nicolevasilevsky
commented
2 years ago Thanks so much to the Protege team (@gouttegd @matthewhorridge and all) for this new version, I am very excited!
Some notes from my testing are below:
- Thank you for adding links to external xrefs, this is going to be immensely useful and helpful for our Mondo editors team. I noted that some external IDs in Mondo are linked and some are not (and maybe that is because some are in identifiers.org and some are not, so maybe this is known/expected). OMIM and GARD IDs are not linked. (OMIM uses omim.org and the URL for GARD is: https://rarediseases.info.nih.gov/)
- @gouttegd warned me I may get a huge diff when editing and I do
- in Protege 5.5.0, if I search for an obsolete term in the search and click on it, it shows up in the class hierarchy, but this does not work in 5.6.0 beta-1
- the tab autocomplete in class expression editor does not seem to work
Thanks for adding these cool new features
-
I like how you can chose the language tag when adding a new annotation
-
I like how the imports or sources are displayed on the annotations
Thanks for all your work! This is all I have time to do right now, but I'll try to test more again later.
gouttegd
rays22
matthewhorridge
ghxiao
thistlillo
(Maintainers: this ticket is not actually an issue, but a set of instructions for users willing to test Protégé.)
Background
Protégé is written in the Java programming language. As such, running it requires a Java Runtime Environment (JRE), which comprises (among other things) a Java Virtual Machine (JVM) and a standard Java Class Library (JCL).
Normally, when a version of Protégé is released, we provide specific packages for GNU/Linux, Mac OS, and Windows operating systems. Those packages already include a JRE for the corresponding system, so that they are “standalone” and can be used directly without requiring any further dependencies.
We have not yet produced such OS-specific packages for the current pre-release, though. It’s a somewhat complicated process and we’d like to first make sure that the upcoming release of Protégé is working fine before committing to packaging it for specific systems.
So for now, we only provide a “platform-independent” package. This is a single package that will work across all systems, but that does not include a JRE – the JRE must be provided by the system or installed independently if your system does not already have one.
Do you already have a JRE?
Your system may already have a JRE installed. Check by running
in a terminal. If you get a
java: command not foundmessage (or similar), you do not have a JRE and will need to install one. Go to the next section.If you get a message more or less like the following:
then you have a JRE. Check that the version is 9 or superior (in this example, it’s 17.0.4). The current pre-release of Protégé will not work with Java 8 of inferior.
While we are especially aiming at compatibility with Java 11 and Java 17, any test performed with any version of Java superior or equal to 9 will be valuable. If you have, say, Java 16, you do not have to install Java 11 or Java 17! You can do that if you want, but we’ll be happy if you just test with Java 16. :)
If you only have Java 8 or inferior, then you do need to install a higher version. Note that you don’t have to upgrade your existing Java 8 (and doing so may actually be a bad idea, as you may have applications on your system that specifically require Java 8); instead, several versions of Java can co-exist on the same system, so you can install, say, Java 17 while also keeping Java 8.
Installing a JRE
On GNU/Linux
On Debian-based distributions, you can install the Java 17 JRE with
On Fedora, OpenSuSE, CentOS, and presumably most RPM-based distributions, the package would normally be called
java-17-openjdk. On ArchLinux, it should bejre17-openjdk.(I won’t even try to cover all the distributions. I will blatantly assume that if you don’t use a “typical” distribution, you know what you are doing and you can find your way around your distribution’s package manager – or even compile OpenJDK from source!)
Of course other versions than 17 may be available, feel free to test another version if you’d like.
On Mac OS
Several distributors provide Java environments for Mac OS. Here I will suggest either Adoptium or Azul, but if you know of another feel free to use them. Protégé should work fine independently of where your Java environment comes from (if it does not, it’s either a bug in Protégé or a bug in the Java environment; in any case, it’s something that should not happen).
Visit Adoptium.net. Your system should be automatically detected and the website should propose you to download a suitable package of Java 17 straight from the home page.
In case it does not, or if you’d like to try another version than 17, go the releases page where you’ll be able to find a suitable package yourself: select your system (
mac OS), your architecture (x64if you have a Mac with an Intel processor, oraarch64if you have a Mac with a M1 chip aka “Apple Silicon”),JREas the “package type”, and then finally the version you want. Then download the corresponding.pkgfile.(If you choose to get your JRE from Azul instead, the procedure is similar.)
Double-click on the downloaded package and follow the installer’s instructions. The JRE will be installed somewhere under
/Library/Java/JavaVirtualMachines.On Windows
Unfortunately I can’t provide instructions for Windows. If someone has such instructions, feel free to add them as a comment to this ticket.
In principle, it should be similar to the procedure for Mac OS: get an installer from either Adoptium or Azul (both provide environments for Windows as well, not only Mac OS), start the installer, then follow whatever steps the installer requires.
Testing Protégé
Now that you have a JRE on your system, you can test Protégé. Download the current pre-release’s platform-independent package and put the archive at the location of your choice, then navigate to that location from your terminal.
From there, unzip the archive…
enter the Protégé folder…
and actually start the program with either
on GNU/Linux, or
on Mac OS, or
on Windows.
Protégé should (hopefully!) start, and you can commence your tests. Try to do everything you would normally do with Protégé, and check that you can still do it with that version.
Of note, this version does not come with any plugins. If you need some plugins (e.g. a reasoner), you have to install them manually by creating a
pluginsfolder in Protégé’s directory (the same directory that contains therun.*scripts), then putting the plugins you need in that folder (you may copy them over from your normal Protégé installation).“Advanced stuff“: choosing the JRE to use
If you happen to have more than one JRE on your system, you can choose the one that Protégé will use by setting the variable
JAVA_HOMEprior to calling therun.shorrun.commandscript (not available on Windows, sorry!).That variable should be set to the main folder (the folder containing the
bindirectory) of the JRE that you want to use.For example, if you’re on Mac OS and you have both the Java 16 JRE from Adoptium and the Java 17 JRE from Azul, they should be located, respectively, in
/Library/Java/JavaVirtualMachines/jdk-16.jre/Contents/Homeand/Library/Java/JavaVirtualMachines/zulu-17.jre/Contents/Home. Then if you want to test Protégé with, say, the Java 17 JRE from Azul, you may invoke therun.commandas follows: