def real_database(database_name, institute_obj, user_obj, genes, panel_info):
"""Setup a real database with populated data"""
mongo_client = pymongo.MongoClient()
mongo_client.drop_database(database_name)
database = mongo_client[database_name]
adapter = MongoAdapter(database)
# Populate the database
adapter.add_institute(institute_obj)
adapter.add_user(user_obj)
load_hgnc_genes(adapter, genes)
adapter.hgnc_collection.create_index([('build', pymongo.ASCENDING),
('hgnc_symbol', pymongo.ASCENDING)])
load_panel(adapter=adapter, panel_info=panel_info)
# load_hpo(adapter=gene_database, hpo_lines=hpo_terms_handle, disease_lines=genemap_handle)
# adapter.add_case(case_obj)
# for variant in variant_objs:
# adapter.load_variant(variant)
yield adapter
mongo_client.drop_database(database_name)
def test_load_panel(gene_database, panel_info):
# GIVEN an database with genes but no panels
assert gene_database.gene_panels().count() == 0
# WHEN loading a gene panel
load_panel(adapter=gene_database, panel_info=panel_info)
# THEN make sure that the panel is loaded
assert gene_database.gene_panel(panel_id=panel_info['panel_name'])
def panel(
path,
date,
display_name,
version,
panel_type,
panel_id,
institute,
maintainer,
omim,
genemap2,
mim2genes,
api_key,
panel_app,
):
"""Add a gene panel to the database."""
adapter = store
institute = institute or "cust000"
if omim:
_panel_omim(adapter, genemap2, mim2genes, api_key, institute,
maintainer)
return
if panel_app:
# try:
load_panel_app(adapter, panel_id, institute=institute)
# except Exception as err:
# LOG.warning(err)
# raise click.Abort()
return
if path is None:
LOG.info("Please provide a panel")
return
try:
load_panel(
panel_path=path,
adapter=adapter,
date=date,
display_name=display_name,
version=version,
panel_type=panel_type,
panel_id=panel_id,
institute=institute,
maintainer=maintainer,
)
except Exception as err:
LOG.warning(err)
raise click.Abort()
return
def panel(path, date, display_name, version, panel_type, panel_id, institute,
omim, api_key, panel_app):
"""Add a gene panel to the database."""
adapter = store
institute = institute or 'cust000'
if not path and not omim:
LOG.warning("Please provide a gene panel file or specify omim")
context.abort()
if omim:
api_key = api_key or current_app.config.get('OMIM_API_KEY')
if not api_key:
LOG.warning(
"Please provide a omim api key to load the omim gene panel")
raise click.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
# Here we know that there is no panel loaded
try:
adapter.load_omim_panel(api_key, institute=institute)
except Exception as err:
LOG.error(err)
raise click.Abort()
if panel_app:
# try:
load_panel_app(adapter, panel_id, institute=institute)
# except Exception as err:
# LOG.warning(err)
# raise click.Abort()
if (omim or panel_app):
return
if path is None:
LOG.info("Please provide a panel")
return
try:
load_panel(path, adapter, date, display_name, version, panel_type,
panel_id, institute)
except Exception as err:
LOG.warning(err)
raise click.Abort()
def test_load_panel(gene_database, panel_info):
# GIVEN an database with genes but no panels
adapter = gene_database
assert sum(1 for i in adapter.gene_panels()) == 0
# WHEN loading a gene panel
load_panel(panel_path=panel_info['file'],
adapter=adapter,
institute=panel_info['institute'],
panel_id=panel_info['panel_name'],
panel_type=panel_info['type'],
version=panel_info['version'],
display_name=panel_info['full_name'])
# THEN make sure that the panel is loaded
assert adapter.gene_panel(panel_id=panel_info['panel_name'])
def test_load_panel(gene_database, panel_info):
# GIVEN an database with genes but no panels
adapter = gene_database
assert adapter.gene_panels().count() == 0
# WHEN loading a gene panel
load_panel(
panel_path=panel_info['file'],
adapter=adapter,
institute=panel_info['institute'],
panel_id=panel_info['panel_name'],
panel_type=panel_info['type'],
version=panel_info['version'],
display_name=panel_info['full_name']
)
# THEN make sure that the panel is loaded
assert adapter.gene_panel(panel_id=panel_info['panel_name'])
def panel(context, path, date, display_name, version, panel_type, panel_id, institute, omim, api_key, panel_app):
"""Add a gene panel to the database."""
adapter = context.obj['adapter']
institute = institute or 'cust000'
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
# Here we know that there is no panel loaded
try:
adapter.load_omim_panel(api_key, institute=institute)
except Exception as err:
LOG.error(err)
context.abort()
if panel_app:
# try:
load_panel_app(adapter, panel_id, institute=institute)
# except Exception as err:
# LOG.warning(err)
# context.abort()
if (omim or panel_app):
return
if path is None:
LOG.info("Please provide a panel")
return
try:
load_panel(path, adapter, date, display_name, version, panel_type, panel_id, institute)
except Exception as err:
LOG.warning(err)
context.abort()
def panel(
path,
date,
display_name,
version,
panel_type,
panel_id,
institute,
omim,
genemap2,
mim2genes,
api_key,
panel_app,
):
"""Add a gene panel to the database."""
adapter = store
institute = institute or "cust000"
if omim:
mim_files = None
if genemap2 and mim2genes:
mim_files = {
"genemap2": list(get_file_handle(genemap2)),
"mim2genes": list(get_file_handle(mim2genes)),
}
api_key = api_key or current_app.config.get("OMIM_API_KEY")
if not api_key and mim_files is None:
LOG.warning(
"Please provide a omim api key to load the omim gene panel")
raise click.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
if not mim_files:
try:
mim_files = fetch_mim_files(api_key=api_key,
genemap2=True,
mim2genes=True)
except Exception as err:
raise err
# Here we know that there is no panel loaded
try:
adapter.load_omim_panel(
genemap2_lines=mim_files["genemap2"],
mim2gene_lines=mim_files["mim2genes"],
institute=institute,
)
except Exception as err:
LOG.error(err)
raise click.Abort()
if panel_app:
# try:
load_panel_app(adapter, panel_id, institute=institute)
# except Exception as err:
# LOG.warning(err)
# raise click.Abort()
if omim or panel_app:
return
if path is None:
LOG.info("Please provide a panel")
return
try:
load_panel(path, adapter, date, display_name, version, panel_type,
panel_id, institute)
except Exception as err:
LOG.warning(err)
raise click.Abort()