def test_pybel_neighborhood_query():
bp = bel.process_pybel_neighborhood(['TP63'],
network_type='graph_jsongz_url',
network_file=small_corpus_url)
assert bp.statements
for stmt in bp.statements:
assert_valid_statement(stmt)
assert all([s.evidence[0].context is not None for s in bp.statements])
assert all([
s.evidence[0].context.cell_line.name == 'MCF 10A'
for s in bp.statements
])
# Locate statement about epidermis development
stmt = [
st for st in bp.statements
if st.agent_list()[1].name == 'epidermis development'
][0]
assert repr(stmt.evidence[0].context) == str(stmt.evidence[0].context)
assert stmt.evidence[0].context == BioContext(
location=RefContext(name="Cytoplasm",
db_refs={'MESH': 'D003593'}),
cell_line=RefContext(name="MCF 10A",
db_refs={'EFO': '0001200'}),
cell_type=RefContext(name="keratinocyte",
db_refs={'CL': 'CL:0000312'}),
organ=RefContext(name="colon",
db_refs={'UBERON': 'UBERON:0001155'}),
disease=RefContext(name="cancer",
db_refs={'DOID': 'DOID:162'}),
species=RefContext(name="Rattus norvegicus",
db_refs={'TAXONOMY': '10116'})), \
stmt.evidence[0].context
# Test annotation manager
assert bp.annot_manager.get_mapping('Species', '9606') == \
'H**o sapiens'
def upload(self, db):
"""Upload the content for this dataset into the database."""
dbid = self._check_reference(db)
stmts = self._get_statements()
# Raise any validity issues with statements as exceptions here
# to avoid uploading invalid content.
for stmt in stmts:
assert_valid_statement(stmt)
insert_db_stmts(db, stmts, dbid)
return