doc/Bioportal_UI_Deployment.rtf
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{\info
{\title Deploying BioPortal Ruby On Rails GUI}
{\author Dorf, Michael}
{\*\company }}\margl1440\margr1440\vieww19380\viewh18920\viewkind1\viewscale150
\deftab720
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\f0\b\fs32 \cf0 Deploying BioPortal Ruby On Rails UI\
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\i\fs28 \cf0 Table of Contents\
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{\field{\*\fldinst{HYPERLINK "%5Cl%20%22_Toc207622116%22"}}{\fldrslt
\f1\i0\b0\fs22 \cf2 \ul \ulc2 System Requirements\cf0 \ulnone 2}}
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{\field{\*\fldinst{HYPERLINK "%5Cl%20%22_Toc207622117%22"}}{\fldrslt \cf2 \ul \ulc2 Source Structure\cf0 \ulnone 2}}\
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{\field{\*\fldinst{HYPERLINK "%5Cl%20%22_Toc207622118%22"}}{\fldrslt \cf2 \ul \ulc2 Installation and Configuration\cf0 \ulnone 3}}\
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{\field{\*\fldinst{HYPERLINK "%5Cl%20%22_Toc207622119%22"}}{\fldrslt \cf2 \ul \ulc2 Deploy BioPortal Ruby on Rails UI\cf0 \ulnone 4}}\
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\f0\i\b\fs28 \cf0 System Requirements\
\pard\pardeftab720\li720\fi-360\ri0\sl276\slmult1\sa200
\ls1\ilvl0
\f1\i0\b0\fs22 \cf0 1. Ruby Programming Language (1.8.5 or greater) -- Ruby Enterprise Edition recommended\
2. RubyGems\
3. Memcache \
4. Libxml2\
5. Apache With Phusion Passenger (aka mod_rails, mod_rack)\
6. MySQL 5.0 Database Server\
\pard\pardeftab720\ri0\sl276\slmult1\sb240\sa60
\f0\i\b\fs28 \cf0 Source Structure\
\itap1\trowd \taflags1 \trgaph108\trleft-108 \trbrdrt\brdrs\brdrw10\brdrcf0 \trbrdrl\brdrs\brdrw10\brdrcf0 \trbrdrr\brdrs\brdrw10\brdrcf0
\clvertalc \clshdrawnil \clwWidth4645\clftsWidth3 \clbrdrt\brdrs\brdrw10\brdrcf0 \clbrdrl\brdrs\brdrw10\brdrcf0 \clbrdrb\brdrs\brdrw10\brdrcf0 \clbrdrr\brdrs\brdrw10\brdrcf0 \clpadl100 \clpadr100 \gaph\cellx4320
\clvertalc \clshdrawnil \clwWidth4571\clftsWidth3 \clbrdrt\brdrs\brdrw10\brdrcf0 \clbrdrl\brdrs\brdrw10\brdrcf0 \clbrdrb\brdrs\brdrw10\brdrcf0 \clbrdrr\brdrs\brdrw10\brdrcf0 \clpadl100 \clpadr100 \gaph\cellx8640
\pard\intbl\itap1\pardeftab720\ri0\sl276\slmult1\sa200
\f1\i0\b0\fs22 \cf0 /config/database.yml\cell
\pard\intbl\itap1\pardeftab720\ri0\sl276\slmult1\sa200
\cf0 File that contains database connection properties.\cell \row
\itap1\trowd \taflags1 \trgaph108\trleft-108 \trbrdrl\brdrs\brdrw10\brdrcf0 \trbrdrr\brdrs\brdrw10\brdrcf0
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\clvertalc \clshdrawnil \clwWidth4571\clftsWidth3 \clbrdrt\brdrs\brdrw10\brdrcf0 \clbrdrl\brdrs\brdrw10\brdrcf0 \clbrdrb\brdrs\brdrw10\brdrcf0 \clbrdrr\brdrs\brdrw10\brdrcf0 \clpadl100 \clpadr100 \gaph\cellx8640
\pard\intbl\itap1\pardeftab720\ri0\sl276\slmult1\sa200
\cf0 /config/bioportal_config.rb.sample\cell
\pard\intbl\itap1\pardeftab720\ri0\sl276\slmult1\sa200\ql\qnatural
\cf0 File containing environment variables such as mail server location, REST service location, and other BioPortal-specific options. Remove \'91.sample\'92 and customize.\cell \row
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\clvertalc \clshdrawnil \clwWidth4571\clftsWidth3 \clbrdrt\brdrs\brdrw10\brdrcf0 \clbrdrl\brdrs\brdrw10\brdrcf0 \clbrdrb\brdrs\brdrw10\brdrcf0 \clbrdrr\brdrs\brdrw10\brdrcf0 \clpadl100 \clpadr100 \gaph\cellx8640
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\cf0 /config/environment.rb\cell
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\cf0 Rails-specific environment settings.\cell \row
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\clvertalc \clshdrawnil \clwWidth4571\clftsWidth3 \clbrdrt\brdrs\brdrw10\brdrcf0 \clbrdrl\brdrs\brdrw10\brdrcf0 \clbrdrb\brdrs\brdrw10\brdrcf0 \clbrdrr\brdrs\brdrw10\brdrcf0 \clpadl100 \clpadr100 \gaph\cellx8640
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\cf0 /config/environments/production.rb,\
/config/environments/development.rb\cell
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\cf0 Files that contain environment variables that are specific to a environment (e.g. memcache settings)\cell \row
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\clvertalc \clshdrawnil \clwWidth4571\clftsWidth3 \clbrdrt\brdrs\brdrw10\brdrcf0 \clbrdrl\brdrs\brdrw10\brdrcf0 \clbrdrb\brdrs\brdrw10\brdrcf0 \clbrdrr\brdrs\brdrw10\brdrcf0 \clpadl100 \clpadr100 \gaph\cellx8640
\pard\intbl\itap1\pardeftab720\ri0\sl276\slmult1\sa200
\cf0 /app\cell
\pard\intbl\itap1\pardeftab720\ri0\sl276\slmult1\sa200
\cf0 The folder containing all the core logic to the ruby on rails application\cell \row
\itap1\trowd \taflags1 \trgaph108\trleft-108 \trbrdrl\brdrs\brdrw10\brdrcf0 \trbrdrr\brdrs\brdrw10\brdrcf0
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\clvertalc \clshdrawnil \clwWidth4571\clftsWidth3 \clbrdrt\brdrs\brdrw10\brdrcf0 \clbrdrl\brdrs\brdrw10\brdrcf0 \clbrdrb\brdrs\brdrw10\brdrcf0 \clbrdrr\brdrs\brdrw10\brdrcf0 \clpadl100 \clpadr100 \gaph\cellx8640
\pard\intbl\itap1\pardeftab720\ri0\sl276\slmult1\sa200
\cf0 /db\cell
\pard\intbl\itap1\pardeftab720\ri0\sl276\slmult1\sa200
\cf0 The folder containing database migrations\cell \row
\itap1\trowd \taflags1 \trgaph108\trleft-108 \trbrdrl\brdrs\brdrw10\brdrcf0 \trbrdrr\brdrs\brdrw10\brdrcf0
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\clvertalc \clshdrawnil \clwWidth4571\clftsWidth3 \clbrdrt\brdrs\brdrw10\brdrcf0 \clbrdrl\brdrs\brdrw10\brdrcf0 \clbrdrb\brdrs\brdrw10\brdrcf0 \clbrdrr\brdrs\brdrw10\brdrcf0 \clpadl100 \clpadr100 \gaph\cellx8640
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\cf0 /lib\cell
\pard\intbl\itap1\pardeftab720\ri0\sl276\slmult1\sa200
\cf0 The folder containing libraries used for talking to services\cell \row
\itap1\trowd \taflags1 \trgaph108\trleft-108 \trbrdrl\brdrs\brdrw10\brdrcf0 \trbrdrr\brdrs\brdrw10\brdrcf0
\clvertalc \clshdrawnil \clwWidth4645\clftsWidth3 \clbrdrt\brdrs\brdrw10\brdrcf0 \clbrdrl\brdrs\brdrw10\brdrcf0 \clbrdrb\brdrs\brdrw10\brdrcf0 \clbrdrr\brdrs\brdrw10\brdrcf0 \clpadl100 \clpadr100 \gaph\cellx4320
\clvertalc \clshdrawnil \clwWidth4571\clftsWidth3 \clbrdrt\brdrs\brdrw10\brdrcf0 \clbrdrl\brdrs\brdrw10\brdrcf0 \clbrdrb\brdrs\brdrw10\brdrcf0 \clbrdrr\brdrs\brdrw10\brdrcf0 \clpadl100 \clpadr100 \gaph\cellx8640
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\cf0 /public\cell
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\cf0 The folder containing public files such as stylesheets and images\cell \row
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\clvertalc \clshdrawnil \clwWidth4645\clftsWidth3 \clbrdrt\brdrs\brdrw10\brdrcf0 \clbrdrl\brdrs\brdrw10\brdrcf0 \clbrdrb\brdrs\brdrw10\brdrcf0 \clbrdrr\brdrs\brdrw10\brdrcf0 \clpadl100 \clpadr100 \gaph\cellx4320
\clvertalc \clshdrawnil \clwWidth4571\clftsWidth3 \clbrdrt\brdrs\brdrw10\brdrcf0 \clbrdrl\brdrs\brdrw10\brdrcf0 \clbrdrb\brdrs\brdrw10\brdrcf0 \clbrdrr\brdrs\brdrw10\brdrcf0 \clpadl100 \clpadr100 \gaph\cellx8640
\pard\intbl\itap1\pardeftab720\ri0\sl276\slmult1\sa200
\cf0 /vendor\cell
\pard\intbl\itap1\pardeftab720\ri0\sl276\slmult1\sa200
\cf0 The folder containing ruby plugins\cell \lastrow\row
\pard\pardeftab720\li360\ri0\sl276\slmult1\sa200
\cf0 \
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\f0\i\b\fs28 \cf0 \page Obtaining Source Code\
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\f1\i0\b0\fs22 \cf0 To get the most recent source code, you must issue the following command:
\f2 \uc0\u8232
\f1 svn checkout https://bmir-gforge.stanford.edu/svn/bioportalui/trunk\
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:
\f2 \uc0\u8232
\f1 svn checkout https://bmir-gforge.stanford.edu/svn/bioportalui/tag/
\i tag_number\
\i0 To get the entire code repository, including all tags, branches, and the trunk, run the following:
\f2 \uc0\u8232
\f1 svn checkout https://bmir-gforge.stanford.edu/svn/bioportalui\
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\f0\i\b\fs28 \cf0 Installation and Configuration\
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\ls2\ilvl0
\f1\i0\b0\fs22 \cf0 1. Install the Ruby Core Library (version 1.8.5 or higher)\
2. Install libxml2 and libxml2-dev (Linux packages: http://xmlsoft.org)\
3. Install Ruby Gems:\
\pard\pardeftab720\li1440\fi-360\ri0\sl276\slmult1\sa200
\ls2\ilvl1\cf0 actionmailer (2.3.5)\
actionpack (2.3.5)\
activerecord (2.3.5)\
activeresource (2.3.5)\
activesupport (2.3.5)\
fastthread (1.0.7)\
libxml-ruby (1.1.3)\
memcache-client (1.7.8)\
mime-types (1.16)\
mysql (2.8.1)\
passenger (2.2.9)\
rack (1.0.1)\
rails (2.3.5)\
rake (0.8.7)\
rest-client (1.3.0)\
SystemTimer (1.1.3)\
xray (1.1)\
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\ls2\ilvl1\cf0 5. Install Apache web server\
5. Install Memcache\
6. Install and configure MySQL 5 database. \
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\ls2\ilvl1\cf0 A. Create a database to contain metadata\
B. Point the config/database.yml file to the newly created database.\
C. Run the following command in the main ruby code directory: rake db:migrate\
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\f0\i\b\fs28 \cf0 Deploy BioPortal UI\
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\ls3\ilvl1
\f1\i0\b0\fs22 \cf0 1. Configure Phusion Passenger to run from the appropriate directory with your desired settings.\
2. Modify the /config/environments/production.rb file to point to the correct location of your memcache server.\
3. Modify the /config/database.yml file to contain the proper connection settings for your MySQL installation.\
4. Rename /config/bioportal_config.rb.sample to /config/bioportal_config.rb and modify the options as described.\
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\f0\i\b\fs28 \cf0 Accessing BioPortal UI\
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\ls4\ilvl1
\f1\i0\b0\fs22 \cf0 1. Start Apache.\
2. Logs are generated in /log/
\i environment_name
\i0 .log where
\i environment_name
\i0 matches production, development, test, etc. from the /config/environments directory. Note:
\i this is most likely production
\i0 .\
}