def make_html(stmts, fname):
ha = HtmlAssembler(
stmts,
title='Small molecule inhibitors of %s assembled by INDRA' % target,
db_rest_url='http://db.indra.bio/latest')
ha.make_model()
ha.save_model(fname)
def assemble_html(stmts_with_counts):
for channel, (stmts, ev_counts, source_counts) in stmts_with_counts.items():
ha = HtmlAssembler(stmts, ev_totals=ev_counts,
source_counts=source_counts,
title='INDRA statements for %s' % channel,
db_rest_url='https://db.indra.bio')
ha.save_model('html/%s.html' % channel)
def html_assembler(indra_stmts, fname):
"""Assemble INDRA statements into a HTML report"""
html_assembler = HtmlAssembler(indra_stmts,
db_rest_url='https://db.indra.bio')
assembled_html_report = html_assembler.make_model(no_redundancy=True)
html_assembler.save_model(fname)
return assembled_html_report
def make_html(stmts, ev_counts, source_counts, fname, drug):
ha = HtmlAssembler(stmts,
ev_totals=ev_counts,
source_counts=source_counts,
title='Effects of %s assembled by INDRA' % drug,
db_rest_url='http://db.indra.bio/latest')
ha.make_model()
ha.save_model(fname)
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
from indra.tools import assemble_corpus as ac
from indra.statements import stmts_to_json_file
from indra.assemblers.html import HtmlAssembler
from indra.sources import reach
tp = reach.process_pmc('PMC4455820', url=reach.local_nxml_url)
if tp:
stmts = tp.statements
print(stmts)
stmts = ac.filter_grounded_only(stmts) # Filter out ungrounded agents
stmts = ac.run_preassembly(
stmts, # Run preassembly
return_toplevel=False,
normalize_equivalences=
True, # Optional: rewrite equivalent groundings to one standard
normalize_opposites=
True, # Optional: rewrite opposite groundings to one standard
normalize_ns='WM'
) # Use 'WM' namespace to normalize equivalences and opposites
stmts = ac.filter_belief(stmts, 0.8) # Apply belief cutoff of e.g., 0.8
stmts_to_json_file(stmts, 'PMC4455820.json')
ha = HtmlAssembler(stmts)
ha.save_model('PMC4455820.html')
#
#
#
#
#attempt to combine many statements
from indra.tools import assemble_corpus as ac
from indra.statements import stmts_to_json_file
from indra.assemblers.html import HtmlAssembler
from indra.sources import reach
pmcids = ["PMC3717945", "PMC5906628"]
stmts = []
for pmcid in pmcids:
tp = reach.process_pmc(pmcid)
stmts += tp.statements
stmts = ac.filter_grounded_only(stmts) # Filter out ungrounded agents
stmts = ac.run_preassembly(
stmts, # Run preassembly
return_toplevel=False,
normalize_equivalences=
True, # Optional: rewrite equivalent groundings to one standard
normalize_opposites=
True, # Optional: rewrite opposite groundings to one standard
normalize_ns='WM'
) # Use 'WM' namespace to normalize equivalences and opposites
stmts = ac.filter_belief(stmts, 0.8) # Apply belief cutoff of e.g., 0.8
stmts_to_json_file(stmts, 'bigresults.json')
ha = HtmlAssembler(stmts)
ha.save_model('bigresults.html')
def assemble_html(stmts, fname_key):
ha = HtmlAssembler(stmts)
ha.make_model()
ha.save_model('%s.html' % fname_key)