Merge pull request #5 from pcvolkmer/add_ihc_therapy

Add IHC report and Therapies

src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcog.java

@@ -3,15 +3,15 @@ package dev.pcvolkmer.mv64e.mtb;
 import com.fasterxml.jackson.annotation.*;
 
 public class CodingEcog {
-    private PurpleCode code;
+    private EcogCode code;
     private String display;
     private String system;
     private String version;
 
     @JsonProperty("code")
-    public PurpleCode getCode() { return code; }
+    public EcogCode getCode() { return code; }
     @JsonProperty("code")
-    public void setCode(PurpleCode value) { this.code = value; }
+    public void setCode(EcogCode value) { this.code = value; }
 
     @JsonProperty("display")
     public String getDisplay() { return display; }

src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionIcScore.java

@@ -0,0 +1,30 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class CodingProteinExpressionIcScore {
+    private ICScoreCode code;
+    private String display;
+    private String system;
+    private String version;
+
+    @JsonProperty("code")
+    public ICScoreCode getCode() { return code; }
+    @JsonProperty("code")
+    public void setCode(ICScoreCode value) { this.code = value; }
+
+    @JsonProperty("display")
+    public String getDisplay() { return display; }
+    @JsonProperty("display")
+    public void setDisplay(String value) { this.display = value; }
+
+    @JsonProperty("system")
+    public String getSystem() { return system; }
+    @JsonProperty("system")
+    public void setSystem(String value) { this.system = value; }
+
+    @JsonProperty("version")
+    public String getVersion() { return version; }
+    @JsonProperty("version")
+    public void setVersion(String value) { this.version = value; }
+}

src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionResult.java

@@ -0,0 +1,30 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class CodingProteinExpressionResult {
+    private ProteinExpressionResultCode code;
+    private String display;
+    private String system;
+    private String version;
+
+    @JsonProperty("code")
+    public ProteinExpressionResultCode getCode() { return code; }
+    @JsonProperty("code")
+    public void setCode(ProteinExpressionResultCode value) { this.code = value; }
+
+    @JsonProperty("display")
+    public String getDisplay() { return display; }
+    @JsonProperty("display")
+    public void setDisplay(String value) { this.display = value; }
+
+    @JsonProperty("system")
+    public String getSystem() { return system; }
+    @JsonProperty("system")
+    public void setSystem(String value) { this.system = value; }
+
+    @JsonProperty("version")
+    public String getVersion() { return version; }
+    @JsonProperty("version")
+    public void setVersion(String value) { this.version = value; }
+}

src/main/java/dev/pcvolkmer/mv64e/mtb/CodingProteinExpressionTcScore.java

@@ -0,0 +1,30 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class CodingProteinExpressionTcScore {
+    private TcScoreCode code;
+    private String display;
+    private String system;
+    private String version;
+
+    @JsonProperty("code")
+    public TcScoreCode getCode() { return code; }
+    @JsonProperty("code")
+    public void setCode(TcScoreCode value) { this.code = value; }
+
+    @JsonProperty("display")
+    public String getDisplay() { return display; }
+    @JsonProperty("display")
+    public void setDisplay(String value) { this.display = value; }
+
+    @JsonProperty("system")
+    public String getSystem() { return system; }
+    @JsonProperty("system")
+    public void setSystem(String value) { this.system = value; }
+
+    @JsonProperty("version")
+    public String getVersion() { return version; }
+    @JsonProperty("version")
+    public void setVersion(String value) { this.version = value; }
+}

src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecist.java

@@ -3,15 +3,15 @@ package dev.pcvolkmer.mv64e.mtb;
 import com.fasterxml.jackson.annotation.*;
 
 public class CodingRecist {
-    private FluffyCode code;
+    private RecistCode code;
     private String display;
     private String system;
     private String version;
 
     @JsonProperty("code")
-    public FluffyCode getCode() { return code; }
+    public RecistCode getCode() { return code; }
     @JsonProperty("code")
-    public void setCode(FluffyCode value) { this.code = value; }
+    public void setCode(RecistCode value) { this.code = value; }
 
     @JsonProperty("display")
     public String getDisplay() { return display; }

src/main/java/dev/pcvolkmer/mv64e/mtb/EcogCode.java

@@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb;
 import java.io.IOException;
 import com.fasterxml.jackson.annotation.*;
 
-public enum PurpleCode {
+public enum EcogCode {
     CODE_0, CODE_1, CODE_2, CODE_3, CODE_4;
 
     @JsonValue
@@ -19,7 +19,7 @@ public enum PurpleCode {
     }
 
     @JsonCreator
-    public static PurpleCode forValue(String value) throws IOException {
+    public static EcogCode forValue(String value) throws IOException {
         switch (value) {
             case "0":
                 return CODE_0;
@@ -32,6 +32,6 @@ public enum PurpleCode {
             case "4":
                 return CODE_4;
         }
-        throw new IOException("Cannot deserialize PurpleCode");
+        throw new IOException("Cannot deserialize EcogCode");
     }
 }

src/main/java/dev/pcvolkmer/mv64e/mtb/ICScoreCode.java

@@ -0,0 +1,34 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import java.io.IOException;
+import com.fasterxml.jackson.annotation.*;
+
+public enum ICScoreCode {
+    CODE_0, CODE_1, CODE_2, CODE_3;
+
+    @JsonValue
+    public String toValue() {
+        switch (this) {
+            case CODE_0: return "0";
+            case CODE_1: return "1";
+            case CODE_2: return "2";
+            case CODE_3: return "3";
+        }
+        return null;
+    }
+
+    @JsonCreator
+    public static ICScoreCode forValue(String value) throws IOException {
+        switch (value) {
+            case "0":
+                return CODE_0;
+            case "1":
+                return CODE_1;
+            case "2":
+                return CODE_2;
+            case "3":
+                return CODE_3;
+        }
+        throw new IOException("Cannot deserialize ICScoreCode");
+    }
+}

src/main/java/dev/pcvolkmer/mv64e/mtb/IHCReport.java

@@ -0,0 +1,58 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+import java.util.Date;
+import java.util.List;
+
+public class IHCReport {
+    private ExternalId blockId;
+    private Date date;
+    private String id;
+    private ExternalId journalId;
+    private List<MSIMmrResult> msiMmrResults;
+    private Reference patient;
+    private List<ProteinExpressionResult> proteinExpressionResults;
+    private Reference specimen;
+
+    @JsonProperty("blockId")
+    public ExternalId getBlockId() { return blockId; }
+    @JsonProperty("blockId")
+    public void setBlockId(ExternalId value) { this.blockId = value; }
+
+    @JsonProperty("date")
+    @JsonFormat(pattern = "yyyy-MM-dd")
+    public Date getDate() { return date; }
+    @JsonProperty("date")
+    @JsonFormat(pattern = "yyyy-MM-dd")
+    public void setDate(Date value) { this.date = value; }
+
+    @JsonProperty("id")
+    public String getId() { return id; }
+    @JsonProperty("id")
+    public void setId(String value) { this.id = value; }
+
+    @JsonProperty("journalId")
+    public ExternalId getJournalId() { return journalId; }
+    @JsonProperty("journalId")
+    public void setJournalId(ExternalId value) { this.journalId = value; }
+
+    @JsonProperty("msiMmrResults")
+    public List<MSIMmrResult> getMsiMmrResults() { return msiMmrResults; }
+    @JsonProperty("msiMmrResults")
+    public void setMsiMmrResults(List<MSIMmrResult> value) { this.msiMmrResults = value; }
+
+    @JsonProperty("patient")
+    public Reference getPatient() { return patient; }
+    @JsonProperty("patient")
+    public void setPatient(Reference value) { this.patient = value; }
+
+    @JsonProperty("proteinExpressionResults")
+    public List<ProteinExpressionResult> getProteinExpressionResults() { return proteinExpressionResults; }
+    @JsonProperty("proteinExpressionResults")
+    public void setProteinExpressionResults(List<ProteinExpressionResult> value) { this.proteinExpressionResults = value; }
+
+    @JsonProperty("specimen")
+    public Reference getSpecimen() { return specimen; }
+    @JsonProperty("specimen")
+    public void setSpecimen(Reference value) { this.specimen = value; }
+}

