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tripal / tripal

The Tripal package is a suite of Drupal modules for creating biological (genomic, genetic, breeding) websites. Visit the Tripal homepage at http://tripal.info for documentation, support, and other information. The Drupal project page is at http://drupal.org/project/tripal.
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Organism name is incorrectly case sensitive for taxonomy loader #1761

Closed dsenalik closed 9 months ago

dsenalik commented 9 months ago

Tripal Version

4.alpha2

Drupal Version

NA

PostgreSQL Version

NA

PHP Version

NA

General Description

The taxonomy loader, when you import existing species 20240123_existing_species is failing due to NCBI returning all lower case organism names.

Steps to reproduce

  1. Create a real organism, e.g. Citrus sinensis
  2. Run the taxonomy importer, just with defaults, don't enter anything.
  3. When the job is run you will see [warning] WARNING: Partial match "citrus sinensis" to query "Citrus sinensis", no taxid available This should have matched, ignoring case. NCBI returned all lower case.
dsenalik commented 9 months ago

The same thing happens in Tripal 3. Probably a change in the NCBI API.

pdtouch commented 9 months ago

Thanks.