From bda8ea32273e5dae66f11a2019a7101832b20bd1 Mon Sep 17 00:00:00 2001
From: Niklas Reimer <n.reimer@uni-luebeck.de>
Date: Tue, 8 Oct 2024 13:53:07 +0200
Subject: [PATCH] fix ci

---
 .env.example                                | 7 +++++--
 .github/workflows/docker-build-dev.yml      | 8 ++++----
 .github/workflows/docker-build-research.yml | 4 ++--
 .github/workflows/docker-build.yml          | 4 ++--
 README.md                                   | 4 ++--
 compose.yml                                 | 5 +++--
 compose/dev.yml                             | 2 +-
 7 files changed, 19 insertions(+), 15 deletions(-)

diff --git a/.env.example b/.env.example
index 7f7cfdd..abb7ba8 100644
--- a/.env.example
+++ b/.env.example
@@ -1,5 +1,8 @@
-# Release version e.g. 2022q2 or simply latest
-RELEASE=2024q1
+# Select flavor: care, research, dev
+FLAVOR=care
+
+# Release version e.g. 2024q4 or simply latest
+RELEASE=2024q4
 
 # Network configuration
 PORT=8080
diff --git a/.github/workflows/docker-build-dev.yml b/.github/workflows/docker-build-dev.yml
index 5159e46..1641155 100644
--- a/.github/workflows/docker-build-dev.yml
+++ b/.github/workflows/docker-build-dev.yml
@@ -18,9 +18,9 @@ jobs:
 
       - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
       - name: Build dev containers
-        run: docker compose -f compose-dev.yml build cbioportal
+        run: FLAVOR=dev docker compose build cbioportal
       - name: Build dev cbioproxy
-        run: docker compose -f compose-dev.yml build cbioproxy
+        run: FLAVOR=dev docker compose build cbioproxy
       - name: Login to Docker registry
         if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' }}
         uses: docker/login-action@v3
@@ -30,7 +30,7 @@ jobs:
           password: ${{ secrets.GITHUB_TOKEN }}
       - name: Push cbioportal
         if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' }}
-        run: docker compose -f compose-dev.yml build cbioportal --push
+        run: FLAVOR=dev docker compose build cbioportal --push
       - name: Push cbioproxy
         if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' }}
-        run: docker compose -f compose-dev.yml build cbioproxy --push
+        run: FLAVOR=dev docker compose build cbioproxy --push
diff --git a/.github/workflows/docker-build-research.yml b/.github/workflows/docker-build-research.yml
index 5a16b3e..c736644 100644
--- a/.github/workflows/docker-build-research.yml
+++ b/.github/workflows/docker-build-research.yml
@@ -11,6 +11,6 @@ jobs:
       - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
 
       - name: Build research containers
-        run: docker compose -f compose-research.yml build cbioportal
+        run: FLAVOR=research docker compose build cbioportal
       - name: Build research cbioproxy
-        run: docker compose -f compose-research.yml build cbioproxy
+        run: FLAVOR=research docker compose build cbioproxy
diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml
index 85d4c4b..e60df85 100644
--- a/.github/workflows/docker-build.yml
+++ b/.github/workflows/docker-build.yml
@@ -11,6 +11,6 @@ jobs:
       - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
 
       - name: Build care cBioPortal
-        run: docker compose -f compose.yml build cbioportal
+        run: FLAVOR=care docker compose build cbioportal
       - name: Build care cbioproxy
-        run: docker compose -f compose.yml build cbioproxy
+        run: FLAVOR=care docker compose build cbioproxy
diff --git a/README.md b/README.md
index 409d2f8..3c3b55c 100644
--- a/README.md
+++ b/README.md
@@ -10,7 +10,7 @@ Installation is described [here](./INSTALL.md)
 
 All images with a `ghcr.io/buschlab/` prefix can be rebuilt using the following command:
 ```
-sudo docker compose -f compose-dev.yml build <service>
+FLAVOR=dev docker compose build <service>
 ```
 
 Such are marked in the table down below.
@@ -53,7 +53,7 @@ The only part that needs a database backup is the HAPI FHIR server. For that ple
 
 ## Ports
 
-| Service | Path (behind OpenResty) | Port (compose-dev.yml) | Image |
+| Service | Path (behind OpenResty) | Port (FLAVOR=dev) | Image |
 | - | - | - | - |
 | OpenResty  | / | 8080 | ghcr.io/buschlab/cbioroxy |
 | cBioPortal | / | 8081 | ghcr.io/buschlab/cbioportal |
diff --git a/compose.yml b/compose.yml
index 7c37463..d67efe9 100644
--- a/compose.yml
+++ b/compose.yml
@@ -1,3 +1,4 @@
 include:
- - ./compose/base.yml
- - ./compose/${FLAVOR:-care}.yml
\ No newline at end of file
+  - path:
+      - ./compose/base.yml
+      - ./compose/${FLAVOR:-care}.yml
\ No newline at end of file
diff --git a/compose/dev.yml b/compose/dev.yml
index 42a02fc..558ecdd 100644
--- a/compose/dev.yml
+++ b/compose/dev.yml
@@ -2,7 +2,7 @@ services:
   cbioportal:
     image: ghcr.io/buschlab/cbioportal:${RELEASE:-latest}
     build:
-      context: services/cbioportal
+      context: ./services/cbioportal
       platforms:
         - "linux/amd64"
         - "linux/arm64"