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

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This commit is contained in:
Dannon Baker
2017-12-21 17:59:16 -05:00
parent d7b9068496 0bf73e4381
commit 0eeb09545f
104 changed files with 1925 additions and 1906 deletions
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client/GruntFile.js
+9 -22
View File
@@ -1,26 +1,13 @@
module.exports = function(grunt) {
"use strict";
var GALAXY_PATHS = {
dist : '../static/scripts',
maps : '../static/maps',
// this symlink allows us to serve uncompressed scripts in DEV_PATH for use with sourcemaps
srcSymlink : '../static/src',
},
TOOLSHED_PATHS = {
dist : '../static/toolshed/scripts',
maps : '../static/toolshed/maps',
srcSymlink : '../static/toolshed/src',
};
grunt.config.set( 'app', 'galaxy' );
grunt.config.set( 'paths', GALAXY_PATHS );
if( grunt.option( 'app' ) === 'toolshed' ){
grunt.config.set( 'app', grunt.option( 'app' ) );
grunt.config.set( 'paths', TOOLSHED_PATHS );
}
dist: "../static/scripts",
maps: "../static/maps",
// this symlink allows us to serve uncompressed scripts in DEV_PATH for use with sourcemaps
srcSymlink: "../static/src"
};
grunt.config.set("app", "galaxy");
grunt.config.set("paths", GALAXY_PATHS);
// see the sub directory grunt-tasks/ for individual task definitions
grunt.loadTasks( 'grunt-tasks' );
grunt.registerTask( 'default', [ 'uglify' ] );
grunt.loadTasks("grunt-tasks");
grunt.registerTask("default", ["style"]);
};
client/README.md
-10
View File
@@ -66,13 +66,3 @@ As mentioned above, 'make client' will also rebuild styles. If you *only* want
to run the style task, use the following command from the `client` directory:
yarn run style
The Toolshed Client Build
=========================
The toolshed client is not tightly integrated with the rest of the build
system. To build the toolshed client, execute the following command from the
`client` directory.
yarn run build-toolshed
client/galaxy/scripts/apps/extended.js
+150 -2
View File
@@ -1,11 +1,37 @@
import _l from "utils/localization";
import GalaxyApp from "galaxy";
import WorkflowView from "mvc/workflow/workflow-view";
import Trackster from "viz/trackster";
import Circster from "viz/circster";
import Phyloviz from "viz/phyloviz";
import Sweepster from "viz/sweepster";
import GalaxyLibrary from "galaxy.library";
import AdminToolshed from "admin.toolshed";
import Masthead from "layout/masthead";
import user from "mvc/user/user-model";
import Modal from "mvc/ui/ui-modal";
import pagesEditorOnload from "galaxy.pages";
import Data from "mvc/dataset/data";
import History from "mvc/history/history-model";
import StructureView from "mvc/history/history-structure-view";
import HistoryContents from "mvc/history/history-contents";
import MultiPanel from "mvc/history/multi-panel";
import HistoryView from "mvc/history/history-view";
import HistoryViewEdit from "mvc/history/history-view-edit";
import HistoryViewAnnotated from "mvc/history/history-view-annotated";
import HistoryCopyDialog from "mvc/history/copy-dialog";
import HDAListItemEdit from "mvc/history/hda-li-edit";
import HDAModel from "mvc/history/hda-model";
import addLogging from "utils/add-logging";
import LegacyGridView from "legacy/grid/grid-view";
import * as run_stats from "reports/run_stats";
import ToolshedGroups from "toolshed/toolshed.groups";
if (window.Galaxy && window.Galaxy.debug === undefined) {
//TODO: (kind of a temporary hack?) Must have Galaxy.logging for some of the imports
//here; remove when imports are all fixed.
addLogging(window.Galaxy, "GalaxyApp");
}
export function mastheadEntry(options) {
if (!Galaxy.user) {
@@ -34,17 +60,139 @@ export function workflowEntry(options) {
new WorkflowView(options);
}
function libraryEntry(options) {
export function libraryEntry(options) {
new GalaxyLibrary.GalaxyApp(options);
}
export function historyEntry(options) {
$("#toggle-deleted").modeButton({
initialMode: options.initialModeDeleted,
modes: [
{ mode: "showing_deleted", html: _l("Exclude deleted") },
{ mode: "not_showing_deleted", html: _l("Include deleted") }
]
});
$("#toggle-hidden").modeButton({
initialMode: options.initialModeHidden,
modes: [
{ mode: "showing_hidden", html: _l("Exclude hidden") },
{ mode: "not_showing_hidden", html: _l("Include hidden") }
]
});
$("#switch").click(function() {
//##HACK:ity hack hack
//##TODO: remove when out of iframe
var hview =
Galaxy.currHistoryPanel || (window.top.Galaxy && window.top.Galaxy.currHistoryPanel)
? window.top.Galaxy.currHistoryPanel
: null;
if (hview) {
hview.switchToHistory("${ history[ 'id' ] }");
} else {
window.location = "${ switch_to_url }";
}
});
// use_panels effects where the the center_panel() is rendered:
// w/o it renders to the body, w/ it renders to #center - we need to adjust a few things for scrolling to work
if (options.hasMasthead) {
$("#center").addClass("flex-vertical-container");
}
let viewClass = options.userIsOwner ? HistoryViewEdit.HistoryViewEdit : HistoryView.HistoryView;
let historyModel = new History.History(options.historyJSON);
// attach the copy dialog to the import button now that we have a history
$("#import").click(function() {
HistoryCopyDialog(historyModel, {
useImport: true,
// use default datasets option to match the toggle-deleted button
allDatasets: $("#toggle-deleted").modeButton("getMode").mode === "showing_deleted"
}).done(function() {
if (window === window.parent) {
window.location = Galaxy.root;
} else if (Galaxy.currHistoryPanel) {
Galaxy.currHistoryPanel.loadCurrentHistory();
}
});
});
let historyView = new viewClass({
el: $("#history-" + options.historyJSON.id),
className: viewClass.prototype.className + " wide",
$scrollContainer: options.hasMasthead
? function() {
return this.$el.parent();
}
: undefined,
model: historyModel,
show_deleted: options.showDeletedJson,
show_hidden: options.showHiddenJson,
purgeAllowed: options.allow_user_dataset_purge
});
historyView.trigger("loading");
historyModel
.fetchContents({ silent: true })
.fail(function() {
alert("Galaxy history failed to load");
})
.done(function() {
historyView.trigger("loading-done");
historyView.render();
});
$("#toggle-deleted").on("click", function() {
historyView.toggleShowDeleted();
});
$("#toggle-hidden").on("click", function() {
historyView.toggleShowHidden();
});
}
export function multiHistoryEntry(options) {
let histories = new History.HistoryCollection([], {
includeDeleted: options.includingDeleted,
order: options.order,
limitOnFirstFetch: options.limit,
limitPerFetch: options.limit,
currentHistoryId: options.current_history_id
});
let multipanel = new MultiPanel.MultiPanelColumns({
el: $("#center").get(0),
histories: histories
});
histories.fetchFirst({ silent: true }).done(function() {
multipanel.createColumns();
multipanel.render(0);
});
}
export const bundleEntries = {
library: libraryEntry,
masthead: mastheadEntry,
workflow: workflowEntry,
trackster: tracksterEntry,
circster: circsterEntry,
adminToolshed: adminToolshedEntry
adminToolshed: adminToolshedEntry,
pages: pagesEditorOnload,
phyloviz: Phyloviz.PhylovizView,
createTabularDatasetChunkedView: Data.createTabularDatasetChunkedView,
multiHistory: multiHistoryEntry,
history: historyEntry,
History: History.History,
HistoryContents: HistoryContents.HistoryContents,
SweepsterVisualization: Sweepster.SweepsterVisualization,
SweepsterVisualizationView: Sweepster.SweepsterVisualizationView,
HistoryCopyDialog,
HistoryViewAnnotated,
Trackster,
StructureView,
HDAListItemEdit,
HDAModel,
GalaxyApp,
LegacyGridView,
run_stats,
ToolshedGroups
};
window.bundleEntries = bundleEntries;
client/galaxy/scripts/galaxy.js
+3
View File
@@ -256,6 +256,9 @@ GalaxyApp.prototype.toString = function toString() {
return `GalaxyApp(${userEmail})`;
};
// This is not great. Rework to be a singleton-style Galaxy app accessible/created by import
window.Galaxy = window.Galaxy || new GalaxyApp();
// ============================================================================
export default {
GalaxyApp: GalaxyApp
client/galaxy/scripts/galaxy.library.js
+1 -1
View File
@@ -176,7 +176,7 @@ var GalaxyLibrary = Backbone.View.extend({
mod_toastr.info("You must select at least one dataset to download");
Galaxy.libraries.library_router.navigate(`folders/${folder_id}`, { trigger: true, replace: true });
} else {
Galaxy.libraries.folderToolbarView.download(folder_id, format);
Galaxy.libraries.folderToolbarView.download(format);
Galaxy.libraries.library_router.navigate(`folders/${folder_id}`, { trigger: false, replace: true });
}
});
client/galaxy/scripts/galaxy.pages.js
+3 -1
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@@ -5,6 +5,8 @@ import "libs/jquery/jquery.wymeditor";
import "libs/jquery/jquery.autocomplete";
import GridView from "mvc/grid/grid-view";
var WYMeditor = window.WYMeditor;
var CONTROLS = {
// Item types.
ITEM_HISTORY: "item_history",
@@ -487,7 +489,7 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
}
};
export default function editor_onload() {
export default function pagesEditorOnload() {
// Generic error handling
$(document).ajaxError((e, x) => {
// console.log( e, x );
client/galaxy/scripts/layout/router.js
+2 -4
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@@ -17,10 +17,8 @@ var Router = Backbone.Router.extend({
data.__identifer = Math.random()
.toString(36)
.substr(2);
if (!$.isEmptyObject(data)) {
url += url.indexOf("?") == -1 ? "?" : "&";
url += $.param(data, true);
}
url += url.indexOf("?") == -1 ? "?" : "&";
url += $.param(data, true);
Galaxy.params = data;
this.navigate(url, { trigger: true });
},
client/galaxy/scripts/libs/jquery/jquery.wymeditor.js
+2
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@@ -4754,3 +4754,5 @@ WYMeditor.WymClassSafari.prototype.getTagForStyle = function(style) {
if(/super/.test(style)) return 'sup';
return false;
};
window.WYMeditor = WYMeditor;
client/galaxy/scripts/mvc/collection/list-collection-creator.js
+2 -2
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@@ -278,8 +278,8 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
/** describe what is wrong with a particular element if anything */
_isElementInvalid: function(element) {
if (element.history_content_type !== "dataset") {
return _l("is not a dataset");
if (element.history_content_type === "dataset_collection") {
return _l("is a collection, this is not allowed");
}
var validState = element.state === STATES.OK || _.contains(STATES.NOT_READY_STATES, element.state);
if (!validState) {
client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
+3 -2
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@@ -1796,7 +1796,8 @@ var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal(datase
oncreate: function(creator, response) {
Galaxy.modal.hide();
deferred.resolve(response);
}
},
title: _l("Create a collection of paired datasets")
});
if (!window.Galaxy || !Galaxy.modal) {
@@ -1805,7 +1806,7 @@ var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal(datase
creator = new PairedCollectionCreator(options);
Galaxy.modal.show({
title: _l("Create a collection of paired datasets"),
title: options.title,
body: creator.$el,
width: "80%",
height: "800px",
client/galaxy/scripts/mvc/dataset/data.js
+1 -3
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@@ -1,8 +1,6 @@
import _l from "utils/localization";
// Additional dependencies: jQuery, underscore.
import Modal from "mvc/ui/ui-modal";
import Frames from "mvc/ui/ui-frames";
import mod_icon_btn from "mvc/ui/icon-button";
// Additional dependencies: jQuery, underscore.
/**
* Dataset metedata.
*/
client/galaxy/scripts/mvc/dataset/dataset-li.js
+29 -37
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@@ -286,47 +286,39 @@ var DatasetListItemView = _super.extend(
return this._renderMetaFileDownloadButton();
}
return $(
[
'<a class="download-btn icon-btn" ',
'href="',
this.model.urls.download,
`" title="${_l("Download")}" download>`,
'<span class="fa fa-floppy-o"></span>',
"</a>"
].join("")
);
return $(`
<a class="download-btn icon-btn" href="${this.model.urls.download}" title="${_l("Download")}">
<span class="fa fa-floppy-o"></span>
</a>`);
},
/** Render the download button which opens a dropdown with links to download assoc. meta files (indeces, etc.) */
/** Render the download button which opens a dropdown with links to download assoc. meta files (indices, etc.) */
_renderMetaFileDownloadButton: function() {
var urls = this.model.urls;
return $(
[
'<div class="metafile-dropdown dropdown">',
'<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',
` title="${_l("Download")}">`,
'<span class="fa fa-floppy-o"></span>',
"</a>",
'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">',
`<li><a href="${urls.download}" 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>"
].join("")
).join("\n"),
"</ul>",
"</div>"
].join("\n")
);
return $(`
<div class="metafile-dropdown dropdown">
<a class="download-btn icon-btn" href="${urls.download}" data-toggle="dropdown" title="${_l(
"Download"
)}">
<span class="fa fa-floppy-o"></span>
</a>
<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">
<li>
<a href="${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")} ${meta_file.file_type}
</a>
</li>`
)}
</ul>
</div>`);
},
_renderNametags: function() {
client/galaxy/scripts/mvc/history/history-item-li.js
+8 -9
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@@ -1,15 +1,14 @@
function _labelIfName(tag) {
if (tag.indexOf("name:") == 0) {
return `<span class="label label-info">${_.escape(tag.slice(5))}</span>`;
} else {
return "";
}
function _templateNametag(tag) {
return `<span class="label label-info">${_.escape(tag.slice(5))}</span>`;
}
function nametagTemplate(historyItem) {
return `<span class="nametags">${_.sortBy(_.uniq(historyItem.tags))
.map(_labelIfName)
.join("")}</span>`;
let uniqueNametags = _.filter(_.uniq(historyItem.tags), t => t.indexOf("name:") === 0);
let nametagsDisplay = _.sortBy(uniqueNametags).map(_templateNametag);
return `
<div class="nametags" title="${uniqueNametags.length} nametags">
${nametagsDisplay.join("")}
</div>`;
}
export default {
client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+417 -228
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client/galaxy/scripts/mvc/ui/ui-modal.js
+10 -11
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@@ -39,17 +39,16 @@ export var View = Backbone.View.extend({
if (!this.visible) {
this.visible = true;
this.$el.fadeIn("fast");
if (this.options.closing_events) {
var self = this;
$(document).on("keyup.ui-modal", e => {
if (e.keyCode == 27) {
self.hide(true);
}
});
this.$backdrop.on("click", () => {
self.hide(true);
});
}
}
if (this.options.closing_events) {
$(document).on("keyup.ui-modal", e => {
if (e.keyCode == 27) {
this.hide(true);
}
});
this.$backdrop.on("click", () => {
this.hide(true);
});
}
},
client/galaxy/scripts/mvc/ui/ui-select-default.js
+71 -50
View File
@@ -5,7 +5,6 @@ import Utils from "utils/utils";
import Buttons from "mvc/ui/ui-buttons";
var View = Backbone.View.extend({
initialize: function(options) {
var self = this;
this.data = [];
this.data2 = [];
this.model =
@@ -28,7 +27,9 @@ var View = Backbone.View.extend({
pagesize: 20
}).set(options);
this.on("change", () => {
self.model.get("onchange") && self.model.get("onchange")(self.value());
if (this.model.get("onchange")) {
this.model.get("onchange")(this.value());
}
});
this.listenTo(this.model, "change:data", this._changeData, this);
this.listenTo(this.model, "change:disabled", this._changeDisabled, this);
@@ -40,8 +41,11 @@ var View = Backbone.View.extend({
},
render: function() {
var self = this;
this.model.get("searchable") ? this._renderSearchable() : this._renderClassic();
if (this.model.get("searchable")) {
this._renderSearchable();
} else {
this._renderClassic();
}
this.$el.addClass(this.model.get("cls")).attr("id", this.model.get("id"));
this.$select
.empty()
@@ -49,8 +53,8 @@ var View = Backbone.View.extend({
.attr("id", `${this.model.get("id")}_select`)
.prop("multiple", this.model.get("multiple"))
.on("change", () => {
self.value(self._getValue());
self.trigger("change");
this.value(this._getValue());
this.trigger("change");
});
this._changeData();
this._changeWait();
@@ -60,7 +64,6 @@ var View = Backbone.View.extend({
/** Renders the classic selection field */
_renderClassic: function() {
var self = this;
this.$el
.addClass(this.model.get("multiple") ? "ui-select-multiple" : "ui-select")
.append((this.$select = $("<select/>")))
@@ -76,12 +79,12 @@ var View = Backbone.View.extend({
.off("mousedown")
.on("mousedown", event => {
var currentY = event.pageY;
var currentHeight = self.$select.height();
self.minHeight = self.minHeight || currentHeight;
var currentHeight = this.$select.height();
this.minHeight = this.minHeight || currentHeight;
$("#dd-helper")
.show()
.on("mousemove", event => {
self.$select.height(Math.max(currentHeight + (event.pageY - currentY), self.minHeight));
this.$select.height(Math.max(currentHeight + (event.pageY - currentY), this.minHeight));
})
.on("mouseup mouseleave", () => {
$("#dd-helper")
@@ -98,25 +101,27 @@ var View = Backbone.View.extend({
/** Renders the default select2 field */
_renderSearchable: function() {
var self = this;
this.$el.append((this.$select = $("<div/>"))).append((this.$dropdown = $("<div/>")));
this.$dropdown.hide();
if (!this.model.get("multiple")) {
this.$dropdown.show().on("click", () => {
self.$select.select2 && self.$select.select2("open");
if (this.$select.select2) {
this.$select.select2("open");
}
});
}
this.all_button = null;
if (this.model.get("multiple") && !this.model.get("individual") && !this.model.get("readonly")) {
this.all_button = new Buttons.ButtonCheck({
onclick: function() {
onclick: () => {
var new_value = [];
self.all_button.value() !== 0 &&
_.each(self.model.get("data"), option => {
if (this.all_button.value() !== 0) {
_.each(this.model.get("data"), option => {
new_value.push(option.value);
});
self.value(new_value);
self.trigger("change");
}
this.value(new_value);
this.trigger("change");
}
});
this.$el.prepend(this.all_button.$el);
@@ -127,7 +132,7 @@ var View = Backbone.View.extend({
_match: function(term, text) {
return (
!term ||
term == "" ||
term === "" ||
String(text)
.toUpperCase()
.indexOf(term.toUpperCase()) >= 0
@@ -136,18 +141,17 @@ var View = Backbone.View.extend({
/** Updates the selection options */
_changeData: function() {
var self = this;
this.data = [];
if (!this.model.get("multiple") && this.model.get("optional")) {
this.data.push({
value: "__null__",
label: self.model.get("empty_text")
label: this.model.get("empty_text")
});
}
_.each(this.model.get("data"), option => {
self.data.push(option);
this.data.push(option);
});
if (this.length() == 0) {
if (this.length() === 0) {
this.data.push({
value: "__null__",
label: this.model.get("error_text")
@@ -156,61 +160,71 @@ var View = Backbone.View.extend({
if (this.model.get("searchable")) {
this.data2 = [];
_.each(this.data, (option, index) => {
self.data2.push({
this.data2.push({
order: index,
id: option.value,
text: option.label,
tags: option.tags
});
});
this.$select.data("select2") && this.$select.select2("destroy");
if (this.$select.data("select2")) {
this.$select.select2("destroy");
}
this.matched_tags = {};
this.$select.select2({
data: self.data2,
data: this.data2,
closeOnSelect: !this.model.get("multiple"),
multiple: this.model.get("multiple"),
query: function(q) {
self.matched_tags = {};
var pagesize = self.model.get("pagesize");
var results = _.filter(self.data2, e => {
query: q => {
this.matched_tags = {};
var pagesize = this.model.get("pagesize");
var results = _.filter(this.data2, e => {
var found = false;
_.each(e.tags, tag => {
if (self._match(q.term, tag)) {
found = self.matched_tags[tag] = true;
if (this._match(q.term, tag)) {
found = this.matched_tags[tag] = true;
}
});
return found || self._match(q.term, e.text);
return found || this._match(q.term, e.text);
});
q.callback({
results: results.slice((q.page - 1) * pagesize, q.page * pagesize),
more: results.length >= q.page * pagesize
});
},
formatResult: function(result) {
return `${_.escape(result.text)}<div class="ui-tags">${_.reduce(
result.tags,
(memo, tag) => {
if (self.matched_tags[tag]) {
formatResult: result => {
let extraTagWarning = "";
let filteredTags = _.filter(result.tags, t => this.matched_tags.hasOwnProperty(t));
if (filteredTags.length > 5) {
extraTagWarning = `&nbsp;<div class="label label-warning">${filteredTags.length -
5} more tags</div>`;
}
return `
${_.escape(result.text)}
<div class="ui-tags">
${_.reduce(
filteredTags.slice(0, 5),
(memo, tag) => {
return `${memo}&nbsp;<div class="label label-info">${_.escape(tag)}</div>`;
}
return memo;
},
""
)}</div>`;
},
""
)}
${extraTagWarning}
</div>`;
}
});
this.$(".select2-container .select2-search input").off("blur");
} else {
this.$select.find("option").remove();
_.each(this.data, option => {
self.$select.append(
this.$select.append(
$("<option/>")
.attr("value", option.value)
.html(_.escape(option.label))
);
});
}
this.model.set("disabled", this.model.get("readonly") || this.length() == 0);
this.model.set("disabled", this.model.get("readonly") || this.length() === 0);
this._changeValue();
},
@@ -252,7 +266,9 @@ var View = Backbone.View.extend({
/** Return/Set current selection */
value: function(new_value) {
new_value !== undefined && this.model.set("value", new_value);
if (new_value !== undefined) {
this.model.set("value", new_value);
}
return this._getValue();
},
@@ -311,9 +327,13 @@ var View = Backbone.View.extend({
/** Update all available options at once */
add: function(options, sorter) {
_.each(this.model.get("data"), v => {
v.keep && !_.findWhere(options, { value: v.value }) && options.push(v);
if (v.keep && !_.findWhere(options, { value: v.value })) {
options.push(v);
}
});
sorter && options && options.sort(sorter);
if (sorter && options) {
options.sort(sorter);
}
this.model.set("data", options);
},
@@ -334,7 +354,6 @@ var View = Backbone.View.extend({
/** Set value to dom */
_setValue: function(new_value) {
var self = this;
if (new_value === null || new_value === undefined) {
new_value = "__null__";
}
@@ -351,8 +370,10 @@ var View = Backbone.View.extend({
if ($.isArray(new_value)) {
var val = [];
_.each(new_value, v => {
var d = _.findWhere(self.data2, { id: v });
d && val.push(d);
var d = _.findWhere(this.data2, { id: v });
if (d) {
val.push(d);
}
});
new_value = val;
} else {
client/galaxy/scripts/mvc/ui/ui-select-library.js
+4 -3
View File
@@ -1,8 +1,7 @@
// dependencies
import Utils from "utils/utils";
import Ui from "mvc/ui/ui-misc";
import Table from "mvc/ui/ui-table";
import List from "mvc/ui/ui-list";
// collection of libraries
var Libraries = Backbone.Collection.extend({
url: `${Galaxy.root}api/libraries?deleted=false`
@@ -85,7 +84,9 @@ var View = Backbone.View.extend({
// add change event. fires on trigger
this.on("change", () => {
options.onchange && options.onchange(self.value());
if (options.onchange) {
options.onchange(self.value());
}
});
// create elements
client/galaxy/scripts/nls/zh/locale.js
+171 -96
View File
@@ -1,169 +1,244 @@
/** zh localization */
/* by steven shen */
define({
// ----------------------------------------------------------------------------- masthead
"Analyze Data": "数据分析",
Workflow: "流程",
"Shared Data": "共享的数据",
"Data Libraries": "数据库",
Histories: "已发布的历史",
Workflows: "已发布的流程",
Visualizations: "已发布的可视化",
Pages: "已发布的页面",
Visualization: "可视化",
"New Track Browser": "创建 Track Browser",
"Saved Visualizations": "已保存的保存",
"Interactive Environments": "交互式环境",
Admin: "管理员",
Help: "帮助",
Support: "支持",
Search: "搜索",
"Mailing Lists": "邮件列表",
Videos: "视频",
Wiki: false,
"How to Cite Galaxy": "引用",
"Interactive Tours": "使用引导",
User: "用户",
Login: "登陆",
Register: "注册",
"Login or Register": "登陆或注册",
"Logged in as": "您已登陆为",
Preferences: "用户偏好性",
"Custom Builds": "自定义构建集",
Logout: "退出",
"Saved Histories": "保存历史",
"Saved Datasets": "保存数据集",
"Saved Pages": "保存页面",
//Tooltip
"Account and saved data": "账号及数据保存",
"Account registration or login": "注册与登录",
"Support, contact, and community": "支持，联系，社区",
"Administer this Galaxy": "管理您的Galaxy",
"Visualize datasets": "数据集可视化",
"Access published resources": "访问发布的资源",
"Chain tools into workflows": "将工具链接到工作流程中",
"Analysis home view": "数据分析主页",
// ---------------------------------------------------------------------------- histories
// ---- history/options-menu
"History Lists": "历史列表",
// Saved histories is defined above.
