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stuckyb / ontopilot

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Possible bug in excluded types functionality #73

Closed jdeck88 closed 7 years ago

jdeck88 commented 7 years ago

The reasoning process using the elk_pipeline + excluded types was working a couple of days and stopped after an update. I've attached a zip file containing files to reproduce the error. The zip file contains an unreasoned file in turtle format, an excluded_types.csv file, a configuration file, and the error messages i receive when running the command.

This command is run like: /somepath/ontopilot/bin/ontopilot inference_pipeline -i /somepath/test_1.csv.ttl -o /somepath/test_1.csv.owl -c /somepath/pre_reasoner.conf

Output of the command is simply NullPointerException and seems to be triggered by line 407 of inferred_axiom_adder.py

jdeck88 commented 7 years ago

OK, more information here, and i think i see the issue, there is a bug in the unreasoned file that we begin with, as it has an unassigned float value (null string)... no wonder a null pointer exception was occurring. Pretty sure this is not a bug with ontopilot but lets leave this open for a bit until i finish testing this... Here is the offending data:

<ppo:?measurementDatum=1> a obo:IAO_0000109 ; obo:PPO_0001000 3 ; obo:PPO_0001001 10 ; obo:PPO_0001003 " "^^xsd:float .

jdeck88 commented 7 years ago

OK, just re-ran process and it all worked as advertised. A slight grumble to the OWL API for cryptic error messaging output , but can't expect ontopilot to intercept and make sense of that!, closing