From 89b47316598719d9f852226b75d1c9820e905ecc Mon Sep 17 00:00:00 2001 From: Berend Weel Date: Fri, 12 Nov 2021 08:51:35 +0100 Subject: [PATCH 1/7] Upgrade gradle to v7.2 --- build.gradle | 6 +++--- gradle/wrapper/gradle-wrapper.properties | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/build.gradle b/build.gradle index f8645e5..cf4cc2e 100644 --- a/build.gradle +++ b/build.gradle @@ -15,7 +15,7 @@ sourceCompatibility = JavaVersion.VERSION_11 targetCompatibility = JavaVersion.VERSION_11 application { - mainClassName = 'nl.esciencecenter.computeservice.rest.Application' + mainClass = 'nl.esciencecenter.computeservice.rest.Application' } @@ -79,14 +79,14 @@ dependencies { } bootJar { - baseName = 'xenonflow' + baseName = 'xenonflow' } // Include some more files in the distribution zip // Don't use include an extra directory in the dist zip. distributions { boot { - baseName = 'xenonflow' + distributionBaseName = 'xenonflow' contents { from(['config/config.yml', 'config/application.properties']) { into '/config' diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index 442d913..e750102 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -1,5 +1,5 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-6.8.3-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-7.3-bin.zip zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists From 006034ab63dab2d65c4c9d51c0ed73c6b16ca4d5 Mon Sep 17 00:00:00 2001 From: Berend Weel Date: Fri, 12 Nov 2021 09:46:00 +0100 Subject: [PATCH 2/7] Update java version in github actions --- .github/workflows/build.yml | 7 +++---- .github/workflows/cwl_compliance.yml | 7 +++---- 2 files changed, 6 insertions(+), 8 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index bf55878..2bba074 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -20,11 +20,10 @@ jobs: steps: - name: Set up java - uses: actions/setup-java@v1 + uses: actions/setup-java@v2 with: - java-version: 11.0.2 - java-package: jdk - architecture: x64 + distribution: 'temurin' + java-version: '17' - name: Set up python uses: actions/setup-python@v2 with: diff --git a/.github/workflows/cwl_compliance.yml b/.github/workflows/cwl_compliance.yml index 966b2ed..f931ec5 100644 --- a/.github/workflows/cwl_compliance.yml +++ b/.github/workflows/cwl_compliance.yml @@ -19,11 +19,10 @@ jobs: steps: - name: Set up java - uses: actions/setup-java@v1 + uses: actions/setup-java@v2 with: - java-version: 11.0.2 - java-package: jdk - architecture: x64 + distribution: 'temurin' + java-version: '17' - name: Set up python uses: actions/setup-python@v2 with: From 71e45ea684ed924d662614235754361ef32dd130 Mon Sep 17 00:00:00 2001 From: Berend Weel Date: Fri, 12 Nov 2021 09:57:47 +0100 Subject: [PATCH 3/7] Updating spring --- .gitignore | 5 +++++ build.gradle | 16 ++++++++-------- 2 files changed, 13 insertions(+), 8 deletions(-) diff --git a/.gitignore b/.gitignore index 83e5feb..ffb8e40 100644 --- a/.gitignore +++ b/.gitignore @@ -6,7 +6,12 @@ build/ .settings *.iws .DS_Store +.vscode +# Ignore yarn +src/main/frontend/yarn-v1.22.0/ + +# Xenonflow logs log/ db/ xenon-flow.log diff --git a/build.gradle b/build.gradle index cf4cc2e..92554b2 100644 --- a/build.gradle +++ b/build.gradle @@ -4,7 +4,7 @@ plugins { id 'idea' id 'eclipse' id 'application' - id 'org.springframework.boot' version '2.2.4.RELEASE' + id 'org.springframework.boot' version '2.5.6' id 'io.spring.dependency-management' version '1.0.7.RELEASE' id 'jacoco' id "com.github.node-gradle.node" version "2.2.2" @@ -43,10 +43,10 @@ dependencies { implementation group: 'nl.esciencecenter.xenon.adaptors', name: 'xenon-adaptors-cloud', version: '3.0.2' //Spring(boot) - implementation group: 'org.springframework.boot', name: 'spring-boot-starter-web', version: '2.2.4.RELEASE' - implementation group: 'org.springframework.boot', name: 'spring-boot-starter', version: '2.2.4.RELEASE' - implementation group: 'org.springframework.boot', name: 'spring-boot-starter-tomcat', version: '2.2.4.RELEASE' - implementation group: 'org.springframework.boot', name: 'spring-boot-devtools', version: '2.2.4.RELEASE' + implementation group: 'org.springframework.boot', name: 'spring-boot-starter-web', version: '2.5.6' + implementation group: 'org.springframework.boot', name: 'spring-boot-starter', version: '2.5.6' + implementation group: 'org.springframework.boot', name: 'spring-boot-starter-tomcat', version: '2.5.6' + implementation group: 'org.springframework.boot', name: 'spring-boot-devtools', version: '2.5.6' implementation group: 'io.springfox', name: 'springfox-boot-starter', version: '3.0.0' //Jackson, match version used in Spring @@ -58,11 +58,11 @@ dependencies { implementation group: 'javax.validation', name: 'validation-api', version: '2.0.1.Final' //JPA, hibernate and h2 database persistance libraries - implementation group: 'org.springframework.boot', name: 'spring-boot-starter-data-jpa', version: '2.2.4.RELEASE' + implementation group: 'org.springframework.boot', name: 'spring-boot-starter-data-jpa', version: '2.5.6' runtimeOnly group: 'com.h2database', name: 'h2', version: '1.4.199' // Security - implementation group: 'org.springframework.boot', name: 'spring-boot-starter-security', version: '2.2.4.RELEASE' + implementation group: 'org.springframework.boot', name: 'spring-boot-starter-security', version: '2.5.6' // Admin Interface @@ -75,7 +75,7 @@ dependencies { testImplementation group: 'org.hamcrest', name:'hamcrest', version:'2.2' testImplementation group: 'org.hamcrest', name:'hamcrest-library', version:'2.2' testImplementation group: 'junit', name:'junit', version:'4.13' - testImplementation group: 'org.springframework.boot', name: 'spring-boot-starter-test', version: '2.2.4.RELEASE' + testImplementation group: 'org.springframework.boot', name: 'spring-boot-starter-test', version: '2.5.6' } bootJar { From ed21f522d28eed571fdd5f6b67de67a92d9f60e0 Mon Sep 17 00:00:00 2001 From: Berend Weel Date: Fri, 12 Nov 2021 11:16:40 +0100 Subject: [PATCH 4/7] updating some more dependencies --- build.gradle | 25 ++++++++++++++----------- 1 file changed, 14 insertions(+), 11 deletions(-) diff --git a/build.gradle b/build.gradle index 92554b2..4238081 100644 --- a/build.gradle +++ b/build.gradle @@ -4,7 +4,7 @@ plugins { id 'idea' id 'eclipse' id 'application' - id 'org.springframework.boot' version '2.5.6' + id 'org.springframework.boot' version '2.3.12.RELEASE' id 'io.spring.dependency-management' version '1.0.7.RELEASE' id 'jacoco' id "com.github.node-gradle.node" version "2.2.2" @@ -43,26 +43,27 @@ dependencies { implementation group: 'nl.esciencecenter.xenon.adaptors', name: 'xenon-adaptors-cloud', version: '3.0.2' //Spring(boot) - implementation group: 'org.springframework.boot', name: 'spring-boot-starter-web', version: '2.5.6' - implementation group: 'org.springframework.boot', name: 'spring-boot-starter', version: '2.5.6' - implementation group: 'org.springframework.boot', name: 'spring-boot-starter-tomcat', version: '2.5.6' - implementation group: 'org.springframework.boot', name: 'spring-boot-devtools', version: '2.5.6' + implementation group: 'org.springframework.boot', name: 'spring-boot-starter-web', version: '2.3.12.RELEASE' + implementation group: 'org.springframework.boot', name: 'spring-boot-starter', version: '2.3.12.RELEASE' + implementation group: 'org.springframework.boot', name: 'spring-boot-starter-tomcat', version: '2.3.12.RELEASE' + implementation group: 'org.springframework.boot', name: 'spring-boot-devtools', version: '2.3.12.RELEASE' + implementation group: 'org.springframework.boot', name: 'spring-boot-starter-validation', version: '2.3.12.RELEASE' implementation group: 'io.springfox', name: 'springfox-boot-starter', version: '3.0.0' //Jackson, match version used in Spring - implementation group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.9.8' - implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.9.8' - implementation group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version: '2.9.8' + implementation group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.11.4' + implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.11.4' + implementation group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version: '2.11.4' //compile group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310' implementation group: 'javax.validation', name: 'validation-api', version: '2.0.1.Final' //JPA, hibernate and h2 database persistance libraries - implementation group: 'org.springframework.boot', name: 'spring-boot-starter-data-jpa', version: '2.5.6' + implementation group: 'org.springframework.boot', name: 'spring-boot-starter-data-jpa', version: '2.3.12.RELEASE' runtimeOnly group: 'com.h2database', name: 'h2', version: '1.4.199' // Security - implementation group: 'org.springframework.boot', name: 'spring-boot-starter-security', version: '2.5.6' + implementation group: 'org.springframework.boot', name: 'spring-boot-starter-security', version: '2.3.12.RELEASE' // Admin Interface @@ -75,7 +76,9 @@ dependencies { testImplementation group: 'org.hamcrest', name:'hamcrest', version:'2.2' testImplementation group: 'org.hamcrest', name:'hamcrest-library', version:'2.2' testImplementation group: 'junit', name:'junit', version:'4.13' - testImplementation group: 'org.springframework.boot', name: 'spring-boot-starter-test', version: '2.5.6' + testImplementation group: 'org.springframework.boot', name: 'spring-boot-starter-test', version: '2.3.12.RELEASE' + + runtimeOnly group: 'org.springframework.boot', name: 'spring-boot-properties-migrator', version: '2.3.12.RELEASE' } bootJar { From 7ec67f403a84d45d1171e40a724052f7c68d66a3 Mon Sep 17 00:00:00 2001 From: Berend Weel Date: Wed, 24 Nov 2021 10:06:01 +0100 Subject: [PATCH 5/7] Added matrix of java versions to build and test --- .github/workflows/build.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 2bba074..e03e0fb 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -15,15 +15,18 @@ on: jobs: build: - name: Build and Test runs-on: ubuntu-latest + strategy: + matrix: + java: ['11', '13', '15', '17' ] + name: Java ${{ matrix.java }} Build and Test steps: - name: Set up java uses: actions/setup-java@v2 with: distribution: 'temurin' - java-version: '17' + java-version: ${{ matrix.java }} - name: Set up python uses: actions/setup-python@v2 with: From ada6a20b9835ce7a059c9a9d785ab8d705895894 Mon Sep 17 00:00:00 2001 From: Berend Weel Date: Wed, 24 Nov 2021 10:06:38 +0100 Subject: [PATCH 6/7] Fixed input being removed if deleteInputTest failed --- .../nl/esciencecenter/computeservice/rest/CwlResultTest.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/test/java/nl/esciencecenter/computeservice/rest/CwlResultTest.java b/src/test/java/nl/esciencecenter/computeservice/rest/CwlResultTest.java index 778668d..1c52619 100644 --- a/src/test/java/nl/esciencecenter/computeservice/rest/CwlResultTest.java +++ b/src/test/java/nl/esciencecenter/computeservice/rest/CwlResultTest.java @@ -54,6 +54,10 @@ public class CwlResultTest { @After public void deleteJob() throws Exception { + if (xenonService.getConfig().getSourceFilesystemConfig().shouldClearOnJobDone()) { + // Make sure we do not throw away the input if the testDeleteInput test fails + xenonService.getConfig().getSourceFilesystemConfig().setClearOnJobDone(false); + } for (Job job : CwlTestUtils.getCreated()) { mockMvc.perform( delete(job.getUri()) From aa5aa877fd37d57fee31f26b5f09aad0fbff88fe Mon Sep 17 00:00:00 2001 From: Berend Weel Date: Wed, 24 Nov 2021 10:08:10 +0100 Subject: [PATCH 7/7] Fixed java versions --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index e03e0fb..7be4acd 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -18,7 +18,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - java: ['11', '13', '15', '17' ] + java: ['11', '16', '17' ] name: Java ${{ matrix.java }} Build and Test steps: