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: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Spring 4 2023 Feb 21, Spring 5 2023 Mar 6, Spring 6 2023 Mar 20, Spring 7 2023 Apr 10
Description
Situation: After updating the OSGI annotations and removing bnd IGB can be built but when attempting to run the jar we are seeing the error below.
Task: Investigate the cause of the below error. Some additional context can be found in the comments of IGBF-3142
09:44:48.140 [main] ERROR com.affymetrix.main.OSGiHandler - Unable to resolve annotation-tab [2](R 2.0): missing requirement [annotation-tab [2](R 2.0)] osgi.wiring.package; (&(osgi.wiring.package=com.affymetrix.genometry.parsers)(version>=9.1.0)(!(version>=10.0.0))) [caused by: Unable to resolve genometry [30](R 30.0): missing requirement [genometry [30](R 30.0)] osgi.wiring.package; (osgi.wiring.package=com.apple.laf)] Unresolved requirements: [[annotation-tab [2](R 2.0)] osgi.wiring.package; (&(osgi.wiring.package=com.affymetrix.genometry.parsers)(version>=9.1.0)(!(version>=10.0.0)))] org.osgi.framework.BundleException: Unable to resolve annotation-tab [2](R 2.0): missing requirement [annotation-tab [2](R 2.0)] osgi.wiring.package; (&(osgi.wiring.package=com.affymetrix.genometry.parsers)(version>=9.1.0)(!(version>=10.0.0))) [caused by: Unable to resolve genometry [30](R 30.0): missing requirement [genometry [30](R 30.0)] osgi.wiring.package; (osgi.wiring.package=com.apple.laf)] Unresolved requirements: [[annotation-tab [2](R 2.0)] osgi.wiring.package; (&(osgi.wiring.package=com.affymetrix.genometry.parsers)(version>=9.1.0)(!(version>=10.0.0)))] at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4398) at org.apache.felix.framework.Felix.startBundle(Felix.java:2308) at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:1006) at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:992) at com.affymetrix.main.OSGiHandler.loadBundles(OSGiHandler.java:83) at com.affymetrix.main.OSGiHandler.startOSGi(OSGiHandler.java:63) at com.affymetrix.main.Main.main(Main.java:30)
Attachments
Issue Links
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IGBF-3310 Investigate com.google.guava error
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Activity
OSGI compendium (osgi.cmpn & osgi.compendium) is an aggregate API artifact of OSGI which is not available in Maven any more. We upgraded the version of compendium from 5 to 6 and 7 to solve the errors in the annotations (Symbol not found error) but it did not solve it. For our purposes, using individual artifacts for annotations as well as the wiring issues seems to be a better option.
Suggestion: Look at maven central and/or other artifact repositories and look at who is downloading osgi bundles to find other projects that use the same code as us
I created a new branch IGBF-3275 from my branch IGBF-3142. I then rebased IGBF-3275 onto master. This resulted in two main merge conflicts:
LoadSessionAction.java - we removed an import (import static com.affymetrix.common.CommonUtils.IS_MAC) in master that needed to be removed in the IGBF-3275 branch.
USeqUtilities.java - we removed all of the USeq files from master so the commit modifying the USeqUtilities.java file needed to be skipped in IGBF-3275.
I will be working from my IGBF-3275 branch. If anyone else wants to rebase their own branches, you will most likely run into the above merge conflicts. An easier way to resolve them may be to revert the commit that modified USeqUtilities.java and to remove the unneeded import and commit it to your branch before attempting to merge.
IGBF-3275 branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3275
To fetch just my branch I think you can use:
git fetch https://bitbucket.org/nfreese/nowlanfork-igb.git IGBF-3275:IGBF-3275
You will then need to switch to the branch which will be named IGBF-3275
Note: I'm not sure if you need your USERNAME@ before the bitbucket.org when fetching. I think I usually leave mine in, but I'm not sure if it matters.
Useful documentation describing how we can create references to each other's branches on each other's forks, using local tracking branches:
A more basic tutorial:
Some notes from meeting with Dr. Loraine:
- Examine the xml file within the bundle. For example, unzip the annotation-tab-9.1.10.jar bundle and within the OSGI-INF folder there should be ANNOTATION_TRACK_PANEL_TAB.xml
- Take a look at the Shared-lib-wrapper pom. The maven-dependency-plugin specifies a version, but we are unsure if this is correct or if it should use the same version as the parent pom.
Comparing manifest files between master and my 3275 branch for annotation tab:
master:
Service-Component: OSGI-INF/ANNOTATION_TRACK_PANEL_TAB.xml
3275:
Service-Component: OSGI-INF/ANNOTATION_TRACK_PANEL_TAB.xml
master:
Tool: Bnd-3.0.0.201509101326
3275:
Tool: Bnd-6.3.1.202206071316
master:
Require-Capability: osgi.ee;filter:="(&(osgi.ee=JavaSE)(version=1.8))"
3275:
Require-Capability: osgi.extender;filter:="(&(osgi.extender=osgi.compo nent)(version>=1.3.0)(!(version>=2.0.0)))",osgi.service;filter:="(obj ectClass=org.lorainelab.igb.services.IgbService)";effective:=active,o sgi.service;filter:="(objectClass=org.lorainelab.igb.track.operations .api.OperationsPanelService)";effective:=active,osgi.ee;filter:="(&(o sgi.ee=JavaSE)(version=11))"
XML from annotation-tab:
master:
<?xml version="1.0" encoding="UTF-8"?> <scr:component xmlns:scr="http://www.osgi.org/xmlns/scr/v1.1.0" name="ANNOTATION_TRACK_PANEL_TAB" immediate="true" activate="activate"> <implementation class="com.affymetrix.igb.tabs.annotation.AnnotationTrackPanel"/> <service> <provide interface="org.lorainelab.igb.services.window.tabs.IgbTabPanelI"/> </service> <reference name="igbService" cardinality="1..1" interface="org.lorainelab.igb.services.IgbService" bind="setIgbService"/> <reference name="operationsPanel" cardinality="1..1" interface="org.lorainelab.igb.track.operations.api.OperationsPanelService" bind="setOperationsPanel"/> </scr:component>
3275:
<?xml version="1.0" encoding="UTF-8"?> <scr:component xmlns:scr="http://www.osgi.org/xmlns/scr/v1.3.0" name="ANNOTATION_TRACK_PANEL_TAB" immediate="true" activate="activate"> <service> <provide interface="org.lorainelab.igb.services.window.tabs.IgbTabPanelI"/> </service> <reference name="IgbService" cardinality="1..1" interface="org.lorainelab.igb.services.IgbService" bind="setIgbService"/> <reference name="OperationsPanel" cardinality="1..1" interface="org.lorainelab.igb.track.operations.api.OperationsPanelService" bind="setOperationsPanel"/> <implementation class="com.affymetrix.igb.tabs.annotation.AnnotationTrackPanel"/> </scr:component>
The service component XML for AnnotationTab shows what this bundle is able to export as a service. Based on the error messages, I would also recommend looking at the services / packages the AnnotationTab requires but are not available.
Currently running Java OpenJDK 64-Bit Server VM Zulu11.60+19-CA (build 11.0.17+8-LTS, mixed mode)
Examining the manifest and errors we are seeing (attached as output.txt):
apollo-library: the last unresolved requirement is com.affymetrix.igb.shared which is included in the Import-Package of the apollo-library-9.1.10.jar manifest. Unclear why the below line also mentions jidesoft ultimate as it is not included in the manifest anywhere.
14:49:00.128 [main] ERROR com.affymetrix.main.OSGiHandler - Unable to resolve apollo-library [3](R 3.0): missing requirement [apollo-library [3](R 3.0)] osgi.wiring.package; (osgi.wiring.package=com.affymetrix.igb.shared) [caused by: Unable to resolve igb [38](R 38.0): missing requirement [igb [38](R 38.0)] osgi.wiring.package; (&(osgi.wiring.package=com.jidesoft.hints)(version>=3.5.0)(!(version>=4.0.0))) [caused by: Unable to resolve com.jidesoft.ultimate [49](R 49.0): missing requirement [com.jidesoft.ultimate [49](R 49.0)] osgi.wiring.package; (osgi.wiring.package=javax.xml.bind.annotation)]] Unresolved requirements: [[apollo-library [3](R 3.0)] osgi.wiring.package; (osgi.wiring.package=com.affymetrix.igb.shared)]
Created ticket IGBF-3302 to address this error.
genometry: every error involving missing requirement genometry also includes com.apple.laf. The manifest for genometry Import-Package includes com.apple.laf
14:49:00.124 [main] ERROR com.affymetrix.main.OSGiHandler - Unable to resolve annotation-tab [2](R 2.0): missing requirement [annotation-tab [2](R 2.0)] osgi.wiring.package; (&(osgi.wiring.package=com.affymetrix.genometry.parsers)(version>=9.1.0)(!(version>=10.0.0))) [caused by: Unable to resolve genometry [30](R 30.0): missing requirement [genometry [30](R 30.0)] osgi.wiring.package; (osgi.wiring.package=com.apple.laf)] Unresolved requirements: [[annotation-tab [2](R 2.0)] osgi.wiring.package; (&(osgi.wiring.package=com.affymetrix.genometry.parsers)(version>=9.1.0)(!(version>=10.0.0)))] org.osgi.framework.BundleException: Unable to resolve annotation-tab [2](R 2.0): missing requirement [annotation-tab [2](R 2.0)] osgi.wiring.package; (&(osgi.wiring.package=com.affymetrix.genometry.parsers)(version>=9.1.0)(!(version>=10.0.0))) [caused by: Unable to resolve genometry [30](R 30.0): missing requirement [genometry [30](R 30.0)] osgi.wiring.package; (osgi.wiring.package=com.apple.laf)] Unresolved requirements: [[annotation-tab [2](R 2.0)] osgi.wiring.package; (&(osgi.wiring.package=com.affymetrix.genometry.parsers)(version>=9.1.0)(!(version>=10.0.0)))]
Created ticket IGBF-3305 to address this error.
slf4j: the manifest for slf4j-api states: Bundle-RequiredExecutionEnvironment: JavaSE-1.8
This is for slf4j version 2.0.6 which was released in December 2022, so it may be possible that the slf4j api only works on Java 8. May be worth looking to see if there is a different artifact that will work with Java 11 but provide the same capabilities.
See stackoverflow.
14:49:00.373 [main] ERROR com.affymetrix.main.OSGiHandler - Unable to resolve org.slf4j.api [85](R 85.0): missing requirement [org.slf4j.api [85](R 85.0)] osgi.extender; (&(osgi.extender=osgi.serviceloader.processor)(version>=1.0.0)(!(version>=2.0.0))) Unresolved requirements: [[org.slf4j.api [85](R 85.0)] osgi.extender; (&(osgi.extender=osgi.serviceloader.processor)(version>=1.0.0)(!(version>=2.0.0)))] org.osgi.framework.BundleException: Unable to resolve org.slf4j.api [85](R 85.0): missing requirement [org.slf4j.api [85](R 85.0)] osgi.extender; (&(osgi.extender=osgi.serviceloader.processor)(version>=1.0.0)(!(version>=2.0.0))) Unresolved requirements: [[org.slf4j.api [85](R 85.0)] osgi.extender; (&(osgi.extender=osgi.serviceloader.processor)(version>=1.0.0)(!(version>=2.0.0)))]
Created ticket IGBF-3311 to address this error.
