+
@@ -57,7 +57,7 @@ export default {
};
diff --git a/client/galaxy/scripts/components/PluginList.vue b/client/galaxy/scripts/components/PluginList.vue
new file mode 100644
index 00000000000..e30094e061e
--- /dev/null
+++ b/client/galaxy/scripts/components/PluginList.vue
@@ -0,0 +1,136 @@
+
+ or create a new session with this dataset as the only track `,
buttons: {
Cancel: () => {
- window.location = `${Galaxy.root}visualizations/list`;
+ window.top.location = `${Galaxy.root}visualizations/list`;
},
"View in saved visualization": () => {
this.view_in_saved(dataset_params);
@@ -456,14 +456,14 @@ class TracksterUIView extends Backbone.View {
body: tracks_grid.$el,
buttons: {
Cancel: () => {
- window.location = `${Galaxy.root}visualizations/list`;
+ window.top.location = `${Galaxy.root}visualizations/list`;
},
"Add to visualization": () => {
$(window.parent.document)
.find("input[name=id]:checked")
.each(() => {
dataset_params.id = $(this).val();
- window.location = `${Galaxy.root}visualization/trackster?${$.param(dataset_params)}`;
+ window.top.location = `${Galaxy.root}visualization/trackster?${$.param(dataset_params)}`;
});
}
}
@@ -509,7 +509,7 @@ class TracksterUIView extends Backbone.View {
body: this.template_view_new(response),
buttons: {
Cancel: () => {
- window.location = `${Galaxy.root}visualizations/list`;
+ window.top.location = `${Galaxy.root}visualizations/list`;
},
Create: () => {
this.create_browser($("#new-title").val(), $("#new-dbkey").val());
@@ -562,7 +562,7 @@ class TracksterUIView extends Backbone.View {
// close selection/finalize template
html += `
+
+
+
+
+
diff --git a/client/galaxy/scripts/layout/menu.js b/client/galaxy/scripts/layout/menu.js
index 8af6fd22d16..6b41b82a345 100644
--- a/client/galaxy/scripts/layout/menu.js
+++ b/client/galaxy/scripts/layout/menu.js
@@ -42,6 +42,33 @@ var Collection = Backbone.Collection.extend({
url: "workflows/list"
});
+ //
+ // Visualization tab.
+ //
+ this.add({
+ id: "visualization",
+ title: _l("Visualize"),
+ url: "visualizations/list",
+ tooltip: _l("Visualize datasets"),
+ disabled: !Galaxy.user.id,
+ menu: [
+ {
+ title: _l("Create Visualization"),
+ url: "visualizations"
+ },
+ {
+ title: _l("Interactive Environments"),
+ url: "visualization/gie_list",
+ target: "galaxy_main"
+ },
+ {
+ title: _l("Saved Visualizations"),
+ url: "visualizations/list",
+ target: "_frame"
+ }
+ ]
+ });
+
//
// 'Shared Items' or Libraries tab.
//
@@ -74,34 +101,6 @@ var Collection = Backbone.Collection.extend({
]
});
- //
- // Visualization tab.
- //
- this.add({
- id: "visualization",
- title: _l("Visualization"),
- url: "visualizations/list",
- tooltip: _l("Visualize datasets"),
- disabled: !Galaxy.user.id,
- menu: [
- {
- title: _l("New Track Browser"),
- url: "visualization/trackster",
- target: "_frame"
- },
- {
- title: _l("Saved Visualizations"),
- url: "visualizations/list",
- target: "_frame"
- },
- {
- title: _l("Interactive Environments"),
- url: "visualization/gie_list",
- target: "galaxy_main"
- }
- ]
- });
-
//
// Webhooks
//
@@ -272,20 +271,25 @@ var Collection = Backbone.Collection.extend({
target: "_top",
divider: true
},
- {
- title: _l("Saved Histories"),
- url: "histories/list",
- target: "_top"
- },
{
title: _l("Saved Datasets"),
url: "datasets/list",
target: "_top"
},
+ {
+ title: _l("Saved Histories"),
+ url: "histories/list",
+ target: "_top"
+ },
{
title: _l("Saved Pages"),
url: "pages/list",
target: "_top"
+ },
+ {
+ title: _l("Saved Visualizations"),
+ url: "visualizations/list",
+ target: "_top"
}
]
};
@@ -340,13 +344,13 @@ var Tab = Backbone.View.extend({
.attr("title", this.model.get("tooltip"))
.tooltip("destroy");
this.model.get("tooltip") && this.$toggle.tooltip({ placement: "bottom" });
- if(!this.model.get("menu")){
+ if (!this.model.get("menu")) {
this.$dropdown
.removeClass()
.addClass("dropdown")
.addClass(this.model.get("disabled") && "disabled")
.addClass(this.model.get("active") && "active");
- };
+ }
if (this.model.get("menu") && this.model.get("show_menu")) {
this.$menu.show();
$("#dd-helper")
diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
index cc38029959c..48d4cc2bd6a 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
@@ -261,7 +261,7 @@ var DatasetListItemEdit = _super.extend(
}
if (visualizations.length >= 1) {
- var url = Galaxy.root + "visualizations/dataset_id=" + this.model.get("id");
+ var url = Galaxy.root + "plugins?dataset_id=" + this.model.get("id");
return $("")
.addClass("visualization-link icon-btn")
.attr("href", url)
diff --git a/client/galaxy/scripts/mvc/form/form-parameters.js b/client/galaxy/scripts/mvc/form/form-parameters.js
index bda898a9322..5c7a9abd89e 100644
--- a/client/galaxy/scripts/mvc/form/form-parameters.js
+++ b/client/galaxy/scripts/mvc/form/form-parameters.js
@@ -84,23 +84,10 @@ export default Backbone.Model.extend({
}
// identify display type
- var SelectClass = Ui.Select;
- switch (input_def.display) {
- case "checkboxes":
- SelectClass = Ui.Checkbox;
- break;
- case "radio":
- SelectClass = Ui.Radio;
- break;
- case "radiobutton":
- SelectClass = Ui.RadioButton;
- break;
- }
-
- // create select field
- return new SelectClass.View({
+ return new Ui.TextSelect({
id: `field-${input_def.id}`,
data: data,
+ display: input_def.display,
error_text: input_def.error_text || "No options available",
readonly: input_def.readonly,
multiple: input_def.multiple,
diff --git a/client/galaxy/scripts/mvc/form/form-wrapper.js b/client/galaxy/scripts/mvc/form/form-wrapper.js
index 49247a8f8c0..5109b7f6aec 100644
--- a/client/galaxy/scripts/mvc/form/form-wrapper.js
+++ b/client/galaxy/scripts/mvc/form/form-wrapper.js
@@ -6,7 +6,7 @@ var View = Backbone.View.extend({
this.model = new Backbone.Model(options);
this.url = this.model.get("url");
this.redirect = this.model.get("redirect");
- if (options && options.active_tab){
+ if (options && options.active_tab) {
this.active_tab = options.active_tab;
}
this.setElement("");
diff --git a/client/galaxy/scripts/mvc/grid/grid-shared.js b/client/galaxy/scripts/mvc/grid/grid-shared.js
index 170ad392ba6..09829e25c1e 100644
--- a/client/galaxy/scripts/mvc/grid/grid-shared.js
+++ b/client/galaxy/scripts/mvc/grid/grid-shared.js
@@ -9,7 +9,7 @@ var View = Backbone.View.extend({
this.model = new Backbone.Model(options);
this.item = this.model.get("item");
this.title = this.model.get("plural");
- if (options && options.active_tab){
+ if (options && options.active_tab) {
this.active_tab = options.active_tab;
}
$.ajax({
diff --git a/client/galaxy/scripts/mvc/history/history-list.js b/client/galaxy/scripts/mvc/history/history-list.js
index 4a470694915..9b4a01b5403 100644
--- a/client/galaxy/scripts/mvc/history/history-list.js
+++ b/client/galaxy/scripts/mvc/history/history-list.js
@@ -107,10 +107,9 @@ var View = Backbone.View.extend({
var self = this;
LoadingIndicator.markViewAsLoading(this);
- if(options.action_id == "list_published"){
+ if (options.action_id == "list_published") {
this.active_tab = "shared";
- }
- else if (options.action_id = "list"){
+ } else if ((options.action_id = "list")) {
this.active_tab = "user";
}
this.model = new Backbone.Model();
diff --git a/client/galaxy/scripts/mvc/tool/tool-form-composite.js b/client/galaxy/scripts/mvc/tool/tool-form-composite.js
index a2123487dcc..45ac7882d83 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-composite.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-composite.js
@@ -15,7 +15,7 @@ var View = Backbone.View.extend({
this.modal = parent.Galaxy.modal || new Modal.View();
this.model = (options && options.model) || new Backbone.Model(options);
this.deferred = new Deferred();
- if (options && options.active_tab){
+ if (options && options.active_tab) {
this.active_tab = options.active_tab;
}
this.setElement(
@@ -303,17 +303,17 @@ var View = Backbone.View.extend({
});
this._append(this.$steps, this.history_form.$el);
},
-
+
/** Render Workflow Options */
_renderResourceParameters: function() {
this.workflow_resource_parameters_form = null;
- if(!_.isEmpty(this.model.get('workflow_resource_parameters'))){
+ if (!_.isEmpty(this.model.get("workflow_resource_parameters"))) {
this.workflow_resource_parameters_form = new Form({
- cls : 'ui-portlet-narrow',
- title : 'Workflow Resource Options',
- inputs : this.model.get('workflow_resource_parameters')
+ cls: "ui-portlet-narrow",
+ title: "Workflow Resource Options",
+ inputs: this.model.get("workflow_resource_parameters")
});
- this._append( this.$steps, this.workflow_resource_parameters_form.$el );
+ this._append(this.$steps, this.workflow_resource_parameters_form.$el);
}
},
@@ -538,7 +538,9 @@ var View = Backbone.View.extend({
var job_def = {
new_history_name: history_form_data["new_history|name"] ? history_form_data["new_history|name"] : null,
history_id: !history_form_data["new_history|name"] ? this.model.get("history_id") : null,
- resource_params: this.workflow_resource_parameters_form ? this.workflow_resource_parameters_form.data.create() : {},
+ resource_params: this.workflow_resource_parameters_form
+ ? this.workflow_resource_parameters_form.data.create()
+ : {},
replacement_params: this.wp_form ? this.wp_form.data.create() : {},
parameters: {},
// Tool form will submit flat maps for each parameter
diff --git a/client/galaxy/scripts/mvc/ui/ui-buttons.js b/client/galaxy/scripts/mvc/ui/ui-buttons.js
index 75dc7033f3b..b496778bfb8 100644
--- a/client/galaxy/scripts/mvc/ui/ui-buttons.js
+++ b/client/galaxy/scripts/mvc/ui/ui-buttons.js
@@ -14,7 +14,8 @@ var ButtonDefault = Backbone.View.extend({
wait_text: "Sending...",
wait_cls: "btn btn-info",
disabled: false,
- percentage: -1
+ percentage: -1,
+ visible: true
}).set(options);
this.setElement(
$("")
@@ -36,6 +37,7 @@ var ButtonDefault = Backbone.View.extend({
.addClass(options.disabled && "disabled")
.attr("id", options.id)
.attr("disabled", options.disabled)
+ .css("display", options.visible ? "inline-block" : "none")
.off("click")
.on("click", () => {
$(".tooltip").hide();
@@ -60,12 +62,12 @@ var ButtonDefault = Backbone.View.extend({
/** Show button */
show: function() {
- this.$el.show();
+ this.model.set("visible", true);
},
/** Hide button */
hide: function() {
- this.$el.hide();
+ this.model.set("visible", false);
},
/** Disable button */
@@ -101,6 +103,7 @@ var ButtonLink = ButtonDefault.extend({
(options && options.model) ||
new Backbone.Model({
id: Utils.uid(),
+ visible: true,
title: "",
icon: "",
cls: ""
@@ -122,6 +125,7 @@ var ButtonLink = ButtonDefault.extend({
target: options.target || "_top",
disabled: options.disabled
})
+ .css("display", options.visible ? "inline-block" : "none")
.tooltip({ placement: "bottom" })
.off("click")
.on("click", () => {
@@ -141,6 +145,7 @@ var ButtonCheck = Backbone.View.extend({
title: "Select/Unselect all",
icons: ["fa-square-o", "fa-minus-square-o", "fa-check-square-o"],
value: 0,
+ visible: true,
onchange: function() {}
}).set(options);
this.setElement(
@@ -157,6 +162,7 @@ var ButtonCheck = Backbone.View.extend({
var options = this.model.attributes;
this.$el
.addClass("ui-button-check")
+ .css("display", options.visible ? "inline-block" : "none")
.off("click")
.on("click", () => {
self.model.set("value", (self.model.get("value") === 0 && 2) || 0);
@@ -196,6 +202,7 @@ var ButtonIcon = ButtonDefault.extend({
id: Utils.uid(),
title: "",
icon: "",
+ visible: true,
cls: "ui-button-icon",
disabled: false
}).set(options);
@@ -217,6 +224,7 @@ var ButtonIcon = ButtonDefault.extend({
.removeClass()
.addClass(options.cls)
.addClass(options.disabled && "disabled")
+ .css("display", options.visible ? "inline-block" : "none")
.attr("disabled", options.disabled)
.attr("id", options.id)
.off("click")
diff --git a/client/galaxy/scripts/mvc/ui/ui-misc.js b/client/galaxy/scripts/mvc/ui/ui-misc.js
index c5ee45392b8..a34ea7fae57 100644
--- a/client/galaxy/scripts/mvc/ui/ui-misc.js
+++ b/client/galaxy/scripts/mvc/ui/ui-misc.js
@@ -47,7 +47,7 @@ export var Message = Backbone.View.extend({
fade: true
}).set(options);
this.listenTo(this.model, "change", this.render, this);
- if (options && options.active_tab){
+ if (options && options.active_tab) {
this.active_tab = options.active_tab;
}
this.render();
@@ -184,6 +184,35 @@ export var Hidden = Backbone.View.extend({
}
});
+/** Creates an input element which switches between select and text field */
+export var TextSelect = Backbone.View.extend({
+ initialize: function(options) {
+ this.text = new Input(options);
+ var classes = {
+ "checkboxes": Checkbox,
+ "radio": Radio,
+ "radiobutton": RadioButton
+ }
+ var SelectClass = classes[options.display] || Select;
+ this.select = new SelectClass.View(options);
+ this.setElement($("").append(this.select.$el)
+ .append(this.text.$el));
+ this.update(options.data);
+ },
+ value: function(new_val) {
+ var element = this.textmode ? this.text : this.select;
+ return element.value(new_val);
+ },
+ update: function(options) {
+ var v = this.value();
+ this.textmode = !$.isArray(options) || options.length === 0;
+ this.text.$el[this.textmode ? "show" : "hide"]();
+ this.select.$el[this.textmode ? "hide" : "show"]();
+ this.select.update(options);
+ this.value(v);
+ }
+});
+
/** Creates a upload element input field */
export var Upload = Backbone.View.extend({
initialize: function(options) {
@@ -266,6 +295,7 @@ export default {
Checkbox: Options.Checkbox,
Radio: Options.Radio,
Select: Select,
+ TextSelect: TextSelect,
Hidden: Hidden,
Slider: Slider,
Drilldown: Drilldown
diff --git a/client/galaxy/scripts/mvc/ui/ui-slider.js b/client/galaxy/scripts/mvc/ui/ui-slider.js
index 2b10bd62454..da091747113 100644
--- a/client/galaxy/scripts/mvc/ui/ui-slider.js
+++ b/client/galaxy/scripts/mvc/ui/ui-slider.js
@@ -100,10 +100,18 @@ var View = Backbone.View.extend({
var options = this.model.attributes;
if (new_val !== undefined) {
if (new_val !== null && new_val !== "" && !this._isParameter(new_val)) {
- isNaN(new_val) && (new_val = 0);
- !options.precise && (new_val = Math.round(new_val));
- options.max !== null && (new_val = Math.min(new_val, options.max));
- options.min !== null && (new_val = Math.max(new_val, options.min));
+ if (isNaN(new_val)) {
+ new_val = 0;
+ }
+ if (!options.precise) {
+ new_val = Math.round(new_val);
+ }
+ if (options.max !== null && !isNaN(options.max)) {
+ new_val = Math.min(new_val, options.max);
+ }
+ if (options.min !== null && !isNaN(options.min)) {
+ new_val = Math.max(new_val, options.min);
+ }
}
this.model.set("value", new_val);
this.model.trigger("change");
diff --git a/client/galaxy/scripts/mvc/visualization/chart/components/model.js b/client/galaxy/scripts/mvc/visualization/chart/components/model.js
index e21015222e0..58d6e44c64b 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/components/model.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/components/model.js
