Merge Develop 2.3 -> Develop

.github/workflows/trivy-scan.yml

@@ -4,6 +4,7 @@ on:
   pull_request:
     branches:
       - develop
+      - develop-*
       - master
 
   workflow_dispatch:  # Allows manual runs from the GitHub UI

build.gradle

@@ -213,7 +213,7 @@ spotless {
 }
 
 // # for this, the cuis with listed sources will have hierarchies computed
-// ./gradlew rrfSample -Pterminology=NCIMTH,ICD10CM,ICD9CM,SNOMEDCT_US,RXNORM,LNC,MDR,RADLEX -PlistFile=src/main/resources/cuis.txt -PinputPath=../data/NCIM
+// ./gradlew rrfSample -Pterminology=NCIMTH,MDR,ICD10CM,ICD9CM,LNC,SNOMEDCT_US,RADLEX,PDQ,ICD10,HL7V3.0 -PlistFile=src/main/resources/cuis-202508.txt -PinputPath=../data/NCIM
 tasks.register('rrfSample', JavaExec) {
   classpath = sourceSets.main.runtimeClasspath
   main = "gov.nih.nci.evs.api.service.SamplingApplication"

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.2.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.14.2-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

src/main/bin/devreset.sh

@@ -22,7 +22,7 @@ if [ $help == 1 ] || [ ${#arr[@]} -ne 1 ]; then
 fi
 dir=${arr[0]}
 # Hardcode the history file
-historyFile=$dir/cumulative_history_21.06e.txt
+historyFile=$dir/NCIT/cumulative_history_25.06e.txt
 
 
 databases=("NCIT2" "CTRP")
@@ -78,41 +78,41 @@ fi
 
 # Check NCIM
 echo "    check NCIM"
-ct=`ls $dir/NCIM | grep RRF | wc -l`
-if [[ $ct -le 20 ]]; then
-    echo "ERROR: unexpectedly small number of NCIM/*RRF files = $ct"
+ct=`ls $dir/NCIM | egrep "(AUI|COLS|CONSO|CUI|DEF|DOC|FILES|HIER|MAP|RANK|REL|SAB|SAT|STY)*RRF" | wc -l`
+if [[ ! $ct -eq 14 ]]; then
+    echo "ERROR: unexpectedly missing NCIM/*RRF files = $dir/NCIM"
     exit 1
 fi
 # Check NCIt weekly
 echo "    check NCIt weekly"
-if [[ ! -e "$dir/ThesaurusInferred_+1weekly.owl" ]]; then
+if [[ ! -e "$dir/NCIT/ThesaurusInferred_+1weekly.owl" ]]; then
     echo "ERROR: unexpectedly ThesaurusInferred_+1weekly.owl file"
     exit 1
 fi
 # Check NCIt monthly
 echo "    check NCIt monthly"
-if [[ ! -e "$dir/ThesaurusInferred_monthly.owl" ]]; then
+if [[ ! -e "$dir/NCIT/ThesaurusInferred_monthly.owl" ]]; then
     echo "ERROR: unexpectedly ThesaurusInferred_monthly.owl file"
     exit 1
 fi
 # Check GO monthly
 echo "    check GO monthly"
-if [[ ! -e "$dir/GO/go.2022-07-01.owl" ]]; then
-    echo "ERROR: unexpectedly missing GO/go.2022-07-01.owl file"
+if [[ ! -e "$dir/GO/GO.20250601.owl" ]]; then
+    echo "ERROR: unexpectedly missing GO/GO.20250601.owl file"
     exit 1
 fi
 
 # Check HGNC monthly
 echo "    check HGNC monthly"
-if [[ ! -e "$dir/HGNC/HGNC_202209.owl" ]]; then
-    echo "ERROR: unexpectedly missing HGNC/HGNC_202209.owl file"
+if [[ ! -e "$dir/HGNC/HGNC.202507.owl" ]]; then
+    echo "ERROR: unexpectedly missing HGNC/HGNC.202507.owl file"
     exit 1
 fi
 
 # Check ChEBI monthly
 echo "    check ChEBI monthly"
-if [[ ! -e "$dir/ChEBI/chebi_213.owl" ]]; then
-    echo "ERROR: unexpectedly missing ChEBI/chebi_213.owl file"
+if [[ ! -e "$dir/ChEBI/chebi_241.owl" ]]; then
+    echo "ERROR: unexpectedly missing ChEBI/chebi_241.owl file"
     exit 1
 fi
 
@@ -290,15 +290,15 @@ load_terminology_data(){
 }
 
 load_data(){
-    load_terminology_data CTRP http://NCI_T_weekly ThesaurusInferred_+1weekly.owl
-    load_terminology_data CTRP http://NCI_T_monthly ThesaurusInferred_monthly.owl
-    load_terminology_data NCIT2 http://NCI_T_monthly ThesaurusInferred_monthly.owl
-    load_terminology_data NCIT2 http://GO_monthly GO/go.2022-07-01.owl
-    load_terminology_data NCIT2 http://HGNC_monthly HGNC/HGNC_202209.owl
-    load_terminology_data NCIT2 http://ChEBI_monthly ChEBI/chebi_213.owl
+    load_terminology_data CTRP http://NCI_T_weekly NCIT/ThesaurusInferred_+1weekly.owl
+    load_terminology_data CTRP http://NCI_T_monthly NCIT/ThesaurusInferred_monthly.owl
+    load_terminology_data NCIT2 http://NCI_T_monthly NCIT/ThesaurusInferred_monthly.owl
+    load_terminology_data NCIT2 http://GO_monthly GO/GO.20250601.owl
+    load_terminology_data NCIT2 http://HGNC_monthly HGNC/HGNC.202507.owl
+    load_terminology_data NCIT2 http://ChEBI_monthly ChEBI/chebi_241.owl
     load_terminology_data NCIT2 http://UmlsSemNet UmlsSemNet/umlssemnet.owl
-    load_terminology_data NCIT2 http://MEDRT MED-RT/medrt.owl
-    load_terminology_data NCIT2 http://Canmed CanMed/canmed.owl
+    load_terminology_data NCIT2 http://Canmed CanMed/CANMED.202506.owl
+    load_terminology_data NCIT2 http://MEDRT MED-RT/MEDRT.2025-06-02.owl
     load_terminology_data NCIT2 http://CTCAE CTCAE/ctcae5.owl
     load_terminology_data NCIT2 http://DUO_monthly DUO/duo_Feb21.owl
     load_terminology_data NCIT2 http://DUO_monthly DUO/iao_Dec20.owl

