SHACL testing

[gaurav]

Provides a Java class that interfaces with TopBraid's SHACL library to validate an RDF/XML file against a file containing SHACL space. Also includes a Python script that can be called by py.test to run validations correctly and to report the result.

This is pretty complicated, so it might be easier to consider two other options:

• 1. Use Docker to create a self-contained installation that contains Apache Jena and the SHACL library. We would still be dependent on Python 2.7 and Java 1.8 (neither Jena nor SHACL will work with Java 1.7) -- unless we could package those too?
• 2. We don't actually do much with Python in here; all we use is rdflib. If we port our code to Java or Scala and use Apache Jena instead, we would end up with a single code base that doesn't depend on Python at all. This would probably make testing and deployment much simpler.

[hlapp]

Minor comment re: the SHACL runner, normally programs shouldn't output to stderr in case of success unless asked to (such as through --verbose or some such). But addressing that can be left to later - it doesn't change the test behavior at all.

[hlapp]

Are you sure that's needed? Is that because of switching to language: java? I thought they had rid themselves of having to specify that. It used to be necessary for Docker-utilizing builds, which this one isn't.

[gaurav]

Unfortunately, it looks like it is: without sudo: required, TravisCI uses the container-based virtualization environments (https://docs.travis-ci.com/user/ci-environment/), which for some reason won't allow pip install --users to work correctly: check out line 375 at https://travis-ci.org/gaurav/phylo2owl/builds/169361177#L375, where it appears to correctly install setuptools>=18.5, but then reports Successfully installed setuptools-12.0.5!

I might be able to download Jena to /tmp and use it from there, instead of sudo-ing a folder in /opt for it. Would that help? I don't think it makes a difference if we need to sudo for pip install anyway.

[hlapp]

Hmm. It used to work as recently as #22: https://travis-ci.org/phyloref/phylo2owl/jobs/147828629

I suppose what makes the difference is switching from language: python to language java. That switch causes pip install to fail without either --user using sudo? (I would not specify the version for setuptools. I vaguely recall that I ran into problems with that and then simply left it at whatever defaulted to the latest version.)

How about the alternative of leaving language: python and then installing Java on the fly? Does that not work because of the license restrictions on Java, which means you can't just download and install it (even if under a custom location and then setting JAVA_HOME)?

[gaurav]

The idea with sending the output to stderr was to ensure that stdout was always well-formed Turtle: I didn't want any error messages getting in there!

[hlapp]

The idea with sending the output to stderr was to ensure that stdout was always well-formed Turtle: I didn't want any error messages getting in there!

Right, but announcing success isn't an error message 😄

[gaurav]

@hlapp: I got rid of the STDERR stuff and the sudo, and I managed to set up Maven so that it creates a JAR file containing all the prerequisites it needs. I still need to build testShacl.jar locally, rather than on Travis, but I've filed that issue for another day: #14

[hlapp]

Great, nice work, @gaurav! There's a lot of commits here now of all the trials and errors. I can just squash the whole PR into a single commit ("squash and merge"), or if you want to retain specific commits, you can do an interactive rebase squashing what can be squashed and keeping commits as individual ones as you would like.

Let me know. By default I would squash into a single commit and merge.

[gaurav]

Yup, let's squash and merge it. The largest changes are the source files needed by the SHACL library; the others are mostly small files, and each file should be pretty straightforward to understand.