Merge pull request #14 from imsweb/mph

Fix MPH support

Author: ctmay4

README.md

@@ -29,14 +29,14 @@ Download [the latest JAR][1] or grab via Maven:
 <dependency>
     <groupId>com.imsweb</groupId>
     <artifactId>seerapi-client-java</artifactId>
-    <version>3.4</version>
+    <version>3.5</version>
 </dependency>
 ```
 
 or via Gradle:
 
 ```
-compile 'com.imsweb:seerapi-client-java:3.4'
+compile 'com.imsweb:seerapi-client-java:3.5'
 ```
 
 ## Usage

build.gradle

@@ -5,10 +5,12 @@ plugins {
     id 'checkstyle'
     id 'findbugs'
     id 'com.bmuschko.nexus' version '2.3.1'
+    id "io.codearte.nexus-staging" version "0.8.0"  // logs into Sonotype OSS and does a "Close" and "Release"
+    id 'net.ossindex.audit' version '0.1.1'
 }
 
 group = 'com.imsweb'
-version = '3.4'
+version = '3.5'
 description = 'Java client library for SEER*API'
 
 println "Starting build using ${Jvm.current()}"
@@ -26,7 +28,7 @@ repositories {
 }
 
 dependencies {
-    compile 'com.squareup.retrofit2:retrofit:2.1.0'
+    compile 'com.squareup.retrofit2:retrofit:2.2.0'
     compile 'com.squareup.retrofit2:converter-jackson:2.1.0'
 
     testCompile 'junit:junit:4.11'
@@ -63,7 +65,7 @@ findbugs {
 
 // Gradle wrapper, this allows to build the project without having to install Gradle!
 task wrapper(type: Wrapper) {
-    gradleVersion = '3.2.1'
+    gradleVersion = '4.0'
 }
 
 modifyPom {

gradle/wrapper/gradle-wrapper.jar

@@ -1,6 +1,6 @@
-#Wed Dec 07 11:32:53 EST 2016
+#Fri Jun 16 16:42:51 EDT 2017
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-3.2.1-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.0-all.zip

gradle/wrapper/gradle-wrapper.properties

@@ -4,6 +4,16 @@
 
 public class MphInput {
 
+    /**
+     * How to consider histology match, if it is strict 8000 is considered a different histology than 8010-9999
+     * for rule : Do the tumors have ICD-O-3 histology codes that are different at the first (Xxxx), second (Xxxx), or third (xxXx) number?
+     * If lenient mode is on 8000 is considered as NOS and be considered to match any 8nnn histologies.
+     */
+    public enum HistologyMatchMode {
+        STRICT,
+        LENIENT
+    }
+
     @JsonProperty("primary_site")
     private String _primarySite;
     @JsonProperty("histology_icd_o3")

gradlew

@@ -0,0 +1,72 @@
+package com.imsweb.seerapi.client.mph;
+
+import java.util.List;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+public class MphOutput {
+
+    // The possible results of determining if two tumors are single or multiple primaries.
+    public enum Result {
+        // indicates the two tumors are the same primary
+        SINGLE_PRIMARY,
+        // indicates the two tumors are different primaries
+        MULTIPLE_PRIMARIES,
+        // indicates there is not enough information to make a proper determination
+        QUESTIONABLE
+    }
+
+    @JsonProperty("result")
+    private Result _result;
+    @JsonProperty("reason")
+    private String _reason;
+    @JsonProperty("applied_rules")
+    private List<MphRule> _appliedRules;
+    @JsonProperty("group_id")
+    private String _groupId;
+    @JsonProperty("step")
+    private String _step;
+
+    public MphOutput() {
+    }
+
+    public Result getResult() {
+        return _result;
+    }
+
+    public void setResult(Result result) {
+        _result = result;
+    }
+
+    public String getReason() {
+        return _reason;
+    }
+
+    public void setReason(String reason) {
+        _reason = reason;
+    }
+
+    public List<MphRule> getAppliedRules() {
+        return _appliedRules;
+    }
+
+    public void setAppliedRules(List<MphRule> appliedRules) {
+        _appliedRules = appliedRules;
+    }
+
+    public String getGroupId() {
+        return _groupId;
+    }
+
+    public void setGroupId(String groupId) {
+        _groupId = groupId;
+    }
+
+    public String getStep() {
+        return _step;
+    }
+
+    public void setStep(String step) {
+        _step = step;
+    }
+}

src/main/java/com/imsweb/seerapi/client/mph/MphInput.java

@@ -0,0 +1,75 @@
+/*
+ * Copyright (C) 2013 Information Management Services, Inc.
+ */
+package com.imsweb.seerapi.client.mph;
+
+import java.util.List;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+public class MphRule {
+
+    @JsonProperty("group_id")
+    private String _groupId;
+    @JsonProperty("step")
+    private String _step;
+    @JsonProperty("question")
+    private String _question;
+    @JsonProperty("reason")
+    private String _reason;
+    @JsonProperty("notes")
+    private List<String> _notes;
+    @JsonProperty("examples")
+    private List<String> _examples;
+
+    public MphRule() {
+    }
+
+    public String getGroupId() {
+        return _groupId;
+    }
+
+    public void setGroupId(String groupId) {
+        _groupId = groupId;
+    }
+
+    public String getStep() {
+        return _step;
+    }
+
+    public void setStep(String step) {
+        _step = step;
+    }
+
+    public String getQuestion() {
+        return _question;
+    }
+
+    public void setQuestion(String question) {
+        _question = question;
+    }
+
+    public String getReason() {
+        return _reason;
+    }
+
+    public void setReason(String reason) {
+        _reason = reason;
+    }
+
+    public List<String> getNotes() {
+        return _notes;
+    }
+
+    public void setNotes(List<String> notes) {
+        _notes = notes;
+    }
+
+    public List<String> getExamples() {
+        return _examples;
+    }
+
+    public void setExamples(List<String> examples) {
+        _examples = examples;
+    }
+}

src/main/java/com/imsweb/seerapi/client/mph/MphOutput.java

@@ -6,15 +6,27 @@
 import retrofit2.Call;
 import retrofit2.http.Body;
 import retrofit2.http.POST;
+import retrofit2.http.Query;
+
+import com.imsweb.seerapi.client.mph.MphInput.HistologyMatchMode;
 
 public interface MphService {
 
+    /**
+     * Uses multiple primary rules to compare two diseases using strict histology matching mode
+     * @param pair a pair of diseases
+     * @return a result indicating whether the two diseases are the same primary
+     */
+    @POST("mph")
+    Call<MphOutput> mph(@Body MphInputPair pair);
+
     /**
      * Uses multiple primary rules to compare two diseases
      * @param pair a pair of diseases
+     * @param matchMode
      * @return a result indicating whether the two diseases are the same primary
      */
     @POST("mph")
-    Call<MphResult> mph(@Body MphInputPair pair);
+    Call<MphOutput> mph(@Body MphInputPair pair, @Query("histology-matching-mode") HistologyMatchMode matchMode);
 
 }