imported>KennethBaclawski: Fix PurpleMediaWiki references

2016-01-09T07:44:58Z

Fix PurpleMediaWiki references

New page

This page describes installation and customization details to the [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance NCBO Virtual Appliance] to create an OOR instance.

== Download ==

Download the OVF image for the [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance NCBO Virtual Appliance]. The URL is not public.

The current version (used in examples below) is ncbo-appliance-0.3.ova.

== VM Conversion ==

The OVF image needs to be converted for the desired VM environment.

=== VMware ===

The image requires a 64-bit host with enabled support for Intel Virtualization Technology (VT).

To convert the OVF image for execution under VMware:

# Download [http://www.vmware.com/resources/techresources/1013 VMware OVF Tool] from http://www.vmware.com/support/developer/ovf/.
# Run ovftool ncbo-appliance-0.3.ova .
# Execute the resulting ncbo-appliance-0.3/ncbo-appliance-0.3.vmx file under VMware, by double-clicking the file icon or opening it within VMware.
# Click through the initial Linux text screen setup questions.

=== Xen ===

* at CIM3 we use para-virtualized guests (and therefore, would prefer vm images for that over fully-virtualized guests.) --ShinyaYamada/2011.10.31

To convert the OVF image for execution under Xen:

# Download <nowiki>XenConvert</nowiki> from http://www.citrix.com/english/ss/downloads/details.asp?downloadId=2306318.
# Run <nowiki>XenConvert</nowiki> under Windows. This requires access to a running <nowiki>XenServer</nowiki>.

This hasn't yet been successfully accomplished.

=== KVM ===

... ''(coming!)''

== Basic Customization: from [[BioPortal]] (ncbo-appliance) to an [[OOR]] instance ==

=== Banner, Logo, etc. ===

# Login to the running image.
# Edit /var/rails/<nowiki>BioPortal</nowiki>/current/config/bioportal_config.rb, changing at least
** ORG (e.g. to SOCoP)
** SITE (e.g. to OOR)
** ORG_URL (e.g. to http://socop.org).
# Replace the <nowiki>BioPortal</nowiki> logo with the OOR logo.
** public/maintenance/nav_logo.jpg (126x43) Medium logo using the color gradient
** public/maintenance/logo_background.jpg (1x43) The color gradient
** public/images/ncbo_logo_portal.gif (463x157) Large logo
** public/images/logo.png (463x157) Large logo copy
** public/images/layout/logo_mini.png (85x20) Small logo using the color gradient
** public/images/layout/nav_logo.png (126x43) Medium logo copy
# Replace the <nowiki>BioPortal</nowiki> IPR policy with the OOR or instance policy.
** The IPR license is at license.txt
# "Send Feedback" form should be mailed to <support [at] oor.net>
** which currently gets forwarded to: [[TejasParikh|Tejas Parikh]], [[User:KennethBaclawski|Ken Baclawski]], [[MikeDean|Mike Dean]], [[PeterYim|Peter P. Yim]] and <oor-users [at] ontolog.cim3.net> (i.e. the [oor-dev] mailing list) --PeterYim/2011.10.14
** admin contact is now routed to <tejas [at] cim3.com> --tejas/2011.12.11
# Run ncborestart.

=== Enable Google Analytics ===

* Enter the appropriate ID below as $ANALYTICS_ID in bioportal_config.rb
* OOR-instance / Web Property ID
** sandbox.oor.net / UA-7295028-10
** dev.oor.net / UA-7295028-11
** socop.oor.net / UA-7295028-12

=== Ontology Categories ===

# Add OOR categories below per the instructions at http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_do_I_add_or_change_categories.3F.
## You may need to download the <nowiki>[[MySQL]]</nowiki> JDBC driver and copy it to the Protege directory as driver.jar per http://protegewiki.stanford.edu/wiki/Working_with_the_Database_Backend_in_OWL#Before_you_start
## Use jdbc:mysql://localhost/bioportal_protege and run, e.g., ssh oor-03.cim3.net -L 3306:localhost:3306
# Run ncborestart.
# Verify the updated categories by opening the Browse panel and clicking the Filter by Category menu

* Category list (based on MikeDean's original list): ([http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_08_05#nid2W6B updated 2011.08.05])
## Upper Ontologies
## Standards (for example, W3C, ISO, OMG, Measurement)
## Science (for example, Biomedical)
## Financial
## Government
## Cultural
## Social Networking (for example, People, Organizations)
## Geospatial
## Commercial
## Literature
## Technology
## Provenance
## Defense
## Metadata (for example, OMV, Dublin Core)
## Process (for example, PSL)
## Other

=== Support / Syndication / Social Network ===

* The twitter and facebook buttons can easily be removed by commenting out the div element with id "social_networking" in .../<nowiki>BioPortal</nowiki>/current/app/views/home/index.rhtml (on lines 154 to 157). If you want to enable them, then you must define home.facebook_button and home.twitter_button.
* As mentioned in [[OOR_SandBox_Customization|above]]: feedback and support goes to <support [at] oor.net>
* The RSS feed citation can be removed from .../<nowiki>BioPortal</nowiki>/current/config/locales/en.rb

=== Home Page Statistics ===

# Edit /srv/ncbo/rails/<nowiki>BioPortal</nowiki>/current/config/locales/en.rb to set :stats => ''.
# Manually edit :most_viewed in the same file, if desired for Most Viewed Ontologies.

=== reCaptcha ===

* This is important for preventing wikispam.
* If you do not have a google account then signup for one.
* Go to http://www.google.com/recaptcha.
* Click on "My Account" and then "Add a new site".
* Enter the domain or IP address of the server (e.g., oor-03.cim3.net).
* Note that you need a different pair of keys for each domain.
* Copy the public and private keys to /srv/ncbo/rails/<nowiki>BioPortal</nowiki>/current/config/bioportal_config.rb as follows (except for replacing the keys):
** ENV['USE_RECAPTCHA'] = 'true'
** ENV['RECAPTCHA_PUBLIC_KEY'] = '6Ld9UM0SAAAAAG9kx-VF6rPb_Be-gHO21[[DnlH2jN]]'
** ENV['RECAPTCHA_PRIVATE_KEY'] = '6Ld9UM0SAAAAADgdc3sw8O_-hEQa-Vab-I9cDov4'
* Restart the services with "sudo ncborestart".

=== Other Updates ===

* All updates in this section are relative to .../<nowiki>BioPortal</nowiki>/current
* app/views/home/all_resources.html.erb Change "Search biomedical resources" to "Search resources"
* app/views/home/help.html.erb Change "How to Cite <<nowiki>BioPortal</nowiki>" to "How to Cite OOR", and then change the citation just below this.
* app/views/home/index.rhtml This is the home page, so make changes as needed. One such change is mentioned [[OOR_SandBox_Customization|above]].

[[Category:WorkSpace]] [[Category:OOR]]

OOR SandBox Customization - Revision history

imported>KennethBaclawski: Fix PurpleMediaWiki references