ACEDB HOWTO
ACeDB is poorly documented and very intimidating to the new user.
Despite this, it is not hard to install the database and get it
running.
OBTAINING THE SOFTWARE
ACeDB is available in both binary and source code form. I strongly
recommend that you install the server from source code. The source
distributions tend to be more up to date than the binary
distributions, and subtle differences between shared libraries can
cause ACeDB binaries linked on one platform to behave differently on
another.
ACeDB distributions are available at:
ftp://ftp.wormbase.org/pub/wormbase/software/
ftp://ncbi.nlm.nih.gov/repository/acedb/
I recommend that you use the ftp.wormbase.org URL, as this contains
the latest stable snapshot of ACeDB that I use for testing and
debugging the current release of AcePerl.
COMPILING THE SOFTWARE
Unpack the software into its own directory:
1) mkdir acedb
2) gunzip -c acedb-latest.tar.gz | tar xvf -
Compile the software. The makefile requires that an environment
variable named ACEDB_MACHINE be defined. This environment variable is
in turn used to select the makefile to be used to compile. To figure
out what to set this environment variable to, type "make". You will
receive an error message listing the alternatives. Choose one for your
system, and run "make again".
3) cd acedb
4) make (error message listing possibilities)
5) setenv ACEDB_MACHINE LINUX_4 (for example)
6) make
This will create a subdirectory named bin.LINUX_4 (or whatever your
operating system is), containing the executables along with a number
of other files.
INSTALLING THE SOFTWARE
ACeDB runs as an Internet server. As such, it should not be run as
root, but as an unprivileged user. My strategy has been to create a
new user and group, both named "acedb". The server runs as "acedb",
and all database developers belong to the "acedb" group, giving them
write access to the database files.
After creating the acedb user, create a "bin" directory and copy the
executables into it:
1) cd ~acedb
2) mkdir bin
3) cd ~/acedb (where the source code was compiled)
4) cd bin.LINUX_4 (or whatever)
5) cp xace tace giface saceserver sgifaceserver makeUserPasswd ~acedb/bin/
Now put ~acedb/bin on your path so that the Ace::Local module can find
the giface and tace programs. This usually involves editing .cshrc or
.bashrc to change the PATH variable. (See your system administrator
if you don't know how to do this).
CREATING DATABASES
Each ACeDB database lives in a separate subdirectory, which I
conventionally place under ~acedb/. You will often be installing a
compressed database archive, such as the C. elegans database (see the
NCBI FTP site). In this case, simply unpack the database into the
~acedb/ directory. Programs like xace, tace, and the servers will
refer to the database by its path. Within the database directory
should be the subdirectories databases/, wspec/, wdoc/, wgf/, wquery/,
and possibly others. If not, make sure that you unpacked the database
package correctly.
Now examine and edit the file ~acedb/wspec/passwd.wrm. This contains
the names of user accounts that are allowed to write to the database.
Make this file readable by everyone, but only writable by you (and
other trusted users). If you will be running an ACeDB server, you
should examine the file ~acedb/wspec/server.wrm. This contains read
and write policies for the server. You can restrict who can read and
write to the database, although currently you are limited to
restricting read and write privileges to local users versus non-local
users.
Creating a new database from scratch is somewhat more difficult,
because you have to create an appropriate models (schema) file.
Please see NEW_DB.HOWTO for help.
Now confirm that the database is correctly installed by running the
xace program.
xace ~acedb/elegans (or whatever)
You should be able browse the data, view graphics, and so on.
INSTALLING AN ACE SERVER
ACEDB comes with two servers called "saceserver" and "sgifaceserver".
The difference between the two is that sgifaceserver has the ability
to serve graphical pictures. Aceserver is text-only. In general, you
will want to use sgifaceserver unless you know you will never need to
serve pictures. If you download a binary distribution of ACEDB, the
two executables may have the name of the operating system appended to
them. Never fear. Just rename the files to "saceserver" and
"sgifaceserver."
A full description of installing s(gif)aceserver is given in the ACEDB
web pages at:
http://www.acedb.org/Development/wdoc/Socket_Server/SOCKET_aceserver.html
However, it is a rather technical description. Here's a brief summary
of what you need to do:
1) Set up server password permissions:
a. Choose an administrative username and password. For example "admin"
and "acepass"
b. Generate a "hash" of the username and password using the makeUserPasswd
program (this comes with the acedb binaries):
% makeUserPasswd admin
// Please enter passwd: ******
// Please re-enter passwd: ******
// The following line is a valid entry for wspec/serverpasswd.wrm
admin e5cc20aa1a8f3e7e5b29728bbd1355d8
c. Find the file named serverpasswd.wrm located in the wspec/ subdirectory
of the acedb database directory. Add these two lines to the end of the file:
admin: admin
admin e5cc20aa1a8f3e7e5b29728bbd1355d8
The first line tells the server that the "admin" user has administrative
access, and can start and stop the server. The second line says that
"admin" has the password encoded in the numbers.
d. If you want to create additional users with read-only or read/write,
permissions, you can do so by generating more user names and password
hashes with makeUserPasswd, and entering them into the serverpasswd.wrm
file as described before. Here is an example that grants "fred" and "ethel"
read/write access, and grants "ricky" read-only access:
admin: admin
write: fred ethel
read: ricky
admin e5cc20aa1a8f3e7e5b29728bbd1355d8
fred 08b622ddf7eb7c8e44cdb3bd6362f966
ricky 64c12094434c3c4a1a24cdd21ad06485
ethel f95557500f46122aacd59ce920aae6e8
2) Try to start the server under your own account, using saceclient.
Assuming that you have installed the acedb databases using your own
user permissions, you can try to run the web server as yourself. Open
up two command windows on your system. In one type this command:
% ~acedb/bin/sgifaceserver ~acedb/elegans 5000
This is telling the server to run on port 5000 and to read data from
the database directory located at ~acedb/elegans. If all is well, you
will see messages like this:
// Database directory: /usr/local/acedb/elegans
// Shared files: /usr/local/acedb
// #### Server started at 2003-05-12_11:54:13
// #### host=brie3.cshl.org listening port=5000
// #### Database dir=/usr/local/acedb/elegans/
// #### Working dir=/usr/local/acedb/elegans/
// #### clientTimeout=600 serverTimeout=600 maxbytes=102400 autoSaveInterval=600
The messages will stop, indicating that the server is waiting for
incoming connections.
In the other window, launch saceclient with this command:
% ~acedb/bin/saceclient localhost -port 5000
It will prompt you for a userid (type "admin") and a password (type
the password). If all goes well, you will get this prompt:
acedb@localhost>
and the server will accept queries. For example, try the command
"Find Model".
3) Try to communicate with the server using aceperl.
When you installed AcePerl, it should have installed a small interface
script named ace.pl. Confirm that it can talk to the server:
% ace.pl -host localhost -port 5000
By default, you will get an "anonymous" read only connection, and you
will see the prompt:
aceperl>
indicating that the database is ready to accept queries.
4) Shut down the server.
When you are ready, shut down the server like this:
% ace.pl -host localhost -port 5000 -user admin -pass acepass
aceperl> shutdown now
5) Try running the server as the "acedb" user.
If you are going to be running the acedb server a lot, it is better to
run it under the "acedb" account than under your personal login. The
reason for this is that bugs in the acedb server code may
inadvertently expose your personal files to snooping or deletion if
the server is running under your personal ID.
To run the server as acedb, you must make its database files writable
by the acedb user. To do this, become the root user, and run the
following commands:
# chown -R acedb ~acedb/elegans/database
# chgrp -R acedb ~acedb/elegans/database
# chmod -R +rw ~acedb/elegans/database
Replace the path ~acedb/elegans with the path to the database that you
want to be accessible. What this is doing is to make the "database"
subdirectory owned by the acedb user and writable by it.
Still running as root, become the acedb user:
# su acedb
Now confirm that you can still launch the server:
% ~acedb/bin/sgifaceserver ~acedb/elegans 5000
and talk to it:
% ace.pl -host localhost -port 5000
Congratulations. You're almost done. The last step is to arrange for
the acedb socket server to start up automatically when needed.
GETTING THE SERVER TO START AUTOMATICALLY
There are two recipes for this, depending on whether your system uses
standard "inetd" "super daemon" to start up services on an as-needed
basis, or uses the new enhanced version called "xinetd." The way to
tell is to look in your /etc directory. If you see a file named
inetd.conf, then you are using the traditional inetd daemon. If you
see instead a directory named xinetd.d/ then you are using xinetd.
1) Configuring for inetd:
a) Find the file /etc/services, and add the following line to the
end of the file:
elegans 5000/tcp
This is defining a new service named "elegans" which runs on
port 5000. You can change this symbolic name to anything you
like. If you have multiple acedb databases running, give each
one a distinctive name and port number. Avoid using any port
numbers that are already mentioned in the file.
b) Find the file /etc/inetd.conf, and add the following line:
elegans stream tcp wait acedb /usr/local/acedb/bin/sgifaceserver
sgifaceserver /usr/local/acedb/elegans
This is all one line, but has been word-wrapped to fit.
The first field refers to the service named "elegans" that you
defined in /etc/services and is necessary for inetd to associate
the service with the proper port number. Modify as you see fit.
c) Tell inetd to reread its configuration files. Use "ps" to find
the ID of the inetd daemon like this:
# ps -elf | grep inetd
140 S root 121 1 0 68 0 - 475 do_sel May11 ? 00:00:00 /usr/sbin/inetd
and use "kill -HUP" to tell the server to reread inetd.conf
(this must be done as root):
# kill -HUP 140
You should now be able to communicate with the server using saceclient
or ace.pl. If it's not working, look in the following log files for
helpful error messages:
/var/log/messages
~acedb/elegans/database/log.wrm
~acedb/elegans/database/serverlog.wrm
2) Configuring for xinetd:
a) Find the file /etc/services, and add the following line to the
end of the file:
elegans 5000/tcp
This is defining a new service named "elegans" which runs on
port 5000. You can change this symbolic name to anything you
like. If you have multiple acedb databases running, give each
one a distinctive name and port number. Avoid using any port
numbers that are already mentioned in the file.
b) Find the directory /etc/xinetd.d. Create a file named after
the service chosen in (a) containing these contents:
# file: elegans
# default: on
# description: C. elegans acedb database
service elegans
{
disable = no
protocol = tcp
socket_type = stream
flags = REUSE
wait = yes
user = acedb
group = acedb
log_on_success += USERID DURATION
log_on_failure += USERID HOST
server = /usr/local/acedb/bin/saceserver
server_args = /usr/local/acedb/elegans
}
Change the line "service elegans" to be the symbolic name chosen
in (a).
c) Tell xinetd to restart. Use "ps" to find the ID of the xinetd
daemon like this:
# ps -elf | grep xinetd
140 S root 457 1 0 69 0 - 557 do_sel Mar09 ? 00:00:21 xinetd
and use "kill -HUP" to tell the server to reread inetd.conf
(this must be done as root):
# kill -HUP 140
You should now be able to communicate with the server using saceclient
or ace.pl. If it's not working, look in the following log files for
helpful error messages:
/var/log/messages
~acedb/elegans/database/log.wrm
~acedb/elegans/database/serverlog.wrm
Lincoln Stein
May 2003