Set up Jenkins job to pull missing content from OWL (Jython) to neo4j

VirtualFlyBrain / VFB_owl

A repository for VFB owl files and the code that generates them

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Set up Jenkins job to pull missing content from OWL (Jython) to neo4j #21

Closed dosumis closed 7 years ago

dosumis commented 8 years ago

Requires latest vfb.owl (earlier versions will fail addition uniqueness constraints necessary for merge statements to work).
Both need python requests. Should be possible to install with pip.
Scripts: VFB_owl/src/code/owl2neo:
- add_refs_for_anat.py neo_server_uri USR PWD path_to_owl_file
- add_anonymous_types.py neo_server_uri USR PWD path_to_owl_file

@Robbie1977 - can you look into setting up dependencies? Once ready, you can assign back to me.

Robbie1977 commented 8 years ago

just run in this virtual env and eveything is installed:

source /disk/data/VFBTools/python-modules-2.6/bin/activate

Assuming you want python 2.6?

dosumis commented 8 years ago

Can this work with Jython? (2.7 better)

dosumis commented 8 years ago

http://seletz.github.io/blog/2012/04/06/jython-classpath-virtualenv/

Robbie1977 commented 8 years ago

not quite that simple unfortunately. What version of Jython are you using?

dosumis commented 8 years ago

2.7.0

Robbie1977 commented 8 years ago

getting it updated as it's currently 2.2 which has issues.

dosumis commented 8 years ago

OK. We've been running it from a JAR up to now. Question is how that could be combined with regular Jython imports. Should be possible to package all into one JAR.

Robbie1977 commented 8 years ago

Have you tried it under the virtual environment? (just use 2.7 instead of 2.6)

On Fri, 26 Feb 2016 at 11:53 David Osumi-Sutherland < notifications@github.com> wrote:

OK. We've been running it from a JAR up to now. Question is how that could be combined with regular Jython imports. Should be possible to package all into one JAR.

— Reply to this email directly or view it on GitHub https://github.com/VirtualFlyBrain/VFB_owl/issues/21#issuecomment-189241509 .

Robbie1977 commented 8 years ago

which jenkins job is it running in?

On Fri, 26 Feb 2016 at 11:57 Robbie Court robbie.court@gmail.com wrote:

Have you tried it under the virtual environment? (just use 2.7 instead of 2.6)

On Fri, 26 Feb 2016 at 11:53 David Osumi-Sutherland < notifications@github.com> wrote:

OK. We've been running it from a JAR up to now. Question is how that could be combined with regular Jython imports. Should be possible to package all into one JAR.

— Reply to this email directly or view it on GitHub https://github.com/VirtualFlyBrain/VFB_owl/issues/21#issuecomment-189241509 .

dosumis commented 8 years ago

The owl conversion uses Jython from jar: https://blanik.inf.ed.ac.uk:8079/view/OWL/job/Build_VFB_ind/ (needs updating #5 )

dosumis commented 8 years ago

In https://github.com/VirtualFlyBrain/VFB_owl/blob/master/src/owl/vfb_ind_release.sh

All Jython scripts are run as:

java -Xmx6000m -cp $CP"*" org.python.util.jython

Robbie1977 commented 8 years ago

working through the errors - resolving the port forwarding first: suspect jenkins isn't authorized for this ATM - ticket in