def test_create_model():
model = Model('test')
case = Node({"handle": "case"})
# set_trace()
case.props['days_to_enrollment'] = Property(
{"handle": 'days_to_enrollment'})
model.add_node(case)
assert isinstance(model.nodes['case'], Node)
assert model.props[('case', 'days_to_enrollment')]
model.add_node({"handle": "sample"})
assert model.nodes["sample"]
assert isinstance(model.nodes["sample"], Node)
assert model.nodes["sample"].model == 'test'
case_id = Property({"handle": "case_id", "value_domain": "string"})
model.add_prop(case, case_id)
assert model.props[("case", "case_id")]
assert model.props[("case", "case_id")].value_domain == 'string'
assert 'case_id' in model.nodes['case'].props
sample = model.nodes["sample"]
of_case = Edge({"handle": "of_case", "src": sample, "dst": case})
of_case.props['operator'] = Property({
"handle": "operator",
"value_domain": "boolean"
})
model.add_edge(of_case)
assert model.edges[('of_case', 'sample', 'case')]
assert model.contains(of_case.props['operator'])
assert of_case.props['operator'].model == 'test'
assert model.props[('of_case', 'sample', 'case', 'operator')]
assert model.props[('of_case', 'sample', 'case',
'operator')].value_domain == 'boolean'
dx = Property({"handle": "diagnosis", "value_domain": "value_set"})
tm = Term({"value": "CRS"})
model.add_prop(case, dx)
model.add_terms(dx, tm, 'rockin_pneumonia', 'fungusamongus')
assert {x.value
for x in dx.terms.values()
} == {'CRS', 'rockin_pneumonia', 'fungusamongus'}
def test_put_model(bento_neo4j):
(b,h)=bento_neo4j
the_mdb = MDB(uri=b)
assert the_mdb
ObjectMap.clear_cache()
m = Model(handle='ICDC',mdb=the_mdb)
m.dget()
prop = m.props[('sample','sample_type')]
sample = m.nodes['sample']
edge = m.edges[('on_visit','sample', 'visit')]
term = Term({"value":"electric_boogaloo"})
m.add_terms(prop, term)
node = m.nodes['lab_exam']
m.dput()
with m.drv.session() as session:
result = session.run('match (v:value_set)-->(t:term {value:"electric_boogaloo"}) return v,t')
rec = result.single()
assert rec['v'].id == prop.value_set.neoid
assert rec['t'].id == term.neoid
assert rec['t']['value'] == term.value
result = session.run('match (n:node {handle:"lab_exam"}) return n')
rec = result.single()
assert rec['n'].id == node.neoid
term = m.props[('demographic','sex')].terms['M']
assert term.concept
assert term.concept._id == "337c0e4f-506a-4f4e-95f6-07c3462b81ff"
concept = term.concept
assert term in concept.belongs.values()
term.concept=None
assert not term in concept.belongs.values()
assert ('concept',concept) in term.removed_entities
m.dput()
with m.drv.session() as session:
result = session.run('match (t:term) where id(t)=$id return t',{"id":term.neoid})
assert result.single() # term there
result = session.run('match (c:concept) where id(c)=$id return c',{"id":concept.neoid})
assert result.single() # concept there
result = session.run('match (t:term)-->(c:concept) where id(t)=$id return t',{"id":term.neoid})
assert not result.single() # but link is gone
concept._id="heydude"
term.concept = concept
prop.model = None
assert not prop.model
m.dput()
with m.drv.session() as session:
result = session.run('match (t:term)--(c:concept) where id(t)=$id return c',{"id":term.neoid})
s = result.single()
assert s
assert s['c'].id == concept.neoid
assert s['c']['id'] == "heydude"
result = session.run('match (p:property) where id(p)=$id return p',{"id":prop.neoid})
s = result.single()
assert s
assert s['p'].id == prop.neoid
assert not 'model' in s['p']
prop.model = 'ICDC'
at_enrollment = m.edges[('at_enrollment','prior_surgery','enrollment')]
prior_surgery = m.nodes['prior_surgery']
with m.drv.session() as session:
result = session.run('match (n:node)<-[:has_src]-(r:relationship {handle:"at_enrollment"})-[:has_dst]->(:node {handle:"enrollment"}) where id(n)=$id return r',{"id":prior_surgery.neoid})
s = result.single()
assert s
m.rm_edge(at_enrollment)
assert not at_enrollment.src
assert not at_enrollment.dst
assert not at_enrollment in m.edges_out(prior_surgery)
m.dput()
with m.drv.session() as session:
result = session.run('match (n:node)<-[:has_src]-(r:relationship {handle:"at_enrollment"})-[:has_dst]->(:node {handle:"enrollment"}) where id(n)=$id return r',{"id":prior_surgery.neoid})
s = result.single()
assert not s
result = session.run('match (e:relationship) where id(e)=$id return e',{"id":at_enrollment.neoid})
s = result.single()
assert s