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Plant Ontology: Developers guide to SVN access

Get an account from SVN administrator

To get your username and password, please run the following command from a Unix/Linux machine (technically you can do it from Windows, but you're on your own to figure it out)
htpasswd -cm password_file username

To get your account created, please email the password_file to Justin Elser and by mentioning

Request for svn account on: palea.cgrb.oregonstate.edu
Your name:
Institution:
Email address:
Office or lab telephone number:(xxx)-xxx-xxxx
Contents of password_file

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

SVN 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:

mkdir ontology
cd ontology

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

svn co http://palea.cgrb.oregonstate.edu:/svn/Poc --username=user_name_supplied

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

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

There is a helpful Subversion Quick Reference Card by Cezary Sobaniec.
If you need help in depositing your ontology please contact one of us
Pankaj Jaiswal, Justin Elser

SVN access via windows

One possible program to access and subversion repository under Windows is TortoiseSVN.  The program integrates with Windows Explorer and can be downloaded from tigris.org.

The following section tells you about setting up and accessing SVN via windows machine by using TortoiseSVN.
After you have downloaded the freeware, install it on your machine.

After installation is completed and the computer is rebooted, create a directory named Poc for the repository files using Windows Explorer.

Right click on the new folder and select SVN checkout (image-1)

Image-1

TortoiseSVN image (image-1)


The URL of the repository is
    http://palea.cgrb.oregonstate.edu/svn/Poc

It will then download the repository for editing.  It may take awhile, the total size of the repository as of this writing was ~62 MBytes.

Make the edits to the files you wish to change.

After your changes have been saved, the icon for the file will have a red exclamation mark, meaning that it different than the repositories version.

To commit your file to the repository, simply right click and choose SVN commit.  It will ask you to type a message explaining the changes you made (image-2)

Image-2

TortoiseSVN message window


After your message is entered, it will ask you for your username and password, enter the ones sent earlier (after acknowledgment of approval).


SVN access using Mac Machines

One possible GUI option is the program SmartSVN.  The program can be downloaded from http://www.syntevo.com/smartsvn/index.html

Download the program and follow the installation instructions.

After the program is installed, choose "My repositories are already set up" and choose "Check out project from repository" from the following screen:

mac svn client figure 1

Do a "Quick Checkout" with the following URL: http://palea.cgrb.oregonstate.edu/svn/Poc
and choose the local directory for the files to be stored.

After you select Ok, the repository will download about 63MB (as of this writing).

Edit the files that you want to change.  Note that a test file you can change is in trunk/private/test/test.  Once any changes you have made are finished, the "Local State" will change to "Modified" as shown below.  You can then commit the file by right-clicking and choosing "commit".

mac svn client figure 2

Write a short message explaining what changes you have made, and then enter the username and password you setup from the top of this page.


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 SVN 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

          -Follow the steps outlined near image-2.


  

Last modified: Fri Jul 23 19:41:05 2010

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