HTTP Error 400 while running Segment_GBM module on the command line

[giemmecci]

Hi,
I got this error while trying to run the Segment_GBM module thru the command line:

urllib.error.HTTPError: HTTP Error 400: Bad Request

It seems to be happening after the file are loaded correctly, here's the full output:

Using TensorFlow backend.
/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/tensorflow/python/framework/dtypes.py:516: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint8 = np.dtype([("qint8", np.int8, 1)])
/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/tensorflow/python/framework/dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/tensorflow/python/framework/dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint16 = np.dtype([("qint16", np.int16, 1)])
/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/tensorflow/python/framework/dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/tensorflow/python/framework/dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint32 = np.dtype([("qint32", np.int32, 1)])
/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/tensorflow/python/framework/dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  np_resource = np.dtype([("resource", np.ubyte, 1)])
/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint8 = np.dtype([("qint8", np.int8, 1)])
/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint16 = np.dtype([("qint16", np.int16, 1)])
/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint32 = np.dtype([("qint32", np.int32, 1)])
/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  np_resource = np.dtype([("resource", np.ubyte, 1)])
File loading completed.
Traceback (most recent call last):
  File "/home/m192229/anaconda3/envs/deepneuroenv/bin/segment_gbm", line 11, in <module>
    sys.exit(main())
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/deepneuro/pipelines/Segment_GBM/cli.py", line 86, in main
    Segment_GBM_cli()
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/deepneuro/pipelines/shared.py", line 22, in __init__
    self.load()
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/deepneuro/pipelines/Segment_GBM/cli.py", line 16, in load
    super(Segment_GBM_cli, self).load()
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/deepneuro/pipelines/shared.py", line 48, in load
    getattr(self, args.command)()
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/deepneuro/pipelines/Segment_GBM/cli.py", line 82, in pipeline
    quiet=args.quiet)
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/deepneuro/pipelines/Segment_GBM/predict.py", line 70, in predict_GBM
    postprocessors=[BinarizeLabel(postprocessor_string='label')])
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/deepneuro/models/model.py", line 284, in load_model_with_output
    model = load_old_model(load(model_name), **kwargs)
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/site-packages/deepneuro/load/load.py", line 70, in load
    urlretrieve(data_dict[dataset][1], dataset_path)
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/urllib/request.py", line 187, in urlretrieve
    with contextlib.closing(urlopen(url, data)) as fp:
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/urllib/request.py", line 162, in urlopen
    return opener.open(url, data, timeout)
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/urllib/request.py", line 471, in open
    response = meth(req, response)
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/urllib/request.py", line 581, in http_response
    'http', request, response, code, msg, hdrs)
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/urllib/request.py", line 503, in error
    result = self._call_chain(*args)
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/urllib/request.py", line 443, in _call_chain
    result = func(*args)
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/urllib/request.py", line 686, in http_error_302
    return self.parent.open(new, timeout=req.timeout)
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/urllib/request.py", line 471, in open
    response = meth(req, response)
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/urllib/request.py", line 581, in http_response
    'http', request, response, code, msg, hdrs)
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/urllib/request.py", line 509, in error
    return self._call_chain(*args)
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/urllib/request.py", line 443, in _call_chain
    result = func(*args)
  File "/home/m192229/anaconda3/envs/deepneuroenv/lib/python3.5/urllib/request.py", line 589, in http_error_default
    raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 400: Bad Request

Thank you

[JonathanChiang]

@giemmecci This is known issue and we are working on updating the links.

[giemmecci]

Thank you

[agatadefr]

I have the same issue. When do you expect to fix this issue ?

C:\Users\krasona\PycharmProjects\BrainLesionSegmentation>segment_gbm pipeline -T1 T1 -T1POST T1POST -FLAIR FLAIR -output_folder output -wholetumor_output wholetumor.nii.gz -en
hancing_output enhancing.nii.gz -debiased -registered -skullstripped -preprocessed
Using TensorFlow backend.
C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\tensorflow\python\framework\dtypes.py:516: FutureWarning: Passing (type, 1) or '1type' as a synonym of
 type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint8 = np.dtype([("qint8", np.int8, 1)])
C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\tensorflow\python\framework\dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of
 type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint8 = np.dtype([("quint8", np.uint8, 1)])
C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\tensorflow\python\framework\dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of
 type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint16 = np.dtype([("qint16", np.int16, 1)])
C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\tensorflow\python\framework\dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of
 type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint16 = np.dtype([("quint16", np.uint16, 1)])
C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\tensorflow\python\framework\dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of
 type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint32 = np.dtype([("qint32", np.int32, 1)])
C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\tensorflow\python\framework\dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of
 type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  np_resource = np.dtype([("resource", np.ubyte, 1)])
C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a syn
onym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint8 = np.dtype([("qint8", np.int8, 1)])
C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a syn
onym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint8 = np.dtype([("quint8", np.uint8, 1)])
C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a syn
onym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint16 = np.dtype([("qint16", np.int16, 1)])
C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a syn
onym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint16 = np.dtype([("quint16", np.uint16, 1)])
C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a syn
onym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint32 = np.dtype([("qint32", np.int32, 1)])
C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a syn
onym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  np_resource = np.dtype([("resource", np.ubyte, 1)])
File loading completed.
Traceback (most recent call last):
  File "C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\Scripts\segment_gbm-script.py", line 11, in <module>
    load_entry_point('deepneuro==0.2.3', 'console_scripts', 'segment_gbm')()
  File "C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\deepneuro\pipelines\Segment_GBM\cli.py", line 86, in main
    Segment_GBM_cli()
  File "C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\deepneuro\pipelines\shared.py", line 22, in __init__
    self.load()
  File "C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\deepneuro\pipelines\Segment_GBM\cli.py", line 16, in load
    super(Segment_GBM_cli, self).load()
  File "C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\deepneuro\pipelines\shared.py", line 48, in load
    getattr(self, args.command)()
  File "C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\deepneuro\pipelines\Segment_GBM\cli.py", line 82, in pipeline
    quiet=args.quiet)
  File "C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\deepneuro\pipelines\Segment_GBM\predict.py", line 70, in predict_GBM
    postprocessors=[BinarizeLabel(postprocessor_string='label')])
  File "C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\deepneuro\models\model.py", line 284, in load_model_with_output
    model = load_old_model(load(model_name), **kwargs)
  File "C:\Users\krasona\PycharmProjects\BrainLesionSegmentation\venv\lib\site-packages\deepneuro\load\load.py", line 70, in load
    urlretrieve(data_dict[dataset][1], dataset_path)
  File "C:\Users\krasona\AppData\Local\Programs\Python\Python37\lib\urllib\request.py", line 248, in urlretrieve
    with contextlib.closing(urlopen(url, data)) as fp:
  File "C:\Users\krasona\AppData\Local\Programs\Python\Python37\lib\urllib\request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "C:\Users\krasona\AppData\Local\Programs\Python\Python37\lib\urllib\request.py", line 532, in open
    response = meth(req, response)
  File "C:\Users\krasona\AppData\Local\Programs\Python\Python37\lib\urllib\request.py", line 642, in http_response
    'http', request, response, code, msg, hdrs)
  File "C:\Users\krasona\AppData\Local\Programs\Python\Python37\lib\urllib\request.py", line 564, in error
    result = self._call_chain(*args)
  File "C:\Users\krasona\AppData\Local\Programs\Python\Python37\lib\urllib\request.py", line 504, in _call_chain
    result = func(*args)
  File "C:\Users\krasona\AppData\Local\Programs\Python\Python37\lib\urllib\request.py", line 756, in http_error_302
    return self.parent.open(new, timeout=req.timeout)
  File "C:\Users\krasona\AppData\Local\Programs\Python\Python37\lib\urllib\request.py", line 532, in open
    response = meth(req, response)
  File "C:\Users\krasona\AppData\Local\Programs\Python\Python37\lib\urllib\request.py", line 642, in http_response
    'http', request, response, code, msg, hdrs)
  File "C:\Users\krasona\AppData\Local\Programs\Python\Python37\lib\urllib\request.py", line 570, in error
    return self._call_chain(*args)
  File "C:\Users\krasona\AppData\Local\Programs\Python\Python37\lib\urllib\request.py", line 504, in _call_chain
    result = func(*args)
  File "C:\Users\krasona\AppData\Local\Programs\Python\Python37\lib\urllib\request.py", line 650, in http_error_default
    raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 400: Bad Request

[changken1]

Hi, We just updated the links - should be working now. Best, Ken

…

On Wed, Aug 28, 2019 at 9:36 AM agata ***@***.***> wrote: I have the same issue. When do you expect to fix this issue ? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#49?email_source=notifications&email_token=AGAKY7EXDYGARIPKO75LYA3QGZ5MTA5CNFSM4INFMSGKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5LEQ4A#issuecomment-525748336>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGAKY7FVONZ4XVHLKS7J3XTQGZ5MTANCNFSM4INFMSGA> .

[agatadefr]

Hmmm ... I just tried and I am getting the same error.

[changken1]

Did you re-pull the github repository? We changed deepneuro/load/load.py

[agatadefr]

Ok. I did that. Thanks for fixing this bug.
Thanks for your help @changken1 !

[agatadefr]

One more issue could update also a link to data sample_gbm_nifti because tutorial doesn't work.
I mean exactly this one:

  'sample_gbm_nifti': [os.path.join ( current_dir, 'Sample_Data', 'TCGA_GBM_NIFTI', 'TCGA_GBM_NIFTI.zip' ),
                                  'https://www.dropbox.com/s/bqclpqzwfsreolb/GBM_NIFTI.zip?dl=1'],

[kbenahmed89]

The links are still not working. We are still getting the same issue.

[TSbme]

the link is not working.