Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:0.25
-
Epic Link:
-
Sprint:Spring 1, Spring 5
Description
When building main-JDK21 using a container built with the new "JDK21" Dockerfile (see this commit), I observed the following warning, shown in the following output from the command "mvn install".
Downloading from repo1: https://maven.bioviz.org/repo1/com/affymetrix/genoviz/1.1.9/genoviz-1.1.9.jar [WARNING] Could not validate integrity of download from https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.jar org.eclipse.aether.transfer.ChecksumFailureException: Checksum validation failed, no checksums available at org.eclipse.aether.internal.impl.AbstractChecksumPolicy.onNoMoreChecksums (AbstractChecksumPolicy.java:63) at org.eclipse.aether.connector.basic.ChecksumValidator.validate (ChecksumValidator.java:112) at org.eclipse.aether.connector.basic.BasicRepositoryConnector$GetTaskRunner.runTask (BasicRepositoryConnector.java:484) at org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run (BasicRepositoryConnector.java:414) at org.eclipse.aether.util.concurrency.RunnableErrorForwarder.lambda$wrap$0 (RunnableErrorForwarder.java:66) at java.util.concurrent.ThreadPoolExecutor.runWorker (ThreadPoolExecutor.java:1144) at java.util.concurrent.ThreadPoolExecutor$Worker.run (ThreadPoolExecutor.java:642) at java.lang.Thread.run (Thread.java:1583) [WARNING] Checksum validation failed, no checksums available from repo1 for https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.jar Downloaded from repo1: https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.jar (115 kB at 1.4 MB/s)
Judging from the error message, probably we need to create and deploy a "checksum" file for this artifact.
Also, since we are building main-JDK21, which I thought replaces javax artifacts with jakarta artifacts (due to a package name change), why is IGB needing to get this artifact from the maven repository?
Investigate and correct the problem.
Info about the version of IGB I was trying to build:
docker.bioviz.org ec2-user $ git status On branch main-JDK21 Your branch is up to date with 'origin/main-JDK21'. nothing to commit, working tree clean docker.bioviz.org ec2-user $ git remote -v origin https://bitbucket.org/hillrunner2008/integrated-genome-browser (fetch) origin https://bitbucket.org/hillrunner2008/integrated-genome-browser (push) docker.bioviz.org ec2-user $ git ls a0860834e (HEAD -> main-JDK21, origin/main-JDK21) removing mac specific code for the right aligned tabs to ensure vertical override is applied 6fe7790d9 rolling back javafx dark mode changes ebf692063 rolling back javafx dark mode changes d15e06b05 fixing yml for new custom task d3c07fc14 fixing yml for new custom task 55080cf74 adding step with reference to maven cache
Info about the container I was using to build it:
docker.bioviz.org ec2-user $ pwd /home/ec2-user/integrated-genome-browser-docker docker.bioviz.org ec2-user $ git status On branch jdk21 Your branch is up to date with 'origin/jdk21'. nothing to commit, working tree clean docker.bioviz.org ec2-user $ git remote -v origin https://aloraine@bitbucket.org/lorainelab/integrated-genome-browser-docker.git (fetch) origin https://aloraine@bitbucket.org/lorainelab/integrated-genome-browser-docker.git (push) docker.bioviz.org ec2-user $ git ls d26649c (HEAD -> jdk21, origin/jdk21) new dockerfile for jdk21 and install4jv10 b138cd9 updates to dockerfile for new jdk21 release 9e155fb (origin/master, origin/HEAD, master) IGBF-3160 Enable Karthik and Nowlan to log in ce91408 IGBF-3160 Add Ann's favorite aliases df458df IGBF-3160 Specify region in aws_vars.yml instead
Attachments
Issue Links
- relates to
-
IGBF-3521 Investigate build problem: effective model for org.lorainelab.igb:affymetrix-common:bundle:10.0.0
-
- Closed
-
-
-
- Closed
-
-
-
- Closed
-
-
-
- Closed
-
-
-
- Closed
-
-
-
- Closed
-
Show 1 more links (1 relates to)
Activity
I am not seeing this error in the build either. I believe it was a transitive dependency in affymetrix-common and that dependency is removed or replaced. I think this ticket can be closed for now.
Seeing the warning after removing the .m2 cache. Bitbucket pipelines will use cache, so it is possible that this warning no longer appears in the pipeline since it is cached.
Most likely just need to create a sha1 and md5 similar to IGBF-3523.
sha1 and md5 files is attached to this ticket
Ann Loraine - please upload the two attached files (jlfgr-1.0.md5 and jlfgr-1.0.sha1) to the following repo: https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/
A request for Karthik Raveendran or Nowlan Freese:
Our three "old school" maven repositories are now being version controlled here: https://bitbucket.org/lorainelab/maven/src/main/
Please submit a PR to the repository to add the above files.
Pull request: https://bitbucket.org/lorainelab/maven/pull-requests/2
PR is merged and changes are deployed to maven.bioviz.org.
To test:
- Check the deployment of the above files. They should now appear in one of the three repos hosted on maven.bioviz.org
- Remove local .m2 to ensure all the things will get downloaded freshly from the maven repositories hosted on maven.bioviz.org
- Compile IGB and check to see if the errors mentioned in the ticket re-occur
The issue seems to still persists despite having the files in the right folders
Downloading from repo1: https://maven.bioviz.org/repo1/com/affymetrix/genoviz/1.1.9/genoviz-1.1.9.jar [WARNING] Could not validate integrity of download from https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.jar org.eclipse.aether.transfer.ChecksumFailureException: Checksum validation failed, no checksums available at org.eclipse.aether.internal.impl.AbstractChecksumPolicy.onNoMoreChecksums (AbstractChecksumPolicy.java:63) at org.eclipse.aether.connector.basic.ChecksumValidator.validate (ChecksumValidator.java:112) at org.eclipse.aether.connector.basic.BasicRepositoryConnector$GetTaskRunner.runTask (BasicRepositoryConnector.java:484) at org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run (BasicRepositoryConnector.java:414) at org.eclipse.aether.util.concurrency.RunnableErrorForwarder.lambda$wrap$0 (RunnableErrorForwarder.java:66) at java.util.concurrent.ThreadPoolExecutor.runWorker (ThreadPoolExecutor.java:1144) at java.util.concurrent.ThreadPoolExecutor$Worker.run (ThreadPoolExecutor.java:642) at java.lang.Thread.run (Thread.java:1583) [WARNING] Checksum validation failed, no checksums available from repo1 for https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.jar
A second similar error for the pom:
[WARNING] Could not validate integrity of download from https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.pom org.eclipse.aether.transfer.ChecksumFailureException: Checksum validation failed, no checksums available at org.eclipse.aether.internal.impl.AbstractChecksumPolicy.onNoMoreChecksums (AbstractChecksumPolicy.java:63) at org.eclipse.aether.connector.basic.ChecksumValidator.validate (ChecksumValidator.java:112) at org.eclipse.aether.connector.basic.BasicRepositoryConnector$GetTaskRunner.runTask (BasicRepositoryConnector.java:484) at org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run (BasicRepositoryConnector.java:414) at org.eclipse.aether.connector.basic.BasicRepositoryConnector.get (BasicRepositoryConnector.java:260) at org.eclipse.aether.internal.impl.DefaultArtifactResolver.performDownloads (DefaultArtifactResolver.java:536) at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve (DefaultArtifactResolver.java:448) at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifacts (DefaultArtifactResolver.java:260) at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifact (DefaultArtifactResolver.java:242) at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.loadPom (DefaultArtifactDescriptorReader.java:231) at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.readArtifactDescriptor (DefaultArtifactDescriptorReader.java:172) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.resolveCachedArtifactDescriptor (DfDependencyCollector.java:382) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.getArtifactDescriptorResult (DfDependencyCollector.java:368) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.processDependency (DfDependencyCollector.java:218) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.processDependency (DfDependencyCollector.java:156) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.process (DfDependencyCollector.java:138) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.doCollectDependencies (DfDependencyCollector.java:108) at org.eclipse.aether.internal.impl.collect.DependencyCollectorDelegate.collectDependencies (DependencyCollectorDelegate.java:222) at org.eclipse.aether.internal.impl.collect.DefaultDependencyCollector.collectDependencies (DefaultDependencyCollector.java:87) at org.eclipse.aether.internal.impl.DefaultRepositorySystem.collectDependencies (DefaultRepositorySystem.java:305) at org.apache.maven.project.DefaultProjectDependenciesResolver.resolve (DefaultProjectDependenciesResolver.java:151) at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.getDependencies (LifecycleDependencyResolver.java:224) at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.resolveProjectDependencies (LifecycleDependencyResolver.java:136) at org.apache.maven.lifecycle.internal.MojoExecutor.ensureDependenciesAreResolved (MojoExecutor.java:369) at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute (MojoExecutor.java:327) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:213) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:175) at org.apache.maven.lifecycle.internal.MojoExecutor.access$000 (MojoExecutor.java:76) at org.apache.maven.lifecycle.internal.MojoExecutor$1.run (MojoExecutor.java:163) at org.apache.maven.plugin.DefaultMojosExecutionStrategy.execute (DefaultMojosExecutionStrategy.java:39) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:160) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:105) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:73) at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:53) at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:118) at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:261) at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:173) at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:101) at org.apache.maven.cli.MavenCli.execute (MavenCli.java:910) at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:283) at org.apache.maven.cli.MavenCli.main (MavenCli.java:206) at jdk.internal.reflect.DirectMethodHandleAccessor.invoke (DirectMethodHandleAccessor.java:103) at java.lang.reflect.Method.invoke (Method.java:580) at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:283) at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:226) at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:407) at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:348) [WARNING] Checksum validation failed, no checksums available from repo1 for https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.pom
The directory https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/ contains these files:
- jlfgr-1.0.jar
- jlfgr-1.0.md5
- jlfgr-1.0.pom
- jlfgr-1.0.sha1
According to other examples, it seems like md4 and sh1 checksum files need to be named after the file they refer to.
As an example, see: https://maven.bioviz.org/repo2/com/affymetrix/genoviz/1.0.1/.
- jlfgr-1.0.jar.md5
- jlfgr-1.0.jar.sha1
- jlfgr-1.0.pom.md5
- jlfgr-1.0.pom.sha1
Made md5 file on MacOS with:
local aloraine$ md5 jlfgr-1.0.jar MD5 (jlfgr-1.0.jar) = 88b00348a6f398a034c4c3999c097f47
Copied 88b00348a6f398a034c4c3999c097f47 into a file.
Made sha1 file on MacOS with:
local aloraine$ shasum jlfgr-1.0.jar ca531553caad2d15ae5b5d4ec1a119ce8a14d70a jlfgr-1.0.jar
Copied ca531553caad2d15ae5b5d4ec1a119ce8a14d70a to a file.
Deployed the new files to maven.bioviz.org. Confirmed that the error now longer appears. Moving to done.
I'm not seeing the error below in the latest bitbucket pipeline logs from main-JDK21-with-javafx-no-theme
[WARNING] Could not validate integrity of download from https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.jarThe warning is correct in that the md5 and sha1 are not present maven.bioviz.org/repo1, though this same artifact is available from the Freehep repository with md5 and sha1. I'm not sure why the warning is no longer present.
I'm not sure what this artifact is being used for. It isn't widely used in the IGB project, though I do see it in the pom for the affymetrix-common module.
Regarding the replacing of javax, it is only certain javax packages that were renamed.
As the warning is no longer appearing I think this is non-critical to address for the JDK21 release.