See commit . Once the user has opted in, the window won't show up again. Please reset the preferences to default to change that.

Thanks Karthik! I am going to try it out using the an installer we build on bitbucket infrastructure and report back.

Adding Karthik's repo as a remote to my local:

git remote add karthik git@bitbucket.org:KarthikRavee91/karthikfork-igb.git

Getting Karthik's branches (all of them, gulp!)

git fetch karthik

Checking out his new branch:

git checkout -b IGBF-4416 --track karthik/IGBF-4416

Commits on IGBF-4416:

e08f83bf16 (HEAD -> IGBF-4416, karthik/IGBF-4416) IGBF-4416 Add Google Analytics opt-in option for users
b46b47c2bb IGBF-4411 Make SAMtags filter case sensitivity
2b34862cbc IGBF-4411 Fix number value comparison issue
ae3f901b4a IGBF-4411 Fix initialization null exception error

Commits on main (team repo):

9b8e7dc660 (HEAD -> main, origin/main, origin/HEAD) Merged in IGBF-4411 (pull request #1108)
2edb6f614b (karthik/IGBF-4411) IGBF-4411 Make SAMtags filter case sensitivity
4266147298 IGBF-4411 Fix number value comparison issue
1b2bd4f35b Merged in IGBF-4411 (pull request #1106)
8eceab1c64 Merged in IGBF-4413 (pull request #1107)
6be4f8214e IGBF-4413: Change quickstart URL to bioviz.org help page

Looks like the new branch is coming from a series of commits that were later squashed and merged into main.

Asking Karthik to add the new IGBF-4416 commit to a new branch from main, not his old IGBF-4413 branch.

emailed KR:

Hi!

I would like to test your new commit (e08f83bf16) to a fresh branch from a completely up-to-date main branch!

Currently, your new branch IGBF-4416 (with it's one commit e08f83bf16) was branched from your old IGBF-4413 branch that has a lot of commits that got squashed later and merged into main.

Please let me know when it's ready!

Ann

Made a new branch on my local from main and cherrypicked the commit from KR onto it. Then tested the build:

Checked out updated main:

git checkout main

Made new branch on my local repo:

git checkout IGBF-4416-AL1

Cherrypicked KR's commit on it:

git cherrypick e08f83bf16

Observed commit history:

aa8f7ddf07 (HEAD -> IGBF-4416-AL1) IGBF-4416 Add Google Analytics opt-in option for users
9b8e7dc660 (origin/main, origin/HEAD, main, karthik/IGBF-4416) Merged in IGBF-4411 (pull request #1108)
2edb6f614b (karthik/IGBF-4411) IGBF-4411 Make SAMtags filter case sensitivity
4266147298 IGBF-4411 Fix number value comparison issue
1b2bd4f35b Merged in IGBF-4411 (pull request #1106)
8eceab1c64 Merged in IGBF-4413 (pull request #1107)
6be4f8214e IGBF-4413: Change quickstart URL to bioviz.org help page

Build code:

mvn clean install

No errors observed.

Ran code with:

I ran the code from the command line inside my clone's top-level directory with:

./run_igb.sh

and observed that a modal dialog appeared with text:

"By continuing to use this software, you consent to this data collection"

This text appears right above to buttons that are labeled:

"Opt out of Analytics" and "I accept."

I clicked the "Opt out of Analytics" option.

Then, IGB started as normal and I was able to use the software.

And yet, the message on the modal dialog says that if I continue to use the software I am consenting to having my usage data collected. But, I chose the "Opt out" option. So I am confused about what is actually happening with the analytics choice I mad.

I then quit IGB and re-ran it.

Again, the same modal dialog appeared.

I was surprised to see it again because I expected that I would not have to re-select the option. Was my selection not getting saved?

Also, I wanted to copy the text from the dialog into this issue, but when I tried to click-and-drag over the text in the dialog in order to copy it, I was unable to do that.

The "About IGB" window shows text and I can copy all the text. It also includes links. Can we use the same interface for the opting out of analytics selection interface? Also, can we save the user's choice somehow, while also giving them an option to change their selection later?

Next, I restarted IGB and chose the option to allow analytics.

I noticed also that startup was extremely slow! I don't know if that is related to the new commit, however. Probably not!

I then used reset my preferences to their default values, as usual, and then re-ran IGB, again using the run_igb.sh script.

Startup was as fast as usual this time, suggesting that whatever slowdown I'd been experiencing was due to some other problem.

It looks like if I chose the "opt out" option, IGB will start as usual. The next time I start IGB (without resetting preferences) then I will see the same dialog again and again have to make a selection.

If I chose "opt in" option, use IGB, quit IGB and then re-launch IGB, the dialog does not appear.

Re-setting preferences to defaults causes the dialog to appear again upon startup even if I have selected the "opt in" option.

I have changed the alert message to make sense for IGB. I have changed the logic as well - once the user makes any choice or closes the alert window it is saved and the alert never shows up unless the user resets the preferences. See commit