def test_cytof_antibody_metadata_end_to_end(monkeypatch, metadata_df):
"""Test addition of antibody metadata for cytof files"""
# Mock an CyTOF downloadable file record
cytof_record = MagicMock()
cytof_record.object_url = "foo.txt"
cytof_record.upload_type = "cytof"
cytof_record.additional_metadata = {"foo": "bar"}
get_by_object_url = MagicMock()
get_by_object_url.return_value = cytof_record
monkeypatch.setattr(DownloadableFiles, "get_by_object_url",
get_by_object_url)
# Mock trial
ct = MagicMock()
ct.metadata_json = {
"assays": {
"cytof": [{
"cytof_antibodies": [
{
"usage": "Ignored"
},
{
"usage": "Used",
"stain_type": "Surface Stain",
"isotope": "000Foo",
"antibody": "Bar",
"clone": "Nx/xxx",
},
{
"usage": "Analysis Only",
"stain_type": "Intracellular",
"isotope": "001Foo",
"antibody": "Baz",
},
],
"object_url":
"foo.txt", # for DeepSearch
}]
}
}
find_by_trial_id = MagicMock()
find_by_trial_id.return_value = ct
monkeypatch.setattr(TrialMetadata, "find_by_trial_id", find_by_trial_id)
# Mock metadata_df
_get_metadata_df = MagicMock()
_get_metadata_df.return_value = metadata_df
monkeypatch.setattr(functions.visualizations, "_get_metadata_df",
_get_metadata_df)
vis_preprocessing(make_pubsub_event("1"), {})
get_by_object_url.assert_called_once()
_get_metadata_df.assert_called_once()
assert cytof_record.additional_metadata == {
"foo":
"bar",
"cytof.antibodies":
"surface 000Foo-Bar (Nx/xxx), intracellular 001Foo-Baz",
}
def test_cytof_clustergrammer_end_to_end(monkeypatch, metadata_df,
upload_type):
"""Test the CyTOF-clustergrammer transform."""
# Test no file found
monkeypatch.setattr(DownloadableFiles, "get_by_object_url",
lambda *args, **kwargs: None)
with pytest.raises(Exception, match="No downloadable file"):
vis_preprocessing(make_pubsub_event("foo/bar"), {})
# Mock a CyTOF summary downloadable file record
cytof_record = MagicMock()
cytof_record.object_url = "foo.txt"
cytof_record.upload_type = upload_type
get_by_object_url = MagicMock()
get_by_object_url.return_value = cytof_record
monkeypatch.setattr(DownloadableFiles, "get_by_object_url",
get_by_object_url)
# Mock GCS call
gcs_blob = MagicMock()
_get_blob_as_stream = MagicMock()
fake_cytof = open(CYTOF_PATH, "rb")
_get_blob_as_stream.return_value = fake_cytof
monkeypatch.setattr(functions.visualizations, "get_blob_as_stream",
_get_blob_as_stream)
# Mock metadata_df
_get_metadata_df = MagicMock()
_get_metadata_df.return_value = metadata_df
monkeypatch.setattr(functions.visualizations, "_get_metadata_df",
_get_metadata_df)
vis_preprocessing(make_pubsub_event("1"), {})
get_by_object_url.assert_called_once()
_get_blob_as_stream.assert_called_once()
_get_metadata_df.assert_called_once()
# Check contents of the clustergrammer output
row_names = [
row["name"] for row in cytof_record.clustergrammer["row_nodes"]
]
col_names = [
col["name"] for col in cytof_record.clustergrammer["col_nodes"]
]
col_cats = [(col["cat-0"], col["cat-1"], col["cat-2"])
for col in cytof_record.clustergrammer["col_nodes"]]
# Based on the contents of fake_cytof_summary.csv...
assert row_names == ["cell1", "cell2"]
assert col_names == ["CIMAC Id: CTTTTPPS1.01", "CIMAC Id: CTTTTPPS2.01"]
# Based on the construction of metadata_df...
assert col_cats == [
("Participant Id: CTTTTPP", "Cohort: Arm_A",
"Collection Event: Event1"),
("Participant Id: CTTTTPP", "Cohort: Arm_A",
"Collection Event: Event2"),
]
fake_cytof.close()
def test_mif_antibody_metadata_end_to_end(monkeypatch, metadata_df):
"""Test addition of antibody metadata for MIF files"""
# Mock an MIF downloadable file record
mif_record = MagicMock()
mif_record.object_url = "foo.txt"
mif_record.upload_type = "mif"
mif_record.additional_metadata = {"foo": "bar"}
get_by_object_url = MagicMock()
get_by_object_url.return_value = mif_record
monkeypatch.setattr(DownloadableFiles, "get_by_object_url",
get_by_object_url)
# Mock GCS call
ct = MagicMock()
ct.metadata_json = {
"assays": {
"mif": [{
"antibodies": [
{
"export_name": "Foo"
},
{
"antibody": "Bar",
"clone": "Nx/xxx",
"fluor_wavelength": 500
},
{
"antibody": "Baz",
"fluor_wavelength": 500
},
],
"object_url":
"foo.txt", # for DeepSearch
}]
}
}
find_by_trial_id = MagicMock()
find_by_trial_id.return_value = ct
monkeypatch.setattr(TrialMetadata, "find_by_trial_id", find_by_trial_id)
# Mock metadata_df
_get_metadata_df = MagicMock()
_get_metadata_df.return_value = metadata_df
monkeypatch.setattr(functions.visualizations, "_get_metadata_df",
_get_metadata_df)
vis_preprocessing(make_pubsub_event("1"), {})
get_by_object_url.assert_called_once()
_get_metadata_df.assert_called_once()
assert mif_record.additional_metadata == {
"foo": "bar",
"mif.antibodies": "Foo, Bar (Nx/xxx - 500), Baz (500)",
}
def test_ihc_combined_end_to_end(monkeypatch, metadata_df):
"""Test the IHC combined transform."""
# Mock an IHC combined downloadable file record
ihc_record = MagicMock()
ihc_record.object_url = "foo.txt"
ihc_record.upload_type = "ihc marker combined"
get_by_object_url = MagicMock()
get_by_object_url.return_value = ihc_record
monkeypatch.setattr(DownloadableFiles, "get_by_object_url",
get_by_object_url)
# Mock GCS call
gcs_blob = MagicMock()
_get_blob_as_stream = MagicMock()
combined_csv = StringIO(
"cimac_id,foo,bar\nCTTTTPPS1.01,1,2\nCTTTTPPS2.01,3,4")
_get_blob_as_stream.return_value = combined_csv
monkeypatch.setattr(functions.visualizations, "get_blob_as_stream",
_get_blob_as_stream)
# Mock metadata_df
_get_metadata_df = MagicMock()
_get_metadata_df.return_value = metadata_df
monkeypatch.setattr(functions.visualizations, "_get_metadata_df",
_get_metadata_df)
vis_preprocessing(make_pubsub_event("1"), {})
get_by_object_url.assert_called_once()
_get_blob_as_stream.assert_called_once()
_get_metadata_df.assert_called_once()
assert ihc_record.ihc_combined_plot == [
{
"cimac_id": "CTTTTPPS1.01",
"foo": 1,
"bar": 2,
"cimac_participant_id": "CTTTTPP",
"cohort_name": "Arm_A",
"collection_event_name": "Event1",
},
{
"cimac_id": "CTTTTPPS2.01",
"foo": 3,
"bar": 4,
"cimac_participant_id": "CTTTTPP",
"cohort_name": "Arm_A",
"collection_event_name": "Event2",
},
]
def test_ihc_antibody_metadata_end_to_end(monkeypatch, metadata_df):
"""Test addition of antibody metadata for IHC files"""
# Mock an IHC downloadable file record
ihc_record = MagicMock()
ihc_record.object_url = "foo.txt"
ihc_record.upload_type = "ihc"
ihc_record.additional_metadata = {"foo": "bar"}
get_by_object_url = MagicMock()
get_by_object_url.return_value = ihc_record
monkeypatch.setattr(DownloadableFiles, "get_by_object_url",
get_by_object_url)
# Mock GCS call
ct = MagicMock()
ct.metadata_json = {
"assays": {
"ihc": [{
"antibody": {
"antibody": "Bar",
"clone": "Nx/xxx"
},
"object_url": "foo.txt", # for DeepSearch
}]
}
}
find_by_trial_id = MagicMock()
find_by_trial_id.return_value = ct
monkeypatch.setattr(TrialMetadata, "find_by_trial_id", find_by_trial_id)
# Mock metadata_df
_get_metadata_df = MagicMock()
_get_metadata_df.return_value = metadata_df
monkeypatch.setattr(functions.visualizations, "_get_metadata_df",
_get_metadata_df)
vis_preprocessing(make_pubsub_event("1"), {})
get_by_object_url.assert_called_once()
_get_metadata_df.assert_called_once()
assert ihc_record.additional_metadata == {
"foo": "bar",
"ihc.antibody": "Bar (Nx/xxx)",
}
def test_loading_lazily(monkeypatch, metadata_df):
"""Test that files aren't loaded if there are no transformations for them"""
record = MagicMock()
record.object_url = "foo.txt"
record.upload_type = "something"
get_by_object_url = MagicMock()
get_by_object_url.return_value = record
monkeypatch.setattr(DownloadableFiles, "get_by_object_url",
get_by_object_url)
get_blob_as_stream = MagicMock()
monkeypatch.setattr(functions.visualizations, "get_blob_as_stream",
get_blob_as_stream)
# Mock metadata_df
_get_metadata_df = MagicMock()
_get_metadata_df.return_value = metadata_df
monkeypatch.setattr(functions.visualizations, "_get_metadata_df",
_get_metadata_df)
vis_preprocessing(make_pubsub_event("1"), {})
get_blob_as_stream.assert_not_called()