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[bioontology-support] NCBO Tree widget: collapsing/expanding the hierarchy

Allyson Lister allyson.lister at oerc.ox.ac.uk
Tue Feb 2 01:00:36 PST 2016


Dear Jennifer,

Thanks - it is all looking great for me now - the updated code has been
installed on BioSharing.

One additional note (which I'm happy to turn into an additional ticket if
you prefer) is that the information returned from a query on an ontology
present as a Summary Only on BioPortal is identical to the info returned
for an unknown record, e.g.:

A record which does not exist:

{
    -"errors": [
        "Ontology 'ZZZ' not found."
    ],
    "status": 404
}

And a record which does exist as a summary only on bioportal:

{
    -"errors": [
        "Ontology PHARMGKB submission not found."
    ],
    "status": 404
}

We would like to treat these two cases differently - is there any way to
get a different error message when the record is present, but as a summary
only?

Thanks :) Allyson

On Sat, 30 Jan 2016 at 19:51 Allyson Lister <allyson.lister at oerc.ox.ac.uk>
wrote:

> Thank you very much! We'll take a look at it next week and get back to
> you. Have a good weekend!
>
> Thanks, Allyson
>
>
> On Sat, 30 Jan 2016 at 03:02 Jennifer Leigh Vendetti <
> vendetti at stanford.edu> wrote:
>
>> I misspoke about the minified version in my last response.  It’s already
>> up:
>>
>>
>> http://bioportal.bioontology.org/widgets/minified/jquery.ncbo.tree-2.0.2.min.js
>>
>> Jennifer
>>
>>
>> On Jan 29, 2016, at 6:56 PM, Jennifer Leigh Vendetti <
>> vendetti at stanford.edu> wrote:
>>
>> Hi Allyson,
>>
>> I published a new version of the NCBO Tree Widget JavaScript here:
>>
>> http://bioportal.bioontology.org/widgets/jquery.ncbo.tree-2.0.2.js
>>
>> The plus icons display properly and expanding/collapsing the hierarchy is
>> working.  I plan to get a minified version of the JavaScript up on our site
>> early next week, but you should be able to try out the non-minified version
>> in the meantime.
>>
>> Best,
>> Jennifer
>>
>>
>>
>> On Jan 22, 2016, at 4:42 PM, Jennifer Leigh Vendetti <
>> vendetti at stanford.edu> wrote:
>>
>> Hi Allyson,
>>
>> I started to look at this today.  The NCBO wiki mentions a version
>> “2.0.0” of this widget [1].  I noticed that there’s a newer version of the
>> JavaScript for this widget on our website that’s not publicized on our wiki
>> [2] - version 2.0.1 (the development of these widgets predates my joining
>> the group).  I experimented with that one a little.  The plus icons do show
>> up, but unfortunately trying to expand anything in the class hierarchy
>> doesn’t work.  It wasn’t immediately apparent to me what’s broken.  Sorry I
>> don’t have better news - I’ll try to find more time next week to make
>> progress on this.
>>
>> Best,
>> Jennifer
>>
>> [1] http://www.bioontology.org/wiki/index.php/Ontology_Widgets#Location
>> [2] https://bioportal.bioontology.org/widgets/jquery.ncbo.tree-2.0.1.js
>>
>>
>>
>> On Jan 13, 2016, at 3:06 AM, Allyson Lister <allyson.lister at oerc.ox.ac.uk>
>> wrote:
>>
>> Dear Jennifer,
>>
>> Thanks very much for helping me with this bug. Please could you let me
>> know if how this is going? It looks like the tracker hasn't had any
>> additional activity.
>>
>> Thanks, and Happy New Year!
>>
>> Allyson :)
>>
>> On Sun, 15 Nov 2015 at 19:10 Allyson Lister <allyson.lister at oerc.ox.ac.uk>
>> wrote:
>>
>>> Thanks very much,
>>> Allyson :)
>>>
>>>
>>> On Sat, 14 Nov 2015 at 01:12 Jennifer Leigh Vendetti <
>>> vendetti at stanford.edu> wrote:
>>>
>>>> Thanks for the bug report Allyson.  I’ve entered an issue in our
>>>> tracker (NCBO-1574).  We’ll look into this.
>>>>
>>>> Best,
>>>> Jennifer
>>>>
>>>>
>>>> On Nov 11, 2015, at 6:24 AM, Allyson Lister <
>>>> allyson.lister at oerc.ox.ac.uk> wrote:
>>>>
>>>> Hi all,
>>>>
>>>> I recently asked about your https setup, and thanks for fixing that!
>>>> However, now on to a related question - when the NCBO tree widget first
>>>> loads, e.g. with https://biosharing.org/bsg-000154 or just on your
>>>> website at
>>>> http://bioportal.bioontology.org/ontologies/BP-METADATA?p=widgets,
>>>> there are no little "+" symbols for me for any of the parent classes. If I
>>>> use the search box to find a class further down in the hierarchy, then all
>>>> of the "+" or "-" that lead to the searched-for class do appear, but none
>>>> of the others. It's as if they're not drawn to start with.
>>>>
>>>> I'm using Chrome Version 46.0.2490.80 (64-bit) on Ubuntu 15.10
>>>>
>>>> thanks! Allyson
>>>> <Screenshot from 2015-11-11 14-21-34.png>
>>>> _______________________________________________
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>>>> bioontology-support at lists.stanford.edu
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>
>>>>
>>>>
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