AceBrowser Version 3.1
September 20, 2001

The AcePerl distribution now includes a collection of CGI scripts that
run on top of AcePerl to provide a simple browsable interface to ACEDB
databases.  Some of the code has been tuned for the C. elegans
database, but most of it is fully generic.

Demos are running at http://stein.cshl.org/elegans/.

REQUIREMENTS:

1. AcePerl 1.76 or higher (available at http://stein.cshl.org/AcePerl/)
2. Perl 5.6.0 or higher
3. CGI.pm 2.77 or higher (available at http://stein.cshl.org/WWW/software/CGI)
4. A Web server
5. sgifaceserver 4.8c or higher.  For best results, use the version of
   sgifaceserver available at http://www.acedb.org/.
   The socket server is generally a better choice than the older RPC-based
   server.

INSTALLATION:

1. Read README first.  This describes how to install AcePerl.  

2. During the installation, you will be asked whether you wish to
install AceBrowser.  Answer "yes."  

3. You will be asked for the installation locations for several groups
of files.  The answers depend on the configuration of your web server
The install script will attempt to create any directories that do not
already exist.

  a. Site-specific configuration file directory

	Acebrowser needs access to one or more configuration files.
	Each file describes a data source and how information from
	the data source is to be rendered.  All configuration files
	are stored in a directory at the location indicated here.

	The default is /usr/local/apache/conf/ace/.

  b. Acebrowser CGI script directory

        The core of Acebrowser is a set of CGI scripts.  This is the
	directory that will contain them.  Choose a directory that will
	be recognized by the web server as containing CGI script.  If
	you are using Apache/mod_perl, select a directory under the 
	control of Apache::Registry.

        The default is /usr/local/apache/cgi-bin/ace/

  c. Acebrowser HTML files and images

	Acebrowser uses a small number of static HTML files and images.
	This is the directory that will contain them.  Choose a directory
	that is located under the web server's document root.

	The default is /usr/local/apache/htdocs/ace/

Depending on the permissions of your web server directories, you may
have to be root in order to create some of these directories.

4. Run "make", "make test" and "make install" as described in the main
README.  If this is successful, run "make install-browser".  This will
copy the acebrowser files into the directories chosen in step (3).
Depending on the permissions of your web server directories, you may
have to be root in order to complete this step.

5. If you installed the CGI scripts in their default location, you
should now be able to search the C. elegans database by fetching the
following URL:

	http://your.host/cgi-bin/ace/searches/text

You can then follow the links to browse the database.  A slightly more 
sophisticated search allows you to search a subset of object classes:

        http://your.host/cgi-bin/ace/searches/basic

or the entire list of object classes:

        http://your.host/cgi-bin/ace/searches/browser

There is also a default Acebrowser "home page" installed at the URL:

	http://your.host/ace/index.html

You may have to adjust these URLs for the locations of the directories
chosen in step (3).

CONFIGURATION

Acebrowser is configured to allow access to multiple ACEDB databases.
You can customize each database extensively by changing the appearance
of pages, adding new search capabilities, and adding new displays for
particular Ace object classes.

Each database has a symbolic name, and each symbolic name corresponds
to a configuration file located in the site-specific configuration
directory.  There are three databases defined in a new Acebrowser
installation: 

  simple   An acedb database running on port 2005 of the 
	   local host

  moviedb  An example database of movies running on port 200008 
	   of stein.cshl.org

  default  An oldish snapshot of the C. elegans database running
	   on port 2005 of stein.cshl.org

To select among the data sources, append the symbolic name to the end
of the URL of the desired CGI script.  For example, to do a text
search on the "moviedb" database, fetch this URL:

  http://your.site/cgi-bin/ace/searches/text/moviedb

If no symbolic name is specified, the default database is assumed.
  http://your.site/cgi-bin/ace/searches/text 

is equivalent to

  http://your.site/cgi-bin/ace/searches/text/default

As described in EXTENDING ACEBROWSER, another way to select among
databases is to place the CGI script itself in a directory with the
same name as the database.  For example, if you have written a
specialized CGI script called screenplay that is designed to work with 
the "moviedb" database, you could place it in a subdirectory named
moviedb, and refer to it this way:

  http://your.site/cgi-bin/ace/moviedb/screenplay

The symbolic name can actually appear anywhere in the path, so this
would work as well:

  http://your.site/cgi-bin/ace/moviedb/custom/screenplay

THE CONFIGURATION FILES

The configuration files are located in the directory selected for
acebrowser configuration.  Their names are formed by appending ".pm"
to the symbolic name of the database.  For example, the configuration
file "simple.pm" corresponds to the database "simple".

Each of the configuration files is actually an executable Perl script.
As such it can use any Perl constructions you wish, including variable
interpolation.  The purpose of the configuration file is to set a
series of configuration variables, which by convention are all
uppercase.  For example, here is an excerpt from the default.pm
configuration file:

 $HOST = 'stein.cshl.org';
 $PORT = 2005;
 $USERNAME = '';
 $PASSWORD = '';

In addition to scalar variables, the configuration file is used to set 
arrays, hashes and specially-named functions.

If you are only interested in accessing a single database, it is
easiest to modify the default.pm configuration file.  To serve
multiple databases, just make a copy of default.pm and edit the copy.

If, for some reason, Acebrowser cannot find its configuration files,
it will generate an internal server error.  The location of the
configuration files directory is stored in the module
Ace::Browser::LocalSiteDefs, typically somewhere inside the
"site_perl" subdirectory of the Perl library directory (use "perl -V"
to see where that is).  You can find out where Acebrowser expects to
find its configuration files by running the following command:

  perl -MAce::Browser::LocalSiteDefs \
       -e 'print $Ace::Browser::LocalSiteDefs::SITE_DEFS,"\n"'

To change this value, either reinstall Aceperl or edit
LocalSiteDefs.pm manually.

EDITING THE CONFIGURATION FILE

The settings in the default.pm configuration file distributed with
AcePerl should work with little, if any modification.  The following
variables may need to be tweaked:

  $ROOT = '/cgi-bin/ace';

This is the root (top level) for all the Acebrowser CGI scripts.
Change this if necessary.

 $DOCROOT = '/ace';

This is the root (top level) for all of Acebrowser's static HTML files
and images.  You will need to change this if the static files are
installed somewhere else.

 $ICONS = "$DOCROOT/ico";

This is where Acebrowser expects to find its icons. This subdirectory
holds icons and other small static images.  Note how the
previously-defined $DOCROOT variable is used.  You will probably not
need to change this.

 $IMAGES = "$DOCROOT/images";

This is where Acebrowser expects to find its "images" subdirectory.
This directory contains images generated dynamically by the ACEDB
database.  It *must* be writable by the web server user, usually
"nobody".  When the AcePerl install script creates this directory, it
makes it world-writable by default.  You may prefer to make it owned
by the "nobody" user and/or group.

 $HOST = 'stein.cshl.org';

This is the name of the host where the desired acedb server can be
found.

 $PORT = 2005;

This is the network port on which the desired acedb server is
listening.  Network ports in the range 1024-65535 are assumed to
correspond to the newer socket-based sgifaceserver.  Ports in the
range 65536-4,294,967,296 are assumed to correspond to the older
RPC-based gifaceserver.

 $USERNAME = '';
 $PASSWORD = '';

For password-protected ACEDB databases, these variables contain the
username and password.

 $STYLESHEET = "$DOCROOT/stylesheets/aceperl.css";

This is the cascading stylesheet used to set the background color,
font, table colors, and so forth.  You probably don't need to change
this, but you might want to modify the stylesheet itself.

 @PICTURES = ($IMAGES => "$HTML_PATH/images");

This array indicates the location of the "images" subdirectory.  The
first element of the array is the location of the directory as a URL,
and the second element is the location of the directory as a physical
path on the file system.  This array is ignored when running under
modperl/Apache::Registry; modperl uses $IMAGES to look up the
corresponding physical path.

 @SEARCHES   = (
	       basic => {
			name   => 'Basic Search',
			url    =>"$ROOT/searches/basic",
		       },
	       text => {
			name   => 'Text Search',
			url    =>"$ROOT/searches/text",
		       },
	       browser => {
			   name => 'Class Browser',
			   url  => "$ROOT/searches/browser",
			  },
	       query => {
			 name => 'Acedb Query',
			 url  => "$ROOT/searches/query",
			 },
	       );
 $SEARCH_ICON = "$ICONS/unknown.gif";

The @SEARCHES array sets the searches made available to users.  The
first element in each pair is the symbolic name for the search.  The
second element is a hash reference containing the keys "name" and
"url".  The name is the bit of human readable text printed in the
list of searches located at the top of the AceBrowser page.  The url
is the URL of the script that performs the search.

