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[bioontology-support] REST query with a slash in the search string

Paul R Alexander palexander at stanford.edu
Thu Dec 8 11:54:33 PST 2011


Marco,

There's a known bug in our server software (Apache Tomcat) that prevents 
the use of encoded slashes in the URL proper. However, you can pass them 
in query string parameters just fine. The URL below does this:
http://rest.bioontology.org/bioportal/search/?query=Mutant+%2F+Wild+type+comparison_design&maxnumhits=10000000&level=1&includeproperties=0&isexactmatch=1&ontologyids=1136&subtreerootconceptid=efo%3AEFO_0003740&apikey={YourAPIKey}

Paul R Alexander
Web / UI Developer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research


On 12/8/11 10:38 AM, Trish Whetzel wrote:
> Hi Marco,
>
> The issue is not with the "/" character. We worked with the Rat Genome 
> Database folks and their Rat Strain Ontology has a lot of interesting 
> characters that we tested the search with so strings like 
> "DA.F344-Aia1/1" can be used with the Search, url-encoded of course. 
> E.g. 
> http://rest.bioontology.org/bioportal/search/?query=DA.F344-Aia1%2F1&apikey={YourAPIKey}. 
> <http://rest.bioontology.org/bioportal/search/?query=DA.F344-Aia1%2F1&apikey=%7BYourAPIKey%7D.> 
> At best I can see right now is that there might be a problem with the 
> search within subtree.
>
> Trish
>
> PS - I don't think the Search call takes the param "level"
>
>
> On Dec 8, 2011, at 11:52 AM, Marco Brandizi wrote:
>
>> Hi all,
>>
>> sorry if the following question has already been asked, I cannot find 
>> a reference to this. Bioportal REST seems to fail when it gets a 
>> string with a slash character in it, for instance this:
>>
>> http://rest.bioontology.org/bioportal/search/Mutant+%2F+Wild+type+comparison_design/?maxnumhits=10000000&apikey=<my-key>&level=1&includeproperties=0&isexactmatch=1&ontologyids=1136&subtreerootconceptid=efo%3AEFO_0003740
>>
>> which I'm trying to use to see if there is 'Mutant / Wild type 
>> comparison_design' under the tree rooted at EFO_0003740, instead 
>> tells me a 404/Not Found, which I interpret as the inability to 
>> recognise that the %2F (note it's escaped) is part of the search string.
>>
>> Is there any massaging/escaping/etc I can do to the input to make it 
>> working?
>>
>> Thanks in advance for any help.
>>
>> -- 
>>
>> ===============================================================================
>> Marco Brandizi, PhD<brandizi at ebi.ac.uk <mailto:brandizi at ebi.ac.uk>>
>>
>> Microarray Group - Sr Software Engineer
>> http://www.ebi.ac.uk/microarray
>>
>> European Bioinformatics Institute
>> Hinxton, CB10 1SD, United Kingdom
>> Office A3141
>>
>> Tel.: +44 (0)1223 492 613
>> Fax: +44 (0)1223 492 620
>>
>> http://www.marcobrandizi.info
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
> Trish Whetzel, PhD
> Outreach Coordinator
> The National Center for Biomedical Ontology
> Ph: 650-721-2378
> http://www.bioontology.org
>
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>
>
>
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