Merge pull request #70 from sanctuuary/dev

Merge pom tags needed to publish to mvn Fix tests
sanctuuary · Aug 1, 2023 · 77f1fbd · 77f1fbd
2 parents 0003126 + dbaa52f
commit 77f1fbd
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Showing 4 changed files with 69 additions and 46 deletions.
diff --git a/.travis.yml b/.travis.yml
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>io.github.sanctuuary</groupId>
 	<artifactId>APE</artifactId>
-	<version>2.1.4</version>
+	<version>2.1.5</version>
 	<packaging>jar</packaging>
 	<name>io.github.sanctuuary:APE</name>
 	<description>APE is a command line tool and an API for the automated exploration of possible computational pipelines (workflows) from large collections of computational tools.</description>
@@ -65,12 +65,30 @@
 					</execution>
 				</executions>
 			</plugin>
+			<plugin>
+          		<groupId>org.apache.maven.plugins</groupId>
+          		<artifactId>maven-surefire-plugin</artifactId>
+          		<version>3.0.0-M5</version>
+        	</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-surefire-plugin</artifactId>
-				<version>3.0.0-M4</version>
+				<artifactId>maven-site-plugin</artifactId>
+				<version>3.7.1</version>
 			</plugin>
- 			<plugin>
+			<plugin>
+		      <groupId>org.apache.maven.plugins</groupId>
+		      <artifactId>maven-source-plugin</artifactId>
+		      <version>3.2.1</version>
+		      <executions>
+		        <execution>
+		          <id>attach-sources</id>
+		          <goals>
+		            <goal>jar-no-fork</goal>
+		          </goals>
+		        </execution>
+		      </executions>
+		    </plugin>
+		    <plugin>
 		      <groupId>org.apache.maven.plugins</groupId>
 		      <artifactId>maven-javadoc-plugin</artifactId>
 		      <version>3.4.0</version>
@@ -83,6 +101,31 @@
 		        </execution>
 		      </executions>
 		    </plugin>
+			<plugin>
+		      <groupId>org.sonatype.plugins</groupId>
+		      <artifactId>nexus-staging-maven-plugin</artifactId>
+		      <version>1.6.13</version>
+		      <extensions>true</extensions>
+		      <configuration>
+		        <serverId>ossrh</serverId>
+		        <nexusUrl>https://oss.sonatype.org/</nexusUrl>
+		        <autoReleaseAfterClose>true</autoReleaseAfterClose>
+		      </configuration>
+		    </plugin>
+		    <plugin>
+		      <groupId>org.apache.maven.plugins</groupId>
+		      <artifactId>maven-gpg-plugin</artifactId>
+		      <version>3.0.1</version>
+		      <executions>
+		        <execution>
+		          <id>sign-artifacts</id>
+		          <phase>verify</phase>
+		          <goals>
+		            <goal>sign</goal>
+		          </goals>
+		        </execution>
+		      </executions>
+		    </plugin>
 		</plugins>
 	</build>
 
@@ -103,7 +146,7 @@
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-lang3</artifactId>
-			<version>3.12.0</version>
+			<version>3.13.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
@@ -119,13 +162,13 @@
 		<dependency>
 			<groupId>org.json</groupId>
 			<artifactId>json</artifactId>
-			<version>20230227</version>
+			<version>20230618</version>
 		</dependency>
 		<!-- https://mvnrepository.com/artifact/org.junit.jupiter/junit-jupiter-api -->
 		<dependency>
 			<groupId>org.junit.jupiter</groupId>
 			<artifactId>junit-jupiter-api</artifactId>
-			<version>5.8.2</version>
+			<version>5.10.0</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
@@ -142,7 +185,7 @@
 		<dependency>
 		    <groupId>org.antlr</groupId>
 		    <artifactId>antlr4-runtime</artifactId>
-		    <version>4.12.0</version>
+		    <version>4.13.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.yaml</groupId>

diff --git a/src/main/java/nl/uu/cs/ape/APE.java b/src/main/java/nl/uu/cs/ape/APE.java
@@ -568,6 +568,10 @@ public static boolean writeControlFlowGraphs(SolutionsList allSolutions, RankDir
 	 * @return true if the execution was successfully performed, false otherwise.
 	 */
 	public static boolean writeCWLWorkflows(SolutionsList allSolutions) {
+
+		if (allSolutions.isEmpty()) {
+			return false;
+		}
 		// Check the configuration before continuing.
 		Path cwlFolder = allSolutions.getRunConfiguration().getSolutionDirPath2CWL();
 		int noCWLFiles = allSolutions.getRunConfiguration().getNoCWL();
@@ -597,17 +601,23 @@ public static boolean writeCWLWorkflows(SolutionsList allSolutions) {
 				DefaultCWLCreator cwlCreator = new DefaultCWLCreator(solution);
 				APEFiles.write2file(cwlCreator.generate(), script, false);
 
-				// Write the cwl input file (in YML) to the file system
-				String titleInputs = solution.getFileName() + "_inp.yml";
-				File inputScipt = cwlFolder.resolve(titleInputs).toFile();
-				APEFiles.write2file(cwlCreator.generateCWLWorkflowInputs(), inputScipt, false);
-
 			} catch (IOException e) {
 				log.error("Error occurred while writing a CWL file to the file system.");
 				e.printStackTrace();
 			}
 		});
 
+		// Write the cwl input file (in YML) to the file system
+		String titleInputs = "input.yml";
+		File inputScipt = cwlFolder.resolve(titleInputs).toFile();
+		DefaultCWLCreator cwlCreator = new DefaultCWLCreator(allSolutions.get(0));
+		try {
+			APEFiles.write2file(cwlCreator.generateCWLWorkflowInputs(), inputScipt, false);
+		} catch (IOException e) {
+			log.error("Error occurred while writing a CWL input file (yml) to the file system.");
+			e.printStackTrace();
+		}
+
 		APEUtils.timerPrintText(timerID, "CWL files have been generated.");
 		return true;
 	}

diff --git a/src/test/java/nl/uu/cs/ape/test/sat/ape/UseCaseTest.java b/src/test/java/nl/uu/cs/ape/test/sat/ape/UseCaseTest.java
@@ -152,10 +152,10 @@ void testUseCase(String name, String evaluationPath)
                 assertNotNull(files);
                 assertEquals(mutation.number_of_cwl_files,
                         Stream.of(files).filter(file -> file.getName().endsWith(".cwl")).count());
-                assertEquals(mutation.number_of_cwl_files,
-                        Stream.of(files).filter(file -> file.getName().endsWith("inp.yml")).count());
+                assertEquals(1,
+                        Stream.of(files).filter(file -> file.getName().startsWith("input.yml")).count());
                 for (File f : files) {
-                    assertTrue(f.getName().startsWith("workflowSolution_"));
+                    assertTrue(f.getName().startsWith("workflowSolution_") || f.getName().startsWith("input.yml"));
                 }
                 success("All %s expected CWL files were generated", mutation.number_of_cwl_files);
             }