fix: Helm chart name

.dockerignore

@@ -0,0 +1,3 @@
+*
+docker/
+**/*

deploy/Chart.yaml

@@ -1,6 +1,6 @@
 apiVersion: v2
-name: biothings-annotator
-description: A Helm chart for Biothings/pending.api-annotator
+name: node-normalization
+description: A Helm chart for NodeNormalizationAPI
 
 # A chart can be either an 'application' or a 'library' chart.
 #

deploy/Jenkinsfile

@@ -15,7 +15,7 @@ pipeline {
         pollSCM('H/5 * * * *')
     }
     environment {
-        DOCKER_REPO_NAME = "853771734544.dkr.ecr.us-east-1.amazonaws.com/translator-bte-pending-api-annotator"
+        DOCKER_REPO_NAME = "853771734544.dkr.ecr.us-east-1.amazonaws.com/translator-nodenormalization-api"
         KUBERNETES_BLUE_CLUSTER_NAME = "translator-eks-ci-blue-cluster"
         KUBERNETES_GREEN_CLUSTER_NAME = "translator-eks-ci-green-cluster"
         PACKAGE_DIR = "docker"

deploy/deploy.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-projectName="biothings-annotator"
+projectName="node-normalization"
 namespace="bte"
 
 #set +x

deploy/templates/NOTES.txt

@@ -6,16 +6,16 @@
   {{- end }}
 {{- end }}
 {{- else if contains "NodePort" .Values.service.type }}
-  export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ include "pendingapi.fullname" . }})
+  export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ include "node-normalization.fullname" . }})
   export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
   echo http://$NODE_IP:$NODE_PORT
 {{- else if contains "LoadBalancer" .Values.service.type }}
      NOTE: It may take a few minutes for the LoadBalancer IP to be available.
-           You can watch the status of by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "pendingapi.fullname" . }}'
-  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "pendingapi.fullname" . }} --template "{{"{{ range (index .status.loadBalancer.ingress 0) }}{{.}}{{ end }}"}}")
+           You can watch the status of by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "node-normalization.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "node-normalization.fullname" . }} --template "{{"{{ range (index .status.loadBalancer.ingress 0) }}{{.}}{{ end }}"}}")
   echo http://$SERVICE_IP:{{ .Values.service.port }}
 {{- else if contains "ClusterIP" .Values.service.type }}
-  export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name={{ include "pendingapi.name" . }},app.kubernetes.io/instance={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
+  export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name={{ include "node-normalization.name" . }},app.kubernetes.io/instance={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
   export CONTAINER_PORT=$(kubectl get pod --namespace {{ .Release.Namespace }} $POD_NAME -o jsonpath="{.spec.containers[0].ports[0].containerPort}")
   echo "Visit http://127.0.0.1:8080 to use your application"
   kubectl --namespace {{ .Release.Namespace }} port-forward $POD_NAME 8080:$CONTAINER_PORT

deploy/templates/_helpers.tpl

@@ -1,7 +1,7 @@
 {{/*
 Expand the name of the chart.
 */}}
-{{- define "biothings-annotator.name" -}}
+{{- define "node-normalization.name" -}}
 {{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" }}
 {{- end }}
 
@@ -10,7 +10,7 @@ Create a default fully qualified app name.
 We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
 If release name contains chart name it will be used as a full name.
 */}}
-{{- define "biothings-annotator.fullname" -}}
+{{- define "node-normalization.fullname" -}}
 {{- if .Values.fullnameOverride }}
 {{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" }}
 {{- else }}
@@ -26,16 +26,16 @@ If release name contains chart name it will be used as a full name.
 {{/*
 Create chart name and version as used by the chart label.
 */}}
-{{- define "biothings-annotator.chart" -}}
+{{- define "node-normalization.chart" -}}
 {{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
 {{- end }}
 
 {{/*
 Common labels
 */}}
-{{- define "biothings-annotator.labels" -}}
-helm.sh/chart: {{ include "biothings-annotator.chart" . }}
-{{ include "biothings-annotator.selectorLabels" . }}
+{{- define "node-normalization.labels" -}}
+helm.sh/chart: {{ include "node-normalization.chart" . }}
+{{ include "node-normalization.selectorLabels" . }}
 {{- if .Chart.AppVersion }}
 app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
 {{- end }}
@@ -45,7 +45,7 @@ app.kubernetes.io/managed-by: {{ .Release.Service }}
 {{/*
 Selector labels
 */}}
-{{- define "biothings-annotator.selectorLabels" -}}
-app.kubernetes.io/name: {{ include "biothings-annotator.name" . }}
+{{- define "node-normalization.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "node-normalization.name" . }}
 app.kubernetes.io/instance: {{ .Release.Name }}
 {{- end }}

deploy/templates/deployment.yaml

@@ -1,9 +1,9 @@
 apiVersion: apps/v1
 kind: Deployment
 metadata:
-  name: {{ include "biothings-annotator.fullname" . }}
+  name: {{ include "node-normalization.fullname" . }}
   labels:
-    {{- include "biothings-annotator.labels" . | nindent 4 }}
+    {{- include "node-normalization.labels" . | nindent 4 }}
 spec:
   strategy:
     type: {{ .Values.deployment.strategy.type }}
@@ -15,11 +15,11 @@ spec:
   replicas: {{ .Values.deployment.replicaCount }}
   selector:
     matchLabels:
-      {{- include "biothings-annotator.selectorLabels" . | nindent 6 }}
+      {{- include "node-normalization.selectorLabels" . | nindent 6 }}
   template:
     metadata:
       labels:
-        {{- include "biothings-annotator.selectorLabels" . | nindent 8 }}
+        {{- include "node-normalization.selectorLabels" . | nindent 8 }}
         {{- toYaml .Values.ncats.labels | nindent 8 }}
     spec:
       containers:
@@ -30,11 +30,9 @@ spec:
             - name: ES_HOST
               value: {{ .Values.containers.es_host }}
             - name: OPENTELEMETRY_ENABLED
-              value: "{{ .Values.containers.OPENTELEMETRY_ENABLED_VALUE }}"  
-            - name: OPENTELEMETRY_JAEGER_HOST
-              value: "{{ .Values.containers.OPENTELEMETRY_JAEGER_HOST_VALUE }}"
-            - name: OPENTELEMETRY_JAEGER_PORT
-              value: "{{ .Values.containers.OPENTELEMETRY_JAEGER_PORT_VALUE }}"      
+              value: "{{ .Values.env.OPENTELEMETRY_ENABLED_VALUE }}"  
+            - name: PORT
+              value: "{{ .Values.containers.port }}"      
           ports:
             - name: http
               containerPort: {{ .Values.containers.port }}

deploy/templates/ingress.yaml

@@ -1,12 +1,12 @@
 {{- if .Values.ingress.enabled -}}
-{{- $fullName := include "biothings-annotator.fullname" . -}}
+{{- $fullName := include "node-normalization.fullname" . -}}
 {{- $svcPort := .Values.service.port -}}
 apiVersion: networking.k8s.io/v1
 kind: Ingress
 metadata:
   name: {{ $fullName }}
   labels:
-    {{- include "biothings-annotator.labels" . | nindent 4 }}
+    {{- include "node-normalization.labels" . | nindent 4 }}
   {{- with .Values.ingress.annotations }}
   annotations:
     {{- toYaml . | nindent 4 }}
@@ -27,7 +27,7 @@ spec:
           pathType: ImplementationSpecific
           backend:
             service:
-              name: {{ include "biothings-annotator.fullname" . }}
+              name: {{ include "node-normalization.fullname" . }}
               port:
                 number: 80
     - host: {{ .Values.ingress.annotatorHost | quote }}
@@ -37,7 +37,7 @@ spec:
           pathType: ImplementationSpecific
           backend:
             service:
-              name: {{ include "biothings-annotator.fullname" . }}
+              name: {{ include "node-normalization.fullname" . }}
               port:
                 number: 80
 {{- end }}

deploy/templates/service.yaml

@@ -1,9 +1,9 @@
 apiVersion: v1
 kind: Service
 metadata:
-  name: {{ include "biothings-annotator.fullname" . }}
+  name: {{ include "node-normalization.fullname" . }}
   labels:
-    {{- include "biothings-annotator.labels" . | nindent 4 }}
+    {{- include "node-normalization.labels" . | nindent 4 }}
 spec:
   type: {{ .Values.service.type }}
   ports:
@@ -12,4 +12,4 @@ spec:
       protocol: TCP
       name: http
   selector:
-    {{- include "biothings-annotator.selectorLabels" . | nindent 4 }}
+    {{- include "node-normalization.selectorLabels" . | nindent 4 }}

deploy/values.yaml

@@ -1,7 +1,10 @@
-# Default values for biothings-annotator.
+# Default values for node-normalization.
 # This is a YAML-formatted file.
 # Declare variables to be passed into your templates.
 
+# Override the full deployment name to prevent release name prefix
+fullnameOverride: "node-normalization"
+
 deployment:
   replicaCount: 1
   strategy:
@@ -14,15 +17,15 @@ deployment:
       # A new pod will only be created after an old pod is taken down.
       maxSurge: 0
 image:
-  repository: 853771734544.dkr.ecr.us-east-1.amazonaws.com/translator-bte-pending-api-annotator
+  repository: 853771734544.dkr.ecr.us-east-1.amazonaws.com/translator-nodenormalization-api
   pullPolicy: Always
   # Overrides the image tag whose default is the chart appVersion.
   tag: DOCKER_VERSION_VALUE
 
 containers:
-  name: biothingsannotator
+  name: node-normalization
   es_host: ES_HOST_VALUE
-  port: 9000
+  port: 8000
 
 env:
   OPENTELEMETRY_ENABLED_VALUE: True
@@ -44,13 +47,13 @@ ingress:
     alb.ingress.kubernetes.io/actions.ssl-redirect: '{"Type": "redirect", "RedirectConfig": { "Protocol": "HTTPS", "Port": "443", "StatusCode": "HTTP_301"}}'
     alb.ingress.kubernetes.io/success-codes: '200'
     alb.ingress.kubernetes.io/load-balancer-attributes: idle_timeout.timeout_seconds=600
-  host: BTEPA_HOSTNAME_VALUE
+  host: NODE_NORM_HOSTNAME_VALUE
 
 ncats:
   labels:
     gov.nih.ncats.appenv: appenv
-    gov.nih.ncats.appname: bte-biothings-annotator
-    gov.nih.ncats.appentry: BTEPA_HOSTNAME_VALUE
+    gov.nih.ncats.appname: bte-node-normalization
+    gov.nih.ncats.appentry: NODE_NORM_HOSTNAME_VALUE
     gov.nih.ncats.appentrytype: https
     gov.nih.ncats.appentryport: tcp
     gov.nih.ncats.appconnnum: '1'

docker/Dockerfile

@@ -1,6 +1,6 @@
 FROM python:3.12 AS builder
 
-ARG NODENORM_REPO=https://github.com/biothings/NodeNormalizationAPI.git
+ARG NODENORM_REPO=https://github.com/chevvak2/NodeNormalizationAPI.git
 ARG NODENORM_BRANCH=main
 
 WORKDIR /build/nodenorm
@@ -16,22 +16,36 @@ RUN apt update -q -y && apt install -y --no-install-recommends git supervisor cu
 RUN useradd -m nodenorm && usermod -aG sudo nodenorm
 USER nodenorm
 WORKDIR /home/nodenorm/
+# Set PyStow home directory to a writable location
+ENV PYSTOW_HOME=/home/nodenorm/.pystow
+RUN mkdir -p /home/nodenorm/.pystow
 RUN python -m venv /home/nodenorm/venv
 COPY --from=builder --chown=nodenorm:nodenorm /build/wheels /home/nodenorm/wheels
 RUN /home/nodenorm/venv/bin/pip install /home/nodenorm/wheels/*.whl && rm -rf /home/nodenorm/wheels
 
+# Apply patches to fix NodeNormalization compatibility issues
+COPY --chown=nodenorm:nodenorm patches/health.py /home/nodenorm/venv/lib/python3.12/site-packages/nodenorm/handlers/health.py
+
 WORKDIR /home/nodenorm/configuration
 COPY --from=builder --chown=nodenorm:nodenorm /build/nodenorm/src/nodenorm/config/config.default.json /home/nodenorm/configuration/default.json
 COPY --from=builder --chown=nodenorm:nodenorm /build/nodenorm/version.txt /home/nodenorm/configuration/version.txt
 
-COPY --chown=nodenorm:nodenorm docker/configuration/supervisord.conf /etc/supervisor/supervisord.conf
-COPY --chown=nodenorm:nodenorm docker/configuration/Caddyfile /etc/caddy/Caddyfile
+# Override with corrected configuration
+COPY --chown=nodenorm:nodenorm configuration/config.json /home/nodenorm/configuration/config.json
 
-COPY --from=caddy_builder --chown=nodenorm:nodenorm /usr/bin/caddy /usr/bin/caddy
+# Switch back to root for system-level operations
+USER root
+COPY configuration/supervisord.conf /etc/supervisor/supervisord.conf
+COPY configuration/Caddyfile /etc/caddy/Caddyfile
+COPY --from=caddy_builder /usr/bin/caddy /usr/bin/caddy
+# Switch back to nodenorm user for runtime
+USER nodenorm
 
 
 STOPSIGNAL SIGINT
-EXPOSE 9000
+EXPOSE 8000
 
+# Run supervisord as root to manage processes 
+USER root
 ENTRYPOINT ["supervisord"]
 CMD ["-c", "/etc/supervisor/supervisord.conf"]

docker/configuration/Caddyfile

@@ -1,4 +1,4 @@
-:9000 {
+:8000 {
 	reverse_proxy localhost:9001
 	encode zstd gzip
   log {

docker/configuration/config.json

@@ -0,0 +1,32 @@
+{
+    "webserver": {
+        "HOST": "localhost",
+        "PORT": 8000,
+        "ENABLE_CURL_CLIENT": true,
+        "SETTINGS": {
+            "debug": true,
+            "autoreload": true
+        }
+    },
+    "api": {
+        "API_PREFIX": "nodenorm",
+        "API_VERSION": ""
+    },
+    "elasticsearch": {
+        "ES_HOST": "http://elasticsearch.es-core-components.svc.cluster.local:9200",
+        "ES_INDEX": "nodenorm",
+        "ES_ALIAS": "nodenorm", 
+        "ES_DOC_TYPE": "node",
+        "ES_INDICES": {},
+        "ES_ARGS": {
+            "sniff": false,
+            "request_timeout": 60
+        }
+    },
+    "telemetry": {
+        "OPENTELEMETRY_ENABLED": false,
+        "OPENTELEMETRY_SERVICE_NAME": "NodeNorm",
+        "OPENTELEMETRY_JAEGER_HOST": "http://localhost",
+        "OPENTELEMETRY_JAEGER_PORT": 6831
+    }
+}

docker/configuration/supervisord.conf

@@ -17,11 +17,13 @@ stderr_logfile_maxbytes=0
 stderr_logfile_backups=0
 
 [program:python_app]
-command=/home/nodenorm/venv/bin/python -m nodenorm --port=9001
+command=/home/nodenorm/venv/bin/python -m nodenorm --conf=/home/nodenorm/configuration/config.json --port=9001
+user=nodenorm
+environment=PYSTOW_HOME=/home/nodenorm/.pystow
 autorestart=true
 stdout_logfile=/dev/stdout
 stdout_logfile_maxbytes=0
 stdout_logfile_backups=0
 stderr_logfile=/dev/stderr
 stderr_logfile_maxbytes=0
-stderr_logfile_backups=0
+stderr_logfile_backups=0