def test_association():
st = [Association([Event(Concept('a')), Event(Concept('b'))])]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_inactivation():
st = [Inhibition(Agent('DUSP4'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_influence():
st = [Influence(Event(Concept('a')), Event(Concept('b')))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_complex():
st = [Complex([Agent('BRAF'), Agent('RAF1'), Agent('YWAH')])]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 3
assert len(ga.graph.edges()) == 3
def test_phosphorylation():
st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_dephosphorylation_noenz():
st = [Dephosphorylation(None, Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 0
assert len(ga.graph.edges()) == 0
def get_pdf_graph(self):
"""Save a graph made with GraphAssembler as pdf, return file name."""
fname = 'indrabot.pdf'
ga = GraphAssembler(self.get_statements())
ga.make_model()
ga.save_pdf(fname)
return fname
def test_phosphorylation():
st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
model = ga.make_model()
assert 'MAP2K1' in model
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def assemble_graph():
"""Assemble INDRA Statements and return Graphviz graph dot string."""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
stmts_json = body.get('statements')
stmts = stmts_from_json(stmts_json)
ga = GraphAssembler(stmts)
model_str = ga.make_model()
res = {'model': model_str}
return res
def assemble_graph():
"""Assemble INDRA Statements and return Graphviz graph dot string."""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
stmts_json = body.get('statements')
stmts = stmts_from_json(stmts_json)
ga = GraphAssembler(stmts)
model_str = ga.make_model()
res = {'model': model_str}
return res
def report_paths_graph(self, paths_list):
from indra.assemblers.graph import GraphAssembler
from indra.util import flatten
path_stmts = [stmts_from_json(l) for l in paths_list]
all_stmts = flatten(path_stmts)
ga = GraphAssembler(all_stmts)
ga.make_model()
resource = get_img_path('qca_paths.png')
ga.save_pdf(resource)
content = KQMLList('display-image')
content.set('type', 'simulation')
content.sets('path', resource)
self.tell(content)
def draw_graph(stmts, fname):
graphpr = {'rankdir': 'TD'}
nodepr = {'fontsize': 12, 'shape': 'plaintext', 'margin': '0,0', 'pad': 0}
ga = GraphAssembler(stmts, graph_properties=graphpr,
node_properties=nodepr)
ga.make_model()
ga.save_dot('%s.dot' % fname)
ga.save_pdf('%s.pdf' % fname)
def test_get_string():
st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
graph_str = ga.get_string()
assert graph_str
def post(self):
"""Assemble INDRA Statements and return Graphviz graph dot string.
Parameters
----------
statements : list[indra.statements.Statement.to_json()]
A list of INDRA Statements to assemble.
Returns
-------
model
Assembled model string.
"""
args = request.json
stmts_json = args.get('statements')
stmts = stmts_from_json(stmts_json)
ga = GraphAssembler(stmts)
model_str = ga.make_model()
res = {'model': model_str}
return res
def test_inactivation():
st = [Inhibition(Agent('DUSP4'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_complex():
st = [Complex([Agent('BRAF'), Agent('RAF1'), Agent('YWAH')])]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 3
assert len(ga.graph.edges()) == 3
def test_influence():
st = [Influence(Concept('a'), Concept('b'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_dephosphorylation_noenz():
st = [Dephosphorylation(None, Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 0
assert len(ga.graph.edges()) == 0
def test_association():
st = [Association([Event(Concept('a')), Event(Concept('b'))])]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def test_dephosphorylation():
st = [Dephosphorylation(Agent('DUSP4'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def get_pdf_graph(self):
"""Save a graph made with GraphAssembler as pdf, return file name."""
fname = 'indrabot.pdf'
ga = GraphAssembler(self.get_statements())
ga.make_model()
ga.save_pdf(fname)
return fname
def test_get_string():
st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
graph_str = ga.get_string()
assert graph_str
def test_influence():
# Add an extra standalone event just to make sure it doesn't error
st = [Influence(Event(Concept('a')), Event(Concept('b'))),
Event(Concept('a'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
assert len(ga.graph.nodes()) == 2
assert len(ga.graph.edges()) == 1
def report_paths_graph(self, paths_list):
from indra.assemblers.graph import GraphAssembler
from indra.util import flatten
path_stmts = [stmts_from_json(l) for l in paths_list]
all_stmts = flatten(path_stmts)
ga = GraphAssembler(all_stmts)
ga.make_model()
resource = get_img_path('qca_paths.png')
ga.save_pdf(resource)
content = KQMLList('display-image')
content.set('type', 'simulation')
content.sets('path', resource)
self.tell(content)
def format_stmts(stmts, output_format, ev_counts=None, source_counts=None):
if output_format == 'tsv':
msg = ''
for stmt in stmts:
if not stmt.evidence:
logger.warning('Statement %s without evidence' % stmt.uuid)
txt = ''
pmid = ''
else:
txt = '"%s"' % stmt.evidence[0].text if \
stmt.evidence[0].text else ''
pmid = stmt.evidence[0].pmid if stmt.evidence[0].pmid else ''
try:
ea_txt = EnglishAssembler([stmt]).make_model()
except Exception as e:
ea_txt = ''
logger.error('English assembly failed for %s' % stmt)
logger.error(e)
line = '%s\t%s\t%s\tPMID%s\n' % (stmt, ea_txt, txt, pmid)
msg += line
return msg
elif output_format == 'pkl':
fname = 'indrabot.pkl'
with open(fname, 'wb') as fh:
pickle.dump(stmts, fh)
return fname
elif output_format == 'pdf':
fname = 'indrabot.pdf'
ga = GraphAssembler(stmts)
ga.make_model()
ga.save_pdf(fname)
return fname
elif output_format == 'json':
msg = json.dumps(stmts_to_json(stmts), indent=1)
return msg
elif output_format == 'html':
ev_counts = {} if not ev_counts else ev_counts
ha = HtmlAssembler(stmts, ev_totals=ev_counts,
source_counts=source_counts)
fname = 'indrabot.html'
ha.save_model(fname)
return fname
return None
def test_save_pdf():
st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
ga.save_pdf('/dev/null')
def test_save_pdf():
st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
ga.save_pdf('/dev/null')