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.