From 1a9aa620cfd86ee8d5341a71d8b792f83f20fa1e Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 6 Jul 2022 07:49:33 +0300
Subject: [PATCH 01/16] Add missing flag to generic item content wrapper

---
 client/src/components/History/Content/GenericItem.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/src/components/History/Content/GenericItem.vue b/client/src/components/History/Content/GenericItem.vue
index abe04cdf46f..982de872647 100644
--- a/client/src/components/History/Content/GenericItem.vue
+++ b/client/src/components/History/Content/GenericItem.vue
@@ -8,6 +8,7 @@
                 :name="item.name"
                 :expand-dataset="expandDataset"
                 :is-dataset="item.history_content_type == 'dataset'"
+                :is-history-item="false"
                 @update:expand-dataset="expandDataset = $event"
                 @view-collection="viewCollection = !viewCollection"
                 @delete="onDelete"

From 1d9ae14bbadf4feac0ac175efa650b753f97b627 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 6 Jul 2022 07:51:13 +0300
Subject: [PATCH 02/16] Remove redundant isHistPanel prop, should be equivalent
 to isHistoryItem?

---
 client/src/components/History/Content/ContentItem.vue         | 3 +--
 client/src/components/History/CurrentHistory/HistoryPanel.vue | 1 -
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/client/src/components/History/Content/ContentItem.vue b/client/src/components/History/Content/ContentItem.vue
index 6504ae300e6..c6dea2e0353 100644
--- a/client/src/components/History/Content/ContentItem.vue
+++ b/client/src/components/History/Content/ContentItem.vue
@@ -80,7 +80,7 @@
             <DatasetDetails
                 v-if="expandDataset"
                 :dataset="item"
-                :show-highlight="isHistoryItem && isHistPanel"
+                :show-highlight="isHistoryItem"
                 @edit="onEdit"
                 @toggleHighlights="toggleHighlights" />
         </b-collapse>
@@ -116,7 +116,6 @@ export default {
         id: { type: Number, required: true },
         isDataset: { type: Boolean, default: true },
         isHistoryItem: { type: Boolean, default: true },
-        isHistPanel: { type: Boolean, default: false },
         item: { type: Object, required: true },
         name: { type: String, required: true },
         selected: { type: Boolean, default: false },
diff --git a/client/src/components/History/CurrentHistory/HistoryPanel.vue b/client/src/components/History/CurrentHistory/HistoryPanel.vue
index f90a3965007..66a1c1cf7f8 100644
--- a/client/src/components/History/CurrentHistory/HistoryPanel.vue
+++ b/client/src/components/History/CurrentHistory/HistoryPanel.vue
@@ -105,7 +105,6 @@
                                         :name="item.name"
                                         :expand-dataset="isExpanded(item)"
                                         :is-dataset="isDataset(item)"
-                                        is-hist-panel
                                         :highlight="getHighlight(item)"
                                         :selected="isSelected(item)"
                                         :selectable="showSelection"

From 6eafb0303a4e24c17ba2eeb3482d1d1ee42790d2 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 6 Jul 2022 08:04:27 +0300
Subject: [PATCH 03/16] Set default for isHistoryItem to false

---
 client/src/components/History/Content/ContentItem.vue           | 2 +-
 client/src/components/History/Content/GenericElement.vue        | 1 -
 client/src/components/History/Content/GenericItem.vue           | 1 -
 .../components/History/CurrentCollection/CollectionPanel.vue    | 1 -
 client/src/components/History/CurrentHistory/HistoryPanel.vue   | 1 +
 5 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/client/src/components/History/Content/ContentItem.vue b/client/src/components/History/Content/ContentItem.vue
index c6dea2e0353..049f11f36ca 100644
--- a/client/src/components/History/Content/ContentItem.vue
+++ b/client/src/components/History/Content/ContentItem.vue
@@ -115,7 +115,7 @@ export default {
         highlight: { type: String, default: null },
         id: { type: Number, required: true },
         isDataset: { type: Boolean, default: true },
-        isHistoryItem: { type: Boolean, default: true },
+        isHistoryItem: { type: Boolean, default: false },
         item: { type: Object, required: true },
         name: { type: String, required: true },
         selected: { type: Boolean, default: false },
diff --git a/client/src/components/History/Content/GenericElement.vue b/client/src/components/History/Content/GenericElement.vue
index c8e8d1b0172..7b8f4068501 100644
--- a/client/src/components/History/Content/GenericElement.vue
+++ b/client/src/components/History/Content/GenericElement.vue
@@ -6,7 +6,6 @@
             :name="item.element_identifier"
             :is-dataset="item.element_type == 'hda'"
             :expand-dataset="expandDataset"
-            :is-history-item="false"
             @update:expand-dataset="expandDataset = $event"
             @view-collection="viewCollection = !viewCollection" />
         <GenericItem v-if="viewCollection" :item-id="item.object.id" :item-src="item.object.history_content_type" />
diff --git a/client/src/components/History/Content/GenericItem.vue b/client/src/components/History/Content/GenericItem.vue
index 982de872647..abe04cdf46f 100644
--- a/client/src/components/History/Content/GenericItem.vue
+++ b/client/src/components/History/Content/GenericItem.vue
@@ -8,7 +8,6 @@
                 :name="item.name"
                 :expand-dataset="expandDataset"
                 :is-dataset="item.history_content_type == 'dataset'"
-                :is-history-item="false"
                 @update:expand-dataset="expandDataset = $event"
                 @view-collection="viewCollection = !viewCollection"
                 @delete="onDelete"
diff --git a/client/src/components/History/CurrentCollection/CollectionPanel.vue b/client/src/components/History/CurrentCollection/CollectionPanel.vue
index 3977d89036f..025f48d74f3 100644
--- a/client/src/components/History/CurrentCollection/CollectionPanel.vue
+++ b/client/src/components/History/CurrentCollection/CollectionPanel.vue
@@ -28,7 +28,6 @@
                                     :name="item.element_identifier"
                                     :expand-dataset="isExpanded(item)"
                                     :is-dataset="item.element_type == 'hda'"
-                                    :is-history-item="false"
                                     @update:expand-dataset="setExpanded(item, $event)"
                                     @view-collection="onViewSubCollection" />
                             </template>
diff --git a/client/src/components/History/CurrentHistory/HistoryPanel.vue b/client/src/components/History/CurrentHistory/HistoryPanel.vue
index 66a1c1cf7f8..dbc3cf438c2 100644
--- a/client/src/components/History/CurrentHistory/HistoryPanel.vue
+++ b/client/src/components/History/CurrentHistory/HistoryPanel.vue
@@ -100,6 +100,7 @@
                                 <template v-slot:item="{ item, currentOffset }">
                                     <ContentItem
                                         v-if="!invisible[item.hid]"
+                                        is-history-item
                                         :id="item.hid"
                                         :item="item"
                                         :name="item.name"

From 6b4c7c8aa36a0da6ca692573e4d40776fff3c6e3 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 7 Jul 2022 00:41:13 +0300
Subject: [PATCH 04/16] Allow deletion, undelete and unhide for datasets
 displayed as generic items?

---
 client/src/components/History/Content/GenericItem.vue | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/client/src/components/History/Content/GenericItem.vue b/client/src/components/History/Content/GenericItem.vue
index abe04cdf46f..57fa3fbf940 100644
--- a/client/src/components/History/Content/GenericItem.vue
+++ b/client/src/components/History/Content/GenericItem.vue
@@ -3,6 +3,7 @@
         <loading-span v-if="loading" message="Loading dataset" />
         <div v-else>
             <ContentItem
+                is-history-item
                 :id="item.hid"
                 :item="item"
                 :name="item.name"
@@ -10,9 +11,9 @@
                 :is-dataset="item.history_content_type == 'dataset'"
                 @update:expand-dataset="expandDataset = $event"
                 @view-collection="viewCollection = !viewCollection"
-                @delete="onDelete"
-                @undelete="onUndelete"
-                @unhide="onUnhide" />
+                @delete="onDelete(item)"
+                @undelete="onUndelete(item)"
+                @unhide="onUnhide(item)" />
             <div v-if="viewCollection">
                 <div v-for="(collectionItem, collectionIndex) in item.elements" :key="collectionIndex">
                     <GenericElement :item="collectionItem" />

From 2b70db9cf72249d7373a3bb072ebc11e7daa27ca Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 8 Jul 2022 06:57:51 -0400
Subject: [PATCH 05/16] Fixes to have deferred data tour work a bit better.

---
 client/src/components/Tour/Tour.vue   | 10 ++++++++--
 client/src/components/Tour/runTour.js |  2 +-
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Tour/Tour.vue b/client/src/components/Tour/Tour.vue
index 00e7206e6d3..244ab085d7e 100644
--- a/client/src/components/Tour/Tour.vue
+++ b/client/src/components/Tour/Tour.vue
@@ -86,6 +86,9 @@ export default {
         isLast() {
             return this.currentIndex === this.steps.length - 1;
         },
+        hasBegun() {
+            return this.currentIndex >= 1;
+        },
     },
     beforeDestroy() {
         window.removeEventListener("keyup", this.handleKeyup);
@@ -105,12 +108,15 @@ export default {
             }
         },
         loginRequired(user) {
-            return this.requirements.indexOf("logged_in") >= 0 && user.isAnonymous;
+            return !this.hasBegun && this.requirements.indexOf("logged_in") >= 0 && user.isAnonymous;
         },
         adminRequired(user) {
-            return this.requirements.indexOf("admin") >= 0 && !user.is_admin;
+            return !this.hasBegun && this.requirements.indexOf("admin") >= 0 && !user.is_admin;
         },
         newHistoryRequired(history) {
+            if (this.hasBegun) {
+                return false;
+            }
             const hasNewNistoryRequirement = this.requirements.indexOf("new_history") >= 0;
             if (!hasNewNistoryRequirement) {
                 return false;
diff --git a/client/src/components/Tour/runTour.js b/client/src/components/Tour/runTour.js
index 39d06756893..9f5292e6b35 100644
--- a/client/src/components/Tour/runTour.js
+++ b/client/src/components/Tour/runTour.js
@@ -4,7 +4,7 @@ import { mountVueComponent } from "utils/mountVueComponent";
 import Tour from "./Tour";
 
 // delays and maximum number of attempts to wait for element
-const attempts = 100;
+const attempts = 200;
 const delay = 200;
 
 // return tour data

From f53cc284211d69113fb37e6245f36c46b93c416a Mon Sep 17 00:00:00 2001
From: Simon Bray <sbray1371@gmail.com>
Date: Fri, 8 Jul 2022 16:46:15 +0200
Subject: [PATCH 06/16] specify time as datetime object in job queries

---
 lib/galaxy/managers/jobs.py           | 3 ++-
 lib/galaxy/schema/schema.py           | 2 +-
 lib/galaxy/webapps/galaxy/api/jobs.py | 9 +++++----
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 35735c41d94..9a5ff96c317 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -1,6 +1,7 @@
 import json
 import logging
 import typing
+from datetime import datetime
 
 from boltons.iterutils import remap
 from pydantic import (
@@ -107,7 +108,7 @@ class JobManager:
 
         def build_and_apply_filters(query, objects, filter_func):
             if objects is not None:
-                if isinstance(objects, str):
+                if isinstance(objects, str) or isinstance(objects, datetime):
                     query = query.filter(filter_func(objects))
                 elif isinstance(objects, list):
                     t = []
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index 576f494e459..6e365384ad4 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1109,7 +1109,7 @@ class JobIndexQueryPayload(Model):
     user_id: Optional[DecodedDatabaseIdField] = None
     tool_ids: Optional[List[str]] = None
     tool_ids_like: Optional[List[str]] = None
-    date_range_min: Optional[str] = None
+    date_range_min: Optional[datetime] = None
     date_range_max: Optional[str] = None
     history_id: Optional[DecodedDatabaseIdField] = None
     workflow_id: Optional[DecodedDatabaseIdField] = None
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index b60cb4b6799..9c33290f9f3 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -5,6 +5,7 @@ API operations on a jobs.
 """
 
 import logging
+from datetime import datetime
 from typing import (
     Any,
     Dict,
@@ -98,13 +99,13 @@ ToolIdLikeQueryParam: Optional[str] = Query(
     description="Limit listing of jobs to those that match one of the included tool ID sql-like patterns. If none, all are returned",
 )
 
-DateRangeMinQueryParam: Optional[str] = Query(
+DateRangeMinQueryParam: Optional[datetime] = Query(
     default=None,
     title="Date Range Minimum",
     description="Limit listing of jobs to those that are updated after specified date (e.g. '2014-01-01')",
 )
 
