Add oaklib

[gouttegd]

This PR adds the Ontology Access Kit to the odkfull image.

This brings in a whole new set of dependencies:

• Obographviz, needed by the runoak viz command;
• Node.js, needed to execute obographviz as it is a Javascript library and script;
• NPM, needed to install obographviz and its Javascript dependencies;
• Graphviz, which provides the dot command needed by obographviz.

closes #584

[matentzn]

This is very very amazing.. Thanks for doing this! Let's wait for @cmungall to review

[cmungall]

I just moved ogv from my org to this org - does this affect the PR?

[gouttegd]

I just moved ogv from my org to this org - does this affect the PR?

We install Obographviz through NPM. I'm not very familiar with the Node/NPM ecosystem but I think as long as the name of the published package doesn't change, the organisation to which the source repository belongs to shouldn't matter.

[kltm]

I created a docker image in this branch as:

docker build .

and entered as

docker run --network host -it 079d3e44c526 /bin/bash

Inside the image, the lib oaklib and the runoak command do not seem exposed:

root@moiraine:/tools# runoak
bash: runoak: command not found

In [1]: import oaklib
---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-1-a904ee677e33> in <module>
----> 1 import oaklib

ModuleNotFoundError: No module named 'oaklib'

Is there something wrong with this test/invocation?

[gouttegd]

I created a docker image in this branch as:

docker build .

That’s not how the ODK should be built. By trying to build it by calling docker build directly, you’re skipping the step of building the intermediate odkbuild image, which among other things assembles all the Python packages (including, in this branch, oaklib).

Build the ODK by running

make build

in the top-level directory.

[kltm]

@gouttegd Ah, cheers--I was looking in the main README, not the dev one.
Retrying my testing, it all looks good to me now.

[gouttegd]

Thanks for the testing @kltm! Merging now, oaklib will be part of the next release.