Plant Ontology: Developers guide to CVS access

Get an account from CVS administrator

Before getting started get your user_login name and password from Peter Van Buren by mentioning

Request for user account on: brebiou.cshl.edu
Your name:
Institution:
Email address:
Office or lab telephone number:(xxx)-xxx-xxxx

If you already have one, do not worry, it will work. Once you have established your account on brebiou.cshl.edu, start with the following depending on the type of machine from which you will be accessing the CVS repository.

CVS access via unix or linux machines

If you prefer a command line access via a unix or linux  machines try this
Set up a directory on your home box: ontology

cd ontology

CSHL servers require that you use secure shell:

setenv CVS_RSH ssh

Get the files by doing a check out (co) of the "Poc" module with the following command:

cvs -d user_name@brebiou.cshl.edu:/home/cvs co Poc

In order to update an ontology do this
-cvs update
-cvs commit for your edited file.

It is good practice always to update a file before revising it.

There is a helpful O'Reilly "CVS Pocket Reference" by G.N. Purdy.
If you need help in depositing your ontology please contact one of us
Doreen Ware, Shuly Avraham, Pankaj Jaiswal

CVS access via windows

If you have an account on the brebiou CVS server, you can use SSH client to access the CVS (it is simple to set up, thus no instructions provided). However, if you are interested in accessing the CVS from your desktop, I suggest using the freeware WinCvs.
For downloading the freeware please go to http://www.wincvs.org/download.html

Following section tells you about setting up and accessing the CVS via windows machine by using WinCvs.
After you have downloaded the freeware, install it on your machine.
It might install in a default directory C:\Program Files\GNU\ on your hard drive.
Look for wincvs.exe file under C:\Program Files\GNU\WinCvs 1.3
Execute the file by clicking on wincvs.exe

It will open a WniCvs panel (image-1). Do not worry if a waring message appears saying you do not have python installed. Just ignore.

Image-1

WinCvs panel image (image-1)

In the mean time, using your windows explorer,  create a SANDBOX directory in your favourite location calling it "ontology"

Now come back to the WinCvs window (image-1)
In the menu section on top, go to "Admin" and "Preferences"
A small window for WinCvs preference (image-2) pops up.

WinCvs preference:

Go to "general" and configure the settings as follows:

In the "Authentication" section after selecting ssh (select from dropdown menu), click on the "settings" button. This opens a new window where you select the "SSH client" and provide the location ssh2.exe file. You can find this by browsing the program directory where you installed the SSH client. Most probably it will be "C:\Program Files\SSH Communications Security\SSH Secure Shell\ssh2.exe"

Image-2

WinCvs preference settings panel

On the same window go to "CVS" section (image-3)

Provide a path under HOME (passwords and ~/.cvs* files) where the information on your passwords etc. will be stored.
You may want to have a path C:\Documents and Settings\My Documents\SELF\wincvs
or any other if you want to have it stored at some different place. Remember you will have to create this directory "wincvs" by using your windows explorer.

Image-3

WinCvs panel CVS section

After you have setp up these configurations say OK.

Checkout module:
Go to WinCvs menu "Remote" on the WinCvs window (image-1) and select "Checkout module"
It opens a new window "Checkout settings" (image-4).

Go to "Checkout settings" and configure the following
Module name and path on the server: Poc
Local folder to checkout to: Select the location of your SANDBOX directory "ontology".

Image-4

Checkout module panel

On the same window go to "General" section and once again confirm the settings as follows (same as Image-2)

After you have setp up these configurations say OK

Hitting the OK on "Checkout settings" window will start connecting to the server brebiou.cshl.edu and will propmt you to enter a password (assigned by Peter van Buren, CSHL) in a command line window. After you enter the password hit Enter key and it should start downloading the Poc module to the designated SANDBOX directory "ontology" on your machine.

After it is done with downloading, you are all set to work on these files. You will see the same files under ontology/Poc/ as available from Steinlab Viewcvs (for more info CLICK HERE).

CVS access using Mac Machines

Download the Apple Developers Tookit. It's a free download (you just need to signup for a userid). When you install the developer kit, it installs cvs.

To do a checkout, all you have to do is setup your environment (.bashrc and/or .cshrc) and then do

This will check out the Poc module in the current directory. What you can do is create a folder inside the desktop folder (call it sandbox), then open a terminal window and cd to Desktop/sandbox. Now when you run a checkout, the Poc module will end up in a folder on the desktop called "sandbox".

The instructions to do an anonymous checkout are the same.

DAG-Edit software:

This Java application provides an interface to browse, query and edit PO files or any other vocabulary that has a DAG data structure. The most current version of DAG-Edit can be downloaded from the publicly accessible source repository at SourceForge. Help documentation is now included in the program, or is available here: dagedit_userguide/dagedit.html

Working on ontology files:

After  you have the DAG-Edit installed and CVS setup woorking, you must be excited to start working on the Ontology files.  In the following sections, I am giving an example of the TAIR anatomy files. Soon we will have the PO files