replace append with concat

Author: rxu17

tests/test_dashboard_table_updater.py

@@ -1,8 +1,33 @@
+import pandas as pd
+from pandas.testing import assert_frame_equal
 import pytest
+from unittest import mock
 
 from genie import dashboard_table_updater as dash_update
 
 
+@pytest.fixture
+def mock_syn(tmp_path):
+    """Fixture for a fake synapse client and test file."""
+    syn = mock.MagicMock()
+
+    # Create a fake clinical file
+    clinical_path = tmp_path / "clinical.txt"
+    clinical_path.write_text("SAMPLE_ID\nS1\nS2\nS3\n")
+
+    # Entity returned by syn.get for the clinical file
+    clinical_entity = mock.MagicMock()
+    clinical_entity.path = str(clinical_path)
+
+    # syn.get() will return this entity when given file_mapping["sample"]
+    syn.get.return_value = clinical_entity
+
+    # Default columns of existing table
+    syn.getTableColumns.return_value = [{"name": "SAMPLE_ID"}]
+
+    return syn
+
+
 @pytest.mark.parametrize(
     "input_string_time, expected_output_time",
     [
@@ -17,3 +42,118 @@ def test_that_string_to_unix_epoch_time_milliseconds_gives_expected_time(
 ):
     output = dash_update.string_to_unix_epoch_time_milliseconds(input_string_time)
     assert output == expected_output_time
+
+
+def test_that_update_samples_in_release_table_adds_column_and_calls_update(
+    tmp_path, mock_syn
+):
+    """Test that a new release column is added and load._update_table gets correct data."""
+    file_mapping = {"sample": "syn123"}
+    release = "5.3-consortium"
+    samples_in_release_synid = "syn999"
+
+    # Fake DataFrames for clinical and existing table
+    clinical_df = pd.DataFrame({"SAMPLE_ID": ["S1", "S2", "S3"]})
+    existing_df = pd.DataFrame({"SAMPLE_ID": ["S1"], release: [1]})
+
+    with (
+        mock.patch.object(pd, "read_csv", return_value=clinical_df) as mock_read,
+        mock.patch.object(
+            dash_update.extract, "get_syntabledf", return_value=existing_df
+        ) as mock_extract,
+        mock.patch.object(dash_update.load, "_update_table") as mock_update,
+    ):
+        dash_update.update_samples_in_release_table(
+            syn=mock_syn,
+            file_mapping=file_mapping,
+            release=release,
+            samples_in_release_synid=samples_in_release_synid,
+        )
+
+        # --- Assertions on Synapse calls ---
+        mock_syn.get.assert_has_calls(
+            [
+                mock.call(file_mapping["sample"], followLink=True),
+                mock.call(samples_in_release_synid),
+            ]
+        )
+        mock_syn.getTableColumns.assert_called_once_with(samples_in_release_synid)
+
+        # --- Assertions on pd.read_csv ---
+        mock_read.assert_called_once()
+        assert list(mock_read.return_value.columns) == ["SAMPLE_ID"]
+
+        # --- Assertions on extract.get_syntabledf ---
+        mock_extract.assert_called_once_with(
+            syn=mock_syn,
+            query_string=f'SELECT SAMPLE_ID, "{release}" FROM {samples_in_release_synid}',
+        )
+
+        # --- Assertions on load._update_table inputs ---
+        mock_update.assert_called_once()
+        args, kwargs = mock_update.call_args
+
+        # Extract arguments
+        _, _, samples_in_releasedf, synid_arg, key_cols = args
+
+        # Ensure correct Synapse ID and key columns
+        assert synid_arg == samples_in_release_synid
+        assert key_cols == ["SAMPLE_ID"]
+
+        # Check that new samples and old samples are in expected order
+        assert_frame_equal(
+            samples_in_releasedf.reset_index(drop=True),
+            pd.DataFrame(
+                {"SAMPLE_ID": ["S2", "S3", "S1"], "5.3-consortium": [1, 1, 1]}
+            ),
+        )
+
+
+def test_that_update_samples_in_release_table_existing_column_calls_update_directly(
+    mock_syn,
+):
+    """If the release column already exists, we skip creating new column but still call _update_table."""
+    release = "5.3-consortium"
+    file_mapping = {"sample": "syn123"}
+    samples_in_release_synid = "syn999"
+
+    # Pretend the release column already exists
+    mock_syn.getTableColumns.return_value = [{"name": "SAMPLE_ID"}, {"name": release}]
+
+    clinical_df = pd.DataFrame({"SAMPLE_ID": ["S1", "S2"]})
+    existing_df = pd.DataFrame({"SAMPLE_ID": ["S2", "S1"], release: [1, 1]})
+
+    with (
+        mock.patch.object(pd, "read_csv", return_value=clinical_df) as mock_read,
+        mock.patch.object(
+            dash_update.extract, "get_syntabledf", return_value=existing_df
+        ) as mock_extract,
+        mock.patch.object(dash_update.load, "_update_table") as mock_update,
+    ):
+
+        dash_update.update_samples_in_release_table(
+            syn=mock_syn,
+            file_mapping=file_mapping,
+            release=release,
+            samples_in_release_synid=samples_in_release_synid,
+        )
+        # --- Assertions on Synapse calls ---
+        mock_syn.get.assert_has_calls(
+            [
+                mock.call(file_mapping["sample"], followLink=True),
+            ]
+        )
+        args, kwargs = mock_update.call_args
+
+        # Extract arguments
+        _, _, samples_in_releasedf, synid_arg, key_cols = args
+
+        # Ensure correct Synapse ID and key columns
+        assert synid_arg == samples_in_release_synid
+        assert key_cols == ["SAMPLE_ID"]
+
+        # Check that new samples and old samples are in expected order
+        assert_frame_equal(
+            samples_in_releasedf.reset_index(drop=True),
+            pd.DataFrame({"SAMPLE_ID": ["S1", "S2"], "5.3-consortium": [1, 1]}),
+        )