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Adding Procedures Resource #8

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2867026
Adding Procedures Resource
KFrazer Apr 24, 2015
cb55816
Moving ProcedureResourceProvider to Correct Location
KFrazer Apr 24, 2015
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148 changes: 147 additions & 1 deletion src/edu/gatech/i3l/HealthPort/HealthPortInfo.java
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Expand Up @@ -28,12 +28,14 @@
import ca.uhn.fhir.model.dstu.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu.composite.CodingDt;
import ca.uhn.fhir.model.dstu.composite.ContainedDt;
import ca.uhn.fhir.model.dstu.composite.PeriodDt;
import ca.uhn.fhir.model.dstu.composite.QuantityDt;
import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
import ca.uhn.fhir.model.dstu.resource.Condition;
import ca.uhn.fhir.model.dstu.resource.Medication;
import ca.uhn.fhir.model.dstu.resource.MedicationPrescription;
import ca.uhn.fhir.model.dstu.resource.Observation;
import ca.uhn.fhir.model.dstu.resource.Procedure;
import ca.uhn.fhir.model.dstu.resource.MedicationPrescription.Dispense;
import ca.uhn.fhir.model.dstu.resource.MedicationPrescription.DosageInstruction;
import ca.uhn.fhir.model.dstu.valueset.ConditionStatusEnum;
Expand Down Expand Up @@ -64,6 +66,7 @@ public class HealthPortInfo {
public static String OBSERVATION = "OBSERVATION";
public static String CONDITION = "CONDITIONS";
public static String MEDICATIONPRESCRIPTION = "MEDICATIONPRESCRIPTION";
public static String PROCEDURE = "PROCEDURES";

private DataSource dataSource;

Expand Down Expand Up @@ -643,7 +646,150 @@ else if (textStatus.equalsIgnoreCase("EXTENSIONS"))
NarrativeStatusEnum.EXTENSIONS);
}
retVal.add(medicationPrescript);
}
} else if (tableName.equals(PROCEDURE)) {
String theId = rs.getString("ID");
String patientId = rs.getString("SUBJECT");
String typeUri = rs.getString("TYPEURI");
String typeCode = rs.getString("TYPECODING");
String typeDisp = rs.getString("TYPEDISPLAY");
String indicationUri = rs.getString("INDICATIONURI");
String indicationCode = rs.getString("INDICATIONCODING");
String indicationText = rs.getString("INDICATIONTEXT");
//String performerName = rs.getString("PERFORMER");
String outcome = rs.getString("OUTCOME");
String report = rs.getString("REPORT");
String complicationUri = rs.getString("COMPLICATIONURI");
String complicationCode = rs.getString("COMPLICATIONCODING");
String complicationText = rs.getString("COMPLICATIONTEXT");
String followup = rs.getString("FOLLOWUP");
String notes = rs.getString("NOTES");

Timestamp startDateTS = rs.getTimestamp("STARTDATE");
java.util.Date startDate = null;
if (startDateTS != null) {
startDate = new Date(startDateTS.getTime());
}

Timestamp endDateTS = rs.getTimestamp("ENDDATE");
java.util.Date endDate = null;
if (endDateTS != null) {
endDate = new Date(endDateTS.getTime());
}

Procedure proc = new Procedure();

// Procedure ID
proc.setId(new IdDt(theId));

// Procedure Subject
proc.setSubject(new ResourceReferenceDt(patientId));

// Procedure Type
CodingDt typeCoding = new CodingDt(typeUri, typeCode);
if (typeDisp != null) {
typeCoding.setDisplay(typeDisp);
}

ArrayList<CodingDt> codingList = new ArrayList<CodingDt>();
codingList.add(typeCoding);

CodeableConceptDt typeDt = new CodeableConceptDt();
typeDt.setCoding(codingList);

proc.setType(typeDt);

// Procedure Indication
if ((indicationUri != null && indicationCode != null) || indicationText != null) {
CodeableConceptDt indicationDt = new CodeableConceptDt();

if (indicationUri != null && indicationCode != null) {
CodingDt indicationCoding = new CodingDt(indicationUri, indicationCode);

ArrayList<CodingDt> indicationList = new ArrayList<CodingDt>();
codingList.add(indicationCoding);
indicationDt.setCoding(indicationList);
}

if (indicationText != null) {
indicationDt.setText(indicationText);
}

ArrayList<CodeableConceptDt> indCodeableList = new ArrayList<CodeableConceptDt>();
indCodeableList.add(indicationDt);

proc.setIndication(indCodeableList);
}

// Procedure Performer. We don't have Performer resource yet.
// Just display it.
// if (performerName != null) {
// ResourceReferenceDt performerRefDt = new ResourceReferenceDt();
// performerRefDt.setDisplay(performerName);
// proc.setPerformer(performerRefDt);
// }

// Procedure Date
if (startDate != null) {
PeriodDt period = new PeriodDt();
period.setStart(new DateTimeDt(startDate));

if (endDate != null) {
period.setEnd(new DateTimeDt(endDate));
}
proc.setDate(period);
}

// Procedure Outcome
if (outcome != null) {
proc.setOutcome(outcome);
}

// Procedure Report. We don't have Report resource yet.
// Just display it.
if (report != null) {
ResourceReferenceDt reportRefDt = new ResourceReferenceDt();
reportRefDt.setDisplay(report);

ArrayList<ResourceReferenceDt> referenceList = new ArrayList<ResourceReferenceDt>();
referenceList.add(reportRefDt);

proc.setReport(referenceList);
}

// Procedure Complications
if ((complicationUri != null && complicationCode != null) || complicationText != null) {
CodeableConceptDt complicationDt = new CodeableConceptDt();

if (complicationUri != null && complicationCode != null) {
CodingDt complicationCoding = new CodingDt(complicationUri, complicationCode);

ArrayList<CodingDt> complicationList = new ArrayList<CodingDt>();
codingList.add(complicationCoding);
complicationDt.setCoding(complicationList);
}

if (complicationText != null) {
complicationDt.setText(complicationText);
}

ArrayList<CodeableConceptDt> compCodeableList = new ArrayList<CodeableConceptDt>();
compCodeableList.add(complicationDt);

proc.setComplication(compCodeableList);
}

// Procedure Follow Up
if (followup != null) {
proc.setFollowUp(followup);
}

// Procedure Notes
if (notes != null) {
proc.setNotes(notes);
}

retVal.add(proc);
}
}
}
} catch (NamingException | SQLException e) {
Expand Down
33 changes: 33 additions & 0 deletions src/edu/gatech/i3l/HealthPort/ProcedureSerializable.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
/**
*
*/
package edu.gatech.i3l.HealthPort;

import java.io.Serializable;

/**
* @author kfrazer3
*
*/
public class ProcedureSerializable implements Serializable {
private static final long serialVersionUID = 1L;

public String ID;
public String SUBJECT;
public String TYPEURI;
public String TYPECODING;
public String TYPEDISPLAY;
public String INDICATIONURI;
public String INDICATIONCODING;
public String INDICATIONTEXT;
//public String PERFORMER;
public String OUTCOME;
public String REPORT;
public String COMPLICATIONURI;
public String COMPLICATIONCODING;
public String COMPLICATIONTEXT;
public String FOLLOWUP;
public String NOTES;
public java.util.Date STARTDATE;
public java.util.Date ENDDATE;
}
2 changes: 2 additions & 0 deletions src/edu/gatech/i3l/HealthPort/RestfulServlet.java
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
import edu.gatech.i3l.HealthPort.providers.MedicationPrescrResource;
import edu.gatech.i3l.HealthPort.providers.ObservationResourceProvider;
import edu.gatech.i3l.HealthPort.providers.PatientResourceProvider;
import edu.gatech.i3l.HealthPort.providers.ProcedureResourceProvider;

import org.slf4j.LoggerFactory;

Expand Down Expand Up @@ -63,6 +64,7 @@ protected void initialize() throws ServletException {
resourceProviders.add(new ObservationResourceProvider());
resourceProviders.add(new ConditionResourceProvider());
resourceProviders.add(new MedicationPrescrResource());
resourceProviders.add(new ProcedureResourceProvider());
setResourceProviders(resourceProviders);

// /*
Expand Down
91 changes: 91 additions & 0 deletions src/edu/gatech/i3l/HealthPort/providers/ProcedureResourceProvider.java
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@@ -0,0 +1,91 @@
package edu.gatech.i3l.HealthPort.providers;

import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;

import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu.resource.Procedure;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Read;
import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.IResourceProvider;
import edu.gatech.i3l.HealthPort.HealthPortInfo;

public class ProcedureResourceProvider implements IResourceProvider {
private HealthPortInfo healthPortUser;

// Constructor
public ProcedureResourceProvider() {
healthPortUser = new HealthPortInfo("jdbc/HealthPort");
}

@Override
public Class<? extends IResource> getResourceType() {
return Procedure.class;
}

@Read()
public Procedure getResourceById(@IdParam IdDt theId) {
List<String>Ids = new ArrayList<String>();
Ids.add(theId.getIdPart());

List<IResource> resourceList = null;
try {
resourceList = healthPortUser.getResourceList(HealthPortInfo.PROCEDURE, Ids);
} catch (SQLException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}

if (resourceList == null || resourceList.isEmpty()) return null;
return (Procedure) resourceList.get(0);
}

@Search()
public IBundleProvider getProceduresByPatient(
@RequiredParam(name = Procedure.SP_SUBJECT) ReferenceParam theSubject) {

final InstantDt searchTime = InstantDt.withCurrentTime();
String patientID = theSubject.getIdPart();

final List<String> matchingResourceIds = healthPortUser.getResourceIdsByPatient(HealthPortInfo.PROCEDURE, patientID);

return new IBundleProvider() {

@Override
public int size() {
return matchingResourceIds.size();
}

@Override
public List<IResource> getResources(int theFromIndex, int theToIndex) {
int end = Math.min(theToIndex, matchingResourceIds.size());
// System.out.println("From:"+theFromIndex+" To:"+theToIndex+" Total:"+matchingResourceIds.size());
List<String> idsToReturn = matchingResourceIds.subList(
theFromIndex, end);

List<IResource> retVal = null;
try {
retVal = healthPortUser.getResourceList(HealthPortInfo.PROCEDURE,
idsToReturn);
} catch (SQLException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}

return retVal;
}

@Override
public InstantDt getPublished() {
return searchTime;
}
};
}
}