Merge from master

.github/workflows/build-staging.yml

@@ -0,0 +1,114 @@
+name: Gigwa Build Staging test
+on:
+  push:
+    tags:
+      - 'STAGING'
+jobs:
+  pre-realese:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/[email protected]
+
+      - name: Set up Java
+        uses: actions/[email protected]
+        with:
+          distribution: 'zulu'
+          java-version: 17
+
+      - name: Build project
+        run: |
+          wget https://raw.githubusercontent.com/${{ github.repository }}/staging/misc/build-staging.sh
+          chmod +x build-staging.sh
+          ./build-staging.sh -P staging
+          pwd
+          ls
+
+      - name: Delete old prelease and tag
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          TAG_NAME=$(basename ${{ github.ref }})
+          echo "Deleting release and tag $TAG_NAME"
+
+          # Get the release ID associated with the tag
+          RELEASE_ID=$(curl -s -H "Authorization: token $GITHUB_TOKEN" \
+            "https://api.github.com/repos/${{ github.repository }}/releases/tags/$TAG_NAME" \
+            | jq -r '.id')
+
+          if [ "$RELEASE_ID" != "null" ]; then
+            echo "Deleting release with ID $RELEASE_ID"
+            # Delete the release
+            curl -s -X DELETE -H "Authorization: token $GITHUB_TOKEN" \
+              "https://api.github.com/repos/${{ github.repository }}/releases/$RELEASE_ID"
+          else
+            echo "No release found for tag $TAG_NAME"
+          fi
+
+          # Delete the tag locally
+          git tag -d $TAG_NAME
+          # Delete the tag from the remote repository
+          git push origin :refs/tags/$TAG_NAME
+
+      - name: Set up variables
+        id: vars
+        run: |
+          echo "DATE=$(date +'%d/%m/%y')" >> $GITHUB_ENV
+          echo "SHORT_SHA=$(git rev-parse --short HEAD)" >> $GITHUB_ENV
+          echo "NEW_NAME=Gigwa2_STAGING" >> $GITHUB_ENV
+
+      - name: Create prerelease
+        id: create_release
+        uses: actions/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: "STAGING"
+          release_name: "STAGING"
+          draft: false
+          prerelease: true
+          body: "This is a staging prerelease ${{ env.DATE }} ${{ env.SHORT_SHA }}"
+
+      - name: Grep release version
+        id: grep_release_version
+        run: |
+          # RESULT=$(grep -m 1 project\\\.version ${{ github.event.repository.name }}/pom.xml | sed -n 's/.*<project\.version>\(.*\)<\/project\.version>.*/\1/p')
+          echo "release_version=$(grep -m 1 project\\\.version ${{ github.event.repository.name }}/pom.xml | sed -n 's/.*<project\.version>\(.*\)<\/project\.version>.*/\1/p')" >>$GITHUB_OUTPUT
+        shell: bash
+
+      - name: Upload main prerelease asset (webapp zip)
+        id: upload-release-asset
+        uses: actions/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }}
+          asset_path: ${{ github.event.repository.name }}/target/Gigwa_V${{ steps.grep_release_version.outputs.release_version }}_Webapp.zip
+          asset_name: ${{ env.NEW_NAME }}.zip
+          asset_content_type: application/zip
+
+#  ssh:
+#    runs-on: ubuntu-latest
+#    needs: build
+#    steps:
+#      - name: Checkout
+#        uses: actions/checkout@v3
+#      - name: Install OpenVPN
+#        run: |
+#          sudo apt update
+#          sudo apt install -y openvpn openvpn-systemd-resolved
+#      - name: Connect to VPN
+#        uses: "kota65535/github-openvpn-connect-action@v2"
+#        with:
+#          config_file: .github/workflows/client.ovpn
+#          username: ${{ secrets.OVPN_USERNAME }}
+#          password: ${{ secrets.OVPN_PASSWORD }}
+#          client_key: ${{ secrets.USER_KEY }}
+#      - name: Use SSH
+#        uses: appleboy/ssh-action@master
+#        with:
+#          host: ${{ secrets.SERVER_HOST }}
+#          username: ${{ secrets.SERVER_USERNAME }}
+#          key: ${{ secrets.SSH_PRIVATE_KEY }}
+#          script: |
+#            ls

.github/workflows/build.yml

@@ -0,0 +1,147 @@
+name: Gigwa Build
+
+on:
+  workflow_dispatch
+
+jobs:
+  setup-and-build:
+    runs-on: ubuntu-latest
+    outputs:
+      # Output the release version to be used in the following steps
+      release_version: ${{ steps.grep_release_version.outputs.release_version }}
+    steps:
+      - uses: actions/checkout@v4
+
+      # Set up Python for the build script
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+
+      # Install Python dependencies for the build script
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install gitpython
+
+      # Set up Java for the maven build
+      - name: Set up Java
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'zulu'
+          java-version: 17
+
+      # Get the release version from the pom.xml file
+      - name: Grep release version
+        id: grep_release_version
+        run: |
+          echo "release_version=$(grep -m 1 project\\\.version pom.xml | sed -n 's/.*<project\.version>\(.*\)<\/project\.version>.*/\1/p')" >> $GITHUB_OUTPUT
+
+      # Run the maven build script which will build the project and create the Webapp zip
+      - name: Run Python build script
+        run: |
+          cd misc
+          python3 build.py
+
+      # Upload the Webapp zip as artifact for upload-release-assets
+      - name: Upload Webapp zip
+        uses: actions/upload-artifact@v3
+        with:
+          name: Gigwa_V${{ steps.grep_release_version.outputs.release_version }}_Webapp.zip
+          path: target/Gigwa_V${{ steps.grep_release_version.outputs.release_version }}_Webapp.zip
+
+      # Upload the Gigwa directory as artifact for the Dockerfile
+      - name: Upload Gigwa directory
+        uses: actions/upload-artifact@v3
+        with:
+          name: gigwa
+          path: target/gigwa/
+
+  create-release:
+    needs: setup-and-build
+    runs-on: ubuntu-latest
+    outputs:
+      # Output the upload URL to be used in the following steps
+      upload_url: ${{ steps.create_release.outputs.upload_url }}
+    steps:
+      # Create a release with the good version and add a description
+      - name: Create Release
+        id: create_release
+        uses: actions/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: "${{ needs.setup-and-build.outputs.release_version }}"
+          release_name: "${{ needs.setup-and-build.outputs.release_version }}"
+          body: |
+            For initial setups not using Docker, download the bundle creation script corresponding to your OS, place it in the desired installation location, and launch it!
+          draft: false
+          prerelease: false
+
+  upload-release-assets:
+    needs: [setup-and-build, create-release]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # Define the assets to be uploaded with their path, name, content type, and add a flag "download" to download the asset before uploading it
+        asset:
+          - { path: "target/Gigwa_V${{ needs.setup-and-build.outputs.release_version }}_Webapp.zip", name: "Gigwa_V${{ needs.setup-and-build.outputs.release_version }}_Webapp.zip", content_type: "application/zip", downloaded: true }
+          - { path: "misc/macos_bundle.command", name: "Gigwa_V${{ needs.setup-and-build.outputs.release_version }}_bundle_creation_osx.command", content_type: "application/x-sh" }
+          - { path: "misc/linux_bundle.sh", name: "Gigwa_V${{ needs.setup-and-build.outputs.release_version }}_bundle_creation_ubuntu.sh", content_type: "application/x-sh" }
+          - { path: "misc/win_bundle.ps1", name: "Gigwa_V${{ needs.setup-and-build.outputs.release_version }}_bundle_creation_windows.ps1", content_type: "application/powershell" }
+          - { path: "docker-compose.yml", name: "Gigwa_V${{ needs.setup-and-build.outputs.release_version }}_docker-compose.yml", content_type: "application/yml" }
+    steps:
+      - uses: actions/checkout@v4
+
+      # Download the asset if the flag "download" is set to true
+      - name: Download Webapp zip
+        if: matrix.asset.downloaded == true
+        uses: actions/download-artifact@v3
+        with:
+          name: Gigwa_V${{ needs.setup-and-build.outputs.release_version }}_Webapp.zip
+          path: target/
+
+      # Upload the asset to the release
+      - name: Upload Release Asset
+        uses: actions/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ needs.create-release.outputs.upload_url }}
+          asset_path: ${{ matrix.asset.path }}
+          asset_name: ${{ matrix.asset.name }}
+          asset_content_type: ${{ matrix.asset.content_type }}
+
+  build-push-docker:
+    needs: [ setup-and-build, create-release ]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      # Set up Docker Buildx for multi-platform builds
+      - name: Set up Docker Buildx
+        uses: docker/[email protected]
+
+      # Login to Docker Hub
+      - name: Login to Docker Hub
+        uses: docker/[email protected]
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      # Download the Gigwa directory artifact for the Dockerfile
+      - name: Download gigwa directory
+        uses: actions/download-artifact@v3
+        with:
+          name: gigwa
+          path: target/gigwa/
+
+      # Build and push the Docker image
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          push: true
+          tags: |
+            ${{ secrets.DOCKERHUB_USERNAME }}/gigwa:${{ needs.setup-and-build.outputs.release_version }}
+            ${{ secrets.DOCKERHUB_USERNAME }}/gigwa:latest

Dockerfile

@@ -1,4 +1,4 @@
-FROM tomcat:8.5.81-jre8-openjdk-slim-bullseye
+FROM tomcat:9.0.58-jdk17-openjdk-slim
 
 ENV LANG C.UTF-8
 ENV LC_ALL C.UTF-8

LICENSE.txt

@@ -0,0 +1,14 @@
+GIGWA - Genotype Investigator for Genome Wide Analyses
+Copyright (C) 2016, 2024 <South Green> <CIRAD> <IRD>
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU Affero General Public License, version 3 as published by
+the Free Software Foundation.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
+details.
+
+See <http://www.gnu.org/licenses/agpl.html> for details about GNU General
+Public License V3.

README.md

@@ -13,12 +13,18 @@ https://github.com/SouthGreenPlatform/Gigwa2/wiki
 
 The source code is available in this repository. It uses Maven for dependency management and requires the following dependencies to be present in your workspace (order matters):
 
-##### https://github.com/SouthGreenPlatform/GenotypeFileManipulation
-##### https://github.com/SouthGreenPlatform/Mgdb2BrapiModel
-##### https://github.com/SouthGreenPlatform/Mgdb2
-##### https://github.com/SouthGreenPlatform/Mgdb2Export
-##### https://github.com/SouthGreenPlatform/role_manager
-##### https://github.com/SouthGreenPlatform/Gigwa2ServiceInterface
-##### https://github.com/SouthGreenPlatform/Gigwa2ServiceImpl
-##### https://github.com/SouthGreenPlatform/Mgdb2BrapiImpl
-##### https://github.com/SouthGreenPlatform/Mgdb2BrapiV2Impl
+##### https://github.com/GuilhemSempere/GenotypeFileManipulation
+##### https://github.com/GuilhemSempere/Mgdb2BrapiModel
+##### https://github.com/GuilhemSempere/Mgdb2
+##### https://github.com/GuilhemSempere/Mgdb2Export
+##### https://github.com/GuilhemSempere/role_manager
+##### https://github.com/GuilhemSempere/Mgdb2BrapiImpl
+##### https://github.com/GuilhemSempere/Mgdb2BrapiV2Impl
+##### https://github.com/GuilhemSempere/Gigwa2ServiceInterface
+##### https://github.com/GuilhemSempere/Gigwa2ServiceImpl
+
+Gigwa2 project now contains **bom/pom.xml** which can be used as a parent project that **treats all required projects as Maven modules**, and thus **allows to build them all with a single mvn install** (all projects, including Gigwa2 have to sit at the same level though)
+
+A quick and convenient way to **build the latest version of Gigwa at once** is to use the following script misc/build.sh:
+- ideally not from within the Gigwa2 source hierarchy, otherwise it will create duplicate source files
+- assuming that for each referenced project, a git tag exists, named after the value found in pom.xml's <project.version>

bom/pom.xml

@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>fr.cirad</groupId>
+    <artifactId>Gigwa2bom</artifactId>
+    <version>1.0-RELEASE</version>
+    <packaging>pom</packaging>
+
+ 	<modules>
+	    <module>../../GenotypeFileManipulation</module>
+   	    <module>../../Mgdb2BrapiModel</module>
+        <module>../../Mgdb2</module>
+	    <module>../../Mgdb2Export</module>
+		<module>../../role_manager</module>
+		<module>../../Mgdb2BrapiImpl</module>
+		<module>../../Mgdb2BrapiV2Impl</module>
+		<module>../../Gigwa2ServiceImpl</module>
+		<module>../../Gigwa2ServiceInterface</module>
+		<module>..</module>
+	</modules>
+</project>

bundle_files/osx/updateGigwa.command

@@ -7,11 +7,24 @@ fi
 
 if [ -d "$1" ]; then
 	if [ -d "$2" ]; then
-
+
+	if [ ! -d "$1/WEB-INF" ]; then
+      echo "Error: $1 does not contain a WEB-INF directory."
+      exit 1
+    fi
+
+    if [ ! -d "$2/WEB-INF" ]; then
+      echo "Error: $2 does not contain a WEB-INF directory."
+      exit 1
+    fi
+
 		DATE=$(date +%Y%m%d%H%M)
 
+		# Get the name of the last directory in the second argument path
+    	backup_dir=$(basename "$2")
+
 		#save old gigwa files
-		mkdir -p $3 && cp -av $2 $3/gigwa.$DATE
+		mkdir -p "$3" && cp -av "$2" "$3/$backup_dir.$DATE"
 
