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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 473820a Updates for ctakes wiki auto-creator.
new b2fdc42 Merge remote-tracking branch 'origin/main' into main
473820a is described below
commit 473820a15d9f117aee621c07a5de0726a98abfa7
Author: Sean Finan <[email protected]>
AuthorDate: Thu Sep 19 16:48:56 2024 -0400
Updates for ctakes wiki auto-creator.
---
.../ctakes/gui/pipeline/bit/PipeBitFinder.java | 6 +-
.../org/apache/ctakes/gui/util/WikiPipeLister.java | 156 +++++++++++++--------
2 files changed, 98 insertions(+), 64 deletions(-)
diff --git
a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java
b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java
index f1bd162..8547224 100644
---
a/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java
+++
b/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java
@@ -75,10 +75,10 @@ public enum PipeBitFinder {
}
final ClassGraph scanner = new ClassGraph().enableAllInfo();
-
+
+ String message = (_allImplementations) ? "all possible " :
"official";
+ LOGGER.info( "Starting Scan for ({}) Pipeline Bits", message );
try ( DotLogger dotter = new DotLogger(); ScanResult result =
scanner.scan()) {
- String message = (_allImplementations) ? "all possible
" : "official";
- LOGGER.info( "Starting Scan for ("+message+") Pipeline
Bits" );
ClassInfoList list = null;
if(_allImplementations)
list = findByType(result);
diff --git
a/ctakes-gui/src/main/java/org/apache/ctakes/gui/util/WikiPipeLister.java
b/ctakes-gui/src/main/java/org/apache/ctakes/gui/util/WikiPipeLister.java
index 9ba7514..fad4181 100644
--- a/ctakes-gui/src/main/java/org/apache/ctakes/gui/util/WikiPipeLister.java
+++ b/ctakes-gui/src/main/java/org/apache/ctakes/gui/util/WikiPipeLister.java
@@ -43,6 +43,15 @@ final public class WikiPipeLister {
// core_AE.md
+ static private final String MODULE_SUB_DIR = "auto/modules/";
+ static private final String PIPER_SUB_DIR = "auto/pipers/";
+ static private final String READER_SUB_DIR = "auto/readers/";
+ static private final String ANNOTATORS_SUB_DIR = "auto/annotators/";
+ static private final String WRITERS_SUB_DIR = "auto/writers/";
+ static private final String UTILS_SUB_DIR = "auto/utils/";
+ static private final String SCRIPTS_SUB_DIR = "auto/scripts/";
+
+
static private final String WIKI = "https://github.com/apache/ctakes/wiki/";;
static private final String PREFIX = "org.apache.ctakes.";
@@ -154,7 +163,7 @@ final public class WikiPipeLister {
.append( "](" )
.append( moduleDesc._name ).append( ")\n" );
}
- try ( Writer writer = new BufferedWriter( new FileWriter( dir + "/" +
moduleDesc._name + ".md" ) ) ) {
+ try ( Writer writer = new BufferedWriter( new FileWriter( dir + "/" +
MODULE_SUB_DIR + moduleDesc._name + ".md" ) ) ) {
writer.write( markdownModule( moduleDesc ) );
} catch ( IOException ioE ) {
System.err.println( ioE.getMessage() );
@@ -225,7 +234,7 @@ final public class WikiPipeLister {
}
private void writeAllPipers( final String dir ) {
- try ( Writer writer = new BufferedWriter( new FileWriter( dir + "/Piper
File List.md" ) ) ) {
+ try ( Writer writer = new BufferedWriter( new FileWriter( dir + "/" +
PIPER_SUB_DIR + "Piper File List.md" ) ) ) {
writer.write( markdownPipers() );
} catch ( IOException ioE ) {
System.err.println( ioE.getMessage() );
@@ -235,7 +244,7 @@ final public class WikiPipeLister {
private String markdownPipers() {
final Collection<PiperDesc> pipers = _pipers.values().stream().flatMap(
Collection::stream )
- .sorted( Comparator.comparing( PiperDesc::getName ) ).collect(
Collectors.toList() );
+ .sorted( Comparator.comparing( PiperDesc::getName ) ).toList();
final StringBuilder sb = new StringBuilder();
sb.append( "# Piper File List\n\n| Name | Description |\n|---|---|\n" );
for ( PiperDesc piper : pipers ) {
@@ -264,17 +273,17 @@ final public class WikiPipeLister {
}
private void writeAllBitTypes( final String dir ) {
- writeBitType( dir, getBitType( "Reader" ), COLLECTION_READERS );
- writeBitType( dir, getBitType( "Annotator" ), ANNOTATION_ENGINES );
- writeBitType( dir, getBitType( "Writer" ), WRITERS_CONSUMERS );
- writeBitType( dir, getBitType( "Special" ), UTILITIES_SPECIAL );
+ writeBitType( dir + "/" + READER_SUB_DIR, getBitType( "Reader" ),
COLLECTION_READERS );
+ writeBitType( dir + "/" + ANNOTATORS_SUB_DIR, getBitType( "Annotator" ),
ANNOTATION_ENGINES );
+ writeBitType( dir + "/" + WRITERS_SUB_DIR, getBitType( "Writer" ),
WRITERS_CONSUMERS );
+ writeBitType( dir + "/" + UTILS_SUB_DIR, getBitType( "Special" ),
UTILITIES_SPECIAL );
}
private void writeBitType( final String dir, final List<PipeBitDesc>
bitDescs, final String title ) {
_sidebar.append( "- [" ).append( title )
.append( "](" )
.append( title.replace( ' ', '-' ) ).append( ")\n" );
- try ( Writer writer = new BufferedWriter( new FileWriter( dir + "/" +
title + ".md" ) ) ) {
+ try ( Writer writer = new BufferedWriter( new FileWriter( dir + title +
".md" ) ) ) {
writer.write( markdownBitType( bitDescs, title ) );
} catch ( IOException ioE ) {
System.err.println( ioE.getMessage() );
@@ -633,58 +642,64 @@ final public class WikiPipeLister {
}
static private final String SH_LICENSE =
- "# Licensed to the Apache Software Foundation (ASF) under one\n" +
- "# or more contributor license agreements. See the NOTICE file\n" +
- "# distributed with this work for additional information\n" +
- "# regarding copyright ownership. The ASF licenses this file\n" +
- "# to you under the Apache License, Version 2.0 (the\n" +
- "# \"License\"); you may not use this file except in compliance\n" +
- "# with the License. You may obtain a copy of the License at\n" +
- "#\n" +
- "# http://www.apache.org/licenses/LICENSE-2.0\n"; +
- "#\n" +
- "# Unless required by applicable law or agreed to in writing,\n" +
- "# software distributed under the License is distributed on an\n" +
- "# \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY\n" +
- "# KIND, either express or implied. See the License for the\n" +
- "# specific language governing permissions and limitations\n" +
- "# under the License.\n";
+ """
+ # 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.
+ """;
static private final String BAT_LICENSE =
- "@REM Licensed to the Apache Software Foundation (ASF) under one\n" +
- "@REM or more contributor license agreements. See the NOTICE file\n"
+
- "@REM distributed with this work for additional information\n" +
- "@REM regarding copyright ownership. The ASF licenses this file\n" +
- "@REM to you under the Apache License, Version 2.0 (the\n" +
- "@REM \"License\"); you may not use this file except in compliance\n"
+
- "@REM with the License. You may obtain a copy of the License at\n" +
- "@REM\n" +
- "@REM http://www.apache.org/licenses/LICENSE-2.0\n"; +
- "@REM\n" +
- "@REM Unless required by applicable law or agreed to in writing,\n" +
- "@REM software distributed under the License is distributed on an\n" +
- "@REM \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY\n" +
- "@REM KIND, either express or implied. See the License for the\n" +
- "@REM specific language governing permissions and limitations\n" +
- "@REM under the License.\n";
+ """
+ @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.
+ """;
static private final String BAT_LICENSE_2 =
- ":: Licensed to the Apache Software Foundation (ASF) under one\n" +
- ":: or more contributor license agreements. See the NOTICE file\n" +
- ":: distributed with this work for additional information\n" +
- ":: regarding copyright ownership. The ASF licenses this file\n" +
- ":: to you under the Apache License, Version 2.0 (the\n" +
- ":: \"License\"); you may not use this file except in compliance\n" +
- ":: with the License. You may obtain a copy of the License at\n" +
- "::\n" +
- ":: http://www.apache.org/licenses/LICENSE-2.0\n"; +
- "::\n" +
- ":: Unless required by applicable law or agreed to in writing,\n" +
- ":: software distributed under the License is distributed on an\n" +
- ":: \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY\n" +
- ":: KIND, either express or implied. See the License for the\n" +
- ":: specific language governing permissions and limitations\n" +
- ":: under the License.\n";
+ """
+ :: 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.
+ """;
static private String getScriptType( final String filename ) {
if ( filename.endsWith( ".sh" ) || filename.endsWith( ".bash" ) ) {
@@ -750,11 +765,11 @@ final public class WikiPipeLister {
private void writeBinScripts( final String dir ) {
_sidebar.append( "- [Scripts](Shell+Scripts)\n" );
final Map<String,String> binScripts = getBinScriptsMap();
- try ( Writer writer = new BufferedWriter( new FileWriter( dir + "/Shell
Scripts.md" ) ) ) {
+ try ( Writer writer = new BufferedWriter( new FileWriter( dir +"/" +
SCRIPTS_SUB_DIR + "Shell Scripts.md" ) ) ) {
writer.write( "Shell Scripts included in the bin/ directory of a
cTAKES installation. \n" );
writer.write( "These scripts can only be run in a cTAKES
installation. \n" );
writer.write( "They cannot be used within a source code project.\n\n"
);
- final List<String> names =
binScripts.keySet().stream().sorted().collect( Collectors.toList() );
+ final List<String> names =
binScripts.keySet().stream().sorted().toList();
for ( String name : names ) {
writer.write( binScripts.get( name ) );
}
@@ -765,8 +780,17 @@ final public class WikiPipeLister {
}
private List<ModuleDesc> parseModules() {
- PipeBitFinder.getInstance().scan();
final Map<String, ModuleDesc> moduleMap = new HashMap<>();
+ final File[] files = new File( "." ).listFiles();
+ if ( files != null ) {
+ for ( File file : files ) {
+ if ( file.isDirectory() && file.getName().startsWith( "ctakes-" )
+ && new File( file.getName(), "src" ).isDirectory() ) {
+ moduleMap.put( file.getName(), new ModuleDesc( file.getName() )
);
+ }
+ }
+ }
+ PipeBitFinder.getInstance().scan();
final Collection<Class<?>> bitClasses =
PipeBitFinder.getInstance().getPipeBits();
for ( Class<?> bitClass : bitClasses ) {
final PipeBitDesc bitDesc = new PipeBitDesc( bitClass );
@@ -810,6 +834,7 @@ final public class WikiPipeLister {
private void startSidebar() {
_sidebar.append( "[[/images/ctakes_logo.jpg|Apache cTAKES]]\n\n" )
.append( "\n### [Home](Home)\n\n" )
+ .append( "- [New in v6](Differences+between+5.0+and+6.0)\n" )
.append( "- [New in v5](Differences+between+4.0+and+5.0)\n" )
.append( "- [Videos](Videos)\n" );
}
@@ -875,7 +900,7 @@ final public class WikiPipeLister {
.append( "- [Get Involved](Get-Involved)\n" )
.append( "- [Apache™
Sponsorship](https://www.apache.org/foundation/sponsorship.html)\n" )
.append( "- [Thank
you](https://www.apache.org/foundation/thanks.html)\n" );
- try ( BufferedWriter writer = new BufferedWriter( new FileWriter( dir +
"/_Sidebar.md" ) ) ) {
+ try ( BufferedWriter writer = new BufferedWriter( new FileWriter( dir +
"/auto_Sidebar.md" ) ) ) {
writer.write( _sidebar.toString() );
} catch ( IOException ioE ) {
System.err.println( ioE.getMessage() );
@@ -898,8 +923,17 @@ final public class WikiPipeLister {
static public void main( final String... args ) {
// final String dir = args[ 0 ];
- final String dir = "C:/temp/wiki_modules";
+ final String dir = "C:/temp/wiki2_modules";
new File( dir ).mkdirs();
+ new File( dir + "/" + MODULE_SUB_DIR ).mkdirs();
+ new File( dir + "/" + PIPER_SUB_DIR ).mkdirs();
+ new File( dir + "/" + READER_SUB_DIR ).mkdirs();
+ new File( dir + "/" + ANNOTATORS_SUB_DIR ).mkdirs();
+ new File( dir + "/" + WRITERS_SUB_DIR ).mkdirs();
+ new File( dir + "/" + UTILS_SUB_DIR ).mkdirs();
+ new File( dir + "/" + SCRIPTS_SUB_DIR ).mkdirs();
+
+ System.out.println( "Run this with the classpath of ctakes-dist,
otherwise you will miss modules." );
final WikiPipeLister tabler = new WikiPipeLister();
tabler.startSidebar();
tabler.sidebarRunCtakes( dir );