src/main/java/dev/pcvolkmer/mv64e/mtb/MSIMmrResult.java

@@ -0,0 +1,48 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class MSIMmrResult {
+    private CodingProteinExpressionIcScore icScore;
+    private String id;
+    private Reference patient;
+    private Coding protein;
+    private CodingProteinExpressionTcScore tcScore;
+    private Long tpsScore;
+    private CodingProteinExpressionResult value;
+
+    @JsonProperty("icScore")
+    public CodingProteinExpressionIcScore getIcScore() { return icScore; }
+    @JsonProperty("icScore")
+    public void setIcScore(CodingProteinExpressionIcScore value) { this.icScore = value; }
+
+    @JsonProperty("id")
+    public String getId() { return id; }
+    @JsonProperty("id")
+    public void setId(String value) { this.id = value; }
+
+    @JsonProperty("patient")
+    public Reference getPatient() { return patient; }
+    @JsonProperty("patient")
+    public void setPatient(Reference value) { this.patient = value; }
+
+    @JsonProperty("protein")
+    public Coding getProtein() { return protein; }
+    @JsonProperty("protein")
+    public void setProtein(Coding value) { this.protein = value; }
+
+    @JsonProperty("tcScore")
+    public CodingProteinExpressionTcScore getTcScore() { return tcScore; }
+    @JsonProperty("tcScore")
+    public void setTcScore(CodingProteinExpressionTcScore value) { this.tcScore = value; }
+
+    @JsonProperty("tpsScore")
+    public Long getTpsScore() { return tpsScore; }
+    @JsonProperty("tpsScore")
+    public void setTpsScore(Long value) { this.tpsScore = value; }
+
+    @JsonProperty("value")
+    public CodingProteinExpressionResult getValue() { return value; }
+    @JsonProperty("value")
+    public void setValue(CodingProteinExpressionResult value) { this.value = value; }
+}

src/main/java/dev/pcvolkmer/mv64e/mtb/MTBMedicationTherapy.java

@@ -5,7 +5,7 @@ import java.util.Date;
 import java.util.List;
 
 public class MTBMedicationTherapy {
-    private String basedOn;
+    private Reference basedOn;
     private String diagnosis;
     private String id;
     private Reference indication;
@@ -19,9 +19,9 @@ public class MTBMedicationTherapy {
     private Long therapyLine;
 
     @JsonProperty("basedOn")
-    public String getBasedOn() { return basedOn; }
+    public Reference getBasedOn() { return basedOn; }
     @JsonProperty("basedOn")
-    public void setBasedOn(String value) { this.basedOn = value; }
+    public void setBasedOn(Reference value) { this.basedOn = value; }
 
     @JsonProperty("diagnosis")
     public String getDiagnosis() { return diagnosis; }

src/main/java/dev/pcvolkmer/mv64e/mtb/Mtb.java

@@ -14,6 +14,7 @@ public class Mtb {
     private List<OncoProdecure> guidelineProcedures;
     private List<MTBMedicationTherapy> guidelineTherapies;
     private List<HistologyReport> histologyReports;
+    private List<IHCReport> ihcReports;
     private List<MolecularTherapy> molecularTherapies;
     private List<SomaticNgsReport> ngsReports;
     private MtbPatient patient;
@@ -22,6 +23,7 @@ public class Mtb {
     private List<Response> responses;
     private List<TumorSpecimen> specimens;
     private List<StudyEnrollmentRecommendation> studyInclusionRequests;
+    private List<Therapy> therapies;
 
     @JsonProperty("carePlans")
     public List<MTBCarePlan> getCarePlans() { return carePlans; }
@@ -73,6 +75,11 @@ public class Mtb {
     @JsonProperty("histologyReports")
     public void setHistologyReports(List<HistologyReport> value) { this.histologyReports = value; }
 
+    @JsonProperty("ihcReports")
+    public List<IHCReport> getIhcReports() { return ihcReports; }
+    @JsonProperty("ihcReports")
+    public void setIhcReports(List<IHCReport> value) { this.ihcReports = value; }
+
     @JsonProperty("molecularTherapies")
     public List<MolecularTherapy> getMolecularTherapies() { return molecularTherapies; }
     @JsonProperty("molecularTherapies")
@@ -112,4 +119,9 @@ public class Mtb {
     public List<StudyEnrollmentRecommendation> getStudyInclusionRequests() { return studyInclusionRequests; }
     @JsonProperty("studyInclusionRequests")
     public void setStudyInclusionRequests(List<StudyEnrollmentRecommendation> value) { this.studyInclusionRequests = value; }
+
+    @JsonProperty("therapies")
+    public List<Therapy> getTherapies() { return therapies; }
+    @JsonProperty("therapies")
+    public void setTherapies(List<Therapy> value) { this.therapies = value; }
 }

src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionResult.java

@@ -0,0 +1,48 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+
+public class ProteinExpressionResult {
+    private CodingProteinExpressionIcScore icScore;
+    private String id;
+    private Reference patient;
+    private Coding protein;
+    private CodingProteinExpressionTcScore tcScore;
+    private Long tpsScore;
+    private CodingProteinExpressionResult value;
+
+    @JsonProperty("icScore")
+    public CodingProteinExpressionIcScore getIcScore() { return icScore; }
+    @JsonProperty("icScore")
+    public void setIcScore(CodingProteinExpressionIcScore value) { this.icScore = value; }
+
+    @JsonProperty("id")
+    public String getId() { return id; }
+    @JsonProperty("id")
+    public void setId(String value) { this.id = value; }
+
+    @JsonProperty("patient")
+    public Reference getPatient() { return patient; }
+    @JsonProperty("patient")
+    public void setPatient(Reference value) { this.patient = value; }
+
+    @JsonProperty("protein")
+    public Coding getProtein() { return protein; }
+    @JsonProperty("protein")
+    public void setProtein(Coding value) { this.protein = value; }
+
+    @JsonProperty("tcScore")
+    public CodingProteinExpressionTcScore getTcScore() { return tcScore; }
+    @JsonProperty("tcScore")
+    public void setTcScore(CodingProteinExpressionTcScore value) { this.tcScore = value; }
+
+    @JsonProperty("tpsScore")
+    public Long getTpsScore() { return tpsScore; }
+    @JsonProperty("tpsScore")
+    public void setTpsScore(Long value) { this.tpsScore = value; }
+
+    @JsonProperty("value")
+    public CodingProteinExpressionResult getValue() { return value; }
+    @JsonProperty("value")
+    public void setValue(CodingProteinExpressionResult value) { this.value = value; }
+}

src/main/java/dev/pcvolkmer/mv64e/mtb/ProteinExpressionResultCode.java

@@ -0,0 +1,40 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import java.io.IOException;
+import com.fasterxml.jackson.annotation.*;
+
+public enum ProteinExpressionResultCode {
+    EXP, NOT_EXP, CODE_1_PLUS, CODE_2_PLUS, CODE_3_PLUS, UNKNOWN;
+
+    @JsonValue
+    public String toValue() {
+        switch (this) {
+            case EXP: return "exp";
+            case NOT_EXP: return "not-exp";
+            case CODE_1_PLUS: return "1+";
+            case CODE_2_PLUS: return "2+";
+            case CODE_3_PLUS: return "3+";
+            case UNKNOWN: return "unknown";
+        }
+        return null;
+    }
+
+    @JsonCreator
+    public static ProteinExpressionResultCode forValue(String value) throws IOException {
+        switch (value) {
+            case "exp":
+                return EXP;
+            case "not-exp":
+                return NOT_EXP;
+            case "1+":
+                return CODE_1_PLUS;
+            case "2+":
+                return CODE_2_PLUS;
+            case "3+":
+                return CODE_3_PLUS;
+            case "unknown":
+                return UNKNOWN;
+        }
+        throw new IOException("Cannot deserialize PurpleCode");
+    }
+}

