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[bioontology-support] BioPortal installation

Paul R Alexander palexander at stanford.edu
Wed Jun 23 11:03:07 PDT 2010


  Mouna,

Ok, go ahead and take my recommended actions and let me know if you run 
into problems.

Paul

On 6/23/10 10:57 AM, Mouna Kettani wrote:
> Paul,
>
> To answer your question, I am running tag 1039 of BioportalUI from the 
> ROOT of my tomcat folder. Regards,
>
> Mouna
>
> On Wed, Jun 23, 2010 at 1:18 PM, Paul R Alexander 
> <palexander at stanford.edu <mailto:palexander at stanford.edu>> wrote:
>
>     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
>
>
>
>
> -- 
> Mouna
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