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uf-hobi-informatics-lab / SODA_Docker

repo for pipeline development
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ClinicalTransformerClassification not available #3

Open rkboyce opened 6 months ago

rkboyce commented 6 months ago

Thank you for sharing your code. Unfortunately, I cannot successfully run git submodule update because it seems that ClinicalTransformerClassification is no longer available. Below is the output of the command, would you have any suggestions on how to move forward?

]$ git submodule update
Cloning into '/home/rdb20/remote-git-repos/SODA_Docker/ClinicalTransformerClassification'...
Username for 'https://github.com': rkboyce
Password for 'https://rkboyce@github.com': 
remote: Repository not found.
fatal: repository 'https://github.com/uf-hobi-informatics-lab/ClinicalTransformerClassification.git/' not found
fatal: clone of 'https://github.com/uf-hobi-informatics-lab/ClinicalTransformerClassification.git' into submodule path '/home/rdb20/remote-git-repos/SODA_Docker/ClinicalTransformerClassification' failed
Failed to clone 'ClinicalTransformerClassification'. Retry scheduled
Cloning into '/home/rdb20/remote-git-repos/SODA_Docker/ClinicalTransformerNER'...
Cloning into '/home/rdb20/remote-git-repos/SODA_Docker/ClinicalTransformerRelationExtraction'...
Cloning into '/home/rdb20/remote-git-repos/SODA_Docker/NLPreprocessing'...
Cloning into '/home/rdb20/remote-git-repos/SODA_Docker/ClinicalTransformerClassification'...
Username for 'https://github.com': rkboyce
Password for 'https://rkboyce@github.com': 
remote: Repository not found.
fatal: repository 'https://github.com/uf-hobi-informatics-lab/ClinicalTransformerClassification.git/' not found
fatal: clone of 'https://github.com/uf-hobi-informatics-lab/ClinicalTransformerClassification.git' into submodule path '/home/rdb20/remote-git-repos/SODA_Docker/ClinicalTransformerClassification' failed
Failed to clone 'ClinicalTransformerClassification' a second time, aborting
sjbost commented 6 months ago

@yonghuiwuf and/or @dparedespardo do you know what's happening with the ClinicalTransformerClassification?

yonghuiwuf commented 6 months ago

It turns out that 'ClinicalTransformerClassification' is set as private. We have changed it back to public, can you test and let us know if it works?

sjbost commented 5 months ago

@rkboyce were you able to access ClinicalTransformerClassification?