#64 filters not working correctly?

closed-out-of-date
AmiGO 1.8 (12)
6
2011-03-25
2011-03-04
Doug Howe
No

When I am on the term page for 'apoptosis', and I apply a filter for Data Source, or a filter for Species, the page refreshes like a filter was applied, but the counts of gene products after the terms seems unchanged, and the buttons that might allow me to remove or change the status of the filters are gone...so I can not change the filter settings any more.

Seems broken to me.

Discussion

  • Doug Howe

    Doug Howe - 2011-03-04

    Actually...I just tried accessing the term 'apoptosis' with a brand new search from the AmiGO home page...going then directly to the apoptosis term page, I don't even get any buttons to set the filters at all! When I posted my last post I had accessed the term from a link in ZFIN.

     
  • Seth Carbon

    Seth Carbon - 2011-03-10
    • assigned_to: nobody --> sjcarbon
     
  • Seth Carbon

    Seth Carbon - 2011-03-10
    • priority: 5 --> 6
    • labels: --> AmiGO 1.8
     
  • Seth Carbon

    Seth Carbon - 2011-03-10

    This is odd--I cannot reproduce your bug at all. Could you get me the following information:

    1) The exact URL of the page you're using, or the process to generate the page starting from amigo.geneontology.org.
    2) The platform and version you're using (e,g, Windows XP SP2, Ubuntu 10.10 x86_64),
    3) Browser and version number you're using (e.g. Firefox 3.6.15).

    With that, hopefully I can reproduce it. I'm guessing that there is something wrong in the JavaScript for your platform...

     
  • Doug Howe

    Doug Howe - 2011-03-10

    I've just realized that no buttons are necessary on the term page...the filters seem to be applied quite spiffily by some AJAX methods or something...I was thrown off because I USED to have buttons on the earlier page..then no buttons on this page..

     
  • Doug Howe

    Doug Howe - 2011-03-10

    Perhaps this is related to how we linked in to AmiGO from within ZFIN? I'll dig up a url from within ZFIN and see if that casts any light...

     
  • Seth Carbon

    Seth Carbon - 2011-03-10
    • status: open --> pending-out-of-date
     
  • Seth Carbon

    Seth Carbon - 2011-03-10

    That's a possibility--the old URLs were kept in the back for various arcane compatibility reasons. On the other hand, they should work as well, but all links should flow back into the new system. I'll switch this to pending for now in case some problem with that crops up.

     
  • Doug Howe

    Doug Howe - 2011-03-10
    • status: pending-out-of-date --> open-out-of-date
     
  • Doug Howe

    Doug Howe - 2011-03-10

    At least part of the issue is a difference in the target page depending on the url.

    From within ZFIN we currently have this url to go to the 'apoptosis' page:

    http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0006915

    This link takes us to a term page with the "Term Lineage" open at the bottom of the page..(see left page in attached image)

    If I navigate to the same term page from within AmiGO, I get this url:
    http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0006915&session_id=9780amigo1299794805
    -that's the right image in the attached graphic
    It takes me to a a term detail page with the "Term Neighborhood for apoptosis" section open at the bottom....I get no buttons for the filters here..but they work automagically when I select items in the filter lists.

    I also see differences in the presentation of the Term Information.

     
  • Doug Howe

    Doug Howe - 2011-03-10

    different views of term details

     
  • Seth Carbon

    Seth Carbon - 2011-03-10

    Ahhh...

    Here's the problem then: in ZFIN you have a URL to the old format that points to the old pages. When you perform any operation (form/filter) or click any link on the old pages, it automatically boots you to the new pages where what you did in the old form resets--not an issue if you clicked a link, but strange if you performed a filter or something. Besides the functional difference, the jump in physical styling and placement is jarring as well.

    Since we (again, for various arcane reasons) can't easily remove the old pages completely right away, how would a warning message and link to the newer style page work for you?

    An alternative would be for AmiGO to try and detect antiquated paths and try and forward the right ones to the new pages. I'll take a look and see if that's doable (it's always hard to keep the various rationals for cruft in my head).

    As a side issue, you may also want to request that your ZFIN links go to the new style pages (which, in a way, makes me want to favor the first possible solution).

     
  • Doug Howe

    Doug Howe - 2011-03-10

    So, if we simply remove the .cgi from "term-details.cgi" in the url...this problem will be gone because we will be going directly to the new pages?

    If that's it...that's easy. These pages in ZFIN are in testing right now...can be changed easily.

     
  • Doug Howe

    Doug Howe - 2011-03-10

    Nope....removing ".cgi" just gets me a Forbidden..

    What url should be used to link directly to new pages in amigo? The urls look the same to me (other than session) when I link in from ZFIN or navigate directly in AmiGO.

    I must be missing something...

     
  • Seth Carbon

    Seth Carbon - 2011-03-10

    Yes, if I'm understanding the problem correctly, the changing the URL to the "term_details" form (note the dash is now an underscore) will make the problem go away for you.

    That said, the problem still exists for others who have not updated, which is why I think a warning message (and small explanation) might be good.

     
  • Doug Howe

    Doug Howe - 2011-03-10

    Ah..beautiful...

    Change the "-" to an "_"...problem solved.

    Should something be announced on the GO list perhaps alerting folks to this small change? Maybe it was...and I just missed it!

     
  • Seth Carbon

    Seth Carbon - 2011-03-11
    • status: open-out-of-date --> pending-out-of-date
     
  • SourceForge Robot

    • status: pending-out-of-date --> closed-out-of-date
     
  • SourceForge Robot

    This Tracker item was closed automatically by the system. It was
    previously set to a Pending status, and the original submitter
    did not respond within 14 days (the time period specified by
    the administrator of this Tracker).

     

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