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OBO importer - fix unsubstituted message #1905

Merged
merged 2 commits into from
Jun 20, 2024
Merged

OBO importer - fix unsubstituted message #1905

merged 2 commits into from
Jun 20, 2024

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dsenalik
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Bug Fix

Closes #1904

Tripal Version: 4.x

Description

During step 1 of importing an OBO file, the namespaces message does not have the actual namespaces substituted for the placeholder. This fixes that.

Testing?

  1. Build a docker

Output before

grep -n 'Found the following namespaces' /tmp/4.x.log
2713:#28 86.38  [notice] Found the following namespaces: @namespaces.
2864:#28 136.9  [notice] Found the following namespaces: @namespaces.
2966:#28 138.5  [notice] Found the following namespaces: @namespaces.
3036:#28 139.4  [notice] Found the following namespaces: @namespaces.

Output on this branch

grep -n 'Found the following namespaces' /tmp/1904.log
2713:#28 86.38  [notice] Found the following namespaces: sequence.
2864:#28 136.9  [notice] Found the following namespaces: taxonomic_rank.
2966:#28 138.5  [notice] Found the following namespaces: tripal_contact.
3036:#28 139.4  [notice] Found the following namespaces: tripal_pub.

@dsenalik dsenalik added bug - confirmed For issues where a core developer has confirmed a bug exists. Tripal 4 Any issue or pull request focused on Tripal 4 Group 4 - Data Importing Any issue relating to importing of biological data into either Chado or any other database. labels Jun 18, 2024
@dsenalik dsenalik changed the title fix unsubstituted message OBO importer - fix unsubstituted message Jun 18, 2024
@dsenalik dsenalik added the Easy PR Review 😀 Small easy to review pull request label Jun 18, 2024
@dsenalik dsenalik mentioned this pull request Jun 19, 2024
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laceysanderson
laceysanderson approved these changes Jun 20, 2024
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✅ Code change looks good
✅ Manual testing shows the correct, fixed output during docker build.

@laceysanderson laceysanderson merged commit d849def into 4.x Jun 20, 2024
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@laceysanderson laceysanderson deleted the tv4g4-issue1904-obo-importer-message branch June 20, 2024 18:08
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@laceysanderson laceysanderson laceysanderson approved these changes

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bug - confirmed For issues where a core developer has confirmed a bug exists. Easy PR Review 😀 Small easy to review pull request Group 4 - Data Importing Any issue relating to importing of biological data into either Chado or any other database. Tripal 4 Any issue or pull request focused on Tripal 4
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Successfully merging this pull request may close these issues.

OBO importer variable not substituted in message
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@dsenalik @laceysanderson