Skip to content

Shell Scripts

Jump to bottom
Sean Finan edited this page Jun 6, 2024 · 4 revisions

Shell Scripts included in the bin/ directory of a cTAKES installation.
These scripts can only be run in a cTAKES installation.
They cannot be used within a source code project.

getUmlsDictionary.bat

Windows shell script 
@ECHO OFF
::
::
::
::   Starts a simple gui to fetch the cTAKES umls (snomed, rxnorm) dictionary.
::::
:: Requires JAVA JDK 1.8+
::

@REM Guess CTAKES_HOME if not defined
set CURRENT_DIR=%cd%
if not "%CTAKES_HOME%" == "" goto gotHome
set CTAKES_HOME=%CURRENT_DIR%
if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome
cd ..
set CTAKES_HOME=%cd%

:gotHome
if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome
echo The CTAKES_HOME environment variable is not defined correctly
echo This environment variable is needed to run this program
goto end

:okHome
@set PATH=%PATH%;%CTAKES_HOME%\lib\auth\x64
@REM use JAVA_HOME if set
if exist "%JAVA_HOME%\bin\java.exe" set PATH=%JAVA_HOME%\bin;%PATH%

cd %CTAKES_HOME%
set CLASS_PATH=%CTAKES_HOME%\desc\;%CTAKES_HOME%\resources\;%CTAKES_HOME%\lib\*
set LOG4J_PARM=-Dlog4j.configuration="file:\%CTAKES_HOME%\config\log4j.xml"
set DICT_DOWNLOADER=org.apache.ctakes.gui.dictionary.DictionaryDownloader
java -cp "%CLASS_PATH%" %LOG4J_PARM% -Xms512M -Xmx3g %DICT_DOWNLOADER% %*
cd %CURRENT_DIR%

:end

getUmlsDictionary.sh

Linux / Mac shell script 
#!/bin/sh
#
#
#
#   Runs the pipeline in a piper file.
#
# Requires JAVA JDK 1.8+
#

PRG="$0"
while [ -h "$PRG" ]; do
  ls=`ls -ld "$PRG"`
  link=`expr "$ls" : '.*-> \(.*\)$'`
  if expr "$link" : '/.*' > /dev/null; then
    PRG="$link"
  else
    PRG=`dirname "$PRG"`/"$link"
  fi
done
PRGDIR=`dirname "$PRG"`

# Only set CTAKES_HOME if not already set
[ -z "$CTAKES_HOME" ] && CTAKES_HOME=`cd "$PRGDIR/.." >/dev/null; pwd`

cd $CTAKES_HOME
java -cp $CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g org.apache.ctakes.gui.dictionary.DictionaryDownloader "$@"

runClinicalPipeline.bat

Windows shell script 
@ECHO OFF
::
::
::
::   Runs the default clinical pipeline on files in the input directory specified by -i {directory}
::   Writes .xmi files to the output directory specified by --xmiOut {directory}
::   Uses UMLS credentials specified by --user {username} --pass {password}
::   Can also use a custom dictionary with -l {dictionaryConfigFile}
::
::
:: Requires JAVA JDK 1.8+
::

@REM Guess CTAKES_HOME if not defined
set CURRENT_DIR=%cd%
if not "%CTAKES_HOME%" == "" goto gotHome
set CTAKES_HOME=%CURRENT_DIR%
if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome
cd ..
set CTAKES_HOME=%cd%

:gotHome
if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome
echo The CTAKES_HOME environment variable is not defined correctly
echo This environment variable is needed to run this program
goto end

:okHome
@set PATH=%PATH%;%CTAKES_HOME%\lib\auth\x64
@REM use JAVA_HOME if set
if exist "%JAVA_HOME%\bin\java.exe" set PATH=%JAVA_HOME%\bin;%PATH%

cd %CTAKES_HOME%
set CLASS_PATH=%CTAKES_HOME%\desc\;%CTAKES_HOME%\resources\;%CTAKES_HOME%\lib\*
set LOG4J_PARM=-Dlog4j.configuration="file:\%CTAKES_HOME%\config\log4j.xml"
set PIPE_RUNNER=org.apache.ctakes.core.pipeline.PiperFileRunner
set FAST_PIPER=resources\org\apache\ctakes\clinical\pipeline\DefaultFastPipeline.piper
java -cp "%CLASS_PATH%" %LOG4J_PARM% -Xms512M -Xmx3g %PIPE_RUNNER% -p %FAST_PIPER% %*
cd %CURRENT_DIR%

:end

runClinicalPipeline.sh

Linux / Mac shell script 
#!/bin/sh
#
#
#
#   Runs the default clinical pipeline on files in the input directory specified by -i {directory}
#   Writes .xmi files to the output directory specified by --xmiOut {directory}
#   Uses UMLS credentials specified by --user {username} --pass {password}
#   Can also use a custom dictionary with -l {dictionaryConfigFile}
#
#
# Requires JAVA JDK 1.8+
#

PRG="$0"
while [ -h "$PRG" ]; do
  ls=`ls -ld "$PRG"`
  link=`expr "$ls" : '.*-> \(.*\)$'`
  if expr "$link" : '/.*' > /dev/null; then
    PRG="$link"
  else
    PRG=`dirname "$PRG"`/"$link"
  fi
done
PRGDIR=`dirname "$PRG"`

# Only set CTAKES_HOME if not already set
[ -z "$CTAKES_HOME" ] && CTAKES_HOME=`cd "$PRGDIR/.." >/dev/null; pwd`

cd $CTAKES_HOME
java -cp $CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g org.apache.ctakes.core.pipeline.PiperFileRunner -p org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper "$@"

runDictionaryCreator.bat

Windows shell script 
@REM
@REM

@REM If you plan to use the UMLS Resources, set/export env variables
@REM  set ctakes.umlsuser=[username]
@REM  set ctakes.umlspw=[password]
@REM For example:
@REM   set ctakes.umlsuser=myusername
@REM   set ctakes.umlspw=mypassword
@REM or add the properties
@REM   -Dctakes.umlsuser=[username] -Dctakes.umlspw=[password]
@REM for example:  
@REM   -Dctakes.umlsuser=myusername -Dctakes.umlspw="mypassw@rd"

@REM Guess CTAKES_HOME if not defined
set CURRENT_DIR=%cd%
if not "%CTAKES_HOME%" == "" goto gotHome
set CTAKES_HOME=%CURRENT_DIR%
if exist "%CTAKES_HOME%\bin\runDictionaryCreator.bat" goto okHome
cd ..
set CTAKES_HOME=%cd%

:gotHome
if exist "%CTAKES_HOME%\bin\runDictionaryCreator.bat" goto okHome
echo The CTAKES_HOME environment variable is not defined correctly
echo This environment variable is needed to run this program
goto end

:okHome
@REM use JAVA_HOME if set
if exist "%JAVA_HOME%\bin\java.exe" set PATH=%JAVA_HOME%\bin;%PATH%
@set PATH=%PATH%;%CTAKES_HOME%\lib\auth\x64

cd %CTAKES_HOME%

java  -cp "%CTAKES_HOME%\desc\;%CTAKES_HOME%\resources\;%CTAKES_HOME%\lib\*"  -Dlog4j.configuration="file:\%CTAKES_HOME%\config\log4j.xml"  -Xms512M -Xmx3g  org.apache.ctakes.gui.dictionary.DictionaryCreator
  
cd %CURRENT_DIR%
:end

runDictionaryCreator.sh

Linux / Mac shell script 
#
#

# If you plan to use the UMLS Resources, set/export env variables
#  set ctakes.umlsuser=[username]
#  set ctakes.umlspw=[password]
# For example:
#   set ctakes.umlsuser=myusername
#   set ctakes.umlspw=mypassword
# or add the properties
#   -Dctakes.umlsuser=[username] -Dctakes.umlspw=[password]
# for example:  
#   -Dctakes.umlsuser=myusername -Dctakes.umlspw="mypassw@rd"

PRG="$0"
while [ -h "$PRG" ]; do
  ls=`ls -ld "$PRG"`
  link=`expr "$ls" : '.*-> \(.*\)$'`
  if expr "$link" : '/.*' > /dev/null; then
    PRG="$link"
  else
    PRG=`dirname "$PRG"`/"$link"
  fi
done
PRGDIR=`dirname "$PRG"`

# Only set CTAKES_HOME if not already set
[ -z "$CTAKES_HOME" ] && CTAKES_HOME=`cd "$PRGDIR/.." >/dev/null; pwd`

cd $CTAKES_HOME
java -cp $CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g org.apache.ctakes.gui.dictionary.DictionaryCreator

runPiperCreator.bat

Windows shell script 
@REM
@REM

@REM If you plan to use the UMLS Resources, set/export env variables
@REM  set ctakes.umlsuser=[username]
@REM  set ctakes.umlspw=[password]
@REM For example:
@REM   set ctakes.umlsuser=myusername
@REM   set ctakes.umlspw=mypassword
@REM or add the properties
@REM   -Dctakes.umlsuser=[username] -Dctakes.umlspw=[password]
@REM for example:  
@REM   -Dctakes.umlsuser=myusername -Dctakes.umlspw="mypassw@rd"

@REM Guess CTAKES_HOME if not defined
set CURRENT_DIR=%cd%
if not "%CTAKES_HOME%" == "" goto gotHome
set CTAKES_HOME=%CURRENT_DIR%
if exist "%CTAKES_HOME%\bin\runPiperCreator.bat" goto okHome
cd ..
set CTAKES_HOME=%cd%


set ALL_IMPL=""
@REM Uncomment the following to add unofficial Piper elements to the list
@REM set ALL_IMPL="-Dctakes.gui.all-impls=XX"

:gotHome
if exist "%CTAKES_HOME%\bin\runPiperCreator.bat" goto okHome
echo The CTAKES_HOME environment variable is not defined correctly
echo This environment variable is needed to run this program
goto end

:okHome
@REM use JAVA_HOME if set
if exist "%JAVA_HOME%\bin\java.exe" set PATH=%JAVA_HOME%\bin;%PATH%
@set PATH=%PATH%;%CTAKES_HOME%\lib\auth\x64

cd %CTAKES_HOME%

java  -cp "%CTAKES_HOME%\desc\;%CTAKES_HOME%\resources\;%CTAKES_HOME%\lib\*"  -Dlog4j.configuration="file:\%CTAKES_HOME%\config\log4j.xml"  %ALL_IMPL% -Xms512M -Xmx3g  org.apache.ctakes.gui.pipeline.PiperCreator
  
cd %CURRENT_DIR%
:end

runPiperCreator.sh

Linux / Mac shell script 
#
#

# If you plan to use the UMLS Resources, set/export env variables
#  set ctakes.umlsuser=[username]
#  set ctakes.umlspw=[password]
# For example:
#   set ctakes.umlsuser=myusername
#   set ctakes.umlspw=mypassword
# or add the properties
#   -Dctakes.umlsuser=[username] -Dctakes.umlspw=[password]
# for example:  
#   -Dctakes.umlsuser=myusername -Dctakes.umlspw="mypassw@rd"

PRG="$0"
while [ -h "$PRG" ]; do
  ls=`ls -ld "$PRG"`
  link=`expr "$ls" : '.*-> \(.*\)$'`
  if expr "$link" : '/.*' > /dev/null; then
    PRG="$link"
  else
    PRG=`dirname "$PRG"`/"$link"
  fi
done
PRGDIR=`dirname "$PRG"`

ALL_IMPL=""
if [ "$1" = "-a" ]; then
  ALL_IMPL="-Dctakes.gui.all-impls=XX"
elif [ "$1" = "-h" ]; then
  echo "Adding -h will also add unofficial components"
  exit
fi

# Only set CTAKES_HOME if not already set
[ -z "$CTAKES_HOME" ] && CTAKES_HOME=`cd "$PRGDIR/.." >/dev/null; pwd`

cd $CTAKES_HOME
java -cp $CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* $ALL_IMPL -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g org.apache.ctakes.gui.pipeline.PiperCreator

runPiperFile.bat

Windows shell script 
@ECHO OFF
::
::
::
::   Runs the pipeline in the piper file specified by -p {piperfile}
::   with any other provided parameters.  Standard parameters are:
::   -i , --inputDir {inputDirectory}
::   -o , --outputDir {outputDirectory}
::   -s , --subDir {subDirectory}  (for i/o)
::   --xmiOut {xmiOutputDirectory} (if different from -o)
::   -l , --lookupXml {dictionaryConfigFile} (fast only)
::   --key {umlsKey}
::   -? , --help
::
::   Other parameters may be declared in the piper file using the cli command:
::     cli {parameterName}={singleCharacter}
::   For instance, for declaration of ParagraphAnnotator path to regex file optional parameter PARAGRAPH_TYPES_PATH,
::   in the custom piper file add the line:
::     cli PARAGRAPH_TYPES_PATH=t
::   and when executing this script use:
::      runPiperFile -p path/to/my/custom.piper -t path/to/my/custom.bsv  ...
::
:: Requires JAVA JDK 1.8+
::

@REM Guess CTAKES_HOME if not defined
set CURRENT_DIR=%cd%
if not "%CTAKES_HOME%" == "" goto gotHome
set CTAKES_HOME=%CURRENT_DIR%
if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome
cd ..
set CTAKES_HOME=%cd%

:gotHome
if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome
echo The CTAKES_HOME environment variable is not defined correctly
echo This environment variable is needed to run this program
goto end

:okHome
@set PATH=%PATH%;%CTAKES_HOME%\lib\auth\x64
@REM use JAVA_HOME if set
if exist "%JAVA_HOME%\bin\java.exe" set PATH=%JAVA_HOME%\bin;%PATH%

cd %CTAKES_HOME%
set CLASS_PATH=%CTAKES_HOME%\desc\;%CTAKES_HOME%\resources\;%CTAKES_HOME%\lib\*
set LOG4J_PARM=-Dlog4j.configuration="file:\%CTAKES_HOME%\config\log4j.xml"
set PIPE_RUNNER=org.apache.ctakes.core.pipeline.PiperFileRunner
java -cp "%CLASS_PATH%" %LOG4J_PARM% -Xms512M -Xmx3g %PIPE_RUNNER% %*
cd %CURRENT_DIR%

:end

runPiperFile.sh

Linux / Mac shell script 
#!/bin/sh
#
#
#
#   Runs the pipeline in the piper file specified by -p (piperfile)
#   with any other provided parameters.  Standard parameters are:
#     -i , --inputDir {inputDirectory}
#     -o , --outputDir {outputDirectory}
#     -s , --subDir {subDirectory}  (for i/o)
#     --xmiOut {xmiOutputDirectory} (if different from -o)
#     -l , --lookupXml {dictionaryConfigFile} (fast only)
#     --key {umlsKey}
#     -? , --help
#
#   Other parameters may be declared in the piper file using the cli command:
#     cli {parameterName}={singleCharacter}
#   For instance, for declaration of ParagraphAnnotator path to regex file optional parameter PARAGRAPH_TYPES_PATH,
#   in the custom piper file add the line:
#     cli PARAGRAPH_TYPES_PATH=t
#   and when executing this script use:
#      runPiperFile -p path/to/my/custom.piper -t path/to/my/custom.bsv  ...
#
# Requires JAVA JDK 1.8+
#

PRG="$0"
while [ -h "$PRG" ]; do
  ls=`ls -ld "$PRG"`
  link=`expr "$ls" : '.*-> \(.*\)$'`
  if expr "$link" : '/.*' > /dev/null; then
    PRG="$link"
  else
    PRG=`dirname "$PRG"`/"$link"
  fi
done
PRGDIR=`dirname "$PRG"`

