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wellcometrust / grants_tagger

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Run and submit bioasq batch 10 results #205

Closed nsorros closed 2 years ago

nsorros commented 2 years ago

Description

Run and submit results for batch 10 of BioASQ. There was a problem with the XLinear model so had to checkout dvc lock to 4606aef9119a542de14ad569551e6afed9834a77 to be able to do dvc pull and get a xlinear model.

Note that DVC is not up to date and this needs to be fixed asap.

Checklist

aCampello commented 2 years ago

For this one I got a dvc issue:

WARNING: Some of the cache files do not exist neither locally nor on remote. Missing cache files:                                                                                    
name: data/processed/bioasq/tagged_data_10_xlinear.json, md5: 99f9b4f24144edb06b81ad85220d4018
name: data/processed/bioasq/tagged_data_10_bertmesh.json, md5: 8adcee49cb65c000800b23c3b98ac0c3
name: data/processed/bioasq/data_10.json, md5: c2cd9f241b748ec5e93cb6d62f798b36
ERROR: unexpected error - [Errno 2] No such file or directory: '/data/grants_tagger/data/processed/bioasq/data_10.json'                                                              

(venv) ubuntu@ip-10-60-49-149:/data/grants_tagger$ dvc pull pipelines/bioasq/dvc.yaml
nsorros commented 2 years ago

For this one I got a dvc issue:

WARNING: Some of the cache files do not exist neither locally nor on remote. Missing cache files:                                                                                    
name: data/processed/bioasq/tagged_data_10_xlinear.json, md5: 99f9b4f24144edb06b81ad85220d4018
name: data/processed/bioasq/tagged_data_10_bertmesh.json, md5: 8adcee49cb65c000800b23c3b98ac0c3
name: data/processed/bioasq/data_10.json, md5: c2cd9f241b748ec5e93cb6d62f798b36
ERROR: unexpected error - [Errno 2] No such file or directory: '/data/grants_tagger/data/processed/bioasq/data_10.json'                                                              

(venv) ubuntu@ip-10-60-49-149:/data/grants_tagger$ dvc pull pipelines/bioasq/dvc.yaml

Should be fixed, try again

aCampello commented 2 years ago

All good to me now:

A       data/processed/bioasq/tagged_data_10_xlinear.json                                                                        
A       data/processed/bioasq/tagged_data_10_bertmesh.json                                                                       
2 files added and 3 files fetched