added some tests

modified CI

Author: maximiliani

.github/workflows/CI.yml

@@ -33,27 +33,37 @@ jobs:
       - name: Build with Gradle
         run: ./gradlew clean build
   test:
-    runs-on: ubuntu-latest
     strategy:
       matrix:
-        jdk: [ 17 ]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        jdk: [17]
+        python-version: [3.10]
+    runs-on: ${{ matrix.os }}
     steps:
       - name: Checkout repo
         uses: actions/checkout@v2
       - name: Set up OpenJDK
         uses: actions/setup-java@v1
         with:
           java-version: ${{ matrix.jdk }}
-      - name: Install python
-        run: sudo apt install -y python3 python3-setuptools python3-pip
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get Python location
+        run: python -c "import os, sys; print(os.path.dirname(sys.executable))"
       - name: Update pip
-        run: pip3 install --upgrade pip
+        run: python3 -m pip install --upgrade pip
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew
       - name: Clean
         run: ./gradlew clean
-      - name: Test with Gradle
-        run: ./gradlew test --scan --stacktrace
+      - if: matrix.os == 'windows-latest'
+        name: Test with Gradle on Windows
+        run: ./gradlew test -DapplicationProperties=src/test/resources/test-config/application-test-windows.properties
+      - if: matrix.os != 'windows-latest'
+        name: Test with Gradle on ${{ matrix.os }}
+        run: ./gradlew test -DapplicationProperties=src/test/resources/test-config/application-test.properties
       - name: Generate report
         run: ./gradlew jacocoTestReport
       - name: Codecov

build.gradle

@@ -30,6 +30,7 @@ repositories {
 
 ext {
     set('snippetsDir', file('build/generated-snippets'))
+    applicationProperties = System.getProperty('applicationProperties', 'src/main/resources/application.properties')
 }
 
 dependencies {
@@ -80,7 +81,9 @@ dependencies {
 test {
     outputs.dir snippetsDir
     finalizedBy jacocoTestReport
-    environment 'spring.config.location', 'classpath:/test-config/'
+    print("Running tests with configuration: ${applicationProperties}")
+    environment 'spring.config.location', applicationProperties
+//    environment 'spring.config.location', 'classpath:/test-config/'
     useJUnitPlatform()
 }
 

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.2-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
 

output

@@ -0,0 +1 @@
+Hello World!Input file: inputMapping schema file: schema

src/main/java/edu/kit/datamanager/mappingservice/util/ShellRunnerUtil.java

@@ -90,6 +90,11 @@ public static MappingPluginState run(OutputStream output, OutputStream error, St
      * @throws MappingPluginException If an error occurs.
      */
     public static MappingPluginState run(OutputStream output, OutputStream error, int timeOutInSeconds, String... command) throws MappingPluginException {
+        if (output == null) throw new MappingPluginException(MappingPluginState.INVALID_INPUT, "Output stream is null.");
+        if (error == null) throw new MappingPluginException(MappingPluginState.INVALID_INPUT, "Error stream is null.");
+        if (timeOutInSeconds <= 0) throw new MappingPluginException(MappingPluginState.INVALID_INPUT, "Timeout is null or negative.");
+        if (command == null || command.length == 0) throw new MappingPluginException(MappingPluginState.INVALID_INPUT, "No command given.");
+
         ExecutorService pool = Executors.newSingleThreadExecutor();
         int result;
         MappingPluginState returnValue = MappingPluginState.SUCCESS;
@@ -123,13 +128,13 @@ public static MappingPluginState run(OutputStream output, OutputStream error, in
                 throw new ExecutionException(new Throwable());
             }
         } catch (IOException ioe) {
-            LOGGER.error("Failed to execute python.", ioe);
+            LOGGER.error("Failed to execute command.", ioe);
             returnValue = MappingPluginState.EXECUTION_ERROR;
         } catch (TimeoutException te) {
-            LOGGER.error("Python script did not return in expected timeframe of " + TIMEOUT + " seconds", te);
+            LOGGER.error("Command did not return in expected timeframe of " + TIMEOUT + " seconds", te);
             returnValue = MappingPluginState.TIMEOUT;
         } catch (InterruptedException | ExecutionException e) {
-            LOGGER.error("Failed to execute python script due to an unknown Exception.", e);
+            LOGGER.error("Failed to execute command due to an unknown exception.", e);
             returnValue = MappingPluginState.UNKNOWN_ERROR;
         } finally {
             pool.shutdown();

src/main/resources/application.properties

@@ -33,7 +33,7 @@ spring.jpa.hibernate.ddl-auto=update
 # Mapping-Service specific settings
 ##################################################
 # Absolute path to the local python interpreter
-mapping-service.pythonLocation=file:///usr/bin/python3
+mapping-service.pythonLocation=file:///usr/bin/python4
 
 # Absolute path to the local gemma mappings folder
 mapping-service.mappingSchemasLocation=file:///tmp/mapping-service/mappingSchemas

src/test/java/edu/kit/datamanager/mappingservice/plugins/PluginManagerTest.java

@@ -99,13 +99,12 @@ void mapFileInvalidParameters() {
     @Test
     void mapFile() {
         try {
-            File outputFile = new File("src/test/resources/testOutput");
-            outputFile.delete();
-            assertFalse(outputFile.exists());
+            File outputFile = new File("/tmp/testOutput");
             PluginManager.soleInstance().mapFile("TEST_0.0.0", new File("mapping-schema").toPath(), new File("input").toPath(), outputFile.toPath());
             assertTrue(outputFile.exists());
             outputFile.delete();
         } catch (MappingPluginException e) {
+            e.printStackTrace();
             fail("Mapping failed");
         }
     }

src/test/java/edu/kit/datamanager/mappingservice/util/ShellRunnerUtilTest.java

@@ -0,0 +1,47 @@
+/*
+ * Copyright 2022 Karlsruhe Institute of Technology.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *        http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.kit.datamanager.mappingservice.util;
+
+import edu.kit.datamanager.mappingservice.plugins.MappingPluginException;
+import edu.kit.datamanager.mappingservice.plugins.MappingPluginState;
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+class ShellRunnerUtilTest {
+
+    @Test
+    void runValid(){
+        try {
+            assertEquals(MappingPluginState.SUCCESS, ShellRunnerUtil.run("echo", "test"));
+            assertEquals(MappingPluginState.SUCCESS, ShellRunnerUtil.run(5, "echo", "test"));
+            assertEquals(MappingPluginState.SUCCESS, ShellRunnerUtil.run(System.out, System.err, "echo", "test"));
+        } catch (MappingPluginException e) {
+            fail(e);
+        }
+    }
+
+    @Test
+    void runInvalid() {
+        assertThrows(MappingPluginException.class, () -> ShellRunnerUtil.run(null));
+        assertThrows(MappingPluginException.class, () -> ShellRunnerUtil.run("blablusdhflakjdsfh"));
+        assertThrows(MappingPluginException.class, () -> ShellRunnerUtil.run(-5, "echo", "test"));
+        assertThrows(MappingPluginException.class, () -> ShellRunnerUtil.run(null, System.err, "echo", "test"));
+        assertThrows(MappingPluginException.class, () -> ShellRunnerUtil.run(System.err, null, "echo", "test"));
+        assertThrows(MappingPluginException.class, () -> ShellRunnerUtil.run(1, "cat", "/dev/urandom"));
+        assertThrows(MappingPluginException.class, () -> ShellRunnerUtil.run(1, "sudo", "cat", "/dev/urandom"));
+    }
+}

src/test/resources/test-config/application-test-windows.properties

@@ -0,0 +1,44 @@
+#
+# Copyright 2022 Karlsruhe Institute of Technology.
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#        http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+# General Spring Boot Settings (do not change!)
+spring.main.allow-bean-definition-overriding=true
+spring.main.allow-circular-references=true
+server.port=8095
+# Data transfer settings, e.g. transfer compression and multipart message size.
+# The properties max-file-size and max-request-size define the maximum size of files 
+# transferred to and from the repository. Setting them to -1 removes all limits.
+server.compression.enabled=false
+spring.servlet.multipart.max-file-size=100MB
+spring.servlet.multipart.max-request-size=100MB
+# Logging settings
+logging.level.root=ERROR
+logging.level.edu.kit.datamanager=INFO
+springdoc.swagger-ui.disable-swagger-default-url=true
+# Actuator settings
+info.app.name=Mapping-Service
+info.app.description=Generic mapping service supporting different mapping implementations.
+info.app.group=edu.kit.datamanager
+info.app.version=1.0.0
+management.endpoint.health.probes.enabled=true
+management.endpoints.web.exposure.include=*
+
+##################################################
+# Mapping-Service specific settings
+##################################################
+# Absolute path to the local python interpreter
+mapping-service.pythonLocation=file:///usr/bin/python3
+# Absolute path to the local gemma mappings folder
+mapping-service.mappingSchemasLocation=file://mapping-service