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bokulich-lab / q2-fondue

Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere
BSD 3-Clause "New" or "Revised" License
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Fetching metadata by sample ID never returns #24

Closed misialq closed 3 years ago

misialq commented 3 years ago

When using an SRA sample ID (#SRS...) to fetch sample metadata, the command hangs and never returns.

Steps to reproduce:

  1. Run the following command: q2 fondue get-metadata --p-sample-ids SRS2162586 --p-email <your email> --o-metadata ~/metadata.qza --verbose.
  2. Observe the behaviour.

Expected behaviour: The command returns and the metadata.qza artifact is created.

Actual behaviour: The command hangs, doesn't print anything and we never get an artifact.

Note: It would seem that we get to the point of entrezpy making a request (but probably never getting a response)...