def test_all_hgnc_ids():
for obj in bp.model.getObjects().toArray():
bpe = bpc._cast_biopax_element(obj)
if bpc._is_protein(bpe):
hgnc_id = bp._get_hgnc_id(bpe)
if hgnc_id is not None:
assert (unicode_strs(hgnc_id))
def test_all_hgnc_ids():
for obj in bp.model.getObjects().toArray():
bpe = bpc._cast_biopax_element(obj)
if bpc._is_protein(bpe):
hgnc_id = bp._get_hgnc_id(bpe)
if hgnc_id is not None:
assert(unicode_strs(hgnc_id))
def test_all_uniprot_ids():
for obj in bp.model.getObjects().toArray():
bpe = bpc._cast_biopax_element(obj)
if bpc._is_protein(bpe):
uniprot_id = bp._get_uniprot_id(bpe)
if uniprot_id is not None:
assert (not uniprot_client.is_secondary(uniprot_id))
assert (unicode_strs(uniprot_id))
def test_all_uniprot_ids():
for obj in bp.model.getObjects().toArray():
bpe = bpc._cast_biopax_element(obj)
if bpc._is_protein(bpe):
uniprot_id = bp._get_uniprot_id(bpe)
if uniprot_id is not None:
assert(not uniprot_client.is_secondary(uniprot_id))
assert(unicode_strs(uniprot_id))
def test_all_protein_db_refs():
unmapped_uniprot_ids = []
for obj in bp.model.getObjects().toArray():
bpe = bpc._cast_biopax_element(obj)
if bpc._is_protein(bpe):
db_refs = bpc.BiopaxProcessor._get_db_refs(bpe)
uniprot_id = db_refs.get('UP')
hgnc_id = db_refs.get('HGNC')
if uniprot_id:
if uniprot_client.is_human(uniprot_id):
if not hgnc_id:
unmapped_uniprot_ids.append(uniprot_id)
unmapped_uniprot_ids = sorted(list(set(unmapped_uniprot_ids)))
# The number of unmapped entries should not increase
# so we check for an upper limit here
assert (len(unmapped_uniprot_ids) < 95)
def test_all_protein_db_refs():
unmapped_uniprot_ids = []
for obj in bp.model.getObjects().toArray():
bpe = bpc._cast_biopax_element(obj)
if bpc._is_protein(bpe):
db_refs = bpc.BiopaxProcessor._get_db_refs(bpe)
uniprot_id = db_refs.get('UP')
hgnc_id = db_refs.get('HGNC')
if uniprot_id:
if uniprot_client.is_human(uniprot_id):
if not hgnc_id:
unmapped_uniprot_ids.append(uniprot_id)
unmapped_uniprot_ids = sorted(list(set(unmapped_uniprot_ids)))
# The number of unmapped entries should not increase
# so we check for an upper limit here
assert(len(unmapped_uniprot_ids) < 95)
