This is an automated email from the ASF dual-hosted git repository.
seanfinan pushed a commit to branch main
in repository https://gitbox.apache.org/repos/asf/ctakes.git
The following commit(s) were added to refs/heads/main by this push:
new 6be23f7 Add short script descriptions.
6be23f7 is described below
commit 6be23f7d5c7005a8623b146c5adf862367f2b866
Author: Sean Finan <[email protected]>
AuthorDate: Fri Sep 20 18:28:52 2024 -0400
Add short script descriptions.
---
.../src/main/bin/deprecated-ctakes.profile | 2 +-
.../src/main/bin/getUmlsDictionary.bat | 12 +++----
.../src/main/bin/getUmlsDictionary.sh | 12 +++----
.../src/main/bin/runClinicalPipeline.bat | 28 +++++++++------
.../src/main/bin/runClinicalPipeline.sh | 25 +++++++------
.../src/main/bin/runDictionaryCreator.bat | 41 +++++++++++----------
.../src/main/bin/runDictionaryCreator.sh | 5 ++-
.../src/main/bin/runPiperCreator.bat | 42 ++++++++++++----------
.../src/main/bin/runPiperCreator.sh | 9 +++--
ctakes-distribution/src/main/bin/runPiperFile.bat | 14 ++++----
ctakes-distribution/src/main/bin/runPiperFile.sh | 10 +++---
ctakes-distribution/src/main/bin/runPiperGUI.bat | 14 ++++----
ctakes-distribution/src/main/bin/runPiperGUI.sh | 11 +++---
.../src/main/bin/runPiperSubmitter.bat | 14 ++++----
.../src/main/bin/runPiperSubmitter.sh | 11 +++---
ctakes-distribution/src/main/bin/runctakesCPE.sh | 2 +-
ctakes-distribution/src/main/bin/runctakesCVD.sh | 2 +-
ctakes-distribution/src/main/bin/setenv.bat | 18 ++++------
ctakes-distribution/src/main/bin/setenv.sh | 25 +++++++++++++
ctakes-distribution/src/main/bin/ytexweb.bat | 2 +-
ctakes-distribution/src/main/bin/ytexweb.sh | 2 +-
21 files changed, 172 insertions(+), 129 deletions(-)
diff --git a/ctakes-distribution/src/main/bin/deprecated-ctakes.profile
b/ctakes-distribution/src/main/bin/deprecated-ctakes.profile
index 41426db..c0cfd06 100644
--- a/ctakes-distribution/src/main/bin/deprecated-ctakes.profile
+++ b/ctakes-distribution/src/main/bin/deprecated-ctakes.profile
@@ -17,7 +17,7 @@
# under the License.
#
-# Requires JAVA JDK 1.6+
+# Requires Java 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
diff --git a/ctakes-distribution/src/main/bin/getUmlsDictionary.bat
b/ctakes-distribution/src/main/bin/getUmlsDictionary.bat
index 4b6dc9d..d46e2d1 100644
--- a/ctakes-distribution/src/main/bin/getUmlsDictionary.bat
+++ b/ctakes-distribution/src/main/bin/getUmlsDictionary.bat
@@ -16,12 +16,12 @@
:: KIND, either express or implied. See the License for the
:: specific language governing permissions and limitations
:: under the License.
-::
-::
-:: Starts a simple gui to fetch the cTAKES umls (snomed, rxnorm) dictionary.
-::::
-:: Requires JAVA JDK 17
-::
+
+
+:: Starts a simple GUI to fetch the cTAKES umls (snomed, rxnorm) dictionary.
+
+:: Requires Java 17
+
@REM The setenv script sets up the environment needed by cTAKES.
@call %~sdp0\setenv.bat
diff --git a/ctakes-distribution/src/main/bin/getUmlsDictionary.sh
b/ctakes-distribution/src/main/bin/getUmlsDictionary.sh
index cb7db4b..ac76604 100644
--- a/ctakes-distribution/src/main/bin/getUmlsDictionary.sh
+++ b/ctakes-distribution/src/main/bin/getUmlsDictionary.sh
@@ -16,12 +16,12 @@
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
-#
-#
-# Starts a simple gui to fetch the cTAKES umls (snomed, rxnorm) dictionary.
-#
-# Requires JAVA JDK 17
-#
+
+
+# Starts a simple GUI to fetch the cTAKES umls (snomed, rxnorm) dictionary.
+
+# Requires Java 17
+
# Sets up environment for cTAKES
. ${HOME}/setenv.sh
diff --git a/ctakes-distribution/src/main/bin/runClinicalPipeline.bat
b/ctakes-distribution/src/main/bin/runClinicalPipeline.bat
index 84290d3..da2c971 100644
--- a/ctakes-distribution/src/main/bin/runClinicalPipeline.bat
+++ b/ctakes-distribution/src/main/bin/runClinicalPipeline.bat
@@ -16,18 +16,24 @@
:: KIND, either express or implied. See the License for the
:: specific language governing permissions and limitations
:: under the License.
-::
-::
-:: 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 The setenv script sets up the environment needed by cTAKES.
+
+:: Runs the default clinical pipeline with provided parameters.
+:: Required parameters are:
+:: -i , --inputDir {inputDirectory}
+:: -o , --outputDir {outputDirectory}
+:: --key {umlsKey}
+
+:: Optional standard parameters are:
+:: -s , --subDir {subDirectory} (for i/o)
+:: --xmiOut {xmiOutputDirectory} (if different from -o)
+:: -l , --lookupXml {dictionaryConfigFile} (fast only)
+:: -? , --help
+
+:: Requires Java 17
+
+
+:: The setenv script sets up the environment needed by cTAKES.
@call %~sdp0\setenv.bat
cd %CTAKES_HOME%
diff --git a/ctakes-distribution/src/main/bin/runClinicalPipeline.sh
b/ctakes-distribution/src/main/bin/runClinicalPipeline.sh
index 49dd1b0..b69732f 100644
--- a/ctakes-distribution/src/main/bin/runClinicalPipeline.sh
+++ b/ctakes-distribution/src/main/bin/runClinicalPipeline.sh
@@ -16,16 +16,21 @@
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
-#
-#
-# 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 --key {umlsKey}
-# Can also use a custom dictionary with -l {dictionaryConfigFile}
-#
-#
-# Requires JAVA JDK 17
-#
+
+# Runs the default clinical pipeline with provided parameters.
+# Required parameters are:
+# -i , --inputDir {inputDirectory}
+# -o , --outputDir {outputDirectory}
+# --key {umlsKey}
+
+# Optional standard parameters are:
+# -s , --subDir {subDirectory} (for i/o)
+# --xmiOut {xmiOutputDirectory} (if different from -o)
+# -l , --lookupXml {dictionaryConfigFile} (fast only)
+# -? , --help
+
+# Requires Java 17
+
# Sets up environment for cTAKES
. ${HOME}/setenv.sh
diff --git a/ctakes-distribution/src/main/bin/runDictionaryCreator.bat
b/ctakes-distribution/src/main/bin/runDictionaryCreator.bat
index b3f63cb..ec73443 100644
--- a/ctakes-distribution/src/main/bin/runDictionaryCreator.bat
+++ b/ctakes-distribution/src/main/bin/runDictionaryCreator.bat
@@ -1,23 +1,26 @@
-@REM
-@REM Licensed to the Apache Software Foundation (ASF) under one
-@REM or more contributor license agreements. See the NOTICE file
-@REM distributed with this work for additional information
-@REM regarding copyright ownership. The ASF licenses this file
-@REM to you under the Apache License, Version 2.0 (the
-@REM "License"); you may not use this file except in compliance
-@REM with the License. You may obtain a copy of the License at
-@REM
-@REM http://www.apache.org/licenses/LICENSE-2.0
-@REM
-@REM Unless required by applicable law or agreed to in writing,
-@REM software distributed under the License is distributed on an
-@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-@REM KIND, either express or implied. See the License for the
-@REM specific language governing permissions and limitations
-@REM under the License.
-@REM
+::
+:: Licensed to the Apache Software Foundation (ASF) under one
+:: or more contributor license agreements. See the NOTICE file
+:: distributed with this work for additional information
+:: regarding copyright ownership. The ASF licenses this file
+:: to you under the Apache License, Version 2.0 (the
+:: "License"); you may not use this file except in compliance
+:: with the License. You may obtain a copy of the License at
+::
+:: http://www.apache.org/licenses/LICENSE-2.0
+::
+:: Unless required by applicable law or agreed to in writing,
+:: software distributed under the License is distributed on an
+:: "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+:: KIND, either express or implied. See the License for the
+:: specific language governing permissions and limitations
+:: under the License.
