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Ace::Browser::AceSubs(User Contributed Perl DocumentatAce::Browser::AceSubs(3)

NAME
       Ace::Browser::AceSubs - Subroutines for AceBrowser

SYNOPSIS
	 use Ace;
	 use Ace::Browser::AceSubs;
	 use CGI qw(:standard);
	 use CGI::Cookie;

	 my $obj = GetAceObject() || AceNotFound();
	 PrintTop($obj);
	 print $obj->asHTML;
	 PrintBottom();

DESCRIPTION
       Ace::Browser::AceSubs exports a set of routines that are	useful for
       creating	search pages and displays for AceBrowser CGI pages. See
       http://stein.cshl.org/AcePerl/AceBrowser.

       The following subroutines are exported by default:

	 AceError
	 AceMissing
	 AceNotFound
	 Configuration
	 DoRedirect
	 GetAceObject
	 Object2URL
	 ObjectLink
	 OpenDatabase
	 PrintTop
	 PrintBottom
	 Url

       The following subroutines are exported if explicitly requested:

	 AceAddCookie
	 AceInit
	 AceHeader
	 AceMultipleChoices
	 AceRedirect
	 DB_Name
	 Footer
	 Header
	 ResolveUrl
	 Style
	 Toggle
	 TypeSelector

       To load the default subroutines load the	module with:

	  use Ace::Browser::AceSubs;

       To bring	in a set of optionally routines, load the module with:

	  use Ace::Browser::AceSubs qw(AceInit AceRedirect);

       To bring	in all the default subroutines,	plus some of the optional
       ones:

	  use Ace::Browser::AceSubs qw(:DEFAULT	AceInit	AceRedirect);

       There are two main types	of AceBrowser scripts:

       display scripts
	   These are called with the CGI parameters b<name> and	b<class>,
	   corresponding to the	name and class of an AceDB object to display.
	   The subroutine GetAceObject() will return the requested object, or
	   undef if the	object does not	exist.

	   To retrieve the parameters, use the CGI.pm param() method:

	     $name  = param('name');
	     $class = param('class');

       search scripts
	   These are not called	with any CGI parameters	on their first
	   invocation, but can define their own	parameter lists	by creating
	   fill-out forms.  The	AceBrowser system remembers the	last search
	   performed by	a search script	in a cookie and	regenerates the	CGI
	   parameters the next time the	user selects that search script.

SUBROUTINES
       The following sections describe the exported subroutines.

       AceError($message)
	   This	subroutine will	print out an error message and exit the
	   script.  The	text of	the message is taken from $message.

       AceHeader()
	   This	function prints	the HTTP header	and issues a number of cookies
	   used	for maintaining	AceBrowser state.  It is not exported by
	   default.

       AceAddCookie(@cookies)
	   This	subroutine, which must be called b<after> OpenDatabase()
	   and/or GetAceObject() and b<before> PrintTop(), will	add one	or
	   more	cookies	to the outgoing	HTTP headers that are emitted by
	   AceHeader().	 Cookies must be CGI::Cookie objects.

       AceInit()
	   This	subroutine initializes the AcePerl connection to the
	   configured database.	 If the	database cannot	be opened, it
	   generates an	error message and exits.  This subroutine is not
	   exported by default,	but is called by PrintTop() and	Header()
	   internally.

       AceMissing([$class,$name])
	   This	subroutine will	print out an error message indicating that an
	   object is present in	AceDB, but that	the information	the user
	   requested is	absent.	It will	then exit the script. This is
	   infrequently	encountered when following XREFed objects. If the
	   class and name of the object	are not	provided as arguments, they
	   are taken from CGI's	param()	function.

       AceMultipleChoices($symbol,$report,$objects)
	   This	function is called when	a search has recovered multiple
	   objects and the user	must make a choice among them.	The user is
	   presented with an ordered list of the objects, and asked to click
	   on one of them.

	   The three arguements	are:

	      $symbol	The keyword or query string the	user was searching
			on, undef if none.

	      $report	The symbolic name of the current display, or undef
			if none.

	      $objects	An array reference containing the Ace objects in
			question.

	   This	subroutine is not exported by default.

       AceNotFound([$class,$name])
	   This	subroutine will	print out an error message indicating that the
	   requested object is not present in AceDB, even as a name. It	will
	   then	exit the script. If the	class and name of the object are not
	   provided as arguments, they are taken from CGI's param() function.

       ($uri,$physical_path) = AcePicRoot($directory)
	   This	function returns the physical and URL paths of a temporary
	   directory in	which the pic script can write pictures.  Not exported
	   by default.	Returns	a two-element list containing the URL and
	   physical path.

       AceRedirect($report,$object)
	   This	function redirects the user to a named display script for
	   viewing an Ace object.  It is used, for example, to convert a
	   request for a sequence into a request for a protein:

	     $obj = GetAceObject();
	     if	($obj->CDS) {
	       my $protein = $obj->Corresponding_protein;
	       AceRedirect('protein',$protein);
	     }

	   AceRedirect must be called b<before>	PrintTop() or  AceHeader().
	   It invokes exit(), so it will not return.

	   This	subroutine is not exported by default.	It differs from
	   DoRedirect()	in that	it displays a message to the user for two
	   seconds before it generates the new page. It	also allows the
	   display to be set explicitly, rather	than determined	automatically
	   by the AceBrowser system.

       $configuration =	Configuration()
	   The Configuration() function	returns	the Ace::Browser::SiteDefs
	   object for the current session.  From this object you can retrieve
	   information from the	configuration file.

       $name = DB_Name()
	   This	function returns the symbolic name of the current database,
	   for example "default".

       DoRedirect($object)
	   This	subroutine immediately redirects to the	default	display	for
	   the Ace::Object indicated by	$object	and exits the script.  It must
	   be called before PrintTop() or any other HTML-generating code.  It
	   differs from	AceRedirect() in that it generates a fast redirect
	   without alerting the	user.

	   This	function is not	exported by default.

       $footer = Footer()
	   This	function returns the contents of the footer as a string, but
	   does	not print it out.  It is not exported by default.

       $object = GetAceObject()
	   This	function is called by display scripts to return	the
	   Ace::Object.that the	user wishes to view.  It automatically opens
	   or refreshes	the database, and performs the request using the
	   values of the "name"	and "class" CGI	variables.

	   If a	single object is found,	the function returns it	as the
	   function result.  If	no objects are found, it returns undef.	 If
	   more	than one object	is found, the function invokes
	   AceMultipleChoices()	and exits the script.

       $html = Header()
	   This	subroutine returns the boilerplate at the top of the HTML page
	   as a	string,	but does not print it out.  It is not exported by
	   default.

       $url = Object2URL($object)
       $url = Object2URL($name,$class)
	   In its single-argument form,	this function takes an AceDB Object
	   and returns an AceBrowser URL.  The URL chosen is determined	by the
	   configuration settings.

	   It is also possible to pass Object2URL an object name and class, in
	   the case that an AceDB object isn't available.

	   The return value is a URL.

       $link = ObjectLink($object [,$link_text])
	   This	function converts an AceDB object into a hypertext link.  The
	   first argument is an	Ace::Object.  The second, optional argument is
	   the text to use for the link.  If not provided, the object's	name
	   becomes the link text.

	   This	function is used extensively to	create cross references
	   between Ace::Objects	on AceBrowser pages.

	   Example:

	     my	$author	= $db->fetch(Author => 'Sulston	JE');
	     print ObjectLink($author,$author->Full_name);

	   This	will print out a link to a page	that will display details on
	   the author page.  The text of the link will be the value of the
	   Full_name tag.

       $db = OpenDatabase()
	   This	function opens the Acedb database designated by	the
	   configuration file.	In modperl environments, this function caches
	   database handles and	reuses them, pinging and reopening them	in the
	   case	of timeouts.

	   This	function is not	exported by default.

       PrintTop($object,$class,$title,@html_headers)
	   The PrintTop() function generates all the boilerplate at the	top of
	   a typical AceBrowser	page, including	the HTTP header	information,
	   the page title, the navigation bar for searches, the	web site
	   banner, the type selector for choosing alternative displays,	and a
	   level-one header.

	   Call	it with	one or more arguments.	The arguments are:

	     $object	An AceDB object.  The navigation bar and title will be
			customized for the object.

	     $class	If no AceDB object is available, then you can pass
			a string containing the	AceDB class that this page is
			designed to display.

	     $title	A title	to use for the HTML page and the first level-one
			header.	 If not	provided, a generic title "Report for
			Object"	is generated.

	     @html_headers  Additional HTML headers to pass to the the CGI.pm
			start_html.

       PrintBottom()
	   The PrintBottom() function outputs all the boilerplate at the
	   bottom of a typical AceBrowser page.	 If a user-defined footer is
	   present in the configuration	file, that is printed.	Otherwise, the
	   method prints a horizontal rule followed by links to	the site home
	   page, the AcePerl home page,	the privacy policy, and	the feedback
	   page.

       $hashref	= Style()
	   This	subroutine returns a hashref containing	a reference to the
	   configured stylesheet, in the following format:

	     { -src => '/ace/stylesheets/current_stylesheet.css' }

	   This	hash is	suitable for passing to	the -style argument of
	   CGI.pm's start_html() function, or for use as an additional header
	   in PrintTop().  You may add locally-defined stylesheet elements to
	   the hash before calling start_html().  See the pic script for an
	   example of how this is done this.

	   This	function is not	exported by default.

       $url = ResolveUrl($url,$param)
	   Given a URL and a set of parameters,	this function does the
	   necessary magic to add the symbolic database	name to	the end	of the
	   URL (if needed) and then tack the parameters	onto the end.

	   A typical call is:

	     $url = ResolveUrl('/cgi-bin/ace/generic/tree','name=fred;class=Author');

	   This	function is not	exported by default.

       $boolean	=
       Toggle($section,[$label,$object_count,$add_plural,$add_count])
       ($link,$bool) =
       Toggle($section,$label,$object_count,$add_plural,$add_count)
	   The Toggle()	subroutine makes it easy to create HTML	sections that
	   open	and close when the user	selects	a toggle icon (a yellow
	   triangle).

	   Toggle() can	be used	to manage multiple collapsible HTML sections,
	   but each section must have a	unique name.  The required first
	   argument is the section name.  Optional arguments are:

	     $label	    The	text of	the generated link, for	example	"sequence"

	     $object_count  The	number of objects that opening the section will	reveal

	     $add_plural    If true, the label will be pluralized when
			    appropriate

	     $add_count	    If true, the label will have the object count added
			    when appropriate

	   In a	scalar context,	Toggle() prints	the link HTML and returns a
	   boolean flag.  A true result	indicates that the section is expanded
	   and should be generated.  A false result indicates that the section
	   is collapsed.

	   In a	list context, Toggle() returns a two-element list.  The	first
	   element is the HTML link that expands and contracts the section.
	   The second element is a boolean that	indicates whether the section
	   is currently	open or	closed.

	   This	example	indicates typical usage:

	     my	$sequence = GetAceObject();
	     print "sequence name = ",$sequence,"\n";
	     print "sequence clone = ",$sequence->Clone,"\n";
	     if	(Toggle('dna','Sequence	DNA')) {
		 print $sequence->asDNA;
	     }

	   An alternative way to do the	same thing:

	     my	$sequence = GetAceObject();
	     print "sequence name = ",$sequence,"\n";
	     print "sequence clone = ",$sequence->Clone,"\n";
	     my	($link,$open) =	Toggle('dna','Sequence DNA');
	     print $link;
	     print $sequence->asDNA if $open;

       $html = TypeSelector($name,$class)
	   This	subroutine generates the HTML for the type selector navigation
	   bar.	 The links in the bar are dynamically generated	based on the
	   values of $name and $class.	This function is called	by PrintTop().
	   It is not exported by default.

       $url = Url($display,$params)
	   Given a symbolic display name, such as "tree" and a set of
	   parameters, this function looks up its URL and then calls
	   ResolveUrl()	to create a single Url.

	   When	hard-coding relative URLs into AceBrowser scripts, it is
	   important to	pass them through Url().  The reason for this is that
	   AceBrowser may need to attach the database name to the URL in order
	   to identify it.

	   Example:

	     my	$url = Url('../sequence_dump',"name=$name;long_dump=yes");
	     print a({-href=>$url},'Dump this sequence');

BUGS
       Please report them.

SEE ALSO
       Ace::Object, Ace::Browser::SiteDefs, Ace::Browsr::SearchSubs, the
       README.ACEBROWSER file.

AUTHOR
       Lincoln Stein <lstein@cshl.org>.

       Copyright (c) 2001 Cold Spring Harbor Laboratory

       This library is free software; you can redistribute it and/or modify it
       under the same terms as Perl itself.  See DISCLAIMER.txt	for
       disclaimers of warranty.

perl v5.32.1			  2005-04-20	      Ace::Browser::AceSubs(3)

NAME | SYNOPSIS | DESCRIPTION | SUBROUTINES | BUGS | SEE ALSO | AUTHOR

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