From 71f0caba492895a778a720c1cc0098f328c4bd5d Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Tue, 13 Aug 2024 11:10:58 -0400 Subject: [PATCH 01/29] java 21 compatibility --- dockstore-cli-integration-testing/pom.xml | 7 +++++-- pom.xml | 22 ++++++++++++++++------ 2 files changed, 21 insertions(+), 8 deletions(-) diff --git a/dockstore-cli-integration-testing/pom.xml b/dockstore-cli-integration-testing/pom.xml index 436c0eafe..251157500 100644 --- a/dockstore-cli-integration-testing/pom.xml +++ b/dockstore-cli-integration-testing/pom.xml @@ -292,8 +292,11 @@ - org.scala-tools - maven-scala-plugin + net.alchim31.maven + scala-maven-plugin + + 2.13.12 + diff --git a/pom.xml b/pom.xml index d322c01ff..d9a7f7265 100644 --- a/pom.xml +++ b/pom.xml @@ -366,6 +366,10 @@ random 1 + + -Djava.security.manager=allow + @{argLine} + @@ -378,6 +382,10 @@ random 1 + + -Djava.security.manager=allow + @{argLine} + @@ -391,7 +399,7 @@ com.github.spotbugs spotbugs-maven-plugin - 4.6.0.0 + 4.8.3.1 org.apache.maven.plugins @@ -424,11 +432,13 @@ maven-javadoc-plugin 3.3.2 - - org.scala-tools - maven-scala-plugin - 2.15.2 + net.alchim31.maven + scala-maven-plugin + 4.8.1 + + 17 + org.codehaus.mojo @@ -542,7 +552,7 @@ 3.8.1 - [11.0.11,18.0) + [17.0.11,22.0) From 6315860ef7000df4bae9773c5b2df0a65ad1ffa3 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Tue, 13 Aug 2024 11:12:12 -0400 Subject: [PATCH 02/29] add build for Java 21 --- .github/workflows/mvnw.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/mvnw.yml b/.github/workflows/mvnw.yml index 070f98bb3..7bbf9b01a 100644 --- a/.github/workflows/mvnw.yml +++ b/.github/workflows/mvnw.yml @@ -7,7 +7,7 @@ jobs: runs-on: ubuntu-22.04 strategy: matrix: - java: [ '17.0.4+8' ] + java: [ '17.0.4+8', '21.0.4+7' ] steps: - name: install git secrets From 69e685e78efd609f7dd5e1c9d1780032c04105a0 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Tue, 13 Aug 2024 11:13:47 -0400 Subject: [PATCH 03/29] trim required java version --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index d9a7f7265..3e694b479 100644 --- a/pom.xml +++ b/pom.xml @@ -552,7 +552,7 @@ 3.8.1 - [17.0.11,22.0) + [17.0,22.0) From 392259ba17ff625b9b2118d1e1340dfe91a2a5b7 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Tue, 13 Aug 2024 11:51:10 -0400 Subject: [PATCH 04/29] test with Java 21 --- .circleci/config.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 1a12f497a..c2e46d072 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -2,7 +2,7 @@ version: 2.1 parameters: java-tag: type: string - default: "17.0.3" + default: "21.0.2" run_against_develop_core: type: boolean default: false @@ -17,14 +17,14 @@ executors: machine_integration_test_exec: machine: # run the steps with Ubuntu VM - image: ubuntu-2204:2023.10.1 + image: ubuntu-2204:2024.04.4 environment: PGHOST: 127.0.0.1 resource_class: medium toil_wes_test_executor: machine: # run the steps with Ubuntu VM - image: ubuntu-2204:2023.10.1 + image: ubuntu-2204:2024.04.4 resource_class: medium common_filters: &common_filters From b1d29bc26fb5751e38a71136c55565f82d02eba5 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Tue, 13 Aug 2024 16:30:18 -0400 Subject: [PATCH 05/29] copy https://github.com/dockstore/dockstore/pull/5961/files --- scripts/install-tests.sh | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/scripts/install-tests.sh b/scripts/install-tests.sh index f14c54c43..d6049ac31 100755 --- a/scripts/install-tests.sh +++ b/scripts/install-tests.sh @@ -14,8 +14,11 @@ fi if [ "${TESTING_PROFILE}" = "toil-integration-tests" ]; then pip3 install --user toil[cwl]==3.15.0 else - pip3 install --user -r https://raw.githubusercontent.com/dockstore/dockstore/develop/dockstore-webservice/src/main/resources/requirements/1.14.0/requirements3.txt -fi + # depending on https://github.com/dockstore/dockstore/pull/5958 we may want to match where we go with the cwltool install, for now apt seems to work well + sudo apt-get update + # https://stackoverflow.com/questions/44331836/apt-get-install-tzdata-noninteractive needed by cwltool + DEBIAN_FRONTEND=noninteractive sudo apt-get -qq --yes --force-yes install tzdata + sudo apt-get -qq --yes --force-yes install cwltool=3.1.20220224085855-1 if [ "${TESTING_PROFILE}" = "singularity-tests" ]; then # Install singularity from source From 798b25369f62802688ac263464a2b7a933362825 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Tue, 13 Aug 2024 16:35:40 -0400 Subject: [PATCH 06/29] syntax --- scripts/install-tests.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/install-tests.sh b/scripts/install-tests.sh index d6049ac31..22b3037fe 100755 --- a/scripts/install-tests.sh +++ b/scripts/install-tests.sh @@ -19,6 +19,7 @@ else # https://stackoverflow.com/questions/44331836/apt-get-install-tzdata-noninteractive needed by cwltool DEBIAN_FRONTEND=noninteractive sudo apt-get -qq --yes --force-yes install tzdata sudo apt-get -qq --yes --force-yes install cwltool=3.1.20220224085855-1 +fi if [ "${TESTING_PROFILE}" = "singularity-tests" ]; then # Install singularity from source From c1548dec8e278a05d8114d44750a946cf2417271 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Tue, 13 Aug 2024 16:48:51 -0400 Subject: [PATCH 07/29] add option for java 21 --- dockstore-cli-integration-testing/pom.xml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dockstore-cli-integration-testing/pom.xml b/dockstore-cli-integration-testing/pom.xml index 251157500..0af08d30f 100644 --- a/dockstore-cli-integration-testing/pom.xml +++ b/dockstore-cli-integration-testing/pom.xml @@ -259,6 +259,8 @@ + + -Djava.security.manager=allow @{argLine} --illegal-access=permit --add-opens java.base/java.lang=ALL-UNNAMED From 2fdfd240eb2e64f0738fb814fc1c0d08aaf13caf Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Tue, 13 Aug 2024 17:03:28 -0400 Subject: [PATCH 08/29] jacoco upgrade for java 21? --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 3e694b479..788697b9f 100644 --- a/pom.xml +++ b/pom.xml @@ -232,7 +232,7 @@ org.jacoco jacoco-maven-plugin - 0.8.8 + 0.8.12 com.googlecode.maven-download-plugin From a0d8b0e8be50e97c5c5cd875528674d5e2bfc009 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Wed, 14 Aug 2024 10:41:00 -0400 Subject: [PATCH 09/29] anything special about order? --- dockstore-cli-integration-testing/pom.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dockstore-cli-integration-testing/pom.xml b/dockstore-cli-integration-testing/pom.xml index 0af08d30f..3a1feeb55 100644 --- a/dockstore-cli-integration-testing/pom.xml +++ b/dockstore-cli-integration-testing/pom.xml @@ -259,8 +259,6 @@ - - -Djava.security.manager=allow @{argLine} --illegal-access=permit --add-opens java.base/java.lang=ALL-UNNAMED @@ -270,6 +268,8 @@ --add-opens java.base/java.base=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED --add-opens java.base/sun.nio.fs=ALL-UNNAMED + + -Djava.security.manager=allow -da:org.hibernate... From 5a405630782acece3c1c9c64c6ee65947522a863 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Wed, 14 Aug 2024 11:28:22 -0400 Subject: [PATCH 10/29] try this --- dockstore-client/pom.xml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dockstore-client/pom.xml b/dockstore-client/pom.xml index b7cbec466..2e065ff64 100644 --- a/dockstore-client/pom.xml +++ b/dockstore-client/pom.xml @@ -529,6 +529,8 @@ --add-opens java.base/java.io=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.base/java.base=ALL-UNNAMED + + -Djava.security.manager=allow ${skipITs} ${excludeGroups} From 9080cd9f413774263423e9df25117da0a778d660 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Thu, 5 Dec 2024 13:53:28 -0500 Subject: [PATCH 11/29] bad merge --- scripts/install-tests.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/install-tests.sh b/scripts/install-tests.sh index 3ae383be5..f07734551 100755 --- a/scripts/install-tests.sh +++ b/scripts/install-tests.sh @@ -14,7 +14,7 @@ fi if [ "${TESTING_PROFILE}" = "toil-integration-tests" ]; then pip3 install --user toil[cwl]==7.0.0 else - pip3 install --user -r https://raw.githubusercontent.com/dockstore/dockstore/develop/dockstore-webservice/src/main/resources/requirements/1.15.0/requirements3.txt + # depending on https://github.com/dockstore/dockstore/pull/5958 we may want to match where we go with the cwltool install, for now apt seems to work well sudo apt-get update # https://stackoverflow.com/questions/44331836/apt-get-install-tzdata-noninteractive needed by cwltool DEBIAN_FRONTEND=noninteractive sudo apt-get -qq --yes --force-yes install tzdata From 7067b6fc13a1657c1404e55a510ffd96c267f30f Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Thu, 5 Dec 2024 13:53:39 -0500 Subject: [PATCH 12/29] fix java version --- .github/workflows/mvnw.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/mvnw.yml b/.github/workflows/mvnw.yml index 7bbf9b01a..30fa93b93 100644 --- a/.github/workflows/mvnw.yml +++ b/.github/workflows/mvnw.yml @@ -7,7 +7,7 @@ jobs: runs-on: ubuntu-22.04 strategy: matrix: - java: [ '17.0.4+8', '21.0.4+7' ] + java: [ '17.0.4+8', '21.0.5+11.0.LTS' ] steps: - name: install git secrets From 4de8628c9f78bdaad1acf88839cddc6320177f90 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Thu, 5 Dec 2024 14:50:24 -0500 Subject: [PATCH 13/29] upgrade cwltool version --- scripts/install-tests.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/install-tests.sh b/scripts/install-tests.sh index f07734551..3018a64b6 100755 --- a/scripts/install-tests.sh +++ b/scripts/install-tests.sh @@ -18,7 +18,7 @@ else sudo apt-get update # https://stackoverflow.com/questions/44331836/apt-get-install-tzdata-noninteractive needed by cwltool DEBIAN_FRONTEND=noninteractive sudo apt-get -qq --yes --force-yes install tzdata - sudo apt-get -qq --yes --force-yes install cwltool=3.1.20220224085855-1 + sudo apt-get -qq --yes --force-yes install cwltool=3.1.20240112164112-2 fi if [ "${TESTING_PROFILE}" = "singularity-tests" ]; then From c84e75e8680159fe8bab21a771a1c13a40105f8b Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Thu, 5 Dec 2024 17:17:34 -0500 Subject: [PATCH 14/29] switch to pipx --- scripts/install-tests.sh | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/scripts/install-tests.sh b/scripts/install-tests.sh index 3018a64b6..06e0a1834 100755 --- a/scripts/install-tests.sh +++ b/scripts/install-tests.sh @@ -17,8 +17,9 @@ else # depending on https://github.com/dockstore/dockstore/pull/5958 we may want to match where we go with the cwltool install, for now apt seems to work well sudo apt-get update # https://stackoverflow.com/questions/44331836/apt-get-install-tzdata-noninteractive needed by cwltool - DEBIAN_FRONTEND=noninteractive sudo apt-get -qq --yes --force-yes install tzdata - sudo apt-get -qq --yes --force-yes install cwltool=3.1.20240112164112-2 + DEBIAN_FRONTEND=noninteractive sudo apt-get -qq --yes --force-yes install tzdata pipx + pipx install cwltool==3.1.20240708091337 + pipx install --user -r https://raw.githubusercontent.com/dockstore/dockstore/develop/dockstore-webservice/src/main/resources/requirements/1.15.0/requirements3.txt fi if [ "${TESTING_PROFILE}" = "singularity-tests" ]; then From a5a64b65572c0bc8e550674765fdcec37e2b478e Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Thu, 5 Dec 2024 17:28:23 -0500 Subject: [PATCH 15/29] match quickstart more closely --- scripts/install-tests.sh | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/scripts/install-tests.sh b/scripts/install-tests.sh index 06e0a1834..e9a4929ff 100755 --- a/scripts/install-tests.sh +++ b/scripts/install-tests.sh @@ -17,9 +17,10 @@ else # depending on https://github.com/dockstore/dockstore/pull/5958 we may want to match where we go with the cwltool install, for now apt seems to work well sudo apt-get update # https://stackoverflow.com/questions/44331836/apt-get-install-tzdata-noninteractive needed by cwltool - DEBIAN_FRONTEND=noninteractive sudo apt-get -qq --yes --force-yes install tzdata pipx + DEBIAN_FRONTEND=noninteractive sudo apt-get -qq --yes --force-yes install tzdata pipx curl + curl -o requirements.txt "https://dockstore.org/api/metadata/runner_dependencies?client_version=1.16.0&python_version=3" pipx install cwltool==3.1.20240708091337 - pipx install --user -r https://raw.githubusercontent.com/dockstore/dockstore/develop/dockstore-webservice/src/main/resources/requirements/1.15.0/requirements3.txt + pipx runpip cwltool install -r requirements.txt # this ensures that your version of cwltool and its dependencies matches what we test with fi if [ "${TESTING_PROFILE}" = "singularity-tests" ]; then From cdfa85031c76a4e2b5528947763ac2724c594478 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Fri, 6 Dec 2024 10:48:23 -0500 Subject: [PATCH 16/29] ensurepath? --- scripts/install-tests.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/install-tests.sh b/scripts/install-tests.sh index e9a4929ff..4fb7e0098 100755 --- a/scripts/install-tests.sh +++ b/scripts/install-tests.sh @@ -21,6 +21,7 @@ else curl -o requirements.txt "https://dockstore.org/api/metadata/runner_dependencies?client_version=1.16.0&python_version=3" pipx install cwltool==3.1.20240708091337 pipx runpip cwltool install -r requirements.txt # this ensures that your version of cwltool and its dependencies matches what we test with + pipx ensurepath fi if [ "${TESTING_PROFILE}" = "singularity-tests" ]; then From 6c8d7cf3948c9ea77e1b0a05bfb2e81fce64bf63 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Fri, 6 Dec 2024 11:20:24 -0500 Subject: [PATCH 17/29] Add schema salad --- scripts/install-tests.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/install-tests.sh b/scripts/install-tests.sh index 4fb7e0098..f72aae1ef 100755 --- a/scripts/install-tests.sh +++ b/scripts/install-tests.sh @@ -20,6 +20,7 @@ else DEBIAN_FRONTEND=noninteractive sudo apt-get -qq --yes --force-yes install tzdata pipx curl curl -o requirements.txt "https://dockstore.org/api/metadata/runner_dependencies?client_version=1.16.0&python_version=3" pipx install cwltool==3.1.20240708091337 + pipx install schema_salad pipx runpip cwltool install -r requirements.txt # this ensures that your version of cwltool and its dependencies matches what we test with pipx ensurepath fi From 149b42610ca26d02bd4c353490eef9cc1c09f2c6 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Fri, 6 Dec 2024 12:00:55 -0500 Subject: [PATCH 18/29] sigh, specific version of schema salad --- scripts/install-tests.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/install-tests.sh b/scripts/install-tests.sh index f72aae1ef..cf8d780ad 100755 --- a/scripts/install-tests.sh +++ b/scripts/install-tests.sh @@ -20,7 +20,7 @@ else DEBIAN_FRONTEND=noninteractive sudo apt-get -qq --yes --force-yes install tzdata pipx curl curl -o requirements.txt "https://dockstore.org/api/metadata/runner_dependencies?client_version=1.16.0&python_version=3" pipx install cwltool==3.1.20240708091337 - pipx install schema_salad + pipx install schema_salad==8.7.20240718183047 pipx runpip cwltool install -r requirements.txt # this ensures that your version of cwltool and its dependencies matches what we test with pipx ensurepath fi From a8c252328e4189b4ce15b80b022eb3c36120da5d Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Fri, 6 Dec 2024 13:53:12 -0500 Subject: [PATCH 19/29] cwlref-runner --- scripts/install-tests.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/install-tests.sh b/scripts/install-tests.sh index cf8d780ad..2f19c7271 100755 --- a/scripts/install-tests.sh +++ b/scripts/install-tests.sh @@ -21,6 +21,7 @@ else curl -o requirements.txt "https://dockstore.org/api/metadata/runner_dependencies?client_version=1.16.0&python_version=3" pipx install cwltool==3.1.20240708091337 pipx install schema_salad==8.7.20240718183047 + pipx install cwlref-runner pipx runpip cwltool install -r requirements.txt # this ensures that your version of cwltool and its dependencies matches what we test with pipx ensurepath fi From 1469ef7e21d5541762a04dd9f3b5d1d5bd4764ae Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Mon, 9 Dec 2024 15:19:23 -0500 Subject: [PATCH 20/29] redirect jelte Docker images to fork --- dockstore-client/src/test/resources/testDirectory3/mutect.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dockstore-client/src/test/resources/testDirectory3/mutect.cwl b/dockstore-client/src/test/resources/testDirectory3/mutect.cwl index 116b98239..d791ef89c 100644 --- a/dockstore-client/src/test/resources/testDirectory3/mutect.cwl +++ b/dockstore-client/src/test/resources/testDirectory3/mutect.cwl @@ -10,7 +10,7 @@ doc: "Mutect 1.1.5" hints: - class: DockerRequirement - dockerPull: quay.io/jeltje/mutect + dockerPull: quay.io/dockstore-testing/mutect requirements: - class: InlineJavascriptRequirement From dfded625852edd1f17307ca7b7084523fd5c1db1 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Mon, 9 Dec 2024 16:16:28 -0500 Subject: [PATCH 21/29] mocked IT seems to work fine with this version locally --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index e20d67762..0e80f5b24 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -2,7 +2,7 @@ version: 2.1 parameters: java-tag: type: string - default: "21.0.2" + default: "21.0.5" run_against_develop_core: type: boolean default: false From 6d6fa4b1449e23f703e44c93145d178189869faa Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Mon, 9 Dec 2024 17:10:49 -0500 Subject: [PATCH 22/29] bump things along and re-test --- .circleci/config.yml | 2 +- .../src/test/java/io/dockstore/client/cli/WDLWorkflowIT.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 0e80f5b24..2fa0ae743 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -24,7 +24,7 @@ executors: toil_wes_test_executor: machine: # run the steps with Ubuntu VM - image: ubuntu-2204:2024.04.4 + image: ubuntu-2204:2024.11.1 resource_class: medium common_filters: &common_filters diff --git a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/WDLWorkflowIT.java b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/WDLWorkflowIT.java index 214933c64..5b8f60947 100644 --- a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/WDLWorkflowIT.java +++ b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/WDLWorkflowIT.java @@ -97,7 +97,7 @@ void testRunningCheckerWDLWorkflow() throws IOException { workflowApi.publish1(refresh.getId(), publishRequest); // get test json - String testVersion = "1.3.0"; + String testVersion = "1.4.0"; // Also test that files can be gotten by owner even though it's hidden List workflowVersions = refresh.getWorkflowVersions(); workflowVersions.stream().filter(v -> v.getName().equals(testVersion)).forEach(v -> v.setHidden(true)); From 8da34b35ae071353693e5de8a323e1b08b8cbebb Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Mon, 9 Dec 2024 17:46:43 -0500 Subject: [PATCH 23/29] finish for the day with newer Ubuntu/Java and disable mockito --- .circleci/config.yml | 2 +- .../src/test/java/io/dockstore/client/cli/MockedIT.java | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 2fa0ae743..8ae716b2f 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -17,7 +17,7 @@ executors: machine_integration_test_exec: machine: # run the steps with Ubuntu VM - image: ubuntu-2204:2024.04.4 + image: ubuntu-2204:2024.11.1 environment: PGHOST: 127.0.0.1 resource_class: medium diff --git a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/MockedIT.java b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/MockedIT.java index ae27f0a2a..f0651a701 100644 --- a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/MockedIT.java +++ b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/MockedIT.java @@ -60,6 +60,7 @@ import org.junit.contrib.java.lang.system.SystemErrRule; import org.junit.contrib.java.lang.system.SystemOutRule; import org.junit.experimental.categories.Category; +import org.junit.jupiter.api.Disabled; import org.junit.runner.RunWith; import org.powermock.core.classloader.annotations.PowerMockIgnore; import org.powermock.core.classloader.annotations.PrepareForTest; @@ -75,6 +76,7 @@ @RunWith(PowerMockRunner.class) @PrepareForTest({ Client.class, ToolClient.class, UsersApi.class }) @Category({ConfidentialTest.class, ToolTest.class }) +@Disabled("leave this till later, will likely need Mockito/Powermock specific-work for Java 21") public class MockedIT { @Rule From 1fa891fe93867959d9050df609283c7545ae7432 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Mon, 9 Dec 2024 17:56:32 -0500 Subject: [PATCH 24/29] sigh@python Toil install --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 8ae716b2f..2fa0ae743 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -17,7 +17,7 @@ executors: machine_integration_test_exec: machine: # run the steps with Ubuntu VM - image: ubuntu-2204:2024.11.1 + image: ubuntu-2204:2024.04.4 environment: PGHOST: 127.0.0.1 resource_class: medium From 9de2336f204d267524530b3d08bec4ae7c64b728 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Mon, 9 Dec 2024 18:19:14 -0500 Subject: [PATCH 25/29] junit 4? --- .../src/test/java/io/dockstore/client/cli/MockedIT.java | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/MockedIT.java b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/MockedIT.java index f0651a701..e94603a9a 100644 --- a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/MockedIT.java +++ b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/MockedIT.java @@ -60,7 +60,6 @@ import org.junit.contrib.java.lang.system.SystemErrRule; import org.junit.contrib.java.lang.system.SystemOutRule; import org.junit.experimental.categories.Category; -import org.junit.jupiter.api.Disabled; import org.junit.runner.RunWith; import org.powermock.core.classloader.annotations.PowerMockIgnore; import org.powermock.core.classloader.annotations.PrepareForTest; @@ -76,7 +75,7 @@ @RunWith(PowerMockRunner.class) @PrepareForTest({ Client.class, ToolClient.class, UsersApi.class }) @Category({ConfidentialTest.class, ToolTest.class }) -@Disabled("leave this till later, will likely need Mockito/Powermock specific-work for Java 21") +@Ignore("leave this till later, will likely need Mockito/Powermock specific-work for Java 21") public class MockedIT { @Rule From dddc979bf4d5110fea31360a70130ec72d840250 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Tue, 10 Dec 2024 10:23:56 -0500 Subject: [PATCH 26/29] Update install-tests.sh --- scripts/install-tests.sh | 1 - 1 file changed, 1 deletion(-) diff --git a/scripts/install-tests.sh b/scripts/install-tests.sh index 2f19c7271..1747c22ef 100755 --- a/scripts/install-tests.sh +++ b/scripts/install-tests.sh @@ -14,7 +14,6 @@ fi if [ "${TESTING_PROFILE}" = "toil-integration-tests" ]; then pip3 install --user toil[cwl]==7.0.0 else - # depending on https://github.com/dockstore/dockstore/pull/5958 we may want to match where we go with the cwltool install, for now apt seems to work well sudo apt-get update # https://stackoverflow.com/questions/44331836/apt-get-install-tzdata-noninteractive needed by cwltool DEBIAN_FRONTEND=noninteractive sudo apt-get -qq --yes --force-yes install tzdata pipx curl From fa84e6801bdeb85adf1eb6556d8b5a7d15d5ce3e Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Tue, 10 Dec 2024 13:30:56 -0500 Subject: [PATCH 27/29] may have been for powermock? --- dockstore-cli-integration-testing/pom.xml | 2 -- dockstore-client/pom.xml | 2 -- 2 files changed, 4 deletions(-) diff --git a/dockstore-cli-integration-testing/pom.xml b/dockstore-cli-integration-testing/pom.xml index 802fb313b..75c2ee41a 100644 --- a/dockstore-cli-integration-testing/pom.xml +++ b/dockstore-cli-integration-testing/pom.xml @@ -268,8 +268,6 @@ --add-opens java.base/java.base=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED --add-opens java.base/sun.nio.fs=ALL-UNNAMED - - -Djava.security.manager=allow -da:org.hibernate... diff --git a/dockstore-client/pom.xml b/dockstore-client/pom.xml index 2e065ff64..b7cbec466 100644 --- a/dockstore-client/pom.xml +++ b/dockstore-client/pom.xml @@ -529,8 +529,6 @@ --add-opens java.base/java.io=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.base/java.base=ALL-UNNAMED - - -Djava.security.manager=allow ${skipITs} ${excludeGroups} From e095d091d2fb290202653dd92aa136a47e8b3315 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Tue, 10 Dec 2024 14:01:31 -0500 Subject: [PATCH 28/29] Revert "may have been for powermock?" This reverts commit fa84e6801bdeb85adf1eb6556d8b5a7d15d5ce3e. --- dockstore-cli-integration-testing/pom.xml | 2 ++ dockstore-client/pom.xml | 2 ++ 2 files changed, 4 insertions(+) diff --git a/dockstore-cli-integration-testing/pom.xml b/dockstore-cli-integration-testing/pom.xml index 75c2ee41a..802fb313b 100644 --- a/dockstore-cli-integration-testing/pom.xml +++ b/dockstore-cli-integration-testing/pom.xml @@ -268,6 +268,8 @@ --add-opens java.base/java.base=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED --add-opens java.base/sun.nio.fs=ALL-UNNAMED + + -Djava.security.manager=allow -da:org.hibernate... diff --git a/dockstore-client/pom.xml b/dockstore-client/pom.xml index b7cbec466..2e065ff64 100644 --- a/dockstore-client/pom.xml +++ b/dockstore-client/pom.xml @@ -529,6 +529,8 @@ --add-opens java.base/java.io=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.base/java.base=ALL-UNNAMED + + -Djava.security.manager=allow ${skipITs} ${excludeGroups} From e628a281277f0de9049866ca8687bdc6ba9c4961 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Tue, 10 Dec 2024 14:07:47 -0500 Subject: [PATCH 29/29] extend comment --- dockstore-cli-integration-testing/pom.xml | 2 +- dockstore-client/pom.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dockstore-cli-integration-testing/pom.xml b/dockstore-cli-integration-testing/pom.xml index 802fb313b..d9ff28b3b 100644 --- a/dockstore-cli-integration-testing/pom.xml +++ b/dockstore-cli-integration-testing/pom.xml @@ -268,7 +268,7 @@ --add-opens java.base/java.base=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED --add-opens java.base/sun.nio.fs=ALL-UNNAMED - + -Djava.security.manager=allow -da:org.hibernate... diff --git a/dockstore-client/pom.xml b/dockstore-client/pom.xml index 2e065ff64..53b232228 100644 --- a/dockstore-client/pom.xml +++ b/dockstore-client/pom.xml @@ -529,7 +529,7 @@ --add-opens java.base/java.io=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.base/java.base=ALL-UNNAMED - + -Djava.security.manager=allow ${skipITs}