Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-3311

Investigate org.slf4j.api error

        Details

          Description

          Situation: Unable to resolve org.slf4j.api. 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)))]

          Task: Determine why this error is appearing, if it can be fixed then update this ticket as needed.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3275 Investigate the OSGI wiring issue

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-3142 [ 21688 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3275 [ IGBF-3275 ]
                nfreese Nowlan Freese made changes -
                Description Situation: Unable to resolve org.slf4j.api. 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|https://stackoverflow.com/questions/56773611/slf4j-logging-not-working-after-upgrading-to-java-11].

                {code}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)))]
                {code}
                		Situation: Unable to resolve org.slf4j.api. 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|https://stackoverflow.com/questions/56773611/slf4j-logging-not-working-after-upgrading-to-java-11].

                {code}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)))]
                {code}

                Task: Determine why this error is appearing, if it can be fixed then update this ticket as needed.
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                https://mvnrepository.com/artifact/org.sonatype.install4j/install4j-slf4j

                Show
                nfreese Nowlan Freese added a comment - https://mvnrepository.com/artifact/org.sonatype.install4j/install4j-slf4j
                nfreese Nowlan Freese made changes -
                Sprint Spring 8 2023 Apr 24 [ 168 ] Spring 9 2023 May 8 [ 169 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Sprint Spring 9 2023 May 8 [ 169 ] Spring 8 2023 Apr 24 [ 168 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked lower
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                Hide
                Permalink
                nfreese Nowlan Freese added a comment - - edited

                The error for org.slf4j.api stated there was a missing requirement for osgi.serviceloader.processor. According to this post on stackoverflow, a number of dependencies are required, including aries spi fly. After adding the required dependencies in this commit, slf4j is able to load. However, there are other bundles that use slf4j that require a version <2, causing their bundles to fail to load.

                Reading through the slf4j faq, it doesn't seem like there is any reason for us to upgrade to >2. According to the slf4j requirements, slf4j version 1.7 works with jdk 1.5 or later (i.e. it should work with 11). Downgrading slf4j from version 2.0.7 to 1.7.36 (released Feb, 2022) and logback core/classic to 1.2.12 (released March 2023) in this commit resolves all of the slf4j errors. I have reverted the commit with the dependencies necessary for slf4j version > 2 so that the code changes are still part of the commit history, in the event that we decide to upgrade in the future.

                To test:

                1. Pull the latest changes to branch IGBF-3275 and build (mvn clean install) IGB.
                2. Check that there are no errors regarding slf4j.
                Show
                nfreese Nowlan Freese added a comment - - edited The error for org.slf4j.api stated there was a missing requirement for osgi.serviceloader.processor. According to this post on stackoverflow , a number of dependencies are required, including aries spi fly . After adding the required dependencies in this commit , slf4j is able to load. However, there are other bundles that use slf4j that require a version <2, causing their bundles to fail to load. Reading through the slf4j faq , it doesn't seem like there is any reason for us to upgrade to >2. According to the slf4j requirements , slf4j version 1.7 works with jdk 1.5 or later (i.e. it should work with 11). Downgrading slf4j from version 2.0.7 to 1.7.36 (released Feb, 2022) and logback core/classic to 1.2.12 (released March 2023) in this commit resolves all of the slf4j errors. I have reverted the commit with the dependencies necessary for slf4j version > 2 so that the code changes are still part of the commit history, in the event that we decide to upgrade in the future. To test: Pull the latest changes to branch IGBF-3275 and build (mvn clean install) IGB. Check that there are no errors regarding slf4j.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese made changes -
                Story Points 2 1
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Update master branch (IGB for JDK 8):

                • slf4j to 1.7.36
                • logback core and logback classic to 1.2.12
                Show
                ann.loraine Ann Loraine added a comment - Update master branch (IGB for JDK 8): slf4j to 1.7.36 logback core and logback classic to 1.2.12
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                Java8:
                Commit updating slf4j-api and logback-core and logback-classic: https://bitbucket.org/nfreese/nowlanfork-igb/commits/fdb32433768301579942db6565bb5f06dffbdba8

                To test:

                1. Download installer for IGBF-3311 branch: https://bitbucket.org/nfreese/nowlanfork-igb/downloads/
                2. Install and run IGB, looking for changes to log.
                Show
                nfreese Nowlan Freese added a comment - Java8: Commit updating slf4j-api and logback-core and logback-classic: https://bitbucket.org/nfreese/nowlanfork-igb/commits/fdb32433768301579942db6565bb5f06dffbdba8 To test: Download installer for IGBF-3311 branch: https://bitbucket.org/nfreese/nowlanfork-igb/downloads/ Install and run IGB, looking for changes to log.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Downloaded and install IGB. No differences in logging detected. Moving to "ready for PR" to add these new changes to the JDK8 branch "master"

                Show
                ann.loraine Ann Loraine added a comment - Downloaded and install IGB. No differences in logging detected. Moving to "ready for PR" to add these new changes to the JDK8 branch "master"
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Assignee Nowlan Freese [ nfreese ]
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/926

                Show
                nfreese Nowlan Freese added a comment - Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/926
                nfreese Nowlan Freese made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Master branch installers are built and deployed to the downloads section of the team repository.
                Ready for testing.

                Show
                ann.loraine Ann Loraine added a comment - Master branch installers are built and deployed to the downloads section of the team repository. Ready for testing.
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Assignee Nowlan Freese [ nfreese ]
                pkulzer Paige Kulzer made changes -
                Fix Version/s 10.0.0 Major Release [ 10900 ]
                nfreese Nowlan Freese made changes -
                Issue Type Task [ 3 ] Bug [ 1 ]

                  People

                  • Assignee:
                    nfreese Nowlan Freese
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: