From d73a82052b35de3c7d8d295986bacf3616962899 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 11 Jun 2024 17:35:13 +0200
Subject: [PATCH 01/15] Increase API test coverage for group update

The second update does not provide a group_name as we are not changing it. This will  fail with the current code as the update payload model is the same as the create one.
---
 lib/galaxy_test/api/test_groups.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy_test/api/test_groups.py b/lib/galaxy_test/api/test_groups.py
index e644392b6151..e6fe63772231 100644
--- a/lib/galaxy_test/api/test_groups.py
+++ b/lib/galaxy_test/api/test_groups.py
@@ -76,10 +76,15 @@ def test_update(self):
 
         group_id = group["id"]
         updated_name = f"group-test-updated-{self.dataset_populator.get_random_name()}"
-        update_payload = {
-            "name": updated_name,
-        }
-        update_response = self._put(f"groups/{group_id}", data=update_payload, admin=True, json=True)
+        update_response = self._put(f"groups/{group_id}", data={"name": updated_name}, admin=True, json=True)
+        self._assert_status_code_is_ok(update_response)
+
+        # Update with another user
+        another_user_id = None
+        with self._different_user():
+            another_user_id = self.dataset_populator.user_id()
+        assert another_user_id is not None
+        update_response = self._put(f"groups/{group_id}", data={"user_ids": [another_user_id]}, admin=True, json=True)
         self._assert_status_code_is_ok(update_response)
 
     def test_update_only_admin(self):

From 0b504cf543a6e8b4c6c553a28671a5e0905a5d49 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 11 Jun 2024 17:36:46 +0200
Subject: [PATCH 02/15] Fix update group payload model

All fields in the payload should be optional when updating.
---
 lib/galaxy/managers/groups.py           | 11 +++++++----
 lib/galaxy/schema/groups.py             |  6 ++++++
 lib/galaxy/webapps/galaxy/api/groups.py |  3 ++-
 3 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/managers/groups.py b/lib/galaxy/managers/groups.py
index 33de69670cf5..da58a2e18807 100644
--- a/lib/galaxy/managers/groups.py
+++ b/lib/galaxy/managers/groups.py
@@ -18,7 +18,10 @@
 from galaxy.model.base import transaction
 from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.schema.fields import Security
-from galaxy.schema.groups import GroupCreatePayload
+from galaxy.schema.groups import (
+    GroupCreatePayload,
+    GroupUpdatePayload,
+)
 from galaxy.structured_app import MinimalManagerApp
 
 
@@ -77,7 +80,7 @@ def show(self, trans: ProvidesAppContext, group_id: int):
         item["roles_url"] = self._url_for(trans, "group_roles", group_id=encoded_id)
         return item
 
-    def update(self, trans: ProvidesAppContext, group_id: int, payload: GroupCreatePayload):
+    def update(self, trans: ProvidesAppContext, group_id: int, payload: GroupUpdatePayload):
         """
         Modifies a group.
         """
@@ -87,9 +90,9 @@ def update(self, trans: ProvidesAppContext, group_id: int, payload: GroupCreateP
             self._check_duplicated_group_name(sa_session, name)
             group.name = name
             sa_session.add(group)
-        user_ids = payload.user_ids
+        user_ids = payload.user_ids or []
         users = get_users_by_ids(sa_session, user_ids)
-        role_ids = payload.role_ids
+        role_ids = payload.role_ids or []
         roles = get_roles_by_ids(sa_session, role_ids)
         self._app.security_agent.set_entity_group_associations(
             groups=[group], roles=roles, users=users, delete_existing_assocs=False
diff --git a/lib/galaxy/schema/groups.py b/lib/galaxy/schema/groups.py
index aebe0796f8cd..1a4bde58f764 100644
--- a/lib/galaxy/schema/groups.py
+++ b/lib/galaxy/schema/groups.py
@@ -9,6 +9,7 @@
 )
 from typing_extensions import Literal
 
+from galaxy.schema import partial_model
 from galaxy.schema.fields import (
     DecodedDatabaseIdField,
     EncodedDatabaseIdField,
@@ -69,3 +70,8 @@ class GroupCreatePayload(Model):
         [],
         title="role IDs",
     )
+
+
+@partial_model()
+class GroupUpdatePayload(GroupCreatePayload):
+    pass
diff --git a/lib/galaxy/webapps/galaxy/api/groups.py b/lib/galaxy/webapps/galaxy/api/groups.py
index 7525e55fd1c0..f23e2a79f976 100644
--- a/lib/galaxy/webapps/galaxy/api/groups.py
+++ b/lib/galaxy/webapps/galaxy/api/groups.py
@@ -17,6 +17,7 @@
     GroupCreatePayload,
     GroupListResponse,
     GroupResponse,
+    GroupUpdatePayload,
 )
 from galaxy.webapps.galaxy.api import (
     depends,
@@ -80,8 +81,8 @@ def show(
     def update(
         self,
         group_id: Annotated[DecodedDatabaseIdField, Path(...)],
+        payload: Annotated[GroupUpdatePayload, Body(...)],
         trans: ProvidesAppContext = DependsOnTrans,
-        payload: GroupCreatePayload = Body(...),
     ) -> GroupResponse:
         return self.manager.update(trans, group_id, payload)
 

From c69e54a12a44ee47f9bbf3b9538b9ab8b4cf5105 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 11 Jun 2024 17:50:52 +0200
Subject: [PATCH 03/15] Update client API schema

---
 client/src/api/schema/schema.ts | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index a68de4e76d45..f592e3f59745 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -5483,6 +5483,15 @@ export interface components {
              */
             url: string;
         };
+        /** GroupUpdatePayload */
+        GroupUpdatePayload: {
+            /** name of the group */
+            name?: string | null;
+            /** role IDs */
+            role_ids?: string[] | null;
+            /** user IDs */
+            user_ids?: string[] | null;
+        };
         /** GroupUserListResponse */
         GroupUserListResponse: components["schemas"]["GroupUserResponse"][];
         /** GroupUserResponse */
@@ -15135,7 +15144,7 @@ export interface operations {
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["GroupCreatePayload"];
+                "application/json": components["schemas"]["GroupUpdatePayload"];
             };
         };
         responses: {

From a8cb547519931361e5c9765c27b0b4377970f896 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 13 Jun 2024 16:53:41 +0200
Subject: [PATCH 04/15] Add tests for replacing and removing group users and
 roles

---
 lib/galaxy_test/api/test_groups.py | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy_test/api/test_groups.py b/lib/galaxy_test/api/test_groups.py
index e6fe63772231..7441c3740663 100644
--- a/lib/galaxy_test/api/test_groups.py
+++ b/lib/galaxy_test/api/test_groups.py
@@ -79,7 +79,7 @@ def test_update(self):
         update_response = self._put(f"groups/{group_id}", data={"name": updated_name}, admin=True, json=True)
         self._assert_status_code_is_ok(update_response)
 
-        # Update with another user
+        # Update replace with another user
         another_user_id = None
         with self._different_user():
             another_user_id = self.dataset_populator.user_id()
@@ -87,6 +87,23 @@ def test_update(self):
         update_response = self._put(f"groups/{group_id}", data={"user_ids": [another_user_id]}, admin=True, json=True)
         self._assert_status_code_is_ok(update_response)
 
+        # get group and check if it was updated
+        response = self._get(f"groups/{group_id}", admin=True)
+        self._assert_status_code_is_ok(response)
+        users = self._get(f"groups/{group_id}/users", admin=True).json()
+        assert len(users) == 1
+        assert users[0]["id"] == another_user_id
+
+        # Remove private role from group
+        update_response = self._put(f"groups/{group_id}", data={"role_ids": []}, admin=True, json=True)
+        self._assert_status_code_is_ok(update_response)
+
+        # get group and check if it was updated
+        response = self._get(f"groups/{group_id}", admin=True)
+        self._assert_status_code_is_ok(response)
+        roles = self._get(f"groups/{group_id}/roles", admin=True).json()
+        assert len(roles) == 0
+
     def test_update_only_admin(self):
         group = self.test_create_valid()
         group_id = group["id"]

From 480358c90e00b94b0f521687a5d168b64a6b878a Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 13 Jun 2024 16:54:35 +0200
Subject: [PATCH 05/15] Fix update group API endpoint

Allow to replace or remove users and roles from the group
---
 lib/galaxy/managers/groups.py | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/managers/groups.py b/lib/galaxy/managers/groups.py
index da58a2e18807..69fcabc5612c 100644
--- a/lib/galaxy/managers/groups.py
+++ b/lib/galaxy/managers/groups.py
@@ -90,13 +90,18 @@ def update(self, trans: ProvidesAppContext, group_id: int, payload: GroupUpdateP
             self._check_duplicated_group_name(sa_session, name)
             group.name = name
             sa_session.add(group)
-        user_ids = payload.user_ids or []
-        users = get_users_by_ids(sa_session, user_ids)
-        role_ids = payload.role_ids or []
-        roles = get_roles_by_ids(sa_session, role_ids)
-        self._app.security_agent.set_entity_group_associations(
-            groups=[group], roles=roles, users=users, delete_existing_assocs=False
-        )
+
+        users = None
+        if payload.user_ids is not None:
+            users = get_users_by_ids(sa_session, payload.user_ids)
+
+        roles = None
+        if payload.role_ids is not None:
+            roles = get_roles_by_ids(sa_session, payload.role_ids)
+
+        if payload.user_ids is not None or payload.role_ids is not None:
+            self._app.security_agent.set_entity_group_associations(groups=[group], roles=roles, users=users)
+
         with transaction(sa_session):
             sa_session.commit()
 

From 1e2348e5553dbd267cf40a9280c94aa5a52e0ac3 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 13 Jun 2024 17:44:09 +0200
Subject: [PATCH 06/15] Fix typing

---
 lib/galaxy/managers/roles.py | 2 +-
 lib/galaxy/managers/users.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/managers/roles.py b/lib/galaxy/managers/roles.py
index 89bf69815e2c..b20244fc7fb4 100644
--- a/lib/galaxy/managers/roles.py
+++ b/lib/galaxy/managers/roles.py
@@ -162,6 +162,6 @@ def undelete(self, trans: ProvidesUserContext, role: model.Role) -> model.Role:
         return role
 
 
-def get_roles_by_ids(session: Session, role_ids):
+def get_roles_by_ids(session: Session, role_ids: List[int]) -> List[Role]:
     stmt = select(Role).where(Role.id.in_(role_ids))
     return session.scalars(stmt).all()
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index 210566025061..519bc6dbfab4 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -874,7 +874,7 @@ def _add_parsers(self):
         self.fn_filter_parsers.update({})
 
 
-def get_users_by_ids(session: Session, user_ids):
+def get_users_by_ids(session: Session, user_ids: List[int]) -> List[User]:
     stmt = select(User).where(User.id.in_(user_ids))
     return session.scalars(stmt).all()
 

From a04942fa7aafd02ea0f3b7acb0a219037ceea36f Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 13 Jun 2024 18:05:16 +0200
Subject: [PATCH 07/15] Keep old API behavior for now

Do not allow to remove or replace, only add users and roles.
---
 lib/galaxy/managers/groups.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/managers/groups.py b/lib/galaxy/managers/groups.py
index 69fcabc5612c..df30b2b39853 100644
--- a/lib/galaxy/managers/groups.py
+++ b/lib/galaxy/managers/groups.py
@@ -99,8 +99,9 @@ def update(self, trans: ProvidesAppContext, group_id: int, payload: GroupUpdateP
         if payload.role_ids is not None:
             roles = get_roles_by_ids(sa_session, payload.role_ids)
 
-        if payload.user_ids is not None or payload.role_ids is not None:
-            self._app.security_agent.set_entity_group_associations(groups=[group], roles=roles, users=users)
+        self._app.security_agent.set_entity_group_associations(
+            groups=[group], roles=roles, users=users, delete_existing_assocs=False
+        )
 
         with transaction(sa_session):
             sa_session.commit()

From fbf903d1e710261a72ea16fb922ee0e44ce9f200 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 13 Jun 2024 18:24:18 +0200
Subject: [PATCH 08/15] Refactor API test for updating a group

---
 lib/galaxy_test/api/test_groups.py | 72 +++++++++++++++++++++++-------
 1 file changed, 56 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy_test/api/test_groups.py b/lib/galaxy_test/api/test_groups.py
index 7441c3740663..7e0d40943868 100644
--- a/lib/galaxy_test/api/test_groups.py
+++ b/lib/galaxy_test/api/test_groups.py
@@ -1,4 +1,7 @@
-from typing import Optional
+from typing import (
+    List,
+    Optional,
+)
 
 from galaxy_test.base.populators import DatasetPopulator
 from ._framework import ApiTestCase
@@ -72,37 +75,62 @@ def test_show_unknown_raises_400(self):
         self._assert_status_code_is(response, 400)
 
     def test_update(self):
-        group = self.test_create_valid(group_name=f"group-test-{self.dataset_populator.get_random_name()}")
+        user_id = self.dataset_populator.user_id()
+        user_private_role_id = self.dataset_populator.user_private_role_id()
+        original_name = f"group-test-{self.dataset_populator.get_random_name()}"
+        group = self.test_create_valid(group_name=original_name)
+
+        self._assert_group_has_expected_values(
+            group["id"],
+            name=original_name,
+            user_ids=[user_id],
+            role_ids=[user_private_role_id],
+        )
 
         group_id = group["id"]
         updated_name = f"group-test-updated-{self.dataset_populator.get_random_name()}"
         update_response = self._put(f"groups/{group_id}", data={"name": updated_name}, admin=True, json=True)
         self._assert_status_code_is_ok(update_response)
 
-        # Update replace with another user
+        # Only the name should be updated
+        self._assert_group_has_expected_values(
+            group_id,
+            name=updated_name,
+            user_ids=[user_id],
+            role_ids=[user_private_role_id],
+        )
+
+        # Add another user to the group
         another_user_id = None
         with self._different_user():
             another_user_id = self.dataset_populator.user_id()
+            another_role_id = self.dataset_populator.user_private_role_id()
         assert another_user_id is not None
         update_response = self._put(f"groups/{group_id}", data={"user_ids": [another_user_id]}, admin=True, json=True)
         self._assert_status_code_is_ok(update_response)
 
-        # get group and check if it was updated
-        response = self._get(f"groups/{group_id}", admin=True)
-        self._assert_status_code_is_ok(response)
-        users = self._get(f"groups/{group_id}/users", admin=True).json()
-        assert len(users) == 1
-        assert users[0]["id"] == another_user_id
+        # Check if the user was added
+        self._assert_group_has_expected_values(
+            group_id,
+            name=updated_name,
+            user_ids=[user_id, another_user_id],
+            role_ids=[user_private_role_id],
+        )
 
-        # Remove private role from group
-        update_response = self._put(f"groups/{group_id}", data={"role_ids": []}, admin=True, json=True)
+        # Add another role to the group
+        update_response = self._put(f"groups/{group_id}", data={"role_ids": [another_role_id]}, admin=True, json=True)
         self._assert_status_code_is_ok(update_response)
 
-        # get group and check if it was updated
-        response = self._get(f"groups/{group_id}", admin=True)
-        self._assert_status_code_is_ok(response)
-        roles = self._get(f"groups/{group_id}/roles", admin=True).json()
-        assert len(roles) == 0
+        # Check if the role was added
+        self._assert_group_has_expected_values(
+            group_id,
+            name=updated_name,
+            user_ids=[user_id, another_user_id],
+            role_ids=[user_private_role_id, another_role_id],
+        )
+
+        # TODO: Test removing users and roles
+        # Currently not possible because the API can only add users and roles
 
     def test_update_only_admin(self):
         group = self.test_create_valid()
@@ -177,6 +205,18 @@ def _assert_valid_group(self, group, assert_id=None):
         if assert_id is not None:
             assert group["id"] == assert_id
 
+    def _assert_group_has_expected_values(self, group_id: str, name: str, user_ids: List[str], role_ids: List[str]):
+        group = self._get(f"groups/{group_id}", admin=True).json()
+        assert group["name"] == name
+        users = self._get(f"groups/{group_id}/users", admin=True).json()
+        assert len(users) == len(user_ids)
+        for user in users:
+            assert user["id"] in user_ids
+        roles = self._get(f"groups/{group_id}/roles", admin=True).json()
+        assert len(roles) == len(role_ids)
+        for role in roles:
+            assert role["id"] in role_ids
+
     def _build_valid_group_payload(self, name: Optional[str] = None):
         name = name or self.dataset_populator.get_random_name()
         user_id = self.dataset_populator.user_id()

From 84d6971d5e9704631e0592799f679a705e775887 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 13 Jun 2024 19:15:40 +0200
Subject: [PATCH 09/15] Use random user in test

Since we cannot remove the user from the group to restore its previous state we need to use a user that will not be part of other tests to avoid unwanted interactions.
---
 lib/galaxy_test/api/test_groups.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy_test/api/test_groups.py b/lib/galaxy_test/api/test_groups.py
index 7e0d40943868..8e4c5510fe98 100644
--- a/lib/galaxy_test/api/test_groups.py
+++ b/lib/galaxy_test/api/test_groups.py
@@ -101,8 +101,9 @@ def test_update(self):
         )
 
         # Add another user to the group
+        another_user_email = f"user-{self.dataset_populator.get_random_name()}@example.com"
         another_user_id = None
-        with self._different_user():
+        with self._different_user(another_user_email):
             another_user_id = self.dataset_populator.user_id()
             another_role_id = self.dataset_populator.user_private_role_id()
         assert another_user_id is not None

From 03001d4d20ce7c60cc6143b6b58387fe4d283e6d Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 13 Jun 2024 20:13:46 +0200
Subject: [PATCH 10/15] Reset current page when changing folders

---
 client/src/components/FilesDialog/FilesDialog.vue    |  1 +
 .../components/SelectionDialog/SelectionDialog.vue   | 12 ++++++++++++
 2 files changed, 13 insertions(+)

diff --git a/client/src/components/FilesDialog/FilesDialog.vue b/client/src/components/FilesDialog/FilesDialog.vue
index 1fb89ae29130..5e6d2bde46e3 100644
--- a/client/src/components/FilesDialog/FilesDialog.vue
+++ b/client/src/components/FilesDialog/FilesDialog.vue
@@ -409,6 +409,7 @@ onMounted(() => {
         :is-busy="isBusy"
         :items="items"
         :items-provider="itemsProvider"
+        :provider-url="currentDirectory?.url"
         :total-items="totalItems"
         :modal-show="modalShow"
         :modal-static="modalStatic"
diff --git a/client/src/components/SelectionDialog/SelectionDialog.vue b/client/src/components/SelectionDialog/SelectionDialog.vue
index c3958b198003..ea501a759411 100644
--- a/client/src/components/SelectionDialog/SelectionDialog.vue
+++ b/client/src/components/SelectionDialog/SelectionDialog.vue
@@ -27,6 +27,7 @@ interface Props {
     isEncoded?: boolean;
     items?: SelectionItem[];
     itemsProvider?: ItemsProvider;
+    providerUrl?: string;
     totalItems?: number;
     leafIcon?: string;
     modalShow?: boolean;
@@ -48,6 +49,7 @@ const props = withDefaults(defineProps<Props>(), {
     isEncoded: false,
     items: () => [],
     itemsProvider: undefined,
+    providerUrl: undefined,
     totalItems: 0,
     leafIcon: "fa fa-file-o",
     modalShow: true,
@@ -127,6 +129,16 @@ watch(
         filtered(props.items);
     }
 );
+
+watch(
+    () => props.providerUrl,
+    () => {
+        // We need to reset the current page when drilling down sub-folders
+        if (props.itemsProvider !== undefined) {
+            currentPage.value = 1;
+        }
+    }
+);
 </script>
 
 <template>

From 5e6afdd5b983ebcac22651c3e914748f57dcec89 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 14 Jun 2024 18:01:42 +0200
Subject: [PATCH 11/15] Fix ``get_accessible_job`` if called without session

Fixes https://github.com/galaxyproject/galaxy/issues/18399:

```
ExceptionGroup: unhandled errors in a TaskGroup
  File "starlette/_utils.py", line 87, in collapse_excgroups
    yield
  File "starlette/middleware/base.py", line 190, in __call__
    async with anyio.create_task_group() as task_group:
  File "anyio/_backends/_asyncio.py", line 678, in __aexit__
    raise BaseExceptionGroup(

AttributeError: 'NoneType' object has no attribute 'id'
(25 additional frame(s) were not displayed)
...
  File "galaxy/webapps/galaxy/fast_app.py", line 109, in add_x_frame_options
    response = await call_next(request)
  File "galaxy/webapps/galaxy/api/jobs.py", line 261, in common_problems
    job = self.service.get_job(trans=trans, job_id=job_id)
  File "galaxy/webapps/galaxy/services/jobs.py", line 121, in get_job
    return self.job_manager.get_accessible_job(trans, decoded_job_id=job_id)
  File "galaxy/managers/jobs.py", line 271, in get_accessible_job
    else (job.session_id == trans.get_galaxy_session().id)
```
---
 lib/galaxy/managers/jobs.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 4e245388a3e2..4a4a1ff13c29 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -260,15 +260,15 @@ def update_job_lock(self, job_lock: JobLock):
         )
         return self.job_lock()
 
-    def get_accessible_job(self, trans, decoded_job_id) -> Job:
+    def get_accessible_job(self, trans: ProvidesUserContext, decoded_job_id) -> Job:
         job = trans.sa_session.get(Job, decoded_job_id)
         if job is None:
             raise ObjectNotFound()
-        belongs_to_user = (
-            (job.user_id == trans.user.id)
-            if job.user_id and trans.user
-            else (job.session_id == trans.get_galaxy_session().id)
-        )
+        belongs_to_user = False
+        if trans.user:
+            belongs_to_user = job.user_id == trans.user.id
+        elif trans.galaxy_session:
+            belongs_to_user = job.session_id == trans.galaxy_session.id
         if not trans.user_is_admin and not belongs_to_user:
             # Check access granted via output datasets.
             if not job.output_datasets:

From a245bd96f2ddb1e38cc3820286137a8af5bf1a75 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 14 Jun 2024 18:21:23 +0200
Subject: [PATCH 12/15] Fix invocation step_job_summary for new collections

Fixes https://github.com/galaxyproject/galaxy/issues/18401
---
 lib/galaxy/managers/jobs.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 4e245388a3e2..403fb7266102 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -832,10 +832,10 @@ def summarize_jobs_to_dict(sa_session, jobs_source):
             "id": jobs_source.id,
             "populated_state": populated_state,
             "model": "ImplicitCollectionJobs",
+            "states": {},
         }
         if populated_state == "ok":
             # produce state summary...
-            states = {}
             join = model.ImplicitCollectionJobs.table.join(
                 model.ImplicitCollectionJobsJobAssociation.table.join(model.Job)
             )
@@ -846,8 +846,7 @@ def summarize_jobs_to_dict(sa_session, jobs_source):
                 .group_by(model.Job.state)
             )
             for row in sa_session.execute(statement):
-                states[row[0]] = row[1]
-            rval["states"] = states
+                rval["states"][row[0]] = row[1]
     return rval
 
 

From a2fa98d97c5d1c63d349d4722d0765a3cf0c6990 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 14 Jun 2024 22:25:27 +0200
Subject: [PATCH 13/15] Allow in_range validator for selects

this is for instance needed if we have a data table with version
information and we want to restrict the chosen options by the version
column.
---
 lib/galaxy/tool_util/linters/inputs.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/tool_util/linters/inputs.py b/lib/galaxy/tool_util/linters/inputs.py
index 7f0e8889543f..6ebd64d83bee 100644
--- a/lib/galaxy/tool_util/linters/inputs.py
+++ b/lib/galaxy/tool_util/linters/inputs.py
@@ -94,6 +94,7 @@
     ],
     "text": ["regex", "length", "empty_field", "value_in_data_table", "value_not_in_data_table", "expression"],
     "select": [
+        "in_range",
         "no_options",
         "regex",
         "length",

From 486f41349d384f8f66defb8e2aaf6ae8f8a80d89 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 16 Jun 2024 19:30:05 +0200
Subject: [PATCH 14/15] Ensure datatypes match on dragging elements into
 FormData

This is pretty common source of cheetah templating issues
where tool authors assume (orrectly, IMO) only datatypes allowed in the format
attribute of an input dataset are allowed.
Here's a hypothetical example:

```
  # set index = $input.cram_index
  # set index = $input.cram_index
ln -s '$index' input.index
```
This is going to fail if a user drag e.g. a txt dataset into the input.

For anything but the valid datatypes this is going to fail.

