def new_panel(store, institute_id, panel_name, display_name, csv_lines):
"""Create a new gene panel."""
institute_obj = store.institute(institute_id)
if institute_obj is None:
flash("{}: institute not found".format(institute_id))
return None
panel_obj = store.gene_panel(panel_name)
if panel_obj:
flash("panel already exists: {} - {}".format(
panel_obj['panel_name'], panel_obj['display_name']))
return None
log.debug("parse genes from CSV input")
try:
new_genes = parse_genes(csv_lines)
except SyntaxError as error:
flash(error.args[0], 'danger')
return None
log.debug("build new gene panel")
panel_data = build_panel(
dict(
panel_name=panel_name,
institute=institute_obj['_id'],
version=1.0,
date=dt.datetime.now(),
display_name=display_name,
genes=new_genes,
), store)
panel_obj = store.add_gene_panel(panel_data)
return panel_obj
def test_build_panel(institute_database, test_gene):
## GIVEN a adapter with a gene and a institute
adapter = institute_database
adapter.load_hgnc_gene(test_gene)
# panel_id and display_name contain leading and trailing whitespaces to test that the spaces are removed
panel_info = {
"panel_id": " panel1",
"institute": "cust000",
"date": datetime.now(),
"display_name": "first panel ",
"description": "first panel description",
"genes": [{
"hgnc_id": 1
}],
"version": 1.0,
}
## WHEN building a gene panel
panel_obj = build_panel(panel_info, adapter)
## THEN assert that the panel was given the right attributes and that the leading and trailing spaces were removed
assert panel_obj["institute"] == panel_info["institute"]
assert panel_obj["panel_name"] == "panel1"
assert panel_obj["display_name"] == "first panel"
assert len(panel_info["genes"]) == len(panel_obj["genes"])
def new_panel(store, institute_id, panel_name, display_name, csv_lines, description=None):
"""Create a new gene panel.
Args:
store(scout.adapter.MongoAdapter)
institute_id(str)
panel_name(str)
display_name(str)
csv_lines(iterable(str)): Stream with genes
description(str)
Returns:
panel_id: the ID of the new panel document created or None
"""
institute_obj = store.institute(institute_id)
if institute_obj is None:
flash("{}: institute not found".format(institute_id))
return None
panel_obj = store.gene_panel(panel_name)
if panel_obj:
flash("panel already exists: {} - {}".format(panel_obj['panel_name'],
panel_obj['display_name']))
return None
log.debug("parse genes from CSV input")
try:
new_genes = parse_genes(csv_lines)
except SyntaxError as error:
flash(error.args[0], 'danger')
return None
log.debug("build new gene panel")
panel_id = None
try:
panel_data = build_panel(dict(
panel_name=panel_name,
institute=institute_obj['_id'],
version=1.0,
date=dt.datetime.now(),
display_name=display_name,
description=description,
genes=new_genes,
), store)
panel_id= store.add_gene_panel(panel_data)
except Exception as err:
log.error('An error occurred while adding the gene panel {}'.format(err))
return panel_id
def new_panel(store, institute_id, panel_name, display_name, csv_lines):
"""Create a new gene panel.
Args:
store(scout.adapter.MongoAdapter)
institute_id(str)
panel_name(str)
display_name(str)
csv_lines(iterable(str)): Stream with genes
Returns:
panel_id: the ID of the new panel document created or None
"""
institute_obj = store.institute(institute_id)
if institute_obj is None:
flash("{}: institute not found".format(institute_id))
return None
panel_obj = store.gene_panel(panel_name)
if panel_obj:
flash("panel already exists: {} - {}".format(panel_obj['panel_name'],
panel_obj['display_name']))
return None
log.debug("parse genes from CSV input")
try:
new_genes = parse_genes(csv_lines)
except SyntaxError as error:
flash(error.args[0], 'danger')
return None
log.debug("build new gene panel")
panel_id = None
try:
panel_data = build_panel(dict(
panel_name=panel_name,
institute=institute_obj['_id'],
version=1.0,
date=dt.datetime.now(),
display_name=display_name,
genes=new_genes,
), store)
panel_id= store.add_gene_panel(panel_data)
except Exception as err:
log.error('An error occurred while adding the gene panel {}'.format(err))
return panel_id
def test_build_panel_no_date(institute_database, test_gene):
## GIVEN a adapter with a gene and a institute
adapter = institute_database
adapter.load_hgnc_gene(test_gene)
## WHEN building a gene panel without date
panel_info = {
'panel_name': 'panel1',
'institute': 'cust000',
'display_name': 'first panel',
'genes': [{'hgnc_id':1}],
'version': 1.0,
}
## THEN assert a KeyError was raised
with pytest.raises(KeyError):
panel_obj = build_panel(panel_info, adapter)
def test_build_panel_no_date(institute_database, test_gene):
## GIVEN a adapter with a gene and a institute
adapter = institute_database
adapter.load_hgnc_gene(test_gene)
## WHEN building a gene panel without date
panel_info = {
"panel_name": "panel1",
"institute": "cust000",
"display_name": "first panel",
"genes": [{"hgnc_id": 1}],
"version": 1.0,
}
## THEN assert a KeyError was raised
with pytest.raises(KeyError):
panel_obj = build_panel(panel_info, adapter)
def test_build_panel_non_existing_insitute(institute_database, test_gene):
## GIVEN a adapter with a gene and a institute
adapter = institute_database
adapter.load_hgnc_gene(test_gene)
assert adapter.institute('cust001') is None
## WHEN building a gene panel with wrong institute
panel_info = {
'panel_name': 'panel1',
'institute': 'cust0001',
'date': datetime.now(),
'display_name': 'first panel',
'genes': [{'hgnc_id':1}],
'version': 1.0,
}
## THEN assert that an IntegrityError is raised
with pytest.raises(IntegrityError):
panel_obj = build_panel(panel_info, adapter)
def test_build_panel_non_existing_insitute(institute_database, test_gene):
## GIVEN a adapter with a gene and a institute
adapter = institute_database
adapter.load_hgnc_gene(test_gene)
assert adapter.institute("cust001") is None
## WHEN building a gene panel with wrong institute
panel_info = {
"panel_name": "panel1",
"institute": "cust0001",
"date": datetime.now(),
"display_name": "first panel",
"genes": [{"hgnc_id": 1}],
"version": 1.0,
}
## THEN assert that an IntegrityError is raised
with pytest.raises(IntegrityError):
panel_obj = build_panel(panel_info, adapter)
def test_build_panel(institute_database, test_gene):
## GIVEN a adapter with a gene and a institute
adapter = institute_database
adapter.load_hgnc_gene(test_gene)
panel_info = {
'panel_id': 'panel1',
'institute': 'cust000',
'date': datetime.now(),
'display_name': 'first panel',
'description' : 'first panel description',
'genes': [{'hgnc_id':1}],
'version': 1.0,
}
## WHEN building a gene panel
panel_obj = build_panel(panel_info, adapter)
## THEN assert that the panel was given the right attributes
assert panel_obj['institute'] == panel_info['institute']
assert len(panel_info['genes']) == len(panel_obj['genes'])
def test_build_panel_non_existing_gene(institute_database, institute_obj):
"""Test creating a panel by proving one gene that is not in database"""
### GIVEN a adapter with an institute and no genes
adapter = institute_database
assert adapter.hgnc_collection.find_one() is None
## WHEN building a gene panel with wrong institute
panel_info = {
"panel_name": "panel1",
"institute": institute_obj["_id"],
"date": datetime.now(),
"display_name": "first panel",
"genes": [{
"hgnc_id": 1
}],
"version": 1.0,
}
## THEN assert that an IntegrityError is raised
with pytest.raises(IntegrityError):
panel_obj = build_panel(panel_info, adapter)
def new_panel(
store,
institute_id,
panel_name,
display_name,
csv_lines,
maintainer=None,
description=None,
):
"""Create a new gene panel.
Args:
store(scout.adapter.MongoAdapter)
institute_id(str)
panel_name(str)
display_name(str)
csv_lines(iterable(str)): Stream with genes
maintainer(list(user._id))
description(str)
Returns:
panel_id: the ID of the new panel document created or None
"""
institute_obj = store.institute(institute_id)
if institute_obj is None:
flash("{}: institute not found".format(institute_id))
return None
panel_obj = store.gene_panel(panel_name)
if panel_obj:
flash(
"panel already exists: {} - {}".format(
panel_obj["panel_name"], panel_obj["display_name"]
),
"danger",
)
return None
LOG.debug("parse genes from CSV input")
try:
new_genes = parse_genes(csv_lines)
except SyntaxError as error:
flash(error.args[0], "danger")
LOG.debug("Ooops!")
return None
LOG.debug("build new gene panel")
panel_id = None
try:
panel_data = build_panel(
dict(
panel_name=panel_name,
institute=institute_obj["_id"],
version=1.0,
maintainer=maintainer,
date=dt.datetime.now(),
display_name=display_name,
description=description,
genes=new_genes,
hidden=False,
),
store,
)
panel_id = store.add_gene_panel(panel_data)
except Exception as err:
flash(str(err), "danger")
return panel_id
