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[bioontology-support] BioPortal installation

Mouna Kettani mouna.kettani at gmail.com
Wed Jun 23 13:16:04 PDT 2010


Paul,

The search is still not working after these changes and I get the error
message: "The rest services did not return successfully". Please find
attached bioportal_config.rb.
The crossdomain.xml file is in the ROOT folder of the my Tomcat webapps
directory.

Regards,

Mouna

On Wed, Jun 23, 2010 at 2:48 PM, Paul R Alexander
<palexander at stanford.edu>wrote:

>  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)*
>    - cd tomcat5.5/webapps/ROOT/
>       - 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
> > 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
>
>


-- 
Mouna
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