Find a better workaround for macOS access to OpenJDK

[ctrueden]

When running imagej.init on a macOS system without Apple Java 6 installed, an error is given when attempting to load Java via JNI:

No Java runtime present, requesting install.

And a dialog box appears saying "You need to install the legacy Java SE 6 runtime." Unfortunately, this is no longer possible on current versions of macOS.

A workaround is to edit the Info.plist of your Java installation to include <string>JNI</string> in the capabilities, as described at kivy/pyjnius#277 (comment). However, there is no guidance to do this. And it would be better if we could automagically make things work without requiring the user to perform an administrator-level action.

[ctrueden]

It seems another workaround is to link to libjli instead of libjvm; see e.g. dotnet/java-interop#198. This might be better since it will not require hacking the installed JRE.

[ctrueden]

It turns out that the ImageJ launcher has already used this libjli hack for years; see imagej/imagej-launcher@efaea16. I don't know how I missed this for so long. But pyjnius would need to use it as well; see kivy/pyjnius#277 (comment).

[jamesbraza]

@ctrueden I am hitting this problem on pyimagej==0.4.0. I followed your install instructions, using miniconda --> conda create -n pyimagej pyimagej openjdk=8.

How can I use dotnet/java-interop#198 in the contexts of the pyimagej environment?

Here is some info on my machine:

• OS: macOS Mojave version 10.14.3
• echo $JAVA_HOME --> /usr/local/Caskroom/miniconda/base/envs/pyimagej
• java -version -->

openjdk version "1.8.0_192"
OpenJDK Runtime Environment (Zulu 8.33.0.1-macosx) (build 1.8.0_192-b01)
OpenJDK 64-Bit Server VM (Zulu 8.33.0.1-macosx) (build 25.192-b01, mixed mode)

[ctrueden]

@JDusub83 On the user side, I do not know a way for you to link to libjli instead of libjvm—I think this is a change we'd need to make upstream in pyjnius.

The way I currently work around this issue is:

brew cask install adoptopenjdk8
sudo sed -i '' -e 's/\(<string>CommandLine<\/string>\)/\1<string>JNI<\/string>/' /Library/Java/JavaVirtualMachines/adoptopenjdk-8.jdk/Contents/Info.plist

In other words: install a system-wide JVM and then add <string>JNI</string> to the JVMCapabilities section of its Info.plist.

Note that this works equally well with adoptopenjdk cask with adoptopenjdk-12.jdk folder—it doesn't matter which Java you hack in that fashion; it won't actually be used by pyimagej. It's just a hack to make Apple's overzealous linkage check happy.

I am sorry this is still necessary. ☹️

[ctrueden]

I quickly checked how hard it would be to fix on the pyjnius side, and it turns out it was extremely simple, so I filed a PR: kivy/pyjnius#441. Hopefully they will merge it soon.

[jamesbraza]

Thank you @ctrueden for getting back quickly and also for opening up a PR for a long-term fix!

A few notes

---

brew cask install adoptopenjdk8

Per this article, I also had to brew tap AdoptOpenJDK/openjdk first.

---

sudo sed -i '' -e 's/(CommandLine</string>) ...

I previously had jdk "12.0.1" 2019-04-16. I ran this command (I just modified directory path):

sudo sed -i '' -e 's/\(<string>CommandLine<\/string>\)/\1<string>JNI<\/string>/' /Library/Java/JavaVirtualMachines/jdk-12.0.1.jdk/Contents/Info.plist

And found it did this:

        <dict>
                <key>JVMCapabilities</key>
                <array>
                        <string>CommandLine</string><string>JNI</string>
                </array>

Not sure that it matters that the </string><string>JNI</string> is not on a new line, you may want to add that to the sed command.

Regardless, I tested it out (without the new line), and found that the change worked anyways.

---

So anyways, thank you for suggesting the temporary fix! Feel free to post again when the PR goes through, and I can test it out.

[jamesbraza]

@ctrueden I tried to make the sed command better. Full disclosure, I don't really know sed.
Using this answer, and manually adding in exact amount of whitespace, I got close:

sudo sed -i '' -e 's/\(<string>CommandLine<\/string>\)/\1\'$'\n''                        <string>JNI<\/string>/' /Library/Java/JavaVirtualMachines/jdk-12.0.1.jdk/Contents/Info.plist

There is probably a better way to do the newline and maintain whitespace, but I couldn't figure it out. Perhaps you would know a better way to do this.

[ctrueden]

I also had to brew tap AdoptOpenJDK/openjdk first.

Right, thanks for pointing that out.

There is probably a better way to do the newline and maintain whitespace, but I couldn't figure it out. Perhaps you would know a better way to do this.

Inserting lines with BSD sed is annoying, which is why I didn't bother. The Info.plist is XML, so the whitespace doesn't matter.

Regardless, I tested it out (without the new line), and found that the change worked anyways.

Glad to hear! 😄

[ctrueden]

I filed a PR to pyjnius that was merged: kivy/pyjnius#441

Once a new pyjnius is released, this issue will go away! 🎉