Implementing AllergyIntollerance and Substance resources

sql/create_ALLERGYINTOLERANCE_table.sql

@@ -0,0 +1,11 @@
+CREATE TABLE `HealthPort`.`ALLERGYINTOLERANCE` (
+  `ID` VARCHAR(255) NOT NULL,
+  `DISPLAY` TEXT NULL,
+  `SUBSTANCE` VARCHAR(255) NULL,
+  `SUBJECT` TEXT NULL,
+  `SENSITIVITY_TYPE` TEXT NULL,
+  `RECORDED_DATE` DATE NULL,
+  `REACTION` TEXT NULL,
+  `CRITICALITY` TEXT NULL,
+  `STATUS` TEXT NULL,
+  PRIMARY KEY (`ID`));

sql/create_SUBSTANCE_table.sql

@@ -0,0 +1,10 @@
+CREATE TABLE `HealthPort`.`SUBSTANCE` (
+  `ID` VARCHAR(255) NOT NULL,
+  `NAME` TEXT NULL,
+  `TYPE_SYSTEM` TEXT NULL,
+  `TYPE_CODE` TEXT NULL,
+  `TYPE_DISPLAY` TEXT NULL,
+  `EXTENSION_SYSTEM` TEXT NULL,
+  `EXTENSION_CODE` TEXT NULL,
+  `EXTENSION_DISPLAY` TEXT NULL,
+  PRIMARY KEY (`ID`));

src/edu/gatech/i3l/HealthPort/AllergyIntoleranceSerializable.java

@@ -0,0 +1,36 @@
+package edu.gatech.i3l.HealthPort;
+
+import java.io.Serializable;
+
+/**
+ * Bean for AllergyIntolerance data.
+ * @author Eric Wallace <ewall@gatech.edu>
+ */
+public class AllergyIntoleranceSerializable implements Serializable {
+	private static final long serialVersionUID = 1L;
+
+    public String ID;
+    public String DISPLAY;
+    public String SUBSTANCE;
+    public String SUBJECT;
+    public String SENSITIVITY_TYPE;
+    public java.util.Date RECORDED_DATE;
+    public String REACTION;
+    public String CRITICALITY;
+    public String STATUS;
+
+    public AllergyIntoleranceSerializable() {};
+
+    public AllergyIntoleranceSerializable(String id, String display, String substId, String subj,
+    		String sensitivity, java.util.Date recDate, String reaction, String criticality, String status) {
+    	this.ID = id;
+    	this.DISPLAY = display;
+    	this.SUBSTANCE = substId;
+    	this.SUBJECT = subj;
+    	this.SENSITIVITY_TYPE = sensitivity;
+    	this.RECORDED_DATE = recDate;
+    	this.REACTION = reaction;
+    	this.CRITICALITY = criticality;
+    	this.STATUS = status;
+    }
+}

src/edu/gatech/i3l/HealthPort/HealthPortInfo.java

@@ -24,26 +24,36 @@
 
 import org.apache.commons.lang3.StringEscapeUtils;
 
+import ca.uhn.fhir.model.api.ExtensionDt;
 import ca.uhn.fhir.model.api.IResource;
 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.NarrativeDt;
 import ca.uhn.fhir.model.dstu.composite.QuantityDt;
 import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
+import ca.uhn.fhir.model.dstu.resource.AdverseReaction;
+import ca.uhn.fhir.model.dstu.resource.AdverseReaction.Symptom;
+import ca.uhn.fhir.model.dstu.resource.AllergyIntolerance;
 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.MedicationPrescription.Dispense;
 import ca.uhn.fhir.model.dstu.resource.MedicationPrescription.DosageInstruction;
+import ca.uhn.fhir.model.dstu.resource.Substance;
 import ca.uhn.fhir.model.dstu.valueset.ConditionStatusEnum;
+import ca.uhn.fhir.model.dstu.valueset.CriticalityEnum;
 import ca.uhn.fhir.model.dstu.valueset.MedicationPrescriptionStatusEnum;
 import ca.uhn.fhir.model.dstu.valueset.NarrativeStatusEnum;
 import ca.uhn.fhir.model.dstu.valueset.ObservationReliabilityEnum;
 import ca.uhn.fhir.model.dstu.valueset.ObservationStatusEnum;
+import ca.uhn.fhir.model.dstu.valueset.SensitivityStatusEnum;
+import ca.uhn.fhir.model.dstu.valueset.SensitivityTypeEnum;
 import ca.uhn.fhir.model.primitive.DateDt;
 import ca.uhn.fhir.model.primitive.DateTimeDt;
 import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.StringDt;
 
 /**
  * @author Myung Choi Constructor requires UserID. - Connects to SQL database to
@@ -64,6 +74,8 @@ public class HealthPortInfo {
 	public static String OBSERVATION = "OBSERVATION";
 	public static String CONDITION = "CONDITIONS";
 	public static String MEDICATIONPRESCRIPTION = "MEDICATIONPRESCRIPTION";
+	public static String ALLERGYINTOLERANCE = "ALLERGYINTOLERANCE";
+	public static String SUBSTANCE = "SUBSTANCE";
 
 	private DataSource dataSource;
 
@@ -202,6 +214,39 @@ public List<String> getResourceIdsByCodeSystem(String tableName,
 		return retVal;
 	}
 
+	public List<String> getResourceIdsBySubstance (String tableName, String substanceId) {
+		List<String> retVal = new ArrayList<String>();
+
+		Connection connection = null;
+		Statement statement = null;
+
+		String SQL_STATEMENT = "SELECT ID FROM " + tableName
+				+ " WHERE SUBSTANCE = 'Substance/" + substanceId + "'";
+
+		System.out.println ("HealthPortInfo: getResourceIdsBySubstance: "+tableName+" for Substance "+substanceId);
+		connection = getConnection();
+		try {
+			statement = connection.createStatement();
+			ResultSet rs = statement.executeQuery(SQL_STATEMENT);
+
+			while (rs.next()) {
+				retVal.add(rs.getString("ID"));
+			}
+		} catch (SQLException e) {
+			e.printStackTrace();
+		} finally {
+			try {
+				connection.close();
+			} catch (SQLException e) {
+				e.printStackTrace(); // TODO Auto-generated catch block
+			}
+		}
+
+		System.out.println ("HealthPortInfo: getResourceIdsBySubstance: Done");
+
+		return retVal;
+	}
+
 	public List<String> getAllResourceIds(String tableName) {
 		List<String> retVal = new ArrayList<String>();
 
@@ -349,7 +394,54 @@ public static void storeResource(String tableName, Object obj0)
 				pstmt.executeUpdate();
 				pstmt.clearParameters();
 				pstmt.close();
+			} else if (tableName.equals(ALLERGYINTOLERANCE)) {
+				AllergyIntoleranceSerializable obj = (AllergyIntoleranceSerializable) obj0;
+				SQL_STATEMENT = "REPLACE INTO " + tableName
+						+ " (ID, DISPLAY, SUBSTANCE, SUBJECT, SENSITIVITY_TYPE,"
+						+ " RECORDED_DATE, REACTION, CRITICALITY, STATUS) VALUES"
+						+ " (?, ?, ?, ?, ?, ?, ?, ?, ?)";
+				PreparedStatement pstmt = connection.prepareStatement(SQL_STATEMENT);
+
+				// set input parameters
+				pstmt.setString(1, obj.ID);
+				pstmt.setString(2, obj.DISPLAY);
+				pstmt.setString(3, obj.SUBSTANCE);
+				pstmt.setString(4, "Patient/" + obj.SUBJECT);
+				pstmt.setString(5, obj.SENSITIVITY_TYPE);
+				if (obj.RECORDED_DATE != null) {
+					Timestamp ts = new Timestamp(obj.RECORDED_DATE.getTime());
+					pstmt.setTimestamp(6, ts);
+				} else {
+					pstmt.setTimestamp(6, null);
+				}
+				pstmt.setString(7, obj.REACTION);
+				pstmt.setString(8, obj.CRITICALITY);
+				pstmt.setString(9, obj.STATUS);
+
+				pstmt.executeUpdate();
+				pstmt.clearParameters();
+				pstmt.close();
+			} else if (tableName.equals(SUBSTANCE)) {
+				SubstanceSerializable obj = (SubstanceSerializable) obj0;
+				SQL_STATEMENT = "REPLACE INTO " + tableName
+						+ " (ID, NAME, TYPE_SYSTEM, TYPE_CODE, TYPE_DISPLAY,"
+						+ " EXTENSION_SYSTEM, EXTENSION_CODE, EXTENSION_DISPLAY) VALUES"
+						+ " (?, ?, ?, ?, ?, ?, ?, ?)";
+				PreparedStatement pstmt = connection.prepareStatement(SQL_STATEMENT);
 
+				// set input parameters
+				pstmt.setString(1, obj.ID);
+				pstmt.setString(2, obj.NAME);
+				pstmt.setString(3, obj.TYPE_SYSTEM);
+				pstmt.setString(4, obj.TYPE_CODE);
+				pstmt.setString(5, obj.TYPE_DISPLAY);
+				pstmt.setString(6, obj.EXTENSION_SYSTEM);
+				pstmt.setString(7, obj.EXTENSION_CODE);
+				pstmt.setString(8, obj.EXTENSION_DISPLAY);
+
+				pstmt.executeUpdate();
+				pstmt.clearParameters();
+				pstmt.close();
 			}
 		} catch (NamingException | SQLException e) {
 			e.printStackTrace();
@@ -703,6 +795,118 @@ else if (textStatus.equalsIgnoreCase("EXTENSIONS"))
 										NarrativeStatusEnum.EXTENSIONS);
 						}
 						retVal.add(medicationPrescript);
+					} else if (tableName.equals(ALLERGYINTOLERANCE)) {
+						String id = rs.getString("ID");
+						String display = rs.getString("DISPLAY");
+						String substId = rs.getString("SUBSTANCE");
+						String subject = rs.getString("SUBJECT");
+						String sensitivity = rs.getString("SENSITIVITY_TYPE");
+						Timestamp rdateTS = rs.getTimestamp("RECORDED_DATE");
+						String reactionText = rs.getString("REACTION");
+						String criticality = rs.getString("CRITICALITY");
+						String status = rs.getString("STATUS");
+
+						AllergyIntolerance allergy = new AllergyIntolerance();
+
+						// set ID
+						allergy.setId(id);
+
+						// set Text
+						NarrativeDt text = new NarrativeDt();
+						text.setDiv(display);
+						allergy.setText(text);
+
+						// set Subject as reference to Patient
+						ResourceReferenceDt subj = new ResourceReferenceDt(subject);
+						allergy.setSubject(subj);
+
+						// set Substance - reference
+						allergy.setSubstance(new ResourceReferenceDt(substId));
+
+						// set Type - valueset http://www.hl7.org/implement/standards/fhir/sensitivitytype.html
+						if (sensitivity.matches("(?i:allergy|drug|immunization)"))
+							allergy.setSensitivityType(SensitivityTypeEnum.ALLERGY);
+						else if (sensitivity.matches("(?i:intolerance|sensitivity"))
+							allergy.setSensitivityType(SensitivityTypeEnum.INTOLERANCE);
+						else
+							allergy.setSensitivityType(SensitivityTypeEnum.UNKNOWN);
+
+						// set Recoded Date
+						java.util.Date rDate = null;
+						if (rdateTS != null)
+							rDate = new Date(rdateTS.getTime());
+						if (rDate != null)
+							allergy.setRecordedDate(new DateTimeDt(rDate));
+
+						// set Reaction - resource AdverseReaction.symptom
+						AdverseReaction reactionObj = new AdverseReaction();
+						reactionObj.setSubject(subj);
+						Symptom symptom = new Symptom();
+						CodeableConceptDt sympCode = new CodeableConceptDt();
+						sympCode.setText(reactionText); // not enough info to fill out code
+						symptom.setCode(sympCode);
+						ArrayList<Symptom> sympList = new ArrayList<Symptom>();
+						sympList.add(symptom);
+						reactionObj.setSymptom(sympList);					
+
+						// set Criticality - valueset http://www.hl7.org/implement/standards/fhir/criticality.html
+						if (criticality.matches("(?i:mild|low)"))
+								allergy.setCriticality(CriticalityEnum.LOW);
+						else if (criticality.matches("(?i:moderate|medium)"))
+								allergy.setCriticality(CriticalityEnum.MEDIUM);
+						else if (criticality.matches("(?i:severe|high)"))
+								allergy.setCriticality(CriticalityEnum.HIGH);
+						else if (criticality.matches("(?i:critical|fatal)"))
+								allergy.setCriticality(CriticalityEnum.FATAL);
+
+						// set Status - valueset http://www.hl7.org/implement/standards/fhir/sensitivitystatus.html
+						if (status.matches("(?i:suspected)"))
+							allergy.setStatus(SensitivityStatusEnum.SUSPECTED);
+						else if (status.matches("(?i:confirmed)"))
+							allergy.setStatus(SensitivityStatusEnum.CONFIRMED);
+						else if (status.matches("(?i:refuted)"))
+							allergy.setStatus(SensitivityStatusEnum.REFUTED);
+						else if (status.matches("(?i:resolved)"))
+							allergy.setStatus(SensitivityStatusEnum.RESOLVED);
+
+						retVal.add(allergy);
+					} else if (tableName.equals(SUBSTANCE)) {
+						String id = rs.getString("ID");
+						String name = rs.getString("NAME");
+						String typeSystem = rs.getString("TYPE_SYSTEM");
+						String typeCode = rs.getString("TYPE_CODE");
+						String typeDisp = rs.getString("TYPE_DISPLAY");
+						String extSystem = rs.getString("EXTENSION_SYSTEM");
+						String extCode = rs.getString("EXTENSION_CODE");
+						String extDisp = rs.getString("EXTENSION_DISPLAY");
+
+						Substance subst = new Substance();
+
+						// set ID
+						subst.setId(id);
+
+						// set Name
+						name = StringEscapeUtils.escapeHtml4(name);
+						subst.setDescription(name);
+
+						// set Type
+						//subst.setType(SubstanceTypeEnum.VALUESET_BINDER.fromCodeString(typeCode, typeSystem));
+						CodingDt typeCoding = new CodingDt();
+						typeCoding.setValueSet(new ResourceReferenceDt("http://hl7.org/fhir/vs/substance-type"));
+						typeCoding.setSystem(typeSystem);
+						typeCoding.setCode(typeCode);
+						typeCoding.setDisplay(typeDisp);
+						ArrayList<CodingDt> codingList = new ArrayList<CodingDt>();
+						codingList.add(typeCoding);
+						subst.getType().setCoding(codingList);
+
+						// add Extension
+						if (!extSystem.equals("") && !extCode.equals("")) {
+							ExtensionDt ext = new ExtensionDt(false, extSystem, new StringDt(extCode));
+							subst.addUndeclaredExtension(ext);
+						}
+
+						retVal.add(subst);
 					}
 				}
 			}

