This great blog post by Matthias Marschall and this thread @ stackoverflow give some very good advice, how to load the required data without the usage of fixtures. The basic idea is simple:  Dump the loaded ontologies  from Postgresql/CHADO. Overwrite a Rake task with system calls that load the sql files and finaly run the rake command to populate the db.  Hence the above mentioned solution presents a convienient way to make use of the ontologies while testing an application that relies on CHADO.

A basic example to solve the situation could look something like this:

Create a file in lib/tasks/load_seed.rake with:

namespace :db do
  namespace :seed do

    desc "load the dumped seed data from db/*.sql into the test database"
    task :load => :environment do
      config = ActiveRecord::Base.configurations['test']
      system("psql --username=#{config['username']} #{config['database']} < db/db_ontologies.sql")
      system("psql --username=#{config['username']} #{config['database']} < db/db_initialize.sql")
     end
  end
end

To populate the test database with the data run

rake:db:seed:load

, in addition to

rake db:test:prepare

and

rake db:test:load

I’m using a single sql dump of the ontologies needed, since the download, conversion and load of the ontologies every time  db:seed:load is called would require an enormous amount of time.

(In this post I’m assuming that the database used is Postgresql and that the sql-file db_ontology.sql  represents a data dump of the chado instance  + ontologies loaded. db_initialize.sql is equal to gmod/load/etc/initialize.sql. See the CHADO installation manuel for more information.)

1. Follow the manual installation described here until the point:

   perl Makefile.PL.

2. Determine the path of YOUR mysql_config file, it is in the bin folder of your installation, or try to determine it with:

   whereis mysql_config

3. call:

   sudo perl Makefile.PL --mysql_config="your_mysql_path/bin/mysql_config"

4. Try to follow the instructions in #1, if an error occours that names a connection problem with:

   tmp/mysql.sock

   set an symlink as follows:

   ln -s /your_path_to_your_mysq/tmp/mysql.sock /tmp/mysql.sock

5. Try again to run make test, and u should be good to go!

1. Conversion from String to Integer

   String example=“1”;
   int value = Integer.parseInt( example );
   

   It is NOT:

   Integer.getInteger( example );

   The getInteger method trys to

   Determines the integer value of the system property with the specified name.

2. The ? – Operator The Java ternary operator (sometimes referred to as the “questionmark operator”) is an elegeant way to deal with boolean (TRUE / FALSE) decisions or assignments in the programming world. The ternary operator differs from an if-else statement due to the fact that it is an expression that returns a value. While the if-else structure  executes a statement. The following Example assigns the maximum Value of two ints to a new variable:

   int a = 5;
   int b = 10;
   int max  = (a > b ? a : b);
   

3. instanceof and isInstance The binary operator instanceof checks if an object is a member of a class:

   SampleObject sample = new SampleObject();
   if(sample instanceof SampleObject) {
   ...
   }
   

   Unfortunately though it is not possible to set the type (which the object is tested against) at runtime and use for example a string at the leftside of the instanceof operator:

   SampleObject sample = new SampleObject();
   String sampleStr = "sampleObject";
   

   if(sample instanceof sampleStr) {

   ...
   }
   

   At runtime it is possible though to check the type of an object with the isInstance method:

   // the object where we know what kind of type it is
   SampleObject sampleold = new SampleObject();
   
   // our "unknown" type object
   Object samplenew = new SampleObject();
   
   if(sampleold.getClass().isInstance(samplenew)) {
   ...
   }
   

   Attention to the switch of the arguments between instanceof and isInstance !

4. Comparator
   
   If I write a Comparator Object I usually implement Comparator<T> and then override  int compare(T t1, T t2). To implement a proper working compare method the following “handrules” apply:
   1. (t1 < t2) ->  return a negative value
   2. (t1 == t2) -> return zero
   3. (t1 > t2) -> return a positive value

   The <, ==, > do NOT have to refer to the standard smaller, greater, etc operators !

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