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:Fall 2 2022 Sep 5, Fall 3 2022 Sep 26, Spring 2 2023 Jan 16
Description
We would like to upgrade IGB to use more recent versions of Java.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM.
IBM talk at https://2022.jconf.dev/
"Making the Move to Java 17"
Alex Motley and Cindy
Discussed migration and migration tools, including tools they made and invite the audience to use.
- slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338
- video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents
Noteworthy updates :
- Module system added with JDK9.
- XML package name change
Attachments
Activity
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Summary | Define scope of work for IGB java upgrade project contract | Investigate: upgrade IGB java |
| Assignee | Karthik Raveendran [ karthik ] |
| Sprint | Fall 2 2022 Sep 5, Fall 3 2022 Sep 26 [ 154, 155 ] | Fall 2 2022 Sep 5, Fall 3 2022 Sep 26, Spring 2 2023 Jan 16 [ 154, 155, 162 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Sprint | Fall 2 2022 Sep 5, Fall 3 2022 Sep 26, Fall 8 2022 Dec 5 [ 154, 155, 160 ] | Fall 2 2022 Sep 5, Fall 3 2022 Sep 26 [ 154, 155 ] |
Thank you very much for the above information Karthik Raveendran ... bon voyage !
| Attachment | Transformer output.png [ 17571 ] |
| Attachment | Transformer output.png [ 17570 ] |
| Attachment | Transformer output.png [ 17570 ] |
| Attachment | Transformer output.png [ 17569 ] |
Eclipse Transformer - to update Java EE libraries to Jakarta. See https://www.youtube.com/watch?v=rS5EJb_QYs8 and https://www.slideshare.net/Jakarta_EE/the-eclipse-transformer-project. After running the transformer a few files were updated as seen in the image.
After cloning the project from https://github.com/eclipse/transformer, go to the project and maven clean install:
mvnw clean install
Open org.eclipse.transformer.cli/target in the project folder
java -jar org.eclipse.transformer.cli-<version>.jar [IGB_Project_Folder] [Output_Folder]
After the changes are made the output folder has a new copy of the project with the changes but its just replacing with Jakarta.
JDeps and Migration Toolkit for Application Binaries are dependency analyser and evaluates application-binary files respectively which may assist in the migration but they are not very .
I did not get a chance to checkout Dependabot(https://github.com/dependabot/dependabot-core)
| Attachment | Transformer output.png [ 17569 ] |
| Attachment | makingthemovetojava17jconf2022-220930162146-738abbe4.pdf [ 17568 ] |
Found two removed Packages/Classes from Java 11 that is being used in IGB
com.sun.awt.AWTUtilities -> PopupInfo.java line 646 (package is not imported)
com.sun.security.auth.X500Principal -> IGBTrustManager (line 65,66)
| Description |
We would like to upgrade IGB to use more recent versions of Java.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/ "Making the Move to Java 17" Alex Motley and Cindy Discussed migration tools, including tools they made and invite the audience to use. * slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 * video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents Noteworthy updates : # Module system added with JDK9. # XML package name change |
We would like to upgrade IGB to use more recent versions of Java.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/ "Making the Move to Java 17" Alex Motley and Cindy Discussed migration and migration tools, including tools they made and invite the audience to use. * slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 * video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents Noteworthy updates : # Module system added with JDK9. # XML package name change |
| Description |
We would like to upgrade IGB to use more recent versions of Java.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/ "Making the Move to Java 17" Alex Motley and Cindy Discussed migration tools, including tools they made and invite the audience to use. * slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 * video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents Noteworthy updates # Module system added with JDK9. # XML package name change |
We would like to upgrade IGB to use more recent versions of Java.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/ "Making the Move to Java 17" Alex Motley and Cindy Discussed migration tools, including tools they made and invite the audience to use. * slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 * video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents Noteworthy updates : # Module system added with JDK9. # XML package name change |
| Description |
We would like to upgrade IGB to use more recent versions of Java.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/ "Making the Move to Java 17" Alex Motley and Cindy Discussed migration tools, including tools they made and invite the audience to use. * slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 * video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents Updates of note: * Module system added with JDK9. * XML package name change |
We would like to upgrade IGB to use more recent versions of Java.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/ "Making the Move to Java 17" Alex Motley and Cindy Discussed migration tools, including tools they made and invite the audience to use. * slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 * video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents Noteworthy updates # Module system added with JDK9. # XML package name change |
| Description |
We would like to upgrade IGB to use more recent versions of Java.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/ "Making the Move to Java 17" Alex Motley and Cindy * migration tools, including tools they made and invite the audience to use. slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents Updates of note: * Module system added with JDK9. * XML package name change |
We would like to upgrade IGB to use more recent versions of Java.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/ "Making the Move to Java 17" Alex Motley and Cindy Discussed migration tools, including tools they made and invite the audience to use. * slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 * video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents Updates of note: * Module system added with JDK9. * XML package name change |
| Description |
We would like to upgrade IGB to use more recent versions of Java.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/ "Making the Move to Java 17" Alex Motley and Cindy They talked about migration tools, including tools they made and invite the audience to use. slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents Updates of note: * Module system added with JDK9. * XML package name change |
We would like to upgrade IGB to use more recent versions of Java.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/ "Making the Move to Java 17" Alex Motley and Cindy * migration tools, including tools they made and invite the audience to use. slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents Updates of note: * Module system added with JDK9. * XML package name change |