src/edu/gatech/i3l/HealthPort/RestfulServlet.java

@@ -9,10 +9,12 @@
 import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.RestfulServer;
+import edu.gatech.i3l.HealthPort.providers.AllergyIntoleranceResourceProvider;
 import edu.gatech.i3l.HealthPort.providers.ConditionResourceProvider;
 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.SubstanceResourceProvider;
 
 import org.slf4j.LoggerFactory;
 
@@ -63,6 +65,8 @@ protected void initialize() throws ServletException {
 		resourceProviders.add(new ObservationResourceProvider());
 		resourceProviders.add(new ConditionResourceProvider());
 		resourceProviders.add(new MedicationPrescrResource());
+		resourceProviders.add(new AllergyIntoleranceResourceProvider());
+		resourceProviders.add(new SubstanceResourceProvider());
 		setResourceProviders(resourceProviders);
 
 //		/*

src/edu/gatech/i3l/HealthPort/SubstanceSerializable.java

@@ -0,0 +1,35 @@
+package edu.gatech.i3l.HealthPort;
+
+import java.io.Serializable;
+
+/**
+ * Bean for Substance data.
+ * @author Eric Wallace <ewall@gatech.edu>
+ */
+public class SubstanceSerializable implements Serializable {
+	private static final long serialVersionUID = 1L;
+
+	public String ID;
+	public String NAME;
+	public String TYPE_SYSTEM;
+	public String TYPE_CODE;
+	public String TYPE_DISPLAY;
+	public String EXTENSION_SYSTEM;
+	public String EXTENSION_CODE;
+	public String EXTENSION_DISPLAY;
+
+	public SubstanceSerializable() {};
+
+	public SubstanceSerializable(String id, String name,
+			String typeSystem, String typeCode, String typeDisp,
+			String extSystem, String extCode, String extDisp) {
+		this.ID = id;
+		this.NAME = name;
+		this.TYPE_SYSTEM = typeSystem;
+		this.TYPE_CODE = typeCode;
+		this.TYPE_DISPLAY = typeDisp;
+		this.EXTENSION_SYSTEM = extSystem;
+		this.EXTENSION_CODE = extCode;
+		this.EXTENSION_DISPLAY = extDisp;
+	}
+}

src/edu/gatech/i3l/HealthPort/UpdateFHIRdB.java

@@ -167,6 +167,10 @@ protected void doGet(HttpServletRequest request,
 					e.printStackTrace();
 				}
 			}
+		} else if (res.equalsIgnoreCase(HealthPortInfo.ALLERGYINTOLERANCE)) {
+			// only ExactDataPort implemented at this time
+			syntheticEHRPort.getAllergyIntolerances();
+			syntheticCancerPort.getAllergyIntolerances();
 		}
 	}