Closed wyli closed 2 years ago
Describe the bug looks like an issue from the server side
01:08:28 Running ./modules/tcia_csv_processing.ipynb 01:08:28 Checking PEP8 compliance... 01:08:29 Running notebook... 01:08:33 MONAI version: 0.9.1rc3+3.gec4c0311 01:08:33 Numpy version: 1.22.4 01:08:33 Pytorch version: 1.10.2+cu102 01:08:33 MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False 01:08:33 MONAI rev id: ec4c03115ba45b2e950103a24db22f16d54c8d40 01:08:33 MONAI __file__: /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/__init__.py 01:08:33 01:08:33 Optional dependencies: 01:08:33 Pytorch Ignite version: 0.4.9 01:08:33 Nibabel version: 4.0.1 01:08:33 scikit-image version: 0.19.3 01:08:33 Pillow version: 9.0.1 01:08:33 Tensorboard version: 2.9.1 01:08:33 gdown version: 4.5.1 01:08:33 TorchVision version: 0.11.3+cu102 01:08:33 tqdm version: 4.64.0 01:08:33 lmdb version: 1.3.0 01:08:33 psutil version: 5.9.1 01:08:33 pandas version: 1.1.5 01:08:33 einops version: 0.4.1 01:08:33 transformers version: 4.20.1 01:08:33 mlflow version: 1.27.0 01:08:33 pynrrd version: 0.4.3 01:08:33 01:08:33 For details about installing the optional dependencies, please visit: 01:08:33 https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies 01:08:33 01:08:33 /opt/conda/lib/python3.8/site-packages/papermill/iorw.py:58: FutureWarning: pyarrow.HadoopFileSystem is deprecated as of 2.0.0, please use pyarrow.fs.HadoopFileSystem instead. 01:08:33 from pyarrow import HadoopFileSystem 01:08:45 Executing: 0%| | 0/18 [00:00<?, ?cell/s] Executing: 6%|▌ | 1/18 [00:01<00:26, 1.55s/cell] Executing: 17%|█▋ | 3/18 [00:06<00:32, 2.17s/cell] Executing: 28%|██▊ | 5/18 [00:08<00:21, 1.64s/cell] Executing: 61%|██████ | 11/18 [00:09<00:03, 1.75cell/s] Executing: 78%|███████▊ | 14/18 [00:10<00:02, 1.84cell/s] Executing: 78%|███████▊ | 14/18 [00:11<00:03, 1.22cell/s] 01:08:45 Traceback (most recent call last): 01:08:45 File "/opt/conda/bin/papermill", line 8, in <module> 01:08:45 sys.exit(papermill()) 01:08:45 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1128, in __call__ 01:08:45 return self.main(*args, **kwargs) 01:08:45 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1053, in main 01:08:45 rv = self.invoke(ctx) 01:08:45 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1395, in invoke 01:08:45 return ctx.invoke(self.callback, **ctx.params) 01:08:45 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 754, in invoke 01:08:45 return __callback(*args, **kwargs) 01:08:45 File "/opt/conda/lib/python3.8/site-packages/click/decorators.py", line 26, in new_func 01:08:45 return f(get_current_context(), *args, **kwargs) 01:08:45 File "/opt/conda/lib/python3.8/site-packages/papermill/cli.py", line 250, in papermill 01:08:45 execute_notebook( 01:08:45 File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 122, in execute_notebook 01:08:45 raise_for_execution_errors(nb, output_path) 01:08:45 File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 234, in raise_for_execution_errors 01:08:45 raise error 01:08:45 papermill.exceptions.PapermillExecutionError: 01:08:45 --------------------------------------------------------------------------- 01:08:45 Exception encountered at "In [7]": 01:08:45 --------------------------------------------------------------------------- 01:08:45 HTTPError Traceback (most recent call last) 01:08:45 Input In [7], in <cell line: 1>() 01:08:45 ----> 1 data = dataset[0] 01:08:45 2 print(f"Series UID is: {data['Series UID']}") 01:08:45 01:08:45 Input In [4], in TCIADataset.__getitem__(self, index) 01:08:45 75 if isinstance(index, int): 01:08:45 76 series_uid = self.data[index]["Series UID"] 01:08:45 ---> 77 self.data[index]["image"] = self._get_image(series_uid) 01:08:45 78 return super().