Update NodeNorm and NameRes to Babel 2025nov4

helm/name-lookup/Chart.yaml

@@ -14,11 +14,11 @@ type: application
 
 # This is the chart version. This version number should be incremented each time you make changes
 # to the chart and its templates, including the app version.
-version: 0.5.1
+version: 0.5.2
 
 # This is the version number of the application being deployed. This version number should be
 # incremented each time you make changes to the application.
 # 
 # NameRes versions are based on the version of the NameRes Docker image concatenated with the
 # Babel release date.
-appVersion: 1.5.1_2025sep1
+appVersion: 1.6.0_2025nov4

helm/name-lookup/ncats-images-meta.yaml

@@ -1,6 +1,6 @@
 nameLookup:
   image: ghcr.io/ncatstranslator/nameresolution
-  version: v1.5.1
+  version: v1.6.0
 
 solr:
   image: solr

helm/name-lookup/templates/scripts-config-map.yaml

@@ -16,7 +16,7 @@ data:
     rm -rf $DATA_DIR/*
 
     # Download the file with retries if the download fails or if there is an existing file we can continue.
-    wget -c --progress=dot:giga --tries=10 --waitretry=10 --timeout=60 --read-timeout=30 -O $DATA_DIR/$BACKUP_ZIP $BACKUP_URL 
+    wget -c --progress=dot:giga --tries=10 --waitretry=10 --timeout=60 --read-timeout=30 -O $DATA_DIR/$BACKUP_ZIP $BACKUP_URL
 
     cd $DATA_DIR
     tar -xf $DATA_DIR/$BACKUP_ZIP -C $DATA_DIR
@@ -159,6 +159,13 @@ data:
                         "stored": true,
                         "multiValued": true
                     },
+                    {
+                        "name":"taxon_specific",
+                        "type":"boolean",
+                        "stored":true,
+                        "multiValued":false,
+                        "sortMissingLast":true
+                    },
                     {
                         "name": "shortest_name_length",
                         "type": "pint",

helm/name-lookup/templates/web-deployment.yaml

@@ -40,6 +40,9 @@ spec:
             value: "{{ .Values.app.otel.jaegerHost }}"
           - name: "JAEGER_PORT"
             value: "{{ .Values.app.otel.jaegerPort }}"
+          # Logging level.
+          - name: LOGLEVEL
+            value: "{{ .Values.app.logLevel }}"
           # Babel version information.
           - name: BABEL_VERSION
             value: "{{ .Values.data.babelVersion }}"

helm/name-lookup/values.yaml

@@ -13,13 +13,13 @@ webServer:
   port: 2433
   image:
     repository: ghcr.io/ncatstranslator/nameresolution
-    tag: v1.5.1
+    tag: v1.6.0
 
-dataUrl: "https://stars.renci.org/var/babel_outputs/2025sep1/nameres/snapshot.backup.tar.gz"
+dataUrl: "https://stars.renci.org/var/babel_outputs/2025nov4/nameres/snapshot.backup.tar.gz"
 forceRun: false
 data:
-  babelVersion: 2025sep1
-  babelVersionURL: https://github.com/ncatstranslator/Babel/blob/master/releases/2025sep1.md
+  babelVersion: 2025nov4
+  babelVersionURL: https://github.com/ncatstranslator/Babel/blob/master/releases/2025nov4.md
 
 downloader:
   image:
@@ -97,6 +97,7 @@ app:
     enabled: false
     jaegerHost:
     jaegerPort:
+  logLevel: INFO
   nodeSelector:
   affinity:
   tolerations:

helm/node-normalization-loader/Chart.yaml

@@ -15,12 +15,12 @@ type: application
 # This is the chart version. This version number should be incremented each time you make changes
 # to the chart and its templates, including the app version.
 # Versions are expected to follow Semantic Versioning (https://semver.org/)
-version: 0.7.0
+version: 0.8.0
 
 # This is the version number of the application being deployed. This version number should be
 # incremented each time you make changes to the application. Versions are not expected to
 # follow Semantic Versioning. They should reflect the version the application is using.
 # 
 # NodeNorm versions are based on the version of the NodeNorm Docker image concatenated with the
 # Babel release date.
-appVersion: 2.3.26_2025sep1
+appVersion: 2.3.28_2025nov4

helm/node-normalization-loader/ncats-images-meta.yaml

@@ -1,3 +1,3 @@
 nodeNormalizationLoader:
   image: "ghcr.io/ncatstranslator/nodenormalization-data-loading"
-  version: "v2.3.26"
+  version: "v2.3.28"

helm/node-normalization-loader/templates/loader-pipe-job.yaml

@@ -8,6 +8,7 @@
 {{- $tag := .Values.restore.tag }}
 {{- $pullPolicy := .Values.restore.pullPolicy }}
 {{- $ephemeralStorage := .Values.restore.ephemeralStorage }}
+{{- $redisConfig := .Values.redis_config }}
 {{- range $dbName, $dbConf := .Values.redis_backend_config }}
 {{- $dbKubeName := $dbName | replace "_" "-"}}
 {{- $dataStorageSize := $dbConf.storageSize }}
@@ -18,6 +19,7 @@
 {{- $sslEnabled := $connectionDetails.ssl_enabled }}
 {{- $isCluster := $connectionDetails.is_cluster }}
 {{- $redisPassword := $connectionDetails.password }}
+{{- $redisVersion := $connectionDetails.redis_version | default $redisConfig.redis_version | default "6.2" }}
 apiVersion: batch/v1
 kind: Job
 metadata:
@@ -103,6 +105,7 @@ data:
     gunzip "{{ $dataDir }}/{{ $dbName }}.rdb.gz"
 
     # Restore the file into the specified database.
+    # We no longer need to support cluster mode, so we can just pipe the data directly to the target host.
     # The `-c` option doesn't work in pipe mode, which is why we generate a ton of MOVED errors when we run this. The `grep -v MOVED` should suppress them
     # to avoid filling up the log.
     # Instead, what we will do is to get the list of cluster nodes and then stream ALL the data to ALL the nodes. Very inefficient, but it should get the job done.
@@ -115,8 +118,9 @@ data:
     for node in $sub_nodes; do
       IFS=':' read -ra node_host_port <<< $node
       sub_host_name="${node_host_port[0]}"
-      echo "... Started piping data to ${sub_host_name} as part of {{ $hostName }} ..." 
-      rdb -c protocol "{{ $dataDir }}/{{ $dbName }}.rdb" | redis-cli {{ if $isCluster }}-c{{end}} -h ${sub_host_name} -p {{ $port }} --pipe {{ if $sslEnabled -}}--tls{{ end }} 2>&1 | grep -v MOVED
+      echo "... Started piping data to ${sub_host_name} as part of {{ $hostName }} ..."
+      bash /home/nru/rdb-to-resp.sh "{{ $dataDir }}/{{ $dbName }}.rdb" "{{$redisVersion}}" | redis-cli {{ if $isCluster }}-c{{end}} -h ${sub_host_name} -p {{ $port }} --pipe {{ if $sslEnabled -}}--tls{{ end }} 2>&1 | grep -v MOVED
+      # rdb -c protocol "{{ $dataDir }}/{{ $dbName }}.rdb" | redis-cli {{ if $isCluster }}-c{{end}} -h ${sub_host_name} -p {{ $port }} --pipe {{ if $sslEnabled -}}--tls{{ end }} 2>&1 | grep -v MOVED
       echo "... Done piping data to ${sub_host_name} as part of {{ $hostName }} ..."
     done
 

helm/node-normalization-loader/values.yaml

@@ -12,14 +12,14 @@ logLevel: INFO
 
 image:
   repository: "ghcr.io/ncatstranslator/nodenormalization"
-  tag: "v2.3.26"
+  tag: "v2.3.28"
   pullPolicy: Always
 fullnameOverride: ""
 
 # Settings to use for a restore job.
 restore:
   repository: "ghcr.io/ncatstranslator/nodenormalization-data-loading"
-  tag: "v2.3.26"
+  tag: "replace-rdb-reader"
   pullPolicy: Always
   dataDir: "/data"
   dataSize: 50G
@@ -33,7 +33,7 @@ app:
 data:
   compendia:
     storageSize: 10G
-    sourceBaseUrl: "https://stars.renci.org/var/babel_outputs/2025sep1/compendia/"
+    sourceBaseUrl: "https://stars.renci.org/var/babel_outputs/2025nov4/compendia/"
     files:
     - AnatomicalEntity.txt
     - BiologicalProcess.txt
@@ -45,14 +45,14 @@ data:
     - ComplexMolecularMixture.txt
     - Disease.txt
     - Drug.txt
-    - GeneFamily.txt
     - Gene.txt.00
     - Gene.txt.01
     - Gene.txt.02
     - Gene.txt.03
     - Gene.txt.04
     - Gene.txt.05
     - Gene.txt.06
+    - GeneFamily.txt
     - GrossAnatomicalStructure.txt
     - MacromolecularComplex.txt
     - MolecularActivity.txt
@@ -82,11 +82,6 @@ data:
     - Protein.txt.18
     - Protein.txt.19
     - Protein.txt.20
-    - Protein.txt.21
-    - Protein.txt.22
-    - Protein.txt.23
-    - Protein.txt.24
-    - Protein.txt.25
     - Publication.txt.00
     - Publication.txt.01
     - Publication.txt.02
@@ -106,7 +101,7 @@ data:
     - umls.txt
   conflations:
     storageSize: 1G
-    sourceBaseUrl: "https://stars.renci.org/var/babel_outputs/2025sep1/conflation/"
+    sourceBaseUrl: "https://stars.renci.org/var/babel_outputs/2025nov4/conflation/"
     configs:
       - file: "GeneProtein.txt"
         types:
@@ -120,33 +115,36 @@ data:
         redis_db: "chemical_drug_db"
 codeDir: /code
 
+redis_config:
+  redis_version: "6.2"
+
 redis_backend_config:
   "eq_id_to_id_db":
-    restoreURL: "https://stars.renci.org/var/babel_outputs/2025sep1/rdb-backups/id-id.rdb.gz"
+    restoreURL: "https://stars.renci.org/var/babel_outputs/2025nov4/rdb-backups/id-id.rdb.gz"
     storageSize: 100G
 
   "id_to_eqids_db":
-    restoreURL: "https://stars.renci.org/var/babel_outputs/2025sep1/rdb-backups/id-eq-id.rdb.gz"
+    restoreURL: "https://stars.renci.org/var/babel_outputs/2025nov4/rdb-backups/id-eq-id.rdb.gz"
     storageSize: 150G
 
   "id_to_type_db":
-    restoreURL: "https://stars.renci.org/var/babel_outputs/2025sep1/rdb-backups/id-categories.rdb.gz"
+    restoreURL: "https://stars.renci.org/var/babel_outputs/2025nov4/rdb-backups/id-categories.rdb.gz"
     storageSize: 30G
 
   "curie_to_bl_type_db":
-    restoreURL: "https://stars.renci.org/var/babel_outputs/2025sep1/rdb-backups/semantic-count.rdb.gz"
+    restoreURL: "https://stars.renci.org/var/babel_outputs/2025nov4/rdb-backups/semantic-count.rdb.gz"
     storageSize: 1G
 
   "gene_protein_db":
-    restoreURL: "https://stars.renci.org/var/babel_outputs/2025sep1/rdb-backups/conflation-db.rdb.gz"
+    restoreURL: "https://stars.renci.org/var/babel_outputs/2025nov4/rdb-backups/conflation-db.rdb.gz"
     storageSize: 10G
 
   "info_content_db":
-    restoreURL: "https://stars.renci.org/var/babel_outputs/2025sep1/rdb-backups/info-content.rdb.gz"
+    restoreURL: "https://stars.renci.org/var/babel_outputs/2025nov4/rdb-backups/info-content.rdb.gz"
     storageSize: 1G
 
   "chemical_drug_db":
-    restoreURL: "https://stars.renci.org/var/babel_outputs/2025sep1/rdb-backups/chemical-drug-db.rdb.gz"
+    restoreURL: "https://stars.renci.org/var/babel_outputs/2025nov4/rdb-backups/chemical-drug-db.rdb.gz"
     storageSize: 1G
 
 securityContext:

helm/node-normalization-web-server/Chart.yaml

@@ -15,12 +15,12 @@ type: application
 # This is the chart version. This version number should be incremented each time you make changes
 # to the chart and its templates, including the app version.
 # Versions are expected to follow Semantic Versioning (https://semver.org/)
-version: 0.4.1
+version: 0.4.3
 
 # This is the version number of the application being deployed. This version number should be
 # incremented each time you make changes to the application. Versions are not expected to
 # follow Semantic Versioning. They should reflect the version the application is using.
 # 
 # NodeNorm versions are based on the version of the NodeNorm Docker image concatenated with the
 # Babel release date.
-appVersion: 2.3.26_2025sep1
+appVersion: 2.3.28_2025nov4

helm/node-normalization-web-server/ncats-images-meta.yaml

@@ -1,4 +1,3 @@
 nodeNormalization:
   image: ghcr.io/ncatstranslator/nodenormalization
-  version: v2.3.26
-
+  version: v2.3.28

helm/node-normalization-web-server/templates/web-server-deployment.yaml

@@ -46,6 +46,8 @@ spec:
               value: "{{ .Values.data.babelVersion }}"
             - name: "BABEL_VERSION_URL"
               value: "{{ .Values.data.babelVersionURL }}"
+            - name: "BIOLINK_MODEL_TAG"
+              value: "{{ .Values.data.biolinkModelTag }}"
             - name: "SERVER_ROOT"
               value: "{{ .Values.web.serverHostName }}"
             - name: "MATURITY_VALUE"

helm/node-normalization-web-server/values.yaml

@@ -8,12 +8,13 @@
 
 image:
   repository: ghcr.io/ncatstranslator/nodenormalization
-  tag: v2.3.26
+  tag: v2.3.28
   pullPolicy: Always
 
 data:
-  babelVersion: "2025sep1"
-  babelVersionURL: "https://github.com/ncatstranslator/Babel/blob/master/releases/2025sep1.md"
+  babelVersion: "2025nov4"
+  babelVersionURL: "https://github.com/ncatstranslator/Babel/blob/master/releases/2025nov4.md"
+  biolinkModelTag: "v4.3.2"
 
 web:
   port: 8080

helm/redis-r3-external/scripts/backup-nn-redis-db0.sh

@@ -5,8 +5,8 @@
 #
 
 # Configuration
-NN_VERSION="${NN_VERSION:-2025sep1}"
-NN_NAMESPACE="${NN_NAMESPACE:-translator-dev}"
+NN_VERSION="${NN_VERSION:-2025nov4}"
+NN_NAMESPACE="${NN_NAMESPACE:-translator-exp}"
 RETRIES=10
 
 # Copy all the dump files.
@@ -22,7 +22,9 @@ function check_and_download() {
     echo Checking RDB file.
     kubectl exec -n "$NN_NAMESPACE" "nn-redis-$NN_VERSION-$name-master-0" -- bash -c 'redis-check-rdb /data/dump.rdb'
     # Backup file.
-    kubectl cp -n "$NN_NAMESPACE" "nn-redis-$NN_VERSION-$name-master-0:/data/compressed.rdb.gz" ./$name.rdb.gz --retries $RETRIES
+    kubectl cp -n "$NN_NAMESPACE" "nn-redis-$NN_VERSION-$name-master-0:/data/dump.rdb" ./$name.rdb --retries $RETRIES && \
+        md5 ./$name.rdb && \
+        gzip ./$name.rdb
 }
 
 # Download files

helm/redis-r3-external/scripts/backup-nn-redis-db1.sh

@@ -5,8 +5,8 @@
 #
 
 # Configuration
-NN_VERSION="${NN_VERSION:-2025sep1}"
-NN_NAMESPACE="${NN_NAMESPACE:-translator-dev}"
+NN_VERSION="${NN_VERSION:-2025nov4}"
+NN_NAMESPACE="${NN_NAMESPACE:-translator-exp}"
 
 # Copy all the dump files.
 function check_and_download() {
@@ -21,7 +21,9 @@ function check_and_download() {
     echo Checking RDB file.
     kubectl exec -n "$NN_NAMESPACE" "nn-redis-$NN_VERSION-$name-master-0" -- bash -c 'redis-check-rdb /data/dump.rdb'
     # Backup file.
-    kubectl cp -n "$NN_NAMESPACE" "nn-redis-$NN_VERSION-$name-master-0:/data/compressed.rdb.gz" ./$name.rdb.gz --retries 10
+    kubectl cp -n "$NN_NAMESPACE" "nn-redis-$NN_VERSION-$name-master-0:/data/dump.rdb" ./$name.rdb --retries 10 && \
+        md5 ./$name.rdb && \
+        gzip ./$name.rdb
 }
 
 # Download files

helm/redis-r3-external/scripts/backup-nn-redis-db2-5-6.sh

@@ -5,8 +5,8 @@
 #
 
 # Configuration
-NN_VERSION="${NN_VERSION:-2025sep1}"
-NN_NAMESPACE="${NN_NAMESPACE:-translator-dev}"
+NN_VERSION="${NN_VERSION:-2025nov4}"
+NN_NAMESPACE="${NN_NAMESPACE:-translator-exp}"
 
 # Copy all the dump files.
 function check_and_download() {

helm/redis-r3-external/scripts/backup-nn-redis-db3.sh

@@ -5,8 +5,8 @@
 #
 
 # Configuration
-NN_VERSION="${NN_VERSION:-2025sep1}"
-NN_NAMESPACE="${NN_NAMESPACE:-translator-dev}"
+NN_VERSION="${NN_VERSION:-2025nov4}"
+NN_NAMESPACE="${NN_NAMESPACE:-translator-exp}"
 
 # Copy all the dump files.
 function check_and_download() {
@@ -21,7 +21,9 @@ function check_and_download() {
     echo Checking RDB file.
     kubectl exec -n "$NN_NAMESPACE" "nn-redis-$NN_VERSION-$name-master-0" -- bash -c 'redis-check-rdb /data/dump.rdb'
     # Backup file.
-    kubectl cp -n "$NN_NAMESPACE" "nn-redis-$NN_VERSION-$name-master-0:/data/compressed.rdb.gz" ./$name.rdb.gz --retries 10
+    kubectl cp -n "$NN_NAMESPACE" "nn-redis-$NN_VERSION-$name-master-0:/data/dump.rdb" ./$name.rdb --retries 10 && \
+        md5 ./$name.rdb && \
+        gzip ./$name.rdb
 }
 
 # Download files

helm/redis-r3-external/scripts/backup-nn-redis-db4.sh

@@ -5,8 +5,8 @@
 #
 
 # Configuration
-NN_VERSION="${NN_VERSION:-2025sep1}"
-NN_NAMESPACE="${NN_NAMESPACE:-translator-dev}"
+NN_VERSION="${NN_VERSION:-2025nov4}"
+NN_NAMESPACE="${NN_NAMESPACE:-translator-exp}"
 
 # Copy all the dump files.
 function check_and_download() {