[SYNPY-1859] When creating entity views for Curator, the name column now goes first

synapseclient/extensions/curator/file_based_metadata_task.py

@@ -65,7 +65,7 @@ def create_json_schema_entity_view(
         synapse_client=syn,
     )
     assert isinstance(entity, (Folder, Project))
-    jsb = entity.get_schema()
+    jsb = entity.get_schema(synapse_client=syn)
     version_info = jsb.json_schema_version_info
     schema = JSONSchema(version_info.schema_name, version_info.organization_name)
     body = schema.get_body(version=version_info.semantic_version, synapse_client=syn)
@@ -77,10 +77,10 @@ def create_json_schema_entity_view(
         view_type_mask=view_type_mask,
         columns=columns,
     ).store(synapse_client=syn)
-    # This reorder is so that these show up in the front of the EntityView in Synapse
-    view.reorder_column(name="createdBy", index=0)
+    # This reorder is so that these show up in the front of the EntityView in Synapse.
     view.reorder_column(name="name", index=0)
-    view.reorder_column(name="id", index=0)
+    view.reorder_column(name="id", index=1)
+    view.reorder_column(name="createdBy", index=2)
     view.store(synapse_client=syn)
     return view.id
 

tests/integration/synapseclient/extensions/curator/test_file_based_metadata_task.py

@@ -0,0 +1,137 @@
+"""Integration tests for create_file_based_metadata_task."""
+
+import uuid
+from typing import Any, Callable, Generator
+
+import pytest
+
+from synapseclient import Synapse
+from synapseclient.core.exceptions import SynapseHTTPError
+from synapseclient.extensions.curator.file_based_metadata_task import (
+    create_file_based_metadata_task,
+)
+from synapseclient.models import (
+    CurationTask,
+    EntityView,
+    Folder,
+    JSONSchema,
+    Project,
+    SchemaOrganization,
+)
+
+
+def _test_name() -> str:
+    random_string = "".join(c for c in str(uuid.uuid4()) if c.isalpha())
+    return f"SYNPY.TEST.{random_string}"
+
+
+@pytest.fixture(scope="module")
+def patient_schema_uri(syn: Synapse, request: pytest.FixtureRequest) -> str:
+    """
+    Create a SchemaOrganization and a Patient JSON schema for the module.
+    Returns the schema URI.
+    """
+    org_name = _test_name()
+    schema_name = "test.schematic.Patient"
+
+    org = SchemaOrganization(name=org_name)
+    org.store(synapse_client=syn)
+
+    schema = JSONSchema(name=schema_name, organization_name=org_name)
+    schema_body = {
+        "$schema": "http://json-schema.org/draft-07/schema#",
+        "$id": f"https://example.com/schema/{org_name}-{schema_name}.json",
+        "title": "Patient",
+        "type": "object",
+        "properties": {
+            "PatientID": {"type": "string"},
+            "Sex": {"type": "string", "enum": ["Male", "Female", "Other"]},
+            "Age": {"type": "integer", "minimum": 0},
+        },
+        "required": ["PatientID"],
+    }
+    schema.store(schema_body=schema_body, synapse_client=syn)
+
+    def cleanup():
+        for js in org.get_json_schemas(synapse_client=syn):
+            js.delete(synapse_client=syn)
+        org.delete(synapse_client=syn)
+
+    request.addfinalizer(cleanup)
+
+    return schema.uri
+
+
+@pytest.fixture(scope="function")
+def folder(
+    syn: Synapse,
+    project: Project,
+    schedule_for_cleanup: Callable[[Any], None],
+) -> Generator[Folder, None, None]:
+    """Returns a Synapse Folder"""
+    folder = Folder(name=_test_name(), parent_id=project.id).store(synapse_client=syn)
+    schedule_for_cleanup(folder.id)
+    yield folder
+    # Unbind any JSON schema from the folder before teardown so the module-scoped
+    # schema cleanup (which runs before the session-scoped folder deletion) is not
+    # blocked by "Cannot delete a schema that is bound to an object".
+    try:
+        folder.unbind_schema(synapse_client=syn)
+    except SynapseHTTPError:
+        # No schema bound to this folder; nothing to unbind.
+        pass
+
+
+class TestCreateFileBasedMetadataTask:
+    """Integration tests for create_file_based_metadata_task."""
+
+    def test_create_file_based_metadata_task(
+        self,
+        syn: Synapse,
+        schedule_for_cleanup: Callable[[Any], None],
+        request: pytest.FixtureRequest,
+        patient_schema_uri: str,
+        folder: Folder,
+    ) -> None:
+        """Test successful creation of CurationTask and EntityView"""
+        # GIVEN a folder, a Patient JSON schema, and a unique task name
+        test_name = _test_name()
+
+        # WHEN a file-based metadata task is created for the folder
+        entity_view_id, task_id = create_file_based_metadata_task(
+            folder_id=folder.id,
+            curation_task_name=test_name,
+            instructions="Contribute Patient data.",
+            entity_view_name=test_name,
+            schema_uri=patient_schema_uri,
+            synapse_client=syn,
+        )
+        schedule_for_cleanup(entity_view_id)
+
+        # The CurationTask is not a deletable entity via syn.delete, so it keeps a
+        # dedicated finalizer. The EntityView it points at is cleaned up via
+        # schedule_for_cleanup above, so delete_source is not needed here.
+        request.addfinalizer(
+            lambda: CurationTask(task_id=task_id).delete(synapse_client=syn)
+        )
+
+        # THEN both the entity view and the curation task were created
+        assert entity_view_id is not None
+        assert task_id is not None
+
+        # AND the entity view exists in Synapse with the expected name
+        view = EntityView(id=entity_view_id).get(
+            include_columns=True, synapse_client=syn
+        )
+        assert view.id == entity_view_id
+        assert view.name == test_name
+
+        # AND the curation task exists in Synapse pointing at that view
+        task = CurationTask(task_id=task_id).get(synapse_client=syn)
+        assert task.task_id == task_id
+        assert task.data_type == test_name
+        assert task.task_properties.file_view_id == entity_view_id
+
+        # AND the leading columns are ordered with "name" first
+        column_names = list(view.columns.keys())
+        assert column_names[:3] == ["name", "id", "createdBy"]

tests/unit/synapseclient/extensions/unit_test_curator.py

@@ -13,7 +13,7 @@
 import tempfile
 import unittest
 from typing import Any
-from unittest.mock import Mock, mock_open, patch
+from unittest.mock import Mock, call, mock_open, patch
 
 import pandas as pd
 import pytest
@@ -1553,9 +1553,13 @@ def test_create_json_schema_entity_view_success(
 
         # THEN the entity view should be created successfully
         assert result == "syn87654321"
-        mock_view.reorder_column.assert_any_call(name="createdBy", index=0)
-        mock_view.reorder_column.assert_any_call(name="name", index=0)
-        mock_view.reorder_column.assert_any_call(name="id", index=0)
+        # AND the columns are reordered so that "name", "id", and "createdBy"
+        # appear first, in that order.
+        assert mock_view.reorder_column.call_args_list == [
+            call(name="name", index=0),
+            call(name="id", index=1),
+            call(name="createdBy", index=2),
+        ]
 
     @patch("synapseclient.extensions.curator.file_based_metadata_task.isinstance")
     @patch("synapseclient.extensions.curator.file_based_metadata_task.EntityView")