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[bioontology-support] BioPortal installation

Paul R Alexander palexander at stanford.edu
Wed Jun 23 11:48:12 PDT 2010


  Mouna,

Please check all of the config options in the bioportal_config.rb file 
and point them to the proper location. I think the one you want to fix 
the problem you are having is:
$REST_DOMAIN = "localhost:8080"

Also, you'll need to make sure you completed the step to put the 
crossdomain.xml file in the ROOT folder of the Tomcat webapps directory:

    * *The following is required for Flex app support (Search,
      Annotator, etc)*
          o |cd tomcat5.5/webapps/ROOT/|
          o |svn export
            https://bmir-gforge.stanford.edu/svn/bioportalui/trunk/public/crossdomain.xml|



Paul


On 6/23/10 11:29 AM, Mouna Kettani wrote:
> Paul,
>
> The UI worked now! Thank you very much! but some links don't. When I 
> search for a term, I get the attached error. I checked 
> tomcat6/logs/bioportal.log and it is writable to everybody.
>
> Regards,
>
>
> On Wed, Jun 23, 2010 at 2:03 PM, Paul R Alexander 
> <palexander at stanford.edu <mailto:palexander at stanford.edu>> wrote:
>
>     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
>
>
>
>
> -- 
> Mouna
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