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Description
Hi Team,
getting issue with fetching the file from tcga repository https://portal.gdc.cancer.gov/repository?facetTab=files
inline below is the error log from jupyter notebook for your reference
Downloading file 'tcga/prostate/6b725022-f1d5-4672-8c6c-de8140345210' from 'https://api.gdc.cancer.gov/data/6b725022-f1d5-4672-8c6c-de8140345210' to '/root/.cache/histolab-images/0.2.5'.
HTTPError Traceback (most recent call last)
/usr/local/lib/python3.8/dist-packages/histolab/data/init.py in _fetch(data_filename)
189 try:
--> 190 resolved_path = image_fetcher.fetch(data_filename)
191 except HTTPError as httperror:
/usr/local/lib/python3.8/dist-packages/pooch/core.py in fetch(self, fname, processor, downloader)
538
--> 539 stream_download(
540 url,
/usr/local/lib/python3.8/dist-packages/pooch/core.py in stream_download(url, fname, known_hash, downloader, pooch, retry_if_failed)
723 with temporary_file(path=str(fname.parent)) as tmp:
--> 724 downloader(url, tmp, pooch)
725 hash_matches(tmp, known_hash, strict=True, source=str(fname.name))
/usr/local/lib/python3.8/dist-packages/pooch/downloaders.py in call(self, url, output_file, pooch)
179 response = requests.get(url, **kwargs)
--> 180 response.raise_for_status()
181 content = response.iter_content(chunk_size=self.chunk_size)
/usr/local/lib/python3.8/dist-packages/requests/models.py in raise_for_status(self)
942 if http_error_msg:
--> 943 raise HTTPError(http_error_msg, response=self)
944
HTTPError: 451 Client Error: UNAVAILABLE FOR LEGAL REASONS for url: https://api.gdc.cancer.gov/data/6b725022-f1d5-4672-8c6c-de8140345210
During handling of the above exception, another exception occurred:
HTTPError Traceback (most recent call last)
in
----> 1 prostate_svs, prostate_path = prostate_tissue()
2 ovarian_svs, ovarian_path = ovarian_tissue()
/usr/local/lib/python3.8/dist-packages/histolab/data/init.py in prostate_tissue()
476 Path where the slide is saved
477 """
--> 478 return _load_svs("tcga/prostate/6b725022-f1d5-4672-8c6c-de8140345210")
/usr/local/lib/python3.8/dist-packages/histolab/data/init.py in _load_svs(filename)
235 """
236 try:
--> 237 svs = openslide.open_slide(_fetch(filename))
238 except PIL.UnidentifiedImageError:
239 raise PIL.UnidentifiedImageError(
/usr/local/lib/python3.8/dist-packages/histolab/data/init.py in _fetch(data_filename)
190 resolved_path = image_fetcher.fetch(data_filename)
191 except HTTPError as httperror:
--> 192 raise HTTPError(f"{httperror}")
193 except ConnectionError: # pragma: no cover
194 # If we decide in the future to suppress the underlying 'requests'
HTTPError: 451 Client Error: UNAVAILABLE FOR LEGAL REASONS for url: https://api.gdc.cancer.gov/data/6b725022-f1d5-4672-8c6c-de8140345210
Is there any option to refer .svs file from local machine in current histolab implementation ?
Regards,
Amit