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[bioontology-support] BioPortal installation

Paul R Alexander palexander at stanford.edu
Wed Jun 9 11:56:55 PDT 2010


  Mouna,

Are you receiving this error when you actually try to check out the code 
with the following command?
svn checkout https://bmir-gforge.stanford.edu/svn/bioportal_core

The direct https link won't get you anything, even with an account. 
Also, you should probably just check out the most recent tag (1026), so 
that command would be:
svn checkout https://bmir-gforge.stanford.edu/svn/bioportal_core/tags/1026

If you need to see a browser representation of the code, you can go to:
https://bmir-gforge.stanford.edu/gf/project/bioportal_core/scmsvn/

Paul R Alexander
Web / UI Developer
NCBO BioPortal

On 6/9/10 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 
> <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
>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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