8000 java 17 and compile issue with trs api by denis-yuen · Pull Request #211 · dockstore/dockstore-cli · GitHub
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Merged
merged 16 commits into from
Dec 20, 2022
Merged

java 17 and compile issue with trs api #211

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9bb2279
java 17 and compile issue with trs api
denis-yuen Dec 14, 2022
d9f2a50
syntax error
denis-yuen Dec 14, 2022
9acc4b2
syntax (stupid whitespace languages)
denis-yuen Dec 14, 2022
42face0
quoting issue?
denis-yuen Dec 14, 2022
efe3d59
cli version of https://github.com/dockstore/dockstore/pull/4792
denis-yuen Dec 14, 2022
8e24e46
Need cli equivalent of https://github.com/dockstore/dockstore/pull/5243
denis-yuen Dec 14, 2022
4c6181a
parameter order changing, Java 17 module issue with system rules
denis-yuen Dec 15, 2022
91a7e56
java 17 module stuff
denis-yuen Dec 15, 2022
a353b05
Bunch more Java 17 issues
denis-yuen Dec 15, 2022
ca423b9
need this jacoco plugin version for official java 17 support
denis-yuen Dec 15, 2022
d7e6403
give this a shot
denis-yuen Dec 15, 2022
5c50f87
match main repo use of mvnw
denis-yuen Dec 16, 2022
f09f0f4
main repo lacks coveralls holdover
denis-yuen Dec 16, 2022
9db97f8
noticed this difference
denis-yuen Dec 16, 2022
6ef7acc
works locally, if this is the issue will need to check main repo too
denis-yuen Dec 16, 2022
d6c2ccc
syntax from
denis-yuen Dec 19, 2022
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20 changes: 10 additions & 10 deletions .circleci/config.yml
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Expand Up @@ -2,7 +2,7 @@ version: 2.1
parameters:
java-tag:
type: string
default: "11.0.12"
default: "17.0.3"
orbs:
build-tools: circleci/build-tools@2.7.0
executors:
Expand All @@ -12,14 +12,14 @@ executors:

machine_integration_test_exec:
machine: # run the steps with Ubuntu VM
image: ubuntu-2004:202104-01
image: ubuntu-2204:2022.10.1
environment:
PGHOST: 127.0.0.1
resource_class: medium

toil_wes_test_executor:
machine: # run the steps with Ubuntu VM
image: ubuntu-2004:202104-01
image: ubuntu-2204:2022.10.1
resource_class: medium

common_filters: &common_filters
Expand Down Expand Up @@ -216,7 +216,7 @@ commands:
- run:
name: decrypt and expand confidential test data
command: |
sudo apt install openssl -y
sudo NEEDRESTART_MODE=a apt install openssl
bash scripts/decrypt.sh

send_coverage:
Expand Down Expand Up @@ -386,14 +386,14 @@ commands:
# but at this time how to do that is unknown
# so we have to add /home/circleci/.local/bin to the PATH
export CWLTOOL_PATH=${HOME}/.local/bin
echo "export CWLTOOL_PATH=${HOME}/.local/bin" >> $BASH_ENV
echo 'export CWLTOOL_PATH=${HOME}/.local/bin' >> $BASH_ENV

export GO_PATH=/usr/local
echo "export GO_PATH=/usr/local" >> $BASH_ENV
echo 'export GO_PATH=/usr/local' >> $BASH_ENV
export SINGULARITY_PATH=${HOME}/go
echo "export SINGULARITY_PATH=${HOME}/go" >> $BASH_ENV
echo 'export SINGULARITY_PATH=${HOME}/go' >> $BASH_ENV

echo "export PATH=${CWLTOOL_PATH}:${GO_PATH}/go/bin:${PATH}:${SINGULARITY_PATH}/bin" >> $BASH_ENV
echo 'export PATH=${CWLTOOL_PATH}:${GO_PATH}/go/bin:${PATH}:${SINGULARITY_PATH}/bin' >> $BASH_ENV
- run:
name: install pip dependencies
command: scripts/install-tests.sh
Expand All @@ -408,10 +408,10 @@ commands:
then
TESTS_TO_RUN=$(cat temp/test-list/IT/all.txt | circleci tests split --split-by=timings --time-default=0.1s | tr '\n' ',')
echo $TESTS_TO_RUN
mvn -B org.jacoco:jacoco-maven-plugin:report org.jacoco:jacoco-maven-plugin:report-aggregate clean $MAVEN_GOAL -Dit.test=$TESTS_TO_RUN -DfailIfNoTests=false \
./mvnw -B org.jacoco:jacoco-maven-plugin:report org.jacoco:jacoco-maven-plugin:report-aggregate clean install -Dit.test=$TESTS_TO_RUN -DfailIfNoTests=false \
-P$TESTING_PROFILE,coverage -ntp | grep -v "^Running Changeset:"
else
mvn -B org.jacoco:jacoco-maven-plugin:report org.jacoco:jacoco-maven-plugin:report-aggregate $MAVEN_GOAL -P$TESTING_PROFILE,coverage -ntp | grep -v "^Running Changeset:"
./mvnw -B org.jacoco:jacoco-maven-plugin:report org.jacoco:jacoco-maven-plugin:report-aggregate clean install -P$TESTING_PROFILE,coverage -ntp | grep -v "^Running Changeset:"
fi
# The piping grep command is a temporary fix to this issue https://github.com/liquibase/liquibase/issues/2396
save_test_results:
Expand Down
12 changes: 11 additions & 1 deletion .github/workflows/cron.yml
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Expand Up @@ -6,7 +6,10 @@ on:

jobs:
build:
runs-on: ubuntu-latest
runs-on: ubuntu-22.04
strategy:
matrix:
java: [ '17.0.4+8' ]

steps:
- name: install git secrets
Expand All @@ -16,6 +19,13 @@ jobs:
cd git-secrets-1.3.0
sudo make install
- uses: actions/checkout@v3

- name: Set up JDK
uses: actions/setup-java@v3
with:
java-version: ${{ matrix.java }}
distribution: 'temurin'

# Step that does that actual cache save and restore
- uses: actions/cache@v3
with:
Expand Down
4 changes: 2 additions & 2 deletions .github/workflows/mvnw.yml
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Expand Up @@ -4,10 +4,10 @@ on: [push]

jobs:
build:
runs-on: ubuntu-latest
runs-on: ubuntu-22.04
strategy:
matrix:
java: [ '11', '17' ]
java: [ '17.0.4+8' ]
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Is it intentional this is different that the Circle CI version (17.0.3)?

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No, I think this is just pinned to the same as in the webservice repo.


steps:
- name: install git secrets
Expand Down
10 changes: 5 additions & 5 deletions THIRD-PARTY-LICENSES.txt
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Expand Up @@ -125,10 +125,10 @@ Lists of 384 third-party dependencies.
(The Apache Software License, Version 2.0) docker-java-transport-httpclient5 (com.github.docker-java:docker-java-transport-httpclient5:3.2.8 - https://github.com/docker-java/docker-java)
(Apache Software License, Version 2.0) dockstore-cli-integration-testing (io.dockstore:dockstore-cli-integration-testing:1.14.0-SNAPSHOT - https://github.com/dockstore/dockstore-cli/dockstore-cli-integration-testing)
(Apache Software License, Version 2.0) dockstore-client (io.dockstore:dockstore-client:1.14.0-SNAPSHOT - https://github.com/dockstore/dockstore-cli/dockstore-client)
(Apache Software License, Version 2.0) dockstore-common (io.dockstore:dockstore-common:1.14.0-alpha.1 - no url defined)
(Apache Software License, Version 2.0) dockstore-common (io.dockstore:dockstore-common:1.14.0-alpha.2 - no url defined)
(Apache Software License, Version 2.0) dockstore-file-plugin-parent (io.dockstore:dockstore-file-plugin-parent:1.14.0-SNAPSHOT - https://github.com/dockstore/dockstore-cli/dockstore-file-plugin-parent)
(Apache Software License, Version 2.0) dockstore-language-plugin-parent (io.dockstore:dockstore-language-plugin-parent:1.14.0-alpha.1 - no url defined)
(Apache Software License, Version 2.0) dockstore-webservice (io.dockstore:dockstore-webservice:1.14.0-alpha.1 - no url defined)
(Apache Software License, Version 2.0) dockstore-language-plugin-parent (io.dockstore:dockstore-language-plugin-parent:1.14.0-alpha.2 - no url defined)
(Apache Software License, Version 2.0) dockstore-webservice (io.dockstore:dockstore-webservice:1.14.0-alpha.2 - no url defined)
(Apache License 2.0) Dropwizard (io.dropwizard:dropwizard-core:2.1.4 - http://www.dropwizard.io/2.1.4/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-core)
(Apache License 2.0) Dropwizard Asset Bundle (io.dropwizard:dropwizard-assets:2.1.4 - http://www.dropwizard.io/2.1.4/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-assets)
(Apache License 2.0) Dropwizard Authentication (io.dropwizard:dropwizard-auth:2.1.4 - http://www.dropwizard.io/2.1.4/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-auth)
Expand Down Expand Up @@ -327,7 +327,7 @@ Lists of 384 third-party dependencies.
(Apache License, Version 2.0) Objenesis (org.objenesis:objenesis:3.2 - http://objenesis.org/objenesis)
(The Apache Software License, Version 2.0) okhttp (com.squareup.okhttp3:okhttp:4.10.0 - https://square.github.io/okhttp/)
(The Apache Software License, Version 2.0) okio (com.squareup.okio:okio-jvm:3.0.0 - https://github.com/square/okio/)
(Apache Software License, Version 2.0) openapi-java-client (io.dockstore:openapi-java-client:1.14.0-alpha.1 - no url defined)
(Apache Software License, Version 2.0) openapi-java-client (io.dockstore:openapi-java-client:1.14.0-alpha.2 - no url defined)
(Apache Software License, Version 2.0) openapi-java-wes-client (io.dockstore:openapi-java-wes-client:1.14.0-SNAPSHOT - https://github.com/dockstore/dockstore-cli/openapi-java-wes-client)
(The Apache License, Version 2.0) OpenCensus (io.opencensus:opencensus-api:0.31.0 - https://github.com/census-instrumentation/opencensus-java)
(Apache 2) opencsv (com.opencsv:opencsv:5.6 - http://opencsv.sf.net)
Expand Down Expand Up @@ -365,7 +365,7 @@ Lists of 384 third-party dependencies.
(Apache License 2.0) swagger-core (io.swagger:swagger-core:1.6.8 - https://github.com/swagger-api/swagger-core/modules/swagger-core)
(Apache License 2.0) swagger-integration (io.swagger.core.v3:swagger-integration:2.2.4 - https://github.com/swagger-api/swagger-core/modules/swagger-integration)
(Apache Software License, Version 2.0) swagger-java-bitbucket-client (io.dockstore:swagger-java-bitbucket-client:2.0.2 - no url defined)
(Apache Software License, Version 2.0) swagger-java-client (io.dockstore:swagger-java-client:1.14.0-alpha.1 - no url defined)
(Apache Software License, Version 2.0) swagger-java-client (io.dockstore:swagger-java-client:1.14.0-alpha.2 - no url defined)
(Apache Software License, Version 2.0) swagger-java-discourse-client (io.dockstore:swagger-java-discourse-client:2.0.0 - no url defined)
(Apache Software License, Version 2.0) swagger-java-quay-client (io.dockstore:swagger-java-quay-client:2.0.1 - no url defined)
(Apache Software License, Version 2.0) swagger-java-sam-client (io.dockstore:swagger-java-sam-client:2.0.1 - no url defined)
Expand Down
6 changes: 3 additions & 3 deletions dockstore-cli-integration-testing/generated/src/main/resources/pom.xml
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Expand Up @@ -36,13 +36,13 @@
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-common</artifactId>
<version>1.14.0-alpha.1</version>
<version>1.14.0-alpha.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-webservice</artifactId>
<version>1.14.0-alpha.1</version>
<version>1.14.0-alpha.2</version>
<scope>compile</scope>
<exclusions>
<exclusion>
Expand All @@ -54,7 +54,7 @@
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>openapi-java-client</artifactId>
<version>1.14.0-alpha.1</version>
<version>1.14.0-alpha.2</version>
<scope>compile</scope>
</dependency>
<dependency>
Expand Down
13 changes: 13 additions & 0 deletions dockstore-cli-integration-testing/pom.xml
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Expand Up @@ -28,6 +28,7 @@

<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<argLine></argLine>
</properties>

<dependencies>
Expand Down Expand Up @@ -206,6 +207,18 @@
<skipTests>${skipITs}</skipTests>
<!-- seems like some form of Jackson fork issue for this module with random order -->
<runOrder>filesystem</runOrder>
<!-- workaround for Java 17 module issues with powermock -->
<argLine>
@{argLine}
--illegal-access=permit
--add-opens java.base/java.lang=ALL-UNNAMED
--add-opens java.base/java.io=ALL-UNNAMED
--add-opens java.base/java.util=ALL-UNNAMED
--add-opens java.base/java.util.stream=ALL-UNNAMED
--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
</argLine>
</configuration>
</plugin>
<plugin>
Expand Down
8 changes: 4 additions & 4 deletions dockstore-cli-integration-testing/src/test/java/io/dockstore/common/CommonTestUtilities.java
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Expand Up @@ -83,7 +83,7 @@ public static void dropAndRecreateNoTestData(DropwizardTestSupport<DockstoreWebs
application.run("db", "drop-all", "--confirm-delete-everything", dropwizardConfigurationFile);
application
.run("db", "migrate", dropwizardConfigurationFile, "--include", "1.3.0.generated,1.3.1.consistency,1.4.0,1.5.0,"
+ "1.6.0,1.7.0,1.8.0,1.9.0,1.10.0,1.11.0,1.12.0,1.13.0");
+ "1.6.0,1.7.0,1.8.0,1.9.0,1.10.0,1.11.0,1.12.0,1.13.0,1.14.0");
}

/**
Expand All @@ -110,7 +110,7 @@ public static void dropAndCreateWithTestData(DropwizardTestSupport<DockstoreWebs

List<String> migrationList = Arrays
.asList("1.3.0.generated", "1.3.1.consistency", "test", "1.4.0", "1.5.0", "test_1.5.0", "1.6.0", "1.7.0",
"1.8.0", "1.9.0", "1.10.0", "1.11.0", "1.12.0", "1.13.0");
"1.8.0", "1.9.0", "1.10.0", "1.11.0", "1.12.0", "1.13.0", "1.14.0");
runMigration(migrationList, application, dropwizardConfigurationFile);
}

Expand Down Expand Up @@ -214,7 +214,7 @@ private static void cleanStatePrivate1(DropwizardTestSupport<DockstoreWebservice
new File("../dockstore-webservice/src/main/resources/migrations.test.confidential1_1.5.0.xml").getAbsolutePath());
runExternalMigration(migrationList, application, configPath);

migrationList = Arrays.asList("1.6.0", "1.7.0", "1.8.0", "1.9.0", "1.10.0", "1.11.0", "1.12.0", "1.13.0");
migrationList = Arrays.asList("1.6.0", "1.7.0", "1.8.0", "1.9.0", "1.10.0", "1.11.0", "1.12.0", "1.13.0", "1.14.0");
runMigration(migrationList, application, configPath);
}

Expand Down Expand Up @@ -299,7 +299,7 @@ private static void cleanStatePrivate2(DropwizardTestSupport<DockstoreWebservice
new File("../dockstore-webservice/src/main/resources/migrations.test.confidential2_1.5.0.xml").getAbsolutePath());
runExternalMigration(migrationList, application, configPath);

migrationList = Arrays.asList("1.6.0", "1.7.0", "1.8.0", "1.9.0", "1.10.0", "1.11.0", "1.12.0", "1.13.0");
migrationList = Arrays.asList("1.6.0", "1.7.0", "1.8.0", "1.9.0", "1.10.0", "1.11.0", "1.12.0", "1.13.0", "1.14.0");
runMigration(migrationList, application, configPath);
}

Expand Down
8 changes: 4 additions & 4 deletions dockstore-client/generated/src/main/resources/pom.xml
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Expand Up @@ -66,7 +66,7 @@
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-common</artifactId>
<version>1.14.0-alpha.1</version>
<version>1.14.0-alpha.2</version>
<scope>compile</scope>
<exclusions>
<exclusion>
Expand All @@ -78,13 +78,13 @@
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>swagger-java-client</artifactId>
<version>1.14.0-alpha.1</version>
<version>1.14.0-alpha.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>openapi-java-client</artifactId>
<version>1.14.0-alpha.1</version>
<version>1.14.0-alpha.2</version>
<scope>compile</scope>
</dependency>
<dependency>
Expand Down Expand Up @@ -337,7 +337,7 @@
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<groupId>org.hibernate.validator</groupId>
<artifactId>hibernate-validator</artifactId>
<version>6.2.5.Final</version>
<scope>compile</scope>
Expand Down
16 changes: 10 additions & 6 deletions dockstore-client/pom.xml
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Expand Up @@ -29,6 +29,7 @@

<properties>
<docker-client.version>3.2.8</docker-client.version>
<argLine></argLine>
</properties>

