Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 10.0.0 Major Release
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Labels:None
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Story Points:4
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Epic Link:
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Sprint:Summer 4 2023 June 26, Summer 5 2023 July 10, Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21
Description
In previous work, we observed that updating SCR syntax to match the OSGI SCR R6 coincided with inability to run IGB using JDK 11.
We do not know why this occurred.
To get a better understanding of how SCR annotations are used in IGB, update the annotations to use R6 instead of R5 syntax, using the master branch of the team repository, version 9.1.12.
Hopefully, we will see how the changes affect IGB and in what way. For example, if we observe wiring errors, we would like to know why these wiring errors would occur if there is only a change in the Component syntax.
This task emerged from work on a different ticket. See this comment from that ticket.
Attachments
Issue Links
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- Closed
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- relates to
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IGBF-3422 Investigate Test Failure that is occurring in QuickloadUtilsTest class.
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- Closed
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- Closed
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- Closed
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- Closed
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Show 1 more links (1 relates to)
Activity
Runtime errors that appear after changes in the annotations include the part (osgi.extender=osgi.component)(version>=1.3.0)(!(version>=2.0.0) as a missing requirement.
Unable to resolve igb [39](R 39.0): missing requirement [igb [39](R 39.0)] osgi.wiring.package; (&(osgi.wiring.package=com.affymetrix.genometry.color)(version>=9.1.0)(!(version>=10.0.0))) [caused by: Unable to resolve genometry [31](R 31.0): missing requirement [genometry [31](R 31.0)] osgi.extender; (&(osgi.extender=osgi.component)(version>=1.3.0)(!(version>=2.0.0)))] Unresolved requirements: [[igb [39](R 39.0)] osgi.wiring.package; (&(osgi.wiring.package=com.affymetrix.genometry.color)(version>=9.1.0)(!(version>=10.0.0)))]
This requirement osgi.extender, which provides osgi.component, is fulfilled by org.apache.felix.scr, a bundle we are trying to avoid.
Another requirement issue is for javax.microedition.io
Unable to resolve igb [39](R 39.0): missing requirement [igb [39](R 39.0)] osgi.wiring.package; (&(osgi.wiring.package=com.affymetrix.genometry.color)(version>=9.1.0)(!(version>=10.0.0))) [caused by: Unable to resolve genometry [31](R 31.0): missing requirement [genometry [31](R 31.0)] osgi.wiring.package; (osgi.wiring.package=javax.microedition.io)] Unresolved requirements: [[igb [39](R 39.0)] osgi.wiring.package; (&(osgi.wiring.package=com.affymetrix.genometry.color)(version>=9.1.0)(!(version>=10.0.0)))]
In order to resolve the javax.microedition.io, felix dependency manager and felix dependency manager shell dependencies that are pulled from maven repo2 was removed. However, the osgi.extender issue is yet to be resolved. Work so far has been committed and pushed, see Commit . In this commit, there are 52 runtime errors that pertains to genometry.
Dr. Nowlan Freese removed dependencies for remote logging in IGBF-3382 and after merging that branch with mine, strangely, there is an com.apple.laf issue. Its strange because the issue occurs only with Java 11 but both of us are making changes in IGB JDK 8. After removing com.apple.laf, however, the number of runtime errors have reduced considerably especially errors pertatining to osgi.extender issue.
The significant difference in both branches apart from the obvious changes is the use of bndlib. Dr. Nowlan Freese uses annotations from bndlib whereas my branch uses osgi annotations.
Branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3379
Builds and runs with all bundles (84) active, but IGB does not appear.
Additional notes about changes:
- ThresholdingAction.java - OSGI was throwing an error about "properties = "name=" + ThresholdingAction.COMPONENT_NAME" so I removed it. Unsure of what it was doing, may break something functionally.
- osgi.cmpn is set at version 6.0.0. However, in the main pom.xml osgi.cmpn was set to a scope of runtime, which is not allowed (see blog post). I changed scope to provided and the error went away, but unsure if this is the correct way of handling the issue.
- Needed to add org.osgi.service.log to resolve a dependency.
- In QuickloadDataProvider.java there is an import for org.osgi.framework that was unable to find the dependency. I'm not sure where org.osgi.framework was being provided originally as I don't think anything changed in its pom, but I had to add org.apache.felix.main to satisfy the dependency.
Suggestions for debugging:
- Dig into the "main" project to investigate when the OSGi bundles get activated and started. Use the debugger to watch how objects get instantiated and so forth. The "kickoff" for all of it might be this: core/igb/src/main/java/com/affymetrix/igb/Activator.java
- Also, use the felix console to manipulate bundle life cycle.
- Observe startup behavior using different methods of launching the application: 1) using IDE "run" 2) running with java -jar igb_exe.jar (with and without the "development mode" option) 3) using one of the "igb run" scripts version-controlled in the project
- Try to modify the annotations for one bundle at a time to observe when the lack of startup occurs; also, read the XML descriptor file in the pre- and post- OSGI v6 annotations update to understand how that descriptor file may or may not be getting made, and its syntax.
- Try running without the apple look and feel option (run time option - a "hail mary" debugging idea
Recall that the OSGi runtime we are now using can handle both types of annotations - v5 and v6? If so, you can update the annotations syntax incrementally, bundle by bundle.
Reminder of the branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3379
Nowlan Freese notes: When he starts the jar file the IGB icon appears in the system tray (on his mac) and the menu bar shows "main". When he clicks on "about main" the proper "about igb" screen appears. He can also see the settings options. [~aloraine]: try manipulating the settings.
- In Activator.java, at the end of initializeWindowService the IGB window appears (after line 150) when running main-JDK8. Nothing appears on the
IGBF-3379branch, though I can't see any obvious differences. - Refreshing the Core IGB bundle through the felix web console does not bring up the IGB window.
- Changing back to using the aQute.bnd bundle instead of org.osgi for declarative services annotations (but using the new version of annotations) will build and all bundles are active, but the IGB window does not appear and I cannot access the IGB menu as I could with the org.osgi annotations.
- Looking at the Core IGB bundle through the felix web console I see the following in
IGBF-3379, which i do not see when I run main-JDK8: java.applet,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.awt,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.awt.datatransfer,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.awt.dnd,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.awt.event,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.awt.font,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.awt.geom,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.awt.im,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.awt.image,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.awt.print,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.beans,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.io,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.lang,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.lang.invoke,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.lang.reflect,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.net,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.nio,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.nio.charset,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.security,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.security.cert,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.sql,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.text,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.util,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.util.concurrent,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.util.function,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.util.logging,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.util.prefs,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.util.regex,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation java.util.stream,version=0.0.0.JavaSE_001_008 from org.apache.felix.framework (0) -- Overwritten by Boot Delegation
Attempting to upgrade the Core - Window Service module by itself to the new annotations, without changing anything else. As soon as the new annotations are used (just changing them from aQute.bnd.annotation.component.Component to aQute.bnd.component.annotations.Component) the IGB window fails to appear. If the new annotations are used in only IgbTabPanelRegistry.java then the IGB window appears with no tabs.
Interesting post on bundle classpath: https://stackoverflow.com/questions/16933929/what-is-the-intended-use-case-for-bundle-classpath-in-osgi-bundles
Medium on Java vs OSGI class loaders: https://technospace.medium.com/java-vs-osgi-class-loading-17a1ad4cc2a5
Following after Dr. Freese's changes in IGBF-3379 and the above comment and trying to replace aQute component annotations to OSGI component annotations. One of the first bundles to fail in this change is synonymlookup bundle, where the compiler is unable to find the symbol, @Component and followed by genometry. Trying to figure out why these bundles specifically are vulnerable to these errors after the changes
After clearing all errors regarding @Component issue by adding osgi.cmpn and osgi.core in the dependencies of the bundles that need them, IGB bundles were started and felix console was up and running as well but IGB did not appear. When I built the project in Intellij and tried running it in debug mode, an error in the OSGIHandler.java popped up:
15:27:15.048 ERROR com.affymetrix.main.Main - Error starting osgi runtime container
java.lang.NoSuchMethodError: org.osgi.service.resolver.ResolveContext.onCancel(Ljava/lang/Runnable;)V
at org.apache.felix.resolver.ResolverImpl$ResolveSession.createSession(ResolverImpl.java:99)
at org.apache.felix.resolver.ResolverImpl.resolve(ResolverImpl.java:419)
at org.apache.felix.resolver.ResolverImpl.resolve(ResolverImpl.java:374)
at org.apache.felix.framework.StatefulResolver.resolve(StatefulResolver.java:488)
at org.apache.felix.framework.Felix.init(Felix.java:778)
at org.apache.felix.framework.Felix.init(Felix.java:648)
at org.apache.felix.framework.Felix.start(Felix.java:1111)
at com.affymetrix.main.OSGiHandler.loadFramework(OSGiHandler.java:170)
at com.affymetrix.main.OSGiHandler.startOSGi(OSGiHandler.java:62)
at com.affymetrix.main.Main.main(Main.java:30)
This is a weird error on further investigation: The error trace leads back to OSGiHandler.java, line 170, which is framework.start() which in turn is a function in the Framework interface in org.osgi.framework.launch package in osgi.core 6.0.0 bundle. There is a @ProviderType annotation in the Framework interface and that annotation is throwing an error. The annotation should apparently come from org.osgi.annotation.versioning.ProviderType but the annotation folder does not exist within osgi.core 6.0.0. Out of curiosity, I went through some classes within osgi.core and there are other annotations with errors like this, annotations like @ConsumerType and @Version.
Not sure if that is why the error is thrown but ResolveContext class in the package org.osgi.service.resolver has a similar issue with its annotation and it does not have the method OnCancel.
In the above mentioned issue the annotations are available in bndlib and I am trying find if there is an alternative as we are trying to use OSGI annotations and not use bndlib as much as possible.
Request for clarification on the previous two comments, based on discussion during daily standup:
1) Please clarify: "the annotations are available in bndlib." In this context, what is meant by "bndlib"? Does is mean: a java library artifact, a jar file, where annotations are defined?
2) When discussing java libraries, please refer to them using their proper full maven names instead of nicknames like "bndlib" or "osgi compendium." Please review this maven project documentation describing maven coordinates. It would be helpful if you could edit all comments above to use the proper names for any java libraries or artifacts you are discussing.
3) If "bndlib" is a java library or a plugin, provide a link to where the particular version you are using resides in maven central or other maven repository where you are getting it from.
attn: Karthik Raveendran or Nowlan Freese
1) AQute bndlib is a java library which is added in the project to provide annotations. We are trying to replace the these annotations with OSGI R6 annotations which is available in OSGI core. However, OSGI Core uses annotations that is provided by bndlib.
3) https://mvnrepository.com/artifact/biz.aQute.bnd/biz.aQute.bndlib
Before realizing that I need to add the bndlib back into the project, I had made changes to fix wiring issues but that was unnecessary because adding bndlib would have solved that so I had to revert back all that changes and add bndlib back. I am currently in a place where the project throws no error but IGB does not seem to start and gets stuck half way. Need to investigate this because incomplete run process without errors is not something I have seen. See log below
05:53:00.302 [main] INFO com.affymetrix.main.Main - Starting OSGI container
05:53:00.312 [main] INFO com.affymetrix.main.OSGiHandler - Loading OSGi framework
05:53:00.913 [main] INFO com.affymetrix.main.OSGiHandler - Loading embedded OSGi bundles
05:53:01.450 [main] INFO com.affymetrix.main.OSGiHandler - loading affymetrix-common-9.1.12.jar
05:53:01.455 [main] INFO com.affymetrix.main.OSGiHandler - loading annotation-tab-9.1.12.jar
05:53:01.460 [main] INFO com.affymetrix.main.OSGiHandler - loading apollo-library-9.1.12.jar
05:53:01.463 [main] INFO com.affymetrix.main.OSGiHandler - loading appstore-9.1.12.jar
05:53:01.469 [main] INFO com.affymetrix.main.OSGiHandler - loading bai-9.1.12.jar
05:53:01.473 [main] INFO com.affymetrix.main.OSGiHandler - loading bam-9.1.12.jar
05:53:01.479 [main] INFO com.affymetrix.main.OSGiHandler - loading bed-9.1.12.jar
05:53:01.485 [main] INFO com.affymetrix.main.OSGiHandler - loading bigBedHandler-9.1.12.jar
05:53:01.489 [main] INFO com.affymetrix.main.OSGiHandler - loading bigWigHandler-9.1.12.jar
05:53:01.493 [main] INFO com.affymetrix.main.OSGiHandler - loading bigwig-2.0.0.jar
05:53:01.498 [main] INFO com.affymetrix.main.OSGiHandler - loading bookmark-9.1.12.jar
05:53:01.503 [main] INFO com.affymetrix.main.OSGiHandler - loading cache-9.1.12.jar
05:53:01.506 [main] INFO com.affymetrix.main.OSGiHandler - loading cache-api-9.1.12.jar
05:53:01.513 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-codec-1.15.jar
05:53:01.523 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-compress-1.23.0.jar
05:53:01.527 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-csv-1.10.0.jar
05:53:01.531 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-fileupload-1.5.jar
05:53:01.537 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-io-2.11.0.jar
05:53:01.543 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-jexl-2.1.1.jar
05:53:01.550 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-lang3-3.12.0.jar
05:53:01.555 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-logging-1.2.jar
05:53:01.560 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-pool-1.6.jar
05:53:01.563 [main] INFO com.affymetrix.main.OSGiHandler - loading console-tab-9.1.12.jar
05:53:01.567 [main] INFO com.affymetrix.main.OSGiHandler - loading context-menu-service-9.1.12.jar
05:53:01.581 [main] INFO com.affymetrix.main.OSGiHandler - loading das-9.1.12.jar
05:53:01.585 [main] INFO com.affymetrix.main.OSGiHandler - loading external-sort-9.1.12.jar
05:53:01.592 [main] INFO com.affymetrix.main.OSGiHandler - loading externalView-9.1.12.jar
05:53:01.596 [main] INFO com.affymetrix.main.OSGiHandler - loading failureaccess-1.0.1.jar
05:53:01.600 [main] INFO com.affymetrix.main.OSGiHandler - loading feedback-9.1.12.jar
05:53:01.604 [main] INFO com.affymetrix.main.OSGiHandler - loading frameManager-9.1.12.jar
05:53:01.614 [main] INFO com.affymetrix.main.OSGiHandler - loading genometry-9.1.12.jar
05:53:01.618 [main] INFO com.affymetrix.main.OSGiHandler - loading genotyping-9.1.12.jar
05:53:01.628 [main] INFO com.affymetrix.main.OSGiHandler - loading genoviz-1.1.9.jar
05:53:01.632 [main] INFO com.affymetrix.main.OSGiHandler - loading graphTab-9.1.12.jar
05:53:01.638 [main] INFO com.affymetrix.main.OSGiHandler - loading gson-2.10.1.jar
05:53:01.659 [main] INFO com.affymetrix.main.OSGiHandler - loading guava-32.1.1-jre.jar
05:53:01.662 [main] INFO com.affymetrix.main.OSGiHandler - loading heatmap-editor-9.1.12.jar
05:53:01.677 [main] INFO com.affymetrix.main.OSGiHandler - loading htsjdk-igb-2.16.3.jar
05:53:01.701 [main] INFO com.affymetrix.main.OSGiHandler - loading igb-9.1.12.jar
05:53:01.706 [main] INFO com.affymetrix.main.OSGiHandler - loading igb-genoviz-extensions-9.1.12.jar
05:53:01.710 [main] INFO com.affymetrix.main.OSGiHandler - loading igb-javafx-util-9.1.12.jar
05:53:01.714 [main] INFO com.affymetrix.main.OSGiHandler - loading igb-preferences-9.1.12.jar
05:53:01.719 [main] INFO com.affymetrix.main.OSGiHandler - loading igb-services-9.1.12.jar
05:53:01.723 [main] INFO com.affymetrix.main.OSGiHandler - loading igbScript-9.1.12.jar
05:53:01.728 [main] INFO com.affymetrix.main.OSGiHandler - loading igbSwingExt-9.1.12.jar
05:53:01.733 [main] INFO com.affymetrix.main.OSGiHandler - loading image-exporter-9.1.12.jar
05:53:01.780 [main] INFO com.affymetrix.main.OSGiHandler - loading jide-ultimate-3.5.15.jar
05:53:01.786 [main] INFO com.affymetrix.main.OSGiHandler - loading keyWordSearch-9.1.12.jar
05:53:01.791 [main] INFO com.affymetrix.main.OSGiHandler - loading keybinding-registry-9.1.12.jar
05:53:01.797 [main] INFO com.affymetrix.main.OSGiHandler - loading logback-classic-1.2.12.jar
05:53:01.804 [main] INFO com.affymetrix.main.OSGiHandler - loading logback-core-1.2.12.jar
05:53:01.808 [main] INFO com.affymetrix.main.OSGiHandler - loading logging-config-9.1.12.jar
05:53:01.812 [main] INFO com.affymetrix.main.OSGiHandler - loading narrowpeak-9.1.12.jar
05:53:01.816 [main] INFO com.affymetrix.main.OSGiHandler - loading ncbiBlast-9.1.12.jar
05:53:01.822 [main] INFO com.affymetrix.main.OSGiHandler - loading org.apache.felix.bundlerepository-2.0.10.jar
05:53:01.826 [main] INFO com.affymetrix.main.OSGiHandler - loading org.apache.felix.configadmin-1.9.26.jar
05:53:01.830 [main] INFO com.affymetrix.main.OSGiHandler - loading org.apache.felix.eventadmin-1.6.4.jar
05:53:01.849 [main] INFO com.affymetrix.main.OSGiHandler - loading org.apache.felix.http.bundle-3.0.0.jar
05:53:01.878 [main] INFO com.affymetrix.main.OSGiHandler - loading org.apache.felix.http.jetty-4.2.12.jar
05:53:01.886 [main] INFO com.affymetrix.main.OSGiHandler - loading org.apache.felix.http.servlet-api-2.1.0.jar
05:53:01.893 [main] INFO com.affymetrix.main.OSGiHandler - loading org.apache.felix.scr-2.0.14.jar
05:53:01.899 [main] INFO com.affymetrix.main.OSGiHandler - loading org.apache.felix.webconsole-4.8.8.jar
05:53:01.902 [main] INFO com.affymetrix.main.OSGiHandler - loading org.lorainelab.igb.menu.api-9.1.12.jar
05:53:01.911 [main] INFO com.affymetrix.main.OSGiHandler - loading osgi.cmpn-5.0.0.jar
05:53:01.914 [main] INFO com.affymetrix.main.OSGiHandler - loading paired-data-preprocessor-9.1.12.jar
05:53:01.921 [main] INFO com.affymetrix.main.OSGiHandler - loading plugins-manager-9.1.12.jar
05:53:01.925 [main] INFO com.affymetrix.main.OSGiHandler - loading propertyView-9.1.12.jar
05:53:01.928 [main] INFO com.affymetrix.main.OSGiHandler - loading quickload-9.1.12.jar
05:53:01.932 [main] INFO com.affymetrix.main.OSGiHandler - loading restrictionSites-9.1.12.jar
05:53:01.936 [main] INFO com.affymetrix.main.OSGiHandler - loading searchModelIdOrProps-9.1.12.jar
05:53:01.940 [main] INFO com.affymetrix.main.OSGiHandler - loading searchView-9.1.12.jar
05:53:01.944 [main] INFO com.affymetrix.main.OSGiHandler - loading sequenceViewer-9.1.12.jar
05:53:01.947 [main] INFO com.affymetrix.main.OSGiHandler - loading session-manager-9.1.12.jar
05:53:01.979 [main] INFO com.affymetrix.main.OSGiHandler - loading shared-lib-wrapper-9.1.12.jar
05:53:01.985 [main] INFO com.affymetrix.main.OSGiHandler - loading slf4j-api-1.7.36.jar
05:53:01.988 [main] INFO com.affymetrix.main.OSGiHandler - loading survey-9.1.12.jar
05:53:01.992 [main] INFO com.affymetrix.main.OSGiHandler - loading synonym-lookup-9.1.12.jar
05:53:01.995 [main] INFO com.affymetrix.main.OSGiHandler - loading thresholding-9.1.12.jar
05:53:01.999 [main] INFO com.affymetrix.main.OSGiHandler - loading track-operations-panel-9.1.12.jar
05:53:02.002 [main] INFO com.affymetrix.main.OSGiHandler - loading update-9.1.12.jar
05:53:02.007 [main] INFO com.affymetrix.main.OSGiHandler - loading weblinks-9.1.12.jar
05:53:02.010 [main] INFO com.affymetrix.main.OSGiHandler - loading window-service-9.1.12.jar
05:53:02.014 [main] INFO com.affymetrix.main.OSGiHandler - loading xz-1.9.jar
05:53:02.014 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.framework
05:53:02.014 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: affymetrix-common
05:53:02.087 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: annotation-tab
05:53:02.107 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: apollo-library
05:53:02.112 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: appstore
05:53:02.117 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bai
05:53:02.121 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bam
05:53:02.124 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bed
05:53:02.127 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigBedHandler
05:53:02.130 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigWigHandler
05:53:02.133 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.broad.igv.bigwig
05:53:02.134 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bookmark
05:53:02.238 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache
05:53:02.242 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache-api
05:53:02.242 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-codec
05:53:02.243 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-compress
05:53:02.243 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-csv
05:53:02.244 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-fileupload
05:53:02.245 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-io
05:53:02.246 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.jexl
05:53:02.247 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.lang3
05:53:02.247 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.logging
05:53:02.248 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.pool
05:53:02.248 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: console-tab
05:53:02.251 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: context-menu-service
05:53:02.252 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: das
05:53:02.255 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.external-sort
05:53:02.256 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: externalView
05:53:02.259 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.guava.failureaccess
05:53:02.261 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.feedback
05:53:02.263 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: frameManager
05:53:02.264 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: genometry
05:53:02.266 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.genotyping
05:53:02.270 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.affymetrix.genoviz
05:53:02.271 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: graphTab
05:53:02.274 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.gson
05:53:02.275 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.guava
05:53:02.275 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: heatmap-editor
05:53:02.276 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: htsjdk-igb
05:53:02.276 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb
05:53:02.290 INFO com.affymetrix.igb.Activator - Verifying Jidesoft license
05:53:02.311 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-genoviz-extensions
05:53:02.311 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-javafx-util
05:53:02.312 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-preferences
05:53:02.313 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-services
05:53:02.313 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbScript
05:53:02.317 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbSwingExt
05:53:02.362 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: image-exporter
05:53:02.363 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.jidesoft.ultimate
05:53:02.363 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keyWordSearch
05:53:02.366 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keybinding-registry
05:53:02.369 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.classic
05:53:02.370 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.core
05:53:02.371 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.logging-config
05:53:02.371 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.narrowpeak
05:53:02.374 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ncbiBlast
05:53:02.378 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.bundlerepository
05:53:02.400 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.configadmin
05:53:02.414 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.eventadmin
05:53:02.424 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.bundle
[INFO] Started bridged http service
05:53:02.434 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.jetty
05:53:02.464 INFO org.eclipse.jetty.util.log - Logging initialized @2328ms to org.eclipse.jetty.util.log.Slf4jLog
05:53:02.508 INFO org.eclipse.jetty.server.Server - jetty-9.4.51.v20230217; built: 2023-02-17T08:19:37.309Z; git: b45c405e4544384de066f814ed42ae3dceacdd49; jvm 1.8.0_372-b07
05:53:02.536 INFO org.eclipse.jetty.server.session - DefaultSessionIdManager workerName=node0
05:53:02.536 INFO org.eclipse.jetty.server.session - No SessionScavenger set, using defaults
05:53:02.539 INFO org.eclipse.jetty.server.session - node0 Scavenging every 600000ms
05:53:02.547 INFO o.e.j.server.handler.ContextHandler - Started o.e.j.s.ServletContextHandler@5bd73d1a{/,null,AVAILABLE}
05:53:02.547 INFO org.eclipse.jetty.server.Server - Started @2413ms
05:53:02.548 INFO org.eclipse.jetty.server.session - node0 Scavenging every 660000ms
05:53:02.587 INFO o.e.jetty.server.AbstractConnector - Started ServerConnector@3d829787{HTTP/1.1, (http/1.1)}{localhost:7080}
[INFO] Started Jetty 9.4.51.v20230217 at port(s) HTTP:7080 on context path / [minThreads=8,maxThreads=200,acceptors=1,selectors=6]
05:53:02.606 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.servlet-api
05:53:02.606 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.scr
05:53:03.378 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.webconsole
05:53:03.443 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.menu.api
05:53:03.446 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: osgi.cmpn
05:53:03.446 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: paired-data-preprocessor
05:53:03.451 INFO o.l.i.p.PairedReadPreprocessor - Initializaing PairedReadPreprocessor
05:53:03.452 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.plugins-manager
05:53:03.520 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: propertyView
05:53:03.526 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: quickload
05:53:03.532 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: restrictionSites
05:53:03.538 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchModelIdOrProps
05:53:03.547 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchView
05:53:03.553 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: sequenceViewer
05:53:03.559 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: session-manager
05:53:03.565 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: shared-lib-wrapper
05:53:03.566 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: slf4j.api
05:53:03.566 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: survey
05:53:03.571 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: synonym-lookup
05:53:03.817 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/rnaseq/
05:53:03.896 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/rnaseq/synonyms.txt
05:53:03.921 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/rnaseq/species.txt
05:53:04.195 INFO c.a.i.p.IgbPreferencesLoadingOrchestrator - Loading server preferences from the Java preferences subsystem
05:53:04.197 INFO c.a.i.p.IgbPreferencesLoadingOrchestrator - Completed loading server preferences from the Java preferences subsystem
05:53:04.198 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: thresholding
05:53:04.204 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: track-operations-panel
05:53:04.208 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: update
05:53:04.212 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: weblinks
05:53:04.227 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: window-service
05:53:04.229 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.tukaani.xz
05:53:04.230 [main] INFO com.affymetrix.main.OSGiHandler - OSGi is started with org.apache.felix.framework version 6.0.3
05:53:04.503 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/quickload/
05:53:04.781 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/blueberry/
05:53:04.847 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/blueberry/synonyms.txt
05:53:04.871 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/blueberry/species.txt
05:53:07.554 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/bar/
05:53:07.618 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/bar/synonyms.txt
05:53:07.642 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/bar/species.txt
05:53:07.643 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/chipseq/
05:53:07.702 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/chipseq/synonyms.txt
05:53:07.723 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/chipseq/species.txt
05:53:07.724 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server https://bioviz.org/quickload/genome-in-a-bottle/
05:53:08.022 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from https://bioviz.org/quickload/genome-in-a-bottle/synonyms.txt
05:53:08.116 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: https://bioviz.org/quickload/genome-in-a-bottle/species.txt
After running the Nowlan Freese IGBF-3379 and launching IGB Project, I saved the logs and compared it with the logs above. The missing log entries are:
10:47:15.509 INFO c.a.igb.IgbServiceDependencyManager - AnnotationContextMenuRegistryI now available. 10:47:15.509 INFO c.a.igb.IgbServiceDependencyManager - ChromosomeSynonymLookupService now available. 10:47:15.509 INFO c.a.igb.IgbServiceDependencyManager - FrameManagerService now available. 10:47:15.509 INFO c.a.igb.IgbServiceDependencyManager - GenomeVersionSynonymLookupService now available. 10:47:15.509 INFO c.a.igb.IgbServiceDependencyManager - QuickloadFactory now available. 10:47:15.509 INFO c.a.igb.IgbServiceDependencyManager - SpeciesSynonymLookupService now available. 10:47:15.509 INFO c.a.igb.IgbServiceDependencyManager - Window Service now available. 10:47:15.509 INFO c.a.igb.IgbServiceDependencyManager - Igb Module Service Dependencies are now available. 10:47:15.510 INFO com.affymetrix.igb.Activator - Starting IGB 10:47:15.920 INFO com.affymetrix.igb.IGB - Starting: Integrated Genome Browser 9.1.12 10:47:15.920 INFO com.affymetrix.igb.IGB - Java version: 1.8.0_372 from Azul Systems, Inc. 10:47:15.922 INFO com.affymetrix.igb.IGB - System memory: 7.6 GB 10:47:17.332 INFO c.a.igb.util.IGBTrustManager - Trusted Certificates:CN=*.bioviz.org; CN=Sectigo RSA Domain Validation Secure Server CA,O=Sectigo Limited,L=Salford,ST=Greater Manchester,C=GB; CN=USERTrust RSA Certification Authority,O=The USERTRUST Network,L=Jersey City,ST=New Jersey,C=US 10:47:17.428 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.HomeAction. But action class com.affymetrix.igb.action.HomeAction exists with same keystroke "ctrl pressed H". Using keystroke with latest action. 10:47:17.850 INFO o.l.i.appstore.IgbAppServerLauncher - setPlugingManagerService START 10:47:18.050 INFO o.l.i.appstore.IgbAppServerLauncher - setPluginManagerService DONE 10:47:18.052 INFO o.l.i.appstore.IgbAppServerLauncher - activate START 10:47:18.053 INFO o.l.i.appstore.IgbAppServerLauncher - org.lorainelab.igb.plugin.manager.service.impl.PluginManagerServiceImpl@6436e181 10:47:18.057 INFO o.l.i.appstore.IgbAppServerLauncher - activate DONE 10:47:20.358 INFO c.a.i.b.action.BookmarkActionManager - Loading bookmarks from file C:\Users\Karthik Raveendran\AppData\Roaming\IGB\bookmarks.html 10:47:20.365 INFO c.a.i.b.action.BookmarkActionManager - Saving bookmarks to file C:\Users\Karthik Raveendran\AppData\Roaming\IGB\bookmarks.html~ 10:47:20.610 INFO com.affymetrix.igb.Activator - IGB Started Starting Bundle: org.tukaani.xz 10:47:20.929 INFO o.l.i.appstore.IgbAppServerLauncher - Started REST endpoint. 10:47:24.105 INFO com.affymetrix.igb.tiers.TrackStyle - Saving user stylesheet to file C:\Users\Karthik Raveendran\AppData\Roaming\IGB\user_stylesheet.xml 10:47:24.110 INFO o.l.i.p.weblink.WebLinkUtils - Saving web links to file "C:\Users\Karthik Raveendran\AppData\Roaming\IGB\weblinks.json" 10:47:24.114 INFO c.a.i.b.action.BookmarkActionManager - Saving bookmarks to file C:\Users\Karthik Raveendran\AppData\Roaming\IGB\bookmarks.html
When running mvn clean install with debugging enabled (-X) I am seeing errors on the IGBF-3379 branch. The primary error has to do with the Genometry bundle having the following error: java.lang.NoClassDefFoundError: org/osgi/framework/FrameworkUtil
Providing the dependency org.apache.felix.framework seems to resolve the missing requirement, but raises some other requirements.
UPDATE: Some blogs on fixing NoClassDefFoundError
I have been looking for articles related to bndlib to OSGi V6 migration. So far, I found two articles which might be helpful for this migration.
- Switching To OSGi R6 And Dumping bnd Annotations
- GitHub issue thread
- However, these articles doesn't provide brief info regarding "How to do". Instead, they just
focused on "what to do", which is not super helpful for us.
Question for Kaushik Gopu:
- Are there resources or mentions newer than Aug. 15, 2015?
After moving from osgi.cmpn to osgi. annotations library, I am facing with several osgi.wiring.package issues. OSGI wiring package error happens when bundle is installed but requirement is not satisfied. This is error should be resolved by adding Export packages properly in the package but in my case it is not working. Need to investigate further.
After reverting other changes on the IGBF-3379 branch I am still seeing the java.lang.NoClassDefFoundError: org/osgi/framework/FrameworkUtil when the DAS bundle runs its tests. The issue occurs when the DasDataProviderTest calls retrieveAssemblyInfo which attempts to instantiate a GenomeVersion from the genometry bundle, which requires FrameworkUtil. The class for FrameworkUtil is satisfied through org.apache.felix.main and the genometry bundle itself builds without issue. After investigating with Karthik, when IGB is built without tests it does complete, and running the JAR results in all bundles being listed as active, but we see "Overwritten by Boot Delegation" in several bundles.
Blog discussing similar issue: https://issues.apache.org/jira/browse/KARAF-6525
Yesterday, while trying to resolve the errors i.e genometry based, I realised that the version of genometry was 9.2.0 which the project having difficulty in recognising.
