add: function(options) {
if (!options.id || this.list[options.id]) {
Galaxy.emit.debug("form-repeat::add()", "Duplicate or invalid repeat block id.");
return;
}
var button_delete = new Ui.Button({
icon: "fa-trash-o",
tooltip: _l("Delete this repeat block"),
cls: "ui-button-icon-plain form-repeat-delete",
onclick: function() {
if (options.ondel) {
options.ondel();
}
}
});
var portlet = new Portlet.View({
id: options.id,
title: _l("placeholder"),
cls: options.cls || "ui-portlet-section",
operations: { button_delete: button_delete }
});
portlet.append(options.$el);
portlet.$el.addClass("section-row").hide();
this.list[options.id] = portlet;
this.$list.append(portlet.$el.fadeIn("fast"));
if (this.options.max > 0 && this.size() >= this.options.max) {
this.button_new.disable();
}
this._refresh();
},
_getDatatype: function() {
var self = this;
var form = new Form({
title: _l("Change datatype"),
operations: {
submit_datatype: new Ui.Button({
tooltip: _l("Change the datatype to a new type."),
title: _l("Change datatype"),
icon: "fa-exchange",
onclick: function() {
self._submit("datatype", form);
}
}),
submit_datatype_detect: new Ui.Button({
tooltip: _l("Detect the datatype and change it."),
title: _l("Detect datatype"),
icon: "fa-undo",
onclick: function() {
self._submit("datatype_detect", form);
}
})
}
});
return form;
},
_renderMetaFileDownloadButton: function() {
var urls = this.model.urls;
return $(`
<div class="metafile-dropdown dropdown">
<a class="download-btn icon-btn" href="${urls.download}" data-toggle="dropdown" title="${_l(
"Download"
)}">
<span class="fa fa-floppy-o"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="${urls.download}">
${_l("Download dataset")}
</a>
</li>
${_.map(
this.model.get("meta_files"),
meta_file =>
`<li>
<a href="${urls.meta_download + meta_file.file_type}">
${_l("Download")} ${meta_file.file_type}
</a>
</li>`
)}
</ul>
</div>`);
},
_getAttribute: function() {
var self = this;
var form = new Form({
title: _l("Edit attributes"),
operations: {
submit_attributes: new Ui.Button({
tooltip: _l("Save attributes of the dataset."),
icon: "fa-floppy-o",
title: _l("Save"),
onclick: function() {
self._submit("attributes", form);
}
}),
submit_autodetect: new Ui.Button({
tooltip:
"This will inspect the dataset and attempt to correct the values of fields if they are not accurate.",
icon: "fa-undo",
title: "Auto-detect",
onclick: function() {
self._submit("autodetect", form);
}
})
}
});
return form;
},
this._loadDataset(dataset_id, (dataset, config) => {
current_dataset = dataset;
self.add(
_.extend(
{
menu: [
{
icon: "fa fa-chevron-circle-left",
tooltip: _l("Previous in History"),
onclick: function(frame) {
_loadDatasetOffset(current_dataset, -1, frame);
},
disabled: function() {
return !_findDataset(current_dataset, -1);
}
},
{
icon: "fa fa-chevron-circle-right",
tooltip: _l("Next in History"),
onclick: function(frame) {
_loadDatasetOffset(current_dataset, 1, frame);
},
disabled: function() {
return !_findDataset(current_dataset, 1);
}
}
]
},
config
)
);
});
createList: function(name) {
if (!this.workingElements.length) {
var message = `${_l("No valid elements for final list")}. `;
message += `<a class="cancel-create" href="javascript:void(0);">${_l("Cancel")}</a> `;
message += _l("or");
message += ` <a class="reset" href="javascript:void(0);">${_l("start over")}</a>.`;
this._showAlert(message);
return;
}
var creator = this;
var elements = this.workingElements.map(element => creator._elementToJSON(element));
creator.blocking = true;
return creator
.creationFn(elements, name, creator.hideOriginals)
.always(() => {
creator.blocking = false;
})
.fail((xhr, status, message) => {
creator.trigger("error", {
xhr: xhr,
status: status,
message: _l("An error occurred while creating this collection")
});
})
.done(function(response, message, xhr) {
creator.trigger("collection:created", response, message, xhr);
creator.metric("collection:created", response);
if (typeof creator.oncreate === "function") {
creator.oncreate.call(this, response, message, xhr);
}
});
},
initialize: function(options) {
options = options || {};
this.frames = new Frames.View({ visible: false });
this.setElement(this.frames.$el);
this.active = false;
this.buttonActive = options.collection.add({
id: "enable-scratchbook",
icon: "fa-th",
tooltip: _l("Enable/Disable Scratchbook"),
onclick: () => {
this.active = !this.active;
this.buttonActive.set({
toggle: this.active,
show_note: this.active,
note_cls: this.active && "fa fa-check"
});
if (!this.active) {
this.frames.hide();
}
},
onbeforeunload: () => {
if (this.frames.length() > 0) {
return `You opened ${this.frames.length()} frame(s) which will be lost.`;
}
}
});
this.buttonLoad = options.collection.add({
id: "show-scratchbook",
icon: "fa-eye",
tooltip: _l("Show/Hide Scratchbook"),
show_note: true,
visible: false,
onclick: e => {
if (this.frames.visible) {
this.frames.hide();
} else {
this.frames.show();
}
}
});
this.frames
.on("add remove", () => {
if (this.frames.visible && this.frames.length() === 0) {
this.frames.hide();
}
this.buttonLoad.set({
note: this.frames.length(),
visible: this.frames.length() > 0
});
})
.on("show hide ", () => {
this.buttonLoad.set({
toggle: this.frames.visible,
icon: (this.frames.visible && "fa-eye") || "fa-eye-slash"
});
});
this.history_cache = {};
},
multiselectActions: function() {
var panel = this;
var actions = [
{
html: _l("Hide datasets"),
func: function() {
var action = HDA_MODEL.HistoryDatasetAssociation.prototype.hide;
panel.getSelectedModels().ajaxQueue(action);
}
},
{
html: _l("Unhide datasets"),
func: function() {
var action = HDA_MODEL.HistoryDatasetAssociation.prototype.unhide;
panel.getSelectedModels().ajaxQueue(action);
}
},
{
html: _l("Delete datasets"),
func: function() {
var action = HDA_MODEL.HistoryDatasetAssociation.prototype["delete"];
panel.getSelectedModels().ajaxQueue(action);
}
},
{
html: _l("Undelete datasets"),
func: function() {
var action = HDA_MODEL.HistoryDatasetAssociation.prototype.undelete;
panel.getSelectedModels().ajaxQueue(action);
}
}
];
if (panel.purgeAllowed) {
actions.push({
html: _l("Permanently delete datasets"),
func: function() {
if (
window.confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))
) {
var action = HDA_MODEL.HistoryDatasetAssociation.prototype.purge;
const historyContents = panel.getSelectedModels();
const selectedDatasets = historyContents.filter(
c => c.get("history_content_type") == "dataset"
);
historyContents.ajaxQueue(action, {}, selectedDatasets);
}
}
});
}
actions = actions.concat(panel._collectionActions());
return actions;
},
_isElementInvalid: function(element) {
if (element.history_content_type === "dataset_collection") {
return _l("is a collection, this is not allowed");
}
var validState = element.state === STATES.OK || _.contains(STATES.NOT_READY_STATES, element.state);
if (!validState) {
return _l("has errored, is paused, or is not accessible");
}
if (element.deleted || element.purged) {
return _l("has been deleted or purged");
}
return null;
},
render: function(options) {
var repo_queue_template = this.templateRepoQueue;
var repositories = this.model.models;
this.$el.html(
repo_queue_template({
title: _l("Repository Installation Queue"),
repositories: repositories,
empty: _l("No repositories in queue."),
queue: toolshed_util.queueLength()
})
);
$("#center").css("overflow", "auto");
this.bindEvents();
},
/** Display a modal showing an error message but fallback to alert if there's no modal */
function errorModal(message, title, details) {
if (!message) {
return;
}
message = _l(message);
title = _l(title) || _l("Error:");
if (window.Galaxy && Galaxy.modal) {
return _errorModal(message, title, details);
}
alert(`${title}\n\n${message}`);
console.log("error details:", JSON.stringify(details));
}
add: function(options) {
if (this.frame_counter >= this.options.frame_max) {
Galaxy.modal.show({
title: _l("Warning"),
body: `You have reached the maximum number of allowed frames (${this.options.frame_max}).`,
buttons: {
Close: function() {
Galaxy.modal.hide();
}
}
});
} else {
var frame_id = `#frame-${this.frame_uid++}`;
if ($(frame_id).length !== 0) {
Galaxy.modal.show({
title: _l("Error"),
body: "This frame already exists. This page might contain multiple frame managers.",
buttons: {
Close: function() {
Galaxy.modal.hide();
}
}
});
} else {
// initialize new frame elements
this.top = this.options.top_min;
var frame = new FrameView(options);
this.$el.append(frame.$el);
// set dimensions
options.width = this._toPixelCoord("width", this.options.frame.cols);
options.height = this._toPixelCoord("height", this.options.frame.rows);
