Details

    • Type: Task
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None

      Description

      Task: Update ProtAnnot so that it can work with main-JDK21.

        Attachments

          Issue Links

            Activity

            nfreese Nowlan Freese created issue -
            nfreese Nowlan Freese made changes -
            Field Original Value New Value
            Epic Link IGBF-1908 [ 17998 ]
            nfreese Nowlan Freese made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            nfreese Nowlan Freese made changes -
            Status In Progress [ 3 ] To-Do [ 10305 ]
            nfreese Nowlan Freese made changes -
            Status To-Do [ 10305 ] Pull Request Submitted [ 10101 ]
            Hide
            nfreese Nowlan Freese added a comment -

            Pull request: https://bitbucket.org/lorainelab/protannot/pull-requests/17

            Note that the pull request is not aimed at the master branch, we will need to merge it to master.

            Show
            nfreese Nowlan Freese added a comment - Pull request: https://bitbucket.org/lorainelab/protannot/pull-requests/17 Note that the pull request is not aimed at the master branch, we will need to merge it to master.
            nfreese Nowlan Freese made changes -
            Link This issue relates to IGBF-3519 [ IGBF-3519 ]
            nfreese Nowlan Freese made changes -
            Assignee Ann Loraine [ aloraine ]
            nfreese Nowlan Freese made changes -
            Epic Link IGBF-1908 [ 17998 ] IGBF-3142 [ 21688 ]
            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 ]
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            Hide
            ann.loraine Ann Loraine added a comment - - edited

            I accepted the new branch and tried to build the jar.

            Bitbucket pipeline failed to build the new ProtAnnot 10.0.0 with this error:

            [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/ProtAnnotAction.java:[23,34] package com.google.common.eventbus does not exist
            [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/ProtAnnotAction.java:[24,34] package com.google.common.eventbus does not exist
            [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/model/ProtannotParser.java:[31,30] package com.google.common.base does not exist
            [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/model/ProtannotParser.java:[32,34] package com.google.common.eventbus does not exist
            [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/ProtAnnotService.java:[13,33] package com.google.common.collect does not exist
            [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/ProtAnnotService.java:[14,33] package com.google.common.collect does not exist
            [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/ProtAnnotService.java:[15,34] package com.google.common.eventbus does not exist
            [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/GenomeView.java:[38,30] package com.google.common.base does not exist
            [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/GenomeView.java:[39,34] package com.google.common.eventbus does not exist
            [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/GenomeView.java:[40,34] package com.google.common.eventbus does not exist
            [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/ProtAnnotPreferencesService.java:[14,34] package com.google.common.eventbus does not exist
            [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/ProtAnnotAction.java:[164,13] cannot find symbol
              symbol:   class EventBus
            

            See: https://bitbucket.org/lorainelab/protannot/pipelines/results/25

            attn: Nowlan Freese

            Show
            ann.loraine Ann Loraine added a comment - - edited I accepted the new branch and tried to build the jar. Bitbucket pipeline failed to build the new ProtAnnot 10.0.0 with this error: [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/ProtAnnotAction.java:[23,34] package com.google.common.eventbus does not exist [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/ProtAnnotAction.java:[24,34] package com.google.common.eventbus does not exist [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/model/ProtannotParser.java:[31,30] package com.google.common.base does not exist [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/model/ProtannotParser.java:[32,34] package com.google.common.eventbus does not exist [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/ProtAnnotService.java:[13,33] package com.google.common.collect does not exist [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/ProtAnnotService.java:[14,33] package com.google.common.collect does not exist [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/ProtAnnotService.java:[15,34] package com.google.common.eventbus does not exist [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/GenomeView.java:[38,30] package com.google.common.base does not exist [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/GenomeView.java:[39,34] package com.google.common.eventbus does not exist [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/GenomeView.java:[40,34] package com.google.common.eventbus does not exist [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/ProtAnnotPreferencesService.java:[14,34] package com.google.common.eventbus does not exist [ERROR] /opt/atlassian/pipelines/agent/build/src/main/java/org/lorainelab/igb/protannot/ProtAnnotAction.java:[164,13] cannot find symbol symbol: class EventBus See: https://bitbucket.org/lorainelab/protannot/pipelines/results/25 attn: Nowlan Freese
            ann.loraine Ann Loraine made changes -
            Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
            ann.loraine Ann Loraine made changes -
            Status Post-merge Testing In Progress [ 10003 ] To-Do [ 10305 ]
            ann.loraine Ann Loraine made changes -
            Assignee Nowlan Freese [ nfreese ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            nfreese Nowlan Freese made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            ann.loraine Ann Loraine made changes -
            Epic Link IGBF-3142 [ 21688 ] IGBF-1908 [ 17998 ]
            Show
            nfreese Nowlan Freese added a comment - Pull request: https://bitbucket.org/lorainelab/protannot/pull-requests/18
            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 -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            Hide
            ann.loraine Ann Loraine added a comment - - edited

            Merged. New jar is built. See: protannot-10.0.0.jar in:

            Show
            ann.loraine Ann Loraine added a comment - - edited Merged. New jar is built. See: protannot-10.0.0.jar in: https://bitbucket.org/lorainelab/protannot/downloads/
            ann.loraine Ann Loraine made changes -
            Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
            ann.loraine Ann Loraine made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            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 ]
            ann.loraine Ann Loraine made changes -
            Sprint Fall 8 [ 184 ] Fall 8, Spring 1 [ 184, 185 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Sprint Fall 8, Spring 1 [ 184, 185 ] Fall 8, Spring 1, Spring 2 [ 184, 185, 186 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            nfreese Nowlan Freese made changes -
            Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ]
            nfreese Nowlan Freese made changes -
            Link This issue relates to IGBF-3433 [ IGBF-3433 ]
            ann.loraine Ann Loraine made changes -
            Sprint Fall 8, Spring 1, Spring 2 [ 184, 185, 186 ] Fall 8, Spring 1, Spring 2, Spring 3 [ 184, 185, 186, 187 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            Hide
            nfreese Nowlan Freese added a comment -

            Was able to test locally on Mac through the App Manager, ProtAnnot installed and ran correctly.

            Note that the branch with the changes currently in bitbucket is IGB_10_Alignment (not master). The bitbucket-pipeline is also pointing at hillrunner2008/igb-maven-install4j:I4J10-jre-21.0.1 whereas we are now using lorainelab/igb-maven-install4j:I4J10-jre-21.0.1-21.0.0 to build IGB, though that may change depending on IGBF-3588.

            Show
            nfreese Nowlan Freese added a comment - Was able to test locally on Mac through the App Manager, ProtAnnot installed and ran correctly. Note that the branch with the changes currently in bitbucket is IGB_10_Alignment (not master). The bitbucket-pipeline is also pointing at hillrunner2008/igb-maven-install4j:I4J10-jre-21.0.1 whereas we are now using lorainelab/igb-maven-install4j:I4J10-jre-21.0.1-21.0.0 to build IGB, though that may change depending on IGBF-3588 .
            nfreese Nowlan Freese made changes -
            Link This issue relates to IGBF-3595 [ IGBF-3595 ]
            nfreese Nowlan Freese made changes -
            Status Post-merge Testing In Progress [ 10003 ] Merged Needs Testing [ 10002 ]
            nfreese Nowlan Freese made changes -
            Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
            nfreese Nowlan Freese made changes -
            Status Post-merge Testing In Progress [ 10003 ] To-Do [ 10305 ]
            ann.loraine Ann Loraine made changes -
            Sprint Fall 8, Spring 1, Spring 2, Spring 3 [ 184, 185, 186, 187 ] Fall 8, Spring 1, Spring 2, Spring 3, Spring 4 [ 184, 185, 186, 187, 188 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Sprint Fall 8, Spring 1, Spring 2, Spring 3, Spring 4 [ 184, 185, 186, 187, 188 ] Fall 8, Spring 1, Spring 2, Spring 3, Spring 4, Spring 5 [ 184, 185, 186, 187, 188, 189 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            nfreese Nowlan Freese made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            Show
            nfreese Nowlan Freese added a comment - Pull request: https://bitbucket.org/lorainelab/protannot/pull-requests/21
            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 -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            nfreese Nowlan Freese made changes -
            Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
            nfreese Nowlan Freese made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            Hide
            ann.loraine Ann Loraine added a comment -

            PR is merged. Ready for next steps.

            attn: Nowlan Freese

            Show
            ann.loraine Ann Loraine added a comment - PR is merged. Ready for next steps. attn: Nowlan Freese
            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
            nfreese Nowlan Freese added a comment -

            Tested on Mac, Windows, and Linux from https://bitbucket.org/lorainelab/protannot/downloads/

            Final step: release to IGB App Store.

            Show
            nfreese Nowlan Freese added a comment - Tested on Mac, Windows, and Linux from https://bitbucket.org/lorainelab/protannot/downloads/ Final step: release to IGB App Store.
            ann.loraine Ann Loraine made changes -
            Sprint Fall 8, Spring 1, Spring 2, Spring 3, Spring 4, Spring 5 [ 184, 185, 186, 187, 188, 189 ] Fall 8, Spring 1, Spring 2, Spring 3, Spring 4, Spring 5, Spring 6 [ 184, 185, 186, 187, 188, 189, 190 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            nfreese Nowlan Freese made changes -
            Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
            nfreese Nowlan Freese made changes -
            Resolution Done [ 10000 ]
            Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
            nfreese Nowlan Freese made changes -
            Resolution Done [ 10000 ]
            Status Closed [ 6 ] To-Do [ 10305 ]
            Hide
            nfreese Nowlan Freese added a comment -

            To do: remove upper bound on IGB version.

            Show
            nfreese Nowlan Freese added a comment - To do: remove upper bound on IGB version.
            nfreese Nowlan Freese made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            Hide
            nfreese Nowlan Freese added a comment -

            Commit: https://bitbucket.org/nfreese/protannot/commits/9d586e6980990e4a1176fa209b1dfc9eb192c2ab

            PR: https://bitbucket.org/lorainelab/protannot/pull-requests/22

            In order to remove the upper bound we have to explicitly declare IGB dependency versions within the Import-Package. This had been done as part of IGBF-1906 for some of the apps, though not all.

            I tested by changing the IGB version to 11 and seeing if ProtAnnot would install and work. ProtAnnot did work and there were no errors in the log.

            Show
            nfreese Nowlan Freese added a comment - Commit: https://bitbucket.org/nfreese/protannot/commits/9d586e6980990e4a1176fa209b1dfc9eb192c2ab PR: https://bitbucket.org/lorainelab/protannot/pull-requests/22 In order to remove the upper bound we have to explicitly declare IGB dependency versions within the Import-Package. This had been done as part of IGBF-1906 for some of the apps, though not all. I tested by changing the IGB version to 11 and seeing if ProtAnnot would install and work. ProtAnnot did work and there were no errors in the log.
            nfreese Nowlan Freese made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            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 ] Ready for Pull Request [ 10304 ]
            nfreese Nowlan Freese made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            nfreese Nowlan Freese made changes -
            Assignee Ann Loraine [ aloraine ]
            Hide
            ann.loraine Ann Loraine added a comment - - edited

            Before proceeding, could you paste (in here) the OSGI tag contents from the MANIFEST.mf file packaged in the ProtAnnot bundle? Please also specify the version of the felix plugin that we're actually using to make the bundle.

            I'd like to see those OSGI tags before and after the commit.

            It just really seems like a weird thing that specifying the required version of IGB platform bundles as 10.0.0 – with no modifiers – would then allow the framework to install and run the bundle in a platform where all the platform bundles declare themselves to be version 11.0.0.

            However, the POM configuration is only for the felix plugin. Who knows how that plugin is going to translate that configuration into the OSGI meta information stored in the bundles' MANIFEST?

            Thank you for taking such care with all this!

            Show
            ann.loraine Ann Loraine added a comment - - edited Before proceeding, could you paste (in here) the OSGI tag contents from the MANIFEST.mf file packaged in the ProtAnnot bundle? Please also specify the version of the felix plugin that we're actually using to make the bundle. I'd like to see those OSGI tags before and after the commit. It just really seems like a weird thing that specifying the required version of IGB platform bundles as 10.0.0 – with no modifiers – would then allow the framework to install and run the bundle in a platform where all the platform bundles declare themselves to be version 11.0.0. However, the POM configuration is only for the felix plugin. Who knows how that plugin is going to translate that configuration into the OSGI meta information stored in the bundles' MANIFEST? Thank you for taking such care with all this!
            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 ] To-Do [ 10305 ]
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ] Nowlan Freese [ nfreese ]
            Hide
            nfreese Nowlan Freese added a comment -

            Before:

            Created-By: Apache Maven Bundle Plugin 5.1.9
            Import-Package: com.affymetrix.common;version="[10.0,11)",com.affymetr
            ix.genometry;version="[10.0,11)",com.affymetrix.genometry.comparator;
            version="[10.0,11)",com.affymetrix.genometry.event;version="[10.0,11)
            ",com.affymetrix.genometry.span;version="[10.0,11)",com.affymetrix.ge
            nometry.symmetry;version="[10.0,11)",com.affymetrix.genometry.symmetr
            y.impl;version="[10.0,11)",com.affymetrix.genometry.thread;version="[
            10.0,11)",com.affymetrix.genometry.util;version="[10.0,11)",com.affym
            etrix.genoviz.awt;version="[1.1,2)",com.affymetrix.genoviz.bioviews;v
            ersion="[1.1,2)",com.affymetrix.genoviz.event;version="[1.1,2)",com.a
            ffymetrix.genoviz.glyph;version="[1.1,2)",com.affymetrix.genoviz.swin
            g;version="[1.1,2)",com.affymetrix.genoviz.util;version="[1.1,2)",com
            .affymetrix.genoviz.widget;version="[1.1,2)",com.affymetrix.genoviz.w
            idget.tieredmap;version="[1.1,2)",com.affymetrix.igb.shared;version="
            [10.0,11)",com.affymetrix.igb.swing;version="[10.0,11)",com.affymetri
            x.igb.swing.jide;version="[10.0,11)",com.google.common.base;version="
            [32.1,33)",com.google.common.collect;version="[32.1,33)",com.google.c
            ommon.eventbus;version="[32.1,33)",jakarta.xml.bind;version="[4.0,5)"
            ,jakarta.xml.bind.annotation;version="[4.0,5)",java.awt,java.awt.data
            transfer,java.awt.event,java.awt.geom,java.io,java.lang,java.lang.inv
            oke,java.lang.reflect,java.math,java.net,java.text,java.util,java.uti
            l.function,java.util.prefs,java.util.regex,java.util.stream,javax.swi
            ng,javax.swing.border,javax.swing.table,javax.xml.namespace,javax.xml
            .parsers,javax.xml.xpath,net.miginfocom.layout,net.miginfocom.swing,o
            rg.apache.commons.io;version="[1.4,2)",org.apache.commons.lang3.text;
            version="[3.4,4)",org.lorainelab.igb.genoviz.extensions;version="[10.
            0,11)",org.lorainelab.igb.genoviz.extensions.glyph;version="[10.0,11)
            ",org.lorainelab.igb.image.exporter.service;version="[10.0,11)",org.l
            orainelab.igb.javafx;version="[10.0,11)",org.lorainelab.igb.menu.api;
            version="[10.0,11)",org.lorainelab.igb.menu.api.model;version="[10.0,
            11)",org.lorainelab.igb.services;version="[10.0,11)",org.osgi.service
            .component;version="[1.2,2)",org.slf4j;version="[1.7,2)",org.w3c.dom,
            org.xml.sax
            Tool: Bnd-6.3.1.202206071316

            Show
            nfreese Nowlan Freese added a comment - Before: Created-By: Apache Maven Bundle Plugin 5.1.9 Import-Package: com.affymetrix.common;version="[10.0,11)",com.affymetr ix.genometry;version="[10.0,11)",com.affymetrix.genometry.comparator; version="[10.0,11)",com.affymetrix.genometry.event;version="[10.0,11) ",com.affymetrix.genometry.span;version="[10.0,11)",com.affymetrix.ge nometry.symmetry;version="[10.0,11)",com.affymetrix.genometry.symmetr y.impl;version="[10.0,11)",com.affymetrix.genometry.thread;version="[ 10.0,11)",com.affymetrix.genometry.util;version="[10.0,11)",com.affym etrix.genoviz.awt;version="[1.1,2)",com.affymetrix.genoviz.bioviews;v ersion="[1.1,2)",com.affymetrix.genoviz.event;version="[1.1,2)",com.a ffymetrix.genoviz.glyph;version="[1.1,2)",com.affymetrix.genoviz.swin g;version="[1.1,2)",com.affymetrix.genoviz.util;version="[1.1,2)",com .affymetrix.genoviz.widget;version="[1.1,2)",com.affymetrix.genoviz.w idget.tieredmap;version="[1.1,2)",com.affymetrix.igb.shared;version=" [10.0,11)",com.affymetrix.igb.swing;version="[10.0,11)",com.affymetri x.igb.swing.jide;version="[10.0,11)",com.google.common.base;version=" [32.1,33)",com.google.common.collect;version="[32.1,33)",com.google.c ommon.eventbus;version="[32.1,33)",jakarta.xml.bind;version="[4.0,5)" ,jakarta.xml.bind.annotation;version="[4.0,5)",java.awt,java.awt.data transfer,java.awt.event,java.awt.geom,java.io,java.lang,java.lang.inv oke,java.lang.reflect,java.math,java.net,java.text,java.util,java.uti l.function,java.util.prefs,java.util.regex,java.util.stream,javax.swi ng,javax.swing.border,javax.swing.table,javax.xml.namespace,javax.xml .parsers,javax.xml.xpath,net.miginfocom.layout,net.miginfocom.swing,o rg.apache.commons.io;version="[1.4,2)",org.apache.commons.lang3.text; version="[3.4,4)",org.lorainelab.igb.genoviz.extensions;version="[10. 0,11)",org.lorainelab.igb.genoviz.extensions.glyph;version="[10.0,11) ",org.lorainelab.igb.image.exporter.service;version="[10.0,11)",org.l orainelab.igb.javafx;version="[10.0,11)",org.lorainelab.igb.menu.api; version="[10.0,11)",org.lorainelab.igb.menu.api.model;version="[10.0, 11)",org.lorainelab.igb.services;version="[10.0,11)",org.osgi.service .component;version="[1.2,2)",org.slf4j;version="[1.7,2)",org.w3c.dom, org.xml.sax Tool: Bnd-6.3.1.202206071316
            Hide
            nfreese Nowlan Freese added a comment -

            After:

            Created-By: Apache Maven Bundle Plugin 5.1.9
            Import-Package: com.affymetrix.common;version="10.0.0",com.affymetrix.
            genometry;version="10.0.0",com.affymetrix.genometry.comparator;versio
            n="10.0.0",com.affymetrix.genometry.event;version="10.0.0",com.affyme
            trix.genometry.span;version="10.0.0",com.affymetrix.genometry.symmetr
            y;version="10.0.0",com.affymetrix.genometry.symmetry.impl;version="10
            .0.0",com.affymetrix.genometry.thread;version="10.0.0",com.affymetrix
            .genometry.util;version="10.0.0",com.affymetrix.igb.shared;version="1
            0.0.0",com.affymetrix.igb.swing;version="10.0.0",com.affymetrix.igb.s
            wing.jide;version="10.0.0",org.lorainelab.igb.genoviz.extensions;vers
            ion="10.0.0",org.lorainelab.igb.genoviz.extensions.glyph;version="10.
            0.0",org.lorainelab.igb.image.exporter.service;version="10.0.0",org.l
            orainelab.igb.javafx;version="10.0.0",org.lorainelab.igb.menu.api;ver
            sion="10.0.0",org.lorainelab.igb.menu.api.model;version="10.0.0",org.
            lorainelab.igb.services;version="10.0.0",com.affymetrix.genoviz.awt;v
            ersion="[1.1,2)",com.affymetrix.genoviz.bioviews;version="[1.1,2)",co
            m.affymetrix.genoviz.event;version="[1.1,2)",com.affymetrix.genoviz.g
            lyph;version="[1.1,2)",com.affymetrix.genoviz.swing;version="[1.1,2)"
            ,com.affymetrix.genoviz.util;version="[1.1,2)",com.affymetrix.genoviz
            .widget;version="[1.1,2)",com.affymetrix.genoviz.widget.tieredmap;ver
            sion="[1.1,2)",com.google.common.base;version="[32.1,33)",com.google.
            common.collect;version="[32.1,33)",com.google.common.eventbus;version
            ="[32.1,33)",jakarta.xml.bind;version="[4.0,5)",jakarta.xml.bind.anno
            tation;version="[4.0,5)",java.awt,java.awt.datatransfer,java.awt.even
            t,java.awt.geom,java.io,java.lang,java.lang.invoke,java.lang.reflect,
            java.math,java.net,java.text,java.util,java.util.function,java.util.p
            refs,java.util.regex,java.util.stream,javax.swing,javax.swing.border,
            javax.swing.table,javax.xml.namespace,javax.xml.parsers,javax.xml.xpa
            th,net.miginfocom.layout,net.miginfocom.swing,org.apache.commons.io;v
            ersion="[1.4,2)",org.apache.commons.lang3.text;version="[3.4,4)",org.
            osgi.service.component;version="[1.2,2)",org.slf4j;version="[1.7,2)",
            org.w3c.dom,org.xml.sax
            Tool: Bnd-6.3.1.202206071316

