def test_parse_panel_info_lines():
## GIVEN a panel with some info
panel_lines = [
'##panel_id=panel1',
'##institute=cust000',
'##version=1.0',
'##date=2016-12-09',
'##display_name=Test panel',
'#hgnc_id\thgnc_symbol',
'7481\tMT-TF'
]
## WHEN parsing the information
panel_info = get_panel_info(panel_lines)
## THEN assert that no information except a date is returned
for key in panel_info:
if key == 'panel_id':
assert panel_info[key] == 'panel1'
elif key == 'institute':
assert panel_info[key] == 'cust000'
elif key == 'version':
assert panel_info[key] == '1.0'
elif key == 'display_name':
assert panel_info[key] == 'Test panel'
elif key == 'date':
assert type(panel_info[key]) is type(datetime.datetime.now())
def test_parse_panel_info_lines():
## GIVEN a panel with some info
panel_lines = [
"##panel_id=panel1",
"##institute=cust000",
"##version=1.0",
"##date=2016-12-09",
"##display_name=Test panel",
"#hgnc_id\thgnc_symbol",
"7481\tMT-TF",
]
## WHEN parsing the information
panel_info = get_panel_info(panel_lines)
## THEN assert that no information except a date is returned
for key in panel_info:
if key == "panel_id":
assert panel_info[key] == "panel1"
elif key == "institute":
assert panel_info[key] == "cust000"
elif key == "version":
assert panel_info[key] == "1.0"
elif key == "display_name":
assert panel_info[key] == "Test panel"
elif key == "date":
assert type(panel_info[key]) is type(datetime.datetime.now())
def test_parse_panel_info_no_info():
## GIVEN no information at all
panel_lines = []
## WHEN parsing the information
panel_info = get_panel_info(panel_lines)
## THEN assert that no information except a date is returned
for key in panel_info:
if key != "date":
assert panel_info[key] is None
else:
assert type(panel_info[key]) is type(datetime.datetime.now())
def test_parse_panel_info_no_info():
## GIVEN no information at all
panel_lines = []
## WHEN parsing the information
panel_info = get_panel_info(panel_lines)
## THEN assert that no information except a date is returned
for key in panel_info:
if key != 'date':
assert panel_info[key] == None
else:
assert type(panel_info[key]) is type(datetime.datetime.now())
def test_parse_panel_file(panel_handle):
## GIVEN a panel with some info
panel_lines = panel_handle
## WHEN parsing the information
panel_info = get_panel_info(panel_lines)
## THEN assert that no information except a date is returned
for key in panel_info:
if key == "panel_id":
assert panel_info[key] == "panel1"
elif key == "institute":
assert panel_info[key] == "cust000"
elif key == "version":
assert panel_info[key] == "1.0"
elif key == "display_name":
assert panel_info[key] == "Test panel"
elif key == "date":
assert type(panel_info[key]) is type(datetime.datetime.now())
def test_parse_panel_file(panel_handle):
## GIVEN a panel with some info
panel_lines = panel_handle
## WHEN parsing the information
panel_info = get_panel_info(panel_lines)
## THEN assert that no information except a date is returned
for key in panel_info:
if key == 'panel_id':
assert panel_info[key] == 'panel1'
elif key == 'institute':
assert panel_info[key] == 'cust000'
elif key == 'version':
assert panel_info[key] == '1.0'
elif key == 'display_name':
assert panel_info[key] == 'Test panel'
elif key == 'date':
assert type(panel_info[key]) is type(datetime.datetime.now())
def test_parse_panel_file(panel_handle):
## GIVEN a panel with some info
panel_lines = panel_handle
## WHEN parsing the information
panel_info = get_panel_info(panel_lines)
## THEN assert that no information except a date is returned
for key in panel_info:
if key == 'panel_id':
assert panel_info[key] == 'panel1'
elif key == 'institute':
assert panel_info[key] == 'cust000'
elif key == 'version':
assert panel_info[key] == '1.0'
elif key == 'display_name':
assert panel_info[key] == 'Test panel'
elif key == 'date':
assert type(panel_info[key]) is type(datetime.datetime.now())
def test_parse_panel_info_lines():
## GIVEN a panel with some info
panel_lines = [
'##panel_id=panel1', '##institute=cust000', '##version=1.0',
'##date=2016-12-09', '##display_name=Test panel',
'#hgnc_id\thgnc_symbol', '7481\tMT-TF'
]
## WHEN parsing the information
panel_info = get_panel_info(panel_lines)
## THEN assert that no information except a date is returned
for key in panel_info:
if key == 'panel_id':
assert panel_info[key] == 'panel1'
elif key == 'institute':
assert panel_info[key] == 'cust000'
elif key == 'version':
assert panel_info[key] == '1.0'
elif key == 'display_name':
assert panel_info[key] == 'Test panel'
elif key == 'date':
assert type(panel_info[key]) is type(datetime.datetime.now())
def panel(context, date, display_name, version, panel_type, panel_id, path, institute, omim, api_key):
"""Add a gene panel to the database."""
adapter = context.obj['adapter']
if not path:
if not omim:
LOG.warning("Please provide a gene panel file or specify omim")
context.abort()
if omim:
api_key = api_key or context.obj.get('omim_api_key')
if not api_key:
LOG.warning("Please provide a omim api key to load the omim gene panel")
context.abort()
#Check if OMIM-AUTO exists
if adapter.gene_panel(panel_id='OMIM-AUTO'):
LOG.warning("OMIM-AUTO already exists in database")
LOG.info("To create a new version use scout update omim")
return
try:
adapter.load_omim_panel(api_key, version=1.0)
except Exception as err:
LOG.error(err)
context.abort()
return
panel_lines = get_file_handle(path)
try:
panel_info = get_panel_info(
panel_lines=panel_lines,
panel_id=panel_id,
institute=institute,
version=version,
date=date,
display_name=display_name
)
except Exception as err:
LOG.warning(err)
context.abort()
version = None
if panel_info.get('version'):
version = float(panel_info['version'])
panel_id = panel_info['panel_id']
display_name = panel_info['display_name'] or panel_id
institute = panel_info['institute']
date = panel_info['date']
if not institute:
LOG.warning("A Panel has to belong to a institute")
context.abort()
#Check if institute exists in database
if not adapter.institute(institute):
LOG.warning("Institute {0} does not exist in database".format(institute))
context.abort()
if not panel_id:
LOG.warning("A Panel has to have a panel id")
context.abort()
if version:
existing_panel = adapter.gene_panel(panel_id, version)
else:
existing_panel = adapter.gene_panel(panel_id)
## Assuming version 1.0
version = 1.0
if existing_panel:
LOG.info("found existing panel")
if version == existing_panel['version']:
LOG.warning("Panel with same version exists in database")
LOG.info("Reload with updated version")
context.abort()
display_name = display_name or existing_panel['display_name']
institute = institute or existing_panel['institute']
try:
adapter.load_panel(
path=path,
institute=institute,
panel_id=panel_id,
date=date,
panel_type=panel_type,
version=version,
display_name=display_name
)
except Exception as err:
LOG.warning(err)
context.abort()
def load_panel(
panel_path,
adapter,
date=None,
display_name=None,
version=None,
panel_type=None,
panel_id=None,
institute=None,
):
"""Load a manually curated gene panel into scout
Args:
panel_path(str): path to gene panel file
adapter(scout.adapter.MongoAdapter)
date(str): date of gene panel on format 2017-12-24
display_name(str)
version(float)
panel_type(str)
panel_id(str)
institute(str)
"""
panel_lines = get_file_handle(panel_path)
try:
# This will parse panel metadata if includeed in panel file
panel_info = get_panel_info(
panel_lines=panel_lines,
panel_id=panel_id,
institute=institute,
version=version,
date=date,
display_name=display_name,
)
except Exception as err:
raise err
version = None
if panel_info.get("version"):
version = float(panel_info["version"])
panel_id = panel_info["panel_id"]
display_name = panel_info["display_name"] or panel_id
institute = panel_info["institute"]
date = panel_info["date"]
if not institute:
raise SyntaxError("A Panel has to belong to a institute")
# Check if institute exists in database
if not adapter.institute(institute):
raise SyntaxError("Institute {0} does not exist in database".format(institute))
if not panel_id:
raise SyntaxError("A Panel has to have a panel id")
if version:
existing_panel = adapter.gene_panel(panel_id, version)
else:
## Assuming version 1.0
existing_panel = adapter.gene_panel(panel_id)
version = 1.0
LOG.info("Set version to %s", version)
if existing_panel:
LOG.info("found existing panel")
if version == existing_panel["version"]:
LOG.warning("Panel with same version exists in database")
LOG.info("Reload with updated version")
raise SyntaxError()
display_name = display_name or existing_panel["display_name"]
institute = institute or existing_panel["institute"]
parsed_panel = parse_gene_panel(
path=panel_path,
institute=institute,
panel_type=panel_type,
date=date,
version=version,
panel_id=panel_id,
display_name=display_name,
)
try:
adapter.load_panel(parsed_panel=parsed_panel)
except Exception as err:
raise err
def panel(context, date, display_name, version, panel_type, panel_id, path,
institute):
"""Add a gene panel to the database."""
adapter = context.obj['adapter']
panel_lines = get_file_handle(path)
try:
panel_info = get_panel_info(panel_lines=panel_lines,
panel_id=panel_id,
institute=institute,
version=version,
date=date,
display_name=display_name)
except Exception as err:
LOG.warning(err)
context.abort()
version = None
if panel_info.get('version'):
version = float(panel_info['version'])
panel_id = panel_info['panel_id']
display_name = panel_info['display_name'] or panel_id
institute = panel_info['institute']
date = panel_info['date']
if not institute:
LOG.warning("A Panel has to belong to a institute")
context.abort()
if not panel_id:
LOG.warning("A Panel has to have a panel id")
context.abort()
if version:
existing_panel = adapter.gene_panel(panel_id, version)
else:
existing_panel = adapter.gene_panel(panel_id)
## Assuming version 1.0
version = 1.0
if existing_panel:
LOG.info("found existing panel")
if version == existing_panel['version']:
LOG.warning("Panel with same version exists in database")
LOG.info("Reload with updated version")
context.abort()
display_name = display_name or existing_panel['display_name']
institute = institute or existing_panel['institute']
try:
adapter.load_panel(path=path,
institute=institute,
panel_id=panel_id,
date=date,
panel_type=panel_type,
version=version,
display_name=display_name)
except Exception as err:
LOG.warning(err)
context.abort()