Merge release_23.1 into dev

.github/workflows/converter_tests.yaml

@@ -68,7 +68,7 @@ jobs:
       - name: Run tests
         run: |
           mapfile -t TOOL_ARRAY < tool_list.txt
-          planemo test --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' "${TOOL_ARRAY[@]}"
+          planemo test --biocontainers --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' "${TOOL_ARRAY[@]}"
       - uses: actions/upload-artifact@v3
         if: failure()
         with:

client/src/components/History/Modals/CopyModal.vue

@@ -2,7 +2,7 @@
     <b-modal v-bind="$attrs" :title="title" title-tag="h2" v-on="$listeners">
         <transition name="fade">
             <b-alert v-localize :show="isAnonymous" variant="warning">
-                As an anonymous user, unless you login or register, you will lose your current history after copying
+                As an anonymous user, unless you log in or register, you will lose your current history after copying
                 this history. You can <a href="/user/login">log in here</a> or <a href="/user/create">register here</a>.
             </b-alert>
         </transition>

client/src/components/Login/RegisterForm.vue

@@ -3,7 +3,8 @@
         <div class="row justify-content-md-center">
             <div class="col col-lg-6">
                 <b-alert :show="!!registrationWarningMessage" variant="info">
-                    {{ registrationWarningMessage }}
+                    <!-- eslint-disable-next-line vue/no-v-html -->
+                    <span v-html="registrationWarningMessage" />
                 </b-alert>
                 <b-alert :show="!!messageText" :variant="messageVariant">
                     {{ messageText }}
@@ -64,19 +65,18 @@
                                         dashes ('.', '_', '-').
                                     </b-form-text>
                                 </b-form-group>
-                                <b-form-group
-                                    v-if="mailingJoinAddr && serverMailConfigured"
-                                    :label="labelSubscribe"
-                                    label-for="register-form-subscribe">
-                                    <input
+                                <b-form-group v-if="mailingJoinAddr && serverMailConfigured">
+                                    <b-form-checkbox
                                         id="register-form-subscribe"
                                         v-model="subscribe"
                                         name="subscribe"
-                                        type="checkbox" />
+                                        type="checkbox">
+                                        {{ labelSubscribe }}
+                                    </b-form-checkbox>
                                 </b-form-group>
-                                <b-button v-localize name="create" type="submit" :disabled="disableCreate"
-                                    >Create</b-button
-                                >
+                                <b-button v-localize name="create" type="submit" :disabled="disableCreate">
+                                    Create
+                                </b-button>
                             </b-card-body>
                         </b-collapse>
                         <b-card-footer v-if="showLoginLink">
@@ -93,8 +93,9 @@
                     </b-card>
                 </b-form>
             </div>
-            <div v-if="termsUrl" class="col">
-                <b-embed type="iframe" :src="termsUrl" aspect="1by1" />
+            <div v-if="termsUrl" class="col position-relative embed-container">
+                <iframe title="terms-of-use" :src="termsUrl" frameborder="0" class="terms-iframe"></iframe>
+                <div v-localize class="scroll-hint">↓ Scroll to review ↓</div>
             </div>
         </div>
     </div>
@@ -204,3 +205,26 @@ export default {
     },
 };
 </script>
+<style scoped>
+.embed-container {
+    position: relative;
+}
+
+.scroll-hint {
+    position: absolute;
+    bottom: 10px;
+    left: 50%;
+    transform: translateX(-50%);
+    background-color: rgba(255, 255, 255, 0.9);
+    border: 1px solid #ccc;
+    padding: 2px 5px;
+    border-radius: 4px;
+}
+
+.terms-iframe {
+    width: 100%;
+    height: 90vh;
+    border: none;
+    overflow-y: auto;
+}
+</style>

client/src/components/PageDisplay/PageDisplay.vue

@@ -8,6 +8,7 @@
                     :enable_beta_markdown_export="config.enable_beta_markdown_export"
                     :download-endpoint="stsUrl(config)"
                     :export-link="exportUrl"
+                    :read-only="!userOwnsPage"
                     @onEdit="onEdit" />
                 <PageHtml v-else :page="page" />
             </div>
@@ -17,7 +18,10 @@
 </template>
 
 <script>
+import { storeToRefs } from "pinia";
+
 import { useConfig } from "@/composables/config";
+import { useUserStore } from "@/stores/userStore";
 import { withPrefix } from "@/utils/redirect";
 import { urlData } from "@/utils/url";
 
@@ -39,14 +43,19 @@ export default {
     },
     setup() {
         const { config, isConfigLoaded } = useConfig(true);
-        return { config, isConfigLoaded };
+        const userStore = useUserStore();
+        const { currentUser } = storeToRefs(userStore);
+        return { config, currentUser, isConfigLoaded };
     },
     data() {
         return {
             page: {},
         };
     },
     computed: {
+        userOwnsPage() {
+            return this.currentUser.username === this.page.username;
+        },
         dataUrl() {
             return `/api/pages/${this.pageId}`;
         },

client/src/entry/analysis/menu.js

@@ -166,7 +166,7 @@ export function fetchMenu(options = {}) {
         if (options.allow_user_creation) {
             userTab = {
                 id: "user",
-                title: _l("Login or Register"),
+                title: _l("Log in or Register"),
                 cls: "loggedout-only",
                 url: "/login",
                 tooltip: _l("Log in or register a new account"),

client/src/nls/de/locale.js

@@ -23,7 +23,7 @@ define({
     User: "Benutzer",
     Login: "Anmeldung",
     Register: "Neu registrieren",
-    "Login or Register": "Einloggen oder Registrieren",
+    "Log in or Register": "Einloggen oder Registrieren",
     "Signed in as": "Angemeldet als",
     Preferences: "Präferenzen",
     "Custom Builds": "Custom Builds",

client/src/nls/es/locale.js

@@ -54,7 +54,7 @@ define({
 
     Register: "Registro",
 
-    "Login or Register": "Iniciar sesión o Registrarse",
+    "Log in or Register": "Iniciar sesión o Registrarse",
     "Subscribe to mailing list": false,
     "Already have an account?": false,
     "Log in here.": false,

client/src/nls/fr/locale.js

@@ -24,7 +24,7 @@ define({
     User: "Utilisateur",
     Login: "Authentification",
     Register: "Enregistrement",
-    "Login or Register": "Authentification et Enregistrement",
+    "Log in or Register": "Authentification et Enregistrement",
     "Signed in as": "Authentifié en tant que",
     Preferences: "Préférences",
     "Custom Builds": "Mes génomes Builds de référence",

client/src/nls/ja/locale.js

@@ -26,7 +26,7 @@ define({
     User: "ユーザー",
     Login: "ログイン",
     Register: "登録",
-    "Login or Register": "ログイン/登録",
+    "Log in or Register": "ログイン/登録",
     Preferences: "設定",
     "Custom Builds": "カスタムビルド",
     Logout: "ログアウト",

client/src/nls/locale.js

@@ -25,7 +25,7 @@ define({
         User: false,
         Login: false,
         Register: false,
-        "Login or Register": false,
+        "Log in or Register": false,
         "Signed in as": false,
         Preferences: false,
         "Custom Builds": false,

client/src/nls/zh/locale.js

@@ -26,7 +26,7 @@ define({
     User: "账号管理",
     Login: "登陆",
     Register: "注册",
-    "Login or Register": "注册登陆",
+    "Log in or Register": "注册登陆",
     "Signed in as": "您已登陆为",
     Preferences: "用户偏好性",
     "Custom Builds": "自定义构建集",

config/plugins/visualizations/example/package.json

@@ -1,13 +1,13 @@
 {
     "name": "visualization",
-    "version": "0.1.0",
+    "version": "0.2.0",
     "keywords": [
         "galaxy",
         "visualization"
     ],
     "license": "AFL-3.0",
     "dependencies": {
-        "@galaxyproject/charts": "^0.0.6",
+        "@galaxyproject/charts": "^0.1.0",
         "babel-preset-env": "^1.6.1",
         "backbone": "^1.3.3",
         "bootstrap": "^3.3.7",

config/plugins/visualizations/heatmap/heatmap_default/package.json

@@ -1,13 +1,13 @@
 {
     "name": "visualization",
-    "version": "0.1.0",
+    "version": "0.2.0",
     "keywords": [
         "galaxy",
         "visualization"
     ],
     "license": "AFL-3.0",
     "dependencies": {
-        "@galaxyproject/charts": "^0.0.6",
+        "@galaxyproject/charts": "^0.1.0",
         "babel-preset-env": "^1.6.1",
         "backbone": "^1.4.0",
         "bootstrap": "^3.3.7",

config/plugins/visualizations/jqplot/jqplot_bar/package.json

@@ -1,13 +1,13 @@
 {
     "name": "visualization",
-    "version": "0.1.0",
+    "version": "0.2.0",
     "keywords": [
         "galaxy",
         "visualization"
     ],
     "license": "AFL-3.0",
     "dependencies": {
-        "@galaxyproject/charts": "^0.0.6",
+        "@galaxyproject/charts": "^0.1.0",
         "babel-preset-env": "^1.6.1",
         "backbone": "^1.3.3",
         "bootstrap": "^3.3.7",

config/plugins/visualizations/nvd3/nvd3_bar/package.json

@@ -1,6 +1,6 @@
 {
     "name": "nvd3",
-    "version": "0.1.0",
+    "version": "0.2.0",
     "description": "NVD3 visualization plugin.",
     "keywords": [
         "galaxy",
@@ -9,7 +9,7 @@
     ],
     "license": "AFL-3.0",
     "dependencies": {
-        "@galaxyproject/charts": "^0.0.6",
+        "@galaxyproject/charts": "^0.1.0",
         "babel-preset-env": "^1.6.1",
         "backbone": "^1.3.3",
         "bootstrap": "^3.3.7",

config/plugins/visualizations/venn/package.json

@@ -1,13 +1,13 @@
 {
     "name": "visualization",
-    "version": "0.1.0",
+    "version": "0.2.0",
     "keywords": [
         "galaxy",
         "visualization"
     ],
     "license": "AFL-3.0",
     "dependencies": {
-        "@galaxyproject/charts": "^0.0.6",
+        "@galaxyproject/charts": "^0.1.0",
         "babel-preset-env": "^1.6.1",
         "backbone": "^1.3.3",
         "bootstrap": "^3.3.7",

lib/galaxy/dependencies/pinned-requirements.txt

@@ -156,6 +156,7 @@ pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.12"
 pyzmq==25.1.1 ; python_version >= "3.7" and python_version < "3.12"
 rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12"
 refgenconf==0.12.2 ; python_version >= "3.7" and python_version < "3.12"
+regex==2023.8.8 ; python_version >= "3.7" and python_version < "3.12"
 repoze-lru==0.7 ; python_version >= "3.7" and python_version < "3.12"
 requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
 requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12"