__getitem__(index=index) 01:08:45 01:08:45 Input In [4], in TCIADataset._get_image(self, series_uid) 01:08:45 69 url = "https://services.cancerimagingarchive.net/nbia-api/services/v1/getImage?SeriesInstanceUID=" + series_uid 01:08:45 70 if not os.path.exists(data_dir): 01:08:45 ---> 71 download_and_extract(url=url, filepath=data_dir + ".zip", output_dir=data_dir) 01:08:45 72 return data_dir 01:08:45 01:08:45 File /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/utils.py:312, in download_and_extract(url, filepath, output_dir, hash_val, hash_type, file_type, has_base, progress) 01:08:45 310 with tempfile.TemporaryDirectory() as tmp_dir: 01:08:45 311 filename = filepath or Path(tmp_dir, _basename(url)).resolve() 01:08:45 --> 312 download_url(url=url, filepath=filename, hash_val=hash_val, hash_type=hash_type, progress=progress) 01:08:45 313 extractall(filepath=filename, output_dir=output_dir, file_type=file_type, has_base=has_base) 01:08:45 01:08:45 File /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/utils.py:203, in download_url(url, filepath, hash_val, hash_type, progress, **gdown_kwargs) 01:08:45 201 gdown.download(url, f"{tmp_name}", quiet=not progress, **gdown_kwargs) 01:08:45 202 else: 01:08:45 --> 203 _download_with_progress(url, tmp_name, progress=progress) 01:08:45 204 if not tmp_name.exists(): 01:08:45 205 raise RuntimeError( 01:08:45 206 f"Download of file from {url} to {filepath} failed due to network issue or denied permission." 01:08:45 207 ) 01:08:45 01:08:45 File /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/utils.py:114, in _download_with_progress(url, filepath, progress) 01:08:45 112 except (URLError, HTTPError, ContentTooShortError, OSError) as e: 01:08:45 113 logger.error(f"Download failed from {url} to {filepath}.") 01:08:45 --> 114 raise e 01:08:45 01:08:45 File /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/utils.py:107, in _download_with_progress(url, filepath, progress) 01:08:45 104 self.update(b * bsize - self.n) # will also set self.n = b * bsize 01:08:45 106 with TqdmUpTo(unit="B", unit_scale=True, unit_divisor=1024, miniters=1, desc=_basename(filepath)) as t: 01:08:45 --> 107 urlretrieve(url, filepath, reporthook=t.update_to) 01:08:45 108 else: 01:08:45 109 if not has_tqdm and progress: 01:08:45 01:08:45 File /opt/conda/lib/python3.8/urllib/request.py:247, in urlretrieve(url, filename, reporthook, data) 01:08:45 230 """ 01:08:45 231 Retrieve a URL into a temporary location on disk. 01:08:45 232 01:08:45 (...) 01:08:45 243 data file as well as the resulting HTTPMessage object. 01:08:45 244 """ 01:08:45 245 url_type, path = _splittype(url) 01:08:45 --> 247 with contextlib.closing(urlopen(url, data)) as fp: 01:08:45 248 headers = fp.info() 01:08:45 250 # Just return the local path and the "headers" for file:// 01:08:45 251 # URLs. No sense in performing a copy unless requested. 01:08:45 01:08:45 File /opt/conda/lib/python3.8/urllib/request.py:222, in urlopen(url, data, timeout, cafile, capath, cadefault, context) 01:08:45 220 else: 01:08:45 221 opener = _opener 01:08:45 --> 222 return opener.open(url, data, timeout) 01:08:45 01:08:45 File /opt/conda/lib/python3.8/urllib/request.py:531, in OpenerDirector.open(self, fullurl, data, timeout) 01:08:45 529 for processor in self.process_response.get(protocol, []): 01:08:45 530 meth = getattr(processor, meth_name) 01:08:45 --> 531 response = meth(req, response) 01:08:45 533 return response 01:08:45 01:08:45 File /opt/conda/lib/python3.8/urllib/request.py:640, in HTTPErrorProcessor.http_response(self, request, response) 01:08:45 637 # According to RFC 2616, "2xx" code indicates that the client's 01:08:45 638 # request was successfully received, understood, and accepted. 01:08:45 639 if not (200 <= code < 300): 01:08:45 --> 640 response = self.parent.error( 01:08:45 641 'http', request, response, code, msg, hdrs) 01:08:45 643 return response 01:08:45 01:08:45 File /opt/conda/lib/python3.8/urllib/request.py:569, in OpenerDirector.error(self, proto, *args) 01:08:45 567 if http_err: 01:08:45 568 args = (dict, 'default', 'http_error_default') + orig_args 01:08:45 --> 569 return self._call_chain(*args) 01:08:45 01:08:45 File /opt/conda/lib/python3.8/urllib/request.py:502, in OpenerDirector._call_chain(self, chain, kind, meth_name, *args) 01:08:45 500 for handler in handlers: 01:08:45 501 func = getattr(handler, meth_name) 01:08:45 --> 502 result = func(*args) 01:08:45 503 if result is not None: 01:08:45 504 return result 01:08:45 01:08:45 File /opt/conda/lib/python3.8/urllib/request.py:649, in HTTPDefaultErrorHandler.http_error_default(self, req, fp, code, msg, hdrs) 01:08:45 648 def http_error_default(self, req, fp, code, msg, hdrs): 01:08:45 --> 649 raise HTTPError(req.full_url, code, msg, hdrs, fp) 01:08:45 01:08:45 HTTPError: HTTP Error 502: Bad Gateway
service is back
wyli
commented
2 years ago wyli
commented
2 years ago
Describe the bug looks like an issue from the server side