"Saved Histories": "保存历史",
"Histories Shared with Me": "分享给您历史",
"Current History": "当前历史",
"Create New": "创建新的历史",
"Copy History": "复制历史",
"Share or Publish": "分享或发布历史",
"Show Structure": "展示结构",
"Extract Workflow": "提取为工作流",
// Delete is defined elsewhere, but is also in this menu.
Delete: "删除",
"Delete Permanently": "永久删除",
"Dataset Actions": "数据操作",
"Copy Datasets": "复制数据集",
"Dataset Security": "数据安全",
"Resume Paused Jobs": "恢复已暂停的任务",
"Collapse Expanded Datasets": false,
"Unhide Hidden Datasets": "取消隐藏的数据集",
"Delete Hidden Datasets": "删除隐藏的数据集",
"Purge Deleted Datasets": "清空已删除的数据集",
Downloads: "下载",
"Export Tool Citations": "导出工具文献引用",
"Export History to File": "导出历史到文件",
"Other Actions": "其他操作",
"Import from File": "从文件导入",
Webhooks: false,
// ---- history-model
// ---- history-view
"This history is empty": "历史已空",
"No matching datasets found": "未找到匹配的数据集",
//"An error occurred while getting updates from the server" :
//false,
//"Please contact a Galaxy administrator if the problem persists" :
//false,
"An error occurred while getting updates from the server": "从服务器更新出现错误",
"Please contact a Galaxy administrator if the problem persists": "如果问题仍然存在，请联系Galaxy管理员",
//TODO:
//"An error was encountered while <% where %>" :
//false,
"Search datasets": "搜索数据集",
"You are currently viewing a deleted history!": "正在查看已删除的历史",
"You are over your disk quota": "您已超过磁盘配额",
//"Tool execution is on hold until your disk usage drops below your allocated quota" :
//false,
All: "皆",
"An error was encountered while <% where %>": "出现错误，当执行以下操作时: <% where %>",
"search datasets": "搜索数据集",
"You are currently viewing a deleted history!": "您正在查看已删除的历史记录",
"You are over your disk quota": "您超出了您的磁盘配额",
"Tool execution is on hold until your disk usage drops below your allocated quota":
"工具执行处于暂停状态，直到您的磁盘使用量低于您分配的配额",
All: "所有的",
None: "一个也没有",
"For all selected": "为每个选定",
// ---- history-view-edit
//"Edit history tags" :
//false,
//"Edit history Annotation" :
//false,
"Edit history tags": "编辑历史标签",
"Edit history Annotation": "编辑历史备注",
"Click to rename history": "单击要重命名的历史",
// multi operations
"Operations on multiple datasets": "编辑多个数据集",
//"Hide datasets" :
//false,
//"Unhide datasets" :
//false,
//"Delete datasets" :
//false,
//"Undelete datasets" :
//false,
"Hide datasets": "隐藏数据集",
"Unhide datasets": "显示数据集",
"Delete datasets": "删除数据集",
"Undelete datasets": "取消删除数据集",
"Permanently delete datasets": "永久删除数据集",
"This will permanently remove the data in your datasets. Are you sure?": "这将永久在你的数据集删除数据。你确定？",
"This will permanently remove the data in your datasets. Are you sure?": "这将永久在您的数据集删除数据。你确定？",
// ---- history-view-annotated
Dataset: "数据集",
//"Annotation" :
//false,
Dataset: "数据",
Annotation: "备注",
// ---- history-view-edit-current
"This history is empty. Click 'Get Data' on the left tool menu to start": "历史已空，请单击左边窗格中‘获取数据’",
"You must be logged in to create histories": "你必须登录后才能创建历史",
//TODO:
//"You can <% loadYourOwn %> or <% externalSource %>" :
"You can ": "您可以 ",
" or ": " 或者 ",
"load your own data": "上传您的个人数据",
"get data from an external source": "从外部来源获取数据",
// these aren't in zh/ginga.po and the template doesn't localize
//"Include Deleted Datasets" :
//false,
//"load your own data" :
//false,
//"get data from an external source" :
//"Include Hidden Datasets" :
//false,
// ---------------------------------------------------------------------------- datasets
// ---- hda-model
//"Unable to purge dataset" :
//false,
"Unable to purge dataset": "无法清除数据集",
// ---- hda-base
// display button
//"Cannot display datasets removed from disk" :
//false,
//"This dataset must finish uploading before it can be viewed" :
//false,
//"This dataset is not yet viewable" :
//false,
"View data": "数据",
"Cannot display datasets removed from disk": "无法显示已从磁盘中删除的数据集",
"This dataset must finish uploading before it can be viewed": "此数据集必须先完成上传, 然后才能查看",
"This dataset is not yet viewable": "此数据集是不可见的",
"View data": "查看数据",
// download button
Download: "下载",
"Download dataset": "下载数据集",
//"Additional files" :
//false,
"Additional files": "其他文件",
// info/show_params
"View details": "查看详情",
// dataset states
// state: new
//"This is a new dataset and not all of its data are available yet" :
//false,
"This is a new dataset and not all of its data are available yet": "这是一个新的数据集，并不是所有的数据都可用",
// state: noPermission
//"You do not have permission to view this dataset" :
//false,
"You do not have permission to view this dataset": "您无权查看此数据集",
// state: discarded
//"The job creating this dataset was cancelled before completion" :
//false,
"The job creating this dataset was cancelled before completion": "创建此数据集的任务在完成之前已被取消",
// state: queued
"This job is waiting to run": "等待运行的进程",
"This job is waiting to run": "任务正在等待运行",
// state: upload
//"This dataset is currently uploading" :
//false,
"This dataset is currently uploading": "此数据集正在上传中",
// state: setting_metadata
//"Metadata is being auto-detected" :
//false,
"Metadata is being auto-detected": "元数据正在被自动检测中",
// state: running
"This job is currently running": "正在运行的进程",
"This job is currently running": "任务正在运行中",
// state: paused
//"This job is paused. Use the \"Resume Paused Jobs\" in the history menu to resume" :
//false,
'This job is paused. Use the "Resume Paused Jobs" in the history menu to resume':
'此任务已暂停。使用历史菜单中的 "恢复已暂停的工作" 来恢复',
// state: error
"An error occurred with this dataset": "进程运行时出错",
"An error occurred with this dataset": "此数据集发生错误",
// state: empty
"No data": "没有数据",
// state: failed_metadata
//"An error occurred setting the metadata for this dataset" :
//false,
"An error occurred setting the metadata for this dataset": "设置此数据集的元数据时发生错误",
// ajax error prefix
//"There was an error getting the data for this dataset" :
//false,
"There was an error getting the data for this dataset": "获取此数据集的数据时出错",
// purged'd/del'd msg
//"This dataset has been deleted and removed from disk" :
//false,
"This dataset has been deleted and removed from disk": "此数据集已被删除并从磁盘中删除",
"This dataset has been deleted": "此数据集已被删除",
"This dataset has been hidden": "此数据集已隐藏",
"This dataset has been hidden": "此数据集已被隐藏",
format: "格式",
database: "数据库",
// ---- hda-edit
"Edit attributes": "编辑属性",
//"Cannot edit attributes of datasets removed from disk" :
//false,
//"Undelete dataset to edit attributes" :
//false,
//"This dataset must finish uploading before it can be edited" :
//false,
//"This dataset is not yet editable" :
//false,
"Cannot edit attributes of datasets removed from disk": "无法编辑已从磁盘中删除的数据集的属性",
"Undelete dataset to edit attributes": "取消删除数据集以编辑属性",
"This dataset must finish uploading before it can be edited": "该数据集必须先上传完成, 然后才能编辑",
"This dataset is not yet editable": "该数据集不可编辑",
Delete: "删除",
//"Dataset is already deleted" :
//false,
"Dataset is already deleted": "数据集已被删除",
"View or report this error": "报告错误",
"View or report this error": "查看或报告此错误",
"Run this job again": "重新运行",
"Run this job again": "重新运行此任务",
Visualize: "图形",
//"Visualize in" :
//false,
Visualize: "可视化",
"Visualize in": "的可视化",
"Undelete it": "反删除",
"Undelete it": "取消删除",
"Permanently remove it from disk": "从磁盘中永久删除",
"Unhide it": "取消隐藏"
"Unhide it": "取消隐藏",
//"You may be able to" :
//false,
//"set it manually or retry auto-detection" :
//false,
"You may be able to": "您可能可以",
"set it manually or retry auto-detection": "手动设置或重试自动检测",
//"Edit dataset tags" :
//false,
//"Edit dataset annotation" :
//false,
"Edit dataset tags": "编辑数据集标签",
"Edit dataset annotation": "编辑数据集备注",
"Tool Help": "工具帮助",
// ---------------------------------------------------------------------------- admin
"Search Tool Shed": "搜索 Tool Shed",
"Monitor installing repositories": "",
"Manage installed tools": "管理已安装的工具",
"Reset metadata": "重置元数据",
"Download local tool": "下载本地工具",
"Tool lineage": false,
"Reload a tool's configuration": "重新加载工具的配置",
"Review tool migration stages": "查看工具迁移状态",
"View Tool Error Logs": "查看工具错误日志",
"Manage Display Whitelist": "管理显示白名单",
"Manage Tool Dependencies": "管理工具依赖",
Users: "用户",
Groups: "组别",
"API keys": false,
"Impersonate a user": "模拟用户",
Data: "数据",
Quotas: "配额",
Roles: "角色",
"Local data": "本地数据",
"Form Definitions": "定义表单",
// ---------------------------------------------------------------------------- Scratchbook
"Enable/Disable Scratchbook": "启用/禁用 Scratchbook",
"Show/Hide Scratchbook": "显示/隐藏 Scratchbook",
// ---------------------------------------------------------------------------- misc. MVC
//"Tags" :
//false,
//"Annotation" :
//false,
//"Edit annotation" :
//false,
Tags: "标签",
"Edit annotation": "编辑备注",
// ----------------------------------------------------------------------------
ja: true,
fr: true,
zh: true
});
client/galaxy/scripts/toolshed/groups/group-detail-view.js
+138
View File
@@ -0,0 +1,138 @@
import * as mod_toastr from "libs/toastr";
import mod_group_model from "toolshed/groups/group-model";
// toolshed group detail view
const GroupDetailView = Backbone.View.extend({
el: "#groups_element",
options: {},
app: null,
initialize: function(options) {
this.options = _.extend(this.options, options);
this.app = window.globalTS.groups;
if (this.app.collection !== null) {
this.model = this.app.collection.get(this.options.group_id);
this.render();
} else {
this.fetchGroup();
}
},
fetchGroup: function(options) {
const that = this;
this.options = _.extend(this.options, options);
this.model = new mod_group_model.Group({ id: this.options.group_id });
this.model.fetch({
success: function(model) {
console.log("received data: ");
console.log(model);
that.render();
},
error: function(model, response) {
if (typeof response.responseJSON !== "undefined") {
mod_toastr.error(response.responseJSON.err_msg);
} else {
mod_toastr.error("An error occurred.");
}
}
});
},
render: function() {
const template = this.templateRow();
this.$el.html(template({ group: this.model }));
$("#center [data-toggle]").tooltip();
$("#center").css("overflow", "auto");
},
templateRow: function() {
return _.template(
[
"<div>",
'<h3><%= _.escape(group.get("name")) %></h3>',
'<p class="" style="color:gray;">',
'A group of <%= group.get("members").length %> members with <%= group.get("repositories").length %> repositories and a total of <%= group.get("total_downloads") %> combined repository clones.</p>',
"<h3>Members</h3>",
'<table class="grid table table-condensed">',
"<thead>",
"<th>Name</th>",
"<th>Repositories</th>",
"<th>Registered</th>",
"</thead>",
"<tbody>",
'<% _.each(group.get("members"), function(member) { %>',
"<tr>",
"<td>",
"<%= _.escape(member.username) %>",
"</td>",
"<td>",
'<a data-toggle="tooltip" data-placement="top" title="Repositories of <%= _.escape(member.username) %>" href="/repository/browse_repositories_by_user?user_id=<%= member.id %>&use_panels=true" id="<%= member.id %>"><%= member.user_repos_count %></a>',
"</td>",
"<td>",
"<%= member.time_created %>",
"</td>",
"</tr>",
"<% }); %>",
"</tbody>",
"</table>",
"<h3>Repositories</h3>",
'<table class="grid table table-condensed">',
"<thead>",
"<th>Name</th>",
"<th>Description</th>",
"<th>Clones</th>",
"<th>Owner</th>",
"<th>Categories</th>",
"<th>Created</th>",
"<th>Updated</th>",
"<th>Rating</th>",
"<th>Verified</th>",
"</thead>",
"<tbody>",
'<% _.each(group.get("repositories"), function(repo) { %>',
"<tr>",
"<td>",
'<a data-toggle="tooltip" data-placement="top" title="Details of <%= _.escape(repo.name) %>" href="/view/<%= _.escape(repo.owner) %>/<%= _escape(repo.name) %>" id="<%= repo.id %>"><%= _.escape(repo.name) %></a>',
"</td>",
"<td>",
"<%= _.escape(repo.description) %>",
"</td>",
"<td>",
"<%= repo.times_downloaded %>",
"</td>",
"<td>",
"<%= _.escape(repo.owner) %>",
"</td>",
"<td>",
"<% _.each((repo.categories), function(cat) { %>",
'<a data-toggle="tooltip" data-placement="top" title="Repositories in <%= cat.name %>" href="/repository/browse_repositories_in_category?id=<%= cat.id %>&use_panels=true"><%= cat.name %></a><br/>',
// '<%= repo.categories %>',
"<% }); %>",
"</td>",
'<td data-toggle="tooltip" data-placement="top" title="<%= repo.time_created_full %>">',
"<%= repo.time_created %>",
"</td>",
'<td data-toggle="tooltip" data-placement="top" title="<%= repo.time_updated_full %>">',
"<%= repo.time_updated %>",
"</td>",
"<td>",
"<%= repo.ratings_mean %>",
"</td>",
"<td>",
"<%= repo.approved %>",
"</td>",
"</tr>",
"<% }); %>",
"</tbody>",
"</table>",
"</div>"
].join("")
);
}
});
export default {
GroupDetailView: GroupDetailView
};
client/galaxy/scripts/toolshed/groups/group-list-view.js
+128
View File
@@ -0,0 +1,128 @@
import * as mod_toastr from "libs/toastr";
import mod_group_model from "toolshed/groups/group-model";
import mod_group_row from "toolshed/groups/group-listrow-view";
const GroupListView = Backbone.View.extend({
el: "#groups_element",
defaults: {},
/**
* Initialize and fetch the groups from server.
* Async render afterwards.
* @param {object} options an object with options
*/
initialize: function(options) {
this.options = _.defaults(this.options || {}, this.defaults, options);
const that = this;
window.globalTS.groups.collection = new mod_group_model.Groups();
window.globalTS.groups.collection.fetch({
success: function(model) {
console.log("received data: ");
console.log(model);
that.render();
},
error: function(model, response) {
if (typeof response.responseJSON !== "undefined") {
mod_toastr.error(response.responseJSON.err_msg);
} else {
mod_toastr.error("An error occurred.");
}
}
});
},
fetch: function() {},
/**
* Render the groups table from the object's own collection.
*/
render: function(options) {
this.options = _.extend(this.options, options);
$(".tooltip").hide();
const template = this.templateGroupsList();
this.$el.html(template({ length: window.globalTS.groups.collection.models.length }));
this.renderRows(window.globalTS.groups.collection.models);
$("#center [data-toggle]").tooltip();
$("#center").css("overflow", "auto");
},
/**
* Render all given models as rows in the groups list
* @param {array} groups_to_render array of group models to render
*/
renderRows: function(groups_to_render) {
for (let i = 0; i < groups_to_render.length; i++) {
const group = groups_to_render[i];
this.renderOne({ group: group });
}
},
/**
* Create a view for the given model and add it to the groups view.
* @param {Group} model of the view that will be rendered
*/
renderOne: function(options) {
const rowView = new mod_group_row.GroupListRowView(options);
this.$el.find("#group_list_body").append(rowView.el);
},
/**
* Table heading was clicked, update sorting preferences and re-render.
* @return {[type]} [description]
*/
// sort_clicked : function(){
// if (Galaxy.libraries.preferences.get('sort_order') === 'asc'){
// Galaxy.libraries.preferences.set({'sort_order': 'desc'});
// } else {
// Galaxy.libraries.preferences.set({'sort_order': 'asc'});
// }
// this.render();
// },
/**
* Sort the underlying collection according to the parameters received.
* Currently supports only sorting by name.
*/
// sortLibraries: function(){
// if (Galaxy.libraries.preferences.get('sort_by') === 'name'){
// if (Galaxy.libraries.preferences.get('sort_order') === 'asc'){
// this.collection.sortByNameAsc();
// } else if (Galaxy.libraries.preferences.get('sort_order') === 'desc'){
// this.collection.sortByNameDesc();
// }
// }
// },
// MMMMMMMMMMMMMMMMMM
// === TEMPLATES ====
// MMMMMMMMMMMMMMMMMM
templateGroupsList: function() {
const tmpl_array = [];
tmpl_array.push('<div id="groups">');
tmpl_array.push("</div>");
tmpl_array.push('<div class="groups_container table-responsive">');
tmpl_array.push("<% if(length === 0) { %>");
tmpl_array.push("<div>There are no groups yet.</div>");
tmpl_array.push("<% } else{ %>");
tmpl_array.push('<table class="grid table table-condensed">');
tmpl_array.push(" <thead>");
tmpl_array.push(" <th>Name</th>");
// tmpl_array.push(' <th style="width:22%;">description</th>');
tmpl_array.push(" <th>Members</th> ");
tmpl_array.push(" <th>Repositories</th>");
tmpl_array.push(" </thead>");
tmpl_array.push(' <tbody id="group_list_body">');
// group item views will attach here
tmpl_array.push(" </tbody>");
tmpl_array.push("</table>");
tmpl_array.push("<% }%>");
tmpl_array.push("</div>");
return _.template(tmpl_array.join(""));
}
});
export default {
GroupListView: GroupListView
};
client/toolshed/scripts/mvc/groups/group-listrow-view.js → client/galaxy/scripts/toolshed/groups/group-listrow-view.js
+13 -17
View File
@@ -1,36 +1,32 @@
define([],
function() {
// toolshed group row view
var GroupListRowView = Backbone.View.extend({
const GroupListRowView = Backbone.View.extend({
events: {},
initialize : function( options ){
this.render( options.group );
initialize: function(options) {
this.render(options.group);
},
render: function( group ){
var tmpl = this.templateRow();
this.setElement(tmpl( { group:group } ));
render: function(group) {
const tmpl = this.templateRow();
this.setElement(tmpl({ group: group }));
this.$el.show();
return this;
},
templateRow: function() {
return _.template([
return _.template(
[
'<tr class="" data-id="<%- group.get("id") %>">',
'<td><a href="groups#/<%= group.get("id") %>"><%= _.escape(group.get("name")) %></a></td>',
// '<td>description</td>',
'<td><%= group.get("total_members") %></td>',
'<td><%= group.get("total_repos") %></td>',
'</tr>'
].join(''));
}
"</tr>"
].join("")
);
}
});
return {
export default {
GroupListRowView: GroupListRowView
};
});
client/galaxy/scripts/toolshed/groups/group-model.js
+17
View File
@@ -0,0 +1,17 @@
// ============================================================================
// TS GROUP RELATED MODELS
const Group = Backbone.Model.extend({
urlRoot: `${Galaxy.root}api/groups`
});
const Groups = Backbone.Collection.extend({
url: `${Galaxy.root}api/groups`,
model: Group
});
export default {
Group: Group,
Groups: Groups
};
client/galaxy/scripts/toolshed/toolshed.groups.js
+42
View File
@@ -0,0 +1,42 @@
// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
// === MAIN TOOLSHED GROUP MODULE ====
// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
import mod_group_list from "toolshed/groups/group-list-view";
import mod_group_detail from "toolshed/groups/group-detail-view";
// ============================================================================
// ROUTER
const ToolshedRouter = Backbone.Router.extend({
routes: {
"": "groups",
":group_id": "group_page"
}
});
const ToolshedGroups = Backbone.View.extend({
groupListView: null,
groupDetailView: null,
collection: null,
initialize: function() {
window.globalTS.groups = this;
this.ts_router = new ToolshedRouter();
this.ts_router.on("route:groups", () => {
window.globalTS.groups.groupListView = new mod_group_list.GroupListView();
});
this.ts_router.on("route:group_page", group_id => {
window.globalTS.groups.groupDetailView = new mod_group_detail.GroupDetailView({
group_id: group_id
});
});
Backbone.history.start({ pushState: false });
}
});
export default {
ToolshedGroups: ToolshedGroups
};
client/galaxy/scripts/viz/circster.js
+7 -9
View File
@@ -1,6 +1,7 @@
import _l from "utils/localization";
import * as _ from "libs/underscore";
import * as d3 from "libs/d3";
import * as d3 from "d3";
import { event as currentEvent } from "d3";
import visualization from "viz/visualization";
import mod_utils from "utils/utils";
import config from "utils/config";
@@ -193,7 +194,6 @@ var CircsterView = Backbone.View.extend({
tracks_start_radii = d3.range(radius_start, min_dimension / 2, dataset_arc_height + track_gap);
// Map from track start to bounds.
var self = this;
return _.map(tracks_start_radii, radius => [radius, radius + dataset_arc_height]);
},
@@ -221,8 +221,8 @@ var CircsterView = Backbone.View.extend({
.call(
d3.behavior.zoom().on("zoom", () => {
// Do zoom, drag.
var scale = d3.event.scale;
svg.attr("transform", `translate(${d3.event.translate}) scale(${scale})`);
var scale = currentEvent.scale;
svg.attr("transform", `translate(${currentEvent.translate}) scale(${scale})`);
// Propagate scale changes to views.
if (self.scale !== scale) {
@@ -628,7 +628,6 @@ var CircsterTrackView = Backbone.View.extend({
* default data bounds.
*/
_update_data_bounds: function(new_bounds) {
var old_bounds = this.data_bounds;
this.data_bounds =
new_bounds || this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));
this._transition_chrom_data();
@@ -962,7 +961,6 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
_data_bounds_ticks_fn: function() {
// Closure vars.
var self = this;
visibleChroms = 0;
// Return function for locating ticks based on chrom arc data.
return (
@@ -1101,9 +1099,9 @@ var Circster = Backbone.View.extend({
// load css
mod_utils.cssLoadFile("static/style/circster.css");
// -- Configure visualization --
var genome = new visualization.Genome(galaxy_config.app.genome);
var genome = new visualization.Genome(window.galaxy_config.app.genome);
var vis = new visualization.GenomeVisualization(galaxy_config.app.viz_config);
var vis = new visualization.GenomeVisualization(window.galaxy_config.app.viz_config);
// Add Circster-specific config options.
vis.get("config").add([
@@ -1143,7 +1141,7 @@ var Circster = Backbone.View.extend({
// setup title
$("#center .unified-panel-header-inner").append(
`${galaxy_config.app.viz_config.title} ${galaxy_config.app.viz_config.dbkey}`
`${window.galaxy_config.app.viz_config.title} ${window.galaxy_config.app.viz_config.dbkey}`
);
// setup menu
client/galaxy/scripts/viz/trackster.js
+20 -17
View File
@@ -2,13 +2,7 @@ import _l from "utils/localization";
/**
* Top-level trackster code, used for creating/loading visualizations and user interface elements.
*/
// global variables
var ui = null;
var view = null;
var browser_router = null;
// trackster viewer
//import * as $ from 'jquery';
import * as _ from "libs/underscore";
import tracks from "viz/trackster/tracks";
import visualization from "viz/visualization";
@@ -25,6 +19,12 @@ import "libs/farbtastic";
import "libs/jquery/jquery.form";
import "libs/jquery/jquery.rating";
import "ui/editable-text";
// trackster global variables
var ui = null;
var view = null;
var browser_router = null;
/**
* Base Object/Model for inhertiance.
*/
@@ -152,7 +152,7 @@ var TracksterUI = Base.extend({
title: _l("Bookmarks"),
on_click: function() {
// HACK -- use style to determine if panel is hidden and hide/show accordingly.
force_right_panel($("div#right").css("right") == "0px" ? "hide" : "show");
window.force_right_panel($("div#right").css("right") == "0px" ? "hide" : "show");
}
},
{
@@ -250,7 +250,7 @@ var TracksterUI = Base.extend({
// Create view.
var self = this;
var view = new tracks.TracksterView(_.extend(view_config, { header: false }));
view = new tracks.TracksterView(_.extend(view_config, { header: false }));
view.editor = true;
$.when(view.load_chroms_deferred).then(chrom_info => {
@@ -408,10 +408,10 @@ var TracksterView = Backbone.View.extend({
});
// hide right panel
force_right_panel("hide");
window.force_right_panel("hide");
// check if id is available
if (galaxy_config.app.id) {
if (window.galaxy_config.app.id) {
this.view_existing();
} else if (query_string.get("dataset_id")) {
this.choose_existing_or_new();
@@ -483,7 +483,7 @@ var TracksterView = Backbone.View.extend({
// view
view_existing: function() {
// get config
var viz_config = galaxy_config.app.viz_config;
var viz_config = window.galaxy_config.app.viz_config;
// view
view = ui.create_visualization(
@@ -533,8 +533,11 @@ var TracksterView = Backbone.View.extend({
// select default
var dbkeys_in_genomes = response.map(r => r[1]);
if (galaxy_config.app.default_dbkey && _.contains(dbkeys_in_genomes, galaxy_config.app.default_dbkey)) {
$("#new-dbkey").val(galaxy_config.app.default_dbkey);
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
@@ -588,7 +591,7 @@ var TracksterView = Backbone.View.extend({
name: name,
dbkey: dbkey
},
galaxy_config.app.gene_region
window.galaxy_config.app.gene_region
);
// initialize editor
@@ -604,9 +607,9 @@ var TracksterView = Backbone.View.extend({
$("#center .unified-panel-title").text(`${view.config.get_value("name")} (${view.dbkey})`);
// add dataset
if (galaxy_config.app.add_dataset)
if (window.galaxy_config.app.add_dataset)
$.ajax({
url: `${Galaxy.root}api/datasets/${galaxy_config.app.add_dataset}`,
url: `${Galaxy.root}api/datasets/${window.galaxy_config.app.add_dataset}`,
data: { hda_ldda: "hda", data_type: "track_config" },
dataType: "json",
success: function(track_data) {
client/galaxy/style/less/history.less
+4 -2
View File
@@ -221,7 +221,9 @@
}
}
}
span.nametags {
div.nametags {
max-height:26px;
overflow-y: auto;
span.label {
display: inline-block;
margin-right: 2px;
@@ -698,4 +700,4 @@
margin-right: 8px;
}
}
}
}
client/galaxy/style/less/library.less
+19 -58
View File
@@ -104,7 +104,7 @@ th.button_heading{
margin-right: 0.2em;
}
.toolbar-item{
margin-left: 1em;
margin-left: 0.5em;
}
}
#libraries_element, #folder_items_element{
@@ -112,7 +112,7 @@ th.button_heading{
margin-left: 0.5em;
}
}
.help-button{
.right-float{
float: right;
}
.pagination-sm{
@@ -128,11 +128,6 @@ th.button_heading{
.libimport-select-all{
margin-left: 0.5em;
}
.library-modal-item{
width:90%;
margin-left: 1em;
margin-right: 1em;
}
.paginator-bottom{
width: 27em;
margin-left: auto;
@@ -143,60 +138,26 @@ th.button_heading{
}
// Extra style for Galaxy modal
.modal-content #selected_history_content{
ul{
list-style-type: none;
.modal-content{
.library_selected_history_content{
ul{
list-style-type: none;
}
}
.library-collection-type-select, .library-collection-history-select{
margin-left:auto;
margin-right:auto;
width:200px;
min-width:200px;
}
.library-modal-item{
width:90%;
margin-left: auto;
margin-right: auto;
margin-top: 1.5em;
}
}
// Follows the style for the deprecated admin libraries interface
#library-grid{
ul{
list-style: none;
}
span.expandLink{
padding-left: 12px;
display: inline-block;
vertical-align: middle;
background: url(../images/silk/resultset_next.png) no-repeat;
}
.folderRow.expanded span.expandLink{
background: url(../images/silk/resultset_bottom.png) no-repeat;
}
.folderRow span.rowIcon{
float: left;
margin-right: 5px;
width: 16px;
height: 16px;
display: inline-block;
vertical-align: middle;
background: url(../images/silk/folder.png);
}
.libraryItem-error{
margin-right: 2px;
padding: 0 2px 0 2px;
border: 1px solid @state-danger-border;
background: @state-danger-bg;
}
.libraryItem-queued{
margin-right: 2px;
padding: 0 2px 0 2px;
border: 1px solid @state-default-border;
background: @state-default-bg;
}
.libraryItem-running{
margin-right: 2px;
padding: 0 2px 0 2px;
border: 1px solid @state-running-border;
background: @state-running-bg;
}
.libraryItem-upload{
margin-right: 2px;
padding: 0 2px 0 2px;
border: 1px solid @state-upload-border;
background: @state-upload-bg;
}
}
.libraryTitle{
th{
text-align: left;
client/grunt-tasks/install-libs.js
-80
View File
@@ -1,80 +0,0 @@
/**
* Grunt task to fetch third-party libraries using bower and copy them to the proper location in client/.
* @param {Object} grunt main grunt file
* @return {Function} callback to build this task
*/
module.exports = function( grunt ){
"use strict";
var dev_path = './galaxy/scripts',
// where to move fetched bower components into the build structure (libName: [ bower-location, libs-location ])
libraryLocations = {
'farbtastic': [ 'src/farbtastic.js', 'farbtastic.js' ],
'bootstrap-tour': [ 'build/js/bootstrap-tour.js', 'bootstrap-tour.js' ],
// these need to be updated and tested
//'jquery-form': [ 'jquery.form.js', 'jquery/jquery.form.js' ],
//'jquery-autocomplete': [ 'src/jquery.autocomplete.js', 'jquery/jquery.autocomplete.js' ],
//'select2': [ 'select2.js', 'jquery/select2.js' ],
//'jStorage': [ 'jstorage.js', 'jquery/jstorage.js' ],
//'dynatree': [ 'dist/jquery.dynatree.js', 'jquery/jquery.dynatree.js' ],
//'jquery.event.drag-drop': [
// [ 'event.drag/jquery.event.drag.js', 'jquery/jquery.event.drag.js' ],
// [ 'event.drag/jquery.event.drop.js', 'jquery/jquery.event.drop.js' ]
//],
// these are complicated by additional css/less
//'toastr': [ 'toastr.js', 'toastr.js' ],
//'wymeditor': [ 'dist/wymeditor/jquery.wymeditor.js', 'jquery/jquery.wymeditor.js' ],
//'jstree': [ 'jstree.js', 'jquery/jstree.js' ],
// these have been customized by Galaxy
//'bootstrap': [ 'dist/js/bootstrap.js', 'bootstrap.js' ],
//'jquery-ui': [
// // multiple components now
// [ '', 'jquery/jquery-ui.js' ]
//],
};
// call bower to install libraries and other external resources
grunt.config( 'bower-install-simple', {
options: {
color: true
},
"prod": {
options: {
production: true
}
},
"dev": {
options: {
production: false
}
}
});
/** copy external libraries from bower components to scripts/libs */
function copyLibs(){
var lib_path = dev_path + '/libs/';
for( var libName in libraryLocations ){
if( libraryLocations.hasOwnProperty( libName ) ){
var bower_dir = 'bower_components',
location = libraryLocations[ libName ],
source = [ bower_dir, libName, location[0] ].join( '/' ),
destination = lib_path + location[1];
grunt.log.writeln( source + ' -> ' + destination );
grunt.file.copy( source, destination );
}
}
}
grunt.loadNpmTasks( 'grunt-bower-install-simple' );
grunt.registerTask( 'copy-libs', 'copy external libraries to src', copyLibs );
grunt.registerTask( 'install-libs', 'fetch external libraries and copy to src',
[ 'bower-install-simple:prod', 'copy-libs' ] );
};
client/grunt-tasks/scripts.js
-123
View File
@@ -1,123 +0,0 @@
/**
* Grunt task to compress/bundle static/scripts.
* @param {Object} grunt main grunt file
* @return {Function} callback to build this task
*/
module.exports = function( grunt ){
"use strict";
var app = grunt.config.get( 'app' ),
paths = grunt.config.get( 'paths' ),
// uglify settings used when scripts are decompressed/not-minified
decompressedSettings = {
mangle : false,
beautify : true,
compress : {
drop_debugger : false
}
},
// uglify settings used when scripts are compressed/minified
compressedSettings = {
mangle : {
screw_ie8 : true
},
compress : {
// high compression options
screw_ie8 : true,
sequences: true,
dead_code : true,
drop_debugger : true,
comparisons : true,
conditionals : true,
evaluate : true,
booleans : true,
loops : true,
unused : true,
hoist_funs : true,
if_return : true,
join_vars : true,
cascade : true,
}
};
grunt.config( 'uglify', {
target : {
files: [{
expand : true,
cwd : paths.srcSymlink,
// NOTE: do not use uglify in the apps dir (webpack will do that section)
src : [ '**/*.js', '!apps/**/*.js' ],
// src : '**/*.js',
dest : paths.dist
}],
}
});
if (grunt.option( 'develop' )){
grunt.config( 'uglify.options', decompressedSettings );
} else {
grunt.config( 'uglify.target.options', {
sourceMap : true,
sourceMapName : function( path ){
// rewrite name to have all source maps in 'static/maps'
return path.replace( paths.dist, paths.maps ) + '.map';
}
});
grunt.config( 'uglify.options', compressedSettings );
}
// -------------------------------------------------------------------------- decompress for easier debugging
grunt.registerTask( 'decompress', function(){
grunt.log.writeln( "decompressing... (don't forget to call 'grunt' again before committing)" );
grunt.config( 'uglify.options', decompressedSettings );
grunt.config( 'uglify.target.options', {});
grunt.task.run( 'uglify' );
});
// alias for symmetry
grunt.registerTask( 'compress', [ 'uglify' ] );
// -------------------------------------------------------------------------- watch & copy,pack only those changed
// use 'grunt watch' (from a new tab in your terminal) to have grunt re-copy changed files automatically
grunt.config( 'watch', {
watch: {
// watch for changes in the src dir
// NOTE: but not in the apps dir (which is only used by webpack)
files: [ paths.srcSymlink + '/**', '!' + paths.srcSymlink + '/apps/**' ],
tasks: [ 'uglify' ],
options: {
spawn: false
}
}
});
// outer scope variable for the event handler and onChange fn - begin with empty hash
var changedFiles = Object.create(null);
// when files are changed, set the copy src and packScripts target to the filenames of the updated files
var onChange = grunt.util._.debounce(function() {
grunt.log.writeln( 'onChange, changedFiles:', Object.keys( changedFiles ) );
grunt.config( 'uglify.target.files', [{
expand : true,
cwd : paths.srcSymlink,
src : Object.keys( changedFiles ),
dest : paths.dist
}]);
changedFiles = Object.create(null);
}, 200);
var addChangedFile = function( action, filepath ) {
// store each filepath in a Files obj, the debounced fn above will use it as an aggregate list for copying
// we need to take galaxy/scripts out of the filepath or it will be copied to the wrong loc
filepath = filepath.replace( paths.srcSymlink + '/', '' );
// grunt.log.writeln( 'on.watch, filepath:', filepath );
changedFiles[ filepath ] = action;
onChange();
};
grunt.event.on( 'watch', addChangedFile );
// --------------------------------------------------------------------------
grunt.loadNpmTasks( 'grunt-contrib-watch' );
grunt.loadNpmTasks( 'grunt-contrib-uglify' );
};
client/toolshed/scripts/mvc/groups/group-detail-view.js
-146
View File
@@ -1,146 +0,0 @@
define([
"libs/toastr",
"toolshed/scripts/mvc/groups/group-model"
],
function(
mod_toastr,
mod_group_model
) {
// toolshed group detail view
var GroupDetailView = Backbone.View.extend({
el: "#groups_element",
options: {},
app: null,
initialize : function( options ){
this.options = _.extend( this.options, options );
this.app = window.globalTS.groups;
if ( this.app.collection !== null ){
this.model = this.app.collection.get( this.options.group_id );
this.render();
} else {
this.fetchGroup();
}
},
fetchGroup: function( options ){
var that = this;
this.options = _.extend( this.options, options );
this.model = new mod_group_model.Group( { id: this.options.group_id } );
this.model.fetch({
success: function( model ){
console.log( 'received data: ' );
console.log( model );
that.render();
},
error: function( model, response ){
if ( typeof response.responseJSON !== "undefined" ){
mod_toastr.error( response.responseJSON.err_msg );
} else {
mod_toastr.error( 'An error occurred.' );
}
}
});
},
render: function(){
var template = this.templateRow();
this.$el.html( template( { group: this.model } ) );
$( "#center [data-toggle]" ).tooltip();
$( "#center" ).css( 'overflow','auto' );
},
templateRow: function() {
return _.template([
'<div>',
'<h3><%= _.escape(group.get("name")) %></h3>',
'<p class="" style="color:gray;">',
'A group of <%= group.get("members").length %> members with <%= group.get("repositories").length %> repositories and a total of <%= group.get("total_downloads") %> combined repository clones.</p>',
'<h3>Members</h3>',
'<table class="grid table table-condensed">',
'<thead>',
'<th>Name</th>',
'<th>Repositories</th>',
'<th>Registered</th>',
'</thead>',
'<tbody>',
'<% _.each(group.get("members"), function(member) { %>',
'<tr>',
'<td>',
'<%= _.escape(member.username) %>',
'</td>',
'<td>',
'<a data-toggle="tooltip" data-placement="top" title="Repositories of <%= _.escape(member.username) %>" href="/repository/browse_repositories_by_user?user_id=<%= member.id %>&use_panels=true" id="<%= member.id %>"><%= member.user_repos_count %></a>',
'</td>',
'<td>',
'<%= member.time_created %>',
'</td>',
'</tr>',
'<% }); %>',
'</tbody>',
'</table>',
'<h3>Repositories</h3>',
'<table class="grid table table-condensed">',
'<thead>',
'<th>Name</th>',
'<th>Description</th>',
'<th>Clones</th>',
'<th>Owner</th>',
'<th>Categories</th>',
'<th>Created</th>',
'<th>Updated</th>',
'<th>Rating</th>',
'<th>Verified</th>',
'</thead>',
'<tbody>',
'<% _.each(group.get("repositories"), function(repo) { %>',
'<tr>',
'<td>',
'<a data-toggle="tooltip" data-placement="top" title="Details of <%= _.escape(repo.name) %>" href="/view/<%= _.escape(repo.owner) %>/<%= _escape(repo.name) %>" id="<%= repo.id %>"><%= _.escape(repo.name) %></a>',
'</td>',
'<td>',
'<%= _.escape(repo.description) %>',
'</td>',
'<td>',
'<%= repo.times_downloaded %>',
'</td>',
'<td>',
'<%= _.escape(repo.owner) %>',
'</td>',
'<td>',
'<% _.each((repo.categories), function(cat) { %>',
'<a data-toggle="tooltip" data-placement="top" title="Repositories in <%= cat.name %>" href="/repository/browse_repositories_in_category?id=<%= cat.id %>&use_panels=true"><%= cat.name %></a><br/>',
// '<%= repo.categories %>',
'<% }); %>',
'</td>',
'<td data-toggle="tooltip" data-placement="top" title="<%= repo.time_created_full %>">',
'<%= repo.time_created %>',
'</td>',
'<td data-toggle="tooltip" data-placement="top" title="<%= repo.time_updated_full %>">',
'<%= repo.time_updated %>',
'</td>',
'<td>',
'<%= repo.ratings_mean %>',
'</td>',
'<td>',
'<%= repo.approved %>',
'</td>',
'</tr>',
'<% }); %>',
'</tbody>',
'</table>',
'</div>'
].join(''));
}
});
return {
GroupDetailView: GroupDetailView
};
});
client/toolshed/scripts/mvc/groups/group-list-view.js
-141
View File
@@ -1,141 +0,0 @@
define([
"libs/toastr",
"toolshed/scripts/mvc/groups/group-model",
"toolshed/scripts/mvc/groups/group-listrow-view"
], function(
mod_toastr,
mod_group_model,
mod_group_row
){
var GroupListView = Backbone.View.extend({
el: '#groups_element',
defaults: {},
/**
* Initialize and fetch the groups from server.
* Async render afterwards.
* @param {object} options an object with options
*/
initialize : function( options ){
this.options = _.defaults( this.options || {}, this.defaults, options );
var that = this;
window.globalTS.groups.collection = new mod_group_model.Groups();
window.globalTS.groups.collection.fetch({
success: function( model ){
console.log( 'received data: ' );
console.log( model );
that.render();
},
error: function( model, response ){
if ( typeof response.responseJSON !== "undefined" ){
mod_toastr.error( response.responseJSON.err_msg );
} else {
mod_toastr.error( 'An error occurred.' );
}
}
});
},
fetch: function(){
},
/**
* Render the groups table from the object's own collection.
*/
render: function ( options ) {
this.options = _.extend( this.options, options );
$( ".tooltip" ).hide();
var template = this.templateGroupsList();
this.$el.html( template( { length: window.globalTS.groups.collection.models.length } ) );
this.renderRows( window.globalTS.groups.collection.models );
$( "#center [data-toggle]" ).tooltip();
$( "#center" ).css( 'overflow','auto' );
},
/**
* Render all given models as rows in the groups list
* @param {array} groups_to_render array of group models to render
*/
renderRows: function( groups_to_render ){
for ( var i = 0; i < groups_to_render.length; i++ ) {
var group = groups_to_render[i];
this.renderOne( { group: group } )
}
},
/**
* Create a view for the given model and add it to the groups view.
* @param {Group} model of the view that will be rendered
*/
renderOne: function( options ){
var rowView = new mod_group_row.GroupListRowView( options );
this.$el.find( '#group_list_body' ).append( rowView.el );
},
/**
* Table heading was clicked, update sorting preferences and re-render.
* @return {[type]} [description]
*/
// sort_clicked : function(){
// if (Galaxy.libraries.preferences.get('sort_order') === 'asc'){
// Galaxy.libraries.preferences.set({'sort_order': 'desc'});
// } else {
// Galaxy.libraries.preferences.set({'sort_order': 'asc'});
// }
// this.render();
// },
/**
* Sort the underlying collection according to the parameters received.
* Currently supports only sorting by name.
*/
// sortLibraries: function(){
// if (Galaxy.libraries.preferences.get('sort_by') === 'name'){
// if (Galaxy.libraries.preferences.get('sort_order') === 'asc'){
// this.collection.sortByNameAsc();
// } else if (Galaxy.libraries.preferences.get('sort_order') === 'desc'){
// this.collection.sortByNameDesc();
// }
// }
// },
// MMMMMMMMMMMMMMMMMM
// === TEMPLATES ====
// MMMMMMMMMMMMMMMMMM
templateGroupsList: function(){
var tmpl_array = [];
tmpl_array.push('<div id="groups">');
tmpl_array.push('</div>');
tmpl_array.push('<div class="groups_container table-responsive">');
tmpl_array.push('<% if(length === 0) { %>');
tmpl_array.push('<div>There are no groups yet.</div>');
tmpl_array.push('<% } else{ %>');
tmpl_array.push('<table class="grid table table-condensed">');
tmpl_array.push(' <thead>');
tmpl_array.push(' <th>Name</th>');
// tmpl_array.push(' <th style="width:22%;">description</th>');
tmpl_array.push(' <th>Members</th> ');
tmpl_array.push(' <th>Repositories</th>');
tmpl_array.push(' </thead>');
tmpl_array.push(' <tbody id="group_list_body">');
// group item views will attach here
tmpl_array.push(' </tbody>');
tmpl_array.push('</table>');
tmpl_array.push('<% }%>');
tmpl_array.push('</div>');
return _.template(tmpl_array.join(''));
},
});
return {
GroupListView: GroupListView
};
});
client/toolshed/scripts/mvc/groups/group-model.js
-22
View File
@@ -1,22 +0,0 @@
define([], function() {
// ============================================================================
// TS GROUP RELATED MODELS
var Group = Backbone.Model.extend({
urlRoot: Galaxy.root + 'api/groups',
});
var Groups = Backbone.Collection.extend({
url: Galaxy.root + 'api/groups',
model: Group,
});
return {
Group: Group,
Groups: Groups
};
});
client/toolshed/scripts/toolshed.groups.js
-51
View File
@@ -1,51 +0,0 @@
// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
// === MAIN TOOLSHED GROUP MODULE ====
// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
define([
'toolshed/scripts/mvc/groups/group-list-view',
'toolshed/scripts/mvc/groups/group-detail-view',
'toolshed/scripts/mvc/groups/group-model'
],
function(
mod_group_list,
mod_group_detail,
mod_group_model
) {
// ============================================================================
// ROUTER
var ToolshedRouter = Backbone.Router.extend({
routes: {
"" : "groups",
":group_id" : "group_page"
}
});
var ToolshedGroups = Backbone.View.extend({
groupListView: null,
groupDetailView: null,
collection: null,
initialize : function(){
window.globalTS.groups = this;
this.ts_router = new ToolshedRouter();
this.ts_router.on( 'route:groups', function() {
window.globalTS.groups.groupListView = new mod_group_list.GroupListView();
});
this.ts_router.on( 'route:group_page', function( group_id ) {
window.globalTS.groups.groupDetailView = new mod_group_detail.GroupDetailView( { group_id: group_id } );
});
Backbone.history.start({pushState: false});
}
});
return {
ToolshedGroups: ToolshedGroups
};
});
config/galaxy.ini.sample
+5
View File
@@ -920,6 +920,11 @@ use_interactive = True
# create symlinks to them).
#user_library_import_symlink_whitelist = None
# In conjunction or alternatively, Galaxy can restrict user library imports to
# those files that the user can read (by checking basic unix permissions).
# For this to work, the username has to match the username on the filesystem.
#user_library_import_check_permissions = False
# Allow admins to paste filesystem paths during upload. For libraries this
# adds an option to the admin library upload tool allowing admins to paste
# filesystem paths to files and directories in a box, and these paths will be
lib/galaxy/actions/library.py
+87 -30
View File
@@ -8,6 +8,11 @@ import os.path
from markupsafe import escape
from galaxy import util
from galaxy.exceptions import (
AdminRequiredException,
ConfigDoesNotAllowException,
RequestParameterInvalidException,
)
from galaxy.tools.actions import upload_common
from galaxy.tools.parameters import populate_state
from galaxy.util.path import (
@@ -19,6 +24,47 @@ from galaxy.util.path import (
log = logging.getLogger(__name__)
def validate_server_directory_upload(trans, server_dir):
if server_dir in [None, 'None', '']:
raise RequestParameterInvalidException("Invalid or unspecified server_dir parameter")
if trans.user_is_admin():
import_dir = trans.app.config.library_import_dir
import_dir_desc = 'library_import_dir'
if not import_dir:
raise ConfigDoesNotAllowException('"library_import_dir" is not set in the Galaxy configuration')
else:
import_dir = trans.app.config.user_library_import_dir
if not import_dir:
raise ConfigDoesNotAllowException('"user_library_import_dir" is not set in the Galaxy configuration')
if server_dir != trans.user.email:
import_dir = os.path.join(import_dir, trans.user.email)
import_dir_desc = 'user_library_import_dir'
full_dir = os.path.join(import_dir, server_dir)
unsafe = None
if safe_relpath(server_dir):
username = trans.user.username if trans.app.config.user_library_import_check_permissions else None
if import_dir_desc == 'user_library_import_dir' and safe_contains(import_dir, full_dir, whitelist=trans.app.config.user_library_import_symlink_whitelist, username=username):
for unsafe in unsafe_walk(full_dir, whitelist=[import_dir] + trans.app.config.user_library_import_symlink_whitelist):
log.error('User attempted to import a path that resolves to a path outside of their import dir: %s -> %s', unsafe, os.path.realpath(unsafe))
else:
log.error('User attempted to import a directory path that resolves to a path outside of their import dir: %s -> %s', server_dir, os.path.realpath(full_dir))
unsafe = True
if unsafe:
raise RequestParameterInvalidException("Invalid server_dir specified")
return full_dir, import_dir_desc
def validate_path_upload(trans):
if not trans.app.config.allow_library_path_paste:
raise ConfigDoesNotAllowException('"allow_path_paste" is not set to True in the Galaxy configuration file')
if not trans.user_is_admin():
raise AdminRequiredException('Uploading files via filesystem paths can only be performed by administrators')
class LibraryActions(object):
"""
Mixin for controllers that provide library functionality.
@@ -42,37 +88,11 @@ class LibraryActions(object):
upload_option = kwd.get('upload_option', 'upload_file')
response_code = 200
if upload_option == 'upload_directory':
if server_dir in [None, 'None', '']:
response_code = 400
if trans.user_is_admin():
import_dir = trans.app.config.library_import_dir
import_dir_desc = 'library_import_dir'
else:
import_dir = trans.app.config.user_library_import_dir
if server_dir != trans.user.email:
import_dir = os.path.join(import_dir, trans.user.email)
import_dir_desc = 'user_library_import_dir'
full_dir = os.path.join(import_dir, server_dir)
unsafe = None
if safe_relpath(server_dir):
if import_dir_desc == 'user_library_import_dir' and safe_contains(import_dir, full_dir, whitelist=trans.app.config.user_library_import_symlink_whitelist):
for unsafe in unsafe_walk(full_dir, whitelist=[import_dir] + trans.app.config.user_library_import_symlink_whitelist):
log.error('User attempted to import a path that resolves to a path outside of their import dir: %s -> %s', unsafe, os.path.realpath(unsafe))
else:
log.error('User attempted to import a directory path that resolves to a path outside of their import dir: %s -> %s', server_dir, os.path.realpath(full_dir))
unsafe = True
if unsafe:
response_code = 403
message = 'Invalid server_dir'
if import_dir:
message = 'Select a directory'
else:
response_code = 403
message = '"%s" is not defined in the Galaxy configuration file' % import_dir_desc
full_dir, import_dir_desc = validate_server_directory_upload(trans, server_dir)
message = 'Select a directory'
elif upload_option == 'upload_paths':
if not trans.app.config.allow_library_path_paste:
response_code = 403
message = '"allow_library_path_paste" is not defined in the Galaxy configuration file'
# Library API already checked this - following check isn't actually needed.
validate_path_upload(trans)
# Some error handling should be added to this method.
try:
# FIXME: instead of passing params here ( which have been processed by util.Params(), the original kwd
@@ -118,6 +138,43 @@ class LibraryActions(object):
uploaded_datasets.append(self._make_library_uploaded_dataset(trans, params, name, file, 'server_dir', library_bunch))
return uploaded_datasets, 200, None
def _get_server_dir_files(self, params, full_dir, import_dir_desc):
files = []
try:
for entry in os.listdir(full_dir):
# Only import regular files
path = os.path.join(full_dir, entry)
link_data_only = params.get('link_data_only', 'copy_files')
if os.path.islink(full_dir) and link_data_only == 'link_to_files':
# If we're linking instead of copying and the
# sub-"directory" in the import dir is actually a symlink,
# dereference the symlink, but not any of its contents.
link_path = os.readlink(full_dir)
if os.path.isabs(link_path):
path = os.path.join(link_path, entry)
else:
path = os.path.abspath(os.path.join(link_path, entry))
elif os.path.islink(path) and os.path.isfile(path) and link_data_only == 'link_to_files':
# If we're linking instead of copying and the "file" in the
# sub-directory of the import dir is actually a symlink,
# dereference the symlink (one dereference only, Vasili).
link_path = os.readlink(path)
if os.path.isabs(link_path):
path = link_path
else:
path = os.path.abspath(os.path.join(os.path.dirname(path), link_path))
if os.path.isfile(path):
files.append(path)
except Exception as e:
message = "Unable to get file list for configured %s, error: %s" % (import_dir_desc, str(e))
response_code = 500
return None, response_code, message
if not files:
message = "The directory '%s' contains no valid files" % full_dir
response_code = 400
return None, response_code, message
return files, None, None
def _get_path_paste_uploaded_datasets(self, trans, params, library_bunch, response_code, message):
preserve_dirs = util.string_as_bool(params.get('preserve_dirs', False))
uploaded_datasets = []
lib/galaxy/config.py
+1
View File
@@ -426,6 +426,7 @@ class Configuration(object):
self.library_import_dir = kwargs.get('library_import_dir', None)
self.user_library_import_dir = kwargs.get('user_library_import_dir', None)
self.user_library_import_symlink_whitelist = listify(kwargs.get('user_library_import_symlink_whitelist', []), do_strip=True)
self.user_library_import_check_permissions = string_as_bool(kwargs.get('user_library_import_check_permissions', False))
# Searching data libraries
self.ftp_upload_dir = kwargs.get('ftp_upload_dir', None)
self.ftp_upload_dir_identifier = kwargs.get('ftp_upload_dir_identifier', 'email') # attribute on user - email, username, id, etc...
lib/galaxy/tools/deps/conda_util.py
+1 -1
View File
@@ -530,7 +530,7 @@ def build_isolated_environment(
# - https://github.com/galaxyproject/galaxy/issues/3635
# - https://github.com/conda/conda/issues/2035
offline_works = (conda_context.conda_version < LooseVersion("4.3")) or \
(conda_context.conda_version >= LooseVersion("4.3.18"))
(conda_context.conda_version >= LooseVersion("4.4"))
if offline_works:
create_args.extend(["--offline"])
else:
lib/galaxy/util/path/__init__.py
+75 -6
View File
@@ -4,16 +4,20 @@ from __future__ import absolute_import
import errno
import imp
import logging
from functools import partial
from grp import getgrgid
from itertools import starmap
from operator import getitem
from os import (
extsep,
makedirs,
walk,
stat,
walk
)
from os.path import (
abspath,
dirname,
exists,
isabs,
join,
@@ -21,10 +25,13 @@ from os.path import (
pardir,
realpath,
relpath,
sep as separator,
)
from pwd import getpwuid
from six import iteritems, string_types
from six.moves import filterfalse, map, zip
from six.moves import map, zip
log = logging.getLogger(__name__)
def safe_contains(prefix, path, whitelist=None):
@@ -82,7 +89,7 @@ def safe_relpath(path):
return not (isabs(path) or normpath(path).startswith(pardir))
def unsafe_walk(path, whitelist=None):
def unsafe_walk(path, whitelist=None, username=None):
"""Walk a path and ensure that none of its contents are symlinks outside the path.
It is assumed that ``path`` itself has already been validated e.g. with :func:`safe_relpath` or
@@ -92,10 +99,72 @@ def unsafe_walk(path, whitelist=None):
:param path: a directory to check for unsafe contents
:type whitelist: list of strings
:param whitelist: list of additional paths under which contents may be located
:rtype: iterator
:returns: Iterator of "bad" files found under ``path``
:rtype: list of strings
:returns: A list of "bad" files found under ``path``
"""
return filterfalse(partial(safe_contains, path, whitelist=whitelist), __walk(abspath(path)))
unsafe_paths = []
for walked_path in __walk(abspath(path)):
is_safe = safe_contains(path, walked_path, whitelist=whitelist)
if username and is_safe:
is_safe = full_path_permission_for_user(path, walked_path, username=username, skip_prefix=True)
if not is_safe:
unsafe_paths.append(walked_path)
return unsafe_paths
def __path_permission_for_user(path, username):
"""
:type path: string
:param path: a directory or file to check
:type username: string
:param username: a username matching the systems username
"""
group_id_of_file = stat(path).st_gid
file_owner = getpwuid(stat(path).st_uid)
group_members = getgrgid(group_id_of_file).gr_mem
oct_mode = oct(stat(path).st_mode)
owner_permissions = int(oct_mode[-3])
group_permissions = int(oct_mode[-2])
other_permissions = int(oct_mode[-1])
if other_permissions >= 4 or \
(file_owner == username and owner_permissions >= 4) or \
(username in group_members and group_permissions >= 4):
return True
return False
def full_path_permission_for_user(prefix, path, username, skip_prefix=False):
"""
Assuming username is identical to the os username, this checks that the
given user can read the specified path by checking the file permission
and each parent directory permission.
