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[bioontology-support] BioPortal installation

Mouna Kettani mouna.kettani at gmail.com
Wed Jun 23 11:29:35 PDT 2010


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>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
> > 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
>
>


-- 
Mouna
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