bigbio/bc5cdr · Dataset Viewer issue: requires bioc

BigScience Biomedical Datasets org Nov 14, 2022

•

edited Jun 6, 2023

The dataset viewer is not working.

Error details:

Error code:   ConfigNamesError
Exception:    ImportError
Message:      To be able to use bigbio/bc5cdr, you need to install the following dependency: bioc.
Please install it using 'pip install bioc' for instance.
Traceback:    The previous step failed, the error is copied to this step:  kind='/config-names' dataset='bigbio/bc5cdr' config=None split=None---Traceback (most recent call last):
                File "/src/workers/datasets_based/src/datasets_based/workers/config_names.py", line 89, in compute_config_names_response
                  for config in sorted(get_dataset_config_names(path=dataset, use_auth_token=use_auth_token))
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/inspect.py", line 323, in get_dataset_config_names
                  dataset_module = dataset_module_factory(
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/load.py", line 1217, in dataset_module_factory
                  raise e1 from None
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/load.py", line 1188, in dataset_module_factory
                  return HubDatasetModuleFactoryWithScript(
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/load.py", line 907, in get_module
                  local_imports = _download_additional_modules(
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/load.py", line 221, in _download_additional_modules
                  raise ImportError(
              ImportError: To be able to use bigbio/bc5cdr, you need to install the following dependency: bioc.
              Please install it using 'pip install bioc' for instance.

https://github.com/bigscience-workshop/biomedical/blob/main/setup.cfg#L10

ImportError: To be able to use bigscience-biomedical/bc5cdr, you need to install the following dependency: bioc.

hyesunyun

Jun 5, 2023

Hello! Is there an update on this? I would like to use this dataset for a research project and would like this to be resolved.

Thanks!

albertvillanova

BigScience Biomedical Datasets org Jun 6, 2023

•

edited Jun 6, 2023

@hyesunyun please note that this issue only affects the dataset viewer.

You can use this dataset as far as you install "bioc" locally on your machine:

pip install bioc

I am changing the title/description of this issue so that is clear that this only affects the dataset viewer.

albertvillanova changed discussion title from requires bioc to Dataset Viewer issue: requires bioc Jun 6, 2023

hyesunyun

Jun 6, 2023

Got it! Thank you for the clarification. Much appreciated.