def test_report_info_no_projects(self): """report: report run with no projects in 'info' mode """ # Make a mock auto-process directory mockdir = MockAnalysisDirFactory.bcl2fastq2( '170901_M00879_0087_000000000-AGEW9', 'miseq', metadata={ "source": "testing", "run_number": 87, "assay": "Nextera" }, top_dir=self.dirn) mockdir.create(no_project_dirs=True) # Make autoprocess instance ap = AutoProcess(analysis_dir=mockdir.dirn) # Generate concise report expected = """Run reference: MISEQ_170901#87 Directory : %s Platform : miseq Unaligned dir: bcl2fastq Summary of data in 'bcl2fastq' dir: - AB: AB1-2 (2 paired end samples) - CDE: CDE3-4 (2 paired end samples) No analysis projects found""" % mockdir.dirn for o, e in zip(report_info(ap).split('\n'), expected.split('\n')): self.assertEqual(o, e)
def test_report_info(self): """report: report run in 'info' mode """ # Make a mock auto-process directory mockdir = MockAnalysisDirFactory.bcl2fastq2( '170901_M00879_0087_000000000-AGEW9', 'miseq', metadata={ "source": "testing", "run_number": 87, "assay": "Nextera" }, project_metadata={ "AB": { "User": "******", "Library type": "RNA-seq", "Organism": "Human", "PI": "Audrey Bower" }, "CDE": { "User": "******", "Library type": "ChIP-seq", "Organism": "Mouse", "PI": "Colin Delaney Eccleston" } }, top_dir=self.dirn) mockdir.create() # Make autoprocess instance ap = AutoProcess(analysis_dir=mockdir.dirn) # Generate concise report expected = """Run reference: MISEQ_170901#87 Directory : %s Platform : miseq Unaligned dir: bcl2fastq Summary of data in 'bcl2fastq' dir: - AB: AB1-2 (2 paired end samples) - CDE: CDE3-4 (2 paired end samples) 3 analysis projects: - AB -- User : Alison Bell PI : Audrey Bower Library : RNA-seq SC Plat.: None Organism: Human Dir : AB #samples: 2 #cells : Samples : AB1-2 QC : not verified Comments: None - CDE --- User : Charles David Edwards PI : Colin Delaney Eccleston Library : ChIP-seq SC Plat.: None Organism: Mouse Dir : CDE #samples: 2 #cells : Samples : CDE3-4 QC : not verified Comments: None - undetermined ------------ User : None PI : None Library : None SC Plat.: None Organism: None Dir : undetermined #samples: 1 #cells : Samples : Undetermined QC : not verified Comments: None""" % mockdir.dirn for o, e in zip(report_info(ap).split('\n'), expected.split('\n')): self.assertEqual(o, e)