Developers SVN Guide - Revision history

Cooperl: /* SVN access using Mac Machines */

2015-09-11T21:02:08Z

SVN access using Mac Machines

Cooperl: /* SVN access via unix or linux machines */

2015-09-11T21:01:37Z

SVN access via unix or linux machines

Cooperl: /* Get an account from SVN administrator */

2015-09-11T21:00:28Z

Get an account from SVN administrator

Elserj at 17:21, 28 August 2015

2015-08-28T17:21:21Z

Elserj: /* SVN access via unix or linux machines */

2015-08-28T17:20:27Z

SVN access via unix or linux machines

Elserj: moved Developers Guide to Developers SVN Guide

2013-10-22T22:52:06Z

moved Developers Guide to Developers SVN Guide

Elserj: Created page with '=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…'

2013-10-22T22:51:40Z

Created page with '=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…'

New page

=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 the following:

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 one of the following sets of instructions, 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:

<code>
mkdir ontology

cd ontology
</code>

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

<code>svn co <nowiki>http://palea.cgrb.oregonstate.edu:/svn/Poc</nowiki> --username=user_name_supplied</code>

In order to update an ontology do this:

<code>svn update</code>

Make your changes to the ontology files, then

<code>svn commit</code>

to save your modified file to the svn repository.

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

There is a helpful [http://www.digilife.be/quickreferences/QRC/Subversion%20Quick%20Reference%20Card.pdf Subversion Quick Reference Card] by Cezary Sobaniec.
If you need help in depositing your files, please contact one of us:
[mailto:jaiswalp@science.oregonstate.edu?Subject=Plantontology%20SVN%20help Pankaj Jaiswal],[mailto:jaiswalp@science.oregonstate.edu?Subject=Plantontology%20SVN%20help Laurel Cooper], [mailto:jaiswalp@science.oregonstate.edu?Subject=Plantontology%20SVN%20help Justin Elser]

==SVN access via windows==

One possible program to access a subversion repository under Windows is TortoiseSVN. The program integrates with Windows Explorer and can be downloaded from [http://tortoisesvn.tigris.org/ tigris.org].

The following section tells you about setting up and accessing SVN via a 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 for the repository files named Poc, using Windows Explorer.

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

'''Image-1'''

[[File:Svn dev 1.jpg]]

The URL of the repository is
<nowiki>http://palea.cgrb.oregonstate.edu/svn/Poc</nowiki>
It will then download the repository for editing. It may take awhile, as the total size of the repository could be rather large.

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 is different from the repository's 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'''

[[File:Svn dev 2.jpg]]

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:

[[File:Mac svn 1.jpg]]

Do a "Quick Checkout" with the following URL: <nowiki>http://palea.cgrb.oregonstate.edu/svn/Poc</nowiki>

and choose the local directory for the files to be stored.

After you select Ok, the repository will download.

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".

[[File:Mac svn 2.jpg]]

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.

==Ontology editing software:==

===Obo-Edit software===

[http://oboedit.org/?page=index OBO-Edit] is an open source ontology editor written in Java that can be used to browse, search, or edit the PO (or any .obo) files.

OBO-Edit features an easy to use editing interface, a simple but fast reasoner, and powerful search capabilities. It is optimized for reading and writing ontologies in the OBO biological ontology file format.

OBO-Edit is developed by the Berkeley Bioinformatics and Open Source Projects, and is funded by the Gene Ontology Consortium.

The latest version of OBO-Edit can be downloaded from [http://sourceforge.net/projects/geneontology/files/ SourceForge].

===Protégé software===

[http://protege.stanford.edu/ Protégé] is a free, open source ontology editor and knowledge-base framework that is useful if you want to edite ontlogies in RDF(S), OWL, or XML Schema.

Protégé is based on Java, is extensible, and provides a plug-and-play environment that makes it a flexible base for rapid prototyping and application development.

===Ontology development===

The [[PO_Developers_Guide|PO Developers Guide]] provides details on the standard practices and principles used in development of the Plant Ontology.

@@ Line 80: / Line 80: @@
 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==
+==SVN access using GUI on Mac Machines==
 One possible GUI option is the program SmartSVN.  The program can be downloaded from http://www.syntevo.com/smartsvn/index.html

@@ Line 17: / Line 17: @@
 If you already have one, do not worry, it will work. Once you have established your account on palea.cgrb.oregonstate.edu, start with one of the following sets of instructions, depending on the type of machine from which you will be accessing the SVN repository.
-==SVN access via unix or linux machines==
+==SVN access via unix or linux machines (including Mac)==
 If you prefer a command line access via a unix or linux machines, try this.

@@ Line 6: / Line 6: @@
 htpasswd -cm password_file username
-To get your account created, please email the password_file to Justin Elser and by mentioning the following:
+To get your account created, please email the password_file to [mailto:jaiswalp@science.oregonstate.edu?Subject=Plantontology%20SVN%20help Justin Elser] and list the following information:
 Request for svn account on: palea.cgrb.oregonstate.edu

@@ Line 29: / Line 29: @@
 </code>
-Get the files by doing a check out (co) of the "Poc" module with the following command:
+Get the files by doing a check out (co) of the "associations" module with the following command:
 <code>svn co <nowiki>http://palea.cgrb.oregonstate.edu:/svn/associations</nowiki> --username=user_name_supplied</code>
@@ Line 56: / Line 56: @@
 After you have downloaded the freeware, install it on your machine.
-After installation is completed and the computer is rebooted, create a directory for the repository files named Poc, using Windows Explorer.
+After installation is completed and the computer is rebooted, create a directory for the repository files named "associations", using Windows Explorer.
 Right click on the new folder and select SVN checkout (Image-1)
@@ Line 65: / Line 65: @@
 The URL of the repository is
-     <nowiki>http://palea.cgrb.oregonstate.edu/svn/Poc</nowiki>
+     <nowiki>http://palea.cgrb.oregonstate.edu/svn/associations</nowiki>
 It will then download the repository for editing.  It may take awhile, as the total size of the repository could be rather large.
@@ Line 90: / Line 90: @@
 [[File:Mac svn 1.jpg]]
-Do a "Quick Checkout" with the following URL: <nowiki>http://palea.cgrb.oregonstate.edu/svn/Poc</nowiki>
+Do a "Quick Checkout" with the following URL: <nowiki>http://palea.cgrb.oregonstate.edu/svn/associations</nowiki>
 and choose the local directory for the files to be stored.

@@ Line 31: / Line 31: @@
 Get the files by doing a check out (co) of the "Poc" module with the following command:
-<code>svn co <nowiki>http://palea.cgrb.oregonstate.edu:/svn/Poc</nowiki> --username=user_name_supplied</code>
+<code>svn co <nowiki>http://palea.cgrb.oregonstate.edu:/svn/associations</nowiki> --username=user_name_supplied</code>
 In order to update an ontology do this:

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