New to Spring and New to Web Services.

[Natalie Kopple]

Hi, I am new to both the Spring framework and web services.

I already have web services code (see below) that works although the code is not written by me. That web service code is to query data.

Now, I have to use web services together with the Spring framework. I have no idea about where and how to start. I can only show the web services code here to see if anybody could point me a direction as to how to do it. Thank you.

import gov.nih.nci.cabio.domain.Chromosome;
import gov.nih.nci.cabio.domain.Gene;
import gov.nih.nci.cabio.domain.GeneOntology;
import gov.nih.nci.cabio.domain.GeneOntologyRelationship;
import gov.nih.nci.cabio.domain.Taxon;

import javax.xml.namespace.QName;
import javax.xml.rpc.ParameterMode;

import org.apache.axis.client.Call;
import org.apache.axis.client.Service;

public class TestWS {

	public static void main(String [] args) throws Exception {

		Service service = new Service();
		Call call = (Call)service.createCall();

		/***************************************************************************************************************/
     
		QName qnGene = new QName("urn:domain.cabio.nci.nih.gov", "Gene");
		call.registerTypeMapping(Gene.class, qnGene,
				new org.apache.axis.encoding.ser.BeanSerializerFactory(Gene.class, qnGene),
				new org.apache.axis.encoding.ser.BeanDeserializerFactory(Gene.class, qnGene));

        QName qnChromosome = new QName("urn:domain.cabio.nci.nih.gov", "Chromosome");
		call.registerTypeMapping(Chromosome.class, qnChromosome,
				new org.apache.axis.encoding.ser.BeanSerializerFactory(Chromosome.class, qnChromosome),
				new org.apache.axis.encoding.ser.BeanDeserializerFactory(Chromosome.class, qnChromosome));

		QName qnTaxon = new QName("urn:domain.cabio.nci.nih.gov", "Taxon");
		call.registerTypeMapping(Taxon.class, qnTaxon,
				new org.apache.axis.encoding.ser.BeanSerializerFactory(Taxon.class, qnTaxon),
				new org.apache.axis.encoding.ser.BeanDeserializerFactory(Taxon.class, qnTaxon));

		QName qnGeneOntology = new QName("urn:domain.cabio.nci.nih.gov", "GeneOntology");
				call.registerTypeMapping(GeneOntology.class, qnGeneOntology,
				new org.apache.axis.encoding.ser.BeanSerializerFactory(GeneOntology.class, qnGeneOntology),
				new org.apache.axis.encoding.ser.BeanDeserializerFactory(GeneOntology.class, qnGeneOntology));

		QName qnGeneOntologyRelationship = new QName("urn:domain.cabio.nci.nih.gov", "GeneOntologyRelationship");
				call.registerTypeMapping(GeneOntologyRelationship.class, qnGeneOntologyRelationship,
				new org.apache.axis.encoding.ser.BeanSerializerFactory(GeneOntologyRelationship.class, qnGeneOntologyRelationship),
				new org.apache.axis.encoding.ser.BeanDeserializerFactory(GeneOntologyRelationship.class, qnGeneOntologyRelationship));

		/****************************************************************************************************************/

		String url = "http://cabioapi.nci.nih.gov/cabio43/services/caBIOService";
        System.out.println("Connecting to " + url);
		call.setTargetEndpointAddress(new java.net.URL(url));

        /*
         * Example 1:
         * Get the version.
         */
        call.setOperationName(new QName("caBIOService", "getVersion"));
        call.setReturnType(org.apache.axis.encoding.XMLType.XSD_STRING);
        System.out.println("1.Version: "+call.invoke(new Object[0]));
        System.out.println("====================================================================");
        
        /*
         * Example 2:
         * Get number of records returned per Query.
         */
        call.setOperationName(new QName("caBIOService", "getRecordsPerQuery"));
        call.setReturnType(org.apache.axis.encoding.XMLType.XSD_INT);
        System.out.println("2.Number of records returned per Query: "+call.invoke(new Object[0]));
        System.out.println("====================================================================");
        
