Perform level 4 files checks in local_run

Because local_run doesn't have a level 4 directory configured, the
checks were skipped.

This change move that conditional to different location, so the checks
are performed in local_run, and adds tests

Partial fix to #675:

jobrunner/executors/local.py

@@ -487,13 +487,18 @@ def persist_outputs(job_definition, outputs, job_metadata):
 
     # Copy out medium privacy files
     medium_privacy_dir = get_medium_privacy_workspace(job_definition.workspace)
-    if medium_privacy_dir:
-        for filename, privacy_level in outputs.items():
-            if privacy_level == "moderately_sensitive":
-                ok, job_msg, file_msg = check_l4_file(
-                    job_definition, filename, sizes[filename], workspace_dir
-                )
 
+    for filename, privacy_level in outputs.items():
+        if privacy_level == "moderately_sensitive":
+            ok, job_msg, file_msg = check_l4_file(
+                job_definition, filename, sizes[filename], workspace_dir
+            )
+
+            if not ok:
+                excluded_files[filename] = job_msg
+
+            # local run currently does not have a level 4 directory
+            if medium_privacy_dir:
                 message_file = medium_privacy_dir / (filename + ".txt")
 
                 if ok:
@@ -503,19 +508,18 @@ def persist_outputs(job_definition, outputs, job_metadata):
                     # if it previously had a too big notice, delete it
                     delete_files_from_directory(medium_privacy_dir, [message_file])
                 else:
-                    excluded_files[filename] = job_msg
                     message_file.parent.mkdir(exist_ok=True, parents=True)
                     message_file.write_text(file_msg)
 
-        # this can be removed once osrelease is dead
-        write_manifest_file(
-            medium_privacy_dir,
-            {
-                # this currently needs to exist, but is not used
-                "repo": None,
-                "workspace": job_definition.workspace,
-            },
-        )
+                # this can be removed once osrelease is dead
+                write_manifest_file(
+                    medium_privacy_dir,
+                    {
+                        # this currently needs to exist, but is not used
+                        "repo": None,
+                        "workspace": job_definition.workspace,
+                    },
+                )
 
     return excluded_files
 

tests/test_local_executor.py

@@ -464,9 +464,17 @@ def test_finalize_failed_oomkilled(docker_cleanup, job_definition, tmp_work_dir)
     assert workspace_log_file_exists(job_definition)
 
 
+@pytest.fixture(params=[True, False])
+def local_run(request, monkeypatch):
+    # local_run does not have a level 4 configured
+    if request.param:
+        monkeypatch.setattr(config, "MEDIUM_PRIVACY_WORKSPACES_DIR", None)
+    return request.param
+
+
 @pytest.mark.needs_docker
 def test_finalize_large_level4_outputs(
-    docker_cleanup, job_definition, tmp_work_dir, volume_api
+    docker_cleanup, job_definition, tmp_work_dir, volume_api, local_run
 ):
     job_definition.args = [
         "truncate",
@@ -498,19 +506,21 @@ def test_finalize_large_level4_outputs(
         "output/output.txt": "File size of 1.0Mb is larger that limit of 0.5Mb.",
     }
 
-    level4_dir = local.get_medium_privacy_workspace(job_definition.workspace)
-    message_file = level4_dir / "output/output.txt.txt"
-    txt = message_file.read_text()
-    assert "output/output.txt" in txt
-    assert "1.0Mb" in txt
-    assert "0.5Mb" in txt
-    log_file = level4_dir / "metadata/action.log"
+    log_file = local.get_log_dir(job_definition) / "logs.txt"
     log = log_file.read_text()
     assert "Invalid moderately_sensitive outputs:" in log
     assert (
         "output/output.txt  - File size of 1.0Mb is larger that limit of 0.5Mb." in log
     )
 
+    if not local_run:
+        level4_dir = local.get_medium_privacy_workspace(job_definition.workspace)
+        message_file = level4_dir / "output/output.txt.txt"
+        txt = message_file.read_text()
+        assert "output/output.txt" in txt
+        assert "1.0Mb" in txt
+        assert "0.5Mb" in txt
+
 
 @pytest.mark.needs_docker
 def test_finalize_invalid_file_type(docker_cleanup, job_definition, tmp_work_dir):
@@ -544,14 +554,16 @@ def test_finalize_invalid_file_type(docker_cleanup, job_definition, tmp_work_dir
     txt = message_file.read_text()
     assert "output/output.rds" in txt
 
-    log_file = level4_dir / "metadata/action.log"
+    log_file = local.get_log_dir(job_definition) / "logs.txt"
     log = log_file.read_text()
     assert "Invalid moderately_sensitive outputs:" in log
     assert "output/output.rds  - File type of .rds is not valid level 4 file" in log
 
 
 @pytest.mark.needs_docker
-def test_finalize_patient_id_header(docker_cleanup, job_definition, tmp_work_dir):
+def test_finalize_patient_id_header(
+    docker_cleanup, job_definition, tmp_work_dir, local_run
+):
     job_definition.args = [
         "sh",
         "-c",
@@ -581,17 +593,19 @@ def test_finalize_patient_id_header(docker_cleanup, job_definition, tmp_work_dir
         "output/output.csv": "File has patient_id column",
     }
 
-    level4_dir = local.get_medium_privacy_workspace(job_definition.workspace)
-    message_file = level4_dir / "output/output.csv.txt"
-    txt = message_file.read_text()
-    assert "output/output.csv" in txt
-    assert "patient_id" in txt
-
-    log_file = level4_dir / "metadata/action.log"
+    log_file = local.get_log_dir(job_definition) / "logs.txt"
     log = log_file.read_text()
     assert "Invalid moderately_sensitive outputs:" in log
     assert "output/output.csv  - File has patient_id column" in log
 
+    if not local_run:
+        level4_dir = local.get_medium_privacy_workspace(job_definition.workspace)
+
+        message_file = level4_dir / "output/output.csv.txt"
+        txt = message_file.read_text()
+        assert "output/output.csv" in txt
+        assert "patient_id" in txt
+
 
 @pytest.mark.needs_docker
 def test_finalize_large_level4_outputs_cleanup(