ESCKAN chore: Replace hardcoded URL with env var

Dockerfile

@@ -1,18 +1,22 @@
 ARG NODE_PARENT=node:18
 
 FROM  ${NODE_PARENT} as frontend
-
+ARG VITE_COMPOSER_API_URL
+ENV VITE_COMPOSER_API_URL=$VITE_COMPOSER_API_URL
 ENV BUILDDIR=/app
 
 WORKDIR ${BUILDDIR}
 COPY package.json ${BUILDDIR}
 COPY yarn.lock ${BUILDDIR}
 COPY nginx/default.conf ${BUILDDIR}
+COPY replace_env_vars.sh ${BUILDDIR}
 
 RUN yarn install
 COPY . ${BUILDDIR}
+RUN /bin/sh replace_env_vars.sh './src/settings.ts'
 RUN yarn build
 
+
 FROM nginx:1.19.3-alpine
 
 RUN cat /etc/nginx/conf.d/default.conf

deploy/codefresh/codefresh.yml

@@ -15,21 +15,23 @@ steps:
     title: "Building SCKANNER"
     type: "build"
     image_name: "sckanner"
-    tag: "${{CF_BUILD_ID}}"
+    tag: "${{CF_SHORT_REVISION}}"
     dockerfile: Dockerfile
     working_directory: ./sckan-explorer
-    buildkit: true    
+    buildkit: true
     registry: "${{CODEFRESH_REGISTRY}}"
+    arguments:
+      build_arguments:
+        - VITE_COMPOSER_API_URL=${{VITE_COMPOSER_API_URL}}
   deploy:
     stage: "deploy"
     title: "Deploying SCKANNER"
-    image: codefresh/kubectl
+    image: codefresh/cf-deploy-kubernetes
+    tag: latest
     working_directory: ./sckan-explorer/deploy/k8s
     commands:
-      - export CLUSTER_NAME="${{CLUSTER_NAME}}"
-      - export NAMESPACE="${{NAMESPACE}}"
-      - export CF_BUILD_ID
-      - export REGISTRY="${{REGISTRY}}/"
-      - export DOMAIN="${{DOMAIN}}"
-      - chmod +x ./deploy.sh
-      - ./deploy.sh
+      - /cf-deploy-kubernetes sckanner.yaml
+      - /cf-deploy-kubernetes ingress.yaml
+    environment:
+      - KUBECONTEXT=${{CLUSTER_NAME}}
+      - KUBERNETES_NAMESPACE=${{NAMESPACE}}

replace_env_vars.sh

@@ -0,0 +1,7 @@
+#!/bin/sh
+
+DEST_FILES=$1
+
+for var in $(printenv | grep VITE_ | awk -F= '{print $1}'); do
+  sed -i 's|import.meta.env.'$var'|"'$(printenv $var)'"|g' "$DEST_FILES"
+done

src/settings.ts

@@ -6,6 +6,7 @@ export const SCKAN_ORDER_JSON_URL =
 export const SCKAN_MAJOR_NERVES_JSON_URL =
   'https://raw.githubusercontent.com/smtifahim/SCKAN-Apps/master/sckan-explorer/json/major-nerves.json';
 
+export const COMPOSER_API_URL = import.meta.env.VITE_COMPOSER_API_URL;
 export const SCKAN_DATABASE_SUMMARY_URL_LATEST =
   'https://raw.githubusercontent.com/smtifahim/SCKAN-Apps/master/sckan-explorer/json/sckan-stats/sckan-version-2024-03-04/';
 
@@ -26,10 +27,6 @@ export const DATABASE_FILES = {
   [FILES.CATEGORY]: 'stats-population-category-count.json',
 };
 
-// TODO: To change to the env variable when the deployment gets integrated with other sckan projects @dario
-export const COMPOSER_API_URL = 'https://composer.scicrunch.io/api';
-//export const COMPOSER_API_URL = import.meta.env.VITE_COMPOSER_API_URL
-
 export const OTHER_X_AXIS_ID = 'OTHER_X';
 export const OTHER_X_AXIS_LABEL = 'Other';
 export const OTHER_PHENOTYPE_LABEL = 'other';