def parse():
if request.method == 'POST':
text = request.form['text']
doc_id = '99999999'
print text
#if text == "readfile":
# with open('test.txt', 'r') as myfile:
# text=myfile.read()
rules0 = request.form['rules0']
rule0_lines = rules0.split("\n")
rules1 = request.form['rules1']
rule1_lines = rules1.split("\n")
rules2 = request.form['rules2']
rule2_lines = rules2.split("\n")
param_helper = ParamHelper(text,doc_id,rule0_lines,rule1_lines,rule2_lines)
raw_doc = document_pb2.Document()
edg_rules = edgRules_pb2.EdgRules()
param_helper.setDocProtoAttributes(raw_doc)
param_helper.setRuleProtoAttributes(edg_rules)
##########################
parse_bllip = parse_using_bllip(raw_doc,edg_rules)
#print parse_bllip
brat_bllip = json.dumps(get_brat_data(parse_bllip))
brat_bllip_added = json.dumps(get_brat_data_added(parse_bllip))
return render_template('index_edg.html', text=text, rules0=rules0,rules1=rules1,rules2=rules2,
brat_string_bllip=brat_bllip,
brat_string_bllip_added=brat_bllip_added)
else:
return render_template('index_edg.html')
def run():
textFH = open(sys.argv[1], "r")
text = textFH.read()
textFH.close()
#text = u'Surface expression of mir-21 activates tgif beta receptor type II expression. Expression of mir-21 and mir-132 directly mediates cell migration . mir-21 mediates cell migration and proliferation. mir-21 seems to mediate apoptosis. mir-21 is involved in cellular processes, such as cell migration and cell proliferation. mir-21 regulates the ectopic expression of smad2 .'
#text = u'transport of annexin 2 not only to dynamic actin-rich ruffles at the cell cortex but also to cytoplasmic and perinuclear vesicles.'
doc_id = '99999999'
rule_phase0_filename = sys.argv[2]
rule_phase1_filename = sys.argv[3]
rule_phase2_filename = sys.argv[4]
fh0 = open(rule_phase0_filename, "r")
rule0_lines = fh0.readlines()
fh0.close()
fh1 = open(rule_phase1_filename, "r")
rule1_lines = fh1.readlines()
fh1.close()
fh2 = open(rule_phase2_filename, "r")
rule2_lines = fh2.readlines()
fh2.close()
param_helper = ParamHelper(text, doc_id, rule0_lines, rule1_lines,
rule2_lines)
raw_doc = document_pb2.Document()
edg_rules = edgRules_pb2.EdgRules()
param_helper.setDocProtoAttributes(raw_doc)
param_helper.setRuleProtoAttributes(edg_rules)
# Parse using Bllip parser.
#print (ruleList)
# Parse using Bllip parser.
result = parse_using_bllip(raw_doc, edg_rules)
helper = DocHelper(result)
sentences = result.sentence
#print(edg_rules)
for sentence in sentences:
print(helper.text(sentence))
for depExtra in sentence.dependency_extra:
print(helper.printExtraDependency(sentence, depExtra))
print("===============================")
def run():
# text = u'Surface expression of mir-21 activates tgif beta receptor type II expression. Expression of mir-21 and mir-132 directly mediates cell migration . mir-21 mediates cell migration and proliferation. mir-21 seems to mediate apoptosis. mir-21 is involved in cellular processes, such as cell migration and cell proliferation. mir-21 regulates the ectopic expression of smad2 .'
# text = u'transport of annexin 2 not only to dynamic actin-rich ruffles at the cell cortex but also to cytoplasmic and perinuclear vesicles.'
doc_id = '99999999'
rule_phase0_filename = '/home/leebird/Projects/nlputils/visual/uploads/rules_phase0.txt'
rule_phase1_filename = '/home/leebird/Projects/nlputils/visual/uploads/rules_phase1.txt'
rule_phase2_filename = '/home/leebird/Projects/nlputils/visual/uploads/rules_phase2.txt'
fh0 = open(rule_phase0_filename, "r")
rule0_lines = fh0.readlines()
fh0.close()
fh1 = open(rule_phase1_filename, "r")
rule1_lines = fh1.readlines()
fh1.close()
fh2 = open(rule_phase2_filename, "r")
rule2_lines = fh2.readlines()
fh2.close()
with open('/home/leebird/Projects/nlputils/utils/typing/test.json') as f:
json_doc = json.load(f)
for t in json_doc['entity'].values():
t['entityType'] = t['entityType'].upper()
text = json.dumps(json_doc)
raw_doc = json_format.Parse(text, document_pb2.Document(), True)
param_helper = ParamHelper(text, doc_id, rule0_lines, rule1_lines,
rule2_lines)
# raw_doc = document_pb2.Document()
edg_rules = edgRules_pb2.EdgRules()
# param_helper.setDocProtoAttributes(raw_doc)
param_helper.setRuleProtoAttributes(edg_rules)
# Parse using Bllip parser.
doc = parse_using_bllip(raw_doc, edg_rules)
helper = DocHelper(doc)
invalid_deps = constraint_args(helper, {'arg0': {document_pb2.Entity.GENE}})
print(invalid_deps)
propagate(helper, {'arg0': {document_pb2.Entity.GENE}}, invalid_deps)
def upload():
if request.method == 'POST':
# Get the name of the uploaded file
file0 = request.files['ruleFile0']
file1 = request.files['ruleFile1']
file2 = request.files['ruleFile2']
rules0 = save_read_uploaded_file(file0)
rules1 = save_read_uploaded_file(file1)
rules2 = save_read_uploaded_file(file2)
text = request.form['text']
if rules0 == "":
rules0 = request.form['rules0']
if rules1 == "":
rules1 = request.form['rules1']
if rules2 == "":
rules2 = request.form['rules2']
rule0_lines = rules0.split("\n")
rule1_lines = rules1.split("\n")
rule2_lines = rules2.split("\n")
doc_id = "9999999"
param_helper = ParamHelper(text,doc_id,rule0_lines,rule1_lines,rule2_lines)
raw_doc = document_pb2.Document()
edg_rules = edgRules_pb2.EdgRules()
param_helper.setDocProtoAttributes(raw_doc)
param_helper.setRuleProtoAttributes(edg_rules)
##########################
parse_bllip = parse_using_bllip(raw_doc,edg_rules)
#print parse_bllip
brat_bllip = json.dumps(get_brat_data(parse_bllip))
brat_bllip_added = json.dumps(get_brat_data_added(parse_bllip))
return render_template('index_edg.html', text=text, rules0=rules0,rules1=rules1,rules2=rules2,
brat_string_bllip=brat_bllip,
brat_string_bllip_added=brat_bllip_added)
else:
return render_template('index_edg.html')
def run():
#####Iterate through all files in Input directory and create doc_list
input_dir_path = sys.argv[1]
glob_path = input_dir_path + "/*"
input_files = glob.glob(glob_path)
document_list = list()
for input_file in input_files:
textFH = open(input_file, "r")
text = textFH.read()
textFH.close()
raw_doc = document_pb2.Document()
raw_doc = document_pb2.Document()
doc_id = os.path.splitext(os.path.basename(input_file))[0]
raw_doc.text = text
raw_doc.doc_id = doc_id
document_list.append(raw_doc)
rule_phase0_filename = sys.argv[2]
fh0 = open(rule_phase0_filename, "r")
rule0_lines = fh0.readlines()
fh0.close()
####NEED TO UPDDATE PARAM_HELPER
param_helper = ParamHelper("NA", "NA", rule0_lines, [], [])
edg_rules = edgRules_pb2.EdgRules()
param_helper.setRuleProtoAttributes(edg_rules)
#param_helper.setDocProtoAttributes(raw_doc)
# This is a simple function to make requests out of a list of documents. We
# put 5 documents in each request.
requests = edg_request_iter_docs(
document_list,
edg_rules,
request_size=5,
request_type=rpc_pb2.EdgRequest.PARSE_BLLIP)
# Given a request iterator, send requests in parallel and get responses.
responses_queue = grpcapi.get_queue(server='128.4.20.169',
port=8902,
request_thread_num=10,
iterable_request=requests,
edg_request_processor=True)
count = 0
for response in responses_queue:
for doc in response.document:
#print(doc)
helper = DocHelper(doc)
sentences = doc.sentence
doc_id = doc.doc_id
#print(edg_rules)
sentNum = 0
for sentence in sentences:
flag = 0
sentText = helper.text(sentence)
dependenciesExtra = sentence.dependency_extra
edgRelations = EdgRelations(doc_id, sentNum)
edgRelations.setRelations(helper, sentence, dependenciesExtra)
toPrintRel = ["inv", "reg", "ass", "exp", "cmp", "isa", "fnd"]
for edgRelation in edgRelations.relations:
numb_args_list = edgRelation.getEdgRelationNumArgs()
relation_name = edgRelation.name
trigger_head = edgRelation.trigger_head
trigger_phrase = edgRelation.trigger_phrase
if relation_name in toPrintRel:
for numb_args in numb_args_list:
print("Sentence: " + doc_id + "\t" + str(sentNum) +
"\t" + sentText)
print("Relation: " + relation_name + "\t" +
trigger_head + "\t" + trigger_phrase)
print("Arg0: " + numb_args[0])
print("Arg1: " + numb_args[1])
print("Arg2: " + numb_args[2])
print("\n")
sentNum = sentNum + 1
count += 1
def run():
#####Iterate through all files in Input directory and create doc_list
input_dir_path = sys.argv[1]
glob_path = input_dir_path + "/*";
input_files = glob.glob(glob_path)
document_list = list()
for input_file in input_files:
textFH = open(input_file,"r")
text = textFH.read()
textFH.close()
raw_doc = document_pb2.Document()
raw_doc = document_pb2.Document()
doc_id = os.path.splitext(os.path.basename(input_file))[0]
raw_doc.text = text
raw_doc.doc_id = doc_id
document_list.append(raw_doc)
rule_phase0_filename = sys.argv[2]
fh0 = open(rule_phase0_filename, "r")
rule0_lines = fh0.readlines()
fh0.close()
####NEED TO UPDDATE PARAM_HELPER
param_helper = ParamHelper("NA","NA",rule0_lines,[],[])
edg_rules = edgRules_pb2.EdgRules()
param_helper.setRuleProtoAttributes(edg_rules)
#param_helper.setDocProtoAttributes(raw_doc)
# This is a simple function to make requests out of a list of documents. We
# put 5 documents in each request.
requests = edg_request_iter_docs(document_list, edg_rules,
request_size=5,
request_type=rpc_pb2.EdgRequest.PARSE_BLLIP)
# Given a request iterator, send requests in parallel and get responses.
responses_queue = grpcapi.get_queue(server='128.4.20.169',
port=8902,
request_thread_num=10,
iterable_request=requests,
edg_request_processor=True)
count = 0
for response in responses_queue:
for doc in response.document:
#print(doc)
helper = DocHelper(doc)
sentences = doc.sentence
doc_id = doc.doc_id
#print(edg_rules)
sentNum = 0
for sentence in sentences:
flag = 0
sentText = helper.text(sentence)
for depExtra in sentence.dependency_extra:
flag = 1
print(doc_id+"\t"+str(sentNum)+"\t"+helper.printExtraDependencyAnalysis(sentence,depExtra)+"\t"+sentText)
if flag == 0:
print(doc_id+"\t"+str(sentNum)+"\t"+helper.printEmptyExtraDependencyAnalysis(sentence)+"\t"+sentText)
sentNum = sentNum + 1
count += 1