From 945bd5db130d1aa206e7cd2467f39d4abe97678a Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 12 Jul 2024 18:16:51 +0100
Subject: [PATCH 1/4] Sync cwl_conformance GitHub workflow with api one

---
 .github/workflows/cwl_conformance.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cwl_conformance.yaml b/.github/workflows/cwl_conformance.yaml
index f9ac963071ac..fc696787fe11 100644
--- a/.github/workflows/cwl_conformance.yaml
+++ b/.github/workflows/cwl_conformance.yaml
@@ -4,10 +4,12 @@ on:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
 env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
 concurrency:
@@ -59,7 +61,7 @@ jobs:
         uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
-          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
       - name: Run tests
         run: ./run_tests.sh --coverage --skip_flakey_fails -cwl lib/galaxy_test/api/cwl -- -m "${{ matrix.marker }} and ${{ matrix.conformance-version }}"
         working-directory: 'galaxy root'

From e0ee749c1638a15c5d4c0df7bde9a8cfc0ae58bd Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 12 Jul 2024 18:17:42 +0100
Subject: [PATCH 2/4] Type annotation fix

---
 lib/galaxy/structured_app.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/structured_app.py b/lib/galaxy/structured_app.py
index 7ab7bcba3977..1d1986dee1a8 100644
--- a/lib/galaxy/structured_app.py
+++ b/lib/galaxy/structured_app.py
@@ -46,7 +46,10 @@
     from galaxy.managers.collections import DatasetCollectionManager
     from galaxy.managers.hdas import HDAManager
     from galaxy.managers.histories import HistoryManager
-    from galaxy.managers.workflows import WorkflowsManager
+    from galaxy.managers.workflows import (
+        WorkflowContentsManager,
+        WorkflowsManager,
+    )
     from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
     from galaxy.tools import ToolBox
     from galaxy.tools.cache import ToolCache
@@ -110,7 +113,7 @@ class MinimalManagerApp(MinimalApp):
     history_manager: "HistoryManager"
     hda_manager: "HDAManager"
     workflow_manager: "WorkflowsManager"
-    workflow_contents_manager: Any  # 'galaxy.managers.workflows.WorkflowContentsManager'
+    workflow_contents_manager: "WorkflowContentsManager"
     library_folder_manager: Any  # 'galaxy.managers.folders.FolderManager'
     library_manager: Any  # 'galaxy.managers.libraries.LibraryManager'
     role_manager: Any  # 'galaxy.managers.roles.RoleManager'

From 5c7b6b6085329154e3afe20d699a83d2c58b8681 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 12 Jul 2024 18:18:38 +0100
Subject: [PATCH 3/4] Easier debugging of assertion

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

diff --git a/lib/galaxy/tool_util/cwl/parser.py b/lib/galaxy/tool_util/cwl/parser.py
index 674b3abcc357..1599955eb796 100644
--- a/lib/galaxy/tool_util/cwl/parser.py
+++ b/lib/galaxy/tool_util/cwl/parser.py
@@ -903,7 +903,7 @@ def split_step_references(step_references, workflow_id=None, multiple=True):
     if multiple:
         return split_references
     else:
-        assert len(split_references) == 1
+        assert len(split_references) == 1, split_references
         return split_references[0]
 
 

From e8e1b4a1605432f32c446bbe4f1b965c294b3566 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 12 Jul 2024 18:20:04 +0100
Subject: [PATCH 4/4] Move try/except one level down

---
 lib/galaxy_test/base/populators.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py
index 1e284135937b..fcf59fd12d1f 100644
--- a/lib/galaxy_test/base/populators.py
+++ b/lib/galaxy_test/base/populators.py
@@ -2532,13 +2532,13 @@ def run_conformance_test(self, version: str, doc: str):
             raise Exception("Expected run to fail but it didn't.")
 
         expected_outputs = test["output"]
-        try:
-            for key, value in expected_outputs.items():
+        for key, value in expected_outputs.items():
+            try:
                 actual_output = run.get_output_as_object(key)
                 cwltest.compare.compare(value, actual_output)
-        except Exception:
-            self.dataset_populator._summarize_history(run.history_id)
-            raise
+            except Exception:
+                self.dataset_populator._summarize_history(run.history_id)
+                raise
 
 
 class LibraryPopulator: