Absolute Smiles JNI-inchi fix

[dkatzel-ncats]

This is the fix for #797 as well as adding the fix for 2.7.1 to the 2.8 branch.

This is as small a change as possible. Alternative approaches are to make the inchi options and return value Strings instead of enums so there wouldn't be a dependency for either JNA or JNI inchi. but there would then be a lot more String parsing into those enums every time which would might lead to performance problems.

Another approach would be to make a CDK inchi interface that wraps the underlying JNI/JNA implementation but that would be more code changes and API breaking changes.

[egonw]

I think the idea is to fix this instead by (runtime?) depending on the new cdk-jniinchi-support module, @johnmay?

[dkatzel-ncats]

yeah I wasn't sure if the idea going forward was to assume JNA-inchi and have additional support for jni so things should default to jna or if you wanted to make it more flexible based on which modules are loaded?

[egonw]

@dkatzel-ncats, can you try the current master (so, without this patch), but add this to your pom.xml:

    <dependency>
      <groupId>org.openscience.cdk</groupId>
      <artifactId>cdk-jniinchi-support</artifactId>
      <version>2.7.1</version>
    </dependency>

Does that solve it?

[dkatzel-ncats]

That would fix the compiler error but my downstream software can't use JNI inchi we must use JNA

[egonw]

No, I think this cdk-jniinchi-support module just provides the two classes, but not actually use the JNI version... checking!

[egonw]

@dkatzel-ncats, check https://github.com/cdk/cdk/tree/master/storage/jniinchi-support/src/main/java/net/sf/jniinchi and if you like that module's pom file too... I think it's really just these two classes.

[johnmay]

Yep include the jniinchi-support-module for now, not doing another release sorry am swamped ATM.

[johnmay]

I'll fix on master though, it's just a mater of not using the INCHI_OPTION etc

[johnmay]

To clarify as Egon said it's jus the Enum's not the actual JNI stuff. It's basically to provide backwards compatible API support, everything still uses JNA inchi.

[dkatzel-ncats]

I can confirm using 2.7.1 with jniinchi-support to my software that uses cdk does make everything work using 2.7.1 thanks!

[johnmay]

Fix on master once pulled, sorry about that - experimenting with optional dependencies and so they are a little magical such that even the tests didn't pick this up. Please let us know if you find other issues.