Updated dependencies

CHANGELOG.md

@@ -1,5 +1,11 @@
 ## Layout Framework Version History
 
+**Changes in version 5.6**
+
+- Added NAACCR 25 XML layout; documentation is not available yet for new data items.
+- Updated NAACCR XML library from version 10.1 to version 11.0.
+- Updated CSV library from version 5.8 to version 5.9.
+
 **Changes in version 5.5**
 
 - Fixed NAACCR 24 Incidence layout having the wrong name.

build.gradle

@@ -4,13 +4,13 @@ plugins {
     id 'java-library'
     id 'checkstyle'
     id 'jacoco'
-    id 'com.github.spotbugs' version '5.2.1'
+    id 'com.github.spotbugs' version '6.0.19'
     id 'maven-publish'
     id 'signing'
-    id 'io.github.gradle-nexus.publish-plugin' version '1.3.0' // publish to Maven Central
-    id 'com.github.ben-manes.versions' version '0.49.0' // check for out-of-date dependencies (run 'dependencyUpdates' manually)
-    id 'org.sonatype.gradle.plugins.scan' version '2.6.1' // scan for vulnerabilities
-    id "org.sonarqube" version "4.4.1.3373"// sonarQube analysis
+    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+    id 'com.github.ben-manes.versions' version '0.51.0' // check for out-of-date dependencies (run 'dependencyUpdates' manually)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.sonarqube' version '5.1.0.4882' // sonarQube analysis
 }
 
 group = 'com.imsweb'
@@ -28,19 +28,19 @@ repositories {
 }
 
 dependencies {
-    api 'com.imsweb:naaccr-xml:10.1'
+    api 'com.imsweb:naaccr-xml:11.0'
 
-    implementation 'commons-io:commons-io:2.15.0'
-    implementation 'com.opencsv:opencsv:5.8'
+    implementation 'commons-io:commons-io:2.16.1'
+    implementation 'com.opencsv:opencsv:5.9'
     implementation 'com.thoughtworks.xstream:xstream:1.4.20'
 
     testImplementation 'junit:junit:4.13.2'
     testImplementation 'com.imsweb:seerutils:5.6'
     testImplementation 'com.imsweb:seerutils-gui:1.20'
     testImplementation 'com.imsweb:naaccr-api-client:1.0' // access NAACCR documentation API
-    testImplementation 'org.commonmark:commonmark:0.21.0' // convert markdown to HTML for NAACCR documentation
-    testImplementation 'org.freemarker:freemarker:2.3.32' // fill it template for NAACCR documentation
-    testImplementation 'org.xhtmlrenderer:flying-saucer-core:9.3.1' // Java Swing HTML renderer for NAACCR documentation lab
+    testImplementation 'org.commonmark:commonmark:0.22.0' // convert markdown to HTML for NAACCR documentation
+    testImplementation 'org.freemarker:freemarker:2.3.33' // fill it template for NAACCR documentation
+    testImplementation 'org.xhtmlrenderer:flying-saucer-core:9.9.0' // Java Swing HTML renderer for NAACCR documentation lab
 }
 
 // enforce UTF-8, display the compilation warnings
@@ -223,7 +223,7 @@ nexusPublishing {
 
 // Gradle wrapper, this allows to build the project without having to install Gradle!
 wrapper {
-    gradleVersion = '8.4'
+    gradleVersion = '8.9'
     distributionType = Wrapper.DistributionType.ALL
 }
 

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.9-all.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

gradlew

@@ -83,7 +83,8 @@ done
 # This is normally unused
 # shellcheck disable=SC2034
 APP_BASE_NAME=${0##*/}
-APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
+# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
+APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
@@ -144,15 +145,15 @@ if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
         # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045
+        # shellcheck disable=SC2039,SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
         # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045
+        # shellcheck disable=SC2039,SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
@@ -201,11 +202,11 @@ fi
 # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
 DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
-# Collect all arguments for the java command;
-#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
-#     shell script including quotes and variable substitutions, so put them in
-#     double quotes to make sure that they get re-expanded; and
-#   * put everything else in single quotes, so that it's not re-expanded.
+# Collect all arguments for the java command:
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#     and any embedded shellness will be escaped.
+#   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
+#     treated as '${Hostname}' itself on the command line.
 
 set -- \
         "-Dorg.gradle.appname=$APP_BASE_NAME" \

src/main/java/com/imsweb/layout/LayoutFactory.java

@@ -46,6 +46,11 @@
 public final class LayoutFactory {
 
     //XML Layouts - constants for the internal layout IDs
+    public static final String LAYOUT_ID_NAACCR_XML_25 = "naaccr-xml-25"; // shortcut for full abstract
+    public static final String LAYOUT_ID_NAACCR_XML_25_ABSTRACT = "naaccr-xml-25-abstract";
+    public static final String LAYOUT_ID_NAACCR_XML_25_MODIFIED = "naaccr-xml-25-modified";
+    public static final String LAYOUT_ID_NAACCR_XML_25_CONFIDENTIAL = "naaccr-xml-25-confidential";
+    public static final String LAYOUT_ID_NAACCR_XML_25_INCIDENCE = "naaccr-xml-25-incidence";
     public static final String LAYOUT_ID_NAACCR_XML_24 = "naaccr-xml-24"; // shortcut for full abstract
     public static final String LAYOUT_ID_NAACCR_XML_24_ABSTRACT = "naaccr-xml-24-abstract";
     public static final String LAYOUT_ID_NAACCR_XML_24_MODIFIED = "naaccr-xml-24-modified";
@@ -130,6 +135,7 @@ public final class LayoutFactory {
 
     // make sure to put all the "aliases" in this list...
     static {
+        _INTERNAL_LAYOUT_ID_ALIASES.put(LAYOUT_ID_NAACCR_XML_25, LAYOUT_ID_NAACCR_XML_25_ABSTRACT);
         _INTERNAL_LAYOUT_ID_ALIASES.put(LAYOUT_ID_NAACCR_XML_24, LAYOUT_ID_NAACCR_XML_24_ABSTRACT);
         _INTERNAL_LAYOUT_ID_ALIASES.put(LAYOUT_ID_NAACCR_XML_23, LAYOUT_ID_NAACCR_XML_23_ABSTRACT);
         _INTERNAL_LAYOUT_ID_ALIASES.put(LAYOUT_ID_NAACCR_XML_22, LAYOUT_ID_NAACCR_XML_22_ABSTRACT);
@@ -152,6 +158,11 @@ public final class LayoutFactory {
     // make sure to add the most recent layouts first, they will be "tried" in that order (important for discovery mechanism)
     static {
         //NAACCR XML
+        _INTERNAL_LAYOUTS.put(LAYOUT_ID_NAACCR_XML_25, "NAACCR XML 25 Abstract");
+        _INTERNAL_LAYOUTS.put(LAYOUT_ID_NAACCR_XML_25_ABSTRACT, "NAACCR XML 25 Abstract");
+        _INTERNAL_LAYOUTS.put(LAYOUT_ID_NAACCR_XML_25_MODIFIED, "NAACCR XML 25 Modified");
+        _INTERNAL_LAYOUTS.put(LAYOUT_ID_NAACCR_XML_25_CONFIDENTIAL, "NAACCR XML 25 Confidential");
+        _INTERNAL_LAYOUTS.put(LAYOUT_ID_NAACCR_XML_25_INCIDENCE, "NAACCR XML 25 Incidence");
         _INTERNAL_LAYOUTS.put(LAYOUT_ID_NAACCR_XML_24, "NAACCR XML 24 Abstract");
         _INTERNAL_LAYOUTS.put(LAYOUT_ID_NAACCR_XML_24_ABSTRACT, "NAACCR XML 24 Abstract");
         _INTERNAL_LAYOUTS.put(LAYOUT_ID_NAACCR_XML_24_MODIFIED, "NAACCR XML 24 Modified");

src/main/java/com/imsweb/layout/naaccrxml/NaaccrXmlLayout.java

@@ -466,6 +466,9 @@ else if (archivedDocStream != null)
     }
 
     protected String getDocFolder() {
+        // there is always a delay before the documentation is released on the NAACCR website...
+        if ("250".equals(_naaccrVersion))
+            return "naaccr24";
         return "naaccr" + _naaccrVersion.substring(0, 2);
     }
 

src/main/resources/layout/fixed/naaccr/items-extra-info.csv

@@ -858,4 +858,31 @@ derivedSummaryGrade2018,Der Sum Grade 18,Stage/Prognostic Factors
 geocodingQualityCode,Geo Qual Code,Demographic
 geocodingQualityCodeDetail,Geo Qual Code Det,Demographic
 rxHospReconBreast,RX Hosp Recon Breast,Hospital-Specific
-rxSummReconBreast,RX Summ Recon Breast,Treatment-1st Course
+rxSummReconBreast,RX Summ Recon Breast,Treatment-1st Course
+chromosome16qLossHeterozygosity,Chrom 16q Heter,Stage/Prognostic Factors
+chromosome1qStatus,Chrom 1q Status,Stage/Prognostic Factors
+derivedPediatricM,Der Ped M,Stage/Prognostic Factors
+derivedPediatricStageGroup,Der Ped Stg Group,Stage/Prognostic Factors
+derivedPediatricT,Der Ped T,Stage/Prognostic Factors
+derivedPediatricTN,Der Ped N,Stage/Prognostic Factors
+ewsr1Fli1Fusion,EWSR1-FLI1 fusion,Stage/Prognostic Factors
+foxo1GeneRearrangements,FOXO1,Stage/Prognostic Factors
+inpc,INPC,Stage/Prognostic Factors
+inrgss,INRGSS,Stage/Prognostic Factors
+irssStageForEye2,IRSS Eye-2,Stage/Prognostic Factors
+nMycAmplification,n-MYC Amp,Stage/Prognostic Factors
+pdl1,PD-L1,Stage/Prognostic Factors
+pediatricId,Ped ID,Stage/Prognostic Factors
+pediatricIdVersionCurrent,Ped ID Ver Cur,Stage/Prognostic Factors
+pediatricIdVersionOriginal,Ped ID Ver Ori,Stage/Prognostic Factors
+pediatricMets,Ped Mets,Stage/Prognostic Factors
+pediatricPrimaryTumor,Ped Prim Tumor,Stage/Prognostic Factors
+pediatricRegionalNodes,Ped Reg Nodes,Stage/Prognostic Factors
+pretextClinicalStaging,Pretext Clin Stg,Stage/Prognostic Factors
+ptld,PTLD,Stage/Prognostic Factors
+torontoM,Tor M,Stage/Prognostic Factors
+torontoN,Tor N,Stage/Prognostic Factors
+torontoStageGroup,Tor Stg Group,Stage/Prognostic Factors
+torontoT,Tor T,Stage/Prognostic Factors
+torontoVersionNumber,Tor Ver Num,Stage/Prognostic Factors
+whiteBloodCellCount,Wh Blood Cell Ct,Stage/Prognostic Factors

src/test/java/com/imsweb/layout/naaccrxml/NaaccrXmlLayoutTest.java

@@ -83,7 +83,7 @@ private void assertStandardNaaccrXmlLayout(String layoutId) {
             Assert.assertNotNull(layoutId + "/" + field.getNaaccrId(), field.getLongLabel());
             Assert.assertNotEquals(layoutId + "/" + field.getNaaccrId(), "?", field.getShortLabel());
             Assert.assertNotEquals(layoutId + "/" + field.getNaaccrId(), "?", field.getSection());
-            if (!"240".equals(layout.getNaaccrVersion())) {
+            if (!"250".equals(layout.getNaaccrVersion())) {
                 Assert.assertNotNull(layoutId + "/" + field.getNaaccrId(), layout.getFieldDocByName(field.getName(), TestingUtils.getArchivedNaaccrDoc()));
                 Assert.assertNotNull(layoutId + "/" + field.getNaaccrId(), layout.getFieldDocByNaaccrItemNumber(field.getNaaccrItemNum(), TestingUtils.getArchivedNaaccrDoc()));
             }