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From "Dligach, Dmitriy" <ddlig...@luc.edu>
Subject file not found error
Date Mon, 11 Apr 2016 14:12:59 GMT
I installed a fresh copy of cTAKES and tried to run org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory
(see below). It completed, but in the process I got a lot of FileNotFoundException(s) that
all referred to a few subdirectories in ctakes-clinical-pipeline/. Did I need to install these
files separately?

Thanks,

Dima

------------------

Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/misc/stopWords.data
(No such file or directory)
** Error: problem of opening/reading stop words file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/misc/stopWords.data'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/misc/nonInfoWords.data
(No such file or directory)
** Error: problem of opening/reading non-Info words file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/misc/nonInfoWords.data'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/misc/conjunctionWord.data
(No such file or directory)
** Error: problem of opening/reading conjunction words file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/misc/conjunctionWord.data'.
** ERR: problem of opening/reading diacritics file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/diacriticMap.data'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/diacriticMap.data
(No such file or directory)
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/ligatureMap.data
(No such file or directory)
** Error: problem of opening/reading ligature file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/ligatureMap.data'.
** Error: problem of opening/reading symbol synonym file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/synonymMap.data'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/synonymMap.data
(No such file or directory)
**Error: problem of opening/reading file '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/misc/removeS.data'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/misc/removeS.data
(No such file or directory)
** Error: problem of opening/reading Unicode symbol file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/symbolMap.data'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/symbolMap.data
(No such file or directory)
** Error: problem of opening/reading Unicode file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/unicodeMap.data'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/unicodeMap.data
(No such file or directory)
** Error: problem of opening/reading nonStripMap file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/nonStripMap.data'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/nonStripMap.data
(No such file or directory)
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/rules/im.rul
(No such file or directory)
**Error: problem of opening/reading file '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline//data/rules/im.rul'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/rules/im.rul
(No such file or directory)
**Error: problem of opening/reading file '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline//data/rules/im.rul'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/rules/dm.rul
(No such file or directory)
**Error: problem of opening/reading file '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline//data/rules/dm.rul'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/rules/dm.rul
(No such file or directory)
**Error: problem of opening/reading file '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline//data/rules/dm.rul'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/misc/stopWords.data
(No such file or directory)
** Error: problem of opening/reading stop words file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/misc/stopWords.data'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/misc/nonInfoWords.data
(No such file or directory)
** Error: problem of opening/reading non-Info words file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/misc/nonInfoWords.data'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/misc/conjunctionWord.data
(No such file or directory)
** Error: problem of opening/reading conjunction words file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/misc/conjunctionWord.data'.
** ERR: problem of opening/reading diacritics file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/diacriticMap.data'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/diacriticMap.data
(No such file or directory)
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/ligatureMap.data
(No such file or directory)
** Error: problem of opening/reading ligature file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/ligatureMap.data'.
** Error: problem of opening/reading symbol synonym file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/synonymMap.data'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/synonymMap.data
(No such file or directory)
**Error: problem of opening/reading file '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/misc/removeS.data'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/misc/removeS.data
(No such file or directory)
** Error: problem of opening/reading Unicode symbol file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/symbolMap.data'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/symbolMap.data
(No such file or directory)
** Error: problem of opening/reading Unicode file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/unicodeMap.data'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/unicodeMap.data
(No such file or directory)
** Error: problem of opening/reading nonStripMap file: '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/nonStripMap.data'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/Unicode/nonStripMap.data
(No such file or directory)
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/rules/im.rul
(No such file or directory)
**Error: problem of opening/reading file '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline//data/rules/im.rul'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/rules/im.rul
(No such file or directory)
**Error: problem of opening/reading file '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline//data/rules/im.rul'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/rules/dm.rul
(No such file or directory)
**Error: problem of opening/reading file '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline//data/rules/dm.rul'.
Exception: java.io.FileNotFoundException: /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline/data/rules/dm.rul
(No such file or directory)
**Error: problem of opening/reading file '/Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline//data/rules/dm.rul'.
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