EBI breaking change this Sunday 1st October

Jalview Developers
1

See https://issues.jalview.org/browse/JAL-2745.

I’ve had clarification that http://www.ebi.ac.uk will redirect to https from 1st Oct (and that this cannot be deferred).

I have tested a similar redirect in Jalview and confirmed that these will cease to work:

  • fetch of Uniprot, PDB or EMBL accessions

  • PDB free text search

Do we need to drop everything and put out a fix build and communications to users to install it?

The changes are simple and already done on the JAL-2745 branch (made off develop - cherry pick to another branch if need be).

Mungo

p.s. don’t be thrown by a separate problem retrieving Uniprot just now. There seems to be an internal problem at their end which I have emailed them about. They are returning “ERROR 11 Unable to connect to database [uniprotkb]”.

The University of Dundee is a registered Scottish Charity, No: SC015096

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Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

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2

Hi Mungo

I’ve had clarification that http://www.ebi.ac.uk will redirect to https from 1st Oct (and that this cannot be deferred).

OK.

I have tested a similar redirect in Jalview and confirmed that these will cease to work:

  • fetch of Uniprot, PDB or EMBL accessions

  • PDB free text search

I see from your tests that HTTP 302 is not handled. much sadness.

Do we need to drop everything and put out a fix build and communications to users to install it?

yes - but by drop everything, I guess you mean:

  1. Port the fix to 2.10.2b1 branch and bump its version to 2.10.2b2.

→ one amendment here: the patch should also make all these endpoints configurable via .jalview_properties. Some already are IIRC.

  1. Post a jalview news article telling everyone who fetches sequences, annotation or 3D structures in Jalview that they will need to upgrade to the latest patch release.

  2. pick everything up, keep calm and carry on…

Jim

The University of Dundee is a registered Scottish Charity, No: SC015096

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On 28/09/2017 16:50, Mungo Carstairs (Staff) wrote: