Merge pull request #4 from CIAT-DAPA/develop

Develop

.github/workflows/test_pipeline.yml

@@ -99,7 +99,7 @@ jobs:
         commit_message: "Update version to ${{ steps.taggerDryRun.outputs.new_tag }}"
     # API Zip
     - name: Zip artifact for deployment
-      run: zip releaseAPI.zip ./src/* -r
+      run: cd ./src && zip -r ../releaseAPI.zip ./* && cd ..
     # Upload Artifacts
     - name: Upload ORM artifact for deployment job
       uses: actions/upload-artifact@v3

Jenkinsfile

@@ -0,0 +1,185 @@
+// Define an empty map for storing remote SSH connection parameters
+def remote = [:]
+
+pipeline {
+    agent any
+
+    environment {
+        server_name = credentials('name_spcat')
+        server_host = credentials('host_spcat')
+        ssh_key = credentials('spcat_key')
+    }
+
+    stages {
+        stage('Connection to AWS server') {
+            steps {
+                script {
+                    // Set up remote SSH connection parameters
+                    remote.allowAnyHosts = true
+                    remote.identityFile = ssh_key
+                    remote.user = ssh_key_USR
+                    remote.name = server_name
+                    remote.host = server_host
+
+                }
+            }
+        }
+
+        stage('Verify Api folder and environment') {
+            steps {
+                script {
+                    sshCommand remote: remote, command: '''
+                        # Verify and create the api_SPCAT folder if it does not exist and the virtual environment
+                        if [ ! -d api_SPCAT ]; then
+                            mkdir ./api_SPCAT
+                            cd ./api_SPCAT
+                            python3 -m venv env
+                        fi
+                    '''
+
+                }
+            }
+        }
+
+        stage('Stop previous API') {
+            steps {
+                script {
+                    sshCommand remote: remote, command: '''
+                        # Stop the API if it is running
+                        
+                        cd ./api_SPCAT
+
+                        if [ -f pid.txt ]; then
+                            PID_API_SPCAT=$(cat pid.txt)
+                            if kill -0 "$PID_API_SPCAT" 2>/dev/null; then
+                                echo "The process exists, stopping it..."
+                                kill "$PID_API_SPCAT"
+                            fi
+                        fi
+                    '''
+                }
+            }
+        }
+
+        stage('Backup previous files') {
+            steps {
+                script {
+                    sshCommand remote: remote, command: '''
+                        # Saving old API files
+                        cd ./api_SPCAT
+                        rm -rf api_antiguo
+                        if [ -d api_actual ]; then
+                            mv api_actual api_antiguo
+                        fi
+                    '''
+                }
+            }
+        }
+
+        stage('Download latest release') {
+            steps {
+                script {
+                    sshCommand remote: remote, command: '''
+                        # Download the latest release from GitHub
+                        cd ./api_SPCAT
+                        rm -rf releaseApi.zip
+                        curl -LOk https://github.com/CIAT-DAPA/spcat_webapi/releases/latest/download/releaseApi.zip
+                        rm -rf api_actual
+                        unzip releaseApi.zip -d api_actual
+                    '''
+                }
+            }
+        }
+
+        stage('Update dependencies') {
+            steps {
+                script {
+                    sshCommand remote: remote, command: '''
+                        cd ./api_SPCAT
+                        # Activate the virtual environment
+                        source env/bin/activate
+                        
+                        # Updating the dependencies
+                        pip install --upgrade setuptools wheel
+                        pip install -r api_actual/requirements.txt
+                    '''
+                }
+            }
+        }
+
+        stage('Start API') {
+            steps {
+                script {
+                    sshCommand remote: remote, command: '''
+                        # Configure variables for deployment
+                        while IFS= read -r line; do
+                            export "$line"
+                        done < variables.txt
+
+                        
+                        # Activate the virtual environment
+                        cd ./api_SPCAT
+                        source env/bin/activate
+
+                        
+
+                        # Start API
+                        cd ./api_actual
+                        nohup python3 api.py > api_spcat.log 2>&1 &
+                        
+                        # Get the new PID and save it to a file
+                        PID_API_SPCAT=$!
+                        echo $PID_API_SPCAT > ../pid.txt
+                    '''
+                }
+            }
+        }
+
+        stage('Verify API') {
+            steps {
+                script {
+                    def apiUrl = "http://127.0.0.1:5000"
+
+                    //def response = sh(script: "curl -sL -w \"%{http_code}\" -o /dev/null ${apiUrl}", returnStdout: true)
+
+                    def response = sshCommand remote: remote, command: "curl -sL -w \"%{http_code}\" -o /dev/null ${apiUrl}"
+
+                    if (response.trim() == '200') {
+                        echo "API is running correctly."
+                    } else {
+                        error "API is not running correctly. Rolling back..."
+                    }
+                }
+            }
+        }
+    }
+
+    post {
+        failure {
+            script {
+                sshCommand remote: remote, command: '''
+                    # Configure variables for deployment
+                    while IFS= read -r line; do
+                        export "$line"
+                    done < variables.txt
+
+                    # Rollback to the previous API if any step fails
+                    cd ./api_SPCAT
+                    rm -rf api_actual
+                    mv api_antiguo api_actual
+
+                    # Activate the virtual environment
+                    source env/bin/activate
+
+                    # Start API
+                    cd ./api_actual
+                    nohup python3 api.py > api_spcat.log 2>&1 &
+                    
+                    # Get the new PID and save it to a file
+                    PID_API_SPCAT=$!
+                    echo $PID_API_SPCAT > ../pid.txt
+                '''
+            }
+        }
+    }
+}

src/api.py

@@ -43,8 +43,4 @@ def send_static(path):
     connect(host=config['CONNECTION_DB'])
     print("Connected DB")
 
-    if config['DEBUG']:
-        app.run(threaded=True, port=config['PORT'], debug=config['DEBUG'])
-    else:
-        app.run(host=config['HOST'], port=config['PORT'],
-                debug=config['DEBUG'])
+    app.run(threaded=True, host=config['HOST'], port=config['PORT'], debug=config['DEBUG'])

src/config.py

@@ -6,9 +6,9 @@
     config['DEBUG'] = True
     config['HOST'] = 'localhost'
     config['PORT'] = 5000
-    config['CONNECTION_DB']='mongodb://root:s3cr3t@localhost:27017/dbgap?authSource=admin'
+    config['CONNECTION_DB']='mongodb://localhost:27017/dbgap'
 else:
     config['DEBUG'] = False
     config['HOST'] = '0.0.0.0'
-    config['PORT'] = os.getenv('PORT')
+    config['PORT'] = os.getenv('API_SPCAT_PORT')
     config['CONNECTION_DB']=os.getenv('CONNECTION_DB')

src/requirements.txt

@@ -8,6 +8,7 @@ Flask==2.2.3
 Flask-Cors==3.0.10
 Flask-RESTful==0.3.9
 flask-swagger-ui==4.11.1
+gunicorn==20.1.0
 itsdangerous==2.1.2
 Jinja2==3.1.2
 jsonschema==4.17.3