FoX_DoX

# FoX documentation.

All in one page

Separate pages

## Introduction

- Versioning

- Configuration and compilation

- Embedding into an existing project

## Other documentation

In January 2007, a workshop was run introducing FoX. This was iFax: Integrating Fortran and XML, organized by the National Institute for Environmental eScience.

The materials for this workshop included several talks, a set of documentation, and a number of example programs and problem sets to work through. All of these materials are available for download.

## API documentation

- FoX has six sets of publically exported interfaces. These are documented here:

### COMMON interfaces

- FoX_common
- FoX_utils

### OUTPUT interfaces

- FoX_wxml
- FoX_wcml

### INPUT interface

- FoX_sax
- FoX_dom

These documents describe all publically usable APIs.

If a subroutine or function, or indeed one of its arguments, is not mentioned above, it is not to be considered part of the stable API, even if it is accessible.

The astute developer is reminded that all times the final reference documentation is the source, which is publically available.

Worked examples of the use of these APIs may be found in the `examples/` subdirectory.

## Other things

- Hints for debugging

- Further information

- Licensing

# FoX versioning

This documentation describes version 3.1.2 of the FoX library.

This version includes output modules for general XML, and for CML, and also a Fortran version of the SAX2 input parser, and a Fortran mapping of the W3C DOM interface.

This is a stable branch, which will be maintained with important bugfixes.

## FoX Changes

As of FoX-3.0, there is one user-visible change that should be noted.

### Configuration/compilation

In previous versions of FoX, the configure script was accessible as `config/configure`. Version 3.0 now follows common practice by placing the script in the main directory, so it is now called as `./configure`.

Previous versions of FoX made it quite hard to compile only portions of the library (eg only the CML output portion; or just the SAX input). This is now possible by specifying arguments to the configuration script. For example,

`./configure --enable-wcml`

will cause the generated Makefile to only compile the CML writing module and its dependencies.

See Compilation for further details.

# Configuration and compilation

You will have received the FoX source code as a tar.gz file.

Unpack it as normal, and change directory into the top-level directory, FoX-$VERSION.

### Requirements for use

FoX requires a Fortran 95 compiler - not just Fortran 90. All currently available versions of Fortran compilers claim to support F95. If your favoured compiler is not listed as working below, I recommend the use of g95, which is free to download and use. And if your favourite compiler is listed as not working, then please send a bug report to your compiler vendor.

In the event that you need to write a code targetted at multiple compilers, including some which have bugs preventing FoX compilation, please note the possibility of producing a dummy library.

The list below shows results as tested at the time of release with the 3.0 release of the FoX code (see a special the note on the PGI compilers below.). An up-to-date list of tested compiler version is maintained here.

- g95 as of 25/5/7
- gfortran as of version 4.2
- Intel version 8.1, 9.1, 10.1
- NAG version 5.1
- XLF version 10.01

Known failures:

- Any version of Compaq Visual Fortran
- g95 prior to 25/5/7
- Intel version 7.1
- NAG version 5.0
- F version of 16/5/6
- All PGI versions (see below)

Results from other compilers are welcome.

As of version 2.0.2, the following other compilers had been tested and are known to work:

- Lahey version 6.20
- Pathscale, version 2.4
- XLF version 9.1

#### PGI compilers

The Portland group compilers are by far the worst performing and buggiest compilers I have had the misfortune to use. Nevertheless, I have tried hard to make FoX work with them. The results are that:

- PGI 5.1 is completely broken. Compilation is impossible, too few F95 features are supported.

- PGI 6.1-6 and 6.2-3, and 7.0-2 are usable. All of FoX will be compiled, and most of the functionality is available, with the exception of any array-output routines, which the compiler runtime cannot handle. In practice, this means that most of WXML, and all of SAX and DOM are safe for use. Segfaults will be generated in the use of WCML.

I cannot recommend the use of PGI compilers. Patches to work around PGI problems will be welcomed, but please direct bug reports to the Portland Group.

## Configuration

- In order to generate the Makefile, make sure that you have a Fortran compiler in your `PATH`, and do:

  `./configure`

This should suffice for most installations. However:

1. You may not be interested in all of the modules that FoX supplies. For example, you may only be interested in output, not input. If so, you can select which modules you want using `--enable-MODULENAME` where MODULENAME is one of `wxml`, `wcml`, `wkml`, `sax`, `dom`. If none are explicitly enabled, then all will be built. (Alternatively, you can exclude modules one at a time with `--disable-MODULENAME`) Thus, for example, if you only care about CML output, and not anything else: `./configure --enable-wcml`

2. If you have more than one Fortran compiler available, or it is not on your `PATH`, you can force the choice by doing:

   `./configure FC=/path/to/compiler/of/choice`

3. It is possible that the configuration fails. In this case

   - please tell me about it so I can fix it
   - all relevant compiler details are placed in the file arch.make; you may be able to edit that file to allow compilation. Again, if so, please let me know what you need to do.

4. By default the resultant files are installed under the objs directory. If you wish them to be installed elsewhere, you may do

   `./configure --prefix=/path/to/installation`

Note that the configure process encodes the current directory location in several places. If you move the FoX directory later on, you will need to re-run configure.

- You may be interested in dummy compilation. This is activated with the `--enable-dummy` switch (but only works for wxml/wcml currently).

  `./configure --enable-wcml --enable-dummy`

## Compilation

In order to compile the full library, now simply do:

    make

This will build all the requested FoX modules, and the relevant examples

## Testing

In the full version of the FoX library, there are several testsuites included.

To run them all, simply run `make check` from the top-level directory. This will run the individual testsuites, and collate their results.

If any failures occur (unrelated to known compiler issues, see the up-to-date list), please send a message to the mailing list (FoX@lists.uszla.me.uk) with details of compiler, hardware platform, and the nature of the failure.

## Linking to an existing program

- The files all having been compiled and installed, you need to link them into your program.

A script is provided which will provide the appropriate compiler and linker flags for you; this will be created after configuration, in the top-level directory, and is called `FoX-config`. It may be taken from there and placed anywhere.

FoX-config takes the following arguments:

- `--fcflags`: return flags for compilation
- `--libs`: return flags for linking
- `--wxml`: return flags for compiling/linking against wxml
- `--wcml`: return flags for compiling/linking against wcml
- `--sax`: return flags for compiling/linking against sax

If it is called with no arguments, it will expand to compile & link flags, thusly:

       f95 -o program program.f90 `FoX-config`

For compiling only against FoX, do the following:

    f95 -c `FoX-config --fcflags` sourcefile.f90

For linking only to the FoX library, do:

    f95 -o program `FoX-config --libs` *.o

or similar, according to your compilation scheme.

Note that by default, `FoX-config` assumes you are using all modules of the library. If you are only using part, then this can be specified by also passing the name of each module required, like so:

    FoX-config --fcflags --wcml

## Compiling a dummy library

Because of the shortcomings in some compilers, it is not possible to compile FoX everywhere. Equally, sometimes it is useful to be able to compile a code both with and without support for FoX (perhaps to reduce executable size). Especially where FoX is being used only for additional output, it is useful to be able to run the code and perform computations even without the possibility of XML output.

For this reason, it is possible to compile a dummy version of FoX. This includes all public interfaces, so that your code will compile and link correctly - however none of the subroutines do anything, so you can retain the same version of your code without having to comment out all FoX calls.

Because this dummy version of FoX contains nothing except empty subroutines, it compiles and links with all known Fortran 95 compilers, regardless of compiler bugs.

To compile the dummy code, use the `--enable-dummy` switch. Note that currently the dummy code is only available for the WXML and WCML modules.

# Using FoX in your own project.

The recommended way to use FoX is to embed the full source code into an existing project.

(It would be possible to extract portions of the code, and embed just the ones that you need, but I recommend against it; it would be easy to lose parts of the code which are essential for generating good XML.)

In order to do this, you need to do something like the following:

1. Put the full source code as a top-level subdirectory of the tree, called FoX. (you can of course delete the DoX/ and examples/ subdirectories if you wish to save space)
2. Incorporate calls to FoX into the program.
3. Incorporate building FoX into your build process.

## To incorporate into the program

There is an example of suggested use in the `examples/` subdirectory.

The easiest, and least intrusive way is probably to create a F90 module for your program, looking something like `example_xml_module.f90`

Then you must somewhere (probably in your main program), use this module, and call `initialize_xml_output()` at the start; and then `end_xml_output()` at the end of the program.

In any of the subroutines where you want to output data to the xml file, you should then insert `use example_cml_moule` at the beginning of the subroutine. You can then use any of the cml output routines with no further worries, as shown in the examples.

It is easy to make the use of FoX optional, by the use of preprocessor defines. This can be done simply by wrapping each call to your XML wrapper routines in `#ifdef XML`, or similar. Alternatively, the use of the dummy FoX interfaces allows you to switch FoX on and off at compile time - see Compilation.

## To incorporate into the build process:

If you have some sort of automatic Makefile configuration; for picking up which compiler to use, etc. then within whatever script you use to do this, you should insert a sequence of commands which instructs FoX to use whichever compiler the rest of your program uses, and ensures that the portion of the FoX libraries you need are compiler. For example, if your Fortran compiler is stored in the variable FORT, and you are using only the WCML part of the library, you should ensure that the following command is run:

    (cd FoX; ./configure FC=$(FORT) --enable-wcml; cd ..)

This will instruct FoX to perform its own automatic configuration process appropriately.

Within the Makefile itself, you need to alter your compiler flags in the following fashion. Assuming that you have some sort of FFLAGS Makefile variable, then it should be amended like so:

    FFLAGS="$(FFLAGS) `FoX/FoX-config --fcflags`"

You must also alter the linking step to include the FoX subroutines Again, assuming that you have some sort of variable LDFLAGS holding your linking flags, then it should be amended like so:

    LDFLAGS="$(LDFLAGS) `FoX/FoX-config --libs`"

If you don't have any automatic Makefile configuration, and rely on the user making hand-edited changes to Makefiles, then you must add to your documentation how to configure & build FoX.

# FoX_common

FoX_common is a module exporting interfaces to a set of convenience functions common to all of the FoX modules, which are of more general use.

Currently, the only publically available function is `str`, which converts primitive datatypes into strings in a consistent fashion, conformant with the expectations of XML processors.

It is fully described in StringFormatting

# String handling in FoX

Many of the routines in wxml, and indeed in wcml which is built on top of wxml, are overloaded so that data may be passed to the same routine as string, integer, logical or real data.

In such cases, a few notes on the conversion of non-textual data to text is on order. The standard Fortran I/O formatting routines do not offer the control required for useful XML output, so FoX performs all its own formatting.

This formatting is done internally through a function which is also available publically to the user, `str`.

To use this in your program, import it via:

    use FoX_common, only; str

and use it like so:

     print*, str(data)

In addition, for ease of use, the `//` concatenation operator is overloaded, such that strings can easily be formed by concatenation of strings to other datatypes. To use this you must import it via:

     use FoX_common, only: operator(//)

and use it like so:

     integer :: data
     print*, "This is a number "//data

This will work for all native Fortran data types - but no floating point formatting is available as described below with concatenation, only with str()

You may pass data of the following primitive types to `str`:

## Scalar data

### Character (default kind)

Character data is returned unchanged.

### Logical (default kind)

Logical data is output such that True values are converted to the string 'true', and False to the string 'false'.

### Integer (default kind)

Integer data is converted to the standard decimal representation.

### Real numbers (single and double precision)

Real numbers, both single and double precision, are converted to strings in one of two ways, with some control offered to the user. The output will conform to the real number formats specified by XML Schema Datatypes.

This may be done in one of two ways:

1. Exponential notation, with variable number of significant figures. Format strings of the form "`s`n" are accepted, where n is the number of significant figures.

   Thus the number `111`, when output with various formats, will produce the following output:

s1 | 1e2
s2 | 1.1e2
s3 | 1.11e2
s4 | 1.110e2

The number of significant figures should lie between 1 and the number of digits precision provided by the real kind. If a larger or smaller number is specified, output will be truncated accordingly. If unspecified, then a sensible default will be chosen.

This format is not permitted by XML Schema Datatypes 1.0, though it is in 2.0

1. Non-exponential notation, with variable number of digits after the decimal point. Format strings of the form "`r`n", where n is the number of digits after the decimal point.

   Thus the number `3.14159`, when output with various formats, will produce the following output:

r0 | 3
r1 | 3.1
r2 | 3.14
r3 | 3.142

The number of decimal places must lie between 0 and whatever would output the maximum digits precision for that real kind. If a larger or smaller number is specified, output will be truncated accorsingly. If unspecified, then a sensible default will be chosen.

This format is the only one permitted by XML Schema Datatypes 1.0

If no format is specified, then a default of exponential notation will be used.

If a format is specified not conforming to either of the two forms above, a run-time error will be generated.

NB Since by using FoX or str, you are passing real numbers through various functions, this means that they must be valid real numbers. A corollary of this is that if you pass in +/-Infinity, or NaN, then the behaviour of FoX is unpredictable, and may well result in a crash. This is a consequence of the Fortran standard, which strictly disallows doing anything at all with such numbers, including even just passing them to a subroutine.

## Complex numbers (single and double precision)

Complex numbers will be output as pairs of real numbers, in the following way:

`(1.0e0)+i(1.0e0)`

where the two halves can be formatted in the way described for 'Real numbers' above; only one format may be specified, and it will apply to both.

All the caveats described above apply for complex number as well; that is, output of complex numbers either of whose components are infinite or NaN is illegal in Fortran, and more than likely will cause a crash in FoX.

## Arrays and matrices

All of the above types of data may be passed in as arrays and matrices as well. In this case, a string containing all the individual elements will be returned, ordered as they would be in memory, each element separated by a single space.

If the data is character data, then there is an additional option to str, `delimiter` which may be any single-character string, and will replace a space as the delimiter.

## wxml/wcml wrappers.

All functions in wxml which can accept arbitrary data (roughly, wherever you put anything that is not an XML name; attribute values, pseudo-attribute values, character data) will take scalars, arrays, and matrices of any of the above data types, with `fmt=` and `delimiter=` optional arguments where appropriate.

Similarly, wcml functions which can accept varied data will behave similarly.

# WXML

`wxml` is a general Fortran XML output library. It offers a Fortran interface, in the form of a number of subroutines, to generate well-formed XML documents. Almost all of the XML features described in XML11 and Namespaces are available, and `wxml` will diagnose almost all attempts to produce an invalid document. Exceptions below describes where `wxml` falls short of these aims.

First, Conventions describes the conventions use in this document.

Then, Functions lists all of `wxml`'s publically exported functions, in three sections:

1. Firstly, the very few functions necessary to create the simplest XML document, containing only elements, attributes, and text.
2. Secondly, those functions concerned with XML Namespaces, and how Namespaces affect the behaviour of the first tranche of functions.
3. Thirdly, a set of more rarely used functions required to access some of the more esoteric corners of the XML specification.

Please note that where the documentation below is not clear, it may be useful to look at some of the example files. There is a very simple example in the `examples/` subdirectory, but which nevertheless shows the use of most of the features you will use.

A more elaborate example, using almost all of the XML features found here, is available in the top-level directory as `wxml_example.f90`. It will be automatically compiled as part of the build porcess.

## Conventions and notes:

#### Conventions used below.

- Function names are in `monospace`
- argument names are in bold
- optional argument names are in (parenthesized bold)
- argument types are in italic and may consist of:
- string: string of arbitrary (unless otherwise specified) length
- integer: default integer
- real(sp): single precision real number
- real(dp): double precision real number
- logical: default logical
- real: either of real(sp) or real(dp)
- anytype: any of logical, integer, real(sp), real(dp), string

Note that where strings are passed in, they will be passed through entirely unchanged to the output file - no truncation of whitespace will occur.

It is strongly recommended that the functions be used with keyword arguments rather than replying on implicit ordering.

#### Derived type: `xmlf_t`

This is an opaque type representing the XML file handle. Each function requires this as an argument, so it knows which file to operate on. (And it is an output of the xml_OpenFile subroutine) Since all subroutines require it, it is not mentioned below.

## Function listing

### Frequently used functions

- `xml_OpenFile`
  filename: string: Filename to be opened
  xf: xmlf_t: XML File handle
  (preserve_whitespace): logical: Is whitespace important in the output? (If not, the XML will be pretty-printed.) default: false
  (channel): integer: What Fortran file handle should the XML file be attached to? default: picked by the library at runtime
  (replace): logical: Should the file be replaced if it already exists? default: no, stop at runtime if file already exists
  (addDecl): logical: Should an XML declaration be added at the start of the file? default: yes (valid): logical: Should wxml carry out any checks on the optional VC constraints specified by XML? default: yes (warning): logical: Should wxml emit warnings when it is unable to guarantee well-formedness? default: no

Open a file for writing XML

By default, the XML will have no extraneous text nodes. This has the effect of it looking slightly ugly, since there will be no newlines inserted between tags.

This behaviour can be changed to produce slightly nicer looking XML, by switching on broken_indenting. This will insert newlines and spaces between some tags where they are unlikely to carry semantics. Note, though, that this does result in the XML produced being not quite what was asked for, since extra characters and text nodes have been inserted.

NB: The replace option should be noted. By default, xml_OpenFile will fail with a runtime error if you try and write to an existing file. If you are sure you want to continue on in such a case, then you can specify `**replace**=.true.` and any existing files will be overwritten. If finer granularity is required over how to proceed in such cases, use the Fortran `inquire` statement in your code. There is no 'append' functionality by design - any XML file created by appending to an existing file would almost certainly be invalid.

- `xml_Close`
  xf: xmlf_t: XML File handle (empty): Can the file be empty? default: .false.

Close an opened XML file, closing all still-opened tags so that it is well-formed.

In the normal run of event, trying to close an XML file with no root element will cause an error, since this is not well-formed. However, an doptional argument, empty is provided in case it is desirable to close files which may be empty. In this case, a warning will still be emitted, but no fatal error generated.

- `xml_NewElement`
  name: string: Name of tag (for namespaced output, you need to include the prefix)

Open a new element tag

- `xml_EndElement`
  name: string: Name of tag to be closed (if it doesn't match currently open tag, you'll get an error)

Close an open tag

- `xml_AddAttribute`
  name: string: Name of attribute
  value: anytype: Value of attribute
  (escape): logical: if the attribute value is a string, should the attribute value be escaped? default: true
  (type): string: the type of the attribute. This must be one of `CDATA`, `ID`, `IDREF`, `IDREFS`, `NMTOKEN`, `NMTOKENS`, `ENTITY`, `ENTITIES`, or `NOTATION` (always upper case). If specified, this must match any attribute declarations that have been previously declared in the DTD. If unspecified this (as the XML standard requires) defaults to `CDATA`.

Add an attribute to the currently open tag.

By default, if the attribute value contains markup characters, they will be escaped automatically by wxml before output.

However, in rare cases you may not wish this to happen - if you wish to output Unicode characters, or entity references. In this case, you should set `escape=.false.` for the relevant subroutine call. Note that if you do this, no checking on the validity of the output string iis performed; the onus is on you to ensure well-formedness

The value to be added may be of any type; it will be converted to text according to FoX's formatting rules, and if it is a 1- or 2-dimensional array, the elements will all be output, separated by spaces (except if it is a character array, in which case the delimiter may be changed to any other single character using an optional argument).

NB The type option is only provided so that in the case of an external DTD which FoX is unaware of, the attribute type can be specified (which gives FoX more information to ensure well-formedness and validity). Specifying the type incorrectly may result in spurious error messages)

- `xml_AddCharacters`
  chars anytype: The text to be output
  (parsed): logical: Should the output characters be parsed (ie should the library replace '&' with '&' etc?) or unparsed (in which case the characters will be surrounded by CDATA tags. default: yes
  (delimiter): character(1): If data is a character array, what should the delimiter between elements be on output? default: a single space
  (ws_significant): logical: Is any whitespace in the string significant? default: unknown

Add text data. The data to be added may be of any type; they will be converted to text according to FoX's formatting rules, and if they are a 1- or 2-dimensional array, the elements will all be output, separated by spaces (except if it is a character array, in which case the delimiter may be changed to any other single character using an optional argument).

- `xml_AddNewline`

Within the context of character output, add a (system-dependent) newline character. This function can only be called wherever `xml_AddCharacters` can be called. (Newlines outside of character context are under FoX's control, and cannot be manipulated by the user.)

### Namespace-aware functions:

- `xml_DeclareNamespace`
  nsURI string: The URI of the namespace
  (prefix) string: The namespace prefix to be used in the document. If absent, then the default namespace is affected.

Add an XML Namespace declaration. This function may be called at any time, and its precise effect depends on when it is called; see below

- `xml_UndeclareNamespace`
  (prefix) string: The namespace prefix to be used in the document. If absent, then the default namespace is affected.

Undeclare an XML namespace. This is equivalent to declaring an namespace with an empty URI, and renders the namespace ineffective for the scope of the declaration. For explanation of its scope, see below.

NB Use of `xml_UndeclareNamespace` implies that the resultant document will be compliant with XML Namespaces 1.1, but not 1.0; wxml will issue an error when trying to undeclare namespaces under XML 1.0.

#### Scope of namespace functions

If `xml_[Un]declareNamespace` is called immediately prior to an `xml_NewElement` call, then the namespace will be declared in that next element, and will therefore take effect in all child elements.

If it is called prior to an `xml_NewElement` call, but that element has namespaced attributes

To explain by means of example: In order to generate the following XML output:

     <cml:cml xmlns:cml="http://www.xml-cml.org/schema"/>

then the following two calls are necessary, in the prescribed order:

      xml_DeclareNamespace(xf, 'cml', 'http://www.xml-cml.org')
      xml_NewElement(xf, 'cml:cml')

However, to generate XML input like so: that is, where the namespace refers to an attribute at the same level, then as long as the `xml_DeclareNamespace` call is made before the element tag is closed (either by `xml_EndElement`, or by a new element tag being opened, or some text being added etc.) the correct XML will be generated.

Two previously mentioned functions are affected when used in a namespace-aware fashion.

- `xml_NewElement`, `xml_AddAttribute`

The element or attribute name is checked, and if it is a QName (ie if it is of the form prefix:tagName) then wxml will check that prefix is a registered namespace prefix, and generate an error if not.

### More rarely used functions:

If you don't know the purpose of any of these, then you don't need to.

- `xml_AddXMLDeclaration`
  (version) string: XML version to be used. default: 1.0
  (encoding) string: character encoding of the document default: absent
  (standalone) logical: is this document standalone? default: absent

Add XML declaration to the first line of output. If used, then the file must have been opened with `addDecl = .false.`, and this must be the first wxml call to the document.o

NB The only XML versions available are 1.0 and 1.1. Attempting to specify anything else will result in an error. Specifying version 1.0 results in additional output checks to ensure the resultant document is XML-1.0-conformant.

NB Note that if the encoding is specified, and is specified to not be UTF-8, then if the specified encoding does not match that supported by the Fortran processor, you may end up with output you do not expect.

- `xml_AddDOCTYPE`
  name string: DOCTYPE name
  (system) string: DOCTYPE SYSTEM ID
  (public) string: DOCTYPE PUBLIC ID

Add an XML document type declaration. If used, this must be used prior to first `xml_NewElement` call, and only one such call must be made.

- `xml_AddInternalEntity`
  name string: name of internal entity
  value string: value of internal entity

Define an internal entity for the document. If used, this call must be made after `xml_AddDOCTYPE` and before the first `xml_NewElement` call.

- `xml_AddExternalEntity`
  name string: name of external entity
  system string: SYSTEM ID of external entity
  (public) string: PUBLIC ID of external entity default: absent
  (notation) string: notation for external entity default: absent

Define an external entity for the document. If used, this call must be made after `xml_AddDOCTYPE` and before the first `xml_NewElement` call.

- `xml_AddParameterEntity`
  name string: name of parameter entity
  (PEdef) string: definition of parameter entity default: absent
  (system) string: SYSTEM ID of parameter entity default: absent
  (public) string: PUBLIC ID of parameter entity default: absent

Define a parameter entity for the document. If used, this call must be made after `xml_AddDOCTYPE` and before the first `xml_NewElement` call.

- `xml_AddNotation`
  name string: name of notation
  (system) string: SYSTEM ID of notation default: absent
  (public) string: PUBLIC ID of notation default: absent

Define a notation for the document. If used, this call must be made after `xml_AddDOCTYPE` and before the first `xml_NewElement` call.

- `xml_AddElementToDTD`
  name string: name of element
  declaration string: declaration of element

Add an ELEMENT declaration to the DTD. The syntax of the declaration is not checked in any way, nor does this affect how elements may be added in the content of the XML document.

If used, this call must be made after `xml_AddDOCTYPE` and before the first `xml_NewElement` call.

- `xml_AddAttlistToDTD`
  name string: name of element
  declaration string: declaration of element

Add an ATTLIST declaration to the DTD. The syntax of the declaration is not checked in any way, nor does this affect how attributes may be added in the content of the XML document.

If used, this call must be made after `xml_AddDOCTYPE` and before the first `xml_NewElement` call.

- `xml_AddPEreferenceToDTD`
  name string: name of PEreference

Add a reference to a Parameter Entity in the DTD. No check is made according to whether the PE exists, has been declared, or may legally be used.

If used, this call must be made after `xml_AddDOCTYPE` and before the first `xml_NewElement` call.

- `xml_AddXMLStylesheet`
  href :string: address of stylesheet
  type: string: type of stylesheet (generally "text/xsl")
  (title): string: title of stylesheet default: none
  (media): string: output media type default: none
  (charset): string charset of media type default:none
  (alternate): string: alternate default:none

Add XML stylesheet processing instruction, as described in [Stylesheets]. If used, this call must be made before the first `xml_NewElement` call.

- `xml_AddXMLPI`
  name: string: name of PI
  (data): string: data for PI
  (xml): logical: (see below) default: false
  (ws_significant): logical: if this is a PI containing only data, then is any whitespace in the data significant? default: unknown

Add an XML Processing Instruction.

If data is present, nothing further can be added to the PI. If it is not present, then pseudoattributes may be added using the call below. Normally, the name is checked to ensure that it is XML-compliant. This requires that PI targets not start with `[Xx][Mm][Ll]`, because such names are reserved. However, some are defined by later W3 specificataions. If you wish to use such PI targets, then set `xml=.true.` when outputting them.

The output PI will look like: `<?name data?>`

- `xml_AddPseudoAttribute`
  name: string: Name of pseudoattribute
  value: anytype: Value of pseudoattribute (ws_significant): logical: If there is any whitespace in the value of this pseudoattribute, is is significant?

Add a pseudoattribute to the currently open PI.

- `xml_AddComment`
  comment: string Contents of comment
  (ws_significant): logical: is any whitespace in the comment string significant? default: unknown

Add an XML comment.

- `xml_AddEntityReference`
  entityref: Entity reference.

This may be used anywhere that `xml_AddCharacters` may be, and will insert an entity reference into the contents of the XML document at that point. Note that if the entity inserted is a character entity, its validity well be checked according to the rules of XML-1.1, not 1.0.

If the entity reference is not a character entity, then no check is made of its validity, and a warning will be issued

### Functions to query XML file objects

These functions may be of use in building wrapper libraries:

- `xmlf_Name` result(string)

Return the filename of an open XML file

- `xmlf_OpenTag` result(string)

Return the currently open tag of the current XML file (or the empty string if none is open)

## Exceptions

Below are explained areas where wxml fails to implement the whole of XML 1.0/1.1; numerical references below are to the sections in [XML11]]. These are divided into two lists; where wxml does not permit the generation of a particular well-formed XML document, and where it does permit the generation of a particular non-well-formed document.

Ways in which wxml renders it impossible to produce a certain sort of well-formed XML document:

1. XML documents which are not namespace-valid may not be produced; that is, attempts to produce documents which are well-formed according to [XML11] but not namespace-well-formed according to [Namespaces] will fail.
2. Unicode support[[2.2]](http://www.w3.org/TR/xml11/#charsets) is limited. Due to the limitations of Fortran, wxmlis unable to manipulate characters outwith 7-bit US-ASCII. wxml will ensure that characters corresponding to those in 7-bit ASCII are output correctly within the constraints of the version of XML in use, for a UTF-8 encoding. Attempts to directly output any other characters will have undefined effects. Output of other unicode characters is possible through the use of character entities.
3. Due to the constraints of the Fortran IO specification, it is impossible to output arbitrary long strings without carriage returns. The size of the limit varies between processors, but may be as low as 1024 characters. To avoid overrunning this limit, wxml will by default insert carriage returns before every new element, and if an unbroken string of attribute or text data is requested greater than 1024 characters, then carriage returns will be inserted as appropriate; within whitespace if possible; to ensure it is broken up into smaller sections to fit within the limits. Thus unwanted text sections are being created, and user output modified.

wxml will try very hard to ensure that output is well-formed. However, it is possible to fool wxml into producing ill-formed XML documents. Avoid doing so if possible; for completeness these ways are listed here. In all cases where ill-formedness is a possibility, a warning can be issued. These warnings can be verbose, so are off by default, but if they are desired, they can be switched on by manipulating the `warning` argument to `xml_OpenFile`.

1. If you specify a non-default text encoding, and then run FoX on a platform which does not use this encoding, then the result will be nonsense, and more than likely ill-formed. FoX will issue a warning in this case.
2. When adding any text, if any characters are passed in (regardless of character set) which do not have equivalants within 7-bit ASCII, then the results are processor-dependent, and may result in an invalid document on output. A warning will be issued if this occurs. If you need a guarantee that such characters will be passed correctly, use character entities.
3. Although entities may be output, their contents are not comprehensively checked. It is therefore possible to output combinations of entities which produce nonsense when referenced and expanded. FoX will issue a warning when this is possible.
4. Whenever an external subset of the DTD is referenced, and the document is not standalone, then FoX is unable to check that any unknown references exist or are used correctly, and can therefore no longer guarantee well-formedness. In this case, a warning will be issued.
5. When adding ELEMENT and ATTLIST declarations in the DTD, no checking at all is done on the contents of the declarations passed in, neither at the level of mere syntax, nor at the level of consistency; so that if the declaration is invalid syntactically, the resultant XML document will be ill-formed. A warning will be issued if either function is used.
6. Within the DTD whenever any External ID is written with a SYSTEM ID, this should be a string which can be resolved to a correctly-formatted URI string. No such check is made by wxml though.

Finally, note that constraints on XML documents are divided into two sets - well-formedness constraints (WFC) and validity constraints (VC. The above only applies to WFC checks. wxml makes some minimal checks on VC checks, but this is by no means complete, nor is it intended to be. If it is necessary to produce invalid but well-formed documents, VC checks may be switched off by manipulating the `valid` argument to `xml_OpenFile`.

## References

[XML10]: W3C Recommendation, http://www.w3.org/TR/REC-xml/

[XML11]: W3C Recommendation, http://www.w3.org/TR/xml11

[Namespaces]: W3C Recommendation, http://www.w3.org/TR/xml-names11

[Stylesheets]: W3C Recommendation, http://www.w3.org/TR/xml-stylesheet

# WCML

WCML is a library for outputting CML data. It wraps all the necessary XML calls, such that you should never need to touch any WXML calls when outputting CML.

The CML output is conformant to version 2.4 of the CML schema.

The available functions and their intended use are listed below. Quite deliberately, no reference is made to the actual CML output by each function.

Wcml is not intended to be a generalized Fortran CML output layer. rather it is intended to be a library which allows the output of a limited set of well-defined syntactical fragments.

Further information on these fragments, and on the style of CML generated here, is available at http://www.uszla.me.uk/specs/subset.html.

This section of the manual will detail the available CML output subroutines.

## Use of WCML

wcml subroutines can be accessed from within a module or subroutine by inserting

     use FoX_wcml

at the start. This will import all of the subroutines described below, plus the derived type `xmlf_t` needed to manipulate a CML file.

No other entities will be imported; public/private Fortran namespaces are very carefully controlled within the library.

## Dictionaries.

The use of dictionaries with WCML is strongly encouraged. (For those not conversant with dictionaries, a fairly detailed explanation is available at http://www.xml-cml.org/information/dictionaries)

In brief, dictionaries are used in two ways.

### Identification

Firstly, to identify and disambiguate output data. Every output function below takes an optional argument, `dictRef=""`. It is intended that every piece of data output is tagged with a dictionary reference, which will look something like `nameOfCode:nameOfThing`.

So, for example, in SIESTA, all the energies are output with different dictRefs, looking like: `siesta:KohnShamEnergy`, or `siesta:kineticEnergy`, etc. By doing this, we can ensure that later on all these numbers can be usefully identified.

We hope that ultimately, dictionaries can be written for codes, which will explain what some of these names might mean. However, it is not in any way necessary that this be done - and using `dictRef` attributes will help merely by giving the ability to disambiguate otherwise indistinguishable quantities.

We strongly recommend this course of action - if you choose to do follow our recommendation, then you should add a suitable Namespace to your code. That is, immediately after `cmlBeginFile` and before `cmlStartCml`, you should add something like:

    call cmlAddNamespace(xf=xf, 'nameOfCode', 'WebPageOfCode')

Again, for SIESTA, we add:

    call cmlAddNamespace(xf, 'siesta, 'http://www.uam.es/siesta')

If you don't have a webpage for your code, don't worry; the address is only used as an identifier, so anything that looks like a URL, and which nobody else is using, will suffice.

### Quantification

Secondly, we use dictionaries for units. This is compulsory (unlike `dictRef`s above). Any numerical quantity that is output through cmlAddProperty or cmlAddParameter is required to carry units. These are added with the `units=""` argument to the function. In addition, every other function below which will take numerical arguments also will take optional units, although default will be used if no units are supplied.

Further details are supplied in section Units below.

### General naming conventions for functions.

Functions are named in the following way:

- All functions begin `cml`

- To begin and end a section of the CML file, a pair of functions will exist:

  - `cmlStart`something
  - `cmlEnd`something

- To output a given quantity/property/concept etc. a function will exist `cmlAdd`something

### Conventions used below.

- Function names are in `monospace`
- argument names are in bold
- optional argument names are in (parenthesized bold)
- argument types are in italic and may consist of:
- string: string of arbitrary (unless otherwise specified) length
- integer: default integer
- real(sp): single precision real number
- real(dp): double precision real number
- logical: default logical
- real: either of real(sp) or real(dp)
- anytype: any of logical, integer, real(sp), real(dp), string

Note that where strings are passed in, they will be passed through entirely unchanged to the output file - no truncation of whitespace will occur.

Also note that wherever a real number can be passed in (including through anytype) then the formatting can be specified using the conventions described in StringFormatting

- scalar: single item
- array: one-dimensional array of items
- matrix: two-dimensional array of items
- anydim: any of scalar, array, matrix

Where an array is passed in, it may be passed either as an assumed-shape array; that is, as an F90-style array with no necessity for specifying bounds; thusly:

    integer :: array(50)
    call cmlAddProperty(xf, 'coords', array)

or as an assumed-size array; that is, an F77-style array, in which case the length must be passed as an additional parameter:

    integer :: array(*)
    call cmlAddProperty(xf, 'coords', array, nitems=50)

Similarly, when a matrix is passed in, it may be passed in both fashions:

    integer :: matrix(50, 50)
    call cmlAddProperty(xf, 'coords', matrix)

or

    integer :: array(3, *)
    call cmlAddProperty(xf, 'coords', matrix, nrows=3, ncols=50)

All functions take as their first argument an XML file object, whose keyword is always `xf`. This file object is initialized by a `cmlBeginFile` function.

It is highly recommended that subroutines be called with keywords specified rather than relying on the implicit ordering of arguments. This is robust against changes in the library calling convention; and also stepsides a significant cause of errors when using subroutines with large numbers of arguments.

### Units

Note below that the functions `cmlAddParameter` and `cmlAddProperty` both require that units be specified for any numerical quantities output.

If you are trying to output a quantity that is genuinely dimensionless, then you should specify `units="units:dimensionless"`; or if you are trying to output a countable quantity (eg number of CPUs) then you may specify `units="units:countable"`.

For other properties, all units should be specified as namespaced quantities. If you are using a very few common units, it may be easiest to borrow definitions from the provided dictionaries;

(These links do not resolve yet.)