:type prefix: string
:param prefix: a directory under which ``path`` is to be checked
:type path: string
:param path: a filename to check
:type username: string
:param username: a username matching the systems username
:type skip_prefix: bool
:param skip_prefix: skip the given prefix from being checked for permissions
"""
full_path = realpath(join(prefix, path))
top_path = realpath(prefix) if skip_prefix else None
can_read = __path_permission_for_user(full_path, username)
if can_read:
depth = 0
max_depth = full_path.count(separator)
parent_path = dirname(full_path)
while can_read and depth != max_depth:
if parent_path in [separator, top_path]:
break
if not __path_permission_for_user(parent_path, username):
can_read = False
depth += 1
parent_path = dirname(parent_path)
return can_read
def joinext(root, ext):
lib/galaxy/webapps/galaxy/api/library_contents.py
+6 -11
View File
@@ -12,9 +12,8 @@ from galaxy import (
exceptions,
managers,
util,
web
)
from galaxy.actions.library import LibraryActions
from galaxy.actions.library import LibraryActions, validate_path_upload
from galaxy.managers.collections_util import (
api_payload_to_create_params,
dictify_dataset_collection_instance
@@ -158,7 +157,7 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
rval['parent_library_id'] = trans.security.encode_id(rval['parent_library_id'])
return rval
@web.expose_api
@expose_api
def create(self, trans, library_id, payload, **kwd):
"""
create( self, trans, library_id, payload, **kwd )
@@ -314,12 +313,8 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
if folder and last_used_build in ['None', None, '?']:
last_used_build = folder.genome_build
error = False
if upload_option == 'upload_paths' and not trans.app.config.allow_library_path_paste:
error = True
message = '"allow_library_path_paste" is not defined in the Galaxy configuration file'
elif upload_option == 'upload_paths' and not is_admin:
error = True
message = 'Uploading files via filesystem paths can only be performed by administrators'
if upload_option == 'upload_paths':
validate_path_upload(trans) # Duplicate check made in _upload_dataset.
elif upload_option not in ('upload_file', 'upload_directory', 'upload_paths'):
error = True
message = 'Invalid upload_option'
@@ -373,7 +368,7 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
# for cross type comparisions, ie "True" == True
yield prefix, ("%s" % (meta)).encode("utf8", errors='replace')
@web.expose_api
@expose_api
def update(self, trans, id, library_id, payload, **kwd):
"""
update( self, trans, id, library_id, payload, **kwd )
@@ -411,7 +406,7 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
else:
raise HTTPBadRequest('Malformed library content id ( %s ) specified, unable to decode.' % str(content_id))
@web.expose_api
@expose_api
def delete(self, trans, library_id, id, **kwd):
"""
delete( self, trans, library_id, id, **kwd )
lib/galaxy/webapps/galaxy/api/library_datasets.py
+13 -3
View File
@@ -25,7 +25,7 @@ from galaxy.managers import (
)
from galaxy.tools.actions import upload_common
from galaxy.tools.parameters import populate_state
from galaxy.util.path import safe_contains, safe_relpath, unsafe_walk
from galaxy.util.path import full_path_permission_for_user, safe_contains, safe_relpath, unsafe_walk
from galaxy.util.streamball import StreamBall
from galaxy.web import (
_future_expose_api as expose_api,
@@ -432,20 +432,30 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
path = os.path.join(import_base_dir, path)
elif source in ['userdir_file', 'userdir_folder']:
unsafe = None
username = trans.user.username if trans.app.config.user_library_import_check_permissions else None
user_login = trans.user.email
user_base_dir = trans.app.config.user_library_import_dir
if user_base_dir is None:
raise exceptions.ConfigDoesNotAllowException('The configuration of this Galaxy instance does not allow upload from user directories.')
full_dir = os.path.join(user_base_dir, user_login)
if not safe_contains(full_dir, path, whitelist=trans.app.config.user_library_import_symlink_whitelist):
# the path is a symlink outside the user dir
path = os.path.join(full_dir, path)
log.error('User attempted to import a path that resolves to a path outside of their import dir: %s -> %s', path, os.path.realpath(path))
raise exceptions.RequestParameterInvalidException('The given path is invalid.')
if trans.app.config.user_library_import_check_permissions and not full_path_permission_for_user(full_dir, path, username):
log.error('User attempted to import a path that resolves to a path outside of their import dir: '
'%s -> %s and cannot be read by them.', path, os.path.realpath(path))
raise exceptions.RequestParameterInvalidException('The given path is invalid.')
path = os.path.join(full_dir, path)
for unsafe in unsafe_walk(path, whitelist=[full_dir] + trans.app.config.user_library_import_symlink_whitelist):
for unsafe in unsafe_walk(path, whitelist=[full_dir] + trans.app.config.user_library_import_symlink_whitelist, username=username):
# the path is a dir and contains files that symlink outside the user dir
log.error('User attempted to import a directory containing a path that resolves to a path outside of their import dir: %s -> %s', unsafe, os.path.realpath(unsafe))
error = 'User attempted to import a path that resolves to a path outside of their import dir: %s -> %s', \
path, os.path.realpath(path)
if trans.app.config.user_library_import_check_permissions:
error += ' or is not readable for them.'
log.error(error)
if unsafe:
raise exceptions.RequestParameterInvalidException('The given path is invalid.')
if not os.path.exists(path):
static/scripts/bundled/admin.bundled.js
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static/scripts/galaxy.js
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@@ -1 +1 @@
define("galaxy",["exports","libs/underscore","libs/backbone","mvc/base-mvc","mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization"],function(e,t,o,a,r,n,l,i){"use strict";function g(e){return e&&e.__esModule?e:{default:e}}function s(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var o in e)Object.prototype.hasOwnProperty.call(e,o)&&(t[o]=e[o]);return t.default=e,t}function c(e,t){return this._init(e||{},t||{})}Object.defineProperty(e,"__esModule",{value:!0});var u=s(t),p=s(o),f=g(a),d=g(r),y=g(n),b=g(l),v=g(i);(0,b.default)(c,"GalaxyApp");var m="galaxy:debug:namespaces",_=!1;try{_="true"==localStorage.getItem("galaxy:debug")}catch(e){console.log((0,v.default)("localStorage not available for debug flag retrieval"))}c.prototype._init=function(e,t){var o=this;return u.extend(o,p.Events),_&&(o.logger=console,console.debug("debugging galaxy:","options:",e,"bootstrapped:",t)),o._processOptions(e),o.root=e.root||"/",o.params=e.params||{},o.session_csrf_token=e.session_csrf_token||null,o._initConfig(e.config||{}),o._patchGalaxy(window.Galaxy),o._initLogger(o.options.loggerOptions||{}),o.debug("GalaxyApp.options: ",o.options),o.debug("GalaxyApp.config: ",o.config),o.debug("GalaxyApp.logger: ",o.logger),o._initLocale(),o.debug("GalaxyApp.localize: ",o.localize),o.config=e.config||{},o.debug("GalaxyApp.config: ",o.config),o._initUser(e.user||{}),o.debug("GalaxyApp.user: ",o.user),o._setUpListeners(),o.trigger("ready",o),o},c.prototype.defaultOptions={patchExisting:!0,root:"/",session_csrf_token:null},c.prototype._processOptions=function(e){var t=this,o=t.defaultOptions;t.options={};for(var a in o)o.hasOwnProperty(a)&&(t.options[a]=e.hasOwnProperty(a)?e[a]:o[a]);return t},c.prototype._initConfig=function(e){var t=this;return t.config=e,t.config.debug=_||t.config.debug,t},c.prototype._patchGalaxy=function(e){var t=this;if(t.options.patchExisting&&e)for(var o in e)e.hasOwnProperty(o)&&(t[o]=e[o])},c.prototype._initLogger=function(e){var t=this;if(t.config.debug){e.consoleLogger=e.consoleLogger||console,e.consoleLevel=e.consoleLevel||y.default.MetricsLogger.ALL;try{e.consoleNamespaceWhitelist=localStorage.getItem(m).split(",")}catch(e){}try{e.consoleFlattenMessages="true"==localStorage.getItem("galaxy:debug:flatten")}catch(e){}console.log(e.consoleFlattenMessages)}return t.logger=new y.default.MetricsLogger(e),t.emit={},["log","debug","info","warn","error","metric"].map(function(e){t.emit[e]=function(o){t.logger.emit(e,arguments[0],Array.prototype.slice.call(arguments,1))}}),t.config.debug&&(f.default.LoggableMixin.logger=t.logger),t},c.prototype._initLocale=function(e){var t=this;return t.debug("_initLocale:",e),t.localize=v.default,window._l=t.localize,t},c.prototype._initUser=function(e){var t=this;return t.debug("_initUser:",e),t.user=new d.default.User(e),t.user.logger=t.logger,t},c.prototype._setUpListeners=function(){var e=this;return e.lastAjax={},$(document).bind("ajaxSend",function(t,o,a){var r=a.data;try{r=JSON.parse(r)}catch(e){}e.lastAjax={url:location.href.slice(0,-1)+a.url,data:r}}),e},c.prototype.debugging=function(e){var t=this;try{if(void 0===e)return"true"===localStorage.getItem("galaxy:debug");if(e)return localStorage.setItem("galaxy:debug",!0),!0;localStorage.removeItem("galaxy:debug"),t.debuggingNamespaces(null)}catch(e){console.log((0,v.default)("localStorage not available for debug flag retrieval"))}return!1},c.prototype.debuggingNamespaces=function(e){var t=this;try{if(void 0===e){var o=localStorage.getItem(m);return"string"==typeof o?o.split(","):[]}null===e?localStorage.removeItem(m):localStorage.setItem(m,e);var a=t.debuggingNamespaces();return t.logger&&(t.logger.options.consoleNamespaceWhitelist=a),a}catch(e){console.log((0,v.default)("localStorage not available for debug namespace retrieval"))}},c.prototype.toString=function(){return"GalaxyApp("+(this.user?this.user.get("email")||"(anonymous)":"uninitialized")+")"},e.default={GalaxyApp:c}});
define("galaxy",["exports","libs/underscore","libs/backbone","mvc/base-mvc","mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization"],function(e,t,o,a,r,n,l,i){"use strict";function g(e){return e&&e.__esModule?e:{default:e}}function s(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var o in e)Object.prototype.hasOwnProperty.call(e,o)&&(t[o]=e[o]);return t.default=e,t}function c(e,t){return this._init(e||{},t||{})}Object.defineProperty(e,"__esModule",{value:!0});var u=s(t),p=s(o),f=g(a),d=g(r),y=g(n),b=g(l),v=g(i);(0,b.default)(c,"GalaxyApp");var m="galaxy:debug:namespaces",_=!1;try{_="true"==localStorage.getItem("galaxy:debug")}catch(e){console.log((0,v.default)("localStorage not available for debug flag retrieval"))}c.prototype._init=function(e,t){var o=this;return u.extend(o,p.Events),_&&(o.logger=console,console.debug("debugging galaxy:","options:",e,"bootstrapped:",t)),o._processOptions(e),o.root=e.root||"/",o.params=e.params||{},o.session_csrf_token=e.session_csrf_token||null,o._initConfig(e.config||{}),o._patchGalaxy(window.Galaxy),o._initLogger(o.options.loggerOptions||{}),o.debug("GalaxyApp.options: ",o.options),o.debug("GalaxyApp.config: ",o.config),o.debug("GalaxyApp.logger: ",o.logger),o._initLocale(),o.debug("GalaxyApp.localize: ",o.localize),o.config=e.config||{},o.debug("GalaxyApp.config: ",o.config),o._initUser(e.user||{}),o.debug("GalaxyApp.user: ",o.user),o._setUpListeners(),o.trigger("ready",o),o},c.prototype.defaultOptions={patchExisting:!0,root:"/",session_csrf_token:null},c.prototype._processOptions=function(e){var t=this,o=t.defaultOptions;t.options={};for(var a in o)o.hasOwnProperty(a)&&(t.options[a]=e.hasOwnProperty(a)?e[a]:o[a]);return t},c.prototype._initConfig=function(e){var t=this;return t.config=e,t.config.debug=_||t.config.debug,t},c.prototype._patchGalaxy=function(e){var t=this;if(t.options.patchExisting&&e)for(var o in e)e.hasOwnProperty(o)&&(t[o]=e[o])},c.prototype._initLogger=function(e){var t=this;if(t.config.debug){e.consoleLogger=e.consoleLogger||console,e.consoleLevel=e.consoleLevel||y.default.MetricsLogger.ALL;try{e.consoleNamespaceWhitelist=localStorage.getItem(m).split(",")}catch(e){}try{e.consoleFlattenMessages="true"==localStorage.getItem("galaxy:debug:flatten")}catch(e){}console.log(e.consoleFlattenMessages)}return t.logger=new y.default.MetricsLogger(e),t.emit={},["log","debug","info","warn","error","metric"].map(function(e){t.emit[e]=function(o){t.logger.emit(e,arguments[0],Array.prototype.slice.call(arguments,1))}}),t.config.debug&&(f.default.LoggableMixin.logger=t.logger),t},c.prototype._initLocale=function(e){var t=this;return t.debug("_initLocale:",e),t.localize=v.default,window._l=t.localize,t},c.prototype._initUser=function(e){var t=this;return t.debug("_initUser:",e),t.user=new d.default.User(e),t.user.logger=t.logger,t},c.prototype._setUpListeners=function(){var e=this;return e.lastAjax={},$(document).bind("ajaxSend",function(t,o,a){var r=a.data;try{r=JSON.parse(r)}catch(e){}e.lastAjax={url:location.href.slice(0,-1)+a.url,data:r}}),e},c.prototype.debugging=function(e){var t=this;try{if(void 0===e)return"true"===localStorage.getItem("galaxy:debug");if(e)return localStorage.setItem("galaxy:debug",!0),!0;localStorage.removeItem("galaxy:debug"),t.debuggingNamespaces(null)}catch(e){console.log((0,v.default)("localStorage not available for debug flag retrieval"))}return!1},c.prototype.debuggingNamespaces=function(e){var t=this;try{if(void 0===e){var o=localStorage.getItem(m);return"string"==typeof o?o.split(","):[]}null===e?localStorage.removeItem(m):localStorage.setItem(m,e);var a=t.debuggingNamespaces();return t.logger&&(t.logger.options.consoleNamespaceWhitelist=a),a}catch(e){console.log((0,v.default)("localStorage not available for debug namespace retrieval"))}},c.prototype.toString=function(){return"GalaxyApp("+(this.user?this.user.get("email")||"(anonymous)":"uninitialized")+")"},window.Galaxy=window.Galaxy||new c,e.default={GalaxyApp:c}});
static/scripts/galaxy.library.js
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static/scripts/galaxy.pages.js
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static/scripts/layout/router.js
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define("layout/router",["exports","jquery","utils/query-string-parsing","mvc/ui/ui-misc"],function(e,t,i,a){"use strict";function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var u=s(t),n=s(i),r=s(a),o=u.default,c=Backbone.Router.extend({initialize:function(e,t){this.page=e,this.options=t},push:function(e,t){(t=t||{}).__identifer=Math.random().toString(36).substr(2),o.isEmptyObject(t)||(e+=-1==e.indexOf("?")?"?":"&",e+=o.param(t,!0)),Galaxy.params=t,this.navigate(e,{trigger:!0})},execute:function(e,t,i){Galaxy.debug("router execute:",e,t,i);var a=n.default.parse(t.pop());t.push(a),e&&(this.authenticate(t,i)?e.apply(this,t):this.access_denied())},authenticate:function(e,t){return!0},access_denied:function(){this.page.display(new r.default.Message({status:"danger",message:"You must be logged in with proper credentials to make this request.",persistent:!0}))}});e.default=c});
define("layout/router",["exports","jquery","utils/query-string-parsing","mvc/ui/ui-misc"],function(e,t,i,a){"use strict";function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var u=s(t),n=s(i),r=s(a),o=u.default,d=Backbone.Router.extend({initialize:function(e,t){this.page=e,this.options=t},push:function(e,t){(t=t||{}).__identifer=Math.random().toString(36).substr(2),e+=-1==e.indexOf("?")?"?":"&",e+=o.param(t,!0),Galaxy.params=t,this.navigate(e,{trigger:!0})},execute:function(e,t,i){Galaxy.debug("router execute:",e,t,i);var a=n.default.parse(t.pop());t.push(a),e&&(this.authenticate(t,i)?e.apply(this,t):this.access_denied())},authenticate:function(e,t){return!0},access_denied:function(){this.page.display(new r.default.Message({status:"danger",message:"You must be logged in with proper credentials to make this request.",persistent:!0}))}});e.default=d});
static/scripts/libs/jquery/jquery.wymeditor.js
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static/scripts/mvc/collection/list-collection-creator.js
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static/scripts/mvc/collection/list-of-pairs-collection-creator.js
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static/scripts/mvc/dataset/data.js
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static/scripts/mvc/dataset/dataset-li.js
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static/scripts/mvc/history/history-item-li.js
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define("mvc/history/history-item-li",["exports"],function(e){"use strict";function n(e){return 0==e.indexOf("name:")?'<span class="label label-info">'+_.escape(e.slice(5))+"</span>":""}Object.defineProperty(e,"__esModule",{value:!0}),e.default={nametagTemplate:function(e){return'<span class="nametags">'+_.sortBy(_.uniq(e.tags)).map(n).join("")+"</span>"}}});
define("mvc/history/history-item-li",["exports"],function(e){"use strict";function n(e){return'<span class="label label-info">'+_.escape(e.slice(5))+"</span>"}Object.defineProperty(e,"__esModule",{value:!0}),e.default={nametagTemplate:function(e){var t=_.filter(_.uniq(e.tags),function(e){return 0===e.indexOf("name:")}),a=_.sortBy(t).map(n);return'\n <div class="nametags" title="'+t.length+' nametags">\n '+a.join("")+"\n </div>"}}});
static/scripts/mvc/library/library-foldertoolbar-view.js
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static/scripts/mvc/ui/ui-modal.js
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define("mvc/ui/ui-modal",["exports"],function(t){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var i=t.View=Backbone.View.extend({className:"ui-modal",optionsDefault:{container:"body",title:"ui-modal",cls:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null,title_separator:!0},buttonList:{},initialize:function(t){this.options=_.defaults(t||{},this.optionsDefault),$(this.options.container).prepend(this.el),t&&this.render()},show:function(t){if(t&&(this.options=_.defaults(t,this.optionsDefault),this.render()),!this.visible&&(this.visible=!0,this.$el.fadeIn("fast"),this.options.closing_events)){var i=this;$(document).on("keyup.ui-modal",function(t){27==t.keyCode&&i.hide(!0)}),this.$backdrop.on("click",function(){i.hide(!0)})}},hide:function(t){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback(t),$(document).off("keyup.ui-modal"),this.$backdrop.off("click")},render:function(){var t=this;if(this.$el.html(this._template()),this.$header=this.$(".modal-header"),this.$dialog=this.$(".modal-dialog"),this.$body=this.$(".modal-body"),this.$footer=this.$(".modal-footer"),this.$backdrop=this.$(".modal-backdrop"),this.$buttons=this.$(".buttons"),"progress"==this.options.body&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"/></div>')),this.$el.removeClass().addClass("modal").addClass(this.options.cls),this.$header.find(".title").html(this.options.title),this.$body.html(this.options.body),this.$buttons.empty(),this.buttonList={},this.options.buttons){var i=0;$.each(this.options.buttons,function(s,o){var e=$("<button/>").attr("id","button-"+i++).text(s).click(o);t.$buttons.append(e).append("&nbsp;"),t.buttonList[s]=e})}else this.$footer.hide();this.$backdrop[this.options.backdrop&&"addClass"||"removeClass"]("in"),this.$header[!this.options.title_separator&&"addClass"||"removeClass"]("no-separator"),this.$body.removeAttr("style"),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width)},getButton:function(t){return this.buttonList[t]},enableButton:function(t){this.getButton(t).prop("disabled",!1)},disableButton:function(t){this.getButton(t).prop("disabled",!0)},showButton:function(t){this.getButton(t).show()},hideButton:function(t){this.getButton(t).hide()},scrollTop:function(){return this.$body.scrollTop()},_template:function(){return'<div class="modal-backdrop fade"/><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><h4 class="title"/></div><div class="modal-body"/><div class="modal-footer"><div class="buttons"/></div></div></div>'}});t.default={View:i}});
define("mvc/ui/ui-modal",["exports"],function(t){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var i=t.View=Backbone.View.extend({className:"ui-modal",optionsDefault:{container:"body",title:"ui-modal",cls:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null,title_separator:!0},buttonList:{},initialize:function(t){this.options=_.defaults(t||{},this.optionsDefault),$(this.options.container).prepend(this.el),t&&this.render()},show:function(t){var i=this;t&&(this.options=_.defaults(t,this.optionsDefault),this.render()),this.visible||(this.visible=!0,this.$el.fadeIn("fast")),this.options.closing_events&&($(document).on("keyup.ui-modal",function(t){27==t.keyCode&&i.hide(!0)}),this.$backdrop.on("click",function(){i.hide(!0)}))},hide:function(t){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback(t),$(document).off("keyup.ui-modal"),this.$backdrop.off("click")},render:function(){var t=this;if(this.$el.html(this._template()),this.$header=this.$(".modal-header"),this.$dialog=this.$(".modal-dialog"),this.$body=this.$(".modal-body"),this.$footer=this.$(".modal-footer"),this.$backdrop=this.$(".modal-backdrop"),this.$buttons=this.$(".buttons"),"progress"==this.options.body&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"/></div>')),this.$el.removeClass().addClass("modal").addClass(this.options.cls),this.$header.find(".title").html(this.options.title),this.$body.html(this.options.body),this.$buttons.empty(),this.buttonList={},this.options.buttons){var i=0;$.each(this.options.buttons,function(s,o){var e=$("<button/>").attr("id","button-"+i++).text(s).click(o);t.$buttons.append(e).append("&nbsp;"),t.buttonList[s]=e})}else this.$footer.hide();this.$backdrop[this.options.backdrop&&"addClass"||"removeClass"]("in"),this.$header[!this.options.title_separator&&"addClass"||"removeClass"]("no-separator"),this.$body.removeAttr("style"),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width)},getButton:function(t){return this.buttonList[t]},enableButton:function(t){this.getButton(t).prop("disabled",!1)},disableButton:function(t){this.getButton(t).prop("disabled",!0)},showButton:function(t){this.getButton(t).show()},hideButton:function(t){this.getButton(t).hide()},scrollTop:function(){return this.$body.scrollTop()},_template:function(){return'<div class="modal-backdrop fade"/><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><h4 class="title"/></div><div class="modal-body"/><div class="modal-footer"><div class="buttons"/></div></div></div>'}});t.default={View:i}});
