def get(self, request):
try:
document = Sentence.objects.get(id=request.GET.get("document"))
except:
raise ValueError("Invalid or missing 'document' value passed in the query string.")
qs = Annotation.objects.filter(document=document)
return {
"total": qs.count(),
"rows": Annotation.as_list(qs=qs, user=request.user)
}
def get(self, request):
try:
document = Sentence.objects.get(id=request.GET.get("document"))
except:
raise ValueError("Invalid or missing 'document' value passed in the query string.")
qs = Annotation.objects.filter(document=document)
return {
"total": qs.count(),
"rows": Annotation.as_list(qs=qs, user=request.user)
}
def load_annotations(annotator):
annotation_df = pd.read_excel('data/all_clinical_human_target_' +
annotator.first_name + '.xlsx')
column_to_index = dict([(c, i + 1)
for i, c in enumerate(annotation_df.columns)])
for record in annotation_df.itertuples():
mdr = record[column_to_index['mdr1']]
if mdr == '<none>':
mdr = record[column_to_index['mdr2']]
annotation = Annotation(
key=Drug.objects.get(
key=record[column_to_index['Drug.Key..Unique.ID.']]),
cui=record[column_to_index['cui']],
mdr1=mdr,
)
annotation.save()
print("Loaded {} annotations".format(len(annotation_df)))
def handle_upload(request, doc_id):
if not request.user.is_authenticated():
raise PermissionDenied(
"You do not have permission to perform this action.")
page = request.POST['next']
has_headers = request.POST['has_headers']
start = 1 if has_headers else 0
# try:
t = [i.strip('\r\n') for i in request.FILES['InputFile'].readlines()]
# f = codecs.open('/home/elmira/heritage_corpus/tempfiles/request.txt', 'w')
# prevsent = 0
# wordn = 1
for ln in range(start, len(t)):
sent, word, wordnum, _, _, tag, corr, annotator = t[ln].split('\t')
sent = int(sent)
# if word == ' ':
# continue
# if sent == prevsent:
# wordn += 1
# else:
# prevsent = sent
# wordn = 1
if tag:
tag1 = [i.strip() for i in tag.split(',')]
# f.write(str(len(word.decode('utf-8'))))
# f.write('\r\n')
sent = Sentence.objects.get(pk=sent)
owner = User.objects.get(username=annotator)
annot = Annotation(owner=owner,
document=sent,
guid=str(uuid.uuid4()),
data=json.dumps({
"ranges": [{
"start":
"/span[" + wordnum + "]",
"end":
"/span[" + wordnum + "]",
"startOffset":
0,
"endOffset":
len(word.decode('utf-8'))
}],
"quote":
word,
"text":
"",
"tags":
tag1,
"corrs":
corr
}))
annot.tag = tag
annot.start, annot.end = int(wordnum), int(wordnum)
annot.save()
a = False
# f.close()
# except:
# a = True
return redirect(page, alert=a)
def handle_upload(request, doc_id):
if not request.user.is_authenticated():
raise PermissionDenied("You do not have permission to perform this action.")
page = request.POST['next']
has_headers = request.POST['has_headers']
start = 1 if has_headers else 0
# try:
t = [i.strip('\r\n') for i in request.FILES['InputFile'].readlines()]
# f = codecs.open('/home/elmira/heritage_corpus/tempfiles/request.txt', 'w')
# prevsent = 0
# wordn = 1
for ln in range(start, len(t)):
sent, word, wordnum, _, _, tag, corr, annotator = t[ln].split('\t')
sent = int(sent)
# if word == ' ':
# continue
# if sent == prevsent:
# wordn += 1
# else:
# prevsent = sent
# wordn = 1
if tag:
tag1 = [i.strip() for i in tag.split(',')]
# f.write(str(len(word.decode('utf-8'))))
# f.write('\r\n')
sent = Sentence.objects.get(pk=sent)
owner = User.objects.get(username=annotator)
annot = Annotation(owner=owner, document=sent, guid=str(uuid.uuid4()),
data=json.dumps({"ranges": [{"start": "/span["+wordnum+"]", "end": "/span["+wordnum+"]", "startOffset": 0, "endOffset": len(word.decode('utf-8'))}], "quote": word, "text": "", "tags": tag1, "corrs": corr}))
annot.tag = tag
annot.start, annot.end = int(wordnum), int(wordnum)
annot.save()
a = False
# f.close()
# except:
# a = True
return redirect(page, alert=a)
def handle_upload(request, doc_id):
if not request.user.is_authenticated():
raise PermissionDenied(
"You do not have permission to perform this action.")
page = request.POST['next']
has_headers = request.POST['has_headers']
start = 1 if has_headers else 0
t = [i.strip('\r\n') for i in request.FILES['InputFile'].readlines()]
for ln in range(start, len(t)):
sent, word, wordnum, _, _, tag, corr, annotator = t[ln].split('\t')
sent = int(sent)
if tag:
tag1 = [i.strip() for i in tag.split(',')]
sent = Sentence.objects.get(pk=sent)
owner = User.objects.get(username=annotator)
annot = Annotation(owner=owner,
document=sent,
guid=str(uuid.uuid4()),
data=json.dumps({
"ranges": [{
"start":
"/span[" + wordnum + "]",
"end":
"/span[" + wordnum + "]",
"startOffset":
0,
"endOffset":
len(word.decode('utf-8'))
}],
"quote":
word,
"text":
"",
"tags":
tag1,
"corrs":
corr
}))
annot.tag = tag
annot.start, annot.end = int(wordnum), int(wordnum)
annot.save()
a = False
return redirect(page, alert=a)
def post(self, request, client_data):
# create. Creates an annotation object and returns a 303.
obj = Annotation()
obj.owner = request.user if request.user.is_authenticated() else None
try:
obj.document = Sentence.objects.get(id=client_data.get("document"))
except:
raise ValueError("Invalid or missing 'document' value passed in annotation data.")
obj.set_guid()
obj.data = "{ }"
obj.update_from_json(client_data)
obj.save()
return obj.as_json(request.user) # Spec wants redirect but warns of browser bugs, so return the object.
def get(self, request):
# index. Returns ALL annotation objects. Seems kind of not scalable.
return Annotation.as_list()
def post(self, request, client_data):
# create. Creates an annotation object and returns a 303.
obj = Annotation()
obj.owner = request.user if request.user.is_authenticated() else None
try:
# print 'get sent'
obj.document = Sentence.objects.get(id=client_data.get("document"))
except:
# print 'bad'
raise ValueError(
"Invalid or missing 'document' value passed in annotation data."
)
# print 'get guid'
obj.set_guid()
# print 'get data'
obj.data = "{ }"
# print 'upd'
obj.update_from_json(client_data)
# print 'save'
obj.save()
# print 'return'
return obj.as_json(
request.user
) # Spec wants redirect but warns of browser bugs, so return the object.
def get(self, request):
# index. Returns ALL annotation objects. Seems kind of not scalable.
return Annotation.as_list()
def post(self, request, format=None):
"""Creates a new task"""
required_fields = [
'question_id', 'answer_id', 'annotation_url', 'task_type', 'phrase'
]
if not all(param in request.data for param in required_fields):
errorMsg = {'Error': "Input Error", 'Message': "Missing fields"}
return Response(errorMsg, status=status.HTTP_400_BAD_REQUEST)
taskType = int(request.data['task_type'])
if not 0 <= taskType <= 2:
errorMsg = {
'Error': "Input Error",
'Message': "Task Type not in range (0-2)"
}
return Response(errorMsg, status=status.HTTP_400_BAD_REQUEST)
# create a new annotation with data
newAnnotation = Annotation()
newAnnotation.question_id = request.data['question_id']
newAnnotation.answer_id = request.data['answer_id']
newAnnotation.phrase = request.data['phrase']
newAnnotation.save()
# append and shorten url
appended_url = request.data['annotation_url'] + "/" \
+ str(newAnnotation.id) \
+ "?taskType=" \
+ str(taskType)
post_url_with_key = settings.POST_URLSHORTENER_GOOGLE_URL +\
"?key=" + settings.GOOGLE_URL_SHORTENER_KEY
post_header = {'Content-Type': 'application/json'}
google_response = requests.post(post_url_with_key,
data=json.dumps(
{'longUrl': appended_url}),
headers=post_header).json()
if 'id' not in google_response:
errorMsg = {
'Error': "Google URL Shortener Error",
'Google Response': google_response.pop('error')
}
newAnnotation.delete()
return Response(errorMsg, status=status.HTTP_400_BAD_REQUEST)
shortened_url = google_response['id']
message = self.create_message(str(request.data['phrase'][:6] + ".."),
taskType, shortened_url)
# post twitter message
auth = OAuth1(settings.TWITTER_CONSUMER_KEY,
settings.TWITTER_CONSUMER_SECRET,
settings.TWITTER_ACCESS_TOKEN,
settings.TWITTER_ACCESS_TOKEN_SECRET)
twitter_response = requests.post(settings.POST_STATUS_TWITTER_URL,
data={'status': message},
auth=auth)
tweet_info = twitter_response.json()
if 'id' not in tweet_info:
errorMsg = {
'Error': "Twitter Error",
'Twitter Response': tweet_info.pop('errors')
}
newAnnotation.delete()
return Response(errorMsg, status=status.HTTP_400_BAD_REQUEST)
# create a new task
task = Task()
task.tweet_id = tweet_info['id']
task.annotation_id = newAnnotation.id
task.task_type = taskType
task.created_on = task.checked_on = timezone.now()
task.save()
return Response(TaskSerializer(task).data,
status=status.HTTP_201_CREATED)
