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[bioontology-support] BioPortal installation

Mouna Kettani mouna.kettani at gmail.com
Wed Jun 23 07:17:57 PDT 2010


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>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> 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/1018bioportal_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/trunkbioportal_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
>
>


-- 
Mouna
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