# Only set CTAKES_HOME if not already set
[ -z "$CTAKES_HOME" ] && CTAKES_HOME=`cd "$PRGDIR/.." >/dev/null; pwd`

cd $CTAKES_HOME
java -cp $CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g org.apache.ctakes.core.pipeline.PiperFileRunner "$@"

runPiperSubmitter.bat

Windows shell script 
@ECHO OFF
::
::
::
::   Runs the pipeline in a piper file.
::::
:: Requires JAVA JDK 1.8+
::

@REM Guess CTAKES_HOME if not defined
set CURRENT_DIR=%cd%
if not "%CTAKES_HOME%" == "" goto gotHome
set CTAKES_HOME=%CURRENT_DIR%
if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome
cd ..
set CTAKES_HOME=%cd%

:gotHome
if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome
echo The CTAKES_HOME environment variable is not defined correctly
echo This environment variable is needed to run this program
goto end

:okHome
@set PATH=%PATH%;%CTAKES_HOME%\lib\auth\x64
@REM use JAVA_HOME if set
if exist "%JAVA_HOME%\bin\java.exe" set PATH=%JAVA_HOME%\bin;%PATH%

cd %CTAKES_HOME%
set CLASS_PATH=%CTAKES_HOME%\desc\;%CTAKES_HOME%\resources\;%CTAKES_HOME%\lib\*
set LOG4J_PARM=-Dlog4j.configuration="file:\%CTAKES_HOME%\config\log4j.xml"
set PIPE_RUNNER=org.apache.ctakes.gui.pipeline.PiperRunnerGui
java -cp "%CLASS_PATH%" %LOG4J_PARM% -Xms512M -Xmx3g %PIPE_RUNNER% %*
cd %CURRENT_DIR%

:end

runPiperSubmitter.sh

Linux / Mac shell script 
#!/bin/sh
#
#
#
#   Runs the pipeline in a piper file.
#
# Requires JAVA JDK 1.8+
#

PRG="$0"
while [ -h "$PRG" ]; do
  ls=`ls -ld "$PRG"`
  link=`expr "$ls" : '.*-> \(.*\)$'`
  if expr "$link" : '/.*' > /dev/null; then
    PRG="$link"
  else
    PRG=`dirname "$PRG"`/"$link"
  fi
done
PRGDIR=`dirname "$PRG"`

# Only set CTAKES_HOME if not already set
[ -z "$CTAKES_HOME" ] && CTAKES_HOME=`cd "$PRGDIR/.." >/dev/null; pwd`

cd $CTAKES_HOME
java -cp $CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g org.apache.ctakes.gui.pipeline.PiperRunnerGui "$@"

runctakesCPE.bat

Windows shell script 
@REM
@REM

@REM Requires JAVA JDK 1.8+
@REM If you plan to use the UMLS Resources, set/export env variables
@REM set ctakes.umlsuser=[username], ctakes.umlspw=[password]
@REM or add the properties
@REM -Dctakes.umlsuser=[username] -Dctakes.umlspw=[password]

@REM Guess CTAKES_HOME if not defined
SETLOCAL
set CURRENT_DIR=%cd%
if not "%CTAKES_HOME%" == "" goto gotHome
set CTAKES_HOME=%CURRENT_DIR%
if exist "%CTAKES_HOME%\bin\runctakesCPE.bat" goto okHome
cd ..
set CTAKES_HOME=%cd%

:gotHome
if exist "%CTAKES_HOME%\bin\runctakesCPE.bat" goto okHome
echo The CTAKES_HOME environment variable is not defined correctly
echo This environment variable is needed to run this program
goto end

:okHome
@REM use JAVA_HOME if set
if exist "%JAVA_HOME%\bin\java.exe" set PATH=%JAVA_HOME%\bin;%PATH%
@set PATH=%PATH%;%CTAKES_HOME%\lib\auth\x64
cd %CTAKES_HOME%
java -cp "%CTAKES_HOME%\desc\;%CTAKES_HOME%\resources\;%CTAKES_HOME%\lib\*" -Dlog4j.configuration="file:\%CTAKES_HOME%\config\log4j.xml" -Xms512M -Xmx3g org.apache.uima.tools.cpm.CpmFrame
cd %CURRENT_DIR%
:end
ENDLOCAL

runctakesCPE.sh

Linux / Mac shell script 
#
#

# Requires JAVA JDK 1.6+
# If you plan to use the UMLS Resources, set/export env variables
# export ctakes.umlsuser=[username], ctakes.umlspw=[password]
# or add the properties
# -Dctakes.umlsuser=[username] -Dctakes.umlspw=[password]

# You can also pass in the name of the XML descriptor to auto load as an arugement
# -desc $CTAKES_HOME/ctakes-clinical-pipeline/desc/AggregatePlaintextUMLSProcessor.xml

PRG="$0"
while [ -h "$PRG" ]; do
  ls=`ls -ld "$PRG"`
  link=`expr "$ls" : '.*-> \(.*\)$'`
  if expr "$link" : '/.*' > /dev/null; then
    PRG="$link"
  else
    PRG=`dirname "$PRG"`/"$link"
  fi
done
PRGDIR=`dirname "$PRG"`

# Only set CTAKES_HOME if not already set
[ -z "$CTAKES_HOME" ] && CTAKES_HOME=`cd "$PRGDIR/.." >/dev/null; pwd`

cd $CTAKES_HOME
java -cp $CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g org.apache.uima.tools.cpm.CpmFrame "$@"

runctakesCVD.bat

Windows shell script 
@REM
@REM

@REM If you plan to use the UMLS Resources, set/export env variables
@REM  set ctakes.umlsuser=[username]
@REM  set ctakes.umlspw=[password]
@REM For example:
@REM   set ctakes.umlsuser=myusername
@REM   set ctakes.umlspw=mypassword
@REM or add the properties
@REM   -Dctakes.umlsuser=[username] -Dctakes.umlspw=[password]
@REM for example:  
@REM   -Dctakes.umlsuser=myusername -Dctakes.umlspw="mypassw@rd"

@REM Guess CTAKES_HOME if not defined
set CURRENT_DIR=%cd%
if not "%CTAKES_HOME%" == "" goto gotHome
set CTAKES_HOME=%CURRENT_DIR%
if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome
cd ..
set CTAKES_HOME=%cd%

:gotHome
if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome
echo The CTAKES_HOME environment variable is not defined correctly
echo This environment variable is needed to run this program
goto end

:okHome
@REM use JAVA_HOME if set
if exist "%JAVA_HOME%\bin\java.exe" set PATH=%JAVA_HOME%\bin;%PATH%
@set PATH=%PATH%;%CTAKES_HOME%\lib\auth\x64

cd %CTAKES_HOME%

IF "%~1"=="" GOTO NoParam

IF NOT "%~2"=="" GOTO MoreThanOneParam

if exist "%CTAKES_HOME%\%1" (
  echo CVD will load AE "%CTAKES_HOME%\%1"
  java -cp "%CTAKES_HOME%\desc\;%CTAKES_HOME%\resources\;%CTAKES_HOME%\lib\*" -Dlog4j.configuration="file:\%CTAKES_HOME%\config\log4j.xml" -Xms512M -Xmx3g org.apache.uima.tools.cvd.CVD -desc "%1"
) else (
  echo Unable to find descriptor "%1"
  GOTO NoParam
)
  
GOTO ChangeBack

:NoParam
  echo Use the GUI to select the AE to load
  java -cp "%CTAKES_HOME%\desc\;%CTAKES_HOME%\resources\;%CTAKES_HOME%\lib\*" -Dlog4j.configuration="file:\%CTAKES_HOME%\config\log4j.xml" -Xms512M -Xmx3g org.apache.uima.tools.cvd.CVD
GOTO ChangeBack


:MoreThanOneParam
  echo You entered more than one parameter. Second parameter is "%2" 