Another way things can fail is if an input datatypes should contain
extra files, but doesn't, for instance in
https://sentry.galaxyproject.org/share/issue/73d7bd51dd2d418e96d563f0ac2383f0/:

```
Exception: __action_for_transfer called on non-existent file - [None]
  File "galaxy/jobs/runners/pulsar.py", line 446, in queue_job
    external_job_id = pulsar_submit_job(client, client_job_description, remote_job_config)
  File "pulsar/client/staging/up.py", line 39, in submit_job
    file_stager = FileStager(client, client_job_description, job_config)
  File "pulsar/client/staging/up.py", line 148, in __init__
    self.__upload_input_files()
  File "pulsar/client/staging/up.py", line 264, in __upload_input_files
    self.__upload_input_metadata_file(client_input.action_source)
  File "pulsar/client/staging/up.py", line 287, in __upload_input_metadata_file
    self.transfer_tracker.handle_transfer_source(input_action_source, path_type.INPUT, name=remote_name)
  File "pulsar/client/staging/up.py", line 495, in handle_transfer_source
    action = self.__action_for_transfer(source, type, contents)
  File "pulsar/client/staging/up.py", line 551, in __action_for_transfer
    raise Exception(message)
```

Fixes https://github.com/galaxyproject/galaxy/issues/8202

We can now easily change datatypes in batch if necessary,
this shouldn't be an argument to not properly implement
datatype filtering.
---
 .../Form/Elements/FormData/FormData.test.js   |  4 ++
 .../Form/Elements/FormData/FormData.vue       | 56 +++++++++++++++----
 .../src/components/Form/FormElement.test.js   |  2 +-
 client/src/components/Form/FormElement.vue    | 21 +++++--
 4 files changed, 65 insertions(+), 18 deletions(-)

diff --git a/client/src/components/Form/Elements/FormData/FormData.test.js b/client/src/components/Form/Elements/FormData/FormData.test.js
index 65b7c9dd6100..bcff5d7e5589 100644
--- a/client/src/components/Form/Elements/FormData/FormData.test.js
+++ b/client/src/components/Form/Elements/FormData/FormData.test.js
@@ -3,6 +3,8 @@ import { mount } from "@vue/test-utils";
 import { PiniaVuePlugin } from "pinia";
 import { dispatchEvent, getLocalVue } from "tests/jest/helpers";
 
+import { testDatatypesMapper } from "@/components/Datatypes/test_fixtures";
+import { useDatatypesMapperStore } from "@/stores/datatypesMapperStore";
 import { useEventStore } from "@/stores/eventStore";
 
 import MountTarget from "./FormData.vue";
@@ -15,6 +17,8 @@ let eventStore;
 function createTarget(propsData) {
     const pinia = createTestingPinia({ stubActions: false });
     eventStore = useEventStore();
+    const datatypesStore = useDatatypesMapperStore();
+    datatypesStore.datatypesMapper = testDatatypesMapper;
     return mount(MountTarget, {
         localVue,
         propsData,
diff --git a/client/src/components/Form/Elements/FormData/FormData.vue b/client/src/components/Form/Elements/FormData/FormData.vue
index 123d24bb43b5..8bb48e50638d 100644
--- a/client/src/components/Form/Elements/FormData/FormData.vue
+++ b/client/src/components/Form/Elements/FormData/FormData.vue
@@ -7,6 +7,7 @@ import { BAlert, BButton, BButtonGroup, BCollapse, BFormCheckbox, BTooltip } fro
 import { computed, onMounted, type Ref, ref, watch } from "vue";
 
 import { getGalaxyInstance } from "@/app";
+import { useDatatypesMapper } from "@/composables/datatypesMapper";
 import { useUid } from "@/composables/utils/uid";
 import { type EventData, useEventStore } from "@/stores/eventStore";
 import { orList } from "@/utils/strings";
@@ -51,8 +52,9 @@ const props = withDefaults(
 );
 
 const eventStore = useEventStore();
+const { datatypesMapper } = useDatatypesMapper();
 
-const $emit = defineEmits(["input"]);
+const $emit = defineEmits(["input", "alert"]);
 
 // Determines wether values should be processed as linked or unlinked
 const currentLinked = ref(true);
@@ -302,6 +304,10 @@ function getSourceType(val: DataOption) {
 function handleIncoming(incoming: Record<string, unknown>, partial = true) {
     if (incoming) {
         const values = Array.isArray(incoming) ? incoming : [incoming];
+        const extensions = values.map((v) => v.extension || v.elements_datatypes).filter((v) => (v ? true : false));
+        if (!canAcceptDatatype(extensions)) {
+            return false;
+        }
         if (values.length > 0) {
             const incomingValues: Array<DataOption> = [];
             values.forEach((v) => {
@@ -349,6 +355,7 @@ function handleIncoming(incoming: Record<string, unknown>, partial = true) {
             }
         }
     }
+    return true;
 }
 
