Replace Peach API with BioStudies in export_atlas_ebeye_xml.pl

[anilthanki]

The goal here is to fix export_atlas_ebeye_xml.pl

As the Peach API is deprecated, the function that returns 'public' or 'private' status will fail:

sub get_privacy{
    ...
     my $url = "http://peach.ebi.ac.uk:8480/api/privacy.txt?acc=$expId";
     my $ua = LWP::UserAgent->new;
     my $response = $ua->get($url)->content;
    ...
}

In this PR https://github.com/ebi-gene-expression-group/atlas-prod/pull/255 we solve it by using an internal file and when not available querying the BioStudies API.

The difference now is that the data resulting from the query comes in JSON format , e.g the following will return true:

curl -sS "https://www.ebi.ac.uk/biostudies/api/v1/search?type=study&accession=E-MTAB-10293" | jq .hits[0] | jq .isPublic

[pmb59]

Hi @anilthanki I 've tested the code locally and it works.

However, I see a fundamental flaw in the logic. Because this is not run with login permissions in AE/Biostudies, all private accessions will report error as "not found"

Take for example this accession E-MTAB-7839 that I know it's private. It's going to log the error "Accession not found".
Possible solutions:

1. We search in first instance in the file provided by BioStudies, and then if necessary into the API, and assume not found equals to private.
2. We directly assume that if it's not found by the API it's private. But that could also bring errors, for instance E-MTAB-100000000000 (not existing) will be reported as Private.

Option 1 will minimise problems. Maybe you can use the same login here using the env variable $ENV{'BIOSTUDIES_AE_PRIVACY_STATUS_FILE'})