Chris Mungall > Data-Stag-0.14 > Data::Stag

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Module Version: 0.14   Source  

NAME ^

  Data::Stag - Structured Tags datastructures

SYNOPSIS ^

  # PROCEDURAL USAGE
  use Data::Stag qw(:all);
  $doc = stag_parse($file);
  @persons = stag_find($doc, "person");
  foreach $p (@persons) {
    printf "%s, %s phone: %s\n",
      stag_sget($p, "family_name"),
      stag_sget($p, "given_name"),
      stag_sget($p, "phone_no"),
    ;
  } 

  # OBJECT-ORIENTED USAGE
  use Data::Stag;
  $doc = Data::Stag->parse($file);
  @persons = $doc->find("person");
  foreach $p (@person) {
    printf "%s, %s phone:%s\n",
      $p->sget("family_name"),
      $p->sget("given_name"),
      $p->sget("phone_no"),
    ;
  }

DESCRIPTION ^

This module is for manipulating data as hierarchical tag/value pairs (Structured TAGs or Simple Tree AGgreggates). These datastructures can be represented as nested arrays, which have the advantage of being native to perl. A simple example is shown below:

  [ person=> [  [ family_name => $family_name ],
                [ given_name  => $given_name  ],
                [ phone_no    => $phone_no    ] ] ],

Data::Stag uses a subset of XML for import and export. This means the module can also be used as a general XML parser/writer (with certain caveats).

The above set of structured tags can be represented in XML as

  <person>
    <family_name>...</family_name>
    <given_name>...</given_name>
    <phone_no>...</phone_no>
  </person>

This datastructure can be examined, manipulated and exported using Stag functions or methods:

  $document = Data::Stag->parse($file);
  @persons = $document->find('person');
  foreach my $person (@person) {
    $person->set('full_name',
                 $person->sget('given_name') . ' ' .
                 $person->sget('family_name'));
  }

Advanced querying is performed by passing functions, for example:

  # get all people in dataset with name starting 'A'
  @persons = 
    $document->where('person',
                     sub {shift->sget('family_name') =~ /^A/});

One of the things that marks this module out against other XML modules is this emphasis on a functional approach as an obect-oriented or procedural approach.

For full information on the stag project, see http://stag.sourceforge.net

PROCEDURAL VS OBJECT-ORIENTED USAGE

Depending on your preference, this module can be used a set of procedural subroutine calls, or as method calls upon Data::Stag objects, or both.

In procedural mode, all the subroutine calls are prefixed "stag_" to avoid namespace clashes. The following three calls are equivalent:

  $person = stag_find($doc, "person");
  $person = $doc->find("person");
  $person = $doc->find_person;

In object mode, you can treat any tree element as if it is an object with automatically defined methods for getting/setting the tag values.

USE OF XML

Nested arrays can be imported and exported as XML, as well as other formats. XML can be slurped into memory all at once (using less memory than an equivalent DOM tree), or a simplified SAX style event handling model can be used. Similarly, data can be exported all at once, or as a series of events.

Although this module can be used as a general XML tool, it is intended primarily as a tool for manipulating hierarchical data using nested tag/value pairs.

This module is more suited to dealing with data-oriented documents than text-oriented documents.

By using a simpler subset of XML equivalent to a basic data tree structure, we can write simpler, cleaner code.

This module is ideally suited to element-only XML (that is, XML without attributes or mixed elements).

If you are using attributes or mixed elements, it is useful to know what is going on under the hood.

All attributes are turned into elements; they are nested inside an element with name '@'.

For example, the following piece of XML

  <foo id="x">
    <bar>ugh</bar>
  </foo>

Gets represented internally as

  <foo>
    <@>
      <id>x</id>
    </@>
    <bar>ugh</bar>
  </foo>

Of course, this is not valid XML. However, it is just an internal representation - when exporting back to XML it will look like normal XML with attributes again.

Mixed content cannot be represented in a simple tree format, so this is also expanded.

The following piece of XML

  <paragraph id="1" color="green">
    example of <bold>mixed</bold>content
  </paragraph>

gets parsed as if it were actually:

  <paragraph>
    <@>
      <id>1</id>
      <color>green</color>
    </@>
    <.>example of</.>
    <bold>mixed</bold>
    <.>content</.>
  </paragraph>

When using stag with attribute or mixed attribute xml, you can treat '@' and '.' as normal elements

SAX

This module can also be used as part of a SAX-style event generation / handling framework - see Data::Stag::BaseHandler

PERL REPRESENTATION

Because nested arrays are native to perl, we can specify an XML datastructure directly in perl without going through multiple object calls.

For example, instead of using XML::Writer for the lengthy

  $obj->startTag("record");
  $obj->startTag("field1");
  $obj->characters("foo");
  $obj->endTag("field1");
  $obj->startTag("field2");
  $obj->characters("bar");
  $obj->endTag("field2");
  $obj->end("record");

We can instead write

  $struct = [ record => [
              [ field1 => 'foo'],
              [ field2 => 'bar']]];

PARSING

The following example is for parsing out subsections of a tree and changing sub-elements

  use Data::Stag qw(:all);
  my $tree = stag_parse($xmlfile);
  my ($subtree) = stag_findnode($tree, $element);
  stag_set($element, $sub_element, $new_val);
  print stag_xml($subtree);

OBJECT ORIENTED

The same can be done in a more OO fashion

  use Data::Stag qw(:all);
  my $tree = Data::Stag->parse($xmlfile);
  my ($subtree) = $tree->findnode($element);
  $element->set($sub_element, $new_val);
  print $subtree->xml;

IN A STREAM

Rather than parsing in a whole file into memory all at once (which may not be suitable for very large files), you can take an event handling approach. The easiest way to do this to register which nodes in the file you are interested in using the makehandler method. The parser will sweep through the file, building objects as it goes, and handing the object to a subroutine that you specify.

For example:

  use Data::Stag;
  # catch the end of 'person' elements
  my $h = Data::Stag->makehandler( person=> sub {
                                               my ($self, $person) = @_;
                                               printf "name:%s phone:%s\n",
                                                 $person->get_name,
                                                 $person->get_phone;
                                               return;   # clear node
                                                });
  Data::Stag->parse(-handler=>$h,
                    -file=>$f);

see Data::Stag::BaseHandler for writing handlers

See the Stag website at http://stag.sourceforge.net for more examples.

STRUCTURED TAGS TREE DATA STRUCTURE

A tree of structured tags is represented as a recursively nested array, the elements of the array represent nodes in the tree.

A node is a name/data pair, that can represent tags and values. A node is represented using a reference to an array, where the first element of the array is the tagname, or element, and the second element is the data

This can be visualised as a box:

  +-----------+
  |Name | Data|
  +-----------+

In perl, we represent this pair as a reference to an array

  [ Name => $Data ]

The Data can either be a list of child nodes (subtrees), or a data value.

The terminal nodes (leafs of the tree) contain data values; this is represented in perl using primitive scalars.

For example:

  [ Name => 'Fred' ]

For non-terminal nodes, the Data is a reference to an array, where each element of the the array is a new node.

  +-----------+
  |Name | Data|
  +-----------+
          |||   +-----------+
          ||+-->|Name | Data|
          ||    +-----------+
          ||    
          ||    +-----------+
          |+--->|Name | Data|
          |     +-----------+
          |     
          |     +-----------+
          +---->|Name | Data|
                +-----------+

In perl this would be:

  [ Name => [
              [Name1 => $Data1],
              [Name2 => $Data2],
              [Name3 => $Data3],
            ]
  ];

The extra level of nesting is required to be able to store any node in the tree using a single variable. This representation has lots of advantages over others, eg hashes and mixed hash/array structures.

MANIPULATION AND QUERYING

The following example is taken from biology; we have a list of species (mouse, human, fly) and a list of genes found in that species. These are cross-referenced by an identifier called tax_id. We can do a relational-style inner join on this identifier, as follows -

  use Data::Stag qw(:all);
  my $tree =
  Data::Stag->new(
    'db' => [
    [ 'species_set' => [
      [ 'species' => [
        [ 'common_name' => 'house mouse' ],
        [ 'binomial' => 'Mus musculus' ],
        [ 'tax_id' => '10090' ]]],
      [ 'species' => [
        [ 'common_name' => 'fruit fly' ],
        [ 'binomial' => 'Drosophila melanogaster' ],
        [ 'tax_id' => '7227' ]]],
      [ 'species' => [
        [ 'common_name' => 'human' ],
        [ 'binomial' => 'Homo sapiens' ],
        [ 'tax_id' => '9606' ]]]]],
    [ 'gene_set' => [
      [ 'gene' => [
        [ 'symbol' => 'HGNC' ],
        [ 'tax_id' => '9606' ],
        [ 'phenotype' => 'Hemochromatosis' ],
        [ 'phenotype' => 'Porphyria variegata' ],
        [ 'GO_term' => 'iron homeostasis' ],
        [ 'map' => '6p21.3' ]]],
      [ 'gene' => [
        [ 'symbol' => 'Hfe' ],
        [ 'synonym' => 'MR2' ],
        [ 'tax_id' => '10090' ],
        [ 'GO_term' => 'integral membrane protein' ],
        [ 'map' => '13 A2-A4' ]]]]]]
   );

  # inner join of species and gene parts of tree,
  # based on 'tax_id' element
  my $gene_set = $tree->find("gene_set");       # get <gene_set> element
  my $species_set = $tree->find("species_set"); # get <species_set> element
  $gene_set->ijoin("gene", "tax_id", $species_set);   # INNER JOIN

  print "Reorganised data:\n";
  print $gene_set->xml;

  # find all genes starting with letter 'H' in where species/common_name=human
  my @genes =
    $gene_set->where('gene',
                     sub { my $g = shift;
                           $g->get_symbol =~ /^H/ &&
                           $g->findval("common_name") eq ('human')});

  print "Human genes beginning 'H'\n";
  print $_->xml foreach @genes;

S-Expression (Lisp) representation

The data represented using this module can be represented as Lisp-style S-Expressions.

See Data::Stag::SxprParser and Data::Stag::SxprWriter

If we execute this code on the XML from the example above

  $stag = Data::Stag->parse($xmlfile);
  print $stag->sxpr;

The following S-Expression will be printed:

  '(db
    (species_set
      (species
        (common_name "house mouse")
        (binomial "Mus musculus")
        (tax_id "10090"))
      (species
        (common_name "fruit fly")
        (binomial "Drosophila melanogaster")
        (tax_id "7227"))
      (species
        (common_name "human")
        (binomial "Homo sapiens")
        (tax_id "9606")))
    (gene_set
      (gene
        (symbol "HGNC")
        (tax_id "9606")
        (phenotype "Hemochromatosis")
        (phenotype "Porphyria variegata")
        (GO_term "iron homeostasis")
        (map
          (cytological
            (chromosome "6")
            (band "p21.3"))))
      (gene
        (symbol "Hfe")
        (synonym "MR2")
        (tax_id "10090")
        (GO_term "integral membrane protein")))
    (similarity_set
      (pair
        (symbol "HGNC")
        (symbol "Hfe"))
      (pair
        (symbol "WNT3A")
        (symbol "Wnt3a"))))

TIPS FOR EMACS USERS AND LISP PROGRAMMERS

If you use emacs, you can save this as a file with the ".el" suffix and get syntax highlighting for editing this file. Quotes around the terminal node data items are optional.

If you know emacs lisp or any other lisp, this also turns out to be a very nice language for manipulating these datastructures. Try copying and pasting the above s-expression to the emacs scratch buffer and playing with it in lisp.

INDENTED TEXT REPRESENTATION

Data::Stag has its own text format for writing data trees. Again, this is only possible because we are working with a subset of XML (no attributes, no mixed elements). The data structure above can be written as follows -

  db:
    species_set:
      species:
        common_name: house mouse
        binomial: Mus musculus
        tax_id: 10090
      species:
        common_name: fruit fly
        binomial: Drosophila melanogaster
        tax_id: 7227
      species:
        common_name: human
        binomial: Homo sapiens
        tax_id: 9606
    gene_set:
      gene:
        symbol: HGNC
        tax_id: 9606
        phenotype: Hemochromatosis
        phenotype: Porphyria variegata
        GO_term: iron homeostasis
        map: 6p21.3
      gene:
        symbol: Hfe
        synonym: MR2
        tax_id: 10090
        GO_term: integral membrane protein
        map: 13 A2-A4
    similarity_set:
      pair:
        symbol: HGNC
        symbol: Hfe
      pair:
        symbol: WNT3A
        symbol: Wnt3a

See Data::Stag::ITextParser and Data::Stag::ITextWriter

NESTED ARRAY SPECIFICATION II

To avoid excessive square bracket usage, you can specify a structure like this:

  use Data::Stag qw(:all);
  
  *N = \&stag_new;
  my $tree =
    N(top=>[
            N('personset'=>[
                            N('person'=>[
                                         N('name'=>'davey'),
                                         N('address'=>'here'),
                                         N('description'=>[
                                                           N('hair'=>'green'),
                                                           N('eyes'=>'two'),
                                                           N('teeth'=>5),
                                                          ]
                                          ),
                                         N('pets'=>[
                                                    N('petname'=>'igor'),
                                                    N('petname'=>'ginger'),
                                                   ]
                                          ),
                                                                          
                                        ],
                             ),
                            N('person'=>[
                                         N('name'=>'shuggy'),
                                         N('address'=>'there'),
                                         N('description'=>[
                                                           N('hair'=>'red'),
                                                           N('eyes'=>'three'),
                                                           N('teeth'=>1),
                                                          ]
                                          ),
                                         N('pets'=>[
                                                    N('petname'=>'thud'),
                                                    N('petname'=>'spud'),
                                                   ]
                                          ),
                                        ]
                             ),
                           ]
             ),
            N('animalset'=>[
                            N('animal'=>[
                                         N('name'=>'igor'),
                                         N('class'=>'rat'),
                                         N('description'=>[
                                                           N('fur'=>'white'),
                                                           N('eyes'=>'red'),
                                                           N('teeth'=>50),
                                                          ],
                                          ),
                                        ],
                             ),
                           ]
             ),

           ]
     );

  # find all people
  my @persons = stag_find($tree, 'person');

  # write xml for all red haired people
  foreach my $p (@persons) {
    print stag_xml($p)
      if stag_tmatch($p, "hair", "red");
  } ;

  # find all people that have name == shuggy
  my @p =
    stag_qmatch($tree, 
                "person",
                "name",
                "shuggy");

NODES AS DATA OBJECTS ^

As well as the methods listed below, a node can be treated as if it is a data object of a class determined by the element.

For example, the following are equivalent.

  $node->get_name;
  $node->get('name');

  $node->set_name('fred');
  $node->set('name', 'fred');

This is really just syntactic sugar. The autoloaded methods are not checked against any schema, although this may be added in future.

INDEXING STAG TREES ^

A stag tree can be indexed as a hash for direct retrieval; see Data::Stag::HashDB

This index can be made persistent as a DB file; see Data::Stag::StagDB

If you wish to use Stag in conjunction with a relational database, you should install DBIx::DBStag

STAG METHODS ^

All method calls are also available as procedural subroutine calls; unless otherwise noted, the subroutine call is the same as the method call, but with the string stag_ prefixed to the method name. The first argument should be a Data::Stag datastructure.

To import all subroutines into the current namespace, use this idiom:

  use Data::Stag qw(:all);
  $doc = stag_parse($file);
  @persons = stag_find($doc, 'person');

If you wish to use this module procedurally, and you are too lazy to prefix all calls with stag_, use this idiom:

  use Data::Stag qw(:lazy);
  $doc = parse($file);
  @persons = find($doc, 'person');

But beware of clashes!

Most method calls also have a handy short mnemonic. Use of these is optional. Software engineering types prefer longer names, in the belief that this leads to clearer code. Hacker types prefer shorter names, as this requires less keystrokes, and leads to a more compact representation of the code. It is expected that if you do use this module, then its usage will be fairly ubiquitous within your code, and the mnemonics will become familiar, much like the qw and s/ operators in perl. As always with perl, the decision is yours.

Some methods take a single parameter or list of parameters; some have large lists of parameters that can be passed in any order. If the documentation states:

  Args: [x str], [y int], [z ANY]

Then the method can be called like this:

  $stag->foo("this is x", 55, $ref);

or like this:

  $stag->foo(-z=>$ref, -x=>"this is x", -y=>55);

INITIALIZATION METHODS

new

       Title: new

        Args: element str, data STAG-DATA
     Returns: Data::Stag node
     Example: $node = stag_new();
     Example: $node = Data::Stag->new;
     Example: $node = Data::Stag->new(person => [[name=>$n], [phone=>$p]]);

creates a new instance of a Data::Stag node

stagify (nodify)

       Title: stagify
     Synonym: nodify
        Args: data ARRAY-REF
     Returns: Data::Stag node
     Example: $node = stag_stagify([person => [[name=>$n], [phone=>$p]]]);

turns a perl array reference into a Data::Stag node.

similar to new

parse

       Title: parse

        Args: [file str], [format str], [handler obj], [fh FileHandle]
     Returns: Data::Stag node
     Example: $node = stag_parse($fn);
     Example: $node = stag_parse(-fh=>$fh, -handler=>$h, -errhandler=>$eh);
     Example: $node = Data::Stag->parse(-file=>$fn, -handler=>$myhandler);

slurps a file or string into a Data::Stag node structure. Will guess the format (xml, sxpr, itext, indent) from the suffix if it is not given.

The format can also be the name of a parsing module, or an actual parser object;

The handler is any object that can take nested Stag events (start_event, end_event, evbody) which are generated from the parse. If the handler is omitted, all events will be cached and the resulting tree will be returned.

See Data::Stag::BaseHandler for writing your own handlers

See Data::Stag::BaseGenerator for details on parser classes, and error handling

parsestr

       Title: parsestr

        Args: [str str], [format str], [handler obj]
     Returns: Data::Stag node
     Example: $node = stag_parsestr('(a (b (c "1")))');
     Example: $node = Data::Stag->parsestr(-str=>$str, -handler=>$myhandler);

Similar to parse(), except the first argument is a string

from

       Title: from

        Args: format str, source str
     Returns: Data::Stag node
     Example: $node = stag_from('xml', $fn);
     Example: $node = stag_from('xmlstr', q[<top><x>1</x></top>]);
     Example: $node = Data::Stag->from($parser, $fn);

Similar to parse

slurps a file or string into a Data::Stag node structure.

The format can also be the name of a parsing module, or an actual parser object

unflatten

       Title: unflatten

        Args: data array
     Returns: Data::Stag node
     Example: $node = stag_unflatten(person=>[name=>$n, phone=>$p, address=>[street=>$s, city=>$c]]);

Creates a node structure from a semi-flattened representation, in which children of a node are represented as a flat list of data rather than a list of array references.

This means a structure can be specified as:

  person=>[name=>$n,
           phone=>$p, 
           address=>[street=>$s, 
                     city=>$c]]

Instead of:

  [person=>[ [name=>$n],
             [phone=>$p], 
             [address=>[ [street=>$s], 
                         [city=>$c] ] ]
           ]
  ]

The former gets converted into the latter for the internal representation

makehandler

       Title: makehandler

        Args: hash of CODEREFs keyed by element name
              OR a string containing the name of a module
     Returns: L<Data::Stag::BaseHandler>
     Example: $h = Data::Stag->makehandler(%subs);
     Example: $h = Data::Stag->makehandler("My::FooHandler");
     Example: $h = Data::Stag->makehandler('xml');

This creates a Stag event handler. The argument is a hash of subroutines keyed by element/node name. After each node is fired by the parser/generator, the subroutine is called, passing the handler object and the stag node as arguments. whatever the subroutine returns is placed back into the tree

For example, for a a parser/generator that fires events with the following tree form

  <person>
    <name>foo</name>
    ...
  </person>

we can create a handler that writes person/name like this:

  $h = Data::Stag->makehandler(
                               person => sub { my ($self,$stag) = @_;
                                               print $stag->name;
                                               return $stag; # dont change tree
                                             });
  $stag = Data::Stag->parse(-str=>"(...)", -handler=>$h)

See Data::Stag::BaseHandler for details on handlers

getformathandler

       Title: getformathandler

        Args: format str OR L<Data::Stag::BaseHandler>
     Returns: L<Data::Stag::BaseHandler>
     Example: $h = Data::Stag->getformathandler('xml');
              $h->file("my.xml");
              Data::Stag->parse(-fn=>$fn, -handler=>$h);

Creates a Stag event handler - this handler can be passed to an event generator / parser. Built in handlers include:

xml

Generates xml tags from events

sxpr

Generates S-Expressions from events

itext

Generates itext format from events

indent

Generates indent format from events

All the above are kinds of Data::Stag::Writer

chainhandler

       Title: chainhandler

        Args: blocked events - str or str[]
              initial handler - handler object
              final handler - handler object
     Returns: 
     Example: $h = Data::Stag->chainhandler('foo', $processor, 'xml')

chains handlers together - for example, you may want to make transforms on an event stream, and then pass the event stream to another handler - for example, and xml handler

  $processor = Data::Stag->makehandler(
                                       a => sub { my ($self,$stag) = @_;
                                                  $stag->set_foo("bar");
                                                  return $stag
                                                },
                                       b => sub { my ($self,$stag) = @_;
                                                  $stag->set_blah("eek");
                                                  return $stag
                                                },
                                       );
  $chainh = Data::Stag->chainhandler(['a', 'b'], $processor, 'xml');
  $stag = Data::Stag->parse(-str=>"(...)", -handler=>$chainh)

If the inner handler has a method CONSUMES(), this method will determine the blocked events if none are specified.

see also the script stag-handle.pl

RECURSIVE SEARCHING

find (f)

       Title: find
     Synonym: f

        Args: element str
     Returns: node[] or ANY
     Example: @persons = stag_find($struct, 'person');
     Example: @persons = $struct->find('person');

recursively searches tree for all elements of the given type, and returns all nodes or data elements found.

if the element found is a non-terminal node, will return the node if the element found is a terminal (leaf) node, will return the data value

the element argument can be a path

  @names = $struct->find('department/person/name');

will find name in the nested structure below:

  (department
   (person
    (name "foo")))

findnode (fn)

       Title: findnode
     Synonym: fn

        Args: element str
     Returns: node[]
     Example: @persons = stag_findnode($struct, 'person');
     Example: @persons = $struct->findnode('person');

recursively searches tree for all elements of the given type, and returns all nodes found.

paths can also be used (see find)

findval (fv)

       Title: findval
     Synonym: fv

        Args: element str
     Returns: ANY[] or ANY
     Example: @names = stag_findval($struct, 'name');
     Example: @names = $struct->findval('name');
     Example: $firstname = $struct->findval('name');

recursively searches tree for all elements of the given type, and returns all data values found. the data values could be primitive scalars or nodes.

paths can also be used (see find)

sfindval (sfv)

       Title: sfindval
     Synonym: sfv

        Args: element str
     Returns: ANY
     Example: $name = stag_sfindval($struct, 'name');
     Example: $name = $struct->sfindval('name');

as findval, but returns the first value found

paths can also be used (see find)

findvallist (fvl)

       Title: findvallist
     Synonym: fvl

        Args: element str[]
     Returns: ANY[]
     Example: ($name, $phone) = stag_findvallist($personstruct, 'name', 'phone');
     Example: ($name, $phone) = $personstruct->findvallist('name', 'phone');

recursively searches tree for all elements in the list

DEPRECATED

DATA ACCESSOR METHODS

these allow getting and setting of elements directly underneath the current one

get (g)

       Title: get
     Synonym: g

        Args: element str
      Return: node[] or ANY
     Example: $name = $person->get('name');
     Example: @phone_nos = $person->get('phone_no');

gets the value of the named sub-element

if the sub-element is a non-terminal, will return a node(s) if the sub-element is a terminal (leaf) it will return the data value(s)

the examples above would work on a data structure like this:

