From 8ee3b902b3fa0daf888e9815c1c0937d5c27035d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 5 Jun 2024 17:59:13 +0200
Subject: [PATCH 01/10] Make repo permissions world-readable

---
 lib/tool_shed/util/repository_util.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/lib/tool_shed/util/repository_util.py b/lib/tool_shed/util/repository_util.py
index 7d4ead78a148..624c67c8bb14 100644
--- a/lib/tool_shed/util/repository_util.py
+++ b/lib/tool_shed/util/repository_util.py
@@ -208,6 +208,9 @@ def create_repository(
         dir=app.config.file_path,
         prefix=f"{repository.user.username}-{repository.name}",
     )
+    # Created directory is readable, writable, and searchable only by the creating user ID,
+    # but we need to make it world-readable so non-shed user can serve files (e.g. hgweb run as different user).
+    os.chmod(repository_path, util.RWXR_XR_X)
     # Create the local repository.
     init_repository(repo_path=repository_path)
     # Create a .hg/hgrc file for the local repository.

From c49a9ef35fdee98444f191ced47b62d357566d78 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 6 Jun 2024 11:20:02 +0200
Subject: [PATCH 02/10] Fix seek in slurm memory check

Fixes
https://sentry.galaxyproject.org/share/issue/e196a12836fe40da83c5e9e24c4c8329/:
```
UnsupportedOperation: can't do nonzero end-relative seeks
  File "galaxy/jobs/runners/slurm.py", line 217, in __check_memory_limit
    f.seek(-2048, os.SEEK_END)
```
which has probably been broken since we moved to python 3.
---
 lib/galaxy/jobs/runners/slurm.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/jobs/runners/slurm.py b/lib/galaxy/jobs/runners/slurm.py
index 98c373d96645..b8764ddea7de 100644
--- a/lib/galaxy/jobs/runners/slurm.py
+++ b/lib/galaxy/jobs/runners/slurm.py
@@ -7,7 +7,10 @@
 
 from galaxy import model
 from galaxy.jobs.runners.drmaa import DRMAAJobRunner
-from galaxy.util import commands
+from galaxy.util import (
+    commands,
+    unicodify,
+)
 from galaxy.util.custom_logging import get_logger
 
 log = get_logger(__name__)
@@ -212,12 +215,12 @@ def __check_memory_limit(self, efile_path):
         """
         try:
             log.debug("Checking %s for exceeded memory message from SLURM", efile_path)
-            with open(efile_path) as f:
+            with open(efile_path, "rb") as f:
                 if os.path.getsize(efile_path) > 2048:
                     f.seek(-2048, os.SEEK_END)
                     f.readline()
                 for line in f.readlines():
-                    stripped_line = line.strip()
+                    stripped_line = unicodify(line)
                     if stripped_line == SLURM_MEMORY_LIMIT_EXCEEDED_MSG:
                         return OUT_OF_MEMORY_MSG
                     elif any(_ in stripped_line for _ in SLURM_MEMORY_LIMIT_EXCEEDED_PARTIAL_WARNINGS):

From cf322eb531ca6ae4a3852138123a08019563f93e Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Thu, 6 Jun 2024 12:47:34 +0200
Subject: [PATCH 03/10] restore line.strip()

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/jobs/runners/slurm.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/jobs/runners/slurm.py b/lib/galaxy/jobs/runners/slurm.py
index b8764ddea7de..db1ed9b3d002 100644
--- a/lib/galaxy/jobs/runners/slurm.py
+++ b/lib/galaxy/jobs/runners/slurm.py
@@ -220,7 +220,7 @@ def __check_memory_limit(self, efile_path):
                     f.seek(-2048, os.SEEK_END)
                     f.readline()
                 for line in f.readlines():
-                    stripped_line = unicodify(line)
+                    stripped_line = unicodify(line.strip())
                     if stripped_line == SLURM_MEMORY_LIMIT_EXCEEDED_MSG:
                         return OUT_OF_MEMORY_MSG
                     elif any(_ in stripped_line for _ in SLURM_MEMORY_LIMIT_EXCEEDED_PARTIAL_WARNINGS):

From c01904803c239f090e44ae864917ed546782952e Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 7 Jun 2024 09:47:06 +0200
Subject: [PATCH 04/10] Allow filtering by type-id in DataDialog

---
 client/src/components/DataDialog/DataDialog.vue | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/client/src/components/DataDialog/DataDialog.vue b/client/src/components/DataDialog/DataDialog.vue
index fd0f86201ea4..0a0d90d5564c 100644
--- a/client/src/components/DataDialog/DataDialog.vue
+++ b/client/src/components/DataDialog/DataDialog.vue
@@ -24,6 +24,7 @@ interface Props {
     allowUpload?: boolean;
     callback?: (results: Array<Record>) => void;
     filterOkState?: boolean;
+    filterByTypeIds?: string[];
     format?: string;
     library?: boolean;
     modalStatic?: boolean;
@@ -36,6 +37,7 @@ const props = withDefaults(defineProps<Props>(), {
     allowUpload: true,
     callback: () => {},
     filterOkState: false,
+    filterByTypeIds: undefined,
     format: "download",
     library: true,
     modalStatic: false,
@@ -96,6 +98,9 @@ function getHistoryUrl() {
     if (props.filterOkState) {
         queryString += "&q=state-eq&qv=ok";
     }
+    if (props.filterByTypeIds.length > 0) {
+        queryString += `&q=type_id-in&qv=${props.filterByTypeIds.join(",")}`;
+    }
     return `${getAppRoot()}api/histories/${props.history}/contents?v=dev${queryString}`;
 }
 

From 2389bc4d7ec9dcb69859e511654392e5c9130f7f Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 7 Jun 2024 09:48:50 +0200
Subject: [PATCH 05/10] Display only compatible datasets in DataDialog for
 Visualizations

---
 .../components/Panels/VisualizationPanel.vue  | 42 ++++++++++++++++++-
 1 file changed, 41 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Panels/VisualizationPanel.vue b/client/src/components/Panels/VisualizationPanel.vue
index fedc8dfab1fd..d9fbf144aa2c 100644
--- a/client/src/components/Panels/VisualizationPanel.vue
+++ b/client/src/components/Panels/VisualizationPanel.vue
@@ -1,5 +1,6 @@
 <script setup lang="ts">
 import { faEye } from "@fortawesome/free-solid-svg-icons";
+import { BAlert, BModal } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, onMounted, type Ref, ref } from "vue";
 import { useRouter } from "vue-router/composables";
@@ -22,6 +23,15 @@ interface Plugin {
     target?: string;
 }
 
+interface Dataset {
+    id: string;
+    name: string;
+}
+
+interface CompatibleDatasetsResponse {
+    hdas: Dataset[];
+}
+
 const { currentHistoryId } = storeToRefs(useHistoryStore());
 const router = useRouter();
 
@@ -29,7 +39,9 @@ const plugins: Ref<Array<Plugin>> = ref([]);
 const query = ref("");
 const isLoading = ref(true);
 const currentPlugin: Ref<Plugin | null> = ref(null);
+const compatibleDatasetIdKeys = ref<string[]>([]);
 const showDataDialog = ref(false);
+const showNoCompatibleDatasetsModal = ref(false);
 
 const filteredPlugins = computed(() => {
     const queryLower = query.value.toLowerCase();
@@ -51,11 +63,31 @@ function createVisualization(dataset: any) {
     }
 }
 
-function selectVisualization(plugin: Plugin) {
+async function selectVisualization(plugin: Plugin) {
     currentPlugin.value = plugin;
+    compatibleDatasetIdKeys.value = await getCompatibleDatasetsInCurrentHistory();
+    if (compatibleDatasetIdKeys.value.length === 0) {
+        showNoCompatibleDatasetsModal.value = true;
+        return;
+    }
     showDataDialog.value = true;
 }
 
+/**
+ * Get compatible datasets in the current history for the selected visualization.
+ * @returns {Promise<string[]>} List of compatible datasets as "type-id" strings. In this case, type will be always "dataset".
+ */
+async function getCompatibleDatasetsInCurrentHistory(): Promise<string[]> {
+    if (!currentPlugin.value || !currentHistoryId.value) {
+        return [];
+    }
+    const result = (await urlData({
+        url: `/api/plugins/${currentPlugin.value.name}`,
+        params: { history_id: currentHistoryId.value },
+    })) as CompatibleDatasetsResponse;
+    return result.hdas.map((dataset: Dataset) => `dataset-${dataset.id}`);
+}
+
 async function getPlugins() {
     plugins.value = await urlData({ url: "/api/plugins" });
     isLoading.value = false;
@@ -97,8 +129,16 @@ onMounted(() => {
             format=""
             :history="currentHistoryId"
             :filter-ok-state="true"
+            :filter-by-type-ids="compatibleDatasetIdKeys"
             @onOk="createVisualization"
             @onCancel="showDataDialog = false" />
+        <BModal v-model="showNoCompatibleDatasetsModal" title="No compatible datasets found" title-tag="h2" ok-only>
+            <p v-localize>
+                No datasets found in your current history that are compatible with
+                <b>{{ currentPlugin?.name ?? "this visualization" }}</b
+                >. Please upload a compatible dataset or select a different visualization.
+            </p>
+        </BModal>
     </ActivityPanel>
 </template>
 

From 205601fb0d0af7dc5cf531e4b76add4a3ef38605 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 7 Jun 2024 09:49:51 +0200
Subject: [PATCH 06/10] Fix Editor visualization to accept only text-based
 datatypes

---
 config/plugins/visualizations/editor/config/editor.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/plugins/visualizations/editor/config/editor.xml b/config/plugins/visualizations/editor/config/editor.xml
index 26aacb9fbd63..8038f9fd2e88 100644
--- a/config/plugins/visualizations/editor/config/editor.xml
+++ b/config/plugins/visualizations/editor/config/editor.xml
@@ -5,7 +5,7 @@
     <data_sources>
         <data_source>
             <model_class>HistoryDatasetAssociation</model_class>
-            <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">data.Text</test>
             <to_param param_attr="id">dataset_id</to_param>
         </data_source>
     </data_sources>

From 8496d0036963061d6df95188944d6b2a44b3fcdc Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 7 Jun 2024 10:12:26 +0200
Subject: [PATCH 07/10] Fix total items count in DataDialog

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

diff --git a/client/src/components/DataDialog/DataDialog.vue b/client/src/components/DataDialog/DataDialog.vue
index 0a0d90d5564c..11e339446680 100644
--- a/client/src/components/DataDialog/DataDialog.vue
+++ b/client/src/components/DataDialog/DataDialog.vue
@@ -197,6 +197,7 @@ watch(
         :disable-ok="!hasValue"
         :fields="fields"
         :items="items"
+        :total-items="items.length"
         :modal-show="modalShow"
         :multiple="multiple"
         :options-show="optionsShow"

From 3aea4940355b35faeae89441f192413ff831931d Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 7 Jun 2024 10:56:42 +0200
Subject: [PATCH 08/10] Fix possible undefined value

---
 client/src/components/DataDialog/DataDialog.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/DataDialog/DataDialog.vue b/client/src/components/DataDialog/DataDialog.vue
index 11e339446680..50a417f0d070 100644
--- a/client/src/components/DataDialog/DataDialog.vue
+++ b/client/src/components/DataDialog/DataDialog.vue
@@ -98,7 +98,7 @@ function getHistoryUrl() {
     if (props.filterOkState) {
         queryString += "&q=state-eq&qv=ok";
     }
-    if (props.filterByTypeIds.length > 0) {
+    if (props.filterByTypeIds && props.filterByTypeIds.length > 0) {
         queryString += `&q=type_id-in&qv=${props.filterByTypeIds.join(",")}`;
     }
     return `${getAppRoot()}api/histories/${props.history}/contents?v=dev${queryString}`;

From 67fd14046bd66eb0cf3749bf17df32b8a0e63d98 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 7 Jun 2024 11:06:06 +0200
Subject: [PATCH 09/10] Fix typing issue in reused variable

---
 lib/galaxy/webapps/galaxy/services/users.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/services/users.py b/lib/galaxy/webapps/galaxy/services/users.py
index 0317af35cacc..4cab9d01ab12 100644
--- a/lib/galaxy/webapps/galaxy/services/users.py
+++ b/lib/galaxy/webapps/galaxy/services/users.py
@@ -259,9 +259,7 @@ def get_index(
                 for key, value in user_dict.items():
                     if key in expose_keys:
                         limited_user[key] = value
-                user = LimitedUserModel(**limited_user)
+                rval.append(LimitedUserModel(**limited_user))
             else:
-                user = UserModel(**user_dict)
-
-            rval.append(user)
+                rval.append(UserModel(**user_dict))
         return rval

From 28e0a5b77e600ae267897ee680922c10d689a2b9 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 7 Jun 2024 11:51:26 +0200
Subject: [PATCH 10/10] Fix linting unnecessary `list` literal

---
 test/integration/test_users.py | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/test/integration/test_users.py b/test/integration/test_users.py
index d47110bc96c1..bc1eaadfcb76 100644
--- a/test/integration/test_users.py
+++ b/test/integration/test_users.py
@@ -1,15 +1,18 @@
-from typing import ClassVar
+from typing import (
+    ClassVar,
+    Set,
+)
 
 from galaxy_test.driver import integration_util
 
-USER_SUMMARY_KEYS = set(["model_class", "id", "email", "username", "deleted", "active", "last_password_change"])
+USER_SUMMARY_KEYS: Set[str] = {"model_class", "id", "email", "username", "deleted", "active", "last_password_change"}
 
 
 class UsersIntegrationCase(integration_util.IntegrationTestCase):
     expose_user_name: ClassVar[bool]
     expose_user_email: ClassVar[bool]
     expected_regular_user_list_count: ClassVar[int]
-    expected_limited_user_keys: ClassVar[set]
+    expected_limited_user_keys: ClassVar[Set[str]]
 
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
@@ -57,7 +60,7 @@ class TestExposeUsersIntegration(UsersIntegrationCase):
     expose_user_email = True
 
     # Since we allow to expose user information, all users are returned.
-    expected_limited_user_keys = set(["id", "username", "email"])
+    expected_limited_user_keys = {"id", "username", "email"}
     expected_regular_user_list_count = 3
 
 
@@ -67,7 +70,7 @@ class TestExposeOnlyUserNameIntegration(UsersIntegrationCase):
 
     # When only username is exposed, only that field is returned in the user list.
     # Since we are exposing user information, all users are returned.
-    expected_limited_user_keys = set(["id", "username"])
+    expected_limited_user_keys = {"id", "username"}
     expected_regular_user_list_count = 3
 
 
@@ -77,7 +80,7 @@ class TestExposeOnlyUserEmailIntegration(UsersIntegrationCase):
 
     # When only email is exposed, only that field is returned in the user list.
     # Since we are exposing user information, all users are returned.
-    expected_limited_user_keys = set(["id", "email"])
+    expected_limited_user_keys = {"id", "email"}
     expected_regular_user_list_count = 3