Valentin Guignon

Order FASTA sequences and added warnings for CDS-prot mismatches

4

FASTA sequences are automatically ordered when loaded through read_FASTA_file_array() (either alphabetically or numerically according to sequence name nature) get_homologues-est.pl warns when it detects CDS and protein sequences that do not...

Add deprecation notices to legacy code

2

### Task Description After a quick look into the code, I saw some (legacy) code that is deprecated ( #1341, #1342, #1343, [cv](https://github.com/tripal/tripal/blob/4.x/tripal_chado/src/api/tripal_chado.cv.api.php), [db](https://github.com/tripal/tripal/blob/4.x/tripal_chado/src/api/tripal_chado.db.api.php),...). That's ok and it's a good...

This version supports multiple query genes and provides outputs by matching OGs. There are small changes in the output files: - added a ".sh.map" file for correspondance between original query...

Changed output directory option and added overwrite option

1

By default, SHOOT outputs a serie of files in the same directory as the input FASTA file. This PR changes that behavior so output files are by default put into...

/traits call uses a "observationVariableDbId" filter which is not in the returned properties

1

The "observationVariableDbId" property, as it can be used as filter, should appear in the returned properties.

/traits call returns "attribute" which should be linked to germplasmAttributes

3

As said in the title, the "/traits" call returns an "attribute" string property ([class](https://github.com/plantbreeding/BrAPI/blob/brapi-V2.1/Specification/Components/Schemas/TraitBaseClass.yaml)) defined as `A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is...

A couple of field name inconsistencies.

3

Plural forms should be used instead of singular (to be consistent): - BrAPI-Genotyping > Variant Sets > /variantsets/{variantSetDbId}/variants (array) variantSetDbId --> variantSetDbIds - BrAPI-Germplasm > Germplasm > /search/germplasm (array) genus...

Normalizing/standardizing data storage (enforcing bestpractices) through PL/pgsql functions

2

I'd like to bring a discussion (yesterday on gather.town) here for the community. The main strength of a schema like Chado is to normalize how biological data are stored. Then,...

Add a table to store environmental data

5

For people doing plant characterization or breeding, it may be useful to store environmental data (climatic data and other). Those data are related to a specific geo-location and are taken...

The old links "https://www.bioversityInternational.org/fileadmin/user_upload/online_library/publications/pdfs/FAOBIOVERSITY_MULTI-CROP_PASSPORT_DESCRIPTORS_V.2.1_2015_2020.pdf" and "https://www.bioversityinternational.org/e-library/publications/detail/faobioversity-multi-crop-passport-descriptors-v21-mcpd-v21/" are not valid anymore and should be changed into "https://cgspace.cgiar.org/items/e2aab885-8e08-4a0a-86eb-4494974c5199". They appear in multiple places. I've identified: - [Wiki/Alternative Standards.wiki](https://github.com/plantbreeding/BrAPI/blob/eed6a7a2dc4dc53d4a93743c5307fce47f43e4ac/Wiki/Alternative%20Standards.wiki#L18) - [Scripts/checkSpellingDictionary.txt](https://github.com/plantbreeding/BrAPI/blob/eed6a7a2dc4dc53d4a93743c5307fce47f43e4ac/Scripts/checkSpellingDictionary.txt#L51) - [docs/docs/best_practices/Alternative_Standards.rst](https://github.com/plantbreeding/BrAPI/blob/eed6a7a2dc4dc53d4a93743c5307fce47f43e4ac/docs/docs/best_practices/Alternative_Standards.rst#L33)...