From b388b81f7b8f046317cb838514b04227a26dd8e1 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 13 May 2024 15:11:57 +0200
Subject: [PATCH 01/13] Drop unnecessary commit() call

---
 lib/galaxy/job_execution/actions/post.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/lib/galaxy/job_execution/actions/post.py b/lib/galaxy/job_execution/actions/post.py
index 10c1e3a57071..8fd85e03dd47 100644
--- a/lib/galaxy/job_execution/actions/post.py
+++ b/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

From 2950ae6ab9bd7f98f56c3dba2ec7796eed16ec84 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 13 May 2024 16:01:38 +0200
Subject: [PATCH 02/13] Fix addition of default collection to history

---
 lib/galaxy/tools/parameters/basic.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 62b29613d1fe..61cb868854d6 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2737,6 +2737,7 @@ def raw_to_galaxy(trans, as_dict_value):
             name=name,
             collection=collection,
         )
+        app.model.session.add(hdca)
 
         def write_elements_to_collection(has_elements, collection_builder):
             element_dicts = has_elements.get("elements")
@@ -2753,8 +2754,9 @@ 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()
-        trans.sa_session.add(hdca)
-        trans.sa_session.flush()
+        history.stage_addition(hdca)
+        history.add_pending_items()
+        app.model.session.flush()
         return hdca
 
 

From 25f8d7ec1d86dba2c16e0ade2f185fa9730090aa Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 14 May 2024 10:31:42 +0200
Subject: [PATCH 03/13] Don't flush for inner elements

---
 lib/galaxy/tools/parameters/basic.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 61cb868854d6..dbe1b065a243 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2675,7 +2675,7 @@ 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(trans, as_dict_value):
+def raw_to_galaxy(trans, as_dict_value, commit=True):
     app = trans.app
     history = trans.history
 
@@ -2725,7 +2725,8 @@ def raw_to_galaxy(trans, as_dict_value):
         trans.sa_session.add(primary_data)
         history.stage_addition(primary_data)
         history.add_pending_items()
-        trans.sa_session.flush()
+        if commit:
+            app.model.session.commit()
         return primary_data
     else:
         name = as_dict_value.get("name")
@@ -2745,7 +2746,8 @@ def write_elements_to_collection(has_elements, collection_builder):
                 element_class = element_dict["class"]
                 identifier = element_dict["identifier"]
                 if element_class == "File":
-                    hda = raw_to_galaxy(trans, element_dict)
+                    # Don't commit for inner elements
+                    hda = raw_to_galaxy(trans, element_dict, commit=False)
                     collection_builder.add_dataset(identifier, hda)
                 else:
                     subcollection_builder = collection_builder.get_level(identifier)
@@ -2756,7 +2758,8 @@ def write_elements_to_collection(has_elements, collection_builder):
         collection_builder.populate()
         history.stage_addition(hdca)
         history.add_pending_items()
-        app.model.session.flush()
+        if commit:
+            app.model.session.commit()
         return hdca
 
 

From 48e1eda42e21d8080a2dd925b7f800f9e2a05d90 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 14 May 2024 12:01:13 -0500
Subject: [PATCH 04/13] [24.0] Fix undefined `reading 'produces_entry_points'`
 TypeError

Fixes https://github.com/galaxyproject/galaxy/issues/18138
---
 client/src/components/Tool/ToolSuccess.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Tool/ToolSuccess.vue b/client/src/components/Tool/ToolSuccess.vue
index 9f039b71598e..30da140a0980 100644
--- a/client/src/components/Tool/ToolSuccess.vue
+++ b/client/src/components/Tool/ToolSuccess.vue
@@ -31,7 +31,7 @@ onMounted(() => {
 
 <template>
     <section>
-        <div v-if="jobResponse.produces_entry_points">
+        <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" />

From a20d1633424502af5139e220826fd79e36d93f77 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 14 May 2024 12:14:39 -0500
Subject: [PATCH 05/13] add a `LoadingSpan` if there is no job response

---
 client/src/components/Tool/ToolSuccess.vue | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Tool/ToolSuccess.vue b/client/src/components/Tool/ToolSuccess.vue
index 30da140a0980..76a3613a7a25 100644
--- a/client/src/components/Tool/ToolSuccess.vue
+++ b/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>

From 81abefe5012f8cda79bcb77ebc010f2cd1e74195 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 14 May 2024 14:02:06 -0400
Subject: [PATCH 06/13] Fix accessing config prior to it potentially being
 populated.  We don't need to gate this behind a loading span, it'll just show
 the alert when and if it needs to on load.

---
 .../src/components/User/DiskUsage/Management/StorageManager.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/User/DiskUsage/Management/StorageManager.vue b/client/src/components/User/DiskUsage/Management/StorageManager.vue
index 20ba62028276..a7834a85f302 100644
--- a/client/src/components/User/DiskUsage/Management/StorageManager.vue
+++ b/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>

From 3180435cd1218e28f27da6fc1ece0dbbb9faa46e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 14 May 2024 21:01:53 +0200
Subject: [PATCH 07/13] Fix Legacy HTML page view

`.children` is a HTMLCollection object which doesn't have a forEach
interface. I confirmed this renders a few old style pages successfully.

Fixes https://github.com/galaxyproject/galaxy/issues/18144
---
 client/src/components/PageDisplay/PageHtml.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/PageDisplay/PageHtml.vue b/client/src/components/PageDisplay/PageHtml.vue
index 2ee0fb20bd66..2110bb5a8909 100644
--- a/client/src/components/PageDisplay/PageHtml.vue
+++ b/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 = Object.values(vDom.children);
                 children.forEach((child) => {
                     if (child.classList.contains("embedded-item")) {
                         const splitId = child.id.split("-");

From 91f7bec6988f316b6db1f1b75b8ad661dd0b4ecc Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Wed, 15 May 2024 08:42:50 +0200
Subject: [PATCH 08/13] Use Array.from instead of Object.values

Co-authored-by: Dannon <dannon.baker@gmail.com>
---
 client/src/components/PageDisplay/PageHtml.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/PageDisplay/PageHtml.vue b/client/src/components/PageDisplay/PageHtml.vue
index 2110bb5a8909..f7476e49b2ad 100644
--- a/client/src/components/PageDisplay/PageHtml.vue
+++ b/client/src/components/PageDisplay/PageHtml.vue
@@ -32,7 +32,7 @@ export default {
             if (content) {
                 const vDom = document.createElement("div");
                 vDom.innerHTML = content;
-                const children = Object.values(vDom.children);
+                const children = Array.from(vDom.children);
                 children.forEach((child) => {
                     if (child.classList.contains("embedded-item")) {
                         const splitId = child.id.split("-");

From 7b509b6b80cd646a474865144e98d6144994ae68 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 15 May 2024 10:36:13 +0200
Subject: [PATCH 09/13] Delay tool form rendering until config is loaded

The config typically is already loaded once you hit the tool form,
so this shouldn't cause a delay, and we already do the same effectively
for the current user and current history id.

Fixes https://github.com/galaxyproject/galaxy/issues/18139
```
TypeError: e.config is null
  at $b (webpack://@galaxyproject/galaxy-client/./src/components/Tool/ToolForm.vue?5639:1:1709)
  at Vue.prototype._render (webpack://@galaxyproject/galaxy-client/./node_modules/vue/dist/vue.esm.js:2540:28)
  at updateComponent (webpack://@galaxyproject/galaxy-client/./node_modules/vue/dist/vue.esm.js:2980:27)
  at Watcher.prototype.get (webpack://@galaxyproject/galaxy-client/./node_modules/vue/dist/vue.esm.js:4164:33)
  at Watcher.prototype.run (webpack://@galaxyproject/galaxy-client/./node_modules/vue/dist/vue.esm.js:4240:30)
...
(3 additional frame(s) were not displayed)
```
---
 client/src/components/Tool/ToolForm.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index 9c524b2c0511..d075ae597d93 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/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>

From 69e79408cde87cb907b8885bdb0bf14e07deb380 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 15 May 2024 13:56:44 +0200
Subject: [PATCH 10/13] Raise RequestParameterInvalidException when url is
 invalid

Fixes https://github.com/galaxyproject/galaxy/issues/18154
---
 lib/galaxy/files/uris.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/files/uris.py b/lib/galaxy/files/uris.py
index 139b09f391fd..42b502d77fdc 100644
--- a/lib/galaxy/files/uris.py
+++ b/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,

From 34404bd87583a0a5a0d6cf42603af44aae8fdfcb Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 15 May 2024 14:15:00 +0200
Subject: [PATCH 11/13] Drop redundant error message

There are only two places in the code where we set the job state to
error
(https://github.com/galaxyproject/galaxy/blob/ad9271cf6a33cb2e22bd7bed72f901e5215309da/lib/galaxy/jobs/handler.py#L722,
https://github.com/galaxyproject/galaxy/blob/ad9271cf6a33cb2e22bd7bed72f901e5215309da/lib/galaxy/jobs/handler.py#L733)
and both log more specific log messages.
---
 lib/galaxy/jobs/handler.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/jobs/handler.py b/lib/galaxy/jobs/handler.py
index 1df3503ffb96..f724bb736b72 100644
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -569,7 +569,8 @@ 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)

From 7c604469464ce343128a6b970823b666965d359d Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 17 May 2024 10:18:31 +0200
Subject: [PATCH 12/13] Fix error message on access to restricted zenodo
 records

---
 lib/galaxy/files/sources/invenio.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index 99b64cdf5a4e..04df3550c28c 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -15,6 +15,7 @@
     TypedDict,
 )
 
+from galaxy.exceptions import AuthenticationRequired
 from galaxy.files.sources import (
     Entry,
     EntryData,
@@ -406,6 +407,10 @@ 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:
+            raise AuthenticationRequired(
+                f"Please make sure you have the necessary permissions to access the requested resource."
+            )
         if response.status_code != expected_status_code:
             error_message = self._get_response_error_message(response)
             raise Exception(

From d6a76f704136fe2a8c934e0a9f0ed3cc740b5979 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 17 May 2024 10:38:46 +0200
Subject: [PATCH 13/13] Display record URL for verification

---
 lib/galaxy/files/sources/invenio.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index 04df3550c28c..921438a446bd 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -408,9 +408,8 @@ def _get_request_headers(self, user_context: OptionalUserContext):
 
     def _ensure_response_has_expected_status_code(self, response, expected_status_code: int):
         if response.status_code == 403:
-            raise AuthenticationRequired(
-                f"Please make sure you have the necessary permissions to access the requested resource."
-            )
+            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(