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_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_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_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 assemble_graph():
"""Assemble INDRA Statements and return Graphviz graph dot string."""
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 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 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_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_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 format_stmts(stmts, output_format):
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 = stmt.evidence[0].text if stmt.evidence[0].text else ''
pmid = stmt.evidence[0].pmid if stmt.evidence[0].pmid else ''
line = '%s\t%s\t%s\n' % (stmt, 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
return None
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)
import sys
from indra import reach
from indra.assemblers import GraphAssembler
orig_txt = [ln.strip() for ln in open('ras_pathway.txt', 'rt').readlines()]
correct_txt = [ln.strip() for ln in open('correction.txt', 'rt').readlines()]
for ln in correct_txt:
if ln.startswith('<'):
remove_line = ln[2:]
orig_txt.remove(remove_line)
elif ln.startswith('>'):
add_line = ln[2:]
orig_txt.append(add_line)
txt = ' '.join(orig_txt)
rp = reach.process_text(txt, offline=True)
st = rp.statements
for s in st:
print '%s\t%s' % (s, s.evidence[0].text)
graphpr = {'rankdir': 'TD'}
nodepr = {'fontsize': 12, 'shape': 'plaintext', 'margin': '0,0', 'pad': 0}
ga = GraphAssembler(st, graph_properties=graphpr, node_properties=nodepr)
ga.make_model()
ga.save_dot('rps6ka_correction.dot')
ga.save_pdf('rps6k1_correction.pdf')
def test_save_pdf():
st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
ga.save_pdf('/dev/null')
import sys
import pickle
from indra import reach
from indra.assemblers import GraphAssembler
if len(sys.argv) < 2:
process_type = 'text'
else:
process_type = sys.argv[1]
if process_type == 'text':
txt = open('ras_pathway.txt', 'rt').read()
rp = reach.process_text(txt, offline=True)
st = rp.statements
elif process_type == 'json':
rp = reach.process_json_file('reach_output.json')
st = rp.statements
else:
st = pickle.load(open('statements.pkl', 'rb'))
for s in st:
print '%s\t%s' % (s, s.evidence[0].text)
graphpr = {'rankdir': 'TD'}
nodepr = {'fontsize': 12, 'shape': 'plaintext', 'margin': '0,0', 'pad': 0}
ga = GraphAssembler(st, graph_properties=graphpr, node_properties=nodepr)
ga.make_model()
ga.save_dot('ras_pathway.dot')
ga.save_pdf('ras_pathway.pdf')
import sys
import pickle
from indra import reach
from indra.assemblers import GraphAssembler
txt = open('extension.txt', 'rt').read()
rp = reach.process_text(txt, offline=True)
st = rp.statements
for s in st:
print '%s\t%s' % (s, s.evidence[0].text)
with open('extension.pkl', 'wb') as fh:
pickle.dump(st, fh)
graphpr = {'rankdir': 'TD'}
nodepr = {'fontsize': 12, 'shape': 'plaintext', 'margin': '0,0', 'pad': 0}
ga = GraphAssembler(st, graph_properties=graphpr, node_properties=nodepr)
ga.make_model()
ga.save_dot('jnk_extension.dot')
ga.save_pdf('jnk_extension.pdf')
def test_save_pdf():
st = [Phosphorylation(Agent('MAP2K1'), Agent('MAPK1'))]
ga = GraphAssembler()
ga.add_statements(st)
ga.make_model()
ga.save_pdf('/dev/null')
