mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools
This commit is contained in:
Daniel Blankenberg
@@ -139,9 +139,6 @@ jobs:
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<<: *set_workdir
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steps:
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- *restore_repo_cache
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- run: sudo apt-get update
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# For uwsgi
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- run: sudo apt-get install -y libpython3.5-dev
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- *install_tox
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- run: tox -e py35-first_startup
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validate_test_tools:
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@@ -1,80 +0,0 @@
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import Backbone from "backbone";
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import { getGalaxyInstance } from "app";
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import mod_shed_list_view from "mvc/toolshed/shed-list-view";
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import mod_categories_view from "mvc/toolshed/categories-view";
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import mod_repositories_view from "mvc/toolshed/repositories-view";
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import mod_repository_view from "mvc/toolshed/repository-view";
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import mod_repoqueue_view from "mvc/toolshed/repository-queue-view";
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import mod_repo_status_view from "mvc/toolshed/repo-status-view";
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import mod_workflows_view from "mvc/toolshed/workflows-view";
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var AdminToolshedRouter = Backbone.Router.extend({
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routes: {
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"": "toolsheds",
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sheds: "toolsheds",
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queue: "queue",
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workflows: "workflows",
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"status/r/:repositories": "status",
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status: "status",
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"categories/s/:tool_shed": "categories",
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"category/s/:tool_shed/c/:category_id/k/:sort_key/p/:page/t/:sort_order": "repositories",
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"repository/s/:tool_shed/r/:repository_id": "repository"
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}
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});
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var GalaxyAdminToolshedApp = Backbone.View.extend({
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app_config: {
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known_views: ["toolsheds", "queue", "status", "categories", "repositories", "repository"]
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},
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initialize: function() {
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const Galaxy = getGalaxyInstance();
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Galaxy.admintoolshedapp = this;
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this.admin_toolshed_router = new AdminToolshedRouter();
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this.admin_toolshed_router.on("route:queue", () => {
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Galaxy.admintoolshedapp.adminRepoQueueView = new mod_repoqueue_view.RepoQueueView();
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});
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this.admin_toolshed_router.on("route:toolsheds", () => {
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Galaxy.admintoolshedapp.adminShedListView = new mod_shed_list_view.ShedListView();
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});
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this.admin_toolshed_router.on("route:categories", tool_shed => {
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Galaxy.admintoolshedapp.adminShedCategoriesView = new mod_categories_view.CategoryView({
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tool_shed: tool_shed.replace(/\//g, "%2f")
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});
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});
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this.admin_toolshed_router.on(
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"route:repositories",
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(tool_shed, category_id, sort_key = "name", page = 1, sort_order = "asc") => {
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Galaxy.admintoolshedapp.adminShedCategoryView = new mod_repositories_view.Category({
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tool_shed: tool_shed.replace(/\//g, "%2f"),
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category_id: category_id,
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page: page,
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sort_order: sort_order,
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sort_key: sort_key
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});
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}
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);
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this.admin_toolshed_router.on("route:repository", (tool_shed, repository_id) => {
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Galaxy.admintoolshedapp.adminRepositoryView = new mod_repository_view.RepoDetails({
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tool_shed: tool_shed.replace(/\//g, "%2f"),
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repository_id: repository_id
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});
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});
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this.admin_toolshed_router.on("route:status", repositories => {
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Galaxy.admintoolshedapp.adminRepoStatusView = new mod_repo_status_view.RepoStatus({
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repositories: repositories.split("|")
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});
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});
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this.admin_toolshed_router.on("route:workflows", () => {
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Galaxy.admintoolshedapp.adminWorkflowsView = new mod_workflows_view.Workflows();
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});
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Backbone.history.start({ pushState: false });
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}
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});
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export default {
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GalaxyApp: GalaxyAdminToolshedApp
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};
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@@ -17,7 +17,6 @@ import Circster from "viz/circster";
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export { PhylovizView as phyloviz } from "viz/phyloviz";
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export { SweepsterVisualization, SweepsterVisualizationView } from "viz/sweepster";
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import GalaxyLibrary from "galaxy.library";
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import AdminToolshed from "admin.toolshed";
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export { default as pages } from "galaxy.pages";
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export { createTabularDatasetChunkedView } from "mvc/dataset/data";
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import { HistoryCollection } from "mvc/history/history-model";
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@@ -36,10 +35,6 @@ export { default as IES } from "galaxy.interactive_environments";
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export { Toast } from "ui/toast"; // TODO: remove when external consumers are updated/gone (IES right now)
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export function adminToolshed(options) {
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new AdminToolshed.GalaxyApp(options);
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}
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export function trackster(options) {
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new TracksterUIView(options);
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}
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@@ -171,7 +171,7 @@ const AdminPanel = Backbone.View.extend({
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_templateSection: function(options) {
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return `<div class="toolSectionWrapper">
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<div class="toolSectionTitle">${_l(options.title)}</div>
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<div class="toolSectionTitle px-3">${_l(options.title)}</div>
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<div class="toolSectionBody"/>
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</div>`;
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},
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@@ -55,7 +55,6 @@ var FolderListView = Backbone.View.extend({
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// start to listen if someone modifies the collection
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this.listenTo(this.collection, "add", this.renderOne);
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this.listenTo(this.collection, "remove", this.removeOne);
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this.listenTo(this.collection, "sort", this.rePaint);
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this.listenTo(this.collection, "reset", this.rePaint);
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this.fetchFolder();
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@@ -273,7 +272,8 @@ var FolderListView = Backbone.View.extend({
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event.preventDefault();
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this.current_sort_order = this.current_sort_order === "asc" ? "desc" : "asc";
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this.current_sort_key = event.currentTarget.className.replace("sort-folder-", "");
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this.collection.sortFolder(this.current_sort_key, this.current_sort_order);
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const sorted_folder = this.folder_container.sortFolder(this.current_sort_key, this.current_sort_order);
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this.collection.reset(sorted_folder.models);
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this.renderSortIcon();
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},
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@@ -75,11 +75,6 @@ var FolderAsModel = LibraryItem.extend({
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var Folder = Backbone.Collection.extend({
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model: LibraryItem,
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sortFolder: function(sort_key, sort_order) {
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this.comparator = mod_util.generateComparator(sort_key, sort_order);
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this.sort();
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}
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});
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var FolderContainer = Backbone.Model.extend({
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||||
@@ -104,6 +99,12 @@ var FolderContainer = Backbone.Model.extend({
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||||
});
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},
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sortFolder: function(sort_key, sort_order) {
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this.get("folder").comparator = mod_util.generateComparator(sort_key, sort_order);
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this.get("folder").sort();
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return this.get("folder");
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},
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parse: function(obj) {
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const Galaxy = getGalaxyInstance();
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// empty the collection
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@@ -280,7 +280,7 @@ export default FormBase.extend({
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||||
}
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}).$mount(vm);
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||||
}
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||||
if (options.xrefs) {
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if (options.xrefs && options.xrefs.length) {
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var xrefInstance = Vue.extend(xrefs);
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vm = document.createElement("div");
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$el.append(vm);
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@@ -1,98 +0,0 @@
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import _ from "underscore";
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import $ from "jquery";
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import Backbone from "backbone";
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import { getAppRoot } from "onload/loadConfig";
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import toolshed_model from "mvc/toolshed/toolshed-model";
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import toolshed_util from "mvc/toolshed/util";
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||||
import "libs/jquery/jquery-ui";
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||||
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||||
var ToolShedCategories = Backbone.View.extend({
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||||
el: "#center",
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||||
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||||
initialize: function(options) {
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this.options = _.defaults(this.options || options, this.defaults);
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this.model = new toolshed_model.Categories();
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this.model.url = `${this.model.url}?tool_shed_url=${this.options.tool_shed}`;
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this.model.tool_shed = options.tool_shed.replace(/\//g, "%2f");
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this.model.fetch();
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this.listenTo(this.model, "sync", this.render);
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},
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||||
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render: function(options) {
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const category_list_template = this.templateCategoryList();
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this.options = _.extend(this.options, options);
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this.options.categories = this.model.models;
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this.options.queue = toolshed_util.queueLength();
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this.$el.html(category_list_template(this.options));
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this.bindEvents();
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$("#center").css("overflow", "auto");
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},
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bindEvents: function() {
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$("#search_box").autocomplete({
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source: (request, response) => {
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var shed_url = this.model.tool_shed.replace(/%2f/g, "/");
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||||
var base_url = `${getAppRoot()}api/tool_shed/search`;
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var params = {
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term: request.term,
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||||
tool_shed_url: shed_url
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};
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$.post(base_url, params, data => {
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console.log(data);
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var result_list = toolshed_util.shedParser(data);
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response(result_list);
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});
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},
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minLength: 3,
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select: (event, ui) => {
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var tsr_id = ui.item.value;
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var new_route = `repository/s/${this.model.tool_shed}/r/${tsr_id}`;
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||||
Backbone.history.navigate(new_route, {
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trigger: true,
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replace: true
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||||
});
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||||
}
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||||
});
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||||
},
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||||
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||||
templateCategoryList: function() {
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return _.template(
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||||
`<div class='shed-style-container'>
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||||
<div class='header'>
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||||
<h2>Categories in <%= tool_shed.replace(/%2f/g, '/') %></h2>
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||||
<span><a href='#/queue'>Repository Queue (<%= queue %>)</a></span>
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||||
<span style='clear:both; '></span>
|
||||
</div>
|
||||
<div id='standard-search' style='height: 2em; margin: 1em;'>
|
||||
<span class='ui-widget' >
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||||
<input class='search-box-input' id='search_box' data-shedurl='<%= tool_shed.replace(/%2f/g, '/') %>' name='search' placeholder='Search repositories' size='30' type='text' />
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||||
</span>
|
||||
</div>
|
||||
<div style='clear: both; margin-top: 1em;'>
|
||||
<table class='grid'>
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||||
<thead id='grid-table-header'>
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||||
<tr>
|
||||
<th>Name</th>
|
||||
<th>Description</th>
|
||||
<th>Repositories</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<% _.each(categories, function(category) { %>
|
||||
<tr>
|
||||
<td>
|
||||
<a href='#/category/s/<%= tool_shed %>/c/<%= category.get('id') %>/k/name/p/1/t/asc'><%= category.get('name') %></a>
|
||||
</td>
|
||||
<td><%= category.get('description') %></td>
|
||||
<td><%= category.get('repositories') %></td>
|
||||
</tr>
|
||||
<% }); %>
|
||||
</table>
|
||||
</div>
|
||||
</div>`
|
||||
);
|
||||
}
|
||||
});
|
||||
|
||||
export default {
|
||||
CategoryView: ToolShedCategories
|
||||
};
|
||||
@@ -1,132 +0,0 @@
|
||||
import $ from "jquery";
|
||||
import Backbone from "backbone";
|
||||
import _ from "underscore";
|
||||
import _l from "utils/localization";
|
||||
import toolshed_model from "mvc/toolshed/toolshed-model";
|
||||
import toolshed_util from "mvc/toolshed/util";
|
||||
|
||||
var ToolShedRepoStatusView = Backbone.View.extend({
|
||||
el: "#center",
|
||||
|
||||
initialize: function(options) {
|
||||
this.options = _.defaults(this.options || [{}], options, this.defaults);
|
||||
this.model = new toolshed_model.RepoStatus();
|
||||
this.listenTo(this.model, "sync", this.render);
|
||||
this.model.url += `?repositories=${this.options.repositories.join("|")}`;
|
||||
this.model.fetch();
|
||||
this.timer = window.setInterval(() => {
|
||||
var terminal_states = ["installed", "error"];
|
||||
var all_done = true;
|
||||
_.some(this.model.models, repository => {
|
||||
var repo_status = repository.get("status").toLowerCase();
|
||||
if (terminal_states.indexOf(repo_status) === -1) {
|
||||
all_done = false;
|
||||
return true;
|
||||
}
|
||||
});
|
||||
if (all_done) {
|
||||
window.clearInterval(this.timer);
|
||||
} else {
|
||||
this.model.fetch();
|
||||
}
|
||||
}, 2000);
|
||||
},
|
||||
|
||||
close: function() {
|
||||
window.clearInterval(this.timer);
|
||||
},
|
||||
|
||||
render: function(options) {
|
||||
this.options = _.extend(this.options, options);
|
||||
var repo_status_template = this.templateRepoStatus();
|
||||
this.$el.html(
|
||||
repo_status_template({
|
||||
title: _l("Repository Status"),
|
||||
repositories: this.model.models,
|
||||
queue: toolshed_util.queueLength()
|
||||
})
|
||||
);
|
||||
$("#center").css("overflow", "auto");
|
||||
},
|
||||
|
||||
templateRepoStatus: function() {
|
||||
return _.template(
|
||||
`<div class="unified-panel-header" id="panel_header" unselectable="on">
|
||||
<div class="unified-panel-header-inner"><%= title %>
|
||||
<a class="ml-auto" href="#/queue">Repository Queue (<%= queue %>)</a>
|
||||
</div>
|
||||
</div>
|
||||
<style type="text/css">
|
||||
.state-color-new,
|
||||
.state-color-deactivated,
|
||||
.state-color-uninstalled { border-color:#bfbfbf; background:#eee }
|
||||
.state-color-cloning,
|
||||
.state-color-setting-tool-versions,
|
||||
.state-color-installing-repository-dependencies,
|
||||
.state-color-installing-tool-dependencies,
|
||||
.state-color-loading-proprietary-datatypes { border-color:#AAAA66; background:#FFFFCC }
|
||||
.state-color-installed { border-color:#20b520; background:#b0f1b0 }
|
||||
.state-color-error { border-color:#dd1b15; background:#f9c7c5 }
|
||||
</style>
|
||||
<table id="grid-table" class="grid">
|
||||
<thead id="grid-table-header">
|
||||
<tr>
|
||||
<th id="null-header">Name<span class="sort-arrow"></span></th>
|
||||
<th id="null-header">Description<span class="sort-arrow"></span></th>
|
||||
<th id="null-header">Owner<span class="sort-arrow"></span></th>
|
||||
<th id="null-header">Revision<span class="sort-arrow"></span></th>
|
||||
<th id="null-header">Installation Status<span class="sort-arrow"></span></th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody id="grid-table-body">
|
||||
<% _.each(repositories, function(repository) { %>
|
||||
<tr>
|
||||
<td>
|
||||
<div id="" class="">
|
||||
<label id="repo-name-<%= repository.get("id") %>" for="<%= repository.get("id") %>">
|
||||
<%= repository.get("name") %>
|
||||
</label>
|
||||
</div>
|
||||
</td>
|
||||
<td>
|
||||
<div id="" class="">
|
||||
<label id="repo-desc-<%= repository.get("id") %>" for="<%= repository.get("id") %>">
|
||||
<%= repository.get("description") %>
|
||||
</label>
|
||||
</div>
|
||||
</td>
|
||||
<td>
|
||||
<div id="" class="">
|
||||
<label id="repo-user-<%= repository.get("id") %>" for="<%= repository.get("id") %>">
|
||||
<%= repository.get("owner") %>
|
||||
</label>
|
||||
</div>
|
||||
</td>
|
||||
<td>
|
||||
<div id="" class="">
|
||||
<label id="repo-changeset-<%= repository.get("id") %>" for="<%= repository.get("id") %>">
|
||||
<%= repository.get("changeset_revision") %>
|
||||
</label>
|
||||
</div>
|
||||
</td>
|
||||
<td>
|
||||
<div id="" class="">
|
||||
<label id="RepositoryStatus-<%= repository.get("id") %>" for="<%= repository.get("id") %>">
|
||||
<div class="repo-status count-box state-color-<%= repository.get("status").toLowerCase().replace(/ /g, "-") %>" id="RepositoryStatus-<%= repository.get("id") %>">
|
||||
<%= repository.get("status") %>
|
||||
</div>
|
||||
</label>
|
||||
</div>
|
||||
</td>
|
||||
</tr>
|
||||
<% }); %>
|
||||
</tbody>
|
||||
<tfoot id="grid-table-footer"></tfoot>
|
||||
</table>`
|
||||
);
|
||||
}
|
||||
});
|
||||
|
||||
export default {
|
||||
RepoStatus: ToolShedRepoStatusView
|
||||
};
|
||||
@@ -1,222 +0,0 @@
|
||||
import _ from "underscore";
|
||||
import $ from "jquery";
|
||||
import Backbone from "backbone";
|
||||
import { getAppRoot } from "onload/loadConfig";
|
||||
import toolshed_model from "mvc/toolshed/toolshed-model";
|
||||
import toolshed_util from "mvc/toolshed/util";
|
||||
import "libs/jquery/jquery-ui";
|
||||
|
||||
var ToolShedCategoryContentsView = Backbone.View.extend({
|
||||
el: "#center",
|
||||
|
||||
initialize: function(params) {
|
||||
this.params = params;
|
||||
this.model = new toolshed_model.CategoryCollection();
|
||||
this.listenTo(this.model, "sync", this.render);
|
||||
var shed = params.tool_shed.replace(/\//g, "%2f");
|
||||
this.model.url += `?tool_shed_url=${shed}`;
|
||||
this.model.url += `&category_id=${params.category_id}`;
|
||||
this.model.url += `&sort_key=${params.sort_key}`;
|
||||
this.model.url += `&sort_order=${params.sort_order}`;
|
||||
this.model.url += `&page=${params.page}`;
|
||||
this.model.tool_shed = shed;
|
||||
this.model.category = params.category_id;
|
||||
this.model.fetch();
|
||||
},
|
||||
|
||||
render: function(options) {
|
||||
this.options = _.defaults(this.options || {}, options);
|
||||
var category_contents_template = this.templateCategoryContents();
|
||||
var page_navigation_template = this.templatePageNavigation();
|
||||
var sorting = {
|
||||
class: { owner: "fa-sort", description: "fa-sort", name: "fa-sort" },
|
||||
direction: { owner: "asc", description: "asc", name: "asc" }
|
||||
};
|
||||
sorting.class[this.params.sort_key] = this.params.sort_order == "desc" ? "fa-sort-down" : "fa-sort-up";
|
||||
sorting.direction[this.params.sort_key] = this.params.sort_order == "asc" ? "desc" : "asc";
|
||||
var previous_page = Math.max(this.params.page - 1, 1);
|
||||
var pages = parseInt(this.model.models[0].get("repository_count") % 25) + 1;
|
||||
var next_page = Math.min(parseInt(this.params.page) + 1, pages);
|
||||
var pagination_params = {
|
||||
page: this.params.page,
|
||||
next: next_page,
|
||||
previous: previous_page,
|
||||
pages: pages
|
||||
};
|
||||
if (pages > 5) {
|
||||
var page = parseInt(this.params.page);
|
||||
var page_slice = Array();
|
||||
var slice_start = Math.max(page - 2, 2);
|
||||
var i = slice_start;
|
||||
var slice_end = Math.min(Math.min(page + 2, slice_start + 4), pages);
|
||||
for (i = slice_start; i <= slice_end; i++) {
|
||||
page_slice.push(i);
|
||||
}
|
||||
pagination_params["page_slice"] = page_slice;
|
||||
}
|
||||
this.$el.html(
|
||||
category_contents_template({
|
||||
page_navigation: page_navigation_template(pagination_params),
|
||||
category: this.model.models[0],
|
||||
tool_shed: this.model.tool_shed,
|
||||
queue: toolshed_util.queueLength(),
|
||||
sorting: sorting,
|
||||
page: this.params.page
|
||||
})
|
||||
);
|
||||
$("#center").css("overflow", "auto");
|
||||
this.bindEvents();
|
||||
},
|
||||
|
||||
bindEvents: function() {
|
||||
$("#search_box").autocomplete({
|
||||
source: (request, response) => {
|
||||
var shed_url = this.model.tool_shed.replace(/%2f/g, "/");
|
||||
var base_url = `${getAppRoot()}api/tool_shed/search`;
|
||||
var params = {
|
||||
term: request.term,
|
||||
tool_shed_url: shed_url
|
||||
};
|
||||
$.post(base_url, params, data => {
|
||||
var result_list = toolshed_util.shedParser(data);
|
||||
response(result_list);
|
||||
});
|
||||
},
|
||||
minLength: 3,
|
||||
select: (event, ui) => {
|
||||
var tsr_id = ui.item.value;
|
||||
var new_route = `repository/s/${this.model.tool_shed}/r/${tsr_id}`;
|
||||
Backbone.history.navigate(new_route, {
|
||||
trigger: true,
|
||||
replace: true
|
||||
});
|
||||
}
|
||||
});
|
||||
$(".fa-fw").on("click", ev => {
|
||||
var parameters = {};
|
||||
parameters.field = $(ev.target).attr("data-field");
|
||||
parameters.direction = $(ev.target).attr("data-direction");
|
||||
var new_route = `category/s/${this.model.tool_shed}/c/${this.model.category}/k/${parameters.field}/p/${
|
||||
this.params.page
|
||||
}/t/${parameters.direction}`;
|
||||
Backbone.history.navigate(new_route, {
|
||||
trigger: true,
|
||||
replace: true
|
||||
});
|
||||
});
|
||||
$(".pagenav").on("click", ev => {
|
||||
var page = $(ev.target).attr("data-page");
|
||||
var new_route = `category/s/${this.model.tool_shed}/c/${this.model.category}/k/${
|
||||
this.params.sort_key
|
||||
}/p/${page}/t/${this.params.sort_order}`;
|
||||
Backbone.history.navigate(new_route, {
|
||||
trigger: true,
|
||||
replace: true
|
||||
});
|
||||
});
|
||||
},
|
||||
|
||||
templatePageNavigation: function() {
|
||||
return _.template(
|
||||
`<div class="navigation">
|
||||
<% if (page != 1) { %>
|
||||
<a data-page="1" class="pagenav fa fa-fast-backward" />
|
||||
<a data-page="<%= previous %>" class="pagenav fa fa-step-backward" />
|
||||
<% } else { %>
|
||||
<a data-page="1" class="pagenav-inactive fa fa-fast-backward" />
|
||||
<a data-page="<%= previous %>" class="pagenav-inactive fa fa-step-backward" />
|
||||
<% } %>
|
||||
<% if (pages > 5) { %>
|
||||
<% if (page != 1) { %>
|
||||
<a data-page="1" class="pagenav fa"><a>1</a>
|
||||
<% if (page != 2) { %>
|
||||
<a class="fa">…</a>
|
||||
<% } %>
|
||||
<% } else { %>
|
||||
<a data-page="1" class="pagenav-inactive fa"><a>1</a>
|
||||
<% } %>
|
||||
<% _.each(page_slice, function(i) { %>
|
||||
<% if (i == page) { %>
|
||||
<a data-page="<%= i %>" class="fa"><strong><%= i %></strong></a>
|
||||
<% } else { %>
|
||||
<a data-page="<%= i %>" class="pagenav fa"><%= i %></a>
|
||||
<% } %>
|
||||
<% }); %>
|
||||
<% var last_pages = [pages - 2, pages - 1, pages]; %>
|
||||
<% if (last_pages.indexOf(parseInt(page)) == -1) { %>
|
||||
<a class="fa">…</a>
|
||||
<a data-page="<%= pages %>" class="pagenav fa"><%= pages %></a>
|
||||
<% } %>
|
||||
<% } else { %>
|
||||
<% for (i = 1; i <= pages; i++) { %>
|
||||
<% if (i == page) { %>
|
||||
<a data-page="<%= i %>" class="fa"><strong><%= i %></strong></a>
|
||||
<% } else { %>
|
||||
<a data-page="<%= i %>" class="pagenav fa"><%= i %></a>
|
||||
<% } %>
|
||||
<% } %>
|
||||
<% } %>
|
||||
<% if (page < pages) { %>
|
||||
<a data-page="<%= next %>" class="pagenav fa fa-step-forward" />
|
||||
<a data-page="<%= pages %>" class="pagenav fa fa-fast-forward" />
|
||||
<% } else { %>
|
||||
<a data-page="<%= next %>" class="pagenav-inactive fa fa-step-forward" />
|
||||
<a data-page="<%= pages %>" class="pagenav-inactive fa fa-fast-forward" />
|
||||
<% } %>
|
||||
</div>`
|
||||
);
|
||||
},
|
||||
|
||||
templateCategoryContents: function() {
|
||||
return _.template(
|
||||
`<style type="text/css">
|
||||
.ui-autocomplete { background-color: #fff; }
|
||||
li.ui-menu-item { list-style-type: none; }
|
||||
div.navigation { width: 100%; text-align: center; }
|
||||
div.navigation a { margin-left: 0.5em; margin-right: 0.5em; display: inline; text-decoration: underline; }
|
||||
a.pagenav-inactive { opacity: 0.5; }
|
||||
</style>
|
||||
<div class="unified-panel-header" id="panel_header" unselectable="on">
|
||||
<div class="unified-panel-header-inner">Repositories in <%= category.get("name") %><a class="ml-auto" href="#/queue">Repository Queue (<%= queue %>)</a></div>
|
||||
</div>
|
||||
<div class="unified-panel-body" id="list_repositories">
|
||||
<div id="standard-search" style="height: 2em; margin: 1em;">
|
||||
<span class="ui-widget" >
|
||||
<input class="search-box-input" id="search_box" name="search" data-shedurl="<%= tool_shed.replace(/%2f/g, "/") %>" placeholder="Search repositories by name or id" size="60" type="text" />
|
||||
</span>
|
||||
</div>
|
||||
<% if (category.get('repository_count') > 25) { %>
|
||||
<%= page_navigation %>
|
||||
<% } %>
|
||||
<div style="clear: both; margin-top: 1em;">
|
||||
<table class="grid table-striped">
|
||||
<thead id="grid-table-header">
|
||||
<tr>
|
||||
<th style="width: 10%;"><a class="fa fa-fw <%= sorting.class.owner %>" data-direction="<%= sorting.direction.owner %>" data-field="owner">Owner</a></th>
|
||||
<th style="width: 15%;"><a class="fa fa-fw <%= sorting.class.name %>" data-direction="<%= sorting.direction.name %>" data-field="name">Name</a></th>
|
||||
<th><a class="fa fa-fw <%= sorting.class.description %>" data-direction="<%= sorting.direction.description %>" data-field="description">Synopsis</a></th>
|
||||
<th style="width: 10%;">Type</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<% _.each(category.get("repositories"), function(repository) { %>
|
||||
<tr>
|
||||
<td><%= repository.owner %></td>
|
||||
<td>
|
||||
<div style="float: left; margin-left: 1px;" class="menubutton split">
|
||||
<a href="#/repository/s/<%= tool_shed %>/r/<%= repository.id %>"><%= repository.name %></a>
|
||||
</div>
|
||||
</td>
|
||||
<td><%= repository.description %></td>
|
||||
<td><%= repository.type %></td>
|
||||
</tr>
|
||||
<% }); %>
|
||||
</table>
|
||||
</div>
|
||||
</div>`
|
||||
);
|
||||
}
|
||||
});
|
||||
|
||||
export default {
|
||||
Category: ToolShedCategoryContentsView
|
||||
};
|
||||
@@ -1,166 +0,0 @@
|
||||
import _ from "underscore";
|
||||
import $ from "jquery";
|
||||
import Backbone from "backbone";
|
||||
import { getAppRoot } from "onload/loadConfig";
|
||||
import _l from "utils/localization";
|
||||
import toolshed_model from "mvc/toolshed/toolshed-model";
|
||||
import toolshed_util from "mvc/toolshed/util";
|
||||
|
||||
var View = Backbone.View.extend({
|
||||
el: "#center",
|
||||
|
||||
defaults: [],
|
||||
|
||||
initialize: function(options) {
|
||||
this.model = new toolshed_model.RepoQueue();
|
||||
this.listenTo(this.model, "sync", this.render);
|
||||
this.model.fetch();
|
||||
this.render();
|
||||
},
|
||||
|
||||
render: function(options) {
|
||||
var repo_queue_template = this.templateRepoQueue();
|
||||
var repositories = this.model.models;
|
||||
this.$el.html(
|
||||
repo_queue_template({
|
||||
repositories: repositories,
|
||||
queue: toolshed_util.queueLength()
|
||||
})
|
||||
);
|
||||
$("#center").css("overflow", "auto");
|
||||
this.bindEvents();
|
||||
},
|
||||
|
||||
bindEvents: function() {
|
||||
$(".install_one").on("click", ev => {
|
||||
const repository_metadata = this.loadFromQueue($(ev.target).attr("data-repokey"));
|
||||
this.installFromQueue(repository_metadata, $(ev.target).attr("data-repokey"));
|
||||
});
|
||||
$(".remove_one").on("click", ev => {
|
||||
const queue_key = $(ev.target).attr("data-repokey");
|
||||
const repo_queue = JSON.parse(window.localStorage.repositories);
|
||||
if (repo_queue.hasOwnProperty(queue_key)) {
|
||||
this.removeRow(repo_queue[queue_key].id);
|
||||
delete repo_queue[queue_key];
|
||||
}
|
||||
window.localStorage.repositories = JSON.stringify(repo_queue);
|
||||
});
|
||||
$("#clear_queue").on("click", () => {
|
||||
const repo_queue = JSON.parse(window.localStorage.repositories);
|
||||
for (const key of Object.keys(repo_queue)) {
|
||||
this.removeRow(repo_queue[key].id);
|
||||
}
|
||||
window.localStorage.repositories = "{}";
|
||||
});
|
||||
$("#from_workflow").on("click", () => {
|
||||
Backbone.history.navigate("workflows", {
|
||||
trigger: true,
|
||||
replace: true
|
||||
});
|
||||
});
|
||||
},
|
||||
|
||||
removeRow: function(row_id) {
|
||||
$(`#queued_repository_${row_id}`).remove();
|
||||
},
|
||||
|
||||
installFromQueue: function(repository_metadata, queue_key) {
|
||||
var params = {};
|
||||
params.install_tool_dependencies = repository_metadata.install_tool_dependencies;
|
||||
params.install_repository_dependencies = repository_metadata.install_repository_dependencies;
|
||||
params.install_resolver_dependencies = repository_metadata.install_resolver_dependencies;
|
||||
params.tool_panel_section = repository_metadata.tool_panel_section;
|
||||
params.shed_tool_conf = repository_metadata.shed_tool_conf;
|
||||
params.repositories = JSON.stringify([
|
||||
[repository_metadata.repository.id, repository_metadata.changeset_revision]
|
||||
]);
|
||||
params.tool_shed_repository_ids = JSON.stringify([repository_metadata.repository.id]);
|
||||
params.tool_shed_url = queue_key.split("|")[0];
|
||||
params.changeset = repository_metadata.changeset_revision;
|
||||
var url = `${getAppRoot()}api/tool_shed_repositories/install?async=True`;
|
||||
$(`#queued_repository_${repository_metadata.repository.id}`).remove();
|
||||
if (window.localStorage.repositories) {
|
||||
if (queue_key === undefined) {
|
||||
queue_key = toolshed_util.queueKey(repository_metadata);
|
||||
}
|
||||
var repository_queue = JSON.parse(window.localStorage.repositories);
|
||||
if (repository_queue.hasOwnProperty(queue_key)) {
|
||||
delete repository_queue[queue_key];
|
||||
window.localStorage.repositories = JSON.stringify(repository_queue);
|
||||
}
|
||||
}
|
||||
|
||||
$.post(url, params, data => {
|
||||
var iri_params = JSON.parse(data);
|
||||
var repositories = iri_params.repositories;
|
||||
var new_route = `status/r/${repositories.join("|")}`;
|
||||
$.post(`${getAppRoot()}admin_toolshed/install_repositories`, iri_params, data => {
|
||||
console.log("Initializing repository installation succeeded");
|
||||
});
|
||||
Backbone.history.navigate(new_route, {
|
||||
trigger: true,
|
||||
replace: true
|
||||
});
|
||||
});
|
||||
},
|
||||
|
||||
loadFromQueue: function(queue_key) {
|
||||
var repository_queue = JSON.parse(window.localStorage.repositories);
|
||||
if (repository_queue.hasOwnProperty(queue_key)) {
|
||||
return repository_queue[queue_key];
|
||||
}
|
||||
return this.defaults;
|
||||
},
|
||||
|
||||
templateRepoQueue: function() {
|
||||
return _.template(
|
||||
`<div class='shed-style-container'>
|
||||
<h2>
|
||||
${_l("Repository Queue")}
|
||||
</h2>
|
||||
<div class='tab-pane' id='panel_header' id='repository_queue'>
|
||||
<table id='queued_repositories' class='grid' border='0' cellpadding='2' cellspacing='2' width='100%'>
|
||||
<thead id='grid-table-header'>
|
||||
<tr>
|
||||
<th class='datasetRow'>Name</th>
|
||||
<th class='datasetRow'>Owner</th>
|
||||
<th class='datasetRow'>Revision</th>
|
||||
<th class='datasetRow'>ToolShed</th>
|
||||
<th class='datasetRow'>Install</th>
|
||||
<th class='datasetRow'></th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<% if (repositories.length > 0) { %>
|
||||
<% _.each(repositories, function(repository) { %>
|
||||
<tr id='queued_repository_<%= repository.get('id') %>'>
|
||||
<td class='datasetRow'><%= repository.get('repository').name %></td>
|
||||
<td class='datasetRow'><%= repository.get('repository').owner %></td>
|
||||
<td class='datasetRow'><%= repository.get('changeset_revision') %></td>
|
||||
<td class='datasetRow'><%= repository.get('tool_shed_url') %></td>
|
||||
<td class='datasetRow'>
|
||||
<input class='btn btn-primary install_one' data-repokey='<%= repository.get('queue_key') %>' type='submit' id='install_repository_<%= repository.get('id') %>' name='install_repository' value='Install now' />
|
||||
</td>
|
||||
<td class='datasetRow'>
|
||||
<input class='btn btn-primary remove_one' data-repokey='<%= repository.get('queue_key') %>' type='submit' id='unqueue_repository_<%= repository.get('id') %>' name='unqueue_repository' value='Remove from queue' />
|
||||
</td>
|
||||
</tr>
|
||||
<% }); %>
|
||||
<% } else { %>
|
||||
<tr><td colspan='6'>
|
||||
${_l("No repositories in queue.")}
|
||||
</td></tr>
|
||||
<% } %>
|
||||
</tbody>
|
||||
</table>
|
||||
<input type='button' class='btn btn-primary' id='from_workflow' value='Add from workflow' />
|
||||
<input class='btn btn-primary' type='submit' id='clear_queue' name='clear_queue' value='Clear queue' />
|
||||
</div>
|
||||
</div>`
|
||||
);
|
||||
}
|
||||
});
|
||||
|
||||
export default {
|
||||
RepoQueueView: View
|
||||
};
|
||||
@@ -1,637 +0,0 @@
|
||||
import _ from "underscore";
|
||||
import $ from "jquery";
|
||||
import Backbone from "backbone";
|
||||
import { getAppRoot } from "onload/loadConfig";
|
||||
import "libs/jquery/jstree";
|
||||
import toolshed_model from "mvc/toolshed/toolshed-model";
|
||||
import Utils from "utils/utils";
|
||||
import Modal from "mvc/ui/ui-modal";
|
||||
import FormView from "mvc/form/form-view";
|
||||
import toolshed_util from "mvc/toolshed/util";
|
||||
|
||||
var ToolShedRepositoryView = Backbone.View.extend({
|
||||
el: "#center",
|
||||
|
||||
initialize: function(params) {
|
||||
this.options = _.defaults(this.options || {}, this.defaults);
|
||||
this.model = new toolshed_model.RepositoryCollection();
|
||||
this.listenTo(this.model, "sync", this.render);
|
||||
var shed = params.tool_shed.replace(/\//g, "%2f");
|
||||
this.model.url += `?tool_shed_url=${shed}&repository_id=${params.repository_id}`;
|
||||
this.model.tool_shed_url = params.tool_shed.replace(/%2f/g, "/");
|
||||
this.model.tool_shed = shed;
|
||||
this.model.category = params.repository_id;
|
||||
this.model.fetch();
|
||||
},
|
||||
|
||||
render: function(options) {
|
||||
var repo_details_template = this.templateRepoDetails();
|
||||
var models = this.model.models[0];
|
||||
this.options = {
|
||||
repository: models.get("repository"),
|
||||
tool_shed: this.model.tool_shed,
|
||||
queue: toolshed_util.queueLength()
|
||||
};
|
||||
var changesets = Object.keys(this.options.repository.metadata).sort(function(a, b) {
|
||||
return parseInt(a.split(":")[0] - b.split(":")[0]);
|
||||
});
|
||||
var ordered_metadata = {};
|
||||
var unordered_metadata = this.options.repository.metadata;
|
||||
changesets.forEach(function(key) {
|
||||
ordered_metadata[key] = unordered_metadata[key];
|
||||
});
|
||||
this.options.repository.metadata = ordered_metadata;
|
||||
this.options.current_changeset = this.options.current_changeset || changesets[changesets.length - 1];
|
||||
this.options.current_metadata = this.options.repository.metadata[this.options.current_changeset];
|
||||
this.options.current_metadata.tool_shed_url = this.model.tool_shed_url;
|
||||
this.options.tools = this.options.current_metadata.tools;
|
||||
this.options.repository_dependencies_template = this.templateRepoDependencies();
|
||||
this.options.repository_dependency_template = this.templateRepoDependency();
|
||||
this.options.tps_template_global_select = this.templateGlobalSectionSelect();
|
||||
this.options.tps_template_global_create = this.templateGlobalSectionCreate();
|
||||
this.options.tps_template_tool_select = this.templateToolSectionSelect();
|
||||
this.options.tps_template_tool_create = this.templateToolSectionCreate();
|
||||
this.options.panel_section_options = this.templatePanelSelectOptions();
|
||||
this.options.tool_dependencies = models.get("tool_dependencies");
|
||||
this.options.shed_tool_conf = this.templateShedToolConf({
|
||||
shed_tool_confs: models.get("shed_conf")
|
||||
});
|
||||
this.options.panel_section_dict = models.get("panel_section_dict");
|
||||
this.options.api_url = `${getAppRoot()}api/tool_shed_repositories/install?async=True`;
|
||||
this.options = _.extend(this.options, options);
|
||||
this.$el.html(repo_details_template(this.options));
|
||||
this.checkInstalled(this.options.current_metadata);
|
||||
this.bindEvents();
|
||||
$("#center").css("overflow", "auto");
|
||||
},
|
||||
|
||||
bindEvents: function() {
|
||||
$("#changeset").on("change", () => {
|
||||
this.options.current_changeset = $("#changeset")
|
||||
.find("option:selected")
|
||||
.text();
|
||||
this.options.current_metadata = this.options.repository.metadata[this.options.current_changeset];
|
||||
this.checkInstalled(this.options.current_metadata);
|
||||
this.reDraw(this.options);
|
||||
});
|
||||
$("#tool_panel_section_select").on("change", () => {
|
||||
this.tpsSelection();
|
||||
});
|
||||
$("#install_repository").on("click", ev => {
|
||||
ev.preventDefault();
|
||||
var params = {};
|
||||
params.repositories = JSON.stringify([
|
||||
[
|
||||
$("#install_repository").attr("data-tsrid"),
|
||||
$("#changeset")
|
||||
.find("option:selected")
|
||||
.val()
|
||||
]
|
||||
]);
|
||||
params.tool_shed_repository_ids = JSON.stringify([$("#install_repository").attr("data-tsrid")]);
|
||||
params.tool_shed_url = this.model.tool_shed_url;
|
||||
params.install_tool_dependencies = $("#install_tool_dependencies").val();
|
||||
params.install_repository_dependencies = $("#install_repository_dependencies").val();
|
||||
params.install_resolver_dependencies = $("#install_resolver_dependencies").val();
|
||||
params.tool_panel_section = JSON.stringify(this.panelSelect(params));
|
||||
params.shed_tool_conf = $("select[name='shed_tool_conf']")
|
||||
.find("option:selected")
|
||||
.val();
|
||||
params.changeset = $("#changeset")
|
||||
.find("option:selected")
|
||||
.val();
|
||||
var url = $("#repository_installation").attr("action");
|
||||
this.prepareInstall(params, url);
|
||||
});
|
||||
$("#queue_install").on("click", ev => {
|
||||
this.options.current_changeset = $("#changeset")
|
||||
.find("option:selected")
|
||||
.text();
|
||||
this.options.current_metadata = this.options.repository.metadata[this.options.current_changeset];
|
||||
var repository_metadata = {};
|
||||
_.each(Object.keys(this.options.current_metadata), key => {
|
||||
if (!repository_metadata[key]) {
|
||||
repository_metadata[key] = this.options.current_metadata[key];
|
||||
}
|
||||
});
|
||||
repository_metadata.install_tool_dependencies = $("#install_tool_dependencies").val();
|
||||
repository_metadata.install_repository_dependencies = $("#install_repository_dependencies").val();
|
||||
repository_metadata.install_resolver_dependencies = $("#install_resolver_dependencies").val();
|
||||
repository_metadata.tool_panel_section = JSON.stringify(this.panelSelect({}));
|
||||
repository_metadata.shed_tool_conf = $("select[name='shed_tool_conf']")
|
||||
.find("option:selected")
|
||||
.val();
|
||||
repository_metadata.tool_shed_url = this.model.tool_shed_url;
|
||||
if (repository_metadata.tool_shed_url.substr(-1) == "/") {
|
||||
repository_metadata.tool_shed_url = repository_metadata.tool_shed_url.substr(
|
||||
0,
|
||||
repository_metadata.tool_shed_url.length - 1
|
||||
);
|
||||
}
|
||||
toolshed_util.addToQueue(repository_metadata);
|
||||
this.checkInstalled(repository_metadata);
|
||||
});
|
||||
this.toolTPSSelectionEvents();
|
||||
$(() => {
|
||||
$("#repository_dependencies").jstree();
|
||||
});
|
||||
$(".tool_form").on("click", ev => {
|
||||
var guid = $(ev.target).attr("data-guid");
|
||||
var name = $(ev.target).attr("data-name");
|
||||
var desc = $(ev.target).attr("data-desc");
|
||||
var tool_shed_url = this.model.tool_shed_url;
|
||||
var tsr_id = $("#repository_details").attr("data-tsrid");
|
||||
var changeset = $("#changeset")
|
||||
.find("option:selected")
|
||||
.val();
|
||||
var api_url = `${getAppRoot()}api/tool_shed/tool_json`;
|
||||
var params = {
|
||||
guid: guid,
|
||||
tool_shed_url: tool_shed_url,
|
||||
tsr_id: tsr_id,
|
||||
changeset: changeset
|
||||
};
|
||||
$.get(api_url, params, data => {
|
||||
var toolform = new FormView(data);
|
||||
Utils.deepeach(data.inputs, input => {
|
||||
if (input.type) {
|
||||
if (["data", "data_collection"].indexOf(input.type) != -1) {
|
||||
input.type = "hidden";
|
||||
input.info = `Data input '${input.name}' (${Utils.textify(input.extensions)})`;
|
||||
}
|
||||
}
|
||||
});
|
||||
var modal = new Modal.View();
|
||||
var modal_title = `<u>${name}</u> ${desc}`;
|
||||
modal.show({
|
||||
closing_events: true,
|
||||
title: modal_title,
|
||||
body: toolform.$el,
|
||||
buttons: {
|
||||
Close: function() {
|
||||
modal.hide();
|
||||
}
|
||||
}
|
||||
});
|
||||
});
|
||||
});
|
||||
$(".select-tps-button").on("click", params => {
|
||||
var changeset = this.selectedChangeset();
|
||||
var guid = params.target.attributes.getNamedItem("data-toolguid");
|
||||
this.showToolTPSSelect(guid, changeset);
|
||||
});
|
||||
$(".create-tps-button").on("click", params => {
|
||||
var changeset = this.selectedChangeset();
|
||||
var guid = params.target.attributes.getNamedItem("data-toolguid");
|
||||
this.showToolTPSCreate(guid, changeset);
|
||||
});
|
||||
$(".global-select-tps-button").on("click", () => {
|
||||
$("#tool_panel_section").replaceWith(this.options.tps_template_global_select(this.options));
|
||||
this.propagateTPS();
|
||||
this.bindEvents();
|
||||
});
|
||||
$(".global-create-tps-button").on("click", () => {
|
||||
$("#tool_panel_section").replaceWith(this.options.tps_template_global_create());
|
||||
this.bindEvents();
|
||||
});
|
||||
},
|
||||
|
||||
checkInstalled: function(metadata) {
|
||||
var params = { name: metadata.name, owner: metadata.owner };
|
||||
var already_installed = false;
|
||||
$.get(`${getAppRoot()}api/tool_shed_repositories`, params, data => {
|
||||
for (var index = 0; index < data.length; index++) {
|
||||
var repository = data[index];
|
||||
var installed = !repository.deleted && !repository.uninstalled;
|
||||
var changeset_match =
|
||||
repository.changeset_revision == metadata.changeset_revision ||
|
||||
repository.installed_changeset_revision == metadata.changeset_revision;
|
||||
if (
|
||||
repository.name == metadata.repository.name &&
|
||||
repository.owner == metadata.repository.owner &&
|
||||
installed &&
|
||||
changeset_match
|
||||
) {
|
||||
already_installed = true;
|
||||
}
|
||||
if (already_installed) {
|
||||
$("#install_repository").prop("disabled", true);
|
||||
$("#install_repository").val("This revision is already installed");
|
||||
} else {
|
||||
$("#install_repository").prop("disabled", false);
|
||||
$("#install_repository").val("Install this revision");
|
||||
}
|
||||
}
|
||||
if (this.repoQueued(metadata) || already_installed) {
|
||||
$("#queue_install").hide();
|
||||
$("#queue_install").val("This revision is already in the queue");
|
||||
} else {
|
||||
$("#queue_install").show();
|
||||
$("#queue_install").val("Install this revision later");
|
||||
}
|
||||
});
|
||||
},
|
||||
|
||||
panelSelect: function(params) {
|
||||
var tool_panel_section = {};
|
||||
if ($("#tool_panel_section_select").length) {
|
||||
params.tool_panel_section_id = $("#tool_panel_section_select")
|
||||
.find("option:selected")
|
||||
.val();
|
||||
} else {
|
||||
params.new_tool_panel_section = $("#new_tool_panel_section").val();
|
||||
}
|
||||
$(".tool_panel_section_picker").each(function() {
|
||||
var element_name = $(this).attr("name");
|
||||
var tool_guid = $(this).attr("data-toolguid");
|
||||
if (element_name === "tool_panel_section_id") {
|
||||
tool_panel_section[tool_guid] = {
|
||||
tool_panel_section: $(this)
|
||||
.find("option:selected")
|
||||
.val(),
|
||||
action: "append"
|
||||
};
|
||||
} else {
|
||||
tool_panel_section[tool_guid] = {
|
||||
tool_panel_section: $(this).val(),
|
||||
action: "create"
|
||||
};
|
||||
}
|
||||
});
|
||||
return tool_panel_section;
|
||||
},
|
||||
|
||||
reDraw: function(options) {
|
||||
this.$el.empty();
|
||||
this.render(options);
|
||||
},
|
||||
|
||||
repoQueued: function(metadata) {
|
||||
if (!window.localStorage.repositories) {
|
||||
return;
|
||||
}
|
||||
var queue_key = this.queueKey(metadata);
|
||||
var queued_repos;
|
||||
if (window.localStorage.repositories) {
|
||||
queued_repos = JSON.parse(window.localStorage.repositories);
|
||||
}
|
||||
if (queued_repos && queued_repos.hasOwnProperty(queue_key)) {
|
||||
return true;
|
||||
}
|
||||
return false;
|
||||
},
|
||||
|
||||
queueKey: function(metadata) {
|
||||
var shed_url = this.model.tool_shed_url;
|
||||
// Make sure there is never a trailing slash on the shed URL.