// set default z-index and add to ui and frame list
this.frame_z = parseInt(frame.$el.css("z-index"));
this.frame_list[frame_id] = frame;
this.frame_counter++;
this._frameInit(frame, frame_id);
this._frameResize(frame, {
width: options.width,
height: options.height
});
this._frameInsert(frame, { top: 0, left: 0 }, true);
!this.visible && this.show();
this.trigger("add");
}
}
},
"click .purge-history": function() {
if (window.confirm(_l("This will permanently remove the data. Are you sure?"))) {
this.model.purge().done(data => {
this.render();
});
}
},
_setUpBehaviors: function($where) {
$where = $where || this.$el;
_super.prototype._setUpBehaviors.call(this, $where);
if (!this.model) {
return;
}
// anon users shouldn't have access to any of the following
if (!Galaxy.user || Galaxy.user.isAnonymous() || Galaxy.user.id !== this.model.get("user_id")) {
return;
}
var panel = this;
var nameSelector = "> .controls .name";
$where
.find(nameSelector)
.attr("title", _l("Click to rename history"))
.tooltip({ placement: "bottom" })
.make_text_editable({
on_finish: function(newName) {
var previousName = panel.model.get("name");
if (newName && newName !== previousName) {
panel.$el.find(nameSelector).text(newName);
panel.model.save({ name: newName }).fail(() => {
panel.$el.find(nameSelector).text(panel.model.previous("name"));
});
} else {
panel.$el.find(nameSelector).text(previousName);
}
}
});
},
_renderSelectButton: function($where) {
$where = $where || this.$el;
// do not render selector option if no actions
if (!this.multiselectActions().length) {
return null;
}
// do not render (and remove even) if nothing to select
if (!this.views.length) {
this.hideSelectors();
$where.find(".controls .actions .show-selectors-btn").remove();
return null;
}
// don't bother rendering if there's one already
var $existing = $where.find(".controls .actions .show-selectors-btn");
if ($existing.length) {
return $existing;
}
return faIconButton({
title: _l("Operations on multiple datasets"),
classes: "show-selectors-btn",
faIcon: "fa-check-square-o",
tooltipConfig: { placement: "top" }
}).prependTo($where.find(".controls .actions"));
},
// ----------------------------------------------------------------------------
/** display a modal (with details) about a failed Backbone ajax operation */
function ajaxErrorModal(model, xhr, options, message, title) {
message = message || DEFAULT_AJAX_ERR_MSG;
message += ` ${CONTACT_MSG}`;
title = title || _l("An error occurred");
var details = _ajaxDetails(model, xhr, options);
return errorModal(message, title, details);
}
func: function() {
if (Galaxy && Galaxy.currHistoryPanel && confirm(_l("Really delete the current history?"))) {
Galaxy.currHistoryPanel.model._delete().done(() => {
Galaxy.currHistoryPanel.loadCurrentHistory();
});
}
}
error: function(response) {
Galaxy.emit.debug("tool-form-composite::submit", "Submission failed.", response);
var input_found = false;
if (response && response.err_data) {
for (var i in self.forms) {
var form = self.forms[i];
var step_related_errors = response.err_data[form.model.get("step_index")];
if (step_related_errors) {
var error_messages = form.data.matchResponse(step_related_errors);
for (var input_id in error_messages) {
form.highlight(input_id, error_messages[input_id]);
input_found = true;
break;
}
}
}
}
if (!input_found) {
self.modal.show({
title: _l("Workflow submission failed"),
body: self._templateError(job_def, response && response.err_msg),
buttons: {
Close: function() {
self.modal.hide();
}
}
});
}
},
success: response => {
// show dialog
Galaxy.modal.show({
title: _l("New Visualization"),
body: this.template_view_new(response),
buttons: {
Cancel: () => {
window.top.location = `${getAppRoot()}visualizations/list`;
},
Create: () => {
this.create_browser($("#new-title").val(), $("#new-dbkey").val());
Galaxy.modal.hide();
}
}
});
// select default
var dbkeys_in_genomes = response.map(r => r[1]);
if (
window.galaxy_config.app.default_dbkey &&
_.contains(dbkeys_in_genomes, window.galaxy_config.app.default_dbkey)
) {
$("#new-dbkey").val(window.galaxy_config.app.default_dbkey);
}
// change focus
$("#new-title").focus();
$("select[name='dbkey']").select2();
// to support the large number of options for dbkey, enable scrolling in overlay.
$("#overlay").css("overflow", "auto");
}
/**
* Handle unsaved changes in visualization.
*/
handle_unsaved_changes(view) {
let Galaxy = getGalaxyInstance();
if (view.has_changes) {
Galaxy.modal.show({
title: _l("Close visualization"),
body: "There are unsaved changes to your visualization which will be lost if you do not save them.",
buttons: {
Cancel: () => {
Galaxy.modal.hide();
},
"Leave without Saving": () => {
$(window).off("beforeunload");
window.top.location = `${getAppRoot()}visualizations/list`;
},
Save: () => {
$.when(this.save_viz()).then(() => {
window.top.location = `${getAppRoot()}visualizations/list`;
});
}
}
});
} else {
window.top.location = `${getAppRoot()}visualizations/list`;
}
}
HDAListItemView.prototype.templates = (() => {
var titleBarTemplate = dataset => `
<div class="title-bar clear" tabindex="0">
<span class="state-icon"></span>
<div class="title">
<span class="hid">${dataset.hid}</span>
<span class="name">${_.escape(dataset.name)}</span>
</div>
</br>
${HISTORY_ITEM_LI.nametagTemplate(dataset)}
</div>
`;
var warnings = _.extend({}, _super.prototype.templates.warnings, {
hidden: BASE_MVC.wrapTemplate(
[
// add a warning when hidden
"<% if( !dataset.visible ){ %>",
'<div class="hidden-msg warningmessagesmall">',
_l("This dataset has been hidden"),
"</div>",
"<% } %>"
],
"dataset"
)
});
return _.extend({}, _super.prototype.templates, {
titleBar: titleBarTemplate,
warnings: warnings
});
})();
initialize: function(options) {
this.list = {};
this.options = Utils.merge(options, {
title: _l("Repeat"),
empty_text: "Not available.",
max: null,
min: null
});
this.button_new = new Ui.Button({
icon: "fa-plus",
title: `Insert ${this.options.title}`,
tooltip: `Add new ${this.options.title} block`,
cls: "btn btn-secondary float-none form-repeat-add",
onclick: function() {
if (options.onnew) {
options.onnew();
}
}
});
this.setElement(
$("<div/>")
.append((this.$list = $("<div/>")))
.append($("<div/>").append(this.button_new.$el))
);
},
/** private helper that builds the modal and handles adding details */
function _errorModal(message, title, details) {
// create and return the modal, adding details button only if needed
Galaxy.modal.show({
title: title,
body: message,
closing_events: true,
buttons: {
Ok: function() {
Galaxy.modal.hide();
}
}
});
Galaxy.modal.$el.addClass("error-modal");
if (details) {
Galaxy.modal
.$(".error-details")
.add(Galaxy.modal.$('button:contains("Details")'))
.remove();
$("<div/>")
.addClass("error-details")
.hide()
.appendTo(Galaxy.modal.$(".modal-content"))
.append([$("<p/>").text(DETAILS_MSG), $("<pre/>").text(JSON.stringify(details, null, " "))]);
$(`<button id="button-1" class="float-left">${_l("Details")}</button>`)
.appendTo(Galaxy.modal.$(".buttons"))
.click(() => {
Galaxy.modal.$(".error-details").toggle();
});
}
return Galaxy.modal;
}
.fail((xhr, status, message) => {
creator.trigger("error", {
xhr: xhr,
status: status,
message: _l("An error occurred while creating this collection")
});
})
xhr.fail((xhr, status, message) => {
// Exception messages are hidden within error page including: '...not allowed in this Galaxy instance.'
// unbury and re-add to xhr
var error = _l("Unable to purge dataset");
var messageBuriedInUnfortunatelyFormattedError =
"Removal of datasets by users " + "is not allowed in this Galaxy instance";
if (xhr.responseJSON && xhr.responseJSON.error) {
error = xhr.responseJSON.error;
} else if (xhr.responseText.indexOf(messageBuriedInUnfortunatelyFormattedError) !== -1) {
error = messageBuriedInUnfortunatelyFormattedError;
}
xhr.responseText = error;
hda.trigger("error", hda, xhr, options, _l(error), {
error: error
});
});
initialize: function(options) {
var self = this;
this.model = (options && options.model) || new Backbone.Model(options);
this.setElement($("<div/>").addClass("corner frame"));
this.$el
.append(
$("<div/>")
.addClass("f-header corner")
.append($("<div/>").addClass("f-title"))
.append(
$("<div/>")
.addClass("f-icon f-close fa fa-close")
.tooltip({
title: _l("Close"),
placement: "bottom"
})
)
)
.append($("<div/>").addClass("f-content"))
.append(
$("<div/>")
.addClass("f-resize f-icon corner fa fa-expand")
.tooltip({ title: "Resize" })
)
.append($("<div/>").addClass("f-cover"));
this.$header = this.$(".f-header");
this.$title = this.$(".f-title");
this.$content = this.$(".f-content");
this.render();
this.listenTo(this.model, "change", this.render, this);
},
_getConversion: function() {
var self = this;
var form = new Form({
title: _l("Convert to new format"),
operations: {
submit_conversion: new Ui.Button({
tooltip: _l("Convert the datatype to a new format."),
title: _l("Convert datatype"),
icon: "fa-exchange",
onclick: function() {
self._submit("conversion", form);
}
})
}
});
return form;
},
_getPermission: function() {
var self = this;
var form = new Form({
title: _l("Manage dataset permissions"),
operations: {
submit_permission: new Ui.Button({
tooltip: _l("Save permissions."),
title: _l("Save permissions"),
icon: "fa-floppy-o ",
onclick: function() {
self._submit("permission", form);
}
})
}
});
return form;
},
show: function() {
var self = this;
if (!Galaxy.currHistoryPanel || !Galaxy.currHistoryPanel.model) {
window.setTimeout(() => {
self.show();
}, 500);
return;
}
this.current_user = Galaxy.user.id;
if (!this.modal) {
this.tabs = new Tabs.View();
this.default_view = new UploadViewDefault(this);
this.tabs.add({
id: "regular",
title: _l("Regular"),
$el: this.default_view.$el
});
this.composite_view = new UploadViewComposite(this);
this.tabs.add({
id: "composite",
title: _l("Composite"),
$el: this.composite_view.$el
});
this.collection_view = new UploadViewCollection(this);
this.tabs.add({
id: "collection",
title: _l("Collection"),
$el: this.collection_view.$el
});
this.rule_based_view = new UploadViewRuleBased(this);
this.tabs.add({
id: "rule-based",
title: _l("Rule-based"),
$el: this.rule_based_view.$el
});
this.modal = new Modal.View({
title: _l("Download from web or upload from disk"),
body: this.tabs.$el,
height: this.options.height,
width: this.options.width,
closing_events: true,
title_separator: false
});
}
this.modal.show();
},
onfirstsearch: searchFor => {
this.$("#search-histories").searchInput("toggle-loading");
this.renderInfo(_l("loading all histories for search"));
this.collection.fetchAll().done(() => {
this.$("#search-histories").searchInput("toggle-loading");
this.renderInfo("");
});
},