Hello,
I'm trying to access the biomart data via WebService described in:
http://www.biomart.org/martservice.html (SOAP access)
I was directed to you by ensembl helpdesk.
I am able to retrieve the list of attributes for my requested dataset:
hsapiens_snp
but when I try to query I get no data, until I get socket time out.
maybe my query line is wrong, this is it:
proxy.query("default", 0, 0, 0, new Dataset[]{dataset});
My client program and output can be seen below
Thanks, Ariel.
Client code:
final String wsAddress = "http://www.biomart.org/biomart/martsoap";;
final MartServiceSoapProxy proxy = new MartServiceSoapProxy();
proxy.setEndpoint(wsAddress);
/*
* Here is where I extract the attributes, this succeeded :)
*/
try
{
AttributePage[] attrPages = proxy.getAttributes("hsapiens_snp",
"default");
for(AttributePage attributePage : attrPages)
{
System.out.println("Attribute Page: [" +
attributePage.getName() + "]");
AttributeGroup[] attrGroup =
attributePage.getAttributeGroup();
for(AttributeGroup attributeGroup : attrGroup)
{
System.out.println("\tAttribute Group: [" +
attributeGroup.getName() + "]");
AttributeCollection[] attrCollect =
attributeGroup.getAttributeCollection();
for(AttributeCollection attributeCollection :
attrCollect)
{
System.out.println("\t\tAttribute Collection: [" +
attributeCollection.getName() + "]");
AttributeInfo[] attrInfo =
attributeCollection.getAttributeInfo();
for(AttributeInfo attributeInfo : attrInfo)
{
System.out.println("\t\t\tAttribute [" +
attributeInfo.getName() + "]");
}
}
}
}
}
catch(RemoteException ex1)
{
final String msg = "Exception: [" + ex1.getMessage() + "]";
sLogger.error(msg);
throw new RimonException(msg, ex1);
}
/*
* Prepare request
*/
final Attribute[] attrs = new Attribute[4];
attrs[0] = new Attribute("dbsnp");
attrs[1] = new Attribute("chr_name");
attrs[2] = new Attribute("chrom_start");
attrs[3] = new Attribute("allele");
final Dataset dataset = new Dataset("hsapiens_snp", null, attrs);
/*
* Send request
*/
String[][] wsResult = null;
try
{
wsResult = proxy.query("default", 0, 0, 0, new Dataset
[]{dataset});
}
catch(RemoteException ex)
{
final String msg = "Exception: [" + ex.getMessage() + "]";
sLogger.error(msg);
throw new RimonException(msg, ex);
}
/*
* Let's see the result
*/
for(String[] array : wsResult)
{
for(String result : array)
{
System.out.println("result [" + result + "]");
}
}
Output
Attribute Page: [snp]
Attribute Group: [snp]
Attribute Collection: [snpsatts]
Attribute [refsnp_id]
Attribute [chr_name]
Attribute [chrom_start]
Attribute [chrom_strand]
Attribute [allele]
Attribute [mapweight]
Attribute [validated]
Attribute [allele_1]
Attribute Collection: [variation_annotation]
Attribute [associated_gene]
Attribute [ega_stable_id]
Attribute [phenotype_name]
Attribute [phenotype_description]
Attribute [associated_variant_risk_allele]
Attribute [risk_allele_freq_in_controls]
Attribute [p_value]
Attribute [variation_names]
Attribute [study]
Attribute [study_type]
Attribute [source_name]
Attribute Collection: [source]
Attribute [dbsnp]
Attribute [uniprot_synonym]
Attribute [affy100]
Attribute [affy500]
Attribute [affy6]
Attribute [ensembl_watson]
Attribute [ensembl_venter]
Attribute [illumina_cytosnp12v1]
Attribute [illumina_human1mduov3]
Attribute [illumina_human660wquad]
Attribute Group: [genesnpatts]
Attribute Collection: [ensemblatts]
Attribute [ensembl_gene_stable_id]
Attribute [ensembl_transcript_stable_id]
Attribute [ensembl_transcript_chrom_strand]
Attribute [ensembl_type]
Attribute [consequence_type_tv]
Attribute [ensembl_peptide_shift]
Attribute [cdna_start]
Attribute [cdna_end]
Attribute [translation_start]
Attribute [translation_end]
Attribute Page: [sequences]
Attribute Group: [sequence]
Attribute Collection: [snp_seq_scope]
Attribute [snp]
Attribute Collection: [upstream]
Attribute [upstream_flank]
Attribute Collection: [downstream]
Attribute [downstream_flank]
Attribute Group: [region]
Attribute Collection: [chromosomeatts]
Attribute [chr_name]
Attribute [chrom_start]
Attribute [chrom_strand]
Attribute Group: [snp]
Attribute Collection: [snpatts]
Attribute [source]
Attribute [refsnp_id]
Attribute [allele]
Attribute [validated]
Attribute [mapweight]
Attribute [ensembl_peptide_shift]
Attribute Page: [poly_strain]
Attribute Group: [snp_atts]
Attribute Collection: [snpatts]
Attribute [refsnp_id]
Attribute [chr_name]
Attribute [chrom_start]
Attribute [chrom_strand]
Attribute [allele]
Attribute [validated]
Attribute [mapweight]
Attribute Collection: [ensemblatts]
Attribute [ensembl_gene_stable_id]
Attribute [ensembl_transcript_stable_id]
Attribute [ensembl_type]
Attribute [consequence_type_tv]
Attribute [ensembl_peptide_shift]
Attribute [cdna_start]
Attribute [cdna_end]
Attribute [ensembl_transcript_chrom_strand]
Attribute [translation_start]
Attribute [translation_end]
Exception in thread "main"
com.ibm.hrl.rimon.common.exception.RimonException: Exception: [; nested
exception is:
java.net.SocketTimeoutException: Read timed out]
at com.ibm.hrl.rimon.bii.ws.client.FetchEnsemblQueryWsClient.main(
FetchEnsemblQueryWsClient.java:105)
Caused by: java.net.SocketTimeoutException: Read timed out
at org.apache.axis.AxisFault.makeFault(AxisFault.java:101)
at org.apache.axis.transport.http.HTTPSender.invoke(
HTTPSender.java:154)
at org.apache.axis.strategies.InvocationStrategy.visit(
InvocationStrategy.java:32)
at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at org.biomart.www.MartServiceSoap.BioMartSoapBindingStub.query(
BioMartSoapBindingStub.java:595)
at org.biomart.www.MartServiceSoap.MartServiceSoapProxy.query(
MartServiceSoapProxy.java:74)
at com.ibm.hrl.rimon.bii.ws.client.FetchEnsemblQueryWsClient.main(
FetchEnsemblQueryWsClient.java:99)
Caused by: java.net.SocketTimeoutException: Read timed out
at java.net.SocketInputStream.read(SocketInputStream.java:140)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:229)
at java.io.BufferedInputStream.read(BufferedInputStream.java:248)
at org.apache.axis.transport.http.HTTPSender.readHeadersFromSocket(
HTTPSender.java:583)
at org.apache.axis.transport.http.HTTPSender.invoke(
HTTPSender.java:143)
... 12 more