-DateRangeMaxQueryParam: Optional[str] = Query(
+DateRangeMaxQueryParam: Optional[datetime] = Query(
     default=None,
     title="Date Range Maximum",
     description="Limit listing of jobs to those that are updated before specified date (e.g. '2014-01-01')",
@@ -186,8 +187,8 @@ class FastAPIJobs:
         view: JobIndexViewEnum = ViewQueryParam,
         tool_id: Optional[str] = ToolIdQueryParam,
         tool_id_like: Optional[str] = ToolIdLikeQueryParam,
-        date_range_min: Optional[str] = DateRangeMinQueryParam,
-        date_range_max: Optional[str] = DateRangeMaxQueryParam,
+        date_range_min: Optional[datetime] = DateRangeMinQueryParam,
+        date_range_max: Optional[datetime] = DateRangeMaxQueryParam,
         history_id: Optional[EncodedDatabaseIdField] = HistoryIdQueryParam,
         workflow_id: Optional[EncodedDatabaseIdField] = WorkflowIdQueryParam,
         invocation_id: Optional[EncodedDatabaseIdField] = InvocationIdQueryParam,

From de4fd14ca71ab0a492918da684fcb97e4f4804a6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?David=20L=C3=B3pez?=
 <46503462+davelopez@users.noreply.github.com>
Date: Fri, 8 Jul 2022 17:03:36 +0200
Subject: [PATCH 07/16] Change date_range_max type to datetime

---
 lib/galaxy/schema/schema.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index 6e365384ad4..9fe7063aeb5 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1110,7 +1110,7 @@ class JobIndexQueryPayload(Model):
     tool_ids: Optional[List[str]] = None
     tool_ids_like: Optional[List[str]] = None
     date_range_min: Optional[datetime] = None
-    date_range_max: Optional[str] = None
+    date_range_max: Optional[datetime] = None
     history_id: Optional[DecodedDatabaseIdField] = None
     workflow_id: Optional[DecodedDatabaseIdField] = None
     invocation_id: Optional[DecodedDatabaseIdField] = None

From e359db2306d1a5ca5292c000a3c500c632280833 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 8 Jul 2022 18:52:56 +0300
Subject: [PATCH 08/16] Fix for encoding Decimal values

Fixes https://sentry.galaxyproject.org/organizations/galaxy/issues/84786/?project=3&query=is%3Aunresolved&statsPeriod=14d
---
 lib/galaxy/util/json.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/util/json.py b/lib/galaxy/util/json.py
index 53d9f5cc71a..2b73556d2c4 100644
--- a/lib/galaxy/util/json.py
+++ b/lib/galaxy/util/json.py
@@ -9,6 +9,7 @@ from collections.abc import (
     Mapping,
     Sequence,
 )
+from decimal import Decimal
 
 from ..util import unicodify
 
@@ -22,7 +23,8 @@ from_json_string = json.loads
 
 def swap_inf_nan(val):
     """
-    This takes an arbitrary object and preps it for jsonifying safely, templating Inf/NaN.
+    This takes an arbitrary object and preps it for jsonifying safely, templating Inf/NaN and
+    casting Decimal instances as strings.
     """
     if isinstance(val, str):
         # basestring first, because it's a sequence and would otherwise get caught below.
@@ -40,6 +42,8 @@ def swap_inf_nan(val):
             return "__-Infinity__"
         else:
             return val
+    elif isinstance(val, Decimal):
+        return str(val)
     else:
         return val
 
@@ -63,12 +67,12 @@ def safe_dumps(obj, **kwargs):
     """
     This is a wrapper around dumps that encodes Infinity and NaN values.  It's a
     fairly rare case (which will be low in request volume).  Basically, we tell
-    json.dumps to blow up if it encounters Infinity/NaN, and we 'fix' it before
-    re-encoding.
+    json.dumps to blow up if it encounters Infinity/NaN, or Decimal values,
+    and we 'fix' it before re-encoding.
     """
     try:
         dumped = json.dumps(obj, allow_nan=False, **kwargs)
-    except ValueError:
+    except (ValueError, TypeError):
         obj = swap_inf_nan(obj)
         dumped = json.dumps(obj, allow_nan=False, **kwargs)
     if kwargs.get("escape_closing_tags", True):

From bd4690d9259e6b46c0214bd2fe7841bfe1f95b3f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 8 Jul 2022 18:56:46 +0300
Subject: [PATCH 09/16] Fix infinity value handling when serailzing tool form

Should fix https://github.com/galaxyproject/galaxy/issues/9576.
Seems like at some point in the past json.dumsp must've raised
a ValueError if you tried to serialize inf, but it doesn't anymore,
so the workaround in swap_inf_nan didn't work for inf.
---
 lib/galaxy/tools/__init__.py | 7 +++++--
 lib/galaxy/util/json.py      | 2 +-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index dee9955881e..d9ae71fcc2d 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -120,7 +120,10 @@ from galaxy.util.bunch import Bunch
 from galaxy.util.dictifiable import Dictifiable
 from galaxy.util.expressions import ExpressionContext
 from galaxy.util.form_builder import SelectField
-from galaxy.util.json import safe_loads
+from galaxy.util.json import (
+    safe_loads,
+    swap_inf_nan,
+)
 from galaxy.util.rules_dsl import RuleSet
 from galaxy.util.template import (
     fill_template,
@@ -2459,7 +2462,7 @@ class Tool(Dictifiable):
                 "enctype": self.enctype,
             }
         )
-        return tool_model
+        return swap_inf_nan(tool_model)
 
     def populate_model(self, request_context, inputs, state_inputs, group_inputs, other_values=None):
         """
diff --git a/lib/galaxy/util/json.py b/lib/galaxy/util/json.py
index 2b73556d2c4..a6980f94036 100644
--- a/lib/galaxy/util/json.py
+++ b/lib/galaxy/util/json.py
@@ -67,7 +67,7 @@ def safe_dumps(obj, **kwargs):
     """
     This is a wrapper around dumps that encodes Infinity and NaN values.  It's a
     fairly rare case (which will be low in request volume).  Basically, we tell
-    json.dumps to blow up if it encounters Infinity/NaN, or Decimal values,
+    json.dumps to blow up if it encounters Infinity/NaN, or Decimal values
     and we 'fix' it before re-encoding.
     """
     try:

From 73c73e0822aa8584edb6ba99717b4ee6c88bab53 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 8 Jul 2022 19:39:38 +0300
Subject: [PATCH 10/16] Test Decimal/inf/nan value dumping

---
 test/unit/util/test_json.py | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 test/unit/util/test_json.py

diff --git a/test/unit/util/test_json.py b/test/unit/util/test_json.py
new file mode 100644
index 00000000000..dc1a3432d50
--- /dev/null
+++ b/test/unit/util/test_json.py
@@ -0,0 +1,25 @@
+from decimal import Decimal
+
+import pytest
+
+from galaxy.util.json import (
+    safe_dumps,
+    swap_inf_nan,
+)
+
+
+@pytest.mark.parametrize(
+    "val,expected_val",
+    [
+        (float("inf"), "__Infinity__"),
+        (float("-inf"), "__-Infinity__"),
+        (float("NaN"), "__NaN__"),
+        (Decimal("1"), "1"),
+    ],
+)
+def test_swap_inf_nan(val, expected_val):
+    assert swap_inf_nan(val) == expected_val
+
+
+def test_safe_dumps():
+    assert safe_dumps({"a": Decimal("0.1")}) == """{"a": "0.1"}"""

From 02125b994a4794d813e4e85edd39748a52c3db9d Mon Sep 17 00:00:00 2001
From: simonbray <sbray1371@gmail.com>
Date: Sat, 9 Jul 2022 16:15:06 +0200
Subject: [PATCH 11/16] fix datetime formatting in test_index_date_filter test

---
 lib/galaxy_test/api/test_jobs.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy_test/api/test_jobs.py b/lib/galaxy_test/api/test_jobs.py
index 992cf4dd89c..6f2c0324ac8 100644
--- a/lib/galaxy_test/api/test_jobs.py
+++ b/lib/galaxy_test/api/test_jobs.py
@@ -82,14 +82,14 @@ class JobsApiTestCase(ApiTestCase, TestsTools):
 
     @uses_test_history(require_new=True)
     def test_index_date_filter(self, history_id):
-        self.__history_with_new_dataset(history_id)
         two_weeks_ago = (datetime.datetime.utcnow() - datetime.timedelta(14)).isoformat()
         last_week = (datetime.datetime.utcnow() - datetime.timedelta(7)).isoformat()
         next_week = (datetime.datetime.utcnow() + datetime.timedelta(7)).isoformat()
         today = datetime.datetime.utcnow().isoformat()
         tomorrow = (datetime.datetime.utcnow() + datetime.timedelta(1)).isoformat()
+        self.__history_with_new_dataset(history_id)
 
-        jobs = self.__jobs_index(data={"date_range_min": today[0:10], "date_range_max": tomorrow[0:10]})
+        jobs = self.__jobs_index(data={"date_range_min": today, "date_range_max": tomorrow})
         assert len(jobs) > 0
         today_job_id = jobs[0]["id"]
 

From 457a627586958a9e25af01e141aee8570f001561 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 9 Jul 2022 17:43:37 +0300
Subject: [PATCH 12/16] Drop dataset controller errors method

The mako is gone, this is all client-side. Also updates the link
generated in the legacy history. Fixes
https://sentry.galaxyproject.org/share/issue/99796552da0246ae982c33e2559fb1f7/:
```
TopLevelLookupException: Can't locate template for uri 'dataset/errors.mako'
  File "uvicorn/protocols/http/h11_impl.py", line 366, in run_asgi
    result = await app(self.scope, self.receive, self.send)
  File "uvicorn/middleware/proxy_headers.py", line 75, in __call__
    return await self.app(scope, receive, send)
  File "fastapi/applications.py", line 269, in __call__
    await super().__call__(scope, receive, send)
  File "starlette/applications.py", line 124, in __call__
    await self.middleware_stack(scope, receive, send)
  File "starlette/middleware/errors.py", line 184, in __call__
    raise exc
  File "starlette/middleware/errors.py", line 162, in __call__
    await self.app(scope, receive, _send)
  File "starlette/middleware/base.py", line 69, in __call__
    await response(scope, receive, send)
  File "starlette/responses.py", line 260, in __call__
    await wrap(partial(self.listen_for_disconnect, receive))
  File "anyio/_backends/_asyncio.py", line 662, in __aexit__
    raise exceptions[0]
  File "starlette/responses.py", line 256, in wrap
    await func()
  File "starlette/responses.py", line 245, in stream_response
    async for chunk in self.body_iterator:
  File "starlette/middleware/base.py", line 58, in body_stream
    raise app_exc
  File "starlette/middleware/base.py", line 36, in coro
    await self.app(scope, request.receive, send_stream.send)
  File "starlette_context/middleware/raw_middleware.py", line 96, in __call__
    await self.app(scope, receive, send_wrapper)
  File "starlette/middleware/base.py", line 69, in __call__
    await response(scope, receive, send)
  File "starlette/responses.py", line 260, in __call__
    await wrap(partial(self.listen_for_disconnect, receive))
  File "anyio/_backends/_asyncio.py", line 662, in __aexit__
    raise exceptions[0]
  File "starlette/responses.py", line 256, in wrap
    await func()
  File "starlette/responses.py", line 245, in stream_response
    async for chunk in self.body_iterator:
  File "starlette/middleware/base.py", line 58, in body_stream
    raise app_exc
  File "starlette/middleware/base.py", line 36, in coro
    await self.app(scope, request.receive, send_stream.send)
  File "starlette/middleware/base.py", line 69, in __call__
    await response(scope, receive, send)
  File "starlette/responses.py", line 260, in __call__
    await wrap(partial(self.listen_for_disconnect, receive))
  File "anyio/_backends/_asyncio.py", line 662, in __aexit__
    raise exceptions[0]
  File "starlette/responses.py", line 256, in wrap
    await func()
  File "starlette/responses.py", line 245, in stream_response
    async for chunk in self.body_iterator:
  File "starlette/middleware/base.py", line 58, in body_stream
    raise app_exc
  File "starlette/middleware/base.py", line 36, in coro
    await self.app(scope, request.receive, send_stream.send)
  File "starlette/exceptions.py", line 93, in __call__
    raise exc
  File "starlette/exceptions.py", line 82, in __call__
    await self.app(scope, receive, sender)
  File "fastapi/middleware/asyncexitstack.py", line 21, in __call__
    raise e
  File "fastapi/middleware/asyncexitstack.py", line 18, in __call__
    await self.app(scope, receive, send)
  File "starlette/routing.py", line 670, in __call__
    await route.handle(scope, receive, send)
  File "starlette/routing.py", line 418, in handle
    await self.app(scope, receive, send)
  File "a2wsgi/wsgi.py", line 140, in __call__
    return await responder(scope, receive, send)
  File "a2wsgi/wsgi.py", line 179, in __call__
    raise self.exc_info[0].with_traceback(
  File "galaxy/web/framework/middleware/error.py", line 165, in __call__
    app_iter = self.application(environ, sr_checker)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.8/site-packages/paste/recursive.py", line 85, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/middleware/statsd.py", line 29, in __call__
    req = self.application(environ, start_response)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.8/site-packages/paste/httpexceptions.py", line 640, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/base.py", line 159, in __call__
    return self.handle_request(environ, start_response)
  File "galaxy/web/framework/base.py", line 244, in handle_request
    body = method(trans, **kwargs)
  File "galaxy/webapps/galaxy/controllers/dataset.py", line 99, in errors
    return trans.fill_template("dataset/errors.mako", hda=hda)
  File "galaxy/webapps/base/webapp.py", line 1095, in fill_template
    return self.fill_template_mako(filename, **kwargs)
  File "galaxy/webapps/base/webapp.py", line 1099, in fill_template_mako
    template = template_lookup.get_template(filename)
  File "mako/lookup.py", line 254, in get_template
    raise exceptions.TopLevelLookupException(
```
---
 client/src/mvc/dataset/dataset-model.js          |  2 +-
 lib/galaxy/webapps/galaxy/controllers/dataset.py | 11 -----------
 2 files changed, 1 insertion(+), 12 deletions(-)

diff --git a/client/src/mvc/dataset/dataset-model.js b/client/src/mvc/dataset/dataset-model.js
index cb62962d54d..e7f7a9d132d 100644
--- a/client/src/mvc/dataset/dataset-model.js
+++ b/client/src/mvc/dataset/dataset-model.js
@@ -75,7 +75,7 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                     display: `datasets/${id}/display/?preview=True`,
                     edit: `datasets/edit?dataset_id=${id}`,
                     download: `api/datasets/${id}/display${this._downloadQueryParameters()}`,
-                    report_error: `dataset/errors?id=${id}`,
+                    report_error: `datasets/error?dataset_id=${id}`,
                     rerun: `tool_runner/rerun?id=${id}`,
                     show_params: `datasets/${id}/details`,
                     visualization: "visualization",
diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index 59da806cf5b..8e7c54cba72 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -10,7 +10,6 @@ from markupsafe import escape
 
 from galaxy import (
     datatypes,
-    model,
     util,
     web,
 )
@@ -88,16 +87,6 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             roles, dataset_association.dataset
         )
 
-    @web.expose
-    def errors(self, trans, id):
-        hda = trans.sa_session.query(model.HistoryDatasetAssociation).get(self.decode_id(id))
-
-        if not hda or not self._can_access_dataset(trans, hda):
-            return trans.show_error_message(
-                "Either this dataset does not exist or you do not have permission to access it."
-            )
-        return trans.fill_template("dataset/errors.mako", hda=hda)
-
     @web.expose
     def stdout(self, trans, dataset_id=None, **kwargs):
         trans.response.set_content_type("text/plain")

From 02bbb4bc4126a61428cc56ac1345915762a5056d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 10 Jul 2022 19:33:40 +0300
Subject: [PATCH 13/16] Fix display_as with authz_method=rbac

Fixes
https://sentry.galaxyproject.org/share/issue/57576c6c0bfe44c498ccd2bf519deceb/:
```
AttributeError: 'HistoryDatasetAssociation' object has no attribute 'actions'
  File "uvicorn/protocols/http/h11_impl.py", line 366, in run_asgi
    result = await app(self.scope, self.receive, self.send)
  File "uvicorn/middleware/proxy_headers.py", line 75, in __call__
    return await self.app(scope, receive, send)
  File "fastapi/applications.py", line 269, in __call__
    await super().__call__(scope, receive, send)
  File "starlette/applications.py", line 124, in __call__
    await self.middleware_stack(scope, receive, send)
  File "starlette/middleware/errors.py", line 184, in __call__
    raise exc
  File "starlette/middleware/errors.py", line 162, in __call__
    await self.app(scope, receive, _send)
  File "starlette/middleware/base.py", line 69, in __call__
    await response(scope, receive, send)
  File "starlette/responses.py", line 260, in __call__
    await wrap(partial(self.listen_for_disconnect, receive))
  File "anyio/_backends/_asyncio.py", line 662, in __aexit__
    raise exceptions[0]
  File "starlette/responses.py", line 256, in wrap
    await func()
  File "starlette/responses.py", line 245, in stream_response
    async for chunk in self.body_iterator:
  File "starlette/middleware/base.py", line 58, in body_stream
    raise app_exc
  File "starlette/middleware/base.py", line 36, in coro
    await self.app(scope, request.receive, send_stream.send)
  File "starlette_context/middleware/raw_middleware.py", line 96, in __call__
    await self.app(scope, receive, send_wrapper)
  File "starlette/middleware/base.py", line 69, in __call__
    await response(scope, receive, send)
  File "starlette/responses.py", line 260, in __call__
    await wrap(partial(self.listen_for_disconnect, receive))
  File "anyio/_backends/_asyncio.py", line 662, in __aexit__
    raise exceptions[0]
  File "starlette/responses.py", line 256, in wrap
    await func()
  File "starlette/responses.py", line 245, in stream_response
    async for chunk in self.body_iterator:
  File "starlette/middleware/base.py", line 58, in body_stream
    raise app_exc
  File "starlette/middleware/base.py", line 36, in coro
    await self.app(scope, request.receive, send_stream.send)
  File "starlette/middleware/base.py", line 69, in __call__
    await response(scope, receive, send)
  File "starlette/responses.py", line 260, in __call__
    await wrap(partial(self.listen_for_disconnect, receive))
  File "anyio/_backends/_asyncio.py", line 662, in __aexit__
    raise exceptions[0]
  File "starlette/responses.py", line 256, in wrap
    await func()
  File "starlette/responses.py", line 245, in stream_response
    async for chunk in self.body_iterator:
  File "starlette/middleware/base.py", line 58, in body_stream
    raise app_exc
  File "starlette/middleware/base.py", line 36, in coro
    await self.app(scope, request.receive, send_stream.send)
  File "starlette/exceptions.py", line 93, in __call__
    raise exc
  File "starlette/exceptions.py", line 82, in __call__
    await self.app(scope, receive, sender)
  File "fastapi/middleware/asyncexitstack.py", line 21, in __call__
    raise e
  File "fastapi/middleware/asyncexitstack.py", line 18, in __call__
    await self.app(scope, receive, send)
  File "starlette/routing.py", line 670, in __call__
    await route.handle(scope, receive, send)
  File "starlette/routing.py", line 418, in handle
    await self.app(scope, receive, send)
  File "a2wsgi/wsgi.py", line 140, in __call__
    return await responder(scope, receive, send)
  File "a2wsgi/wsgi.py", line 179, in __call__
    raise self.exc_info[0].with_traceback(
  File "galaxy/web/framework/middleware/error.py", line 165, in __call__
    app_iter = self.application(environ, sr_checker)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.8/site-packages/paste/recursive.py", line 85, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/middleware/statsd.py", line 29, in __call__
    req = self.application(environ, start_response)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.8/site-packages/paste/httpexceptions.py", line 640, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/base.py", line 159, in __call__
    return self.handle_request(environ, start_response)
  File "galaxy/web/framework/base.py", line 244, in handle_request
    body = method(trans, **kwargs)
  File "galaxy/webapps/galaxy/controllers/root.py", line 111, in display_as
    if authz_method == "rbac" and trans.app.security_agent.can_access_dataset(current_user_roles, data):
  File "galaxy/model/security.py", line 506, in can_access_dataset
    retval = self.dataset_is_public(dataset) or self.allow_action(
  File "galaxy/model/security.py", line 1132, in dataset_is_public
    return self.permitted_actions.DATASET_ACCESS.action not in [a.action for a in dataset.actions]
```
---
 lib/galaxy/model/security.py                  | 4 ++--
 lib/galaxy/webapps/galaxy/controllers/root.py | 5 +++--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/model/security.py b/lib/galaxy/model/security.py
index 738db0b548c..3e5690e78fc 100644
--- a/lib/galaxy/model/security.py
+++ b/lib/galaxy/model/security.py
@@ -500,7 +500,7 @@ class GalaxyRBACAgent(RBACAgent):
     def item_permission_map_for_add(self, trans, user_roles, libitems):
         return self.allow_action_on_libitems(trans, user_roles, self.permitted_actions.LIBRARY_ADD, libitems)
 
-    def can_access_dataset(self, user_roles, dataset):
+    def can_access_dataset(self, user_roles, dataset: galaxy.model.Dataset):
         # SM: dataset_is_public will access dataset.actions, which is a
         # backref that causes a query to be made to DatasetPermissions
         retval = self.dataset_is_public(dataset) or self.allow_action(
@@ -1122,7 +1122,7 @@ class GalaxyRBACAgent(RBACAgent):
             if not dataset.purged and not self.dataset_is_public(dataset):
                 self.make_dataset_public(dataset)
 
-    def dataset_is_public(self, dataset):
+    def dataset_is_public(self, dataset: galaxy.model.Dataset):
         """
         A dataset is considered public if there are no "access" actions
         associated with it.  Any other actions ( 'manage permissions',
diff --git a/lib/galaxy/webapps/galaxy/controllers/root.py b/lib/galaxy/webapps/galaxy/controllers/root.py
index eda5a45ae26..ce48fc68c00 100644
--- a/lib/galaxy/webapps/galaxy/controllers/root.py
+++ b/lib/galaxy/webapps/galaxy/controllers/root.py
@@ -107,8 +107,9 @@ class RootController(controller.JSAppLauncher, UsesAnnotations):
         if "authz_method" in kwd:
             authz_method = kwd["authz_method"]
         if data:
-            current_user_roles = trans.get_current_user_roles()
-            if authz_method == "rbac" and trans.app.security_agent.can_access_dataset(current_user_roles, data):
+            if authz_method == "rbac" and trans.app.security_agent.can_access_dataset(
+                trans.get_current_user_roles(), data.dataset
+            ):
                 trans.response.set_content_type(data.get_mime())
                 trans.log_event(f"Formatted dataset id {str(id)} for display at {display_app}")
                 return data.as_display_type(display_app, **kwd)

From e52130b0121d712c0a4d761874851fc5756a11a4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 10 Jul 2022 18:12:08 +0300
Subject: [PATCH 14/16] Urlencode parameters in tagService.js

Fixes
https://sentry.galaxyproject.org/share/issue/ff9f4891f34e4308b8183ef604970761/:
```
TypeError: tag_autocomplete_data() got an unexpected keyword argument 'd'
  File "uvicorn/protocols/http/h11_impl.py", line 366, in run_asgi
    result = await app(self.scope, self.receive, self.send)
  File "uvicorn/middleware/proxy_headers.py", line 75, in __call__
    return await self.app(scope, receive, send)
  File "fastapi/applications.py", line 269, in __call__
    await super().__call__(scope, receive, send)
  File "starlette/applications.py", line 124, in __call__
    await self.middleware_stack(scope, receive, send)
  File "starlette/middleware/errors.py", line 184, in __call__
    raise exc
  File "starlette/middleware/errors.py", line 162, in __call__
    await self.app(scope, receive, _send)
  File "starlette/middleware/base.py", line 69, in __call__
    await response(scope, receive, send)
  File "starlette/responses.py", line 260, in __call__
    await wrap(partial(self.listen_for_disconnect, receive))
  File "anyio/_backends/_asyncio.py", line 662, in __aexit__
    raise exceptions[0]
  File "starlette/responses.py", line 256, in wrap
    await func()
  File "starlette/responses.py", line 245, in stream_response
    async for chunk in self.body_iterator:
  File "starlette/middleware/base.py", line 58, in body_stream
    raise app_exc
  File "starlette/middleware/base.py", line 36, in coro
    await self.app(scope, request.receive, send_stream.send)
  File "starlette_context/middleware/raw_middleware.py", line 96, in __call__
    await self.app(scope, receive, send_wrapper)
  File "starlette/middleware/base.py", line 69, in __call__
    await response(scope, receive, send)
  File "starlette/responses.py", line 260, in __call__
    await wrap(partial(self.listen_for_disconnect, receive))
  File "anyio/_backends/_asyncio.py", line 662, in __aexit__
    raise exceptions[0]
  File "starlette/responses.py", line 256, in wrap
    await func()
  File "starlette/responses.py", line 245, in stream_response
    async for chunk in self.body_iterator:
  File "starlette/middleware/base.py", line 58, in body_stream
    raise app_exc
  File "starlette/middleware/base.py", line 36, in coro
    await self.app(scope, request.receive, send_stream.send)
  File "starlette/middleware/base.py", line 69, in __call__
    await response(scope, receive, send)
  File "starlette/responses.py", line 260, in __call__
    await wrap(partial(self.listen_for_disconnect, receive))
  File "anyio/_backends/_asyncio.py", line 662, in __aexit__
    raise exceptions[0]
  File "starlette/responses.py", line 256, in wrap
    await func()
  File "starlette/responses.py", line 245, in stream_response
    async for chunk in self.body_iterator:
  File "starlette/middleware/base.py", line 58, in body_stream
    raise app_exc
  File "starlette/middleware/base.py", line 36, in coro
    await self.app(scope, request.receive, send_stream.send)
  File "starlette/exceptions.py", line 93, in __call__
    raise exc
  File "starlette/exceptions.py", line 82, in __call__
    await self.app(scope, receive, sender)
  File "fastapi/middleware/asyncexitstack.py", line 21, in __call__
    raise e
  File "fastapi/middleware/asyncexitstack.py", line 18, in __call__
    await self.app(scope, receive, send)
  File "starlette/routing.py", line 670, in __call__
    await route.handle(scope, receive, send)
  File "starlette/routing.py", line 418, in handle
    await self.app(scope, receive, send)
  File "a2wsgi/wsgi.py", line 140, in __call__
    return await responder(scope, receive, send)
  File "a2wsgi/wsgi.py", line 179, in __call__
    raise self.exc_info[0].with_traceback(
  File "galaxy/web/framework/middleware/error.py", line 165, in __call__
    app_iter = self.application(environ, sr_checker)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.8/site-packages/paste/recursive.py", line 85, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/middleware/statsd.py", line 29, in __call__
    req = self.application(environ, start_response)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.8/site-packages/paste/httpexceptions.py", line 640, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/base.py", line 159, in __call__
    return self.handle_request(environ, start_response)
  File "galaxy/web/framework/base.py", line 244, in handle_request
    body = method(trans, **kwargs)
  File "galaxy/web/framework/decorators.py", line 84, in decorator
    return func(self, trans, *args, **kwargs)
```