@@ -8,9 +8,9 @@ export default Backbone.Model.extend({
date: null,
state: "",
state_info: "",
- modified: false,
+ modified: true,
dataset_id: "",
- dataset_id_job: ""
+ dataset_id_job: null
},
initialize: function(options, viz_options) {
@@ -89,15 +89,16 @@ export default Backbone.Model.extend({
}
console.debug("model::save() - Saving failed.");
});
- console.debug("model::save() - Saved with configuration:");
- console.debug(this.chart_last);
+ console.debug("model::save() - Saving with configuration.");
},
/** Load nested models/collections from packed dictionary */
load: function(chart_parsed) {
var d = chart_parsed || this.chart_dict;
- console.debug("model::load() - Attempting to load with configuration:");
- console.debug(d);
+ if (d) {
+ console.debug("model::load() - Attempting to load with configuration:");
+ console.debug(d);
+ }
this.reset();
if (d && d.attributes) {
this.set(d.attributes);
@@ -109,9 +110,11 @@ export default Backbone.Model.extend({
this.trigger("load");
console.debug("model::load() - Loading chart model " + d.attributes.type + ".");
return true;
+ } else {
+ this.set("modified", true);
+ this.trigger("load");
+ console.debug("model::load() - Visualization attributes unavailable.");
+ return false;
}
- this.trigger("load");
- console.debug("model::load() - Visualization attributes unavailable.");
- return false;
}
});
diff --git a/client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js b/client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js
index af6a80d0fb5..d6f7affdc0c 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js
@@ -125,6 +125,9 @@ var _fillFromCache = function(options) {
});
if (limit === 0) {
console.debug("tabular-datasets::_fillFromCache() - No data available.");
+ if (options.chart) {
+ options.chart.state("failed", "No data available.");
+ }
}
var results = [];
groups.each(function(group, group_index) {
diff --git a/client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js b/client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
index 81268775d0b..9f2486f2fd7 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
@@ -28,7 +28,7 @@ var requestCharts = function(chart, module) {
});
columns_string = columns_string.substring(0, columns_string.length - 2);
return {
- tool_id: "charts",
+ tool_id: "toolshed.g2.bx.psu.edu/repos/iuc/charts/charts/1.0.1",
inputs: {
input: {
id: chart.get("dataset_id"),
@@ -44,12 +44,19 @@ var requestCharts = function(chart, module) {
/** Submit job request to charts tool */
var request = function(chart, parameters, success, error) {
chart.state("wait", "Requesting job results...");
- if (chart.get("modified")) {
- cleanup(chart);
+ if (chart.get("modified") && chart.get("dataset_id_job")) {
+ Utils.request({
+ type: "PUT",
+ url: Galaxy.root + "api/histories/none/contents/" + chart.get("dataset_id_job"),
+ data: { deleted: true },
+ success: () => {
+ refreshHdas();
+ }
+ });
+ chart.set("dataset_id_job", null);
chart.set("modified", false);
}
- var dataset_id_job = chart.get("dataset_id_job");
- if (dataset_id_job !== "") {
+ if (chart.get("dataset_id_job")) {
wait(chart, success, error);
} else {
chart.state("wait", "Sending job request...");
@@ -95,22 +102,6 @@ var request = function(chart, parameters, success, error) {
}
};
-/* Remove previous data when re-running jobs */
-var cleanup = function(chart) {
- var previous = chart.get("dataset_id_job");
- if (previous !== "") {
- Utils.request({
- type: "PUT",
- url: Galaxy.root + "api/histories/none/contents/" + previous,
- data: { deleted: true },
- success: function() {
- refreshHdas();
- }
- });
- chart.set("dataset_id_job", "");
- }
-};
-
/** Request job details */
var wait = function(chart, success, error) {
Utils.request({
diff --git a/client/galaxy/scripts/mvc/visualization/chart/views/groups.js b/client/galaxy/scripts/mvc/visualization/chart/views/groups.js
index 8faa516c7e9..363b51f4ad4 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/views/groups.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/views/groups.js
@@ -66,6 +66,7 @@ var GroupView = Backbone.View.extend({
cls: "ui-portlet-plain",
onchange: function() {
self.group.set(self.form.data.create());
+ self.chart.set("modified", true);
self.chart.trigger("redraw");
}
});
diff --git a/client/galaxy/scripts/mvc/visualization/chart/views/menu.js b/client/galaxy/scripts/mvc/visualization/chart/views/menu.js
index e4994549b06..266a4de5263 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/views/menu.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/views/menu.js
@@ -7,6 +7,13 @@ export default Backbone.View.extend({
initialize: function(app) {
this.app = app;
this.model = new Backbone.Model({ visible: true });
+ this.execute_button = new Ui.ButtonIcon({
+ icon: "fa-check-square",
+ tooltip: "Confirm",
+ onclick: () => {
+ app.chart.trigger("redraw", true);