src/main/bin/load.sh

@@ -23,7 +23,7 @@ fi
 dir=${arr[0]}
 
 # Hardcode the history file
-historyFile=$dir/cumulative_history_21.06e.txt
+historyFile=$dir/NCIT/cumulative_history_25.06e.txt
 
 
 databases=("NCIT2" "CTRP")
@@ -64,34 +64,34 @@ echo "  Check prerequisites"
 
 # Check NCIt weekly
 echo "    check NCIt weekly"
-if [[ ! -e "$dir/ThesaurusInferred_+1weekly.owl" ]]; then
+if [[ ! -e "$dir/NCIT/ThesaurusInferred_+1weekly.owl" ]]; then
     echo "ERROR: unexpectedly ThesaurusInferred_+1weekly.owl file"
     exit 1
 fi
 # Check NCIt monthly
 echo "    check NCIt monthly"
-if [[ ! -e "$dir/ThesaurusInferred_monthly.owl" ]]; then
+if [[ ! -e "$dir/NCIT/ThesaurusInferred_monthly.owl" ]]; then
     echo "ERROR: unexpectedly ThesaurusInferred_monthly.owl file"
     exit 1
 fi
 # Check GO monthly
 echo "    check GO monthly"
-if [[ ! -e "$dir/GO/go.2022-07-01.owl" ]]; then
-    echo "ERROR: unexpectedly missing GO/go.2022-07-01.owl file"
+if [[ ! -e "$dir/GO/GO.20250601.owl" ]]; then
+    echo "ERROR: unexpectedly missing GO/GO.20250601.owl file"
     exit 1
 fi
 
 # Check HGNC monthly
 echo "    check HGNC monthly"
-if [[ ! -e "$dir/HGNC/HGNC_202209.owl" ]]; then
-    echo "ERROR: unexpectedly missing HGNC/HGNC_202209.owl file"
+if [[ ! -e "$dir/HGNC/HGNC.202507.owl" ]]; then
+    echo "ERROR: unexpectedly missing HGNC/HGNC.202507.owl file"
     exit 1
 fi
 
 # Check ChEBI monthly
 echo "    check ChEBI monthly"
-if [[ ! -e "$dir/ChEBI/chebi_213.owl" ]]; then
-    echo "ERROR: unexpectedly missing ChEBI/chebi_213.owl file"
+if [[ ! -e "$dir/ChEBI/chebi_241.owl" ]]; then
+    echo "ERROR: unexpectedly missing ChEBI/chebi_241.owl file"
     exit 1
 fi
 
@@ -177,15 +177,15 @@ load_terminology_data(){
 }
 
 load_data(){
-    load_terminology_data CTRP http://NCI_T_weekly ThesaurusInferred_+1weekly.owl
-    load_terminology_data CTRP http://NCI_T_monthly ThesaurusInferred_monthly.owl
-    load_terminology_data NCIT2 http://NCI_T_monthly ThesaurusInferred_monthly.owl
-    load_terminology_data NCIT2 http://GO_monthly GO/go.2022-07-01.owl
-    load_terminology_data NCIT2 http://HGNC_monthly HGNC/HGNC_202209.owl
-    load_terminology_data NCIT2 http://ChEBI_monthly ChEBI/chebi_213.owl
+    load_terminology_data CTRP http://NCI_T_weekly NCIT/ThesaurusInferred_+1weekly.owl
+    load_terminology_data CTRP http://NCI_T_monthly NCIT/ThesaurusInferred_monthly.owl
+    load_terminology_data NCIT2 http://NCI_T_monthly NCIT/ThesaurusInferred_monthly.owl
+    load_terminology_data NCIT2 http://GO_monthly GO/GO.20250601.owl
+    load_terminology_data NCIT2 http://HGNC_monthly HGNC/HGNC.202507.owl
+    load_terminology_data NCIT2 http://ChEBI_monthly ChEBI/chebi_241.owl
     load_terminology_data NCIT2 http://UmlsSemNet UmlsSemNet/umlssemnet.owl
-    load_terminology_data NCIT2 http://MEDRT MED-RT/medrt.owl
-    load_terminology_data NCIT2 http://Canmed CanMed/canmed.owl
+    load_terminology_data NCIT2 http://MEDRT MED-RT/MEDRT.2025-06-02.owl
+    load_terminology_data NCIT2 http://Canmed CanMed/CANMED.202506.owl
     load_terminology_data NCIT2 http://CTCAE CTCAE/ctcae5.owl
     load_terminology_data NCIT2 http://DUO_monthly DUO/duo_Feb21.owl
     load_terminology_data NCIT2 http://DUO_monthly DUO/iao_Dec20.owl