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[bioontology-support] BioPortal installation

Mouna Kettani mouna.kettani at gmail.com
Wed Jun 23 10:57:51 PDT 2010


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>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
> > 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
>
>


-- 
Mouna
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