Release IGB 9.1.10 to BioViz.org

Made release branch and edited README. Pushed branch to team repository. This triggered the release pipeline, which completed successfully. Downloaded the Apple "dmg" installer. Commencing notarization.

Notarization complete. Uploaded notarized installer.
Installers are now ready to deploy.

A little wrinkle:

TASK [igb : get installer and jar files for release] **************************************************************************************************************************************************************************************************************************************************
changed: [bioviztest3] => (item=IGB-macos-9.1.10.dmg)
changed: [bioviztest3] => (item=IGB-unix-9.1.10.sh)
failed: [bioviztest3] (item=IGB-windows-x32-9.1.10.exe) =>

Unknown macro: {"ansible_loop_var"}

changed: [bioviztest3] => (item=IGB-windows-x64-9.1.10.exe)
changed: [bioviztest3] => (item=igb_exe-9.1.10.jar)

We stopped support windows 32-bit because we no longer have access to a JVM for that architecture.
We need to make sure that our HTML / JS code no longer checks for that architecture.

Deployed IGB 9.1.10 to test site bioviztest3.bioviz.org.
Looks like links and so forth were correctly made:

bioviztest3.bioviz.org root $ ls -lh
total 427M
-rw-r--r-- 1 root root  56M Nov  3 19:10 igb_exe-9.1.10.jar
-rw-r--r-- 1 root root 148M Nov  3 19:09 IGB-macos-9.1.10.dmg
lrwxrwxrwx 1 root root   67 Nov  3 19:12 IGB_macos_current.dmg -> /var/www/bioviz/htdocs/igb/releases/igb-9.1.10/IGB-macos-9.1.10.dmg
-rw-r--r-- 1 root root 116M Nov  3 19:09 IGB-unix-9.1.10.sh
lrwxrwxrwx 1 root root   65 Nov  3 19:12 IGB_unix_current.sh -> /var/www/bioviz/htdocs/igb/releases/igb-9.1.10/IGB-unix-9.1.10.sh
-rw-r--r-- 1 root root 108M Nov  3 19:10 IGB-windows-x64-9.1.10.exe
lrwxrwxrwx 1 root root   73 Nov  3 19:12 IGB_windows-x64_current.exe -> /var/www/bioviz/htdocs/igb/releases/igb-9.1.10/IGB-windows-x64-9.1.10.exe
-rw-r--r-- 1 root root 1.4K Nov  3 19:12 updates.xml
bioviztest3.bioviz.org root $ cat updates.xml 
<?xml version="1.0" encoding="UTF-8"?>
<updateDescriptor baseUrl="">
  <entry targetMediaFileId="23" updatableVersionMin="" updatableVersionMax="" fileName="IGB-windows-x64-9.1.10.exe" newVersion="9.1.10" newMediaFileId="23" fileSize="112635304" md5Sum="ab498876ec4ce9f4025fe468156ccab3" sha256Sum="f3d1cbbb380653e14497d2cd755429cd5d8f7b02e0374624a2e3e67bf6c20ca7" bundledJre="windows-amd64-1.8.0_332.tar.gz" archive="false" singleBundle="false">
    <comment language="en" />
  </entry>
  <entry targetMediaFileId="25" updatableVersionMin="" updatableVersionMax="" fileName="IGB-unix-9.1.10.sh" newVersion="9.1.10" newMediaFileId="25" fileSize="121565846" md5Sum="e0beb237501d907145f1c8184f6ddbe5" sha256Sum="00fc8d6ea42b3a4bf967b3c42fb64fc29c44447081250ac3cc36a8b72f4afeb1" bundledJre="linux-amd64-1.8.0_332.tar.gz" archive="false" singleBundle="false">
    <comment language="en" />
  </entry>
  <entry targetMediaFileId="552" updatableVersionMin="" updatableVersionMax="" fileName="IGB-macos-9.1.10.dmg" newVersion="9.1.10" newMediaFileId="552" fileSize="155026667" md5Sum="051c00cf11d20ef8c1e6a3262ed2702e" sha256Sum="384845352806c5bec6116188e6e4ced9ab65fbe737e02fde4c7bd0fd96d1dde7" bundledJre="macos-universal-1.8.0_332.tar.gz" archive="false" singleBundle="false">
    <comment language="en" />
  </entry>
</updateDescriptor>

macOS 12.6 with Intel processor or M1 processor:

• Starting 9.1.8 brought up the update prompt for 9.1.10 which was able to be successfully downloaded and installed.
• Installing 9.1.10 from bioviz.org worked successfully.

Linux Ubuntu 22:

• Starting 9.1.8 brought up the update prompt for 9.1.10, however, the installer appeared oddly and the installation did not advance.
• Installing 9.1.10 from bioviz.org worked successfully.

Windows 10:

• Starting 9.1.8 brought up the update prompt for 9.1.10 which was able to be successfully downloaded and installed.
• Installing 9.1.10 from bioviz.org worked successfully.

Because the update for Linux was not able to advance, should we de-activate the update mechanism for Linux until we can figure out what is going wrong?
We can halt the update process (I think) by editing the updates.xml file.

Potentially. I would like to try to reproduce the issue on another Linux machine. I can test it on my Ubuntu desktop at home early tomorrow.

Please note: I deleted the Linux update entry in the updates.xml file on our server pending investigation as to why Linux 9.1.8 is not able to complete updating to 9.1.10.

cc: Nowlan Freese and Logan Weidenhammer

Please check that now, running IGB 9.1.8 on Linux does not activate the update to 9.1.10 workflow.

attn: Nowlan Freese and Logan Weidenhammer

when starting up IGB 9.1.8 on Linux the updater for 9.1.10 is triggered normally but has difficult to see white-on-white text. This was present on both light-mode and dark-mode. See screenshot.
On this updater window:
When I choose Yes, update > nothing happens.
When I chooser No, don't update > 9.1.8 opens.

When downloading IGB 9.1.10 directly from bioviz.org the installer runs normally.

OK. I will restore the update mechanism tomorrow morning for your testing convenience. thank you!!!

attn: Nowlan Freese

[~aloraine], sorry, I didn't see your comment until after I had posted my comment.
Now, running 9.1.8 does not activate the update to 9.1.10 workflow.

Ran the "release to nexus" pipeline on the release-9.1.10 branch in the team repository, which is configured with the correct credentials to write to our maven repository nexus.bioviz.org.

I checked it and observed that nexus.bioviz.org appears to be properly updated with 9.1.10 artifacts, dated Nov 3 (today).
Example:

• https://nexus.bioviz.org/#browse/browse:maven-releases:org%2Florainelab%2Figb%2Faffymetrix-common%2F9.1.10%2Faffymetrix-common-9.1.10.jar

16.04 lts

• installed 9.1.8 from sourceforge
• ran installer
• started igb from terminal
• asked if i wanted to update
• downloaded updater
• Ran updater immediately (it gives option to run now or later, i ran now)
• Update existing installation
• Install worked correctly
• IGB 9.1.10 installed and running

Updating to 18.04 and will test again

The update process from 9.1.8 to 9.1.10 on Ubuntu 18.04 had no issues.
The update process from 9.1.8 to 9.1.10 on Ubuntu 20.04 had no issues.

Closing ticket.