Hi,
I've followed the instructions found in this mailing list to set up and run the
dictionary tool. I made a quick summary of what I found:
Change the configuration at /data/default/CtakesSources.txt to include ICD10 or
other extensions; there can be zero or more sources.
Copy ctakesumls.properties and ctakesumls.script from resource/memdbtemplate to
a new folder to put the new UMLS DB
Run DictionaryCreator2
java -cp dictionarytool.jar;lib/*
org.apache.ctakes.dictionarytool.DictionaryCreator2
-umls "/2015AB/META"
-atui ./data/tiny/CtakesAnatTuis.txt
-tui ./data/tiny/CtakesSnomedTuis.txt
-src ./data/tiny/CtakesSources.txt
-fd ./data/tiny
-db jdbc:hsqldb:file:pathTonewDB/snorx2015
-tbl CUI_TERMS
Run CodeMapCreator
java -cp dictionarytool.jar;lib/*
org.apache.ctakes.dictionarytool.CodeMapCreator
-umls "/2015AB/META"
-atui ./data/tiny/CtakesAnatTuis.txt
-db jdbc:hsqldb:file:pathTonewDB/snorx2015
-fd ./data/tiny
-tbl CUI_TERMS
Copy new DB files to new location and create a copy of cTakesHsql.xml and
update dictionary location
I'm failing at step 3 when running the DictionaryCreator2 with the output:
lib/hsqldb.jar: warning: cannot start debugger; debugging mode disabled
lib/hsqldb.jar: line 1: $'PK\003\004': command not found
lib/hsqldb.jar: line 2: META-INF/��PK: No such file or directory
lib/hsqldb.jar: line 3: syntax error near unexpected token `('
lib/hsqldb.jar: line 3:
�p�<�_��xMETA-INF/MANIFEST.MFm�Ok!����c{��f�o�m�{(.���\5������uf���5ڙR���N�8F+w����@�V�%m"�
=]�/�U���{�D��Hc���9eٹ�=b�tf0�Υ��&[��U��m��g&���w�������@�p��%�)`����kQe�z{'�w���ͩ�H+.�/f՜�Z��]���Q���S���/vHG��ٔ�e�h[�-F}PK'
The path should be correctly pointing to the UMLS folder. I'm running Mac OS
Sierra.
Any help is greatly appreciated.
Leander