            Show
            nfreese Nowlan Freese added a comment - After: Created-By: Apache Maven Bundle Plugin 5.1.9 Import-Package: com.affymetrix.common;version="10.0.0",com.affymetrix. genometry;version="10.0.0",com.affymetrix.genometry.comparator;versio n="10.0.0",com.affymetrix.genometry.event;version="10.0.0",com.affyme trix.genometry.span;version="10.0.0",com.affymetrix.genometry.symmetr y;version="10.0.0",com.affymetrix.genometry.symmetry.impl;version="10 .0.0",com.affymetrix.genometry.thread;version="10.0.0",com.affymetrix .genometry.util;version="10.0.0",com.affymetrix.igb.shared;version="1 0.0.0",com.affymetrix.igb.swing;version="10.0.0",com.affymetrix.igb.s wing.jide;version="10.0.0",org.lorainelab.igb.genoviz.extensions;vers ion="10.0.0",org.lorainelab.igb.genoviz.extensions.glyph;version="10. 0.0",org.lorainelab.igb.image.exporter.service;version="10.0.0",org.l orainelab.igb.javafx;version="10.0.0",org.lorainelab.igb.menu.api;ver sion="10.0.0",org.lorainelab.igb.menu.api.model;version="10.0.0",org. lorainelab.igb.services;version="10.0.0",com.affymetrix.genoviz.awt;v ersion="[1.1,2)",com.affymetrix.genoviz.bioviews;version="[1.1,2)",co m.affymetrix.genoviz.event;version="[1.1,2)",com.affymetrix.genoviz.g lyph;version="[1.1,2)",com.affymetrix.genoviz.swing;version="[1.1,2)" ,com.affymetrix.genoviz.util;version="[1.1,2)",com.affymetrix.genoviz .widget;version="[1.1,2)",com.affymetrix.genoviz.widget.tieredmap;ver sion="[1.1,2)",com.google.common.base;version="[32.1,33)",com.google. common.collect;version="[32.1,33)",com.google.common.eventbus;version ="[32.1,33)",jakarta.xml.bind;version="[4.0,5)",jakarta.xml.bind.anno tation;version="[4.0,5)",java.awt,java.awt.datatransfer,java.awt.even t,java.awt.geom,java.io,java.lang,java.lang.invoke,java.lang.reflect, java.math,java.net,java.text,java.util,java.util.function,java.util.p refs,java.util.regex,java.util.stream,javax.swing,javax.swing.border, javax.swing.table,javax.xml.namespace,javax.xml.parsers,javax.xml.xpa th,net.miginfocom.layout,net.miginfocom.swing,org.apache.commons.io;v ersion="[1.4,2)",org.apache.commons.lang3.text;version="[3.4,4)",org. osgi.service.component;version="[1.2,2)",org.slf4j;version="[1.7,2)", org.w3c.dom,org.xml.sax Tool: Bnd-6.3.1.202206071316
            Hide
            nfreese Nowlan Freese added a comment -

            I'm following the same logic discussed and applied in IGBF-1906. The changes made in IGBF-1906 were undone by David for ProtAnnot when we were refactoring the app for JDK 21. I am now re-implementing them for the IGB dependencies. By declaring an import-package in the maven-bundle-plugin for the IGB dependencies with just a single version(i.e. 10.0.0), it sets the manifest's import-package version for those IGB dependencies to anything 10.0.0 or greater. Compare this to the normal convention of not passing anything in to the import-package as part of maven-bundle-plugin, which leads to the manifest giving an upper bound of version="[10.0,11)". It would be more "correct" to have the upper bound, as the assumption is that by changing to a new major version we are indicating that there are new changes that would break backwards compatibility. However, it would mean that anytime we changed the major version of IGB, we would need to re-release all apps, whether or not they were compatible.

            Show
            nfreese Nowlan Freese added a comment - I'm following the same logic discussed and applied in IGBF-1906 . The changes made in IGBF-1906 were undone by David for ProtAnnot when we were refactoring the app for JDK 21. I am now re-implementing them for the IGB dependencies. By declaring an import-package in the maven-bundle-plugin for the IGB dependencies with just a single version(i.e. 10.0.0), it sets the manifest's import-package version for those IGB dependencies to anything 10.0.0 or greater. Compare this to the normal convention of not passing anything in to the import-package as part of maven-bundle-plugin, which leads to the manifest giving an upper bound of version="[10.0,11)". It would be more "correct" to have the upper bound, as the assumption is that by changing to a new major version we are indicating that there are new changes that would break backwards compatibility. However, it would mean that anytime we changed the major version of IGB, we would need to re-release all apps, whether or not they were compatible.
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ]
            nfreese Nowlan Freese made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            nfreese Nowlan Freese made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            nfreese Nowlan Freese made changes -
            Assignee Ann Loraine [ aloraine ]
            Hide
            ann.loraine Ann Loraine added a comment -

            Yes, I think what you have said is correct. I just wanted to double-check.

            IBM WebSphere Application server documentation writes:

            ...Import-Package: org.apache.commons.logging;version="1.0.4"
            Import-Package
            This header declares the external dependencies of the bundle that the OSGi Framework uses to resolve the bundle. Specific versions or version ranges for each package can be declared. In this example manifest file, the org.apache.commons.logging package is required at Version 1.0.4 or later.

            Link: https://www.ibm.com/docs/en/was/9.0.5?topic=files-example-osgi-bundle-manifest-file

            Show
            ann.loraine Ann Loraine added a comment - Yes, I think what you have said is correct. I just wanted to double-check. IBM WebSphere Application server documentation writes: ...Import-Package: org.apache.commons.logging;version="1.0.4" Import-Package This header declares the external dependencies of the bundle that the OSGi Framework uses to resolve the bundle. Specific versions or version ranges for each package can be declared. In this example manifest file, the org.apache.commons.logging package is required at Version 1.0.4 or later. Link: https://www.ibm.com/docs/en/was/9.0.5?topic=files-example-osgi-bundle-manifest-file
            Hide
            ann.loraine Ann Loraine added a comment - - edited

            The authoritative answer is available from osgi.org:

            If a version range is specified as a single version, it must be interpreted as the range [version, infinity)

            See:

            Show
            ann.loraine Ann Loraine added a comment - - edited The authoritative answer is available from osgi.org: If a version range is specified as a single version, it must be interpreted as the range [version, infinity) See: https://docs.osgi.org/specification/osgi.core/8.0.0/framework.module.html#i3189032 (source of the above quote) https://docs.osgi.org/specification/osgi.core/8.0.0/framework.module.html#framework.module.importpackage
            ann.loraine Ann Loraine made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            Hide
            ann.loraine Ann Loraine added a comment -

            All ProtAnnot PR's are now merged.

            Show
            ann.loraine Ann Loraine added a comment - All ProtAnnot PR's are now merged.
            ann.loraine Ann Loraine made changes -
            Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
            ann.loraine Ann Loraine made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            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 ]
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ]
            nfreese Nowlan Freese made changes -
            Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
            Hide
            nfreese Nowlan Freese added a comment -

            ProtAnnot 10.0.1 has been released to the app store: https://apps.bioviz.org/apps/org.lorainelab.igb.protannot#

            Tested on Mac on IGB 10.0.0 as well as a development version of IGB with the IGB version set to 11. I was able to install and run ProtAnnot from the app store or app manager. The ProtAnnot icon was also visible from either the Tools menu or the right-click menu.

            Closing ticket.

            Show
            nfreese Nowlan Freese added a comment - ProtAnnot 10.0.1 has been released to the app store: https://apps.bioviz.org/apps/org.lorainelab.igb.protannot# Tested on Mac on IGB 10.0.0 as well as a development version of IGB with the IGB version set to 11. I was able to install and run ProtAnnot from the app store or app manager. The ProtAnnot icon was also visible from either the Tools menu or the right-click menu. Closing ticket.
            nfreese Nowlan Freese made changes -
            Resolution Done [ 10000 ]
            Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

              People

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

                Dates

                • Created:
                  Updated:
                  Resolved: