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Bio::EnsEMBL::DataCheck Framework

ensembl-datacheck uses a set of base modules and scripts to define and execute tests using the Test::More suite.

Modules

Bio::EnsEMBL::DataCheck::BaseCheck

BaseCheck defines the minimal code needed for a test. All datachecks inherit from this module and provide values for the following attributes:

  • name - (required) name of the test
  • description - (required) description of the test
  • datacheck_type - (required) datachecks are "critical" (default) or "advisory"
  • groups - (optional) list of groups to which the datacheck belongs

Instances of this test are invoked by run which uses Test::More to return test results in standard TAP format.

Bio::EnsEMBL::DataCheck::DbCheck

DbCheck supports tests that deal with Ensembl database adaptors. The following variables can be set:

  • db_types - (optional) list of Ensembl database types that the test applies to (core, variation, otherfeatures, compara, funcgen)
  • tables - (optional) list of tables that are related to the datacheck
  • per_db - (optional) whether the datacheck runs on a whole database rather than individual species

After the test runs, the database adaptor is disconnected to avoid connection leaks.

Bio::EnsEMBL::DataCheck::Manager

The Manager module can be used to retrieve a set of datachecks, and optionally run them in a test harness. The history of datachecks' pass/fail status can be read from and written to a file, in order for datachecks to determine if they need to be run.

Bio::EnsEMBL::DataCheck::Test::DataCheck

This module contains Test::More-style methods for dealing with Ensembl databases, e.g. is_rows for checking the number of rows returned.

Scripts

run_datachecks.pl

This script runs one or more datachecks for the specified database e.g.

perl -I lib/ scripts/run_datachecks.pl
  -groups core_handover 
  -history_file /path/to/history/file
  -host localhost -port 3306 -user anonymous 
  -dbname schizosaccharomyces_pombe_core_39_92_2

create_datacheck.pl

This script generates a datacheck file in a standard format, such that only the tests method (and optionally the skip_tests method) then need to be written e.g.

perl -I lib/ scripts/create_datacheck.pl 
  -name AssemblyAccession 
  -description 'Meta key "assembly.accession" is set.' 
  -db_types core 
  -tables 'meta'