Merge branch 'release_24.1' into dev

client/src/components/Form/FormElement.vue

@@ -3,9 +3,12 @@ import { library } from "@fortawesome/fontawesome-svg-core";
 import { faCaretSquareDown, faCaretSquareUp } from "@fortawesome/free-regular-svg-icons";
 import { faArrowsAltH, faExclamation, faTimes } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { sanitize } from "dompurify";
 import type { ComputedRef } from "vue";
 import { computed, ref, useAttrs } from "vue";
 
+import { linkify } from "@/utils/utils";
+
 import type { FormParameterAttributes, FormParameterTypes, FormParameterValue } from "./parameterTypes";
 
 import FormBoolean from "./Elements/FormBoolean.vue";
@@ -181,7 +184,9 @@ const isOptional = computed(() => !isRequired.value && attrs.value["optional"] !
         :class="{ alert: hasAlert, 'alert-info': hasAlert }">
         <div v-if="hasAlert" class="ui-form-error">
             <FontAwesomeIcon class="mr-1" icon="fa-exclamation" />
-            <span class="ui-form-error-text" v-html="props.error || props.warning" />
+            <span
+                class="ui-form-error-text"
+                v-html="linkify(sanitize(props.error || props.warning, { USE_PROFILES: { html: true } }))" />
         </div>
 
         <div class="ui-form-title">

client/src/components/Sharing/Embeds/WorkflowEmbed.vue

@@ -6,8 +6,8 @@ import { useDebounce } from "@vueuse/core";
 import { BButton, BFormCheckbox, BFormInput, BInputGroup, BInputGroupAppend } from "bootstrap-vue";
 import { computed, reactive, ref } from "vue";
 
-import { getAppRoot } from "@/onload/loadConfig";
 import { copy } from "@/utils/clipboard";
+import { getFullAppUrl } from "@/utils/utils";
 
 import ZoomControl from "@/components/Workflow/Editor/ZoomControl.vue";
 import WorkflowPublished from "@/components/Workflow/Published/WorkflowPublished.vue";
@@ -39,13 +39,8 @@ function onChangePosition(event: Event, xy: "x" | "y") {
     }
 }
 
-const root = computed(() => {
-    const port = window.location.port ? `:${window.location.port}` : "";
-    return `${window.location.protocol}//${window.location.hostname}${port}${getAppRoot()}`;
-});
-
 const embedUrl = computed(() => {
-    let url = `${root.value}published/workflow?id=${props.id}&embed=true`;
+    let url = getFullAppUrl(`published/workflow?id=${props.id}&embed=true`);
     url += `&buttons=${settings.buttons}`;
     url += `&about=${settings.about}`;
     url += `&heading=${settings.heading}`;

client/src/components/Sharing/SharingPage.vue

@@ -9,6 +9,7 @@ import { getGalaxyInstance } from "@/app";
 import { useToast } from "@/composables/toast";
 import { getAppRoot } from "@/onload/loadConfig";
 import { errorMessageAsString } from "@/utils/simple-error";
+import { getFullAppUrl } from "@/utils/utils";
 
 import type { Item, ShareOption } from "./item";
 
@@ -52,11 +53,6 @@ const item = ref<Item>({
     extra: defaultExtra(),
 });
 
-const itemRoot = computed(() => {
-    const port = window.location.port ? `:${window.location.port}` : "";
-    return `${window.location.protocol}//${window.location.hostname}${port}${getAppRoot()}`;
-});
-
 const itemUrl = reactive({
     prefix: "",
     slug: "",
@@ -68,7 +64,7 @@ watch(
         if (value) {
             const index = value.lastIndexOf("/");
 
-            itemUrl.prefix = itemRoot.value + value.substring(0, index + 1);
+            itemUrl.prefix = getFullAppUrl(value.substring(0, index + 1));
             itemUrl.slug = value.substring(index + 1);
         }
     },

client/src/components/Workflow/Published/WorkflowInformation.vue

@@ -5,8 +5,8 @@ import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { computed } from "vue";
 import { RouterLink } from "vue-router";
 
-import { getAppRoot } from "@/onload/loadConfig";
 import { useUserStore } from "@/stores/userStore";
+import { getFullAppUrl } from "@/utils/utils";
 
 import Heading from "@/components/Common/Heading.vue";
 import CopyToClipboard from "@/components/CopyToClipboard.vue";
@@ -42,17 +42,12 @@ const gravatarSource = computed(
 
 const publishedByUser = computed(() => `/workflows/list_published?owner=${props.workflowInfo?.owner}`);
 
