Mercurial > repos > earlhaminst > ensembl_get_sequences
changeset 6:7af66c2b3831 draft default tip
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 17c65045b726d0695814bfe761e534f6521786f1"
| author | earlhaminst |
|---|---|
| date | Tue, 20 Oct 2020 15:07:23 +0000 |
| parents | 0fa1d1cc417d |
| children | |
| files | get_feature_info.py get_genetree.py get_sequences.py get_sequences.xml |
| diffstat | 4 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/get_feature_info.py Thu Oct 31 07:50:07 2019 -0400 +++ b/get_feature_info.py Tue Oct 20 15:07:23 2020 +0000 @@ -23,7 +23,7 @@ raise Exception('-i option must be specified') -server = 'http://rest.ensembl.org' +server = 'https://rest.ensembl.org' ext = 'lookup/id' headers = {'Content-Type': 'application/json', 'Accept': 'application/json'} @@ -42,7 +42,7 @@ print(",") data = {'ids': ids} r = requests.post(urljoin(server, ext), params=params, headers=headers, - data=json.dumps(data)) + data=json.dumps(data), allow_redirects=False) if not r.ok: r.raise_for_status()
--- a/get_genetree.py Thu Oct 31 07:50:07 2019 -0400 +++ b/get_genetree.py Tue Oct 20 15:07:23 2020 +0000 @@ -31,7 +31,7 @@ if options.input is None: raise Exception('-i option must be specified') -server = 'http://rest.ensembl.org' +server = 'https://rest.ensembl.org' if options.id_type == 'gene_id': ext = 'genetree/member/id'
--- a/get_sequences.py Thu Oct 31 07:50:07 2019 -0400 +++ b/get_sequences.py Tue Oct 20 15:07:23 2020 +0000 @@ -23,7 +23,7 @@ if options.input is None: raise Exception('-i option must be specified') -server = 'http://rest.ensembl.org' +server = 'https://rest.ensembl.org' ext = 'sequence/id' headers = {'Content-Type': 'text/x-fasta', 'Accept': 'text/x-fasta'} @@ -36,7 +36,7 @@ break data = {'ids': ids} r = requests.post(urljoin(server, ext), params=params, headers=headers, - data=json.dumps(data)) + data=json.dumps(data), allow_redirects=False) if not r.ok: r.raise_for_status()
--- a/get_sequences.xml Thu Oct 31 07:50:07 2019 -0400 +++ b/get_sequences.xml Tue Oct 20 15:07:23 2020 +0000 @@ -54,7 +54,7 @@ Uses the `"POST sequence/id"`_ API endpoint. -.. _"POST sequence/id": http://rest.ensembl.org/documentation/info/sequence_id_post +.. _"POST sequence/id": https://rest.ensembl.org/documentation/info/sequence_id_post ]]> </help> <citations>