Support for GCA/GCF URLs based on identifiers.org
Problem
MVP will have assemblies tagged as both GCA and GCF, and both the species table and the species pages will need to have links to ENA and NCBI respectively.
Description
The PR uses resolver services https://identifiers.irg to provide URLs for assembly.
JIRA
https://www.ebi.ac.uk/panda/jira/browse/ENSWBSITES-2257
Example
Current Response
curl 'https://beta.ensembl.org/api/search/genomes?query=human' | jq '.["matches"][0]["assembly"]'
{
"accession_id": "GCA_000001405.29",
"name": "GRCh38.p14",
"url": "https://www.ebi.ac.uk/ena/browser/view/GCA_000001405.29"
}
After the Changes
$ curl 'http://localhost:8083/api/search/genomes?query=human' | jq '.["matches"][0]["assembly"]'
{
"accession_id": "GCA_000001405.29",
"name": "GRCh38.p14",
"url": "https://identifiers.org/insdc.gca/GCA_000001405.29"
}
Review App URL
No available
Note
This requires change in the environment variable. Instead of ENA_ASSEMBLY_URL it will need IDENTIFIERS_ORG_BASE_URL. Before merging this to main please merge the PR in new-api-config
Related PRs
Metadata API
To make it consistent across all API https://github.com/Ensembl/ensembl-web-metadata-api/pull/48
Config Update
To expose IDENTIFIERS_ORG_BASE_URL environment variable https://gitlab.ebi.ac.uk/ensembl-web/newsite-api-config-setup/-/merge_requests/12
Edited by Kamal Dodiya