In Doxygen 1.11.0, Include Graphs are not made for Java

[tkaken]

Describe the bug

Include Graphs are not generated for Java files.

Screenshots

This shows that the pkg1.Class1a Include Graph is missing:

This is pkg1.Class1a's class diagram that shows that pkg1.Class1a uses pkg1.Class1b and pkg2.Class2:

Here is a couple pkg.Class1a call graphs which verify that graphviz is working:

To Reproduce

Source code

Here are the source code files used. You'll see that pkg1.Class1a uses both pkg1.Class1b and pkg2.Class2.

// File: Class1a.java
package pkg1;

import pkg2.Class2;

public class Class1a {
	public Class1a()
	{
		this.theClass1b = new Class1b();
		this.theClass2 = new Class2();
	}
	
	public void useClass1b()
	{
		this.theClass1b.doClass1bStuff();
	}
	
	public void useClass2()
	{
		this.theClass2.doClass2Stuff();
	}
	
	private Class1b theClass1b;
	private Class2 theClass2;
}

//File: Class1b.java
package pkg1;

public class Class1b {
	
	public void doClass1bStuff() {
	}
}

//File: Class2.java
package pkg2;

import pkg1.Class1a;

public class Class2 {
	public void doClass2Stuff() {
	}
}

Config file

Note that the following settings are all set to YES:

• INCLUDE_GRAPH
• INCLUDED_BY_GRAPH
• OPTIMIZE_OUTPUT_JAVA
• HAVE_DOT

Here is the full list of settings:

# Doxyfile 1.11.0

#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
DOXYFILE_ENCODING      = UTF-8
PROJECT_NAME           = "JavaCode 1.11.0"
PROJECT_NUMBER         =
PROJECT_BRIEF          =
PROJECT_LOGO           =
PROJECT_ICON           =
OUTPUT_DIRECTORY       = doxy_output/java/1_11
CREATE_SUBDIRS         = NO
CREATE_SUBDIRS_LEVEL   = 8
ALLOW_UNICODE_NAMES    = NO
OUTPUT_LANGUAGE        = English
BRIEF_MEMBER_DESC      = YES
REPEAT_BRIEF           = YES
ABBREVIATE_BRIEF       = "The $name class" \
                         "The $name widget" \
                         "The $name file" \
                         is \
                         provides \
                         specifies \
                         contains \
                         represents \
                         a \
                         an \
                         the
ALWAYS_DETAILED_SEC    = NO
INLINE_INHERITED_MEMB  = NO
FULL_PATH_NAMES        = YES
STRIP_FROM_PATH        =
STRIP_FROM_INC_PATH    =
SHORT_NAMES            = YES
JAVADOC_AUTOBRIEF      = NO
JAVADOC_BANNER         = NO
QT_AUTOBRIEF           = NO
MULTILINE_CPP_IS_BRIEF = NO
PYTHON_DOCSTRING       = YES
INHERIT_DOCS           = YES
SEPARATE_MEMBER_PAGES  = NO
TAB_SIZE               = 4
ALIASES                =
OPTIMIZE_OUTPUT_FOR_C  = NO
OPTIMIZE_OUTPUT_JAVA   = YES
OPTIMIZE_FOR_FORTRAN   = NO
OPTIMIZE_OUTPUT_VHDL   = NO
OPTIMIZE_OUTPUT_SLICE  = NO
EXTENSION_MAPPING      =
MARKDOWN_SUPPORT       = YES
TOC_INCLUDE_HEADINGS   = 5
MARKDOWN_ID_STYLE      = DOXYGEN
AUTOLINK_SUPPORT       = YES
BUILTIN_STL_SUPPORT    = NO
CPP_CLI_SUPPORT        = NO
SIP_SUPPORT            = NO
IDL_PROPERTY_SUPPORT   = YES
DISTRIBUTE_GROUP_DOC   = NO
GROUP_NESTED_COMPOUNDS = NO
SUBGROUPING            = YES
INLINE_GROUPED_CLASSES = NO
INLINE_SIMPLE_STRUCTS  = NO
TYPEDEF_HIDES_STRUCT   = NO
LOOKUP_CACHE_SIZE      = 0
NUM_PROC_THREADS       = 1
TIMESTAMP              = NO
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
EXTRACT_ALL            = YES
EXTRACT_PRIVATE        = YES
EXTRACT_PRIV_VIRTUAL   = NO
EXTRACT_PACKAGE        = NO
EXTRACT_STATIC         = NO
EXTRACT_LOCAL_CLASSES  = YES
EXTRACT_LOCAL_METHODS  = NO
EXTRACT_ANON_NSPACES   = NO
RESOLVE_UNNAMED_PARAMS = YES
HIDE_UNDOC_MEMBERS     = NO
HIDE_UNDOC_CLASSES     = NO
HIDE_FRIEND_COMPOUNDS  = NO
HIDE_IN_BODY_DOCS      = NO
INTERNAL_DOCS          = NO
CASE_SENSE_NAMES       = NO
HIDE_SCOPE_NAMES       = NO
HIDE_COMPOUND_REFERENCE= NO
SHOW_HEADERFILE        = YES
SHOW_INCLUDE_FILES     = YES
SHOW_GROUPED_MEMB_INC  = NO
FORCE_LOCAL_INCLUDES   = NO
INLINE_INFO            = YES
SORT_MEMBER_DOCS       = YES
SORT_BRIEF_DOCS        = NO
SORT_MEMBERS_CTORS_1ST = NO
SORT_GROUP_NAMES       = NO
SORT_BY_SCOPE_NAME     = NO
STRICT_PROTO_MATCHING  = NO
GENERATE_TODOLIST      = YES
GENERATE_TESTLIST      = YES
GENERATE_BUGLIST       = YES
GENERATE_DEPRECATEDLIST= YES
ENABLED_SECTIONS       =
MAX_INITIALIZER_LINES  = 30
SHOW_USED_FILES        = YES
SHOW_FILES             = YES
SHOW_NAMESPACES        = YES
FILE_VERSION_FILTER    =
LAYOUT_FILE            =
CITE_BIB_FILES         =
#---------------------------------------------------------------------------
# Configuration options related to warning and progress messages
#---------------------------------------------------------------------------
QUIET                  = NO
WARNINGS               = YES
WARN_IF_UNDOCUMENTED   = YES
WARN_IF_DOC_ERROR      = YES
WARN_IF_INCOMPLETE_DOC = YES
WARN_NO_PARAMDOC       = NO
WARN_IF_UNDOC_ENUM_VAL = NO
WARN_AS_ERROR          = NO
WARN_FORMAT            = "$file:$line: $text"
WARN_LINE_FORMAT       = "at line $line of file $file"
WARN_LOGFILE           =
#---------------------------------------------------------------------------
# Configuration options related to the input files
#---------------------------------------------------------------------------
INPUT                  = Java/src
INPUT_ENCODING         = UTF-8
INPUT_FILE_ENCODING    =
FILE_PATTERNS          = *.c \
                         *.cc \
                         *.cxx \
                         *.cpp \
                         *.c++ \
                         *.java \
                         *.ii \
                         *.ixx \
                         *.ipp \
                         *.i++ \
                         *.inl \
                         *.idl \
                         *.ddl \
                         *.odl \
                         *.h \
                         *.hh \
                         *.hxx \
                         *.hpp \
                         *.h++ \
                         *.cs \
                         *.d \
                         *.php \
                         *.php4 \
                         *.php5 \
                         *.phtml \
                         *.inc \
                         *.m \
                         *.markdown \
                         *.md \
                         *.mm \
                         *.dox \
                         *.py \
                         *.pyw \
                         *.f90 \
                         *.f95 \
                         *.f03 \
                         *.f08 \
                         *.f18 \
                         *.f \
                         *.for \
                         *.vhd \
                         *.vhdl \
                         *.ucf \
                         *.qsf \
                         *.ice
RECURSIVE              = YES
EXCLUDE                =
EXCLUDE_SYMLINKS       = NO
EXCLUDE_PATTERNS       =
EXCLUDE_SYMBOLS        =
EXAMPLE_PATH           =
EXAMPLE_PATTERNS       = *
EXAMPLE_RECURSIVE      = NO
IMAGE_PATH             =
INPUT_FILTER           =
FILTER_PATTERNS        =
FILTER_SOURCE_FILES    = NO
FILTER_SOURCE_PATTERNS =
USE_MDFILE_AS_MAINPAGE =
FORTRAN_COMMENT_AFTER  = 72
#---------------------------------------------------------------------------
# Configuration options related to source browsing
#---------------------------------------------------------------------------
SOURCE_BROWSER         = YES
INLINE_SOURCES         = NO
STRIP_CODE_COMMENTS    = YES
REFERENCED_BY_RELATION = NO
REFERENCES_RELATION    = NO
REFERENCES_LINK_SOURCE = YES
SOURCE_TOOLTIPS        = YES
USE_HTAGS              = NO
VERBATIM_HEADERS       = YES
CLANG_ASSISTED_PARSING = NO
CLANG_ADD_INC_PATHS    = YES
CLANG_OPTIONS          =
CLANG_DATABASE_PATH    =
#---------------------------------------------------------------------------
# Configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
ALPHABETICAL_INDEX     = YES
IGNORE_PREFIX          =
#---------------------------------------------------------------------------
# Configuration options related to the HTML output
#---------------------------------------------------------------------------
GENERATE_HTML          = YES
HTML_OUTPUT            = html
HTML_FILE_EXTENSION    = .html
HTML_HEADER            =
HTML_FOOTER            =
HTML_STYLESHEET        =
HTML_EXTRA_STYLESHEET  =
HTML_EXTRA_FILES       =
HTML_COLORSTYLE        = AUTO_LIGHT
HTML_COLORSTYLE_HUE    = 220
HTML_COLORSTYLE_SAT    = 100
HTML_COLORSTYLE_GAMMA  = 80
HTML_DYNAMIC_MENUS     = YES
HTML_DYNAMIC_SECTIONS  = NO
HTML_CODE_FOLDING      = YES
HTML_COPY_CLIPBOARD    = YES
HTML_PROJECT_COOKIE    =
HTML_INDEX_NUM_ENTRIES = 100
GENERATE_DOCSET        = NO
DOCSET_FEEDNAME        = "Doxygen generated docs"
DOCSET_FEEDURL         =
DOCSET_BUNDLE_ID       = org.doxygen.Project
DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
DOCSET_PUBLISHER_NAME  = Publisher
GENERATE_HTMLHELP      = NO
CHM_FILE               =
HHC_LOCATION           =
GENERATE_CHI           = NO
CHM_INDEX_ENCODING     =
BINARY_TOC             = NO
TOC_EXPAND             = NO
SITEMAP_URL            =
GENERATE_QHP           = NO
QCH_FILE               =
QHP_NAMESPACE          = org.doxygen.Project
QHP_VIRTUAL_FOLDER     = doc
QHP_CUST_FILTER_NAME   =
QHP_CUST_FILTER_ATTRS  =
QHP_SECT_FILTER_ATTRS  =
QHG_LOCATION           =
GENERATE_ECLIPSEHELP   = NO
ECLIPSE_DOC_ID         = org.doxygen.Project
DISABLE_INDEX          = NO
GENERATE_TREEVIEW      = NO
FULL_SIDEBAR           = NO
ENUM_VALUES_PER_LINE   = 4
TREEVIEW_WIDTH         = 250
EXT_LINKS_IN_WINDOW    = NO
OBFUSCATE_EMAILS       = YES
HTML_FORMULA_FORMAT    = png
FORMULA_FONTSIZE       = 10
FORMULA_MACROFILE      =
USE_MATHJAX            = NO
MATHJAX_VERSION        = MathJax_2
MATHJAX_FORMAT         = HTML-CSS
MATHJAX_RELPATH        = https://cdn.jsdelivr.net/npm/mathjax@2
MATHJAX_EXTENSIONS     =
MATHJAX_CODEFILE       =
SEARCHENGINE           = YES
SERVER_BASED_SEARCH    = NO
EXTERNAL_SEARCH        = NO
SEARCHENGINE_URL       =
SEARCHDATA_FILE        = searchdata.xml
EXTERNAL_SEARCH_ID     =
EXTRA_SEARCH_MAPPINGS  =
#---------------------------------------------------------------------------
# Configuration options related to the LaTeX output
#---------------------------------------------------------------------------
GENERATE_LATEX         = NO
LATEX_OUTPUT           = latex
LATEX_CMD_NAME         =
MAKEINDEX_CMD_NAME     = makeindex
LATEX_MAKEINDEX_CMD    = makeindex
COMPACT_LATEX          = NO
PAPER_TYPE             = a4
EXTRA_PACKAGES         =
LATEX_HEADER           =
LATEX_FOOTER           =
LATEX_EXTRA_STYLESHEET =
LATEX_EXTRA_FILES      =
PDF_HYPERLINKS         = YES
USE_PDFLATEX           = YES
LATEX_BATCHMODE        = NO
LATEX_HIDE_INDICES     = NO
LATEX_BIB_STYLE        = plain
LATEX_EMOJI_DIRECTORY  =
#---------------------------------------------------------------------------
# Configuration options related to the RTF output
#---------------------------------------------------------------------------
GENERATE_RTF           = NO
RTF_OUTPUT             = rtf
COMPACT_RTF            = NO
RTF_HYPERLINKS         = NO
RTF_STYLESHEET_FILE    =
RTF_EXTENSIONS_FILE    =
RTF_EXTRA_FILES        =

#---------------------------------------------------------------------------
# Configuration options related to the man page output
#---------------------------------------------------------------------------
GENERATE_MAN           = NO
MAN_OUTPUT             = man
MAN_EXTENSION          = .3
MAN_SUBDIR             =
MAN_LINKS              = NO
#---------------------------------------------------------------------------
# Configuration options related to the XML output
#---------------------------------------------------------------------------
GENERATE_XML           = NO
XML_OUTPUT             = xml
XML_PROGRAMLISTING     = YES
XML_NS_MEMB_FILE_SCOPE = NO
#---------------------------------------------------------------------------
# Configuration options related to the DOCBOOK output
#---------------------------------------------------------------------------
GENERATE_DOCBOOK       = NO
DOCBOOK_OUTPUT         = docbook
#---------------------------------------------------------------------------
# Configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
GENERATE_AUTOGEN_DEF   = NO
#---------------------------------------------------------------------------
# Configuration options related to Sqlite3 output
#---------------------------------------------------------------------------
GENERATE_SQLITE3       = NO
SQLITE3_OUTPUT         = sqlite3
SQLITE3_RECREATE_DB    = YES
#---------------------------------------------------------------------------
# Configuration options related to the Perl module output
#---------------------------------------------------------------------------
GENERATE_PERLMOD       = NO
PERLMOD_LATEX          = NO
PERLMOD_PRETTY         = YES
PERLMOD_MAKEVAR_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
ENABLE_PREPROCESSING   = YES
MACRO_EXPANSION        = NO
EXPAND_ONLY_PREDEF     = NO
SEARCH_INCLUDES        = YES
INCLUDE_PATH           =
INCLUDE_FILE_PATTERNS  =
PREDEFINED             =
EXPAND_AS_DEFINED      =
SKIP_FUNCTION_MACROS   = YES
#---------------------------------------------------------------------------
# Configuration options related to external references
#---------------------------------------------------------------------------
TAGFILES               =
GENERATE_TAGFILE       =
ALLEXTERNALS           = NO
EXTERNAL_GROUPS        = YES
EXTERNAL_PAGES         = YES
#---------------------------------------------------------------------------
# Configuration options related to diagram generator tools
#---------------------------------------------------------------------------
HIDE_UNDOC_RELATIONS   = YES
HAVE_DOT               = YES
DOT_NUM_THREADS        = 0
DOT_COMMON_ATTR        = "fontname=Helvetica,fontsize=10"
DOT_EDGE_ATTR          = "labelfontname=Helvetica,labelfontsize=10"
DOT_NODE_ATTR          = "shape=box,height=0.2,width=0.4"
DOT_FONTPATH           =
CLASS_GRAPH            = YES
COLLABORATION_GRAPH    = YES
GROUP_GRAPHS           = YES
UML_LOOK               = NO
UML_LIMIT_NUM_FIELDS   = 10
DOT_UML_DETAILS        = NO
DOT_WRAP_THRESHOLD     = 17
TEMPLATE_RELATIONS     = YES
INCLUDE_GRAPH          = YES
INCLUDED_BY_GRAPH      = YES
CALL_GRAPH             = YES
CALLER_GRAPH           = YES
GRAPHICAL_HIERARCHY    = YES
DIRECTORY_GRAPH        = YES
DIR_GRAPH_MAX_DEPTH    = 1
DOT_IMAGE_FORMAT       = png
INTERACTIVE_SVG        = NO
DOT_PATH               =
DOTFILE_DIRS           =
DIA_PATH               =
DIAFILE_DIRS           =
PLANTUML_JAR_PATH      =
PLANTUML_CFG_FILE      =
PLANTUML_INCLUDE_PATH  =
DOT_GRAPH_MAX_NODES    = 50
MAX_DOT_GRAPH_DEPTH    = 0
DOT_MULTI_TARGETS      = NO
GENERATE_LEGEND        = YES
DOT_CLEANUP            = YES
MSCGEN_TOOL            =
MSCFILE_DIRS           =

Files to reproduce the issue

Here is a zip file containing the files you can use to reproduce the issue.

Expected behavior

I expected to see the Include Graph showing that Class1a.java includes Class1b.java and Class2.java.

Version

I had this happen on version 1.11.0 on Windows 10, 64bit.

Additional information

I saw that in version 1.9.8, an Include Graph was created for this code, but the included item was shown as a class rather than as a file. Starting in 1.10.0 the entire Include Graph did not get generated.

[albert-github]

The Include graph was only shown in the 1.9.8 version in the doxygen 1.9.7 version it was not present either (neither in some earlier versions).
This change of behavior was cause by (44a8353 ):

Commit: 44a8353ae451b25db7ba20748db742bd7670da14 [44a8353]
Date: Monday, October 30, 2023 8:43:45 PM

Merge pull request #10385 from albert-github/feature/bug_import_non_cpp

Handling of `import` in non cpp files

So just undoing this is not an option.
The JavaImport are already handled in the scanner.l so we can add here some relevant code.

I've just pushed a proposed patch, pull request #11018

[albert-github]

Code has been integrated in master on GitHub (please don't close the issue as this will be done at the moment of an official release).

[doxygen]

This issue was previously marked 'fixed but not released',
which means it should be fixed in doxygen version 1.12.0.
Please verify if this is indeed the case. Reopen the
issue if you think it is not fixed and please include any additional information
that you think can be relevant (preferably in the form of a self-contained example).