def load(self, path):
for f in utils.get_files_in_path(path):
if not f.endswith(".json"):
continue
config_name = Path(f).stem
logging.debug("Loading {}".format(f))
with open(f, "r") as fp:
self.configs[config_name] = json.load(fp)
logging.debug("Loaded config: %s", self.configs)
def upload_filepaths(self, filepaths):
# Convert a directory to a list of files
if len(filepaths) == 1 and os.path.isdir(filepaths[0]):
filepaths = get_files_in_path(filepaths[0])
# Zip up files
s = StringIO.StringIO()
zip_file = ZipFile(s, 'w')
for filepath in filepaths:
zip_file.write(filepath)
zip_file.close()
content = s.getvalue()
self.upload_file('temp.zip', content, zip_files=False)
def add_files(self, filepaths):
# Convert a directory to a list of files
if len(filepaths) == 1 and os.path.isdir(filepaths[0]):
filepaths = get_files_in_path(filepaths[0])
# Zip up files
s = StringIO.StringIO()
zip_file = ZipFile(s, 'w')
for filepath in filepaths:
filename = os.path.basename(filepath)
if os.path.getsize(filepath) < 5:
raise DataverseException('The Dataverse does not currently accept files less than 5 bytes. '
'{} cannot be uploaded.'.format(filename))
elif filename in [f.name for f in self.get_files()]:
raise DataverseException('The file {} already exists on the Dataverse'.format(filename))
zip_file.write(filepath)
zip_file.close()
content = s.getvalue()
self.upload_file('temp.zip', content, zip=False)
sentence_attrs = dict(sentence.attributes.items())
text=sentence_attrs["text"]
sentence_id=sentence_attrs["id"]
path=utils.construct_path(write_path,sentence_id)
output_file=open(path,'w')
output_file.write(text)
output_file.close()
test_medline_path= "./Test/Test for DDI Extraction task/MedLine"
test_drugbank_path= "./Test/Test for DDI Extraction task/DrugBank"
train_medline_path="./Train/MedLine"
train_drugbank_path="./Train/DrugBank"
test_medline_path_files=utils.get_files_in_path(test_medline_path)
test_drugbank_path_files=utils.get_files_in_path(test_drugbank_path)
train_medline_path_files=utils.get_files_in_path(train_medline_path)
train_drugbank_path_files=utils.get_files_in_path(train_drugbank_path)
for file in test_drugbank_path_files:
file=utils.construct_path(test_drugbank_path,file)
write_sentences_to_file(file,"./test_sentences")
for file in test_medline_path_files:
file=utils.construct_path(test_medline_path,file)
write_sentences_to_file(file,"./test_sentences")
for file in train_drugbank_path_files:
file=utils.construct_path(train_drugbank_path,file)
write_sentences_to_file(file,"./train_sentences")
for file in train_drugbank_path_files:
file=utils.construct_path(train_drugbank_path,file)