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gdc.py: Show error code of failed download request #20

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gdc.py: Show error code of failed download request #20

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gdc.py: Show error code of failed download request
roshnet Apr 6, 2019
d734cc3
test_gdc.py: Add test to show error code
roshnet Apr 7, 2019
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8 changes: 8 additions & 0 deletions tests/test_gdc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,11 @@ def test_download():
os.unlink(file_path)


def test_download_error():
uuid = "something-invalid-0101"
gdc.download(uuid)
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@ayan-b ayan-b Apr 7, 2019 •
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Great start! However, you are not asserting the output to some expected output, so the test is not running. You may take a look at the other tests in the same file for some inspiration. 😃

uuid = "something-invalid-0101"
actual = gdc.download(uuid)
expected = <insert the string here>
assert actual == expected

Also, take a look at the CONTRIBUTING file in #17 .



def test_get_project_info():
project_name = "TCGA-THCA"
assert 'TCGA-BRCA' in gdc.get_project_info().index
Expand All @@ -88,3 +93,6 @@ def test_get_samples_clinical():
project_id = "TCGA-OV"
actual = gdc.get_samples_clinical(project_id)
assert actual['case_id'][0] == "71faa2c1-0d5b-4dcc-bdf9-f2405f29907c"


test_download_error()
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You need not to execute the function. pytest will discover the test and will run by itself.

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Oops, I forgot to remove that part after testing locally, will remove it.

4 changes: 3 additions & 1 deletion xena_gdc_etl/gdc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -348,7 +348,9 @@ def download(uuids, download_dir='.', chunk_size=4096):
sys.stdout.flush()
download_list.append(path)
else:
print('\rFail to download file {}.'.format(uuid))
print('\rFailed to download file {filename}.'
'Error code: {errcode}'.format(filename=uuid,
errcode=response.status_code))
print('')
return download_list

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