  [person => [ [name => 'fred'],
               [phone_no => '1-800-111-2222'],
               [phone_no => '1-415-555-5555']]]

will return an array or single value depending on the context

[equivalent to findval(), except that only direct children (as opposed to all descendents) are checked]

paths can also be used, like this:

 @phones_nos = $struct->get('person/phone_no')

sget (sg)

       Title: sget
     Synonym: sg

        Args: element str
      Return: ANY
     Example: $name = $person->sget('name');
     Example: $phone = $person->sget('phone_no');
     Example: $phone = $person->sget('department/person/name');

as get but always returns a single value

[equivalent to sfindval(), except that only direct children (as opposed to all descendents) are checked]

getl (gl getlist)

       Title: gl
     Synonym: getl
     Synonym: getlist

        Args: element str[]
      Return: node[] or ANY[]
     Example: ($name, @phone) = $person->getl('name', 'phone_no');

returns the data values for a list of sub-elements of a node

[equivalent to findvallist(), except that only direct children (as opposed to all descendents) are checked]

getn (gn getnode)

       Title: getn
     Synonym: gn
     Synonym: getnode

        Args: element str
      Return: node[]
     Example: $namestruct = $person->getn('name');
     Example: @pstructs = $person->getn('phone_no');

as get but returns the whole node rather than just the data value

[equivalent to findnode(), except that only direct children (as opposed to all descendents) are checked]

sgetmap (sgm)

       Title: sgetmap
     Synonym: sgm

        Args: hash
      Return: hash
     Example: %h = $person->sgetmap('social-security-no'=>'id', 
                                    'name'              =>'label',
                                    'job'               =>0,
                                    'address'           =>'location');

returns a hash of key/val pairs based on the values of the data values of the subnodes in the current element; keys are mapped according to the hash passed (a value of '' or 0 will map an identical key/val).

no multivalued data elements are allowed

set (s)

       Title: set
     Synonym: s

        Args: element str, datavalue ANY (list)
      Return: ANY
     Example: $person->set('name', 'fred');    # single val
     Example: $person->set('phone_no', $cellphone, $homephone);

sets the data value of an element for any node. if the element is multivalued, all the old values will be replaced with the new ones specified.

ordering will be preserved, unless the element specified does not exist, in which case, the new tag/value pair will be placed at the end.

for example, if we have a stag node $person

  person:
    name: shuggy
    job:  bus driver

if we do this

  $person->set('name', ());

we will end up with

  person:
    job:  bus driver

then if we do this

  $person->set('name', 'shuggy');

the 'name' node will be placed as the last attribute

  person:
    job:  bus driver
    name: shuggy

You can also use magic methods, for example

  $person->set_name('shuggy');
  $person->set_job('bus driver', 'poet');
  print $person->itext;

will print

  person:
    name: shuggy
    job:  bus driver
    job:  poet

note that if the datavalue is a non-terminal node as opposed to a primitive value, then you have to do it like this:

  $people  = Data::Stag->new(people=>[
                                      [person=>[[name=>'Sherlock Holmes']]],
                                      [person=>[[name=>'Moriarty']]],
                                     ]);
  $address = Data::Stag->new(address=>[
                                       [address_line=>"221B Baker Street"],
                                       [city=>"London"],
                                       [country=>"Great Britain"]]);
  ($person) = $people->qmatch('person', (name => "Sherlock Holmes"));
  $person->set("address", $address->data);

If you are using XML data, you can set attributes like this:

  $person->set('@'=>[[id=>$id],[foo=>$foo]]);

unset (u)

       Title: unset
     Synonym: u

        Args: element str, datavalue ANY
      Return: ANY
     Example: $person->unset('name');
     Example: $person->unset('phone_no');

prunes all nodes of the specified element from the current node

You can use magic methods, like this

  $person->unset_name;
  $person->unset_phone_no;

free

       Title: free
     Synonym: u

        Args: 
      Return: 
     Example: $person->free;

removes all data from a node. If that node is a subnode of another node, it is removed altogether

for instance, if we had the data below:

  <person>
    <name>fred</name>
    <address>
    ..
    </address>
  </person>

and called

  $person->get_address->free

then the person node would look like this:

  <person>
    <name>fred</name>
  </person>

add (a)

       Title: add
     Synonym: a

        Args: element str, datavalues ANY[]
              OR
              Data::Stag
      Return: ANY
     Example: $person->add('phone_no', $cellphone, $homephone);
     Example: $person->add_phone_no('1-555-555-5555');
     Example: $dataset->add($person)

adds a datavalue or list of datavalues. appends if already existing, creates new element value pairs if not already existing.

if the argument is a stag node, it will add this node under the current one.

For example, if we have the following node in $dataset

 <dataset>
   <person>
     <name>jim</name>
   </person>
 </dataset>

And then we add data to it:

  ($person) = $dataset->qmatch('person', name=>'jim');
  $person->add('phone_no', '555-1111', '555-2222');

We will be left with:

 <dataset>
   <person>
     <name>jim</name>
     <phone_no>555-1111</phone_no>
     <phone_no>555-2222</phone_no>
   </person>
 </dataset>

The above call is equivalent to:

  $person->add_phone_no('555-1111', '555-2222');

As well as adding data values, we can add whole nodes:

  $dataset->add(person=>[[name=>"fred"],
                         [phone_no=>"555-3333"]]);

Which is equivalent to

  $dataset->add_person([[name=>"fred"],
                        [phone_no=>"555-3333"]]);

Remember, the value has to be specified as an array reference of nodes. In general, you should use the addkid() method to add nodes and used add() to add values

element (e name)

       Title: element
     Synonym: e
     Synonym: name

        Args:
      Return: element str
     Example: $element = $struct->element

returns the element name of the current node.

This is illustrated in the different representation formats below

sxpr
  (element "data")

or

  (element
   (sub_element "..."))
xml
  <element>data</element>

or

  <element>
    <sub_element>...</sub_element>
  </element>
perl
  [element => $data ]

or

  [element => [
                [sub_element => "..." ]]]
itext
  element: data

or

  element:
    sub_element: ...
indent
  element "data"

or

  element
    sub_element "..."

kids (k children)

       Title: kids
     Synonym: k
     Synonym: children

        Args:
      Return: ANY or ANY[]
     Example: @nodes = $person->kids
     Example: $name = $namestruct->kids

returns the data value(s) of the current node; if it is a terminal node, returns a single value which is the data. if it is non-terminal, returns an array of nodes

addkid (ak addchild)

       Title: addkid
     Synonym: ak
     Synonym: addchild

        Args: kid node
      Return: ANY
     Example: $person->addkid($job);

adds a new child node to a non-terminal node, after all the existing child nodes

You can use this method/procedure to add XML attribute data to a node:

  $person->addkid(['@'=>[[id=>$id]]]);

subnodes

       Title: subnodes

        Args: 
      Return: ANY[]
     Example: @nodes = $person->subnodes

returns the child nodes; returns empty list if this is a terminal node

ntnodes

       Title: ntnodes

        Args: 
      Return: ANY[]
     Example: @nodes = $person->ntnodes

returns all non-terminal children of current node

tnodes

       Title: tnodes

        Args: 
      Return: ANY[]
     Example: @nodes = $person->tnodes

returns all terminal children of current node

QUERYING AND ADVANCED DATA MANIPULATION

ijoin (j)

       Title: ijoin
     Synonym: j
     Synonym: ij

        Args: element str, key str, data Node
      Return: undef

does a relational style inner join - see previous example in this doc

key can either be a single node name that must be shared (analagous to SQL INNER JOIN .. USING), or a key1=key2 equivalence relation (analagous to SQL INNER JOIN ... ON)

qmatch (qm)

       Title: qmatch
     Synonym: qm

        Args: return-element str, match-element str, match-value str
      Return: node[]
     Example: @persons = $s->qmatch('person', 'name', 'fred');
     Example: @persons = $s->qmatch('person', (job=>'bus driver'));

queries the node tree for all elements that satisfy the specified key=val match - see previous example in this doc

for those inclined to thinking relationally, this can be thought of as a query that returns a stag object:

  SELECT <return-element> FROM <stag-node> WHERE <match-element> = <match-value>

this always returns an array; this means that calling in a scalar context will return the number of elements; for example

  $n = $s->qmatch('person', (name=>'fred'));

the value of $n will be equal to the number of persons called fred

tmatch (tm)

       Title: tmatch
     Synonym: tm

        Args: element str, value str
      Return: bool
     Example: @persons = grep {$_->tmatch('name', 'fred')} @persons

returns true if the the value of the specified element matches - see previous example in this doc

tmatchhash (tmh)

       Title: tmatchhash
     Synonym: tmh

        Args: match hashref
      Return: bool
     Example: @persons = grep {$_->tmatchhash({name=>'fred', hair_colour=>'green'})} @persons

returns true if the node matches a set of constraints, specified as hash.

tmatchnode (tmn)

       Title: tmatchnode
     Synonym: tmn

        Args: match node
      Return: bool
     Example: @persons = grep {$_->tmatchnode([person=>[[name=>'fred'], [hair_colour=>'green']]])} @persons

returns true if the node matches a set of constraints, specified as node

cmatch (cm)

       Title: cmatch
     Synonym: cm

        Args: element str, value str
      Return: bool
     Example: $n_freds = $personset->cmatch('name', 'fred');

counts the number of matches

where (w)

       Title: where
     Synonym: w

        Args: element str, test CODE
      Return: Node[]
     Example: @rich_persons = $data->where('person', sub {shift->get_salary > 100000});

the tree is queried for all elements of the specified type that satisfy the coderef (must return a boolean)

  my @rich_dog_or_cat_owners =
    $data->where('person',
                 sub {my $p = shift;
                      $p->get_salary > 100000 &&
                      $p->where('pet',
                                sub {shift->get_type =~ /(dog|cat)/})});

iterate (i)

       Title: iterate
     Synonym: i

        Args: CODE
      Return: Node[]
     Example: $data->iterate(sub {
                                 my $stag = shift;
                                 my $parent = shift;
                                 if ($stag->element eq 'pet') {
                                     $parent->set_pet_name($stag->get_name);
                                 }
                             });

iterates through whole tree calling the specified subroutine.

the first arg passed to the subroutine is the stag node representing the tree at that point; the second arg is for the parent.

for instance, the example code above would turn this

  (person
   (name "jim")
   (pet
    (name "fluffy")))

into this

  (person
   (name "jim")
   (pet_name "fluffy")
   (pet
    (name "fluffy")))

maptree

       Title: maptree

        Args: CODE
      Return: Node[]
     Example: $data->maptree(sub {
                                 my $stag = shift;
                                 my $parent = shift;
                                 if ($stag->element eq 'pet') {
                                     [pet=>$stag->sget_foo]
                                 }
                                 else {
                                     $stag
                                 }
                             });

MISCELLANEOUS METHODS

duplicate (d)

       Title: duplicate
     Synonym: d

        Args:
      Return: Node
     Example: $node2 = $node->duplicate;

does a deep copy of a stag structure

isanode

       Title: isanode

        Args:
      Return: bool
     Example: if (stag_isanode($node)) { ... }

hash

       Title: hash

        Args:
      Return: hash
     Example: $h = $node->hash;

turns a tree into a hash. all data values will be arrayrefs

pairs

       Title: pairs

turns a tree into a hash. all data values will be scalar (IMPORTANT: this means duplicate values will be lost)

write

       Title: write

        Args: filename str, format str[optional]
      Return:
     Example: $node->write("myfile.xml");
     Example: $node->write("myfile", "itext");

will try and guess the format from the extension if not specified

xml

       Title: xml

        Args: filename str, format str[optional]
      Return:
     Example: $node->write("myfile.xml");
     Example: $node->write("myfile", "itext");


        Args:
      Return: xml str
     Example: print $node->xml;

XML METHODS

xslt

       Title: xslt

        Args: xslt_file str
      Return: Node
     Example: $new_stag = $stag->xslt('mytransform.xsl');

transforms a stag tree using XSLT

xsltstr

       Title: xsltstr

        Args: xslt_file str
      Return: str
     Example: print $stag->xsltstr('mytransform.xsl');

As above, but returns the string of the resulting transform, rather than a stag tree

sax

       Title: sax

        Args: saxhandler SAX-CLASS
      Return:
     Example: $node->sax($mysaxhandler);

turns a tree into a series of SAX events

xpath (xp tree2xpath)

       Title: xpath
     Synonym: xp
     Synonym: tree2xpath

        Args:
      Return: xpath object
     Example: $xp = $node->xpath; $q = $xp->find($xpathquerystr);

xpquery (xpq xpathquery)

       Title: xpquery
     Synonym: xpq
     Synonym: xpathquery

        Args: xpathquery str
      Return: Node[]
     Example: @nodes = $node->xqp($xpathquerystr);

STAG SCRIPTS ^

The following scripts come with the stag module

stag-autoschema.pl

writes the implicit stag-schema for a stag file

stag-db.pl

persistent storage and retrieval for stag data (xml, sxpr, itext)

stag-diff.pl

finds the difference between two stag files

stag-drawtree.pl

draws a stag file (xml, itext, sxpr) as a PNG diagram

stag-filter.pl

filters a stag file (xml, itext, sxpr) for nodes of interest

stag-findsubtree.pl

finds nodes in a stag file

stag-flatten.pl

turns stag data into a flat table

stag-grep.pl

filters a stag file (xml, itext, sxpr) for nodes of interest

stag-handle.pl

streams a stag file through a handler into a writer

stag-join.pl

joins two stag files together based around common key

stag-mogrify.pl

mangle stag files

stag-parse.pl

parses a file and fires events (e.g. sxpr to xml)

stag-query.pl

aggregare queries

stag-split.pl

splits a stag file (xml, itext, sxpr) into multiple files

stag-splitter.pl

splits a stag file into multiple files

stag-view.pl

draws an expandable Tk tree diagram showing stag data

To get more documentation, type

  stag_<script> -h

BUGS ^

none known so far, possibly quite a few undocumented features!

Not a bug, but the underlying default datastructure of nested arrays is more heavyweight than it needs to be. More lightweight implementations are possible. Some time I will write a C implementation.

WEBSITE ^

http://stag.sourceforge.net

AUTHOR ^

Chris Mungall <cjm AT fruitfly DOT org>

COPYRIGHT ^

Copyright (c) 2004 Chris Mungall

This module is free software. You may distribute this module under the same terms as perl itself

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