AlexsLemonade / AlexsLemonade/refinebio

Migrate to new ArrayExpress API

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#3,243 1 comment 0 reactions 1 assignee Assigned to @davidsmejia View on GitHub
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Description

### Context

In order to be able to process ArrayExpress platform experiments we need to migrate to a new API endpoint:
`The endpoint has changed from https://www.ebi.ac.uk/arrayexpress/xml/v3 to https://www.ebi.ac.uk/biostudies/api/v1`

### Problem or idea
https://www.ebi.ac.uk/biostudies/arrayexpress/help#programmatic describes the new API format/response/endpoint changes.

An accession endpoint provides most of the data, additionally available IDF, SDRF, raw/processed data.

Examples for `E-MTAB-3050` accession:
Study data https://www.ebi.ac.uk/biostudies/api/v1/studies/E-MTAB-3050
IDF data - https://www.ebi.ac.uk/biostudies/files/E-MTAB-3050/E-MTAB-3050.idf.txt
SDRF data - https://www.ebi.ac.uk/biostudies/files/E-MTAB-3050/E-MTAB-3050.sdrf.txt
The study files are available at http://ftp.ebi.ac.uk/biostudies/nfs/E-MTAB-/050/E-MTAB-3050/

### Solution or next step

Migrate refine.bio to the new ArrayExpress API.

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