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renaud / neuroNER

named entity recognizer for neuronal cells, based on UIMA Ruta rules
GNU Lesser General Public License v3.0
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updates to obo resource files breaks sherlok parsing #58

Open stripathy opened 8 years ago

stripathy commented 8 years ago

@renaud the commits that you and @tgbugs have made to the .obo resource files have broken the sherlok pipelines so that the simple process of reimporting the most up-to-date resource files from the github repo using the "clean" method no longer works.

Moving forward we'll need to have some way of ensuring that the changes to the .obo files doesn't break the sherlok infrastructure.

tgbugs commented 8 years ago

@stripathy pretty much everything I did was cosmetic (so that it would work in my parser), if the issue happens on the obo files that are generated from robo files then there's not issue deleting them. If the issue happens on the obo files that are not generated from robo files let me know and I can take a look.

renaud commented 8 years ago 
Caused by: java.lang.NullPointerException: null
    at org.apache.uima.ruta.action.MarkTableAction.execute(MarkTableAction.java:111) ~[ruta-core-2.3.1.jar:2.3.1]
    at org.apache.uima.ruta.rule.AbstractRuleElement.apply(AbstractRuleElement.java:132) ~[ruta-core-2.3.1.jar:2.3.1]