Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] BioPortal installation

Paul R Alexander palexander at stanford.edu
Wed Jun 23 10:18:26 PDT 2010


  Mouna,

It sounds like one of the tables didn't get created. Can you update your 
UI code from the SVN repository and then run "rake db:migrate" from the 
root of the Rails project? Just to make sure, can you let me know if 
you're running the trunk or one of the tags (and if so, which one)?

Thanks.

Paul Alexander
Web / UI Developer
NCBO BioPortal


On 6/23/10 7:17 AM, Mouna Kettani wrote:
> Hello Paul,
>
> Yes, both the Core and the UI are on the same machine inside the 
> tomcat folder: /var/lib/tomcat6/webapps/ROOT. when I type 
> http://localhost:8080/bioportal/ontologies in a browser, I get the 
> page in attached snapshot1.
> I changed $REST_URL="http://localhost:8080/bioportal" 
> <http://localhost:8080/bioportal> in /config/bioportal_config.rb file 
> and this time, it is a different error message (snapshot2 attached).
>
> Thank you,
>
> Mouna
>
>
> On Tue, Jun 22, 2010 at 5:32 PM, Paul R Alexander 
> <palexander at stanford.edu <mailto:palexander at stanford.edu>> wrote:
>
>     Mouna,
>
>     It looks like the UI is timing out when trying to connect to the
>     Core. Is the Core on the same machine? Is the address defined
>     properly in the /config/bioportal_config.rb file?
>
>     There should be a line like this in the bioportal_config.rb file
>     that should point to your Core installation:
>     $REST_URL="http://localhost:8080/bioportal"
>     <http://localhost:8080/bioportal>
>
>     The URL it's timing out on is this (assuming you have the Core
>     running on localhost:8080):
>     http://localhost:8080/bioportal/ontologies
>
>     If that doesn't come up in a browser, you have something wrong
>     with the Core installation or it's not running.
>
>     Let me know if you have further questions.
>
>     Paul Alexander
>
>     Web / UI Developer
>     NCBO BioPortal
>
>     On 6/22/10 9:41 AM, Mouna Kettani wrote:
>>     Dear Natasha,
>>
>>     We have finished the steps in the provided Bioportal installation
>>     instructions. However, we have some issues testing the UI. Please
>>     find attached two snapshots of the errors we get when  starting
>>     Ruby web servers and typing http://localhost:3000 in firefox
>>     browser.
>>     Thank you very much for your support.
>>
>>     Best Regards,
>>
>>     Mouna Kettani
>>
>>
>>
>>     On Thu, Jun 3, 2010 at 3:33 PM, Kettani, Mouna <kettanim at ornl.gov
>>     <mailto:kettanim at ornl.gov>> wrote:
>>
>>         Hello Natasha,
>>
>>         Thank you very much for the instructions. I'll let know of
>>         the progress of our team.
>>
>>         Best Regards,
>>
>>         Mouna Kettani
>>         ________________________________________
>>         From: Natasha Noy [noy at stanford.edu <mailto:noy at stanford.edu>]
>>         Sent: Thursday, June 03, 2010 2:29 PM
>>         To: Kettani, Mouna
>>         Cc: Pouchard, Line Catherine
>>         Subject: Re: BioPortal installation
>>
>>         Dear Mouna,
>>
>>         Please find the installation instructions below. Again, let
>>         us know if you run into trouble. These are instructions for
>>         installing BioPortal itself. ONce you have it up and running,
>>         we'll get you the instructions for installing the Annotator
>>         -- we are still cleaning those up a bit.
>>
>>         Best of luck!
>>
>>         Natasha
>>         How to install Bioportal
>>         Contents
>>          [hide<javascript:toggleToc()>]
>>
>>          *   1
>>         Prerequisities<http://www.bioontology.org/wiki-internal/index.php/How_to_install_Bioportal#Prerequisities>
>>          *   2 Install BP
>>         backend<http://www.bioontology.org/wiki-internal/index.php/How_to_install_Bioportal#Install_BP_backend>
>>            *   2.1
>>         Troubleshooting<http://www.bioontology.org/wiki-internal/index.php/How_to_install_Bioportal#Troubleshooting>
>>          *   3 Install BioPortal UI Development
>>         Environment<http://www.bioontology.org/wiki-internal/index.php/How_to_install_Bioportal#Install_BioPortal_UI_Development_Environment>
>>            *   3.1