You can test this by editing a history tag in the history menu, by
writing `tag;d`, there should be no 500 error on the Galaxy logs.
---
 client/src/components/Tags/tagService.js      | 21 +++---
 client/src/components/Tags/tagService.test.js | 64 +++++--------------
 2 files changed, 28 insertions(+), 57 deletions(-)

diff --git a/client/src/components/Tags/tagService.js b/client/src/components/Tags/tagService.js
index 304d9c1c224..dff2439d3a1 100644
--- a/client/src/components/Tags/tagService.js
+++ b/client/src/components/Tags/tagService.js
@@ -57,10 +57,11 @@ export class TagService {
         if (!tag.valid) {
             throw new Error("Invalid tag");
         }
-        const url = `${getAppRoot()}tag/add_tag_async?item_id=${id}&item_class=${itemClass}&context=${context}&new_tag=${
-            tag.text
-        }`;
-        const response = await axios.get(url);
+        const url = `${getAppRoot()}tag/add_tag_async`;
+        const config = {
+            params: { item_id: id, item_class: itemClass, context: context, new_tag: tag.text },
+        };
+        const response = await axios.get(url, config);
         if (response.status !== 200) {
             throw new Error(`Unable to save tag: ${tag}`);
         }
@@ -75,10 +76,9 @@ export class TagService {
     async delete(rawTag) {
         const { id, itemClass, context } = this;
         const tag = createTag(rawTag);
-        const url = `${getAppRoot()}tag/remove_tag_async?item_id=${id}&item_class=${itemClass}&context=${context}&tag_name=${
-            tag.text
-        }`;
-        const response = await axios.get(url);
+        const url = `${getAppRoot()}tag/remove_tag_async`;
+        const config = { params: { item_id: id, item_class: itemClass, context: context, tag_name: tag.text } };
+        const response = await axios.get(url, config);
         if (response.status !== 200) {
             throw new Error(`Unable to delete tag: ${tag}`);
         }
@@ -92,8 +92,9 @@ export class TagService {
      */
     async autocomplete(searchText) {
         const { id, itemClass } = this;
-        const url = `${getAppRoot()}tag/tag_autocomplete_data?item_id=${id}&item_class=${itemClass}&q=${searchText}`;
-        const response = await axios.get(url);
+        const url = `${getAppRoot()}tag/tag_autocomplete_data`;
+        const config = { params: { item_id: id, item_class: itemClass, q: searchText } };
+        const response = await axios.get(url, config);
         if (response.status !== 200) {
             throw new Error(`Unable to retrieve autocomplete tags for search string: ${searchText}`);
         }
diff --git a/client/src/components/Tags/tagService.test.js b/client/src/components/Tags/tagService.test.js
index 79ba1025758..c8fb78145ee 100644
--- a/client/src/components/Tags/tagService.test.js
+++ b/client/src/components/Tags/tagService.test.js
@@ -2,9 +2,6 @@ import axios from "axios";
 import MockAdapter from "axios-mock-adapter";
 import { TagService } from "./tagService";
 import { createTag } from "./model";
-//import { interval } from "rxjs";
-//import { take, takeUntil } from "rxjs/operators";
-// test response
 import autocompleteResponse from "./testData/autocompleteResponse.txt";
 
 describe("Tags/tagService.js", () => {
@@ -15,6 +12,12 @@ describe("Tags/tagService.js", () => {
         context: "",
         debounceInterval: 50, // shorter value than default for unit tests
     };
+    const testLabel = "fo0bar123";
+    const expectedParams = {
+        item_id: 123,
+        item_class: "fooClass",
+        context: "",
+    };
 
     const svc = new TagService(svcParams);
     beforeEach(() => {
@@ -26,43 +29,43 @@ describe("Tags/tagService.js", () => {
     });
 
     describe("save", () => {
-        const testLabel = "fo0bar123";
         const testTag = createTag(testLabel);
 
-        const { id, itemClass, context } = svcParams;
-        const expectedSaveUrl = `/tag/add_tag_async?item_id=${id}&item_class=${itemClass}&context=${context}&new_tag=${testLabel}`;
+        const expectedSaveUrl = `/tag/add_tag_async`;
 
         it("should save a string tag", async () => {
             const savedTag = await svc.save(testLabel);
             expect(savedTag.text).toBe(testLabel);
             expect(axiosMock.history.get[0].url).toBe(expectedSaveUrl);
+            expect(axiosMock.history.get[0].params).toEqual({ ...expectedParams, new_tag: testLabel });
         });
 
         it("should save an object tag", async () => {
             const savedTag = await svc.save(testTag);
             expect(savedTag.text).toBe(testLabel);
             expect(axiosMock.history.get[0].url).toBe(expectedSaveUrl);
+            expect(axiosMock.history.get[0].params).toEqual({ ...expectedParams, new_tag: testLabel });
         });
 
         // TODO: test error conditions
     });
     describe("delete", () => {
-        const testLabel = "fo0bar123";
         const testTag = createTag(testLabel);
 