 		#remove gigwa folder
 		rm -rf $2
@@ -20,15 +33,16 @@ if [ -d "$1" ]; then
 		cp -av $1 $2
 
 		#copy configuration files from saved folder to new gigwa folder
-		cp -av $3/gigwa.$DATE/WEB-INF/classes/applicationContext-data.xml $2/WEB-INF/classes/applicationContext-data.xml
-#		cp -av $3/gigwa.$DATE/WEB-INF/classes/applicationContext-security.xml $2/WEB-INF/classes/applicationContext-security.xml
-		cp -av $3/gigwa.$DATE/WEB-INF/classes/datasources.properties $2/WEB-INF/classes/datasources.properties
-		cp -av $3/gigwa.$DATE/WEB-INF/classes/users.properties $2/WEB-INF/classes/users.properties
-		cp -av $3/gigwa.$DATE/WEB-INF/classes/config.properties $2/WEB-INF/classes/config.properties
-		cp -av $3/gigwa.$DATE/WEB-INF/classes/log4j.xml $2/WEB-INF/classes/log4j.xml
+		cp -av $3/$backup_dir.$DATE/WEB-INF/classes/applicationContext-data.xml $2/WEB-INF/classes/applicationContext-data.xml
+#		cp -av $3/$backup_dir.$DATE/WEB-INF/classes/applicationContext-security.xml $2/WEB-INF/classes/applicationContext-security.xml
+		cp -av $3/$backup_dir.$DATE/WEB-INF/classes/datasources.properties $2/WEB-INF/classes/datasources.properties
+		cp -av $3/$backup_dir.$DATE/WEB-INF/classes/users.properties $2/WEB-INF/classes/users.properties
+		cp -av $3/$backup_dir.$DATE/WEB-INF/classes/config.properties $2/WEB-INF/classes/config.properties
+		cp -av $3/$backup_dir.$DATE/WEB-INF/classes/log4j.xml $2/WEB-INF/classes/log4j.xml
 
 		# Changes specific to migration to v2.5
-		sed -i 's/project\$CREATOR/SUPERVISOR/g' $2/WEB-INF/classes/users.properties	# replace the deprecated project-CREATOR role with the new DB-level SUPERVISOR role
+
+		sed -i '' 's/project\$CREATOR/SUPERVISOR/g' "$2"/WEB-INF/classes/users.properties # replace the deprecated project-CREATOR role with the new DB-level SUPERVISOR role
 
 		if [ "$(grep -c dumpFolder $2/WEB-INF/classes/config.properties)" -eq 0 ]; then
 			printf "\n\ndumpFolder=$HOME/gigwaDumps" >> $2/WEB-INF/classes/config.properties	# add dumpFolder entry to config.properties it not present
@@ -39,8 +53,8 @@ if [ -d "$1" ]; then
 		fi
 
 		# applicationContext-security.xml has changed much in v2.5 so we don't want to keep that of the previous version. However, still make sure we keep the same passwordEncoder we had
-		if [ "$(grep 'id="passwordEncoder"' $3/gigwa.$DATE/WEB-INF/classes/applicationContext-security.xml | grep -v '<!--')" != "$(grep 'id="passwordEncoder"' $2/WEB-INF/classes/applicationContext-security.xml | grep -v '<!--')" ]; then
-			sed -i "s/.*PasswordEncoder.*//g;s/.*Only one passwordEncoder bean should be enabled at a time.*//g;s|</secur:http>|</secur:http>\n\n\n$(grep 'id="passwordEncoder"' $3/gigwa.$DATE/WEB-INF/classes/applicationContext-security.xml | grep -v '<!--')|g;" $2/WEB-INF/classes/applicationContext-security.xml
+		if [ "$(grep 'id="passwordEncoder"' $3/$backup_dir.$DATE/WEB-INF/classes/applicationContext-security.xml | grep -v '<!--')" != "$(grep 'id="passwordEncoder"' $2/WEB-INF/classes/applicationContext-security.xml | grep -v '<!--')" ]; then
+			sed -i '' "s/.*PasswordEncoder.*//g;s/.*Only one passwordEncoder bean should be enabled at a time.*//g;s|</secur:http>|</secur:http>\n\n\n$(grep 'id="passwordEncoder"' $3/$backup_dir.$DATE/WEB-INF/classes/applicationContext-security.xml | grep -v '<!--')|g;" $2/WEB-INF/classes/applicationContext-security.xml
 		fi
 	fi
 fi