search

ucam-department-of-psychiatry / crate

Create and use de-identified research databases. Preprocess, extract text, anonymise/de-identify, link, apply natural language processing, query for research, manage consent for contact.
GNU General Public License v3.0
19 stars 7 forks source link

Gate 861 plugin fix #27

Closed martinburchell closed 4 years ago

martinburchell commented 4 years ago

The ANNIE plugin is no longer bundled with GATE 8.6.1 so we need to load it ourselves from Maven. Also allow any number of GATE plugins to be loaded from Maven via an INI file.

Francesca did the work, I've documented it and fixed a load of other things in the process of rebuilding the documentation.

RudolfCardinal commented 4 years ago

Looks great. Good to merge, I think. Incidentally, I bumped the AMQP/Celery/Kombu trio too as the previous versions were incompatible with Python 3.8 (but still load fine under 3.6). I've added a specimen GATE plugin INI file. However -- although the ANNIE and Lewy body dementia apps run fine, the pharmacotherapy one doesn't: java.lang.NoSuchMethodError: 'gate.jape.parser.ParseCpsl gate.Factory.newJapeParser(java.net.URL, java.lang.String)'. Do you get that too?

martinburchell commented 4 years ago

Looks great. Good to merge, I think. Incidentally, I bumped the AMQP/Celery/Kombu trio too as the previous versions were incompatible with Python 3.8 (but still load fine under 3.6). I've added a specimen GATE plugin INI file. However -- although the ANNIE and Lewy body dementia apps run fine, the pharmacotherapy one doesn't: java.lang.NoSuchMethodError: 'gate.jape.parser.ParseCpsl gate.Factory.newJapeParser(java.net.URL, java.lang.String)'. Do you get that too?

Yes. Just looking into it now

martinburchell commented 4 years ago

I don't get the error if I use this ini file. Not sure if it's working though!

[ANNIE]
name = annie
location = uk.ac.gate.plugins
version = 8.6

[Tools]
name = tools
location = uk.ac.gate.plugins
version = 8.6

[JAPE]
name = jape-plus
location = uk.ac.gate.plugins
version = 8.6
martinburchell commented 4 years ago

Thanks! Good to merge now?