Fields move record_id_term to parent class #1889
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| $ft_uniqname_term = $mapping->getColumnTermId( 'feature', 'name' ); | ||
| $ft_uniqname_term = $mapping->getColumnTermId('feature', 'name'); | ||
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| $feature_id_term = $mapping->getColumnTermId('featureloc', 'feature_id'); |
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Good catch! I agree with getting the term for the featureloc.feature_id in case we want to be more specific there :-)
laceysanderson
approved these changes
Jun 11, 2024
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Tripal 4 Core Dev Task
Closes #1879
Tripal Version: 4.x
Description
We have a hardcoded
$record_id_term = 'SIO:000729';in most fields.This moves this to the parent
ChadoFieldItemBaseclass.Three fields weren't consistent so they now also use this term, they can get extra careful code review 😼
ChadoSourceDataTypeDefault
ChadoUnitTypeDefault
ChadoSequenceCoordinatesDefault
Testing?
Automated testing will test some of this. But I suppose ideally we need to create at least one instance of every field type. Importing all of the field type collections should do this.
To test these three fields, create an organism and analysis.
The analysis will test the source data field.
Run the GFF3 importer. I used this file for testing from issue #1824
issue1824.gff3.txt
Publish gene
Check the sequence coordinates field, should be
NC_001133.9:1806..2169-Create a genetic map to test the unit field.