src/main/java/dev/pcvolkmer/mv64e/mtb/RecistCode.java

@@ -3,7 +3,7 @@ package dev.pcvolkmer.mv64e.mtb;
 import java.io.IOException;
 import com.fasterxml.jackson.annotation.*;
 
-public enum FluffyCode {
+public enum RecistCode {
     CR, MR, NA, NYA, PD, PR, SD;
 
     @JsonValue
@@ -21,7 +21,7 @@ public enum FluffyCode {
     }
 
     @JsonCreator
-    public static FluffyCode forValue(String value) throws IOException {
+    public static RecistCode forValue(String value) throws IOException {
         switch (value) {
             case "CR":
                 return CR;
@@ -38,6 +38,6 @@ public enum FluffyCode {
             case "SD":
                 return SD;
         }
-        throw new IOException("Cannot deserialize FluffyCode");
+        throw new IOException("Cannot deserialize RecistCode");
     }
 }

src/main/java/dev/pcvolkmer/mv64e/mtb/TcScoreCode.java

@@ -0,0 +1,43 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import java.io.IOException;
+import com.fasterxml.jackson.annotation.*;
+
+public enum TcScoreCode {
+    CODE_0, CODE_1, CODE_2, CODE_3, CODE_4, CODE_5, CODE_6;
+
+    @JsonValue
+    public String toValue() {
+        switch (this) {
+            case CODE_0: return "0";
+            case CODE_1: return "1";
+            case CODE_2: return "2";
+            case CODE_3: return "3";
+            case CODE_4: return "4";
+            case CODE_5: return "5";
+            case CODE_6: return "6";
+        }
+        return null;
+    }
+
+    @JsonCreator
+    public static TcScoreCode forValue(String value) throws IOException {
+        switch (value) {
+            case "0":
+                return CODE_0;
+            case "1":
+                return CODE_1;
+            case "2":
+                return CODE_2;
+            case "3":
+                return CODE_3;
+            case "4":
+                return CODE_4;
+            case "5":
+                return CODE_5;
+            case "6":
+                return CODE_6;
+        }
+        throw new IOException("Cannot deserialize TcScoreCode");
+    }
+}

src/main/java/dev/pcvolkmer/mv64e/mtb/Therapy.java

@@ -0,0 +1,13 @@
+package dev.pcvolkmer.mv64e.mtb;
+
+import com.fasterxml.jackson.annotation.*;
+import java.util.List;
+
+public class Therapy {
+    private List<MTBMedicationTherapy> history;
+
+    @JsonProperty("history")
+    public List<MTBMedicationTherapy> getHistory() { return history; }
+    @JsonProperty("history")
+    public void setHistory(List<MTBMedicationTherapy> value) { this.history = value; }
+}

src/test/java/dev/pcvolkmer/mv64e/mtb/ConverterTest.java

@@ -4,13 +4,14 @@ import org.junit.jupiter.api.Test;
 
 import java.io.IOException;
 
-public class ConverterTest {
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+
+class ConverterTest {
 
     @Test
     void shouldDeserializeJsonString() throws IOException {
         var ressource = getClass().getClassLoader().getResource("mv64e-mtb-fake-patient.json");
-
+        assertNotNull(Converter.fromJsonString(new String(ressource.openStream().readAllBytes())));
-        Converter.fromJsonString(new String(ressource.openStream().readAllBytes()));
     }
 
 }