Fixed two minor issues in N25 dictionary

Author: depryf

build.gradle

@@ -14,12 +14,12 @@ plugins {
     id 'java-library'
     id 'checkstyle'
     id 'jacoco'
-    id 'com.github.spotbugs' version '6.0.19'
+    id 'com.github.spotbugs' version '6.0.20'
     id 'maven-publish'
     id 'signing'
     id 'io.github.gradle-nexus.publish-plugin' version '2.0.0' // publish to Maven Central
     id 'com.github.ben-manes.versions' version '0.51.0' // check for out-of-date dependencies (run 'dependencyUpdates' manually)
-    id 'org.sonatype.gradle.plugins.scan' version '2.8.2' // scan for vulnerabilities
+    id 'org.sonatype.gradle.plugins.scan' version '2.8.3' // scan for vulnerabilities
     id "org.sonarqube" version "5.1.0.4882"// sonarQube analysis
 }
 
@@ -37,10 +37,11 @@ dependencies {
     api 'com.thoughtworks.xstream:xstream:1.4.20'
 
     implementation 'commons-io:commons-io:2.16.1'
-    implementation 'org.apache.commons:commons-lang3:3.14.0'
+    implementation 'org.apache.commons:commons-lang3:3.16.0'
 
     testImplementation 'junit:junit:4.13.2'
     testImplementation 'com.imsweb:data-generator:1.32'
+    testImplementation 'com.imsweb:layout:5.6'
     testImplementation 'com.opencsv:opencsv:5.9'
 }
 

docs/naaccr-xml-items-250.csv

@@ -95,7 +95,7 @@ censusTractCertainty2020,369,"Census Tract Certainty 2020",,1,"A,M,C,I",Tumor,di
 chromosome16qLossHeterozygosity,1189,"Chromosome 16q: Loss of Heterozygosity",,1,"A,M,C,I",Tumor,numeric
 chromosome19qLossHeterozygosity,3802,"Chromosome 19q: Loss of Heterozygosity (LOH)",,1,"A,M,C,I",Tumor,digits
 chromosome1pLossHeterozygosity,3801,"Chromosome 1p: Loss of Heterozygosity (LOH)",,1,"A,M,C,I",Tumor,digits
-chromosome1qStatus,1190,"Chromosome 1q Status",,3,"A,M,C,I",Tumor,numeric
+chromosome1qStatus,1190,"Chromosome 1q Status",,1,"A,M,C,I",Tumor,numeric
 chromosome3Status,3821,"Chromosome 3 Status",,1,"A,M,C,I",Tumor,digits
 chromosome8qStatus,3822,"Chromosome 8q Status",,1,"A,M,C,I",Tumor,text
 circumferentialResectionMargin,3823,"Circumferential Resection Margin (CRM)",,4,"A,M,C,I",Tumor,text
@@ -208,9 +208,9 @@ derivedEod2018N,815,"Derived EOD 2018 N",,15,"A,M,C,I",Tumor,text
 derivedEod2018StageGroup,818,"Derived EOD 2018 Stage Group",,15,"A,M,C,I",Tumor,text
 derivedEod2018T,785,"Derived EOD 2018 T",,15,"A,M,C,I",Tumor,text
 derivedPediatricM,1144,"Derived Pediatric M",,3,"A,M,C,I",Tumor,text
+derivedPediatricN,1143,"Derived Pediatric N",,3,"A,M,C,I",Tumor,text
 derivedPediatricStageGroup,1145,"Derived Pediatric Stage Group",,3,"A,M,C,I",Tumor,text
 derivedPediatricT,1142,"Derived Pediatric T",,3,"A,M,C,I",Tumor,text
-derivedPediatricTN,1143,"Derived Pediatric N",,3,"A,M,C,I",Tumor,text
 derivedRaiStage,3955,"Derived Rai Stage",,1,"A,M,C,I",Tumor,text
 derivedSeerClinStgGrp,3610,"Derived SEER Clin Stg Grp",,5,"A,M,C,I",Tumor,text
 derivedSeerCmbMSrc,3626,"Derived SEER Cmb M Src",,1,"A,M,C,I",Tumor,digits

docs/samples/naaccr-xml-sample-v250-abstract-10.xml.gz

@@ -1,4 +1,5 @@
 <!-- Changelog
+ - 08/23/2024: changed length of chromosome1qStatus from 3 to 1 and changed derivedPediatricTN to derivedPediatricN
  - 05/28/2024: changed length and type of pdl1.
  - 05/20/2024: Initial version.
 -->

docs/samples/naaccr-xml-sample-v250-abstract-100.xml.gz

@@ -5,6 +5,7 @@
      Visit https://www.naaccr.org/ for more information about the NAACCR XML Data Exchange Standard. -->
 
 <!-- Changelog
+ - 08/23/2024: changed length of chromosome1qStatus from 3 to 1 and changed derivedPediatricTN to derivedPediatricN
  - 05/28/2024: changed length and type of pdl1.
  - 05/20/2024: Initial version.
 -->
@@ -650,7 +651,7 @@
         <ItemDef naaccrId="chromosome1qStatus"
             naaccrNum="1190"
             naaccrName="Chromosome 1q Status"
-            length="3"
+            length="1"
             recordTypes="A,M,C,I"
             parentXmlElement="Tumor"
             dataType="numeric"/>
@@ -1471,7 +1472,7 @@
             length="3"
             recordTypes="A,M,C,I"
             parentXmlElement="Tumor"/>
-        <ItemDef naaccrId="derivedPediatricTN"
+        <ItemDef naaccrId="derivedPediatricN"
             naaccrNum="1143"
             naaccrName="Derived Pediatric N"
             length="3"

docs/samples/naaccr-xml-sample-v250-abstract-1000.xml.gz

@@ -22,28 +22,28 @@
 public class CreateSamplesZipFile {
 
     public static void main(String[] args) throws IOException {
-        try (ZipOutputStream zos = new ZipOutputStream(Files.newOutputStream(Paths.get("docs/samples/naaccr-xml-samples-v240.zip").toFile().toPath()))) {
+        try (ZipOutputStream zos = new ZipOutputStream(Files.newOutputStream(Paths.get("docs/samples/naaccr-xml-samples-v250.zip").toFile().toPath()))) {
             Path dir = Paths.get("src/test/resources/data/validity");
             Files.newDirectoryStream(dir.resolve("valid")).forEach(path -> addToZip(path.toFile(), zos));
             Files.newDirectoryStream(dir.resolve("invalid")).forEach(path -> addToZip(path.toFile(), zos));
             Files.newDirectoryStream(dir.resolve("invalid_relaxed")).forEach(path -> addToZip(path.toFile(), zos));
             Files.newDirectoryStream(dir.resolve("invalid_library_only")).forEach(path -> addToZip(path.toFile(), zos));
         }
 
-        NaaccrXmlDataGenerator absGenerator = new NaaccrXmlDataGenerator(LayoutFactory.LAYOUT_ID_NAACCR_XML_24_INCIDENCE);
+        NaaccrXmlDataGenerator absGenerator = new NaaccrXmlDataGenerator(LayoutFactory.LAYOUT_ID_NAACCR_XML_25_INCIDENCE);
         IntStream.of(10, 100, 1000).forEach(i -> {
             try {
-                absGenerator.generateFile(Paths.get("docs/samples/naaccr-xml-sample-v240-incidence-" + i + ".xml.gz").toFile(), i);
+                absGenerator.generateFile(Paths.get("docs/samples/naaccr-xml-sample-v250-incidence-" + i + ".xml.gz").toFile(), i);
             }
             catch (IOException e) {
                 throw new IllegalStateException(e);
             }
         });
 
-        NaaccrXmlDataGenerator incGenerator = new NaaccrXmlDataGenerator(LayoutFactory.LAYOUT_ID_NAACCR_XML_24_ABSTRACT);
+        NaaccrXmlDataGenerator incGenerator = new NaaccrXmlDataGenerator(LayoutFactory.LAYOUT_ID_NAACCR_XML_25_ABSTRACT);
         IntStream.of(10, 100, 1000).forEach(i -> {
             try {
-                incGenerator.generateFile(Paths.get("docs/samples/naaccr-xml-sample-v240-abstract-" + i + ".xml.gz").toFile(), i);
+                incGenerator.generateFile(Paths.get("docs/samples/naaccr-xml-sample-v250-abstract-" + i + ".xml.gz").toFile(), i);
             }
             catch (IOException e) {
                 throw new IllegalStateException(e);