METLIN SOAP API

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METLIN SOAP API

April 26, 2012, 05:53:07 PM

Hi all,

We now launched SOAP API for METLIN (http://http://metlin.scripps.edu/soap/), currently there are 2 major features (Batch search and Spectrum Match for MS/MS data) that you can use for this.
Please feel free to use it, and let us know if there are any issues or suggestions.

By the way, don't forget to register to receive token for this service

Thank you,
Kevin

Re: METLIN SOAP API

Reply #1 – July 13, 2012, 09:20:34 AM

Thank you very much for the public service. It will be very helpful to us.

I am using the web service to search your metlin database. The request is as follows:
MetaboliteSearchRequest request = new MetaboliteSearchRequest()
{
token = m_sToken,
mass = m_ArraySingleMass, // 541.46315
adduct = m_ArrayNeutralMol, // { “M” }
tolerance = fMassRange, // 0.05
tolunits = "Da"
};
The exception is as follows:
Message: There is an error in XML document (2, 369).
Inner Exception: The specified type was not recognized: name='singleSearchResult', namespace='Metlin', at <result xmlns=''>.
Your help is very much appreciated!

Re: METLIN SOAP API

Reply #2 – August 03, 2012, 04:47:23 PM

I am generating fragmentation without precursor ion selection: is the parent ion necessary using the MSMS soap client? Thanks,
Corey

Re: METLIN SOAP API

Reply #3 – August 03, 2012, 06:17:04 PM

The backend does support a similarity search (search without precursor match) but it is not implemented in the SOAP API at the moment.

Re: METLIN SOAP API

Reply #4 – August 06, 2012, 08:27:20 AM

Thanks for the update Ralf, Not to sound impatient, but any idea when this might be available?

Re: METLIN SOAP API

Reply #5 – December 04, 2012, 01:23:21 PM

I tried to generate java bindings for wsdl using instructions on the web site..
wsdl2java resulted in following error

java.io.IOException: Error: Message part result of operation or fault MetaboliteSearch has no element or type attribute.
   at org.apache.axis.wsdl.symbolTable.SymbolTable.getParametersFromParts(SymbolTable.java:2119)
   at org.apache.axis.wsdl.symbolTable.SymbolTable.getOperationParameters(SymbolTable.java:1761)
   at org.apache.axis.wsdl.symbolTable.SymbolTable.populateParameters(SymbolTable.java:1682)
   at org.apache.axis.wsdl.symbolTable.SymbolTable.add(SymbolTable.java:546)
   at org.apache.axis.wsdl.symbolTable.SymbolTable.populate(SymbolTable.java:518)
   at org.apache.axis.wsdl.symbolTable.SymbolTable.populate(SymbolTable.java:495)
   at org.apache.axis.wsdl.gen.Parser$WSDLRunnable.run(Parser.java:361)
   at java.lang.Thread.run(Thread.java:722)

Any suggestions or anyway to get the java sources..

Re: METLIN SOAP API

Reply #6 – May 29, 2013, 08:52:11 AM

I'm trying to use the Metlin SOAP API as part of my final MSc Bix project, integrating the SpectrumMatch within a Matlab script.

I noticed that the wsdl: http://metlin.scripps.edu/soap/metlin-1.0.wsdl throws errors when used in Matlab

Errors:
>> url = 'http://metlin.scripps.edu/soap/metlin-1.0.wsdl';
>> createClassFromWsdl(url)

Error using ==> createClassFromWsdl>parseWsdl at 76
java.io.IOException: Error: Message part result of operation or fault MetaboliteSearch has no element or type
attribute.

Error in ==> createClassFromWsdl at 32
R = parseWsdl(wsdlUrl);

I've tried to get the java example working in order to adapt the code so that I can pass the necessary parameters to the java class from Matlab. However, I've had no luck with getting it to work. When it comes to executing:
java -cp .;* org.apache.axis.wsdl.WSDL2Java http://metlin.scripps.edu/soap/metlin-1.1.wsdl

I just get an error: ClassNotFoundException

Can anyone help please?

Phil

Re: METLIN SOAP API

Reply #7 – June 12, 2013, 09:08:02 AM

I have been having problems with getting the Metlin SOAP API to work. The wsdl address provided (http://metlin.scripps.edu/soap/metlin-1.1.wsdl) throws the following errors. Can anyone help?

Exception in thread "main" org.apache.axis2.wsdl.codegen.CodeGenerationException
: java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
at org.apache.axis2.wsdl.codegen.CodeGenerationEngine.generate(CodeGener
ationEngine.java:293)
at org.apache.axis2.wsdl.WSDL2Code.main(WSDL2Code.java:35)
at org.apache.axis2.wsdl.WSDL2Java.main(WSDL2Java.java:24)
Caused by: java.lang.RuntimeException: java.lang.reflect.InvocationTargetExcepti
on
at org.apache.axis2.wsdl.codegen.extension.SimpleDBExtension.engage(Simp
leDBExtension.java:53)
at org.apache.axis2.wsdl.codegen.CodeGenerationEngine.generate(CodeGener
ationEngine.java:246)
... 2 more
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.
java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
sorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at org.apache.axis2.wsdl.codegen.extension.SimpleDBExtension.engage(Simp
leDBExtension.java:50)
... 3 more
Caused by: org.apache.axis2.schema.SchemaCompilationException: can not find type
{http://schemas.xmlsoap.org/soap/encoding/}Array from the parent schema Metlin
at org.apache.axis2.schema.SchemaCompiler.copyMetaInfoHierarchy(SchemaCo
mpiler.java:1371)
at org.apache.axis2.schema.SchemaCompiler.processComplexContent(SchemaCo
mpiler.java:1333)
at org.apache.axis2.schema.SchemaCompiler.processContentModel(SchemaComp
iler.java:1228)
at org.apache.axis2.schema.SchemaCompiler.processComplexType(SchemaCompi
ler.java:1172)
at org.apache.axis2.schema.SchemaCompiler.processNamedComplexSchemaType(
SchemaCompiler.java:1092)
at org.apache.axis2.schema.SchemaCompiler.processSchema(SchemaCompiler.j
ava:1006)
at org.apache.axis2.schema.SchemaCompiler.processElement(SchemaCompiler.
java:645)
at org.apache.axis2.schema.SchemaCompiler.processElement(SchemaCompiler.
java:604)
at org.apache.axis2.schema.SchemaCompiler.process(SchemaCompiler.java:20
69)
at org.apache.axis2.schema.SchemaCompiler.processParticle(SchemaCompiler
.java:1952)
at org.apache.axis2.schema.SchemaCompiler.processComplexType(SchemaCompi
ler.java:1156)
at org.apache.axis2.schema.SchemaCompiler.processAnonymousComplexSchemaT
ype(SchemaCompiler.java:1055)
at org.apache.axis2.schema.SchemaCompiler.processSchema(SchemaCompiler.j
ava:1009)
at org.apache.axis2.schema.SchemaCompiler.processElement(SchemaCompiler.
java:645)
at org.apache.axis2.schema.SchemaCompiler.processElement(SchemaCompiler.
java:615)
at org.apache.axis2.schema.SchemaCompiler.compile(SchemaCompiler.java:42
3)
at org.apache.axis2.schema.SchemaCompiler.compile(SchemaCompiler.java:29
2)
at org.apache.axis2.schema.ExtensionUtility.invoke(ExtensionUtility.java
:102)
... 8 more

Re: METLIN SOAP API

Reply #8 – March 17, 2014, 09:23:52 AM

Is the SOAP API working yet?

Re: METLIN SOAP API

Reply #9 – November 14, 2014, 04:13:10 AM

Is the SOAP API working? I get this following error while accessing.

SOAP server unavailable temporarily.
Please contact rinehart@scripps.edu with any questions.
8-NOV-2013

Re: METLIN SOAP API

Reply #10 – December 09, 2014, 06:45:10 AM

Unfortunately, I don't think anyone answers queries on this forum anymore. I asked this same question back in March and then I contacted them directly. Their response was that the only way to access their database is to do so manually via the web page!!