+::
-@REM The setenv script sets up the environment needed by cTAKES.
+:: Starts a GUI that can facilitate creation of a dictionary for the
+:: [ctakes-dictionary-lookup-fast](ctakes-dictionary-lookup-fast) module.
+
+:: The setenv script sets up the environment needed by cTAKES.
@call %~sdp0\setenv.bat
cd %CTAKES_HOME%
diff --git a/ctakes-distribution/src/main/bin/runDictionaryCreator.sh
b/ctakes-distribution/src/main/bin/runDictionaryCreator.sh
index 5f1e16f..ae36710 100644
--- a/ctakes-distribution/src/main/bin/runDictionaryCreator.sh
+++ b/ctakes-distribution/src/main/bin/runDictionaryCreator.sh
@@ -16,7 +16,10 @@
# specific language governing permissions and limitations
# under the License.
#
-# Requires JAVA JDK 17
+# Starts a GUI that can facilitate creation of a dictionary for the
+# [ctakes-dictionary-lookup-fast](ctakes-dictionary-lookup-fast) module.
+#
+# Requires Java 17
#
# Sets up environment for cTAKES
diff --git a/ctakes-distribution/src/main/bin/runPiperCreator.bat
b/ctakes-distribution/src/main/bin/runPiperCreator.bat
index cc650dd..9bb7c8d 100644
--- a/ctakes-distribution/src/main/bin/runPiperCreator.bat
+++ b/ctakes-distribution/src/main/bin/runPiperCreator.bat
@@ -1,23 +1,27 @@
-@REM
-@REM Licensed to the Apache Software Foundation (ASF) under one
-@REM or more contributor license agreements. See the NOTICE file
-@REM distributed with this work for additional information
-@REM regarding copyright ownership. The ASF licenses this file
-@REM to you under the Apache License, Version 2.0 (the
-@REM "License"); you may not use this file except in compliance
-@REM with the License. You may obtain a copy of the License at
-@REM
-@REM http://www.apache.org/licenses/LICENSE-2.0
-@REM
-@REM Unless required by applicable law or agreed to in writing,
-@REM software distributed under the License is distributed on an
-@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-@REM KIND, either express or implied. See the License for the
-@REM specific language governing permissions and limitations
-@REM under the License.
-@REM
+::
+:: Licensed to the Apache Software Foundation (ASF) under one
+:: or more contributor license agreements. See the NOTICE file
+:: distributed with this work for additional information
+:: regarding copyright ownership. The ASF licenses this file
+:: to you under the Apache License, Version 2.0 (the
+:: "License"); you may not use this file except in compliance
+:: with the License. You may obtain a copy of the License at
+::
+:: http://www.apache.org/licenses/LICENSE-2.0
+::
+:: Unless required by applicable law or agreed to in writing,
+:: software distributed under the License is distributed on an
+:: "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+:: KIND, either express or implied. See the License for the
+:: specific language governing permissions and limitations
+:: under the License.
-@REM The setenv script sets up the environment needed by cTAKES.
+:: Starts a GUI that can facilitate creation of a pipeline.
+
+:: Requires Java 17
+
+
+:: The setenv script sets up the environment needed by cTAKES.
@call %~sdp0\setenv.bat
cd %CTAKES_HOME%
diff --git a/ctakes-distribution/src/main/bin/runPiperCreator.sh
b/ctakes-distribution/src/main/bin/runPiperCreator.sh
index 633ad68..311a6fb 100644
--- a/ctakes-distribution/src/main/bin/runPiperCreator.sh
+++ b/ctakes-distribution/src/main/bin/runPiperCreator.sh
@@ -15,9 +15,12 @@
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
-#
-# Requires JAVA JDK 17
-#
+
+
+# Starts a GUI that can facilitate creation of a pipeline.
+
+# Requires Java 17
+
# Sets up environment for cTAKES
. ${HOME}/setenv.sh
diff --git a/ctakes-distribution/src/main/bin/runPiperFile.bat
b/ctakes-distribution/src/main/bin/runPiperFile.bat
index b92ada8..42dc2f4 100644
--- a/ctakes-distribution/src/main/bin/runPiperFile.bat
+++ b/ctakes-distribution/src/main/bin/runPiperFile.bat
@@ -16,8 +16,8 @@
:: KIND, either express or implied. See the License for the
:: specific language governing permissions and limitations
:: under the License.
-::
-::
+
+
:: Runs the pipeline in the piper file specified by -p {piperfile}
:: with any other provided parameters. Standard parameters are:
:: -i , --inputDir {inputDirectory}
@@ -27,7 +27,7 @@
:: -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,
@@ -35,11 +35,11 @@
:: 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 17
-::
-@REM The setenv script sets up the environment needed by cTAKES.
+:: Requires Java 17
+
+
+:: The setenv script sets up the environment needed by cTAKES.
@call %~sdp0\setenv.bat
cd %CTAKES_HOME%
diff --git a/ctakes-distribution/src/main/bin/runPiperFile.sh
b/ctakes-distribution/src/main/bin/runPiperFile.sh
index 16fd22e..0bda7db 100644
--- a/ctakes-distribution/src/main/bin/runPiperFile.sh
+++ b/ctakes-distribution/src/main/bin/runPiperFile.sh
@@ -16,8 +16,8 @@
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
-#
-#
+
+
# Runs the pipeline in the piper file specified by -p (piperfile)
# with any other provided parameters. Standard parameters are:
# -i , --inputDir {inputDirectory}
@@ -35,9 +35,9 @@
# 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 17
-#
+
+# Requires Java 17
+
# Sets up environment for cTAKES
. ${HOME}/setenv.sh
diff --git a/ctakes-distribution/src/main/bin/runPiperGUI.bat
b/ctakes-distribution/src/main/bin/runPiperGUI.bat
index 0f5cacc..8fe6583 100644
--- a/ctakes-distribution/src/main/bin/runPiperGUI.bat
+++ b/ctakes-distribution/src/main/bin/runPiperGUI.bat
@@ -16,14 +16,14 @@
:: KIND, either express or implied. See the License for the
:: specific language governing permissions and limitations
:: under the License.
-::
-::
-:: Runs the pipeline in a piper file using a GUI.
-::::
-:: Requires JAVA JDK 1.8+
-::
-@REM The setenv script sets up the environment needed by cTAKES.
+
+:: Starts a GUI that can run a pipeline.
+
+:: Requires Java 17
+
+
+:: The setenv script sets up the environment needed by cTAKES.
@call %~sdp0\setenv.bat
cd %CTAKES_HOME%
diff --git a/ctakes-distribution/src/main/bin/runPiperGUI.sh
b/ctakes-distribution/src/main/bin/runPiperGUI.sh
index c86479c..89bb75d 100644
--- a/ctakes-distribution/src/main/bin/runPiperGUI.sh
+++ b/ctakes-distribution/src/main/bin/runPiperGUI.sh
@@ -16,12 +16,11 @@
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
-#
-#
-# Runs the pipeline in a piper file using a GUI.
-#
-# Requires JAVA JDK 17
-#
+
+# Starts a GUI that can run a pipeline.
+
+# Requires Java 17
+
# Sets up environment for cTAKES
. ${HOME}/setenv.sh
diff --git a/ctakes-distribution/src/main/bin/runPiperSubmitter.bat
b/ctakes-distribution/src/main/bin/runPiperSubmitter.bat
index 0f5cacc..0dc7d35 100644
--- a/ctakes-distribution/src/main/bin/runPiperSubmitter.bat
+++ b/ctakes-distribution/src/main/bin/runPiperSubmitter.bat
@@ -16,14 +16,14 @@
:: KIND, either express or implied. See the License for the
:: specific language governing permissions and limitations
:: under the License.
-::
-::
-:: Runs the pipeline in a piper file using a GUI.
-::::
-:: Requires JAVA JDK 1.8+
-::
-@REM The setenv script sets up the environment needed by cTAKES.
+:: Starts a GUI that can run a pipeline.
+:: Deprecated: Identical to the runPiperGUI script.
+
+:: Requires Java 17
+
+
+:: The setenv script sets up the environment needed by cTAKES.
@call %~sdp0\setenv.bat
cd %CTAKES_HOME%
diff --git a/ctakes-distribution/src/main/bin/runPiperSubmitter.sh
b/ctakes-distribution/src/main/bin/runPiperSubmitter.sh
index c86479c..b22a4a2 100644
--- a/ctakes-distribution/src/main/bin/runPiperSubmitter.sh
+++ b/ctakes-distribution/src/main/bin/runPiperSubmitter.sh
@@ -16,12 +16,11 @@
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
-#
-#
-# Runs the pipeline in a piper file using a GUI.
-#
-# Requires JAVA JDK 17
-#
+
+# Starts a GUI that can run a pipeline.
+# Deprecated: Identical to the runPiperGUI script.
+
+# Requires Java 17
# Sets up environment for cTAKES
. ${HOME}/setenv.sh
diff --git a/ctakes-distribution/src/main/bin/runctakesCPE.sh
b/ctakes-distribution/src/main/bin/runctakesCPE.sh
index 1b3ea68..3704fd9 100644
--- a/ctakes-distribution/src/main/bin/runctakesCPE.sh
+++ b/ctakes-distribution/src/main/bin/runctakesCPE.sh
@@ -17,7 +17,7 @@
# under the License.
#
-# Requires JAVA JDK 17+
+# Requires Java 17+
# Sets up environment for cTAKES
. ${HOME}/setenv.sh
diff --git a/ctakes-distribution/src/main/bin/runctakesCVD.sh
b/ctakes-distribution/src/main/bin/runctakesCVD.sh
index b544799..6d594a5 100644
--- a/ctakes-distribution/src/main/bin/runctakesCVD.sh
+++ b/ctakes-distribution/src/main/bin/runctakesCVD.sh
@@ -17,7 +17,7 @@
# under the License.
#
-# Requires JAVA JDK 17
+# Requires Java 17
# Sets up environment for cTAKES
. ${HOME}/setenv.sh
diff --git a/ctakes-distribution/src/main/bin/setenv.bat
b/ctakes-distribution/src/main/bin/setenv.bat
index 2a39d19..33c4c96 100644
--- a/ctakes-distribution/src/main/bin/setenv.bat
+++ b/ctakes-distribution/src/main/bin/setenv.bat
@@ -16,18 +16,14 @@
:: KIND, either express or implied. See the License for the
:: specific language governing permissions and limitations
:: under the License.
-::
-::
-:: 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
+
+:: Sets up the standard environment for cTAKES.
+
+:: Requires Java 17
+
+
+:: Guess CTAKES_HOME if not defined
set CURRENT_DIR=%cd%
if not "%CTAKES_HOME%" == "" goto gotHome
set CTAKES_HOME=%CURRENT_DIR%
diff --git a/ctakes-distribution/src/main/bin/setenv.sh
b/ctakes-distribution/src/main/bin/setenv.sh
index e70c788..9db1d1e 100644
--- a/ctakes-distribution/src/main/bin/setenv.sh
+++ b/ctakes-distribution/src/main/bin/setenv.sh
@@ -1,3 +1,28 @@
+#!/bin/sh
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+
+# Sets up the standard environment for cTAKES.
+
+# Requires Java 17
+
+
PRG="$0"
while [ -h "$PRG" ]; do
ls=`ls -ld "$PRG"`
diff --git a/ctakes-distribution/src/main/bin/ytexweb.bat
b/ctakes-distribution/src/main/bin/ytexweb.bat
index 1f8db8a..7d2b7b0 100644
--- a/ctakes-distribution/src/main/bin/ytexweb.bat
+++ b/ctakes-distribution/src/main/bin/ytexweb.bat
@@ -18,7 +18,7 @@
@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 YOU MUST use a Java, 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
diff --git a/ctakes-distribution/src/main/bin/ytexweb.sh
b/ctakes-distribution/src/main/bin/ytexweb.sh
index a25b343..5105ea7 100644
--- a/ctakes-distribution/src/main/bin/ytexweb.sh
+++ b/ctakes-distribution/src/main/bin/ytexweb.sh
@@ -19,7 +19,7 @@
#
# simple script to start jetty with the desc/ctakes-ytex-web web app
-# Requires JAVA JDK 17
+# Requires Java 17
#
# Sets up environment for cTAKES
. ${HOME}/setenv.sh