>>         Troubleshooting<http://www.bioontology.org/wiki-internal/index.php/How_to_install_Bioportal#Troubleshooting_2>
>>          *   4 Install the bioportal admin application
>>         (optional)<http://www.bioontology.org/wiki-internal/index.php/How_to_install_Bioportal#Install_the_bioportal_admin_application_.28optional.29>
>>          *   5 What to do
>>         next<http://www.bioontology.org/wiki-internal/index.php/How_to_install_Bioportal#What_to_do_next>
>>
>>
>>         [edit<http://www.bioontology.org/wiki-internal/index.php?title=How_to_install_Bioportal&action=edit&section=1
>>         <http://www.bioontology.org/wiki-internal/index.php?title=How_to_install_Bioportal&action=edit&section=1>>]Prerequisities
>>
>>          *   Install Sun Java 1.6 or higher (On ubuntu you may need
>>         to make it the default jre: sudo update-alternatives --config
>>         java)
>>            *   Note: Java 1.6 is required as of BioPortal Core 2.4,
>>         released April 28, 2010.
>>
>>          *   Install tomcat
>>            *   On ubuntu, it will run on port 8180 - this will create
>>         problems with the BP UI (which assumes 8080 and 80), solution
>>         in the UI section below
>>               *   The BioPortal core port can now be configured in
>>         the environment.rb file of the Rails app.
>>         --Paul<http://www.bioontology.org/wiki-internal/index.php?title=User:Palexand&action=edit&redlink=1
>>         <http://www.bioontology.org/wiki-internal/index.php?title=User:Palexand&action=edit&redlink=1>>
>>         14:27, 23 October 2009 (PDT)
>>            *   sudo apt-get install tomcat5.5
>>
>>          *   Install MySQL (5.1)
>>            *   sudo apt-get install mysql-server
>>
>>         [edit<http://www.bioontology.org/wiki-internal/index.php?title=How_to_install_Bioportal&action=edit&section=2
>>         <http://www.bioontology.org/wiki-internal/index.php?title=How_to_install_Bioportal&action=edit&section=2>>]Install
>>         BP backend
>>
>>          *   In MySQL, create databases:
>>            *   mysql -u root -p
>>            *   create database bioportal;
>>            *   create database bioportal_protege;
>>            *   create database bioportal_lexgrid;
>>
>>          *   Add user: bioportal_prd/bioportal_prd (change password,
>>         if you want, but make sure you keep it in sync with the
>>         build.properties)
>>            *   create user bioportal_prd identified by 'bioportal_prd'
>>
>>          *   grant all rights to bioportal_prd on the 3 databases
>>            *   grant all on *.* to 'bioportal_prd'@'localhost'
>>
>>          *   on the bioportal database, grant also the SUPER and the
>>         TRIGGER rights
>>            *   grant SUPER, TRIGGER on *.* to 'bioportal_prd'@'localhost'
>>
>>          *   create user ncboadmin; (needed!)
>>            *   create user ncboadmin identified by 'ncboadmin'
>>
>>          *   Checkout bioportal_core sources from SVN:
>>            * https://bmir-gforge.stanford.edu/svn/bioportal_core
>>            *   trunk or some tag (ask Misha) - usually take latest tag
>>            *   svn co
>>         https://bmir-gforge.stanford.edu/svn/bioportal_core/tags/1018
>>         bioportal_core
>>
>>          *   Create some directory on your computer to hold the
>>         bioportal resources, e.g.: /work/tools/bioportal/resources
>>
>>          *   Edit the build.properties from the bioportal_core
>>         folder, especially:
>>
>>         bioportal.resource.path/work/tools/bioportal/resources
>>         appserver.home/usr/share/tomcat5.5
>>         bioportal.jdbc.urljdbc:mysql://localhost:3306/bioportal
>>         bioportal.jdbc.drivercom.mysql.jdbc.Driver
>>         bioportal.jdbc.usernamebioportal_prd
>>         bioportal.jdbc.passwordbioportal_prd
>>
>>         protege.jdbc.urljdbc:mysql://localhost/bioportal
>>         protege.jdbc.drivercom.mysql.jdbc.Driver
>>         protege.jdbc.usernamebioportal_prd
>>         protege.jdbc.passwordbioportal_prd
>>
>>         lexgrid.db.urljdbc:mysql://localhost/bioportal_lexgrid
>>         lexgrid.db.userbioportal_prd
>>         lexgrid.db.passwordbioportal_prd
>>
>>         lexgrid.email.totudorache at stanford.edu
>>         <mailto:lexgrid.email.totudorache at stanford.edu><mailto:lexgrid.email.totudorache at stanford.edu
>>         <mailto:lexgrid.email.totudorache at stanford.edu>>
>>
>>
>>          *   Execute:
>>            *   mysql -u root -p < db/sql/bioportal_db.sql
>>            *   mysql -u root -p < db/sql/bioportal_lookup_data.sql
>>            *   mysql -u root -p <
>>         db/sql/bioportal_metadata_base_inclBPcategories.sql
>>
>>          *   The following is required for Flex app support (Search,
>>         Annotator, etc)
>>            *   cd tomcat5.5/webapps/ROOT/
>>            *   svn export
>>         https://bmir-gforge.stanford.edu/svn/bioportalui/public/crossdomain.xml
>>
>>
>>          *   Make following steps only if you are using tag 1018
>>            *   mysql -u root -p < db/sql/bioportal_db_changes_1017.sql
>>            *   mysql
>>            *   use bioportal;
>>            *   alter table ncbo_usage_log modify request_parameters
>>         varchar(2048);
>>
>>          *   Execute:
>>            *   sudo ant clean deploywar
>>
>>         This should create a war file that is deployed in your tomcat
>>         folder. You might get a permission exception, in which case,
>>         you either run as root, or give your user write access to
>>         tomcat/webapps.
>>
>>          *   Test the backend, by going to a browser and try:
>>            * http://localhost:8180/bioportal/ontologies (your port
>>         might be different)
>>            *   You should get back an empty list of ontologies.
>>
>>         [edit<http://www.bioontology.org/wiki-internal/index.php?title=How_to_install_Bioportal&action=edit&section=3
>>         <http://www.bioontology.org/wiki-internal/index.php?title=How_to_install_Bioportal&action=edit&section=3>>]Troubleshooting
>>
>>          *   If you get in catalina.out a access security exception
>>         (something like could not parse default web.xml), then edit
>>         CATALINA_HOME/conf/policy.d/01system.policy
>>
>>         //Added by Tania to make BP run, not a good idea to grant to
>>         all, all permisson... well, it's a hack
>>         grant {
>>             permission java.security.AllPermission;
>>         };
>>
>>
>>         (I had problems with the file permission in tomcat, so I have
>>         given all write permission to webapps. Not recommended, but
>>         solved many problems. Alex can tell you how to do it right)
>>
>>          *   Always look in the tomcat logs: catalina.out and
>>         bioportal.log
>>
>>         [edit<http://www.bioontology.org/wiki-internal/index.php?title=How_to_install_Bioportal&action=edit&section=4
>>         <http://www.bioontology.org/wiki-internal/index.php?title=How_to_install_Bioportal&action=edit&section=4>>]Install
>>         BioPortal UI Development Environment
>>
>>          *   Install ruby, rubygems, rails:
>>         http://rubyonrails.org/download
>>            *   sudo apt-get install ruby
>>            *   sudo apt-get install rubygems
>>            *   sudo apt-get install rails
>>            *   gem install rails
>>
>>          *   Install MySQL
>>            *   sudo gem install mysql -- --with-mysql-dir/usr/share/mysql
>>               *   if you get error "'require': no such file to load
>>         -- mkmf (LoadError)", you need to install:
>>                  *   sudo apt-get install libmysqlclient15-dev
>>                  *   sudo apt-get install ruby-dev
>>
>>          *   Install memcached
>>            *   sudo apt-get install memcached
>>
>>          *   Install ruby gems
>>            *   gem install rails -v 2.3.5
>>            *   gem install fastthread
>>            *   gem install memcache-client
>>            *   gem install SystemTimer
>>            *   gem install rest-client
>>
>>          *   Install LibXML and related gem
>>            *   sudo apt-get install libxml2 libxml2-dev
>>            *   gem install libxml-ruby
>>
>>          *   Decide whether you want to run bleeding-edge code or a
>>         particular tag (running the latest tag from the BioPoral UI
>>         and the BioPortal Core is a good method for getting a stable
>>         system)
>>            *   To get the most recent production-ready tag, look in
>>         the tag folder in the code repository, find the highest tag
>>         number, then issue the following command:

>>               *   svn checkout
>>         https://bmir-gforge.stanford.edu/svn/bioportalui/tag/tag_number
>>            *   To get the most recent, bleeding-edge source code, you
>>         must issue the following command:
>>               *   svn checkout
>>         https://bmir-gforge.stanford.edu/svn/bioportalui/trunk
>>
>>          *   Go to the checked out code and edit config/database.yml
>>         and edit the database connection for "development". E.g.:
>>
>>         development:
>>          adapter: mysql
>>          encoding: utf8
>>          database: BioPortalGui_development
>>          username: bioportal_prd
>>          password: bioportal_prd
>>          host: localhost
>>
>>
>>          *   In MySql give all permission on BioPortalGui_development
>>         to the bioportal user that you have set up in the backend
>>         (e.g., bioportal_prd)
>>
>>          *   Run the database rake task from the root of the
>>         BioPortal UI directory:
>>            *   rake db:migrate
>>
>>          *   Modify config/environments/production.rb file to point
>>         to the correct location of your memcache server
>>
>>          *   Rename /config/environment.rb.sample to
>>         /config/environment.rb and modify the following:
>>            *   Point to the correct SMTP server
>>            *   Point to the proper BioPortal Core and Open Biomedical
>>         Services Resource Index rest URLs (no trailing slashes)
>>            *   Provide the port number of your BioPortal Core Tomcat
>>         installation
>>            *   Enable and configure reCAPTCHA if desired
>>            *   If tomcat runs on a different port (e.g., 8180), like
>>         in ubuntu, change the $REST_PORT setting in config/environment.rb
>>
>>          *   Start the webserver
>>            *   Webrick or Mongrel are Ruby-based webservers, which
>>         can be started from the BioPortal UI directory:
>>               *   ruby script/server
>>               *   Webrick and Mongrel default to port 3000
>>            *   Alternatively, you can use Phusion Passenger (aka
>>         mod_rails, mod_rack). This is recommended for production
>>         environments. More information:
>>         http://www.modrails.com<http://www.modrails.com/>
>>
>>          *   UI should be up now. Make sure backend in Tomcat is
>>         running. To test UI go to:
>>            * http://localhost:3000/
>>            *   You should see BioPortal start page
>>
>>          *   If search is not working, make the
>>         tomcat/logs/bioportal.log writable to everybody
>>
>>         [edit<http://www.bioontology.org/wiki-internal/index.php?title=How_to_install_Bioportal&action=edit&section=5
>>         <http://www.bioontology.org/wiki-internal/index.php?title=How_to_install_Bioportal&action=edit&section=5>>]Troubleshooting
>>         If something goes wrong, then look in:
>>
>>          *   Webrick console
>>          *   Tomcat logs: catalina.out and bioportal.log
>>
>>         [edit<http://www.bioontology.org/wiki-internal/index.php?title=How_to_install_Bioportal&action=edit&section=6
>>         <http://www.bioontology.org/wiki-internal/index.php?title=How_to_install_Bioportal&action=edit&section=6>>]Install
>>         the bioportal admin application (optional)
>>
>>          *   This is optional, and only if you want to do things
>>         directly on the backend (e.g. start parsing, indexing,
>>         deleting ontologies, etc.)
>>
>>          *   Checkout the bioportal admin from SVN
>>
>>         svn co
>>         https://bmir-gforge.stanford.edu/svn/bioportal_admin/trunk
>>         bioportal_admin
>>         cd bioportal_admin
>>
>>          *   make a copy of the build.properties.sample and rename it
>>         to build.properties
>>
>>          *   edit the build.properties (entries similar to the ones
>>         in build.properties for bioportal_core, see above)
>>          *   you'll have to edit bioportal.admin.encryption.key . See
>>         comments for valid values
>>
>>          *   run the build:
>>
>>         ant clean deplywar
>>
>>          *   try it out on:
>>
>>         http://localhost:8180/bioportal_admin (your port might be
>>         different)
>>
>>         [edit<http://www.bioontology.org/wiki-internal/index.php?title=How_to_install_Bioportal&action=edit&section=7
>>         <http://www.bioontology.org/wiki-internal/index.php?title=How_to_install_Bioportal&action=edit&section=7>>]What
>>         to do next
>>
>>          *   Go get a coffee; if you succeeded, then you deserve it :)
>>
>>          *   Create a user from the Bioportal UI
>>
>>          *   Try to upload a small ontology
>>
>>          *   If you want to use the bioportal_admin, you will have to
>>         give your user admin privileges. You can do this, by first
>>         looking into the
>>
>>         bioportal databse, ncbo.l.role table, what is the id for
>>         ROLE_ADMINISTRATOR (e.g., 2824). Then, look in the ncbo_user
>>         table for your user (firstname and lastname col), and write
>>         down the user id from the id column (e.g. 38312). Then go to
>>         ncbo_user_role table and edit the row that contains your user
>>         id in the user_id column, and put in the role_id column the
>>         administrator role id. E.g. (user_id:38312,role_id:2824).
>>         Restart the backend and try to log into the bioportal_admin
>>
>>
>>
>>
>>     -- 
>>     Mouna
>
>
>
>
> -- 
> Mouna
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20100623/cbdf1361/attachment.html>


More information about the bioontology-support mailing list