-        const { id, itemClass, context } = svcParams;
-        const expectedDeleteUrl = `/tag/remove_tag_async?item_id=${id}&item_class=${itemClass}&context=${context}&tag_name=${testLabel}`;
+        const expectedDeleteUrl = `/tag/remove_tag_async`;
 
         it("should delete a text tag", async () => {
             const result = await svc.delete(testTag);
             expect(result).toBeTruthy();
             expect(axiosMock.history.get[0].url).toBe(expectedDeleteUrl);
+            expect(axiosMock.history.get[0].params).toEqual({ ...expectedParams, tag_name: testLabel });
         });
 
         it("should delete an object tag", async () => {
             const result = await svc.delete(testTag);
             expect(result).toBeTruthy();
             expect(axiosMock.history.get[0].url).toBe(expectedDeleteUrl);
+            expect(axiosMock.history.get[0].params).toEqual({ ...expectedParams, tag_name: testLabel });
         });
 
         // TODO: test error conditions
@@ -70,8 +73,7 @@ describe("Tags/tagService.js", () => {
 
     describe("autocomplete", () => {
         const searchString = "foo";
-        const { id, itemClass } = svcParams;
-        const expectedSearchUrl = `/tag/tag_autocomplete_data?item_id=${id}&item_class=${itemClass}&q=${searchString}`;
+        const expectedSearchUrl = `/tag/tag_autocomplete_data`;
 
         const checkAutocompleteResult = (result) => {
             expect(result).toBeTruthy();
@@ -83,46 +85,14 @@ describe("Tags/tagService.js", () => {
 
         // straight ajax request, unused in practice, but it's easier to
         // test this call if we just expose it
+        const { ...searchParams } = expectedParams;
+        delete searchParams.context;
+
         it("ajax call should return tag objects", async () => {
             const result = await svc.autocomplete(searchString);
             expect(axiosMock.history.get[0].url).toBe(expectedSearchUrl);
+            expect(axiosMock.history.get[0].params).toEqual({ ...searchParams, q: searchString });
             checkAutocompleteResult(result);
         });
-
-        /*
-
-        // hit the search input with multiple entries, only one ajax call
-        // should result because of debouncing
-        it("should debounce autocomplete search inputs", (done) => {
-            // stub ajax request to return the success response if the
-            // searchString is the expected input
-
-            // take first emission, debouncing should guarantee the first
-            // emission is the last thing we sent, should be searchString
-            const timer$ = interval(100).pipe(take(1));
-            const option$ = svc.autocompleteOptions.pipe(takeUntil(timer$));
-
-            const nextHandler = jest.fn();
-
-            option$.subscribe({
-                next: nextHandler,
-                error: (err) => console.warn("error", err),
-                complete: () => {
-                    expect(nextHandler).toHaveBeenCalledTimes(1);
-                    expect(axiosMock.history.get.length).toBe(1);
-                    done();
-                },
-            });
-
-            // spam a bunch of key inputs followed by the correct input
-            const spamCount = 2 + Math.floor(Math.random() * 10);
-            for (let i = 0; i < spamCount; i++) {
-                const spamVal = new String(Math.random());
-                svc.autocompleteSearchText = spamVal;
-            }
-            svc.autocompleteSearchText = searchString;
-        });
-
-        */
     });
 });

From ac3625eb20e7c0a4a7ed17d8c9e7b6e8e809551d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 11 Jul 2022 11:07:31 +0300
Subject: [PATCH 15/16] Check for app_name and link_name before unquoting

Should fix
https://sentry.galaxyproject.org/share/issue/f20a1d47fab04ca8bca7a657d81fb568/:
```
AttributeError: 'NoneType' object has no attribute 'replace'
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.8/site-packages/paste/recursive.py", line 85, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/middleware/statsd.py", line 29, in __call__
    req = self.application(environ, start_response)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.8/site-packages/paste/httpexceptions.py", line 640, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/base.py", line 159, in __call__
    return self.handle_request(environ, start_response)
  File "galaxy/web/framework/base.py", line 244, in handle_request
    body = method(trans, **kwargs)
  File "galaxy/web/framework/decorators.py", line 138, in set_nocache_headers
    return func(self, trans, *args, **kwargs)
  File "galaxy/webapps/galaxy/controllers/dataset.py", line 738, in display_application
    link_name = unquote_plus(link_name)
  File "urllib/parse.py", line 777, in unquote_plus
    string = string.replace('+', ' ')
```
---
 lib/galaxy/webapps/galaxy/controllers/dataset.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index 8e7c54cba72..f07d2c66d5a 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -702,6 +702,10 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         **kwds,
     ):
         """Access to external display applications"""
+        if None in [app_name, link_name]:
+            return trans.show_error_message("A display application name and link name must be provided.")
+        app_name = unquote_plus(app_name)
+        link_name = unquote_plus(link_name)
         # Build list of parameters to pass in to display application logic (app_kwds)
         app_kwds = {}
         for name, value in dict(kwds).items():  # clone kwds because we remove stuff as we go.
@@ -723,10 +727,6 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         else:
             user_roles = []
         # Decode application name and link name
-        app_name = unquote_plus(app_name)
-        link_name = unquote_plus(link_name)
-        if None in [app_name, link_name]:
-            return trans.show_error_message("A display application name and link name must be provided.")
         if self._can_access_dataset(trans, data, additional_roles=user_roles):
             msg = []
             preparable_steps = []

From fc8594aee551a90e86dd70a7f895e269456efa2a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 11 Jul 2022 11:46:51 +0300
Subject: [PATCH 16/16] Avoid race condition in disk object store delete

Fixes
https://sentry.galaxyproject.org/share/issue/f48a997e238e46519b67d455ac9bf8bd/:
```
/corral4/main/objects/b/e/1/dataset_be145ee3-580b-48c3-8a40-e55929d3bb81.dat delete error [Errno 2] No such file or directory: '/corral4/main/objects/b/e/1/dataset_be145ee3-580b-48c3-8a40-e55929d3bb81.dat'
```
---
 lib/galaxy/objectstore/__init__.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index 62c531ffaae..2455132fa10 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -653,9 +653,11 @@ class DiskObjectStore(ConcreteObjectStore):
             if entire_dir and (extra_dir or obj_dir):
                 shutil.rmtree(path)
                 return True
-            if self._exists(obj, **kwargs):
-                os.remove(path)
-                return True
+            os.remove(path)
+            return True
+        except FileNotFoundError:
+            # Absolutely possible that a delete request races, but that's "fine".
+            return True
         except OSError as ex:
             log.critical(f"{self.__get_filename(obj, **kwargs)} delete error {ex}")
         return False