 /**
@@ -372,10 +379,36 @@ function onBrowse() {
     }
 }
 
+function canAcceptDatatype(itemDatatypes: string | Array<string>) {
+    if (!(props.extensions?.length > 0)) {
+        return true;
+    }
+    let datatypes: Array<string>;
+    if (!Array.isArray(itemDatatypes)) {
+        datatypes = [itemDatatypes];
+    } else {
+        datatypes = itemDatatypes;
+    }
+    const incompatibleItem = datatypes.find(
+        (extension) => !datatypesMapper.value?.isSubTypeOfAny(extension, props.extensions)
+    );
+    if (incompatibleItem) {
+        return false;
+    }
+    return true;
+}
+
 // Drag/Drop event handlers
 function onDragEnter(evt: MouseEvent) {
     const eventData = eventStore.getDragData();
     if (eventData) {
+        const extensions = (eventData.extension as string) || (eventData.elements_datatypes as Array<string>);
+        if (!canAcceptDatatype(extensions)) {
+            currentHighlighting.value = "warning";
+            $emit("alert", `${extensions} is not an acceptable format for this parameter.`);
+        } else {
+            currentHighlighting.value = "success";
+        }
         dragTarget.value = evt.target;
         dragData.value = eventData;
     }
@@ -384,23 +417,24 @@ function onDragEnter(evt: MouseEvent) {
 function onDragLeave(evt: MouseEvent) {
     if (dragTarget.value === evt.target) {
         currentHighlighting.value = null;
-    }
-}
-
-function onDragOver() {
-    if (dragData.value !== null) {
-        currentHighlighting.value = "warning";
+        $emit("alert", undefined);
     }
 }
 
 function onDrop() {
     if (dragData.value) {
+        let accept = false;
         if (eventStore.multipleDragData) {
-            handleIncoming(Object.values(dragData.value) as any, false);
+            accept = handleIncoming(Object.values(dragData.value) as any, false);
+        } else {
+            accept = handleIncoming(dragData.value);
+        }
+        if (accept) {
+            currentHighlighting.value = "success";
         } else {
-            handleIncoming(dragData.value);
+            currentHighlighting.value = "warning";
         }
-        currentHighlighting.value = "success";
+        $emit("alert", undefined);
         dragData.value = null;
         clearHighlighting();
     }
@@ -468,7 +502,7 @@ const noOptionsWarningMessage = computed(() => {
         :class="currentHighlighting && `ui-dragover-${currentHighlighting}`"
         @dragenter.prevent="onDragEnter"
         @dragleave.prevent="onDragLeave"
-        @dragover.prevent="onDragOver"
+        @dragover.prevent
         @drop.prevent="onDrop">
         <div class="d-flex flex-column">
             <BButtonGroup v-if="variant && variant.length > 1" buttons class="align-self-start">
diff --git a/client/src/components/Form/FormElement.test.js b/client/src/components/Form/FormElement.test.js
index 9aac1c55c0f6..a3cd69f50f74 100644
--- a/client/src/components/Form/FormElement.test.js
+++ b/client/src/components/Form/FormElement.test.js
@@ -30,7 +30,7 @@ describe("FormElement", () => {
         const error = wrapper.find(".ui-form-error-text");
         expect(error.text()).toBe("error_text");
 
-        await wrapper.setProps({ error: "" });
+        await wrapper.setProps({ error: undefined });
         const no_error = wrapper.findAll(".ui-form-error");
         expect(no_error.length).toBe(0);
 
diff --git a/client/src/components/Form/FormElement.vue b/client/src/components/Form/FormElement.vue
index 34baae64c846..50bdeb5aa923 100644
--- a/client/src/components/Form/FormElement.vue
+++ b/client/src/components/Form/FormElement.vue
@@ -127,7 +127,7 @@ function onConnect() {
 
 const isHidden = computed(() => attrs.value["hidden"]);
 const elementId = computed(() => `form-element-${props.id}`);
-const hasAlert = computed(() => Boolean(props.error || props.warning));
+const hasAlert = computed(() => alerts.value.length > 0);
 const showPreview = computed(() => (collapsed.value && attrs.value["collapsible_preview"]) || props.disabled);
 const showField = computed(() => !collapsed.value && !props.disabled);
 
@@ -174,6 +174,16 @@ const isEmpty = computed(() => {
 const isRequired = computed(() => attrs.value["optional"] === false);
 const isRequiredType = computed(() => props.type !== "boolean");
 const isOptional = computed(() => !isRequired.value && attrs.value["optional"] !== undefined);
+const formAlert = ref<string>();
+const alerts = computed(() => {
+    return [formAlert.value, props.error, props.warning]
+        .filter((v) => v !== undefined && v !== null)
+        .map((v) => linkify(sanitize(v!, { USE_PROFILES: { html: true } })));
+});
+
+function onAlert(value: string | undefined) {
+    formAlert.value = value;
+}
 </script>
 
 <template>
@@ -182,11 +192,9 @@ const isOptional = computed(() => !isRequired.value && attrs.value["optional"] !
         :id="elementId"
         class="ui-form-element section-row"
         :class="{ alert: hasAlert, 'alert-info': hasAlert }">
-        <div v-if="hasAlert" class="ui-form-error">
+        <div v-for="(alert, index) in alerts" :key="index" class="ui-form-error">
             <FontAwesomeIcon class="mr-1" icon="fa-exclamation" />
-            <span
-                class="ui-form-error-text"
-                v-html="linkify(sanitize(props.error || props.warning, { USE_PROFILES: { html: true } }))" />
+            <span class="ui-form-error-text" v-html="alert" />
         </div>
 