-const root = computed(() => {
-    const port = window.location.port ? `:${window.location.port}` : "";
-    return `${window.location.protocol}//${window.location.hostname}${port}${getAppRoot()}`;
-});
-
 const relativeLink = computed(() => {
     return `/published/workflow?id=${props.workflowInfo.id}`;
 });
 
 const fullLink = computed(() => {
-    return `${root.value}${relativeLink.value.substring(1)}`;
+    return getFullAppUrl(relativeLink.value.substring(1));
 });
 
 const userOwned = computed(() => {

client/src/components/Workflow/WorkflowActionsExtend.vue

@@ -1,15 +1,6 @@
 <script setup lang="ts">
 import { library } from "@fortawesome/fontawesome-svg-core";
-import { faStar as farStar } from "@fortawesome/free-regular-svg-icons";
-import {
-    faCaretDown,
-    faCopy,
-    faDownload,
-    faFileExport,
-    faShareAlt,
-    faStar,
-    faTrashRestore,
-} from "@fortawesome/free-solid-svg-icons";
+import { faCopy, faDownload, faLink, faShareAlt, faTrashRestore } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BButton } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
@@ -19,9 +10,11 @@ import { copyWorkflow, undeleteWorkflow } from "@/components/Workflow/workflows.
 import { useConfirmDialog } from "@/composables/confirmDialog";
 import { Toast } from "@/composables/toast";
 import { useUserStore } from "@/stores/userStore";
+import { copy } from "@/utils/clipboard";
 import { withPrefix } from "@/utils/redirect";
+import { getFullAppUrl } from "@/utils/utils";
 
-library.add(faCaretDown, faCopy, faDownload, faFileExport, faShareAlt, farStar, faStar, faTrashRestore);
+library.add(faCopy, faDownload, faLink, faShareAlt, faTrashRestore);
 
 interface Props {
     workflow: any;
@@ -72,11 +65,36 @@ async function onRestore() {
         Toast.info("Workflow restored");
     }
 }
+
+const relativeLink = computed(() => {
+    return `/published/workflow?id=${props.workflow.id}`;
+});
+
+const fullLink = computed(() => {
+    return getFullAppUrl(relativeLink.value.substring(1));
+});
+
+function onCopyPublicLink() {
+    copy(fullLink.value);
+    Toast.success("Link to workflow copied");
+}
 </script>
 
 <template>
     <div class="workflow-actions-extend flex-gapx-1">
         <BButtonGroup>
+            <BButton
+                v-if="workflow.published && !workflow.deleted"
+                id="workflow-copy-public-button"
+                v-b-tooltip.hover.noninteractive
+                :size="buttonSize"
+                title="Copy link to workflow"
+                variant="outline-primary"
+                @click="onCopyPublicLink">
+                <FontAwesomeIcon :icon="faLink" fixed-width />
+                <span class="compact-view">Link to Workflow</span>
+            </BButton>
+
             <BButton
                 v-if="!isAnonymous && !shared && !workflow.deleted"
                 id="workflow-copy-button"

client/src/components/Workflow/WorkflowIndicators.vue

@@ -1,6 +1,6 @@
 <script setup lang="ts">
 import { library } from "@fortawesome/fontawesome-svg-core";
-import { faGlobe, faLink, faShieldAlt, faUser, faUsers } from "@fortawesome/free-solid-svg-icons";
+import { faFileImport, faGlobe, faShieldAlt, faUser, faUsers } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BBadge, BButton } from "bootstrap-vue";
 import { computed } from "vue";
@@ -12,7 +12,7 @@ import { copy } from "@/utils/clipboard";
 
 import UtcDate from "@/components/UtcDate.vue";
 
-library.add(faShieldAlt, faLink, faGlobe, faUsers, faUser);
+library.add(faFileImport, faGlobe, faShieldAlt, faUsers, faUser);
 
 interface Props {
     workflow: any;
@@ -116,7 +116,7 @@ function onViewUserPublished() {
             size="sm"
             class="workflow-external-link inline-icon-button"
             :title="sourceTitle">
-            <FontAwesomeIcon :icon="faLink" fixed-width @click="onCopyLink" />
+            <FontAwesomeIcon :icon="faFileImport" fixed-width @click="onCopyLink" />
         </BButton>
 
         <span class="mr-1">

client/src/utils/utils.test.js

@@ -101,4 +101,16 @@ describe("test utils", () => {
             ]);
         });
     });
+
+    describe("test getFullAppUrl", () => {
+        it("should return the full app url", () => {
+            const appUrl = Utils.getFullAppUrl();
+            expect(appUrl).toBe("http://localhost/");
+        });
+
+        it("should return the full app url", () => {
+            const appUrl = Utils.getFullAppUrl("home");
+            expect(appUrl).toBe("http://localhost/home");
+        });
+    });
 });

client/src/utils/utils.ts

@@ -442,6 +442,21 @@ export function hasKeys(object: unknown, keys: string[]) {
     }
 }
 
+/**
+ * Get the full URL path of the app
+ *
+ * @param path Path to append to the URL path
+ * @returns Full URL path of the app
+ */
+export function getFullAppUrl(path: string = ""): string {
+    const protocol = window.location.protocol;
+    const hostname = window.location.hostname;
+    const port = window.location.port ? `:${window.location.port}` : "";
+    const appRoot = getAppRoot();
+
+    return `${protocol}//${hostname}${port}${appRoot}${path}`;
+}
+
 export default {
     cssLoadFile,
     get,
@@ -460,4 +475,5 @@ export default {
     waitForElementToBePresent,
     wait,
     mergeObjectListsById,
+    getFullAppUrl,
 };

lib/galaxy/managers/users.py

@@ -147,15 +147,13 @@ def create(self, email=None, username=None, password=None, **kwargs):
         else:
             # Activation is off, every new user is active by default.
             user.active = True
-        self.session().add(user)
+        session = self.session()
+        session.add(user)
         try:
-            session = self.session()
-            with transaction(session):
-                session.commit()
-            # TODO:?? flush needed for permissions below? If not, make optional
+            # Creating a private role will commit the session
+            self.app.security_agent.create_user_role(user, self.app)
         except exc.IntegrityError as db_err:
             raise exceptions.Conflict(str(db_err))
-        self.app.security_agent.create_user_role(user, self.app)
         return user
 
     def delete(self, user, flush=True):
@@ -200,6 +198,10 @@ def purge(self, user, flush=True):
         if not user.deleted:
             raise exceptions.MessageException(f"User '{user.email}' has not been deleted, so they cannot be purged.")
         private_role = self.app.security_agent.get_private_user_role(user)
+        if private_role is None:
+            raise exceptions.InconsistentDatabase(
+                "User '%s' private role is missing while attempting to purge deleted user." % user.email
+            )
         # Delete History
         for active_history in user.active_histories:
             self.session().refresh(active_history)

lib/galaxy/model/security.py

@@ -758,6 +758,9 @@ def create_private_user_role(self, user):
         return self.get_private_user_role(user)
 
     def get_private_user_role(self, user, auto_create=False):
+        if auto_create and user.id is None:
+            # New user, directly create private role
+            return self.create_private_user_role(user)
         role = get_private_user_role(user, self.sa_session)
         if not role and auto_create:
             role = self.create_private_user_role(user)

lib/galaxy/tool_util/lint.py

@@ -102,12 +102,21 @@ def name(cls) -> str:
         return cls.__name__
 
     @classmethod
-    def list_listers(cls) -> List[str]:
+    def list_linters(cls) -> List[str]:
         """
         list the names of all linter derived from Linter
         """
+        submodules.import_submodules(galaxy.tool_util.linters)
         return [s.__name__ for s in cls.__subclasses__()]
 
+    list_listers: Callable[[], List[str]]  # deprecated alias
+
+
+# Define the `list_listers` alias outside of the `Linter` class so that
+# @classmethod's change to `list_linters`s signature has taken effect and mypy
+# doesn't report an [assignment] error
+Linter.list_listers = Linter.list_linters
+
 
 class LintMessage:
     """

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -22,7 +22,6 @@
     status,
 )
 from gxformat2._yaml import ordered_dump
-from markupsafe import escape
 from pydantic import (
     UUID1,
     UUID4,
@@ -86,7 +85,6 @@
 from galaxy.tools import recommendations
 from galaxy.tools.parameters import populate_state
 from galaxy.tools.parameters.workflow_utils import workflow_building_modes
-from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web import (
     expose_api,
     expose_api_raw_anonymous_and_sessionless,
@@ -268,7 +266,7 @@ def create(self, trans: GalaxyWebTransaction, payload=None, **kwd):
                         )
                         import_source = "URL"
                     except Exception:
-                        raise exceptions.MessageException(f"Failed to open URL '{escape(archive_source)}'.")
+                        raise exceptions.MessageException(f"Failed to open URL '{archive_source}'.")
             elif hasattr(archive_file, "file"):
                 uploaded_file = archive_file.file
                 uploaded_file_name = uploaded_file.name
@@ -448,7 +446,7 @@ def update(self, trans: GalaxyWebTransaction, id, payload, **kwds):
             name_updated = new_workflow_name and new_workflow_name != stored_workflow.name
             steps_updated = "steps" in workflow_dict
             if name_updated and not steps_updated:
-                sanitized_name = sanitize_html(new_workflow_name or old_workflow.name)
+                sanitized_name = new_workflow_name or old_workflow.name
                 if not sanitized_name:
                     raise exceptions.MessageException("Workflow must have a valid name.")
                 workflow = old_workflow.copy(user=trans.user)
@@ -472,7 +470,7 @@ def update(self, trans: GalaxyWebTransaction, id, payload, **kwds):
                 require_flush = True
 
             if "annotation" in workflow_dict and not steps_updated:
-                newAnnotation = sanitize_html(workflow_dict["annotation"])
+                newAnnotation = workflow_dict["annotation"]
                 self.add_item_annotation(trans.sa_session, trans.user, stored_workflow, newAnnotation)
                 require_flush = True
 
@@ -599,7 +597,7 @@ def __api_import_from_archive(self, trans: GalaxyWebTransaction, archive_data, s
         workflow = workflow.latest_workflow
 
         response = {
-            "message": f"Workflow '{escape(workflow.name)}' imported successfully.",
+            "message": f"Workflow '{workflow.name}' imported successfully.",
             "status": "success",
             "id": trans.security.encode_id(workflow_id),
         }