def token_auth_error(status):
'''用于在 Token Auth 认证失败的情况下返回错误响应'''
print('错误状态吗', status)
# return error_response(401)
if status == 401:
return restfulResponse(data="", msg="认证失败,token非法或过期", code=status)
elif status == 403:
return restfulResponse(data="",
msg=f"权限不足,当前角色为{g.current_user.role}",
code=status)
def get_user():
'''返回一个用户'''
id = request.args.get('id', None, type=int)
if id:
user = User.query.get_or_404(id)
if id is None:
user = g.current_user
return restfulResponse(user.to_dict(include_email=True))
data = user.to_dict()
return restfulResponse(data)
def get_token():
token = g.current_user.get_jwt()
# 每次用户登录（即成功获取 JWT 后），更新 last_seen 时间
g.current_user.ping()
db.session.commit()
print(token)
return restfulResponse({'token': token})
def update_post():
'''修改病人信息'''
data = request.get_json()
print('sa', data)
if not data:
return bad_request('You must post JSON data.')
id = data.get('id', 0)
post = PatientBasicInformation.query.get_or_404(id)
# if g.current_user != post.author and not g.current_user.is_administrator():
# return error_response(403)
message = {}
if 'name' not in data or not data.get('name').strip():
message['name'] = 'name is required.'
# if 'date' not in data or not data.get('date').strip():
# message['date'] = 'date is required.'
if 'sex' not in data or not data.get('sex').strip():
message['sex'] = 'sex is required.'
if len(data.get('address')) > 255:
message['address'] = 'address must less than 255 characters.'
if message:
return bad_request(message)
post.from_dict(data)
db.session.commit()
return restfulResponse(post.to_dict())
def get_disease(id):
'''返回当前患病详情'''
post = DiseaseInformation.query.get_or_404(id)
data = post.to_dict()
# 下一个病人信息
next_basequery = DiseaseInformation.query.order_by(
DiseaseInformation.timestamp.desc()).filter(
DiseaseInformation.timestamp > post.timestamp)
if next_basequery.all():
data['next_id'] = next_basequery[-1].id
data['next_title'] = next_basequery[-1].name
data['_links']['next'] = url_for('api.get_disease',
id=next_basequery[-1].id)
else:
data['_links']['next'] = None
# 上一个病人信息
prev_basequery = DiseaseInformation.query.order_by(
DiseaseInformation.timestamp.desc()).filter(
DiseaseInformation.timestamp < post.timestamp)
if prev_basequery.first():
data['prev_id'] = prev_basequery.first().id
data['prev_title'] = prev_basequery.first().name
data['_links']['prev'] = url_for('api.get_disease',
id=prev_basequery.first().id)
else:
data['_links']['prev'] = None
return restfulResponse(data)
def create_post():
'''添加新的病人基础信息'''
data = request.get_json()
print(data)
if not data:
return bad_request('You must post JSON data.')
message = {}
if 'name' not in data or not data.get('name').strip():
message['name'] = 'name is required.'
if 'date' not in data or not data.get('date').strip():
message['date'] = 'date is required.'
if 'sex' not in data or not data.get('sex').strip():
message['sex'] = 'sex is required.'
if len(data.get('address')) > 255:
message['address'] = 'address must less than 255 characters.'
if message:
return bad_request(message)
patient = PatientBasicInformation()
patient.from_dict(data)
db.session.add(patient)
db.session.commit()
response = restfulResponse(patient.to_dict())
response.status_code = 201
# HTTP协议要求201响应包含一个值为新资源URL的Location头部
response.headers['Location'] = url_for('api.get_patients', id=patient.id)
return response
def get_patients():
'''返回病人集合，分页'''
page = request.args.get('page', 1, type=int)
per_page = min(
request.args.get('limit',
current_app.config['POSTS_PER_PAGE'],
type=int), 100)
queryMap = []
queryMap.append(PatientBasicInformation.deleted == False) # 非删除
name = request.args.get('name', None)
sex = request.args.get('sex', None)
if name:
queryMap.append(PatientBasicInformation.name == name)
if sex:
queryMap.append(PatientBasicInformation.sex == sex)
querySort = []
sort = request.args.get('sort', '+id')
if sort == "+id":
querySort.append(PatientBasicInformation.id.asc())
else:
querySort.append(PatientBasicInformation.id.desc())
data = PatientBasicInformation.to_collection_dict(
PatientBasicInformation.query.filter(*queryMap).order_by(*querySort),
page, per_page, 'api.get_patients')
return restfulResponse(data)
def error_response(status_code, message=None):
# payload = {'error': HTTP_STATUS_CODES.get(status_code, 'Unknown error')}
# if message:
# payload['message'] = message
# response = jsonify(payload)
# response.status_code = status_code
# return response
return restfulResponse(data="", msg=message, code=status_code)
def delete_post(id):
'''删除一位病人信息'''
post = PatientBasicInformation.query.get_or_404(id)
# if g.current_user != post.author and not g.current_user.is_administrator():
# return error_response(403)
if post.diseases_history is not None:
return restfulResponse({'msg': '此病人还有关联信息尚未清除，不能删除'})
db.session.delete(post)
db.session.commit()
return '', 204
def delete_disease(id):
'''删除一条疾病信息'''
post = DiseaseInformation.query.get_or_404(id)
# if g.current_user != post.author and not g.current_user.is_administrator():
# return error_response(403)
# if post.sequences is not None:
# return restfulResponse({'msg':'此疾病还有关联测序信息尚未清除，不能删除'})
post.deleted = True
db.session.commit()
return restfulResponse({})
def export_posts():
'''导出当前用户的所有文章，RQ 后台任务'''
if g.current_user.get_task_in_progress(
'export_posts'): # 如果用户已经有同名的后台任务在运行中时
return bad_request('上一个导出文章的后台任务尚未结束')
else:
# 将 app.utils.tasks.export_posts 放入任务队列中
g.current_user.launch_task('export_posts',
'正在导出文章...',
kwargs={'user_id': g.current_user.id})
return restfulResponse(message='正在运行导出文章后台任务')
def update_user():
'''修改一个用户'''
print('dsddsd', g.current_user.id)
user = User.query.get_or_404(g.current_user.id)
print(user)
data = request.get_json()
if not data:
return bad_request(_('You must post JSON data.'))
email = data.get('email', None)
name = data.get('name', None)
pattern = '^(([^<>()\[\]\\.,;:\s@"]+(\.[^<>()\[\]\\.,;:\s@"]+)*)|(".+"))@((\[[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\])|(([a-zA-Z\-0-9]+\.)+[a-zA-Z]{2,}))$'
if not email or not re.match(pattern, email):
return restfulResponse(data={}, msg="请提供正确的邮箱地址.", code=403)
if not name:
return restfulResponse(data={}, msg="用户名不能为空.", code=403)
user.from_dict(data, new_user=False)
db.session.commit()
return restfulResponse(user.to_dict())
def update_disease():
'''修改疾病信息'''
# if g.current_user != post.author and not g.current_user.is_administrator():
# return error_response(403)
data = request.get_json()
post = DiseaseInformation.query.get_or_404(data['id'])
if not data:
return bad_request('You must post JSON data.')
post.from_dict(data)
db.session.commit()
return restfulResponse(post.to_dict())
def get_patient_diseases():
'''获取所有疾病信息'''
page = request.args.get('page', 1, type=int)
per_page = min(
request.args.get('limit',
current_app.config['POSTS_PER_PAGE'],
type=int), 100)
data = DiseaseInformation.to_collection_dict(
DiseaseInformation.query.filter(
DiseaseInformation.deleted == False).order_by(
DiseaseInformation.timestamp.desc()), page, per_page,
'api.get_sequences')
print('疾病', data)
print(type(data))
return restfulResponse(data)
def excel_create_disease():
'''excel导入样本疾病信息'''
data = request.get_json()
if not data:
return bad_request('excel表内容为空')
sample_data = data['data']
# print(sample_data)
sample_header = data['header']
# print(sample_header)
n = 1
with db.session.no_autoflush:
for data in sample_data:
n += 1
name = data.get('姓名', None)
origin = data.get('样品来源', None)
if not name or not origin or name == '姓名':
continue
patient = PatientBasicInformation.query.filter(
PatientBasicInformation.name == name).filter(
PatientBasicInformation.name ==
data['样品来源']).first() or PatientBasicInformation()
patient.from_dict(data, trans=True)
sequence_id = data.get('Sequence ID', None)
sequence = SampleSequence.query.get(
sequence_id) or SampleSequence()
sequence.from_dict(data, trans=True)
disease = DiseaseInformation.query.filter(
sequence.disease_info.patient_id == patient.id).first(
) if sequence.disease_info else DiseaseInformation()
disease.from_dict(data, trans=True)
disease.patient_id = patient.id
sequence.disease_id = disease.id
db.session.add(disease)
db.session.add(patient)
db.session.add(sequence)
if sequence.sequence_id == 'Sequence ID':
print('id:', sequence.sequence_id)
print(n, data)
db.session.commit()
return restfulResponse({})
def search():
'''Elasticsearch全文检索博客文章'''
q = request.args.get('q')
if not q:
return bad_request(message='keyword is required.')
page = request.args.get('page', 1, type=int)
per_page = min(
request.args.get('per_page',
current_app.config['POSTS_PER_PAGE'],
type=int), 100)
total, hits_basequery = PatientBasicInformation.search(q, page, per_page)
# 总页数
total_pages, div = divmod(total, per_page)
if div > 0:
total_pages += 1
# 不能使用 PatientBasicInformation.to_collection_dict()，因为查询结果已经分页过了
data = {
'items': [item.to_dict() for item in hits_basequery],
'_meta': {
'page': page,
'per_page': per_page,
'total_pages': total_pages,
'total_items': total
},
'_links': {
'self':
url_for('api.search', q=q, page=page, per_page=per_page),
'next':
url_for('api.search', q=q, page=page +
1, per_page=per_page) if page < total_pages else None,
'prev':
url_for('api.search', q=q, page=page -
1, per_page=per_page) if page > 1 else None
}
}
return restfulResponse(data=data,
message='Total items: {}, current page: {}'.format(
total, page))
def create_disease():
'''添加新的病人患病信息'''
data = request.get_json()
print(data)
if not data:
return bad_request('You must post JSON data.')
# patient = PatientBasicInformation.query.get_or_404(id)
# if not patient:
# return bad_request('该病人信息不存在')
disease_info = DiseaseInformation()
disease_info.from_dict(data)
# disease_info.patient_id = id
db.session.add(disease_info)
db.session.commit()
response = restfulResponse(disease_info.to_dict())
response.status_code = 201
# HTTP协议要求201响应包含一个值为新资源URL的Location头部
# response.headers['Location'] = url_for('api.get_patient_diseases', id=data.id)
return response
def get_search_post(id):
'''从搜索结果列表页跳转到文章详情'''
q = request.args.get('q')
page = request.args.get('page', type=int)
per_page = request.args.get('per_page', type=int)
if q and page and per_page: # 说明是从搜索结果页中过来查看文章详情的，所以要高亮关键字
total, hits_basequery = PatientBasicInformation.search(
q, page, per_page)
post = hits_basequery.first() # 只会有唯一的一篇文章
data = post.to_dict() # 会高亮关键字
else:
post = PatientBasicInformation.query.get_or_404(id)
data = post.to_dict() # 不会高亮关键字
# 下一篇文章
next_basequery = PatientBasicInformation.query.order_by(
PatientBasicInformation.timestamp.desc()).filter(
PatientBasicInformation.timestamp > post.timestamp)
if next_basequery.all():
data['next_id'] = next_basequery[-1].id
data['next_title'] = next_basequery[-1].title
data['_links']['next'] = url_for('api.get_post',
id=next_basequery[-1].id)
else:
data['_links']['next'] = None
# 上一篇文章
prev_basequery = PatientBasicInformation.query.order_by(
PatientBasicInformation.timestamp.desc()).filter(
PatientBasicInformation.timestamp < post.timestamp)
if prev_basequery.first():
data['prev_id'] = prev_basequery.first().id
data['prev_title'] = prev_basequery.first().title
data['_links']['prev'] = url_for('api.get_post',
id=prev_basequery.first().id)
else:
data['_links']['prev'] = None
return restfulResponse(data)
def logout():
"""用户退出"""
return restfulResponse({})
def create_user(api=True):
'''注册一个新用户'''
data = request.get_json()
if not data and api:
return bad_request(_('You must post JSON data.'))
message = {}
if 'username' not in data or not data.get('username', None).strip():
message['username'] = _('Please provide a valid username.')
pattern = '^(([^<>()\[\]\\.,;:\s@"]+(\.[^<>()\[\]\\.,;:\s@"]+)*)|(".+"))@((\[[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\])|(([a-zA-Z\-0-9]+\.)+[a-zA-Z]{2,}))$'
if 'email' not in data or not re.match(pattern, data.get('email', None)):
message['email'] = _('Please provide a valid email address.')
if 'password' not in data or not data.get('password', None).strip():
message['password'] = _('Please provide a valid password.')
if User.query.filter_by(username=data.get('username', None)).first():
message['username'] = _('Please use a different username.')
if User.query.filter_by(email=data.get('email', None)).first():
message['email'] = _('Please use a different email address.')
if message:
return bad_request(message)
user = User()
user.from_dict(data, new_user=True)
user.confirmed = True
db.session.add(user)
db.session.commit()
# 发送确认账户的邮件
token = user.generate_confirm_jwt()
if not data.get('confirm_email_base_url'):
confirm_url = 'http://127.0.0.1:5000/api/confirm/' + token
else:
confirm_url = data.get('confirm_email_base_url') + token
text_body = '''
Dear {},
Welcome to Madblog!
To confirm your account please click on the following link: {}
Sincerely,
The Madblog Team
Note: replies to this email address are not monitored.
'''.format(user.username, confirm_url)
html_body = '''
<p>Dear {0},</p>
<p>Welcome to <b>Madblog</b>!</p>
<p>To confirm your account please <a href="{1}">click here</a>.</p>
<p>Alternatively, you can paste the following link in your browser's address bar:</p>
<p><b>{1}</b></p>
<p>Sincerely,</p>
<p>The Madblog Team</p>
<p><small>Note: replies to this email address are not monitored.</small></p>
'''.format(user.username, confirm_url)
# send_email('[Madblog] Confirm Your Account',
# sender=current_app.config['MAIL_SENDER'],
# recipients=[user.email],
# text_body=text_body,
# html_body=html_body)
response = restfulResponse(user.to_dict())
response.status_code = 201
# HTTP协议要求201响应包含一个值为新资源URL的Location头部
response.headers['Location'] = url_for('api.get_user', id=user.id)
return response
def basic_auth_error():
'''用于在认证失败的情况下返回错误响应'''
# return error_response(401)
return restfulResponse(data="", msg="用户名或密码错误", code=50000)