mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge branch 'release_21.05' into dev
This commit is contained in:
mvdbeek
@@ -9,7 +9,9 @@
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Library
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</b-button>
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<SearchField :typing-delay="0" @updateSearch="searchValue($event)" />
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<b-form-checkbox class="mr-1" @input="toggle_include_deleted($event)"> include deleted </b-form-checkbox>
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<b-form-checkbox v-if="isAdmin" class="mr-1" @input="toggle_include_deleted($event)">
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include deleted
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</b-form-checkbox>
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<b-form-checkbox class="mr-1" @input="toggle_exclude_restricted($event)">
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exclude restricted
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</b-form-checkbox>
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@@ -158,6 +160,7 @@
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id="paginationPerPage"
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autocomplete="off"
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type="number"
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onkeyup="this.value|=0;if(this.value<1)this.value=1"
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v-model="perPage"
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/>
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</td>
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@@ -303,12 +303,13 @@ export default {
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// helper function to make legacy code compatible
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findCheckedItems: async function (idOnly = true) {
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const datasets = [];
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const folder = [];
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const folders = [];
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const selected = await this.getSelected();
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selected.forEach((item) => {
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item.type === "file" ? datasets.push(idOnly ? item.id : item) : idOnly ? item.id : item;
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const selected_item = idOnly ? item.id : item;
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item.type === "file" ? datasets.push(selected_item) : folders.push(selected_item);
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});
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return { datasets: datasets, folders: folder };
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return { datasets: datasets, folders: folders };
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},
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importToHistoryModal: function (isCollection) {
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this.findCheckedItems(!isCollection).then(({ datasets, folders }) => {
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+2
-2
@@ -79,13 +79,13 @@ var ImportDatasetModal = Backbone.View.extend({
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Toast.error("An error occurred.");
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})
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.always(() => {
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this.modal.enableButton("Import");
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this.modal.disableButton("Import");
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});
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} else {
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var history_id = $("select[name=import_to_history] option:selected").val();
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var history_name = $("select[name=import_to_history] option:selected").text();
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this.processImportToHistory(history_id, history_name);
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this.modal.enableButton("Import");
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this.modal.disableButton("Import");
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}
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},
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@@ -13,9 +13,12 @@ export function onError(error) {
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// legacy code
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export function extractRoles(role_list) {
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const selected_roles = [];
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role_list.forEach((item) => {
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selected_roles.push({ name: item[0], id: item[1] });
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});
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if (role_list) {
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role_list.forEach((item) => {
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selected_roles.push({ name: item[0], id: item[1] });
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});
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}
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return selected_roles;
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}
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@@ -242,6 +242,7 @@ export default {
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file_mode: file.mode || "local",
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file_path: file.path,
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file_data: file,
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file_uri: file.uri,
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extension: this.extension,
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genome: this.genome,
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};
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@@ -249,6 +249,7 @@ export default {
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file_size: file.size,
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file_mode: file.mode || "local",
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file_path: file.path,
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file_uri: file.uri,
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file_data: file,
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};
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},
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@@ -242,6 +242,7 @@ export default {
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name: ftp_file.path,
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size: ftp_file.size,
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path: ftp_file.path,
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uri: ftp_file.uri,
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},
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]);
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},
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@@ -292,24 +292,23 @@ export default {
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auto_decompress: true,
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};
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// Composite does not use the fetch API, so we can just
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// index into the first element of items
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const item = items[0];
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let urls;
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if (item.get("file_mode") == "ftp") {
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urls = [item.get("file_path")];
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} else {
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urls = item.get("url_paste").split("\n");
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}
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urls.forEach((url) => {
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if (url != "") {
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data.targets[0].elements.push({
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url: url.trim(),
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src: "url",
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dbkey: item.get("genome", "?"),
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ext: item.get("extension", "auto"),
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});
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items.forEach((item) => {
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let urls;
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if (item.get("file_mode") == "ftp") {
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urls = [item.get("file_uri") || item.get("file_path")];
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} else {
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urls = item.get("url_paste").split("\n");
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}
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urls.forEach((url) => {
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if (url != "") {
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data.targets[0].elements.push({
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url: url.trim(),
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src: "url",
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dbkey: item.get("genome", "?"),
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ext: item.get("extension", "auto"),
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});
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}
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});
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});
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return data;
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},
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@@ -469,7 +469,7 @@ export default {
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}
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},
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onUpgrade() {
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this.attemptRefactor([{ action_type: "upgrade_all_steps" }]);
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this.onAttemptRefactor([{ action_type: "upgrade_all_steps" }]);
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},
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onEdit() {
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this.isCanvas = true;
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@@ -105,9 +105,20 @@ export default {
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this.trsTool = tool;
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this.errorMessage = null;
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if (this.isAutoImport) {
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const version = this.trsTool.versions.find((version) => version.id === this.queryTrsVersionId);
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/* Resolve discrepancy between workflowhub, which sends an id as query parameter,
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and dockstore, which uses the version name as the query parameter.
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Should just be one of them eventually. */
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let versionField = "name";
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const version = this.trsTool.versions.find((version) => {
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if (version.name === this.queryTrsVersionId) {
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return true;
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} else if (version.id === this.queryTrsVersionId) {
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versionField = "id";
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return true;
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}
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});
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if (version) {
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this.importVersion(this.trsTool.id, version, this.isRun);
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this.importVersion(this.trsTool.id, version[versionField], this.isRun);
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} else {
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Toast.warning(`Specified version: ${this.queryTrsVersionId} doesn't exist`);
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this.isAutoImport = false;
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@@ -11,7 +11,7 @@ export default {
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methods: {
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importVersion(toolId, version, isRunFormRedirect = false) {
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this.services
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.importTrsTool(this.trsSelection.id, toolId, version.name)
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.importTrsTool(this.trsSelection.id, toolId, version)
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.then((response_data) => {
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redirectOnImport(getAppRoot(), response_data, isRunFormRedirect);
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})
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@@ -492,12 +492,12 @@ var LibraryDatasetView = Backbone.View.extend({
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<!-- BREADCRUMBS -->
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<ol class="breadcrumb">
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<li class="breadcrumb-item">
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<a title="Return to the list of libraries" href="<% rootPath %>libraries">Libraries</a>
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<a title="Return to the list of libraries" href="<% rootPath %>/libraries">Libraries</a>
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</li>
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<% _.each(item.get("full_path"), function(path_item) { %>
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<% if (path_item[0] != item.id) { %>
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<li class="breadcrumb-item">
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<a title="Return to this folder" href="<% rootPath %>folders/<%- path_item[0] %>">
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<a title="Return to this folder" href="<% rootPath %>/libraries/folders/<%- path_item[0] %>">
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<%- path_item[1] %>
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</a>
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</li>
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@@ -12,6 +12,7 @@ var Model = Backbone.Model.extend({
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file_size: 0,
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file_type: null,
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file_path: "",
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file_uri: null,
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file_data: null,
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percentage: 0,
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space_to_tab: false,
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@@ -147,32 +147,35 @@ class LibraryManager:
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query = query.filter(trans.app.model.Library.table.c.deleted == false())
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else:
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# Nonadmins can't see deleted libraries
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query = query.filter(trans.app.model.Library.table.c.deleted == false())
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current_user_role_ids = [role.id for role in trans.get_current_user_roles()]
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all_actions = trans.sa_session.query(trans.model.LibraryPermissions).filter(trans.model.LibraryPermissions.table.c.role_id.in_(current_user_role_ids))
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library_add_action = trans.app.security_agent.permitted_actions.LIBRARY_ADD.action
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library_modify_action = trans.app.security_agent.permitted_actions.LIBRARY_MODIFY.action
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library_manage_action = trans.app.security_agent.permitted_actions.LIBRARY_MANAGE.action
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accessible_restricted_library_ids = set()
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allowed_library_add_ids = set()
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allowed_library_modify_ids = set()
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allowed_library_manage_ids = set()
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for action in all_actions:
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if action.action == library_access_action:
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accessible_restricted_library_ids.add(action.library_id)
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if action.action == library_add_action:
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allowed_library_add_ids.add(action.library_id)
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if action.action == library_modify_action:
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allowed_library_modify_ids.add(action.library_id)
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if action.action == library_manage_action:
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allowed_library_manage_ids.add(action.library_id)
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query = query.filter(or_(
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not_(trans.model.Library.table.c.id.in_(restricted_library_ids)),
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trans.model.Library.table.c.id.in_(accessible_restricted_library_ids)
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))
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prefetched_ids['allowed_library_add_ids'] = allowed_library_add_ids
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prefetched_ids['allowed_library_modify_ids'] = allowed_library_modify_ids
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prefetched_ids['allowed_library_manage_ids'] = allowed_library_manage_ids
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if deleted:
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raise exceptions.AdminRequiredException()
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else:
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query = query.filter(trans.app.model.Library.table.c.deleted == false())
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current_user_role_ids = [role.id for role in trans.get_current_user_roles()]
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all_actions = trans.sa_session.query(trans.model.LibraryPermissions).filter(trans.model.LibraryPermissions.table.c.role_id.in_(current_user_role_ids))
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library_add_action = trans.app.security_agent.permitted_actions.LIBRARY_ADD.action
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library_modify_action = trans.app.security_agent.permitted_actions.LIBRARY_MODIFY.action
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library_manage_action = trans.app.security_agent.permitted_actions.LIBRARY_MANAGE.action
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accessible_restricted_library_ids = set()
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allowed_library_add_ids = set()
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allowed_library_modify_ids = set()
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allowed_library_manage_ids = set()
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for action in all_actions:
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if action.action == library_access_action:
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accessible_restricted_library_ids.add(action.library_id)
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if action.action == library_add_action:
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allowed_library_add_ids.add(action.library_id)
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if action.action == library_modify_action:
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allowed_library_modify_ids.add(action.library_id)
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if action.action == library_manage_action:
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allowed_library_manage_ids.add(action.library_id)
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query = query.filter(or_(
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not_(trans.model.Library.table.c.id.in_(restricted_library_ids)),
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trans.model.Library.table.c.id.in_(accessible_restricted_library_ids)
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))
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prefetched_ids['allowed_library_add_ids'] = allowed_library_add_ids
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prefetched_ids['allowed_library_modify_ids'] = allowed_library_modify_ids
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prefetched_ids['allowed_library_manage_ids'] = allowed_library_manage_ids
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return query, prefetched_ids
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def secure(self, trans, library, check_accessible=True):
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@@ -20,20 +20,40 @@ class UploadFtpSeleniumIntegrationTestCase(SeleniumIntegrationTestCase):
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def ftp_dir(cls):
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return cls.temp_config_dir("ftp")
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@selenium_test
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def test_upload_simplest(self):
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email = self.get_logged_in_user()["email"]
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user_ftp_dir = os.path.join(self.ftp_dir(), email)
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os.makedirs(user_ftp_dir)
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file_path = os.path.join(user_ftp_dir, "1.txt")
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with open(file_path, "w")as f:
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f.write("Hello World!")
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def _upload_all(self):
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self.home()
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self.components.upload.start.wait_for_and_click()
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self.components.upload.ftp_add.wait_for_and_click()
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self.components.upload.ftp_popup.wait_for_visible()
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self.components.upload.ftp_items().all()[0].click()
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for item in self.components.upload.ftp_items().all():
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item.click()
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self.components.upload.ftp_close.wait_for_and_click()
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self.components.upload.row(n=0).wait_for_visible()
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self.upload_start()
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self.sleep_for(self.wait_types.UX_RENDER)
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self.wait_for_history()
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def _create_ftp_dir(self):
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email = self.get_logged_in_user()["email"]
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user_ftp_dir = os.path.join(self.ftp_dir(), email)
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os.makedirs(user_ftp_dir)
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return user_ftp_dir
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@selenium_test
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def test_upload_simplest(self):
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user_ftp_dir = self._create_ftp_dir()
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file_path = os.path.join(user_ftp_dir, "1.txt")
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with open(file_path, "w") as f:
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f.write("Hello World!")
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self._upload_all()
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@selenium_test
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def test_upload_multiple(self):
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user_ftp_dir = self._create_ftp_dir()
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file_path = os.path.join(user_ftp_dir, "1.txt")
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with open(file_path, "w") as f:
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f.write("Hello World!")
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file_path = os.path.join(user_ftp_dir, "2.txt")
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with open(file_path, "w") as f:
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f.write("Hello Galaxy!")
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self._upload_all()
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@@ -26,7 +26,7 @@ def safe_bed_file(infile):
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https://lists.soe.ucsc.edu/pipermail/genome/2007-May/013561.html
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"""
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fix_pat = re.compile("^(track|browser)")
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with tempfile.NamedTemporaryFile(mode='w', delete=False) as out_handle, open(infile, 'w') as in_handle:
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with tempfile.NamedTemporaryFile(mode='w', delete=False) as out_handle, open(infile, 'r') as in_handle:
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for line in in_handle:
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if fix_pat.match(line):
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line = "#" + line
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Reference in New Issue
Block a user