After changing version back to 9.1.12, The errors seem to be resolved.However, we want version to be 9.2.0.So, I changed every module version to 9.2.0, led to reduction of errors to about 6-7 and most of those errors are JavaFX based.
Branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3379-bind
Working off of main-JDK8 I have created a new branch using the new annotations for the bndlib library. IGB with tests builds with no issues (compared to IGBF-3379 which fails tests) and all bundles are Active (using maven-bundle-plugin 3.5.1), but am still seeing the "Overwritten by Boot Delegation" in multiple bundles using the felix web console.
Branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3379-updateModule
Updating individual modules to use the osgi components using org.osgi.service.component.annotations (instead of osgi.cmpn) is working so far. This is important as based on OSGI documentation there is a move away from using osgi.cmpn and instead using individual dependencies. Furthermore, osgi.cmpn >= 6 cannot be used at runtime and will throw an error if tried. So it is good to try to migrate to using annotations from org.osgi.service.component.annotations now.
When I tried to use the new annotations from biz.aQute.bndlib it did not work (IGB started fine, but the feature, for example the image export button, failed to appear in IGB). I am now updating each module, testing to make the specific feature is still working, then committing and pushing the changes.
I tried to load and install every bundle in apache karaf, while some of them were able to start, others were generating wiring issues. So far, karaf isn't helping much, but would like follow module-by-module upgrade, suggested by Nowlan Freese and try to investigate the issues.
After discussing with Dr. Freese about updating each module one by one as mentioned above in his comment, I cloned his branch and started updating Core modules and so far its been working and I completed all the core bundles. See commits .
I have created the epic: Implement r6 Annotations in IGB
[~aloraine] - pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/938
PR is merged into main-JDK8-r6. Installers are built and available for download and testing from https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/.
attn: Nowlan Freese, Kaushik Gopu, and Karthik Raveendran
More plugins have been updated to R6. See commit . When issues were found with some of the updates have been, the commit is reverted and new ticket is created for it.
During scrum, Karthik Raveendran mentioned a problem with installing an App.
Karthik Raveendran: please document the error in a new ticket.
App Manager - Tested with errors
While testing the App Manager, I installed SNP file converter app and the tabbed pane at the bottom of IGB stopped responding. The issue did not happen with ProtAnnot app. The following error appeared in the log:
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at javax.swing.plaf.basic.BasicTabbedPaneUI.scrollableTabLayoutEnabled(BasicTabbedPaneUI.java:263)
at javax.swing.plaf.basic.BasicTabbedPaneUI.tabForCoordinate(BasicTabbedPaneUI.java:1497)
at javax.swing.plaf.basic.BasicTabbedPaneUI.setRolloverTab(BasicTabbedPaneUI.java:575)
at javax.swing.plaf.basic.BasicTabbedPaneUI.access$2100(BasicTabbedPaneUI.java:54)
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mouseEntered(BasicTabbedPaneUI.java:3629)
at com.affymetrix.igb.window.service.def.JTabbedTrayPane$2.mouseEntered(JTabbedTrayPane.java:158)
at java.awt.AWTEventMulticaster.mouseEntered(AWTEventMulticaster.java:299)
at java.awt.AWTEventMulticaster.mouseEntered(AWTEventMulticaster.java:299)
at java.awt.Component.processMouseEvent(Component.java:6548)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6304)
at java.awt.Container.processEvent(Container.java:2239)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2297)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
at java.awt.LightweightDispatcher.retargetMouseEnterExit(Container.java:4686)
at java.awt.LightweightDispatcher.trackMouseEnterExit(Container.java:4664)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4515)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
at java.awt.Container.dispatchEventImpl(Container.java:2283)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
at java.awt.EventQueue$4.run(EventQueue.java:733)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
request for Karthik Raveendran:
- Please provide a step-by-step instruction for how to reproduce the bug. For example, how did you install the app? Did you use App Store? Did you use the App Manager interface within IGB? What version of the app did you try to install?
- As described in the various testing protocols, please also state whether or not earlier versions have the bug, or not. Test them, and report the result. This is called regression testing. You should check main-JDK8 in this case.
- After downloading and running the latest main-jdk8-r6 installer from https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/ and follow the steps in https://wiki.bioviz.org/confluence/display/ITD/App+Manager to reproduce the bug. The bug should appear after installing the app from the App Manager and there should be an error in the log. The Log tab at the bottom of IGB will be unresponsive so go to Help > Show Log to see the error trace.
- The error does not appear in the main-jdk8 installer and release 9.1.10
- I can able to install SNP file plugin in main-JDK-r6 with out any issues. This is the similar issue(check in the comments for error) that we encountered before in ProtAnnot, and it was occurred because of version conflicts between protannot, and IGB. Make sure you don't have old versions of plugins in local. if the issue still persists even after following the above instructions, it needs to be investigated further.
Kaushik Gopu I tried it again and its installing smoothly but another issue persists. When mi-bundle app is installed after any of the genomes is selected and when the home button is clicked, it is unresponsive and the following error appears in log:
INFO: Species: Homo sapiens / 9606
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at it.iit.genomics.cru.igb.bundles.mi.view.SearchPanel$18.groupSelectionChanged(SearchPanel.java:685)
at com.affymetrix.genometry.GenometryModel.fireGroupSelectionEvent(GenometryModel.java:161)
at com.affymetrix.genometry.GenometryModel.setSelectedGenomeVersion(GenometryModel.java:147)
at com.affymetrix.igb.action.HomeAction.actionPerformed(HomeAction.java:27)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at com.affymetrix.igb.view.IGBToolBar$JRPButtonTLP.fireActionPerformed(IGBToolBar.java:314)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
at java.awt.Component.processMouseEvent(Component.java:6539)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6304)
at java.awt.Container.processEvent(Container.java:2239)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2297)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
at java.awt.Container.dispatchEventImpl(Container.java:2283)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
at java.awt.EventQueue$4.run(EventQueue.java:733)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Subsystems Test on Windows:
1) Add Data Source endpoint - Tested well
2) App Manager - Tested with errors
3) Bioviz Connect - Tested well
4) Bookmarks - Tested well
5) Cache - Tested well
6) Data Provider - Tested partially
Test for secured dataproviders is incomplete because the links provided in the protocal is not working.
