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wip on importing from library to history as a collection

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+ various es6 additions; cleanup; refactoring

I tried to separate it into more commits but it kept growing too fast, sorry
This commit is contained in:
Martin Cech
2017-12-18 13:16:50 -05:00
parent e8e12a6026
commit 96565e9b84
6 changed files with 335 additions and 139 deletions
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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/mvc/collection/list-collection-creator.js
+3 -3
View File
@@ -278,9 +278,9 @@ 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") {
// return _l("is not a dataset");
// }
var validState = element.state === STATES.OK || _.contains(STATES.NOT_READY_STATES, element.state);
if (!validState) {
return _l("has errored, is paused, or is not accessible");
client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+306 -119
View File
@@ -3,19 +3,21 @@ import mod_utils from "utils/utils";
import mod_toastr from "libs/toastr";
import mod_library_model from "mvc/library/library-model";
import mod_select from "mvc/ui/ui-select";
import LIST_COLLECTION_CREATOR from "mvc/collection/list-collection-creator";
import HDCA_MODEL from "mvc/history/hdca-model";
import "libs/jquery/jstree";
var FolderToolbarView = Backbone.View.extend({
el: "#center",
events: {
"click #toolbtn_create_folder": "createFolderFromModal",
"click #toolbtn_bulk_import": "historyImportModal",
"click #include_deleted_datasets_chk": "checkIncludeDeleted",
"click #toolbtn_bulk_delete": "deleteSelectedItems",
"click .toolbtn-create-folder": "createFolderFromModal",
"click .toolbtn-bulk-import": "importToHistoryModal",
"click .include-deleted-datasets-chk": "checkIncludeDeleted",
"click .toolbtn-bulk-delete": "deleteSelectedItems",
"click .toolbtn-show-locinfo": "showLocInfo",
"click .page_size_prompt": "showPageSizePrompt"
"click .page-size-prompt": "showPageSizePrompt",
"click .toolbtn-collection-import": "showCollectionSelect"
},
defaults: {
@@ -139,7 +141,6 @@ var FolderToolbarView = Backbone.View.extend({
this.$el.find("[data-toggle]").tooltip();
},
// shows modal for creating folder
createFolderFromModal: function(event) {
event.preventDefault();
event.stopPropagation();
@@ -151,7 +152,7 @@ var FolderToolbarView = Backbone.View.extend({
body: template(),
buttons: {
Create: () => {
this.create_new_folder_event();
this.createNewFolderEvent();
},
Close: () => {
Galaxy.modal.hide();
@@ -160,10 +161,9 @@ var FolderToolbarView = Backbone.View.extend({
});
},
// create the new folder from modal
create_new_folder_event: function() {
var folderDetails = this.serialize_new_folder();
if (this.validate_new_folder(folderDetails)) {
createNewFolderEvent: function() {
var folderDetails = this.serializeNewFolder();
if (this.validateNewFolder(folderDetails)) {
var folder = new mod_library_model.FolderAsModel();
var url_items = Backbone.history.fragment.split("/");
var current_folder_id;
@@ -196,30 +196,27 @@ var FolderToolbarView = Backbone.View.extend({
return false;
},
// serialize data from the modal
serialize_new_folder: function() {
serializeNewFolder: function() {
return {
name: $("input[name='Name']").val(),
description: $("input[name='Description']").val()
};
},
// validate new folder info
validate_new_folder: function(folderDetails) {
validateNewFolder: function(folderDetails) {
return folderDetails.name !== "";
},
// show history import modal
historyImportModal: function() {
importToHistoryModal: function(e) {
e.preventDefault();
var $checkedValues = this.findCheckedRows();
var template = this.templateImportIntoHistoryModal();
if ($checkedValues.length === 0) {
mod_toastr.info("You must select some datasets first.");
} else {
this.histories = new mod_library_model.GalaxyHistories();
this.histories
.fetch()
var promise = this.fetchUserHistories();
promise
.done(() => {
var template = this.templateBulkImportInModal();
this.modal = Galaxy.modal;
this.modal.show({
closing_events: true,
@@ -247,18 +244,18 @@ var FolderToolbarView = Backbone.View.extend({
}
},
/**
* Import all selected datasets into history.
*/
fetchUserHistories: function() {
this.histories = new mod_library_model.GalaxyHistories();
var promise = this.histories.fetch();
return promise;
},
importAllIntoHistory: function() {
this.modal.disableButton("Import");
var new_history_name = this.modal.$("input[name=history_name]").val();
if (new_history_name !== "") {
$.post(`${Galaxy.root}api/histories`, {
name: new_history_name
})
this.createNewHistory(new_history_name)
.done(new_history => {
this.options.last_used_history_id = new_history.id;
this.processImportToHistory(new_history.id, new_history.name);
})
.fail((xhr, status, error) => {
@@ -268,62 +265,52 @@ var FolderToolbarView = Backbone.View.extend({
this.modal.enableButton("Import");
});
} else {
var history_id = $("select[name=dataset_import_bulk] option:selected").val();
this.options.last_used_history_id = history_id;
var history_name = $("select[name=dataset_import_bulk] option:selected").text();
var history_id = $("select[name=import_to_history] option:selected").val();
var history_name = $("select[name=import_to_history] option:selected").text();
this.processImportToHistory(history_id, history_name);
this.modal.enableButton("Import");
}
},
createNewHistory: function(new_history_name) {
var promise = $.post(`${Galaxy.root}api/histories`, { name: new_history_name });
return promise;
},
processImportToHistory: function(history_id, history_name) {
var dataset_ids = [];
var folder_ids = [];
this.findCheckedRows().each(function() {
var row_id = $(this)
.closest("tr")
.data("id");
if (row_id.substring(0, 1) == "F") {
folder_ids.push(row_id);
} else {
dataset_ids.push(row_id);
}
});
var checked_items = this.findCheckedItems();
var items_to_import = [];
// prepare the dataset objects to be imported
var datasets_to_import = [];
for (var i = dataset_ids.length - 1; i >= 0; i--) {
var library_dataset_id = dataset_ids[i];
for (let i = checked_items.dataset_ids.length - 1; i >= 0; i--) {
var library_dataset_id = checked_items.dataset_ids[i];
var historyItem = new mod_library_model.HistoryItem();
historyItem.url = `${historyItem.urlRoot + history_id}/contents`;
historyItem.content = library_dataset_id;
historyItem.source = "library";
datasets_to_import.push(historyItem);
items_to_import.push(historyItem);
}
// prepare the folder objects to be imported
var folders_to_import = [];
for (var i = folder_ids.length - 1; i >= 0; i--) {
var library_folder_id = folder_ids[i];
for (let i = checked_items.folder_ids.length - 1; i >= 0; i--) {
var library_folder_id = checked_items.folder_ids[i];
var historyItem = new mod_library_model.HistoryItem();
historyItem.url = `${historyItem.urlRoot + history_id}/contents`;
historyItem.content = library_folder_id;
historyItem.source = "library_folder";
datasets_to_import.push(historyItem);
items_to_import.push(historyItem);
}
this.initChainCallControl({
length: datasets_to_import.length,
length: items_to_import.length,
action: "to_history",
history_name: history_name
});
// set the used history as current so user will see the last one
// that he imported into in the history panel on the 'analysis' page
jQuery.getJSON(`${Galaxy.root}history/set_as_current?id=${history_id}`);
this.chainCallImportingIntoHistory(datasets_to_import, history_name);
this.chainCallImportingIntoHistory(items_to_import, history_name);
},
/**
* Update the progress bar in modal window.
* Update progress bar in modal.
*/
updateProgress: function() {
this.progress += this.progressStep;
@@ -333,25 +320,13 @@ var FolderToolbarView = Backbone.View.extend({
},
/**
* download selected datasets
* @param {str} folder_id id of the current folder
* Download selected datasets. Called from the router.
