def hpo():
"""
Update the hpo terms in the database. Fetch the latest release and update terms.
"""
LOG.info("Running scout update hpo")
adapter = store
LOG.info("Dropping HPO terms")
adapter.hpo_term_collection.drop()
LOG.debug("HPO terms dropped")
load_hpo_terms(adapter)
def hpo(context):
"""
Update the hpo terms in the database. Fetch the latest release and update terms.
"""
LOG.info("Running scout update hpo")
adapter = context.obj['adapter']
LOG.info("Dropping HPO terms")
adapter.hpo_term_collection.drop()
LOG.debug("HPO terms dropped")
load_hpo_terms(adapter)
def test_load_hpo_terms(gene_database, hpo_terms_handle):
adapter = gene_database
alias_genes = adapter.genes_by_alias()
# GIVEN a populated database with genes
assert len([term for term in adapter.hpo_terms()]) == 0
assert len([gene for gene in adapter.all_genes()]) > 0
# WHEN loading the disease terms
load_hpo_terms(adapter=adapter,
hpo_lines=hpo_terms_handle,
genes=alias_genes)
# THEN make sure that the disease terms are in the database
hpo_terms_objs = adapter.hpo_terms()
assert len([term for term in hpo_terms_objs]) > 0
def hpo(context):
"""
Update the hpo terms in the database. Fetch the latest release and update terms.
"""
LOG.info("Running scout update hpo")
adapter = context.obj['adapter']
LOG.info("Dropping HPO terms")
adapter.hpo_term_collection.drop()
LOG.debug("HPO terms dropped")
# Fetch the latest version of the hpo terms
hpo_lines = fetch_hpo_terms()
# Fetch the connection to genes from hpo source
hpo_gene_lines = fetch_hpo_to_genes()
load_hpo_terms(adapter, hpo_lines, hpo_gene_lines)
def hpo(hpoterms, hpo_to_genes):
"""
Update the hpo terms in the database. Fetch the latest release and update terms.
"""
LOG.info("Running scout update hpo")
adapter = store
LOG.info("Dropping HPO terms")
adapter.hpo_term_collection.delete_many({})
LOG.debug("HPO terms dropped")
if hpoterms:
hpoterms = get_file_handle(hpoterms)
if hpo_to_genes:
hpo_to_genes = get_file_handle(hpo_to_genes)
load_hpo_terms(adapter, hpo_lines=hpoterms, hpo_gene_lines=hpo_to_genes)
def test_load_hpo_terms(gene_database, hpo_terms_handle, hpo_to_genes_handle):
adapter = gene_database
alias_genes = adapter.genes_by_alias()
# GIVEN a populated database with genes but no hpo terms
assert len([term for term in adapter.hpo_terms()]) == 0
assert len([gene for gene in adapter.all_genes()]) > 0
# WHEN loading the hpo terms
load_hpo_terms(
adapter=adapter,
hpo_lines=hpo_terms_handle,
hpo_gene_lines=hpo_to_genes_handle,
alias_genes=alias_genes
)
# THEN make sure that the disease terms are in the database
hpo_terms_objs = adapter.hpo_terms()
assert len([term for term in hpo_terms_objs]) > 0
def hpo(ctx, hpo_terms):
"""
Load the hpo terms to the mongo database.
"""
adapter = ctx.obj['adapter']
logger.info("Dropping HpoTerms")
adapter.hpo_term_collection.drop()
logger.debug("HpoTerms dropped")
logger.info("Loading hpo terms from file {0}".format(hpo_terms))
hpo_terms_handle = get_file_handle(hpo_terms)
alias_genes = adapter.genes_by_alias()
load_hpo_terms(
adapter=adapter,
hpo_lines=hpo_terms_handle,
genes=alias_genes,
)
logger.info("Successfully loaded all hpo terms")