/**
* mark the pv if NVP concept
*
* @param curBean evs bean object
* @param session HttpSession object
*/
@SuppressWarnings("unchecked")
public void markNVPConcept(EVS_Bean curBean, HttpSession session) {
Vector<String> vNVP = (Vector) session.getAttribute("NVPConcepts");
if (vNVP == null) vNVP = new Vector<String>();
String conID = curBean.getCONCEPT_IDENTIFIER();
if (conID != null && vNVP.contains(conID)) curBean.setNAME_VALUE_PAIR_IND(1);
else curBean.setNAME_VALUE_PAIR_IND(0);
}
private void getConceptDerivation() {
try {
ConceptForm condata = new ConceptForm();
Vector<EVS_Bean> vCon = new Vector<EVS_Bean>();
EVS_Bean eBean = new EVS_Bean();
eBean.setIDSEQ(
"F37D0428-B66C-6787-E034-0003BA3F9857"); // ("11F45981-C7AC-5747-E044-0003BA0B1A09");
vCon.addElement(eBean);
eBean = new EVS_Bean();
eBean.setIDSEQ("17B24111-A29F-73AC-E044-0003BA0B1A09");
vCon.addElement(eBean);
condata.setConceptList(vCon);
// open teh cadsr connection
Connection conn = varCon.openConnection();
condata.setDBConnection(conn);
ConceptAction conact = new ConceptAction();
String condr = conact.getConDerivation(condata);
varCon.closeConnection(); // close the connection
} catch (SQLException 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);
}
@SuppressWarnings("unchecked")
private void switchCaseEx(int argc) {
switch (argc) /* Switch evaluates an expression (argc) */ {
/* If expression resolves to 1, jump here */
case 1:
System.out.println("Only the command was entered.");
/* break; /* break - cases the execution to jump
out of the 'switch' block. */
/* If expression resolves to 2, jump here */
case 2:
System.out.println("Command plus one parm entered");
// break;
/* If expression resolves to 3, jump here */
case 3:
System.out.println("Command plus two parm entered");
break;
/* Any other value jumps here. */
default:
System.out.println("Command plus %d parms entered\n");
break;
}
// test number combinations
Vector comb = new Vector();
int i = 10;
do {
int j = 1;
do {
int k = i + j;
System.out.println(i + " + " + j + " = " + k);
if (comb.contains(k)) System.out.println("Already exists : " + k);
comb.addElement(k);
j += 1;
} while (j < 10);
i += 10;
} while (i < 150);
// 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);
}
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();
}
}
/** @param copyBean evs bean object ot copy to */
public EVS_Bean(EVS_Bean copyBean) {
this.setLONG_NAME(copyBean.getLONG_NAME());
this.setCONDR_IDSEQ(copyBean.getCONDR_IDSEQ());
this.setCON_AC_SUBMIT_ACTION(copyBean.getCON_AC_SUBMIT_ACTION());
this.setCONCEPT_NAME(copyBean.getCONCEPT_NAME());
this.setCONTE_IDSEQ(copyBean.getCONTE_IDSEQ());
this.setDISPLAY_ORDER(copyBean.getDISPLAY_ORDER());
this.setPREFERRED_DEFINITION(copyBean.getPREFERRED_DEFINITION());
this.setEVS_CONCEPT_SOURCE(copyBean.getEVS_CONCEPT_SOURCE());
this.setEVS_DATABASE(copyBean.getEVS_DATABASE());
this.setEVS_DEF_SOURCE(copyBean.getEVS_DEF_SOURCE());
this.setEVS_ORIGIN(copyBean.getEVS_ORIGIN());
this.setEVS_SEMANTIC(copyBean.getEVS_SEMANTIC());
this.setID(copyBean.getID());
this.setIDSEQ(copyBean.getIDSEQ());
this.setASL_NAME(copyBean.getASL_NAME());
this.setLEVEL(copyBean.getLEVEL());
this.setDEC_USING(copyBean.getDEC_USING());
this.setCONCEPT_IDENTIFIER(copyBean.getCONCEPT_IDENTIFIER());
this.setNCI_CC_TYPE(copyBean.getNCI_CC_TYPE());
this.setNAME_VALUE_PAIR_IND(copyBean.getNAME_VALUE_PAIR_IND());
this.setNVP_CONCEPT_VALUE(copyBean.getNVP_CONCEPT_VALUE());
}