|
||||
if (shed_url.substr(-1) == "/") {
|
||||
shed_url = shed_url.substr(0, shed_url.length - 1);
|
||||
}
|
||||
return `${shed_url}|${metadata.repository_id}|${metadata.changeset_revision}`;
|
||||
},
|
||||
|
||||
tpsSelection: function() {
|
||||
var new_tps = $("#tool_panel_section_select")
|
||||
.find("option:selected")
|
||||
.val();
|
||||
$('.tool_panel_section_picker[default="active"]').each(function() {
|
||||
$(this).val(new_tps);
|
||||
});
|
||||
},
|
||||
|
||||
prepareInstall: function(params, api_url) {
|
||||
$.post(api_url, params, data => {
|
||||
var iri_parameters = JSON.parse(data);
|
||||
this.doInstall(iri_parameters);
|
||||
});
|
||||
},
|
||||
|
||||
doInstall: function(params) {
|
||||
var controller_url = `${getAppRoot()}admin_toolshed/install_repositories`;
|
||||
var repositories = params.repositories;
|
||||
var new_route = `status/r/${repositories.join("|")}`;
|
||||
$.post(controller_url, params, data => {
|
||||
console.log("Initializing repository installation succeeded");
|
||||
});
|
||||
Backbone.history.navigate(new_route, {
|
||||
trigger: true,
|
||||
replace: true
|
||||
});
|
||||
},
|
||||
|
||||
selectedChangeset: function() {
|
||||
return $("#changeset")
|
||||
.find("option:selected")
|
||||
.val();
|
||||
},
|
||||
|
||||
showToolTPSCreate: function(guid, changeset) {
|
||||
var metadata = this.options.current_metadata;
|
||||
var tools = metadata.tools;
|
||||
var tool = toolshed_util.toolByGuid(guid, changeset, tools);
|
||||
var selector = "#tool_tps_" + tool.clean;
|
||||
$(selector).empty();
|
||||
$(selector).append(this.options.tps_template_tool_create({ tool: tool }));
|
||||
$(".select-tps-button").click(ev => {
|
||||
var changeset = this.selectedChangeset();
|
||||
var guid = ev.target.attributes.getNamedItem("data-toolguid");
|
||||
this.showToolTPSSelect(guid, changeset);
|
||||
});
|
||||
this.bindEvents();
|
||||
},
|
||||
|
||||
showToolTPSSelect: function(guid, changeset) {
|
||||
var metadata = this.options.current_metadata;
|
||||
var tools = metadata.tools;
|
||||
var tool = toolshed_util.toolByGuid(guid, changeset, tools);
|
||||
var selector = "#tool_tps_" + tool.clean;
|
||||
$(selector).empty();
|
||||
$(selector).append(
|
||||
this.options.tps_template_tool_select({
|
||||
tool: tool,
|
||||
panel_section_dict: this.options.panel_section_dict,
|
||||
panel_section_options: this.options.panel_section_options
|
||||
})
|
||||
);
|
||||
$(".create-tps-button").click(ev => {
|
||||
var changeset = this.selectedChangeset();
|
||||
var guid = ev.target.attributes.getNamedItem("data-toolguid");
|
||||
this.showToolTPSCreate(guid, changeset);
|
||||
});
|
||||
this.bindEvents();
|
||||
},
|
||||
|
||||
propagateTPS: function() {
|
||||
$("#tool_panel_section_select").change(() => {
|
||||
var new_tps = $("#tool_panel_section_select")
|
||||
.find("option:selected")
|
||||
.val();
|
||||
$('.tool_panel_section_picker[default="active"]').each(obj => {
|
||||
obj.val(new_tps);
|
||||
});
|
||||
});
|
||||
this.toolTPSSelectionEvents();
|
||||
},
|
||||
|
||||
toolTPSSelectionEvents: function() {
|
||||
$(".tool_panel_section_picker").on("change", ev => {
|
||||
const element = $(ev.target);
|
||||
var new_value = element.find("option:selected").val();
|
||||
var default_tps = $("#tool_panel_section_select")
|
||||
.find("option:selected")
|
||||
.val();
|
||||
if (new_value == default_tps) {
|
||||
element.attr("default", "active");
|
||||
} else {
|
||||
element.removeAttr("default");
|
||||
}
|
||||
});
|
||||
},
|
||||
|
||||
templateRepoDetails: function() {
|
||||
return _.template(
|
||||
`<div class="unified-panel-header" id="panel_header" unselectable="on">
|
||||
<div class="unified-panel-header-inner">Repository information for <strong><%= repository.name %></strong> from <strong><%= repository.owner %></strong><a class="ml-auto" href="#/queue">Repository Queue (<%= queue %>)</a></div>
|
||||
</div>
|
||||
<div class="unified-panel-body" id="repository_details" data-tsrid="<%= repository.id %>">
|
||||
<form id="repository_installation" name="install_repository" method="post" action="<%= api_url %>">
|
||||
<input type="hidden" id="repositories" name="<%= repository.id %>" value="ID" />
|
||||
<input type="hidden" id="tool_shed_url" name="tool_shed_url" value="<%= tool_shed %>" />
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Changeset</div>
|
||||
<div class="toolFormBody changeset">
|
||||
<select id="changeset" name="changeset" style="margin: 5px;">
|
||||
<% _.each(Object.keys(repository.metadata), function(changeset) { %>
|
||||
<% if (changeset == current_changeset) { var selected = "selected "; } else { var selected = ""; } %>
|
||||
<option <%= selected %>value="<%= changeset.split(":")[1] %>"><%= changeset %></option>
|
||||
<% }); %>
|
||||
</select>
|
||||
<input class="btn btn-primary preview-button" data-tsrid="<%= current_metadata.repository.id %>" type="submit" id="install_repository" name="install_repository" value="Install this revision now" />
|
||||
<input class="btn btn-primary preview-button" type="button" id="queue_install" name="queue_install" value="Install this revision later" />
|
||||
<div class="toolParamHelp" style="clear: both;">Please select a revision and review the settings below before installing.</div>
|
||||
</div>
|
||||
</div>
|
||||
<%= shed_tool_conf %>
|
||||
<% if (current_metadata.has_repository_dependencies) { %>
|
||||
<div class="toolFormTitle">Repository dependencies for <strong id="current_changeset"><%= current_changeset %></strong></div>
|
||||
<div class="toolFormBody">
|
||||
<p id="install_repository_dependencies_checkbox">
|
||||
<input type="checkbox" checked id="install_repository_dependencies" />
|
||||
<label for="install_repository_dependencies">Install repository dependencies</label>
|
||||
</p>
|
||||
<% current_metadata.repository_dependency_template = repository_dependency_template; %>
|
||||
<div class="tables container-table" id="repository_dependencies">
|
||||
<div class="expandLink">
|
||||
<a class="toggle_folder" data_target="repository_dependencies_table">
|
||||
Repository dependencies – <em>installation of these additional repositories is required</em>
|
||||
</a>
|
||||
</div>
|
||||
<%= repository_dependencies_template(current_metadata) %>
|
||||
</div>
|
||||
</div>
|
||||
<% } %>
|
||||
<% if (current_metadata.includes_tool_dependencies) { %>
|
||||
<div class="toolFormTitle">Tool dependencies</div>
|
||||
<div class="toolFormBody">
|
||||
<p id="install_resolver_dependencies_checkbox">
|
||||
<input type="checkbox" checked id="install_resolver_dependencies" />
|
||||
<label for="install_resolver_dependencies">Install resolver dependencies</label>
|
||||
</p>
|
||||
<p id="install_tool_dependencies_checkbox">
|
||||
<input type="checkbox" checked id="install_tool_dependencies" />
|
||||
<label for="install_tool_dependencies">Install tool dependencies</label>
|
||||
</p>
|
||||
<div class="tables container-table" id="tool_dependencies">
|
||||
<div class="expandLink">
|
||||
<a class="toggle_folder" data_target="tool_dependencies_table">
|
||||
Tool dependencies – <em>repository tools require handling of these dependencies</em>
|
||||
</a>
|
||||
</div>
|
||||
<table class="tables container-table" id="tool_dependencies_table" border="0" cellpadding="2" cellspacing="2" width="100%">
|
||||
<thead>
|
||||
<tr style="display: table-row;" class="datasetRow" parent="0" id="libraryItem-rt-f9cad7b01a472135">
|
||||
<th style="padding-left: 40px;">Name</th>
|
||||
<th>Version</th>
|
||||
<th>Type</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody id="tool_deps">
|
||||
<% _.each(tool_dependencies[current_changeset], function(dependency) { %>
|
||||
<tr class="datasetRow tool_dependency_row" style="display: table-row;">
|
||||
<td style="padding-left: 40px;">
|
||||
<%= dependency.name %></td>
|
||||
<td><%= dependency.version %></td>
|
||||
<td><%= dependency.type %></td>
|
||||
</tr>
|
||||
<% }); %>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
<% } %>
|
||||
<% if (current_metadata.includes_tools_for_display_in_tool_panel) { %>
|
||||
<div class="toolFormTitle">Tools – <em>click the name to preview the tool and use the pop-up menu to inspect all metadata</em></div>
|
||||
<div class="toolFormBody">
|
||||
<div class="tables container-table" id="tools_toggle">
|
||||
<table class="tables container-table" id="valid_tools" border="0" cellpadding="2" cellspacing="2" width="100%">
|
||||
<thead>
|
||||
<tr style="display: table-row;" class="datasetRow" parent="0" id="libraryItem-rt-f9cad7b01a472135">
|
||||
<th style="padding-left: 40px;">Name</th>
|
||||
<th>Description</th>
|
||||
<th>Version</th>
|
||||
<th><%= tps_template_global_select({panel_section_dict: panel_section_dict, panel_section_options: panel_section_options}) %></tr>
|
||||
</thead>
|
||||
<tbody id="tools_in_repo">
|
||||
<% _.each(current_metadata.tools, function(tool) { %>
|
||||
<tr id="libraryItem-<%= tool.clean %>" class="tool_row" style="display: table-row;" style="width: 15%">
|
||||
<td style="padding-left: 40px;">
|
||||
<div id="tool-<%= tool.clean %>" class="menubutton split popup" style="float: left;">
|
||||
<a class="tool_form view-info" data-toggle="modal" data-target="toolform_<%= tool.clean %>" data-clean="<%= tool.clean %>" data-guid="<%= tool.guid %>" data-name="<%= tool.name %>" data-desc="<%= tool.description %>"><%= tool["name"] %></a>
|
||||
</div>
|
||||
</td>
|
||||
<td><%= tool.description %></td>
|
||||
<td style="width: 15%"><%= tool.version %></td>
|
||||
<td style="width: 35%" id="tool_tps_<%= tool.clean %>">
|
||||
<%= tps_template_tool_select({tool: tool, panel_section_dict: panel_section_dict, panel_section_options: panel_section_options}) %>
|
||||
</td>
|
||||
</tr>
|
||||
<% }); %>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
<% } %>
|
||||
</form>
|
||||
</div>`
|
||||
);
|
||||
},
|
||||
|
||||
templateRepoDependencies: function() {
|
||||
return _.template(
|
||||
`<div class="toolFormTitle">Repository Dependencies</div>
|
||||
<div class="toolFormBody tables container-table" id="repository_dependencies">
|
||||
<ul>
|
||||
<li>Repository installation requires the following
|
||||
<% if (has_repository_dependencies) { %>
|
||||
<% _.each(repository_dependencies, function(dependency) { %>
|
||||
<% dependency.repository_dependency_template = repository_dependency_template; %>
|
||||
<%= repository_dependency_template(dependency) %>
|
||||
<% }); %>
|
||||
<% } %>
|
||||
</li>
|
||||
</ul>
|
||||
</div>`
|
||||
);
|
||||
},
|
||||
|
||||
templateRepoDependency: function() {
|
||||
return _.template(
|
||||
`<li id="metadata_<%= id %>" class="datasetRow repository_dependency_row">
|
||||
Repository <b><%= repository.name %></b> revision <b><%= changeset_revision %></b> owned by <b><%= repository.owner %></b>
|
||||
<% if (has_repository_dependencies) { %>
|
||||
<ul class="child_dependencies">
|
||||
<% _.each(repository_dependencies, function(dependency) { %>
|
||||
<% dependency.repository_dependency_template = repository_dependency_template; %>
|
||||
<%= repository_dependency_template(dependency) %>
|
||||
<% }); %>
|
||||
</ul>
|
||||
<% } %>
|
||||
</li>`
|
||||
);
|
||||
},
|
||||
|
||||
templateShedToolConf: function() {
|
||||
return _.template(
|
||||
`<div class="toolFormTitle">Shed tool configuration file:</div>
|
||||
<div class="toolFormBody">
|
||||
<div class="form-row">
|
||||
<select name="shed_tool_conf">
|
||||
<% _.each(shed_tool_confs.options, function(conf) { %>
|
||||
<option value="<%= conf.value %>"><%= conf.label %></option>
|
||||
<% }); %>
|
||||
</select>
|
||||
<div class="toolParamHelp" style="clear: both;">Select the file whose <b>tool_path</b> setting you want used for installing repositories.</div>
|
||||
</div>
|
||||
</div>`
|
||||
);
|
||||
},
|
||||
|
||||
// templateToolDependency: function(){
|
||||
// return _.template(
|
||||
// `<% if (has_repository_dependencies) { %>
|
||||
// <% _.each(repository_dependencies, function(dependency) { %>
|
||||
// <% if (dependency.includes_tool_dependencies) { %>
|
||||
// <% dependency.tool_dependency_template = tool_dependency_template %>
|
||||
// <%= tool_dependency_template(dependency) %>
|
||||
// <% } %>
|
||||
// <% }); %>
|
||||
// <% } %>`
|
||||
// );
|
||||
// },
|
||||
|
||||
templateGlobalSectionCreate: function() {
|
||||
return _.template(
|
||||
`<div id="tool_panel_section">
|
||||
<div class="form-row" id="new_tps">
|
||||
<input id="new_tool_panel_section" name="new_tool_panel_section" type="textfield" value="" size="40"/>
|
||||
<input class="btn btn-primary global-select-tps-button" type="button" id="select_existing" value="Select existing" />
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Add a new tool panel section to contain the installed tools (optional).
|
||||
</div>
|
||||
</div>
|
||||
</div>`
|
||||
);
|
||||
},
|
||||
|
||||
templateGlobalSectionSelect: function() {
|
||||
return _.template(
|
||||
`<div id="tool_panel_section">
|
||||
<div class="toolFormTitle">Tool Panel Section</div>
|
||||
<div class="toolFormBody">
|
||||
<div class="tab-pane" id="select_tps">
|
||||
<select name="<%= name %>" id="<%= panel_section_dict.id %>">
|
||||
<%= panel_section_options({sections: panel_section_dict.sections}) %>
|
||||
</select>
|
||||
<input class="btn btn-primary global-create-tps-button" type="button" id="create_new" value="Create new" />
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Select an existing tool panel section to contain the installed tools (optional).
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div>`
|
||||
);
|
||||
},
|
||||
|
||||
templateToolSectionCreate: function() {
|
||||
return _.template(
|
||||
`<div id="new_tps_<%= tool.clean %>" data-clean="<%= tool.clean %>" class="form-row">
|
||||
<input data-toolguid="<%= tool.guid %>" class="tool_panel_section_picker" size="40" name="new_tool_panel_section" id="new_tool_panel_section_<%= tool.clean %>" type="text">
|
||||
<input id="per_tool_select_<%= tool.clean %>" class="btn btn-primary select-tps-button" data-toolguid="<%= tool.guid %>" value="Select existing" id="select_existing_<%= tool.clean %>" type="button">
|
||||
</div>`
|
||||
);
|
||||
},
|
||||
|
||||
templateToolSectionSelect: function() {
|
||||
return _.template(
|
||||
`<div id="select_tps_<%= tool.clean %>" data-clean="<%= tool.clean %>" class="tps_creator">
|
||||
<select default="active" style="width: 30em;" data-toolguid="<%= tool.guid %>" class="tool_panel_section_picker" name="tool_panel_section_id" id="tool_panel_section_select_<%= tool.clean %>">
|
||||
<%= panel_section_options({sections: panel_section_dict.sections}) %>
|
||||
</select>
|
||||
<input id="per_tool_create_<%= tool.clean %>" data-clean="<%= tool.clean %>" class="btn btn-primary create-tps-button" data-toolguid="<%= tool.guid %>" value="Create new" id="create_new_<%= tool.clean %>" type="button">
|
||||
<div style="clear: both;" class="toolParamHelp"></div>
|
||||
</div>`
|
||||
);
|
||||
},
|
||||
|
||||
templatePanelSelectOptions: function() {
|
||||
return _.template(
|
||||
`<% _.each(sections, function(section) { %>
|
||||
<option value="<%= section.id %>"><%= section.name %></option>
|
||||
<% }); %>`
|
||||
);
|
||||
}
|
||||
});
|
||||
|
||||
export default {
|
||||
RepoDetails: ToolShedRepositoryView
|
||||
};
|
||||
@@ -1,53 +0,0 @@
|
||||
import Backbone from "backbone";
|
||||
import $ from "jquery";
|
||||
import _ from "underscore";
|
||||
import _l from "utils/localization";
|
||||
import toolshed_model from "mvc/toolshed/toolshed-model";
|
||||
import toolshed_util from "mvc/toolshed/util";
|
||||
|
||||
var ShedListView = Backbone.View.extend({
|
||||
initialize: function(options) {
|
||||
this.options = _.defaults(this.options || {}, this.defaults);
|
||||
this.model = new toolshed_model.ShedsCollection();
|
||||
this.listenTo(this.model, "sync", this.render);
|
||||
this.model.fetch();
|
||||
},
|
||||
|
||||
el: "#center",
|
||||
|
||||
render: function(options) {
|
||||
this.options = _.defaults(this.options || {}, options, this.defaults);
|
||||
var toolshed_list_template = this.templateToolshedList();
|
||||
this.$el.html(
|
||||
toolshed_list_template({
|
||||
title: _l("Configured Galaxy Tool Sheds"),
|
||||
tool_sheds: this.model.models,
|
||||
queue: toolshed_util.queueLength()
|
||||
})
|
||||
);
|
||||
$("#center").css("overflow", "auto");
|
||||
},
|
||||
|
||||
templateToolshedList: function() {
|
||||
return _.template(
|
||||
`<div class='shed-style-container'>
|
||||
<div class='header'>
|
||||
<h2>
|
||||
${_l("Configured Tool Sheds")}
|
||||
</h2>
|
||||
<span><a href='#/queue'>Repository Queue (<%= queue %>)</a></span>
|
||||
<div style='clear:both;'></div>
|
||||
</div'>
|
||||
<% _.each(tool_sheds, function(shed) { %>
|
||||
<div>
|
||||
<a href='#/categories/s/<%= shed.get('url') %>'><%= shed.get('name') %></a>
|
||||
</div>
|
||||
<% }); %>
|
||||
</div>`
|
||||
);
|
||||
}
|
||||
});
|
||||
|
||||
export default {
|
||||
ShedListView: ShedListView
|
||||
};
|
||||
@@ -1,106 +0,0 @@
|
||||
import _ from "underscore";
|
||||
import Backbone from "backbone";
|
||||
import { getAppRoot } from "onload/loadConfig";
|
||||
|
||||
var ToolShedModel = Backbone.Model.extend({
|
||||
defaults: {
|
||||
url: "https://toolshed.g2.bx.psu.edu/",
|
||||
name: "Galaxy Main Tool Shed"
|
||||
},
|
||||
urlRoot: `${getAppRoot()}api/tool_shed`
|
||||
});
|
||||
|
||||
var ToolShedsCollection = Backbone.Collection.extend({
|
||||
url: `${getAppRoot()}api/tool_shed`,
|
||||
model: ToolShedModel
|
||||
});
|
||||
|
||||
var ToolShedCategoriesModel = Backbone.Model.extend({
|
||||
defaults: [{}],
|
||||
urlRoot: `${getAppRoot()}api/tool_shed/contents`
|
||||
});
|
||||
|
||||
var ToolShedCategoriesCollection = Backbone.Collection.extend({
|
||||
url: `${getAppRoot()}api/tool_shed/contents`,
|
||||
model: ToolShedCategoriesModel
|
||||
});
|
||||
|
||||
var ToolShedCategoryModel = Backbone.Model.extend({
|
||||
defaults: [{}],
|
||||
urlRoot: `${getAppRoot()}api/tool_shed/category`
|
||||
});
|
||||
|
||||
var ToolShedCategoryCollection = Backbone.Collection.extend({
|
||||
url: `${getAppRoot()}api/tool_shed/category`,
|
||||
model: ToolShedCategoryModel
|
||||
});
|
||||
|
||||
var ToolShedRepositoryModel = Backbone.Model.extend({
|
||||
defaults: [{}],
|
||||
urlRoot: `${getAppRoot()}api/tool_shed/repository`
|
||||
});
|
||||
|
||||
var ToolShedRepositoryCollection = Backbone.Collection.extend({
|
||||
url: `${getAppRoot()}api/tool_shed/repository`,
|
||||
model: ToolShedRepositoryModel
|
||||
});
|
||||
|
||||
var RepoQueueModel = Backbone.Model.extend({
|
||||
url: "#"
|
||||
});
|
||||
|
||||
var RepoQueueCollection = Backbone.Collection.extend({
|
||||
url: "#",
|
||||
model: RepoQueueModel,
|
||||
fetch: function() {
|
||||
var repositories = Array();
|
||||
var repositories_enc;
|
||||
if (window.localStorage.hasOwnProperty("repositories")) {
|
||||
repositories_enc = JSON.parse(window.localStorage.repositories);
|
||||
} else {
|
||||
repositories_enc = [];
|
||||
}
|
||||
var queue_keys = Object.keys(repositories_enc);
|
||||
_.each(queue_keys, key => {
|
||||
var repo = repositories_enc[key];
|
||||
repo.queue_key = key;
|
||||
repositories.push(repo);
|
||||
});
|
||||
this.reset(repositories);
|
||||
return Backbone.Collection.prototype.fetch.call(this);
|
||||
}
|
||||
});
|
||||
|
||||
var RepoStatusModel = Backbone.Model.extend({
|
||||
defaults: [{}],
|
||||
urlRoot: `${getAppRoot()}api/tool_shed/status`
|
||||
});
|
||||
|
||||
var RepoStatusCollection = Backbone.Collection.extend({
|
||||
url: `${getAppRoot()}api/tool_shed/status`,
|
||||
model: RepoStatusModel
|
||||
});
|
||||
|
||||
var WorkflowToolsModel = Backbone.Model.extend({
|
||||
defaults: [{}],
|
||||
urlRoot: `${getAppRoot()}api/workflows?missing_tools=True`
|
||||
});
|
||||
|
||||
var WorkflowToolsCollection = Backbone.Collection.extend({
|
||||
url: `${getAppRoot()}api/workflows?missing_tools=True`,
|
||||
model: WorkflowToolsModel
|
||||
});
|
||||
|
||||
export default {
|
||||
ShedModel: ToolShedModel,
|
||||
ShedsCollection: ToolShedsCollection,
|
||||
Category: ToolShedCategoriesModel,
|
||||
Categories: ToolShedCategoriesCollection,
|
||||
CategoryModel: ToolShedCategoryModel,
|
||||
CategoryCollection: ToolShedCategoryCollection,
|
||||
RepositoryModel: ToolShedRepositoryModel,
|
||||
RepositoryCollection: ToolShedRepositoryCollection,
|
||||
RepoQueue: RepoQueueCollection,
|
||||
RepoStatus: RepoStatusCollection,
|
||||
WorkflowTools: WorkflowToolsCollection
|
||||
};
|
||||
@@ -1,65 +0,0 @@
|
||||
import $ from "jquery";
|
||||
import { getAppRoot } from "onload/loadConfig";
|
||||
|
||||
var searchShed = function(request, response) {
|
||||
var shed_url = this.shed_url;
|
||||
var base_url = `${getAppRoot()}api/tool_shed/search`;
|
||||
$.get(base_url, { term: request.term, tool_shed_url: shed_url }, data => {
|
||||
var result_list = this.shedParser(data);
|
||||
response(result_list);
|
||||
});
|
||||
};
|
||||
|
||||
var shedParser = jsondata => {
|
||||
var results = [];
|
||||
var hits = jsondata.hits;
|
||||
$.each(hits, hit => {
|
||||
var record = hits[hit];
|
||||
var label = `${record.repository.name} by ${record.repository.repo_owner_username}: ${
|
||||
record.repository.description
|
||||
}`;
|
||||
var result = { value: record.repository.id, label: label };
|
||||
results.push(result);
|
||||
});
|
||||
return results;
|
||||
};
|
||||
|
||||
var addToQueue = metadata => {
|
||||
if (metadata.tool_shed_url.substr(-1) == "/") {
|
||||
metadata.tool_shed_url = metadata.tool_shed_url.substr(0, metadata.tool_shed_url.length - 1);
|
||||
}
|
||||
var key = `${metadata.tool_shed_url}|${metadata.repository_id}|${metadata.changeset_revision}`;
|
||||
var queued_repos = {};
|
||||
if (window.localStorage.repositories) {
|
||||
queued_repos = JSON.parse(window.localStorage.repositories);
|
||||
}
|
||||
queued_repos[key] = metadata;
|
||||
window.localStorage.repositories = JSON.stringify(queued_repos);
|
||||
};
|
||||
|
||||
var queueLength = () => {
|
||||
if (window.localStorage.hasOwnProperty("repositories")) {
|
||||
var repo_queue = JSON.parse(window.localStorage.repositories);
|
||||
return Object.keys(repo_queue).length;
|
||||
} else {
|
||||
return 0;
|
||||
}
|
||||
};
|
||||
|
||||
var toolByGuid = function(guid, changeset, tools) {
|
||||
var returned_tool;
|
||||
tools.forEach(function(tool) {
|
||||
if (tool.guid == guid.value) {
|
||||
returned_tool = tool;
|
||||
}
|
||||
});
|
||||
return returned_tool;
|
||||
};
|
||||
|
||||
export default {
|
||||
searchShed: searchShed,
|
||||
shedParser: shedParser,
|
||||
addToQueue: addToQueue,
|
||||
queueLength: queueLength,
|
||||
toolByGuid: toolByGuid
|
||||
};
|
||||
@@ -1,133 +0,0 @@
|
||||
import _ from "underscore";
|
||||
import $ from "jquery";
|
||||
import Backbone from "backbone";
|
||||
import { getAppRoot } from "onload/loadConfig";
|
||||
import _l from "utils/localization";
|
||||
import toolshed_model from "mvc/toolshed/toolshed-model";
|
||||
import toolshed_util from "mvc/toolshed/util";
|
||||
|
||||
var View = Backbone.View.extend({
|
||||
el: "#center",
|
||||
|
||||
defaults: [{}],
|
||||
|
||||
initialize: function(options) {
|
||||
this.model = new toolshed_model.WorkflowTools();
|
||||
this.listenTo(this.model, "sync", this.render);
|
||||
this.model.fetch();
|
||||
this.render();
|
||||
},
|
||||
|
||||
render: function(options) {
|
||||
var workflows_missing_tools = this.templateWorkflows();
|
||||
var workflows = this.model.models;
|
||||
this.$el.html(
|
||||
workflows_missing_tools({
|
||||
title: _l("Workflows Missing Tools"),
|
||||
workflows: workflows,
|
||||
queue: toolshed_util.queueLength()
|
||||
})
|
||||
);
|
||||
$("#center").css("overflow", "auto");
|
||||
this.bindEvents();
|
||||
},
|
||||
|
||||
bindEvents: function() {
|
||||
var repository_id;
|
||||
$(".show_wf_repo").on("click", ev => {
|
||||
var tool_ids = $(ev.target).attr("data-toolids");
|
||||
var toolshed = $(ev.target).attr("data-shed");
|
||||
var api_url = `${getAppRoot()}api/tool_shed/repository`;
|
||||
var params = { tool_ids: tool_ids };
|
||||
$.get(api_url, params, data => {
|
||||
repository_id = data.repository.id;
|
||||
var new_route = `repository/s/${toolshed.replace(/:/g, "%3a").replace(/\//g, "%2f")}/r/${
|
||||
data.repository.id
|
||||
}`;
|
||||
Backbone.history.navigate(new_route, {
|
||||
trigger: true,
|
||||
replace: true
|
||||
});
|
||||
});
|
||||
});
|
||||
$(".queue_wf_repo").on("click", ev => {
|
||||
var elem = $(ev.target);
|
||||
var tool_ids = elem.attr("data-toolids");
|
||||
var toolshed = elem.attr("data-shed");
|
||||
var api_url = `${getAppRoot()}api/tool_shed/repository`;
|
||||
var params = { tool_ids: tool_ids };
|
||||
$.get(api_url, params, data => {
|
||||
repository_id = data.repository.id;
|
||||
params = {
|
||||
tool_shed_url: toolshed,
|
||||
repository_id: repository_id
|
||||
};
|
||||
$.get(api_url, params, data => {
|
||||
var changesets = Object.keys(data.repository.metadata);
|
||||
var current_changeset = changesets[0];
|
||||
var current_metadata = data.repository.metadata[current_changeset];
|
||||
current_metadata.tool_shed_url = toolshed;
|
||||
toolshed_util.addToQueue(current_metadata);
|
||||
elem.remove();
|
||||
});
|
||||
});
|
||||
});
|
||||
$("#from_workflow").on("click", this.loadWorkflows);
|
||||
},
|
||||
|
||||
templateWorkflows: function() {
|
||||
_.template(
|
||||
`<div class="unified-panel-header" id="panel_header" unselectable="on">
|
||||
<div class="unified-panel-header-inner"><%= title %><a class="ml-auto" href="#/queue">Repository Queue (<%= queue %>)</a></div>
|
||||
</div>
|
||||
<style type="text/css">
|
||||
.workflow_names, .workflow_tools { list-style-type: none; } ul.workflow_tools, ul.workflow_names { padding-left: 0px; }
|
||||
</style>
|
||||
<table id="workflows_missing_tools" class="grid" border="0" cellpadding="2" cellspacing="2" width="100%">
|
||||
<thead id="grid-table-header">
|
||||
<tr>
|
||||
<th class="datasetRow">Workflows</th>
|
||||
<th class="datasetRow">Tool IDs</th>
|
||||
<th class="datasetRow">Shed</th>
|
||||
<th class="datasetRow">Name</th>
|
||||
<th class="datasetRow">Owner</th>
|
||||
<th class="datasetRow">Actions</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<% _.each(workflows, function(workflow) { %>
|
||||
<tr>
|
||||
<td class="datasetRow">
|
||||
<ul class="workflow_names">
|
||||
<% _.each(workflow.get("workflows"), function(name) { %>
|
||||
<li class="workflow_names"><%= name %></li>
|
||||
<% }); %>
|
||||
</ul>
|
||||
</td>
|
||||
<td class="datasetRow">
|
||||
<ul class="workflow_tools">
|
||||
<% _.each(workflow.get("tools"), function(tool) { %>
|
||||
<li class="workflow_tools"><%= tool %></li>
|
||||
<% }); %>
|
||||
</ul>
|
||||
</td>
|
||||
<td class="datasetRow"><%= workflow.get("shed") %></td>
|
||||
<td class="datasetRow"><%= workflow.get("repository") %></td>
|
||||
<td class="datasetRow"><%= workflow.get("owner") %></td>
|
||||
<td class="datasetRow">
|
||||
<ul class="workflow_tools">
|
||||
<li class="workflow_tools">
|
||||
<input type="button" class="show_wf_repo btn btn-primary" data-shed="<%= workflow.get("shed") %>" data-owner="<%= workflow.get("owner") %>" data-repo="<%= workflow.get("repository") %>" data-toolids="<%= workflow.get("tools").join(",") %>" value="Show Repository" /></li>
|
||||
</ul>
|
||||
</td>
|
||||
</tr>
|
||||
<% }); %>
|
||||
</ul>
|
||||
</div>`
|
||||
);
|
||||
}
|
||||
});
|
||||
|
||||
export default {
|
||||
Workflows: View
|
||||
};
|
||||
@@ -74,7 +74,7 @@ class ScrollPanel {
|
||||
}
|
||||
|
||||
// Zoom levels to use for zooming the workflow canvas
|
||||
const zoomLevels = [0.25, 0.33, 0.5, 0.67, 0.75, 0.8, 0.9, 1, 1.1, 1.25, 1.5, 1.75, 2, 2.5, 3, 4];
|
||||
const zoomLevels = [0.25, 0.33, 0.5, 0.67, 0.75, 0.8, 0.9, 1, 1.1, 1.25, 1.33, 1.5, 2, 2.5, 3, 4];
|
||||
|
||||
// Default zoome level (1)
|
||||
const defaultZoomLevel = 7;
|
||||
@@ -97,7 +97,7 @@ class CanvasManager {
|
||||
this.init_copy_paste();
|
||||
}
|
||||
setZoom(zoomLevel) {
|
||||
this.zoomLevel = Math.min(Math.max(0, zoomLevel), zoomLevels.length);
|
||||
this.zoomLevel = Math.min(Math.max(0, zoomLevel), zoomLevels.length-1);
|
||||
this.canvasZoom = zoomLevels[this.zoomLevel];
|
||||
// Set CSS transform to appropriate zoom level
|
||||
this.cv.css("transform-origin", "top left");
|
||||
@@ -109,16 +109,33 @@ class CanvasManager {
|
||||
this.app.workflow.fit_canvas_to_nodes();
|
||||
}
|
||||
initZoomControls() {
|
||||
var zoomControl = $('<div class="btn-group-vertical"/>').css({
|
||||
var zoomControl = $('<div class="btn-group-horizontal"/>').css({
|
||||
position: "absolute",
|
||||
left: "1rem",
|
||||
bottom: "1rem"
|
||||
bottom: "1rem",
|
||||
cursor: "pointer"
|
||||
});
|
||||
const zoomButton = $(`<a class="btn btn-light" title="Reset Zoom Level">${zoomLevels[defaultZoomLevel] * 100}%</a>`).css({
|
||||
width: "4rem"
|
||||
});
|
||||
|
||||
zoomControl.append(
|
||||
$('<div class="btn btn-secondary fa fa-plus"/>').click(() => this.setZoom(this.zoomLevel + 1))
|
||||
$('<a class="btn btn-secondary fa fa-minus"/>').click(() => {
|
||||
this.setZoom(this.zoomLevel - 1);
|
||||
zoomButton.text(Math.floor(zoomLevels[this.zoomLevel] * 100) + '%');
|
||||
})
|
||||
);
|
||||
zoomControl.append(
|
||||
$('<div class="btn btn-secondary fa fa-minus"/>').click(() => this.setZoom(this.zoomLevel - 1))
|
||||
zoomButton.click(() => {
|
||||
this.setZoom(defaultZoomLevel);
|
||||
zoomButton.text(Math.floor(zoomLevels[this.zoomLevel] * 100) + '%');
|
||||
})
|
||||
);
|
||||
zoomControl.append(
|
||||
$('<a class="btn btn-secondary fa fa-plus"/>').click(() => {
|
||||
this.setZoom(this.zoomLevel + 1);
|
||||
zoomButton.text(Math.floor(zoomLevels[this.zoomLevel] * 100) + '%');
|
||||
})
|
||||
);
|
||||
this.cv.closest("#workflow-canvas-body").append(zoomControl);
|
||||
}
|
||||
|
||||
@@ -1429,7 +1429,7 @@ div.permissionContainer {
|
||||
.toolMenuContainer {
|
||||
color: $panel-text-color;
|
||||
a {
|
||||
color: $panel-text-color;
|
||||
color: $panel-text-color;
|
||||
}
|
||||
background: $panel-bg-color;
|
||||
min-height: 100%;
|
||||
@@ -1438,9 +1438,6 @@ div.permissionContainer {
|
||||
div.toolSectionTitle {
|
||||
font-weight: 500;
|
||||
font-size: $h4-font-size;
|
||||
&:hover {
|
||||
background: darken($panel-bg-color, 5%);
|
||||
}
|
||||
}
|
||||
|
||||
div.toolPanelLabel {
|
||||
@@ -1457,28 +1454,26 @@ div.toolSectionTitle, div.toolTitle, div.toolTitleNoSection {
|
||||
.labels {
|
||||
float: right;
|
||||
}
|
||||
|
||||
a {
|
||||
@extend .px-3;
|
||||
@extend .py-1;
|
||||
text-decoration: none;
|
||||
display: block;
|
||||
&:hover {
|
||||
@extend .px-3;
|
||||
@extend .py-1;
|
||||
text-decoration: none;
|
||||
display: block;
|
||||
&:hover {
|
||||
background: darken($panel-bg-color, 5%);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
&.text-muted a {
|
||||
&:hover {
|
||||
background: inherit;
|
||||
}
|
||||
&:hover {
|
||||
background: inherit;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
div.toolSectionWrapper {
|
||||
div.toolTitle a, div.toolPanelLabel {
|
||||
@extend .pl-4;
|
||||
font-size: inherit;
|
||||
div.toolTitle a {
|
||||
@extend .pl-4;
|
||||
font-size: inherit;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@@ -0,0 +1,7 @@
|
||||
<?xml version="1.0"?>
|
||||
<display id="icn3d_simple" version="1.0.0" name="view in iCn3D at">
|
||||
<dynamic_links from_data_table="icn3d_simple_display" skip_startswith="#" id="value" name="name">
|
||||
<url>${ url % { 'icn3d_file_type': $icn3d_file.ext, 'icn3d_file_url_qp': $icn3d_file.qp } }</url>
|
||||
<param type="data" name="icn3d_file" url="galaxy_${DATASET_HASH}.${dataset.ext}" />
|
||||
</dynamic_links>
|
||||
</display>
|
||||
@@ -228,7 +228,7 @@ previous section:
|
||||
```yaml
|
||||
uwsgi:
|
||||
#...
|
||||
socket: unix:///srv/galaxy/var/uwsgi.sock
|
||||
socket: /srv/galaxy/var/uwsgi.sock
|
||||
mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()
|
||||
manage-script-name: true
|
||||
# `module` MUST NOT be set when `mount` is in use
|
||||
|
||||
@@ -220,7 +220,7 @@ previous section:
|
||||
```yaml
|
||||
uwsgi:
|
||||
#...
|
||||
socket: unix:///srv/galaxy/var/uwsgi.sock
|
||||
socket: /srv/galaxy/var/uwsgi.sock
|
||||
mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()
|
||||
manage-script-name: true
|
||||
# `module` MUST NOT be set when `mount` is in use
|
||||
|
||||
@@ -0,0 +1,20 @@
|
||||
galaxy.config package
|
||||
=====================
|
||||
|
||||
.. automodule:: galaxy.config
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.config.script module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.config.script
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
@@ -25,4 +25,12 @@ galaxy.datatypes.util.gff\_util module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.util.maf\_utilities module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.util.maf_utilities
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -14,6 +14,7 @@ Subpackages
|
||||
galaxy.actions
|
||||
galaxy.auth
|
||||
galaxy.authnz
|
||||
galaxy.config
|
||||
galaxy.containers
|
||||
galaxy.datatypes
|
||||
galaxy.dependencies
|
||||
@@ -30,6 +31,7 @@ Subpackages
|
||||
galaxy.openid
|
||||
galaxy.quota
|
||||
galaxy.security
|
||||
galaxy.selenium
|
||||
galaxy.tool_util
|
||||
galaxy.tools
|
||||
galaxy.tours
|
||||
@@ -53,10 +55,10 @@ galaxy.app module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.config module
|
||||
--------------------
|
||||
galaxy.config\_watchers module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.config
|
||||
.. automodule:: galaxy.config_watchers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -0,0 +1,83 @@
|
||||
galaxy.selenium package
|
||||
=======================
|
||||
|
||||
.. automodule:: galaxy.selenium
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
|
||||
galaxy.selenium.scripts
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.selenium.cli module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.cli
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.selenium.components module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.components
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.selenium.data module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.data
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.selenium.driver\_factory module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.driver_factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.selenium.has\_driver module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.has_driver
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.selenium.navigates\_galaxy module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.navigates_galaxy
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.selenium.sizzle module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.sizzle
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.selenium.smart\_components module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.smart_components
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
@@ -0,0 +1,20 @@
|
||||
galaxy.selenium.scripts package
|
||||
===============================
|
||||
|
||||
.. automodule:: galaxy.selenium.scripts
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.selenium.scripts.dump\_tour module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.scripts.dump_tour
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
@@ -0,0 +1,92 @@
|
||||
galaxy.tool\_util.linters package
|
||||
=================================
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tool\_util.linters.citations module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.citations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.command module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.command
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.cwl module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.cwl
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.general module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.general
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.help module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.help
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.inputs module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.inputs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.outputs module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.outputs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.stdio module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.stdio
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.tests module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.tests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.xml\_order module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.xml_order
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
@@ -13,8 +13,10 @@ Subpackages
|
||||
|
||||
galaxy.tool_util.cwl
|
||||
galaxy.tool_util.deps
|
||||
galaxy.tool_util.linters
|
||||
galaxy.tool_util.locations
|
||||
galaxy.tool_util.parser
|
||||
galaxy.tool_util.verify
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -27,6 +29,14 @@ galaxy.tool\_util.fetcher module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.lint module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.lint
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.loader module
|
||||
-------------------------------
|
||||
|
||||
|
||||
@@ -0,0 +1,52 @@
|
||||
galaxy.tool\_util.verify.asserts package
|
||||
========================================
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.asserts
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tool\_util.verify.asserts.archive module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.asserts.archive
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.verify.asserts.hdf5 module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.asserts.hdf5
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.verify.asserts.tabular module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.asserts.tabular
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.verify.asserts.text module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.asserts.text
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.verify.asserts.xml module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.asserts.xml
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
@@ -0,0 +1,43 @@
|
||||
galaxy.tool\_util.verify package
|
||||
================================
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
|
||||
galaxy.tool_util.verify.asserts
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tool\_util.verify.interactor module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.interactor
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.verify.script module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.script
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.verify.test\_data module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.test_data
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
@@ -1,92 +0,0 @@
|
||||
galaxy.tools.linters package
|
||||
============================
|
||||
|
||||
.. automodule:: galaxy.tools.linters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tools.linters.citations module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.citations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.linters.command module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.command
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.linters.cwl module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.cwl
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.linters.general module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.general
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.linters.help module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.help
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.linters.inputs module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.inputs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.linters.outputs module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.outputs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.linters.stdio module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.stdio
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.linters.tests module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.tests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.linters.xml\_order module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.xml_order
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
@@ -18,12 +18,10 @@ Subpackages
|
||||
galaxy.tools.expressions
|
||||
galaxy.tools.filters
|
||||
galaxy.tools.imp_exp
|
||||
galaxy.tools.linters
|
||||
galaxy.tools.parameters
|
||||
galaxy.tools.search
|
||||
galaxy.tools.toolbox
|
||||
galaxy.tools.util
|
||||
galaxy.tools.verify
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -76,22 +74,6 @@ galaxy.tools.execute module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.lint module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.lint
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.lint\_util module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.lint_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.repositories module
|
||||
--------------------------------
|
||||
|
||||
|
||||
@@ -1,52 +0,0 @@
|
||||
galaxy.tools.verify.asserts package
|
||||
===================================
|
||||
|
||||
.. automodule:: galaxy.tools.verify.asserts
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tools.verify.asserts.archive module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.verify.asserts.archive
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.verify.asserts.hdf5 module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.verify.asserts.hdf5
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.verify.asserts.tabular module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.verify.asserts.tabular
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.verify.asserts.text module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.verify.asserts.text
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.verify.asserts.xml module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.verify.asserts.xml
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
@@ -1,43 +0,0 @@
|
||||
galaxy.tools.verify package
|
||||
===========================
|
||||
|
||||
.. automodule:: galaxy.tools.verify
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
|
||||
galaxy.tools.verify.asserts
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tools.verify.interactor module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.verify.interactor
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.verify.script module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.verify.script
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.verify.test\_data module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.verify.test_data
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
@@ -14,6 +14,7 @@ Subpackages
|
||||
galaxy.util.logging
|
||||
galaxy.util.pastescript
|
||||
galaxy.util.path
|
||||
galaxy.util.tool_shed
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
@@ -0,0 +1,36 @@
|
||||
galaxy.util.tool\_shed package
|
||||
==============================
|
||||
|
||||
.. automodule:: galaxy.util.tool_shed
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.util.tool\_shed.common\_util module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.tool_shed.common_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.tool\_shed.encoding\_util module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.tool_shed.encoding_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.tool\_shed.xml\_util module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.tool_shed.xml_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
@@ -1,20 +0,0 @@
|
||||
galaxy.web.base package
|
||||
=======================
|
||||
|
||||
.. automodule:: galaxy.web.base
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.web.base.controller module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.base.controller
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
@@ -11,7 +11,6 @@ Subpackages
|
||||
|
||||
.. toctree::
|
||||
|
||||
galaxy.web.base
|
||||
galaxy.web.framework
|
||||
galaxy.web.proxy
|
||||
|
||||
|
||||
@@ -0,0 +1,20 @@
|
||||
galaxy.webapps.base package
|
||||
===========================
|
||||
|
||||
.. automodule:: galaxy.webapps.base
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.base.controller module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.base.controller
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
@@ -25,12 +25,4 @@ galaxy.webapps.galaxy.buildapp module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.galaxy.config\_watchers module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.config_watchers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -11,6 +11,7 @@ Subpackages
|
||||
|
||||
.. toctree::
|
||||
|
||||
galaxy.webapps.base
|
||||
galaxy.webapps.galaxy
|
||||
galaxy.webapps.reports
|
||||
galaxy.webapps.tool_shed
|
||||
|
||||
@@ -6,6 +6,13 @@ galaxy.webapps.tool\_shed.model.migrate package
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
|
||||
galaxy.webapps.tool_shed.model.migrate.versions
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
|
||||
@@ -0,0 +1,220 @@
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions package
|
||||
========================================================
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0001\_initial\_tables module
|
||||
-----------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0001_initial_tables
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0002\_add\_tool\_suite\_column module
|
||||
--------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0002_add_tool_suite_column
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0003\_review\_and\_review\_association\_tables module
|
||||
------------------------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0003_review_and_review_association_tables
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0004\_repository\_tables module
|
||||
--------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0004_repository_tables
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0005\_drop\_tool\_related\_tables module
|
||||
-----------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0005_drop_tool_related_tables
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0006\_add\_email\_alerts\_column module
|
||||
----------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0006_add_email_alerts_column
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0007\_add\_long\_description\_times\_downloaded\_columns module
|
||||
----------------------------------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0007_add_long_description_times_downloaded_columns
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0008\_add\_repository\_metadata\_table module
|
||||
----------------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0008_add_repository_metadata_table
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0009\_add\_malicious\_column module
|
||||
------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0009_add_malicious_column
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0010\_add\_new\_repo\_alert\_column module
|
||||
-------------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0010_add_new_repo_alert_column
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0011\_add\_tool\_versions\_column module
|
||||
-----------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0011_add_tool_versions_column
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0012\_add\_downloadable\_column module
|
||||
---------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0012_add_downloadable_column
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0013\_add\_review\_tables module
|
||||
---------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0013_add_review_tables
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0014\_add\_deprecated\_column module
|
||||
-------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0014_add_deprecated_column
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0015\_add\_api\_keys\_table module
|
||||
-----------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0015_add_api_keys_table
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0016\_add\_do\_not\_test\_tools\_functionally\_correct\_errors\_columns module
|
||||
-------------------------------------------------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0016_add_do_not_test_tools_functionally_correct_errors_columns
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0017\_add\_galaxy\_utility\_columns\_to\_repository\_metadata\_table module
|
||||
----------------------------------------------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0017_add_galaxy_utility_columns_to_repository_metadata_table
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0018\_add\_repository\_metadata\_flag\_columns module
|
||||
------------------------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0018_add_repository_metadata_flag_columns
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0019\_add\_skip\_tool\_test\_table\_and\_test\_install\_error\_column module
|
||||
-----------------------------------------------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0019_add_skip_tool_test_table_and_test_install_error_column
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0020\_add\_repository\_type\_column module
|
||||
-------------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0020_add_repository_type_column
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0021\_change\_repository\_type\_value module
|
||||
---------------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0021_change_repository_type_value
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0022\_add\_repository\_admin\_roles module
|
||||
-------------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0022_add_repository_admin_roles
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0023\_add\_repository\_url\_and\_hompeage\_url module
|
||||
------------------------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0023_add_repository_url_and_hompeage_url
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0024\_password\_reset module
|
||||
-----------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0024_password_reset
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0025\_session\_timeout module
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0025_session_timeout
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool\_shed.model.migrate.versions.0026\_add\_numeric\_revision\_column module
|
||||
--------------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0026_add_numeric_revision_column
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
@@ -6,6 +6,13 @@ tool\_shed.galaxy\_install.migrate package
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
|
||||
tool_shed.galaxy_install.migrate.versions
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
|
||||
@@ -0,0 +1,108 @@
|
||||
tool\_shed.galaxy\_install.migrate.versions package
|
||||
===================================================
|
||||
|
||||
.. automodule:: tool_shed.galaxy_install.migrate.versions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
tool\_shed.galaxy\_install.migrate.versions.0001\_tools module
|
||||
--------------------------------------------------------------
|
||||
|
||||
.. automodule:: tool_shed.galaxy_install.migrate.versions.0001_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
tool\_shed.galaxy\_install.migrate.versions.0002\_tools module
|
||||
--------------------------------------------------------------
|
||||
|
||||
.. automodule:: tool_shed.galaxy_install.migrate.versions.0002_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
tool\_shed.galaxy\_install.migrate.versions.0003\_tools module
|
||||
--------------------------------------------------------------
|
||||
|
||||
.. automodule:: tool_shed.galaxy_install.migrate.versions.0003_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
tool\_shed.galaxy\_install.migrate.versions.0004\_tools module
|
||||
--------------------------------------------------------------
|
||||
|
||||
.. automodule:: tool_shed.galaxy_install.migrate.versions.0004_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
tool\_shed.galaxy\_install.migrate.versions.0005\_tools module
|
||||
--------------------------------------------------------------
|
||||
|
||||
.. automodule:: tool_shed.galaxy_install.migrate.versions.0005_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
tool\_shed.galaxy\_install.migrate.versions.0006\_tools module
|
||||
--------------------------------------------------------------
|
||||
|
||||
.. automodule:: tool_shed.galaxy_install.migrate.versions.0006_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
tool\_shed.galaxy\_install.migrate.versions.0007\_tools module
|
||||
--------------------------------------------------------------
|
||||
|
||||
.. automodule:: tool_shed.galaxy_install.migrate.versions.0007_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
tool\_shed.galaxy\_install.migrate.versions.0008\_tools module
|
||||
--------------------------------------------------------------
|
||||
|
||||
.. automodule:: tool_shed.galaxy_install.migrate.versions.0008_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
tool\_shed.galaxy\_install.migrate.versions.0009\_tools module
|
||||
--------------------------------------------------------------
|
||||
|
||||
.. automodule:: tool_shed.galaxy_install.migrate.versions.0009_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
tool\_shed.galaxy\_install.migrate.versions.0010\_tools module
|
||||
--------------------------------------------------------------
|
||||
|
||||
.. automodule:: tool_shed.galaxy_install.migrate.versions.0010_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
tool\_shed.galaxy\_install.migrate.versions.0011\_tools module
|
||||
--------------------------------------------------------------
|
||||
|
||||
.. automodule:: tool_shed.galaxy_install.migrate.versions.0011_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
tool\_shed.galaxy\_install.migrate.versions.0012\_tools module
|
||||
--------------------------------------------------------------
|
||||
|
||||
.. automodule:: tool_shed.galaxy_install.migrate.versions.0012_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
+4
-2
@@ -23,6 +23,7 @@ from galaxy.model.database_heartbeat import DatabaseHeartbeat
|
||||
from galaxy.model.tags import GalaxyTagHandler
|
||||
from galaxy.queue_worker import GalaxyQueueWorker
|
||||
from galaxy.tool_util.deps.views import DependencyResolversView
|
||||
from galaxy.tool_util.verify import test_data
|
||||
from galaxy.tools.cache import (
|
||||
ToolCache,
|
||||
ToolShedRepositoryCache
|
||||
@@ -30,7 +31,6 @@ from galaxy.tools.cache import (
|
||||
from galaxy.tools.data_manager.manager import DataManagers
|
||||
from galaxy.tools.error_reports import ErrorReports
|
||||
from galaxy.tools.special_tools import load_lib_tools
|
||||
from galaxy.tools.verify import test_data
|
||||
from galaxy.tours import ToursRegistry
|
||||
from galaxy.util import (
|
||||
ExecutionTimer,
|
||||
@@ -184,7 +184,9 @@ class UniverseApplication(config.ConfiguresGalaxyMixin):
|
||||
|
||||
if self.config.enable_oidc:
|
||||
from galaxy.authnz import managers
|
||||
self.authnz_manager = managers.AuthnzManager(self, self.config.oidc_config, self.config.oidc_backends_config)
|
||||
self.authnz_manager = managers.AuthnzManager(self,
|
||||
self.config.oidc_config,
|
||||
self.config.oidc_backends_config)
|
||||
|
||||
self.sentry_client = None
|
||||
if self.config.sentry_dsn:
|
||||
|
||||
@@ -304,10 +304,14 @@ class AuthnzManager(object):
|
||||
ca = CloudAuthz()
|
||||
log.info("Requesting credentials using CloudAuthz with config id `{}` on be half of user `{}`.".format(
|
||||
cloudauthz.id, user_id))
|
||||
return ca.authorize(cloudauthz.provider, config)
|
||||
credentials = ca.authorize(cloudauthz.provider, config)
|
||||
return credentials
|
||||
except CloudAuthzBaseException as e:
|
||||
log.info(e)
|
||||
raise exceptions.AuthenticationFailed(e)
|
||||
except NotImplementedError as e:
|
||||
log.info(e)
|
||||
raise exceptions.RequestParameterInvalidException(e)
|
||||
|
||||
def get_cloud_access_credentials_in_file(self, new_file_path, cloudauthz, sa_session, user_id, request=None):
|
||||
"""
|
||||
|
||||
@@ -100,7 +100,7 @@ def resolve_path(path, root):
|
||||
|
||||
|
||||
def find_root(kwargs):
|
||||
root = kwargs.get('root_dir', '.')
|
||||
root = os.path.abspath(kwargs.get('root_dir', '.'))
|
||||
return root
|
||||
|
||||
|
||||
@@ -556,9 +556,10 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
|
||||
|
||||
involucro_path = kwargs.get('involucro_path', None)
|
||||
if involucro_path is None:
|
||||
target_dir = resolve_path(kwargs.get("tool_dependency_dir", "dependencies"), self.data_dir)
|
||||
target_dir = kwargs.get("tool_dependency_dir", "dependencies")
|
||||
if target_dir == "none":
|
||||
target_dir = "database"
|
||||
target_dir = "dependencies"
|
||||
target_dir = resolve_path(target_dir, self.data_dir)
|
||||
involucro_path = os.path.join(target_dir, "involucro")
|
||||
self.involucro_path = resolve_path(involucro_path, self.root)
|
||||
self.involucro_auto_init = string_as_bool(kwargs.get('involucro_auto_init', True))
|
||||
|
||||
@@ -593,6 +593,7 @@
|
||||
<converter file="sdf_to_inchi_converter.xml" target_datatype="inchi"/>
|
||||
<converter file="sdf_to_mol2_converter.xml" target_datatype="mol2"/>
|
||||
<converter file="sdf_to_cml_converter.xml" target_datatype="cml"/>
|
||||
<display file="icn3d/icn3d_simple.xml"/>
|
||||
</datatype>
|
||||
<datatype extension="inchi" type="galaxy.datatypes.molecules:InChI" display_in_upload="true">
|
||||
<converter file="inchi_to_smi_converter.xml" target_datatype="smi"/>
|
||||
@@ -613,6 +614,7 @@
|
||||
<converter file="mol2_to_inchi_converter.xml" target_datatype="inchi"/>
|
||||
<converter file="mol2_to_mol_converter.xml" target_datatype="mol"/>
|
||||
<converter file="mol2_to_cml_converter.xml" target_datatype="cml"/>
|
||||
<display file="icn3d/icn3d_simple.xml"/>
|
||||
</datatype>
|
||||
<datatype extension="cml" type="galaxy.datatypes.molecules:CML" display_in_upload="true">
|
||||
<converter file="cml_to_smi_converter.xml" target_datatype="smi"/>
|
||||
@@ -624,7 +626,9 @@
|
||||
<datatype extension="obfs" type="galaxy.datatypes.molecules:OBFS" mimetype="text/html" display_in_upload="true"/>
|
||||
<datatype extension="drf" type="galaxy.datatypes.molecules:DRF" display_in_upload="true"/>
|
||||
<datatype extension="phar" type="galaxy.datatypes.molecules:PHAR" display_in_upload="false"/>
|
||||
<datatype extension="pdb" type="galaxy.datatypes.molecules:PDB" display_in_upload="true"/>
|
||||
<datatype extension="pdb" type="galaxy.datatypes.molecules:PDB" display_in_upload="true">
|
||||
<display file="icn3d/icn3d_simple.xml"/>
|
||||
</datatype>
|
||||
<datatype extension="pdbqt" type="galaxy.datatypes.molecules:PDBQT" display_in_upload="true"/>
|
||||
<datatype extension="pqr" type="galaxy.datatypes.molecules:PQR" display_in_upload="true" />
|
||||
<datatype extension="trr" type="galaxy.datatypes.binary:Trr" display_in_upload="true"/>
|
||||
|
||||
@@ -216,6 +216,11 @@
|
||||
zero (no execution) and the stderr/stdout of the k8s job is reported in galaxy (and the galaxy job set
|
||||
to failed) -->
|
||||
|
||||
<!-- <param id="k8s_walltime_limit">172800</param> -->
|
||||
<!-- Controls the maximum time before kubernetes terminates the job. Sets activeDeadlineSeconds
|
||||
in the kubernetes job spec. Once a Job reaches activeDeadlineSeconds, all of its running Pods are
|
||||
terminated and the Job status will become `type: Failed` with `reason: DeadlineExceeded`. -->
|
||||
|
||||
<!-- <param id="k8s_galaxy_instance_id">my-instance</param> -->
|
||||
<!-- Identifies the Galaxy instance where this runner belongs. Setting this variable means that the runner
|
||||
will trust k8s Jobs with the structure galaxy-my-instance-<number> to be its own. This variable needs
|
||||
|
||||
@@ -105,4 +105,9 @@
|
||||
<columns>value, name, url</columns>
|
||||
<file path="tool-data/intermine_simple_display.loc" />
|
||||
</table>
|
||||
<!-- simple iCn3D Structure Viewer servers -->
|
||||
<table name="icn3d_simple_display" comment_char="#" allow_duplicate_entries="False">
|
||||
<columns>value, name, url</columns>
|
||||
<file path="tool-data/icn3d_simple_display.loc" />
|
||||
</table>
|
||||
</tables>
|
||||
|
||||
@@ -694,13 +694,16 @@ class BaseFastq(Sequence):
|
||||
>>> fname = get_test_fname('1.fastqsanger')
|
||||
>>> FastqSanger().sniff(fname)
|
||||
True
|
||||
>>> fname = get_test_fname('4.fastqsanger')
|
||||
>>> FastqSanger().sniff(fname)
|
||||
True
|
||||
>>> fname = get_test_fname('3.fastq')
|
||||
>>> FastqSanger().sniff(fname)
|
||||
False
|
||||
>>> Fastq().sniff(fname)
|
||||
True
|
||||
>>> fname = get_test_fname('2.fastq')
|
||||
>>> Fastq().sniff( fname )
|
||||
>>> Fastq().sniff(fname)
|
||||
True
|
||||
>>> FastqSanger().sniff(fname)
|
||||
False
|
||||
@@ -819,7 +822,7 @@ class FastqSanger(Fastq):
|
||||
def quality_check(lines):
|
||||
"""Presuming lines are lines from a fastq file, return True if the qualities are compatible with sanger encoding"""
|
||||
for line in islice(lines, 3, None, 4):
|
||||
if not all(_ >= '!' and _ <= 'M' for _ in line[0]) or ' ' in line:
|
||||
if not all(_ >= '!' and _ <= 'S' for _ in line[0]):
|
||||
return False
|
||||
return True
|
||||
|
||||
|
||||
Binary file not shown.
@@ -0,0 +1,8 @@
|
||||
@DCW97JN1:309:C0C42ACXX:4:2206:12976:57510/1
|
||||
AAATGGGCATAATATAGATGTAGAGATGTGTTGAATTTATGACTCATTT
|
||||
+
|
||||
ADECJJJJDCCECCCCMCCNCCMCNBCLBJBCLADCDC=CNDJILEDDD
|
||||
@DCW97JN1:309:C0C42ACXX:4:2211:6915:3569/1
|
||||
AAAGAAATTAAATGGGCATAATATAGATGTAGAGATGTGTTGAATTTAT
|
||||
+
|
||||
@DEJAAA?B@ECCEFFGDBBFC8ABGCBK=BI=66@HE@@JACCCDCCI
|
||||
@@ -68,7 +68,7 @@ bioblend = "*"
|
||||
boto = "*"
|
||||
kombu = "*"
|
||||
psutil = "*"
|
||||
pulsar-galaxy-lib = "*"
|
||||
pulsar-galaxy-lib = "==0.12.1"
|
||||
sqlalchemy-migrate = "*"
|
||||
sqlparse = "*"
|
||||
svgwrite = "*"
|
||||
@@ -77,7 +77,7 @@ pyparsing = "*"
|
||||
paramiko = "*"
|
||||
python-genomespaceclient = "<2.0"
|
||||
social_auth_core = {version = "==3.1.0+gx0", extras = ['openidconnect']}
|
||||
cloudauthz = "<=0.4.0"
|
||||
cloudauthz = "==0.6.0"
|
||||
gxformat2 = "*"
|
||||
|
||||
[requires]
|
||||
|
||||
@@ -38,11 +38,11 @@ pygithub3==0.5.1 ; python_version < '3'
|
||||
pygments==2.4.2
|
||||
pyparsing==2.4.0
|
||||
pytest-cov==2.7.1
|
||||
pytest-html==1.20.0
|
||||
pytest-html==1.21.1
|
||||
pytest-metadata==1.8.0
|
||||
pytest-postgresql==1.4.1
|
||||
pytest-pythonpath==0.7.3
|
||||
pytest==4.6.3
|
||||
pytest==4.6.4
|
||||
pytz==2019.1
|
||||
pyyaml==5.1.1
|
||||
recommonmark==0.5.0
|
||||
@@ -50,14 +50,14 @@ requests==2.22.0
|
||||
scandir==1.10.0 ; python_version < '3.5'
|
||||
selenium==3.141.0
|
||||
six==1.11.0
|
||||
snowballstemmer==1.2.1
|
||||
snowballstemmer==1.9.0
|
||||
sphinx-markdown-tables==0.0.9
|
||||
sphinx-rtd-theme==0.4.3
|
||||
sphinx==1.8.5
|
||||
sphinxcontrib-websupport==1.1.2
|
||||
testfixtures==6.9.0
|
||||
testfixtures==6.10.0
|
||||
twill==0.9.1 ; python_version < '3'
|
||||
typing==3.6.6 ; python_version < '3.5'
|
||||
typing==3.7.4 ; python_version < '3.5'
|
||||
urllib3==1.25.3 ; python_version == '2.7'
|
||||
watchdog==0.9.0
|
||||
wcwidth==0.1.7 ; sys_platform != 'win32'
|
||||
|
||||
@@ -21,7 +21,7 @@ azure-storage-common==1.4.2
|
||||
azure-storage-nspkg==3.1.0
|
||||
babel==2.7.0
|
||||
bagit==1.6.4
|
||||
bcrypt==3.1.6
|
||||
bcrypt==3.1.7
|
||||
bdbag==1.4.1
|
||||
beaker==1.10.1
|
||||
bioblend==0.12.0
|
||||
@@ -29,8 +29,8 @@ bleach==3.1.0
|
||||
boltons==19.1.0
|
||||
boto3==1.9.114
|
||||
boto==2.49.0
|
||||
botocore==1.12.169
|
||||
bx-python==0.8.2
|
||||
botocore==1.12.180
|
||||
bx-python==0.8.4
|
||||
bz2file==0.98 ; python_version < '3.3'
|
||||
cachecontrol==0.11.7
|
||||
cachetools==3.1.1
|
||||
@@ -39,7 +39,7 @@ cffi==1.12.3
|
||||
chardet==3.0.4
|
||||
cheetah3==3.2.3
|
||||
cliff==2.15.0
|
||||
cloudauthz==0.4.0
|
||||
cloudauthz==0.6.0
|
||||
cloudbridge==2.0.0
|
||||
cmd2==0.8.9
|
||||
contextlib2==0.5.5 ; python_version < '3.5'
|
||||
@@ -64,7 +64,7 @@ galaxy-sequence-utils==1.1.3
|
||||
google-api-python-client==1.7.8
|
||||
google-auth-httplib2==0.0.3
|
||||
google-auth==1.6.3
|
||||
gxformat2==0.8.3
|
||||
gxformat2==0.8.4
|
||||
h5py==2.9.0
|
||||
httplib2==0.13.0
|
||||
idna==2.8
|
||||
@@ -101,7 +101,7 @@ oauthlib==3.0.1
|
||||
openstacksdk==0.17.0
|
||||
os-client-config==1.32.0
|
||||
os-service-types==1.7.0
|
||||
osc-lib==1.12.1
|
||||
osc-lib==1.13.0
|
||||
oslo.config==6.10.0
|
||||
oslo.context==2.22.1
|
||||
oslo.i18n==3.23.1
|
||||
@@ -109,13 +109,13 @@ oslo.log==3.44.0
|
||||
oslo.serialization==2.29.1
|
||||
oslo.utils==3.41.0
|
||||
packaging==19.0
|
||||
paramiko==2.5.0
|
||||
paramiko==2.6.0
|
||||
parsley==1.3
|
||||
paste==3.0.8
|
||||
pastedeploy==2.0.1
|
||||
pastescript==3.1.0
|
||||
pathlib2==2.3.2 ; python_version < '3'
|
||||
pbr==5.3.0
|
||||
pbr==5.3.1
|
||||
prettytable==0.7.2
|
||||
prov==1.5.1
|
||||
psutil==5.6.3
|
||||
@@ -168,15 +168,15 @@ six==1.11.0
|
||||
social-auth-core[openidconnect]==3.1.0+gx0
|
||||
sqlalchemy-migrate==0.12.0
|
||||
sqlalchemy-utils==0.34.0
|
||||
sqlalchemy==1.3.4
|
||||
sqlalchemy==1.3.5
|
||||
sqlparse==0.3.0
|
||||
stevedore==1.30.1
|
||||
subprocess32==3.5.4 ; python_version < '3.0'
|
||||
svgwrite==1.2.1
|
||||
svgwrite==1.3.1
|
||||
tempita==0.5.2
|
||||
tenacity==4.12.0
|
||||
typing-extensions==3.7.2
|
||||
typing==3.6.6 ; python_version < '3.5'
|
||||
typing-extensions==3.7.4
|
||||
typing==3.7.4 ; python_version < '3.5'
|
||||
tzlocal==1.5.1
|
||||
unicodecsv==0.14.1 ; python_version < '3.0'
|
||||
uritemplate==3.0.0
|
||||
@@ -188,4 +188,4 @@ wcwidth==0.1.7 ; sys_platform != 'win32'
|
||||
webencodings==0.5.1
|
||||
webob==1.8.5
|
||||
whoosh==2.7.4
|
||||
wrapt==1.11.1
|
||||
wrapt==1.11.2
|
||||
|
||||
@@ -8,4 +8,4 @@ functools32==3.2.3.post2 ; python_version < '3.2'
|
||||
mccabe==0.6.1
|
||||
pycodestyle==2.5.0
|
||||
pyflakes==2.1.1
|
||||
typing==3.6.6 ; python_version < '3.5'
|
||||
typing==3.7.4 ; python_version < '3.5'
|
||||
|
||||
@@ -58,7 +58,8 @@ class KubernetesJobRunner(AsynchronousJobRunner):
|
||||
k8s_default_limits_cpu=dict(map=str, default=None),
|
||||
k8s_default_limits_memory=dict(map=str, default=None),
|
||||
k8s_pod_retries=dict(map=int, valid=lambda x: int >= 0, default=3),
|
||||
k8s_pod_retrials=dict(map=int, valid=lambda x: int >= 0, default=3))
|
||||
k8s_pod_retrials=dict(map=int, valid=lambda x: int >= 0, default=3),
|
||||
k8s_walltime_limit=dict(map=int, valid=lambda x: int(x) >= 0, default=172800))
|
||||
|
||||
if 'runner_param_specs' not in kwargs:
|
||||
kwargs['runner_param_specs'] = dict()
|
||||
@@ -220,8 +221,10 @@ class KubernetesJobRunner(AsynchronousJobRunner):
|
||||
return produce_unique_k8s_job_name(app_prefix='galaxy', instance_id=instance_id, job_id=galaxy_internal_job_id)
|
||||
|
||||
def __get_k8s_job_spec(self, ajs):
|
||||
"""Creates the k8s Job spec. For a Job spec, the only requirement is to have a .spec.template."""
|
||||
k8s_job_spec = {"template": self.__get_k8s_job_spec_template(ajs)}
|
||||
"""Creates the k8s Job spec. For a Job spec, the only requirement is to have a .spec.template.
|
||||
If the job hangs around unlimited it will be ended after k8s wall time limit, which sets activeDeadlineSeconds"""
|
||||
k8s_job_spec = {"template": self.__get_k8s_job_spec_template(ajs),
|
||||
"activeDeadlineSeconds": int(self.runner_params['k8s_walltime_limit'])}
|
||||
return k8s_job_spec
|
||||
|
||||
def __get_k8s_job_spec_template(self, ajs):
|
||||
@@ -427,23 +430,18 @@ class KubernetesJobRunner(AsynchronousJobRunner):
|
||||
job_state.running = False
|
||||
self.mark_as_finished(job_state)
|
||||
return None
|
||||
elif failed > 0 and self.__job_failed_due_to_low_memory(job_state):
|
||||
return self._handle_job_failure(job, job_state, reason="OOM")
|
||||
elif active > 0 and failed <= max_pod_retries:
|
||||
if not job_state.running:
|
||||
job_state.running = True
|
||||
job_state.job_wrapper.change_state(model.Job.states.RUNNING)
|
||||
return job_state
|
||||
elif failed > max_pod_retries:
|
||||
return self._handle_job_failure(job, job_state)
|
||||
elif job_state.job_wrapper.get_job().state == model.Job.states.DELETED:
|
||||
# Job has been deleted via stop_job, cleanup and remove from watched_jobs by returning `None`
|
||||
if job_state.job_wrapper.cleanup_job in ("always", "onsuccess"):
|
||||
job_state.job_wrapper.cleanup()
|
||||
return None
|
||||
else:
|
||||
# We really shouldn't reach this point, but we might if the job has been killed by the kubernetes admin
|
||||
log.info("Kubernetes job '%s' not classified as succ., active or failed. Full Job object: \n%s", job.name, job.obj)
|
||||
return self._handle_job_failure(job, job_state)
|
||||
|
||||
elif len(jobs.response['items']) == 0:
|
||||
# there is no job responding to this job_id, it is either lost or something happened.
|
||||
@@ -460,12 +458,17 @@ class KubernetesJobRunner(AsynchronousJobRunner):
|
||||
self.mark_as_failed(job_state)
|
||||
return job_state
|
||||
|
||||
def _handle_job_failure(self, job, job_state, reason=None):
|
||||
def _handle_job_failure(self, job, job_state):
|
||||
# Figure out why job has failed
|
||||
with open(job_state.error_file, 'a') as error_file:
|
||||
if reason == "OOM":
|
||||
if self.__job_failed_due_to_low_memory(job_state):
|
||||
error_file.write("Job killed after running out of memory. Try with more memory.\n")
|
||||
job_state.fail_message = "Tool failed due to insufficient memory. Try with more memory."
|
||||
job_state.runner_state = JobState.runner_states.MEMORY_LIMIT_REACHED
|
||||
elif self.__job_failed_due_to_walltime_limit(job):
|
||||
error_file.write("DeadlineExceeded")
|
||||
job_state.fail_message = "Job was active longer than specified deadline"
|
||||
job_state.runner_state = JobState.runner_states.WALLTIME_REACHED
|
||||
else:
|
||||
error_file.write("Exceeded max number of Kubernetes pod retrials allowed for job\n")
|
||||
job_state.fail_message = "More pods failed than allowed. See stdout for pods details."
|
||||
@@ -474,6 +477,10 @@ class KubernetesJobRunner(AsynchronousJobRunner):
|
||||
job.scale(replicas=0)
|
||||
return None
|
||||
|
||||
def __job_failed_due_to_walltime_limit(self, job):
|
||||
conditions = job.obj['status']['conditions']
|
||||
return any(True for c in conditions if c['type'] == 'Failed' and c['reason'] == 'DeadlineExceeded')
|
||||
|
||||
def __job_failed_due_to_low_memory(self, job_state):
|
||||
"""
|
||||
checks the state of the pod to see if it was killed
|
||||
@@ -483,8 +490,10 @@ class KubernetesJobRunner(AsynchronousJobRunner):
|
||||
|
||||
pods = Pod.objects(self._pykube_api).filter(selector="app=%s" % job_state.job_id,
|
||||
namespace=self.runner_params['k8s_namespace'])
|
||||
pod = Pod(self._pykube_api, pods.response['items'][0])
|
||||
if not pods.response['items']:
|
||||
return False
|
||||
|
||||
pod = Pod(self._pykube_api, pods.response['items'][0])
|
||||
if pod.obj['status']['phase'] == "Failed" and \
|
||||
pod.obj['status']['containerStatuses'][0]['state']['terminated']['reason'] == "OOMKilled":
|
||||
return True
|
||||
|
||||
@@ -147,6 +147,9 @@ class CloudManager(sharable.SharableModelManager):
|
||||
'os_project_domain_name': prj_domain_name,
|
||||
'os_user_domain_name': user_domain_name}
|
||||
connection = CloudProviderFactory().create_provider(ProviderList.OPENSTACK, config)
|
||||
elif provider == "gcp":
|
||||
config = {"gcp_service_creds_dict": credentials}
|
||||
connection = CloudProviderFactory().create_provider(ProviderList.GCP, config)
|
||||
else:
|
||||
raise RequestParameterInvalidException("Unrecognized provider '{}'; the following are the supported "
|
||||
"providers: {}.".format(provider, SUPPORTED_PROVIDERS.keys()))
|
||||
@@ -340,8 +343,8 @@ class CloudManager(sharable.SharableModelManager):
|
||||
try:
|
||||
object_label = hda.name.replace(" ", "_")
|
||||
args = {
|
||||
# We encode ID here because it the tool wrapper assumes
|
||||
# it receives an encoded ID and attempts decoding it.
|
||||
# We encode ID here because the tool wrapper expects
|
||||
# an encoded ID and attempts decoding it.
|
||||
"authz_id": trans.security.encode_id(cloudauthz.id),
|
||||
"bucket": bucket_name,
|
||||
"object_label": object_label,
|
||||
|
||||
@@ -78,6 +78,23 @@ class FolderManager(object):
|
||||
folder = self.check_accessible(trans, folder)
|
||||
return folder
|
||||
|
||||
def check_modifyable(self, trans, folder):
|
||||
"""
|
||||
Check whether the user can modify the folder (name and description).
|
||||
|
||||
:returns: the original folder
|
||||
:rtype: LibraryFolder
|
||||
|
||||
:raises: AuthenticationRequired, InsufficientPermissionsException
|
||||
"""
|
||||
if not trans.user:
|
||||
raise AuthenticationRequired("Must be logged in to manage Galaxy items.", type='error')
|
||||
current_user_roles = trans.get_current_user_roles()
|
||||
if not trans.app.security_agent.can_modify_library_item(current_user_roles, folder):
|
||||
raise InsufficientPermissionsException("You don't have permissions to modify this folder.", type='error')
|
||||
else:
|
||||
return folder
|
||||
|
||||
def check_manageable(self, trans, folder):
|
||||
"""
|
||||
Check whether the user can manage the folder.
|
||||
@@ -171,8 +188,7 @@ class FolderManager(object):
|
||||
"""
|
||||
changed = False
|
||||
if not trans.user_is_admin:
|
||||
if not self.check_manageable(trans, folder):
|
||||
raise InsufficientPermissionsException("You do not have proper permission to update the library folder.")
|
||||
folder = self.check_modifyable(trans, folder)
|
||||
if folder.deleted is True:
|
||||
raise ItemAccessibilityException("You cannot update a deleted library folder. Undelete it first.")
|
||||
if name is not None and name != folder.name:
|
||||
|
||||
@@ -98,7 +98,7 @@ class SelectorTemplate(Target):
|
||||
if name in self._children:
|
||||
return self._children[name](**{"_": self.selector})
|
||||
else:
|
||||
raise KeyError("Could not find child [%s] in %s" % (name, self._children))
|
||||
raise AttributeError("Could not find child [%s] in %s" % (name, self._children))
|
||||
|
||||
__getitem__ = __getattr__
|
||||
|
||||
@@ -193,7 +193,7 @@ class Component(object):
|
||||
elif attr in self._text:
|
||||
return self._text[attr]
|
||||
else:
|
||||
raise Exception("Failed to find referenced sub-component/selector/label/text [%s]" % attr)
|
||||
raise AttributeError("Failed to find referenced sub-component/selector/label/text [%s]" % attr)
|
||||
|
||||
__getitem__ = __getattr__
|
||||
|
||||
@@ -5,9 +5,7 @@ import os
|
||||
import sys
|
||||
import time
|
||||
|
||||
sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'test')))
|
||||
|
||||
from galaxy_selenium import cli
|
||||
from galaxy.selenium import cli
|
||||
|
||||
DESCRIPTION = "Walk a Galaxy tour and dump screenshots."
|
||||
|
||||
@@ -8,7 +8,7 @@ class SmartComponent(object):
|
||||
"""Wrap a Component with driver aware methods.
|
||||
|
||||
Allows smarter selectors that know how to wait for themselves, test themselves,
|
||||
click themselvers, etc.... More "magic", but much cleaner usage.
|
||||
click themselves, etc.... More "magic", but much cleaner usage.
|
||||
"""
|
||||
|
||||
def __init__(self, component, has_driver):
|
||||
+1
-1
@@ -14,7 +14,7 @@ assertion_module_names = ['text', 'tabular', 'xml', 'hdf5', 'archive']
|
||||
# <MODULE_NAME> to the list of assertion module names defined above.
|
||||
assertion_modules = []
|
||||
for assertion_module_name in assertion_module_names:
|
||||
full_assertion_module_name = 'galaxy.tools.verify.asserts.' + assertion_module_name
|
||||
full_assertion_module_name = 'galaxy.tool_util.verify.asserts.' + assertion_module_name
|
||||
try:
|
||||
# Dynamically import module
|
||||
__import__(full_assertion_module_name)
|
||||
@@ -5,7 +5,10 @@ import argparse
|
||||
import json
|
||||
import sys
|
||||
|
||||
from galaxy.tools.verify.interactor import GalaxyInteractorApi, verify_tool
|
||||
from .interactor import (
|
||||
GalaxyInteractorApi,
|
||||
verify_tool,
|
||||
)
|
||||
|
||||
DESCRIPTION = """Script to quickly run a tool test against a running Galaxy instance."""
|
||||
ALL_TESTS = "*all_tests*"
|
||||
@@ -1631,7 +1631,7 @@ many of the default assertion tags that come with Galaxy and examples of each
|
||||
can be found below.
|
||||
|
||||
The implementation of these tags are simply Python functions defined in the
|
||||
[/lib/galaxy/tools/verify/asserts](https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/tools/verify/asserts)
|
||||
[/lib/galaxy/tool_util/verify/asserts](https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/tool_util/verify/asserts)
|
||||
module.
|
||||
]]>
|
||||
</xs:documentation>
|
||||
|
||||
@@ -14,6 +14,8 @@
|
||||
<option value="numeric">numerically (strips all characters except numbers)</option>
|
||||
<option value="file">Sort collection using order of identifiers in text file</option>
|
||||
</param>
|
||||
<when value="alpha" />
|
||||
<when value="numeric" />
|
||||
<when value="file">
|
||||
<param name="sort_file" type="data" format="txt" label="Select file that contains the new order of collection elements" help="Lines in text file must match collection"></param>
|
||||
</when>
|
||||
|
||||
@@ -6,7 +6,7 @@ from six import string_types
|
||||
|
||||
import galaxy.tools.parameters.basic
|
||||
import galaxy.tools.parameters.grouping
|
||||
from galaxy.tools.verify.interactor import ToolTestDescription
|
||||
from galaxy.tool_util.verify.interactor import ToolTestDescription
|
||||
from galaxy.util import (
|
||||
string_as_bool,
|
||||
unicodify,
|
||||
|
||||
@@ -1685,14 +1685,14 @@ def download_to_file(url, dest_file_path, timeout=30, chunk_size=2 ** 20):
|
||||
f.write(chunk)
|
||||
|
||||
|
||||
def _executable():
|
||||
def get_executable():
|
||||
exe = sys.executable
|
||||
if exe.endswith('uwsgi'):
|
||||
virtualenv = None
|
||||
if uwsgi is not None:
|
||||
for name in ('home', 'virtualenv', 'venv', 'pyhome'):
|
||||
if name in uwsgi.opt:
|
||||
virtualenv = uwsgi.opt[name]
|
||||
virtualenv = unicodify(uwsgi.opt[name])
|
||||
break
|
||||
if virtualenv is None and 'VIRTUAL_ENV' in os.environ:
|
||||
virtualenv = os.environ['VIRTUAL_ENV']
|
||||
@@ -1705,9 +1705,6 @@ def _executable():
|
||||
return exe
|
||||
|
||||
|
||||
executable = _executable()
|
||||
|
||||
|
||||
class ExecutionTimer(object):
|
||||
|
||||
def __init__(self):
|
||||
|
||||
@@ -47,8 +47,13 @@ def get_fileobj_raw(filename, mode="r", compressed_formats=None):
|
||||
compressed_format = 'bz2'
|
||||
elif 'zip' in compressed_formats and zipfile.is_zipfile(filename):
|
||||
# Return fileobj for the first file in a zip file.
|
||||
with zipfile.ZipFile(filename, mode) as zh:
|
||||
fh = zh.open(zh.namelist()[0], mode)
|
||||
# 'b' is not allowed in the ZipFile mode argument
|
||||
# since it always opens files in binary mode.
|
||||
# For emulating text mode, we will be returning the binary fh in a
|
||||
# TextIOWrapper.
|
||||
zf_mode = mode.replace('b', '')
|
||||
with zipfile.ZipFile(filename, zf_mode) as zh:
|
||||
fh = zh.open(zh.namelist()[0], zf_mode)
|
||||
compressed_format = 'zip'
|
||||
elif 'b' in mode:
|
||||
return compressed_format, open(filename, mode)
|
||||
|
||||
@@ -777,6 +777,27 @@ class DeletedColumn(GridColumn):
|
||||
return query
|
||||
|
||||
|
||||
class PurgedColumn(GridColumn):
|
||||
""" Column that tracks and filters for items with purged attribute. """
|
||||
|
||||
def get_accepted_filters(self):
|
||||
""" Returns a list of accepted filters for this column. """
|
||||
accepted_filter_labels_and_vals = {"nonpurged" : "False", "purged" : "True", "all": "All"}
|
||||
accepted_filters = []
|
||||
for label, val in accepted_filter_labels_and_vals.items():
|
||||
args = {self.key: val}
|
||||
accepted_filters.append(GridColumnFilter(label, args))
|
||||
return accepted_filters
|
||||
|
||||
def filter(self, trans, user, query, column_filter):
|
||||
"""Modify query to filter self.model_class by state."""
|
||||
if column_filter == "All":
|
||||
pass
|
||||
elif column_filter in ["True", "False"]:
|
||||
query = query.filter(self.model_class.purged == (column_filter == "True"))
|
||||
return query
|
||||
|
||||
|
||||
class StateColumn(GridColumn):
|
||||
"""
|
||||
Column that tracks and filters for items with state attribute.
|
||||
|
||||
@@ -130,7 +130,8 @@ class UserListGrid(grids.Grid):
|
||||
ActivatedColumn("Activated", attach_popup=False),
|
||||
APIKeyColumn("API Key", attach_popup=False),
|
||||
# Columns that are valid for filtering but are not visible.
|
||||
grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced")
|
||||
grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
|
||||
grids.PurgedColumn("Purged", key="purged", visible=False, filterable="advanced")
|
||||
]
|
||||
columns.append(grids.MulticolFilterColumn("Search",
|
||||
cols_to_filter=[columns[0], columns[1]],
|
||||
@@ -170,6 +171,8 @@ class UserListGrid(grids.Grid):
|
||||
]
|
||||
num_rows_per_page = 50
|
||||
use_paging = True
|
||||
default_filter = dict(purged="False")
|
||||
use_default_filter = True
|
||||
|
||||
def get_current_item(self, trans, **kwargs):
|
||||
return trans.user
|
||||
|
||||
@@ -159,18 +159,6 @@ class AdminToolshed(AdminGalaxy):
|
||||
message=message,
|
||||
status=status)
|
||||
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def browse_toolsheds(self, trans, **kwd):
|
||||
app = {
|
||||
'jscript': "adminToolshed"
|
||||
}
|
||||
return trans.fill_template('galaxy.panels.mako',
|
||||
config={
|
||||
'title': 'Galaxy Tool Sheds',
|
||||
'app': app,
|
||||
'bundle': 'extended'})
|
||||
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def check_for_updates(self, trans, **kwd):
|
||||
|
||||
@@ -6,7 +6,7 @@ import sys
|
||||
from migrate.versioning import repository, schema
|
||||
from sqlalchemy import create_engine, MetaData, Table
|
||||
|
||||
from galaxy.util import executable
|
||||
from galaxy.util import get_executable
|
||||
from galaxy.util.odict import odict
|
||||
from tool_shed.util import common_util
|
||||
|
||||
@@ -57,7 +57,7 @@ def verify_tools(app, url, galaxy_config_file=None, engine_options={}):
|
||||
if tool_shed_accessible:
|
||||
# Automatically update the value of the migrate_tools.version database table column.
|
||||
manage_tools = os.path.abspath(os.path.join(os.path.dirname(__file__), 'scripts', 'manage_tools.py'))
|
||||
cmd = [executable, manage_tools, 'upgrade', 'tools']
|
||||
cmd = [get_executable(), manage_tools, 'upgrade', 'tools']
|
||||
if galaxy_config_file:
|
||||
cmd[2:2] = ['-c', galaxy_config_file]
|
||||
proc = subprocess.Popen(args=cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
|
||||
|
||||
Symlink
+1
@@ -0,0 +1 @@
|
||||
../../../lib/galaxy/config
|
||||
@@ -1 +0,0 @@
|
||||
../../../lib/galaxy/config.py
|
||||
@@ -63,8 +63,6 @@ PACKAGES = [
|
||||
'galaxy.tools.toolbox.lineages',
|
||||
'galaxy.tools.util',
|
||||
'galaxy.tools.util.galaxyops',
|
||||
'galaxy.tools.verify',
|
||||
'galaxy.tools.verify.asserts',
|
||||
'galaxy.tours',
|
||||
'galaxy.visualization',
|
||||
'galaxy.visualization.data_providers',
|
||||
@@ -102,6 +100,8 @@ PACKAGES = [
|
||||
]
|
||||
ENTRY_POINTS = '''
|
||||
[console_scripts]
|
||||
galaxy-main=galaxy.main:main
|
||||
galaxy-config=galaxy.config.script:main
|
||||
'''
|
||||
PACKAGE_DATA = {
|
||||
# Be sure to update MANIFEST.in for source dist.
|
||||
|
||||
@@ -47,7 +47,8 @@ PACKAGES = [
|
||||
]
|
||||
ENTRY_POINTS = '''
|
||||
[console_scripts]
|
||||
gx-build-objects=galaxy.model.store.build_objects:main
|
||||
galaxy-build-objects=galaxy.model.store.build_objects:main
|
||||
galaxy-manage-db=galaxy.model.orm.scripts:manage_db
|
||||
'''
|
||||
PACKAGE_DATA = {
|
||||
# Be sure to update MANIFEST.in for source dist.
|
||||
|
||||
@@ -32,10 +32,6 @@ TEST_DIR = 'tests'
|
||||
PACKAGES = []
|
||||
ENTRY_POINTS = '''
|
||||
[console_scripts]
|
||||
galaxy-paster=galaxy.util.pastescript.serve:run
|
||||
galaxy-main=galaxy.main:main
|
||||
galaxy-config=galaxy.config.script:main
|
||||
galaxy-manage-db=galaxy.model.orm.scripts:manage_db
|
||||
'''
|
||||
PACKAGE_DATA = {
|
||||
# Be sure to update MANIFEST.in for source dist.
|
||||
|
||||
@@ -0,0 +1,12 @@
|
||||
.. :changelog:
|
||||
|
||||
History
|
||||
-------
|
||||
|
||||
.. to_doc
|
||||
|
||||
---------------------
|
||||
19.9.0.dev0
|
||||
---------------------
|
||||
|
||||
* Initial import from dev branch of Galaxy during 19.09 development cycle.
|
||||
Symlink
+1
@@ -0,0 +1 @@
|
||||
../../LICENSE.txt
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user