7) eFP-Seq Browser - Tested well
8) External View - Tested well
9) File Chooser - Tested well
10) File Formats - Tested well
11) Galaxy - Tested well
12) Image Export - Tested well
13) Installer - Tested well
14) Local Quickload - Tested well
15) Navigation - Tested well
16) ProtAnnot - Tested well
17) Quickload Saver - Tested well
18) Search - Tested well
19) Soft-Clipping - Tested well
20) Synonyms - Tested well
21) Tabbed Panels - Tested well
22) Toolbar - Tested well
23) Track Operators: Annotation Tracks - Tested well
24) Track Operators: Graph Tracks - Tested well
25) Track View - Tested well
Subsystems Test on Mac:
File used: main-JDK8-r6.jar
1) Add Data Source endpoint - Tested well
2) App Manager - Tested well
3) Bioviz Connect - Tested Partially
Issues loading data Chr1:2,257,393-2,260,187; SEVERE: java.lang.OutOfMemoryError: Java heap space
4) Bookmarks - Tested well
5) Cache - Tested well
6) Data Provider - Tested Partially
Secured Data Providers, secured quickload links not responding
7) eFP-Seq Browser - Tested well
8) External View - Tested well
9) File Chooser - Tested well
10) File Formats - Tested well
11) Galaxy - Tested well
12) Image Export - Tested well
13) Installer - Tested well
Had to use main-JDK8-r6.jar for MAC I am unsure if this works with wizard
14) Local Quickload - Tested well
15) Navigation - Tested well
16) ProtAnnot - Tested well
17) Quickload Saver - Tested well
18) Search - Tested well
19) Soft-Clipping - Tested well
20) Synonyms - Tested well
21) Tabbed Panels - Tested well
22) Toolbar - Tested well
23) Track Operators: Annotation Tracks - Tested well
24) Track Operators: Graph Tracks - Tested well
25) Track View - Tested well
after installing mi-bundle and recreating the issue in various IGB releases, observed the following results:
- I can see the see the same exception in the release 9.1.10 and 9.1.12.
- However, when I was trying to install mi-bundle in earlier versions, before 9.1.10, the installation is not happening. In other words, when I hit the install button, nothing is getting triggered and there were no errors in the logs as well. its not only with mi- bundle, but also with rest of the plugins. A lot of things has changed since 9.1.10 release, and that could be one of the reason.
- created a separate ticket and will be posting further updates about this issue on that ticket.
Windows Testing is complete. See above comment
Testing on Mac macOS 13.5.1
- BioViz Connect - I am able to load data, however I am seeing an error for java.io.FileNotFoundException cache/data.dat. However, this issue is present in IGB 9.1.10 and 9.1.8 so it is unrelated to R6 annotations. New ticket -
IGBF-3425 - Data Provider - The secure quickload link does not appear to be responding. This issue is present in IGB 9.1.10 so it is unrelated to R6. New ticket - IGBF-3426
- Script Handler - There is an issue where an IGB script loaded through the menu causes IGB to freeze (tested on 9.1.10, 9.1.8, 9.1.6 with the same effect). If the script file is dragged and dropped into IGB it works fine, it is only when the user attempts to load the script through the menu interface that it causes IGB to freeze. The issue is unrelated to R6 annotations. New ticket -
IGBF-3427 - File Handler - Genotyping Results - I am unsure how the syms are supposed to appear when loading data, but they seem to be invisible (tested on 9.1.10). The issue is unrelated to R6 annotations.
Tests are complete. Issues unrelated to R6 have new tickets.
Closing ticket.
Migration of aQute annotations to OSGI Release 6 annotations have been pushed: https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/538f8efed53dedd96bdf232234153b398844c1e7
The changes are mostly in library imports and attributes of the annotations:
'multiple = true, optional = false' :: cardinality = ReferenceCardinality.AT_LEAST_ONE
'multiple=false & optional = true' :: cardinality = ReferenceCardinality.OPTIONAL
'multiple = true' :: cardinality = ReferenceCardinality.AT_LEAST_ONE
'optional=false' :: cardinality = ReferenceCardinality.MANDATORY
'dynamic = true' :: policy = ReferencePolicy.DYNAMIC
Changes in pom.xml is also included:
<plugin> <groupId>org.apache.felix</groupId> <artifactId>maven-bundle-plugin</artifactId> <version>4.2.1</version> </plugin><dependency> <groupId>org.osgi</groupId> <artifactId>org.osgi.service.component.annotations</artifactId> <version>1.5.1</version> </dependency> <dependency> <groupId>org.osgi</groupId> <artifactId>org.osgi.annotation</artifactId> <version>6.0.0</version> </dependency> <dependency> <groupId>org.osgi</groupId> <artifactId>org.osgi.service.metatype.annotations</artifactId> <version>1.4.1</version> </dependency> <dependency> <groupId>org.osgi</groupId> <artifactId>osgi.cmpn</artifactId> <version>6.0.0</version> <scope>provided</scope> </dependency>