[IGBF-3335] Update IGB java 1.8 dependencies - JIRA UNCC

Details

Type: Improvement
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: 10.0.0 Major Release
Labels:
None

Story Points:
5
Epic Link:
Run IGB in Java 21
Sprint:
Summer 1 2023 May 15, Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26, Summer 5 2023 July 10

Description

Situation: We have reached a blocker in the upgrade to java 11 as IGB will not start but there are no additional errors. I think there may be an issue with the OSGI wiring, but we need a way to check if that is the issue keeping IGB from running or if it is a java 11 issue.

Task: Update the various project dependencies for IGB in Java 8. Ensure that IGB starts and that all of the bundles are able to load.

Attachments

Issue Links

relates to

IGBF-3382 Remove remote error dependencies

Closed

IGBF-3384 Branch from master to create new development branch main-JDK8

Closed

IGBF-3331 Investigate com.sun.java.swing.plaf.windows requirement

Closed

Activity

Ascending order - Click to sort in descending order

Hide

Permalink

Nowlan Freese added a comment - 16/May/23 9:20 AM - edited

Side note:

While attempting to install netbeans version 11.3, I ran into a bug where the installer will fail because it cannot find the jdk. The steps here fixed the issue.

The problem seems to be the fact that /usr/libexec/java_home seems to be broken in BigSur (see here: https://developer.apple.com/forums/thread/666681).

The Netbeans installer checks if the JDK is installed by using /usr/libexec/java_home, gets the wrong answer and quits with an error.

One way to fix that behaviour is to patch the installer. It can be done as follows:

assuming there is no directory called "a" in tmp:

Open the dmg, but do not run the installer

In a shell give the following command:

pkgutil --expand /Volumes/NetBeans\ 8.2\ RC/NetBeans\ 8.2\ RC.pkg /tmp/a

(if your Netbeans installer has a different name, change the command to reflect the actual name of your installer)

This opens the package, and copies it s content in /tmp/a.

Edit the installation script. Using a text editor, open the file /tmp/a/Distribution.

on line 13, replace:

var java_result = checkJavaVersion();

with

var java_result = true;

and save the file. This will skip the check on the Java version. It is your responsibility to make sure you have JDK 8 or following on your machine, and that this version is used when you use the java command. You can make sure that's fine by checking with the command

java -version

Let's wrap it up:
pkgutil --flatten /tmp/a ~/a.pkg

At this point you have in your home directory a package called a.pkg. Double click on it, and the Netbeans installer will do its job.

Show

Nowlan Freese added a comment - 16/May/23 9:20 AM - edited Side note: While attempting to install netbeans version 11.3, I ran into a bug where the installer will fail because it cannot find the jdk. The steps here fixed the issue. The problem seems to be the fact that /usr/libexec/java_home seems to be broken in BigSur (see here: https://developer.apple.com/forums/thread/666681 ). The Netbeans installer checks if the JDK is installed by using /usr/libexec/java_home, gets the wrong answer and quits with an error. One way to fix that behaviour is to patch the installer. It can be done as follows: assuming there is no directory called "a" in tmp: Open the dmg, but do not run the installer In a shell give the following command: pkgutil --expand /Volumes/NetBeans\ 8.2\ RC/NetBeans\ 8.2\ RC.pkg /tmp/a (if your Netbeans installer has a different name, change the command to reflect the actual name of your installer) This opens the package, and copies it s content in /tmp/a. Edit the installation script. Using a text editor, open the file /tmp/a/Distribution. on line 13, replace: var java_result = checkJavaVersion(); with var java_result = true; and save the file. This will skip the check on the Java version. It is your responsibility to make sure you have JDK 8 or following on your machine, and that this version is used when you use the java command. You can make sure that's fine by checking with the command java -version Let's wrap it up: pkgutil --flatten /tmp/a ~/a.pkg At this point you have in your home directory a package called a.pkg. Double click on it, and the Netbeans installer will do its job.

21 older comments

Hide

Permalink

Ann Loraine added a comment - 13/Jul/23 12:32 PM

OK - I will make the target branch and push it to the team repository shortly.

Show

Ann Loraine added a comment - 13/Jul/23 12:32 PM OK - I will make the target branch and push it to the team repository shortly.

Hide

Permalink

Ann Loraine added a comment - 13/Jul/23 12:40 PM

I have pushed the new development branch. It is ready to receive your PR.

See:

https://bitbucket.org/lorainelab/integrated-genome-browser/src/main-JDK8/

Show

Ann Loraine added a comment - 13/Jul/23 12:40 PM I have pushed the new development branch. It is ready to receive your PR. See: https://bitbucket.org/lorainelab/integrated-genome-browser/src/main-JDK8/

Hide

Permalink

Nowlan Freese added a comment - 13/Jul/23 1:07 PM

Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/934

Show

Nowlan Freese added a comment - 13/Jul/23 1:07 PM Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/934

Hide

Permalink

Ann Loraine added a comment - 14/Jul/23 4:23 AM

Merged and the new main-JDK8 branch installers are deployed to BioViz early access section.

Show

Ann Loraine added a comment - 14/Jul/23 4:23 AM Merged and the new main-JDK8 branch installers are deployed to BioViz early access section.

Hide

Permalink

Kaushik Gopu added a comment - 17/Jul/23 3:57 PM - edited

Tested in local. all 95/95 bundles are active, I am able to load data and everything else looks fine. closing this ticket

Show

Kaushik Gopu added a comment - 17/Jul/23 3:57 PM - edited Tested in local. all 95/95 bundles are active, I am able to load data and everything else looks fine. closing this ticket

People

Assignee:

Nowlan Freese

Reporter:

Nowlan Freese

Votes:

0 Vote for this issue

Watchers:

3 Start watching this issue

Dates

Created:

15/May/23 9:36 AM

Updated:

07/Feb/24 1:48 PM

Resolved:

18/Jul/23 10:16 AM