def test_model_unit(self):
"""Test to make sure that Unit is working properly.
"""
unit_type = Property(name="unit_type", value="section")
number = 1
unit = Unit()
unit.properties = [unit_type]
unit.number = number
assert unit.number == number
sentence = Sentence()
sentence.words = [Word(lemma="hello"), Word(lemma="world")]
prop = Property(name="title", value="Hello World")
unit.sentences.append(sentence)
unit.properties.append(prop)
assert unit.sentences == [sentence]
assert unit.properties.all() == [unit_type, prop]
unit.save()
prop.save()
retrieved_prop = Property.query.filter(Property.name=="title").\
filter(Property.value == "Hello World").first()
assert retrieved_prop.unit.type == "unit"
assert retrieved_prop.unit.number == unit.number
def load_sentences():
"""Load the content of data.yml into the English / Latin tables"""
yaml = open('data/quiz_data.yml')
data = ruamel.yaml.load(yaml, ruamel.yaml.RoundTripLoader)
print data
for topic_name, quiz in data.items():
topic = (Topic.query.filter_by(name=topic_name).first()
or Topic(name=topic_name))
print topic
topic.save()
for quiz_name, sentences in quiz.items():
quiz = Quiz(name=quiz_name, topic=topic)
print quiz
quiz.save()
for question, answers in sentences.items():
type = answers.pop(0)['type']
q = Sentence(type=type, text=question, quiz=quiz)
for answer in answers:
a = Sentence(text=answer, )
q.translations.append(a)
a.translations.append(q)
db.session.add(q)
db.session.commit()
def test_model_unit(self):
"""Test to make sure that Unit is working properly.
"""
unit_type = Property(name="unit_type", value="section")
number = 1
unit = Unit()
unit.properties = [unit_type]
unit.number = number
assert unit.number == number
sentence = Sentence()
sentence.words = [Word(word="hello"), Word(word="world")]
prop = Property(name="title", value="Hello World")
unit.sentences.append(sentence)
unit.properties.append(prop)
assert unit.sentences == [sentence]
assert unit.properties.all() == [unit_type, prop]
unit.save()
prop.save()
retrieved_prop = Property.query.filter(Property.name=="title").\
filter(Property.value == "Hello World").first()
assert retrieved_prop.unit.type == "unit"
assert retrieved_prop.unit.number == unit.number
def find_sentence(word):
if len(word.sentence) < 3:
url = "https://twinword-word-graph-dictionary.p.rapidapi.com/example/"
querystring = {"entry": word.word}
headers = {
'x-rapidapi-host':
"twinword-word-graph-dictionary.p.rapidapi.com",
'x-rapidapi-key': os.getenv('RAPID_API_KEY')
}
response = requests.request("GET",
url,
headers=headers,
params=querystring)
raw_sentence_response = response.json()
while True:
index_choice = random.choice(
range(len(raw_sentence_response["example"])))
sentence_response = raw_sentence_response["example"][
index_choice]
if Sentence.query.filter_by(
example=sentence_response).count() == 0:
break
sentence = Sentence(example=sentence_response,
from_api=True,
word_id=word.id)
sentence.save()
return sentence.example
else:
return random.choice(word.sentence).example
def test_add_sequence(self):
"""Test the ``add_sequence()`` method of ``Sentence``.
"""
project = Project()
sentence = Sentence(text="foo", project=project)
sequence = Sequence(lemmatized=False)
project.save()
sentence.save()
sequence.save()
rel = sentence.add_sequence(sequence, position=1, project=project)
assert rel.sequence == sequence
assert rel.sentence == sentence
assert rel.position == 1
assert rel.project == project
def test_add_sequence(self):
"""Test the ``add_sequence()`` method of ``Sentence``.
"""
sentence = Sentence(text="foo")
sequence = Sequence(lemmatized=False)
project = Project()
project.save()
sentence.save()
sequence.save()
rel = sentence.add_sequence(sequence, position=1, project=project)
assert rel.sequence == sequence
assert rel.sentence == sentence
assert rel.position == 1
assert rel.project == project
def test_add_word(self):
"""Test the ``add_word()`` method of ``Sentence``.
"""
sentence = Sentence(text="foo")
word = Word(word="foo")
project = Project()
project.save()
sentence.save()
word.save()
rel = sentence.add_word(word, position=4, space_before=" ",
part_of_speech="ADF", project=project)
assert rel.word == word
assert rel.sentence == sentence
assert rel.position == 4
assert rel.space_before == " "
assert rel.part_of_speech == "ADF"
assert rel.project == project
def insert_into_db():
for episode_link in get_all_episode_links():
season, episode, sentences = parse_episode(episode_link)
for sentence in sentences:
if sentence.text:
sen = Sentence(
season=season,
episode=episode,
sentence=sentence.text.strip()
)
db.session.add(sen)
db.session.commit()
def test_add_dependency(self):
"""Test the ``add_dependency()`` method of ``Sentence``.
"""
sentence = Sentence(text="foo")
word = Word(word="foo")
dependency = Dependency(governor=word)
project = Project()
project.save()
sentence.save()
dependency.save()
word.save()
rel = sentence.add_dependency(dependency, governor_index=1,
dependent_index=2, project=project)
assert rel.dependency == dependency
assert rel.sentence == sentence
assert rel.governor_index == 1
assert rel.dependent_index == 2
assert rel.project == project
def test_add_word(self):
"""Test the ``add_word()`` method of ``Sentence``.
"""
project = Project()
sentence = Sentence(text="foo", project=project)
word = Word(lemma="foo")
project.save()
sentence.save()
word.save()
rel = sentence.add_word(word,
position=4,
space_before=" ",
project=project)
assert rel.word == word
assert rel.sentence == sentence
assert rel.position == 4
assert rel.space_before == " "
assert rel.project == project
def new_question():
form = SentenceForm()
if form.validate_on_submit():
sentence = Sentence(question=form.question.data,
answer=form.answer.data,
author=current_user)
db.session.add(sentence)
db.session.commit()
flash('Your question has been created!', 'success')
return redirect(url_for('questions'))
return render_template('create_question.html',
title='New Question',
form=form,
legend='New Question')
def test_add_dependency(self):
"""Test the ``add_dependency()`` method of ``Sentence``.
"""
project = Project()
sentence = Sentence(text="foo", project=project)
word = Word(lemma="foo")
dependency = Dependency(governor=word)
project.save()
sentence.save()
dependency.save()
word.save()
rel = sentence.add_dependency(dependency,
governor_index=1,
dependent_index=2,
project=project)
assert rel.dependency == dependency
assert rel.sentence == sentence
assert rel.governor_index == 1
assert rel.dependent_index == 2
assert rel.project == project
def test_model_sentence(self):
"""Test to make sure that Sentence is working properly.
"""
text = "hello world"
sentence = Sentence()
sentence.text = text
assert sentence.text == text
word_1 = Word(lemma="hello")
word_2 = Word(lemma="world")
sentence.words.append(word_1)
sentence.words.append(word_2)
assert sentence.words == [word_1, word_2]
sentence.save()
#Test with Dependencies
dependency1 = Dependency()
dependency2 = Dependency()
sentence.dependencies = [dependency1, dependency2]
db.session.add_all([dependency1, dependency2])
db.session.commit()
#Test with Sequences
sequence1 = Sequence()
sequence2 = Sequence()
sentence.sequences = [sequence1, sequence2]
db.session.add_all([sequence1, sequence2])
db.session.commit()
#Test with Project
project = Project()
sentence.project = project
db.session.add_all([project])
db.session.commit()
def read_chinese_sentences():
"""
Reads sentences from txt and creates Sentence objects
"""
location = os.path.join(os.getcwd(), 'files')
with open(os.path.join(location, 'sentences.txt'), encoding='utf-8') as f:
raw = f.read()
lines = raw.split('\n')
structures = set(len(l.split('\t')) for l in lines)
assert len(structures) == 1
for l in lines:
data = l.split('\t')
fields = {
'zi_simp': get_chinese(data[0]),
'pinyin_tone': data[1],
'english': data[2],
}
s = Sentence(**fields)
db.session.add(s)
db.session.commit()
def test_model_sentence(self):
"""Test to make sure that Sentence is working properly.
"""
text = "hello world"
sentence = Sentence()
sentence.text = text
assert sentence.text == text
word_1 = Word(word="hello")
word_2 = Word(word="world")
sentence.words.append(word_1)
sentence.words.append(word_2)
assert sentence.words == [word_1, word_2]
sentence.save()
#Test with Dependencies
dependency1 = Dependency()
dependency2 = Dependency()
sentence.dependencies = [dependency1, dependency2]
db.session.add_all([dependency1, dependency2])
db.session.commit()
#Test with Sequences
sequence1 = Sequence()
sequence2 = Sequence()
sentence.sequences = [sequence1, sequence2]
db.session.add_all([sequence1, sequence2])
db.session.commit()
def xmlImport(inputFile):
def named_parameters(model):
columns = [m.key for m in model.__table__.columns]
return columns
# Truncate DB
Sentence.query.delete()
Entity.query.delete()
Interaction.query.delete()
OntologyAnnotation.query.delete()
db.session.commit()
tree = ET.parse(inputFile)
root = tree.getroot()
for sentence in root:
sentence_attr = {
el.tag: el.text
for el in sentence
if el.text and el.tag in named_parameters(Sentence)
}
# Entity
entities = []
for entity in sentence.iter("entity"):
entity_attr = {
el.tag: el.text
for el in entity
if el.text and el.tag in named_parameters(Entity)
}
# Ontology Annotation
ontologyAnnotations = []
for ontologyAnnotation in entity.iter("ontologyAnnotation"):
ontologyAnnotation_attr = {
el.tag: el.text
for el in ontologyAnnotation if el.text
and el.tag in named_parameters(OntologyAnnotation)
}
ontologyAnnotation_attr["default"] = (
ontologyAnnotation_attr["default"] == 'True')
ontologyAnnotations.append(
OntologyAnnotation(**ontologyAnnotation_attr))
if not "comment" in entity_attr: entity_attr["comment"] = ""
entity_attr["ontologyAnnotations"] = ontologyAnnotations
entities.append(Entity(**entity_attr))
# Interaction
interactions = []
for interaction in sentence.iter("interaction"):
interaction_attr = {
el.tag: el.text
for el in interaction
if el.text and el.tag in named_parameters(Interaction)
}
if not "comment" in interaction_attr:
interaction_attr["comment"] = ""
interactions.append(Interaction(**interaction_attr))
sentence_attr["entities"] = entities
sentence_attr["interactions"] = interactions
if not "comment" in sentence_attr: sentence_attr["comment"] = ""
s = Sentence(**sentence_attr)
db.session.add(s)
db.session.commit()
def tweetSentimentAnalysis(self):
outFile = codecs.open("testTweetsLineByLine.txt", 'w', "utf-8")
# Read all the tweets from "testTweets.txt" and
# split + store them to tweets_list
tweets = codecs.open("testTweets.txt", 'r', "utf-8").read()
tweets_list = tweets.split('\n')
#tweets.close() - AttributeError: 'str' object has no attribute 'close'
positive_counter = 0
negative_counter = 0
sentences = []
#implementation of topic modelling
for idx, tweet in enumerate(tweets_list):
if (len(tweet)):
print(tweet)
stop = set(stopwords.words('english'))
exclude = set(string.punctuation)
lemma = WordNetLemmatizer()
def clean(data):
stop_free = " ".join(
[i for i in data.lower().split() if i not in stop])
punc_free = ''.join(ch for ch in stop_free
if ch not in exclude)
normalized = " ".join(
lemma.lemmatize(word) for word in punc_free.split())
return normalized
tweet_clean = [clean(tweet).split()]
print(tweet_clean)
dictionary = corpora.Dictionary(tweet_clean)
doc_term_matrix = [
dictionary.doc2bow(doc) for doc in tweet_clean
]
Lda = gensim.models.ldamodel.LdaModel
ldamodel = Lda(doc_term_matrix,
num_topics=1,
id2word=dictionary,
passes=50)
ldamodel = ldamodel.print_topics(num_topics=1, num_words=3)
words = ldamodel[0][1]
words = words.split("+")
import re
topicModelingValues = []
for word in words:
word = re.sub(r'[?|$|.|!]', r'', word)
word = re.sub(r'[^a-zA-Z0-9 ]', r'', word)
result = ''.join(
[word for word in word if not word.isdigit()])
topicModelingValues.append(result)
# Call outputo`unt() on each tweet stored in tweets_list and
# increment positive_counter and negative_counter accordingly
p, n = self.posNegCount(tweet)
positive_counter += p
negative_counter += n
temp = p - n
dataToBeSaved = "tweet with idx : --- {} --- \n , have the following postivity : {} \n\n".format(
tweet, temp)
#print(dataToBeSaved.encode("utf-8"))
outFile.write(dataToBeSaved)
ner = self.nerfun(tweet)
if p > n:
sentiment_sent = "POSITIVE"
elif p < n:
sentiment_sent = "NEGATIVE"
else:
sentiment_sent = "NEUTRAL"
ts = time.time()
sentences.append(
Sentence(ts, tweet, sentiment_sent,
str(datetime.datetime.now()), ner,
topicModelingValues, "temp"))
outFile.close()
if positive_counter > negative_counter:
sentiment = "POSITIVE"
elif positive_counter < negative_counter:
sentiment = "NEGATIVE"
else:
sentiment = "NEUTRAL"
valuesSum = positive_counter + negative_counter
neural_counter = len(tweets_list) - valuesSum
output = {
'positive': positive_counter,
'negative': negative_counter,
'sentiment': sentiment,
'valuesSum': valuesSum,
'neural': neural_counter
}
blockchain = Blockchain()
ts = time.time()
call = blockchain.add_topic(id=ts,
keyword=self.keyword,
sentiment_result=output,
date=str(datetime.datetime.now()))
topicId = str(ts)
for sent in sentences:
sent.topicId = topicId
blockchain.add_sentence(sent.id, sent.content,
sent.sentiment_result, sent.date, sent.ner,
sent.topicModelingValues, sent.topicId)
print(
"//////////////////////////////////////////////////////////////////////////"
)
print("positive_counter:", positive_counter, "negative_counter:",
negative_counter, "valuesSum", valuesSum)
print(
"//////////////////////////////////////////////////////////////////////////"
)
# Hopefully, this is self-explanatory
return (output)
def createBlock(blockLines):
headLineComponents = blockLines[0].split("\t")
ids = headLineComponents[1].split("__")
pmid = ids[0]
sentenceID = ids[1]
sentence = headLineComponents[2]
score = float(headLineComponents[3])
# add Sentence
s = Sentence(pubmedID=pmid,
sentenceID=sentenceID,
literal=sentence,
score=score,
grade=defaultGrade,
comment=defaultComment)
db.session.add(s)
for line in blockLines[1:]:
lineComponents = line.split("\t")
# Possible forms:
# PROTEIN_EXACT\tstart end\tword\tdatabase id
# PROTEIN_GENIA\tstart end\tword\tPROTEIN_REFLECT\tstart end\tword\tdatabase id
# PATTERN\tstart end\tinteraction_type
try:
kind = lineComponents[0]
if kind == "PATTERN":
start, end = startEnd(lineComponents[1])
type = lineComponents[2]
# add Interaction
i = Interaction(type=type,
start=start,
end=end,
sentence=s,
grade=defaultGrade,
comment=defaultComment)
db.session.add(i)
else:
type, software = typeSoftware(
kind.replace("GO_PROCESS",
"GO-PROCESS").replace("CHEM", "CHEMICAL"))
if type.upper() != "PROTEIN" or software.upper() == "EXACT":
start, end = startEnd(lineComponents[1])
name = lineComponents[2]
databaseID = lineComponents[3]
# add Entity
e = Entity(type=type,
software=software,
name=name,
databaseID=databaseID,
start=start,
end=end,
sentence=s,
grade=defaultGrade,
comment=defaultComment)
db.session.add(e)
else:
# partial overlap
databaseID = lineComponents[6]
type1, software1 = typeSoftware(lineComponents[0])
start1, end1 = startEnd(lineComponents[1])
name1 = lineComponents[2]
# add Entity
e1 = Entity(type=type1,
software=software1,
name=name1,
databaseID=databaseID,
start=start1,
end=end1,
sentence=s,
grade=defaultGrade,
comment=defaultComment)
db.session.add(e1)
type2, software2 = typeSoftware(lineComponents[3])
start2, end2 = startEnd(lineComponents[4])
name2 = lineComponents[5]
# add Entity
e2 = Entity(type=type2,
software=software2,
name=name2,
databaseID=databaseID,
start=start2,
end=end2,
sentence=s,
grade=defaultGrade,
comment=defaultComment)
db.session.add(e2)
except:
raise "Error: {}\n\nLine Components: {}".format(
sys.exc_info()[0], lineComponents)
db.session.commit()
