30 Sept deadline to update NCBI sources!

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

30 Sept deadline to update NCBI sources!

Julie Sullivan-2
Hi InterMiners

See:

        http://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/

NCBI is switching to use HTTPS only. This is an issue for InterMine
because we use NCBI web services in our data sources -- specifically:

        entrez-organism
        update-publications

** You need to update your code before 30 September or these sources
will fail. **

Options:

1. update to the latest InterMine, v 1.6.7. Specifically, this is the
patch you need:

        https://github.com/intermine/intermine/pull/1416

2. update NCBI URLs yourself to be HTTPS instead of HTTP

ENTREZ-ORGANISM

https://github.com/intermine/intermine/blob/dev/bio/sources/entrez-organism/main/src/org/intermine/bio/dataconversion/EntrezOrganismRetriever.java#L55

UPDATE PUBLICATIONS

https://github.com/intermine/intermine/blob/dev/bio/sources/update-publications/main/src/org/intermine/bio/dataconversion/EntrezPublicationsRetriever.java#L78-L82

It's an easy, safe update. Both HTTP and HTTPS NCBI URLs work currently.
HTTP will stop working on 30 Sept. So update your code!

Please let me know if you have any concerns!

Julie

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev