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)