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DI-809 - fix upload of output file to job destination #15

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merged 1 commit into from
Sep 25, 2024
Merged

DI-809 - fix upload of output file to job destination #15

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17 changes: 13 additions & 4 deletions src/vcf_qc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -281,13 +281,22 @@ def upload_output_file(outfile) -> None:
outfile : str
name of file to upload
"""
print(f"\nUploading {outfile}")
output_project = os.environ.get("DX_PROJECT_CONTEXT_ID")
output_folder = (
dxpy.bindings.dxjob.DXJob(os.environ.get("DX_JOB_ID"))
.describe()
.get("folder", "/")
)
print(f"\nUploading {outfile} to {output_project}:{output_folder}")

dxpy.set_workspace_id(output_project)
dxpy.api.project_new_folder(
output_project, input_params={"folder": output_folder, "parents": True}
)

url_file = dxpy.upload_local_file(
filename=outfile,
folder=dxpy.bindings.dxjob.DXJob(
os.environ.get("DX_JOB_ID")
).describe()["folder"],
folder=output_folder,
wait_on_close=True,
)

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7 changes: 5 additions & 2 deletions tests/test_vcf_qc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -372,9 +372,10 @@ def test_output_file_contents_correctly_written(self):


@patch("src.vcf_qc.dxpy.upload_local_file")
@patch("src.vcf_qc.dxpy.api.project_new_folder")
@patch("src.vcf_qc.dxpy.bindings.dxjob.DXJob")
class TestUploadOutputFile(unittest.TestCase):
def test_upload_params_correct(self, mock_job, mock_upload):
def test_upload_params_correct(self, mock_job, mock_folder, mock_upload):
mock_job.return_value.describe.return_value = {
"folder": "/output/sub_folder"
}
Expand All @@ -389,7 +390,9 @@ def test_upload_params_correct(self, mock_job, mock_upload):

self.assertEqual(mock_upload.call_args[1], expected_args)

def test_expected_dxlink_format_returned(self, mock_job, mock_upload):
def test_expected_dxlink_format_returned(
self, mock_job, mock_folder, mock_upload
):
mock_upload.return_value = "file-xxx"

self.assertEqual(
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