initialize: function(options) {
this.options = Utils.merge(options, this.options);
// create view for upload/progress button
this.ui_button = new UploadButton.View({
onclick: e => {
e.preventDefault();
this.show();
},
onunload: () => {
var percentage = this.ui_button.model.get("percentage", 0);
if (percentage > 0 && percentage < 100) {
return "Several uploads are queued.";
}
}
});
// set element to button view
this.setElement(this.ui_button.$el);
// load extensions
UploadUtils.getUploadDatatypes(
list_extensions => {
this.list_extensions = list_extensions;
},
this.options.datatypes_disable_auto,
this.options.auto
);
// load genomes
UploadUtils.getUploadGenomes(list_genomes => {
this.list_genomes = list_genomes;
}, this.default_genome);
},
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))
);
},
_workflowLoadAjax: function(workflowId, version, options) {
$.ajax(
Utils.merge(options, {
url: this.urls.load_workflow,
data: { id: workflowId, _: "true", version: version },
dataType: "json",
cache: false
})
);
},
addMenu: function(options) {
this.collection.add(
Utils.merge(options, {
title: "",
target: "",
href: "",
onclick: null,
divider: false,
visible: true,
icon: null,
cls: "button-menu btn-group"
})
);
}
initialize: function(options) {
this.options = Utils.merge(options, {
content: "No content available.",
onchange: null,
ondblclick: null,
onconfirm: null,
cls: "grid",
selectable: true
});
this.setElement(this._template());
this.$thead = this.$("thead");
this.$tbody = this.$("tbody");
this.$tmessage = this.$("tmessage");
this.row = $("<tr/>");
this.row_count = 0;
},
_.each(this.model.get("steps"), (step, i) => {
Galaxy.emit.debug("tool-form-composite::initialize()", `${i} : Preparing workflow step.`);
var icon = WorkflowIcons[step.step_type];
var title = `${parseInt(i + 1)}: ${step.step_label || step.step_name}`;
if (step.annotation) {
title += ` - ${step.annotation}`;
}
if (step.step_version) {
title += ` (Galaxy Version ${step.step_version})`;
}
step = Utils.merge(
{
index: i,
fixed_title: _.escape(title),
icon: icon || "",
help: null,
citations: null,
collapsible: true,
collapsed: i > 0 && !self._isDataStep(step),
sustain_version: true,
sustain_repeats: true,
sustain_conditionals: true,
narrow: true,
text_enable: "Edit",
text_disable: "Undo",
cls_enable: "fa fa-edit",
cls_disable: "fa fa-undo",
errors: step.messages,
initial_errors: true,
cls: "ui-portlet-section",
hide_operations: true,
needs_refresh: false,
always_refresh: step.step_type != "tool"
},
step
);
self.steps[i] = step;
self.links[i] = [];
self.parms[i] = {};
});
initialize: function(options) {
// configure options
this.options = Utils.merge(options, this.optionsDefault);
// create new element
this.setElement(this._template(this.options));
// check if container exists
if (!this.options.container) {
console.log("ui-select::initialize() : container not specified.");
return;
}
// add to dom
this.options.container.append(this.$el);
// link selection dictionary
this.select_data = this.options.data;
// refresh
this._refresh();
if (!this.options.multiple) {
// initial value
if (this.options.value) {
this._setValue(this.options.value);
}
// add change event
var self = this;
if (this.options.onchange) {
this.$el.on("change", () => {
self.options.onchange(self.value());
});
}
}
},
this.deferred.execute(promise => {
self.$steps.addClass("ui-steps");
if (step.step_type == "tool") {
step.postchange = function(process, form) {
var current_state = {
tool_id: step.id,
tool_version: step.version,
inputs: $.extend(true, {}, form.data.create())
};
form.wait(true);
Galaxy.emit.debug("tool-form-composite::postchange()", "Sending current state.", current_state);
Utils.request({
type: "POST",
url: `${getAppRoot()}api/tools/${step.id}/build`,
data: current_state,
success: function(data) {
form.update(data);
form.wait(false);
Galaxy.emit.debug("tool-form-composite::postchange()", "Received new model.", data);
process.resolve();
},
error: function(response) {
Galaxy.emit.debug("tool-form-composite::postchange()", "Refresh request failed.", response);
process.reject();
}
});
};
form = new ToolFormBase(step);
if (step.post_job_actions && step.post_job_actions.length) {
form.portlet.append(
$("<div/>")
.addClass("ui-form-element-disabled")
.append(
$("<div/>")
.addClass("ui-form-title")
.html("<b>Job Post Actions</b>")
)
.append(
$("<div/>")
.addClass("ui-form-preview")
.html(
_.reduce(
step.post_job_actions,
(memo, value) => `${memo} ${value.short_str}`,
""
)
)
)
);
}
} else {
var is_simple_input = ["data_input", "data_collection_input"].indexOf(step.step_type) != -1;
_.each(step.inputs, input => {
input.flavor = "module";
input.hide_label = is_simple_input;
});
form = new Form(
Utils.merge(
{
title: step.fixed_title,
onchange: function() {
_.each(self.links[step.index], link => {
self._refreshStep(link);
});
},
inputs:
step.inputs && step.inputs.length > 0
? step.inputs
: [
{
type: "hidden",
name: "No options available.",
ignore: null
}
]
},
step
)
);
if (step.step_label) {
form.$el.attr("step-label", step.step_label);
}
}
self.forms[step.index] = form;
self._append(self.$steps, form.$el);
if (step.needs_refresh) {
self._refreshStep(step);
}
form.portlet[!self.show_progress ? "enable" : "disable"]();
if (self.show_progress) {
self.execute_btn.model.set({
wait: true,
wait_text: "Preparing...",
percentage: ((step.index + 1) * 100.0) / self.steps.length
});
}
Galaxy.emit.debug("tool-form-composite::initialize()", `${step.index} : Workflow step state ready.`, step);
window.setTimeout(() => {
promise.resolve();
}, 0);
});
initialize: function(options) {
var self = this;
this.options = Utils.merge(options, this.options);
// create view for upload/progress button
this.ui_button = new UploadButton.View({
onclick: function(e) {
e.preventDefault();
self.show();
},
onunload: function() {
var percentage = self.ui_button.model.get("percentage", 0);
if (percentage > 0 && percentage < 100) {
return "Several uploads are queued.";
}
}
});
// set element to button view
this.setElement(this.ui_button.$el);
// load extensions
var self = this;
Utils.get({
url: `${Galaxy.root}api/datatypes?extension_only=False`,
success: function(datatypes) {
for (var key in datatypes) {
self.list_extensions.push({
id: datatypes[key].extension,
text: datatypes[key].extension,
description: datatypes[key].description,
description_url: datatypes[key].description_url,
composite_files: datatypes[key].composite_files
});
}
self.list_extensions.sort((a, b) => {
var a_text = a.text && a.text.toLowerCase();
var b_text = b.text && b.text.toLowerCase();
return a_text > b_text ? 1 : a_text < b_text ? -1 : 0;
});
if (!self.options.datatypes_disable_auto) {
self.list_extensions.unshift(self.options.auto);
}
}
});
// load genomes
Utils.get({
url: `${Galaxy.root}api/genomes`,
success: function(genomes) {
for (var key in genomes) {
self.list_genomes.push({
id: genomes[key][1],
text: genomes[key][0]
});
}
self.list_genomes.sort((a, b) => {
if (a.id == self.options.default_genome) {
return -1;
}
if (b.id == self.options.default_genome) {
return 1;
}
return a.text > b.text ? 1 : a.text < b.text ? -1 : 0;
});
}
});
},