+ }
+ });
this.export_button = new Ui.ButtonMenu({
icon: "fa-camera",
tooltip: "Export"
@@ -72,53 +79,50 @@ export default Backbone.View.extend({
});
}
});
- this.buttons = [
- new Ui.ButtonIcon({
- icon: "fa-angle-double-left",
- tooltip: "Show",
- cls: "ui-button-icon charts-fullscreen-button",
- onclick: () => {
- this.model.set("visible", true);
- window.dispatchEvent(new Event("resize"));
+ this.left_button = new Ui.ButtonIcon({
+ icon: "fa-angle-double-left",
+ tooltip: "Show",
+ onclick: () => {
+ this.model.set("visible", true);
+ window.dispatchEvent(new Event("resize"));
+ }
+ });
+ this.right_button = new Ui.ButtonIcon({
+ icon: "fa-angle-double-right",
+ tooltip: "Hide",
+ onclick: () => {
+ this.model.set("visible", false);
+ window.dispatchEvent(new Event("resize"));
+ }
+ });
+ this.save_button = new Ui.ButtonIcon({
+ icon: "fa-save",
+ tooltip: "Save",
+ onclick: () => {
+ if (app.chart.get("title")) {
+ app.message.update({
+ message: `Saving '${app.chart.get(
+ "title"
+ )}'. It will appear in the list of 'Saved Visualizations'.`,
+ status: "success"
+ });
+ app.chart.save({
+ error: () => {
+ app.message.update({
+ message: "Could not save visualization.",
+ status: "danger"
+ });
+ }
+ });
+ } else {
+ app.message.update({
+ message: "Please provide a name.",
+ status: "danger"
+ });
}
- }),
- new Ui.ButtonIcon({
- icon: "fa-angle-double-right",
- tooltip: "Hide",
- onclick: () => {
- this.model.set("visible", false);
- window.dispatchEvent(new Event("resize"));
- }
- }),
- this.export_button,
- new Ui.ButtonIcon({
- icon: "fa-save",
- tooltip: "Save",
- onclick: () => {
- if (app.chart.get("title")) {
- app.message.update({
- message: `Saving '${app.chart.get(
- "title"
- )}'. It will appear in the list of 'Saved Visualizations'.`,
- status: "success"
- });
- app.chart.save({
- error: () => {
- app.message.update({
- message: "Could not save visualization.",
- status: "danger"
- });
- }
- });
- } else {
- app.message.update({
- message: "Please provide a name.",
- status: "danger"
- });
- }
- }
- })
- ];
+ }
+ });
+ this.buttons = [this.left_button, this.right_button, this.execute_button, this.export_button, this.save_button];
this.setElement("");
for (let b of this.buttons) {
this.$el.append(b.$el);
@@ -130,7 +134,11 @@ export default Backbone.View.extend({
render: function() {
var visible = this.model.get("visible");
this.app.$el[visible ? "removeClass" : "addClass"]("charts-fullscreen");
+ this.execute_button.model.set("visible", visible && !!this.app.chart.plugin.specs.confirm);
+ this.save_button.model.set("visible", visible);
this.export_button.model.set("visible", visible);
+ this.right_button.model.set("visible", visible);
+ this.left_button.model.set("visible", !visible);
var exports = this.app.chart.plugin.specs.exports || [];
this.export_button.collection.each(model => {
model.set("visible", exports.indexOf(model.get("key")) !== -1);
diff --git a/client/galaxy/scripts/mvc/visualization/chart/views/viewer.js b/client/galaxy/scripts/mvc/visualization/chart/views/viewer.js
index bb422366cba..b36df06a9af 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/views/viewer.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/views/viewer.js
@@ -25,11 +25,15 @@ export default Backbone.View.extend({
this.$text = this.$(".text");
this._fullscreen(this.$el, 20);
this._createContainer("div");
- this.chart.on("redraw", function() {
- self.app.deferred.execute(function(process) {
- console.debug("viewer:redraw() - Redrawing...");
- self._draw(process, self.chart);
- });
+ this.chart.on("redraw", function(confirmed) {
+ if (!self.chart.get("modified") || !self.chart.plugin.specs.confirm || confirmed) {
+ self.app.deferred.execute(function(process) {
+ console.debug("viewer:redraw() - Redrawing...");
+ self._draw(process, self.chart);
+ });
+ } else {
+ self.chart.state("info", "Please confirm the settings before rendering the results.");
+ }
});
this.chart.on("set:state", function() {
var $container = self.$(".charts-viewer-container");
@@ -49,6 +53,10 @@ export default Backbone.View.extend({
$icon.addClass("icon fa fa-warning");
$container.hide();
break;
+ case "info":
+ $icon.addClass("icon fa fa-info");
+ $container.hide();
+ break;
default:
$icon.addClass("icon fa fa-spinner fa-spin");
$container.show();
diff --git a/client/galaxy/scripts/mvc/visualization/visualization-model.js b/client/galaxy/scripts/mvc/visualization/visualization-model.js
index 40b56109554..4c246b71db1 100644
--- a/client/galaxy/scripts/mvc/visualization/visualization-model.js
+++ b/client/galaxy/scripts/mvc/visualization/visualization-model.js
@@ -1,4 +1,8 @@
-import * as Backbone from "libs/backbone";
+import * as Backbone from "backbone";
+import * as _ from "underscore";
+
+/* global Galaxy */
+
//==============================================================================
/** @class Model for a saved Galaxy visualization.
