#5 Change to archived ensembl

open
nobody
None
5
2013-05-16
2012-06-11
No

This changes the URL for ensembl to sep2011.archive.ensembl.org so that it matches the version used at the time of the release of 1.1.21. This should allow perlprimer to continue to work even if ensembl change the page format of the main site in future.

Related

Patches: #5

Discussion

  • Nick Kennedy

    Nick Kennedy - 2012-06-11
     
  • Charles Plessy

    Charles Plessy - 2013-05-16

    Thanks for the patch ! Could you or somebody else enhance it by either detecting the latest Ensembl archive, or providing a way to the user for selecting another one ?

    Cheers,

    --
    Charles Plessy
    Tsurumi, Kanagawa, Japan

     
  • Nick Kennedy

    Nick Kennedy - 2013-05-29

    Hi,

    The issue is that perlprimer currently works by screenscraping the Ensembl
    website. This makes the assumption that the website never changes its
    format, but unfortunately this is not the case, and every time ensemble
    makes a change, perlprimer breaks. To avoid this, I changed the code to
    reference a fixed version of Ensembl, but as you've noted this has the side
    effect of also fixing the data at the point in time.

    Making changes to support the current version of Ensembl would be not too
    difficult, but would undoubtedly break again next time they change the
    website. The better long term solution is to switch to using the Ensembl
    perl API. The main author Owen has indicated he intends to do that at some
    point, but I don't know when. I don't myself really have the time to do it
    just now.

    Kind regards,

    Nick Kennedy

    From: Charles Plessy [mailto:plessy@users.sf.net]
    Sent: 16 May 2013 02:30
    To: [perlprimer:patches]
    Subject: [perlprimer:patches] #5 Change to archived ensembl

    Thanks for the patch ! Could you or somebody else enhance it by either
    detecting the latest Ensembl archive, or providing a way to the user for
    selecting another one ?

    Cheers,

    --
    Charles Plessy
    Tsurumi, Kanagawa, Japan


    [patches:#5] Change to archived ensembl

    Status: open
    Created: Mon Jun 11, 2012 02:49 PM UTC by Nick Kennedy
    Last Updated: Mon Jun 11, 2012 02:49 PM UTC
    Owner: nobody

    This changes the URL for ensembl to sep2011.archive.ensembl.org so that it
    matches the version used at the time of the release of 1.1.21. This should
    allow perlprimer to continue to work even if ensembl change the page format
    of the main site in future.


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    Related

    Patches: #5


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