Broke out API functions in the core into separate files

docs/tripal_doxygen.config

@@ -0,0 +1,1716 @@
+# Doxyfile 1.7.4
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project.
+#
+# All text after a hash (#) is considered a comment and will be ignored.
+# The format is:
+#       TAG = value [value, ...]
+# For lists items can also be appended using:
+#       TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (" ").
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the config file
+# that follow. The default is UTF-8 which is also the encoding used for all
+# text before the first occurrence of this tag. Doxygen uses libiconv (or the
+# iconv built into libc) for the transcoding. See
+# http://www.gnu.org/software/libiconv for the list of possible encodings.
+
+DOXYFILE_ENCODING      = UTF-8
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
+# by quotes) that should identify the project.
+
+PROJECT_NAME           = Tripal
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number.
+# This could be handy for archiving the generated documentation or
+# if some version control system is used.
+
+PROJECT_NUMBER         = "v1.0 (6.x-1.0)"
+
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer
+# a quick idea about the purpose of the project. Keep the description short.
+
+PROJECT_BRIEF          = 
+
+# With the PROJECT_LOGO tag one can specify an logo or icon that is
+# included in the documentation. The maximum height of the logo should not
+# exceed 55 pixels and the maximum width should not exceed 200 pixels.
+# Doxygen will copy the logo to the output directory.
+
+PROJECT_LOGO           = 
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
+# base path where the generated documentation will be put.
+# If a relative path is entered, it will be relative to the location
+# where doxygen was started. If left blank the current directory will be used.
+
+OUTPUT_DIRECTORY       = docs
+
+# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
+# 4096 sub-directories (in 2 levels) under the output directory of each output
+# format and will distribute the generated files over these directories.
+# Enabling this option can be useful when feeding doxygen a huge amount of
+# source files, where putting all generated files in the same directory would
+# otherwise cause performance problems for the file system.
+
+CREATE_SUBDIRS         = YES
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# The default language is English, other supported languages are:
+# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
+# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
+# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
+# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
+# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
+# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
+
+OUTPUT_LANGUAGE        = English
+
+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
+# include brief member descriptions after the members that are listed in
+# the file and class documentation (similar to JavaDoc).
+# Set to NO to disable this.
+
+BRIEF_MEMBER_DESC      = YES
+
+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
+# the brief description of a member or function before the detailed description.
+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# brief descriptions will be completely suppressed.
+
+REPEAT_BRIEF           = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator
+# that is used to form the text in various listings. Each string
+# in this list, if found as the leading text of the brief description, will be
+# stripped from the text and the result after processing the whole list, is
+# used as the annotated text. Otherwise, the brief description is used as-is.
+# If left blank, the following values are used ("$name" is automatically
+# replaced with the name of the entity): "The $name class" "The $name widget"
+# "The $name file" "is" "provides" "specifies" "contains"
+# "represents" "a" "an" "the"
+
+ABBREVIATE_BRIEF       =
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# Doxygen will generate a detailed section even if there is only a brief
+# description.
+
+ALWAYS_DETAILED_SEC    = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
+# operators of the base classes will not be shown.
+
+INLINE_INHERITED_MEMB  = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
+# path before files name in the file list and in the header files. If set
+# to NO the shortest path that makes the file name unique will be used.
+
+FULL_PATH_NAMES        = YES
+
+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
+# can be used to strip a user-defined part of the path. Stripping is
+# only done if one of the specified strings matches the left-hand part of
+# the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the
+# path to strip.
+
+STRIP_FROM_PATH        =
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
+# the path mentioned in the documentation of a class, which tells
+# the reader which header file to include in order to use a class.
+# If left blank only the name of the header file containing the class
+# definition is used. Otherwise one should specify the include paths that
+# are normally passed to the compiler using the -I flag.
+
+STRIP_FROM_INC_PATH    =
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
+# (but less readable) file names. This can be useful if your file system
+# doesn't support long names like on DOS, Mac, or CD-ROM.
+
+SHORT_NAMES            = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
+# will interpret the first line (until the first dot) of a JavaDoc-style
+# comment as the brief description. If set to NO, the JavaDoc
+# comments will behave just like regular Qt-style comments
+# (thus requiring an explicit @brief command for a brief description.)
+
+JAVADOC_AUTOBRIEF      = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
+# interpret the first line (until the first dot) of a Qt-style
+# comment as the brief description. If set to NO, the comments
+# will behave just like regular Qt-style comments (thus requiring
+# an explicit \brief command for a brief description.)
+
+QT_AUTOBRIEF           = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
+# treat a multi-line C++ special comment block (i.e. a block of //! or ///
+# comments) as a brief description. This used to be the default behaviour.
+# The new default is to treat a multi-line C++ comment block as a detailed
+# description. Set this tag to YES if you prefer the old behaviour instead.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
+# member inherits the documentation from any documented member that it
+# re-implements.
+
+INHERIT_DOCS           = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
+# a new page for each member. If set to NO, the documentation of a member will
+# be part of the file/class/namespace that contains it.
+
+SEPARATE_MEMBER_PAGES  = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab.
+# Doxygen uses this value to replace tabs by spaces in code fragments.
+
+TAB_SIZE               = 8
+
+# This tag can be used to specify a number of aliases that acts
+# as commands in the documentation. An alias has the form "name=value".
+# For example adding "sideeffect=\par Side Effects:\n" will allow you to
+# put the command \sideeffect (or @sideeffect) in the documentation, which
+# will result in a user-defined paragraph with heading "Side Effects:".
+# You can put \n's in the value part of an alias to insert newlines.
+
+ALIASES                =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
+# sources only. Doxygen will then generate output that is more tailored for C.
+# For instance, some of the names that are used will be different. The list
+# of all members will be omitted, etc.
+
+OPTIMIZE_OUTPUT_FOR_C  = NO
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
+# sources only. Doxygen will then generate output that is more tailored for
+# Java. For instance, namespaces will be presented as packages, qualified
+# scopes will look different, etc.
+
+OPTIMIZE_OUTPUT_JAVA   = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources only. Doxygen will then generate output that is more tailored for
+# Fortran.
+
+OPTIMIZE_FOR_FORTRAN   = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for
+# VHDL.
+
+OPTIMIZE_OUTPUT_VHDL   = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given extension.
+# Doxygen has a built-in mapping, but you can override or extend it using this
+# tag. The format is ext=language, where ext is a file extension, and language
+# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C,
+# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make
+# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
+# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions
+# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
+
+EXTENSION_MAPPING      =
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should
+# set this tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
+# func(std::string) {}). This also makes the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+
+BUILTIN_STL_SUPPORT    = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+
+CPP_CLI_SUPPORT        = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
+# Doxygen will parse them like normal C++ but will assume all classes use public
+# instead of private inheritance when no explicit protection keyword is present.
+
+SIP_SUPPORT            = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate getter
+# and setter methods for a property. Setting this option to YES (the default)
+# will make doxygen replace the get and set methods by a property in the
+# documentation. This will only work if the methods are indeed getting or
+# setting a simple type. If this is not the case, or you want to show the
+# methods anyway, you should set this option to NO.
+
+IDL_PROPERTY_SUPPORT   = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES, then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+
+DISTRIBUTE_GROUP_DOC   = NO
+
+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
+# the same type (for instance a group of public functions) to be put as a
+# subgroup of that type (e.g. under the Public Functions section). Set it to
+# NO to prevent subgrouping. Alternatively, this can be done per class using
+# the \nosubgrouping command.
+
+SUBGROUPING            = YES
+
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and
+# unions are shown inside the group in which they are included (e.g. using
+# @ingroup) instead of on a separate page (for HTML and Man pages) or
+# section (for LaTeX and RTF).
+
+INLINE_GROUPED_CLASSES = NO
+
+# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
+# is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically
+# be useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+
+TYPEDEF_HIDES_STRUCT   = NO
+
+# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
+# determine which symbols to keep in memory and which to flush to disk.
+# When the cache is full, less often used symbols will be written to disk.
+# For small to medium size projects (<1000 input files) the default value is
+# probably good enough. For larger projects a too small cache size can cause
+# doxygen to be busy swapping symbols to and from disk most of the time
+# causing a significant performance penalty.
+# If the system has enough physical memory increasing the cache will improve the
+# performance by keeping more symbols in memory. Note that the value works on
+# a logarithmic scale so increasing the size by one will roughly double the
+# memory usage. The cache size is given by this formula:
+# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols
+
+SYMBOL_CACHE_SIZE      = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
+# documentation are documented, even if no documentation was available.
+# Private class members and static file members will be hidden unless
+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+
+EXTRACT_ALL            = YES
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
+# will be included in the documentation.
+
+EXTRACT_PRIVATE        = YES
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file
+# will be included in the documentation.
+
+EXTRACT_STATIC         = YES
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
+# defined locally in source files will be included in the documentation.
+# If set to NO only classes defined in header files are included.
+
+EXTRACT_LOCAL_CLASSES  = YES
+
+# This flag is only useful for Objective-C code. When set to YES local
+# methods, which are defined in the implementation section but not in
+# the interface are included in the documentation.
+# If set to NO (the default) only methods in the interface are included.
+
+EXTRACT_LOCAL_METHODS  = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base
+# name of the file that contains the anonymous namespace. By default
+# anonymous namespaces are hidden.
+
+EXTRACT_ANON_NSPACES   = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
+# undocumented members of documented classes, files or namespaces.
+# If set to NO (the default) these members will be included in the
+# various overviews, but no documentation section is generated.
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS     = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy.
+# If set to NO (the default) these classes will be included in the various
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES     = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
+# friend (class|struct|union) declarations.
+# If set to NO (the default) these declarations will be included in the
+# documentation.
+
+HIDE_FRIEND_COMPOUNDS  = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
+# documentation blocks found inside the body of a function.
+# If set to NO (the default) these blocks will be appended to the
+# function's detailed documentation block.
+
+HIDE_IN_BODY_DOCS      = NO
+
+# The INTERNAL_DOCS tag determines if documentation
+# that is typed after a \internal command is included. If the tag is set
+# to NO (the default) then the documentation will be excluded.
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS          = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
+# file names in lower-case letters. If set to YES upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+
+CASE_SENSE_NAMES       = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
+# will show members with their full class and namespace scopes in the
+# documentation. If set to YES the scope will be hidden.
+
+HIDE_SCOPE_NAMES       = NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
+# will put a list of the files that are included by a file in the documentation
+# of that file.
+
+SHOW_INCLUDE_FILES     = YES
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
+# will list include files with double quotes in the documentation
+# rather than with sharp brackets.
+
+FORCE_LOCAL_INCLUDES   = NO
+
+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
+# is inserted in the documentation for inline members.
+
+INLINE_INFO            = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
+# will sort the (detailed) documentation of file and class members
+# alphabetically by member name. If set to NO the members will appear in
+# declaration order.
+
+SORT_MEMBER_DOCS       = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
+# brief documentation of file, namespace and class members alphabetically
+# by member name. If set to NO (the default) the members will appear in
+# declaration order.
+
+SORT_BRIEF_DOCS        = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
+# will sort the (brief and detailed) documentation of class members so that
+# constructors and destructors are listed first. If set to NO (the default)
+# the constructors will appear in the respective orders defined by
+# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
+# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
+# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
+# hierarchy of group names into alphabetical order. If set to NO (the default)
+# the group names will appear in their defined order.
+
+SORT_GROUP_NAMES       = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
+# sorted by fully-qualified names, including namespaces. If set to
+# NO (the default), the class list will be sorted only by class name,
+# not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the
+# alphabetical list.
+
+SORT_BY_SCOPE_NAME     = NO
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
+# do proper type resolution of all parameters of a function it will reject a
+# match between the prototype and the implementation of a member function even
+# if there is only one candidate or it is obvious which candidate to choose
+# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
+# will still accept a match between prototype and implementation in such cases.
+
+STRICT_PROTO_MATCHING  = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or
+# disable (NO) the todo list. This list is created by putting \todo
+# commands in the documentation.
+
+GENERATE_TODOLIST      = NO
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or
+# disable (NO) the test list. This list is created by putting \test
+# commands in the documentation.
+
+GENERATE_TESTLIST      = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or
+# disable (NO) the bug list. This list is created by putting \bug
+# commands in the documentation.
+
+GENERATE_BUGLIST       = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
+# disable (NO) the deprecated list. This list is created by putting
+# \deprecated commands in the documentation.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional
+# documentation sections, marked by \if sectionname ... \endif.
+
+ENABLED_SECTIONS       =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
+# the initial value of a variable or macro consists of for it to appear in
+# the documentation. If the initializer consists of more lines than specified
+# here it will be hidden. Use a value of 0 to hide initializers completely.
+# The appearance of the initializer of individual variables and macros in the
+# documentation can be controlled using \showinitializer or \hideinitializer
+# command in the documentation regardless of this setting.
+
+MAX_INITIALIZER_LINES  = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
+# at the bottom of the documentation of classes and structs. If set to YES the
+# list will mention the files that were used to generate the documentation.
+
+SHOW_USED_FILES        = YES
+
+# If the sources in your project are distributed over multiple directories
+# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
+# in the documentation. The default is NO.
+
+SHOW_DIRECTORIES       = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
+# This will remove the Files entry from the Quick Index and from the
+# Folder Tree View (if specified). The default is YES.
+
+SHOW_FILES             = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
+# Namespaces page.
+# This will remove the Namespaces entry from the Quick Index
+# and from the Folder Tree View (if specified). The default is YES.
+
+SHOW_NAMESPACES        = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command <command> <input-file>, where <command> is the value of
+# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
+# provided by doxygen. Whatever the program writes to standard output
+# is used as the file version. See the manual for examples.
+
+FILE_VERSION_FILTER    =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. The create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option.
+# You can optionally specify a file name after the option, if omitted
+# DoxygenLayout.xml will be used as the name of the layout file.
+
+LAYOUT_FILE            =
+
+#---------------------------------------------------------------------------
+# configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+QUIET                  = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated by doxygen. Possible values are YES and NO. If left blank
+# NO is used.
+
+WARNINGS               = YES
+
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
+# automatically be disabled.
+
+WARN_IF_UNDOCUMENTED   = YES
+
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some
+# parameters in a documented function, or documenting parameters that
+# don't exist or using markup commands wrongly.
+
+WARN_IF_DOC_ERROR      = YES
+
+# The WARN_NO_PARAMDOC option can be enabled to get warnings for
+# functions that are documented, but have no documentation for their parameters
+# or return value. If set to NO (the default) doxygen will only warn about
+# wrong or incomplete parameter documentation, but not about the absence of
+# documentation.
+
+WARN_NO_PARAMDOC       = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that
+# doxygen can produce. The string should contain the $file, $line, and $text
+# tags, which will be replaced by the file and line number from which the
+# warning originated and the warning text. Optionally the format may contain
+# $version, which will be replaced by the version of the file (if it could
+# be obtained via FILE_VERSION_FILTER)
+
+WARN_FORMAT            = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning
+# and error messages should be written. If left blank the output is written
+# to stderr.
+
+WARN_LOGFILE           =
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain
+# documented source files. You may enter file names like "myfile.cpp" or
+# directories like "/usr/src/myproject". Separate the files or directories
+# with spaces.
+
+INPUT                  = tripal_core tripal_db tripal_cv tripal_organism tripal_analysis tripal_feature tripal_stock tripal_project tripal_natural_diversity tripal_genetic tripal_views tripal_bulk_loader tripal_library tripal_contact tripal_featuremap tripal_phenotype 
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
+# also the default input encoding. Doxygen uses libiconv (or the iconv built
+# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
+# the list of possible encodings.
+
+INPUT_ENCODING         = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank the following patterns are tested:
+# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh
+# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
+# *.f90 *.f *.for *.vhd *.vhdl
+
+FILE_PATTERNS          = *.php *.inc *.module
+
+# The RECURSIVE tag can be used to turn specify whether or not subdirectories
+# should be searched for input files as well. Possible values are YES and NO.
+# If left blank NO is used.
+
+RECURSIVE              = YES
+
+# The EXCLUDE tag can be used to specify files and/or directories that should
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+
+EXCLUDE                = 
+
+# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
+# from the input.
+
+EXCLUDE_SYMLINKS       = YES
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories. Note that the wildcards are matched
+# against the file with absolute path, so to exclude all test directories
+# for example use the pattern */test/*
+
+EXCLUDE_PATTERNS       =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+
+EXCLUDE_SYMBOLS        =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or
+# directories that contain example code fragments that are included (see
+# the \include command).
+
+EXAMPLE_PATH           =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank all files are included.
+
+EXAMPLE_PATTERNS       =
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude
+# commands irrespective of the value of the RECURSIVE tag.
+# Possible values are YES and NO. If left blank NO is used.
+
+EXAMPLE_RECURSIVE      = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or
+# directories that contain image that are included in the documentation (see
+# the \image command).
+
+IMAGE_PATH             =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command <filter> <input-file>, where <filter>
+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
+# input file. Doxygen will then use the output that the filter program writes
+# to standard output.
+# If FILTER_PATTERNS is specified, this tag will be
+# ignored.
+
+INPUT_FILTER           =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis.
+# Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match.
+# The filters are a list of the form:
+# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
+# info on how filters are used. If FILTER_PATTERNS is empty or if
+# non of the patterns match the file name, INPUT_FILTER is applied.
+
+FILTER_PATTERNS        =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will be used to filter the input files when producing source
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+
+FILTER_SOURCE_FILES    = NO
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any)
+# and it is also possible to disable source filtering for a specific pattern
+# using *.ext= (so without naming a filter). This option only has effect when
+# FILTER_SOURCE_FILES is enabled.
+
+FILTER_SOURCE_PATTERNS =
+
+#---------------------------------------------------------------------------
+# configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will
+# be generated. Documented entities will be cross-referenced with these sources.
+# Note: To get rid of all source code in the generated output, make sure also
+# VERBATIM_HEADERS is set to NO.
+
+SOURCE_BROWSER         = YES
+
+# Setting the INLINE_SOURCES tag to YES will include the body
+# of functions and classes directly in the documentation.
+
+INLINE_SOURCES         = YES
+
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
+# doxygen to hide any special comment blocks from generated source code
+# fragments. Normal C and C++ comments will always remain visible.
+
+STRIP_CODE_COMMENTS    = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES
+# then for each documented function all documented
+# functions referencing it will be listed.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES
+# then for each documented function all documented entities
+# called/used by that function will be listed.
+
+REFERENCES_RELATION    = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
+# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
+# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
+# link to the source code.
+# Otherwise they will link to the documentation.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code
+# will point to the HTML generated by the htags(1) tool instead of doxygen
+# built-in source browser. The htags tool is part of GNU's global source
+# tagging system (see http://www.gnu.org/software/global/global.html). You
+# will need version 4.8.6 or higher.
+
+USE_HTAGS              = NO
+
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
+# will generate a verbatim copy of the header file for each class for
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS       = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
+# of all compounds will be generated. Enable this if the project
+# contains a lot of classes, structs, unions or interfaces.
+
+ALPHABETICAL_INDEX     = YES
+
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
+# in which this list will be split (can be a number in the range [1..20])
+
+COLS_IN_ALPHA_INDEX    = 5
+
+# In case all classes in a project start with a common prefix, all
+# classes will be put under the same header in the alphabetical index.
+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
+# should be ignored while generating the index headers.
+
+IGNORE_PREFIX          =
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
+# generate HTML output.
+
+GENERATE_HTML          = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `html' will be used as the default path.
+
+HTML_OUTPUT            = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
+# doxygen will generate files with .html extension.
+
+HTML_FILE_EXTENSION    = .html
+
+# The HTML_HEADER tag can be used to specify a personal HTML header for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard header. Note that when using a custom header you are responsible
+# for the proper inclusion of any scripts and style sheets that doxygen
+# needs, which is dependent on the configuration options used.
+# It is adviced to generate a default header using "doxygen -w html
+# header.html footer.html stylesheet.css YourConfigFile" and then modify
+# that header. Note that the header is subject to change so you typically
+# have to redo this when upgrading to a newer version of doxygen or when changing the value of configuration settings such as GENERATE_TREEVIEW!
+
+HTML_HEADER            =
+
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard footer.
+
+HTML_FOOTER            =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
+# style sheet that is used by each HTML page. It can be used to
+# fine-tune the look of the HTML output. If the tag is left blank doxygen
+# will generate a default style sheet. Note that doxygen will try to copy
+# the style sheet file to the HTML output directory, so don't put your own
+# stylesheet in the HTML output directory as well, or it will be erased!
+
+HTML_STYLESHEET        =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that
+# the files will be copied as-is; there are no commands or markers available.
+
+HTML_EXTRA_FILES       =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
+# Doxygen will adjust the colors in the stylesheet and background images
+# according to this color. Hue is specified as an angle on a colorwheel,
+# see http://en.wikipedia.org/wiki/Hue for more information.
+# For instance the value 0 represents red, 60 is yellow, 120 is green,
+# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
+# The allowed range is 0 to 359.
+
+HTML_COLORSTYLE_HUE    = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
+# the colors in the HTML output. For a value of 0 the output will use
+# grayscales only. A value of 255 will produce the most vivid colors.
+
+HTML_COLORSTYLE_SAT    = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
+# the luminance component of the colors in the HTML output. Values below
+# 100 gradually make the output lighter, whereas values above 100 make
+# the output darker. The value divided by 100 is the actual gamma applied,
+# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
+# and 100 does not change the gamma.
+
+HTML_COLORSTYLE_GAMMA  = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting
+# this to NO can help when comparing the output of multiple runs.
+
+HTML_TIMESTAMP         = YES
+
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
+# files or namespaces will be aligned in HTML using tables. If set to
+# NO a bullet list will be used.
+
+HTML_ALIGN_MEMBERS     = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded. For this to work a browser that supports
+# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
+# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
+
+HTML_DYNAMIC_SECTIONS  = YES
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files
+# will be generated that can be used as input for Apple's Xcode 3
+# integrated development environment, introduced with OSX 10.5 (Leopard).
+# To create a documentation set, doxygen will generate a Makefile in the
+# HTML output directory. Running make will produce the docset in that
+# directory and running "make install" will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
+# it at startup.
+# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
+
+GENERATE_DOCSET        = NO
+
+# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
+# feed. A documentation feed provides an umbrella under which multiple
+# documentation sets from a single provider (such as a company or product suite)
+# can be grouped.
+
+DOCSET_FEEDNAME        = "Doxygen generated docs"
+
+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
+# should uniquely identify the documentation set bundle. This should be a
+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
+# will append .docset to the name.
+
+DOCSET_BUNDLE_ID       = org.doxygen.Project
+
+# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+
+DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
+
+# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
+
+DOCSET_PUBLISHER_NAME  = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files
+# will be generated that can be used as input for tools like the
+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP      = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
+# be used to specify the file name of the resulting .chm file. You
+# can add a path in front of the file if the result should not be
+# written to the html output directory.
+
+CHM_FILE               =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
+# be used to specify the location (absolute path including file name) of
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
+# the HTML help compiler on the generated index.hhp.
+
+HHC_LOCATION           =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
+# controls if a separate .chi index file is generated (YES) or that
+# it should be included in the master .chm file (NO).
+
+GENERATE_CHI           = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
+# is used to encode HtmlHelp index (hhk), content (hhc) and project file
+# content.
+
+CHM_INDEX_ENCODING     =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
+# controls whether a binary table of contents is generated (YES) or a
+# normal table of contents (NO) in the .chm file.
+
+BINARY_TOC             = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members
+# to the contents of the HTML help documentation and to the tree view.
+
+TOC_EXPAND             = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
+# that can be used as input for Qt's qhelpgenerator to generate a
+# Qt Compressed Help (.qch) of the generated HTML documentation.
+
+GENERATE_QHP           = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
+# be used to specify the file name of the resulting .qch file.
+# The path specified is relative to the HTML output folder.
+
+QCH_FILE               =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#namespace
+
+QHP_NAMESPACE          = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#virtual-folders
+
+QHP_VIRTUAL_FOLDER     = doc
+
+# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to
+# add. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#custom-filters
+
+QHP_CUST_FILTER_NAME   =
+
+# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see
+# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">
+# Qt Help Project / Custom Filters</a>.
+
+QHP_CUST_FILTER_ATTRS  =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's
+# filter section matches.
+# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">
+# Qt Help Project / Filter Attributes</a>.
+
+QHP_SECT_FILTER_ATTRS  =
+
+# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
+# be used to specify the location of Qt's qhelpgenerator.
+# If non-empty doxygen will try to run qhelpgenerator on the generated
+# .qhp file.
+
+QHG_LOCATION           =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
+#  will be generated, which together with the HTML files, form an Eclipse help
+# plugin. To install this plugin and make it available under the help contents
+# menu in Eclipse, the contents of the directory containing the HTML and XML
+# files needs to be copied into the plugins directory of eclipse. The name of
+# the directory within the plugins directory should be the same as
+# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
+# the help appears.
+
+GENERATE_ECLIPSEHELP   = NO
+
+# A unique identifier for the eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have
+# this name.
+
+ECLIPSE_DOC_ID         = org.doxygen.Project
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
+# top of each HTML page. The value NO (the default) enables the index and
+# the value YES disables it.
+
+DISABLE_INDEX          = NO
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values
+# (range [0,1..20]) that doxygen will group on one line in the generated HTML
+# documentation. Note that a value of 0 will completely suppress the enum
+# values from appearing in the overview section.
+
+ENUM_VALUES_PER_LINE   = 4
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information.
+# If the tag value is set to YES, a side panel will be generated
+# containing a tree-like index structure (just like the one that
+# is generated for HTML Help). For this to work a browser that supports
+# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
+# Windows users are probably better off using the HTML help feature.
+
+GENERATE_TREEVIEW      = YES
+
+# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
+# and Class Hierarchy pages using a tree view instead of an ordered list.
+
+USE_INLINE_TREES       = YES
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
+# used to set the initial width (in pixels) of the frame in which the tree
+# is shown.
+
+TREEVIEW_WIDTH         = 250
+
+# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
+# links to external symbols imported via tag files in a separate window.
+
+EXT_LINKS_IN_WINDOW    = NO
+
+# Use this tag to change the font size of Latex formulas included
+# as images in the HTML documentation. The default is 10. Note that
+# when you change the font size after a successful doxygen run you need
+# to manually remove any form_*.png images from the HTML output directory
+# to force them to be regenerated.
+
+FORMULA_FONTSIZE       = 10
+
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are
+# not supported properly for IE 6.0, but are supported on all modern browsers.
+# Note that when changing this option you need to delete any form_*.png files
+# in the HTML output before the changes have effect.
+
+FORMULA_TRANSPARENT    = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
+# (see http://www.mathjax.org) which uses client side Javascript for the
+# rendering instead of using prerendered bitmaps. Use this if you do not
+# have LaTeX installed or if you want to formulas look prettier in the HTML
+# output. When enabled you also need to install MathJax separately and
+# configure the path to it using the MATHJAX_RELPATH option.
+
+USE_MATHJAX            = NO
+
+# When MathJax is enabled you need to specify the location relative to the
+# HTML output directory using the MATHJAX_RELPATH option. The destination
+# directory should contain the MathJax.js script. For instance, if the mathjax
+# directory is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the
+# mathjax.org site, so you can quickly see the result without installing
+# MathJax, but it is strongly recommended to install a local copy of MathJax
+# before deployment.
+
+MATHJAX_RELPATH        = http://www.mathjax.org/mathjax
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box
+# for the HTML output. The underlying search engine uses javascript
+# and DHTML and should work on any modern browser. Note that when using
+# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
+# (GENERATE_DOCSET) there is already a search function so this one should
+# typically be disabled. For large projects the javascript based search engine
+# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
+
+SEARCHENGINE           = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a PHP enabled web server instead of at the web client
+# using Javascript. Doxygen will generate the search PHP script and index
+# file to put on the web server. The advantage of the server
+# based approach is that it scales better to large projects and allows
+# full text search. The disadvantages are that it is more difficult to setup
+# and does not have live searching capabilities.
+
+SERVER_BASED_SEARCH    = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
+# generate Latex output.
+
+GENERATE_LATEX         = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `latex' will be used as the default path.
+
+LATEX_OUTPUT           = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked. If left blank `latex' will be used as the default command name.
+# Note that when enabling USE_PDFLATEX this option is only used for
+# generating bitmaps for formulas in the HTML output, but not in the
+# Makefile that is written to the output directory.
+
+LATEX_CMD_NAME         = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
+# generate index for LaTeX. If left blank `makeindex' will be used as the
+# default command name.
+
+MAKEINDEX_CMD_NAME     = makeindex
+
+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
+# LaTeX documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_LATEX          = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used
+# by the printer. Possible values are: a4, letter, legal and
+# executive. If left blank a4wide will be used.
+
+PAPER_TYPE             = a4
+
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
+# packages that should be included in the LaTeX output.
+
+EXTRA_PACKAGES         =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
+# the generated latex document. The header should contain everything until
+# the first chapter. If it is left blank doxygen will generate a
+# standard header. Notice: only use this tag if you know what you are doing!
+
+LATEX_HEADER           =
+
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for
+# the generated latex document. The footer should contain everything after
+# the last chapter. If it is left blank doxygen will generate a
+# standard footer. Notice: only use this tag if you know what you are doing!
+
+LATEX_FOOTER           =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
+# is prepared for conversion to pdf (using ps2pdf). The pdf file will
+# contain links (just like the HTML output) instead of page references
+# This makes the output suitable for online browsing using a pdf viewer.
+
+PDF_HYPERLINKS         = YES
+
+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
+# plain latex in the generated Makefile. Set this option to YES to get a
+# higher quality PDF documentation.
+
+USE_PDFLATEX           = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
+# command to the generated LaTeX files. This will instruct LaTeX to keep
+# running if errors occur, instead of asking the user for help.
+# This option is also used when generating formulas in HTML.
+
+LATEX_BATCHMODE        = NO
+
+# If LATEX_HIDE_INDICES is set to YES then doxygen will not
+# include the index chapters (such as File Index, Compound Index, etc.)
+# in the output.
+
+LATEX_HIDE_INDICES     = NO
+
+# If LATEX_SOURCE_CODE is set to YES then doxygen will include
+# source code with syntax highlighting in the LaTeX output.
+# Note that which sources are shown also depends on other settings
+# such as SOURCE_BROWSER.
+
+LATEX_SOURCE_CODE      = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
+# The RTF output is optimized for Word 97 and may not look very pretty with
+# other RTF readers or editors.
+
+GENERATE_RTF           = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `rtf' will be used as the default path.
+
+RTF_OUTPUT             = rtf
+
+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
+# RTF documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_RTF            = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
+# will contain hyperlink fields. The RTF file will
+# contain links (just like the HTML output) instead of page references.
+# This makes the output suitable for online browsing using WORD or other
+# programs which support those fields.
+# Note: wordpad (write) and others do not support links.
+
+RTF_HYPERLINKS         = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's
+# config file, i.e. a series of assignments. You only have to provide
+# replacements, missing definitions are set to their default value.
+
+RTF_STYLESHEET_FILE    =
+
+# Set optional variables used in the generation of an rtf document.
+# Syntax is similar to doxygen's config file.
+
+RTF_EXTENSIONS_FILE    =
+
+#---------------------------------------------------------------------------
+# configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
+# generate man pages
+
+GENERATE_MAN           = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `man' will be used as the default path.
+
+MAN_OUTPUT             = man
+
+# The MAN_EXTENSION tag determines the extension that is added to
+# the generated man pages (default is the subroutine's section .3)
+
+MAN_EXTENSION          = .3
+
+# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
+# then it will generate one additional man file for each entity
+# documented in the real man page(s). These additional files
+# only source the real man page, but without them the man command
+# would be unable to find the correct page. The default is NO.
+
+MAN_LINKS              = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES Doxygen will
+# generate an XML file that captures the structure of
+# the code including all documentation.
+
+GENERATE_XML           = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `xml' will be used as the default path.
+
+XML_OUTPUT             = xml
+
+# The XML_SCHEMA tag can be used to specify an XML schema,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_SCHEMA             =
+
+# The XML_DTD tag can be used to specify an XML DTD,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_DTD                =
+
+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
+# dump the program listings (including syntax highlighting
+# and cross-referencing information) to the XML output. Note that
+# enabling this will significantly increase the size of the XML output.
+
+XML_PROGRAMLISTING     = YES
+
+#---------------------------------------------------------------------------
+# configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
+# generate an AutoGen Definitions (see autogen.sf.net) file
+# that captures the structure of the code including all
+# documentation. Note that this feature is still experimental
+# and incomplete at the moment.
+
+GENERATE_AUTOGEN_DEF   = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES Doxygen will
+# generate a Perl module file that captures the structure of
+# the code including all documentation. Note that this
+# feature is still experimental and incomplete at the
+# moment.
+
+GENERATE_PERLMOD       = NO
+
+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
+# the necessary Makefile rules, Perl scripts and LaTeX code to be able
+# to generate PDF and DVI output from the Perl module output.
+
+PERLMOD_LATEX          = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
+# nicely formatted so it can be parsed by a human reader.
+# This is useful
+# if you want to understand what is going on.
+# On the other hand, if this
+# tag is set to NO the size of the Perl module output will be much smaller
+# and Perl will parse it just the same.
+
+PERLMOD_PRETTY         = YES
+
+# The names of the make variables in the generated doxyrules.make file
+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
+# This is useful so different doxyrules.make files included by the same
+# Makefile don't overwrite each other's variables.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
+# evaluate all C-preprocessor directives found in the sources and include
+# files.
+
+ENABLE_PREPROCESSING   = YES
+
+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
+# names in the source code. If set to NO (the default) only conditional
+# compilation will be performed. Macro expansion can be done in a controlled
+# way by setting EXPAND_ONLY_PREDEF to YES.
+
+MACRO_EXPANSION        = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
+# then the macro expansion is limited to the macros specified with the
+# PREDEFINED and EXPAND_AS_DEFINED tags.
+
+EXPAND_ONLY_PREDEF     = NO
+
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
+# pointed to by INCLUDE_PATH will be searched when a #include is found.
+
+SEARCH_INCLUDES        = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by
+# the preprocessor.
+
+INCLUDE_PATH           =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will
+# be used.
+
+INCLUDE_FILE_PATTERNS  =
+
+# The PREDEFINED tag can be used to specify one or more macro names that
+# are defined before the preprocessor is started (similar to the -D option of
+# gcc). The argument of the tag is a list of macros of the form: name
+# or name=definition (no spaces). If the definition and the = are
+# omitted =1 is assumed. To prevent a macro definition from being
+# undefined via #undef or recursively expanded use the := operator
+# instead of the = operator.
+
+PREDEFINED             =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
+# this tag can be used to specify a list of macro names that should be expanded.
+# The macro definition that is found in the sources will be used.
+# Use the PREDEFINED tag if you want to use a different macro definition that
+# overrules the definition found in the source code.
+
+EXPAND_AS_DEFINED      =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
+# doxygen's preprocessor will remove all references to function-like macros
+# that are alone on a line, have an all uppercase name, and do not end with a
+# semicolon, because these will confuse the parser if not removed.
+
+SKIP_FUNCTION_MACROS   = YES
+
+#---------------------------------------------------------------------------
+# Configuration::additions related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES option can be used to specify one or more tagfiles.
+# Optionally an initial location of the external documentation
+# can be added for each tagfile. The format of a tag file without
+# this location is as follows:
+#
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+#
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where "loc1" and "loc2" can be relative or absolute paths or
+# URLs. If a location is present for each tag, the installdox tool
+# does not have to be run to correct the links.
+# Note that each tag file must have a unique name
+# (where the name does NOT include the path)
+# If a tag file is not located in the directory in which doxygen
+# is run, you must also specify the path to the tagfile here.
+
+TAGFILES               =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create
+# a tag file that is based on the input files it reads.
+
+GENERATE_TAGFILE       =
+
+# If the ALLEXTERNALS tag is set to YES all external classes will be listed
+# in the class index. If set to NO only the inherited external classes
+# will be listed.
+
+ALLEXTERNALS           = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will
+# be listed.
+
+EXTERNAL_GROUPS        = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of `which perl').
+
+PERL_PATH              = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
+# or super classes. Setting the tag to NO turns the diagrams off. Note that
+# this option also works with HAVE_DOT disabled, but it is recommended to
+# install and use dot, since it yields more powerful graphs.
+
+CLASS_DIAGRAMS         = YES
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see
+# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
+
+MSCGEN_PATH            =
+
+# If set to YES, the inheritance and collaboration graphs will hide
+# inheritance and usage relations if the target is undocumented
+# or is not a class.
+
+HIDE_UNDOC_RELATIONS   = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz, a graph visualization
+# toolkit from AT&T and Lucent Bell Labs. The other options in this section
+# have no effect if this option is set to NO (the default)
+
+HAVE_DOT               = NO
+
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is
+# allowed to run in parallel. When set to 0 (the default) doxygen will
+# base this on the number of processors available in the system. You can set it
+# explicitly to a value larger than 0 to get control over the balance
+# between CPU load and processing speed.
+
+DOT_NUM_THREADS        = 0
+
+# By default doxygen will write a font called Helvetica to the output
+# directory and reference it in all dot files that doxygen generates.
+# When you want a differently looking font you can specify the font name
+# using DOT_FONTNAME. You need to make sure dot is able to find the font,
+# which can be done by putting it in a standard location or by setting the
+# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
+# containing the font.
+
+DOT_FONTNAME           = Helvetica
+
+# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
+# The default size is 10pt.
+
+DOT_FONTSIZE           = 10
+
+# By default doxygen will tell dot to use the output directory to look for the
+# FreeSans.ttf font (which doxygen will put there itself). If you specify a
+# different font using DOT_FONTNAME you can set the path where dot
+# can find it using this tag.
+
+DOT_FONTPATH           =
+
+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect inheritance relations. Setting this tag to YES will force the
+# the CLASS_DIAGRAMS tag to NO.
+
+CLASS_GRAPH            = YES
+
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect implementation dependencies (inheritance, containment, and
+# class references variables) of the class with other documented classes.
+
+COLLABORATION_GRAPH    = YES
+
+# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for groups, showing the direct groups dependencies
+
+GROUP_GRAPHS           = YES
+
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+
+UML_LOOK               = NO
+
+# If set to YES, the inheritance and collaboration graphs will show the
+# relations between templates and their instances.
+
+TEMPLATE_RELATIONS     = NO
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
+# tags are set to YES then doxygen will generate a graph for each documented
+# file showing the direct and indirect include dependencies of the file with
+# other documented files.
