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Support for GCA/GCF URLs based on identifiers.org

Kamal Dodiya requested to merge support-gca-gcf into master

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

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