From fbd1be9b70895a81d884dca8616f18a4b7a42313 Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Tue, 17 May 2022 17:36:06 +0200 Subject: [PATCH 1/7] Setup pom for mvn repo --- pom.xml | 49 ++++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 46 insertions(+), 3 deletions(-) diff --git a/pom.xml b/pom.xml index f52b45a0..8929fbce 100644 --- a/pom.xml +++ b/pom.xml @@ -65,12 +65,30 @@ + + org.apache.maven.plugins + maven-surefire-plugin + 3.0.0-M5 + org.apache.maven.plugins - maven-surefire-plugin - 3.0.0-M4 + maven-site-plugin + 3.7.1 - + + org.apache.maven.plugins + maven-source-plugin + 3.2.1 + + + attach-sources + + jar-no-fork + + + + + org.apache.maven.plugins maven-javadoc-plugin 3.4.0 @@ -83,6 +101,31 @@ + + org.sonatype.plugins + nexus-staging-maven-plugin + 1.6.8 + true + + ossrh + https://oss.sonatype.org/ + true + + + + org.apache.maven.plugins + maven-gpg-plugin + 3.0.1 + + + sign-artifacts + verify + + sign + + + + From 692a6e6129f9d6272327e851d5c940d80e9e9f15 Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Thu, 2 Jun 2022 20:22:27 +0200 Subject: [PATCH 2/7] Keep mvn pom dependencies --- pom.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index bda5ef0d..3b1c400e 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ 4.0.0 io.github.sanctuuary APE - 2.0.0 + 2.0.1 jar io.github.sanctuuary:APE APE is a command line tool and an API for the automated exploration of possible computational pipelines (workflows) from large collections of computational tools. @@ -188,4 +188,4 @@ 1.30 - \ No newline at end of file + From 84e83f4125ba790196566f0cb407e3ed8fcc9d6d Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Tue, 1 Aug 2023 10:30:27 +0200 Subject: [PATCH 3/7] Remove the travis CI file --- .travis.yml | 30 ------------------------------ 1 file changed, 30 deletions(-) delete mode 100644 .travis.yml diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 81e86ce7..00000000 --- a/.travis.yml +++ /dev/null @@ -1,30 +0,0 @@ -notifications: - webhooks: https://outlook.office.com/webhook/3d8e5085-15c4-4958-a6b3-2b60c8b797e4@d72758a0-a446-4e0f-a0aa-4bf95a4a10e7/TravisCI/1d6d563ba4014e34b073eab8c200d61f/8c18a7c8-be05-4398-8ba1-0d22da27a984 -stages: - - Test - -jobs: - include: - # Unit tests - - stage: Test - name: "Unit tests" - language: java - - # CWL test - - stage: Test - name: "Validate CWL output" - dist: focal - language: java - before_install: - - sudo apt-get -y install python3 python3-pip - - pip3 install cwlref-runner - script: - # Build JAR - - mvn package -DskipTests=true - # Run use case - - git clone https://github.com/Workflomics/domain-annotations - - cd domain-annotations - - java -jar ../target/APE-*-executable.jar WombatP_tools/config_local.json - # Validate with CWL runner - - cd ./WombatP_tools/CWL - - cwltool --enable-dev --validate workflowSolution_0.cwl From c5eb60712f28228bf08a05f05ba554d16d032c66 Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Tue, 1 Aug 2023 11:04:13 +0200 Subject: [PATCH 4/7] Input file rename --- src/main/java/nl/uu/cs/ape/APE.java | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/src/main/java/nl/uu/cs/ape/APE.java b/src/main/java/nl/uu/cs/ape/APE.java index 7e51da9b..6599cdba 100644 --- 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; } From 91f969a2917350ef0af018165301ec6807930b7a Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Tue, 1 Aug 2023 13:08:37 +0200 Subject: [PATCH 5/7] Update nexus-staging version --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 84cd963d..890bb5c0 100644 --- a/pom.xml +++ b/pom.xml @@ -104,7 +104,7 @@ org.sonatype.plugins nexus-staging-maven-plugin - 1.6.8 + 1.6.13 true ossrh From 514c7c77d9e41275e8ac3f325a4dc4506d907007 Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Tue, 1 Aug 2023 13:49:19 +0200 Subject: [PATCH 6/7] Updated dependencies and tests --- pom.xml | 8 ++++---- src/test/java/nl/uu/cs/ape/test/sat/ape/UseCaseTest.java | 6 +++--- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/pom.xml b/pom.xml index 890bb5c0..9ac928e1 100644 --- a/pom.xml +++ b/pom.xml @@ -146,7 +146,7 @@ org.apache.commons commons-lang3 - 3.12.0 + 3.13.0 org.apache.logging.log4j @@ -162,13 +162,13 @@ org.json json - 20230227 + 20230618 org.junit.jupiter junit-jupiter-api - 5.8.2 + 5.10.0 test @@ -185,7 +185,7 @@ org.antlr antlr4-runtime - 4.12.0 + 4.13.0 org.yaml 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 index f2febc54..97d6d34e 100644 --- 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); } From dbaa52fdb34d630d42fdbe8af0b31f5dfd10074a Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Tue, 1 Aug 2023 13:52:20 +0200 Subject: [PATCH 7/7] Version update --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 9ac928e1..77f1bf09 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ 4.0.0 io.github.sanctuuary APE - 2.1.4 + 2.1.5 jar io.github.sanctuuary:APE APE is a command line tool and an API for the automated exploration of possible computational pipelines (workflows) from large collections of computational tools.