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[bioontology-support] BioPortal installation

Natasha Noy noy at stanford.edu
Wed Jun 9 11:57:08 PDT 2010


Hi Mouna,

You can go to https://bmir-gforge.stanford.edu/gf/ to create a new  
account.

Natasha


On Jun 9, 2010, at 11:48 AM, Mouna Kettani wrote:

> Dear Natasha,
>
> We have installed java 1.6, tomcat 6 and Mysql-server successfully.  
> We have created the required databases and users with the access  
> rights. However, we have an issue checking bioportal core sources  
> from SVN and editing build.properties. The provided websites require  
> a login:
> 1. https://bmir-gforge.stanford.edu/svn/bioportal_core
> 2. https://bmir-gforge.stanford.edu/svn/bioportal_core/tags/1018
> 3. https://bmir-gforge.stanford.edu/svn/bioportalui/public/crossdomain.xml
>
> Thank you for letting us know,
>
> Best Regards,
>
> Mouna Kettani
>
>
> On Thu, Jun 3, 2010 at 3:33 PM, Kettani, Mouna <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]
> 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 
> >]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 
> > 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 
> >]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 
> >
>
>
>  *   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 
> >]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 
> >]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 
> >]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 
> >]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 
> >]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




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