static/scripts/mvc/ui/ui-select-default.js
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static/scripts/mvc/ui/ui-select-library.js
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define("mvc/ui/ui-select-library",["exports","utils/utils","mvc/ui/ui-misc","mvc/ui/ui-table","mvc/ui/ui-list"],function(e,t,i,a,l){"use strict";function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});n(t);var s=n(i),r=(n(a),n(l)),c=Backbone.Collection.extend({url:Galaxy.root+"api/libraries?deleted=false"}),o=Backbone.Collection.extend({initialize:function(){var e=this;this.config=new Backbone.Model({library_id:null}),this.config.on("change",function(){e.fetch({reset:!0})})},url:function(){return Galaxy.root+"api/libraries/"+this.config.get("library_id")+"/contents"}}),u=Backbone.View.extend({initialize:function(e){var t=this;this.libraries=new c,this.datasets=new o,this.options=e,this.library_select=new s.default.Select.View({onchange:function(e){t.datasets.config.set("library_id",e)}}),this.dataset_list=new r.default.View({name:"dataset",optional:e.optional,multiple:e.multiple,onchange:function(){t.trigger("change")}}),this.libraries.on("reset",function(){var e=[];t.libraries.each(function(t){e.push({value:t.id,label:t.get("name")})}),t.library_select.update(e)}),this.datasets.on("reset",function(){var e=[];null!==t.library_select.text()&&t.datasets.each(function(t){"file"===t.get("type")&&e.push({value:t.id,label:t.get("name")})}),t.dataset_list.update(e)}),this.on("change",function(){e.onchange&&e.onchange(t.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){t.library_select.trigger("change"),void 0!==t.options.value&&t.value(t.options.value)}})},value:function(e){return this.dataset_list.value(e)},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div></div>'}});e.default={View:u}});
define("mvc/ui/ui-select-library",["exports","mvc/ui/ui-misc","mvc/ui/ui-list"],function(e,t,i){"use strict";function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var n=a(t),l=a(i),s=Backbone.Collection.extend({url:Galaxy.root+"api/libraries?deleted=false"}),r=Backbone.Collection.extend({initialize:function(){var e=this;this.config=new Backbone.Model({library_id:null}),this.config.on("change",function(){e.fetch({reset:!0})})},url:function(){return Galaxy.root+"api/libraries/"+this.config.get("library_id")+"/contents"}}),c=Backbone.View.extend({initialize:function(e){var t=this;this.libraries=new s,this.datasets=new r,this.options=e,this.library_select=new n.default.Select.View({onchange:function(e){t.datasets.config.set("library_id",e)}}),this.dataset_list=new l.default.View({name:"dataset",optional:e.optional,multiple:e.multiple,onchange:function(){t.trigger("change")}}),this.libraries.on("reset",function(){var e=[];t.libraries.each(function(t){e.push({value:t.id,label:t.get("name")})}),t.library_select.update(e)}),this.datasets.on("reset",function(){var e=[];null!==t.library_select.text()&&t.datasets.each(function(t){"file"===t.get("type")&&e.push({value:t.id,label:t.get("name")})}),t.dataset_list.update(e)}),this.on("change",function(){e.onchange&&e.onchange(t.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){t.library_select.trigger("change"),void 0!==t.options.value&&t.value(t.options.value)}})},value:function(e){return this.dataset_list.value(e)},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div></div>'}});e.default={View:c}});
static/scripts/nls/zh/locale.js
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static/scripts/toolshed/groups/group-detail-view.js
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define("toolshed/groups/group-detail-view",["exports","libs/toastr","toolshed/groups/group-model"],function(e,t,o){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var r=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var o in e)Object.prototype.hasOwnProperty.call(e,o)&&(t[o]=e[o]);return t.default=e,t}(t),i=function(e){return e&&e.__esModule?e:{default:e}}(o),a=Backbone.View.extend({el:"#groups_element",options:{},app:null,initialize:function(e){this.options=_.extend(this.options,e),this.app=window.globalTS.groups,null!==this.app.collection?(this.model=this.app.collection.get(this.options.group_id),this.render()):this.fetchGroup()},fetchGroup:function(e){var t=this;this.options=_.extend(this.options,e),this.model=new i.default.Group({id:this.options.group_id}),this.model.fetch({success:function(e){console.log("received data: "),console.log(e),t.render()},error:function(e,t){void 0!==t.responseJSON?r.error(t.responseJSON.err_msg):r.error("An error occurred.")}})},render:function(){var e=this.templateRow();this.$el.html(e({group:this.model})),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},templateRow:function(){return _.template(["<div>",'<h3><%= _.escape(group.get("name")) %></h3>','<p class="" style="color:gray;">','A group of <%= group.get("members").length %> members with <%= group.get("repositories").length %> repositories and a total of <%= group.get("total_downloads") %> combined repository clones.</p>',"<h3>Members</h3>",'<table class="grid table table-condensed">',"<thead>","<th>Name</th>","<th>Repositories</th>","<th>Registered</th>","</thead>","<tbody>",'<% _.each(group.get("members"), function(member) { %>',"<tr>","<td>","<%= _.escape(member.username) %>","</td>","<td>",'<a data-toggle="tooltip" data-placement="top" title="Repositories of <%= _.escape(member.username) %>" href="/repository/browse_repositories_by_user?user_id=<%= member.id %>&use_panels=true" id="<%= member.id %>"><%= member.user_repos_count %></a>',"</td>","<td>","<%= member.time_created %>","</td>","</tr>","<% }); %>","</tbody>","</table>","<h3>Repositories</h3>",'<table class="grid table table-condensed">',"<thead>","<th>Name</th>","<th>Description</th>","<th>Clones</th>","<th>Owner</th>","<th>Categories</th>","<th>Created</th>","<th>Updated</th>","<th>Rating</th>","<th>Verified</th>","</thead>","<tbody>",'<% _.each(group.get("repositories"), function(repo) { %>',"<tr>","<td>",'<a data-toggle="tooltip" data-placement="top" title="Details of <%= _.escape(repo.name) %>" href="/view/<%= _.escape(repo.owner) %>/<%= _escape(repo.name) %>" id="<%= repo.id %>"><%= _.escape(repo.name) %></a>',"</td>","<td>","<%= _.escape(repo.description) %>","</td>","<td>","<%= repo.times_downloaded %>","</td>","<td>","<%= _.escape(repo.owner) %>","</td>","<td>","<% _.each((repo.categories), function(cat) { %>",'<a data-toggle="tooltip" data-placement="top" title="Repositories in <%= cat.name %>" href="/repository/browse_repositories_in_category?id=<%= cat.id %>&use_panels=true"><%= cat.name %></a><br/>',"<% }); %>","</td>",'<td data-toggle="tooltip" data-placement="top" title="<%= repo.time_created_full %>">',"<%= repo.time_created %>","</td>",'<td data-toggle="tooltip" data-placement="top" title="<%= repo.time_updated_full %>">',"<%= repo.time_updated %>","</td>","<td>","<%= repo.ratings_mean %>","</td>","<td>","<%= repo.approved %>","</td>","</tr>","<% }); %>","</tbody>","</table>","</div>"].join(""))}});e.default={GroupDetailView:a}});
static/scripts/toolshed/groups/group-list-view.js
+1
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@@ -0,0 +1 @@
define("toolshed/groups/group-list-view",["exports","libs/toastr","toolshed/groups/group-model","toolshed/groups/group-listrow-view"],function(e,o,t,s){"use strict";function r(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var i=function(e){if(e&&e.__esModule)return e;var o={};if(null!=e)for(var t in e)Object.prototype.hasOwnProperty.call(e,t)&&(o[t]=e[t]);return o.default=e,o}(o),n=r(t),l=r(s),u=Backbone.View.extend({el:"#groups_element",defaults:{},initialize:function(e){this.options=_.defaults(this.options||{},this.defaults,e);var o=this;window.globalTS.groups.collection=new n.default.Groups,window.globalTS.groups.collection.fetch({success:function(e){console.log("received data: "),console.log(e),o.render()},error:function(e,o){void 0!==o.responseJSON?i.error(o.responseJSON.err_msg):i.error("An error occurred.")}})},fetch:function(){},render:function(e){this.options=_.extend(this.options,e),$(".tooltip").hide();var o=this.templateGroupsList();this.$el.html(o({length:window.globalTS.groups.collection.models.length})),this.renderRows(window.globalTS.groups.collection.models),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},renderRows:function(e){for(var o=0;o<e.length;o++){var t=e[o];this.renderOne({group:t})}},renderOne:function(e){var o=new l.default.GroupListRowView(e);this.$el.find("#group_list_body").append(o.el)},templateGroupsList:function(){var e=[];return e.push('<div id="groups">'),e.push("</div>"),e.push('<div class="groups_container table-responsive">'),e.push("<% if(length === 0) { %>"),e.push("<div>There are no groups yet.</div>"),e.push("<% } else{ %>"),e.push('<table class="grid table table-condensed">'),e.push(" <thead>"),e.push(" <th>Name</th>"),e.push(" <th>Members</th> "),e.push(" <th>Repositories</th>"),e.push(" </thead>"),e.push(' <tbody id="group_list_body">'),e.push(" </tbody>"),e.push("</table>"),e.push("<% }%>"),e.push("</div>"),_.template(e.join(""))}});e.default={GroupListView:u}});
static/scripts/toolshed/groups/group-listrow-view.js
+1
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@@ -0,0 +1 @@
define("toolshed/groups/group-listrow-view",["exports"],function(e){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var t=Backbone.View.extend({events:{},initialize:function(e){this.render(e.group)},render:function(e){var t=this.templateRow();return this.setElement(t({group:e})),this.$el.show(),this},templateRow:function(){return _.template(['<tr class="" data-id="<%- group.get("id") %>">','<td><a href="groups#/<%= group.get("id") %>"><%= _.escape(group.get("name")) %></a></td>','<td><%= group.get("total_members") %></td>','<td><%= group.get("total_repos") %></td>',"</tr>"].join(""))}});e.default={GroupListRowView:t}});
static/scripts/toolshed/groups/group-model.js
+1
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@@ -0,0 +1 @@
define("toolshed/groups/group-model",["exports"],function(o){"use strict";Object.defineProperty(o,"__esModule",{value:!0});var e=Backbone.Model.extend({urlRoot:Galaxy.root+"api/groups"}),r=Backbone.Collection.extend({url:Galaxy.root+"api/groups",model:e});o.default={Group:e,Groups:r}});
static/scripts/toolshed/toolshed.groups.js
+1
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@@ -0,0 +1 @@
define("toolshed/toolshed.groups",["exports","toolshed/groups/group-list-view","toolshed/groups/group-detail-view"],function(o,e,t){"use strict";function u(o){return o&&o.__esModule?o:{default:o}}Object.defineProperty(o,"__esModule",{value:!0});var i=u(e),r=u(t),s=Backbone.Router.extend({routes:{"":"groups",":group_id":"group_page"}}),l=Backbone.View.extend({groupListView:null,groupDetailView:null,collection:null,initialize:function(){window.globalTS.groups=this,this.ts_router=new s,this.ts_router.on("route:groups",function(){window.globalTS.groups.groupListView=new i.default.GroupListView}),this.ts_router.on("route:group_page",function(o){window.globalTS.groups.groupDetailView=new r.default.GroupDetailView({group_id:o})}),Backbone.history.start({pushState:!1})}});o.default={ToolshedGroups:l}});
static/scripts/viz/circster.js
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static/scripts/viz/trackster.js
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static/style/blue/base.css
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static/style/blue/library.css
+1 -1
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@@ -1 +1 @@
a{text-decoration:underline}label{font-weight:normal}.library_style_container{width:95%;margin:auto;margin-top:2em;overflow:auto !important}.library_style_container .fa{font-size:12px}.library_style_container .fa-globe,.library_style_container .fa-shield,.library_style_container .fa-key,.library_style_container .fa-ban{font-size:initial;margin-left:.6em}.library_style_container .libraryRow{background-color:#ebd9b2}.library_style_container .datasetHighlighted{background-color:#f9f9f9}.library_style_container .libraryItemDeleted-True{font-style:italic}.library_style_container div.libraryItemBody{padding:4px 4px 2px 4px}.library_style_container li.folderRow,.library_style_container li.datasetRow{border-top:solid 1px #c6bfa8}.library_style_container li.folderRow:hover,.library_style_container li.datasetRow:hover{background-color:#f9f9f9}.library_style_container td.right-center{vertical-align:middle !important;text-align:right}.library_style_container .library-genome-select{max-width:350px}.library_style_container .library-extension-select{max-width:140px}.library_style_container .library_table td{border-top:1px solid #5f6990 !important}.library_style_container .library_table th{border-bottom:2px solid #5f6990 !important}.library_style_container .library_table a{color:#0A143D}.library_style_container .library_table a:hover{color:maroon}.library_style_container tr.light td{background-color:white;color:black}.library_style_container tr.light:hover td{background-color:#f5e8cc}.library_style_container tr.dark td{background-color:#d6b161;color:white}.library_style_container tr.dark:hover td{background-color:#ebd4a4;color:white}.library_style_container a.dark{color:white}.library_style_container .dataset_table tr,.library_style_container .dataset_table th,.library_style_container .dataset_table td{border:none}.library_style_container .dataset_table .dataset-first-column{width:30%}.library_style_container th.button_heading{width:2em}.library_style_container .bigdrop.select2-container .select2-results{max-height:300px}.library_style_container .bigdrop .select2-results{max-height:300px}.library_style_container .select2-container-multi{width:100%}.library_style_container .roles-selection{width:66%}.library_style_container #library_toolbar{margin-bottom:.5em}.library_style_container #library_toolbar span{margin-right:.2em}.library_style_container #library_toolbar .toolbar-item{margin-left:1em}.library_style_container #libraries_element button,.library_style_container #folder_items_element button{margin-left:.5em}.library_style_container .help-button{float:right}.library_style_container .pagination-sm{height:15px}.library_style_container .library-paginator{margin-left:2em}.library_style_container .import-type-switch{text-decoration:underline}.library_style_container .libimport-select-none,.library_style_container .libimport-select-all{margin-left:.5em}.library_style_container .library-modal-item{width:90%;margin-left:1em;margin-right:1em}.library_style_container .paginator-bottom{width:27em;margin-left:auto;margin-right:auto;margin-top:2em;margin-bottom:2em}.modal-content #selected_history_content ul{list-style-type:none}#library-grid ul{list-style:none}#library-grid span.expandLink{padding-left:12px;display:inline-block;vertical-align:middle;background:url(../images/silk/resultset_next.png) no-repeat}#library-grid .folderRow.expanded span.expandLink{background:url(../images/silk/resultset_bottom.png) no-repeat}#library-grid .folderRow span.rowIcon{float:left;margin-right:5px;width:16px;height:16px;display:inline-block;vertical-align:middle;background:url(../images/silk/folder.png)}#library-grid .libraryItem-error{margin-right:2px;padding:0 2px 0 2px;border:1px solid #dd1b15;background:#f9c7c5}#library-grid .libraryItem-queued{margin-right:2px;padding:0 2px 0 2px;border:1px solid #bfbfbf;background:#eee}#library-grid .libraryItem-running{margin-right:2px;padding:0 2px 0 2px;border:1px solid #AAAA66;background:#FFFFCC}#library-grid .libraryItem-upload{margin-right:2px;padding:0 2px 0 2px;border:1px solid #119ac2;background:#a8e5f7}.libraryTitle th{text-align:left}.libraryTitle .rowTitle{padding:2px}
a{text-decoration:underline}label{font-weight:normal}.library_style_container{width:95%;margin:auto;margin-top:2em;overflow:auto !important}.library_style_container .fa{font-size:12px}.library_style_container .fa-globe,.library_style_container .fa-shield,.library_style_container .fa-key,.library_style_container .fa-ban{font-size:initial;margin-left:.6em}.library_style_container .libraryRow{background-color:#ebd9b2}.library_style_container .datasetHighlighted{background-color:#f9f9f9}.library_style_container .libraryItemDeleted-True{font-style:italic}.library_style_container div.libraryItemBody{padding:4px 4px 2px 4px}.library_style_container li.folderRow,.library_style_container li.datasetRow{border-top:solid 1px #c6bfa8}.library_style_container li.folderRow:hover,.library_style_container li.datasetRow:hover{background-color:#f9f9f9}.library_style_container td.right-center{vertical-align:middle !important;text-align:right}.library_style_container .library-genome-select{max-width:350px}.library_style_container .library-extension-select{max-width:140px}.library_style_container .library_table td{border-top:1px solid #5f6990 !important}.library_style_container .library_table th{border-bottom:2px solid #5f6990 !important}.library_style_container .library_table a{color:#0A143D}.library_style_container .library_table a:hover{color:maroon}.library_style_container tr.light td{background-color:white;color:black}.library_style_container tr.light:hover td{background-color:#f5e8cc}.library_style_container tr.dark td{background-color:#d6b161;color:white}.library_style_container tr.dark:hover td{background-color:#ebd4a4;color:white}.library_style_container a.dark{color:white}.library_style_container .dataset_table tr,.library_style_container .dataset_table th,.library_style_container .dataset_table td{border:none}.library_style_container .dataset_table .dataset-first-column{width:30%}.library_style_container th.button_heading{width:2em}.library_style_container .bigdrop.select2-container .select2-results{max-height:300px}.library_style_container .bigdrop .select2-results{max-height:300px}.library_style_container .select2-container-multi{width:100%}.library_style_container .roles-selection{width:66%}.library_style_container #library_toolbar{margin-bottom:.5em}.library_style_container #library_toolbar span{margin-right:.2em}.library_style_container #library_toolbar .toolbar-item{margin-left:.5em}.library_style_container #libraries_element button,.library_style_container #folder_items_element button{margin-left:.5em}.library_style_container .right-float{float:right}.library_style_container .pagination-sm{height:15px}.library_style_container .library-paginator{margin-left:2em}.library_style_container .import-type-switch{text-decoration:underline}.library_style_container .libimport-select-none,.library_style_container .libimport-select-all{margin-left:.5em}.library_style_container .paginator-bottom{width:27em;margin-left:auto;margin-right:auto;margin-top:2em;margin-bottom:2em}.modal-content .library_selected_history_content ul{list-style-type:none}.modal-content .library-collection-type-select,.modal-content .library-collection-history-select{margin-left:auto;margin-right:auto;width:200px;min-width:200px}.modal-content .library-modal-item{width:90%;margin-left:auto;margin-right:auto;margin-top:1.5em}.libraryTitle th{text-align:left}.libraryTitle .rowTitle{padding:2px}
templates/base.mako
+1
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@@ -61,6 +61,7 @@
## TODO: remove when all libs are required directly in modules
'bundled/libs.bundled',
'libs/require',
'bundled/extended.bundled'
)}
<script type="text/javascript">
templates/base/base_panels.mako
+3 -2
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@@ -54,6 +54,7 @@
## TODO: remove when all libs are required directly in modules
'bundled/libs.bundled',
'libs/require',
'bundled/extended.bundled'
)}
<script type="text/javascript">
@@ -98,13 +99,13 @@
%if self.has_left_panel:
var lp = new panels.LeftPanel({ el: '#left' });
force_left_panel = function( x ) { lp.force_panel( x ) };
window.force_left_panel = function( x ) { lp.force_panel( x ) };
%endif
%if self.has_right_panel:
var rp = new panels.RightPanel({ el: '#right' });
window.handle_minwidth_hint = function( x ) { rp.handle_minwidth_hint( x ) };
force_right_panel = function( x ) { rp.force_panel( x ) };
window.force_right_panel = function( x ) { rp.force_panel( x ) };
%endif
%if t.webapp.name == 'galaxy' and app.config.ga_code:
templates/galaxy_client_app.mako
+9 -12
View File
@@ -24,19 +24,16 @@ ${ h.dumps( dictionary, indent=( 2 if trans.debug else 0 ) ) }
## 1) bootstrap kwargs (as above), 2) build Galaxy global var, 3) load 'app' by AMD (optional)
${ self.bootstrap( **kwargs ) }
<script type="text/javascript">
require([ 'require', 'galaxy' ], function( require, galaxy ){
//TODO: global...
