File: remove_SBMLDoclet.patch

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Description: Deal with issue in doclets by removing docs/src/SBMLDoclet.java
Bug-Debian: https://bugs.debian.org/896531
Author: Andreas Tille <tille@debian.org>
Last-Update: Mon, 14 May 2018 10:55:58 +0200

--- a/docs/src/SBMLDoclet.java
+++ /dev/null
@@ -1,525 +0,0 @@
-/**
- * @file    SBMLDoclet.java
- * @brief   Exclude files, allow tag "@internal", and more.
- * @author  Michael Hucka
- * 
- * <!-- -----------------------------------------------------------------------
- * Portions of this code are under the following copyright terms:
- *
- * Copyright 2004 Sun Microsystems, Inc. All Rights Reserved.
- * 
- * Redistribution and use in source and binary forms, with or without 
- * modification, are permitted provided that the following conditions are met:
- * 
- *  - Redistribution of source code must retain the above copyright notice, 
- *    this list of conditions and the following disclaimer.
- *
- *  - Redistribution in binary form must reproduce the above copyright notice, 
- *    this list of conditions and the following disclaimer in the documentation 
- *    and/or other materials provided with the distribution.
- *
- * Neither the name of Sun Microsystems, Inc. nor the names of contributors may be 
- * used to endorse or promote products derived from this software without specific 
- * prior written permission.
- *  
- * This software is provided "AS IS," without a warranty of any kind. ALL EXPRESS 
- * OR IMPLIED CONDITIONS, REPRESENTATIONS AND WARRANTIES, INCLUDING ANY IMPLIED 
- * WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT, 
- * ARE HEREBY EXCLUDED. SUN MICROSYSTEMS, INC. ("SUN") AND ITS LICENSORS SHALL NOT 
- * BE LIABLE FOR ANY DAMAGES SUFFERED BY LICENSEE AS A RESULT OF USING, MODIFYING 
- * OR DISTRIBUTING THIS SOFTWARE OR ITS DERIVATIVES. IN NO EVENT WILL SUN OR ITS 
- * LICENSORS BE LIABLE FOR ANY LOST REVENUE, PROFIT OR DATA, OR FOR DIRECT, INDIRECT, 
- * SPECIAL, CONSEQUENTIAL, INCIDENTAL OR PUNITIVE DAMAGES, HOWEVER CAUSED AND 
- * REGARDLESS OF THE THEORY OF LIABILITY, ARISING OUT OF THE USE OF OR INABILITY 
- * TO USE THIS SOFTWARE, EVEN IF SUN HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH 
- * DAMAGES.
- *  
- * You acknowledge that this software is not designed, licensed or intended for 
- * use in the design, construction, operation or maintenance of any nuclear facility. 
- *
- * ------------------------------------------------------------------------ -->
- *
- * Portions of this code was originally obtained on 24 Feb. 2008 from
- * http://java.sun.com/developer/JDCTechTips/2004/tt1214.html
- * Author: Jamie Ho, Sun Microsystems, Inc.
- *
- * The following documentation was copied from that page.
- *
- * java -classpath <path to doclet and path to tools.jar>
- *     ExcludeDoclet  -excludefile <path to exclude file>  <javadoc options>
- *
- * In response to the command, the validOptions method of the Doclet class
- * looks for the -excludefile option. If it finds it, the method reads the
- * contents of the exclude file -- these are the set of classes and
- * packages to ignore. Then the start method is called. As each class or
- * package is processed, the method throws away the classes and packages in
- * the exclude set. The doclet includes the optionLength method, this
- * allows the doclet to run under both J2SE 1.4 and 5.0.
- *
- * Compile the doclet as follows:
- *
- *   javac -classpath tools.jar ExcludeDoclet.java
- *
- * Replace tools.jar with the appropriate location of your JDK
- * installation. For example, if you're running in the Windows environment
- * and your JDK is installed in the c:\jdk1.5.0 directory, specify
- * c:\jdk1.5.0\lib\tools.jar.
- *
- * Next, create a file such as skip.txt to identify which classes to
- * skip. For this example, run ExcludeDoclet with the standard JDK
- * classes, and ignore a set in the java.lang package:
- *
- *    java.lang.Math
- *    java.lang.Long
- *    java.lang.InternalError 
- *    java.lang.InterruptedException 
- *    java.lang.Iterable 
- *    java.lang.LinkageError
- *
- * Then run the following command (on one line):
- *
- * java -classpath .;c:\jdk1.5.0\lib\tools.jar ExcludeDoclet 
- *    -d docs -excludefile skip.txt -sourcepath c:\jdk1.5.0\src 
- *    -source 1.5 java.lang
- *
- * The command will generate the javadoc for the java.lang package,
- * excluding the six classes and interfaces identified in skip.txt.
- *
- * ----------------------------------------------------------------------------
- * Additional notes (M. Hucka):
- * - "tools.jar" is called "classes.jar" on MacOS and it's located in
- *   /System/Library/Frameworks/JavaVM.framework/Classes/classes.jar
- *   See http://lists.apple.com/archives/java-dev/2002/Jun/msg00901.html
- *
- * - 2008-02-25 I made a small tweak to the diagnostic msgs printed by start()
- *
- * - 2011-11-03 I added the @exclude tag processing code written by
- * Chris Nokleberg and made available from the following URL:
- * http://www.sixlegs.com/blog/java/exclude-javadoc-tag.html The page was
- * dated 22 Feb 2005.  The page stated that the code is in the public
- * domain.  The file was originally also named ExcludeDoclet.java.  What I
- * did is take the code and make it a subclass within this file, and took
- * the bulk of the previous doclet code and put it in *another* subclass in
- * this file, then hooked them together through the main() method.
- *
- * - 2011-11-08 Changed @exclude to @internal, which is what Doxygen uses
- * for the purpose we're using this for.
- */
-
-import java.io.*;
-import java.util.*;
-import java.lang.reflect.*;
-import com.sun.tools.doclets.standard.Standard;
-import com.sun.tools.javadoc.Main;
-import jdk.javadoc.doclet.*;
-
-
-/**
- * A wrapper for Javadoc.  Accepts additional options:
- *
- * * "-excludefile": specifies which classes and packages should be excluded
- *   from the output.
- *
- * * "-listskipped": print things that get skipped because they are SWIG
- *   things we don't want in the documentation.
- *
- * @author Jamie Ho
- * @author Michael Hucka
- */
-public class SBMLDoclet extends Doclet
-{
-    private static List m_args = new ArrayList();
-    private static Set m_excludeSet = new HashSet();
-    static boolean m_list_skipped = false;
-
-    /**
-     * First executes the doclet that exclude files.
-     * Then it executes the doclet that processes the classes and excludes
-     * things marked with @exclude.
-     *
-     * @param args  the Javadoc arguments from the command line
-     */
-    public static void main(String[] args)
-    {
-        String name;
-
-        name = FileExclusionDoclet.class.getName();
-        Main.execute(name, name, args);
-
-        name = SBMLProcessingDoclet.class.getName();
-        Main.execute(name, name, (String[]) m_args.toArray(new String[] {}));
-    }
-
-    /* --------------------------------------------------------------------- */
-
-    /**
-     * File exclusion handler class.
-     *
-     * This code was originally taken from:
-     * @(#)SBMLDoclet.java	1.1 04/08/31
-     * http://java.sun.com/developer/JDCTechTips/2004/tt1214.html
-     */
-    public static class FileExclusionDoclet
-        extends Doclet
-    {
-        /**
-         * Iterate through the documented classes and remove the ones that should
-         * be excluded.
-         * 
-         * @param root the initial RootDoc (before filtering).
-         */
-        public static boolean start(RootDoc root)
-        {
-            root.printNotice("SBMLDoclet removing excluded source files...");
-            ClassDoc[] classes = root.classes();
-            for (int i = 0; i < classes.length; i++) {
-                if (m_excludeSet.contains(classes[i].qualifiedName()) ||
-                    m_excludeSet.contains(classes[i].containingPackage().name())) {
-                    root.printNotice("Excluding " + classes[i].qualifiedName());
-                    continue;
-                }
-                m_args.add(classes[i].position().file().getPath());   
-            }
-            return true;
-        }
-
-        /**
-         * Let every option be valid.  The real validation happens in the
-         * standard doclet, not here.  Remove the "-excludefile" and
-         * "-subpackages" options because they are not needed by the standard
-         * doclet.  Similarly, process SBMLDoclet's -listexcludes flag here
-         * and also remove it.
-         * 
-         * @param options   the options from the command line
-         * @param reporter  the error reporter
-         */
-        public static boolean validOptions(String[][] options,
-                                           DocErrorReporter reporter)
-        {
-            for (int i = 0; i < options.length; i++) {
-                if (options[i][0].equalsIgnoreCase("-excludefile")) {
-                    try {
-                        readExcludeFile(options[i][1]);
-                    } catch (Exception e) {
-                        e.printStackTrace();
-                    }
-                    continue;
-                }
-                if (options[i][0].equals("-subpackages")) {
-                    continue;
-                }
-                if (options[i][0].equals("-listskipped")) {
-                    m_list_skipped = true;
-                    continue;
-                }
-                for (int j = 0; j < options[i].length; j++) {
-                    m_args.add(options[i][j]);
-                }
-            }
-            return true;
-        }
-
-        /**
-         * Parse the file that specifies which classes and packages to exclude from
-         * the output. You can write comments in this file by starting the line with
-         * a '#' character.
