BASE_MVC.mixin(
searchableMixin,
/** @lends DatasetAssociation.prototype */ {
_logNamespace: logNamespace,
/** default attributes for a model */
defaults: {
state: STATES.NEW,
deleted: false,
purged: false,
name: "(unnamed dataset)",
accessible: true,
// sniffed datatype (sam, tabular, bed, etc.)
data_type: "",
file_ext: "",
file_size: 0,
// array of associated file types (eg. [ 'bam_index', ... ])
meta_files: [],
misc_blurb: "",
misc_info: "",
tags: []
// do NOT default on annotation, as this default is valid and will be passed on 'save'
// which is incorrect behavior when the model is only partially fetched (annos are not passed in summary data)
//annotation : ''
},
/** instance vars and listeners */
initialize: function(attributes, options) {
this.debug(`${this}(Dataset).initialize`, attributes, options);
//!! this state is not in trans.app.model.Dataset.states - set it here -
if (!this.get("accessible")) {
this.set("state", STATES.NOT_VIEWABLE);
}
/** Datasets rely/use some web controllers - have the model generate those URLs on startup */
this.urls = this._generateUrls();
this._setUpListeners();
},
_getDatasetId: function() {
return this.get("id");
},
/** returns misc. web urls for rendering things like re-run, display, etc. */
_generateUrls: function() {
const id = this._getDatasetId();
if (!id) {
return {};
}
var urls = {
purge: `datasets/${id}/purge_async`,
display: `datasets/${id}/display/?preview=True`,
edit: `datasets/edit?dataset_id=${id}`,
download: `datasets/${id}/display${this._downloadQueryParameters()}`,
report_error: `dataset/errors?id=${id}`,
rerun: `tool_runner/rerun?id=${id}`,
show_params: `datasets/${id}/show_params`,
visualization: "visualization",
meta_download: `dataset/get_metadata_file?hda_id=${id}&metadata_name=`
};
_.each(urls, (value, key) => {
urls[key] = getAppRoot() + value;
});
this.urls = urls;
return urls;
},
_downloadQueryParameters: function() {
return `?to_ext=${this.get("file_ext")}`;
},
/** set up any event listeners
* event: state:ready fired when this DA moves into/is already in a ready state
*/
_setUpListeners: function() {
// if the state has changed and the new state is a ready state, fire an event
this.on("change:state", function(currModel, newState) {
this.log(`${this} has changed state:`, currModel, newState);
if (this.inReadyState()) {
this.trigger("state:ready", currModel, newState, this.previous("state"));
}
});
// the download url (currently) relies on having a correct file extension
this.on("change:id change:file_ext", function(currModel) {
this._generateUrls();
});
},
// ........................................................................ common queries
/** override to add urls */
toJSON: function() {
var json = Backbone.Model.prototype.toJSON.call(this);
//console.warn( 'returning json?' );
//return json;
return _.extend(json, {
urls: this.urls
});
},
/** Is this dataset deleted or purged? */
isDeletedOrPurged: function() {
return this.get("deleted") || this.get("purged");
},
/** Is this dataset in a 'ready' state; where 'Ready' states are states where no
* processing (for the ds) is left to do on the server.
*/
inReadyState: function() {
var ready = _.contains(STATES.READY_STATES, this.get("state"));
return this.isDeletedOrPurged() || ready;
},
/** Does this model already contain detailed data (as opposed to just summary level data)? */
hasDetails: function() {
// if it's inaccessible assume it has everything it needs
if (!this.get("accessible")) {
return true;
}
return this.has("annotation");
},
/** Convenience function to match dataset.has_data. */
hasData: function() {
return this.get("file_size") > 0;
},
// ........................................................................ ajax
fetch: function(options) {
var dataset = this;
return Backbone.Model.prototype.fetch.call(this, options).always(() => {
dataset._generateUrls();
});
},
/** override to use actual Dates objects for create/update times */
parse: function(response, options) {
var parsed = Backbone.Model.prototype.parse.call(this, response, options);
if (parsed.create_time) {
parsed.create_time = new Date(parsed.create_time);
}
if (parsed.update_time) {
parsed.update_time = new Date(parsed.update_time);
}
return parsed;
},
/** override to wait by default */
save: function(attrs, options) {
options = options || {};
options.wait = _.isUndefined(options.wait) ? true : options.wait;
return Backbone.Model.prototype.save.call(this, attrs, options);
},
//NOTE: subclasses of DA's will need to implement url and urlRoot in order to have these work properly
/** save this dataset, _Mark_ing it as deleted (just a flag) */
delete: function(options) {
if (this.get("deleted")) {
return jQuery.when();
}
return this.save({ deleted: true }, options);
},
/** save this dataset, _Mark_ing it as undeleted */
undelete: function(options) {
if (!this.get("deleted") || this.get("purged")) {
return jQuery.when();
}
return this.save({ deleted: false }, options);
},
/** remove the file behind this dataset from the filesystem (if permitted) */
purge: function _purge(options) {
//TODO: use, override model.destroy, HDA.delete({ purge: true })
if (this.get("purged")) {
return jQuery.when();
}
options = options || {};
options.url = this.urls.purge;
//TODO: ideally this would be a DELETE call to the api
// using purge async for now
var hda = this;
var xhr = jQuery.ajax(options);
xhr.done((message, status, responseObj) => {
hda.set({ deleted: true, purged: true });
});
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
});
});
return xhr;
},
// ........................................................................ searching
/** what attributes of an HDA will be used in a text search */
searchAttributes: ["name", "file_ext", "genome_build", "misc_blurb", "misc_info", "annotation", "tags"],
/** our attr keys don't often match the labels we display to the user - so, when using
* attribute specifiers ('name="bler"') in a term, allow passing in aliases for the
* following attr keys.
*/
searchAliases: {
title: "name",
format: "file_ext",
database: "genome_build",
blurb: "misc_blurb",
description: "misc_blurb",
info: "misc_info",
tag: "tags"
},
// ........................................................................ misc
/** String representation */
toString: function() {
var nameAndId = this.get("id") || "";
if (this.get("name")) {
nameAndId = `"${this.get("name")}",${nameAndId}`;
}
return `Dataset(${nameAndId})`;
}
}
)
BASE_MVC.mixin(BASE_MVC.SelectableViewMixin, BASE_MVC.DraggableViewMixin, {
tagName: "div",
className: "list-item",
/** Set up the base class and all mixins */
initialize: function(attributes) {
ExpandableView.prototype.initialize.call(this, attributes);
BASE_MVC.SelectableViewMixin.initialize.call(this, attributes);
BASE_MVC.DraggableViewMixin.initialize.call(this, attributes);
this._setUpListeners();
},
/** event listeners */
_setUpListeners: function() {
// hide the primary actions in the title bar when selectable and narrow
this.on(
"selectable",
function(isSelectable) {
if (isSelectable) {
this.$(".primary-actions").hide();
} else {
this.$(".primary-actions").show();
}
},
this
);
return this;
},
// ........................................................................ rendering
/** In this override, call methods to build warnings, titlebar and primary actions */
_buildNewRender: function() {
var $newRender = ExpandableView.prototype._buildNewRender.call(this);
$newRender.children(".warnings").replaceWith(this._renderWarnings());
$newRender.children(".title-bar").replaceWith(this._renderTitleBar());
$newRender.children(".primary-actions").append(this._renderPrimaryActions());
$newRender.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle());
return $newRender;
},
/** In this override, render the selector controls and set up dragging before the swap */
_swapNewRender: function($newRender) {
ExpandableView.prototype._swapNewRender.call(this, $newRender);
if (this.selectable) {
this.showSelector(0);
}
if (this.draggable) {
this.draggableOn();
}
return this.$el;
},
/** Render any warnings the item may need to show (e.g. "I'm deleted") */
_renderWarnings: function() {
var view = this;
var $warnings = $('<div class="warnings"></div>');
var json = view.model.toJSON();
//TODO:! unordered (map)
_.each(view.templates.warnings, templateFn => {
$warnings.append($(templateFn(json, view)));
});
return $warnings;
},
/** Render the title bar (the main/exposed SUMMARY dom element) */
_renderTitleBar: function() {
return $(this.templates.titleBar(this.model.toJSON(), this));
},
/** Return an array of jQ objects containing common/easily-accessible item controls */
_renderPrimaryActions: function() {
// override this
return [];
},
/** Render the title bar (the main/exposed SUMMARY dom element) */
_renderSubtitle: function() {
return $(this.templates.subtitle(this.model.toJSON(), this));
},
// ......................................................................... events
/** event map */
events: {
// expand the body when the title is clicked or when in focus and space or enter is pressed
"click .title-bar": "_clickTitleBar",
"keydown .title-bar": "_keyDownTitleBar",
"click .selector": "toggleSelect"
},
/** expand when the title bar is clicked */
_clickTitleBar: function(event) {
event.stopPropagation();
if (event.altKey) {
this.toggleSelect(event);
if (!this.selectable) {
this.showSelector();
}
} else {
this.toggleExpanded();
}
},
/** expand when the title bar is in focus and enter or space is pressed */
_keyDownTitleBar: function(event) {
// bail (with propagation) if keydown and not space or enter
var KEYCODE_SPACE = 32;
var KEYCODE_RETURN = 13;
if (
event &&
event.type === "keydown" &&
(event.keyCode === KEYCODE_SPACE || event.keyCode === KEYCODE_RETURN)
) {
this.toggleExpanded();
event.stopPropagation();
return false;
}
return true;
},
// ......................................................................... misc
/** String representation */
toString: function() {
var modelString = this.model ? `${this.model}` : "(no model)";
return `ListItemView(${modelString})`;
}
})
import DATASET from "mvc/dataset/dataset-model";
import HISTORY_CONTENT from "mvc/history/history-content-model";
import BASE_MVC from "mvc/base-mvc";
import _l from "utils/localization";
//==============================================================================
var _super = DATASET.DatasetAssociation;
var hcontentMixin = HISTORY_CONTENT.HistoryContentMixin;
/** @class (HDA) model for a Galaxy dataset contained in and related to a history.
*/
var HistoryDatasetAssociation = _super.extend(
BASE_MVC.mixin(
hcontentMixin,
/** @lends HistoryDatasetAssociation.prototype */ {
/** default attributes for a model */
defaults: _.extend({}, _super.prototype.defaults, hcontentMixin.defaults, {
history_content_type: "dataset",
model_class: "HistoryDatasetAssociation"
})
}
)
);
//==============================================================================
export default {
HistoryDatasetAssociation: HistoryDatasetAssociation
};
BASE_MVC.mixin(
searchableMixin,
/** @lends Job.prototype */ {
_logNamespace: logNamespace,
/** default attributes for a model */
defaults: {
model_class: "Job",
tool_id: null,
exit_code: null,
inputs: {},
outputs: {},
params: {},
create_time: null,
update_time: null,
state: STATES.NEW
},
/** override to parse params on incomming */
parse: function(response, options) {
response.params = this.parseParams(response.params);
return response;
},
/** override to treat param values as json */
parseParams: function(params) {
var newParams = {};
_.each(params, (value, key) => {
newParams[key] = JSON.parse(value);
});
return newParams;
},
/** instance vars and listeners */
initialize: function(attributes, options) {
this.debug(`${this}(Job).initialize`, attributes, options);
this.set("params", this.parseParams(this.get("params")), {
silent: true
});
this.outputCollection = attributes.outputCollection || new HISTORY_CONTENTS.HistoryContents([]);
this._setUpListeners();
},
/** set up any event listeners
* event: state:ready fired when this DA moves into/is already in a ready state
*/
_setUpListeners: function() {
// if the state has changed and the new state is a ready state, fire an event
this.on("change:state", function(currModel, newState) {
this.log(`${this} has changed state:`, currModel, newState);
if (this.inReadyState()) {
this.trigger("state:ready", currModel, newState, this.previous("state"));
}
});
},
// ........................................................................ common queries
/** Is this job in a 'ready' state; where 'Ready' states are states where no
* processing is left to do on the server.
*/
inReadyState: function() {
return _.contains(STATES.READY_STATES, this.get("state"));
},
/** Does this model already contain detailed data (as opposed to just summary level data)? */
hasDetails: function() {
//?? this may not be reliable
return !_.isEmpty(this.get("outputs"));
},
// ........................................................................ ajax
/** root api url */
urlRoot: `${Galaxy.root}api/jobs`,
//url : function(){ return this.urlRoot; },
// ........................................................................ searching
// see base-mvc, SearchableModelMixin
/** what attributes of an Job will be used in a text search */
//searchAttributes : [
// 'tool'
//],
// ........................................................................ misc
/** String representation */
toString: function() {
return ["Job(", this.get("id"), ":", this.get("tool_id"), ")"].join("");
}
}
)