Merge pull request #45 from helxplatform/develop

Release 5.2.0
helxplatform · Aug 14, 2024 · cb00c4b · cb00c4b
2 parents e0c773c + ddcce5d
commit cb00c4b
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Showing 9 changed files with 531 additions and 311 deletions.
diff --git a/Chart.yaml b/Chart.yaml
@@ -15,10 +15,10 @@ 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: 5.1.0
+version: 5.2.0
+engine: gotpl
 
-
-appVersion: "2.10.2"
+appVersion: "v2.13.2"
 
 # For dynamic updates to dependencies, versions must specify a range. 
 # Apart from version constrains operators = != > < >= <= the following shorthand notations are supported:
@@ -29,26 +29,26 @@ appVersion: "2.10.2"
 
 dependencies:
   - name: airflow
-    version: "^8.6.1"
+    version: "8.8.0"
     condition: airflow.enabled
     repository: "https://airflow-helm.github.io/charts"
   - name: elasticsearch
-    version: "^8.5.1"
+    version: "8.5.1"
     repository: "https://helm.elastic.co"
     condition: elasticsearch.enabled
   - name: redis
-    version: "^18.1.1"
+    version: "18.1.1"
     repository: "https://charts.bitnami.com/bitnami"
     condition: redis.enabled
   - name: tranql
-    version: "^0.4.2"
+    version: "0.4.2"
     condition: tranql.enabled
     repository: "@helx-charts"
   - name: redis-insight
-    version: "^0.1.0"
+    version: "0.1.0"
     condition: redis-insight.enabled
     repository: "@helx-charts"
   - name: ui
     condition: ui.enabled
-    version: "^1.3.0"
-    repository: "@helx-charts"
+    version: "^1.4.0"
+    repository: "@helx-charts"
diff --git a/README.md b/README.md
diff --git a/README.md.gotmpl b/README.md.gotmpl
@@ -0,0 +1,11 @@
+{{ template "chart.header" . }}
+{{ template "chart.description" . }}
+
+### Architecture of Search Chart
+
+For full architeture overview please refer to our documentation [here](https://dug.readthedocs.io/en/latest/architecture/roger/).
+
+{{ template "chart.versionBadge" . }}{{ template "chart.typeBadge" . }}{{ template "chart.appVersionBadge" . }}
+
+
+{{ template "chart.valuesSection" . }}
diff --git a/templates/_helpers.tpl b/templates/_helpers.tpl
@@ -189,10 +189,27 @@ Environment vars for API pods
   {{- end }}
   {{- end }}
   {{- if .Values.api.deployment.extraEnv }}
-  {{- toYaml .Values.api.deployment.extraEnv | nindent 10 }}
+  {{- toYaml .Values.api.deployment.extraEnv | nindent 0 }}
   {{- end }}
 - name: ROOT_PATH
   value: /search-api
+  {{ if .Values.config.program_config }}
+- name: PROGRAM_DESCRIPTION
+  value: {{ .Values.config.program_config | toJson | quote }}
+  {{ end }}
+  {{ if .Values.config.consent_id_config }}
+- name: CONSENT_ID_PATH
+  value: "/home/dug/dug/consent-id.json"
+  {{ end }}
+  {{ if .Values.config.missing_programs }}
+- name: MISSING_PROGRAM_PATH
+  value: "/home/dug/dug/missing_programs.json"
+  {{ end }}
+  {{ if .Values.config.missing_studies }}
+- name: MISSING_STUDIES_PATH
+  value: "/home/dug/dug/missing_studies.json"
+  {{ end }}
+
 {{- end -}}
 
 {{/*

diff --git a/templates/api-deployment.yaml b/templates/api-deployment.yaml
@@ -40,6 +40,26 @@ spec:
         resources:
           {{- toYaml .Values.api.deployment.resources | nindent 10 }}
         volumeMounts:
+          {{ if .Values.config.program_config }}
+          - name: program-config
+            mountPath: "/home/dug/dug/program-names.json"
+            subPath: "program_names.json"
+          {{ end }}
+          {{ if .Values.config.consent_id_config }}
+          - name: consent-id-config
+            mountPath: "/home/dug/dug/consent-id.json"
+            subPath: "consent_id.json"
+          {{ end }}
+          {{ if .Values.config.missing_studies }}
+          - name: missing-studies-config
+            mountPath: "/home/dug/dug/missing_studies.json"
+            subPath: "missing_studies.json"
+          {{ end }}
+          {{ if .Values.config.missing_programs }}
+          - name: missing-programs-config
+            mountPath: "/home/dug/dug/missing_programs.json"
+            subPath: "missing_programs.json"
+          {{ end }}
           - name: gunicorn-config
             mountPath: "/home/dug/dug/uvicorn_custom.py"
             subPath: "uvicorn_custom.py"
@@ -51,6 +71,30 @@ spec:
         configMap:
           name: {{ include "search.api.web.fullname" . }}-gunicorn-conf
           defaultMode: 0777
+      {{ if .Values.config.program_config }}
+      - name: program-config
+        configMap:
+          name: {{ include "search.api.web.fullname" . }}-program-names
+          defaultMode: 0777
+      {{ end }}
+      {{ if .Values.config.consent_id_config }}
+      - name: consent-id-config
+        configMap:
+          name: {{ include "search.api.web.fullname" . }}-consent-id-config
+          defaultMode: 0777
+      {{ end }}
+      {{ if .Values.config.missing_programs }}
+      - name: missing-programs-config
+        configMap:
+          name: {{ include "search.api.web.fullname" . }}-missing-programs-config
+          defaultMode: 0777
+      {{ end }}
+      {{ if .Values.config.missing_studies }}
+      - name: missing-studies-config
+        configMap:
+          name: {{ include "search.api.web.fullname" . }}-missing-studies-config
+          defaultMode: 0777
+      {{ end }}
       - name: elastic-ca
         secret:
           secretName: {{ include "search.api.elasticsearch.uname" . }}-certs

diff --git a/templates/api-service.yaml b/templates/api-service.yaml
@@ -17,4 +17,27 @@ spec:
       targetPort: {{ .Values.api.deployment.apiPort }}
   selector:
     app: {{ .Values.api.appName }}
-  type: {{ .Values.api.service.type }}
+  type: {{ .Values.api.service.type }}
+---
+{{ if .Values.chat.enabled }}
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ include "search.api.web.fullname" . }}-chat
+  {{- if .Values.api.service.annotations }}
+  annotations:
+    {{- toYaml .Values.api.service.annotations | nindent 4}}
+  {{- end }}
+  labels:
+    app: {{ .Values.api.appName }}-chat
+    {{- include "search.api.labels" . | nindent 4 }}
+spec:
+  ports:
+    - name: chat-port
+      protocol: TCP
+      port: {{ .Values.chat.apiPort }}
+      targetPort: {{ .Values.chat.apiPort }}
+  selector:
+    app: {{ .Values.api.appName }}-chat
+  type: {{ .Values.chat.service.type }}
+{{ end }}
diff --git a/templates/chat-bot-deployment.yaml b/templates/chat-bot-deployment.yaml
@@ -0,0 +1,41 @@
+{{ if .Values.chat.enabled }}
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "search.api.web.fullname" . }}-chat
+  labels:
+    app: {{ .Values.api.appName}}
+spec:
+  replicas: {{ .Values.chat.replicas }}
+  selector:
+    matchLabels:
+      app: {{ .Values.api.appName }}-chat
+  template:
+    metadata:
+      labels:
+        app: {{ .Values.api.appName}}-chat
+    spec:
+      imagePullSecrets:
+        {{- toYaml .Values.api.deployment.imagePullSecrets | nindent 8 }}
+      containers:
+      - image: {{ .Values.chat.image.repository }}:{{ .Values.chat.image.tag }}
+        imagePullPolicy: {{ .Values.api.image.pullPolicy }}
+        name: {{ include "search.api.web.fullname" . }}-container
+        env:
+          - name: API_URL
+            value: {{ .Values.chat.config.api_url }}
+          - name: SCRIPT_NAME
+            value: {{ .Values.chat.root_path }}
+        ports:
+          - containerPort: {{ .Values.chat.apiPort }}
+        command: [
+            "gunicorn",
+            "app:app",
+            "-b",
+            "0.0.0.0:{{ .Values.chat.apiPort }}"
+        ]
+        tty: true
+        stdin: true
+        resources:
+          {{- toYaml .Values.chat.resources | nindent 10 }}
+{{ end }}
diff --git a/templates/configmap.yaml b/templates/configmap.yaml
@@ -41,6 +41,13 @@ data:
   annotator_monarch_url: {{ .Values.config.annotation.monarch.url | quote }}
   annotator_sapbert_classification_url: {{ .Values.config.annotation.sapbert.classification_url | quote }}
   annotator_sapbert_annotator_url: {{ .Values.config.annotation.sapbert.annotator_url | quote }}
+  annotator_sapbert_bagel_enabled: {{ .Values.config.annotation.sapbert.bagel.enabled | quote }}
+  annotator_sapbert_bagel_url: {{ .Values.config.annotation.sapbert.bagel.url | quote }}
+  annotator_sapbert_bagel_prompt: {{ .Values.config.annotation.sapbert.bagel.prompt | quote }}
+  annotator_sapbert_bagel_llm_model_name: {{ .Values.config.annotation.sapbert.bagel.llm_args.llm_model_name | quote }}
+  annotator_sapbert_bagel_llm_organization: {{ .Values.config.annotation.sapbert.bagel.llm_args.organization | quote }}
+  annotator_sapbert_bagel_llm_access_key: {{ .Values.config.annotation.sapbert.bagel.llm_args.access_key | quote }}
+  annotator_sapbert_score_threshold: {{ .Values.config.annotation.sapbert.score_threshold | quote }}
   s3_access_key: {{ .Values.config.s3.access_key }}
   s3_bucket: {{ .Values.config.s3.bucket }}
   s3_host: {{ .Values.config.s3.host }}
@@ -68,4 +75,44 @@ data:
     from uvicorn.workers import UvicornWorker
     class SubPathWorker(UvicornWorker):
        CONFIG_KWARGS = {"root_path": "/search-api" }
+{{ if .Values.config.program_config }}
+---
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: {{ include "search.api.web.fullname" . }}-program-names
+data:
+  program_names.json: |-
+    {{ .Values.config.program_config | toJson }}
+{{ end }}
 
+{{ if .Values.config.consent_id_config }}
+---
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: {{ include "search.api.web.fullname" . }}-consent-id-config
+data:
+  consent_id.json: |-
+    {{ .Values.config.consent_id_config | toJson }}
+{{ end }}
+---
+{{ if .Values.config.missing_studies }}
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: {{ include "search.api.web.fullname" . }}-missing-studies-config
+data:
+  missing_studies.json: |-
+    {{ .Values.config.missing_studies | toJson }}
+{{ end }}
+---
+{{ if .Values.config.missing_programs }}
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: {{ include "search.api.web.fullname" . }}-missing-programs-config
+data:
+  missing_programs.json: |-
+    {{ .Values.config.missing_programs | toJson }}
+{{ end }}