caCORE 3.0.1 API Presenters: Nafis Zebarjadi, SAIC - SDK Technical Trainer Michael Connolly, SAIC - caBIO Developer Jennifer Zeng, SAIC - caBIO Developer

1
caCORE 3.0.1 APIPresenters Nafis Zebarjadi,
SAIC - SDK Technical Trainer Michael
Connolly, SAIC - caBIO Developer
Jennifer Zeng, SAIC - caBIO Developer

• Developer Boot Camp
• August 2005
• caCORE SDK Development Team
• SAIC

2
Summary

• Learning Objectives
• Introduction
• API Demonstration
• Hands On Exercise
• Known Issues
• How to get help?

3
Learning Objectives

• How to use caCORE 3.0.1 API Using
• caCORE Java API
• Domain Object Based Search Criteria
• Hibernate Detached Criteria
• Web Services API

4
Introduction

• caCORE 3.0.1 API is
• Programmatic interface to caCORE hosted
  vocabulary, metadata, and biomedical data
• Output of caCORE SDK 1.0.3

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Introduction (cont.)

• caCORE 3.0.1 Provides
• Domain Objects
• ApplicationService class
• static getLocalInstance()
• static getRemoteInstance(String serverURL)
• search(Class targetObjectClass, Object
  criteriaObject)
• search(Class targetObjectClass, List
  criteriaObjectList)
• search(String path-to-targetObject, Object
  criteriaObject)
• search(String path-to-targetObject, List
  criteriaObjectList)
• query(Object criteria, String targetClassName)
• various print utility methods

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API Demonstration

• We will use code samples to demonstrate how to
  apply each of these three query methods to
  implement the following two use cases

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API Demonstration (cont.)

• Use Case 1 Search for GeneOntology based on a
  Gene whose symbol is NAT2

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API Demonstration (cont.)

• Method 1
• ApplicationService appService
  ApplicationService.getRemoteInstance("http//cabio
  .nci.nih.gov/cacore30/server/HTTPServer")
• Gene gene1 new GeneImpl()
• gene1.setSymbol("NAT2")
• List resultList1 appService.search(GeneOntology.
  class, gene1)

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API Demonstration (cont.)

• Method 2
• ApplicationService appService
  ApplicationService.getRemoteInstance(
  "http//cabio.nci.nih.gov/cacore30/server/HTTPServ
  er")
• Gene gene1 new GeneImpl()
• gene1.setSymbol("NAT2")
• List resultList1 appService.search(Gene.class,
  gene1)
• for (Iterator resultsIterator
  resultList1.iterator() resultsIterator.hasNext()
  )
• Gene returnedGene (Gene)resultsIterator.next()
• List geneOntologyList (List)returnedGene.getGene
  OntologyCollection()

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API Demonstration (cont.)

• Use Case 2 Seach for the disease category of a
  Disease which can be treated by an Agent with the
  name Gleevec.

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API Demonstration (cont.)

• Method 1
• ApplicationService appService
  ApplicationService.getRemoteInstance("http//cabio
  .nci.nih.gov/cacore30/server/HTTPServer")
• Agent agent2 new AgentImpl()
• agent2.setName("Gleevec")
• List resultList2 appService.search(
  gov.nih.nci.cabio.domain.ProtocolAss
  ociation, gov.nih.nci.cabio.domain.ClinicalTrialPr
  otocol", agent2)

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API Demonstration (cont.)

• Method 2
• ApplicationService appService
  ApplicationService.getRemoteInstance("http//cabio
  .nci.nih.gov/cacore30/server/HTTPServer")
• List agentList new ArrayList()
• Agent agent2 new AgentImpl()
• agent2.setName("Gleevec")
• agentList.add(agent2)
• ClinicalTrialProtocol ctp new
  ClinicalTrialProtocolImpl()
• ctp.setAgentCollection(agentList)
• List resultList2 appService.search(
  ProtocolAssociation.class, ctp)

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API Demonstration (cont.)

• Hibernate Detached Criteria Scenario for Use Case
  2
• DetachedCriteria dCriteria2 DetachedCriteria.for
  Class(ProtocolAssociation.class)
• dCriteria2.createAlias("clinicalTrialProtocol",
  "clinical")
• .createAlias("clinical.agentCollection", "agent")
• .add(Restrictions.ilike("agent.name",
  "Gleevec"))
• List resultList2 appService.query(dCriteria2,Pro
  tocolAssociationImpl.class.getName())

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API Demonstration (cont.)

• Use Case 3 Get Description Logic Concepts from
  the NCI Thesaurus for the term Organ.
• ApplicationService appService ApplicationService.
  getRemoteInstance(
• 
  "http//cabio.nci.nih.gov/cacore30/serv
  er/HTTPServer")
• try
• String vocabularyName "NCI_Thesaurus"
• EVSQuery evsQuery new EVSQueryImpl()
• List evsResults new ArrayList()
• evsQuery.getDescLogicConcept("NCI_Thesaurus","O
  rgan",false)
• evsResults (List)appService.evsSearch(evsQuer
  y)
• appService.printEVSResults(evsResults)
• System.out.println("\n\n"evsResults.size()
  " records found")
• catch(Exception ex)

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API Demonstration (cont.)

• Steps to use caCORE 3.0.1 Web Services
• download WSDL file from http//cabio.nci.nih.gov/c
  acore30/ws/caCOREService?wsdl
• download axis1-2
• run wsdl2java program
• java org.apache.axis.wsdl.WSDL2Java cacore30.wsdl
• create a web service client (two variations)
• DII (Dynamic Invocation Interface) Client
• JAX-RPC Client

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API Demonstration (cont.)

• caCORE Web Service Expose 2 Methods
• queryObject(String pathToTarget, Object
  criteriaObject)
• query(String pathToTarget, Object criteriaObject,
  int startRow, int resultSizeLimit)

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• Lets give it a try
• cd to C\wsClient
• run classpathenv.bat
• create domain objects and stubs
• run java org.apache.axis.wsdl.WSDL2Java
  cacore30.wsdl
• compiling and running web service test clients
• javac WSTestClientDII.java
• java WSTestClientDII
• javac WSTestClientRPC.java
• java WSTestClientRPC

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Hands On Exercise (1)

• Modify your existing caCORE3.0.1 Test Client to
  do the following query
• Question Find the Chromosome object(s) that
  contain the Gene whose symbol is Gup1.
• Model Relationship

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Hands On Exercise (1)

• Our Solution

ApplicationService appService
ApplicationService.getRemoteInstance(
"http//cabio.nci.nih.gov/cacore30/server/HTTPSer
ver") Gene gene new GeneImpl() gene.setSymbol
("Gup1") List resultList3 appService.search("go
v.nih.nci.cabio.domain.Chromosome",
gene) if((resultList3 ! null)
(resultList3.size()lt1)) System.out.println(
"No records found") for (Iterator iterator
resultList3.iterator()iterator.hasNext())
Chromosome chrom (Chromosome)iterator.next()
System.out.println("Chromosome number "
chrom.getNumber())
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Hands On Exercise (2)

• Modify your existing caCORE3.0.1 Test Client to
  do the following query
• Question Search for a ProteinAlias based on
  Chromosome number 8 going through Protein and
  then Gene.
• Model Relationship

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Hands On Exercise (2)

• Our Solution

Chromosome chrom new ChromosomeImpl() chrom.set
Number("8") List resultList5
appService.search("gov.nih.nci.cabio.domain.Protei
nAlias," "gov.nih.nci.cabio.domain.Protei
n," "gov.nih.nci.cabio.domain.Gene",
chrom) if((resultList5 ! null)
(resultList5.size()lt1)) System.out.println(
"No records found") for (Iterator
iterator resultList5.iterator()iterator.hasNext
()) ProteinAlias proteinA
(ProteinAlias)iterator.next()
System.out.println("ProteinAlias name "
proteinA.getName())
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Hands On Exercise (3)

• Modify your existing caCORE3.0.1 Test Client to
  do the following query
• Question Search for Anomalies based on an Agent
  name "FLAVOPIRIDOL" through the Target object.
• Model Relationship

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Hands On Exercise (3)

• Our Nested Object Solution

Agent agent new AgentImpl() agent.setName("FLAV
OPIRIDOL") List agentList new
ArrayList() agentList.add(agent) Target target
new TargetImpl() target.setAgentCollection(agen
tList) List resultList7 appService.search("gov.
nih.nci.cabio.domain.Anomaly", target) if ((
resultList7 ! null)(resultList7.size() 0))
System.out.println("No Anomaly record
found.") for (Iterator iterator
resultList7.iterator()iterator.hasNext())
Anomaly anomaly (Anomaly)iterator.next()
System.out.println(" Anomaly
description " anomaly.getDescription())

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Hands on Exercise

• Our Path-to-Object Solution

Agent agent new AgentImpl() agent.setName("FLAV
OPIRIDOL") List resultList7 appService.search(
gov.nih.nci.cabio.domain.Anomaly,
gov.nih.nci.cabio.domain.Target", agent) if ((
resultList7 ! null)(resultList7.size() 0))
System.out.println("\nNo Anomaly record
found.") for (Iterator iterator
resultList7.iterator()iterator.hasNext())
Anomaly anomaly (Anomaly)iterator.next()
System.out.println(" Anomaly
description " anomaly.getDescription())

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Known Issues

• Range searching not supported.
• Data provenance package objects are empty.
• Must use get methods when retrieving objects
  associated to Gene/Diseease/OrganOntology.
• Consult release notes.

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How to get Help?

• NCICB Application Support
• http//ncicbsupport.nci.nih.gov/sw/
• Telephone [phone] or toll free
  888-478-4423
• ncicb_at_pop.nih.gov
• Sign up for the caBIO Users Listserv when you
  downlaod caCORE 3.0.1
• Open Development Initiative
• http//ncicb.nci.nih.gov/ODI
• NCICBOpenDevelopment_at_mail.nih.gov

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Further Reading

• caCORE SDK Programmers Guide
• ftp//ftp1.nci.nih.gov/pub/cacore/SDK/caCORE_SDK1.
  0.3_Programmers_Guide.pdf
• caCORE SDK Installation and Basic Test Guide
• ftp//ftp1.nci.nih.gov/pub/cacore/SDK/caCORE_SDK1.
  0.3_Installation_and_Basic_Test_Guide.pdf
• caCORE Technical Guide
• ftp//ftp1.nci.nih.gov/pub/cacore/caCORE2.0_Tech_G
  uide.pdf
• ftp//ftp1.nci.nih.gov/pub/cacore/caCORE3.0.1_Tech
  _Supp.pdf
• caCORE Web site
• http//ncicb.nci.nih.gov/core

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Questions?