window.Galaxy = new galaxy.default.GalaxyApp({
root : '${h.url_for( "/" )}',
config : ${ render_json( get_config_dict() )},
user : ${ render_json( get_user_dict() )},
session_csrf_token : '${ trans.session_csrf_token }'
}, window.bootstrapped );
window.Galaxy = new window.bundleEntries.GalaxyApp.GalaxyApp({
root : '${h.url_for( "/" )}',
config : ${ render_json( get_config_dict() )},
user : ${ render_json( get_user_dict() )},
session_csrf_token : '${ trans.session_csrf_token }'
}, window.bootstrapped );
%if app:
require([ '${app}' ]);
%endif
});
%if app:
require([ '${app}' ]);
%endif
</script>
</%def>
templates/legacy/grid_base.mako
+2 -4
View File
@@ -64,10 +64,8 @@
## load javascript
<script type="text/javascript">
require(['legacy/grid/grid-view'], function(GridView) {
$(function() {
var gridView = new GridView.default( ${ h.dumps( self.get_grid_config( embedded=embedded, insert=insert ) ) } );
});
$(function() {
var gridView = new window.bundleEntries.LegacyGridView( ${ h.dumps( self.get_grid_config( embedded=embedded, insert=insert ) ) } );
});
</script>
</%def>
templates/webapps/galaxy/base_panels.mako
-1
View File
@@ -7,7 +7,6 @@
<%def name="javascripts()">
${parent.javascripts()}
${h.js("bundled/extended.bundled")}
</%def>
<%def name="late_javascripts()">
templates/webapps/galaxy/dataset/display.mako
+14 -21
View File
@@ -5,31 +5,24 @@
<%def name="javascripts()">
${parent.javascripts()}
${h.js("bundled/extended.bundled")}
## If data is chunkable, use JavaScript for display.
%if item.datatype.CHUNKABLE:
<script type="text/javascript">
require(['mvc/dataset/data'], function(data) {
//
// Use tabular data display progressively by deleting data from page body
// and then showing dataset view.
//
$('.page-body').children().remove();
data.default.createTabularDatasetChunkedView({
// TODO: encode id.
dataset_config:
_.extend( ${h.dumps( item.to_dict() )}, {
chunk_url: "${h.url_for( controller='/dataset', action='display',
dataset_id=trans.security.encode_id( item.id ))}",
first_data_chunk: ${first_chunk}
}),
parent_elt: $('.page-body')
<script type="text/javascript">
$(function(){
// Use tabular data display progressively by deleting data from page body
// and then showing dataset view.
var dataset_config = _.extend( ${h.dumps( item.to_dict() )}, {
chunk_url: "${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( item.id ))}",
first_data_chunk: ${first_chunk}});
$('.page-body').children().remove();
window.bundleEntries.createTabularDatasetChunkedView({
dataset_config: dataset_config,
parent_elt: $('.page-body')
});
});
});
</script>
</script>
%endif
</%def>
templates/webapps/galaxy/dataset/tabular_chunked.mako
+3 -2
View File
@@ -5,10 +5,11 @@
<%def name="javascripts()">
${parent.javascripts()}
${h.js("bundled/extended.bundled")}
<script type="text/javascript">
require([ 'mvc/dataset/data' ], function( data ) {
data.default.createTabularDatasetChunkedView({
$(function(){
bundleEntries.createTabularDatasetChunkedView({
dataset_config : _.extend( ${ h.dumps( trans.security.encode_dict_ids( dataset.to_dict() ) )}, {
first_data_chunk: ${ chunk }
}),
templates/webapps/galaxy/galaxy.panels.mako
+3 -2
View File
@@ -110,6 +110,7 @@
// extra configuration global
var galaxy_config = ${ h.dumps( self.galaxy_config ) };
window.galaxy_config = galaxy_config;
</script>
${h.js(
@@ -146,14 +147,14 @@
## configure left panel
%if self.galaxy_config['left_panel']:
var lp = new panels.LeftPanel({ el: '#left' });
force_left_panel = function( x ) { lp.force_panel( x ) };
window.force_left_panel = function( x ) { lp.force_panel( x ) };
%endif
## configure right panel
%if self.galaxy_config['right_panel']:
var rp = new panels.RightPanel({ el: '#right' });
window.handle_minwidth_hint = function( x ) { rp.handle_minwidth_hint( x ) };
force_right_panel = function( x ) { rp.force_panel( x ) };
window.force_right_panel = function( x ) { rp.force_panel( x ) };
%endif
</script>
</%def>
templates/webapps/galaxy/history/display.mako
+7 -17
View File
@@ -47,18 +47,8 @@
.css( 'height', '100%' )
.addClass( 'flex-vertical-container' );
require.config({
baseUrl : "${h.url_for( '/static/scripts' )}",
urlArgs: 'v=${app.server_starttime}'
})([
'mvc/history/history-view-annotated',
'mvc/history/copy-dialog',
], function( panelMod, historyCopyDialog ){
// history module is already in the dpn chain from the panel. We can re-scope it here.
var HISTORY = require( 'mvc/history/history-model' );
var HISTORY_CONTENTS = require( 'mvc/history/history-contents' );
var HistoryContentsWithAnnotations = HISTORY_CONTENTS.default.HistoryContents.extend({
$(function(){
var HistoryContentsWithAnnotations = window.bundleEntries.HistoryContents.extend({
_buildFetchData : function( options ){
console.log( '_buildFetchData:' );
options = options || {};
@@ -66,10 +56,10 @@
options.view = 'summary';
options.keys = 'annotation,tags';
}
return HISTORY_CONTENTS.default.HistoryContents.prototype._buildFetchData.call( this, options );
return window.bundleEntries.HistoryContents.prototype._buildFetchData.call( this, options );
}
});
var HistoryWithAnnotations = HISTORY.default.History.extend({
var HistoryWithAnnotations = window.bundleEntries.History.extend({
contentsClass : HistoryContentsWithAnnotations
});
@@ -78,16 +68,16 @@
});
$( '.history-copy-link' ).click( function( ev ){
historyCopyDialog.default( historyModel, { useImport: true, allowAll: false })
window.bundleEntries.HistoryCopyDialog( historyModel, { useImport: true, allowAll: false })
.done( function(){
var mainWindow = ( window && ( window !== window.parent ) )? window.top : window;
mainWindow.location.href = Galaxy.root;
});
});
window.historyView = new panelMod.default.AnnotatedHistoryView({
window.historyView = new window.bundleEntries.HistoryViewAnnotated.AnnotatedHistoryView({
el : $( "#history-" + historyJSON.id ),
className : panelMod.default.AnnotatedHistoryView.prototype.className + ' wide',
className : window.bundleEntries.HistoryViewAnnotated.AnnotatedHistoryView.prototype.className + ' wide',
model : historyModel,
show_deleted : false,
show_hidden : false,
templates/webapps/galaxy/history/display_structured.mako
+10 -11
View File
@@ -141,22 +141,21 @@
hda_dicts.append( hda_dict )
%>
${parent.javascripts()}
${h.js("bundled/extended.bundled")}
## load edit views for each of the hdas
<script type="text/javascript">
define( 'display-structured', function(){
require([ 'mvc/history/hda-li-edit', 'mvc/history/hda-model' ], function( hdaEdit, hdaModel ){
var hdaJSON = ${ h.dumps( hda_dicts, indent=( 2 if trans.debug else 0 ) ) };
var hdaJSON = ${ h.dumps( hda_dicts, indent=( 2 if trans.debug else 0 ) ) };
window.hdas = hdaJSON.map( function( hda ){
return new hdaEdit.default.HDAListItemEdit({
model : new hdaModel.default.HistoryDatasetAssociation( hda ),
el : $( '#hda-' + hda.id ),
linkTarget : '_self',
purgeAllowed : Galaxy.config.allow_user_dataset_purge,
logger : Galaxy.logger
}).render( 0 );
});
window.hdas = hdaJSON.map( function( hda ){
return new window.bundleEntries.HDAListItemEdit.HDAListItemEdit({
model : new window.bundleEntries.HDAModel.HistoryDatasetAssociation( hda ),
el : $( '#hda-' + hda.id ),
linkTarget : '_self',
purgeAllowed : Galaxy.config.allow_user_dataset_purge,
logger : Galaxy.logger
}).render( 0 );
});
});
templates/webapps/galaxy/history/embed.mako
+74 -86
View File
@@ -40,99 +40,87 @@
// In order to handle this, find this script and cache the previous node (the div above).
// (Since we need thisScript to be locally scoped or it will get overwritten, enclose in self-calling function)
(function(){
var scripts = document.getElementsByTagName( 'script' ),
var scripts = document.getElementsByTagName( 'script' );
// this is executed immediately, so the last script will be this script
thisScript = scripts[ scripts.length - 1 ],
$embeddedHistory = $( thisScript ).prev();
var thisScript = scripts[ scripts.length - 1 ];
var $embeddedHistory = $( thisScript ).prev();
require.config({
baseUrl: "${h.url_for( '/static/scripts' )}",
urlArgs: 'v=${app.server_starttime}'
});
require([
'mvc/history/history-view-annotated',
'mvc/history/copy-dialog'
], function( viewMod, historyCopyDialog ){
var $embeddedHistory = $( thisScript ).prev();
$embeddedHistory.find( '.item-content' ).addClass( 'flex-vertical-container' );
var $embeddedHistory = $( thisScript ).prev();
$embeddedHistory.find( '.item-content' ).addClass( 'flex-vertical-container' );
$(function(){
var HISTORY = require( 'mvc/history/history-model' );
var HISTORY_CONTENTS = require( 'mvc/history/history-contents' );
$(function(){
var HistoryContentsWithAnnotations = window.bundleEntries.HistoryContents.extend({
_buildFetchData : function( options ){
console.log( '_buildFetchData:' );
options = options || {};
if( !options.keys && !options.view ){
options.view = 'summary';
options.keys = 'annotation,tags';
}
return window.bundleEntries.HistoryContents.prototype._buildFetchData.call( this, options );
}
});
var HistoryWithAnnotations = window.bundleEntries.History.extend({
contentsClass : HistoryContentsWithAnnotations
});
var HistoryContentsWithAnnotations = HISTORY_CONTENTS.default.HistoryContents.extend({
_buildFetchData : function( options ){
console.log( '_buildFetchData:' );
options = options || {};
if( !options.keys && !options.view ){
options.view = 'summary';
options.keys = 'annotation,tags';
}
return HISTORY_CONTENTS.default.HistoryContents.prototype._buildFetchData.call( this, options );
var historyJSON = ${h.dumps( history_dict )};
var historyModel = new HistoryWithAnnotations( historyJSON, null, {
order : 'hid-asc',
});
var historyView = new window.bundleEntries.HistoryViewAnnotated.AnnotatedHistoryView({
el : $embeddedHistory.find( ".history-panel" ),
className : window.bundleEntries.HistoryViewAnnotated.AnnotatedHistoryView.prototype.className + ' wide',
model : historyModel
});
historyView.trigger( 'loading' );
historyModel.fetchContents({ silent: true })
.fail( function(){ alert( 'Galaxy history failed to load' ); })
.done( function(){
historyView.trigger( 'loading-done' );
historyView.render();
});
function toggleExpanded( ev ){
ev.preventDefault();
$embeddedHistory.find( '.expand-content-btn' ).toggleClass( 'toggle-expand' ).toggleClass( 'toggle' );
$embeddedHistory.find( ".summary-content" ).slideToggle( "fast" );
$embeddedHistory.find( ".annotation" ).slideToggle( "fast" );
$embeddedHistory.find( ".expanded-content" ).slideToggle( "fast" );
}
$embeddedHistory.find( '.expand-content-btn' ).click( toggleExpanded );
$embeddedHistory.find( '.toggle-embed' ).click( toggleExpanded );
function showConfirmationModal( name ){
var body = [
'<div class="donemessagelarge">',
_l( 'History imported' ), ': ', _.escape( historyModel.get( 'name' ) ),
'</div>'
].join('');
Galaxy.modal.show({
title : _l( 'Success!' ),
body : $( body ),
buttons : {
'Return to the published page' : function(){
Galaxy.modal.hide();
},
'Start using the history' : function(){
window.location = Galaxy.root;
},
}
});
var HistoryWithAnnotations = HISTORY.default.History.extend({
contentsClass : HistoryContentsWithAnnotations
});
Galaxy.modal.$( '.modal-header' ).hide();
Galaxy.modal.$( '.modal-body' ).css( 'padding-bottom', 0 );
Galaxy.modal.$( '.modal-footer' ).css({ border : 0, 'padding-top': 0 });
}
var historyJSON = ${h.dumps( history_dict )};
var historyModel = new HistoryWithAnnotations( historyJSON, null, {
order : 'hid-asc',
});
var historyView = new viewMod.default.AnnotatedHistoryView({
el : $embeddedHistory.find( ".history-panel" ),
className : viewMod.default.AnnotatedHistoryView.prototype.className + ' wide',
model : historyModel
});
historyView.trigger( 'loading' );
historyModel.fetchContents({ silent: true })
.fail( function(){ alert( 'Galaxy history failed to load' ); })
.done( function(){
historyView.trigger( 'loading-done' );
historyView.render();
});
function toggleExpanded( ev ){
ev.preventDefault();
$embeddedHistory.find( '.expand-content-btn' ).toggleClass( 'toggle-expand' ).toggleClass( 'toggle' );
$embeddedHistory.find( ".summary-content" ).slideToggle( "fast" );
$embeddedHistory.find( ".annotation" ).slideToggle( "fast" );
$embeddedHistory.find( ".expanded-content" ).slideToggle( "fast" );
}
$embeddedHistory.find( '.expand-content-btn' ).click( toggleExpanded );
$embeddedHistory.find( '.toggle-embed' ).click( toggleExpanded );
function showConfirmationModal( name ){
var body = [
'<div class="donemessagelarge">',
_l( 'History imported' ), ': ', _.escape( historyModel.get( 'name' ) ),
'</div>'
].join('');
Galaxy.modal.show({
title : _l( 'Success!' ),
body : $( body ),
buttons : {
'Return to the published page' : function(){
Galaxy.modal.hide();
},
'Start using the history' : function(){
window.location = Galaxy.root;
},
}
});
Galaxy.modal.$( '.modal-header' ).hide();
Galaxy.modal.$( '.modal-body' ).css( 'padding-bottom', 0 );
Galaxy.modal.$( '.modal-footer' ).css({ border : 0, 'padding-top': 0 });
}
$embeddedHistory.find( '.import' ).click( function( ev ){
var dialogOptions = { useImport: true, allowAll: false, autoClose: false };
historyCopyDialog.default( historyModel, dialogOptions ).done( showConfirmationModal );
})
});
$embeddedHistory.find( '.import' ).click( function( ev ){
var dialogOptions = { useImport: true, allowAll: false, autoClose: false };
window.bundleEntries.HistoryCopyDialog( historyModel, dialogOptions ).done( showConfirmationModal );
})
});
})();
</script>
templates/webapps/galaxy/history/structure.mako
+15 -18
View File
@@ -6,6 +6,11 @@
</%def>
## -----------------------------------------------------------------------------
<%def name="javascripts()">
${ parent.javascripts() }
${h.js("bundled/extended.bundled")}
</%def>
<%def name="stylesheets()">
${ parent.stylesheets() }
@@ -68,26 +73,18 @@ ${ parent.stylesheets() }
<%def name="javascript_app()">
<script type="text/javascript">
define( 'app', function(){
require([
'mvc/history/history-model',
'mvc/history/history-structure-view'
], function( HISTORY, StructureView ){
console.debug(HISTORY);
console.debug(StructureView);
var historyModel = new HISTORY.default.History( bootstrapped.history, bootstrapped.contents );
console.debug("Got here?");
window.historymodel = historyModel;
window.jobs = bootstrapped.jobs;
window.tools = bootstrapped.tools;
var historyModel = new window.bundleEntries.History( bootstrapped.history, bootstrapped.contents );
window.historymodel = historyModel;
window.jobs = bootstrapped.jobs;
window.tools = bootstrapped.tools;
var structure = new StructureView.default({
model : historyModel,
jobs : bootstrapped.jobs,
tools : bootstrapped.tools
});
window.structure = structure;
structure.render().$el.appendTo( 'body' );
var structure = new window.bundleEntries.StructureView({
model : historyModel,
jobs : bootstrapped.jobs,
tools : bootstrapped.tools
});
window.structure = structure;
structure.render().$el.appendTo( 'body' );
});
</script>
${ galaxy_client.load( app='app', historyId=historyId, history=history, contents=contents, jobs=jobs, tools=tools ) }
templates/webapps/galaxy/history/view.mako
+16 -103
View File
@@ -102,109 +102,22 @@ a.btn {
<script type="text/javascript">
// use_panels effects where the the center_panel() is rendered:
// w/o it renders to the body, w/ it renders to #center - we need to adjust a few things for scrolling to work
var hasMasthead = ${ 'true' if use_panels else 'false' },
userIsOwner = ${ 'true' if user_is_owner else 'false' },
isCurrent = ${ 'true' if history_is_current else 'false' },
historyJSON = ${ h.dumps( history ) },
viewToUse = ( userIsOwner )?
//TODO: change class names
({ location: 'mvc/history/history-view-edit', className: 'HistoryViewEdit' }):
({ location: 'mvc/history/history-view', className: 'HistoryView' });
require.config({
baseUrl : "${h.url_for( '/static/scripts' )}",
paths : {
'jquery' : 'libs/jquery/jquery'
},
urlArgs: 'v=${app.server_starttime}'
})([
'mvc/user/user-model',
viewToUse.location,
'mvc/history/copy-dialog',
'utils/localization',
'ui/mode-button'
], function( user, viewMod, historyCopyDialog, _l ){
+(function setUpBehaviors(){
$( '#toggle-deleted' ).modeButton({
initialMode : "${ 'showing_deleted' if show_deleted else 'not_showing_deleted' }",
modes: [
{ mode: 'showing_deleted', html: _l( 'Exclude deleted' ) },
{ mode: 'not_showing_deleted', html: _l( 'Include deleted' ) }
]
});
$( '#toggle-hidden' ).modeButton({
initialMode : "${ 'showing_hidden' if show_hidden else 'not_showing_hidden' }",
modes: [
{ mode: 'showing_hidden', html: _l( 'Exclude hidden' ) },
{ mode: 'not_showing_hidden', html: _l( 'Include hidden' ) }
]
});
$( '#switch' ).click( function( ev ){
//##HACK:ity hack hack
//##TODO: remove when out of iframe
var hview = Galaxy.currHistoryPanel
|| ( top.Galaxy && top.Galaxy.currHistoryPanel )? top.Galaxy.currHistoryPanel : null;
if( hview ){
hview.switchToHistory( "${ history[ 'id' ] }" );
} else {
window.location = "${ switch_to_url }";
}
});
})();
$(function(){
if( hasMasthead ){
$( '#center' ).addClass( 'flex-vertical-container' );
}
var viewClass = viewMod.default[ viewToUse.className ],
// history module is already in the dpn chain from the view. We can re-scope it here.
HISTORY = require( 'mvc/history/history-model' ),
historyModel = new HISTORY.default.History( historyJSON );
// attach the copy dialog to the import button now that we have a history
$( '#import' ).click( function( ev ){
historyCopyDialog.default( historyModel, {
useImport : true,
// use default datasets option to match the toggle-deleted button
allDatasets : $( '#toggle-deleted' ).modeButton( 'getMode' ).mode === 'showing_deleted',
}).done( function(){
if( window === window.parent ){
window.location = Galaxy.root;
} else if( Galaxy.currHistoryPanel ){
Galaxy.currHistoryPanel.loadCurrentHistory();
}
});
});
window.historyView = new viewClass({
el : $( "#history-" + historyJSON.id ),
className : viewClass.prototype.className + ' wide',
$scrollContainer: hasMasthead? function(){ return this.$el.parent(); } : undefined,
model : historyModel,
show_deleted : ${show_deleted_json},
show_hidden : ${show_hidden_json},
purgeAllowed : Galaxy.config.allow_user_dataset_purge,
});
historyView.trigger( 'loading' );
historyModel.fetchContents({ silent: true })
.fail( function(){ alert( 'Galaxy history failed to load' ); })
.done( function(){
historyView.trigger( 'loading-done' );
historyView.render();
});
$( '#toggle-deleted' ).on( 'click', function(){
historyView.toggleShowDeleted();
});
$( '#toggle-hidden' ).on( 'click', function(){
historyView.toggleShowHidden();
});
});
$(function(){
options = {
hasMasthead: ${ 'true' if use_panels else 'false' },
userIsOwner: ${ 'true' if user_is_owner else 'false' },
isCurrent: ${ 'true' if history_is_current else 'false' },
historyJSON: ${ h.dumps( history ) },
showDeletedJson: ${ show_deleted_json },
showHiddenJson: ${ show_hidden_json },
initialModeDeleted: "${ 'showing_deleted' if show_deleted else 'not_showing_deleted' }",
initialModeHidden: "${ 'showing_hidden' if show_hidden else 'not_showing_hidden' }",
allowUserDatasetPurge: ${ 'true' if trans.app.config.allow_user_dataset_purge else 'false' }
};
options.viewToUse = options.userIsOwner ?
({ location: 'mvc/history/history-view-edit', className: 'HistoryViewEdit' }):
({ location: 'mvc/history/history-view', className: 'HistoryView' });
window.bundleEntries.history(options);
});
</script>
templates/webapps/galaxy/history/view_multiple.mako
+10 -31
View File
@@ -1,4 +1,3 @@
<%inherit file="/webapps/galaxy/base_panels.mako"/>
<%namespace file="/galaxy_client_app.mako" name="galaxy_client"/>
@@ -24,36 +23,16 @@
<%def name="javascript_app()">
<script type="text/javascript">
define( 'app', function(){
require([
'mvc/history/history-model',
'mvc/history/multi-panel'
], function( HISTORY_MODEL, MULTI_HISTORY ){
$(function(){
histories = new HISTORY_MODEL.default.HistoryCollection( [], {
includeDeleted : bootstrapped.includingDeleted,
order : bootstrapped.order,
limitOnFirstFetch : bootstrapped.limit,
limitPerFetch : bootstrapped.limit,
// lastFetched : bootstrapped.limit,
currentHistoryId : bootstrapped.current_history_id,
});
multipanel = new MULTI_HISTORY.default.MultiPanelColumns({
el : $( '#center' ).get(0),
histories : histories,
})
histories.fetchFirst({ silent: true })
.done( function(){
multipanel.createColumns();
multipanel.render( 0 );
});
});
define( 'app', function(){
bundleEntries.multiHistory(bootstrapped);
});
});
</script>
${ galaxy_client.load( app='app', current_history_id=current_history_id,
includingDeleted=include_deleted_histories, order=order, limit=limit ) }
##${ galaxy_client.load( app='app', histories=histories,
## includingDeleted=include_deleted_histories, order=order, limit=limit ) }
${galaxy_client.load(
app='app',
current_history_id=current_history_id,
includingDeleted=include_deleted_histories,
order=order,
limit=limit
)}
</%def>
templates/webapps/galaxy/page/editor.mako
+2 -2
View File
@@ -22,8 +22,8 @@
iframe_base_path = "${h.url_for('/static/wymeditor/iframe/galaxy')}/",
save_url = "${h.url_for(controller='page', action='save' )}";
require(['galaxy.pages'], function(Pages){
Pages.default();
$(function(){
bundleEntries.pages()
});
</script>
templates/webapps/galaxy/visualization/display.mako
+33 -47
View File
@@ -18,9 +18,7 @@
<%def name="stylesheets()">
${parent.stylesheets()}
${h.css(
"trackster"
)}
${h.css("trackster")}
## Style changes needed for display.
<style type="text/css">
@@ -53,56 +51,44 @@
<div id="${trans.security.encode_id( visualization.id )}" class="unified-panel-body" style="overflow:none;top:0px;"></div>
<script type="text/javascript">
require.config({
baseUrl: "${h.url_for('/static/scripts') }",
shim: {
"libs/underscore": { exports: "_" },
"libs/backbone": { exports: "Backbone" },
},
urlArgs: 'v=${app.server_starttime}'
});
require( ["viz/trackster"], function(trackster) {
// FIXME: deliberate global required for now due to requireJS integration.
view = null;
// FIXME: deliberate global required for now due to requireJS integration.
view = null;
var ui = new (window.bundleEntries.Trackster.TracksterUI)( "${h.url_for('/')}" );
var container_element = $("#${trans.security.encode_id( visualization.id )}");
var ui = new (trackster.default.TracksterUI)( "${h.url_for('/')}" )
container_element = $("#${trans.security.encode_id( visualization.id )}");
$(function() {
var is_embedded = (container_element.parents(".item-content").length > 0);
$(function() {
var is_embedded = (container_element.parents(".item-content").length > 0);
// HTML setup.
if (is_embedded) {
container_element.css( { "position": "relative" } );
} else { // Viewing just one shared viz
$("#right-border").click(function() { view.resize_window(); });
}
// HTML setup.
if (is_embedded) {
container_element.css( { "position": "relative" } );
} else { // Viewing just one shared viz
$("#right-border").click(function() { view.resize_window(); });
}
// Create visualization.
var callback;
%if 'viewport' in config:
var callback = function() { view.change_chrom( '${config['viewport']['chrom']}', ${config['viewport']['start']}, ${config['viewport']['end']} ); }
%endif
view = ui.create_visualization( {
container: container_element,
name: "${config.get('title') | h}",
vis_id: "${config.get('vis_id')}",
dbkey: "${config.get('dbkey')}"
},
${ h.dumps( config.get( 'viewport', dict() ) ) },
${ h.dumps( config['tracks'] ) },
${ h.dumps( config.get('bookmarks') ) }
);
// Create visualization.
var callback;
%if 'viewport' in config:
var callback = function() { view.change_chrom( '${config['viewport']['chrom']}', ${config['viewport']['start']}, ${config['viewport']['end']} ); }
%endif
view = ui.create_visualization( {
container: container_element,
name: "${config.get('title') | h}",
vis_id: "${config.get('vis_id')}",
dbkey: "${config.get('dbkey')}"
},
${ h.dumps( config.get( 'viewport', dict() ) ) },
${ h.dumps( config['tracks'] ) },
${ h.dumps( config.get('bookmarks') ) }
);
// Set up keyboard navigation.
ui.init_keyboard_nav(view);
// HACK: set viewport height because it cannot be set automatically. Currently, max height for embedded
// elts is 25em, so use 20em.
view.viewport_container.height("20em");
});
// Set up keyboard navigation.
ui.init_keyboard_nav(view);
// HACK: set viewport height because it cannot be set automatically. Currently, max height for embedded
// elts is 25em, so use 20em.
view.viewport_container.height("20em");
});
</script>
templates/webapps/galaxy/visualization/phyloviz.mako
+12 -30
View File
@@ -138,41 +138,23 @@
<%def name="javascripts()">
${parent.javascripts()}
${h.js( "libs/require" )}
<script type="text/javascript">
require.config({
baseUrl: "${h.url_for('/static/scripts')}",
shim: {
"libs/underscore": { exports: "_" },
"libs/d3": { exports: "d3" }
},
urlArgs: 'v=${app.server_starttime}'
});
$(function(){
var config = ${ h.dumps( config )};
var data = ${h.dumps(data['data'])};
require(["viz/phyloviz"], function(phyloviz_mod) {
function initPhyloViz(data, config) {
var phyloviz;
// -- Initialization code |-->
phyloviz = new phyloviz_mod.default.PhylovizView({
data : data,
layout : "Linear",
config : config
});
// -- Render viz. --
phyloviz.render();
};
$(function firstVizLoad(){ // calls when viz is loaded for the first time
var config = ${ h.dumps( config )};
var data = ${h.dumps(data['data'])};
initPhyloViz(data, config);
// -- Initialization code |-->
var phyloviz = new bundleEntries.phyloviz({
data : data,
layout : "Linear",
config : config
});
// -- Render viz. --
phyloviz.render();
});
</script>
templates/webapps/galaxy/visualization/sweepster.mako
+7 -25
View File
@@ -109,31 +109,13 @@
${h.js( "libs/jquery/jquery-ui" )}
<script type="text/javascript">
// require.config({
// baseUrl: "${h.url_for('/static/scripts') }",
// shim: {
// "libs/underscore": { exports: "_" },
// "libs/backbone": {
// deps: [ 'jquery', 'libs/underscore' ],
// exports: "Backbone"
// },
// "libs/d3": { exports: "d3" },
// },
// // cache buster based on templated server (re)start time
// urlArgs: 'v=${app.server_starttime}'
// });
require(["viz/sweepster"], function(sweepster) {
var viz;
$(function() {
// -- Viz set up. --
var viz = new sweepster.default.SweepsterVisualization(
${ h.dumps( config )}
);
var viz_view = new sweepster.default.SweepsterVisualizationView({ model: viz });
viz_view.render();
});
$(function() {
// -- Viz set up. --
var viz = new window.bundleEntries.SweepsterVisualization(
${ h.dumps( config )}
);
var viz_view = new window.bundleEntries.SweepsterVisualizationView({ model: viz });
viz_view.render();
});
</script>
</%def>
templates/webapps/reports/run_stats.mako
+7 -7
View File
@@ -5,13 +5,13 @@
${parent.javascripts()}
<script type="text/javascript">
require(['reports/run_stats'], function(run_stats){
run_stats.create_chart(${jf_hr_data}, "jf_hr_chart", "hours", "Jobs Finished per Hour");
run_stats.create_chart(${jf_dy_data}, "jf_dy_chart", "days", "Jobs Finished per Day");
run_stats.create_chart(${jc_hr_data}, "jc_hr_chart", "hours", "Jobs Created per Hour");
run_stats.create_chart(${jc_dy_data}, "jc_dy_chart", "days", "Jobs Created per Day");
run_stats.create_histogram(${et_hr_data}, "et_hr_chart", "Job Run Times (past day)");
run_stats.create_histogram(${et_dy_data}, "et_dy_chart", "Job Run Time (past 30 days)");
$(function(){
window.bundleEntries.run_stats.create_chart(${jf_hr_data}, "jf_hr_chart", "hours", "Jobs Finished per Hour");
window.bundleEntries.run_stats.create_chart(${jf_dy_data}, "jf_dy_chart", "days", "Jobs Finished per Day");
window.bundleEntries.run_stats.create_chart(${jc_hr_data}, "jc_hr_chart", "hours", "Jobs Created per Hour");
window.bundleEntries.run_stats.create_chart(${jc_dy_data}, "jc_dy_chart", "days", "Jobs Created per Day");
window.bundleEntries.run_stats.create_histogram(${et_hr_data}, "et_hr_chart", "Job Run Times (past day)");
window.bundleEntries.run_stats.create_histogram(${et_dy_data}, "et_dy_chart", "Job Run Time (past 30 days)");
});
</script>
</%def>
templates/webapps/tool_shed/group/index.mako
+1 -8
View File
@@ -41,14 +41,7 @@
<script type="text/javascript">
window.globalTS = new Object();
$( function(){
require.config({
paths: {
'toolshed': '../toolshed'
}
});
require([ '${config.get( "app" ).get( "jscript" )}' ], function( groups ){
app = new groups.default.ToolshedGroups();
});
new window.bundleEntries.ToolshedGroups.ToolshedGroups();
});
</script>
<div id="groups_element" style="width: 95%; margin:auto; margin-top:2em; "></div>
test/api/test_configuration.py
+1 -1
View File
@@ -29,7 +29,7 @@ class ConfigurationApiTestCase(api.ApiTestCase):
def setUp(self):
super(ConfigurationApiTestCase, self).setUp()
self.library_populator = LibraryPopulator(self)
self.library_populator = LibraryPopulator(self.galaxy_interactor)
def test_normal_user_configuration(self):
config = self._get_configuration()
test/api/test_history_contents.py
+1 -1
View File
@@ -22,7 +22,7 @@ class HistoryContentsApiTestCase(api.ApiTestCase, TestsDatasets):
self.history_id = self._new_history()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
self.library_populator = LibraryPopulator(self)
self.library_populator = LibraryPopulator(self.galaxy_interactor)
def test_index_hda_summary(self):
hda1 = self._new_dataset(self.history_id)
test/api/test_libraries.py
+1 -1
View File
@@ -13,7 +13,7 @@ class LibrariesApiTestCase(api.ApiTestCase, TestsDatasets):
super(LibrariesApiTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
self.library_populator = LibraryPopulator(self)
self.library_populator = LibraryPopulator(self.galaxy_interactor)
def test_create(self):
data = dict(name="CreateTestLibrary")
test/api/test_tools.py
+1 -1
View File
@@ -259,7 +259,7 @@ class ToolsTestCase(api.ApiTestCase):
@skip_without_tool("library_data")
def test_library_data_param(self):
with self.dataset_populator.test_history() as history_id:
ld = LibraryPopulator(self).new_library_dataset("lda_test_library")
ld = LibraryPopulator(self.galaxy_interactor).new_library_dataset("lda_test_library")
inputs = {
"library_dataset": ld["ldda_id"],
"library_dataset_multiple": [ld["ldda_id"], ld["ldda_id"]]
test/base/populators.py
+25 -13
View File
@@ -461,9 +461,8 @@ class WorkflowPopulator(BaseWorkflowPopulator, ImporterGalaxyInterface):
class LibraryPopulator(object):
def __init__(self, api_test_case):
self.api_test_case = api_test_case
self.galaxy_interactor = api_test_case.galaxy_interactor
def __init__(self, galaxy_interactor):
self.galaxy_interactor = galaxy_interactor
def new_private_library(self, name):
library = self.new_library(name)
@@ -500,44 +499,57 @@ class LibraryPopulator(object):
def user_private_role_id(self):
user_email = self.user_email()
roles_response = self.api_test_case.galaxy_interactor.get("roles", admin=True)
roles_response = self.galaxy_interactor.get("roles", admin=True)
users_roles = [r for r in roles_response.json() if r["name"] == user_email]
assert len(users_roles) == 1
return users_roles[0]["id"]
def create_dataset_request(self, library, **kwds):
upload_option = kwds.get("upload_option", "upload_file")
create_data = {
"folder_id": kwds.get("folder_id", library["root_folder_id"]),
"create_type": "file",
"files_0|NAME": kwds.get("name", "NewFile"),
"upload_option": kwds.get("upload_option", "upload_file"),
"upload_option": upload_option,
"file_type": kwds.get("file_type", "auto"),
"db_key": kwds.get("db_key", "?"),
}
files = {
"files_0|file_data": kwds.get("file", StringIO(kwds.get("contents", "TestData"))),
}
if upload_option == "upload_file":
files = {
"files_0|file_data": kwds.get("file", StringIO(kwds.get("contents", "TestData"))),
}
elif upload_option == "upload_paths":
create_data["filesystem_paths"] = kwds["paths"]
files = {}
elif upload_option == "upload_directory":
create_data["server_dir"] = kwds["server_dir"]
files = {}
return create_data, files
def new_library_dataset(self, name, **create_dataset_kwds):
library = self.new_private_library(name)
payload, files = self.create_dataset_request(library, **create_dataset_kwds)
url_rel = "libraries/%s/contents" % (library["id"])
dataset = self.api_test_case.galaxy_interactor.post(url_rel, payload, files=files).json()[0]
dataset = self.raw_library_contents_create(library["id"], payload, files=files).json()[0]
def show():
return self.api_test_case.galaxy_interactor.get("libraries/%s/contents/%s" % (library["id"], dataset["id"]))
return self.galaxy_interactor.get("libraries/%s/contents/%s" % (library["id"], dataset["id"]))
wait_on_state(show, timeout=DEFAULT_TIMEOUT)
return show().json()
def raw_library_contents_create(self, library_id, payload, files={}):
url_rel = "libraries/%s/contents" % library_id
return self.galaxy_interactor.post(url_rel, payload, files=files)
def show_ldda(self, library_id, library_dataset_id):
return self.api_test_case.galaxy_interactor.get("libraries/%s/contents/%s" % (library_id, library_dataset_id))
return self.galaxy_interactor.get("libraries/%s/contents/%s" % (library_id, library_dataset_id))
def new_library_dataset_in_private_library(self, library_name="private_dataset", wait=True):
library = self.new_private_library(library_name)
payload, files = self.create_dataset_request(library, file_type="txt", contents="create_test")
create_response = self.api_test_case.galaxy_interactor.post("libraries/%s/contents" % library["id"], payload, files=files)
create_response = self.galaxy_interactor.post("libraries/%s/contents" % library["id"], payload, files=files)
api_asserts.assert_status_code_is(create_response, 200)
library_datasets = create_response.json()
assert len(library_datasets) == 1
test/galaxy_selenium/navigates_galaxy.py
+26 -2
View File
@@ -612,6 +612,11 @@ class NavigatesGalaxy(HasDriver):
self.components.masthead.libraries.wait_for_and_click()
self.components.libraries.selector.wait_for_visible()
def libraries_open_with_name(self, name):
self.libraries_open()
self.libraries_index_search_for(name)
self.libraries_index_table_elements()[0].find_element_by_css_selector("td a").click()
@retry_during_transitions
def libraries_index_table_elements(self):
container = self.wait_for_selector_visible(".library_container")
@@ -657,8 +662,7 @@ class NavigatesGalaxy(HasDriver):
self.driver.execute_script("$(arguments[0]).keyup();", search_box)
def libraries_folder_create(self, name):
create_folder_button = self.wait_for_selector_clickable("#toolbtn_create_folder")
create_folder_button.click()
self.components.libraries.folder.add_folder.wait_for_and_click()
name_text_box = self.wait_for_selector_clickable("input[name='Name']")
name_text_box.send_keys(name)
@@ -681,6 +685,26 @@ class NavigatesGalaxy(HasDriver):
self.wait_for_visible(self.navigation.libraries.folder.selectors.add_items_menu)
self.wait_for_and_click(self.navigation.libraries.folder.labels.from_path)
def libraries_dataset_import_from_history_select(self, to_select_items):
self.wait_for_visible(self.navigation.libraries.folder.selectors.import_history_content)
history_elements = self.find_elements(self.navigation.libraries.folder.selectors.import_history_contents_items)
for to_select_item in to_select_items:
found = False
for history_element in history_elements:
if to_select_item in history_element.text:
history_element.find_element_by_css_selector("input").click()
found = True
break
if not found:
raise Exception("Failed to find history item [%s] to select" % to_select_item)
def libraries_dataset_import_from_history_click_ok(self, wait=True):
self.wait_for_and_click(self.navigation.libraries.folder.selectors.import_datasets_ok_button)
if wait:
# Let the progress bar disappear...
self.wait_for_absent_or_hidden(self.navigation.libraries.folder.selectors.import_progress_bar)
def libraries_table_elements(self):
tbody_element = self.wait_for_selector_visible("#folder_list_body")
return tbody_element.find_elements_by_css_selector("tr")[1:]

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