Adding another stackoverflow here that may help to understand the problem
guava: Guava was updated in the pom to Bundle-Version: 31.1.0.jre. However, Guava is unable to be resolved. The package com.google.common.util.concurrent.internal is in every error line that also mentions Guava. The com.google.common.util.concurrent.internal package is set as an Import-Package in the Guava manifest.
14:49:00.226 [main] ERROR com.affymetrix.main.OSGiHandler - Unable to resolve com.google.guava [35](R 35.0): missing requirement [com.google.guava [35](R 35.0)] osgi.wiring.package; (&(osgi.wiring.package=com.google.common.util.concurrent.internal)(version>=1.0.0)(!(version>=2.0.0))) Unresolved requirements: [[com.google.guava [35](R 35.0)] osgi.wiring.package; (&(osgi.wiring.package=com.google.common.util.concurrent.internal)(version>=1.0.0)(!(version>=2.0.0)))]
Created ticket IGBF-3310 to address this error.
osgi.cmpn: This is interesting as the osgi.cmpn artifact version 6.0.0 was added for this branch (to match the osgi.core version 6.0.0 that replaced bndlib). The osgi.cmpn artifact is included in the master branch of IGB, but in a previous version with the artifact id org.osgi.compendium. Unclear why it is not working, but the "must.not.resolve=*" appears in every error that mentions the osgi.cmpn artifact.
14:49:00.362 [main] ERROR com.affymetrix.main.OSGiHandler - Unable to resolve osgi.cmpn [74](R 74.0): missing requirement [osgi.cmpn [74](R 74.0)] osgi.compile.time.only; (&(must.not.resolve=*)(!(must.not.resolve=*))) Unresolved requirements: [[osgi.cmpn [74](R 74.0)] osgi.compile.time.only; (&(must.not.resolve=*)(!(must.not.resolve=*)))]
Created ticket IGBF-3309 to address this error.
org.apache.felix.scr: The only other bundle affected by org.apache.felix.scr is the graphTab bundle. Both bundles state that they are missing the required org.osgi.service.component.
14:49:00.346 [main] ERROR com.affymetrix.main.OSGiHandler - Unable to resolve org.apache.felix.scr [64](R 64.0): missing requirement [org.apache.felix.scr [64](R 64.0)] osgi.wiring.package; (&(osgi.wiring.package=org.osgi.service.component)(version>=1.5.0)(!(version>=1.6.0))) Unresolved requirements: [[org.apache.felix.scr [64](R 64.0)] osgi.wiring.package; (&(osgi.wiring.package=org.osgi.service.component)(version>=1.5.0)(!(version>=1.6.0)))]
Created ticket IGBF-3308 to address this error.
org.apache.felix.dm: The only remaining errors (errors are all in org.lorainelab.igb.remote.services) all have the same thing in common, a missing requirement for org.apache.felix.dm. The pom does include a dependency for org.apache.felix.dependencymanager, which seems similar. The dependencymanager dependency was updated to the most recent version.
14:49:00.356 [main] ERROR com.affymetrix.main.OSGiHandler - Unable to resolve org.lorainelab.igb.remote.services.discovery.provider.configured [70](R 70.0): missing requirement [org.lorainelab.igb.remote.services.discovery.provider.configured [70](R 70.0)] osgi.wiring.package; (&(osgi.wiring.package=org.apache.felix.dm)(version>=3.0.0)(!(version>=4.0.0))) Unresolved requirements: [[org.lorainelab.igb.remote.services.discovery.provider.configured [70](R 70.0)] osgi.wiring.package; (&(osgi.wiring.package=org.apache.felix.dm)(version>=3.0.0)(!(version>=4.0.0)))]
Created ticket IGBF-3307 to address this error.
The error mentioned in the description is one of many similar types of errors that are triggered during run time. The errors is believed to be caused by OSGI compendium version. Upgrading the OSGI compendium to the latest releases, 6 and 7 solves the issues. However, OSGI component annotations packages does not exist and an error is thrown.