| Description |
We would like to upgrade IGB to use more recent versions of Java.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/ "Making the Move to Java 17" Alex Motley and Cindy They talked about migration tools, including tools they made and invite the audience to use. slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents |
We would like to upgrade IGB to use more recent versions of Java.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/ "Making the Move to Java 17" Alex Motley and Cindy They talked about migration tools, including tools they made and invite the audience to use. slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents Updates of note: * Module system added with JDK9. * XML package name change |
| Description |
We would like to upgrade IGB to use more recent versions of Java. Currently the recommended java to use is java 17. There is jdk 18 but it's not yet fully released, pending further work and testing and so on.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/ "Making the Move to Java 17" Alex Motley and Cindy They talked about migration tools, including tools they made and invite the audience to use. slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents |
We would like to upgrade IGB to use more recent versions of Java.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/ "Making the Move to Java 17" Alex Motley and Cindy They talked about migration tools, including tools they made and invite the audience to use. slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents |
| Description |
We would like to upgrade IGB to use more recent versions of Java. Currently the recommended java to use is java 17. There is jdk 18 but it's not yet fully released, pending further work and testing and so on.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/: "Making the Move to Java 17" Alex Motley and Cindy They talked about tools one can use to make the migration. slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents |
We would like to upgrade IGB to use more recent versions of Java. Currently the recommended java to use is java 17. There is jdk 18 but it's not yet fully released, pending further work and testing and so on.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/ "Making the Move to Java 17" Alex Motley and Cindy They talked about migration tools, including tools they made and invite the audience to use. slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents |
| Sprint | Fall 2 2022 Sep 5, Fall 3 2022 Sep 26 [ 154, 155 ] | Fall 2 2022 Sep 5, Fall 3 2022 Sep 26, Fall 8 2022 Dec 5 [ 154, 155, 160 ] |
| Description |
We would like to upgrade IGB to use more recent versions of Java. Currently the recommended java to use is java 17. There is jdk 18 but it's not yet fully released, pending further work and testing and so on.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/: "Making the Move to Java 17" Alex Motley and Cindy They talked about tools one can use to make the migration. slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 |
We would like to upgrade IGB to use more recent versions of Java. Currently the recommended java to use is java 17. There is jdk 18 but it's not yet fully released, pending further work and testing and so on.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/: "Making the Move to Java 17" Alex Motley and Cindy They talked about tools one can use to make the migration. slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 video: https://www.youtube.com/watch?v=VN7GQexxpnc&ab_channel=connectevents |
Also, Ann has experimented a bit with moving to Java 18 and made a branch where she made some progress. She was able to get IGB to compile but not run under JDK 18. The branch is here: https://bitbucket.org/aloraine/integrated-genome-browser/branch/IGBF-3142
| Description |
We would like to upgrade IGB to use more recent versions of Java. Currently the recommended java to use is java 17. There is jdk 18 but it's not yet fully released, pending further work and testing and so on.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/: "Making the Move to Java 17" Alex Motley and Cindy They talked about tools one can use to make the migration. |
We would like to upgrade IGB to use more recent versions of Java. Currently the recommended java to use is java 17. There is jdk 18 but it's not yet fully released, pending further work and testing and so on.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/: "Making the Move to Java 17" Alex Motley and Cindy They talked about tools one can use to make the migration. slides: https://www.slideshare.net/AlexMotley3/making-the-move-to-java-17-jconf-2022-253278338 |
| Description |
We would like to upgrade IGB to use more recent versions of Java. Currently the recommended java to use is java 17. There is jdk 18 but it's not yet fully released, pending further work and testing and so on.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk: "Making the Move to Java 17" Alex Motley and Cindy They talked about tools one can use to make the migration. |
We would like to upgrade IGB to use more recent versions of Java. Currently the recommended java to use is java 17. There is jdk 18 but it's not yet fully released, pending further work and testing and so on.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk at https://2022.jconf.dev/: "Making the Move to Java 17" Alex Motley and Cindy They talked about tools one can use to make the migration. |
| Description |
We would like to upgrade IGB to use more recent versions of Java. Currently the recommended java to use is java 17. There is jdk 18 but it's not yet fully released, pending further work and testing and so on.
There are some tools that could be helpful in this. Ann attended a conference where the upgrade path to java 17 was discussed in a talk by IBM. IBM talk: "Making the Move to Java 17" Alex Motley and Cindy They talked about tools one can use to make the migration. |
| Assignee | Ann Loraine [ aloraine ] | Karthik Raveendran [ karthik ] |
| Rank | Ranked higher |
| Sprint | Fall 2 2022 Sep 5, Fall 3 2022 Sep 26, Fall 4 2022 Oct 10 [ 154, 155, 156 ] | Fall 2 2022 Sep 5, Fall 3 2022 Sep 26 [ 154, 155 ] |
| Rank | Ranked higher |
| Sprint | Fall 2 2022 Sep 5, Fall 3 2022 Sep 26 [ 154, 155 ] | Fall 2 2022 Sep 5, Fall 3 2022 Sep 26, Fall 4 2022 Oct 10 [ 154, 155, 156 ] |
Attended "deep dish java" conference and talked with experts from IBM and elsewhere on upgrading IGB to use JDK 17, currently the preferred option. Learned about several command-line tools that can aid and even automate the migration process. See Description above.
| Rank | Ranked higher |
| Sprint | Fall 2 2022 Sep 5 [ 154 ] | Fall 2 2022 Sep 5, Fall 3 2022 Sep 26 [ 154, 155 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Talked with Kim and others in Purchasing and got information on how to proceed. Relevant attachments and emails are in my "Budgets" email folder.
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1531 [ 17617 ] |
Many notes were made. Moving forward with the next phase of this project in linked ticket IGBF-3142.