def diseases(api_key, genemap2):
"""
Update disease terms in mongo database.
If no file is specified the file will be fetched from OMIM with the api-key
"""
adapter = store
# Fetch the omim information
api_key = api_key or current_app.config.get("OMIM_API_KEY")
if genemap2:
genemap_lines = get_file_handle(genemap2)
else:
if not api_key:
LOG.warning("Please provide a omim api key to load the omim gene panel")
raise click.Abort()
try:
mim_files = fetch_mim_files(api_key, genemap2=True)
genemap_lines = mim_files["genemap2"]
except Exception as err:
LOG.warning(err)
raise click.Abort()
LOG.info("Dropping DiseaseTerms")
adapter.disease_term_collection.drop()
LOG.debug("DiseaseTerms dropped")
load_disease_terms(adapter=adapter, genemap_lines=genemap_lines)
LOG.info("Successfully loaded all disease terms")
def diseases(context, api_key):
"""
Update disease terms in mongo database.
"""
adapter = context.obj['adapter']
# 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()
try:
mim_files = fetch_mim_files(api_key, genemap2=True)
except Exception as err:
LOG.warning(err)
context.abort()
LOG.info("Dropping DiseaseTerms")
adapter.disease_term_collection.drop()
LOG.debug("DiseaseTerms dropped")
load_disease_terms(
adapter=adapter,
genemap_lines=mim_files['genemap2'],
)
LOG.info("Successfully loaded all disease terms")
def diseases(api_key):
"""
Update disease terms in mongo database.
"""
adapter = store
# 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 to load the omim gene panel")
raise click.Abort()
try:
mim_files = fetch_mim_files(api_key, genemap2=True)
except Exception as err:
LOG.warning(err)
raise click.Abort()
LOG.info("Dropping DiseaseTerms")
adapter.disease_term_collection.drop()
LOG.debug("DiseaseTerms dropped")
load_disease_terms(
adapter=adapter,
genemap_lines=mim_files['genemap2'],
)
LOG.info("Successfully loaded all disease terms")
def diseases(ctx):
"""
Load the disease terms to the mongo database.
"""
adapter = ctx.obj['adapter']
logger.info("Dropping Disease Terms")
adapter.disease_term_collection.drop()
logger.debug("Disease Terms dropped")
logger.info("Loading disease info from file {0}".format(genemap2_path))
logger.info("Loading hpo info from file {0}".format(hpo_phenotype_to_terms_path))
disease_handle = get_file_handle(genemap2_path)
hpo_handle = get_file_handle(hpo_phenotype_to_terms_path)
alias_genes = adapter.genes_by_alias()
load_disease_terms(
adapter=adapter,
genemap_lines=disease_handle,
genes=alias_genes,
hpo_disease_lines=hpo_handle,
)
logger.info("Successfully loaded all hpo terms")
def test_load_disease_terms(gene_database, genemap_handle, hpo_disease_handle):
adapter = gene_database
alias_genes = adapter.genes_by_alias()
# GIVEN a populated database with genes and no disease terms
assert len([term for term in adapter.disease_terms()]) == 0
# WHEN loading the disease terms
load_disease_terms(
adapter=adapter,
genemap_lines=genemap_handle,
genes=alias_genes,
hpo_disease_lines=hpo_disease_handle,
)
# THEN make sure that the disease terms are in the database
disease_objs = adapter.disease_terms()
assert len([disease for disease in disease_objs]) > 0
def diseases(downloads_folder, api_key):
"""
Update disease terms in mongo database. Use pre-downloaded resource files (phenotype_to_genes and genemap2) or download them from OMIM.
Both options require using a valid omim api key.
"""
adapter = store
api_key = api_key or current_app.config.get("OMIM_API_KEY")
resources = {}
if downloads_folder:
api_key = None
# Fetch required resource lines after making sure that are present in downloads folder and that contain valid data
_fetch_downloaded_resources(resources, downloads_folder)
else:
# Download resources
if not api_key:
LOG.warning(
"Please provide a omim api key to load the omim gene panel")
raise click.Abort()
try:
mim_files = fetch_mim_files(api_key, genemap2=True)
resources["genemap_lines"] = mim_files["genemap2"]
resources["hpo_gene_lines"] = fetch_hpo_to_genes_to_disease()
except Exception as err:
LOG.warning(err)
raise click.Abort()
_check_resources(resources)
LOG.info("Dropping DiseaseTerms")
adapter.disease_term_collection.delete_many({})
LOG.debug("DiseaseTerms dropped")
load_disease_terms(
adapter=adapter,
genemap_lines=resources["genemap_lines"],
hpo_disease_lines=resources["hpo_gene_lines"],
)
LOG.info("Successfully loaded all disease terms")
def test_load_disease_terms(gene_database, genemap_file, hpo_disease_handle):
adapter = gene_database
alias_genes = adapter.genes_by_alias()
# GIVEN a populated database with genes and no disease terms
assert len([term for term in adapter.disease_terms()]) == 0
genemap_handle = get_file_handle(genemap_file)
# WHEN loading the disease terms
load_disease_terms(
adapter=adapter,
genemap_lines=genemap_handle,
genes=alias_genes,
hpo_disease_lines=hpo_disease_handle,
)
# THEN make sure that the disease terms are in the database
disease_objs = adapter.disease_terms()
assert len([disease for disease in disease_objs]) > 0