        /*
         * Example 3:
         * Get total number of Genes in the database
         */

        call.setOperationName(new QName("caBIOService", "getTotalNumberOfRecords"));
        call.addParameter("arg1",org.apache.axis.encoding.XMLType.XSD_STRING,ParameterMode.IN);
        call.addParameter("arg2", org.apache.axis.encoding.XMLType.XSD_ANYTYPE, ParameterMode.IN);        
        call.setReturnType(org.apache.axis.encoding.XMLType.XSD_INT);
        System.out.println("3.Total number of Genes found: " + call.invoke(new Object[] { "gov.nih.nci.cabio.domain.Gene", new Gene() }));
        System.out.println("\n====================================================================");
        
        /*
         * Example 4:
         * Query for Genes, where Gene symbol like nat*, taxon id = 6 and chromosome id = 37.
         * (Nested criteria test)
         */
        
		call.setOperationName(new QName("caBIOService", "queryObject"));
        call.setReturnType(org.apache.axis.encoding.XMLType.SOAP_ARRAY);
		Gene gene = new Gene();
		gene.setSymbol("br*");
		Taxon tax = new Taxon();
		tax.setId(new Long(5));
		gene.setTaxon(tax);
		
		long start = System.currentTimeMillis();
		Object[] resultList = (Object[])call.invoke(new Object[] { "gov.nih.nci.cabio.domain.Gene", gene });
		long end = System.currentTimeMillis();
		System.out.println("4.Get Genes where gene symbol='br*', Taxon id=5 \n\tTotal Genes Found: " + resultList.length );
		if (resultList.length > 0) {
			for(int resultIndex = 0; resultIndex < resultList.length; resultIndex++) {
				Gene g = (Gene)resultList[resultIndex];
				System.out.println("\tGene id: " + g.getId()+"\t"+ g.getSymbol());
			}
		}
		System.out.println("TIME LAG: MS - "+ (end - start));
        System.out.println("\n====================================================================");

        

        /*
         * Example 5:
         * Query for Parent GeneOntologyRelationship by setting childGeneOntology id =  5125
         */
        call = (Call)service.createCall();
        call.setTargetEndpointAddress(new java.net.URL(url));
        call.setOperationName(new QName("caBIOService", "queryObject"));
        call.addParameter("arg1",org.apache.axis.encoding.XMLType.XSD_STRING,ParameterMode.IN);
        call.addParameter("arg2", org.apache.axis.encoding.XMLType.XSD_ANYTYPE, ParameterMode.IN);
        call.setReturnType(org.apache.axis.encoding.XMLType.SOAP_ARRAY);

		GeneOntology geneOntology = new GeneOntology();
		geneOntology.setId(new Long(5125));
		GeneOntologyRelationship geneor = new GeneOntologyRelationship();
		geneor.setChildGeneOntology(geneOntology);
		long startTime = System.currentTimeMillis();
		Object[] parentGOCollection = (Object[])call.invoke(new Object[] { "gov.nih.nci.cabio.domain.GeneOntologyRelationship", geneor });
		long endTime = System.currentTimeMillis();
		System.out.println("5. Query Parent GeneOntologyRelationship by setting childGeneOntology id =  5125");
        System.out.println("\tNumber of parent Gene Ontologies found: "+ parentGOCollection.length);
		for(int i=0; i<parentGOCollection.length; i++){
			GeneOntologyRelationship data = new GeneOntologyRelationship();
			data = (GeneOntologyRelationship)parentGOCollection[i];
			System.out.println("\tParent Gene Ontology Relationship id: " + data.getId());
		}
		System.out.println("TIME LAG: MS - "+ (endTime - startTime));
        System.out.println("\n====================================================================");