+
+INCLUDE_GRAPH          = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
+# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
+# documented header file showing the documented files that directly or
+# indirectly include this file.
+
+INCLUDED_BY_GRAPH      = YES
+
+# If the CALL_GRAPH and HAVE_DOT options are set to YES then
+# doxygen will generate a call dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable call graphs
+# for selected functions only using the \callgraph command.
+
+CALL_GRAPH             = NO
+
+# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
+# doxygen will generate a caller dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable caller
+# graphs for selected functions only using the \callergraph command.
+
+CALLER_GRAPH           = NO
+
+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
+# will generate a graphical hierarchy of all classes instead of a textual one.
+
+GRAPHICAL_HIERARCHY    = YES
+
+# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# then doxygen will show the dependencies a directory has on other directories
+# in a graphical way. The dependency relations are determined by the #include
+# relations between the files in the directories.
+
+DIRECTORY_GRAPH        = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. Possible values are svg, png, jpg, or gif.
+# If left blank png will be used.
+
+DOT_IMAGE_FORMAT       = png
+
+# The tag DOT_PATH can be used to specify the path where the dot tool can be
+# found. If left blank, it is assumed the dot tool can be found in the path.
+
+DOT_PATH               =
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the
+# \dotfile command).
+
+DOTFILE_DIRS           =
+
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the
+# \mscfile command).
+
+MSCFILE_DIRS           =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
+# nodes that will be shown in the graph. If the number of nodes in a graph
+# becomes larger than this value, doxygen will truncate the graph, which is
+# visualized by representing a node as a red box. Note that doxygen if the
+# number of direct children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
+# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+
+DOT_GRAPH_MAX_NODES    = 50
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
+# graphs generated by dot. A depth value of 3 means that only nodes reachable
+# from the root by following a path via at most 3 edges will be shown. Nodes
+# that lay further from the root node will be omitted. Note that setting this
+# option to 1 or 2 may greatly reduce the computation time needed for large
+# code bases. Also note that the size of a graph can be further restricted by
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+
+MAX_DOT_GRAPH_DEPTH    = 0
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+# background. This is disabled by default, because dot on Windows does not
+# seem to support this out of the box. Warning: Depending on the platform used,
+# enabling this option may lead to badly anti-aliased labels on the edges of
+# a graph (i.e. they become hard to read).
+
+DOT_TRANSPARENT        = NO
+
+# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10)
+# support this, this feature is disabled by default.
+
+DOT_MULTI_TARGETS      = NO
+
+# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
+# generate a legend page explaining the meaning of the various boxes and
+# arrows in the dot generated graphs.
+
+GENERATE_LEGEND        = YES
+
+# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
+# remove the intermediate dot files that are used to generate
+# the various graphs.
+
+DOT_CLEANUP            = YES

tripal_core/api/tripal_core_custom_tables.api.inc

@@ -0,0 +1,206 @@
+<?php
+/**
+ * @file
+ * Contains functions for the Custom Tables API
+
+ * @defgroup tripal_custom_tables_api Custom Tables API
+ * @ingroup tripal_core_api
+ * @{
+ * Provides an API to manage custom tables in Chado.
+ * @}
+ */
+
+/**
+ * Edits a custom table in the chado database. It supports 
+ * using the Drupal Schema API array.
+ *
+ * @param $table_id
+ *   The table_id of the table to edit
+ * @param $table_name
+ *   The name of the custom table
+ * @param $schema
+ *   Use the Schema API array to define the custom table.
+ * @param $skip_creation
+ *   Set as TRUE to skip dropping and re-creation of the table.  This is
+ *   useful if the table was already created through another means and you
+ *   simply want to make Tripal aware of the table schema.
+ *
+ * @ingroup tripal_custom_tables_api
+ */
+function tripal_core_edit_custom_table($table_id, $table_name, $schema, $skip_creation = 1) {
+
+  // Create a new record
+  $record = new stdClass();
+  $record->table_id = $table_id;
+  $record->table_name = $table_name;
+  $record->schema = serialize($schema);
+
+  // get the current custom table record
+  $sql = "SELECT * FROM {tripal_custom_tables} WHERE table_id = %d";
+  $custom_table = db_fetch_object(db_query($sql, $table_id));
+  
+  // if the user changed the table name, we want to drop the old one and force
+  // creation of the new one.
+  if ($custom_table->table_name != $table_name) {
+    chado_query("DROP TABLE %s", $custom_table->table_name);  
+    $skip_creation = 0; // we want to create the table
+  }
+
+  // if skip creation is not set, then drop the table from chado if it exists
+  if(!$skip_creation){
+    if (db_table_exists($custom_table->table_name)) {
+      chado_query("DROP TABLE %s", $custom_table->table_name);
+      drupal_set_message(t("Custom Table '%name' dropped", array('%name' => $custom_table->table_name)));
+    }
+  }
+
+  // update the custom table record and re-create the table in Chado
+  if (drupal_write_record('tripal_custom_tables', $record, 'table_id')) {
+
+    // drop the table from chado if it exists
+    if(!$skip_creation){
+      if (db_table_exists($custom_table->table_name)) {
+        chado_query("DROP TABLE %s", $custom_table->table_name);
+        drupal_set_message(t("Custom Table '%name' dropped", array('%name' => $custom_table->table_name)));
+      }
+
+      // re-create the table
+      if (!tripal_core_create_custom_table ($ret, $table_name, $schema)) {
+        drupal_set_message(t("Could not create the custom table. Check Drupal error report logs."));
+      }
+      else {
+        drupal_set_message(t("Custom table '%name' created", array('%name' => $table_name)));
+      }
+    }
+    // TODO: add FK constraints
+  }
+}
+
+/**
+ * Add a new table to the Chado schema. This function is simply a wrapper for
+ * the db_create_table() function of Drupal, but ensures the table is created
+ * inside the Chado schema rather than the Drupal schema.  If the table already
+ * exists then it will be dropped and recreated using the schema provided.
+ * However, it will only drop a table if it exsits in the tripal_custom_tables
+ * table. This way the function cannot be used to accidentally alter existing
+ * non custom tables.  If $skip_creation is set then the table is simply
+ * added to the tripal_custom_tables and no table is created in Chado.
+ *
+ * @param $ret
+ *   Array to which query results will be added.
+ * @param $table
+ *   The name of the table to create.
+ * @param $schema
+ *   A Drupal-style Schema API definition of the table
+ * @param $skip_creation
+ *   Set as TRUE to skip dropping and re-creation of the table if it already
+ *   exists.  This is useful if the table was already created through another 
+ *   means and you simply want to make Tripal aware of the table schema.  If the
+ *   table does not exist it will be created.
+ *
+ * @return
+ *   A database query result resource for the new table, or FALSE if table was not constructed.
+ *
+ * @ingroup tripal_custom_tables_api
+ */
+function tripal_core_create_custom_table(&$ret, $table, $schema, $skip_creation = 1) {
+  $ret = array();
+      
+  // see if the table entry already exists in the tripal_custom_tables table.
+  $sql = "SELECT * FROM {tripal_custom_tables} WHERE table_name = '%s'";
+  $centry = db_fetch_object(db_query($sql, $table));
+  
+  // check to see if the table already exists in the chado schema  
+  $previous_db = tripal_db_set_active('chado');  // use chado database
+  $exists = db_table_exists($table);
+  tripal_db_set_active($previous_db);  // now use drupal database
+
+  
+  // if the table does not exist then create it
+  if (!$exists) {
+    $previous_db = tripal_db_set_active('chado');  // use chado database
+    db_create_table($ret, $table, $schema);
+    tripal_db_set_active($previous_db);  // now use drupal database
+    if (count($ret)==0) {
+      watchdog('tripal_core', "Error adding custom table '!table_name'.",
+        array('!table_name' => $table), WATCHDOG_ERROR);
+      return FALSE;
+    }
+  }  
+
+  // if the table exists in Chado and in our custom table and
+  // skip creation is turned off then drop and re-create the table 
+  if ($exists and is_object($centry) and !$skip_creation) {    
+    
+    // drop the table we'll recreate it with the new schema
+    $previous_db = tripal_db_set_active('chado');  // use chado database
+    db_drop_table($ret, $table);
+    db_create_table($ret, $table, $schema);
+    tripal_db_set_active($previous_db);  // now use drupal database
+  }
+
+  // add an entry in the tripal_custom_table
+  $record = new stdClass();
+  $record->table_name = $table;
+  $record->schema = serialize($schema);
+
+  // if an entry already exists then remove it
+  if ($centry) {
+    $sql = "DELETE FROM {tripal_custom_tables} WHERE table_name = '%s'";
+    db_query($sql, $table);
+  }
+  $success = drupal_write_record('tripal_custom_tables', $record);
+  if (!$success) {
+    watchdog('tripal_core', "Error adding custom table %table_name.",
+      array('%table_name' => $table), WATCHDOG_ERROR);
+    drupal_set_message(t("Could not add custom table %table_name. 
+      Please check the schema array.", array('%table_name' => $table)), 'error');      
+    return FALSE;
+  }
+  
+  // now add any foreign key constraints
+  if(!$skip_creation and array_key_exists('foreign keys', $schema)){
+    $fkeys = $schema['foreign keys'];
+    foreach ($fkeys as $fktable => $fkdetails) {
+      $relations = $fkdetails['columns'];
+      foreach ($relations as $left => $right) {
+        $sql = "ALTER TABLE $table ADD CONSTRAINT " . 
+          $table . "_" . $left . "_fkey FOREIGN KEY ($left) REFERENCES  $fktable ($right) " .
+          "ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED";
+        if(!chado_query($sql)){
+          watchdog('tripal_core', "Error, could not add foreign key contraint to custom table.",
+            array('!table_name' => $table), WATCHDOG_ERROR);
+          drupal_set_message(t("Could not add foreign key contraint to table %table_name. 
+            Please check the schema array and the report log for errors.", 
+            array('%table_name' => $table)), 'error');      
+          return FALSE;
+        }
+      }
+    }
+  }
+
+  return TRUE;
+}
+/**
+ * Retrieve the custom table id given the name
+ *
+ * @param $table_name
+ *   The name of the custom table
+ *
+ * @return
+ *   The unique identifier for the given table
+ *
+ * @ingroup tripal_custom_tables_api
+ */
+function tripal_custom_tables_get_table_id($table_name) {
+  $sql = "SELECT * FROM {tripal_custom_tables} ".
+         "WHERE table_name = '%s'";
+  if (db_table_exists('tripal_custom_tables')) {
+    $custom_table = db_fetch_object(db_query($sql, $table_name));
+    if ($custom_table) {
+      return $custom_table->table_id;
+    }
+  }
+
+  return FALSE;
+}

tripal_core/api/tripal_core_files.api.inc

@@ -0,0 +1,63 @@
+<?php 
+/**
+ * @file
+ * The Tripal Files API
+ *
+ * This file provides the API to help Tripal modules to storing files
+ * in a consistent directory strcuture.
+ *
+ * @defgroup tripal_files_api  Files API
+ * @ingroup tripal_core_api
+ * @{
+ * Provides an application programming interface (API) for managing files within
+ * the Tripal data directory structure.
+ *
+ * @}
+ *
+ */
+ 
+/**
+ * This function is typically used in the '.install' file for a Tripal module
+ * Each module should call this function during installation to create
+ * the module data directory which is sites/default/files/tripal/[module_name]
+ * for default Drupal settings.  This directory can then be used by the module
+ * for storing files.
+ *
+ * @param $module_name
+ *   the name of the module being installed.
+ *
+ * @returns
+ *   nothing
+ *
+ * @ingroup tripal_files_api
+ */
+function tripal_create_moddir($module_name) {
+
+  // make the data directory for this module
+  $data_dir = file_directory_path() . "/tripal/$module_name";
+  if (!file_check_directory($data_dir, FILE_CREATE_DIRECTORY | FILE_MODIFY_PERMISSIONS)) {
+    $message = "Cannot create directory $data_dir. This module may not ".
+               "behave correctly without this directory.  Please  create ".
+               "the directory manually or fix the problem and reinstall.";
+    drupal_set_message(check_plain(t($message)), 'error');
+    watchdog('tripal_core', $message, array(), WATCHDOG_ERROR);
+  }
+}
+
+/**
+ * Each Tripal module has a unique data directory which was creatd using the
+ * tripal_create_moddir function during installation.  This function
+ * retrieves the directory path.
+ *
+ * @param $module_name
+ *   The name of the module
+ *
+ * @returns
+ *   The path within the Drupal installation where the data directory resides
+ *   
+ * @ingroup tripal_files_api
+ */
+function tripal_get_moddir($module_name) {
+  $data_dir = file_directory_path() . "/tripal/$module_name";
+  return $data_dir;
+}

tripal_core/api/tripal_core_jobs.api.inc

@@ -0,0 +1,358 @@
+<?php
+/**
+ * @file
+ * Contains functions related to the Tripal Jobs API
+ *
+ * @defgroup tripal_jobs_api Jobs API
+ * @ingroup tripal_core_api
+ * @{
+ * Tripal offers a job management subsystem for managing tasks that may require an extended period of time for
+ * completion.  Drupal uses a UNIX-based cron job to handle tasks such as  checking  the  availability of updates,
+ * indexing new nodes for searching, etc.   Drupal's cron uses the web interface for launching these tasks, however,
+ * Tripal provides several administrative tasks that may time out and not complete due to limitations of the web
+ * server.  Examples including syncing of a large number of features between chado and Drupal.  To circumvent this,
+ * as well as provide more fine-grained control and monitoring, Tripal uses a jobs management sub-system built into
+ * the Tripal Core module.   It is anticipated that this functionality will be used for managing analysis jobs provided by
+ * future tools, with eventual support for distributed computing.
+ *
+ * The  Tripal jobs management system allows administrators to submit tasks to be performed which can then  be
+ * launched through a UNIX command-line PHP script or cron job.  This command-line script can be added to a cron
+ * entry along-side the Drupal cron entry for automatic, regular launching of Tripal jobs.  The order of execution of
+ * waiting jobs is determined first by priority and second by the order the jobs were entered.
+ *
+ * The API functions described below provide a programmatic interface for adding, checking and viewing jobs.
+ * @} 
+ */
+
+/**
+ * Adds a job to the Tripal Jbo queue
+ *
+ * @param $job_name
+ *    The human readable name for the job
+ * @param $modulename
+ *    The name of the module adding the job
+ * @param $callback
+ *    The name of a function to be called when the job is executed
+ * @param $arguments
+ *    An array of arguements to be passed on to the callback
+ * @param $uid
+ *    The uid of the user adding the job
+ * @param $priority
+ *    The priority at which to run the job where the highest priority is 10 and the lowest priority
+ *    is 1. The default priority is 10.
+ *
+ * @return
+ *    The job_id of the registered job
+ *
+ * Example usage:
+ * @code
+ *  $args = array($dfile, $organism_id, $type, $library_id, $re_name, $re_uname,
+ *        $re_accession, $db_id, $rel_type, $re_subject, $parent_type, $method,
+ *         $user->uid, $analysis_id, $match_type);
+ *
+ * tripal_add_job("Import FASTA file: $dfile", 'tripal_feature',
+ *   'tripal_feature_load_fasta', $args, $user->uid);
+ * @endcode
+ * The code above is copied from the tripal_feature/fasta_loader.php file. The
+ * snipped first builds an array of arguments that will then be passed to the
+ * tripal_add_job function.  The number of arguments provided in the $arguments
+ * variable should match the argument set for the callback function provided
+ * as the third argument.
+ *
+ * @ingroup tripal_jobs_api
+ */
+function tripal_add_job($job_name, $modulename, $callback, $arguments, $uid, $priority = 10) {
+
+  // convert the arguments into a string for storage in the database
+  $args = implode("::", $arguments);
+  $record = new stdClass();
+  $record->job_name = $job_name;
+  $record->modulename = $modulename;
+  $record->callback = $callback;
+  $record->status = 'Waiting';
+  $record->submit_date = time();
+  $record->uid = $uid;
+  $record->priority = $priority;  # the lower the number the higher the priority
+  if ($args) {
+    $record->arguments = $args;
+  }
+  if (drupal_write_record('tripal_jobs', $record)) {
+    $jobs_url = url("admin/tripal/tripal_jobs");
+    drupal_set_message(t("Job '%job_name' submitted.  Check the <a href='!jobs_url'>jobs page</a> for status", array('%job_name' => $job_name, '!jobs_url' => $jobs_url)));
+  }
+  else {
+    drupal_set_message(t("Failed to add job %job_name.", array('%job_name' => $job_name)), 'error');
+  }
+
+  return $record->job_id;
+}
+
+/**
+ * Returns a list of running tripal jobs
+ *
+ * @return
+ *    and array of objects where each object describes a running job or FALSE if no jobs are running
+ *
+ * @ingroup tripal_jobs_api
+ */
+function tripal_jobs_check_running() {
+
+  // iterate through each job that has not ended
+  // and see if it is still running. If it is not
+  // running but does not have an end_time then
+  // set the end time and set the status to 'Error'
+  $sql =  "SELECT * FROM {tripal_jobs} TJ ".
+          "WHERE TJ.end_time IS NULL and NOT TJ.start_time IS NULL ";
+  $jobs = db_query($sql);
+  while ($job = db_fetch_object($jobs)) {
+    $status = `ps --pid=$job->pid --no-header`;
+    if ($job->pid && $status) {
+      // the job is still running so let it go
+      // we return 1 to indicate that a job is running
+      return TRUE;
+    }
+    else {
+      // the job is not running so terminate it
+      $record = new stdClass();
+      $record->job_id = $job->job_id;
+      $record->end_time = time();
+      $record->status = 'Error';
+      $record->error_msg = 'Job has terminated unexpectedly.';
+      drupal_write_record('tripal_jobs', $record, 'job_id');
+    }
+  }
+
+  // return 1 to indicate that no jobs are currently running.
+  return FALSE;
+}
+
+/**
+ * Returns the start time for a given job
+ *
+ * @param $job
+ *   An object describing the job
+ *
+ * @return
+ *   The start time of the job if it was already run and either "Cancelled" or "Not Yet Started" otherwise
+ *
+ * @ingroup tripal_jobs_api
+ */
+function tripal_jobs_get_start_time($job) {
+
+  if ($job->start_time > 0) {
+    $start = format_date($job->start_time);
+  }
+  else {
+    if (strcmp($job->job_status, 'Cancelled')==0) {
+      $start = 'Cancelled';
+    }
+    else {
+      $start = 'Not Yet Started';
+    }
+  }
+  return $start;
+}
+
+/**
+ * Returns the end time for a given job
+ *
+ * @param $job
+ *   An object describing the job
+ *
+ * @return
+ *   The end time of the job if it was already run and empty otherwise
+ *
+ * @ingroup tripal_jobs_api
+ */
+function tripal_jobs_get_end_time($job) {
+
+  if ($job->end_time > 0) {
+    $end = format_date($job->end_time);
+  }
+  else {
+    $end = '';
+  }
+
+  return $end;
+}
+/**
+ * Set a job to be re-ran (ie: add it back into the job queue)
+ *
+ * @param $job_id
+ *   The job_id of the job to be re-ran
+ *
+ * @ingroup tripal_jobs_api
+ */
+function tripal_jobs_rerun($job_id, $goto_jobs_page = TRUE) {
+  global $user;
+
+  $sql = "SELECT * FROM {tripal_jobs} WHERE job_id = %d";
+  $job = db_fetch_object(db_query($sql, $job_id));
+  $args = explode("::", $job->arguments);
+  $job_id = tripal_add_job(
+    $job->job_name,
+    $job->modulename,
+    $job->callback,
+    $args,
+    $user->uid,
+    $job->priority);
+
+  if ($goto_jobs_page) {
+    drupal_goto("admin/tripal/tripal_jobs");
+  }
+  return $job_id;
+}
+
+/**
+ * Cancel a Tripal Job currently waiting in the job queue
+ *
+ * @param $job_id
+ *   The job_id of the job to be cancelled
+ *
+ * @ingroup tripal_jobs_api
+ */
+function tripal_jobs_cancel($job_id, $redirect = TRUE) {
+  $sql = "SELECT * FROM {tripal_jobs} WHERE job_id = %d";
+  $job = db_fetch_object(db_query($sql, $job_id));
+
+  // set the end time for this job
+  if ($job->start_time == 0) {
+    $record = new stdClass();
+    $record->job_id = $job->job_id;
+    $record->end_time = time();
+    $record->status = 'Cancelled';
+    $record->progress = '0';
+    drupal_write_record('tripal_jobs', $record, 'job_id');
+    drupal_set_message(t("Job #%job_id cancelled", array('%job_id' => $job_id)));
+  }
+  else {
+    drupal_set_message(t("Job %job_id cannot be cancelled. It is in progress or has finished.", array('%job_id' => $job_id)));
+  }
+  if ($redirect) {
+    drupal_goto("admin/tripal/tripal_jobs");
+  }
+}
+
+/**
+ * A function used to manually launch all queued tripal jobs
+ *
+ * @param $do_parallel
+ *   A boolean indicating whether jobs should be attempted to run in parallel
+ *
+ * @param $job_id
+ *   To launch a specific job provide the job id.  This option should be
+ *   used sparingly as the jobs queue managment system should launch jobs
+ *   based on order and priority.  However there are times when a specific
+ *   job needs to be launched and this argument will allow it.  Only jobs
+ *   which have not been run previously will run.
+ *
+ * @ingroup tripal_jobs_api
+ */
+function tripal_jobs_launch($do_parallel = 0, $job_id = NULL) {
+
+  // first check if any jobs are currently running
+  // if they are, don't continue, we don't want to have
+  // more than one job script running at a time
+  if (!$do_parallel and tripal_jobs_check_running()) {
+    print "Jobs are still running. Use the --parallel=1 option with the Drush command to run jobs in parallel.";
+    return;
+  }
+
+  // get all jobs that have not started and order them such that
+  // they are processed in a FIFO manner.
+  if ($job_id) {
+    $sql =  "SELECT * FROM {tripal_jobs} TJ ".
+            "WHERE TJ.start_time IS NULL and TJ.end_time IS NULL and TJ.job_id = %d ".
+            "ORDER BY priority ASC,job_id ASC";
+    $job_res = db_query($sql,$job_id);
+  }
+  else {
+    $sql =  "SELECT * FROM {tripal_jobs} TJ ".
+            "WHERE TJ.start_time IS NULL and TJ.end_time IS NULL ".
+            "ORDER BY priority ASC,job_id ASC";
+    $job_res = db_query($sql);
+  }
+  while ($job = db_fetch_object($job_res)) {
+    // set the start time for this job
+    $record = new stdClass();
+    $record->job_id = $job->job_id;
+    $record->start_time = time();
+    $record->status = 'Running';
+    $record->pid = getmypid();
+    drupal_write_record('tripal_jobs', $record, 'job_id');
+
+    // call the function provided in the callback column.
+    // Add the job_id as the last item in the list of arguments. All
+    // callback functions should support this argument.
+    $callback = $job->callback;
+    $args = split("::", $job->arguments);
+    $args[] = $job->job_id;
+    print "Calling: $callback(" . implode(", ", $args) . ")\n";
+    call_user_func_array($callback, $args);
+    // set the end time for this job
+    $record->end_time = time();
+    $record->status = 'Completed';
+    $record->progress = '100';
+    drupal_write_record('tripal_jobs', $record, 'job_id');
+
+    // send an email to the user advising that the job has finished
+  }
+}
+
+/**
+ * An internal function for setting the progress for a current job
+ *
+ * @param $job_id
+ *   The job_id to set the progress for
+ * @param $percentage
+ *   The progress to set the job to
+ *
+ * @return
+ *   True on success and False otherwise
+ *
+ * @ingroup tripal_core
+ */
+function tripal_job_set_progress($job_id, $percentage) {
+
+  if (preg_match("/^(\d+|100)$/", $percentage)) {
+    $record = new stdClass();
+    $record->job_id = $job_id;
+    $record->progress = $percentage;
+    if (drupal_write_record('tripal_jobs', $record, 'job_id')) {
+      return TRUE;
+    }
+  }
+
+  return FALSE;
+}
+/**
+ * Returns a list of jobs associated with the given module
+ *
+ * @param $modulename
+ *    The module to return a list of jobs for
+ *
+ * @return
+ *    An array of objects where each object describes a tripal job
+ *
+ * @ingroup tripal_jobs_api
+ */
+function tripal_get_module_active_jobs($modulename) {
+  $sql =  "SELECT * FROM {tripal_jobs} TJ ".
+           "WHERE TJ.end_time IS NULL and TJ.modulename = '%s' ";
+  return db_fetch_object(db_query($sql, $modulename));
+}
+
+/**
+ * Returns the date the job was added to the queue
+ *
+ * @param $job
+ *   An object describing the job
+ *
+ * @return
+ *   The date teh job was submitted
+ *
+ * @ingroup tripal_jobs_api
+ */
+function tripal_jobs_get_submit_date($job) {
+  return format_date($job->submit_date);
+}

tripal_core/api/tripal_core_mviews.api.inc

@@ -0,0 +1,382 @@
+<?php
+/**
+ * @file
+ * Contains functions for the Materialized Views API
+
+ * @defgroup tripal_mviews_api Materalized Views API
+ * @ingroup tripal_core_api
+ * @{
+ * Provides an application programming interface (API) to manage materialized views in Chado.
+ * The Perl-based chado comes with an interface for managing materialzed views.  This
+ * API provides an alternative Drupal-based method.
+ * @}
+ */
+
+/**
+ * Add a materialized view to the chado database to help speed data access. This
+ * function supports the older style where postgres column specifications
+ * are provided using the $mv_table, $mv_specs and $indexed variables. It also
+ * supports the newer preferred method where the materialized view is described
+ * using the Drupal Schema API array.
+ *
+ * @param $name
+ *   The name of the materialized view.
+ * @param $modulename
+ *   The name of the module submitting the materialized view (e.g. 'tripal_library')
+ * @param $mv_table
+ *   The name of the table to add to chado. This is the table that can be queried.
+ * @param $mv_specs
+ *   The table definition
+ * @param $indexed
+ *   The columns that are to be indexed
+ * @param $query
+ *   The SQL query that loads the materialized view with data
+ * @param $special_index
+ *   currently not used
+ * @param $comment
+ *   A string containing a description of the materialized view
+ * @param $mv_schema
+ *   If using the newer Schema API array to define the materialized view then
+ *   this variable should contain the array or a string representation of the 
+ *   array.
+ * 
+ * @ingroup tripal_mviews_api
+ */
+function tripal_add_mview($name, $modulename, $mv_table, $mv_specs, $indexed,
+  $query, $special_index, $comment = NULL, $mv_schema = NULL) {
+
+  // get the table name from the schema array
+  $schema_arr = array();
+  if ($mv_schema) {
+    // if the schema is provided as a string then convert it to an array
+    if (!is_array($mv_schema)) {
+      eval("\$schema_arr = $mv_schema;");
+    }
+    // if the schema is provided as an array then create a string
+    // copy of it for storage in the mview 
+    else {
+      $schema_arr = $mv_schema;
+      $mv_schema = var_export($schema_arr, 1);
+    }
+    $mv_table = $schema_arr['table'];
+  }
+
+  // Create a new record
+  $record = new stdClass();
+  $record->name = $name;
+  $record->modulename = $modulename;
+  $record->mv_table = $mv_table;
+  $record->mv_specs = $mv_specs;
+  $record->indexed = $indexed;
+  $record->query = $query;
+  $record->special_index = $special_index;
+  $record->comment = $comment;
+  $record->mv_schema = $mv_schema;
+
+  // add the record to the tripal_mviews table and if successful
+  // create the new materialized view in the chado schema
+  if (drupal_write_record('tripal_mviews', $record)) {
+
+    // drop the table from chado if it exists
+    $previous_db = tripal_db_set_active('chado');  // use chado database
+    if (db_table_exists($mv_table)) {
+      $sql = "DROP TABLE $mv_table";
+      db_query($sql);
+    }
+    tripal_db_set_active($previous_db);  // now use drupal database
+
+    // now construct the indexes
+    $index = '';
+    if ($indexed) {
+      // add to the array of values
+      $vals = preg_split("/[\n,]+/", $indexed);
+      $index = '';
+      foreach ($vals as $field) {
+        $field = trim($field);
+        $index .= "CREATE INDEX idx_${mv_table}_${field} ON $mv_table ($field);";
+      }
+    }
+
+    // create the table differently depending on if it the traditional method
+    // or the Drupal Schema API method
+    if ($mv_schema) {
+      if (!tripal_core_create_custom_table ($ret, $mv_table, $schema_arr, 0)) {
+        drupal_set_message(t("Could not create the materialized view. Check Drupal error report logs."), 'error');
+      }
+      else {
+        drupal_set_message(t("View '%name' created", array('%name' => $name)));
+      }
+    }
+    else {
+      // add the table to the database
+      $sql = "CREATE TABLE {$mv_table} ($mv_specs); $index";
+      $previous_db = tripal_db_set_active('chado');  // use chado database
+      $results = db_query($sql);
+      tripal_db_set_active($previous_db);  // now use drupal database
+      if ($results) {
+        drupal_set_message(t("View '%name' created", array('%name' => $name)));
+      }
+      else {
+        drupal_set_message(t("Failed to create the materialized view table: '%mv_table'", array('%mv_table' => $mv_table)), 'error');
+      }
+    }
+  }
+}
+
+/**
+ * Edits a materialized view to the chado database to help speed data access.This
+ * function supports the older style where postgres column specifications
+ * are provided using the $mv_table, $mv_specs and $indexed variables. It also
+ * supports the newer preferred method where the materialized view is described
+ * using the Drupal Schema API array.
+ *
+ * @param $mview_id
+ *   The mview_id of the materialized view to edit
+ * @param $name
+ *   The name of the materialized view.
+ * @param $modulename
+ *   The name of the module submitting the materialized view (e.g. 'tripal_library')
+ * @param $mv_table
+ *   The name of the table to add to chado. This is the table that can be queried.
+ * @param $mv_specs
+ *   The table definition
+ * @param $indexed
+ *   The columns that are to be indexed
+ * @param $query
+ *   The SQL query that loads the materialized view with data
+ * @param $special_index
+ *   currently not used
+ * @param $comment
+ *   A string containing a description of the materialized view
+ * @param $mv_schema
+ *   If using the newer Schema API array to define the materialized view then
+ *   this variable should contain the array.
+ *
+ * @ingroup tripal_mviews_api
+ */
+function tripal_edit_mview($mview_id, $name, $modulename, $mv_table, $mv_specs,
+  $indexed, $query, $special_index, $comment = NULL, $mv_schema = NULL) {
+
+  // get the table name from the schema array
+  $schema_arr = array();
+  if ($mv_schema) {
+    // get the schema from the mv_specs and use it to add the custom table
+    eval("\$schema_arr = $mv_schema;");
+    $mv_table = $schema_arr['table'];
+  }
+
+  $record = new stdClass();
+  $record->mview_id = $mview_id;
+  $record->name = $name;
+  $record->modulename = $modulename;
+  $record->query = $query;
+  $record->last_update = 0;
+  $record->status = '';
+  $record->comment = $comment;
+
+  // get the view before we update and check to see if the table structure has
+  // changed. IF so, then we want to drop and recreate the table. If not, then
+  // just save the updated SQL.
+  $create_table = 1;  
+  $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = %d";
+  $mview = db_fetch_object(db_query($sql, $mview_id));  
+  if($mview->mv_schema == $mv_schema and $mview->mv_table == $mv_table and 
+     $mview->mv_specs == $mv_specs and $mview->indexed == $indexed and 
+     $mview->special_index == $special_index) {
+    // nothing has changed so simpy update the SQL and other fields 
+    $create_table = 0;
+  }
+  else {
+    // add in the table structure fields
+    $record->mv_schema = $mv_schema;
+    $record->mv_table = $mv_table;
+    $record->mv_specs = $mv_specs;
+    $record->indexed = $indexed;
+    $record->query = $query;
+    $record->special_index = $special_index;
+  }
+  
+  // if we are going to create the table then we must first drop it if it exists
+  if ($create_table) {
+    $previous_db = tripal_db_set_active('chado');  // use chado database
+    if (db_table_exists($mview->mv_table)) {
+      $sql = "DROP TABLE %s";
+      db_query($sql, $mview->mv_table);
+      drupal_set_message(t("View '%name' dropped", array('%name' => $name)));
+    }
+    tripal_db_set_active($previous_db);  // now use drupal database
+  }
+
+  // update the record to the tripal_mviews table and if successful
+  // create the new materialized view in the chado schema
+  if (drupal_write_record('tripal_mviews', $record, 'mview_id')) {
+    // construct the indexes SQL if needed
+    $index = '';
+    if ($indexed) {
+      // add to the array of values
+      $vals = preg_split("/[\n,]+/", $indexed);
+      $index = '';
+      foreach ($vals as $field) {
+        $field = trim($field);
+        $index .= "CREATE INDEX idx_${mv_table}_${field} ON $mv_table ($field);";
+      }
+    }
+
+    // re-create the table differently depending on if it the traditional method
+    // or the Drupal Schema API method
+    if ($create_table and $mv_schema) {     
+      if (!tripal_core_create_custom_table($ret, $mv_table, $schema_arr, 0)) {
+        drupal_set_message(t("Could not create the materialized view. Check Drupal error report logs."));
+      }
+      else {
+        drupal_set_message(t("View '%name' created", array('%name' => $name)));
+      }
+    }
+    if ($create_table and !$mv_schema) {
+      $sql = "CREATE TABLE {$mv_table} ($mv_specs); $index";
+      $results = chado_query($sql);
+      if ($results) {
+        drupal_set_message(t("View '%name' created.  All records cleared. Please re-populate the view.", 
+          array('%name' => $name)));
+      }
+      else {
+        drupal_set_message(t("Failed to create the materialized view table: '%mv_table'", 
+          array('%mv_table' => $mv_table)), 'error');
+      }
+    }
+    if (!$create_table) {
+      $message = "View '%name' updated.  All records remain. ";
+      if ($query != $mview->query) {
+        $message .= "Please repopulate the view to use updated query.";
+      }
+      drupal_set_message(t($message, array('%name' => $name)));  
+    }
+  }
+  else {
+    drupal_set_message(t("Failed to update the materialized view: '%mv_table'", 
+      array('%mv_table' => $mv_table)), 'error');  
+  }
+}
+
+/**
+ * Retrieve the materialized view_id given the name
+ *
+ * @param $view_name
+ *   The name of the materialized view
+ *
+ * @return
+ *   The unique identifier for the given view
+ *
+ * @ingroup tripal_mviews_api
+ */
+function tripal_mviews_get_mview_id($view_name) {
+  $sql = "SELECT * FROM {tripal_mviews} ".
+        "WHERE name = '%s'";
+  if (db_table_exists('tripal_mviews')) {
+    $mview = db_fetch_object(db_query($sql, $view_name));
+    if ($mview) {
+      return $mview->mview_id;
+    }
+  }
+
+  return FALSE;
+}
+
+/**
+ * Does the specified action for the specified Materialized View
+ *
+ * @param $op
+ *   The action to be taken. One of update or delete
+ * @param $mview_id
+ *   The unique ID of the materialized view for the action to be performed on
+ * @param $redirect
+ *   TRUE/FALSE depending on whether you want to redirect the user to admin/tripal/mviews
+ *
+ * @ingroup tripal_core
+ */
+function tripal_mviews_action($op, $mview_id, $redirect = FALSE) {
+  global $user;
+
+  $args = array("$mview_id");
+  if (!$mview_id) {
+    return '';
+  }
+
+  // get this mview details
+  $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = %d";
+  $mview = db_fetch_object(db_query($sql, $mview_id));
+
+  // add a job or perform the action based on the given operation
+  if ($op == 'update') {
+    tripal_add_job("Populate materialized view '$mview->name'", 'tripal_core',
+       'tripal_update_mview', $args, $user->uid);
+  }
+  if ($op == 'delete') {
+    // remove the mview from the tripal_mviews table
+    $sql = "DELETE FROM {tripal_mviews} ".
+           "WHERE mview_id = $mview_id";
+    db_query($sql);
+    // drop the table from chado if it exists
+    $previous_db = tripal_db_set_active('chado');  // use chado database
+    if (db_table_exists($mview->mv_table)) {
+      $sql = "DROP TABLE $mview->mv_table";
+      db_query($sql);
+    }
+    tripal_db_set_active($previous_db);  // now use drupal database
+  }
+
+  // Redirect the user
+  if ($redirect) {
+    drupal_goto("admin/tripal/mviews");
+  }
+}
+
+/**
+ * Update a Materialized View
+ *
+ * @param $mview_id
+ *   The unique identifier for the materialized view to be updated
+ *
+ * @return
+ *   True if successful, FALSE otherwise
+ *
+ * @ingroup tripal_mviews_api
+ */
+function tripal_update_mview($mview_id) {
+  $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = %d ";
+  $mview = db_fetch_object(db_query($sql, $mview_id));
+  if ($mview) {    
+    // execute the query inside a transaction so that it doesn't destroy existing data
+    // that may leave parts of the site unfunctional
+    tripal_db_start_transaction();
+    $previous_db = tripal_db_set_active('chado');  // use chado database
+    $results = db_query("DELETE FROM {%s}", $mview->mv_table);
+    $results = db_query("INSERT INTO {%s} ($mview->query)", $mview->mv_table);    
+    tripal_db_set_active($previous_db);  // now use drupal database
+    if ($results) {
+      // commit the transaction
+      tripal_db_commit_transaction();
+      $sql = "SELECT count(*) as cnt FROM {%s}";
+      $previous_db = tripal_db_set_active('chado');  // use chado database
+      $count = db_fetch_object(db_query($sql, $mview->mv_table));
+      tripal_db_set_active($previous_db);  // now use drupal database
+      $record = new stdClass();
+      $record->mview_id = $mview_id;
+      $record->last_update = time();
+      $record->status = "Populated with " . number_format($count->cnt) . " rows";
+      drupal_write_record('tripal_mviews', $record, 'mview_id');
+      return TRUE;
+    }
+    else {
+      // rollback the transaction
+      tripal_db_rollback_transaction();
+      // print and save the error message
+      $record = new stdClass();
+      $record->mview_id = $mview_id;
+      $record->status = "ERROR populating. See Drupal's recent log entries for details.";
+      print $record->status . "\n";
+      drupal_write_record('tripal_mviews', $record, 'mview_id');
+      return FALSE;
+    }
+  }
+}