ENA - changes in API broke getSeqENA

[cimendes]

Hello,

Recently ENA has made changes to their API (https://www.ebi.ac.uk/ena/portal/api/) that deeply affect getSeqENA implementation.

When a request is made, the only fields that are shown for the read_run data are the ones related to the read location in the ftp server, and the md5 values for validation (example: https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERR744165&result=read_run)

The API has an endpoint named returnFields that shows all the possible columnId's for the read_run request (https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=json&result=read_run).

To address this problem, the request to ENA's API needs to be adjusted to include all fields (https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERR744165&result=read_run&fields=all) (attention that fieldnames have changed).

This is also a good oportunity to do some code-cleanup and address some implementation issues that have been overlooked. Additionally, ENA and SRA no longer suppor Aspera Connect.

Another possible addition is to allow the download of all accessions based on a selection criteria (taxon, instrument, layout...)

Work has been started in the branch ENA_API_changes.

API: https://www.ebi.ac.uk/ena/portal/api/
API docs: https://www.ebi.ac.uk/ena/portal/api/doc (last update: 2019-12-10)