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vedran-kasalicavedran-kasalica
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Merge pull request #70 from sanctuuary/dev
Merge pom tags needed to publish to mvn Fix tests
2 parents 0003126 + dbaa52f commit 77f1fbd

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-46
lines changed

4 files changed

+69
-46
lines changed

‎.travis.yml‎

Lines changed: 0 additions & 30 deletions
This file was deleted.

‎pom.xml‎

Lines changed: 51 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
<modelVersion>4.0.0</modelVersion>
55
<groupId>io.github.sanctuuary</groupId>
66
<artifactId>APE</artifactId>
7-
<version>2.1.4</version>
7+
<version>2.1.5</version>
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<packaging>jar</packaging>
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<name>io.github.sanctuuary:APE</name>
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<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 @@
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-surefire-plugin</artifactId>
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<version>3.0.0-M5</version>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
70-
<artifactId>maven-surefire-plugin</artifactId>
71-
<version>3.0.0-M4</version>
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<artifactId>maven-site-plugin</artifactId>
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<version>3.7.1</version>
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</plugin>
73-
<plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-source-plugin</artifactId>
81+
<version>3.2.1</version>
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<executions>
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<execution>
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<id>attach-sources</id>
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<goals>
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<goal>jar-no-fork</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-javadoc-plugin</artifactId>
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<version>3.4.0</version>
@@ -83,6 +101,31 @@
83101
</execution>
84102
</executions>
85103
</plugin>
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<plugin>
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<groupId>org.sonatype.plugins</groupId>
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<artifactId>nexus-staging-maven-plugin</artifactId>
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<version>1.6.13</version>
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<extensions>true</extensions>
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<configuration>
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<serverId>ossrh</serverId>
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<nexusUrl>https://oss.sonatype.org/</nexusUrl>
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<autoReleaseAfterClose>true</autoReleaseAfterClose>
113+
</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-gpg-plugin</artifactId>
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<version>3.0.1</version>
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<executions>
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<execution>
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<id>sign-artifacts</id>
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<phase>verify</phase>
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<goals>
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<goal>sign</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
86129
</plugins>
87130
</build>
88131

@@ -103,7 +146,7 @@
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-lang3</artifactId>
106-
<version>3.12.0</version>
149+
<version>3.13.0</version>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
@@ -119,13 +162,13 @@
119162
<dependency>
120163
<groupId>org.json</groupId>
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<artifactId>json</artifactId>
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<version>20230227</version>
165+
<version>20230618</version>
123166
</dependency>
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<!-- https://mvnrepository.com/artifact/org.junit.jupiter/junit-jupiter-api -->
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<dependency>
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<groupId>org.junit.jupiter</groupId>
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<artifactId>junit-jupiter-api</artifactId>
128-
<version>5.8.2</version>
171+
<version>5.10.0</version>
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<scope>test</scope>
130173
</dependency>
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<dependency>
@@ -142,7 +185,7 @@
142185
<dependency>
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<groupId>org.antlr</groupId>
144187
<artifactId>antlr4-runtime</artifactId>
145-
<version>4.12.0</version>
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<version>4.13.0</version>
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</dependency>
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<dependency>
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<groupId>org.yaml</groupId>

‎src/main/java/nl/uu/cs/ape/APE.java‎

Lines changed: 15 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -568,6 +568,10 @@ public static boolean writeControlFlowGraphs(SolutionsList allSolutions, RankDir
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* @return true if the execution was successfully performed, false otherwise.
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*/
570570
public static boolean writeCWLWorkflows(SolutionsList allSolutions) {
571+
572+
if (allSolutions.isEmpty()) {
573+
return false;
574+
}
571575
// Check the configuration before continuing.
572576
Path cwlFolder = allSolutions.getRunConfiguration().getSolutionDirPath2CWL();
573577
int noCWLFiles = allSolutions.getRunConfiguration().getNoCWL();
@@ -597,17 +601,23 @@ public static boolean writeCWLWorkflows(SolutionsList allSolutions) {
597601
DefaultCWLCreator cwlCreator = new DefaultCWLCreator(solution);
598602
APEFiles.write2file(cwlCreator.generate(), script, false);
599603

600-
// Write the cwl input file (in YML) to the file system
601-
String titleInputs = solution.getFileName() + "_inp.yml";
602-
File inputScipt = cwlFolder.resolve(titleInputs).toFile();
603-
APEFiles.write2file(cwlCreator.generateCWLWorkflowInputs(), inputScipt, false);
604-
605604
} catch (IOException e) {
606605
log.error("Error occurred while writing a CWL file to the file system.");
607606
e.printStackTrace();
608607
}
609608
});
610609

610+
// Write the cwl input file (in YML) to the file system
611+
String titleInputs = "input.yml";
612+
File inputScipt = cwlFolder.resolve(titleInputs).toFile();
613+
DefaultCWLCreator cwlCreator = new DefaultCWLCreator(allSolutions.get(0));
614+
try {
615+
APEFiles.write2file(cwlCreator.generateCWLWorkflowInputs(), inputScipt, false);
616+
} catch (IOException e) {
617+
log.error("Error occurred while writing a CWL input file (yml) to the file system.");
618+
e.printStackTrace();
619+
}
620+
611621
APEUtils.timerPrintText(timerID, "CWL files have been generated.");
612622
return true;
613623
}

‎src/test/java/nl/uu/cs/ape/test/sat/ape/UseCaseTest.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -152,10 +152,10 @@ void testUseCase(String name, String evaluationPath)
152152
assertNotNull(files);
153153
assertEquals(mutation.number_of_cwl_files,
154154
Stream.of(files).filter(file -> file.getName().endsWith(".cwl")).count());
155-
assertEquals(mutation.number_of_cwl_files,
156-
Stream.of(files).filter(file -> file.getName().endsWith("inp.yml")).count());
155+
assertEquals(1,
156+
Stream.of(files).filter(file -> file.getName().startsWith("input.yml")).count());
157157
for (File f : files) {
158-
assertTrue(f.getName().startsWith("workflowSolution_"));
158+
assertTrue(f.getName().startsWith("workflowSolution_") || f.getName().startsWith("input.yml"));
159159
}
160160
success("All %s expected CWL files were generated", mutation.number_of_cwl_files);
161161
}

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