Revert "replace append with concat"

This reverts commit 344ddbd.

Author: rxu17

tests/test_dashboard_table_updater.py

@@ -1,33 +1,8 @@
-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",
     [
@@ -42,118 +17,3 @@ 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]}),
-        )