Reference

Utilities

Test helper functions.

class resolwe_bio.utils.test.BioProcessTestCase(methodName='runTest')

Base class for writing bioinformatics process tests.

It is a subclass of Resolwe’s ProcessTestCase with some specific functions used for testing bioinformatics processes.

prepare_annotation(fn='sp_test.gtf', source='DICTYBASE', species='Dictyostelium discoideum', build='dd-05-2009')

Prepare annotation GTF.

prepare_annotation_gff(fn='annotation dicty.gff.gz', source='DICTYBASE', species='Dictyostelium discoideum', build='dd-05-2009')

Prepare annotation GFF3.

prepare_bam(fn='sp_test.bam', species='Dictyostelium discoideum', build='dd-05-2009')

Prepare alignment BAM.

prepare_expression(f_rc='exp_1_rc.tab.gz', f_exp='exp_1_tpm.tab.gz', f_type='TPM', name='Expression', source='DICTYBASE', descriptor=None, feature_type='gene', species='Dictyostelium discoideum', build='dd-05-2009')

Prepare expression.

prepare_paired_reads(mate1=['fw reads.fastq.gz'], mate2=['rw reads.fastq.gz'])

Prepare NGS reads FASTQ.

prepare_reads(fn=['reads.fastq.gz'])

Prepare NGS reads FASTQ.

prepare_ref_seq(fn='adapters.fasta', species='Other', build='Illumina adapters')

Prepare reference sequence FASTA.

setUp()

Initialize test files path and species annotation.

class resolwe_bio.utils.test.KBBioProcessTestCase(methodName='runTest')

Class for bioinformatics process tests that use knowledge base.

It is based on BioProcessTestCase and Django’s LiveServerTestCase. The latter launches a live Django server in a separate thread so that the tests may use it to query the knowledge base.

run_process(*args, **kwargs)

Run processes in collection.

setUp()

Set up test gene information knowledge base, create collection.

resolwe_bio.utils.test.skipDockerFailure(reason)

Skip decorated tests due to failures when run in Docker.

Unless TESTS_SKIP_DOCKER_FAILURES Django setting is set to False. reason should describe why the test is being skipped.

resolwe_bio.utils.test.skipUnlessLargeFiles(*files)

Skip decorated tests unless large files are available.

Parameters:

*files (list) – variable lenght files list, where each element represents a large file path relative to the TEST_LARGE_FILES_DIR directory