task/refactor-architecture

pom.xml

@@ -68,5 +68,11 @@
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.projectlombok</groupId>
+			<artifactId>lombok</artifactId>
+			<version>1.18.38</version>
+			<scope>provided</scope>
+		</dependency>
 	</dependencies>
 </project>

src/main/java/org/aktin/dwh/PreferenceKey.java

@@ -1,6 +1,6 @@
 package org.aktin.dwh;
 
-import org.aktin.dwh.optinout.PatientReference;
+import org.aktin.dwh.optinout.model.PatientReference;
 
 /**
  * Preferences keys for the data warehouse

src/main/java/org/aktin/dwh/optinout/model/ErrorType.java

@@ -0,0 +1,9 @@
+package org.aktin.dwh.optinout.model;
+
+// errors that occur during CRUD operations on opt-in data
+public enum ErrorType {
+    STUDY_NOT_FOUND,
+    PATIENT_NOT_FOUND,
+    PATIENT_ALREADY_EXISTS,
+    SIC_ALREADY_EXISTS,
+}

src/main/java/org/aktin/dwh/optinout/model/Participation.java

@@ -0,0 +1,28 @@
+package org.aktin.dwh.optinout.model;
+
+import java.util.Arrays;
+
+public enum Participation {
+	/** Patient specifically wants to participate */
+	OptIn("I"),
+	/** Patient wants to be excluded */
+	OptOut("O");
+
+	/**
+	 * helper functions for (de-)serialization
+	 */
+	private String code;
+
+	Participation(String code) {
+		this.code = code;
+	}
+
+	public String getCode() {
+		return code;
+	}
+
+	public static Participation fromCode(String code) {
+		return Arrays.stream(values()).filter(a -> a.code.equals(code)).findFirst()
+				.orElseThrow(() -> new IllegalArgumentException("Unknown database value: " + code));
+	}
+}

src/main/java/org/aktin/dwh/optinout/PatientEncounter.java → src/main/java/org/aktin/dwh/optinout/model/PatientEncounter.java

@@ -1,10 +1,9 @@
-package org.aktin.dwh.optinout;
+package org.aktin.dwh.optinout.model;
 
 import java.time.Instant;
 
 public interface PatientEncounter {
-    int getEncounterId();
-    int getPatientId();
+    String getPseudonym();
     Instant getStartDate();
     Instant getEndDate();
 }

src/main/java/org/aktin/dwh/optinout/model/PatientEntry.java

@@ -0,0 +1,21 @@
+package org.aktin.dwh.optinout.model;
+
+import java.time.Instant;
+
+public interface PatientEntry {
+	Participation getParticipation();
+	PatientReference getReference();
+	String getIdRoot();
+	String getIdExt();
+	String getSIC();
+	String getUser();
+	Instant getTimestamp();
+	String getComment();
+
+	/**
+	 * Get the i2b2 patient_num field. Only available, if the patient was linked
+	 * to existing data. The link is established automatically and periodically
+	 * @return patient_num from i2b2, or {@code null} if no link is available.
+	 */
+	Integer getI2b2PatientNum();
+}

src/main/java/org/aktin/dwh/optinout/model/PatientEntryData.java

@@ -0,0 +1,22 @@
+package org.aktin.dwh.optinout.model;
+
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+/**
+ * This class serves as input POJO for (batch) patient entry write actions (create, update)
+ */
+
+@Data
+@AllArgsConstructor
+@NoArgsConstructor
+public class PatientEntryData {
+    private String root;
+    private String extension;
+    private String sic;
+    private String comment;
+    private boolean generateSic;
+    private Participation participation;
+    private PatientReference reference;
+}

src/main/java/org/aktin/dwh/optinout/PatientMasterData.java → src/main/java/org/aktin/dwh/optinout/model/PatientMasterData.java

@@ -1,9 +1,9 @@
-package org.aktin.dwh.optinout;
+package org.aktin.dwh.optinout.model;
 
 import java.time.Instant;
 
 public interface PatientMasterData {
-    int getPatientId();
+    String getPseudonym();
     String getSex();
     String getZip();
     Instant getBirthDate();

src/main/java/org/aktin/dwh/optinout/PatientReference.java → src/main/java/org/aktin/dwh/optinout/model/PatientReference.java

@@ -1,23 +1,45 @@
-package org.aktin.dwh.optinout;
+package org.aktin.dwh.optinout.model;
+
+import java.util.Arrays;
 
 public enum PatientReference {
 	/** patient specific id 
 	 * CDA element: /ClinicalDocument/recordTarget/patientRole/id
 	 * hash in i2b2 DB: i2b2crcdata.patient_mapping in column patient_ide [type: character varying(200) 
 	 */
-	Patient,
+	Patient("PAT"),
 	/** visit id, a visit can contain multiple encounters 
 	 * Not used in this project.
 	 */
-	Visit,
+	Visit("VIS"),
 	/** encounter (with a practitioner) 
 	 * CDA element: /ClinicalDocument/componentOf/encompassingEncounter/id[1]
 	 * hash in i2b2 DB: i2b2crcdata.encounter_mapping in column encounter_ide [type: character varying(200) 
 	 */
-	Encounter,
+	Encounter("ENC"),
 	/** billing / accounting number of the hospital, used for financial transactions 
 	 * CDA element: /ClinicalDocument/componentOf/encompassingEncounter/id[2]
 	 * hash in i2b2 DB: i2b2crcdata.observation_fact in column tval_char where concept_cd=AKTIN:Fallkennzeichen [type: character varying(255)]
 	 */
-	Billing
+	Billing("BIL");
+
+
+	/**
+	 * helper functions for (de-)serialization
+	 */
+
+	private final String code;
+
+	PatientReference(String code) {
+		this.code = code;
+	}
+
+	public String getCode() {
+		return code;
+	}
+
+	public static PatientReference fromCode(String code) {
+		return Arrays.stream(values()).filter(a -> a.code.equals(code)).findFirst()
+				.orElseThrow(() -> new IllegalArgumentException("Unknown value: " + code));
+	}
 }

src/main/java/org/aktin/dwh/optinout/SICGeneration.java → src/main/java/org/aktin/dwh/optinout/model/SICGeneration.java

@@ -1,4 +1,4 @@
-package org.aktin.dwh.optinout;
+package org.aktin.dwh.optinout.model;
 
 /**
  * Method of Sic generation