Merge branch 'master' of https://github.com/ESIPFed/Geoweaver into do…

…cker-image

.github/workflows/commit_workflow.yml

@@ -36,3 +36,107 @@ jobs:
         with:
           name: geoweaver-jacoco-coverage-report
           path: target/site/jacoco
+  test-mysql:
+    runs-on: ubuntu-latest
+
+    services:
+      mysql:
+        image: mysql:latest
+        env:
+          MYSQL_ROOT_PASSWORD: geoweaver
+          MYSQL_DATABASE: geoweaver
+        ports:
+          - 3306:3306
+        options: --health-cmd="mysqladmin ping -h localhost" --health-interval=10s --health-timeout=5s --health-retries=5
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up JDK 11
+      uses: actions/setup-java@v3
+      with:
+        java-version: '11'
+        distribution: 'temurin'
+        architecture: x64
+
+    - name: Create geoweaver directory and application.properties
+      run: |
+        mkdir -p ~/geoweaver
+        echo "spring.datasource.url=jdbc:mysql://localhost:3306/geoweaver" >> ~/geoweaver/application.properties
+        echo "spring.datasource.username=root" >> ~/geoweaver/application.properties
+        echo "spring.datasource.password=geoweaver" >> ~/geoweaver/application.properties
+        echo "spring.datasource.driver-class-name=com.mysql.cj.jdbc.Driver" >> ~/geoweaver/application.properties
+        echo "spring.jpa.database-platform=org.hibernate.dialect.MySQL8Dialect" >> ~/geoweaver/application.properties
+
+    - name: Run Tests
+      run: |
+        mvn test jacoco:report
+      working-directory: ${{ github.workspace }}
+
+    - name: Check If All Tests Pass
+      run: |
+        if [ $? -eq 0 ]; then
+          echo "All tests passed successfully."
+        else
+          echo "Tests failed."
+          exit 1  # Exit with an error code to stop the workflow
+        fi
+
+    - name: Save Geoweaver JaCoCo HTML Report
+      uses: actions/upload-artifact@v2
+      with:
+        name: geoweaver-jacoco-coverage-report
+        path: target/site/jacoco
+
+  test-postgresql:
+    runs-on: ubuntu-latest
+
+    services:
+      postgres:
+        image: postgres:latest
+        env:
+          POSTGRES_PASSWORD: geoweaver
+          POSTGRES_DB: geoweaver
+        ports:
+          - 5432:5432
+        options: --health-cmd="pg_isready -U postgres" --health-interval=10s --health-timeout=5s --health-retries=5
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up JDK 11
+      uses: actions/setup-java@v3
+      with:
+        java-version: '11'
+        distribution: 'temurin'
+        architecture: x64
+
+    - name: Create geoweaver directory and application.properties
+      run: |
+        mkdir -p ~/geoweaver
+        echo "spring.datasource.url=jdbc:postgresql://localhost:5432/geoweaver" >> ~/geoweaver/application.properties
+        echo "spring.datasource.username=postgres" >> ~/geoweaver/application.properties
+        echo "spring.datasource.password=geoweaver" >> ~/geoweaver/application.properties
+        echo "spring.datasource.driver-class-name=org.postgresql.Driver" >> ~/geoweaver/application.properties
+        echo "spring.jpa.database-platform=org.hibernate.dialect.PostgreSQLDialect" >> ~/geoweaver/application.properties
+
+    - name: Run Tests
+      run: |
+        mvn test jacoco:report
+      working-directory: ${{ github.workspace }}
+
+    - name: Check If All Tests Pass
+      run: |
+        if [ $? -eq 0 ]; then
+          echo "All tests passed successfully."
+        else
+          echo "Tests failed."
+          exit 1  # Exit with an error code to stop the workflow
+        fi
+
+    - name: Save Geoweaver JaCoCo HTML Report
+      uses: actions/upload-artifact@v2
+      with:
+        name: geoweaver-jacoco-coverage-report
+        path: target/site/jacoco
+

pom.xml

@@ -11,7 +11,7 @@
 	</parent>
 	<groupId>com.gw</groupId>
 	<artifactId>geoweaver</artifactId>
-	<version>1.4.8</version>
+	<version>1.4.9</version>
 	<name>geoweaver</name>
 	<description>A lightweight workflow management software for organizing data analysis workflows, 
 	preserving history of every workflow run, and improving scientist producitvity and workflow FAIRness,
@@ -79,6 +79,19 @@
 		</dependency>
 
 
+		<dependency>
+			<groupId>org.postgresql</groupId>
+			<artifactId>postgresql</artifactId>
+			<version>42.3.8</version>
+		</dependency>
+
+		<dependency>
+			<groupId>com.mysql</groupId>
+			<artifactId>mysql-connector-j</artifactId>
+			<version>8.3.0</version>
+		</dependency>
+
+
 		<dependency>
 			<groupId>org.projectlombok</groupId>
 			<artifactId>lombok</artifactId>

src/main/java/com/gw/database/CheckpointRepository.java

@@ -5,6 +5,9 @@
 import java.util.UUID;
 import org.springframework.data.jpa.repository.JpaRepository;
 
+import javax.transaction.Transactional;
+
+@Transactional
 public interface CheckpointRepository extends JpaRepository<Checkpoint, UUID> {
   List<Checkpoint> findByWorkflowId(String workflowId);
 

src/main/java/com/gw/database/EnvironmentRepository.java

@@ -5,11 +5,14 @@
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.CrudRepository;
 
+import javax.transaction.Transactional;
+
 /**
  * The EnvironmentRepository interface provides methods for querying environment configurations from
  * a database. It extends the CrudRepository interface to handle database operations for the
  * Environment entity.
  */
+@Transactional
 public interface EnvironmentRepository extends CrudRepository<Environment, String> {
 
   /**
@@ -22,13 +25,8 @@ public interface EnvironmentRepository extends CrudRepository<Environment, Strin
    * @param basedir The base directory.
    * @return A collection of environment configurations matching the specified criteria.
    */
-  @Query(
-      value =
-          "select * from environment where hostid = ?1 and bin = ?2 and pyenv = ?3 and basedir ="
-              + " ?4",
-      nativeQuery = true)
-  Collection<Environment> findEnvByID_BIN_ENV_BaseDir(
-      String hostid, String bin, String pyenv, String basedir);
+  @Query("SELECT e FROM Environment e WHERE e.hostobj.id = :hostid AND e.bin = :bin AND e.pyenv = :pyenv AND e.basedir = :basedir")
+  Collection<Environment> findEnvByID_BIN_ENV_BaseDir(String hostid, String bin, String pyenv, String basedir);
 
   /**
    * Find environment configurations based on the provided host ID and binary path.
@@ -37,7 +35,7 @@ Collection<Environment> findEnvByID_BIN_ENV_BaseDir(
    * @param bin The binary path.
    * @return A collection of environment configurations matching the specified host and binary path.
    */
-  @Query(value = "select * from environment where hostid = ?1 and bin = ?2", nativeQuery = true)
+  @Query("SELECT e FROM Environment e WHERE e.hostobj.id = :hostid AND e.bin = :bin")
   Collection<Environment> findEnvByID_BIN(String hostid, String bin);
 
   /**
@@ -46,6 +44,7 @@ Collection<Environment> findEnvByID_BIN_ENV_BaseDir(
    * @param hostid The ID of the host.
    * @return A collection of environment configurations associated with the specified host.
    */
-  @Query(value = "select * from environment where hostid = ?1", nativeQuery = true)
+  @Query("SELECT e FROM Environment e WHERE e.hostobj.id = :hostid")
   Collection<Environment> findEnvByHost(String hostid);
+
 }