def test_load_min_missingvalues(self):
loader = ProjectDataLoader(
dbsession, self.project.geid,
'python/tests/pytest_min_missingvalues.xlsx')
with pytest.raises(
LoaderException,
match=r"Column target_gene_id needs a value in Target tab"):
loader.load()
def test_load_min(self):
loader = ProjectDataLoader(dbsession, self.project.geid,
'python/tests/pytest_min.xlsx')
assert not loader.xls.parse('Target').empty
assert not loader.xls.parse('Guide').empty
assert not loader.xls.parse('Amplicon').empty
assert not loader.xls.parse('Layout').empty
loader.load()
dbsession.commit()
target = dbsession.query(Target)\
.join(Project)\
.filter(Project.geid == self.project.geid)\
.filter(Target.name == 'test_target').one()
assert target
guide = dbsession.query(Guide)\
.join(Target)\
.join(Project)\
.filter(Project.geid == self.project.geid)\
.filter(Guide.name == 'test_guide')\
.one()
assert guide
amplicon = dbsession.query(Amplicon)\
.join(Project)\
.filter(Project.geid == self.project.geid)\
.filter(Amplicon.chromosome == 1)\
.filter(Amplicon.start == 1)\
.one()
assert amplicon
primer = dbsession.query(Primer)\
.join(Amplicon)\
.join(Project)\
.filter(Project.geid == self.project.geid)\
.filter(Amplicon.chromosome == 1)\
.filter(Amplicon.start == 1)\
.filter(Primer.sequence == 'AAAAA')\
.filter(Primer.strand == 'forward')\
.filter(Primer.start == 1)\
.filter(Primer.end == 10)\
.one()
assert primer
primer = dbsession.query(Primer)\
.join(Amplicon)\
.join(Project)\
.filter(Project.geid == self.project.geid)\
.filter(Amplicon.chromosome == 1)\
.filter(Amplicon.start == 1)\
.filter(Primer.sequence == 'CCCCC')\
.filter(Primer.strand == 'reverse')\
.filter(Primer.start == 101)\
.filter(Primer.end == 110)\
.one()
assert primer
def test_load_min_withlayouterror2(self):
loader = ProjectDataLoader(
dbsession, self.project.geid,
'python/tests/pytest_min_withlayouterror2.xlsx')
with pytest.raises(
sqlalchemy.exc.IntegrityError,
match=
r".*UNIQUE constraint failed: layout_content.sequencing_barcode, layout_content.layout_id.*"
):
try:
loader.load()
except sqlalchemy.exc.IntegrityError as e:
dbsession.rollback()
raise
def test_load_mouse(self):
loader = ProjectDataLoader(dbsession, self.project.geid,
'python/tests/pytest_mouse.xlsx')
assert not loader.xls.parse('Target').empty
assert not loader.xls.parse('Guide').empty
assert not loader.xls.parse('Amplicon').empty
assert not loader.xls.parse('Layout').empty
loader.load()
dbsession.commit()
target = dbsession.query(Target)\
.join(Project)\
.filter(Project.geid == self.project.geid)\
.filter(Target.name == 'test_mouse_target').one()
assert target
assert target.genome.name == 'Mus_musculus'
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--layout", dest="file_layout", action="store", help="The file layout e.g. '20170118_GEP00001.xlsx'", required=True)
parser.add_argument("--geid", dest="geid", action="store", help="Project GEP ID e.g. 'GEP00001'", required=True)
options = parser.parse_args()
log = logger.get_custom_logger(os.path.join(cfg['PROJECTS_FOLDER'], 'load_layout.log'))
try:
loader = ProjectDataLoader(dbsession, options.geid, options.file_layout)
loader.load()
session.commit()
except Exception as e:
log.exception(e)
session.rollback()
finally:
session.close()
def test_init_empty(self):
loader = ProjectDataLoader(dbsession, self.project.geid,
'python/tests/pytest_empty.xlsx')
assert loader.project.name == self.project.name
assert loader.xls
assert loader.xls.parse('Target').empty
assert loader.xls.parse('Guide').empty
assert loader.xls.parse('Amplicon').empty
assert loader.xls.parse('Layout').empty
def project(self):
gepid = self.request.matchdict['gepid']
project = self.dbsession.query(Project).filter(
Project.geid == gepid).one()
plotter = Plotter(self.dbsession, project.geid)
# Tables
project_header, project_rows = self.get_project_table(project)
target_header, target_rows = self.get_target_table(project)
guide_header, guide_rows = self.get_guide_table(project)
amplicon_header, amplicon_rows = self.get_amplicon_table(project)
layout_header, layout_rows = self.get_layout_table(project)
return_map = {
'project': project,
'title': "GenEditID",
'subtitle': "Project: {}".format(project.geid),
'info': False,
'error': False,
'project_header': project_header,
'project_rows': project_rows,
'target_header': target_header,
'target_rows': target_rows,
'guide_header': guide_header,
'guide_rows': guide_rows,
'amplicon_header': amplicon_header,
'amplicon_rows': amplicon_rows,
'layout_header': layout_header,
'layout_rows': layout_rows,
'config_header': plotter.config_header(),
'config_rows': plotter.config_rows(),
'coverage_plot': plotter.coverage_plot(),
'coverage_header': plotter.coverage_header(),
'coverage_rows': plotter.coverage_rows(),
'impact_plot': plotter.variant_impact_plot(),
'impact_header': plotter.impact_header(),
'impact_rows': plotter.impact_rows(),
'variant_header': plotter.variant_header(),
'variant_rows': plotter.variant_rows(),
'amplicount_header': plotter.amplicount_header(),
'amplicount_rows': plotter.amplicount_rows(),
'heatmap_plot': plotter.heatmap_plot(),
'koscores_header': plotter.koscores_header(),
'koscores_rows': plotter.koscores_rows(),
'tsearch_plot': plotter.targeted_search_plot(),
'tsearch_config_header': plotter.tsearch_config_header(),
'tsearch_config_rows': plotter.tsearch_config_rows(),
'tsearch_header': plotter.tsearch_header(),
'tsearch_rows': plotter.tsearch_rows(),
}
self.logger.debug('project return_map')
if 'submit_project_data' in self.request.params:
file_path = None
try:
error = False
file_path = self._upload("layoutfile", ".xlsx")
self.dbsession.begin_nested()
loader = ProjectDataLoader(self.dbsession, project.geid,
file_path)
loader.load()
self.dbsession.commit()
shutil.copyfile(
file_path,
os.path.join(project.project_folder,
"{}.xlsx".format(project.geid)))
project_header, project_rows = self.get_project_table(project)
target_header, target_rows = self.get_target_table(project)
guide_header, guide_rows = self.get_guide_table(project)
amplicon_header, amplicon_rows = self.get_amplicon_table(
project)
layout_header, layout_rows = self.get_layout_table(project)
return_map = {
'project': project,
'title': "GenEditID",
'subtitle': "Project: {}".format(project.geid),
'info':
"Project configuration file has been uploaded successfully.",
'error': False,
'project_header': project_header,
'project_rows': project_rows,
'target_header': target_header,
'target_rows': target_rows,
'guide_header': guide_header,
'guide_rows': guide_rows,
'amplicon_header': amplicon_header,
'amplicon_rows': amplicon_rows,
'layout_header': layout_header,
'layout_rows': layout_rows,
'config_header': plotter.config_header(),
'config_rows': plotter.config_rows(),
'coverage_plot': plotter.coverage_plot(),
'coverage_header': plotter.coverage_header(),
'coverage_rows': plotter.coverage_rows(),
'impact_plot': plotter.variant_impact_plot(),
'impact_header': plotter.impact_header(),
'impact_rows': plotter.impact_rows(),
'variant_header': plotter.variant_header(),
'variant_rows': plotter.variant_rows(),
'amplicount_header': plotter.amplicount_header(),
'amplicount_rows': plotter.amplicount_rows(),
'heatmap_plot': plotter.heatmap_plot(),
'koscores_header': plotter.koscores_header(),
'koscores_rows': plotter.koscores_rows(),
'tsearch_plot': plotter.targeted_search_plot(),
'tsearch_config_header': plotter.tsearch_config_header(),
'tsearch_config_rows': plotter.tsearch_config_rows(),
'tsearch_header': plotter.tsearch_header(),
'tsearch_rows': plotter.tsearch_rows(),
}
return HTTPFound(
self.request.route_url('project', gepid=project.geid))
except FinderException as e:
self.dbsession.rollback()
error = "Unexpected finder error: {}".format(e)
self.logger.error(error)
except LoaderException as e:
self.dbsession.rollback()
error = "Unexpected loader error: {}".format(e)
self.logger.error(error)
except ValueError as e:
self.dbsession.rollback()
error = "Unexpected value error: {}".format(e)
self.logger.error(error)
except DBAPIError as e:
self.dbsession.rollback()
error = "Unexpected database error: {}".format(e)
self.logger.error(error)
except AttributeError as e:
self.dbsession.rollback()
error = "Unexpected error: {}".format(e)
if not file_path:
error = "No file selected. Please select a file before uploading."
self.logger.error(error)
finally:
if file_path:
try:
os.remove(file_path)
except OSError:
pass
return_map['error'] = error
return return_map
return return_map