`cmlUnits: http://www.xml-cml.org/units/units` `siUnits: <http://www.xml-cml.org/units/siUnits` `atomicUnits: http://www.xml-cml.org/units/atomic`

A default units dictionary, containing only the very basic units that wcml needs to know about, which has a namespace of: `http://www.uszla.me.uk/FoX/units`, and wcml assigns it automatically to the prefix `units`.

This is added automatically, so attempts to add it manually will fail.

The contents of all of these dictionaries, plus the wcml dictionary, may be viewed at: http://www.uszla.me.uk/unitsviz/units.cgi.

Otherwise, you should feel at liberty to construct your own namespace; declare it using `cmlAddNamespace`, and markup all your units as:

     units="myNamespace:myunit"

## Functions for manipulating the CML file:

- `cmlBeginFile`
  filename: string scalar: Filename to be opened.
  unit: integer scalar: what unit number should the file be opened on? If you don't care, you may specify '-1' as the unit number, in which case wcml will make a guess (replace): logical scalar: should the file be replaced if it already exists? default: yes

This takes care of all calls to open a CML output file.

- `cmlFinishFile`

This takes care of all calls to close an open CML output file, once you have finished with it. It is compulsory to call this - if your program finished without calling this, then your CML file will be invalid.

- `cmlAddNamespace`
  prefix string scalar: prefix to be used
  nsURI string scalar: namespace URI to be used

This adds a namespace to a CML file.
NB This may only ever be called immediately after a `cmlBeginFile` call, before any output has been performed. Attempts to do otherwise will result in a runtime error.

This will be needed if you are adding dictionary references to your output. Thus for siesta, we do:

    call cmlAddNamespace(xf, 'siesta', 'http://www.uam.es/siesta')

and then output all our properties and parameters with `dictRef="siesta:something"`.

- `cmlStartCml`
  (fileId) string scalar: name of originating file. (default: current filename) (version) string scalar: version of CML in use. (default: 2.4)

- `cmlEndCml`

This pair of functions begin and end the CML output to an existing CML file. It takes care of namespaces.

Note that unless specified otherwise, there will be a `convention` attribute added to the `cml` tag specifying `FoX_wcml-2.0` as the convention. (see http://www.uszla.me.uk/FoX for details)

## Start/End sections

- `cmlStartMetadataList`
  (name) string scalar: name for the metadata list
  (role) string scalar role which the element plays

- `cmlEndMetadataList`

This pair of functions open & close a metadataList, which is a wrapper for metadata items.

- `cmlStartParameterList`
  (ref) string scalar: Reference an `id` attribute of another element (generally deprecated)
  (role) string scalar role which the element plays

- `cmlEndParameterList`

This pair of functions open & close a parameterList, which is a wrapper for input parameters.

- `cmlStartPropertyList`
  (ref) string scalar: Reference an `id` attribute of another element (generally deprecated)
  (role) string scalar role which the element plays

- `cmlEndPropertyList`

This pair of functions open & close a propertyList, which is a wrapper for output properties.

- `cmlStartBandList`
- `cmlEndBandList`

Start/end a list of bands (added using `cmlAddBand` below)

- `cmlStartKpointList`
- `cmlEndKpointList`

Start/end a list of k-points (added using `cmlAddKpoint` below)

- `cmlStartModule`
  (serial) string scalar: serial id for the module
  (role) string scalar role which the element plays

Note that in most cases where you might want to use a serial number, you should probably be using the `cmlStartStep` subroutine below.

- `cmlEndModule`

This pair of functions open & close a module of a computation which is unordered, or loosely-ordered. For example, METADISE uses one module for each surface examined.

- `cmlStartStep`
  (index) integer scalar: index number for the step. In the absence of an index, steps will be assumed to be consecutively numbered. Specifying this is useful if you wish to output eg every hundredth step.
  (type) string scalar: what sort of step is this? This should be a namespaced string, for example: `siesta:CG` is a Conjugate Gradient step in siesta.

- `cmlEndStep`

This pair of functions open and close a module of a computation which is strongly ordered. For example, DLPOLY uses steps for each step of the simulation.

## Adding items.

- `cmlAddMetadata`
  name: string scalar: Identifying string for metadata
  content: character scalar: Content of metadata

This adds a single item of metadata. Metadata vocabulary is completely uncontrolled within WCML. This means that metadata values may only be strings of characters. If you need your values to contain numbers, then you need to define the representation yourself, and construct your own strings.

- `cmlAddParameter`
  name: string scalar: Identifying title for parameter
  value:anytype anydim: value of parameter
  units: string scalar: units of parameter value (optional for logical/character values, compulsory otherwise; see note above)
  (constraint) string scalar: Constraint under which the parameter is set (this can be an arbitrary string)
  (ref) string scalar: Reference an `id` attribute of another element (generally deprecated)
  (role) string scalar role which the element plays

This function adds a tag representing an input parameter

- `cmlAddProperty`
  title: string scalar
  value: any anydim
  units: string scalar units of property value (optional for logical/character values, compulsory otherwise; see note above)
  (ref) string scalar: Reference an `id` attribute of another element (generally deprecated)
  (role) string scalar role which the element plays

This function adds a tag representing an output property

- `cmlAddMolecule`
  coords: real: a 3xn matrix of real numbers representing atomic coordinates (either fractional or Cartesian) . These must be specified in Angstrom or fractional units (see style below.)
  OR
  x, y, z: real: 3 one-dimensional arrays containing the x, y, and z coordinates of the atoms in the molecule. These must be specified in Angstrom or fractional units (see style below.)
  elements: string array: a length-n array of length-2 strings containing IUPAC chemical symbols for the atoms
  (natoms) integer scalar: number of atoms in molecule (default: picked up from length of coords array)
  (occupancies): real array : a length-n array of the occupancies of each atom.
  (atomRefs): string array: a length-n array of strings containing references which may point to IDs elsewhere of, for example, pseudopotentials or basis sets defining the element's behaviour.
  (atomIds): string array: a length-n array of strings containing IDs for the atoms.
  (style): string scalar: `cartesian` - the coordinates are Cartesian, or `fractional` - the coordinates are fractional. The default is Cartesian.
  (ref) string scalar: Reference an `id` attribute of another element (generally deprecated)
  (formula) string scalar: An IUPAC chemical formula
  (chirality) string scalar: The chirality of the molecule. No defined vocabulary.
  (role) string scalar: Role of molecule. No defined vocabulary.

Outputs an atomic configuration.

- `cmlAddLattice`
  cell: real matrix a 3x3 matrix of the unit cell
  (spaceType): string scalar: `real` or `reciprocal` space.
  (latticeType): string scalar Space group of the lattice. No defined vocabulary
  (units): string scalar units of (reciprocal) distance that cell vectors is given in; default: Angstrom

Outputs information about a unit cell, in lattice-vector form

- `cmlAddCrystal`
  a: real scalar the 'a' parameter (must be in Angstrom)
  b: real scalar the 'b' parameter
  c: real scalar the 'c' parameter
  alpha: real scalar the 'alpha' parameter
  beta: real scalar the 'beta' parameter
  gamma: real scalar the 'gamma' parameter
  (z): integer scalar the 'z' parameter: number of molecules per unit cell.
  (lenunits): string scalar: Units of length: default is `units:angstrom`
  (angunits): string scalar: Units of angle: default is `units:degrees`
  (lenfmt): string scalar: format for crystal lengths
  (angfmt): string scalar: format for crystal angles
  (spaceGroup): string scalar Space group of the crystal. No defined vocabulary.

Outputs information about a unit cell, in crystallographic form

- `cmlAddBand`
  kptref: string scalar: Reference id of relevant kpoint.
  bands: real array: array of eigenvalues
  units: * string* scalar: energy units of eigenvalues
  (fmt): string scalar: format to output eigenvalues
  (label): string scalar: label for band.

Output eigenvalues for a band.

- `cmlAddKpoint`
  kpoint: real array length-3 array defining k-point
  (weight): real scalar: weight of k-point
  (kptfmt): string scalar: format for outputting k-point (default: `"r3"`)
  (weightfmt): string scalar: format for outputting weight (default: `"r3"`)
  (label): string scalar: label for k-point

Output a k-point

- `cmlAddEigen`
  eigvec: real matrix nxn array of eigenvectors
  eigval: real array length-n array of eigenvalues
  (n): number of eigenvalues/eigenvectors (default: picked up from length of eigval)
  units: units of eigenvalues
  eigenOrientationType: string scalar: is the eigenvector matrix `column` or `row` oriented?
  (vecfmt): string scalar: format for outputting eigenvectors
  (valfmt): string scalar: format for outputting eigenvalues
  (type): string scalar: what sort of thing are these eigenvectors? No defined vocabulary.

Output a set of eigenvalues and eigenvectors

## Common arguments

All `cmlAdd` and `cmlStart` routines take the following set of optional arguments:

- `id`: Unique identifying string for element. (Uniqueness is not enforced, though duplicated ids on output are usually an error and may cause later problems)
- `title`: Human-readable title of element for display purposes
- `dictRef`: reference to disambiguate element. Should be a QName; a namespaced string. An actual dictionary entry may or may not exist. It is not an error for it not to.
- `convention`: convention by which the element is to be read.
  (The wording of the definitions for `convention` is deliberately loose.)

# Debugging with FoX.

Following experience integrating FoX into several codes, here are a few tips for debugging any problems you may encounter.

## Compilation problems

You may encounter problems at the compiling or linking stage, with error messages along the lines of: 'No Specific Function can be found for this Generic Function' (exact phrasing depending on compiler, of course.)

If this is the case, it is possible that you have accidentally got the arguments to the offending out of order. If so, then use the keyword form of the argument to ensure correctness; that is, instead of doing:

    call cmlAddProperty(file, name, value)

do:

    call cmlAddProperty(xf=file, name=name, value=value)

This will prevent argument mismatches, and is recommended practise in any case.

## Runtime problems

You may encounter run-time issues. FoX performs many run-time checks to ensure the validity of the resultant XML code. In so far as it is possible, FoX will either issue warnings about potential problems, or try and safely handle any errors it encounters. In both cases, warning will be output on stderr, which will hopefully help diagnose the problem.

Sometimes, however, FoX will encounter a problem it can do nothing about, and must stop. In all cases, it will try and write out an error message highlighting the reason, and generate a backtrace pointing to the offending line. Occasionally though, the compiler will not generate this information, and the error message will be lost.

If this is the case, you can either investigate the coredump to find the problem, or (if you are on a Mac) look in ~/Library/Logs/CrashReporter to find a human-readable log.

If this is not enlightening, or you cannot find the problem, then some of the most common issues we have encountered are listed below. Many of them are general Fortran problems, but sometimes are not easily spotted in the context of FoX.

### Incorrect formatting.

Make sure, whenever you are writing out a real number through one of FoX's routines, and specifying a format, that the format is correct according to StringFormatting. Fortran-style formats are not permitted, and will cause crashes at runtime.

### Array overruns

If you are outputting arrays or matrices, and are doing so in the traditional Fortran style - by passing both the array and its length to the routine, like so:

     call xml_AddAttribute(xf=file, name=name, value=array, nvalue=n)

then if `n` is wrong, you may end up with an array overrun, and cause a crash.

We highly recommend wherever possible using the Fortran-90 style, like so:

     call xml_AddAttribute(xf=file, name=name, value=array)

where the array length will be passed automatically.

### Uninitialized variables

If you are passing variables to FoX which have not been initialized, you may well cause a crash. This is especially true, and easy to cause if you are passing in an array which (due to a bug elsewhere) has been partly but not entirely initialized. To diagnose this, try printing out suspect variables just before passing them to FoX, and look for suspiciously wrong values.

### Invalid floating point numbers.

If during the course of your calculation you accidentally generate Infinities, or NaNs, then passing them to any Fortran subroutine can result in a crash - therefore trying to pass them to FoX for output may result in a crash.

If you suspect this is happening, try printing out suspect variables before calling FoX.

# SAX

SAX stands for Simple API for XML, and was originally a Java API for reading XML. (Full details at http://saxproject.org). SAX implementations exist for most common modern computer languages.

