[MOBY-dev] createInstanceFromDOM

[Sylvie Huchet]

Thanks Paul,

Now it works.

Sylvie.

gordonp at ucalgary.ca a écrit :
> 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
>>>>
>>>>
>>>>!DSPAM:60005,47b1bec010950204642575!
>>>>
>>>
>>>
>>>
>>>_______________________________________________
>>>MOBY-dev mailing list
>>>MOBY-dev at lists.open-bio.org
>>>http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>>>
>>
>>
>>!DSPAM:60005,47b2a29c109502586129532!
>>_______________________________________________
>>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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