[MOBY-dev] createInstanceFromDOM

[gordonp at ucalgary.ca]

Hi Sylvie,

I've fixed it to throw an explanatory MobyException.

Regards,

Paul

> Hi Paul,
>
> Below is the XML file containing the parameters I want to send to a
> Biomoby service.
> With this XML file, I created a DOM object that I use to create a
> MobyContentInstance (this mobycontentInstance should then be used to fill
> the
> data field of a mobyRequest).
> As the simple parameter contains data of a wrong type, I thought I could
> catch a
> MOBYException during the MobycontentInstance constructor call. But the
> inner
> MobyDatacomposite constructor throws a NullPointerException.
>
> Thanks for hour help,
> Sylvie.
>
>
> <?xml version="1.0" encoding="UTF-8"?>
> <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
> <moby:mobyContent>
>     <moby:mobyData moby:queryID="sip_1_">
>       <moby:Simple moby:articleName="alignment">
>         <moby:aWrongType xmlns:moby="http://www.biomoby.org/moby"
> moby:id=""
> moby:namespace="">
>           <moby:String moby:id="" moby:namespace=""
> moby:articleName="content">8
>    6
> Alpha1    AAGAAG
> Alpha2    AAGAAG
> Beta1     AAGGGG
> Beta2     AAGGGG
> Gamma1    AGGAAG
> Gamma2    AGGAAG
> Delta     GGAGGA
> Epsilon   GGAAAG
>           </moby:String>
>         </moby:aWrongType>
>       </moby:Simple>
>       <moby:Parameter moby:articleName="outgroup_root">
> 	<moby:Value>no</moby:Value>
>       </moby:Parameter >
>       <moby:Parameter moby:articleName="howoften">
>         <moby:Value>100</moby:Value>
>       </moby:Parameter >
>       <moby:Parameter moby:articleName="numgroups">
> 	<moby:Value>1000</moby:Value>
>       </moby:Parameter >
>       <moby:Parameter moby:articleName="simple">
> 	<moby:Value>no</moby:Value>
>       </moby:Parameter >
>       <moby:Parameter moby:articleName="threshold">
> 	<moby:Value>1.0</moby:Value>
>       </moby:Parameter >
>       <moby:Parameter moby:articleName="outgnum">
> 	<moby:Value>1</moby:Value>
>       </moby:Parameter >
>     </moby:mobyData>
>   </moby:mobyContent>
> </moby:MOBY>
>
> gordonp at ucalgary.ca a écrit :
>> Hi Sylvie,
>>
>>  If you send me the example XML, that will help me determine the issue.
>> It should be able to parse the data, even if the datatypes are not in
>> the
>> ontology.
>>
>> Regards,
>>
>> Paul
>>
>> If you could send the example file to me, it would
>>
>>
>>>Hi,
>>>
>>>I would like to create a biomoby instance from a file that contains
>>> data.
>>>
>>>The data file is an XML file that comply (or should comply) with
>>> biomoby
>>>format.
>>>I thought that if the file contained a data type that is not a biomoby
>>>data type
>>>(doesn't belong to the object ontology), the createInstanceFromDOM
>>> method
>>>would
>>>throw an exception, but that is not the case. A NullPointerException is
>>>thrown
>>>by an inner method (MobyDatacomposite constructor).
>>>
>>>Should I use another method to check that the data type present in the
>>>data file
>>>is correct or is it a problem with createInstanceFromDOM that should
>>> throw
>>>an
>>>exception ?
>>>
>>>Thanks, and
>>>Best regards,
>>>Sylvie.
>>>
>>>
>>>
>>>_______________________________________________
>>>MOBY-dev mailing list
>>>MOBY-dev at lists.open-bio.org
>>>http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>>>
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>>>
>>
>>
>>
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>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>>
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