def main(**kwargs):
parse = argparse.ArgumentParser(
prog=script_name,
usage='{} KEY_WORD'.format(script_name),
description='A tiny downloader that scrapes the web',
add_help=True,
)
parse.add_argument('-v',
'--version',
action='store_true',
help='Print version and exit',
required=False)
parse.add_argument('KEY_WORD', nargs='*', type=str, help='search keyword')
args = parse.parse_args()
if args.version:
print("%s: version %s" % (script_name, __version__))
sys.exit()
if args.KEY_WORD:
search({
"searchword": args.KEY_WORD[0].encode('gbk'),
"searchtype": "-1"
})
else:
parse.print_help()
def get(self):
parse = reqparse.RequestParser()
parse.add_argument('task_id', type=str, required=True)
args = parse.parse_args()
task_id = args['task_id']
# retrieve file type
conn = MySQLdb.connect(self.db_host, self.db_user, self.db_passwd,
self.db_name)
with conn:
cursor = conn.cursor()
cursor.execute("SELECT file_type from tasks where task_id =%s",
(task_id, ))
conn.commit()
dataset = cursor.fetchall()
# this task_id is not existed.
if cursor.rowcount == 0:
response_packet = {
"msg": 'Bad request.',
"ret": HTTP_400_BAD_REQUEST,
"data": {}
}
return make_response(jsonify(response_packet),
HTTP_400_BAD_REQUEST)
print('Total Row(s) fetched:', cursor.rowcount)
for row in dataset:
file_type = row[0]
self.mFileType = file_type
# return thumbnail picture for specific task_id
filepath = UPLOAD_FOLDER + "/" + task_id + "_thumbnail." + self.mFileType
print(filepath)
with open(filepath, "rb") as image:
image_b64encode_string = base64.b64encode(image.read())
# result here: dict obj
response_packet = {
"msg": 'Access webpage success.',
"ret": HTTP_200_SUCCESS,
"data": {
"task_id": task_id,
"file_type": self.mFileType,
"imageb64": image_b64encode_string,
}
}
return make_response(
jsonify(response_packet),
HTTP_200_SUCCESS) # <- the status_code displayed code on console
def main():
import argparse
parse = argparse.ArgumentParser()
parse.add_argument("--root",
type=str,
help="your http file root",
default='.')
parse.add_argument("--port", type=int, help="http socket port", default=80)
args = parse.parse_args()
reg_ext_handler(".md", _md_handler)
if platform.system() == 'Windows':
os.startfile(f"http://localhost:{args.port}")
start(args.root, args.port)
def parse_args():
parser = argparse.ArgumentParser()
parser.add_argument('host', help='Hostname to scan')
parser.add_argument('-s',
help='Resolve the status for each URL',
action="store_true")
parser.add_argument('-o',
help='Include urls not at the host',
action="store_true")
parser.add_argument('--depth',
help='Depth of search. Default: 3',
default=3)
return parser.parse_args()
def DivideAPI():
parse = reqparse.RequestParser()
parse.add_argument('ip', type=str, help='错误的ip', default='192.168.5.1')
parse.add_argument('username',
type=str,
help='错误的username',
default='root')
parse.add_argument('password',
type=str,
help='错误的password',
default='123456')
args = parse.parse_args()
# 从前端请求中解析参数
Router_ip = args.get('ip')
username = args.get('username')
Router_password = args.get('password')
# 这里调用（操作/验证）脚本
# 将Router fa0/0划分为两个子接口
flag, message = excute(Router_ip, username, Router_password,
'./scripts/Router.txt', socketio)
data = {}
ret = ReturnJ()
ret.data = data
ret.flag = flag
ret.message = message
return ret.toJson()
def VlanAPI():
parse = reqparse.RequestParser()
parse.add_argument('ip', type=str, help='错误的ip', default='192.168.5.5')
parse.add_argument('username',
type=str,
help='错误的username',
default='root')
parse.add_argument('password',
type=str,
help='错误的password',
default='CISCO')
args = parse.parse_args()
# 获取当前文件夹id
Switch_ip = args.get('ip')
username = args.get('username')
Switch_password = args.get('password')
# 这里调用（操作/验证）脚本
# 配置Switch1划分VLAN10和VLAN20
flag, message = excute(Switch_ip, username, Switch_password,
'./scripts/Split_Vlan.txt', socketio)
data = {}
ret = ReturnJ()
ret.data = data
ret.flag = flag
ret.message = message
return ret.toJson()
def get(self):
parse = reqparse.RequestParser()
parse.add_argument('user_id', type=int, required=True)
parse.add_argument('task_id', type=str, required=True)
parse.add_argument('file_type', type=str, required=True)
args = parse.parse_args()
user_id = args['user_id']
task_id = args['task_id']
file_type = args['file_type']
response_data = self.getInternal(user_id, task_id, file_type)
if response_data == "":
response_packet = {
"msg": 'bad request.',
"ret": HTTP_400_BAD_REQUEST,
"data": {}
}
return make_response(jsonify(response_packet), HTTP_400_BAD_REQUEST) # <- the status_code displayed code on console
else:
response_packet = {
"msg": 'Access webpage success.',
"ret": HTTP_200_SUCCESS,
"data" : response_data,
}
return make_response(jsonify(response_packet), HTTP_200_SUCCESS) # <- the status_code displayed code on console
def post(self):
parse = reqparse.RequestParser()
parse.add_argument('user_file', type=FileStorage, location='files')
parse.add_argument('user_id', type=int, location='form')
args = parse.parse_args()
file = args['user_file']
if file:
if file.filename == '':
response_data = {
"msg": 'Upload filename is null.',
"ret": HTTP_400_BAD_REQUEST
}
return make_response(
jsonify(response_data), HTTP_400_BAD_REQUEST
) # <- the status_code displayed code on console
print("recieved a new file.")
fext, s = self.allowed_file(file.filename)
if s:
if not os.path.exists(UPLOAD_FOLDER):
os.makedirs(UPLOAD_FOLDER)
filename = secure_filename(file.filename)
file.save(os.path.join(UPLOAD_FOLDER, filename))
filename_with_path = os.path.join(UPLOAD_FOLDER, filename)
md5filename = self.md5(filename_with_path)
md5filename_with_ext = md5filename + "." + fext
md5thumbnail_with_ext = md5filename + "_thumbnail." + fext
# record this file info in db.
url = "http://localhost:5000/api/insert/record"
values = {
"user_id": args['user_id'],
"task_id": md5filename,
"file_type": fext
}
print("values=>", values)
self.send_request(url, values)
newfilename = os.path.join(UPLOAD_FOLDER, md5filename_with_ext)
newfilename_thumbnail = os.path.join(UPLOAD_FOLDER,
md5thumbnail_with_ext)
if os.path.exists(newfilename):
response_data = {
"msg": 'Please do not upload the file repeatedly.',
"ret": HTTP_400_BAD_REQUEST
}
return make_response(jsonify(response_data),
HTTP_400_BAD_REQUEST)
print("newfilename=>", newfilename)
os.rename(filename_with_path, newfilename)
try:
baseheight = 320
img = Image.open(newfilename)
hpercent = (baseheight / float(img.size[1]))
wsize = int((float(img.size[0]) * float(hpercent)))
img = img.resize((wsize, baseheight), Image.ANTIALIAS)
img.save(newfilename_thumbnail)
except IOError:
print("cannot create thumbnail for '%s'" %
newfilename_thumbnail)
#if not os.path.exists(PREPROC_FOLDER):
# os.makedirs(PREPROC_FOLDER)
#destfile = os.path.join(PREPROC_FOLDER, md5filename_with_ext)
#copyfile(newfilename, destfile)
#self.preprocess_images(newfilename, preproc_filepath)
response_data = {
"data": {
"user_id": args['user_id'],
"task_id": md5filename,
},
"msg": 'Upload file successfully',
"ret": HTTP_201_CREATED
}
return make_response(jsonify(response_data), HTTP_201_CREATED)
else:
response_data = {
"msg": 'Upload is not allowed filetype.',
"ret": HTTP_400_BAD_REQUEST
}
return make_response(jsonify(response_data),
HTTP_400_BAD_REQUEST)
else:
response_data = {
"status": 'user_file is invalid.',
"status_code": HTTP_400_BAD_REQUEST
}
return make_response(jsonify(response_data), HTTP_400_BAD_REQUEST)
outputfile = args.outputfile
if args.versionFile:
targetgenes = VersionConvert(args)
else:
targetgenes = EvidenceLevel(evidence, queryvcf, outputfile)
if __name__ == "__main__":
scriptpath = os.path.split(os.path.realpath(__file__))[0]
parse = argparse.ArgumentParser(formatter_class = HelpFormatter, description = '''
Usage:
python3 {scriptpath}/FilterSNP.py <args> <args>....
NOTE:
This script was used to filterout SNPs that failed to pass GATK criterion and with missing rate in population above threshold.
'''.format(scriptpath = scriptpath))
parse.add_argument('-query', '--queryvcf', required = True, dest = "queryvcf", help = "vcf file without intergenic regions info", metavar = "vcf file without intergenic regions info", type = str, nargs = '?')
parse.add_argument('-outfile', '--out', required = True, dest = "outputfile", help = "outputfile record condidates SNP/Indel", metavar = "outputfile record condidates SNP/Indel", type = str, nargs = '?')
parse.add_argument('-genenamefile', '--namefile', required = True, dest = "genefile", help = "condidate genes with their corresponding names of another version", type = str, nargs = '?')
parse.add_argument('-logfile', '--logfile', required = True, dest = "logfile", help = "Log file to record procedures of processing of this script", metavar = "Log file to record procedures of processing of this script", type = str, nargs = '?')
parse.add_argument('-evidence', '--evidence', required = True, dest = "evidence", default = "exonic downstream intronic splicing upstream UTR3 UTR5",
help = "Positon where SNP/indel located in will be further studied", type = str, nargs = '*')
versiongroup = parse.add_argument_group("verion conversion")
versiongroup.add_argument('-versionFile', '--versionFile', required = False, dest = "versionFile", help = "Responding relationship between two versions", type = str, nargs = '?')
versiongroup.add_argument('-versionname', '--versionname', required = False, dest = "versionName", help = "version name should be consistent with that in verionfile", type = str, nargs = '?')
args = parse.parse_args()
main(args)
def get(self):
try:
parse = reqparse.RequestParser()
parse.add_argument('task_id', type=str, required=True)
parse.add_argument('user_id', type=int, required=True)
args = parse.parse_args()
task_id = args['task_id']
user_id = args['user_id']
# retrieve file type from task_id
conn= MySQLdb.connect(self.db_host, self.db_user, self.db_passwd, self.db_name)
with conn:
cursor = conn.cursor()
cursor.execute("SELECT id from users where id = %s", (user_id, ))
conn.commit()
dataset = cursor.fetchall()
if cursor.rowcount == 0:
raise ValueError("invalid user_id:", user_id)
cursor.execute("SELECT file_type from tasks where task_id =%s ", (task_id, ))
conn.commit()
dataset = cursor.fetchall()
# this task_id is not existed.
if cursor.rowcount == 0:
raise ValueError("task_id is not existed.")
print('Total Row(s) fetched:', cursor.rowcount)
for row in dataset:
file_type = row[0]
self.mFileType = file_type
if task_id and user_id and file_type:
# attempt to retrieve info from backend directory.
# bypass post2 if result exists.
sdir = os.path.join(RESULT_FOLDER, task_id)
response_file = os.path.join(sdir, 'response.json')
if os.path.exists(sdir) and os.path.exists(response_file):
with open(response_file, 'r') as file:
json_string = json.load(file)
response_packet = {
"msg": 'Success.',
"ret": HTTP_200_SUCCESS,
"data": json_string,
}
return make_response(jsonify(response_packet), HTTP_200_SUCCESS) # <- the status_code displayed code on console
res = self.post2(task_id, UPLOAD_FOLDER)
if res['code'] == HTTP_400_BAD_REQUEST:
raise ValueError('bad request in post2 query')
else:
IMGDIR=os.path.join(RESULT_FOLDER, task_id, "step1")
# do tesseract to recognize the docnumber and doctype
print("CMD=>", TESS_CMD + " " + RESULT_FOLDER +"/" + task_id + "/step1/roi-DocNumber.jpg" + " docnumres -l lancejie_fapiao3")
if self.ocr_type == 'google':
os.system(TESS_CMD + " " + RESULT_FOLDER + \
"/" + task_id + "/step1/roi-DocNumber.jpg" + " docnumres -l lancejie_fapiao3")
os.system(TESS_CMD + " " + RESULT_FOLDER + \
"/" + task_id + "/step1/roi-DocType.jpg" + " doctyperes -l lancejie_shuipiao2")
with open("docnumres.txt") as file:
docnumres = file.read().rstrip()
print("docnumres=>", docnumres)
with open("doctyperes.txt") as file:
doctyperes = file.read().rstrip()
print("doctyperes=>", doctyperes)
else:
if self.ocr_type == 'baidu':
fba=FetchBaiduApi.FetchBaiduApi(self.db_host, self.db_user, self.db_passwd, self.db_name)
responseBaiduData = fba.getInternal(user_id, task_id, file_type)
if responseBaiduData == "":
if self.ocr_policy == 'tryout':
responseBaiduData = fba.getInternal(user_id, task_id, file_type)
if responseBaiduData == "":
responseBaiduData = fba.getInternal(user_id, task_id, file_type)
if responseBaidudata == "":
print("Internal error happened!")
raise ValueError("Internal server error", HTTP_407_INTERNAL_ERROR )
else:
self.ocr_type=="google"
else:
print("response=>", responseBaiduData)
with open(IMGDIR+"/roi-DocNumber.jpg", "rb") as image:
# base64 encode read data
# result: bytes
docnum_b64encode_bytes = base64.b64encode(image.read())
docnum_b64encode_string= docnum_b64encode_bytes.decode('utf-8')
with open(IMGDIR+"/roi-DocType.jpg", "rb") as image:
doctype_b64encode_bytes = base64.b64encode(image.read())
doctype_b64encode_string = doctype_b64encode_bytes.decode('utf-8')
if self.ocr_type == 'google':
response_data = {
"task_id": task_id,
"user_id": user_id,
"file_type": file_type,
"words_result": {
"InvoiceNum": docnumres,
"InvoiceCode": doctyperes,
},
"InvoiceNumEncode": docnum_b64encode_string,
"InvoiceCodeEncode": doctype_b64encode_string,
}
else:
if self.ocr_type == 'baidu':
response_data = {
"task_id": task_id,
"user_id": user_id,
"file_type": file_type,
"InvoiceNumEncode": docnum_b64encode_string,
"InvoiceCodeEncode": doctype_b64encode_string,
"words_result": responseBaiduData,
}
# store the parse result
with open(os.path.join(sdir, "response.json"), 'w') as outfile:
# now encoding the data into json
# result: string
json_data=json.dumps(response_data)
outfile.write(json_data)
response_packet = {
"msg": 'Access webpage success.',
"ret": HTTP_200_SUCCESS,
"data" : response_data,
}
return make_response(jsonify(response_packet), HTTP_200_SUCCESS) # <- the status_code displayed code on console
else:
raise ValueError("invalid user_id ,task_id or file_type", user_id, task_id, file_type)
except ValueError as err:
print(err.args)
if err.args[1] == HTTP_407_INTERNAL_ERROR:
response_packet = {
"msg": 'Server internal error.',
"ret": HTTP_407_INTERNAL_ERROR,
"data": {}
}
return make_response(jsonify(response_packet), HTTP_400_BAD_REQUEST) # <- the status_code displayed code on console
else:
response_packet = {
"msg": 'bad request.',
"ret": HTTP_400_BAD_REQUEST,
"data": {}
}
return make_response(jsonify(response_packet), HTTP_400_BAD_REQUEST) # <- the status_code displayed code on console
fname = fname.replace("#yenotroot#", root)
print(f"Load SQL script {fname}")
try:
with conn.cursor() as c, open(fname, "r") as sqlfile:
sql = sqlfile.read()
c.execute(sql)
conn.commit()
except Exception as e:
raise InitError(f"Error loading {ddl} -- {str(e)}")
if __name__ == "__main__":
parse = argparse.ArgumentParser("initialize a yenot database")
parse.add_argument(
"dburl",
help=
"database identifier in url form (e.g. postgresql://user@host/dbname)",
)
parse.add_argument(
"--db-reset",
default=False,
action="store_true",
help="drop (if necessary) and recreate the database",
)
parse.add_argument(
"--db-create",
default=False,
action="store_true",
help="create the database (error if existing)",
)
parse.add_argument(
def get(self):
try:
parse = reqparse.RequestParser()
parse.add_argument('task_id', type=str, required=True)
parse.add_argument('user_id', type=int, required=True)
args = parse.parse_args()
task_id = args['task_id']
user_id = args['user_id']
# retrieve file type from task_id
conn = MySQLdb.connect(self.db_host, self.db_user, self.db_passwd,
self.db_name)
with conn:
cursor = conn.cursor()
cursor.execute("SELECT id from users where id = %s",
(user_id, ))
conn.commit()
dataset = cursor.fetchall()
if cursor.rowcount == 0:
raise ValueError("invalid user_id:", user_id)
cursor.execute(
"SELECT file_type from tasks where task_id =%s ",
(task_id, ))
conn.commit()
dataset = cursor.fetchall()
# this task_id is not existed.
if cursor.rowcount == 0:
raise ValueError("task_id is not existed.")
print('Total Row(s) fetched:', cursor.rowcount)
for row in dataset:
file_type = row[0]
self.mFileType = file_type
if task_id and user_id and file_type:
# attempt to retrieve info from backend directory.
# bypass post2 if result exists.
sdir = os.path.join(RESULT_FOLDER, task_id)
response_file = os.path.join(sdir, 'response.json')
if os.path.exists(sdir) and os.path.exists(response_file):
with open(response_file, 'r') as file:
json_string = json.load(file)
response_packet = {
"msg": 'Success.',
"ret": HTTP_200_SUCCESS,
"data": json_string,
}
return make_response(
jsonify(response_packet), HTTP_200_SUCCESS
) # <- the status_code displayed code on console
if self.ocr_type == 'baidu':
fba = FetchBaiduApi.FetchBaiduApi(self.db_host,
self.db_user,
self.db_passwd,
self.db_name)
responseBaiduData = fba.getInternal(
user_id, task_id, file_type)
if responseBaiduData == "":
if self.ocr_policy == 'tryout':
responseBaiduData = fba.getInternal(
user_id, task_id, file_type)
if responseBaiduData == "":
responseBaiduData = fba.getInternal(
user_id, task_id, file_type)
if responseBaiduData == "":
print("Internal error happened!")
raise ValueError("Internal server error",
HTTP_407_INTERNAL_ERROR)
else:
print("response=>", responseBaiduData)
response_data = {
"task_id": task_id,
"user_id": user_id,
"file_type": file_type,
"words_result": responseBaiduData,
}
# store the parse result
with open(os.path.join(sdir, "response.json"),
'w') as outfile:
# now encoding the data into json
# result: string
json_data = json.dumps(response_data)
outfile.write(json_data)
response_packet = {
"msg": 'Access webpage success.',
"ret": HTTP_200_SUCCESS,
"data": response_data,
}
return make_response(
jsonify(response_packet), HTTP_200_SUCCESS
) # <- the status_code displayed code on console
else:
raise ValueError("invliad ocr_type setting.")
else:
raise ValueError("invalid input setting:", task_id, user_id,
file_type)
except ValueError as err:
print(err.args)
if err.args[1] == HTTP_407_INTERNAL_ERROR:
response_packet = {
"msg": 'Server internal error.',
"ret": HTTP_407_INTERNAL_ERROR,
"data": {}
}
return make_response(
jsonify(response_packet), HTTP_400_BAD_REQUEST
) # <- the status_code displayed code on console
else:
response_packet = {
"msg": 'bad request.',
"ret": HTTP_400_BAD_REQUEST,
"data": {}
}
return make_response(
jsonify(response_packet), HTTP_400_BAD_REQUEST
) # <- the status_code displayed code on console
