def test_search_down_no_output_files_does_not_raise(mocker):
"""
Regression test related to PIP-1163. If the current file being searched does not
have any output files, then the _search_down should not throw an error in the call
to reduce(), and instead yield nothing.
"""
mocker.patch(
"builtins.open", mocker.mock_open(read_data='{"workflowRoot": "gs://foo/bar"}')
)
analysis = Analysis(MetaData("foo"), auto_populate=False, backend="")
no_outputs_task = Task("foo", {"inputs": {"bar": "gs://baz"}, "outputs": {}})
result = list(analysis._search_down(no_outputs_task, "searching_for", "a_file"))
assert result == []
def mock_accession_unreplicated(
mocker: MockFixture,
mock_accession_gc_backend: MockGCBackend,
mock_metadata: MockMetaData,
lab: str,
award: str,
) -> Accession:
"""
Mocked accession instance with dummy __init__ that doesn't do anything and pre-baked
assembly property. @properties must be patched before instantiation
"""
mocker.patch.object(
Accession,
"experiment",
new_callable=PropertyMock(
return_value=EncodeExperiment(
{
"@id": "foo",
"assay_term_name": "microRNA",
"replicates": [{"biological_replicate_number": 1}],
}
)
),
)
mocked_accession = AccessionMicroRna(
"imaginary_steps.json",
Analysis(mock_metadata, backend=mock_accession_gc_backend),
"mock_server.biz",
EncodeCommonMetadata(lab, award),
no_log_file=True,
)
return mocked_accession
def test_invalid_metadata_raises():
"""
Trying to create an Analysis from invalid JSON should raise an error.
"""
current_dir = Path(__file__).resolve()
metadata_json = current_dir.parent / "data" / "invalid_metadata.json"
with pytest.raises(Exception):
Analysis(metadata_json)
def mock_accession(
mocker: MockFixture,
mock_accession_gc_backend: MockGCBackend,
mock_metadata: MockMetaData,
mock_accession_steps: MockAccessionSteps,
server_name: str,
common_metadata: EncodeCommonMetadata,
) -> Accession:
"""
Mocked accession instance with dummy __init__ that doesn't do anything and pre-baked
assembly property. @properties must be patched before instantiation
"""
mocker.patch.object(
AccessionMicroRna, "assembly", new_callable=PropertyMock(return_value="hg19")
)
mocker.patch.object(
AccessionMicroRna,
"genome_annotation",
new_callable=PropertyMock(return_value="V19"),
)
mocker.patch.object(
Accession,
"experiment",
new_callable=PropertyMock(
return_value=EncodeExperiment(
{
"@id": "foo",
"assay_term_name": "microRNA",
"replicates": [
{"biological_replicate_number": 1},
{"biological_replicate_number": 2},
],
"analyses": [{"files": ["/files/1/"]}],
}
)
),
)
mocker.patch.object(Accession, "preflight_helper", new_callable=PropertyMock())
mocked_accession = AccessionMicroRna(
mock_accession_steps,
Analysis(mock_metadata, backend=mock_accession_gc_backend),
create_autospec(Connection, dcc_url=server_name),
common_metadata,
no_log_file=True,
)
return mocked_accession
def mock_accession_chip(
mocker: MockFixture,
mock_accession_gc_backend: MockGCBackend,
mock_metadata: MockMetaData,
mock_accession_steps: MockAccessionSteps,
server_name: str,
common_metadata: EncodeCommonMetadata,
) -> Accession:
"""
Mocked accession instance with dummy __init__ that doesn't do anything and pre-baked
assembly property. @properties must be patched before instantiation
"""
mocker.patch.object(
AccessionChip, "assembly", new_callable=PropertyMock(return_value="hg19")
)
mocker.patch.object(
AccessionChip,
"genome_annotation",
new_callable=PropertyMock(return_value="V19"),
)
mocker.patch.object(
Accession,
"experiment",
new_callable=PropertyMock(
return_value=EncodeExperiment(
{
"@id": "foo",
"assay_term_name": "TF ChIP-seq",
"replicates": [
{"biological_replicate_number": 1},
{"biological_replicate_number": 2},
],
}
)
),
)
mocked_accession = AccessionChip(
mock_accession_steps,
Analysis(mock_metadata, backend=mock_accession_gc_backend),
server_name,
common_metadata,
no_log_file=True,
)
return mocked_accession
def mock_accession_not_patched(
mocker,
mock_accession_gc_backend,
mock_metadata,
mock_accession_steps,
server_name,
common_metadata,
mock_file,
):
mocker.patch.object(
Analysis, "raw_fastqs", new_callable=PropertyMock(return_value=[mock_file])
)
mock_accession = AccessionMicroRna(
mock_accession_steps,
Analysis(mock_metadata, backend=mock_accession_gc_backend),
create_autospec(Connection, dcc_url=server_name),
common_metadata,
no_log_file=True,
)
return mock_accession
def empty_analysis(mock_gc_backend, metadata_json_path): # noqa: F811
empty = Analysis(
MetaData(metadata_json_path), auto_populate=False, backend=mock_gc_backend
)
return empty
def test_search_up_disallow_tasks(
mock_metadata, mock_gc_backend, condition, disallow_tasks, expected
):
metadata = {
"workflowRoot": "gs://foo/bar/",
"calls": {
"chip.bam2ta": [
{
"dockerImageUsed": "arch:latest",
"inputs": {"bam": "gs://foo/bar/ENCFF295YVN.nodup.bam"},
"outputs": {
"ta": "gs://foo/bar/call-bam2ta/shard-0/glob-35/ENCFF295YVN.nodup.tagAlign.gz"
},
},
{
"dockerImageUsed": "arch:latest",
"inputs": {"bam": "gs://foo/bar/ENCFF279HDE.nodup.bam"},
"outputs": {
"ta": "gs://foo/bar/call-bam2ta/shard-1/glob-35/ENCFF279HDE.nodup.tagAlign.gz"
},
},
],
"chip.macs2_signal_track": [
{
"dockerImageUsed": "arch:latest",
"inputs": {
"tas": [
"gs://foo/bar/call-bam2ta/shard-0/glob-35/ENCFF295YVN.nodup.tagAlign.gz",
"gs://foo/bar/call-choose_ctl/glob-99/ctl_for_rep1.tagAlign.gz",
]
},
"outputs": {
"fc_bw": "gs://foo/bar/call-macs2_signal_track/shard-0/glob-10/ENCFF295YVN.bigwig",
"pval_bw": "gs://foo/bar/call-macs2_signal_track/shard-0/glob-89/ENCFF295YVN.bigwig",
},
}
],
"chip.choose_ctl": [
{
"dockerImageUsed": "arch:latest",
"inputs": {
"tas": [
"gs://foo/bar/call-bam2ta/shard-0/glob-35/ENCFF295YVN.nodup.tagAlign.gz",
"gs://foo/bar/call-bam2ta/shard-1/glob-35/ENCFF279HDE.nodup.tagAlign.gz",
]
},
"outputs": {
"chosen_ctl_tas": [
"gs://foo/bar/call-choose_ctl/glob-99/ctl_for_rep1.tagAlign.gz",
"gs://foo/bar/call-choose_ctl/glob-99/ctl_for_rep2.tagAlign.gz",
]
},
}
],
},
}
mock_metadata.content = metadata
analysis = Analysis(mock_metadata, backend=mock_gc_backend)
start_task = analysis.get_tasks("macs2_signal_track")[0]
with condition:
results = analysis.search_up(
start_task=start_task,
task_name="bam2ta",
filekey="bam",
inputs=True,
disallow_tasks=disallow_tasks,
)
result = [i.filename for i in results]
assert sorted(result) == sorted(expected)
def normal_analysis(
mock_gc_backend: MockFixture, metadata_json_path: Path
) -> Analysis: # noqa: F811
normal_analysis = Analysis(MetaData(metadata_json_path), backend=mock_gc_backend)
return normal_analysis
def mirna_replicated_analysis(
mock_accession_gc_backend: MockFixture,
mirna_replicated_metadata_path: str) -> Analysis: # noqa: F811
analysis = Analysis(MetaData(mirna_replicated_metadata_path),
backend=mock_accession_gc_backend)
return analysis