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Merge pull request #13 from imsweb/mph
Add support for MPH
2 parents 2957b4b + e47c363 commit a7878ea

10 files changed

Lines changed: 306 additions & 12 deletions

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‎build.gradle‎

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@@ -8,7 +8,7 @@ plugins {
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}
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group = 'com.imsweb'
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version = '3.3'
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version = '3.4'
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description = 'Java client library for SEER*API'
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println "Starting build using ${Jvm.current()}"
@@ -63,7 +63,7 @@ findbugs {
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// Gradle wrapper, this allows to build the project without having to install Gradle!
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task wrapper(type: Wrapper) {
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gradleVersion = '3.1'
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gradleVersion = '3.2.1'
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}
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modifyPom {

‎gradle/wrapper/gradle-wrapper.jar‎

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‎gradle/wrapper/gradle-wrapper.properties‎

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#Mon Oct 03 09:46:00 EDT 2016
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#Wed Dec 07 11:32:53 EST 2016
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distributionBase=GRADLE_USER_HOME
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distributionPath=wrapper/dists
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zipStoreBase=GRADLE_USER_HOME
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zipStorePath=wrapper/dists
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distributionUrl=https\://services.gradle.org/distributions/gradle-3.1-all.zip
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distributionUrl=https\://services.gradle.org/distributions/gradle-3.2.1-all.zip

‎gradlew‎

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‎src/main/java/com/imsweb/seerapi/client/SeerApi.java‎

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import com.imsweb.seerapi.client.disease.DiseaseService;
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import com.imsweb.seerapi.client.glossary.GlossaryService;
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import com.imsweb.seerapi.client.mph.MphService;
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import com.imsweb.seerapi.client.naaccr.NaaccrService;
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import com.imsweb.seerapi.client.ndc.NdcService;
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import com.imsweb.seerapi.client.rx.RxService;
@@ -37,6 +38,7 @@ public final class SeerApi {
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private DiseaseService _diseaseService;
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private GlossaryService _glossaryService;
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private MphService _mphService;
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private NaaccrService _naaccrService;
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private NdcService _ndcService;
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private RxService _rxService;
@@ -78,6 +80,7 @@ private SeerApi(String baseUrl, final String apiKey) {
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// create cached service entities
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_diseaseService = retrofit.create(DiseaseService.class);
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_glossaryService = retrofit.create(GlossaryService.class);
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_mphService = retrofit.create(MphService.class);
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_naaccrService = retrofit.create(NaaccrService.class);
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_ndcService = retrofit.create(NdcService.class);
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_rxService = retrofit.create(RxService.class);
@@ -125,6 +128,14 @@ public GlossaryService glossary() {
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return _glossaryService;
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}
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/**
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* Return the multiple primary service
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* @return an interface to the multiple APIs
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*/
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public MphService mph() {
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return _mphService;
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}
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/**
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* Return the NAACCR service
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* @return an inteface to all the NAACCR APIs

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

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package com.imsweb.seerapi.client.mph;
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import com.fasterxml.jackson.annotation.JsonProperty;
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public class MphInput {
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@JsonProperty("primary_site")
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private String _primarySite;
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@JsonProperty("histology_icd_o3")
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private String _histologyIcdO3;
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@JsonProperty("histology_icd_o2")
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private String _histologyIcdO2;
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@JsonProperty("behavior_icd_o3")
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private String _behaviorIcdO3;
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@JsonProperty("behavior_icd_o2")
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private String _behaviorIcdO2;
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@JsonProperty("laterality")
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private String _laterality;
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@JsonProperty("date_of_diagnosis_year")
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private String _dateOfDiagnosisYear;
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@JsonProperty("date_of_diagnosis_month")
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private String _dateOfDiagnosisMonth;
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@JsonProperty("date_of_diagnosis_day")
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private String _dateOfDiagnosisDay;
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@JsonProperty("tx_status")
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private String _txStatus;
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public String getPrimarySite() {
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return _primarySite;
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}
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public void setPrimarySite(String primarySite) {
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_primarySite = primarySite;
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}
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public String getHistologyIcdO3() {
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return _histologyIcdO3;
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}
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public void setHistologyIcdO3(String histologyIcdO3) {
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_histologyIcdO3 = histologyIcdO3;
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}
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public String getHistologyIcdO2() {
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return _histologyIcdO2;
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}
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public void setHistologyIcdO2(String histologyIcdO2) {
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_histologyIcdO2 = histologyIcdO2;
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}
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public String getBehaviorIcdO3() {
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return _behaviorIcdO3;
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}
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public void setBehaviorIcdO3(String behaviorIcdO3) {
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_behaviorIcdO3 = behaviorIcdO3;
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}
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public String getBehaviorIcdO2() {
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return _behaviorIcdO2;
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}
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public void setBehaviorIcdO2(String behaviorIcdO2) {
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_behaviorIcdO2 = behaviorIcdO2;
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}
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public String getLaterality() {
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return _laterality;
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}
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public void setLaterality(String laterality) {
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_laterality = laterality;
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}
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public String getDateOfDiagnosisYear() {
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return _dateOfDiagnosisYear;
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}
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public void setDateOfDiagnosisYear(String dateOfDiagnosisYear) {
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_dateOfDiagnosisYear = dateOfDiagnosisYear;
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}
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public String getDateOfDiagnosisMonth() {
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return _dateOfDiagnosisMonth;
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}
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public void setDateOfDiagnosisMonth(String dateOfDiagnosisMonth) {
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_dateOfDiagnosisMonth = dateOfDiagnosisMonth;
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}
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public String getDateOfDiagnosisDay() {
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return _dateOfDiagnosisDay;
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}
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public void setDateOfDiagnosisDay(String dateOfDiagnosisDay) {
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_dateOfDiagnosisDay = dateOfDiagnosisDay;
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}
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public String getTxStatus() {
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return _txStatus;
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}
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public void setTxStatus(String txStatus) {
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_txStatus = txStatus;
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}
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}

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

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package com.imsweb.seerapi.client.mph;
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import com.fasterxml.jackson.annotation.JsonProperty;
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public class MphInputPair {
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public MphInputPair() {
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}
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public MphInputPair(MphInput input1, MphInput input2) {
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_input1 = input1;
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_input2 = input2;
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}
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@JsonProperty("input1")
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private MphInput _input1;
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@JsonProperty("input2")
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private MphInput _input2;
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public MphInput getInput1() {
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return _input1;
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}
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public void setInput1(MphInput input1) {
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_input1 = input1;
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}
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public MphInput getInput2() {
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return _input2;
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}
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public void setInput2(MphInput input2) {
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_input2 = input2;
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}
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}

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

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package com.imsweb.seerapi.client.mph;
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import com.fasterxml.jackson.annotation.JsonProperty;
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public class MphResult {
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/**
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* The possible result of determining if two tumors are single or multiple primaries.
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*/
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public enum Result {
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// indicates the two tumors are the same primary
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SINGLE_PRIMARY,
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// indicates the two tumors are different primaries
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MULTIPLE_PRIMARIES,
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// indicates there is not enough information to make a proper determination
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QUESTIONABLE
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}
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@JsonProperty("result")
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private Result _result;
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public Result getResult() {
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return _result;
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}
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public void setResult(Result result) {
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_result = result;
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}
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}

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

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/*
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* Copyright (C) 2016 Information Management Services, Inc.
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*/
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package com.imsweb.seerapi.client.mph;
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import retrofit2.Call;
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import retrofit2.http.Body;
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import retrofit2.http.POST;
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public interface MphService {
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/**
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* Uses multiple primary rules to compare two diseases
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* @param pair a pair of diseases
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* @return a result indicating whether the two diseases are the same primary
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*/
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@POST("mph")
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Call<MphResult> mph(@Body MphInputPair pair);
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}

‎src/test/java/com/imsweb/seerapi/client/mph/MphTest.java‎

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package com.imsweb.seerapi.client.mph;
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import java.io.IOException;
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import org.junit.BeforeClass;
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import org.junit.Test;
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import com.imsweb.seerapi.client.BadRequestException;
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import com.imsweb.seerapi.client.SeerApi;
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import static org.junit.Assert.assertEquals;
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public class MphTest {
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private static MphService _MPH;
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@BeforeClass
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public static void setup() {
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_MPH = new SeerApi.Builder().connect().mph();
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}
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@Test(expected = BadRequestException.class)
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public void testMissingAllInput() throws IOException {
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_MPH.mph(new MphInputPair()).execute();
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}
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@Test(expected = BadRequestException.class)
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public void testMissingSite() throws IOException {
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MphInput input1 = new MphInput();
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// site is missing
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input1.setHistologyIcdO3("8000");
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input1.setBehaviorIcdO3("3");
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input1.setDateOfDiagnosisYear("2016");
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input1.setLaterality("1");
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MphInput input2 = new MphInput();
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input2.setPrimarySite("C501");
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input2.setHistologyIcdO3("8000");
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input2.setBehaviorIcdO3("3");
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input2.setDateOfDiagnosisYear("2016");
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input2.setLaterality("1");
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_MPH.mph(new MphInputPair(input1, input2)).execute();
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}
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@Test
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public void testResults() throws IOException {
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MphInput input1 = new MphInput();
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input1.setPrimarySite("C509");
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input1.setHistologyIcdO3("8000");
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input1.setBehaviorIcdO3("3");
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input1.setDateOfDiagnosisYear("2016");
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input1.setLaterality("1");
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MphInput input2 = new MphInput();
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input2.setPrimarySite("C501");
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input2.setHistologyIcdO3("8000");
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input2.setBehaviorIcdO3("3");
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input2.setDateOfDiagnosisYear("2016");
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input2.setLaterality("1");
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// first test single primary (only differs by site code)
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MphResult result = _MPH.mph(new MphInputPair(input1, input2)).execute().body();
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assertEquals(MphResult.Result.SINGLE_PRIMARY, result.getResult());
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// next test questionable (setting laterality to unknown for one of the diseases)
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input2.setLaterality("9");
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result = _MPH.mph(new MphInputPair(input1, input2)).execute().body();
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assertEquals(MphResult.Result.QUESTIONABLE, result.getResult());
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// finally test difffernt diseases; set everything the same except for the DX year
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input1.setPrimarySite("C501");
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input1.setHistologyIcdO3("8000");
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input1.setBehaviorIcdO3("3");
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input1.setDateOfDiagnosisYear("2016");
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input1.setLaterality("1");
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input2.setPrimarySite("C501");
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input2.setHistologyIcdO3("8000");
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input2.setBehaviorIcdO3("3");
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input2.setDateOfDiagnosisYear("1998");
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input2.setLaterality("1");
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result = _MPH.mph(new MphInputPair(input1, input2)).execute().body();
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assertEquals(MphResult.Result.MULTIPLE_PRIMARIES, result.getResult());
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}
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}

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