FoX includes a SAX implementation, which translates most of the Java API into Fortran, and makes it accessible to Fortran programs, enabling them to read in XML documents in a fashion as close and familiar as possible to other languages.

SAX is a stream-based, event callback API. Conceptually, running a SAX parser over a document results in the parser generating events as it encounters different XML components, and sends the events to the main program, which can read them and take suitable action.

### Events

Events are generated when the parser encounters, for example, an element opening tag, or some text, and most events carry some data with them - the name of the tag, or the contents of the text.

The full list of events is quite extensive, and may be seen below. For most purposes, though, it is unlikely that most users will need more than the 5 most common events, documented here.

- `startDocument` - generated when the parser starts reading the document. No accompanying data.
- `endDocument` - generated when the parser reaches the end of the document. No accompanying data.
- `startElement` - generated by an element opening tag. Accompanied by tag name, namespace information, and a list of attributes
- `endElement` - generated by an element closing tag. Accompanied by tag name, and namespace information.
- `characters` - generated by text between tags. Accompanied by contents of text.

Given these events and accompanying information, a program can extract data from an XML document.

### Invoking the parser.

Any program using the FoX SAX parser must a) use the FoX module, and b) declare a derived type variable to hold the parser, like so:

       use FoX_sax
       type(xml_t) :: xp

The FoX SAX parser then works by requiring the programmer to write a module containing subroutines to receive any of the events they are interested in, and passing these subroutines to the parser.

Firstly, the parser must be initialized, by passing it XML data. This can be done either by giving a filename, which the parser will manipulate, or by passing a string containing an XML document. Thus:

      call open_xml_file(xp, "input.xml", iostat)

The `iostat` variable will report back any errors in opening the file.

Alternatively,

      call open_xml_string(xp, XMLstring)

where `XMLstring` is a character variable.

To now run the parser over the file, you simply do:

     call parse(xp, list_of_event_handlers)

And once you're finished, you can close the file, and clean up the parser, with:

     call close_xml_t(xp)

#### Options to parser

It is unlikely that most users will need to operate any of these options, but the following are available for use; all are optional boolean arguments to `parse`.

- `namespaces`
  Does namespace processing occur? Default is `.true.`, and if on, then any non-namespace-well-formed documents will be rejected, and namespace URI resolution will be performed according to the version of XML in question. If off, then documents will be processed without regard for namespace well-formedness, and no namespace URI resolution will be performed.

- `namespace_prefixes` Are `xmlns` attributes reported through the SAX parser? Default is `.false.`; all such attributes are removed by the parser, and transparent namespace URI resolution is performed. If on, then such attributes will be reported, and treated according to the value of `xmlns-uris` below. (If `namespaces` is false, this flag has no effect)

- `validate` Should partial validation be performed? Default is `.false.`, no validation checks are made, and the influence of the DTD on the XML Infoset is ignored. (Ill-formed DTD's will still cause fatal errors, of course.) If on, then a limited amount of validation will be performed, and the Infoset modified accordingly. (Validation will be incomplete if any external subset or entities are referenced.)

- `xmlns_uris` Should `xmlns` attributes have a namespace of `http://www.w3.org/2000/xmlns/`? Default is `.false.`. If such attributes are reported, they have no namespace. If `.true.` then they are supplied with the appropriate namespace. (if `namespaces` or `namespace-prefixes` are `.false.`, then this flag has no effect.)

### Receiving events

To receive events, you must construct a module containing event handling subroutines. These are subroutines of a prescribed form - the input & output is predetermined by the requirements of the SAX interface, but the body of the subroutine is up to you.

The required forms are shown in the API documentation below, but here are some simple examples.

To receive notification of character events, you must write a subroutine which takes as input one string, which will contain the characters received. So:

    module event_handling
      use FoX_sax
    contains

      subroutine characters_handler(chars)
        character(len=*), intent(in) :: chars

        print*, chars
      end subroutine
    end module

That does very little - it simply prints out the data it receives. However, since the subroutine is in a module, you can save the data to a module variable, and manipulate it elsewhere; alternatively you can choose to call other subroutines based on the input.

So, a complete program which reads in all the text from an XML document looks like this:

    module event_handling
      use FoX_sax
    contains

      subroutine characters_handler(chars)
        character(len=*), intent(in) :: chars

        print*, chars
      end subroutine
    end module

    program XMLreader
      use FoX_sax
      use event_handling
      type(xml_t) :: xp
      call open_xml_file(xp, 'input.xml')
      call parse(xp, characters_handler=characters_handler)
      call close_xml_t(xp)
    end program

### Attribute dictionaries.

The other likely most common event is the startElement event. Handling this involves writing a subroutine which takes as input three strings (which are the local name, namespace URI, and fully qualified name of the tag) and a dictionary of attributes.

An attribute dictionary is essentially a set of key:value pairs - where the key is the attributes name, and the value is its value. (When considering namespaces, each attribute also has a URI and localName.)

Full details of all the dictionary-manipulation routines are given in AttributeDictionaries(#AttributeDictionaries), but here we shall show the most common.

- `len(dictionary)` - returns the number of entries in the dictionary (the number of attributes declared)

- `getKey(dictionary, i)` (where `i` is an integer) returns a string containing the key of the `i`th dictionary entry (ie, the name of the `i`th attribute.

- `getValue(dictionary, i)` (where `i` is an integer) returns a string containing the value of the `i`th dictionary entry (ie the value of the `i`th attribute.

- `hasKey(dictionary, key)` (where `key` is a string) returns `.true.` or `.false.` depending on whether an attribute named `key` is present.

- `hasKey(dictionary, URI, localname)` (where `URI` and `localname` are strings) returns `.true.` or `.false.` depending on whether an attribute with the appropriate `URI` and `localname` is present.

- `getValue(dictionary, URI, localname)` (where `URI` and `localname` are strings) returns a string containing the value of the attribute with the appropriate `URI` and `localname` (if it is present)

So, a simple subroutine to receive a startElement event would look like:

    module event_handling

    contains

     subroutine startElement_handler(URI, localname, name,attributes)
       character(len=*), intent(in)   :: URI
       character(len=*), intent(in)   :: localname
       character(len=*), intent(in)   :: name
       type(dictionary_t), intent(in) :: attributes

       integer :: i

       print*, name

       do i = 1, len(attributes)
          print*, getKey(attributes, i), '=', getValue(attributes, i)
       enddo

      end subroutine startElement_handler
    end module

    program XMLreader
     use FoX_sax
     use event_handling
     type(xml_t) :: xp
     call open_xml_file(xp, 'input.xml')
     call parse(xp, startElement_handler=startElement_handler)
     call close_xml_t(xp)
    end program

Again, this does nothing but print out the name of the element, and the names and values of all of its attributes. However, by using module variables, or calling other subroutines, the data could be manipulated further.

### Error handling

The SAX parser detects all XML well-formedness errors. By default, when it encounters an error, it will simply halt the program with a suitable error message. However, it is possible to pass in an error handling subroutine if some other behaviour is desired - for example it may be nice to report the error to the user, and carry on with some other task.

In any case, once an error is encountered, the parser will finish. There is no way to continue reading past an error.

An error handling suubroutine works in the same way as any other event handler, with the event data being an error message. Thus, you could write:

    subroutine error_handler(msg)
      character(len=*), intent(in) :: msg

      print*, "The SAX parser encountered an error:"
      print*, msg
      print*, "Never mind, carrying on with the rest of the calcaulation."
    end subroutine

## Full API

### Derived types

There is one derived type, `xml_t`. This is entirely opaque, and is used as a handle for the parser.

### Subroutines

There are four subroutines:

- `open_xml_file
  type(xml_t), intent(inout) :: xp
  character(len=*), intent(in) :: string
  integer, intent(out), optional :: iostat`

This opens a file. `xp` is initialized, and prepared for parsing. `string` must contain the name of the file to be opened. `iostat` reports on the success of opening the file. A value of `0` indicates success.

- `open_xml_string
  type(xml_t), intent(inout) :: xpi
  character(len=*), intent(in) :: string`

  This prepares to parse a string containing XML data. `xp` is initialized. `string` must contain the XML data.

- `close_xml_t
  type(xml_t), intent(inout) :: xp`

This closes down the parser (and closes the file, if input was coming from a file.) `xp` is left uninitialized, ready to be used again if necessary.

- `parse
  type(xml_t), intent(inout) :: xp
  external :: list of event handlers
  logical, optional, intent(in) :: validate`

  This tells `xp` to start parsing its document.

(Advanced: By default, this will be done in a non-validating way, testing only for well-formedness errors. However, if `validate` is set to true. FoX will attempt to diagnose validation errors. Note that FoX is not a full validating parser, and will not read external entities, so do not rely on this behaviour)

The full list of event handlers is in the next section. To use them, the interface must be placed in a module, and the body of the subroutine filled in as desired; then it should be specified as an argument to `parse` as:
`name_of_event_handler = name_of_user_written_subroutine`
Thus a typical call to `parse` might look something like:

      call parse(xp, startElement_handler = mystartelement, endElement_handler = myendelement, characters_handler = mychars)

where `mystartelement`, `myendelement`, and `mychars` are all subroutines written by you according to the interfaces listed below.

## Callbacks.

All of the callbacks specified by SAX 2 are implemented. Documentation of the SAX 2 interfaces is available in the JavaDoc at http://saxproject.org, but as the interfaces needed adjustment for Fortran, they are listed here.

For documentation on the meaning of the callbacks and of their arguments, please refer to the Java SAX documentation.

- `characters_handler
  subroutine characters_handler(chunk)
  character(len=*), intent(in) :: chunk
  end subroutine characters_handler`

Triggered when some character data is read from between tags.

NB Note that all character data is reported, including whitespace. Thus you will probably get a lot of empty `characters` events in a typical XML document.

NB Note also that it is not required that large chunks of character data all come as one event - they may come as multiple consecutive events.

- `endDocument_handler
  subroutine endDocument_handler()
  end subroutine endDocument_handler`

Triggered when the parser reaches the end of the document.

- `endElement_handler
  subroutine endElement_handler(namespaceURI, localName, name)
  character(len=*), intent(in) :: namespaceURI
  character(len=*), intent(in) :: localName
  character(len=*), intent(in) :: name
  end subroutine endElement_handler`

Triggered by a closing tag.

- `endPrefixMapping_handler
  subroutine endPrefixMapping_handler(prefix)
  character(len=*), intent(in) :: prefix
  end subroutine endPrefixMapping_handler`

Triggered when a namespace prefix mapping goes out of scope.

- `ignorableWhitespace
  subroutine ignorableWhitespace_handler(chars)
  character(len=*), intent(in) :: chars
  end subroutine ignorableWhitespace_handler`

Triggered when whitespace is encountered within an element declared as having no PCDATA. (Only active in validating mode.)

- `processingInstruction_handler
  subroutine processingInstruction_handler(name, content)
  character(len=*), intent(in) :: name
  character(len=*), intent(in) :: content
  end subroutine processingInstruction_handler`

Triggered by a Processing Instruction

- `skippedEntity_handler
  subroutine skippedEntity_handler(name)
  character(len=*), intent(in) :: name
  end subroutine skippedEntity_handler`

Triggered when either an external entity, or an undeclared entity, is skipped.

- `startDocument_handler
  subroutine startDocument_handler()
  end subroutine startDocument_handler`

Triggered when the parser starts reading the document.

- `startElement_handler
  subroutine startElement_handler(namespaceURI, localName, name, attributes)
  character(len=*), intent(in) :: namespaceUri
  character(len=*), intent(in) :: localName
  character(len=*), intent(in) :: name
  type(dictionary_t), intent(in) :: attributes
  end subroutine startElement_handler`

Triggered when an opening tag is encountered. (see LINK for documentation on handling attribute dictionaries.

- `startPrefixMapping_handler
  subroutine startPrefixMapping_handler(namespaceURI, prefix)
  character(len=*), intent(in) :: namespaceURI
  character(len=*), intent(in) :: prefix
  end subroutine startPrefixMapping_handler`

Triggered when a namespace prefix mapping start.

