Pubmed Web Service Deserializing Error In C#

Question

[chi-hawk]

I have a web service setup with the following address: http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_snp.wsdl

The confiruration in app.config is as follows:

<binding name="eUtilsServiceSoap3" closeTimeout="00:01:00" openTimeout="00:01:00" receiveTimeout="00:10:00" sendTimeout="00:01:00" allowCookies="false" bypassProxyOnLocal="false" hostNameComparisonMode="StrongWildcard" maxBufferSize="999999999" maxBufferPoolSize="524288" maxReceivedMessageSize="999999999" messageEncoding="Text" textEncoding="utf-8" transferMode="Buffered" useDefaultWebProxy="true">
    <readerQuotas maxDepth="32" maxStringContentLength="999999999" maxArrayLength="16384" maxBytesPerRead="4096" maxNameTableCharCount="16384"/>
    <security mode="None">
    <transport clientCredentialType="None" proxyCredentialType="None" realm=""/>
    <message clientCredentialType="UserName" algorithmSuite="Default"/>
    </security>
</binding>
...
<endpoint address="&lt;a href=" http:="" eutils.ncbi.nlm.nih.gov="" soap="" v2.0="" soap_adapter_2_0.cgi?db="snp" "="" rel="nofollow">http://eutils.ncbi.nlm.nih.gov/soap/v2.0/soap_adapter_2_0.cgi?db=snp"
    binding="basicHttpBinding" bindingConfiguration="eUtilsServiceSoap3"
    contract="PubMedWebServiceEfetch_snp.eUtilsServiceSoap" name="eUtilsServiceSoap3" />

I run the code as follows:

PubMedWebServiceEfetch_snp.eUtilsServiceSoapClient snpServer = new PubMedWebServiceEfetch_snp.eUtilsServiceSoapClient();
PubMedWebServiceEfetch_snp.eFetchRequest snpRequest = new PubMedWebServiceEfetch_snp.eFetchRequest();
snpRequest.id = "1870372";
PubMedWebServiceEfetch_snp.eFetchResult snpResult = snpServer.run_eFetch(snpRequest);
PubMedWebServiceEfetch_snp.ExchangeSet snpInfoFromSnpResult = snpResult.ExchangeSet; 
...

If I run the code with the id = "1870377" it will return and I can access the information in the "ExchangeSet". If I use "1870372" (as in the example above) I get the following error:

Error in deserializing body of reply message for operation 'run_eFetch'.

Upon further investigaion of the inner error message in C# I find that it says:

{"Instance validation error: 'intron-variant' is not a valid value for FxnSetFxnClass."}

Has anyone else found this error? As you can see, I tried to up the maxBufferSize, maxReceivedMessageSize, and maxStringContentLength. You can also see from this page what should be returned: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=SNP&id=1870372

I appreciate any help on ways to avoid this error.

Answer 1

[Pierre Lindenbaum]

I think the problem comes from the NCBI. The XSD schema associated to :

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=SNP&id=1870372&rettype=xml

is

ftp://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_3.1.xsd

but the latest schema is:

ftp://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_3.3.xsd

it contains the following enum that doesn't exist in 3.1:

(...)
<xsd:enumeration value="intron-variant">
(...)

[chi-hawk]

@Pierre - thank you for this. Great explanation. I am contacting PubMed in hopes they can resolve this issue. I will post when I hear more.

Answer 2

[Chris Maloney]

I agree that it is a bug. As Pierre points out, the XML returned by the URI he gives is not valid according to the XSD schema referenced in the returned document. You can send an email to [e-mail] to submit this as a bug report.

[chi-hawk]

This is the reply I received from NIH on 1/23/2012:

Hi, Thanks for sending your feedback to us.

Discussing this with our developers, the decision is not to patch this up since the new released (version 2.5) will be available in a few weeks.

We sincerely apologize for the inconvenience.

[Chris Maloney]

Seems to be fixed now.