Bob,
I guess you missed it. I pointed out a similar problem with Safari last week or
early this week. I put this in a note with my response to you about SJmol
speed. I should have started a new email chain.
The response type is not the only thing that's changed at PubChem. SMILES
queries with \ seem to be broken even if url escaped. I did not report this
because I'm still trying to make sure it's not an issue with my server.
I should note that the PubChem name search works for me on Safari when I have
my server relay the file after a server read. I assumed this was a new cross
domain issue. After your note, this may well work because I change the response
type before I send it from the server - i.e. unrelated to cross domain.
Otis
--
Otis Rothenberger
[email protected]
http://chemagic.com
On Mar 7, 2014, at 12:42 PM, Robert Hanson <[email protected]> wrote:
> I could swear this was working yesterday, so I think it is quite new.
> Something has changed at PubChem or with Firefox. I don't think it is
> Firefox, because I downgraded to FF 26.0 temporarily, and the problem
> persists.
>
> Problem: JSmol/HTML5 cannot download PubChem SDF files.
>
> Configuration: Firefox 27.0.1/Windows 8
>
> Example: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm -- click on
> :caffeine link
>
> Observation 1: JSmol reports "unrecognized file format"
> Observation 2: No problem in MSIE or Chrome
> Observation 3: Same problem local or website
> Observation 4: Same problem with older, stable version of Jmol at
> http://chemapps.stolaf.edu/jmol/jsmol-2014-01-24/jsmol.htm
>
> Observation 5: The following simple direct AJAX call fails under the exact
> same conditions as above:
>
> alert($.ajax({"dataType":"text","async":false,"type":"GET","url":"http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/caffeine/SDF?record_type=3d"}).responseText)
>
> Observation 6: The following simple AJAX call
>
> alert($.ajax({"dataType":"text","async":false,"type":"GET","url":"http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/caffeine/SDF?record_type=3d"}).statusText)
>
> reports "OK" in other browsers but
>
> [Exception... "Failure" nsresult: "0x80004005 (NS_ERROR_FAILURE)" location:
> "JS frame :: file:///C:/jmol-dev/workspace/JSmol/site/jsmol/jquery/jquery.js
> :: .send :: line 8707" data: no]
>
> in Firefox.
>
> Observation 7:
> The following simple AJAX calls to a similar site work fine:
>
> alert($.ajax({"dataType":"text","async":false,"type":"GET","url":"http://cactus.nci.nih.gov/chemical/structure/caffeine/file?format=sdf&get3d=True"}).responseText)
>
> alert($.ajax({"dataType":"text","async":false,"type":"GET","url":"http://cactus.nci.nih.gov/chemical/structure/caffeine/file?format=sdf&get3d=True"}).statusText)
>
> The difference appears to be that PubChem is returning data with response
> type of chemical/x-mdl-sdfile, which forces a special download, as with PDF.
>
>
> Comments welcome.
>
> Bob
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
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With Perforce, you get hassle-free workflows. Merge that actually works.
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freedom to use Git, Perforce or both. Make the move to Perforce.
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