Structure

There are two parts to the system.

"Track" run is the part that the administrator uses to add people, publications and curation sessions to the database. In the web interface this is access using the Admin link in the top right of the page.

"Curs" handles the user curation sessions.

Track - user, publication and session tracking

Database storage

SQLite for main database

Curs - curation sessions

Each curation session has a corresponding SQLite database.

Code

Canto is written in Perl, implemented using the Catalyst framework and running on a Plack server.

Autocomplete searching

• implemented using CLucene
• short names are weighted more highly so they appear at the top of the search list
• the term names and synonyms are passed to CLucene for indexing
• all words appearing in the name or synonyms are joined into one string for separate indexing by CLucene

Developing Canto

Running tests

The environment needs to be initialised with perl Makefile.PL. This command creates the Makefile and only needs to be run once.

In general the tests can be run with: make test in the main canto directory. If the schema or test genes or ontologies are is changed the test data will need to be re-initialised.

Helper scripts

Scripts to help developers:

• etc/db_initialise.pl - create empty template database from the schemas and recreate the database classes in lib/Canto/TrackDB and lib/Canto/CursDB
• etc/test_data_initialise.pl - re-create test data files that don't change very often. e.g. the test PubMed XML file. Currently this script only needs to be run if the list of publications for the test database changes
• etc/test_initialise.pl - initialise the test databases in t/data with a small number of genes and a mini version of the Gene Ontology database
• etc/local_initialise.pl - create a test instance of Canto in ./local

Initialising test data

Run the following commands in the canto directory to create the test database and to populate it with test data:

./etc/db_initialise.pl
./etc/test_initialise.pl

That will need to be done each time the schemas or test data change.

To create a local test instance of Canto, run local_initialise.pl

Running the test instance

The server can be run from the top level directory with this command:

CANTO_CONFIG_LOCAL_SUFFIX=local PERL5LIB=lib ./script/canto_server.pl -p 5000 -r -d