*
diff --git a/client/galaxy/scripts/mvc/visualization/visualization-view.js b/client/galaxy/scripts/mvc/visualization/visualization-view.js
deleted file mode 100644
index 63137e1539b..00000000000
--- a/client/galaxy/scripts/mvc/visualization/visualization-view.js
+++ /dev/null
@@ -1,71 +0,0 @@
-/**
- * Visualization selection grid
- */
-import * as Backbone from "backbone";
-import * as _ from "underscore";
-import Thumbnails from "mvc/ui/ui-thumbnails";
-
-/* global $ */
-/* global Galaxy */
-
-var View = Backbone.View.extend({
- initialize: function(options) {
- this.setElement($(""));
- this.model = new Backbone.Model();
- this.active_tab = "visualization";
- $.ajax({
- url: `${Galaxy.root}api/datasets/${options.dataset_id}`
- }).done(dataset => {
- if (dataset.visualizations.length === 0) {
- this.$el.append(
- $("")
- .addClass("errormessagelarge")
- .append(
- $("").text(
- "Unfortunately we could not identify a suitable plugin. Feel free to contact us if you are aware of visualizations for this datatype."
- )
- )
- );
- } else {
- this.model.set({ dataset: dataset });
- this.render();
- }
- });
- },
-
- render: function() {
- var dataset = this.model.get("dataset");
- this.vis_index = {};
- this.vis_array = [];
- _.each(
- dataset.visualizations.sort((a, b) => {
- return a.html < b.html ? -1 : 1;
- }),
- (v, id) => {
- var dict = {
- id: id,
- name: v.name,
- keywords: v.keywords || [],
- title: v.html,
- image_src: v.logo ? Galaxy.root + v.logo : null,
- description: v.description || "No description available.",
- regular: v.regular,
- visualization: v
- };
- this.vis_index[dict.id] = dict;
- this.vis_array.push(dict);
- }
- );
- this.types = new Thumbnails.View({
- title_default: "Suggested plugins",
- title_list: "List of available plugins",
- collection: this.vis_array,
- onclick: id => {
- var vis_type = this.vis_index[id];
- $("#galaxy_main").attr("src", vis_type.visualization.href);
- }
- });
- this.$el.empty().append(this.types.$el);
- }
-});
-export default { View: View };
diff --git a/client/galaxy/scripts/ui/pagination.js b/client/galaxy/scripts/ui/pagination.js
index 87176338a2a..f3fa2cc94ed 100644
--- a/client/galaxy/scripts/ui/pagination.js
+++ b/client/galaxy/scripts/ui/pagination.js
@@ -1,13 +1,16 @@
-import jQuery from "jquery";
-("use_strict");
+//import $ from "jquery";
+// TODO: This manipulates whatever jquery is available -- needs restructuring,
+// or removal (jquery plugins are a bad design choice for us at this point)
+// It is *only* used in the scatterplot viz, so this is safe.
+/* global $ */
-var $ = jQuery;
/** Builds (twitter bootstrap styled) pagination controls.
* If the totalDataSize is not null, a horizontal list of page buttons is displayed.
* If totalDataSize is null, two links ('Prev' and 'Next) are displayed.
* When pages are changed, a 'pagination.page-change' event is fired
* sending the event and the (0-based) page requested.
*/
+
function Pagination(element, options) {
/** the total number of pages */
this.numPages = null;
@@ -37,7 +40,7 @@ Pagination.prototype.defaults = {
Pagination.prototype.init = function _init($element, options) {
options = options || {};
this.$element = $element;
- this.options = jQuery.extend(true, {}, this.defaults, options);
+ this.options = $.extend(true, {}, this.defaults, options);
this.currPage = this.options.startingPage;
if (this.options.totalDataSize !== null) {
@@ -203,12 +206,12 @@ Pagination.create = function _create($element, options) {
};
// as jq plugin
-jQuery.fn.extend({
+$.fn.extend({
pagination: function $pagination(options) {
- var nonOptionsArgs = jQuery.makeArray(arguments).slice(1);
+ var nonOptionsArgs = $.makeArray(arguments).slice(1);
// if passed an object - use that as an options map to create pagination for each selected
- if (jQuery.type(options) === "object") {
+ if ($.type(options) === "object") {
return this.map(function() {
Pagination.create($(this), options);
return this;
@@ -222,9 +225,9 @@ jQuery.fn.extend({
// if a pagination control was found for this element, either...
if (previousControl) {
// invoke a function on the pagination object if passed a string (the function name)
- if (jQuery.type(options) === "string") {
+ if ($.type(options) === "string") {
var fn = previousControl[options];
- if (jQuery.type(fn) === "function") {
+ if ($.type(fn) === "function") {
return fn.apply(previousControl, nonOptionsArgs);
}
diff --git a/client/galaxy/scripts/ui/peek-column-selector.js b/client/galaxy/scripts/ui/peek-column-selector.js
index f804c1e0dca..dd091d6380c 100644
--- a/client/galaxy/scripts/ui/peek-column-selector.js
+++ b/client/galaxy/scripts/ui/peek-column-selector.js
@@ -1,7 +1,8 @@
-// from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js
-// Uses AMD or browser globals to create a jQuery plugin.
-import jQuery from "jquery";
-var $ = jQuery;
+//import $ from "jquery";
+// TODO: This manipulates whatever jquery is available -- needs restructuring,
+// or removal (jquery plugins are a bad design choice for us at this point)
+// It is *only* used in the scatterplot viz, so this is safe.
+/* global $ */
//==============================================================================
/** Column selection using the peek display as the control.
@@ -63,38 +64,38 @@ var defaults = {
topLeftContent: "Columns:"
};
-var /** class added to the pre.peek element (to allow css on just the control) */
-PEEKCONTROL_CLASS = "peek-column-selector";
+/** class added to the pre.peek element (to allow css on just the control) */
+const PEEKCONTROL_CLASS = "peek-column-selector";
-var /** the string of the event fired when a control row changes */
-CHANGE_EVENT = "peek-column-selector.change";
+/** the string of the event fired when a control row changes */
+const CHANGE_EVENT = "peek-column-selector.change";
-var /** the string of the event fired when a column is renamed */
-RENAME_EVENT = "peek-column-selector.rename";
+/** the string of the event fired when a column is renamed */
+const RENAME_EVENT = "peek-column-selector.rename";
-var /** class added to the control rows */
-ROW_CLASS = "control";
+/** class added to the control rows */
+const ROW_CLASS = "control";
-var /** class added to the left-hand cells that serve as row prompts */
-PROMPT_CLASS = "control-prompt";
+/** class added to the left-hand cells that serve as row prompts */
+const PROMPT_CLASS = "control-prompt";
-var /** class added to selected _cells_/tds */
-SELECTED_CLASS = "selected";
+/** class added to selected _cells_/tds */
+const SELECTED_CLASS = "selected";
-var /** class added to disabled/un-clickable cells/tds */
-DISABLED_CLASS = "disabled";
+/** class added to disabled/un-clickable cells/tds */
+const DISABLED_CLASS = "disabled";
-var /** class added to the clickable surface within a cell to select it */
-BUTTON_CLASS = "button";
+/** class added to the clickable surface within a cell to select it */
+const BUTTON_CLASS = "button";
-var /** class added to peek table header (th) cells to indicate they can be clicked and are renamable */
-RENAMABLE_HEADER_CLASS = "renamable-header";
+/** class added to peek table header (th) cells to indicate they can be clicked and are renamable */
+const RENAMABLE_HEADER_CLASS = "renamable-header";
-var /** the data key used for each cell to store the column index ('data-...') */
-COLUMN_INDEX_DATA_KEY = "column-index";
+/** the data key used for each cell to store the column index ('data-...') */
+const COLUMN_INDEX_DATA_KEY = "column-index";
-var /** renamable header data key used to store the column name (w/o the number and dot: '1.Bler') */
-COLUMN_NAME_DATA_KEY = "column-name";
+/** renamable header data key used to store the column name (w/o the number and dot: '1.Bler') */
+const COLUMN_NAME_DATA_KEY = "column-name";
//TODO: not happy with pure functional here - rows should polymorph (multi, single, etc.)
//TODO: needs clean up, move handlers to outer scope
@@ -102,10 +103,10 @@ COLUMN_NAME_DATA_KEY = "column-name";
// ........................................................................
/** validate the control data sent in for each row */
function validateControl(control) {
- if (control.disabled && jQuery.type(control.disabled) !== "array") {
+ if (control.disabled && $.type(control.disabled) !== "array") {
throw new Error(`"disabled" must be defined as an array of indeces: ${JSON.stringify(control)}`);
}
- if (control.multiselect && control.selected && jQuery.type(control.selected) !== "array") {
+ if (control.multiselect && control.selected && $.type(control.selected) !== "array") {
throw new Error(`Mulitselect rows need an array for "selected": ${JSON.stringify(control)}`);
}
if (!control.label || !control.id) {
@@ -212,7 +213,7 @@ function buildMultiSelectCell(control, columnIndex) {
var eventData = {};
var key = $cell.parent().attr("id");
- var val = jQuery.makeArray(selectedColumnIndeces);
+ var val = $.makeArray(selectedColumnIndeces);
eventData[key] = val;
$cell.parents(".peek").trigger(CHANGE_EVENT, eventData);
});
@@ -252,7 +253,7 @@ function buildControlRow(cellCount, control, includePrompts) {
// ........................................................................
/** add to the peek, using options for configuration, return the peek */
function peekColumnSelector(options) {
- options = jQuery.extend(true, {}, defaults, options);
+ options = $.extend(true, {}, defaults, options);
var $peek = $(this).addClass(PEEKCONTROL_CLASS);
var $peektable = $peek.find("table");
@@ -312,7 +313,7 @@ function peekColumnSelector(options) {
var index = $this.index() + (options.includePrompts ? 0 : 1);
var prevName = $this.data(COLUMN_NAME_DATA_KEY);
- var newColumnName = prompt("New column name:", prevName);
+ var newColumnName = window.prompt("New column name:", prevName);
if (newColumnName !== null && newColumnName !== prevName) {
// set the new text and data
$this
@@ -320,7 +321,7 @@ function peekColumnSelector(options) {
.data(COLUMN_NAME_DATA_KEY, newColumnName)
.attr("data-", COLUMN_NAME_DATA_KEY, newColumnName);
// fire event for new column names
- var columnNames = jQuery.makeArray(
+ var columnNames = $.makeArray(
$this
.parent()
.children("th:not(.top-left)")
@@ -344,7 +345,7 @@ function peekColumnSelector(options) {
// ........................................................................
// as jq plugin
-jQuery.fn.extend({
+$.fn.extend({
peekColumnSelector: function $peekColumnSelector(options) {
return this.map(function() {
return peekColumnSelector.call(this, options);
diff --git a/client/galaxy/scripts/viz/circster.js b/client/galaxy/scripts/viz/circster.js
index a246f2cf577..b5686f87317 100644
--- a/client/galaxy/scripts/viz/circster.js
+++ b/client/galaxy/scripts/viz/circster.js
@@ -1211,7 +1211,7 @@ var Circster = Backbone.View.extend({
icon_class: "cross-circle",
title: _l("Close"),
on_click: function() {
- window.location = `${Galaxy.root}visualizations/list`;
+ window.top.location = `${Galaxy.root}visualizations/list`;
}
}
],
diff --git a/client/galaxy/scripts/viz/sweepster.js b/client/galaxy/scripts/viz/sweepster.js
index abfcc88355b..0af95091924 100644
--- a/client/galaxy/scripts/viz/sweepster.js
+++ b/client/galaxy/scripts/viz/sweepster.js
@@ -874,7 +874,7 @@ var SweepsterVisualizationView = Backbone.View.extend({
icon_class: "cross-circle",
title: _l("Close"),
on_click: function() {
- window.location = "${h.url_for( controller='visualization', action='list' )}";
+ window.top.location = `${Galaxy.root}visualizations/list`;
}
}
],
diff --git a/client/galaxy/scripts/viz/trackster.js b/client/galaxy/scripts/viz/trackster.js
index 37b1dfccbbb..1088bb3b3f7 100644
--- a/client/galaxy/scripts/viz/trackster.js
+++ b/client/galaxy/scripts/viz/trackster.js
@@ -95,7 +95,7 @@ class TracksterUI extends Backbone.Model {
this.view.has_changes = false;
// Needed to set URL when first saving a visualization.
- window.history.pushState({}, "", vis_info.url + window.location.hash);
+ window.history.pushState({}, "", vis_info.url + window.top.location.hash);
})
.error(() => {
// show dialog
@@ -151,7 +151,7 @@ class TracksterUI extends Backbone.Model {
icon_class: "globe",
title: _l("Circster"),
on_click: () => {
- window.location = `${this.baseURL}visualization/circster?id=${this.view.vis_id}`;
+ window.top.location = `${this.baseURL}visualization/circster?id=${this.view.vis_id}`;
}
},
{
@@ -354,17 +354,17 @@ class TracksterUI extends Backbone.Model {
},
"Leave without Saving": () => {
$(window).off("beforeunload");
- window.location = `${Galaxy.root}visualization`;
+ window.top.location = `${Galaxy.root}visualization`;
},
Save: () => {
$.when(this.save_viz()).then(() => {
- window.location = `${Galaxy.root}visualization`;
+ window.top.location = `${Galaxy.root}visualization`;
});
}
}
});
} else {
- window.location = `${Galaxy.root}visualization`;
+ window.top.location = `${Galaxy.root}visualization`;
}
}
}
@@ -433,7 +433,7 @@ class TracksterUIView extends Backbone.View {
"Not available."}
+
+
+
+
+
+
+ |
+ |
+
+
+ {{ plugin.html }}
+
+
+ {{ plugin.description }}
+
+ |
+
| + |
+
+
+
+ Select a dataset to visualize:
+
+
+
+
+
+ |
+
Is the build not listed here? Add a Custom Build
`;
+ }custom_builds" target="_top">Add a Custom Build