[IGBF-2291] Upgrade JDK version to 1.8.0.241 for loraine lab java repositories - JIRA UNCC

Noor Zahara (Inactive) created issue - 18/Mar/20 3:58 PM

Noor Zahara (Inactive) made changes - 18/Mar/20 4:00 PM

Field	Original Value	New Value
Epic Link		IGBF-1531 [ 17617 ]

Noor Zahara (Inactive) made changes - 18/Mar/20 4:00 PM

Assignee

Ann Loraine [ aloraine ]

Noor Zahara [ noor91zahara ]

Noor Zahara (Inactive) made changes - 18/Mar/20 4:00 PM

Link

This issue blocks ~~IGBF-2280~~ [ ~~IGBF-2280~~ ]

Noor Zahara (Inactive) made changes - 18/Mar/20 11:01 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Noor Zahara (Inactive) added a comment - 18/Mar/20 11:02 PM

[~aloraine] -

Could you help me figure out the repositories which needs an upgrade?

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Noor Zahara (Inactive) added a comment - 18/Mar/20 11:02 PM [~aloraine] - Could you help me figure out the repositories which needs an upgrade?

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Ann Loraine added a comment - 19/Mar/20 8:28 AM - edited

Sure. Here are some options:

If you log in to bitbucket and visit https://bitbucket.org/lorainelab/ you *may* see a green check (or exclamation point) in the "Builds" column. But you might not – I am not sure if your user would be able to view build status. Anyway, any repo with a check mark is getting built using the Docker image and needs to be updated.
Any repository with a "bitbucket_pipelines.yml" file. Unfortunately there does not seem to be a way to search for repositories with that file using the bitbucket interface.
Go to: https://bitbucket.org/lorainelab/profile/projects. Every repository in the "IGB Apps" project should have a bitbucket_pipelines.yml" file which needs to be updated to use the new Docker image.
Also go to: https://bitbucket.org/account/user/lorainelab/projects/IGB. Projects that need to be updated include: GenoViz SDK, GenoViz SDK Demos, IGB for Testing App Workflow, Integrated Genome Browser.

Also, I see you have updated "JRE Bundles Install4j" Downloads section. Thanks!

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Ann Loraine added a comment - 19/Mar/20 8:28 AM - edited Sure. Here are some options: If you log in to bitbucket and visit https://bitbucket.org/lorainelab/ you * may * see a green check (or exclamation point) in the "Builds" column. But you might not – I am not sure if your user would be able to view build status. Anyway, any repo with a check mark is getting built using the Docker image and needs to be updated. Any repository with a "bitbucket_pipelines.yml" file. Unfortunately there does not seem to be a way to search for repositories with that file using the bitbucket interface. Go to: https://bitbucket.org/lorainelab/profile/projects . Every repository in the "IGB Apps" project should have a bitbucket_pipelines.yml" file which needs to be updated to use the new Docker image. Also go to: https://bitbucket.org/account/user/lorainelab/projects/IGB . Projects that need to be updated include: GenoViz SDK, GenoViz SDK Demos, IGB for Testing App Workflow, Integrated Genome Browser. Also, I see you have updated "JRE Bundles Install4j" Downloads section. Thanks!

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Noor Zahara (Inactive) added a comment - 24/Mar/20 10:20 PM - edited

Code changes to the repositories -

https://bitbucket.org/noorzahara/2bit-reader-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/genoviz-sdk-demos-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/igb-for-testing-app-workflow-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/app-for-testing-app-workflow-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/get-average-score-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/23andme-snp-converter-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/bundlemarkdownencoder-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/command-socket-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/experimental-apps-for-igb-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/geometric-mean-operator-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/merge-annotation-operator-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/protannot-local/branch/IGBF-2291#diff

https://bitbucket.org/noorzahara/super-simple-igb-app-local/branch/IGBF-2291#diff

https://bitbucket.org/nzahara/genoviz-sdk-local/branch/IGBF-2291#diff

Testing steps - Follow the readme in each repositories.

