *  rendering a tour menu.
  */
 
-import * as BootstrapTour from "libs/bootstrap-tour";
+// bootstrap-tour configures a window.Tour object; keep a local ref.
+import "libs/bootstrap-tour";
+let Tour = window.Tour;
+
 var gxy_root = typeof Galaxy === "undefined" ? "/" : Galaxy.root;
 
 var tourpage_template = `<h2>Galaxy Tours</h2>
@@ -93,31 +96,8 @@ var Tours = Backbone.Collection.extend({
     model: TourItem
 });
 
-var giveTour = tour_id => {
-    var url = `${gxy_root}api/tours/${tour_id}`;
-    $.getJSON(url, data => {
-        // Set hooks for additional click and data entry actions.
-        var tourdata = hooked_tour_from_data(data);
-        sessionStorage.setItem("activeGalaxyTour", JSON.stringify(data));
-        // Store tour steps in sessionStorage to easily persist w/o hackery.
-        var tour = new Tour(
-            _.extend(
-                {
-                    steps: tourdata.steps
-                },
-                tour_opts
-            )
-        );
-        // Always clean restart, since this is a new, explicit giveTour execution.
-        tour.init();
-        tour.goTo(0);
-        tour.restart();
-    });
-};
-
-var ToursView = Backbone.View.extend({
+export var ToursView = Backbone.View.extend({
     title: _l("Tours"),
-    // initialize
     initialize: function() {
         var self = this;
         this.setElement("<div/>");
@@ -165,7 +145,7 @@ var ToursView = Backbone.View.extend({
             )
             .on("click", ".tourItem", function(e) {
                 e.preventDefault();
-                giveTour($(this).data("tour.id"));
+                giveTourById($(this).data("tour.id"));
             })
             .on("click", ".tag-selector-button", e => {
                 var elem = $(e.target);
@@ -183,9 +163,53 @@ var ToursView = Backbone.View.extend({
     }
 });
 
+export function giveTourWithData(data) {
+    let hookedTourData = hooked_tour_from_data(data);
+    sessionStorage.setItem("activeGalaxyTour", JSON.stringify(data));
+    // Store tour steps in sessionStorage to easily persist w/o hackery.
+    let tour = new Tour(_.extend({ steps: hookedTourData.steps }, tour_opts));
+    // Always clean restart, since this is a new, explicit execution.
+    tour.init();
+    tour.goTo(0);
+    tour.restart();
+    return tour;
+}
+
+export function giveTourById(tour_id) {
+    var url = `${gxy_root}api/tours/${tour_id}`;
+    $.getJSON(url, data => {
+        giveTourWithData(data);
+    });
+}
+
+export function activeGalaxyTourRunner() {
+    var et = JSON.parse(sessionStorage.getItem("activeGalaxyTour"));
+    if (et) {
+        et = hooked_tour_from_data(et);
+        if (et && et.steps) {
+            if (window && window.self === window.top) {
+                // Only kick off a new tour if this is the toplevel window (non-iframe).  This
+                // functionality actually *could* be useful, but we'd need to handle it better and
+                // come up with some design guidelines for tours jumping between windows.
+                // Disabling for now.
+                var tour = new Tour(
+                    _.extend(
+                        {
+                            steps: et.steps
+                        },
+                        tour_opts
+                    )
+                );
+                tour.init();
+                tour.restart();
+            }
+        }
+    }
+}
+
 export default {
     ToursView: ToursView,
-    hooked_tour_from_data: hooked_tour_from_data,
-    tour_opts: tour_opts,
-    giveTour: giveTour
+    giveTourWithData: giveTourWithData,
+    giveTourById: giveTourById,
+    activeGalaxyTourRunner: activeGalaxyTourRunner
 };

client/galaxy/scripts/mvc/workflow/workflow-canvas.js

@@ -106,7 +106,10 @@ $.extend(CanvasManager.prototype, {
             // If it appears that the user is trying to copy/paste text, we
             // pass that through.
             if (window.getSelection().toString() === "") {
-                if (this.app.workflow.active_node) {
+                if (
+                    this.app.workflow.active_node &&
+                    this.app.workflow.active_node.type !== "subworkflow"
+                ) {
                     e.clipboardData.setData(
                         "application/json",
                         JSON.stringify({

client/galaxy/scripts/mvc/workflow/workflow-terminals.js

@@ -8,10 +8,10 @@ function CollectionTypeDescription(collectionType) {
 
 var NULL_COLLECTION_TYPE_DESCRIPTION = {
     isCollection: false,
-    canMatch: function(other) {
+    canMatch: function() {
         return false;
     },
-    canMapOver: function(other) {
+    canMapOver: function() {
         return false;
     },
     toString: function() {
@@ -30,13 +30,13 @@ var ANY_COLLECTION_TYPE_DESCRIPTION = {
     canMatch: function(other) {
         return NULL_COLLECTION_TYPE_DESCRIPTION !== other;
     },
-    canMapOver: function(other) {
+    canMapOver: function() {
         return false;
     },
     toString: function() {
         return "AnyCollectionType[]";
     },
-    append: function(otherCollectionType) {
+    append: function() {
         throw "Cannot append to ANY_COLLECTION_TYPE_DESCRIPTION";
     },
     equal: function(other) {
@@ -50,7 +50,7 @@ $.extend(CollectionTypeDescription.prototype, {
             return this;
         }
         if (otherCollectionTypeDescription === ANY_COLLECTION_TYPE_DESCRIPTION) {
-            return otherCollectionType;
+            return otherCollectionTypeDescription;
         }
         return new CollectionTypeDescription(`${this.collectionType}:${otherCollectionTypeDescription.collectionType}`);
     },
@@ -143,7 +143,9 @@ var Terminal = Backbone.Model.extend({
     },
     destroyInvalidConnections: function() {
         _.each(this.connectors, connector => {
-            connector && connector.destroyIfInvalid();
+            if (connector) {
+                connector.destroyIfInvalid();
+            }
         });
     },
     setMapOver: function(val) {
@@ -258,7 +260,7 @@ var BaseInputTerminal = Terminal.extend({
                 if (this._collectionAttached()) {
                     // Can only attach one collection to multiple input
                     // data parameter.
-                    inputsFilled = true;
+                    inputFilled = true;
                 } else {
                     inputFilled = false;
                 }
@@ -317,17 +319,17 @@ var BaseInputTerminal = Terminal.extend({
             if (thisDatatype == "input") {
                 return true;
             }
-            var cat_outputs = new Array();
+            var cat_outputs = [];
             cat_outputs = cat_outputs.concat(other.datatypes);
             if (other.node.post_job_actions) {
                 for (var pja_i in other.node.post_job_actions) {
                     var pja = other.node.post_job_actions[pja_i];
                     if (
                         pja.action_type == "ChangeDatatypeAction" &&
-                        (pja.output_name == "" || pja.output_name == other.name) &&
+                        (pja.output_name === "" || pja.output_name == other.name) &&
                         pja.action_arguments
                     ) {
-                        cat_outputs.push(pja.action_arguments["newtype"]);
+                        cat_outputs.push(pja.action_arguments.newtype);
                     }
                 }
             }

client/galaxy/scripts/mvc/workflow/workflow-view.js

@@ -764,13 +764,15 @@ export default Backbone.View.extend({
         // Fix width to computed width
         // Now add floats
         var buttons = $("<div class='buttons' style='float: right;'></div>");
-        buttons.append(
-            $("<div/>")
-                .addClass("fa-icon-button fa fa-files-o")
-                .click(e => {
-                    node.clone();
-                })
-        );
+        if (type !== "subworkflow") {
+            buttons.append(
+                $("<div/>")
+                    .addClass("fa-icon-button fa fa-files-o")
+                    .click(e => {
+                        node.clone();
+                    })
+            );
+        }
         buttons.append(
             $("<div/>")
                 .addClass("fa-icon-button fa fa-times")

client/galaxy/scripts/onload.js

@@ -19,13 +19,12 @@ import layout_modal from "layout/modal";
 _.extend(window, layout_modal);
 import async_save_text from "utils/async-save-text";
 window.async_save_text = async_save_text;
-import POPUPMENU from "ui/popupmenu";
-window.make_popupmenu = POPUPMENU.make_popupmenu;
-window.make_popup_menus = POPUPMENU.make_popup_menus;
+import Popupmenu from "ui/popupmenu";
+window.make_popupmenu = Popupmenu.make_popupmenu;
+window.make_popup_menus = Popupmenu.make_popup_menus;
 import init_tag_click_function from "ui/autocom_tagging";
 window.init_tag_click_function = init_tag_click_function;
-import TOURS from "mvc/tours";
-import QUERY_STRING from "utils/query-string-parsing";
+import Tours from "mvc/tours";
 // console.debug( 'galaxy globals loaded' );
 
 // ============================================================================
@@ -89,10 +88,7 @@ function init_refresh_on_change() {
         .change(function() {
             var select_field = $(this);
             var select_val = select_field.val();
-            var refresh = false;
-
             var ref_on_change_vals = select_field.attr("refresh_on_change_values");
-
             if (ref_on_change_vals) {
                 ref_on_change_vals = ref_on_change_vals.split(",");
                 var last_selected_value = select_field.attr("last_selected_value");
@@ -114,10 +110,7 @@ function init_refresh_on_change() {
         .click(function() {
             var select_field = $(this);
             var select_val = select_field.val();
-            var refresh = false;
-
             var ref_on_change_vals = select_field.attr("refresh_on_change_values");
-
             if (ref_on_change_vals) {
                 ref_on_change_vals = ref_on_change_vals.split(",");
                 var last_selected_value = select_field.attr("last_selected_value");
@@ -156,7 +149,7 @@ $(document).ready(() => {
         $("[title]").tooltip();
     }
     // Make popup menus.
-    make_popup_menus();
+    Popupmenu.make_popup_menus();
 
     // Replace big selects.
     replace_big_select_inputs(20, 1500);
@@ -165,7 +158,7 @@ $(document).ready(() => {
     // add use_panels=True and set target to self.
     $("a").click(function() {
         var anchor = $(this);
-        var galaxy_main_exists = parent.frames && parent.frames.galaxy_main;
+        var galaxy_main_exists = window.parent.frames && window.parent.frames.galaxy_main;
         if (anchor.attr("target") == "galaxy_main" && !galaxy_main_exists) {
             var href = anchor.attr("href");
             if (href.indexOf("?") == -1) {
@@ -180,44 +173,26 @@ $(document).ready(() => {
         return anchor;
     });
 
-    var et = JSON.parse(sessionStorage.getItem("activeGalaxyTour"));
-    if (et) {
-        et = TOURS.hooked_tour_from_data(et);
-        if (et && et.steps) {
-            if (window && window.self === window.top) {
-                // Only kick off a new tour if this is the toplevel window (non-iframe).  This
-                // functionality actually *could* be useful, but we'd need to handle it better and
-                // come up with some design guidelines for tours jumping between windows.
-                // Disabling for now.
-                var tour = new Tour(
-                    _.extend(
-                        {
-                            steps: et.steps
-                        },
-                        TOURS.tour_opts
-                    )
-                );
-                tour.init();
-                tour.restart();
-            }
-        }
-    }
+    Tours.activeGalaxyTourRunner();
 
     function onloadWebhooks() {
-        if (Galaxy.root !== undefined) {
-            // Load all webhooks with the type 'onload'
-            $.getJSON(`${Galaxy.root}api/webhooks/onload/all`, webhooks => {
-                _.each(webhooks, webhook => {
-                    if (webhook.activate && webhook.script) {
-                        $("<script/>", { type: "text/javascript" })
-                            .text(webhook.script)
-                            .appendTo("head");
-                        $("<style/>", { type: "text/css" })
-                            .text(webhook.styles)
-                            .appendTo("head");
-                    }
+        // Wait until Galaxy.config is loaded.
+        if (Galaxy.config) {
+            if (Galaxy.config.enable_webhooks) {
+                // Load all webhooks with the type 'onload'
+                $.getJSON(`${Galaxy.root}api/webhooks/onload/all`, webhooks => {
+                    _.each(webhooks, webhook => {
+                        if (webhook.activate && webhook.script) {
+                            $("<script/>", { type: "text/javascript" })
+                                .text(webhook.script)
+                                .appendTo("head");
+                            $("<style/>", { type: "text/css" })
+                                .text(webhook.styles)
+                                .appendTo("head");
+                        }
+                    });
                 });
-            });
+            }
         } else {
             setTimeout(onloadWebhooks, 100);
         }

config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample

@@ -6,6 +6,6 @@
 # appropriate files.
 ---
 -
-    image: bgruening/docker-hicbrowser
+    image: quay.io/bgruening/hicbrowser
     description: |
         A simple web browser to visualize Hi-C and other genomic tracks

config/plugins/webhooks/demo/tour_generator/static/script.js

@@ -58,17 +58,7 @@ $(document).ready(function() {
             },
 
             _generateTour: function(data) {
-                var tourData = Tours.default.hooked_tour_from_data(data);
-                sessionStorage.setItem('activeGalaxyTour', JSON.stringify(data));
-
-                // Generate and run the tour
-                var tour = new Tour(_.extend({
-                    steps: tourData.steps
-                }));
-                tour.init();
-                tour.goTo(0);
-                tour.restart();
-
+                var tour = Tours.giveTourWithData(data);
                 // Force ending the tour when pressing the Execute button
                 $('#execute').on('mousedown', function() {
                     if (tour) {