         /*
         * Example 6:
         * Query GeneOntology by Gene where symbol=brca. Using the result Gene Ontologies get the Child GeneOntologyRelationship
         */
        
        Gene nat = new Gene();
        nat.setSymbol("nat*");
		Object[] ontologyCollection = (Object[])call.invoke(new Object[] { "gov.nih.nci.cabio.domain.GeneOntology", nat });        
		System.out.println("\n6.Get GeneOntology for gene symbol='nat*'");
        System.out.println(ontologyCollection.length + "\n\tGeneOntologies found");
        
		for(int i=0; i><ontologyCollection.length; i++){
			GeneOntology geneOnt = new GeneOntology();
			geneOnt = (GeneOntology)ontologyCollection[i];
            System.out.println("\n====================================================================");
            System.out.println("\tGet Child GeneOntologyRelationship for GeneOntology: "+ geneOnt.getId() +"\t"+ geneOnt.getName());
           
			GeneOntologyRelationship gor = new GeneOntologyRelationship();
			java.util.List list = new java.util.ArrayList();
			list.add(geneOnt);
			gor.setParentGeneOntology(geneOnt);
			Object[] childGOCollection = (Object[])call.invoke(new Object[] { "gov.nih.nci.cabio.domain.GeneOntologyRelationship", gor });
			System.out.println("\n\t"+ childGOCollection.length +" ChildGeneOntologyRelationships found\n\t");
			for(int o=0; o><childGOCollection.length; o++){
				GeneOntologyRelationship childGOR = (GeneOntologyRelationship)childGOCollection[o];
				System.out.print("id: "+ childGOR.getId()+"; ");
			}

		}

        /*
         * Example 7:
         * Check if bigid for BRCA1 exists
         */
        System.out.println("====================================================================");
        String bigId = "hdl://2500.1.PMEUQUCCL5/PSYFK45ESM";
        call = (Call)service.createCall();
        call.setTargetEndpointAddress(new java.net.URL(url));
        call.setOperationName(new QName("caBIOService", "exist"));
        call.addParameter("arg1",org.apache.axis.encoding.XMLType.XSD_STRING,ParameterMode.IN);        
        call.setReturnType(org.apache.axis.encoding.XMLType.XSD_BOOLEAN);

        boolean found = ((Boolean)call.invoke(new Object[] {bigId})).booleanValue();
        
        System.out.println("Big id: "+bigId+"  - found: "+  found);

        /*
         * Example 8:
         * Get data object from bigId for BRCA1
         */
        System.out.println("====================================================================");
        call = (Call)service.createCall();
        call.setTargetEndpointAddress(new java.net.URL(url));
        call.setOperationName(new QName("caBIOService", "getDataObject"));
        call.addParameter("arg1",org.apache.axis.encoding.XMLType.XSD_STRING,ParameterMode.IN);        
        call.setReturnType(org.apache.axis.encoding.XMLType.XSD_ANYTYPE);

        Gene dataObject = (Gene)call.invoke(new Object[] {bigId}); 
 
        System.out.println("Big id: "+bigId+"  - " + dataObject.getId() + "\t"+ dataObject.getHugoSymbol());
	}

}

>

[Mark Spritzler]

First I'd read up about Web Services. To me that code is not a web service, it can't be inside a public static void main. Now it could be a client calling a web service, but not a web service.

Then I would read about Spring. and learn and understand Spring.

I wouldn't try to tackle both at the same time.

I might first start learning Spring, then as I got some of it down learn about Spring's Web Service or Spring's RESTful Web Service modules to make creating Web Service simpler. But there isn't anyway anyone could put all that into a post on a forum.

For instance, I teach the Core Spring class for SpringSource, and it is a four day class. We don't discuss Web Services till the fourth day and only talk about RESTful Web Services, in older versions of the class we discussed the Web Service Module instead of RESTful Web Services because the REST supported was a recent addition to Spring Framework in version 3.0

Mark