/** @param args */
public static void main(String[] args) {
// Initialize the Log4j environment.
String logXML = "log4j.xml";
if (args.length > 0) {
logXML = args[0];
}
// logger.initLogger(logXML);
// initialize connection
String connXML = "";
if (args.length > 1) connXML = args[1];
varCon = new TestConnections(connXML, logger);
VMForm vmdata = new VMForm();
try {
vmdata.setDBConnection(varCon.openConnection());
CurationServlet cdeserv = new CurationServlet();
cdeserv.setConn(varCon.openConnection());
vmdata.setCurationServlet(cdeserv);
} catch (SQLException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
TestVM testvm = new TestVM();
// logger.start();
// logger.info("started vm test");
// if (args.length >2)
// VMpropFile = args[2];
VMpropFile = "/Users/ag/demo/cdecurate/src/gov/nih/nci/cadsr/cdecurate/test/TestVMCase.xml";
// load properties with prop file name from input parameter
// if (args.length >2)
// testvm.loadProp(args[2]);
// call the search method
// testvm.doSearchVMValues(vmdata);
// call the validate method
testvm.doValidateValues(vmdata);
// testvm.getConceptDerivation();
// testvm.switchCaseEx(2);
// end the logger
// logger.end();
}
private void readVMdata(NamedNodeMap attr, VMForm vmdata, boolean readMore) {
VM_Bean vm = vmdata.getVMBean();
VM_Bean selvm = vmdata.getSelectVM();
// validate the old vm first before reading the next vm data
if (vm != null && !vm.getVM_LONG_NAME().equals("")) {
// do the search;
VMAction vmact = new VMAction();
vmact.validateVMData(vmdata); // doChangeVM(vmdata);
}
if (readMore) {
// reset the vm
vm = new VM_Bean();
selvm = new VM_Bean();
// get teh next vm data
for (int i = 0; i < attr.getLength(); i++) {
String attName = attr.item(i).getNodeName();
String attValue = attr.item(i).getNodeValue();
if (attName != null && !attName.equals("")) {
if (attName.equals("editvmname"))
// vm.setVM_SHORT_MEANING(attValue);
vm.setVM_LONG_NAME(attValue);
else if (attName.equals("editvmlongname")) vm.setVM_LONG_NAME(attValue);
else if (attName.equals("editvmdesc")) vm.setVM_PREFERRED_DEFINITION(attValue);
else if (attName.equals("selvmname"))
// selvm.setVM_SHORT_MEANING(attValue);
selvm.setVM_LONG_NAME(attValue);
else if (attName.equals("selvmlongname")) selvm.setVM_LONG_NAME(attValue);
else if (attName.equals("selvmdesc")) selvm.setVM_PREFERRED_DEFINITION(attValue);
else if (attName.equals("selvmidseq")) selvm.setVM_IDSEQ(attValue);
else if (attName.equals("selvmcondr")) selvm.setVM_CONDR_IDSEQ(attValue);
}
// add the beans to data object
vmdata.setVMBean(vm);
vmdata.setSelectVM(selvm);
// logger.info(i + " Validating VM for " + vm.getVM_SHORT_MEANING() + " : desc : " +
// vm.getVM_DESCRIPTION() + " conlist " + vm.getVM_CONCEPT_LIST().size());
}
}
}
private void doValidateValues(VMForm vmdata) {
try {
// check if test data is avialable
if (VMpropFile != null && !VMpropFile.equals("")) {
// open teh cadsr connection
Connection conn = varCon.openConnection();
vmdata.setDBConnection(conn);
// get the root data
Element node = parseXMLData(VMpropFile);
StringBuffer sVM = new StringBuffer();
this.exploreNode(node, sVM, vmdata);
}
varCon.closeConnection(); // close the connection
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
private void readConData(NamedNodeMap attr, VMForm data) {
VM_Bean vm = data.getVMBean();
EVS_Bean vmCon = new EVS_Bean();
Vector<EVS_Bean> conList = vm.getVM_CONCEPT_LIST();
for (int i = 0; i < attr.getLength(); i++) {
// System.out.println(i + " ConAttr : " + attr.item(i).getNodeName() + " value " +
// attr.item(i).getNodeValue());
String attName = attr.item(i).getNodeName();
String attValue = attr.item(i).getNodeValue();
if (attName != null && !attName.equals("")) {
if (attName.equals("conname")) vmCon.setLONG_NAME(attValue);
else if (attName.equals("conid")) vmCon.setCONCEPT_IDENTIFIER(attValue);
else if (attName.equals("condefn")) vmCon.setPREFERRED_DEFINITION(attValue);
else if (attName.equals("condefnsrc")) vmCon.setEVS_DEF_SOURCE(attValue);
else if (attName.equals("conorigin")) vmCon.setEVS_ORIGIN(attValue);
else if (attName.equals("consrc")) vmCon.setEVS_CONCEPT_SOURCE(attValue);
else if (attName.equals("conidseq")) vmCon.setIDSEQ(attValue);
}
}
conList.addElement(vmCon);
vm.setVM_CONCEPT_LIST(conList);
}
private void doValidateValuesOld(VMForm vmdata) {
try {
// setting up the data
VM_Bean vm = new VM_Bean();
// vm.setVM_SHORT_MEANING("Nanomaterials");
// vm.setVM_SHORT_MEANING("Metastatic");
// vm.setVM_SHORT_MEANING("Dose");
// vm.setVM_SHORT_MEANING("Fludeoxyglucose F 18");
// vm.setVM_SHORT_MEANING("Adverse Event");
// vm.setVM_SHORT_MEANING("Adverse Event Domain");
// vm.setVM_SHORT_MEANING("Adverse Event Capture");
// vm.setVM_SHORT_MEANING("Low");
vm.setVM_LONG_NAME("Hypersensitivity");
// vm.setVM_DESCRIPTION("need definiton");
// vm.setVM_DESCRIPTION("Any unfavorable and unintended sign (including an abnormal
// laboratory finding), symptom, syndrome, or disease, temporally associated with the use of a
// medical product or procedure, regardless of whether or not it is considered related to the
// product or procedure (attribution of unrelated, unlikely, possible, probable, or definite).
// The concept refers to events that could be medical product related, dose related, route
// related, patient related, caused by an interaction with another therapy or procedure, or
// caused by opioid initiation or dose escalation. The term also is referred to as an adverse
// experience. The old term Side Effect is retired and should not be used.");
// vm.setVM_DESCRIPTION("No Value Exists.");
// vm.setVM_DESCRIPTION("The Adverse Events dataset includes. Adverse events may be captured
// either as free text or a pre-specified list of terms.");
// vm.setVM_DESCRIPTION("Adverse events may be captured either as free text or a pre-specified
// list of terms.");
// vm.setVM_DESCRIPTION("A procedure that uses ultrasonic waves directed over the chest wall
// to obtain a graphic record of the heart's position, motion of the walls, or internal parts
// such as the valves.");
// vm.setVM_DESCRIPTION("The amount of medicine taken, or radiation given, at one time.");
// vm.setVM_DESCRIPTION("(MET-uh-STAT-ik) Having to do with metastasis, which is the spread
// of cancer from one part of the body to another.");
// vm.setVM_DESCRIPTION("Metastatic");
// vm.setVM_DESCRIPTION("Research aimed at discovery of novel nanoscale and nanostructured
// materials and at a comprehensive understanding of the properties of nanomaterials (ranging
// across length scales, and including interface interactions). Also, R&D leading to the
// ability to design and synthesize, in a controlled manner, nanostructured materials with
// targeted properties.");
// vm.setVM_DESCRIPTION("Lower than reference range");
vm.setVM_PREFERRED_DEFINITION("Hypersensitivity");
// get concepts for vm
Vector<EVS_Bean> conList = new Vector<EVS_Bean>();
EVS_Bean vmCon = new EVS_Bean();
vmCon.setLONG_NAME("Hypersensitivity"); // ("Low"); //("Metastatic"); //("Nanomaterials");
vmCon.setCONCEPT_IDENTIFIER("C3114"); // ("C54722"); //("C14174"); // ("C53671");
vmCon.setPREFERRED_DEFINITION(
"Hypersensitivity; a local or general reaction of an organism following contact with a specific allergen to which it has been previously exposed and to which it has become sensitized.");
// ("A minimum level or position or degree; less than normal in degree or intensity or
// amount.");
// ("(MET-uh-STAT-ik) Having to do with metastasis, which is the spread of cancer from one
// part of the body to another.");
// ("Research aimed at discovery of novel nanoscale and nanostructured materials and at a
// comprehensive understanding of the properties of nanomaterials (ranging across length
// scales, and including interface interactions). Also, R&D leading to the ability to design
// and synthesize, in a controlled manner, nanostructured materials with targeted
// properties.");
vmCon.setEVS_ORIGIN("NCI Thesaurus");
vmCon.setEVS_DEF_SOURCE("NCI"); // ("NCI-GLOSS");
vmCon.setIDSEQ(
"F37D0428-B65C-6787-E034-0003BA3F9857"); // ("");
// //("F37D0428-DE70-6787-E034-0003BA3F9857");
conList.addElement(vmCon);
// vmdata.setConceptVMList(conceptVMList)
vm.setVM_CONCEPT_LIST(conList);
vmdata.setVMBean(vm);
VM_Bean selvm = new VM_Bean();
selvm.setVM_LONG_NAME("Hypersensitivity"); // ("Adverse Event Domain");
selvm.setVM_PREFERRED_DEFINITION("Hypersensitivity"); // ("need definiton");
vmdata.setSelectVM(selvm);
logger.info(
"Validating VM for "
+ vm.getVM_LONG_NAME()
+ " : desc : "
+ vm.getVM_PREFERRED_DEFINITION());
// open teh cadsr connection
Connection conn = varCon.openConnection();
vmdata.setDBConnection(conn);
// do the search;
VMAction vmact = new VMAction();
vmact.validateVMData(vmdata); // doChangeVM(vmdata);
varCon.closeConnection(); // close the connection
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
private void doValidateValuesProp(VMForm vmdata) {
try {
// check if test data is avialable
if (VMprop != null) {
String sProp = VMprop.getProperty("vm0");
System.out.println("got the key " + sProp);
// open teh cadsr connection
Connection conn = varCon.openConnection();
vmdata.setDBConnection(conn);
// loop through the data to test one by one
for (int i = 1; true; ++i) {
// setting up the data
VM_Bean vm = new VM_Bean();
VM_Bean selvm = new VM_Bean();
// edited value meaning from the page
String curvmname = VMprop.getProperty("current.vmname." + i);
if (curvmname == null || curvmname.equals("")) break;
if (curvmname != null) vm.setVM_LONG_NAME(curvmname);
String curvmdesc = VMprop.getProperty("current.vmdesc." + i);
if (curvmdesc != null) vm.setVM_PREFERRED_DEFINITION(curvmdesc);
String curvmln = VMprop.getProperty("current.vmlongname." + i);
if (curvmln != null) vm.setVM_LONG_NAME(curvmln);
// concept associated with the edited value meaning
String connm = VMprop.getProperty("current.conname." + i);
if (connm != null) {
Vector<EVS_Bean> conList = new Vector<EVS_Bean>();
EVS_Bean vmCon = new EVS_Bean();
vmCon.setLONG_NAME(connm);
String conid = VMprop.getProperty("current.conid." + i);
if (conid != null) vmCon.setCONCEPT_IDENTIFIER(conid);
String condefn = VMprop.getProperty("current.condefn." + i);
if (condefn != null) vmCon.setPREFERRED_DEFINITION(condefn);
String conorgn = VMprop.getProperty("current.conorigin." + i);
if (conorgn != null) vmCon.setEVS_ORIGIN(conorgn);
String consrc = VMprop.getProperty("current.consrc." + i);
if (consrc != null) vmCon.setEVS_DEF_SOURCE(consrc);
String conidseq = VMprop.getProperty("current.conidseq." + i);
if (conidseq != null) vmCon.setIDSEQ(conidseq);
// add the concept bean to conlist vector and to the vm bean
conList.addElement(vmCon);
vm.setVM_CONCEPT_LIST(conList);
}
// selected value meaning before the change
String selvmname = VMprop.getProperty("selected.vmname." + i);
if (selvmname != null) {
selvm.setVM_LONG_NAME(selvmname);
String selvmdesc = VMprop.getProperty("selected.vmdesc." + i);
if (selvmdesc != null) selvm.setVM_PREFERRED_DEFINITION(selvmdesc);
String selvmln = VMprop.getProperty("selected.vmlongname." + i);
if (selvmln != null) selvm.setVM_LONG_NAME(selvmln);
String selvmid = VMprop.getProperty("selected.vmidseq." + i);
if (selvmid != null) selvm.setVM_IDSEQ(selvmid);
String selvmcondr = VMprop.getProperty("selected.vmcondr." + i);
if (selvmcondr != null) selvm.setVM_CONDR_IDSEQ(selvmcondr);
// add teh selected vm to the vm data
vmdata.setSelectVM(selvm);
}
// add the beans to data object
vmdata.setVMBean(vm);
logger.info(
i
+ " Validating VM for "
+ vm.getVM_LONG_NAME()
+ " : desc : "
+ vm.getVM_PREFERRED_DEFINITION()
+ " conlist "
+ vm.getVM_CONCEPT_LIST().size());
// do the search;
VMAction vmact = new VMAction();
vmact.validateVMData(vmdata); // doChangeVM(vmdata);
}
}
varCon.closeConnection(); // close the connection
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
