def encode_file():
return EncodeFile(
{
"@id": "1",
"status": "foo",
"output_type": "reads",
"dataset": "chip",
"md5sum": "123",
"quality_metrics": [{"@type": "Yes"}],
}
)
def test_preflight_helper_make_log_messages_from_records(preflight_helper):
matches = [
MatchingMd5Record(
"file",
[
EncodeFile({
"@id": "/files/foo/",
"status": "released",
"dataset": "bar"
})
],
)
]
messages = preflight_helper.make_log_messages_from_records(matches)
assert messages == [
"File Path | Matching Portal Files | Portal Status | Portal File Dataset",
"file | foo | released | bar ",
]
def test_encode_file_from_template(encode_common_metadata):
result = EncodeFile.from_template(
aliases=["foo"],
assembly="mm10",
common_metadata=encode_common_metadata,
dataset="dataset_id",
derived_from=["bar"],
file_params=FileParams(
{
"filekey": "foo",
"file_format": "bam",
"file_format_type": "bar",
"output_type": "reads",
"derived_from_files": [],
}
),
file_size="123",
file_md5sum="456",
step_run_id="step_run_id",
genome_annotation="V29",
extras={"extra": "cool"},
)
assert result == {
"_profile": "file",
"aliases": ["foo"],
"assembly": "mm10",
"award": "award",
"dataset": "dataset_id",
"derived_from": ["bar"],
"extra": "cool",
"file_format": "bam",
"file_format_type": "bar",
"file_size": "123",
"genome_annotation": "V29",
"lab": "/labs/lab/",
"md5sum": "456",
"output_type": "reads",
"status": "uploading",
"step_run": "step_run_id",
}
@pytest.fixture
def preflight_helper(mocker):
return PreflightHelper(mocker.create_autospec(Logger))
@pytest.mark.parametrize(
"matches,expected",
[
(
[
MatchingMd5Record(
"gs://foo/a.b",
[
EncodeFile({
"@id": "/files/ENCFF123ABC/",
"status": "released",
"dataset": "ENCSRCBA321",
}),
EncodeFile({
"@id": "/files/ENCFF456DEF/",
"status": "in progress",
"dataset": "ENCSRCBA321",
}),
],
),
MatchingMd5Record(
"gs://foo/c.d",
[
EncodeFile({
"@id": "/files/ENCFF000AAA/",
"status": "revoked",
def test_encode_file_filter_encode_files_by_status(files, expected):
assert len(EncodeFile.filter_encode_files_by_status(files)) == expected
"type": "text/plain",
"download": "my_text_file.txt",
"href": "data:text/plain;base64,Zm9vIGJhciBiYXo=",
}
@pytest.mark.parametrize(
"other_file,expected",
[
(1, False),
(
EncodeFile(
{
"@id": "1",
"status": "foo",
"output_type": "reads",
"dataset": "chip",
"md5sum": "123",
"quality_metrics": [{"@type": "Yes"}],
}
),
True,
),
(
EncodeFile(
{
"@id": "1",
"status": "foo",
"output_type": "reads",
"dataset": "atac",
"md5sum": "123",
"quality_metrics": [{"@type": "Yes"}],
def encode_file_no_qc():
return EncodeFile({"@id": "/files/foo/", "quality_metrics": []})