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Noor Zahara (Inactive) added a comment - 24/Mar/20 10:20 PM - edited Code changes to the repositories - https://bitbucket.org/noorzahara/2bit-reader-local/branch/IGBF-2291#diff https://bitbucket.org/noorzahara/genoviz-sdk-demos-local/branch/IGBF-2291#diff https://bitbucket.org/noorzahara/igb-for-testing-app-workflow-local/branch/IGBF-2291#diff https://bitbucket.org/noorzahara/app-for-testing-app-workflow-local/branch/IGBF-2291#diff https://bitbucket.org/noorzahara/get-average-score-local/branch/IGBF-2291#diff https://bitbucket.org/noorzahara/23andme-snp-converter-local/branch/IGBF-2291#diff https://bitbucket.org/noorzahara/bundlemarkdownencoder-local/branch/IGBF-2291#diff https://bitbucket.org/noorzahara/command-socket-local/branch/IGBF-2291#diff https://bitbucket.org/noorzahara/experimental-apps-for-igb-local/branch/IGBF-2291#diff https://bitbucket.org/noorzahara/geometric-mean-operator-local/branch/IGBF-2291#diff https://bitbucket.org/noorzahara/merge-annotation-operator-local/branch/IGBF-2291#diff https://bitbucket.org/noorzahara/protannot-local/branch/IGBF-2291#diff https://bitbucket.org/noorzahara/super-simple-igb-app-local/branch/IGBF-2291#diff https://bitbucket.org/nzahara/genoviz-sdk-local/branch/IGBF-2291#diff Testing steps - Follow the readme in each repositories.

Noor Zahara (Inactive) made changes - 24/Mar/20 10:21 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Noor Zahara (Inactive) made changes - 24/Mar/20 10:21 PM

Assignee

Noor Zahara [ noor91zahara ]

Nowlan Freese made changes - 30/Mar/20 8:51 AM

Sprint

Spring 5 : 16 Mar to 27 Mar [ 90 ]

Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10 [ 90, 91 ]

Nowlan Freese made changes - 30/Mar/20 8:51 AM

Rank

Ranked higher

Shamika Gajanan Kulkarni (Inactive) made changes - 10/Apr/20 6:22 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Shamika Gajanan Kulkarni (Inactive) made changes - 10/Apr/20 6:22 PM

Assignee

Shamika Gajanan Kulkarni [ shamika ]

Ann Loraine made changes - 13/Apr/20 7:47 PM

Sprint

Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10 [ 90, 91 ]

Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr [ 90, 91, 92 ]

Ann Loraine made changes - 13/Apr/20 7:48 PM

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Shamika Gajanan Kulkarni (Inactive) added a comment - 15/Apr/20 2:24 PM

I have reviewed each of the above links. I was not able to test the 'App for testing App workflow' since the downloads link did not contain repository.xml file. Noor Zahara can you please look into it and rebuild your branch? Rest all are working fine.

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Shamika Gajanan Kulkarni (Inactive) added a comment - 15/Apr/20 2:24 PM I have reviewed each of the above links. I was not able to test the 'App for testing App workflow' since the downloads link did not contain repository.xml file. Noor Zahara can you please look into it and rebuild your branch? Rest all are working fine.

Shamika Gajanan Kulkarni (Inactive) made changes - 15/Apr/20 2:26 PM

Assignee

Shamika Gajanan Kulkarni [ shamika ]

Noor Zahara [ noor91zahara ]

Shamika Gajanan Kulkarni (Inactive) made changes - 15/Apr/20 2:26 PM

Status

First Level Review in Progress [ 10301 ]

Needs 1st Level Review [ 10005 ]

Shamika Gajanan Kulkarni (Inactive) made changes - 15/Apr/20 2:26 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Shamika Gajanan Kulkarni (Inactive) made changes - 15/Apr/20 2:26 PM

Status

First Level Review in Progress [ 10301 ]

Needs 1st Level Review [ 10005 ]

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Shamika Gajanan Kulkarni (Inactive) added a comment - 15/Apr/20 3:03 PM

I have tested the 'App for testing App workflow' using Appstore. It is working fine. Noor Zahara please submit a PR for the same.

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Shamika Gajanan Kulkarni (Inactive) added a comment - 15/Apr/20 3:03 PM I have tested the 'App for testing App workflow' using Appstore. It is working fine. Noor Zahara please submit a PR for the same.

Noor Zahara (Inactive) made changes - 15/Apr/20 3:08 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Shamika Gajanan Kulkarni (Inactive) made changes - 15/Apr/20 3:09 PM

Status

First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]

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Noor Zahara (Inactive) added a comment - 15/Apr/20 4:11 PM

PR Created

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Noor Zahara (Inactive) added a comment - 15/Apr/20 4:11 PM PR Created https://bitbucket.org/lorainelab/2bit-reader/pull-requests/4/igbf-2291/diff https://bitbucket.org/lorainelab/genoviz-sdk-demos/pull-requests/3/upgrade-jdk-version-to-180241/diff https://bitbucket.org/lorainelab/igb-for-testing-app-workflow/pull-requests/1/upgrade-jdk-version-to-180241/diff https://bitbucket.org/lorainelab/app-for-testing-app-workflow/pull-requests/1/upgrade-jdk-version-to-180241/diff https://bitbucket.org/lorainelab/get-average-score/pull-requests/7/upgrade-jdk-version-to-180241/diff https://bitbucket.org/lorainelab/23andme-snp-converter/pull-requests/9/upgrade-jdk-version-to-180241/diff https://bitbucket.org/lorainelab/bundlemarkdownencoder/pull-requests/2/upgrade-jdk-version-to-180241/diff https://bitbucket.org/lorainelab/command-socket/pull-requests/15/upgrade-jdk-version-to-180241/diff https://bitbucket.org/lorainelab/experimental-apps-for-igb/pull-requests/11/upgrade-jdk-version-to-180241/diff https://bitbucket.org/lorainelab/geometric-mean-operator/pull-requests/10/upgrade-jdk-version-to-180241/diff https://bitbucket.org/lorainelab/protannot/pull-requests/13/igbf-2291-upgrade-jdk-version-to-180241/diff https://bitbucket.org/lorainelab/super-simple-igb-app/pull-requests/10/upgrade-jdk-version-to-180241/diff https://bitbucket.org/lorainelab/genoviz-sdk/pull-requests/19/upgrade-jdk-version-to-180241/diff https://bitbucket.org/lorainelab/merge-annotation-operator/pull-requests/12/upgrade-jdk-version-to-180241/diff

Noor Zahara (Inactive) made changes - 15/Apr/20 4:11 PM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

Noor Zahara (Inactive) made changes - 15/Apr/20 4:11 PM

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Noor Zahara [ noor91zahara ]

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Ann Loraine added a comment - 16/Apr/20 6:23 AM

Please check Command Socket PR for comment.
cc: Noor Zahara

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Ann Loraine added a comment - 16/Apr/20 6:23 AM Please check Command Socket PR for comment. cc: Noor Zahara

Ann Loraine made changes - 16/Apr/20 6:23 AM

Status

Pull Request Submitted [ 10101 ]

Reviewing Pull Request [ 10303 ]

Ann Loraine made changes - 16/Apr/20 6:23 AM

Status

Reviewing Pull Request [ 10303 ]

To-Do [ 10305 ]

Noor Zahara (Inactive) made changes - 16/Apr/20 11:53 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Noor Zahara (Inactive) made changes - 16/Apr/20 11:53 AM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Noor Zahara (Inactive) made changes - 16/Apr/20 11:53 AM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Noor Zahara (Inactive) made changes - 16/Apr/20 11:53 AM

Status

First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]

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Noor Zahara (Inactive) added a comment - 16/Apr/20 11:54 AM

I have removed the git.properties file

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Noor Zahara (Inactive) added a comment - 16/Apr/20 11:54 AM I have removed the git.properties file

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Ann Loraine added a comment - 16/Apr/20 12:09 PM

Command socket merged.
Moving to "Ready for Testing" as all PRs are now merged to their respective master branches.

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Ann Loraine added a comment - 16/Apr/20 12:09 PM Command socket merged. Moving to "Ready for Testing" as all PRs are now merged to their respective master branches.

Ann Loraine made changes - 16/Apr/20 12:09 PM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

Ann Loraine made changes - 16/Apr/20 12:09 PM

Status

Pull Request Submitted [ 10101 ]

Reviewing Pull Request [ 10303 ]

Ann Loraine made changes - 16/Apr/20 12:09 PM

Status

Reviewing Pull Request [ 10303 ]

Merged Needs Testing [ 10002 ]

Ann Loraine made changes - 24/Apr/20 10:11 PM

Sprint

Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr [ 90, 91, 92 ]

Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May [ 90, 91, 92, 93 ]

Ann Loraine made changes - 24/Apr/20 10:11 PM

Rank

Ranked higher

Ann Loraine made changes - 10/May/20 8:01 PM

Sprint

Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May [ 90, 91, 92, 93 ]

Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May [ 90, 91, 92, 93, 94 ]

Ann Loraine made changes - 10/May/20 8:01 PM

Rank

Ranked higher

Ann Loraine made changes - 24/May/20 8:27 PM

Sprint

Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May [ 90, 91, 92, 93, 94 ]

Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun [ 90, 91, 92, 93, 94, 95 ]

Ann Loraine made changes - 24/May/20 8:27 PM

Rank

Ranked higher

Ann Loraine made changes - 05/Jun/20 8:28 PM

Sprint

Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun [ 90, 91, 92, 93, 94, 95 ]

Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun [ 90, 91, 92, 93, 94, 95, 96 ]

Ann Loraine made changes - 05/Jun/20 8:28 PM

Rank

Ranked higher

Ann Loraine made changes - 16/Jun/20 7:25 AM

Summary

Upgrade JDK version to 1.8.0.241 for all the loraine lab repositories

Upgrade JDK version to 1.8.0.241 for loraine lab java repositories

Ann Loraine made changes - 16/Jun/20 7:26 AM

Description

Upgrade JDK version to 1.8.0.241 for all the loraine lab repositories.

Change the image tag name in bitbucket pipeline and install 4j files.

Upgrade JDK version to 1.8.0.241 for all the loraine lab java repositories that are using bitbucket pipelines.

Change the image tag name in bitbucket pipeline and install 4j files.

Philip Badzuh (Inactive) made changes - 17/Jun/20 10:22 AM

Status

Merged Needs Testing [ 10002 ]

Post-merge Testing In Progress [ 10003 ]

Philip Badzuh (Inactive) made changes - 17/Jun/20 10:22 AM

Assignee

Philip Badzuh [ pbadzuh ]

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Philip Badzuh (Inactive) added a comment - 17/Jun/20 1:17 PM - edited

All projects were successfully built, except for 'igb-for-testing-app-workflow', which fails at genometry tests, with the following exception:

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.19:test (default-test) on project genometry: There are test failures.

All project except the above that failed to build can be successfully installed using IGB app manager. Tested on macOS

Update: The error seems to the same one that was fixed in ~~IGBF-2357~~. However, the repo below is behind the main IGB repo containing the merged fix.

https://bitbucket.org/lorainelab/igb-for-testing-app-workflow/src/Mock-rel-9.1.0/

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Philip Badzuh (Inactive) added a comment - 17/Jun/20 1:17 PM - edited All projects were successfully built, except for 'igb-for-testing-app-workflow', which fails at genometry tests, with the following exception: [ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.19:test (default-test) on project genometry: There are test failures. All project except the above that failed to build can be successfully installed using IGB app manager. Tested on macOS Update: The error seems to the same one that was fixed in IGBF-2357 . However, the repo below is behind the main IGB repo containing the merged fix. https://bitbucket.org/lorainelab/igb-for-testing-app-workflow/src/Mock-rel-9.1.0/

Philip Badzuh (Inactive) made changes - 17/Jun/20 1:17 PM

Status

Post-merge Testing In Progress [ 10003 ]

To-Do [ 10305 ]

Philip Badzuh (Inactive) made changes - 17/Jun/20 1:17 PM

Assignee

Philip Badzuh [ pbadzuh ]

Philip Badzuh (Inactive) made changes - 17/Jun/20 1:35 PM

Link

This issue relates to ~~IGBF-2357~~ [ ~~IGBF-2357~~ ]

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Ann Loraine added a comment - 19/Jun/20 3:02 PM

To fix, Loraine needs to pull changes from main repo into this fork.

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Ann Loraine added a comment - 19/Jun/20 3:02 PM To fix, Loraine needs to pull changes from main repo into this fork.

Ann Loraine made changes - 19/Jun/20 3:02 PM

Assignee

Ann Loraine [ aloraine ]

Ann Loraine made changes - 19/Jun/20 8:59 PM

Sprint

Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun [ 90, 91, 92, 93, 94, 95, 96 ]

Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 July [ 90, 91, 92, 93, 94, 95, 96, 97 ]

Ann Loraine made changes - 19/Jun/20 8:59 PM

Rank

Ranked higher

Ann Loraine made changes - 19/Jun/20 9:51 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Ann Loraine added a comment - 19/Jun/20 10:01 PM

Pull changes and now the fork builds. Moving to closed.

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Ann Loraine added a comment - 19/Jun/20 10:01 PM Pull changes and now the fork builds. Moving to closed.

Ann Loraine made changes - 19/Jun/20 10:01 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Ann Loraine made changes - 19/Jun/20 10:01 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Ann Loraine made changes - 19/Jun/20 10:01 PM

Status

First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]

Ann Loraine made changes - 19/Jun/20 10:01 PM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

Ann Loraine made changes - 19/Jun/20 10:01 PM

Status

Pull Request Submitted [ 10101 ]

Reviewing Pull Request [ 10303 ]

Ann Loraine made changes - 19/Jun/20 10:01 PM

Status

Reviewing Pull Request [ 10303 ]

Merged Needs Testing [ 10002 ]

Ann Loraine made changes - 19/Jun/20 10:01 PM

Status

Merged Needs Testing [ 10002 ]

Post-merge Testing In Progress [ 10003 ]

Ann Loraine made changes - 19/Jun/20 10:01 PM

Resolution		Done [ 10000 ]
Status	Post-merge Testing In Progress [ 10003 ]	Closed [ 6 ]

Upgrade JDK version to 1.8.0.241 for loraine lab java repositories

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