def panel(panel, version, update_date, update_version):
"""
Update a panel in the database
"""
adapter = store
# Check that the panel exists
panel_obj = adapter.gene_panel(panel, version=version)
if not panel_obj:
LOG.warning("Panel %s (version %s) could not be found" % (panel, version))
click.Abort()
date_obj = None
if update_date:
try:
date_obj = get_date(update_date)
except Exception as err:
LOG.warning(err)
click.Abort()
update_panel(
adapter,
panel,
panel_version=panel_obj["version"],
new_version=update_version,
new_date=date_obj,
)
def panel(context, panel, version, update_date, update_version):
"""
Update a panel in the database
"""
adapter = context.obj['adapter']
#Check that the panel exists
panel_obj = adapter.gene_panel(panel, version=version)
# for panel_obj in adapter.panel_collection.find({'panel_name': 'CAN'}):
# print(panel_obj['panel_name'], panel_obj['version'])
#
# print(panel_obj)
if not panel_obj:
LOG.warning("Panel %s (version %s) could not be found" % (panel, version))
context.abort()
date_obj = None
if update_date:
try:
date_obj = get_date(update_date)
except Exception as err:
LOG.warning(err)
context.abort()
updated_panel = update_panel(
adapter,
panel,
panel_version=panel_obj['version'],
new_version=update_version,
new_date=date_obj
)
def test_update_panel_version(panel_database, case_obj):
adapter = panel_database
adapter._add_case(case_obj)
## GIVEN an adapter with a case with gene panels
case_obj = adapter.case_collection.find_one()
panel_obj = adapter.panel_collection.find_one()
case_id = case_obj['_id']
# There is infirmation about a panel both in the panel collection
# and on the case object. This is fine until one starts to manipulate the objects
panel = case_obj['panels'][0]
panel_version = panel['version']
panel_name = panel['panel_name']
panel_id = panel['panel_id']
new_panel_version = panel_version + 1
## WHEN updating the panel version
updated_panel = update_panel(adapter, panel_name, panel_version,
new_panel_version)
## THEN assert that the panel version was updated both in panel and case
panel_obj = adapter.panel_collection.find_one({'_id': panel_id})
assert panel_obj['version'] == new_panel_version
case_obj = adapter.case_collection.find_one({'_id': case_id})
for panel in case_obj['panels']:
assert panel['version'] == new_panel_version
def test_update_panel_date(adapter, case_obj, testpanel_obj):
adapter.case_collection.insert_one(case_obj)
adapter.panel_collection.insert_one(testpanel_obj)
## GIVEN an adapter with a case with gene panels
new_date_obj = get_date("2015-03-12")
case_obj = adapter.case_collection.find_one()
panel_obj = adapter.panel_collection.find_one()
case_id = case_obj["_id"]
# There is infirmation about a panel both in the panel collection
# and on the case object. This is fine until one starts to manipulate the objects
case_panel = case_obj["panels"][0]
panel_version = case_panel["version"]
panel_name = case_panel["panel_name"]
panel_id = case_panel["panel_id"]
## WHEN updating the panel version
update_panel(adapter,
panel_name,
panel_version=None,
new_date=new_date_obj)
## THEN assert that the panel version was updated both in panel and case
updated_panel_obj = adapter.panel_collection.find_one({
"panel_name":
panel_name,
"version":
panel_version
})
assert updated_panel_obj["date"] == new_date_obj
case_obj = adapter.case_collection.find_one({"_id": case_id})
for panel in case_obj["panels"]:
assert panel["updated_at"] == new_date_obj
def test_update_panel_date(adapter, case_obj, dummypanel_obj):
adapter.case_collection.insert_one(case_obj)
adapter.panel_collection.insert_one(dummypanel_obj)
## GIVEN an adapter with a case with gene panels
new_date_obj = get_date('2015-03-12')
case_obj = adapter.case_collection.find_one()
panel_obj = adapter.panel_collection.find_one()
case_id = case_obj['_id']
# There is infirmation about a panel both in the panel collection
# and on the case object. This is fine until one starts to manipulate the objects
case_panel = case_obj['panels'][0]
panel_version = case_panel['version']
panel_name = case_panel['panel_name']
panel_id = case_panel['panel_id']
## WHEN updating the panel version
update_panel(adapter,
panel_name,
panel_version=None,
new_date=new_date_obj)
## THEN assert that the panel version was updated both in panel and case
updated_panel_obj = adapter.panel_collection.find_one({
'panel_name':
panel_name,
'version':
panel_version
})
assert updated_panel_obj['date'] == new_date_obj
case_obj = adapter.case_collection.find_one({'_id': case_id})
for panel in case_obj['panels']:
assert panel['updated_at'] == new_date_obj
def test_update_panel_version_multiple(adapter, case_obj, testpanel_obj):
adapter.case_collection.insert_one(case_obj)
adapter.panel_collection.insert_one(testpanel_obj)
case_obj["_id"] = "test_2"
# Add another case with same panels
adapter.case_collection.insert_one(case_obj)
## GIVEN an adapter with a case with gene panels
case_obj = adapter.case_collection.find_one()
panel_obj = adapter.panel_collection.find_one()
# There is infirmation about a panel both in the panel collection
# and on the case object. This is fine until one starts to manipulate the objects
panel = case_obj["panels"][0]
panel_version = panel["version"]
panel_name = panel["panel_name"]
panel_id = panel["panel_id"]
new_panel_version = panel_version + 1
## WHEN updating the panel version
update_panel(adapter, panel_name, panel_version, new_panel_version)
## THEN assert that the panel version was updated both in panel and case
updated_panel_obj = adapter.panel_collection.find_one({
"panel_name":
panel_name,
"version":
new_panel_version
})
assert updated_panel_obj["version"] == new_panel_version
for case_obj in adapter.case_collection.find():
for panel in case_obj["panels"]:
assert panel["version"] == new_panel_version
def test_update_panel_version(panel_database, case_obj):
adapter = panel_database
adapter._add_case(case_obj)
## GIVEN an adapter with a case with gene panels
case_obj = adapter.case_collection.find_one()
panel_obj = adapter.panel_collection.find_one()
case_id = case_obj['_id']
# There is infirmation about a panel both in the panel collection
# and on the case object. This is fine until one starts to manipulate the objects
panel = case_obj['panels'][0]
panel_version = panel['version']
panel_name = panel['panel_name']
panel_id = panel['panel_id']
new_panel_version = panel_version + 1
## WHEN updating the panel version
update_panel(adapter, panel_name, panel_version, new_panel_version)
## THEN assert that the panel version was updated for the panel object
updated_panel_obj = adapter.panel_collection.find_one(
{
'panel_name': panel_name,
'version': new_panel_version
})
assert updated_panel_obj['version'] == new_panel_version
case_obj = adapter.case_collection.find_one({'_id': case_id})
for panel in case_obj['panels']:
assert panel['version'] == new_panel_version
def test_update_panel_version(adapter, case_obj, testpanel_obj):
adapter.case_collection.insert_one(case_obj)
adapter.panel_collection.insert_one(testpanel_obj)
## GIVEN an adapter with a case with gene panels
case_obj = adapter.case_collection.find_one()
panel_obj = adapter.panel_collection.find_one()
assert case_obj
assert panel_obj
case_id = case_obj["_id"]
# There is information about a panel both in the panel collection
# and on the case object. This is fine until one starts to manipulate the objects
panel = case_obj["panels"][0]
panel_version = panel["version"]
panel_name = panel["panel_name"]
panel_id = panel["panel_id"]
new_panel_version = panel_version + 1
## WHEN updating the panel version
update_panel(adapter, panel_name, panel_version, new_panel_version)
## THEN assert that the panel version was updated for the panel object
updated_panel_obj = adapter.panel_collection.find_one({
"panel_name":
panel_name,
"version":
new_panel_version
})
assert updated_panel_obj["version"] == new_panel_version
case_obj = adapter.case_collection.find_one({"_id": case_id})
for panel in case_obj["panels"]:
assert panel["version"] == new_panel_version
def test_update_panel_date(panel_database, case_obj):
adapter = panel_database
adapter._add_case(case_obj)
## GIVEN an adapter with a case with gene panels
new_date_obj = get_date('2015-03-12')
case_obj = adapter.case_collection.find_one()
panel_obj = adapter.panel_collection.find_one()
case_id = case_obj['_id']
# There is infirmation about a panel both in the panel collection
# and on the case object. This is fine until one starts to manipulate the objects
case_panel = case_obj['panels'][0]
panel_version = case_panel['version']
panel_name = case_panel['panel_name']
panel_id = case_panel['panel_id']
## WHEN updating the panel version
update_panel(adapter, panel_name, panel_version=None, new_date=new_date_obj)
## THEN assert that the panel version was updated both in panel and case
updated_panel_obj = adapter.panel_collection.find_one(
{
'panel_name': panel_name,
'version': panel_version
})
assert updated_panel_obj['date'] == new_date_obj
case_obj = adapter.case_collection.find_one({'_id': case_id})
for panel in case_obj['panels']:
assert panel['updated_at'] == new_date_obj
def panel(
panel, version, update_date, update_version, add_maintainer, revoke_maintainer
):
"""
Update a panel in the database
"""
adapter = store
# Check that the panel exists
panel_obj = adapter.gene_panel(panel, version=version)
if not panel_obj:
LOG.warning("Panel %s (version %s) could not be found", panel, version)
raise click.Abort()
date_obj = None
if update_date:
try:
date_obj = get_date(update_date)
except Exception as err:
LOG.warning(err)
raise click.Abort()
# Any mintainer updates?
new_maintainer = None
if add_maintainer:
user_obj = adapter.user(user_id=add_maintainer)
if not user_obj:
# Check if maintainers exist in the user database
LOG.warning(
"Maintainer user id %s does not exist in user database", add_maintainer
)
raise click.Abort()
new_maintainer = panel_obj.get("maintainer", [])
if add_maintainer in new_maintainer:
LOG.warning("User %s already in maintainer list.", add_maintainer)
raise click.Abort()
new_maintainer.append(add_maintainer)
if revoke_maintainer:
current_maintainers = panel_obj.get("maintainer", [])
try:
current_maintainers.remove(revoke_maintainer)
new_maintainer = current_maintainers
except ValueError:
LOG.warning(
"Maintainer user id %s is not a maintainer for panel %s. Current maintainers: %s",
revoke_maintainer,
panel,
current_maintainers,
)
update_panel(
adapter,
panel,
panel_version=panel_obj["version"],
new_version=update_version,
new_maintainer=new_maintainer,
new_date=date_obj,
)