def main(self):
"""Upload the files"""
for file_name in os.listdir(self.args.files_directory):
file_path = os.path.join(self.args.files_directory, file_name)
file_size = os.path.getsize(file_path)
file_path_on_askomics = None
file_ext = os.path.splitext(file_name)[1]
files = FilesHandler(self.application, self.session)
fp = open(file_path)
first = True
for (last, chunk) in self.generator_is_last(
self.read_in_chunks(fp, self.chunk_size)):
data = {
"first": first,
"last": last,
"chunk": chunk,
"path": file_path_on_askomics,
"name": file_name,
"size": file_size,
"type": files.get_type(file_ext)
}
first = False
file_path_on_askomics = files.persist_chunk(data)
def upload_chunk():
"""Upload a file chunk
Returns
-------
json
path: name of the local file. To append the next chunk into it
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
files_utils = FilesUtils(current_app, session)
disk_space = files_utils.get_size_occupied_by_user(
) if "user" in session else None
if session["user"]["quota"] > 0 and disk_space >= session["user"]["quota"]:
return jsonify({
'errorMessage': "Exceeded quota",
"path": '',
"error": True
}), 400
data = request.get_json()
if not (data and all([
key in data for key in
["first", "last", "size", "name", "type", "size", "chunk"]
])):
return jsonify({
"path": '',
"error": True,
"errorMessage": "Missing parameters"
}), 400
if not (data["first"] or data.get("path")):
return jsonify({
"path": '',
"error": True,
"errorMessage": "Missing path parameter"
}), 400
try:
files = FilesHandler(current_app, session)
path = files.persist_chunk(data)
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
"path": '',
"error": True,
"errorMessage": str(e)
}), 500
return jsonify({"path": path, "error": False, "errorMessage": ""})
def upload_file(self, file_path):
"""Summary
Parameters
----------
file_path : TYPE
Description
Returns
-------
TYPE
Description
"""
file_name = file_path.split("/")[-1]
file_extension = os.path.splitext(file_path)[1]
file_type = {
".tsv": "text/tab-separated-values",
".csv": "text/tab-separated-values",
".gff3": "null",
".bed": "null"
}
with open(file_path, 'r') as file_content:
content = file_content.read()
file_data = {
"first": True,
"last": True,
"chunk": content,
"name": file_name,
"type": file_type[file_extension],
"size": os.path.getsize(file_path)
}
files = FilesHandler(self.app, self.session)
filepath = files.persist_chunk(file_data)
filedate = files.date
return {
"file_path": filepath,
"file_date": filedate
}