- `notationDecl_handler
  subroutine notationDecl_handler(name, publicId, systemId)
  character(len=*), intent(in) :: name
  character(len=*), intent(in) :: publicId
  character(len=*), intent(in) :: systemId
  end subroutine notationDecl_handler`

Triggered when a NOTATION declaration is made in the DTD

- `unparsedEntityDecl_handler
  subroutine unparsedEntityDecl_handler(name, publicId, systemId, notation)
  character(len=*), intent(in) :: name
  character(len=*), intent(in) :: publicId
  character(len=*), intent(in) :: systemId
  character(len=*), intent(in) :: notation
  end subroutine unparsedEntityDecl_handler`

Triggered when an unparsed entity is declared

- `error_handler
  subroutine error_handler(msg)
  character(len=*), intent(in) :: msg
  end subroutine error_handler`

Triggered when a error is encountered in parsing. Parsing will cease after this event. (NB Note that according to the XML specification, parsers MAY recoved continue parsing after an error. FoX will not.)

Note that FoX is not entirely compliant with the standard; both normal errors and fatal errors will be reported through the errorhandler; fatalErrorhandler below is currently inactive.

- `fatalError_handler
  subroutine fatalError_handler(msg)
  character(len=*), intent(in) :: msg
  end subroutine fatalError_handler`

Triggered when a fatal error is encountered in parsing. Parsing will cease after this event.

Note that FoX is not entirely compliant with the standard; both normal errors and fatal errors will be reported through the errorhandler above; fatalErrorhandler is currently inactive.

- `warning_handler
  subroutine warning_handler(msg)
  character(len=*), intent(in) :: msg
  end subroutine warning_handler`

Triggered when a parser warning is generated. Parsing will continue after this event.

- `attributeDecl_handler
  subroutine attributeDecl_handler(eName, aName, type, mode, value)
  character(len=*), intent(in) :: eName
  character(len=*), intent(in) :: aName
  character(len=*), intent(in) :: type
  character(len=*), intent(in) :: mode
  character(len=*), intent(in) :: value
  end subroutine attributeDecl_handler`

Triggered when an attribute declaration is encountered in the DTD.

- `elementDecl_handler
  subroutine elementDecl_handler(name, model)
  character(len=*), intent(in) :: name
  character(len=*), intent(in) :: model
  end subroutine elementDecl_handler`

Triggered when an element declaration is enountered in the DTD.

- `externalEntityDecl_handler
  subroutine externalEntityDecl_handler(name, publicId, systemId)
  character(len=*), intent(in) :: name
  character(len=*), intent(in) :: publicId
  character(len=*), intent(in) :: systemId
  end subroutine externalEntityDecl_handler`

Triggered when a parsed external entity is declared in the DTD.

- `internalEntityDecl_handler
  subroutine internalEntityDecl_handler(name, value)
  character(len=*), intent(in) :: name
  character(len=*), intent(in) :: value
  end subroutine internalEntityDecl_handler`

Triggered when an internal entity is declared in the DTD.

- `comment_handler
  subroutine comment_handler(comment)
  character(len=*), intent(in) :: comment
  end subroutine comment_handler`

Triggered when a comment is encountered.

- `endCdata_handler
  subroutine endCdata_handler()
  end subroutine endCdata_handler`

Triggered by the end of a CData section.

- `endDTD_handler
  subroutine endDTD_handler()
  end subroutine endDTD_handler`

Triggered by the end of a DTD.

- `endEntity_handler
  subroutine endEntity_handler(name)
  character(len=*), intent(in) :: name
  end subroutine endEntity_handler`

Triggered at the end of entity expansion.

- `startCdata_handler
  subroutine startCdata_handler()
  end subroutine startCdata_handler`

Triggered by the start of a CData section.

- `startDTD_handler
  subroutine startDTD_handler(name, publicId, systemId)
  character(len=*), intent(in) :: name
  character(len=*), intent(in) :: publicId
  character(len=*), intent(in) :: systemId
  end subroutine startDTD_handler`

Triggered by the start of a DTD section.

- `startEntity_handler
  subroutine startEntity_handler(name)
  character(len=*), intent(in) :: name
  end subroutine startEntity_handler`

Triggered by the start of entity expansion.

### Exceptions.

Although FoX tries very hard to work to the letter of the XML and SAX standards, it falls short in a few areas.

- Unicode support is completely absent. It is unfortunately impossible to implement Unicode reading in standard Fortran 95. FoX will work perfectly well on documents of any encoding that only contain characters equivalent to those in US-ASCII, but its behaviour on documents containing other characters is not well-defined.

(This includes non-ASCII characters present only by character reference.)

It will, however, happily accept documents labelled as UTF-8 encoded.

- XML specifies that all SYSTEM IDs reported by events should be converted to URIs before the application receives them. FoX does no such conversion, and as a result, will allow through invalid SYSTEM IDs.

- FoX performs no checking on the validity of Namespace URIs.

Beyond this, any aspects of XML and SAX which FoX fails to do justice to are bugs.

Note that (as permissable within XML) FoX acts primarily as a non-validating parser, and thus all constraints marked as Validity Constraints by XML-1.0/1.1 are ignored by default. A subset of them will be picked up by FoX's validation mode, but only a small subset.

Note also that FoX will not read external entities when processing an XML document.

### What of Java SAX 2 is not included in FoX?

The difference betweek Java & Fortran means that none of the SAX APIs can be copied directly. However, FoX offers data types, subroutines, and interfaces covering a large proportion of the facilities offered by SAX. Where it does not, this is mentioned here.

org.sax.xml:

- Querying/setting of feature flags/property values for the XML parser.
- XML filters - Java SAX makes it possible to write filters to intercept the flow of events. FoX does not support this.
- Namespace configuration - SAX 2 allows changing the ways in which namespaces are interpreted
  by the parser. FoX supports only the SAX 2 default.
- Entity resolution - SAX 2 exports an interface to the application for entity resolution, but
  FOX does not - all entities are resolved within the parser.
- Locator - SAX 2 offers an interface to export information regarding object locations within the document, FoX does not.
- XMLReader - FoX only offers the parse() method - no other methods really make sense in Fortran.
- AttributeList/DocumentHandler/Parser - FoX only offers namespace aware attributes, not the pre-namespace versions.

org.sax.xml.ext:

- Attributes2 - FoX does not implement these attribute-declaration querying functions
- EntityResolver2 - see above
- Locator2 - not implemented

org.sax.xml.helpers:

- None of these helper methods are implemented.

# Attributes dictionaries.

When parsing XML using the FoX SAX module, attributes are returned contained within a dictionary object.

All of the attribute dictionary objects and functions are exported through FoXcommon and FoXsax - you must USE the module to enable them. The dictionary API is described here.

An attribute dictionary consists of a list of entries, one for each attribute. The entries all have the following pieces of data:

- key - the attribute's full name
- value - the attribute's value

and for namespaced attributes:

- nsURI - the namespace URI (if any) of the attribute
- localname - the local name of the attribute

## Derived types

There is one derived type of interest, `dictionary_t`.

It is opaque - that is, it should only be manipulated through the functions described here.

## Functions

- `len
  type(dictionary_t), intent(in) :: dict`

Returns an integer with the length of the dictionary, ie the number of dictionary entries.

- `getLength
  type(dictionary_t), intent(in) :: dict`

Returns an integer with the length of the dictionary, ie the number of dictionary entries. Identical to the `len` function.

- `hasKey
  type(dictionary_t), intent(in) :: dict
  character(len=*), intent(in) :: key`

Returns a logical value according to whether the dictionary contains an attribute named `key` or not.

- `hasKey
  type(dictionary_t), intent(in) :: dict
  character(len=*), intent(in) :: uri
  character(len=*), intent(in) :: localname`

Returns a logical value according to whether the dictionary contains an attribute with the correct `URI` and `localname`.

The following functions may be used to retrieve data from a dictionary

- `getQName
  type(dictionary_t), intent(in) :: dict
  integer, intent(in) :: i`

Return the full name of the `i`th dictionary entry.

- `getValue
  type(dictionary_t), intent(in)
  integer, intent(in) :: i`

If an integer is passed in - the value of the `i`th attribute.

- `getValue
  type(dictionary_t), intent(in)
  character(len=*), intent(in) :: key`

If a single string is passed in, the value of the attribute with that name.

- `getValue
  type(dictionary_t), intent(in)
  character(len=*), intent(in) :: uri, localname`

If two strings are passed in, the value of the attribute with that uri and localname.

- `getURI
  type(dictionary_t), intent(in)
  integer, intent(in), optional :: i`

Returns a string containing the nsURI of the `i`th attribute.

- `getlocalName
  type(dictionary_t), intent(in)
  integer, intent(in), optional :: i`

Returns a string containing the localName of the `i`th attribute.

# DOM

## Overview

The FoX DOM interface exposes an API as specified by the W3C DOM Working group.

FoX implements essentially all of DOM Core Levels 1 and 2, (there are a number of minor exceptions which are listed below) and a substantial portion of DOM Core Level 3.

- Quick overview of how to map the DOM interface to Fortran
- More detailed explanation of Fortran interface
- Additional (non-DOM) utility functions
- String handling
- Exception handling
- Live nodelists
- DOM Configuration
- Miscellanea

## Interface Mapping

FoX implements all objects and methods mandated in DOM Core Level 1 and 2. (A listing of supported DOM Core Level 3 interfaces is given below.)

In all cases, the mapping from DOM interface to Fortran implementation is as follows:

1. All DOM objects are available as Fortran types, and should be referenced only as pointers (though see 7 and 8 below). Thus, to use a Node, it must be declared first as:
   `type(Node), pointer :: aNode`
2. A flat (non-inheriting) object hierarchy is used. All DOM objects which inherit from Node are represented as Node types.
3. All object method calls are modelled as functions or subroutines with the same name, whose first argument is the object. Thus:
   `aNodelist = aNode.getElementsByTagName(tagName)`
   should be converted to Fortran as:
   `aNodelist => getElementsByTagName(aNode, tagName)`
4. All object method calls whose return type is void are modelled as subroutines. Thus:
   `aNode.normalize()`
   becomes `call normalize(aNode)`
5. All object attributes are modelled as a pair of get/set calls (or only get where the attribute is readonly), with the naming convention being merely to prepend get or set to the attribute name. Thus:
   `name = node.nodeName`
   `node.nodeValue = string`
   should be converted to Fortran as
   `name = getnodeName(node)`
   `call setnodeValue(string)`
6. Where an object method or attribute getter returns a DOM object, the relevant Fortran function must always be used as a pointer function. Thus:
   `aNodelist => getElementsByTagName(aNode, tagName)`
7. No special DOMString object is used - all string operations are done on the standard Fortran character strings, and all functions that return DOMStrings return Fortran character strings.
8. Exceptions are modelled by every DOM subroutine/function allowing an optional additional argument, of type DOMException. For further information see (#DOM Exceptions) below.

### String handling

The W3C DOM requires that a `DOMString` object exist, capable of holding Unicode strings; and that all DOM functions accept and emit DOMString objects when string data is to be transferred.

FoX does not follow this model. Since (as mentioned elsewhere) it is impossible to perform Unicode I/O in standard Fortran, it would be obtuse to require users to manipulate additional objects merely to transfer strings. Therefore, wherever the DOM mandates use of a `DOMString`, FoX merely uses standard Fortran character strings.

All functions or subroutines which expect DOMString input arguments should be used with normal character strings.
All functions which should return DOMString objects will return Fortran character strings.

### Using the FoX DOM library.

All functions are exposed through the module `FoX_DOM`. `USE` this in your program:

    program dom_example

      use FoX_DOM
      type(Node) :: myDoc

      myDoc => parseFile("fileIn.xml")
      call serialize(myDoc, "fileOut.xml")
    end program dom_example

## Documenting DOM functions

This manual will not exhaustively document the functions available through the `Fox_DOM` interface. Primary documentation may be found in the W3C DOM specifications:`

- DOM Core Level 1
- DOM Core Level 2
- DOM Core Level 3

The systematic rules for translating the DOM interfaces to Fortran are given in the previous section. For completeness, though, there is a list here. The W3C specifications should be consulted for the use of each.

DOMImplementation:
`type(DOMImplementation), pointer`

- `hasFeature(impl, feature, version)`
- `createDocumentType(impl, qualifiedName, publicId, systemId)`
- `createDocument(impl, qualifiedName, publicId, systemId)`

Document: `type(Node), pointer`

- `getDocType(doc)`
- `getImplementation(doc)`
- `getDocumentElement(doc)`
- `createElement(doc, tagname)`
- `createDocumentFragment(doc)`
- `createTextNode(doc, data)`
- `createComment(doc, data)`
- `createCDataSection(doc, data)`
- `createProcessingInstruction(doc, target, data)`
- `createAttribute(doc, name)`
- `createEntityReference(doc, name)`
- `getElementsByTagName(doc, tagname)`
- `importNode(doc, importedNode, deep)`
- `createElementNS(doc, namespaceURI, qualifiedName)`
- `createAttributeNS(doc, namespaceURI, qualifiedName)`
- `getElementsByTagNameNS(doc, namespaceURI, qualifiedName)`
- `getElementById(doc, elementId)`

Node:
`type(Node), pointer`

- `getNodeName(arg)`
- `getNodeValue(arg)`
- `setNodeValue(arg, value)`
- `getNodeType(arg)`
- `getParentNode(arg)`
- `getChildNodes(arg)`
- `getFirstChild(arg)`
- `getLastChild(arg)`
- `getPreviousSibling(arg)`
- `getNextSibling(arg)`
- `getAttributes(arg)`
- `getOwnerDocument(arg)`
- `insertBefore(arg, newChild, refChild)`
- `replaceChild(arg, newChild, refChild)`
- `removeChild(arg, oldChild)`
- `appendChild(arg, newChild)`
- `hasChildNodes(arg)`
- `cloneNode(arg, deep)`
- `normalize`
- `isSupported(arg, feature, version)`
- `getNamespaceURI(arg)`
- `getPrefix(arg)`
- `setPrefix(arg, prefix)`
- `getLocalName(arg)`
- `hasAttributes(arg)`

NodeList:
`type(NodeList), pointer`

- `item(arg, index)`
- `getLength(arg)`

NamedNodeMap:
`type(NamedNodeMap), pointer`

- `getNamedItem(map, name)`
- `setNamedItem(map, arg)`
- `removeNamedItem(map, name)`
- `item(map, index)`
- `getLength(map)`
- `getNamedItemNS(map, namespaceURI, qualifiedName)`
- `setNamedItemNS(map, arg)`
- `removeNamedItemNS(map, namespaceURI, qualifiedName)`

CharacterData:
`type(Node), pointer`

- `getData(np)`
- `setData(np, data)`
- `getLength(np)`
- `substringData(np, offset, count)`
- `appendData(np, arg)`
- `deleteData(np, offset, count)`
- `replaceData(np, offset, count, arg)`

Attr:
`type(Node), pointer`

- `getName(np)`
- `getSpecified(np)`
- `getValue(np)`
- `setValue(np, value)`
- `getOwnerElement(np)`

Element:
`type(Node), pointer`

- `getTagName(np)`
- `getAttribute(np, name)`
- `setAttribute(np, name, value)`
- `removeAttribute(np, name)`
- `getAttributeNode(np, name)`
- `setAttributeNode(np, newAttr)`
- `removeAttributeNode(np, oldAttr)`
- `getElementsByTagName(np, name)`
- `getAttributeNS(np, namespaceURI, qualifiedName)`
- `setAttributeNS(np, namespaceURI, qualifiedName, value)`
- `removeAttributeNS(np, namespaceURI, qualifiedName)`
- `getAttributeNode(np, namespaceURI, qualifiedName)`
- `setAttributeNode(np, newAttr)`
- `removeAttributeNode(np, oldAttr)`
- `getElementsByTagNameNS(np, namespaceURI, qualifiedName)`
- `hasAttribute(np, name)`
- `hasAttributeNS(np, namespaceURI, qualifiedName)`

Text:
`type(Node), pointer`

- `splitText(np, offset)`

DocumentType:
`type(Node), pointer`

- `getName(np)`
- `getEntites(np)`
- `getNotations(np)`
- `getPublicId(np)`
- `getSystemId(np)`
- `getInternalSubset(np)`

Notation:
`type(Node), pointer`

- `getPublicId(np)`
- `getSystemId(np)`

Entity:
`type(Node), pointer`

- `getPublicId(np)`
- `getSystemId(np)`
- `getNotationName(np)`

ProcessingInstruction:
`type(Node), pointer`

- `getTarget(np)`
- `getData(np)`
- `setData(np, data)`

In addition, the following DOM Core Level 3 functions are available:

Document:

- `getDocumentURI(np)`
- `setDocumentURI(np, documentURI)`
- `getDomConfig(np)`
- `getInputEncoding(np)`
- `getStrictErrorChecking(np)`
- `setStrictErrorChecking(np, strictErrorChecking)`
- `getXmlEncoding(np)`
- `getXmlStandalone(np)`
- `setXmlStandalone(np, xmlStandalone)`
- `getXmlVersion(np)`
- `setXmlVersion(np, xmlVersion)`
- `normalizeDocument(np)`

Node:

- `getTextContent(np)`
- `setTextContent(np, textContent)`
- `isEqualNode(np, other)`
- `isSameNode(np)`
- `isDefaultNamespace(np, namespaceURI)`
- `lookupPrefix(np, namespaceURI)`
- `lookupNamespaceURI(np, prefix)`

Attr:

- `getIsId(np)`

Entity:

- `getInputEncoding(np)`
- `getXmlVersion(np)`
- `getXmlEncoding(np)`

Text:

- `getIsElementContentWhitespace(np)`

DOMConfiguration:
`type(DOMConfiguration)`

- `canSetParameter(arg, name, value)`
- `getParameter(arg, name)`
- `getParameterNames(arg)`
- `setParameter(arg, name)`

NB For details on DOMConfiguration, see below

### Object Model

The DOM is written in terms of an object model involving inheritance, but also permits a flattened model. FoX implements this flattened model - all objects descending from the Node are of the opaque type `Node`. Nodes carry their own type, and attempts to call functions defined on the wrong nodetype (for example, getting the `target` of a node which is not a PI) will result in a `FoX_INVALID_NODE` exception.

The other types available through the FoX DOM are:

- `DOMConfiguration`
- `DOMException`
- `DOMImplementation`
- `NodeList`
- `NamedNodeMap`

### FoX DOM and pointers

All DOM objects exposed to the user may only be manipulated through pointers. Attempts to access them directly will result in compile-time or run-time failures according to your environment.

This should have little effect on the structure of your programs, except that you must always remember, when calling a DOM function, to perform pointer assignment, not direct assignment, thus:
`child => getFirstChild(parent)`
and not
`child = getFirstChild(parent)`

### Memory handling

Fortran offers no garbage collection facility, so unfortunately a small degree of memory handling is necessarily exposed to the user.

However, this has been kept to a minimum. FoX keeps track of all memory allocated and used when calling DOM routines, and keeps references to all DOM objects created.

The only memory handling that the user needs to take care of is destroying any DOM Documents (whether created manually, or by the `parse()` routine.) All other nodes or node structures created will be destroyed automatically by the relevant `destroy()` call.

As a consequence of this, all DOM objects which are part of a given document will become inaccessible after the document object is destroyed.

## Additional functions.

Several additional utility functions are provided by FoX.

### Input and output of XML data

Firstly, to construct a DOM tree, from either a file or a string containing XML data.

- `parseFile`
  filename: string
  (configuration): DOMConfiguration
  (ex): DOMException

filename should be an XML document. It will be opened and parsed into a DOM tree. The parsing is performed by the FoX SAX parser; if the XML document is not well-formed, a `PARSE_ERR` exception will be raised. configuration is an optional argument - see DOMConfiguration for its meaning.

- `parseString`
  XMLstring: string
  (configuration): DOMConfiguration
  (ex): DOMException

XMLstring should be a string containing XML data. It will be parsed into a DOM tree. The parsing is performed by the FoX SAX parser; if the XML document is not well-formed, a `PARSE_ERR` exception will be raised. configuration is an optional argument - see DOMConfiguration for its meaning.

Both `parseFile` and `parseString` return a pointer to a `Node` object containing the Document Node.`

Secondly, to output an XML document:

- `serialize`
  arg: Node, pointer fileName: string

This will open `fileName` and serialize the DOM tree by writing into the file. If `fileName` already exists, it will be overwritten. If an problem arises in serializing the document, then a fatal error will result.

(Control over serialization options is done through the configuration of the arg's ownerDocument, see below.)

Finally, to clean up all memory associated with the DOM, it is necessary to call:

- `destroy`
  np: Node, pointer

This will clear up all memory usage associated with the document (or documentType) node passed in.

### Extraction of data from an XML file.

The standard DOM functions only deal with string data. When dealing with numerical (or logical) data, the following functions may be of use.

- `extractDataContent`
- `extractDataAttribute`
- `extractDataAttributeNS`

These extract data from, respectively, the text content of an element, from one of its attributes, or from one of its namespaced attributes. They are used like so:

(where `p` is an element which has been selected by means of the other DOM functions)

    call extractDataContent(p, data)

The subroutine will look at the text contents of the element, and interpret according to the type of `data`. That is, if `data` has been declared as an `integer`, then the contents of `p` will be read as such an placed into `data`.

`data` may be a `string`, `logical`, `integer`, `real`, `double precision`, `complex` or `double complex` variable.

In addition, if `data` is supplied as a rank-1 or rank-2 variable (ie an array or a matrix) then the data will be read in assuming it to be a space- or comma-separated list of such data items.

Thus, the array of integers within the XML document:

    <element> 1 2 3 4 5 6 </element>

could be extracted by the following Fortran program:

    type(Node), pointer :: doc, p
    integer :: i_array(6)

    doc => parseFile(filename)
    p => item(getElementsByTagName(doc, "element"), 0)
    call extractDataContent(p, i_array)

#### Contents and Attributes

For extracting data from text content, the example above suffices. For data in a non-namespaced attribute (in this case, a 2x2 matrix of real numbers)

    <element att="0.1, 2.3 7.56e23, 93"> Some uninteresting text </element>

then use a Fortran program like:

    type(Node), pointer :: doc, p
    real :: r_matrix(2,2)

    doc => parseFile(filename)
    p => item(getElementsByTagName(doc, "element"), 0)
    call extractDataAttribute(p, "att", r_matrix)

or for extracting from a namespaced attribute (in this case, a length-2 array of complex numbers):

    <myml xmlns:ns="http://www.example.org">
      <element ns:att="0.1,2.3  3.4e2,5.34"> Some uninteresting text </element>
    </myml>

then use a Fortran program like:

    type(Node), pointer :: doc, p
    complex :: c_array(2)

    doc => parseFile(filename)
    p => item(getElementsByTagName(doc, "element"), 0)
    call extractDataAttributeNS(p, &
         namespaceURI="http://www.example.org", localName="att", &
         data=c_array)

#### Error handling

The extraction may fail of course, if the data is not of the sort specified, or if there are not enough elements to fill the array or matrix. In such a case, this can be detected by the optional arguments `num` and `iostat`.

`num` will hold the number of items successfully read. Hopefully this should be equal to the expected number of items; but it may be less if reading failed for some reason, or if there were less items than expected in the element.

`iostat` will hold an integer - this will be `0` if the extraction went ok; `-1` if too few elements were found, `1` if although the read went ok, there were still some elements left over, or `2` if the extraction failed due to either a badly formatted number, or due to the wrong data type being found.

#### String arrays

For all data types apart from strings, arrays and matrices are specified by space- or comma-separated lists. For strings, some additional options are available. By default, arrays will be extracted assuming that separators are spaces (and multiple spaces are ignored). So:

    <element> one two     three </element>

will result in the string array `(/"one", "two", "three"/)`.

However, you may specify an optional argument `separator`, which specifies another single-character separator to use (and does not ignore multiple spaces). So:

    <element>one, two, three </element>

will result in the string array `(/"one", " two", " three "/)`. (note the leading and trailing spaces).

Finally, you can also specify an optional logical argument, `csv`. In this case, the `separator` is ignored, and the extraction proceeds assuming that the data is a list of comma-separated values. (see: CSV)

### Other utility functions

- `setFoX_checks`
  FoX_checks: logical

This affects whether additional FoX-only checks are made (see DomExceptions below).

- `getFoX_checks`
  arg: DOMImplementation, pointer

Retrieves the current setting of FoX_checks.

Note that FoX_checks can only be turned on and off globally, not on a per-document basis.

- `setLiveNodeLists`
  arg: Node, pointer
  liveNodeLists: logical

arg must be a Document Node. Calling this function affects whether any nodelists active on the document are treated as live - ie whether updates to the documents are reflected in the contents of nodelists (see DomLiveNodelists below).

- `getLiveNodeLists`
  arg: Node, pointer

Retrieves the current setting of liveNodeLists.

Note that the live-ness of nodelists is a per-document setting.

### Exception handling

Exception handling is important to the DOM. The W3C DOM standards provide not only interfaces to the DOM, but also specify the error handling that should take place when invalid calls are made.

The DOM specifies these in terms of a `DOMException` object, which carries a numeric code whose value reports the kind of error generated. Depending upon the features available in a particular computer language, this DOMException object should be generated and thrown, to be caught by the end-user application.

Fortran of course has no mechanism for throwing and catching exceptions. However, the behaviour of an exception can be modelled using Fortran features.

FoX defines an opaque `DOMException` object. Every DOM subroutine and function implemented by FoX will take an optional argument, 'ex', of type `DOMException`.

If the optional argument is not supplied, any errors within the DOM will cause an immediate abort, with a suitable error message. However, if the optional argument is supplied, then the error will be captured within the `DOMException` object, and returned to the caller for inspection. It is then up to the application to decide how to proceed.

Functions for inspecting and manipulating the `DOMException` object are described below:

- `inException`:
  ex: DOMException

A function returning a logical value, according to whether `ex` is in exception - that is, whether the last DOM function or subroutine, from which `ex` returned, caused an error. Note that this will not change the status of the exception.

- `getExceptionCode`
  ex: DOMException

A function returning an integer value, describing the nature of the exception reported in `ex`. If the integer is 0, then `ex` does not hold an exception. If the integer is less than 200, then the error encountered was of a type specified by the DOM standard; for a full list, see below, and for explanations, see the various DOM standards. If the integer is 200 or greater, then the code represents a FoX-specific error. See the list below.

Note that calling `getExceptionCode` will clean up all memory associated with the DOMException object, and reset the object such that it is no longer in exception.

#### Exception handling and memory usage.

Note that when an Exception is thrown, memory is allocated within the DOMException object. Calling `getExceptionCode` on a DOMEXception will clean up this memory. If you use the exception-handling interfaces of FoX, then you must check every exception, and ensure you check its code, otherwise your program will leak memory.

#### FoX exceptions.

The W3C DOM interface allows the creation of unserializable XML document in various ways. For example, it permits characters to be added to a text node which would be invalid XML. FoX performs multiple additional checks on all DOM calls to prevent the creation of unserializable trees. These are reported through the DOMException mechanisms noted above, using additional exception codes. However, if for some reason, you want to create such trees, then it is possible to switch off all FoX-only checks. (DOM-mandated checks may not be disabled.) To do this, use the `setFoX_checks` function described in DomUtilityFunctions.

Note that FoX does not yet currently check for all ways that a tree may be made non-serializable.

### Live nodelists

The DOM specification requires that all NodeList objects are live - that is, that any change in the document structure is immediately reflected in the contents of any nodelists.

For example, any nodelists returned by getElementsByTagName or getElementsByTagNameNS must be updated whenever nodes are added to or removed from the document; and the order of nodes in the nodelists must be changed if the document structure changes.

Though FoX does keep all nodelists live, this can impose a significant performance penalty when manipulating large documents. Therefore, FoX can be instructed to inly use 'dead' nodelists - that is, nodelists which reflect a snapshot of the document structure at the point they were created. To do this, call `setLiveNodeLists` (see API documentation).

However, note that the nodes within the nodelist remain live - any changes made to the nodes will be reflected in accessing them through the nodelist.

Furthermore, since the nodelists are still associated with the document, they and their contents will be rendered inaccessible when the document is destroyed.

## DOM Configuration

Multiple valid DOM trees may be produced from a single document. When parsing input, some of these choices are made available to the user.

By default, the DOM tree presented to the user will be produced according to the following criteria:

- there will be no adjacent text nodes
- Cdata nodes will appear as such in the DOM tree
- EntityReference nodes will appear in the DOM tree.

However, if another tree is desired, the user may change this. For example, very often you would rather be working with the fully canonicalized tree, with all cdata sections replaced by text nodes and merged, and all entity references replaced with their contents.

The mechanism for doing this is the optional `configuration` argument to `parseFile` and `parseString`. `configuration` is a `DOMConfiguration` object (which can be generated by simple declaration), which may be manipulated by `setParameter` calls.

Note that FoX's implementation of `DOMConfiguration` does not follow the specification precisely. One `DOMConfiguration` object controls all of parsing, normalization and serialization. It can be used like so:

    ! Declare a new configuration object
    type(DOMConfiguration) :: config
    ! Request full canonicalization
    ! ie convert CDATA sections to text sections, remove all entity references etc.
    call setParameter(config, "canonical-form", .true.)
    ! parse the document
    doc => parseFile("doc.xml", config)

    ! Do a whole lot of DOM processing ...

    ! change the configuration to allow cdata-sections to be preserved.
    call setParameter(getDomConfig(doc), "cdata-sections", .true.)
    ! normalize the document again
    call normalizeDocument(doc)
    ! change the configuration to influence the output - make sure there is an XML declaration
    call setParameter(getDomConfig(doc), "xml-declaration", .true.)
    ! and write the document out.
    call serialize(doc)

The available configuration options are fully explained in:

- DOM Core 3
- DOM Core LSParser
- DOM Core LSSerializer

and are all implemented, with the exceptions of:

- `error-handler`
- `schema-location`
- `schema-type`

### External entities

The FoX SAX processor does not read external entities, therefore these will not be made available through the DOM interface, nor will the document represented be affected by any declarations made in referenced external entities (thus, for example, any externally-declared default attributes will not be made available.)

## DOM Miscellanea

Other issues

- As mentioned in the documentation for WXML, it is impossible within Fortran to reliably output lines longer than 1024 characters. While text nodes containing such lines may be created in the DOM, on serialization newlines will be inserted as described in the documentation for WXML.
- All caveats with regard to the FoX SAX processor apply to reading documents through the DOM interface. In particular, note that documents containing characters beyond the US-ASCII set will not be readable.

It was decided to implement W3C DOM interfaces primarily because they are specified in a language-agnostic fashion, and thus made Fortran implementation possible. A number of criticisms have been levelled at the W3C DOM, but many apply only from the perspective of Java developers. However, more importantly, the W3C DOM suffers from a lack of sufficient error checking so it is very easy to create a DOM tree, or manipulate an existing DOM tree into a state, that cannot be serialized into a legal XML document.

(Although the Level 3 DOM specifications finally addressed this issue, they did so in a fashion that was neither very useful, nor easily translatable into a Fortran API.)

Therefore, FoX will by default produce errors about many attempts to manipulate the DOM in such a way as would result in invalid XML. These errors can be switched off if standards-compliant behaviour is wanted. Although extensive, these checks are not complete. In particular, the way the W3C DOM mandates namespace handling makes it trivial to produce namespace non-well-formed document trees, and very difficult for the processor to automatically detect the non-well-formedness. Thus a fully well-formed tree is only guaranteed after a suitable `normalizeDocument` call.

- This DOM implementation has been written with an eye more for correctness and standards-compliance than for efficiency. Certainly, where efficiency of speed or memory usage are at a premium, another language's DOM should be used. Nevertheless, the FoX DOM performs perfectly adequately on the tasks it has been presented with. For example, parsing, canonicalizing, and re-serializing a document of 52Kb (1205 nodes) takes approximately 0.3 seconds on a 2GHz Intel Core Duo processor, and consumes approximately 3.5Mb of memory. Both the parsing time and memory usage scale approximately linearly in number of nodes.

# UTILS

`FoX_utils` is a collection of general utility functions that the rest of FoX depends on, but which may be of independent use. They are documented here.

All functions are accessible from the `FoX_utils` module.

NB Unlike the APIs of WXML, WCML, and SAX, the UTILS APIs may not remain constant between FoX versions. While some effort will be expended to ensure they don't change unnecessarily, no guarantees are made.

For any end-users interested in the code who are worried about interface changes, it is recommended that the relevant code (all found in the `utils/` directory be lifted directly and imported into other projects, rather than accessed through the FoX interfaces.

Currently only one utility function is provided, `generate_UUID`.

## UUID

UUIDs (see RFC 4122) are Universally Unique IDentifiers. They are a 128-bit number, represented as a 36-character string. For example:

     f81d4fae-7dec-11d0-a765-00a0c91e6bf6

The intention of UUIDs is to enable distributed systems to uniquely identify information without significant central coordination. Thus, anyone can create a UUID and use it to identify something with reasonable confidence that the identifier will never be unintentionally used by anyone for anything else.

This property also makes them useful as Uniform Resource Names, to refer to a given document without requiring a position in a particular URI scheme. Thus the above UUID could be referred to as

    urn:uuid:f81d4fae-7dec-11d0-a765-00a0c91e6bf6

UUIDs are used by WCML to ensure that every document generated has a unique ID. This enables users to go back later on and have confidence that they are examining the same document, regardless of where it might have ended up in file-system hierarchies or databases.

In addition, UUIDs come in several flavours, one of which stores the time of creation to 100-nanosecond accuracy. This can later be extracted (see, for example this service) to verify creation time.

This may well be useful for other XML document types, or indeed in non-XML applications. Thus, UUIDs may be generated by the following function, with one optional argument.

- `generate_UUID`
  version: integer

This function returns a 36-character string containing the UUID.

version identifies the version of UUID to be used (see section 4.1.3 of the RFC). Only versions 0, 1, and 4 are supported. Version 0 generates a nil UUID; version 1 a time-based UUID, and version 4 a pseudo-randomly-generated UUID.

Version 1 is the default, and is recommended.

(Note: all pseudo-random-numbers are generated using the high-quality Mersenne Twister algorithm, using the Fortran implementation of Scott Robert Ladd.)

# Further information

FoX evolved from the initial codebase of xmlf90, which was written largely by Alberto Garcia <albertog@icmab.es> and Jon Wakelin <jon.wakelin@bristol.ac.uk>.

FoX is the work of Toby White <tow21@cam.ac.uk>, and all bug reports/complaints/bouquets of roses should be sent to him.

There is a FoX website at http://www.uszla.me.uk/software/FoX/.

There is also a mailing list for announcements/queries/bug reports. Information on how to subscribe may be found at http://www.uszla.me.uk/cgi-bin/mailman/listinfo/FoX/,

This manual is © Toby White 2006-2007.

# Licensing

FoX is licensed under the agreement below. This is intended to make it as freely available as possible, subject only to retaining copyright notices and acknowledgements.

If for any reason this license causes issues with your intended use of the code, please contect the author.

The license can also be found within the distributed source, in the file FoX/LICENSE

Copyright:
© 2003, 2004, Alberto Garcia, Jon Wakelin
© 2005-2007, Toby White
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

- Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

- Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

- Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

### Third-party code.

In addition, FoX includes a random number library, written by Scott Robert Ladd, which is licensed as follows:

! This computer program source file is supplied "AS IS". Scott Robert
! Ladd (hereinafter referred to as "Author") disclaims all warranties,
! expressed or implied, including, without limitation, the warranties
! of merchantability and of fitness for any purpose. The Author
! assumes no liability for direct, indirect, incidental, special,
! exemplary, or consequential damages, which may result from the use
! of this software, even if advised of the possibility of such damage.
!
! The Author hereby grants anyone permission to use, copy, modify, and
! distribute this source code, or portions hereof, for any purpose,
! without fee, subject to the following restrictions:
!
! 1. The origin of this source code must not be misrepresented.
!
! 2. Altered versions must be plainly marked as such and must not
! be misrepresented as being the original source.
!
! 3. This Copyright notice may not be removed or altered from any
! source or altered source distribution.
!
! The Author specifically permits (without fee) and encourages the use
! of this source code for entertainment, education, or decoration. If
! you use this source code in a product, acknowledgment is not required
! but would be appreciated.