The $SEARCH_ICON variable selects an icon to use for the search
button.

 @HOME      = (
	      $DOCROOT => 'Home Page'
	     );

Select the URL and label for the "home" link appearing on the bottom
of each Acebrowser-generated page.  By default, the home will point to 
"/ace" directory on the local machine.

 %DISPLAYS = (	
	     tree => {
		      'url'     => "generic/tree",
		      'label'   => 'Tree Display',
		      'icon'    => '/ico/text.gif' },
	     pic => {
		     'url'     => "generic/pic",
		     'label'   => 'Graphic Display',    
		     'icon'    => '/ico/image2.gif' },
	    );

As described in EXTENDING ACEBROWSER, the %DISPLAYS hash declares a
set of pages, or "displays", to be used for displaying certain Ace
object types.

 %CLASSES = (	
	     Default => [ qw/tree pic/ ],
	   );

As described in EXTENDING ACEBROWSER, the %CLASSES hash describes how
Acedb classes correspond to displays.

 sub URL_MAPPER {
   my ($display,$name,$class) = @_;
   ...
 }

As described in EXTENDING ACEBROWSER, the URL_MAPPER subroutine allows
you to tinker with the way in which Acedb classes are turned into
links.

 $BANNER = <<END;
 
Default Database
<p>
 END

The $BANNER variable contains HTML text that will be displayed at the
top of each generated page.  You will probably want to change this.

 $FOOTER = '';

The $FOOTER variable contains HTML text that is displayed at the
bottom of each generated page.  You will probably want to change this.

 $PRINT_PRIVACY_STATEMENT = 1;

If this variable is set to true, then AceBrowser will generate a link
in the footer that displays a privacy statement explaining
AceBrowser's use of cookies.

 @FEEDBACK_RECIPIENTS = (
			[ " $ENV{SERVER_ADMIN}", 'general complaints and suggestions', 1 ]
 );

This array contains a list of recipient e-mail addresses for the
"feedback" page.  Each recipient is an array reference containing
least two elements, the e-mail address and a comment.  A third,
optional, element, if true, indicates that this recipient should be
selected by default.  The default is the webmaster's e-mail address.
Comment out the entire section of you do not want the feedback link to 
appear.

 # configuration for the "basic" search script
 @BASIC_OBJECTS = 
   ('Any'          =>   'Anything',
    'Locus'        =>   'Confirmed Gene',
    'Predicted_gene'    =>   'Predicted Gene',
    'Sequence'     =>   'Sequence (any)',
    'Genome_sequence', => 'Sequence (genomic)',
    'Author'       =>    'Author',
    'Genetic_map'  => 'Genetic Map',
    'Sequence_map' => 'Sequence Map',
    'Strain'       =>  'Worm Strain',
    'Clone'        => 'Clone'
   );

The @BASIC_OBJECTS array is used by the "basic" search script.  It
indicates the Acedb classes to offer to the user to search on, and the
labels to use for each class.  For example, the default configuration
will present the user with a radio button labeled "Confirmed Gene" for
use in searching the Acedb class "Locus".

USING ACEBROWSER WITH MOD-PERL

Acebrowser is designed to work well with modperl
(http://perl.apache.org).  In fact, using it with a modperl-enabled
Apache server will increase its performance dramatically.

To use Acebrowser with modperl, install the CGI scripts into a
directory that is under the control of Apache::Registry.  The
<Location> section in httpd.conf should look like this:

 Alias /acedb/ /usr/local/apache/cgi-bin/ace/

 <Location /acedb>
   SetHandler Perl-script
   PerlHandler Apache::Registry
   PerlSendHeader On
   Options +ExecCGI +Indexes
 </Location>

Change the paths as appropriate.  The Acebrowser scripts located in
/usr/local/apache/cgi-bin/ace can now be accessed under modperl at the 
URL /acedb, as in:

  http://your.site/acedb/searches/text

When running under modperl, you can force all the CGI scripts in a
directory to use a particular configuration file by defining the
AceBrowserConf configuration variable .  For example, to create a
virtual directory named /movies and force all the scripts within it to
use the moviedb configuration file:

 Alias /movies/ /usr/local/apache/cgi-bin/ace/

 <Location /movies>
   SetHandler Perl-script
   PerlHandler Apache::Registry
   PerlSendHeader On
   Options +ExecCGI +Indexes
   PerlSetVar AceBrowserConf /usr/local/apache/conf/acebrowser/moviedb.pm
 </Location>

Be sure also to edit moviedb.pm $ROOT variable to indicate the correct
location of scripts in URL space:

 $ROOT = '/movies';

EXTENDING ACEBROWSER

Acedb is fundamentally object based.  In addition to having a name,
each object has a class, such as "Sequence".  Acebrowser takes
advantage of this object structure by allowing you to assign one or
more displays to a class.  Each display is a CGI script that fetches
the desired object from the database, formats it, and displays it as
HTML or an image.

Whenever Acebrowser is called upon to display an object, it consults
the configuration file to determine what displays are registered for
the object, and then presents a row of display names across the top of
the window.  In Acebrowser jargon, this line of displays is called the
"type selector."  The user can change the display to use by selecting
the corresponding link.

Three generic displays, which will work with all databases, come with
Acebrowser:

  tree  an HTML representation of the Acedb object which
	presents the object in the form of a collapsible outline.

  xml   an XML representation of the Acedb object

  pic   a clickable GIF image, as returned from gifaceserver.

Writing New Display Scripts
---------------------------

To register a new display script with the system, you will need to do
three things:

1. Write the script.  The easiest way to do this is to take the
moviedb "misc/movie" script, copy it, and go from there. 

The script will be invoked with the CGI parameters "name" and "class",
corresponding to the name and class of the Acedb object to display.
For example, if the script is located in /cgi-bin/ace/newscript, it
will be invoked as:

  http://your.site/cgi-bin/ace/newscript?name=foo;class=bar

2. Register the display with the %DISPLAYS hash in the configuration
file, by adding a hash entry like the following:

	     newdisplay => {
		 url   => "/cgi-bin/ace/newscript",
		 label => 'New Display',
		 icon  => '/ico/layout.gif',
		 },

The hash key, in this case "newdisplay", is a symbolic name for the
display.  It can correspond to the acual name of the CGI script, or
not.  The hash value is itself an anonymous hash containing the
required keys "url" and "label", and the optional key "icon".  "url"
gives the path to the script that will display, and "label" gives a
human readable label for the link that Acebrowser puts in the type
selector. The "icon" key, if present, will display the indicated icon
in the type selector.

3. Bind this display to the class (or classes) for which this display
is valid, by adding an entry to the %CLASSES array.  For example:

	  NewObject    => ['newdisplay'],

This indicates that whenever Acebrowser is called upon to display an
object of type "NewObject", it will display the object using the CGI
script designated by the "newdisplay" display.  If you have several
displays that are appropriate for a class, you can bind them all to
the class in the following fashion:

          NewObject => ['newdisplay','newerdisplay','newestdisplay'],

When creating a link for an Acedb object, Acebrowser will choose the
first display in the array.  When the object is displayed, all three
of the alternative displays will appear in the type selector.

More information on writing display scripts can be found in the
documentation for Ace::Browser::AceSubs.  From the command line, run:

  perldoc Ace::Browser::AceSubs

Writing New Searches
--------------------

To create a new search, 

1. Write a script following the model of one of the existing scripts.
Ace::Browser::SearchSubs exports subroutines that are useful in
managing the multiple pages of results produced by most search
scripts.

2. Register the new script in the @SEARCHES array.  Provide an
explanatory name for the search script, and a pointer to its URL.

More information on writing search scripts can be found in the
documentation for Ace::Browser::SearchSubs.  From the command line, run:

  perldoc Ace::Browser::SearchSubs

FOR HELP

Please write to the Acedb newsgroup, acedb@sanger.ac.uk for help or to
report possible bugs.  If you get really stuck, write to the author,
lstein@cshl.org.

Lincoln D. Stein
September 24, 2001
