def test_import_project(self):
"""import_project: check project is imported
"""
# Make an auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'160621_M00879_0087_000000000-AGEW9', 'miseq', top_dir=self.dirn)
mockdir.create()
# Check that the project is not currently present
ap = AutoProcess(mockdir.dirn)
self.assertFalse(
'NewProj' in [p.name for p in ap.get_analysis_projects()])
self.assertFalse(
'NewProj' in
[p.name for p in ap.get_analysis_projects_from_dirs()])
self.assertFalse(
os.path.exists(os.path.join(ap.analysis_dir, 'NewProj')))
# Import the project
import_project(ap, self.new_project_dir)
self.assertTrue(
'NewProj' in [p.name for p in ap.get_analysis_projects()])
self.assertTrue('NewProj' in
[p.name for p in ap.get_analysis_projects_from_dirs()])
self.assertTrue(
os.path.exists(os.path.join(ap.analysis_dir, 'NewProj')))
# Verify via fresh AutoProcess object
ap2 = AutoProcess(mockdir.dirn)
self.assertTrue(
'NewProj' in [p.name for p in ap2.get_analysis_projects()])
self.assertTrue(
'NewProj' in
[p.name for p in ap2.get_analysis_projects_from_dirs()])
self.assertTrue(
os.path.exists(os.path.join(ap2.analysis_dir, 'NewProj')))
def test_import_project(self):
"""Check AutoProcess.import_project imports a project
"""
# Make an auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'160621_M00879_0087_000000000-AGEW9',
'miseq',
top_dir=self.dirn)
mockdir.create()
# Check that the project is not currently present
ap = AutoProcess(mockdir.dirn)
self.assertFalse('NewProj' in [p.name
for p in ap.get_analysis_projects()])
self.assertFalse('NewProj' in [p.name
for p in ap.get_analysis_projects_from_dirs()])
self.assertFalse(os.path.exists(os.path.join(ap.analysis_dir,'NewProj')))
# Import the project
ap.import_project(self.new_project_dir)
self.assertTrue('NewProj' in [p.name
for p in ap.get_analysis_projects()])
self.assertTrue('NewProj' in [p.name
for p in ap.get_analysis_projects_from_dirs()])
self.assertTrue(os.path.exists(os.path.join(ap.analysis_dir,'NewProj')))
# Verify via fresh AutoProcess object
ap2 = AutoProcess(mockdir.dirn)
self.assertTrue('NewProj' in [p.name
for p in ap2.get_analysis_projects()])
self.assertTrue('NewProj' in [p.name
for p in ap2.get_analysis_projects_from_dirs()])
self.assertTrue(os.path.exists(os.path.join(ap2.analysis_dir,'NewProj')))
def test_import_project_with_qc(self):
"""import_project: check project with QC outputs is imported
"""
# Make mock multiqc
MockMultiQC.create(os.path.join(self.bin, "multiqc"))
os.environ['PATH'] = "%s:%s" % (self.bin, os.environ['PATH'])
# Make an auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'160621_M00879_0087_000000000-AGEW9', 'miseq', top_dir=self.dirn)
mockdir.create()
# Add QC outputs to the project to be imported
UpdateAnalysisProject(AnalysisProject(
'NewProj',
self.new_project_dir)).add_qc_outputs(include_multiqc=False)
print(os.listdir(os.path.join(self.dirn, 'NewProj')))
# Check that the project is not currently present
ap = AutoProcess(mockdir.dirn)
self.assertFalse(
'NewProj' in [p.name for p in ap.get_analysis_projects()])
self.assertFalse(
'NewProj' in
[p.name for p in ap.get_analysis_projects_from_dirs()])
self.assertFalse(
os.path.exists(os.path.join(ap.analysis_dir, 'NewProj')))
# Import the project
import_project(ap, self.new_project_dir)
self.assertTrue(
'NewProj' in [p.name for p in ap.get_analysis_projects()])
self.assertTrue('NewProj' in
[p.name for p in ap.get_analysis_projects_from_dirs()])
self.assertTrue(
os.path.exists(os.path.join(ap.analysis_dir, 'NewProj')))
# Verify via fresh AutoProcess object
ap2 = AutoProcess(mockdir.dirn)
self.assertTrue(
'NewProj' in [p.name for p in ap2.get_analysis_projects()])
self.assertTrue(
'NewProj' in
[p.name for p in ap2.get_analysis_projects_from_dirs()])
self.assertTrue(
os.path.exists(os.path.join(ap2.analysis_dir, 'NewProj')))
# Check for QC report and ZIP file
print(os.listdir(os.path.join(ap2.analysis_dir, 'NewProj')))
for f in (
"qc_report.html",
"multiqc_report.html",
"qc_report.NewProj.160621_M00879_0087_000000000-AGEW9.zip",
):
f = os.path.join(ap2.analysis_dir, 'NewProj', f)
self.assertTrue(os.path.exists(f), "Missing %s" % f)
def test_import_project_with_comment(self):
"""import_project: check comment is appended
"""
# Make an auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'160621_M00879_0087_000000000-AGEW9', 'miseq', top_dir=self.dirn)
mockdir.create()
# Check that the project is not currently present
ap = AutoProcess(mockdir.dirn)
self.assertFalse(
'NewProj' in [p.name for p in ap.get_analysis_projects()])
self.assertFalse(
'NewProj' in
[p.name for p in ap.get_analysis_projects_from_dirs()])
self.assertFalse(
os.path.exists(os.path.join(ap.analysis_dir, 'NewProj')))
# Import the project and append a comment
import_project(ap,
self.new_project_dir,
comment="imported from elsewhere")
self.assertTrue(
'NewProj' in [p.name for p in ap.get_analysis_projects()])
self.assertTrue('NewProj' in
[p.name for p in ap.get_analysis_projects_from_dirs()])
self.assertTrue(
os.path.exists(os.path.join(ap.analysis_dir, 'NewProj')))
# Verify via fresh AutoProcess object
ap2 = AutoProcess(mockdir.dirn)
self.assertTrue(
'NewProj' in [p.name for p in ap2.get_analysis_projects()])
self.assertTrue(
'NewProj' in
[p.name for p in ap2.get_analysis_projects_from_dirs()])
self.assertTrue(
os.path.exists(os.path.join(ap2.analysis_dir, 'NewProj')))
# Check the comment has been updated
with open(os.path.join(mockdir.dirn,'NewProj','README.info'),'rt') \
as fp:
self.assertTrue(
"Comments\t1% PhiX spike in; imported from elsewhere" in
fp.read())
