Protégé problems with modules

[l-emele]

Description of the issue

In PRs #470 and #453 some weird behaviour of Protégé occurred, see commits 7b9249f and 585327b. It changes the prefix, deletes relation imports and adds URLs.

Ideas of solution

If you already have ideas for the solution describe them here

Workflow checklist

• I am aware of the workflow for this repository

[akleinau]

for all I see protégé just changes the standard prefix which means all entities using that get explixit IRIs instead of the implicit ones using the standard prefix. Anything else that you experienced?

[l-emele]

Might opening the wrong module in protégé cause that problem?

[akleinau]

you're opening oeo-physical, right?
I think protégé just somewhere saved the wrong thing.
If you do changes, does this prefix change always happen? Can you reproduce it?

[l-emele]

The strange thing is that this prefix change does not always happen but only sometimes. And as it occurs only sometimes I was not able so far to force it to happen.

My usual procedure is to open oeo.omn first and then switch in Protégé via the drop-down menu to the module I want to work with (in 99% of the cases oeo-physical.omn).

[akleinau]

one idea would be to try to open directly from file browser instead of through the dropdown, but without a way to reproduce it this is just guessing. This really shoudln't cause problems, it would be a bug of protégé if this helps.

[l-emele]

As Protégé needs about half an hour to start at my computer I basically have Protégé all the times open and the files from Protégé. So opening the file from the file browser is no option. The reason for the long start time is an annoying antivirus program which does always in depth search in java files (and due to company administration I am not able to change this).

[akleinau]

then maybe doing that fix I wrote in #470 is for now the easiest option

[l-emele]

Today I had this problem again. I think this problem has something to do with creating or changing branches while protégé is open.

[l-emele]

I am now sure that this problem is caused by changing between branches while protégé is open. So probably I have to close protégé, then change the branch and finally reopen protégé again.

[l-emele]

The trick from #471 does not work anymore. :(

[akleinau]

Can/ have you published your current state somewhere? Then I‘ll have a look on it

[l-emele]

Thanks for your offer. For the moment I fixed it - somehow, see #523.

As far as I can tell it has something to do with the order in which I open files in Protégé. I suspect Protégé some gets my sometimes confused what belongs to what and thus makes these weird changes.

[l-emele]

An update: Protégé seems to work without troubles if I use the following work flow:

1. Reboot Windows.
2. Switch via git branch to the branch I want to work on.
3. Launch Protégé without being connect to our VPN (else Protégé cannot import external modules).
4. Open oeo.omn in Protégé.
5. Select the module to work with.

I am still not clear what causes the problem, but actions that might be involved in causing this problem:

• Being connected to the our VPN.
• Switching branches while Protégé is running.
• Opening a module file directly.

[l-emele]

For documentation: I installed version 5.5.0 (stable) now because of #620. Let's see whether this brings some improvements here, too.

[stap-m]

Can we close this issue? Maybe the described workflow finds a place in the Q&A Discussion page?!

[l-emele]

I close this issue now. Since I got version 5.5.0 (stable) and a new antivirus program the problem has never occurred again. As the problem seemed to be very specific to my computer I don't think we need to document this anywhere. So I close the issue.