Plant Ontology Consortium

Home Search/Browse Plant Ontologies Download Ontologies Request PO terms Documentation Tutorials Mail Archives Site Map Feedback

Plant Ontology: Developers guide to SVN access

---

Get anaccount from SVN administrator

To get your usernameand password, please run the following command from a Unix/Linuxmachine (technically you can do it from Windows, but you're on your ownto 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 haveestablished your account on palea.cgrb.oregonstate.edu, start with thefollowing depending on the type of machine from which you will beaccessing the SVN repository.

---

SVN access via unix orlinux machines

If you prefer a command line access via a unix or linux  machinestry 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 thefollowing 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
PankajJaiswal, Justin Elser

---

SVN access via windows

Onepossible program to access and subversion repository under Windows isTortoiseSVN.  The program integrates with Windows Explorer and canbe downloaded from tigris.org.

The following section tells you about setting up and accessing SVN viawindows 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 WindowsExplorer.

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

Image-1

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

It will then download the repository for editing.  It maytake 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 ared exclamation mark, meaning that it different than the repositoriesversion.

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

Image-2

After your message is entered, it will ask you for your username andpassword, enter the ones sent earlier (after acknowledgment ofapproval).

---

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 setup" and choose "Check out project from repository" from the followingscreen:



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 youcan change is in trunk/private/test/test.  Once any changes youhave made are finished, the "Local State" will change to "Modified" asshown below.  You can then commit the file by right-clicking andchoosing "commit".



Write a short message explaining what changes you have made, and thenenter 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 editPO files or any other vocabulary that has a DAG data structure. Themost current version of DAG-Edit can be downloaded from the publiclyaccessible source repository at SourceForge.Help documentation is now included in the program, or is availablehere: 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.  Inthe following sections, I am giving an example of the TAIR anatomyfiles. Soon we will have the PO files

anatomy.ontology	--	Anatomical terms and relationships
anatomy.defs	--	Definitions of anatomical terms
development.ontology	--	Developmental and growth stage terms and relationships
development.defs	--	Definitions of developmental and growth stage terms

Open the DAG-Edit program andgo to File menu and select Load Terms. This willopen a window

-Choose data adapter: GO flat file adapter
-File collection:create a new profile Poc
-File paths: Add Toadd a new file browser for the Ontology file you are interested inlooking e.g. anatomy.tair see next
-File Name or URL: Enter or browse tofind the file \Poc\anatomy\anatomy.tairin your SANDBOX directory"ontology" where you checked out the Poc module.
-Definition file name: Same as above browse to enter the definitionfile e.g. \Poc\definitions\tair.definition in your SANDBOX directory "ontology" where you checked out the Poc module
-After you have setp up the file pathssay OK
-This will start loading theontology files. In this example the TAIR anatomy ontology.
-If you have made any changes in definition/added a new term/merged twoterms/modified the tree etc. you need to save the file by going to "File" menu and selecting "Save".
-After saving, you would like to commit those changes to SVN. Follow the instructions as follows:

For command line users:

-go to the respective directory by cdontology/Poc/anatomy/
-then type:svn commit (name of your file with new saves).
-this will commit the changes to the file in SVN


For Windows users:

          -Follow the steps outlined near image-2.

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
Justin Elser, Laurel Cooper, Pankaj Jaiswal

Last modified: Fri Mar 16 16:36:18 2012

| Feedback/Contact Us | Copyright Statement

Plant Ontology by Plantontology.org is licensed under a Creative Commons Attribution-NoDerivs 3.0 United States License. Based on a work at www.plantontology.org.