:ChangeBack
cd %CURRENT_DIR%
:end

runctakesCVD.sh

Linux / Mac shell script 
#
#

# Requires JAVA JDK 1.6+
# If you plan to use the UMLS Resources, set/export env variables
# export ctakes.umlsuser=[username], ctakes.umlspw=[password]
# or add the properties
# -Dctakes.umlsuser=[username] -Dctakes.umlspw=[password]

# You can also pass in the name of the XML descriptor to auto load as an arugement
# -desc $CTAKES_HOME/ctakes-clinical-pipeline/desc/AggregatePlaintextUMLSProcessor.xml

PRG="$0"
while [ -h "$PRG" ]; do
  ls=`ls -ld "$PRG"`
  link=`expr "$ls" : '.*-> \(.*\)$'`
  if expr "$link" : '/.*' > /dev/null; then
    PRG="$link"
  else
    PRG=`dirname "$PRG"`/"$link"
  fi
done
PRGDIR=`dirname "$PRG"`

# Only set CTAKES_HOME if not already set
[ -z "$CTAKES_HOME" ] && CTAKES_HOME=`cd "$PRGDIR/.." >/dev/null; pwd`

cd $CTAKES_HOME
java -cp $CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g org.apache.uima.tools.cvd.CVD "$@"

setenv.bat

Windows shell script 
@REM
@REM


@rem determine CTAKES_HOME - set it to the parent of the directory in which this file is located
@set CURDIR=%cd%
@set BINDIR=%~dp0
@rem change to CTAKES_HOME dir and save the directory
@cd %BINDIR%..
@set CTAKES_HOME=%cd%
@rem change back to the original directory
@cd %CURDIR%

@rem -------------------------------------------
@rem customize these variables to match your environment
@rem -------------------------------------------

@rem add 64-bit MS SQL Server authentication library to path
@rem modify this accordingly if you are using the 32-bit jdk
@set PATH=%PATH%;%CTAKES_HOME%\lib\auth\x64

@rem -------------------------------------------
@rem end customizations.  The following is environment-independent
@rem -------------------------------------------

@set ANT_CP=%CTAKES_HOME%\lib\ant-1.9.2.jar;%CTAKES_HOME%\lib\ant-launcher-1.9.2.jar;%CTAKES_HOME%\lib\ant-contrib-1.0b3.jar
@set CLASSPATH="%CTAKES_HOME%\desc\;%CTAKES_HOME%\resources\;%CTAKES_HOME%\lib\*"

ytexweb.bat

Windows shell script 
@REM
@REM

@rem simple script to start jetty with the desc\ctakes-ytex-web web app
@rem YOU MUST use a java JDK, not JRE.
@rem typical windows Paths include the JRE, not the JDK
@rem do one of the following:
@rem * change java in this script to the full path of java from the JDK
@rem * or modify setenv.bat to put the JDK bin directory at the beginning of the path
@rem * or modify the PATH system environment variable and put the JDK bin directory at the beginning
@setlocal
@call %~dp0setenv.bat
java -cp "%CLASSPATH%" -Dlog4j.configuration="file:\%CTAKES_HOME%\config\log4j.xml" -XX:MaxPermSize=128m -Xmx512m org.eclipse.jetty.runner.Runner "%CTAKES_HOME%\desc\ctakes-ytex-web"
@endlocal

ytexweb.sh

Linux / Mac shell script 
#! /bin/sh
#
#

# simple script to start jetty with the desc/ctakes-ytex-web web app
. ${HOME}/ctakes.profile
java -cp ${CLASSPATH} -Dlog4j.configuration=file:${CTAKES_HOME}/config/log4j.xml -XX:MaxPermSize=128m -Xmx512m org.eclipse.jetty.runner.Runner ${CTAKES_HOME}/desc/ctakes-ytex-web

Home

Running cTAKES

Pipelines

GUI Tools

  • PLACEHOLDER

Code Modules

Pipeline Components

Examples

Python Bridge to Java

General

Clone this wiki locally