<dependencies>
Expand Down Expand Up @@ -293,7 +294,7 @@
<artifactId>jakarta.annotation-api</artifactId>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<groupId>org.hibernate.validator</groupId>
<artifactId>hibernate-validator</artifactId>
<version>6.2.5.Final</version>
</dependency>
Expand Down Expand Up @@ -389,7 +390,7 @@
<usedDependencies>
<usedDependency>com.fasterxml.jackson.jaxrs:jackson-jaxrs-base</usedDependency>
<usedDependency>io.spray:spray-json_2.13</usedDependency>
<usedDependency>org.hibernate:hibernate-validator</usedDependency>
<usedDependency>org.hibernate.validator:hibernate-validator</usedDependency>
<usedDependency>org.glassfish:jakarta.el</usedDependency>
</usedDependencies>
<ignoredNonTestScopedDependencies>
Expand Down Expand Up @@ -417,10 +418,6 @@
<groupId>com.github.spotbugs</groupId>
<artifactId>spotbugs-maven-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.eluder.coveralls</groupId>
<artifactId>coveralls-maven-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
Expand All @@ -439,6 +436,13 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<configuration>
<argLine>
@{argLine}
--add-opens java.base/java.lang=ALL-UNNAMED
--add-opens java.base/java.io=ALL-UNNAMED
--add-opens java.base/java.util=ALL-UNNAMED
--add-opens java.base/java.base=ALL-UNNAMED
</argLine>
<skipTests>${skipITs}</skipTests>
<excludedGroups>${excludeGroups}</excludedGroups>
</configuration>
Expand Down
2 changes: 1 addition & 1 deletion dockstore-client/src/main/java/io/dockstore/client/cli/nested/AbstractEntryClient.java
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Expand Up @@ -816,7 +816,7 @@ public List<ToolFile> getAllToolDescriptors(String type, String entryPath, Strin

// get all the tool files and filter out anything not a descriptor
try {
return ga4ghv20api.toolsIdVersionsVersionIdTypeFilesGet(type, entryPath, versionID).stream()
return ga4ghv20api.toolsIdVersionsVersionIdTypeFilesGet(entryPath, type, versionID, null).stream()
.filter(toolFile -> ToolFile.FileTypeEnum.SECONDARY_DESCRIPTOR.equals(toolFile.getFileType()) || ToolFile.FileTypeEnum.PRIMARY_DESCRIPTOR.equals(toolFile.getFileType()))
.collect(Collectors.toList());
} catch (io.dockstore.openapi.client.ApiException ex) {
Expand Down
2 changes: 1 addition & 1 deletion dockstore-client/src/main/java/io/dockstore/client/cli/nested/BaseLanguageClient.java
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Expand Up @@ -249,7 +249,7 @@ public void validateDescriptorChecksum(ToolDescriptor.TypeEnum type, String entr
Optional<Checksum> remoteDescriptorChecksum = Optional.empty();
try {
// The TRS endpoint only discovers published entries
final FileWrapper remoteDescriptor = ga4ghv20api.toolsIdVersionsVersionIdTypeDescriptorRelativePathGet(type.toString(), ga4ghv20Path, versionID, toolFile.getPath());
final FileWrapper remoteDescriptor = ga4ghv20api.toolsIdVersionsVersionIdTypeDescriptorRelativePathGet(ga4ghv20Path, type.toString(), versionID, toolFile.getPath());
10000 remoteDescriptorChecksum = remoteDescriptor.getChecksum()
.stream()
.filter(c -> c.getType().equals(checksumFunction))
Expand Down
2 changes: 1 addition & 1 deletion dockstore-client/src/main/java/io/dockstore/client/cli/nested/NextflowLauncher.java
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Expand Up @@ -25,7 +25,7 @@ public void initialize() {
@Override
public List<String> buildRunCommand() {
ArrayList<String> command = new ArrayList<>(
Arrays.asList("java", "-jar", executionFile.getAbsolutePath(), "run", "-with-docker", "--outdir", workingDirectory,
Arrays.asList("java", "--add-opens java.management/com.sun.jmx.mbeanserver=ALL-UNNAMED", "-jar", executionFile.getAbsolutePath(), "run", "-with-docker", "--outdir", workingDirectory,
"-work-dir", workingDirectory));
if (originalParameterFile != null) {
command.addAll(Arrays.asList("-params-file", originalParameterFile));
Expand Down
5 changes: 5 additions & 0 deletions dockstore-client/src/test/java/io/dockstore/client/cli/AbstractEntryClientTestIT.java
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Expand Up @@ -34,7 +34,12 @@ public class AbstractEntryClientTestIT {
public final SystemErrRule systemErrRule = new FlushingSystemErrRule().enableLog().muteForSuccessfulTests();
@Rule
public final SystemOutRule systemOutRule = new FlushingSystemOutRule().enableLog().muteForSuccessfulTests();

/**
* @deprecated does not seem to play well with Java 17
*/
@Rule
@Deprecated(since = "1.14")
public final EnvironmentVariables environmentVariables = new EnvironmentVariables();

/**
Expand Down
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