Merge 24.0 into dev

client/src/components/PageDisplay/PageHtml.vue

@@ -32,7 +32,7 @@ export default {
             if (content) {
                 const vDom = document.createElement("div");
                 vDom.innerHTML = content;
-                const children = vDom.children;
+                const children = Array.from(vDom.children);
                 children.forEach((child) => {
                     if (child.classList.contains("embedded-item")) {
                         const splitId = child.id.split("-");

client/src/components/Tool/ToolForm.vue

@@ -1,5 +1,5 @@
 <template>
-    <div v-if="currentUser && currentHistoryId">
+    <div v-if="currentUser && currentHistoryId && isConfigLoaded">
         <b-alert :show="messageShow" :variant="messageVariant">
             {{ messageText }}
         </b-alert>

client/src/components/Tool/ToolSuccess.vue

@@ -1,10 +1,12 @@
 <script setup lang="ts">
+import { BAlert } from "bootstrap-vue";
 import { computed, onMounted } from "vue";
 import { useRouter } from "vue-router/composables";
 
 import { useConfig } from "@/composables/config";
 import { useJobStore } from "@/stores/jobStore";
 
+import LoadingSpan from "../LoadingSpan.vue";
 import ToolRecommendation from "../ToolRecommendation.vue";
 import ToolSuccessMessage from "./ToolSuccessMessage.vue";
 import Webhook from "@/components/Common/Webhook.vue";
@@ -31,10 +33,15 @@ onMounted(() => {
 
 <template>
     <section>
-        <div v-if="jobResponse.produces_entry_points">
-            <ToolEntryPoints v-for="job in jobResponse.jobs" :key="job.id" :job-id="job.id" />
+        <BAlert v-if="!jobResponse" variant="info" show>
+            <LoadingSpan message="Waiting on a job response" />
+        </BAlert>
+        <div v-else>
+            <div v-if="jobResponse?.produces_entry_points">
+                <ToolEntryPoints v-for="job in jobResponse.jobs" :key="job.id" :job-id="job.id" />
+            </div>
+            <ToolSuccessMessage :job-response="jobResponse" :tool-name="toolName" />
         </div>
-        <ToolSuccessMessage :job-response="jobResponse" :tool-name="toolName" />
         <Webhook type="tool" :tool-id="jobDef.tool_id" />
         <ToolRecommendation v-if="showRecommendation" :tool-id="jobDef.tool_id" />
     </section>

client/src/components/User/DiskUsage/Management/StorageManager.vue

@@ -63,7 +63,7 @@ async function onConfirmCleanupSelected(selectedItems: CleanableItem[]) {
             </b-alert>
         </b-row>
         <b-row class="justify-content-md-center mb-5">
-            <b-alert v-if="config.enable_quotas" show>
+            <b-alert v-if="config?.enable_quotas" show>
                 {{ localize("The storage manager only shows elements that count towards your disk quota.") }}
                 <b-link :href="config.quota_url" target="_blank">{{ localize("Learn more") }}</b-link>
             </b-alert>

lib/galaxy/files/sources/invenio.py

@@ -18,6 +18,7 @@
     Unpack,
 )
 
+from galaxy.exceptions import AuthenticationRequired
 from galaxy.files import OptionalUserContext
 from galaxy.files.sources import (
     AnyRemoteEntry,
@@ -434,6 +435,9 @@ def _get_request_headers(self, user_context: OptionalUserContext):
         return headers
 
     def _ensure_response_has_expected_status_code(self, response, expected_status_code: int):
+        if response.status_code == 403:
+            record_url = response.url.replace("/api", "").replace("/files", "")
+            raise AuthenticationRequired(f"Please make sure you have the necessary permissions to access: {record_url}")
         if response.status_code != expected_status_code:
             error_message = self._get_response_error_message(response)
             raise Exception(

lib/galaxy/files/uris.py

@@ -12,6 +12,7 @@
 from galaxy.exceptions import (
     AdminRequiredException,
     ConfigDoesNotAllowException,
+    RequestParameterInvalidException,
 )
 from galaxy.files import (
     ConfiguredFileSources,
@@ -125,7 +126,11 @@ def validate_non_local(uri: str, ip_allowlist: List[IpAllowedListEntryT]) -> str
     # safe to log out, no credentials/request path, just an IP + port
     log.debug("parsed url %s, port:  %s", parsed_url, port)
     # Call getaddrinfo to resolve hostname into tuples containing IPs.
-    addrinfo = socket.getaddrinfo(parsed_url, port)
+    try:
+        addrinfo = socket.getaddrinfo(parsed_url, port)
+    except socket.gaierror as e:
+        log.debug("Could not resolve url '%': %'", url, e)
+        raise RequestParameterInvalidException(f"Could not verify url '{url}'.")
     # Get the IP addresses that this entry resolves to (uniquely)
     # We drop:
     #   AF_* family: It will resolve to AF_INET or AF_INET6, getaddrinfo(3) doesn't even mention AF_UNIX,

lib/galaxy/job_execution/actions/post.py

@@ -8,7 +8,6 @@
 from markupsafe import escape
 
 from galaxy.model import PostJobActionAssociation
-from galaxy.model.base import transaction
 from galaxy.util import send_mail
 from galaxy.util.custom_logging import get_logger
 
@@ -370,8 +369,6 @@ def execute(cls, app, sa_session, action, job, replacement_dict, final_job_state
         # POTENTIAL ISSUES:  When many outputs are being finish()ed
         # concurrently, sometimes non-terminal steps won't be cleaned up
         # because of the lag in job state updates.
-        with transaction(sa_session):
-            sa_session.commit()
         if not job.workflow_invocation_step:
             log.debug("This job is not part of a workflow invocation, delete intermediates aborted.")
             return

lib/galaxy/jobs/handler.py

@@ -568,7 +568,8 @@ def __handle_waiting_jobs(self):
                         self.sa_session.add(dataset_assoc.dataset.dataset)
                     self.sa_session.add(job)
                 elif job_state == JOB_ERROR:
-                    log.error("(%d) Error checking job readiness" % job.id)
+                    # A more informative message is shown wherever the job state is set to error
+                    pass
                 else:
                     log.error("(%d) Job in unknown state '%s'" % (job.id, job_state))
                     new_waiting_jobs.append(job.id)

lib/galaxy/tools/parameters/basic.py

@@ -2681,7 +2681,9 @@ def to_text(self, value):
 
 # Code from CWL branch to massage in order to be shared across tools and workflows,
 # and for CWL artifacts as well as Galaxy ones.
-def raw_to_galaxy(app: "MinimalApp", history: "History", as_dict_value: Dict[str, Any]) -> "HistoryItem":
+def raw_to_galaxy(
+    app: "MinimalApp", history: "History", as_dict_value: Dict[str, Any], commit: bool = True
+) -> "HistoryItem":
     object_class = as_dict_value["class"]
     if object_class == "File":
         # TODO: relative_to = "/"
@@ -2728,7 +2730,8 @@ def raw_to_galaxy(app: "MinimalApp", history: "History", as_dict_value: Dict[str
         app.model.session.add(primary_data)
         history.stage_addition(primary_data)
         history.add_pending_items()
-        app.model.session.flush()
+        if commit:
+            app.model.session.commit()
         return primary_data
     else:
         name = as_dict_value.get("name")
@@ -2740,14 +2743,16 @@ def raw_to_galaxy(app: "MinimalApp", history: "History", as_dict_value: Dict[str
             name=name,
             collection=collection,
         )
+        app.model.session.add(hdca)
 
         def write_elements_to_collection(has_elements, collection_builder):
             element_dicts = has_elements.get("elements")
             for element_dict in element_dicts:
                 element_class = element_dict["class"]
                 identifier = element_dict["identifier"]
                 if element_class == "File":
-                    hda = raw_to_galaxy(app, history, element_dict)
+                    # Don't commit for inner elements
+                    hda = raw_to_galaxy(app, history, element_dict, commit=False)
                     collection_builder.add_dataset(identifier, hda)
                 else:
                     subcollection_builder = collection_builder.get_level(identifier)
@@ -2756,8 +2761,10 @@ def write_elements_to_collection(has_elements, collection_builder):
         collection_builder = builder.BoundCollectionBuilder(collection)
         write_elements_to_collection(as_dict_value, collection_builder)
         collection_builder.populate()
-        app.model.session.add(hdca)
-        app.model.session.flush()
+        history.stage_addition(hdca)
+        history.add_pending_items()
+        if commit:
+            app.model.session.commit()
         return hdca