         <div class="ui-form-title">
@@ -288,7 +296,8 @@ const isOptional = computed(() => !isRequired.value && attrs.value["optional"] !
                 :optional="attrs.optional"
                 :options="attrs.options"
                 :tag="attrs.tag"
-                :type="props.type" />
+                :type="props.type"
+                @alert="onAlert" />
             <FormDrilldown
                 v-else-if="props.type === 'drill_down'"
                 :id="id"

From 74ae35413ea809012a1eaf54251b71ed4b3bf6eb Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 17 Jun 2024 17:23:52 +0200
Subject: [PATCH 15/15] Fix collection map over status for dragged collections

Fixes https://github.com/galaxyproject/galaxy/issues/12614, which is the
source of many templating errors such as
https://sentry.galaxyproject.org/share/issue/008a129bf7e44b3086491789f4bfb07e/:

```
NotFound: cannot find 'forward'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1718305116_116218_60583.py", line 206, in respond
```

If we don't set `batch` and `map_over_type` (this is correctly done by
the backend when building the parameter options from the history) we
pass
in the whole collection, which likely won't have a `forward` element.
---
 .../Form/Elements/FormData/FormData.vue        | 18 +++++++++++++++++-
 .../components/Form/Elements/FormData/types.ts |  1 +
 client/src/components/Form/FormElement.vue     |  3 ++-
 lib/galaxy/tools/parameters/basic.py           |  1 +
 4 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Form/Elements/FormData/FormData.vue b/client/src/components/Form/Elements/FormData/FormData.vue
index 123d24bb43b5..ee65daad081d 100644
--- a/client/src/components/Form/Elements/FormData/FormData.vue
+++ b/client/src/components/Form/Elements/FormData/FormData.vue
@@ -35,6 +35,7 @@ const props = withDefaults(
         };
         extensions?: Array<string>;
         type?: string;
+        collectionTypes?: Array<string>;
         flavor?: string;
         tag?: string;
     }>(),
@@ -45,6 +46,7 @@ const props = withDefaults(
         value: undefined,
         extensions: () => [],
         type: "data",
+        collectionTypes: undefined,
         flavor: undefined,
         tag: undefined,
     }
@@ -311,14 +313,28 @@ function handleIncoming(incoming: Record<string, unknown>, partial = true) {
                 const newName = v.name ? v.name : newId;
                 const newSrc =
                     v.src || (v.history_content_type === "dataset_collection" ? SOURCE.COLLECTION : SOURCE.DATASET);
-                const newValue = {
+                const newValue: DataOption = {
                     id: newId,
                     src: newSrc,
+                    batch: false,
+                    map_over_type: undefined,
                     hid: newHid,
                     name: newName,
                     keep: true,
                     tags: [],
                 };
+                if (v.collection_type && props.collectionTypes?.length > 0) {
+                    if (!props.collectionTypes.includes(v.collection_type)) {
+                        const mapOverType = props.collectionTypes.find((collectionType) =>
+                            v.collection_type.endsWith(collectionType)
+                        );
+                        if (!mapOverType) {
+                            return false;
+                        }
+                        newValue["batch"] = true;
+                        newValue["map_over_type"] = mapOverType;
+                    }
+                }
                 // Verify that new value has corresponding option
                 const keepKey = `${newId}_${newSrc}`;
                 const existingOptions = props.options && props.options[newSrc];
diff --git a/client/src/components/Form/Elements/FormData/types.ts b/client/src/components/Form/Elements/FormData/types.ts
index 52c8a418897e..acdf8299eca6 100644
--- a/client/src/components/Form/Elements/FormData/types.ts
+++ b/client/src/components/Form/Elements/FormData/types.ts
@@ -3,6 +3,7 @@ export type DataOption = {
     hid: number;
     is_dataset?: boolean;
     keep: boolean;
+    batch: boolean;
     map_over_type?: string;
     name: string;
     src: string;
diff --git a/client/src/components/Form/FormElement.vue b/client/src/components/Form/FormElement.vue
index 34baae64c846..10bf6cc0ccc9 100644
--- a/client/src/components/Form/FormElement.vue
+++ b/client/src/components/Form/FormElement.vue
@@ -288,7 +288,8 @@ const isOptional = computed(() => !isRequired.value && attrs.value["optional"] !
                 :optional="attrs.optional"
                 :options="attrs.options"
                 :tag="attrs.tag"
-                :type="props.type" />
+                :type="props.type"
+                :collection-types="attrs.collection_types" />
             <FormDrilldown
                 v-else-if="props.type === 'drill_down'"
                 :id="id"
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index dbe1b065a243..1fe481570601 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2511,6 +2511,7 @@ def to_dict(self, trans, other_values=None):
         # create dictionary and fill default parameters
         other_values = other_values or {}
         d = super().to_dict(trans)
+        d["collection_types"] = self.collection_types
         d["extensions"] = self.extensions
         d["multiple"] = self.multiple
         d["options"] = {"hda": [], "hdca": [], "dce": []}