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Merge pom tags needed to publish to mvn #70

Merged
merged 12 commits into from
Aug 1, 2023
Merged

Merge pom tags needed to publish to mvn #70

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fbd1be9
Setup pom for mvn repo
vedran-kasalica May 17, 2022
5781e08
Merge branch 'dev' into mvn_repo_release
vedran-kasalica Jun 2, 2022
692a6e6
Keep mvn pom dependencies
vedran-kasalica Jun 2, 2022
a1f9222
Merge branch 'main' into mvn_repo_release
vedran-kasalica Mar 22, 2023
84e83f4
Remove the travis CI file
vedran-kasalica Aug 1, 2023
c5eb607
Input file rename
vedran-kasalica Aug 1, 2023
fc8b808
Merge branch 'main' into mvn_repo_release
vedran-kasalica Aug 1, 2023
0980004
Merge branch 'main' into mvn_repo_release
vedran-kasalica Aug 1, 2023
dc16fa2
Merge branch 'CWL-yaml-fix' into mvn_repo_release
vedran-kasalica Aug 1, 2023
91f969a
Update nexus-staging version
vedran-kasalica Aug 1, 2023
514c7c7
Updated dependencies and tests
vedran-kasalica Aug 1, 2023
dbaa52f
Version update
vedran-kasalica Aug 1, 2023
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30 changes: 0 additions & 30 deletions .travis.yml
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59 changes: 51 additions & 8 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down Expand Up @@ -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>
Expand All @@ -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>

Expand All @@ -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>
Expand All @@ -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>
Expand All @@ -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>
Expand Down
20 changes: 15 additions & 5 deletions src/main/java/nl/uu/cs/ape/APE.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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();
Expand Down Expand Up @@ -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;
}
Expand Down
6 changes: 3 additions & 3 deletions src/test/java/nl/uu/cs/ape/test/sat/ape/UseCaseTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
}
Expand Down
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