Merge pull request #20 from monikadrajer/master

Improved performance by multi threading
onc-healthit · Nov 28, 2017 · 97e0fce · 97e0fce
2 parents 5f3ef1f + bc6e22c
commit 97e0fce
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Showing 46 changed files with 823 additions and 219 deletions.
diff --git a/pom.xml b/pom.xml
@@ -30,6 +30,32 @@
 			<artifactId>apache-log4j-extras</artifactId>
 			<version>1.2.17</version>
 		</dependency>
+
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-context</artifactId>
+			<version>4.2.4.RELEASE</version>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.data</groupId>
+			<artifactId>spring-data-jpa</artifactId>
+			<version>1.9.2.RELEASE</version>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-webmvc</artifactId>
+			<version>4.2.4.RELEASE</version>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-web</artifactId>
+			<version>4.2.4.RELEASE</version>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-oxm</artifactId>
+			<version>4.2.4.RELEASE</version>
+		</dependency>
 	</dependencies>
 	<build>
 		<plugins>

diff --git a/src/main/java/org/sitenv/ccdaparsing/model/CCDAAllergy.java b/src/main/java/org/sitenv/ccdaparsing/model/CCDAAllergy.java
@@ -1,6 +1,7 @@
 package org.sitenv.ccdaparsing.model;
 
 import java.util.ArrayList;
+import java.util.List;
 
 public class CCDAAllergy extends CCDAXmlSnippet {
 
@@ -9,6 +10,7 @@ public class CCDAAllergy extends CCDAXmlSnippet {
 	private CCDACode                 		sectionCode;
 	private ArrayList<CCDAAllergyConcern>	allergyConcern;
 	private ArrayList<String> referenceLinks;
+	private List<CCDAID> idList;
 
 	public boolean isSectionNullFlavourWithNI() {
 		return isSectionNullFlavourWithNI;
@@ -54,6 +56,14 @@ public void setReferenceLinks(ArrayList<String> referenceLinks) {
 		this.referenceLinks = referenceLinks;
 	}
 
+	public List<CCDAID> getIdList() {
+		return idList;
+	}
+
+	public void setIdList(List<CCDAID> idList) {
+		this.idList = idList;
+	}
+
 	public CCDAAllergy()
 	{
 

diff --git a/src/main/java/org/sitenv/ccdaparsing/model/CCDAEncounter.java b/src/main/java/org/sitenv/ccdaparsing/model/CCDAEncounter.java
@@ -1,6 +1,7 @@
 package org.sitenv.ccdaparsing.model;
 
 import java.util.ArrayList;
+import java.util.List;
 
 public class CCDAEncounter extends CCDAXmlSnippet {
 
@@ -9,6 +10,7 @@ public class CCDAEncounter extends CCDAXmlSnippet {
 	private CCDACode  sectionCode;
 	private ArrayList<CCDAEncounterActivity> encActivities;
 	private ArrayList<String> referenceLinks;
+	private List<CCDAID> idLIst;
 
 	public boolean isSectionNullFlavourWithNI() {
 		return isSectionNullFlavourWithNI;
@@ -53,6 +55,14 @@ public ArrayList<String> getReferenceLinks() {
 	public void setReferenceLinks(ArrayList<String> referenceLinks) {
 		this.referenceLinks = referenceLinks;
 	}
+
+	public List<CCDAID> getIdLIst() {
+		return idLIst;
+	}
+
+	public void setIdLIst(List<CCDAID> idLIst) {
+		this.idLIst = idLIst;
+	}
 
 	@Override
 	public int hashCode() {

diff --git a/src/main/java/org/sitenv/ccdaparsing/model/CCDAImmunization.java b/src/main/java/org/sitenv/ccdaparsing/model/CCDAImmunization.java
@@ -1,6 +1,7 @@
 package org.sitenv.ccdaparsing.model;
 
 import java.util.ArrayList;
+import java.util.List;
 
 public class CCDAImmunization extends CCDAXmlSnippet {
 
@@ -9,6 +10,7 @@ public class CCDAImmunization extends CCDAXmlSnippet {
 	private CCDACode                 			sectionCode;
 	private ArrayList<CCDAImmunizationActivity> immActivity;
 	private ArrayList<String> referenceLinks;
+	private List<CCDAID> idList;
 
 	public boolean isSectionNullFlavourWithNI() {
 		return isSectionNullFlavourWithNI;
@@ -55,6 +57,14 @@ public ArrayList<String> getReferenceLinks() {
 	public void setReferenceLinks(ArrayList<String> referenceLinks) {
 		this.referenceLinks = referenceLinks;
 	}
+
+	public List<CCDAID> getIdList() {
+		return idList;
+	}
+
+	public void setIdList(List<CCDAID> idList) {
+		this.idList = idList;
+	}
 
 	public CCDAImmunization() 
 	{

diff --git a/src/main/java/org/sitenv/ccdaparsing/model/CCDALabResult.java b/src/main/java/org/sitenv/ccdaparsing/model/CCDALabResult.java
@@ -1,6 +1,7 @@
 package org.sitenv.ccdaparsing.model;
 
 import java.util.ArrayList;
+import java.util.List;
 
 public class CCDALabResult extends CCDAXmlSnippet{
 
@@ -10,6 +11,7 @@ public class CCDALabResult extends CCDAXmlSnippet{
 	private Boolean						isLabTestInsteadOfResult;
 	private ArrayList<String> referenceLinks;
 	private boolean isSectionNullFlavourWithNI;
+	private List<CCDAID> idList = new ArrayList<>();
 
 	public CCDALabResult()
 	{
@@ -71,6 +73,14 @@ public boolean isSectionNullFlavourWithNI() {
 	public void setSectionNullFlavourWithNI(boolean isSectionNullFlavourWithNI) {
 		this.isSectionNullFlavourWithNI = isSectionNullFlavourWithNI;
 	}
+
+	public List<CCDAID> getIdList() {
+		return idList;
+	}
+
+	public void setIdList(List<CCDAID> idList) {
+		this.idList = idList;
+	}
 
 	@Override
 	public int hashCode() {

diff --git a/src/main/java/org/sitenv/ccdaparsing/model/CCDAMedication.java b/src/main/java/org/sitenv/ccdaparsing/model/CCDAMedication.java
@@ -1,6 +1,7 @@
 package org.sitenv.ccdaparsing.model;
 
 import java.util.ArrayList;
+import java.util.List;
 
 public class CCDAMedication extends CCDAXmlSnippet{
 
@@ -9,6 +10,7 @@ public class CCDAMedication extends CCDAXmlSnippet{
 	private CCDACode                 			sectionCode;
 	private ArrayList<CCDAMedicationActivity>  	medActivities;
 	private ArrayList<String> referenceLinks;
+	private List<CCDAID> idList;
 
 	public boolean isSectionNullFlavourWithNI() {
 		return isSectionNullFlavourWithNI;
@@ -58,6 +60,14 @@ public ArrayList<CCDAMedicationActivity> getMedActivities() {
 	public void setMedActivities(ArrayList<CCDAMedicationActivity> medActivities) {
 		this.medActivities = medActivities;
 	}
+
+	public List<CCDAID> getIdList() {
+		return idList;
+	}
+
+	public void setIdList(List<CCDAID> idList) {
+		this.idList = idList;
+	}
 
 	@Override
 	public int hashCode() {

diff --git a/src/main/java/org/sitenv/ccdaparsing/model/CCDAPOT.java b/src/main/java/org/sitenv/ccdaparsing/model/CCDAPOT.java
@@ -1,6 +1,7 @@
 package org.sitenv.ccdaparsing.model;
 
 import java.util.ArrayList;
+import java.util.List;
 
 public class CCDAPOT extends CCDAXmlSnippet{
 
@@ -12,6 +13,7 @@ public class CCDAPOT extends CCDAXmlSnippet{
 	private ArrayList<CCDAProcActProc> plannedProcedure; 
 	private ArrayList<CCDAMedicationActivity> plannedMedicationActivity; 
 	private ArrayList<CCDAEncounterActivity> plannedEncounter;
+	private List<CCDAID> idList;
 
 
 	public boolean isSectionNullFlavourWithNI() {
@@ -66,6 +68,14 @@ public void setPlannedEncounter(
 			ArrayList<CCDAEncounterActivity> plannedEncounter) {
 		this.plannedEncounter = plannedEncounter;
 	}
+	public List<CCDAID> getIdList() {
+		return idList;
+	}
+
+	public void setIdList(List<CCDAID> idList) {
+		this.idList = idList;
+	}
+
 	@Override
 	public int hashCode() {
 		final int prime = 31;

diff --git a/src/main/java/org/sitenv/ccdaparsing/model/CCDAProblem.java b/src/main/java/org/sitenv/ccdaparsing/model/CCDAProblem.java
@@ -1,6 +1,7 @@
 package org.sitenv.ccdaparsing.model;
 
 import java.util.ArrayList;
+import java.util.List;
 
 public class CCDAProblem extends CCDAXmlSnippet{
 
@@ -9,6 +10,7 @@ public class CCDAProblem extends CCDAXmlSnippet{
 	private CCDACode                 		sectionCode;
 	private ArrayList<CCDAProblemConcern>  	problemConcerns;
 	private ArrayList<String> referenceLinks;
+	private List<CCDAID> idList;
 
 	public boolean isSectionNullFlavourWithNI() {
 		return isSectionNullFlavourWithNI;
@@ -53,6 +55,14 @@ public ArrayList<String> getReferenceLinks() {
 	public void setReferenceLinks(ArrayList<String> referenceLinks) {
 		this.referenceLinks = referenceLinks;
 	}
+
+	public List<CCDAID> getIdList() {
+		return idList;
+	}
+
+	public void setIdList(List<CCDAID> idList) {
+		this.idList = idList;
+	}
 
 	public CCDAProblem()
 	{

diff --git a/src/main/java/org/sitenv/ccdaparsing/model/CCDAProcedure.java b/src/main/java/org/sitenv/ccdaparsing/model/CCDAProcedure.java
@@ -1,6 +1,7 @@
 package org.sitenv.ccdaparsing.model;
 
 import java.util.ArrayList;
+import java.util.List;
 
 public class CCDAProcedure extends CCDAXmlSnippet{
 
@@ -9,6 +10,7 @@ public class CCDAProcedure extends CCDAXmlSnippet{
 	private CCDACode                 		sectionCode;
 	private ArrayList<CCDAProcActProc>		procActsProcs;
 	private ArrayList<String> referenceLinks;
+	private List<CCDAID> idList;
 
 
 
@@ -60,6 +62,14 @@ public ArrayList<String> getReferenceLinks() {
 	public void setReferenceLinks(ArrayList<String> referenceLinks) {
 		this.referenceLinks = referenceLinks;
 	}
+
+	public List<CCDAID> getIdList() {
+		return idList;
+	}
+
+	public void setIdList(List<CCDAID> idList) {
+		this.idList = idList;
+	}
 
 	@Override
 	public int hashCode() {

diff --git a/src/main/java/org/sitenv/ccdaparsing/model/CCDASocialHistory.java b/src/main/java/org/sitenv/ccdaparsing/model/CCDASocialHistory.java
@@ -1,6 +1,7 @@
 package org.sitenv.ccdaparsing.model;
 
 import java.util.ArrayList;
+import java.util.List;
 
 public class CCDASocialHistory extends CCDAXmlSnippet{
 
@@ -11,6 +12,7 @@ public class CCDASocialHistory extends CCDAXmlSnippet{
 	private ArrayList<CCDATobaccoUse>			tobaccoUse;
 	private CCDASocialHistoryGenderObs          socialHistoryGenderObs;
 	private ArrayList<String> referenceLinks;
+	private List<CCDAID> idList;
 
 	public boolean isSectionNullFlavourWithNI() {
 		return isSectionNullFlavourWithNI;
@@ -76,6 +78,14 @@ public CCDASocialHistoryGenderObs getSocialHistoryGenderObs() {
 	public void setSocialHistoryGenderObs(CCDASocialHistoryGenderObs socialHistoryGenderObs) {
 		this.socialHistoryGenderObs = socialHistoryGenderObs;
 	}
+
+	public List<CCDAID> getIdList() {
+		return idList;
+	}
+
+	public void setIdList(List<CCDAID> idList) {
+		this.idList = idList;
+	}
 
 	@Override
 	public int hashCode() {

diff --git a/src/main/java/org/sitenv/ccdaparsing/model/CCDAVitalSigns.java b/src/main/java/org/sitenv/ccdaparsing/model/CCDAVitalSigns.java
@@ -1,6 +1,7 @@
 package org.sitenv.ccdaparsing.model;
 
 import java.util.ArrayList;
+import java.util.List;
 
 public class CCDAVitalSigns extends CCDAXmlSnippet{
 
@@ -9,6 +10,7 @@ public class CCDAVitalSigns extends CCDAXmlSnippet{
 	private CCDACode					sectionCode;
 	private ArrayList<CCDAVitalOrg>		vitalsOrg;
 	private ArrayList<String> referenceLinks;
+	List<CCDAID> idList;
 
 	public boolean isSectionNullFlavourWithNI() {
 		return isSectionNullFlavourWithNI;
@@ -53,6 +55,14 @@ public ArrayList<String> getReferenceLinks() {
 	public void setReferenceLinks(ArrayList<String> referenceLinks) {
 		this.referenceLinks = referenceLinks;
 	}
+
+	public List<CCDAID> getIdList() {
+		return idList;
+	}
+
+	public void setIdList(List<CCDAID> idList) {
+		this.idList = idList;
+	}
 
 	public CCDAVitalSigns()
 	{

diff --git a/src/main/java/org/sitenv/ccdaparsing/processing/CareTeamMemberProcessor.java b/src/main/java/org/sitenv/ccdaparsing/processing/CareTeamMemberProcessor.java
@@ -1,24 +1,36 @@
 package org.sitenv.ccdaparsing.processing;
 
 import java.util.ArrayList;
+import java.util.concurrent.Future;
 
 import javax.xml.transform.TransformerException;
 import javax.xml.xpath.XPath;
 import javax.xml.xpath.XPathConstants;
 import javax.xml.xpath.XPathExpressionException;
 
+import org.apache.log4j.Logger;
 import org.sitenv.ccdaparsing.model.CCDACareTeamMember;
 import org.sitenv.ccdaparsing.model.CCDAParticipant;
 import org.sitenv.ccdaparsing.util.ApplicationConstants;
 import org.sitenv.ccdaparsing.util.ApplicationUtil;
+import org.springframework.scheduling.annotation.Async;
+import org.springframework.scheduling.annotation.AsyncResult;
+import org.springframework.stereotype.Service;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.w3c.dom.NodeList;
 
+@Service
 public class CareTeamMemberProcessor {
 
-	public static CCDACareTeamMember retrieveCTMDetails(XPath xPath , Document doc) throws XPathExpressionException,TransformerException
+	private static final Logger logger = Logger.getLogger(CareTeamMemberProcessor.class);
+
+	@Async()
+	public Future<CCDACareTeamMember> retrieveCTMDetails(XPath xPath , Document doc) throws XPathExpressionException,TransformerException
 	{
+		long startTime = System.currentTimeMillis();
+    	logger.info("care team members parsing Start time:"+ startTime);
+
 		NodeList performerNodeList = (NodeList) xPath.compile(ApplicationConstants.CTM_EXPRESSION).evaluate(doc, XPathConstants.NODESET);
 		CCDACareTeamMember careTeamMember = new CCDACareTeamMember();
 		ArrayList<CCDAParticipant> participantList = new ArrayList<>();
@@ -39,11 +51,12 @@ public static CCDACareTeamMember retrieveCTMDetails(XPath xPath , Document doc)
 			participantList.add(participant);
 		}
 		careTeamMember.setMembers(participantList);
+		logger.info("care team members parsing End time:"+ (System.currentTimeMillis() - startTime));
 
-		return careTeamMember;
+		return new AsyncResult<CCDACareTeamMember>(careTeamMember);
 	}
 
-	public static void readName(Element nameElement,CCDAParticipant participant,XPath xPath) throws XPathExpressionException
+	private void readName(Element nameElement,CCDAParticipant participant,XPath xPath) throws XPathExpressionException
 	{
 		if(nameElement != null)
 		{