Make sure we are running the right version of Ruby
$ eselect ruby show Current Ruby version: ruby19 Current Rubygems version: gem19
Check also postgresql version
$ eselect postgresql show 8.4 $ rc-status Runlevel: default postgresql-8.4
Launching oddbd
$ cd /var/www/oddb.org $ bin/oddbd
Several errors of the following type, which can be ignored for the time being
ERROR: relation "object" already exists
The error that needs to be fixed now is
process: Oddb (OddbApp)
init system
/home/alex/.gem/ruby/1.9.1/gems/odba-1.0.8/lib/odba/marshal.rb:15:in `load': undefined class/module CSV::Cell (ArgumentError)
This error will need to be solved by applying the patch
http://dev.ywesee.com/uploads/att/csv.rb.patch.20111123.txt
Save it to my home folder
$ sudo updatedb Password: $ locate csv.rb /home/alex/csv.rb.patch.20111123.txt /usr/lib64/ruby/1.8/csv.rb /usr/lib64/ruby/1.9.1/csv.rb /var/www/oddb.org/src/state/companies/fipi_csv.rb /var/www/oddb.org/src/view/companies/fipi_csv.rb /var/www/oddb.org/test/test_view/companies/fipi_csv.rb $ cd /usr/lib64/ruby/1.9.1/ $ sudo patch -p 0 < ~/csv.rb.patch.20111123.txt
Milestone: oddbd is now running: it proceeds to printing
system initialized
(still some errors are displayed, but they can be ignored)
$ sudo emerge yaml
$ sudo emerge apache $ sudo /etc/init.d/apache2 start Password: * Starting apache2 ... apache2: apr_sockaddr_info_get() failed for alex apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.0.1 for ServerName * start-stop-daemon: failed to start `/usr/sbin/apache2'
It doesn't appear to be running, despite
$ rc-status Dynamic Runlevel: manual apache2 $ sudo /etc/init.d/apache2 status * status: started $ ps aux | grep apache2 alex 2934 0.0 0.0 8360 880 pts/0 S+ 10:10 0:00 grep --colour=auto apache2
Stopped the server and checked the error log file
$ sudo /etc/init.d/apache2 stop $ sudo cat /var/log/apache2/error_log [Fri May 04 10:01:22 2012] [alert] (EAI 2)Name or service not known: mod_unique_id: unable to find IPv4 address of "alex" Configuration Failed
Locate the configuration file
$ locate httpd.conf /etc/apache2/httpd.confGot rid of the first error about apr_sockaddr_info_get() by appending this line to the end of the configuration file
ServerName localhost$ sudo vim /etc/apache2/httpd.conf
Now starting apache
$ sudo /etc/init.d/apache2 start * Starting apache2 ... * start-stop-daemon: failed to start `/usr/sbin/apache2'
Check the hostname
$ cat /etc/conf.d/hostname # Set to the hostname of this machine hostname="alex" $ hostname alex
Fixed the remaining problem by modifying the hostname and restarting the server
$ hostname localhost $ sudo /etc/init.d/apache2 restart * apache2 not running (no pid file) * Starting apache2 ...
Milestone: http server works for localhost
http://localhost
$ sudo vim /etc/hosts 127.0.0.1 localhost 127.0.0.1 localhost oddb.alex.org
Wrong way of creating the virtual host configuration file:
$ cd /etc/apache2/vhosts.d/
$ sudo cp 00_default_vhost.conf 01_oddb_vhost.conf
$ sudo vim 01_oddb_vhost.conf
changed from
ServerName localhost
to
ServerName oddb.alex.org
Correct way of creating the virtual host configuration file:
$ cd /etc/apache2/vhosts.d/ $ wget http://dev.ywesee.com/uploads/att/02_oddb_vhost.conf.txt
Then edit the file to have the correctServerName oddb.alex.org
and sbsm versionRubyAddPath /home/alex/.gem/ruby/1.9.1/gems/sbsm-1.1.6/lib
which was discovered from the gem list command
$ sudo vim /etc/conf.d/apache2 added "-D RUBY" to APACHE2_OPTS
$ sudo /etc/init.d/apache2 restart Password: * apache2 has detected an error in your setup: Syntax error on line 16 of /etc/apache2/vhosts.d/01_oddb_vhost.conf: Invalid command 'RubyAddPath', perhaps misspelled or defined by a module not included in the server configuration * ERROR: apache2 failed to stop
Next: I need to get mod_ruby and compile it against ruby 1.9
In principle, there are two possible ways of proceeding:
The second way is the preferred one, because the same procedure will need to be repeated later on to compile it against ruby 1.8
$ cd ~/sw $ git clone https://github.com/shugo/mod_ruby.git $ cd mod_ruby $ sudo /usr/bin/ruby ./configure.rb --with-apxs --with-apr-includes=/usr/include/apr-1 $ sudo make $ sudo make install $ cd ~ $ wget http://dev.ywesee.com/uploads/att/21_mod_ruby.conf.txt $ mv 21_mod_ruby.conf.txt 21_mod_ruby.conf $ sudo mv 21_mod_ruby.conf /etc/apache2/modules.d/ $ /etc/init.d/apache2 restart
Start (or restart) apache
$ sudo /etc/init.d/apache2 start * Starting apache2 ...
Browsing to
http://oddb.alex.org
no longer displays "Unable to connect"
but "Internal Server Error"
Stopped the server and checked the error log file
$ sudo /etc/init.d/apache2 stop $ sudo cat /var/log/apache2/error_log [Fri May 04 11:34:07 2012] [error] mod_ruby: error in ruby [Fri May 04 11:34:07 2012] [error] mod_ruby: /usr/lib64/ruby/site_ruby/1.9.1/rubygems/custom_require.rb:36:in `require': cannot load such file -- /usr/local/lib/ruby/gems/1.9.1/gems/sbsm-1.1.6/lib/sbsm/request (LoadError) [Fri May 04 11:34:07 2012] [error] mod_ruby: from /usr/lib64/ruby/site_ruby/1.9.1/rubygems/custom_require.rb:36:in `require' [Fri May 04 11:34:07 2012] [error] mod_ruby: from /var/www/oddb.org/doc/index.rbx:7:in `<top (required)>' [Fri May 04 11:34:07 2012] [error] mod_ruby: from /usr/lib64/ruby/1.9.1/apache/ruby-run.rb:53:in `load' [Fri May 04 11:34:07 2012] [error] mod_ruby: from /usr/lib64/ruby/1.9.1/apache/ruby-run.rb:53:in `handler' ruby: warning: already initialized constant TMP_RUBY_PREFIX ruby: warning: already initialized constant TMP_RUBY_PREFIX ruby: warning: already initialized constant TMP_RUBY_PREFIX ruby: warning: already initialized constant TMP_RUBY_PREFIX ruby: warning: already initialized constant TMP_RUBY_PREFIX ruby: warning: already initialized constant TMP_RUBY_PREFIX [Fri May 04 11:35:53 2012] [notice] caught SIGTERM, shutting down
The error is due to the fact that mod ruby is trying to find the sbsm gem in
/usr/local/lib/ruby/gems/1.9.1/gems/sbsm-1.1.6/lib/sbsm/
instead of
/home/alex/.gem/ruby/1.9.1/gems/sbsm-1.1.6/lib/sbsm
$ gem env
RubyGems Environment:
- RUBYGEMS VERSION: 1.8.15
- RUBY VERSION: 1.9.3 (2011-10-30 patchlevel 0) [x86_64-linux]
- INSTALLATION DIRECTORY: /home/alex/.gem/ruby/1.9.1
- RUBY EXECUTABLE: /usr/bin/ruby19
- EXECUTABLE DIRECTORY: /home/alex/.gem/ruby/1.9.1/bin
- RUBYGEMS PLATFORMS:
- ruby
- x86_64-linux
- GEM PATHS:
- /home/alex/.gem/ruby/1.9.1
- /usr/local/lib64/ruby/gems/1.9.1
- /usr/lib64/ruby/gems/1.9.1
- GEM CONFIGURATION:
- :update_sources => true
- :verbose => true
- :benchmark => false
- :backtrace => false
- :bulk_threshold => 1000
- REMOTE SOURCES:
- http://rubygems.org/
Interesting information in
$ cat /usr/lib64/ruby/site_ruby/1.9.1/rubygems/custom_require.rb # When RubyGems is required, Kernel#require is replaced with our own which # is capable of loading gems on demand. # # When you call <tt>require 'x'</tt>, this is what happens: # * If the file can be loaded from the existing Ruby loadpath, it # is. # * Otherwise, installed gems are searched for a file that matches. # If it's found in gem 'y', that gem is activated (added to the # loadpath). # # The normal <tt>require</tt> functionality of returning false if # that file has already been loaded is preserved.
This is the lead to the right solution to the problem:
$ sudo vim /var/www/oddb.org/doc/index.rbx replaced require '/usr/local/lib/ruby/gems/1.9.1/gems/sbsm-1.1.6/lib/sbsm/request' with require '/home/alex/.gem/ruby/1.9.1/gems/sbsm-1.1.6/lib/sbsm/request'
Start (or restart) apache
$ sudo /etc/init.d/apache2 restart * Starting apache2 ...
Milestone: the server appears to be running, showing the open drug database colorful home page,
but with the following message:
We are sorry
The application is currently down due to a software-update
Launching oddbd
$ cd /var/www/oddb.org $ bin/oddbd
the browser refreshed itself and the main page got displayed
$ sudo gem install ycurrency $ currencyd &
Milestone: now when we do a search for a drug the results are displayed correctly
Rationale
Notes
Reference links
Acquire the sources
$ cd ~/sw $ git clone git://scm.ywesee.com/yus/.git yus
Now read the document
yus/Guide.txt
Switch to Ruby 1.8
$ eselect ruby list
Available Ruby profiles:
[1] ruby18 (with Rubygems)
[2] ruby19 (with Rubygems)
alex@localhost ~ $ sudo eselect ruby set 1
Successfully switched to profile:
ruby18
$ gem env
RubyGems Environment:
- RUBYGEMS VERSION: 1.8.15
- RUBY VERSION: 1.8.7 (2011-12-28 patchlevel 357) [x86_64-linux]
- INSTALLATION DIRECTORY: /home/alex/.gem/ruby/1.8
- RUBY EXECUTABLE: /usr/bin/ruby18
- EXECUTABLE DIRECTORY: /home/alex/.gem/ruby/1.8/bin
- RUBYGEMS PLATFORMS:
- ruby
- x86_64-linux
- GEM PATHS:
- /home/alex/.gem/ruby/1.8
- /usr/local/lib64/ruby/gems/1.8
- /usr/lib64/ruby/gems/1.8
- GEM CONFIGURATION:
- :update_sources => true
- :verbose => true
- :benchmark => false
- :backtrace => false
- :bulk_threshold => 1000
- REMOTE SOURCES:
- http://rubygems.org/
alex@localhost ~ $ gem -v
1.8.15
alex@localhost ~ $ gem list
*** LOCAL GEMS ***
deprecated (2.0.1)
json (1.6.4)
pg (0.13.2)
racc (1.4.7)
rake (0.9.2.2)
rdoc (3.12)
$ sudo gem install needle --version '=1.3.0' $ sudo gem install pg --version '=0.9.0' $ sudo gem install postgres --version '=0.7.9.2008.01.28' $ sudo gem install ruby-password
Note: it installs
ruby-password (0.15.5)
but Guide.txt says to install
ruby-password (0.5.3) from sources
We shall not worry so much about this for the moment.
At this point yus is not installed for ruby 1.8 yet, so if I try to start yus, this is what happens:
$ locate yusd /home/alex/.gem/ruby/1.9.1/bin/yusd /home/alex/.gem/ruby/1.9.1/gems/yus-1.0.0/bin/yusd $ /home/alex/.gem/ruby/1.9.1/bin/yusd /home/alex/.gem/ruby/1.9.1/gems/needle-1.3.0/lib/needle/definition-context.rb:36: warning: undefining `initialize' may cause serious problems /home/alex/.gem/ruby/1.9.1/gems/needle-1.3.0/lib/needle/definition-context.rb:36: warning: undefining `object_id' may cause serious problems /home/alex/.gem/ruby/1.9.1/gems/needle-1.3.0/lib/needle/definition-context.rb:36: warning: undefining `__send__' may cause serious problems /home/alex/.gem/ruby/1.9.1/gems/dbi-0.4.5/lib/dbi.rb:300:in `block in load_driver': Unable to load driver 'pg' (underlying error: wrong constant name pg) (DBI::InterfaceError)
Note how all the paths are pointing to the wrong version.
$ sudo gem install yus $ gem list yus *** LOCAL GEMS *** yus (1.0.0) $ sudo mkdir -p /etc/yus/data $ locate yus.crt /home/alex/.gem/ruby/1.9.1/gems/yus-1.0.0/data/yus.crt /home/alex/sw/yus/data/yus.crt /usr/local/lib64/ruby/gems/1.8/gems/yus-1.0.0/data/yus.crt $ locate yus.key /home/alex/.gem/ruby/1.9.1/gems/yus-1.0.0/data/yus.key /home/alex/sw/yus/data/yus.key /usr/local/lib64/ruby/gems/1.8/gems/yus-1.0.0/data/yus.key
Maybe it would be okay to use the existing yus.crt and yus.crt from one of the locations above, and copying them to the intended destination, but we might as well go ahead and generate new keys and certificates:
Create public/private keys
$ ssh-keygen -t rsa Generating public/private rsa key pair. Enter file in which to save the key (/home/alex/.ssh/id_rsa): Enter passphrase (empty for no passphrase): Enter same passphrase again: Your identification has been saved in /home/alex/.ssh/id_rsa. Your public key has been saved in /home/alex/.ssh/id_rsa.pub. The key fingerprint is: b4:99:d7:c1:63:c9:02:ae:db:ec:05:65:51:0f:2c:86
Generate certificate (left all info blank by pressing the ENTER key immediately at each prompt)
$ cd ~ $ openssl req -new -x509 -key .ssh/id_rsa -out .ssh/id_rsa.crt You are about to be asked to enter information that will be incorporated into your certificate request. What you are about to enter is what is called a Distinguished Name or a DN. There are quite a few fields but you can leave some blank For some fields there will be a default value, If you enter '.', the field will be left blank. ----- Country Name (2 letter code) [AU]: State or Province Name (full name) [Some-State]: Locality Name (eg, city) []: Organization Name (eg, company) [Internet Widgits Pty Ltd]: Organizational Unit Name (eg, section) []: Common Name (e.g. server FQDN or YOUR name) []: Email Address []:
Copy the key and certificate into the intended folder where the yaml configuration file is expecting them
$ sudo cp /home/alex/.ssh/id_rsa /etc/yus/data/yus.key $ sudo cp /home/alex/.ssh/id_rsa.crt /etc/yus/data/yus.crt
yaml
$ locate sha256.rb /home/alex/.gem/ruby/1.9.1/gems/yus-1.0.0/sha256.rb /home/alex/sw/yus/sha256.rb /usr/local/lib64/ruby/gems/1.8/gems/yus-1.0.0/sha256.rb $ ruby /usr/local/lib64/ruby/gems/1.8/gems/yus-1.0.0/sha256.rb hatakeyama2 password: hatakeyama2 SHA256 encoding: 8fc68bf10a98d0a3874aaefa546edd4ec5e3f04b1a777310e9b1c798ef698d93
$ sudo vim /etc/yus/yus.yml root_name: alex@filzmail.com root_pass: 8fc68bf10a98d0a3874aaefa546edd4ec5e3f04b1a777310e9b1c798ef698d93 log_level: DEBUG ssl_key: /etc/yus/data/yus.key ssl_cert: /etc/yus/data/yus.crt session_timeout: 3600
Try to add the user
$ yus_add_user alex@filzmail.com login org.oddb.RootUser /usr/lib64/ruby/site_ruby/1.8/rubygems/custom_require.rb:36:in `gem_original_require': no such file to load -- rclconf (LoadError) $ gem install rclconf $ yus_add_user alex@filzmail.com login org.oddb.RootUser /usr/lib64/ruby/1.8/drb/drb.rb:736:in `open': drbssl://localhost:9997 - #<Errno::ECONNREFUSED: Connection refused - connect(2)> (DRb::DRbConnError)
Note: yusd must be running before we can add the user
$ yusd /usr/lib64/ruby/site_ruby/1.8/rubygems/custom_require.rb:36:in `gem_original_require': no such file to load -- odba (LoadError) $ gem install odba $ yusd /usr/lib64/ruby/site_ruby/1.8/rubygems/custom_require.rb:36:in `gem_original_require': no such file to load -- dbi (LoadError) $ gem install dbi $ yusd /usr/local/lib64/ruby/gems/1.8/gems/yus-1.0.0/lib/yus/server.rb:9: warning: already initialized constant VERSION /home/alex/.gem/ruby/1.8/gems/dbi-0.4.5/lib/dbi.rb:300:in `load_driver': Unable to load driver 'pg' (underlying error: wrong constant name pg) (DBI::InterfaceError)
SETUP POSTGRES DB
alex$ sudo su - postgres Password: postgres$ createuser yus (replied 'n' to all 3 questions) postgres$ createdb yus postgres$ exit alex$ $ cd ~/sw/yus $ ruby bin/yusd /home/alex/sw/yus/lib/yus/server.rb:9: warning: already initialized constant VERSION /home/alex/.gem/ruby/1.8/gems/dbi-0.4.5/lib/dbi.rb:300:in `load_driver': Unable to load driver 'pg' (underlying error: wrong constant name pg) (DBI::InterfaceError)
$ sudo emerge =ruby-dbi-0.4.3 $ sudo emerge =pg-0.12.2 $ sudo emerge =dbd-pg-0.3.9
$ ruby bin/yusd /usr/lib64/ruby/site_ruby/1.8/dbi/utils/date.rb:57: undefined method `deprecate' for DBI::Date:Class (NoMethodError)
Note:
Removed deprecated(3.0.0)
$ gem uninstall deprecated
Changed yus.key permissions
$ ls -la /etc/yus/data/ -rw------- 1 root root 1675 May 4 15:17 yus.key $ sudo chmod 644 /etc/yus/data/yus.key $ ls -la /etc/yus/data/ -rw-r--r-- 1 root root 1675 May 4 15:17 yus.key
$ yusd /usr/local/lib64/ruby/gems/1.8/gems/yus-1.0.0/lib/yus/server.rb:9: warning: already initialized constant VERSION ERROR: relation "object" already exists ERROR: relation "prefetchable_index" already exists ERROR: relation "extent_index" already exists ERROR: relation "object_connection" already exists ERROR: relation "target_id_index" already exists ERROR: relation "collection" already exists I, [2012-05-04T16:33:52.956793 #13783] INFO -- start: starting yus-server on drbssl://localhost:9997
Milestone: now yusd is running
Reference:
Created temporary email address to receive the password
http://filzmail.com/
alex@filzmail.com
Actually, it turns out that it needs to be a gmail address (this functionality has only been tested with gmail)
Add the user
$ yus_add_user alex@filzmail.com login org.oddb.RootUser /usr/lib64/ruby/1.8/drb/drb.rb:736:in `open': drbssl://localhost:9997 - #<Errno::ECONNREFUSED: Connection refused - connect(2)> (DRb::DRbConnError) $ yus_add_user alex@filzmail.com login org.oddb.RootUser Password for alex@filzmail.com: hatakeyama2 New Password for alex@filzmail.com: alex Repeat Password for alex@filzmail.com: alex
Then try logging in from the web interface
(Login link at the bottom right of the home page)
specify E-mail: alex@filzmail.com
and password: alex
but it's not going to work because we need to click on "Lost password ?" to receive an email to a valid gmail account
Updated oddb.yml with new email account information
$ sudo cp oddb.yml /var/www/oddb.yml
Restarted oddb
$ sudo eselect ruby set 2 $ bin/oddbd
TODO: