OOR SandBox Customization

This page describes installation and customization details to the NCBO Virtual Appliance to create an OOR instance.    (2X2W)

Download    (2X2X)

Download the OVF image for the NCBO Virtual Appliance. The URL is not public.    (2X2Y)

The current version (used in examples below) is ncbo-appliance-0.3.ova.    (2X2Z)

VM Conversion    (2X30)

The OVF image needs to be converted for the desired VM environment.    (2X31)

VMware    (2X32)

The image requires a 64-bit host with enabled support for Intel Virtualization Technology (VT).    (2XD5)

To convert the OVF image for execution under VMware:    (2X33)

1. Download VMware OVF Tool from http://www.vmware.com/support/developer/ovf/.    (2X34)
2. Run ovftool ncbo-appliance-0.3.ova .    (2X35)
3. 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.    (2X36)
4. Click through the initial Linux text screen setup questions.    (2X3S)

Xen    (2X37)

• at CIM3 we use para-virtualized guests (and therefore, would prefer vm images for that over fully-virtualized guests.) --ShinyaYamada/2011.10.31    (2YD0)

To convert the OVF image for execution under Xen:    (2X38)

1. Download XenConvert from http://www.citrix.com/english/ss/downloads/details.asp?downloadId=2306318.    (2X39)
2. Run XenConvert under Windows. This requires access to a running XenServer.    (2X3A)

This hasn't yet been successfully accomplished.    (2X3B)

KVM    (34AO)

... (coming!)    (34AP)

Basic Customization: from BioPortal (ncbo-appliance) to an OOR instance    (30R7)

Banner, Logo, etc.    (2X3C)

1. Login to the running image.    (2X3D)
2. Edit /var/rails/BioPortal/current/config/bioportal_config.rb, changing at least    (2X3M)
   • ORG (e.g. to SOCoP)    (2X3N)
   • SITE (e.g. to OOR)    (2X3O)
   • ORG_URL (e.g. to http://socop.org).    (2X3E)
3. Replace the BioPortal logo with the OOR logo.    (2X3F)
   • public/maintenance/nav_logo.jpg (126x43) Medium logo using the color gradient    (2XCX)
   • public/maintenance/logo_background.jpg (1x43) The color gradient    (2XCY)
   • public/images/ncbo_logo_portal.gif (463x157) Large logo    (2XCZ)
   • public/images/logo.png (463x157) Large logo copy    (2XD0)
   • public/images/layout/logo_mini.png (85x20) Small logo using the color gradient    (2XD1)
   • public/images/layout/nav_logo.png (126x43) Medium logo copy    (2XD2)
4. Replace the BioPortal IPR policy with the OOR or instance policy.    (2X3G)
   • The IPR license is at license.txt    (2XD3)
5. "Send Feedback" form should be mailed to <support [at] oor.net>    (2YD1)
   • which currently gets forwarded to: TejasParikh, KenBaclawski, MikeDean, PeterYim and <oor-users [at] ontolog.cim3.net> (i.e. the [oor-dev] mailing list) --PeterYim/2011.10.14    (2YD2)
   • admin contact is now routed to <tejas [at] cim3.com> --tejas/2011.12.11    (30RY)
6. Run ncborestart.    (2X3H)

Enable Google Analytics    (30RB)

• Enter the appropriate ID below as $ANALYTICS_ID in bioportal_config.rb    (317K)
• OOR-instance / Web Property ID    (30RC)
  • sandbox.oor.net / UA-7295028-10    (30RD)
  • dev.oor.net / UA-7295028-11    (30RE)
  • socop.oor.net / UA-7295028-12    (30RF)

Ontology Categories    (2X3P)

1. 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.    (2X3Q)
   1. You may need to download the MySQL 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    (317H)
   2. Use jdbc:mysql://localhost/bioportal_protege and run, e.g., ssh oor-03.cim3.net -L 3306:localhost:3306    (317I)
2. Run ncborestart.    (2X3R)
3. Verify the updated categories by opening the Browse panel and clicking the Filter by Category menu    (317J)

• Category list (based on MikeDean's original list): (updated 2011.08.05)    (30RG)
  1. Upper Ontologies    (30RH)
  2. Standards (for example, W3C, ISO, OMG, Measurement)    (30RI)
  3. Science (for example, Biomedical)    (30RJ)
  4. Financial    (30RK)
  5. Government    (30RL)
  6. Cultural    (30RM)
  7. Social Networking (for example, People, Organizations)    (30XJ)
  8. Geospatial    (30RN)
  9. Commercial    (30RO)
  10. Literature    (30RP)
  11. Technology    (30RQ)
  12. Provenance    (30RR)
  13. Defense    (30RS)
  14. Metadata (for example, OMV, Dublin Core)    (30RT)
  15. Process (for example, PSL)    (30RU)
  16. Other    (30RV)

Support / Syndication / Social Network    (30RW)

• The twitter and facebook buttons can easily be removed by commenting out the div element with id "social_networking" in .../BioPortal/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.    (3406)
• As mentioned in above: feedback and support goes to <support [at] oor.net>    (30RX)
• The RSS feed citation can be removed from .../BioPortal/current/config/locales/en.rb    (30S0)

Home Page Statistics    (32O9)

1. Edit /srv/ncbo/rails/BioPortal/current/config/locales/en.rb to set :stats => ''.    (32OA)
2. Manually edit :most_viewed in the same file, if desired for Most Viewed Ontologies.    (32OB)

reCaptcha    (34KM)

• This is important for preventing wikispam.    (34KN)
• If you do not have a google account then signup for one.    (34KO)
• Go to http://www.google.com/recaptcha.    (34KP)
• Click on "My Account" and then "Add a new site".    (34KQ)
• Enter the domain or IP address of the server (e.g., oor-03.cim3.net).    (34KR)
• Note that you need a different pair of keys for each domain.    (34KS)
• Copy the public and private keys to /srv/ncbo/rails/BioPortal/current/config/bioportal_config.rb as follows (except for replacing the keys):    (34KT)
  • ENV['USE_RECAPTCHA'] = 'true'    (34KU)
  • ENV['RECAPTCHA_PUBLIC_KEY'] = '6Ld9UM0SAAAAAG9kx-VF6rPb_Be-gHO21DnlH2jN'    (34KV)
  • ENV['RECAPTCHA_PRIVATE_KEY'] = '6Ld9UM0SAAAAADgdc3sw8O_-hEQa-Vab-I9cDov4'    (34KW)
• Restart the services with "sudo ncborestart".    (34KX)

Other Updates    (3407)

• All updates in this section are relative to .../BioPortal/current    (3408)
• app/views/home/all_resources.html.erb Change "Search biomedical resources" to "Search resources"    (3409)
• app/views/home/help.html.erb Change "How to Cite <BioPortal" to "How to Cite OOR", and then change the citation just below this.    (340A)
• app/views/home/index.rhtml This is the home page, so make changes as needed. One such change is mentioned above.    (340B)