Downloading SARS-CoV-2 Variation Data fails in dataprep/01c-CNCBVariant.ipynb notebook

covid-19-net / covid-19-community

Community effort to build a Neo4j Knowledge Graph (KG) that links heterogeneous data about COVID-19

MIT License

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Downloading SARS-CoV-2 Variation Data fails in dataprep/01c-CNCBVariant.ipynb notebook #319

Closed shophine closed 3 years ago

shophine commented 3 years ago

It throws 'error_prem: 550 Failed to change directory' while downloading and caching data files with variant information. Can you please upload the data itself to the repository if possible?

pwrose commented 3 years ago

The variant information is downloaded incrementally daily into the cache directory (on our server) with this script: https://github.com/covid-19-net/covid-19-community/blob/master/scripts/download.sh (note, there is a single file for each strain, so currently there are about 1 million files!)

However, the download of these data currently fails (see #321) since CNCB is reorganizing their data. I'm in contact with CNCB to resolve this issue.

pwrose commented 3 years ago

The CNCB ftp site is back up. The download.sh script should work again.