* @param {str} format requested archive format
*/
download: function(folder_id, format) {
var dataset_ids = [];
var folder_ids = [];
this.findCheckedRows().each(function() {
var row_id = $(this)
.closest("tr")
.data("id");
if (row_id.substring(0, 1) == "F") {
folder_ids.push(row_id);
} else {
dataset_ids.push(row_id);
}
});
download: function(format) {
var checked_items = this.findCheckedItems();
var url = `${Galaxy.root}api/libraries/datasets/download/${format}`;
var data = { ld_ids: dataset_ids, folder_ids: folder_ids };
var data = { ld_ids: checked_items.dataset_ids, folder_ids: checked_items.folder_ids };
this.processDownload(url, data, "get");
},
@@ -368,7 +343,7 @@ var FolderToolbarView = Backbone.View.extend({
data = typeof data === "string" ? data : $.param(data);
// split params into form inputs
var inputs = "";
$.each(data.split("&"), () => {
$.each(data.split("&"), function() {
var pair = this.split("=");
inputs += `<input type="hidden" name="${pair[0]}" value="${pair[1]}" />`;
});
@@ -424,7 +399,6 @@ var FolderToolbarView = Backbone.View.extend({
/**
* Create modal for importing from Galaxy path.
* This feature is admin-only.
*/
importFilesFromPathModal: function() {
this.modal = Galaxy.modal;
@@ -453,14 +427,14 @@ var FolderToolbarView = Backbone.View.extend({
/**
* Request all extensions and genomes from Galaxy
* and save them sorted in arrays.
* and save them in sorted arrays.
*/
fetchExtAndGenomes: function() {
mod_utils.get({
url: `${Galaxy.root}api/datatypes?extension_only=False`,
success: datatypes => {
this.list_extensions = [];
for (var key in datatypes) {
for (let key in datatypes) {
this.list_extensions.push({
id: datatypes[key].extension,
text: datatypes[key].extension,
@@ -477,7 +451,7 @@ var FolderToolbarView = Backbone.View.extend({
url: `${Galaxy.root}api/genomes`,
success: genomes => {
this.list_genomes = [];
for (var key in genomes) {
for (let key in genomes) {
this.list_genomes.push({
id: genomes[key][1],
text: genomes[key][0]
@@ -492,8 +466,6 @@ var FolderToolbarView = Backbone.View.extend({
renderSelectBoxes: function() {
// This won't work properly unlesss we already have the data fetched.
// See this.fetchExtAndGenomes()
// TODO switch to common resources:
// https://trello.com/c/dIUE9YPl/1933-ui-common-resources-and-data-into-galaxy-object
this.select_genome = new mod_select.View({
css: "library-genome-select",
data: this.list_genomes,
@@ -630,7 +602,7 @@ var FolderToolbarView = Backbone.View.extend({
} else {
this.modal.disableButton("Import");
paths = paths.split("\n");
for (var i = paths.length - 1; i >= 0; i--) {
for (let i = paths.length - 1; i >= 0; i--) {
var trimmed = paths[i].trim();
if (trimmed.length !== 0) {
valid_paths.push(trimmed);
@@ -718,7 +690,7 @@ var FolderToolbarView = Backbone.View.extend({
mod_toastr.info("Please select some items first.");
} else {
this.modal.disableButton("Import");
for (var i = selected_nodes.length - 1; i >= 0; i--) {
for (let i = selected_nodes.length - 1; i >= 0; i--) {
if (selected_nodes[i].li_attr.full_path !== undefined) {
paths.push(selected_nodes[i].li_attr.full_path);
}
@@ -764,16 +736,16 @@ var FolderToolbarView = Backbone.View.extend({
success: history_contents => {
var history_contents_template = this.templateHistoryContents();
this.histories.get(history_id).set({ contents: history_contents });
this.modal.$el.find("#selected_history_content").html(
this.modal.$el.find(".library_selected_history_content").html(
history_contents_template({
history_contents: history_contents.models.reverse()
})
);
this.modal.$el.find(".history-import-select-all").bind("click", () => {
$("#selected_history_content [type=checkbox]").prop("checked", true);
$(".library_selected_history_content [type=checkbox]").prop("checked", true);
});
this.modal.$el.find(".history-import-unselect-all").bind("click", () => {
$("#selected_history_content [type=checkbox]").prop("checked", false);
$(".library_selected_history_content [type=checkbox]").prop("checked", false);
});
},
error: (model, response) => {
@@ -790,7 +762,7 @@ var FolderToolbarView = Backbone.View.extend({
* Import all selected datasets from history into the current folder.
*/
addAllDatasetsFromHistory: function() {
var checked_hdas = this.modal.$el.find("#selected_history_content").find(":checked");
var checked_hdas = this.modal.$el.find(".library_selected_history_content").find(":checked");
var history_item_ids = []; // can be hda or hdca
var history_item_types = [];
var items_to_add = [];
@@ -798,7 +770,7 @@ var FolderToolbarView = Backbone.View.extend({
mod_toastr.info("You must select some datasets first.");
} else {
this.modal.disableButton("Add");
checked_hdas.each(() => {
checked_hdas.each(function() {
var hid = $(this)
.closest("li")
.data("id");
@@ -810,7 +782,7 @@ var FolderToolbarView = Backbone.View.extend({
history_item_types.push(item_type);
}
});
for (var i = history_item_ids.length - 1; i >= 0; i--) {
for (let i = history_item_ids.length - 1; i >= 0; i--) {
var history_item_id = history_item_ids[i];
var folder_item = new mod_library_model.Item();
folder_item.url = `${Galaxy.root}api/folders/${this.options.id}/contents`;
@@ -1095,7 +1067,7 @@ var FolderToolbarView = Backbone.View.extend({
// init the control counters
this.options.chain_call_control.total_number = 0;
this.options.chain_call_control.failed_number = 0;
$checkedValues.each(() => {
$checkedValues.each(function() {
var row_id = $(this)
.closest("tr")
.data("id");
@@ -1114,13 +1086,13 @@ var FolderToolbarView = Backbone.View.extend({
// prepare the dataset items to be added
var items_to_delete = [];
for (var i = dataset_ids.length - 1; i >= 0; i--) {
for (let i = dataset_ids.length - 1; i >= 0; i--) {
var dataset = new mod_library_model.Item({
id: dataset_ids[i]
});
items_to_delete.push(dataset);
}
for (var i = folder_ids.length - 1; i >= 0; i--) {
for (let i = folder_ids.length - 1; i >= 0; i--) {
var folder = new mod_library_model.FolderAsModel({
id: folder_ids[i]
});
@@ -1221,6 +1193,158 @@ var FolderToolbarView = Backbone.View.extend({
return $("#folder_list_body").find(":checked");
},
findCheckedItems: function() {
var folder_ids = [];
var dataset_ids = [];
this.findCheckedRows().each(function() {
var row_id = $(this)
.closest("tr")
.data("id");
if (row_id.substring(0, 1) == "F") {
folder_ids.push(row_id);
} else {
dataset_ids.push(row_id);
}
});
return { folder_ids: folder_ids, dataset_ids: dataset_ids };
},
showCollectionSelect: function(e) {
e.preventDefault();
var checked_items = this.findCheckedItems();
var template = this.templateCollectionSelectModal();
this.modal = Galaxy.modal;
console.log(checked_items.dataset_ids.length);
this.modal.show({
closing_events: true,
title: "Create Collection from Datasets",
body: template({ selected_datasets: checked_items.dataset_ids.length }),
buttons: {
Continue: () => {
this.showColectionBuilder(checked_items.dataset_ids);
},
Close: () => {
Galaxy.modal.hide();
}
}
});
this.prepareCollectionTypeSelect();
this.prepareHistoryTypeSelect();
},
prepareCollectionTypeSelect: function() {
this.collectionType = "list";
this.select_collection_type = new mod_select.View({
css: "library-collection-type-select",
container: this.modal.$el.find(".library-collection-type-select"),
data: [
{ id: "list", text: "List" },
{ id: "paired", text: "Paired" },
{ id: "list:paired", text: "List of Pairs" }
],
value: "list",
onchange: collectionType => {
this.updateCollectionType(collectionType);
}
});
},
prepareHistoryTypeSelect: function() {
var promise = this.fetchUserHistories();
promise.done(() => {
var history_options = [];
for (let i = this.histories.length - 1; i >= 0; i--) {
history_options.unshift({
id: this.histories.models[i].id,
text: this.histories.models[i].get("name")
});
}
this.select_collection_history = new mod_select.View({
css: "library-collection-history-select",
container: this.modal.$el.find(".library-collection-history-select"),
data: history_options,
value: history_options[0].id
});
});
},
/** Update collection type */
updateCollectionType: function(collectionType) {
this.collectionType = collectionType;
},
showColectionBuilder: function(checked_items) {
console.log(this.collectionType);
var collection_elements = [];
var elements_source = this.modal.$('input[type="radio"]:checked').val();
if (elements_source === "selection") {
for (let i = checked_items.length - 1; i >= 0; i--) {
let collection_item = {};
let dataset = Galaxy.libraries.folderListView.folder_container.get("folder").get(checked_items[i]);
collection_item.id = checked_items[i];
collection_item.name = dataset.get("name");
collection_item.deleted = dataset.get("deleted");
collection_item.state = dataset.get("state");
collection_elements.push(collection_item);
}
} else if (elements_source === "folder") {
collection_elements = new Backbone.Collection(
Galaxy.libraries.folderListView.folder_container.get("folder").where({type: "file"})
).toJSON();
}
var new_history_name = this.modal.$("input[name=history_name]").val();
if (new_history_name !== "") {
this.createNewHistory(new_history_name)
.done(new_history => {
mod_toastr.success("History created");
this.collectionImport(collection_elements, new_history.id, new_history.name);
})
.fail((xhr, status, error) => {
mod_toastr.error("An error occurred.");
});
} else {
var selected_history_id = this.select_collection_history.value();
var selected_history_name = this.select_collection_history.text();
this.collectionImport(collection_elements, selected_history_id, selected_history_name);
}
},
collectionImport: function(collection_elements, history_id, history_name) {
var modal_title = `Creating collection in ${history_name}`;
var createFunc = LIST_COLLECTION_CREATOR.ListCollectionCreator;
var creationFn = (elements, name, hideSourceItems = true) => {
elements = elements.map(element => ({
id: element.id,
name: element.name,
src: "ldda"
}));
return this.createHDCA(elements, "list", name, hideSourceItems, history_id);
};
var deferred = LIST_COLLECTION_CREATOR.collectionCreatorModal(
collection_elements,
{ creationFn: creationFn, title: modal_title },
createFunc
);
},
createHDCA: function(elementIdentifiers, collectionType, name, hideSourceItems, history_id, options) {
var hdca = new HDCA_MODEL.HistoryListDatasetCollection({
history_content_type: "dataset_collection",
collection_type: collectionType,
history_id: history_id,
name: name,
hide_source_items: hideSourceItems || false,
// should probably be able to just send in a bunch of json here and restruct per class
// note: element_identifiers is now (incorrectly) an attribute
element_identifiers: elementIdentifiers
// do not create the model on the client until the ajax returns
});
// normally collection.create returns the new model, but we need the promise from the ajax, so we fake create
//precondition: elementIdentifiers is an array of plain js objects
// in the proper form to create the collectionType
return hdca.save(options);
},
templateToolBar: function() {
return _.template(
[
@@ -1232,18 +1356,21 @@ var FolderToolbarView = Backbone.View.extend({
"<span><strong>DATA LIBRARIES</strong></span>",
// paginator will append here
'<span class="library-paginator folder-paginator"></span>',
// include deleted checkbox
'<div class="checkbox toolbar-item logged-dataset-manipulation" style="height: 20px; display:none;">',
"<label>",
'<input id="include_deleted_datasets_chk" type="checkbox">include deleted</input>',
'<input type="checkbox" class="include-deleted-datasets-chk">include deleted</input>',
"</label>",
"</div>",
'<button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items toolbar-item" type="button">',
'<span class="fa fa-plus"></span><span class="fa fa-folder"></span>',
// create new folder button
'<button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" class="btn btn-default primary-button toolbtn-create-folder add-library-items toolbar-item" type="button">',
'<span class="fa fa-plus"></span><span class="fa fa-folder"></span> Create Folder ',
"</button>",
// add datasets button
"<% if(mutiple_add_dataset_options) { %>",
'<div class="btn-group add-library-items" style="display:none;">',
'<div class="btn-group add-library-items toolbar-item" style="display:none;">',
'<button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">',
'<span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>',
'<span class="fa fa-plus"></span><span class="fa fa-file"></span> Add Datasets <span class="caret"></span>',
"</button>",
'<ul class="dropdown-menu" role="menu">',
'<li><a href="#folders/<%= id %>/import/history"> from History</a></li>',
@@ -1263,17 +1390,24 @@ var FolderToolbarView = Backbone.View.extend({
"</ul>",
"</div>",
"<% } else { %>",
'<a data-placement="top" title="Add Datasets to Current Folder" style="display:none;" class="btn btn-default add-library-items" href="#folders/<%= id %>/import/history" role="button">',
'<a data-placement="top" title="Add Datasets to Current Folder" style="display:none;" class="btn btn-default add-library-items" href="#folders/<%= id %>/import/history" role="button">',
'<span class="fa fa-plus"></span><span class="fa fa-file"></span>',
"</a>",
"<% } %>",
'<button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button">',
'<span class="fa fa-book"></span>',
"&nbsp;to History",
// import to history button
'<div class="btn-group toolbar-item">',
'<button title="Import to history" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">',
'<span class="fa fa-book"></span> To History <span class="caret"></span>',
"</button>",
'<div class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">',
'<button title="Download selected items as archive" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">',
'<span class="fa fa-download"></span> Download <span class="caret"></span>',
'<ul class="dropdown-menu" role="menu">',
'<li><a href="" class="toolbtn-bulk-import">as Datasets</a></li>',
'<li><a href="" class="toolbtn-collection-import">as a Collection</a></li>',
"</ul>",
"</div>",
// download button
'<div class="btn-group dataset-manipulation toolbar-item" style="display:none; ">',
'<button title="Download items as archive" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">',
'<span class="fa fa-save"></span> Download <span class="caret"></span>',
"</button>",
'<ul class="dropdown-menu" role="menu">',
'<li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>',
@@ -1281,13 +1415,12 @@ var FolderToolbarView = Backbone.View.extend({
'<li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>',
"</ul>",
"</div>",
'<button data-toggle="tooltip" data-placement="top" title="Mark selected items deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button">',
'<span class="fa fa-times"></span> Delete</button>',
'<button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show location details" class="primary-button toolbtn-show-locinfo" style="margin-left: 0.5em;" type="button">',
'<span class="fa fa-info-circle"></span>',
"&nbsp;Details",
// delete button
'<button data-toggle="tooltip" data-placement="top" title="Mark items deleted" class="primary-button toolbtn-bulk-delete logged-dataset-manipulation toolbar-item" style="display:none;" type="button">',
'<span class="fa fa-trash"></span> Delete',
"</button>",
'<span class="help-button" data-toggle="tooltip" data-placement="top" title="See this screen annotated">',
// help button
'<span class="right-float" data-toggle="tooltip" data-placement="top" title="See this screen annotated">',
'<a href="https://galaxyproject.org/data-libraries/screen/folder-contents/" target="_blank">',
'<button class="primary-button" type="button">',
'<span class="fa fa-question-circle"></span>',
@@ -1295,13 +1428,20 @@ var FolderToolbarView = Backbone.View.extend({
"</button>",
"</a>",
"</span>",
// location button
'<span class="right-float" data-toggle="tooltip" data-placement="top" title="Show location details">',
'<button data-id="<%- id %>" class="primary-button toolbtn-show-locinfo toolbar-item" type="button">',
'<span class="fa fa-info-circle"></span>',
"&nbsp;Details",
"</button>",
"</span>",
// toolbar end
"</div>",
"</form>",
// toolbar end
'<div id="folder_items_element">',
"</div>",
// folder contents will append here
'<div id="folder_items_element" />',
// paginator will append here
'<div class="folder-paginator paginator-bottom"></div>',
'<div class="folder-paginator paginator-bottom" />',
// container end
"</div>"
].join("")
@@ -1386,13 +1526,13 @@ var FolderToolbarView = Backbone.View.extend({
);
},
templateBulkImportInModal: function() {
templateImportIntoHistoryModal: function() {
return _.template(
[
"<div>",
'<div class="library-modal-item">',
"Select history: ",
'<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; " autofocus>',
'<select name="import_to_history" style="width:50%; margin-bottom: 1em; " autofocus>',
"<% _.each(histories, function(history) { %>",
'<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',
"<% }); %>",
@@ -1400,8 +1540,7 @@ var FolderToolbarView = Backbone.View.extend({
"</div>",
'<div class="library-modal-item">',
"or create new: ",
'<input type="text" name="history_name" value="" placeholder="name of the new history" style="width:50%;">',
"</input>",
'<input type="text" name="history_name" value="" placeholder="name of the new history" style="width:50%;" />',
"</div>",
"</div>"
].join("")
@@ -1567,7 +1706,7 @@ var FolderToolbarView = Backbone.View.extend({
"</select>",
"</div>",
"<br/>",
'<div id="selected_history_content">',
'<div class="library_selected_history_content">',
"</div>",
"</div>"
].join("")
@@ -1652,13 +1791,61 @@ var FolderToolbarView = Backbone.View.extend({
"<% } %>",
"</ul>",
"<span>",
' <%- items_shown %> items shown <a href="" data-toggle="tooltip" data-placement="top" title="currently <%- folder_page_size %> per page" class="page_size_prompt">(change)</a>',
' <%- items_shown %> items shown <a href="" data-toggle="tooltip" data-placement="top" title="currently <%- folder_page_size %> per page" class="page-size-prompt">(change)</a>',
"</span>",
"<span>",
" <%- total_items_count %> total",
"</span>"
].join("")
);
},
templateCollectionSelectModal: function() {
return _.template(
[
"<div>",
// elements selection
'<div class="library-modal-item">',
"<h4>From which datasets?</h4>",
'<form class="form-inline">',
'<label class="radio-inline">',
'<input type="radio" name="radio_elements" id="selection_radio" value="selection" <% if (!selected_datasets) { %> disabled <% } %> > current selection',
"<% if (selected_datasets) { %>",
" (<%- selected_datasets %>)",
"<% } %>",
"</label>",
'<label class="radio-inline">',
'<input type="radio" name="radio_elements" id="folder_radio" value="folder"> all datasets in current folder',
"</label>",
"</form>",
"</div>",
// type selection
'<div class="library-modal-item">',
"<h4>Collection type</h4>",
'<span class="library-collection-type-select"/>',
"<h5>Which type to choose?</h5>",
"<ul>",
"<li>",
"List: Generic collection which groups any number of datasets into a set; similar to file system folder.",
"</li>",
"<li>",
"Paired: Simple collection containing exactly two sequence datasets; one reverse and the other forward.",
"</li>",
"<li>",
"List of Pairs: Advanced collection containing any number of Pairs; imagine as Pair-type collections inside of a List-type collection.",
"</li>",
"</ul>",
"</div>",
// history selection/creation
'<div class="library-modal-item">',
"<h4>Select history</h4>",
'<span class="library-collection-history-select"/>',
" or create new: ",
'<input type="text" name="history_name" value="" placeholder="name of the new history" />',
"</div>",
"</div>"
].join("")
);
}
});
client/galaxy/style/less/library.less
+19 -10
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;
@@ -143,9 +138,23 @@ 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;
}
}
static/style/blue/library.css
+1 -1
View File
@@ -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}.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: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}
test/galaxy_selenium/navigation.yml
+5 -5
View File
@@ -30,8 +30,8 @@ masthead:
user:
type: xpath
selector: '//ul[@id="user"]'
workflow:
workflow:
type: xpath
selector: '//ul[@id="workflow"]'
@@ -123,7 +123,7 @@ history_panel:
name: '.title .name'
name_edit_input: '.name input'
contents: '#current-history-panel .list-items div.history-content'
empty_message: '.empty-message'
size: '.history-size'
tag_icon: '.actions .history-tag-btn'
@@ -249,8 +249,8 @@ libraries:
import_datasets_ok_button: '.modal-footer .buttons #button-0'
import_datasets_cancel_button: '.modal-footer .buttons #button-1'
import_progress_bar: '.progress-bar-import'
import_history_content: '#selected_history_content'
import_history_contents_items: '#selected_history_content ul li'
import_history_content: '.library_selected_history_content'
import_history_contents_items: '.library_selected_history_content ul li'
import_from_path_textarea: '#import_paths'
labels: