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'.
