Find file History
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
..
Failed to load latest commit information.
SQL
data
Analysis.t
BatchSubmission.t
BiopipeTestDB.conf
BiopipeTestDB.conf.example
BiopipeTestDB.pm
BlastPipe.t
Blat.t
Cdna2Genome.t
Feature_filter.t
Genewise.t
Genscan.t
Input.t
Job.t
JobAdaptor.t
Output.t
PhylipPipe.t
Promoterwise.t
README
Transformer.t

README

Tests for Bioperl Pipeline

Different functionalities and bioperl pipleline objects are tested in different tests as follows.

Input.t
Input Handling(IoHandler with datahandlers to read in the input)
Classes tested : IOHandler(fetching input), DataHandler, InputAdaptor, Input

Output.t
Output Handling ( IOHandler with datahandlers to write the output)
Classes tested : IOHandler (writing output), DataHandler, AnalysisAdaptor

Job.t
Job (Fetching of jobs, running, creation of next job according to the rules) 
Classes tested : Job, JobAdaptoar, Rule, RuleAdaptor

BatchSubmission.t
BatchSubmission (Submitting the jobs through Batch submission interface) 
Classes tested : BatchSubmission, LSF

Analysis.t
Classes tested : Analysis, AnalysisAdaptor


RunnableI, RunnableDB are implicitly tested throuh Job.t , a TestRunnable is used to test Job
DataTypes is implicitly tested through Input.t

BiopipeTestDB.conf need to be modified to point to the schema required to create the test database. The schema
file also contains the test data required for the tests to run.
Some Adaptor clases needed for testing are in SQL dir

Runnables are not tested as yet. coming soon..
PipelineManager.pl is not tested.. havent figured out how to write a test case...