CK-83 Production deployment setup

.github/ISSUE_TEMPLATE/feature_request.yaml

@@ -0,0 +1,79 @@
+name: Feature request
+description: Form to request a new feature or enhancement to ELIXIR Biovalidator
+title: "[Feature request]: "
+labels: ["enhancement"]
+assignees:
+  - theisuru
+body:
+  - type: markdown
+    attributes:
+      value: |
+        This form serves as a template for **feature requests** to be added to ELIXIR Biovalidator. It can be used to request, for example, a new custom keyword for asynchronous validation (similar to ``graphRestriction``).
+        Thank you for contributing to the improvement of ELIXIR Biovalidator!
+
+  - type: textarea
+    id: feature-summary
+    attributes:
+      label: Summary
+      description: Provide a summary of what the requested feature is. 
+      placeholder: e.g. Addition of information to Biovalidator's logs
+    validations:
+      required: true
+
+  - type: dropdown
+    id: related-field
+    attributes:
+      label: Related topic
+      description: What are the topic(s) that your requested feature is related to? You can select multiple topics if applicable.
+      multiple: true
+      options:
+        - Custom keywords
+        - Installation
+        - Server usage
+        - Command Line Interface (CLI) usage
+        - Tool's documentation
+        - Other
+    validations:
+      required: true
+
+  - type: textarea
+    id: request-motivation
+    attributes:
+      label: Request motivation
+      description: What is the motivation of your request. In other words, what would be the benefits to Biovalidator were your feature to be added. 
+      placeholder: e.g. The addition of the information ``...`` to the logs would greatly improve the traceability of validation requests...
+    validations:
+      required: true
+
+  - type: textarea
+    id: use-cases
+    attributes:
+      label: Use cases
+      description: List examples of the use-cases for the requested feature. 
+      placeholder: |
+        e.g. 
+        - Monitoring the server requests...
+        - Traceability of errors during validation...
+        - Generation of statistics...
+        - ...
+    validations:
+      required: false
+
+  - type: textarea
+    id: examples
+    attributes:
+      label: Examples
+      description: List examples of how you envision the feature to work and its output. 
+      placeholder: |
+        e.g. Example 1: with an example request ``curl ...``, the logs would look like...
+    validations:
+      required: true
+
+  - type: textarea
+    id: additional-context
+    attributes:
+      label: Additional context
+      description: Use this text area to add all additional context needed to create the new feature, including related issues and PRs,images, etc.
+      placeholder: e.g. This feature relates to issue "X", and here is a screenshot of...
+    validations:
+      required: false

.gitlab-ci.yml

@@ -1,34 +1,86 @@
 variables:
   DOCKER_DRIVER: overlay2
   DOCKER_TLS_CERTDIR: ""
+  DOCKER_TAG: $CI_COMMIT_REF_SLUG-$CI_COMMIT_SHORT_SHA
+  DOCKER_IMAGE_NAME: $CI_REGISTRY_IMAGE:$DOCKER_TAG
+  DOCKER_PULL_SECRET: docker-registry-secret
+  DOCKER_AUTH_CONFIG: $DOCKER_CONFIG_JSON
 
 stages:
   - build
   - deploy
 
-build_docker_image: 
+build_docker_image:
   image: docker:latest
   services:
     - docker:dind
   stage: build
   script:
-    - docker login $CI_REGISTRY -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD
-    - docker build -t $CI_REGISTRY_IMAGE:$CI_COMMIT_TAG .
-    - docker push $CI_REGISTRY_IMAGE:$CI_COMMIT_TAG
+    - echo "$CI_DEPLOY_PASSWORD" | docker login $CI_REGISTRY -u $CI_DEPLOY_USER --password-stdin
+    - echo $DOCKER_IMAGE_NAME
+    - docker build -t $DOCKER_IMAGE_NAME .
+    - docker push $DOCKER_IMAGE_NAME
   after_script:
     - docker logout ${CI_REGISTRY}
 
-hx-production:
-  stage: deploy
-  script:
-     - sed -i s#%DOCKER_IMAGE%#$CI_REGISTRY_IMAGE\:$CI_COMMIT_TAG#g k8s-deployment.yaml
-     - export KUBECONFIG=/home/gitlab-runner/.kube/hx-wp-webadmin-01-team-admin &&  kubectl apply -f k8s-deployment.yaml
+deploy_dev:
+  variables:
+    NAMESPACE: biosamples-dev
+    HOST: wwwint.ebi.ac.uk
+  environment:
+    name: dev
+    url: https://wwwint.ebi.ac.uk/biosamples/biovalidator
+  when: manual
+  extends: .kube_deploy_script
+
+deploy_test:
+  variables:
+    NAMESPACE: biosamples-dev
+    HOST: wwwdev.ebi.ac.uk
+  environment:
+    name: test
+    url: https://wwwdev.ebi.ac.uk/biosamples/biovalidator
+  only:
+    - main
+    - dev
+  when: manual
+  extends: .kube_deploy_script
+
+deploy_prod:
+  variables:
+    NAMESPACE: biosamples-prod
+    HOST: www.ebi.ac.uk
+  environment:
+    name: prod
+    url: https://www.ebi.ac.uk/biosamples/biovalidator
   only:
-    - disable
-hh-production:
+    - main
+  when: manual
+  extends: .kube_deploy_script
+
+# todo discuss: do we need AIT biovalidator to share with others?
+# todo discuss: what are the options to make biosamples internal only: remove ingress and make service=ClusterIP?
+#deploy_prod_ait:
+#  variables:
+#    NAMESPACE: ait-prod
+#    HOST: www.ebi.ac.uk
+#  environment:
+#    name: prod-ait
+#    url: https://www.ebi.ac.uk/ait/biovalidator
+#  when: manual
+#  extends: .kube_deploy_script
+
+.kube_deploy_script:
   stage: deploy
+  image: dtzar/helm-kubectl
   script:
-     - sed -i s#%DOCKER_IMAGE%#$CI_REGISTRY_IMAGE\:$CI_COMMIT_TAG#g k8s-deployment.yaml
-     - export KUBECONFIG=/home/gitlab-runner/.kube/hh-wp-webadmin-01-team-admin &&  kubectl apply -f k8s-deployment.yaml
-  only:
-    - disable
+    - kubectl create namespace $NAMESPACE || true
+    - kubectl config set-context --current --namespace=${NAMESPACE}
+    - kubectl delete secret $DOCKER_PULL_SECRET || true
+    - kubectl create secret docker-registry $DOCKER_PULL_SECRET --docker-server=$CI_REGISTRY --docker-username=$CI_DEPLOY_USER --docker-password=$CI_DEPLOY_PASSWORD
+    - envsubst < deployment.yaml > kubernetes.yaml
+    - kubectl apply -f kubernetes.yaml
+    - envsubst < ingress_template.yaml > ingress.yaml
+    - cat ingress.yaml
+    - kubectl apply -f ingress.yaml
+    - kubectl rollout restart deployments biovalidator

README.md

@@ -1,5 +1,5 @@
-# ELIXIR biovalidator - Extended JSON Schema validator with ontology validation
-[![Build Status](https://travis-ci.org/EMBL-EBI-SUBS/json-schema-validator.svg?branch=master)](https://travis-ci.org/EMBL-EBI-SUBS/json-schema-validator) [![Codacy Badge](https://api.codacy.com/project/badge/Grade/7fbabc981e294249a9a0967965418058)](https://www.codacy.com/app/fpenim/json-schema-validator?utm_source=github.com&utm_medium=referral&utm_content=EMBL-EBI-SUBS/json-schema-validator&utm_campaign=Badge_Grade)
+# ELIXIR biovalidator - Extended JSON Schema validator with ontology validation 
+<img src="./media/20240216_Biovalidator_logo.png" alt="Biovalidator logo" width="100" height="auto">  [![Build Status](https://travis-ci.org/EMBL-EBI-SUBS/json-schema-validator.svg?branch=master)](https://travis-ci.org/EMBL-EBI-SUBS/json-schema-validator) [![Codacy Badge](https://api.codacy.com/project/badge/Grade/7fbabc981e294249a9a0967965418058)](https://www.codacy.com/app/fpenim/json-schema-validator?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=EMBL-EBI-SUBS/json-schema-validator&amp;utm_campaign=Badge_Grade)
 [![tested with jest](https://img.shields.io/badge/tested_with-jest-99424f.svg)](https://github.com/facebook/jest)
 
 ELIXIR biovalidator is a [JSON Schema](http://json-schema.org/) validator extended from popular javascript library [AJV](https://ajv.js.org/). 
@@ -434,15 +434,15 @@ This image can be used to run the validator without cloning this repository.
 
 Pull docker image from [quay.io](https://quay.io/repository/ebi-ait/biovalidator)
 ```shell
-docker pull quay.io/ebi-ait/biovalidator:2.0.0
+docker pull quay.io/ebi-ait/biovalidator:2.2.2
 ```
 Run in server mode
 ```shell
-docker run -p 3020:3020 -d quay.io/ebi-ait/biovalidator:2.0.0
+docker run -p 3020:3020 -d quay.io/ebi-ait/biovalidator:2.2.2
 ```
 Run in onetime CLI mode
 ```shell
-docker run quay.io/ebi-ait/biovalidator:2.0.0 --schema /path/to/schema.json --data /path/to/data.json
+docker run quay.io/ebi-ait/biovalidator:2.2.2 --schema /path/to/schema.json --data /path/to/data.json
 ```
 
 ## Development

deployment.yaml

@@ -0,0 +1,39 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  labels:
+    app: biovalidator
+  name: biovalidator
+spec:
+  replicas: 2
+  revisionHistoryLimit: 2
+  selector:
+    matchLabels:
+      app: biovalidator
+  template:
+    metadata:
+      labels:
+        app: biovalidator
+    spec:
+      imagePullSecrets:
+        - name: $DOCKER_PULL_SECRET
+      containers:
+        - name: biovalidator
+          image: $DOCKER_IMAGE_NAME
+          imagePullPolicy: Always
+          ports:
+            - containerPort: 3020
+
+---
+apiVersion: v1
+kind: Service
+metadata:
+  name: biovalidator-service
+spec:
+  type: NodePort
+  selector:
+    app: biovalidator
+  ports:
+    - protocol: TCP
+      port: 3020
+      targetPort: 3020

ingress_template.yaml

@@ -0,0 +1,22 @@
+apiVersion: networking.k8s.io/v1
+kind: Ingress
+metadata:
+  name: biovalidator-ingress
+  namespace: ${NAMESPACE}
+  labels:
+    app: biovalidator-service
+  annotations:
+    nginx.ingress.kubernetes.io/rewrite-target: /$2
+spec:
+  ingressClassName: nginx
+  rules:
+    - host: ${HOST}
+      http:
+        paths:
+          - path: /biosamples/biovalidator(/|$)(.*)
+            pathType: Prefix
+            backend:
+              service:
+                name: biovalidator-service
+                port:
+                  number: 3020

package.json

@@ -1,6 +1,6 @@
 {
   "name": "biovalidator",
-  "version": "2.2.1",
+  "version": "2.2.2",
   "description": "A nodejs JSON schema validator, extended from Ajv to include ontology validation.",
   "main": "src/biovalidator.js",
   "bin": {
@@ -26,6 +26,7 @@
   "license": "Apache-2.0",
   "dependencies": {
     "ajv": "8.12.0",
+    "ajv-errors": "^3.0.0",
     "ajv-formats": "2.1.1",
     "axios": "^1.3.2",
     "express": "^4.17.1",

src/core/biovalidator-core.js

@@ -154,6 +154,7 @@ class BioValidator {
         const draft7MetaSchema = require("ajv/dist/refs/json-schema-draft-07.json")
         ajvInstance.addMetaSchema(draft7MetaSchema)
         addFormats(ajvInstance);
+        require("ajv-errors")(ajvInstance)
 
         this._addCustomKeywordValidators(ajvInstance);
         this._preCompileLocalSchemas(ajvInstance, localSchemaPath);

src/core/server.js

@@ -44,7 +44,7 @@ class BioValidatorServer {
     this.router = express.Router();
     this.router.use(express.static('src/views'));
 
-    this.app.use(bodyParser.json());
+    this.app.use(express.json({limit:'1mb'}));
 
     this.app.use(function(req, res, next) {
       res.header("Access-Control-Allow-Origin", "*");