AcePerl
view release on metacpan or search on metacpan
Ace/Browser/AceSubs.pm view on Meta::CPAN
=item 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.
=back
=head1 SUBROUTINES
The following sections describe the exported subroutines.
=over 4
=cut
use strict;
use Ace::Browser::SiteDefs;
use Ace 1.76;
use CGI qw(:standard escape);
use CGI::Cookie;
use File::Path 'mkpath';
use vars qw/@ISA @EXPORT @EXPORT_OK $VERSION %EXPORT_TAGS
%DB %OPEN $HEADER $TOP @COOKIES
$APACHE_CONF/;
require Exporter;
@ISA = qw(Exporter);
$VERSION = 1.21;
######################### This is the list of exported subroutines #######################
@EXPORT = qw(
GetAceObject AceError AceNotFound AceMissing DoRedirect
OpenDatabase Object2URL Url
ObjectLink Configuration PrintTop PrintBottom);
@EXPORT_OK = qw(AceRedirect Toggle ResolveUrl AceInit AceAddCookie
AceHeader TypeSelector Style AcePicRoot
Header Footer DB_Name AceMultipleChoices);
%EXPORT_TAGS = ( );
use constant DEFAULT_DATABASE => 'default';
use constant PRIVACY => 'misc/privacy'; # privacy/cookie statement
use constant SEARCH_BROWSE => 'search'; # a fallback search script
my %VALID; # cache for get_symbolic() lookups
=item AceError($message)
This subroutine will print out an error message and exit the script.
The text of the message is taken from $message.
=cut
sub AceError {
my $msg = shift;
PrintTop(undef,undef,'Error');
print CGI::font({-color=>'red'},$msg);
PrintBottom();
Apache->exit(0) if defined &Apache::exit;
exit(0);
}
=item AceHeader()
This function prints the HTTP header and issues a number of cookies
used for maintaining AceBrowser state. It is not exported by default.
=cut
=item 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.
=cut
sub AceAddCookie {
push @COOKIES,@_; # add caller's to our globals
}
################## canned header ############
sub AceHeader {
my %searches = map {$_=>1} Configuration()->searches;
my $quovadis = url(-relative=>1);
my $db = get_symbolic();
my $referer = referer();
$referer =~ s!^http://[^/]+!! if defined $referer;
my $home = Configuration()->Home->[0] if Configuration()->Home;
if ($referer && $home && index($referer,$home) >= 0) {
my $bookmark = cookie(
-name=>"HOME_${db}",
-value=>$referer,
-path=>'/');
push(@COOKIES,$bookmark);
}
if ($searches{$quovadis}) {
Delete('Go');
my $search_name = "SEARCH_${db}_${quovadis}";
my $search_data = cookie(-name => $search_name,
-value => query_string(),
-path=>'/',
);
my $last_search = cookie(-name=>"ACEDB_$db",
-value=>$quovadis,
-path=>'/');
push(@COOKIES,$search_data,$last_search);
}
print @COOKIES ? header(-cookie=>\@COOKIES,@_) : header(@_);
Ace/Browser/AceSubs.pm view on Meta::CPAN
from CGI's param() function.
=cut
sub AceMissing {
my ($class,$name) = @_;
$class ||= param('class');
$name ||= param('name');
PrintTop(undef,undef,$name);
print strong('There is no further information about this object in the database.');
PrintBottom();
Apache->exit(0) if defined &Apache::exit;
exit(0);
}
=item 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.
$objects An array reference containing the Ace objects in
question.
This subroutine is not exported by default.
=cut
sub AceMultipleChoices {
my ($symbol,$report,$objects) = @_;
if ($objects && @$objects == 1) {
my $destination = Object2URL($objects->[0]);
AceHeader(-Refresh => "1; URL=$destination");
print start_html (
'-Title' => 'Redirect',
'-Style' => Style(),
),
h1('Redirect'),
p("Automatically transforming this query into a request for corresponding object",
ObjectLink($objects->[0],$objects->[0]->class.':'.$objects->[0])),
p("Please wait..."),
Footer(),
end_html();
return;
}
PrintTop(undef,undef,'Multiple Choices');
print
p("Multiple $report objects correspond to $symbol.",
"Please choose one:"),
ol(
li([
map {ObjectLink($_,font({-color=>'red'},$_->class).': '.$_)} @$objects
])
);
PrintBottom();
}
=item AceNotFound([$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.
=cut
sub AceNotFound {
my $class = shift || param('class');
my $name = shift || param('name');
PrintTop(undef,undef,"$class: $name not found");
print p(font({-color => 'red'},
strong("The $class named \"$name\" is not found in the database.")));
PrintBottom();
Apache->exit(0) if defined &Apache::exit;
exit(0);
}
=item ($uri,$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.
=cut
sub AcePicRoot {
my $path = shift;
my $umask = umask();
umask 002; # want this writable by group
my ($picroot,$uri);
if ($ENV{MOD_PERL} && Apache->can('request')) { # we have apache, so no reason not to take advantage of it
my $r = Apache->request;
$uri = join('/',Configuration()->Pictures->[0],"/",$path);
my $subr = $r->lookup_uri($uri);
$picroot = $subr->filename if $subr;
} else {
($uri,$picroot) = @{Configuration()->Pictures} if Configuration()->Pictures;
$uri .= "/$path";
$picroot .= "/$path";
}
mkpath ($picroot,0,0777) || AceError("Can't create directory to store image in") unless -d $picroot;
umask $umask;
return ($uri,$picroot);
}
=item AceRedirect($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.
=cut
############### redirect to a different report #####################
Ace/Browser/AceSubs.pm view on Meta::CPAN
"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.
=cut
# open database, return object requested by CGI parameters
sub GetAceObject {
my $db = OpenDatabase() || AceError("Couldn't open database."); # exits
my $name = param('name') or return;
my $class = param('class') or return;
my @objs = $db->fetch($class => $name);
if (@objs > 1) {
AceMultipleChoices($name,'',\@objs);
Apache->exit(0) if defined &Apache::exit;
exit(0);
}
return $objs[0];
}
=item $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.
=cut
sub Header {
my $config = Configuration();
my $dbname = get_symbolic();
return unless my $searches = $config->Searches;
my $banner = $config->Banner;
# next select the correct search script
my @searches = @{$searches};
my $self = url(-relative=>1);
my $modperl = $ENV{MOD_PERL} && Apache->can('request') && eval {Apache->request->dir_config('AceBrowserConf')};
my @row;
foreach (@searches) {
my ($name,$url,$on,$off,$size) = @{$config->searches($_)}{qw/name url onimage
offimage size/};
my $active = $url =~ /\b$self\b/;
my $image = $active ? $on : $off;
# replace the url with a cookie, if one is defined
my $cookie_name = "SEARCH_${dbname}_${_}";
my $query_string = cookie($cookie_name) unless /blast/;
$url .= "/$dbname" unless $url =~ /\b$dbname\b/ or $modperl;
$url .= "?$query_string" if $query_string;
if ($image) {
push @row,a({-href=>$url},img({-src=>$image,-border=>0,
-width=>$size->[0],-height=>$size->[1],
-alt=>$name}));
} else {
push @row,$active ? font({-color=>'black'},$name) : a({-href=>$url,-class=>'searchbanner'},$name);
}
}
my ($home,$label) = @{$config->Home} if $config->Home;
return table({-border=>0,-cellspacing=>1,-width=>'100%'},
Tr(td({-align=>'CENTER',-class=>'searchbanner'},\@row)),
Tr(td({-align=>'CENTER',-valign=>'BOTTOM',colspan=>scalar(@row)},
a({-href=>$home},$banner))
)
);
}
=item $url = Object2URL($object)
=item $url = Object2URL($name,$class)
In its single-argument form, this function takes an AceDB Object and
returns an AceBrowser URL. The URL chosen is determined by the
configuration settings.
It is also possible to pass Object2URL an object name and class, in
the case that an AceDB object isn't available.
The return value is a URL.
=cut
# general mapping from a display to a url
sub Object2URL {
my ($object,$extra) = @_;
my ($name,$class);
if (ref($object)) {
($name,$class) = ($object,$object->class);
} else {
($name,$class) = ($object,$extra);
}
my $display = url(-relative=>1);
my ($disp,$parameters) = Configuration()->map_url($display,$name,$class);
return $disp unless $parameters;
return Url($disp,$parameters);
}
=item $link = ObjectLink($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
Ace/Browser/AceSubs.pm view on Meta::CPAN
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 $open;
=cut
# Toggle a subsection open and close
sub Toggle {
my ($section,$label,$count,$addplural,$addcount,$max_open) = @_;
$OPEN{$section}++ if defined($max_open) && $count <= $max_open;
my %open = %OPEN;
$label ||= $section;
my $img;
if (exists $open{$section}) {
delete $open{$section};
$img = img({-src=>'/ico/triangle_down.gif',-alt=>'^',
-height=>6,-width=>11,-border=>0}),
} else {
$open{$section}++;
$img = img({-src=>'/ico/triangle_right.gif',-alt=>'>',
-height=>11,-width=>6,-border=>0}),
my $plural = ($addplural and $label !~ /s$/) ? "${label}s" : "$label";
$label = font({-class=>'toggle'},!$addcount ? $plural : "$count $plural");
}
param(-name=>'open',-value=>join(' ',keys %open));
my $url = url(-absolute=>1,-path_info=>1,-query=>1);
my $link = a({-href=>"$url#$section",-name=>$section},$img.' '.$label);
if (wantarray ){
return ($link,$OPEN{$section})
} else {
print $link,br;
return $OPEN{$section};
}
}
=item $html = TypeSelector($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 $class. This function is called by PrintTop().
It is not exported by default.
=cut
# Choose a set of displayers based on the type.
sub TypeSelector {
my ($name,$class) = @_;
return unless $class;
my ($n,$c) = (escape("$name"),escape($class));
my @rows;
# add the special displays
my @displays = Configuration()->class2displays($class,$name);
my @basic_displays = Configuration()->class2displays('default');
@basic_displays = Ace::Browser::SiteDefs->getConfig(DEFAULT_DATABASE)->class2displays('default')
unless @basic_displays;
my $display = url(-absolute=>1,-path=>1);
foreach (@displays,@basic_displays) {
my ($url,$icon,$label) = @{$_}{qw/url icon label/};
next unless $url;
my $u = ResolveUrl($url,"name=$n;class=$c");
($url = $u) =~ s/[?\#].*$//;
my $active = $url =~ /^$display/;
my $cell;
unless ($active) {
$cell = defined $icon ? a({-href=>$u,-target=>'_top'},
img({-src=>$icon,-border=>0}).br().$label)
: a({-href=>$u,-target=>'_top'},$label);
} else {
$cell = defined $icon ? img({-src=>$icon,-border=>0}).br().font({-color=>'red'},$label)
: font({-color=>'red'},$label);
}
push (@rows,td({-align=>'CENTER',-class=>'small'},$cell));
}
return table({-width=>'100%',-border=>0,-class=>'searchtitle'},
TR({-valign=>'bottom'},@rows));
}
=item $url = Url($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=>$url},'Dump this sequence');
=cut
sub Url {
my ($display,$parameters) = @_;
my $url = Configuration()->display($display,'url');
return ResolveUrl($url,$parameters);
}
sub Open_table{
print '<table width=660>
<tr>
<td>';
}
sub Close_table{
print '</tr>
</td>
</table>';
}
# return host and port for symbolic database name
sub getDatabasePorts {
my $name = shift;
my $config = Ace::Browser::SiteDefs->getConfig($name);
return ($config->Host,$config->Port,
$config->Username,$config->Password,
$config->Cacheroot,$config->Cachesize,$config->Cacheexpires,$config->Cachepurge,
) if $config;
# If we get here, then try getservbynam()
# I think this is a bit of legacy code.
my @s = getservbyname($name,'tcp');
return unless @s;
return unless $s[2]>1024; # don't allow connections to reserved ports
return ('localhost',$s[2]);
( run in 0.761 second using v1.01-cache-2.11-cpan-ceb78f64989 )