-         * 
-         * @param filePath the path to the exclude file.
-         */
-        private static void readExcludeFile(String filePath)
-            throws Exception
-        {
-            LineNumberReader reader = new LineNumberReader(new FileReader(filePath));
-            String line;
-            while ((line = reader.readLine()) != null) {
-                if (line.trim().startsWith("#"))
-                    continue;
-                m_excludeSet.add(line.trim());
-            }
-        }
-
-        /**
-         * Method required to validate the length of the given option.  This is a
-         * bit ugly but the options must be hard coded here.  Otherwise, Javadoc
-         * will throw errors when parsing options.  We could delegate to the 
-         * Standard doclet when computing option lengths, but then this doclet would
-         * be dependent on the version of J2SE used.  Prefer to hard code options
-         * here so that this doclet can be used with 1.4.x or 1.5.x .
-         * 
-         * @param option  the option to compute the length for
-         */
-        public static int optionLength(String option)
-        {
-            if (option.equalsIgnoreCase("-excludefile")) {
-                return 2;   
-            }
-
-            //General options
-            if (option.equals("-author") ||
-                option.equals("-docfilessubdirs") ||
-                option.equals("-keywords") ||
-                option.equals("-linksource") ||
-                option.equals("-nocomment") ||
-                option.equals("-nodeprecated") ||
-                option.equals("-nosince") ||
-                option.equals("-notimestamp") ||
-                option.equals("-quiet") ||
-                option.equals("-xnodate") ||
-                option.equals("-version")) {
-                return 1;
-            } else if (option.equals("-d") ||
-                       option.equals("-docencoding") ||
-                       option.equals("-encoding") ||
-                       option.equals("-excludedocfilessubdir") ||
-                       option.equals("-link") ||
-                       option.equals("-sourcetab") ||
-                       option.equals("-noqualifier") ||
-                       option.equals("-output") ||
-                       option.equals("-sourcepath") ||
-                       option.equals("-tag") ||
-                       option.equals("-taglet") ||
-                       option.equals("-tagletpath")) {
-                return 2;
-            } else if (option.equals("-group") ||
-                       option.equals("-linkoffline")) {
-                return 3;
-            }
-
-            //Standard doclet options
-            option = option.toLowerCase();
-            if (option.equals("-nodeprecatedlist") ||
-                option.equals("-noindex") ||
-                option.equals("-notree") ||
-                option.equals("-nohelp") ||
-                option.equals("-splitindex") ||
-                option.equals("-serialwarn") ||
-                option.equals("-use") ||
-                option.equals("-nonavbar") ||
-                option.equals("-nooverview")) {
-                return 1;
-            } else if (option.equals("-footer") ||
-                       option.equals("-header") ||
-                       option.equals("-packagesheader") ||
-                       option.equals("-doctitle") ||
-                       option.equals("-windowtitle") ||
-                       option.equals("-bottom") ||
-                       option.equals("-helpfile") ||
-                       option.equals("-stylesheetfile") ||
-                       option.equals("-charset") ||
-                       option.equals("-overview")) {
-                return 2;
-            } else {
-                return 0;
-            }
-        }
-    }
-
-    /* --------------------------------------------------------------------- */
-
-    /**
-     * Our own processing doclet.
-     *
-     * The code to handle @internal was originally taken from:
-     * http://www.sixlegs.com/blog/java/exclude-javadoc-tag.html
-     * Author:  Chris Nokleberg.
-     * It looks for @internal in documentation strings and excludes the
-     * method or class marked by it.
-     *
-     * This has added code to substitute a documentation string for
-     * delete().  I have not been able to find a way to do otherwise.  SWIG
-     * will simply not let me attach doc strings to delete() at all, so I
-     * have to do it outside.  Grafting the code here was the best
-     * solution, though this code could stand to be reorganized and
-     * modularized better.
-     */
-
-    public static class SBMLProcessingDoclet
-        extends Doclet
-    {
-        private static RootDoc the_root;
-
-        public static boolean validOptions(String[][] options,
-                                           DocErrorReporter reporter)
-        {
-            return Standard.validOptions(options, reporter);
-        }
-
-        public static int optionLength(String option)
-        {
-            return Standard.optionLength(option);
-        }
-
-        public static boolean start(RootDoc root)
-        {
-            the_root = root;
-            return Standard.start((RootDoc) process(root, RootDoc.class));
-        }
-
-        private static boolean markedInternal(Doc doc)
-        {
-            if (doc instanceof ProgramElementDoc)
-            {
-                ProgramElementDoc pdoc = (ProgramElementDoc) doc;
-                if (pdoc.containingPackage().tags("internal").length > 0)
-                    return true;
-            }
-            return doc.tags("internal").length > 0;
-        }
-
-        private static boolean isSWIGWrapper(Doc doc)
-        {
-            if (doc instanceof ProgramElementDoc)
-            {
-                ProgramElementDoc pdoc = (ProgramElementDoc) doc;
-                if (pdoc.containingPackage().name().startsWith("SWIGTYPE_p"))
-                    return true;
-            }
-            return doc.name().startsWith("SWIGTYPE_p");
-        }
-
-        private static boolean isJNIclass(Doc doc)
-        {
-            if (doc instanceof ProgramElementDoc)
-            {
-                ProgramElementDoc pdoc = (ProgramElementDoc) doc;
-                if (pdoc.containingPackage().name().startsWith("libsbmlJNI"))
-                    return true;
-            }
-            return doc.name().startsWith("libsbmlJNI");
-        }
-
-        private static boolean isSWIGOwnershipMethod(Doc doc)
-        {
-            if (doc instanceof ProgramElementDoc)
-            {
-                ProgramElementDoc pdoc = (ProgramElementDoc) doc;
-                if (pdoc.qualifiedName().endsWith("swigReleaseOwnership")
-                    || pdoc.qualifiedName().endsWith("swigTakeOwnership"))
-                    return true;
-            }
-            return (doc.isMethod()
-                    && (doc.name().equals("swigReleaseOwnership")
-                        || doc.name().equals("swigTakeOwnership")));
-        }
-
-        private static boolean isDeleteMethod(Doc doc)
-        {
-            if (doc instanceof ProgramElementDoc)
-            {
-                ProgramElementDoc pdoc = (ProgramElementDoc) doc;
-                if (pdoc.qualifiedName().endsWith("delete"))
-                    return true;
-            }
-            return (doc.isMethod() && doc.name().equals("delete"));
-        }
-
-        private static Object process(Object obj, Class expect)
-        {
-            if (obj == null)
-                return null;
-            Class cls = obj.getClass();
-            if (cls.getName().startsWith("com.sun."))
-            {
-                return Proxy.newProxyInstance(cls.getClassLoader(),
-                                              cls.getInterfaces(),
-                                              new InternalTagHandler(obj));
-            }
-            else if (obj instanceof Object[])
-            {
-                Class componentType = expect.getComponentType();
-                Object[] array = (Object[])obj;
-                List list = new ArrayList(array.length);
-                for (int i = 0; i < array.length; i++)
-                {
-                    Object entry = array[i];
-                    if (entry instanceof Doc)
-                    {
-                        Doc item = (Doc) entry;
-
-                        if (markedInternal(item))
-                            continue;
-
-                        if (isSWIGWrapper(item) || isJNIclass(item) ||
-                            isSWIGOwnershipMethod(item))
-                        {
-                            if (m_list_skipped)
-                            {
-                                the_root.printNotice("SBMLDoclet: skipping "
-                                                     + item);
-                            }
-                            continue;
-                        }
-
-                        if (isDeleteMethod(item))
-                        {
-                            item.setRawCommentText(
-                                 "Explicitly deletes the underlying native object." +
-                                 "<p>" +
-                                 "In general, application software will not need to call this method " +
-                                 "directly.  The Java language binding for libSBML is implemented as a " +
-                                 "language wrapper that provides a Java interface to libSBML's " +
-                                 "underlying C++/C code.  Some of the Java methods return objects that " +
-                                 "are linked to objects created not by Java code, but by C++ code.  The " +
-                                 "Java objects wrapped around them will be deleted when the garbage " +
-                                 "collector invokes the corresponding C++ <code>finalize()</code> methods for the " +
-                                 "objects.  The <code>finalize()</code> methods in turn call " +
-                                 "the {@link #delete()} method on the libSBML object. " +
-                                 "<p>" +
-                                 "This method is exposed in case calling programs want to ensure that " +
-                                 "the underlying object is freed immediately, and not at some arbitrary " +
-                                 "time determined by the Java garbage collector.  In normal usage, " +
-                                 "callers do not need to invoke {@link #delete()} themselves.");
-                        }
-                    }
-                    list.add(process(entry, componentType));
-                }
-                return list.toArray((Object[])Array.newInstance(componentType, list.size()));
-            }
-            else
-            {
-                return obj;
-            }
-        }
-
-        private static class InternalTagHandler
-            implements InvocationHandler
-        {
-            private Object target;
-
-            public InternalTagHandler(Object target)
-            {
-                this.target = target;
-            }
-
-            public Object invoke(Object proxy, Method method, Object[] args)
-                throws Throwable
-            {
-                if (args != null)
-                {
-                    String mName = method.getName();
-                    if (mName.equals("compareTo") || mName.equals("equals") ||
-                        mName.equals("overrides") || mName.equals("subclassOf"))
-                    {
-                        args[0] = unwrap(args[0]);
-                    }
-                }
-                try
-                {
-                    return process(method.invoke(target, args), method.getReturnType());
-                }
-                catch (InvocationTargetException e)
-                {
-                    throw e.getTargetException();
-                }
-            }
-
-            private Object unwrap(Object proxy)
-            {
-                if (proxy instanceof Proxy)
-                    return ((InternalTagHandler) Proxy.getInvocationHandler(proxy)).target;
-                return proxy;
-            }
-        }
-    }
-
-}
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -229,67 +229,10 @@ if (WITH_JAVA)
 		file(COPY ${graphic} DESTINATION ${CMAKE_CURRENT_SOURCE_DIR}/formatted/java-api/org/sbml/libsbml/)
 	endforeach()
 
+	# Do not care about Java api doc
+	#add_custom_target(api_docs_java ALL DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/formatted/java-api/index.html)
 
-	ADD_CUSTOM_COMMAND(
-		OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/formatted/java-api/index.html
-		COMMAND ${Java_JAVAC_EXECUTABLE}
-		ARGS -nowarn
-			 -cp "${Java_JAVADOC_JAR}"
-			 ${CMAKE_CURRENT_SOURCE_DIR}/src/SBMLDoclet.java
-			  -d "${current_dir}"
-		COMMAND ${Java_JAVA_EXECUTABLE}
-		ARGS  -cp "${Java_JAVADOC_JAR}${FILE_SEP}${current_dir}"
-		      SBMLDoclet
-			  -use -public -version -author -sourcetab 4 -keywords -nohelp
-			  -link http://docs.oracle.com/javase/1.6.0/docs/api
-			  -tag note:a:"Note:"
-			  -tag warning:a:"Warning:"
-			  -excludefile java-skip.txt
-			  -header "${LIBSBML_JAVADOC_HEADER}"
-			  -bottom "${LIBSBML_JAVADOC_FOOTER}"
-			  -windowtitle ${LIBSBML_JAVADOC_WINDOWTITLE}
-			  -doctitle ${LIBSBML_JAVADOC_DOCTITLE}
-			  -overview libsbml-java-fake-overview.html
-			  -stylesheetfile css/libsbml-javadoc-stylesheet.css
-			  -d ${output_dir}
-	          -sourcepath ${java_dir} org.sbml.libsbml
-		COMMENT "Generate Java-API Documentation"
-		VERBATIM
-		WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/src
-
-		COMMAND "${CMAKE_COMMAND}"
-		ARGS -E copy
-			"${logo_file}"
-			"${output_dir}"
-
-		COMMAND "${CMAKE_COMMAND}"
-		ARGS -E copy
-			"${sbml_js}"
-			"${output_dir}"
-
-#		COMMAND "${CMAKE_COMMAND}"
-#		ARGS -E copy
-#			"${tabs_css}"
-#			"${output_dir}"
-
-#		COMMAND "${CMAKE_COMMAND}"
-#		ARGS -E copy
-#			${logo_file}
-#			${java_output_dir}
-#
-		COMMAND "${CMAKE_COMMAND}"
-		ARGS -DPACKAGE_VERSION=\"${PACKAGE_VERSION}\"
-			-Djava_manual=${CMAKE_CURRENT_SOURCE_DIR}/formatted/java-api
-			-P ${CMAKE_CURRENT_SOURCE_DIR}/process-java-doc.cmake
-
-		DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/CMakeLists.txt
-				${CMAKE_CURRENT_SOURCE_DIR}/process-java-doc.cmake
-
-		)
-
-	add_custom_target(api_docs_java ALL DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/formatted/java-api/index.html)
-
-	install(DIRECTORY ${output_dir} DESTINATION ${MISC_PREFIX}docs )
+	#install(DIRECTORY ${output_dir} DESTINATION ${MISC_PREFIX}docs )
 
 endif()