def database(context, institute_name, user_name, user_mail, api_key):
"""Setup a scout database."""
LOG.info("Running scout setup database")
# Fetch the omim information
api_key = api_key or context.obj.get('omim_api_key')
if not api_key:
LOG.warning("Please provide a omim api key with --api-key")
context.abort()
institute_name = institute_name or context.obj['institute_name']
user_name = user_name or context.obj['user_name']
user_mail = user_mail or context.obj['user_mail']
adapter = context.obj['adapter']
LOG.info("Setting up database %s", context.obj['mongodb'])
setup_scout(
adapter=adapter,
institute_id=institute_name,
user_name=user_name,
user_mail = user_mail,
api_key=api_key
)
def test_setup_scout(real_adapter):
"""Test to populate a demo instance of scout"""
adapter = real_adapter
## GIVEN an empty adapter
assert adapter.all_genes().count() == 0
## WHEN setting up a demo instance of scout
setup_scout(adapter=adapter, demo=True)
## THEN make sure that stuff has been added
assert adapter.all_genes().count() > 0
def demo(context):
"""Setup a scout demo instance. This instance will be populated with a
case, a gene panel and some variants.
"""
LOG.info("Running scout setup demo")
institute_name = context.obj['institute_name']
user_name = context.obj['user_name']
user_mail = context.obj['user_mail']
adapter = context.obj['adapter']
LOG.info("Setting up database %s", context.obj['mongodb'])
setup_scout(
adapter=adapter,
institute_id=institute_name,
user_name=user_name,
user_mail = user_mail,
demo=True
)
def database(context, institute_name, user_name, user_mail, api_key):
"""Setup a scout database."""
LOG.info("Running scout setup database")
# Fetch the omim information
api_key = api_key or current_app.config.get('OMIM_API_KEY')
if not api_key:
LOG.warning("Please provide a omim api key with --api-key")
raise click.Abort()
institute_name = institute_name or context.obj['institute_name']
user_name = user_name or context.obj['user_name']
user_mail = user_mail or context.obj['user_mail']
adapter = context.obj['adapter']
LOG.info("Setting up database %s", context.obj['mongodb'])
setup_scout(adapter=adapter,
institute_id=institute_name,
user_name=user_name,
user_mail=user_mail,
api_key=api_key)
def database(context, institute_name, user_name, user_mail, api_key):
"""Setup a scout database."""
LOG.info("Running scout setup database")
# Fetch the omim information
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()
institute_name = institute_name or context.obj['institute_name']
user_name = user_name or context.obj['user_name']
user_mail = user_mail or context.obj['user_mail']
adapter = context.obj['adapter']
LOG.info("Setting up database %s", context.obj['mongodb'])
setup_scout(adapter=adapter,
institute_id=institute_name,
user_name=user_name,
user_mail=user_mail,
api_key=api_key)
def database(
context,
institute_name,
user_name,
user_mail,
api_key,
mim2gene,
genemap,
hgnc,
exac,
ensgenes37,
ensgenes38,
enstx37,
enstx38,
hpogenes,
hpoterms,
hpo_to_genes,
files,
):
"""Setup a scout database."""
LOG.info("Running scout setup database")
# Fetch the omim information
api_key = api_key or current_app.config.get("OMIM_API_KEY")
if not api_key:
LOG.warning("No omim api key provided. This means information will be lost in scout")
LOG.info("Please request an OMIM api key and run scout update genes")
institute_name = institute_name or context.obj["institute_name"]
user_name = user_name or context.obj["user_name"]
user_mail = user_mail or context.obj["user_mail"]
adapter = context.obj["adapter"]
resource_files = {
"mim2gene_path": mim2gene,
"genemap_path": genemap,
"hgnc_path": hgnc,
"exac_path": exac,
"genes37_path": ensgenes37,
"genes38_path": ensgenes38,
"transcripts37_path": enstx37,
"transcripts38_path": enstx38,
"hpogenes_path": hpogenes,
"hpoterms_path": hpoterms,
"hpo_to_genes_path": hpo_to_genes,
}
LOG.info("Setting up database %s", context.obj["mongodb"])
if files:
for path in pathlib.Path(files).glob("**/*"):
if path.stem == "mim2genes":
resource_files["mim2gene_path"] = str(path.resolve())
if path.stem == "genemap2":
resource_files["genemap_path"] = str(path.resolve())
if path.stem == "hgnc":
resource_files["hgnc_path"] = str(path.resolve())
if path.stem == "fordist_cleaned_exac_r03_march16_z_pli_rec_null_data":
resource_files["exac_path"] = str(path.resolve())
if path.stem == "ensembl_genes_37":
resource_files["genes37_path"] = str(path.resolve())
if path.stem == "ensembl_genes_38":
resource_files["genes38_path"] = str(path.resolve())
if path.stem == "ensembl_transcripts_37":
resource_files["transcripts37_path"] = str(path.resolve())
if path.stem == "ensembl_transcripts_38":
resource_files["transcripts38_path"] = str(path.resolve())
if path.stem == "genes_to_phenotype":
resource_files["hpogenes_path"] = str(path.resolve())
if path.stem == "hpo":
resource_files["hpoterms_path"] = str(path.resolve())
if path.stem == "phenotype_to_genes":
resource_files["hpo_to_genes_path"] = str(path.resolve())
setup_scout(
adapter=adapter,
institute_id=institute_name,
user_name=user_name,
user_mail=user_mail,
api_key=api_key,
resource_files=resource_files,
)