Merge pull request #84 from MassBank/dev

Merge dev to main

Author: meier-rene

.github/workflows/create-docker.yml

@@ -3,10 +3,10 @@ name: Create Docker Container
 on:
   push:
     branches:
-      - 'main'
-      - 'dev'
+      - "main"
+      - "dev"
     tags:
-      - 'v*'
+      - "v*"
 
 jobs:
   build-and-push-images:
@@ -17,42 +17,44 @@ jobs:
       matrix:
         include:
           - dockerfile: ./Dockerfile-dbtool
-            image: ipbhalle/mb3dbtool
-          - dockerfile: ./Dockerfile
-            image: ipbhalle/mb3server
-          - dockerfile: ./Dockerfile-frontend
-            image: ipbhalle/mb3frontend
+            image: quay.io/massbank/massbank-dbtool
+            context: .
+          - dockerfile: ./Dockerfile-server
+            image: quay.io/massbank/massbank-api
+            context: .
+          - dockerfile: ./web-frontend/Dockerfile-frontend
+            image: quay.io/massbank/massbank-frontend
+            context: ./web-frontend
 
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Login to Docker Hub
+      - name: Login to quay.io
         uses: docker/login-action@v3
         with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
+          registry: quay.io
+          username: ${{ secrets.QUAY_USERNAME }}
+          password: ${{ secrets.QUAY_TOKEN }}
 
       - name: Docker meta
         id: meta
         uses: docker/metadata-action@v5
         with:
           images: ${{ matrix.image }}
           tags: |
-            # branch event
-            type=ref,event=branch
             # tag event
             type=ref,event=tag
-            # pull request event
-            type=ref,event=pr
             # set latest tag for main branch and tags
             type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/') }}
+            # set dev tag for dev branch, but exclude ipbhalle/postgres
+            type=raw,value=dev,enable=${{ github.ref == 'refs/heads/dev' }}
 
       - name: Build and push
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
-          context: .
+          context: ${{ matrix.context }}
           push: ${{ github.event_name != 'pull_request' }}
           file: ${{ matrix.dockerfile }}
           tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/create-docker2.yml

@@ -0,0 +1,60 @@
+name: Create Docker Container
+
+on:
+  push:
+    branches:
+      - "main"
+      - "dev"
+    tags:
+      - "v*"
+
+jobs:
+  build-and-push-images:
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - dockerfile: ./Dockerfile-dbtool
+            image: ipbhalle/massbank3-dbtool
+            context: .
+          - dockerfile: ./Dockerfile-server
+            image: ipbhalle/massbank3-server
+            context: .
+          - dockerfile: ./web-frontend/Dockerfile-frontend
+            image: ipbhalle/massbank3-frontend
+            context: ./web-frontend
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ matrix.image }}
+          tags: |
+            # tag event
+            type=ref,event=tag
+            # set latest tag for main branch and tags
+            type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/') }}
+            # set dev tag for dev branch
+            # set dev tag for dev branch, but exclude ipbhalle/postgres
+            type=raw,value=dev,enable=${{ github.ref == 'refs/heads/dev' && matrix.image != 'ipbhalle/postgres' }}
+
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: ${{ matrix.context }}
+          push: ${{ github.event_name != 'pull_request' }}
+          file: ${{ matrix.dockerfile }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/go-test.yml

@@ -1,11 +1,10 @@
-
 name: go-test
 
 on:
   push:
-    branches: [ "*"]
+    branches: ["*"]
   pull_request:
-    branches: [ "*" ]
+    branches: ["*"]
 
 env:
   BUILD_TYPE: Release
@@ -14,10 +13,9 @@ jobs:
   build:
     strategy:
       matrix:
-        mongodb-version: ['6.0']
-        os: [ 'ubuntu-22.04', 'ubuntu-20.04']
-        postgres-images: [ 'postgres:latest']
-        go-version: ['1.20']
+        os: ["ubuntu-latest", "ubuntu-24.04"]
+        postgres-images: ["postgres:latest"]
+        go-version: ["1.20"]
     runs-on: ${{ matrix.os }}
 
     services:
@@ -37,25 +35,16 @@ jobs:
           --health-retries 5
 
     steps:
-    - uses: actions/checkout@v3
-
-    - name: Start MongoDB
-      uses: supercharge/mongodb-github-action@1.8.0
-      with:
-        mongodb-version: ${{ matrix.mongodb-version }}
-        mongodb-username: mbtestuser
-        mongodb-password: mbtestpwd
-        mongodb-db: mbtestdb
-
-    - uses: actions/setup-go@v3
-      with:
-        go-version: ${{matrix.go-version}}
-
-    - name: Run all go tests
-      run: go test ./... -v -race -coverprofile=coverage.txt -covermode=atomic
-      env:
-        MONGODB_HOST: localhost
-        POSTGRES_HOST: localhost
-        TEST_DATA_DIR: /home/runner/work/MassBank3/MassBank3/
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-go@v3
+        with:
+          go-version: ${{matrix.go-version}}
+
+      # - name: Run all go tests
+      #   run: go test ./... -v -race -coverprofile=coverage.txt -covermode=atomic
+      #   env:
+      #     POSTGRES_HOST: localhost
+      #     TEST_DATA_DIR: /home/runner/work/MassBank3/MassBank3/
+      # - name: Upload coverage to Codecov
+      #   uses: codecov/codecov-action@v3

.gitignore

@@ -14,10 +14,14 @@
 # Dependency directories (remove the comment below to include it)
 # vendor/
 /docker/.env
-/.idea/
+.idea/
 /docker/debuglog/
 /scripts/bin/
 /docker/deploy.sh
+/docker/deploy_with_init.sh
 
 # misc
-.DS_Store
+.DS_Store/
+.vscode/
+/compose/.env
+

cmd/mb3server/.openapi-generator-ignore renamed to .openapi-generator-ignore

@@ -21,6 +21,13 @@
 #docs/*.md
 # Then explicitly reverse the ignore rule for a single file:
 #!docs/README.md
+
+Dockerfile
+README.md
+api/*
 go.mod
-src/api_default_service.go
-Dockerfile
+main.go
+pkg/mb3server/db_interface.go
+pkg/mb3server/api-impl.go
+pkg/mb3server/api_default_service.go
+

.openapi-generator/FILES

@@ -0,0 +1,42 @@
+pkg/mb3server/api.go
+pkg/mb3server/api_default.go
+pkg/mb3server/error.go
+pkg/mb3server/helpers.go
+pkg/mb3server/impl.go
+pkg/mb3server/logger.go
+pkg/mb3server/model_ac_chromatography_inner.go
+pkg/mb3server/model_ac_general_inner.go
+pkg/mb3server/model_ac_ion_mobility_inner.go
+pkg/mb3server/model_ac_mass_spec.go
+pkg/mb3server/model_ac_mass_spec_subtags_inner.go
+pkg/mb3server/model_authors_inner.go
+pkg/mb3server/model_browse_options.go
+pkg/mb3server/model_database_object.go
+pkg/mb3server/model_get_status_200_response.go
+pkg/mb3server/model_get_status_200_response_export_service.go
+pkg/mb3server/model_get_status_200_response_postgres.go
+pkg/mb3server/model_get_status_200_response_similarity_service.go
+pkg/mb3server/model_mb_record.go
+pkg/mb3server/model_mb_record_acquisition.go
+pkg/mb3server/model_mb_record_comments_inner.go
+pkg/mb3server/model_mb_record_comments_inner_one_of.go
+pkg/mb3server/model_mb_record_compound.go
+pkg/mb3server/model_mb_record_date.go
+pkg/mb3server/model_mb_record_deprecated.go
+pkg/mb3server/model_mb_record_mass_spectrometry.go
+pkg/mb3server/model_mb_record_peak.go
+pkg/mb3server/model_mb_record_peak_annotation.go
+pkg/mb3server/model_mb_record_peak_neutral_loss_inner.go
+pkg/mb3server/model_mb_record_peak_peak.go
+pkg/mb3server/model_mb_record_peak_peak_values_inner.go
+pkg/mb3server/model_mb_record_species.go
+pkg/mb3server/model_metadata.go
+pkg/mb3server/model_metadata_compound_class_inner.go
+pkg/mb3server/model_ms_data_processing_inner.go
+pkg/mb3server/model_ms_focused_ion_inner.go
+pkg/mb3server/model_search_result.go
+pkg/mb3server/model_search_result_data_inner.go
+pkg/mb3server/model_similarity_search_result.go
+pkg/mb3server/model_similarity_search_result_data_inner.go
+pkg/mb3server/model_string_count_inner.go
+pkg/mb3server/routers.go

.openapi-generator/VERSION

@@ -0,0 +1 @@
+7.12.0

.vscode/settings.json

@@ -1,6 +1,6 @@
-FROM docker.io/golang:1.20 AS build
+FROM docker.io/golang:1.23 AS build
 WORKDIR /go/src
-COPY cmd/mb3dbtool/main.go ./cmd/mb3dbtool/
+COPY pkg/mb3dbtool/main.go ./cmd/mb3dbtool/
 COPY pkg/ ./pkg
 COPY go.mod .
 
@@ -9,7 +9,14 @@ RUN go get -d -v ./...
 
 RUN go build -a -installsuffix cgo -o mb3dbtool ./cmd/mb3dbtool
 
-FROM docker.io/alpine AS runtime
+FROM docker.io/alpine:3.21 AS runtime
 COPY --from=build /go/src/mb3dbtool ./
+RUN printf 'case $MB_DB_INIT in\n\
+  true) echo Initialize database...\n\
+  ./mb3dbtool;;\n\
+  *) echo Skip database initialization...;;\n\
+  esac' > ./entrypoint.sh
+RUN chmod +x ./entrypoint.sh
+
 EXPOSE 8080/tcp
-ENTRYPOINT ["./mb3dbtool"]
+CMD ["/bin/sh","./entrypoint.sh"]