fake_datasets

test/plugins/tabular/fake_data_test.py

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+"""Tests that the fake covariate/pheno/metabolomics feather datasets under
+res/datasets/fake/ (used by downstream demos, e.g. the OGM repository's
+train_demo.yaml) actually load via TabularPlugin.
+
+These feather files are derived directly from the existing fake h5ad
+triplets in the same directories (same eids, same values, just reformatted
+for TabularPlugin instead of H5adPlugin), so this mirrors
+test/plugins/h5ad/h5ad_plugin_test.py's geno/cov/metabol/pheno fixtures.
+"""
+import os
+
+import hydra
+import pytest
+from hydra.core.global_hydra import GlobalHydra
+
+from udm.plugins.tabular.tabular_plugin import TabularPlugin
+from test.utils import try_clear_hydra
+
+UDM_HOME = "../../.."
+UDM_HOME_ABSPATH = os.path.abspath(os.path.join(os.path.dirname(__file__), UDM_HOME))
+
+FAKE_FEATHER_FILES = {
+    "covariates_new_base": "covariate/covariates_new_base_all.feather",
+    "covariates_new_extended": "covariate/covariates_new_extended_all.feather",
+    "covariates_new_extended_categorical": "covariate/covariates_new_extended_categorical_all.feather",
+    "covariates_new_extended_continous": "covariate/covariates_new_extended_continous_all.feather",
+    "cad": "pheno/cad_all.feather",
+    "additional_pheno": "additional_pheno/additional_pheno_all.feather",
+    "metabolomics": "metabolomics/metabolomics_all.feather",
+}
+
+# First eid of res/datasets/fake/geno/genetic_extended_tr.obs.csv; every fake
+# dataset under res/datasets/fake/ shares this eid across geno/covariate/
+# pheno/additional_pheno/metabolomics, none of it is real UK Biobank data.
+FIRST_EID = 5797
+
+
+def _config_for(name):
+    try_clear_hydra()
+    config_path = os.path.join(UDM_HOME, "config", "plugins", "tabular")
+    hydra.initialize(version_base=None, config_path=config_path)
+    data_path = os.path.join(
+        UDM_HOME_ABSPATH, "res/datasets/fake", FAKE_FEATHER_FILES[name]
+    )
+    return hydra.compose("default.yaml", overrides=[f"data_paths={data_path}"])
+
+
+@pytest.fixture(params=list(FAKE_FEATHER_FILES))
+def fake_feather_config(request):
+    yield _config_for(request.param)
+
+
+class TestFakeTabularData(object):
+    def setUp(self) -> None:
+        if GlobalHydra.instance().is_initialized():
+            GlobalHydra().instance().clear()
+
+    def test__init__(self, fake_feather_config):
+        TabularPlugin.from_config(fake_feather_config)
+
+    def test_prepare_data(self, fake_feather_config):
+        plugin = TabularPlugin.from_config(fake_feather_config)
+        plugin.prepare_data()
+
+    def test_setup(self, fake_feather_config):
+        plugin = TabularPlugin.from_config(fake_feather_config)
+        plugin.prepare_data()
+        plugin.setup()
+
+    def test__len__(self, fake_feather_config):
+        plugin = TabularPlugin.from_config(fake_feather_config)
+        plugin.prepare_data()
+        plugin.setup()
+        assert len(plugin) == 4096
+
+    def test__getitem__(self, fake_feather_config):
+        plugin = TabularPlugin.from_config(fake_feather_config)
+        plugin.prepare_data()
+        plugin.setup()
+        item = plugin[FIRST_EID]
+        assert "tabular_data" in item
+        assert item["tabular_data"].numel() > 0