def test_report_concise(self):
"""report: report run in 'concise' 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
self.assertEqual(
report_concise(ap),
"Paired end: 'AB': Alison Bell, Human RNA-seq (PI: Audrey Bower) (2 samples); 'CDE': Charles David Edwards, Mouse ChIP-seq (PI: Colin Delaney Eccleston) (2 samples)"
)
def test_report_concise_no_projects(self):
"""report: report run with no projects in 'concise' mode
"""
# Make a mock auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'170901_M00879_0087_000000000-AGEW9',
'miseq',
metadata={
"source": "testing",
"run_number": 87,
},
top_dir=self.dirn)
mockdir.create(no_project_dirs=True)
# Make autoprocess instance
ap = AutoProcess(analysis_dir=mockdir.dirn)
# Generate concise report
self.assertEqual(
report_concise(ap),
"Paired end: no projects found; contents of 'bcl2fastq' are: 'AB' (2 samples), 'CDE' (2 samples)"
)