def read_token(self):
with open('token.txt', 'r') as f:
token = f.readline().strip()
if utils.validate_token(token):
self.token = token
return True
else:
return False
def query_account(request):
logger = utils.CloudLogger().log_request(request)
try:
# 1) Validate the token
token = utils.extract_token(request.headers, None)
if token is None:
return ({
'error': 'Bad Request',
'message': 'Token must be provided in header or body'
}, 400)
token_info = utils.get_token_info(token)
if 'error' in token_info:
return ({
'error':
'Invalid Token',
'message':
token_info['error_description'] if 'error_description'
in token_info else 'Google rejected the client token'
}, 401)
if not utils.validate_token(token_info):
return ({
'error':
'Rejected token',
'message':
'Token was valid but did not meet Lapdog security requirements. Token must have email, profile, openid, and devstorage.read_write scopes.'
' Broad users must authenticate via a LapdogToken'
}, 403)
# 2) Check service account
default_session = utils.generate_default_session(
scopes=['https://www.googleapis.com/auth/cloud-platform'])
account_email = utils.ld_acct_in_project(token_info['email'])
response = utils.query_service_account(default_session, account_email)
if response.status_code >= 400:
return ({
'error': 'Unable to query service account',
'message': response.text
}, 400)
if response.json()['email'] != account_email:
return ({
'error':
'Service account email did not match expected value',
'message':
response.json()['email'] + ' != ' + account_email
}, 400)
return account_email, 200
except:
logger.log_exception()
return ({
'error': 'Unknown Error',
'message': traceback.format_exc()
}, 500)
def change_email(token):
if validate_token(user=current_user,
token=token,
operation=Operations.CHANGE_EMAIL):
flash('Email updated.', 'success')
return redirect(url_for('.index', username=current_user.username))
else:
flash('Invalid or expired token.', 'warning')
return redirect(url_for('.change_email_request'))
def download(data):
db = DbClient()
if not validate_token(request):
return render_template("error_page.html")
user = get_data_by_token(request.cookies.get('token', None))
if data == 'full':
sensors = db.sensors.get_sensors()
sensors = [tuple(sensor.values()) for sensor in sensors]
utils.write_sensors_to_csv(sensors)
return send_file('export.csv', attachment_filename='export.csv')
def confirm(token):
if current_user.confirmed:
return redirect(url_for('main.index'))
if validate_token(user=current_user,
token=token,
operation=Operations.CONFIRM):
flash('Account confirmed.', 'success')
return redirect(url_for('main.index'))
else:
flash('Invalid or expired token.', 'danger')
return redirect(url_for('.resend_confirm_email'))
def confirm(token):
print('token')
if current_user.confirmed:
print(current_user.username)
return redirect(url_for('main.index'))
if validate_token(user=current_user,token=token,operation=Operations.CONFIRM):
print('验证成功')
flash('验证成功','success')
return redirect(url_for('main.index'))
else:
print('验证失败')
flash('验证失败','danger')
return redirect(url_for('.resend_confirmation'))
def new_databins():
db = DbClient()
if not validate_token(request):
return render_template("error_page.html")
user = get_data_by_token(request.cookies.get('token', None))
if request.method == 'POST':
result = request.form
if result['radio-stacked'] == "capacity":
sensors = db.sensors.get_sensor_between_capacity(
result['capacity'], 100)
if not sensors:
return render_template("databins.html")
elif result['radio-stacked'] == 'id':
sensors = db.sensors.get_sensor_by_id(result['Bin_ID'])
if sensors is not None:
pass
else:
return render_template("databins.html")
else:
sensors = db.sensors.get_sensor_by_address(result['address'])
if not sensors:
return render_template("databins.html")
else:
sensors_low = db.sensors.get_sensor_between_capacity(0, 25)
if not sensors_low:
sensors_low = []
sensors_mid = db.sensors.get_sensor_between_capacity(26, 75)
if not sensors_mid:
sensors_mid = []
sensors_full = db.sensors.get_sensor_between_capacity(76, 100)
if not sensors_full:
sensors_full = []
sensors = sensors_low + sensors_mid + sensors_full
if type(sensors) is dict:
tuple_sensors = [
tuple(sensors.values()),
]
sensors = [
sensors,
]
else:
tuple_sensors = [tuple(sensor.values()) for sensor in sensors]
utils.write_sensors_to_csv(tuple_sensors)
return render_template("databins.html", sensors=sensors)
def reset_password(token):
if current_user.is_authenticated:
return redirect(url_for('main.index'))
form = ResetPasswordForm()
if form.validate_on_submit():
user = User.query.filter_by(email=form.email.data.lower()).first()
if user is None:
return redirect(url_for('main.index'))
if validate_token(user=user,
token=token,
operation=Operations.RESET_PASSWORD,
new_password=form.password.data):
flash('Password updated.', 'success')
return redirect(url_for('.login'))
else:
flash('Invalid or expired link.', 'danger')
return redirect(url_for('.forget_password'))
return render_template('auth/reset_password.html', form=form)
def login():
'''
POST login to system and generate JWT token
:param request: flask request object
'''
db = DbClient()
if validate_token(request):
sensors = []
sensors_low = db.sensors.get_sensor_between_capacity(0, 25)
if sensors_low:
sensors += sensors_low
sensors_mid = db.sensors.get_sensor_between_capacity(26, 75)
if sensors_mid:
sensors += sensors_mid
sensors_full = db.sensors.get_sensor_between_capacity(76, 100)
if sensors_full:
sensors += sensors_full
sensors = [tuple(sensor.values()) for sensor in sensors]
utils.write_sensors_to_csv(sensors)
sensors = [[x[1], x[4], x[5], x[3], x[2], x[0]] for x in sensors]
return render_template("index.html",
sensors=sensors,
persent_count=len(sensors),
total_count=len(sensors))
if request.method == 'POST':
try:
data = request.values
user = data.get('username')
password = data.get('password')
if not (user and password):
logger.info(
f'Login failed on {request.remote_addr}, missing credentials'
)
raise InvalidCredentials(user, password)
user_data = db.users.get_user_by_username(user)
if not user_data:
raise UserNotExists(user)
elif not (str.encode(password) == decrypt(
conf.PASSWORD_ENCRYPTION_KEY, user_data['password'])):
raise InvalidCredentials(user)
else:
token = generate_token(user_data['id'])
logger.info(f'Token for user {user} created. token: {token}')
sensors = []
sensors_low = db.sensors.get_sensor_between_capacity(0, 25)
if sensors_low:
sensors += sensors_low
sensors_mid = db.sensors.get_sensor_between_capacity(26, 75)
if sensors_mid:
sensors += sensors_mid
sensors_full = db.sensors.get_sensor_between_capacity(76, 100)
if sensors_full:
sensors += sensors_full
sensors = [tuple(sensor.values()) for sensor in sensors]
utils.write_sensors_to_csv(sensors)
sensors = [[x[1], x[4], x[5], x[3], x[2], x[0]]
for x in sensors]
resp = make_response(
render_template("index.html", sensors=sensors))
resp.set_cookie('token', token)
return resp
except UserNotVerified as e:
logger.warning(e.__str__())
return render_template("error_page.html", error_msg=e.__str__())
except UserNotExists as e:
logger.warning(e.__str__())
error_result = e.__str__()
return render_template("error_page.html", error_msg=error_result)
except InvalidCredentials as e:
logger.warning(e.__str__())
return render_template("error_page.html", error_msg=e.__str__())
except Exception as e:
logger.exception(f'Failed login from {request.remote_addr}')
return render_template("error_page.html", error_msg=e.__str__())
else:
return render_template('login.html')
def register(request):
logger = utils.CloudLogger().log_request(request)
try:
data = request.get_json()
# 1) Validate the token
if not isinstance(data, dict):
return ({
'error':
"Bad Request",
'message': ("No data was provided" if data is None else
"Expected JSON dictionary in request body")
}, 400)
token = utils.extract_token(request.headers, data)
if token is None:
return ({
'error': 'Bad Request',
'message': 'Token must be provided in header or body'
}, 400)
token_info = utils.get_token_info(token)
if 'error' in token_info:
return ({
'error':
'Invalid Token',
'message':
token_info['error_description'] if 'error_description'
in token_info else 'Google rejected the client token'
}, 401)
if not utils.validate_token(token_info):
return ({
'error':
'Rejected token',
'message':
'Token was valid but did not meet Lapdog security requirements. Token must have email, profile, openid, and devstorage.read_write scopes.'
' Broad users must authenticate via a LapdogToken'
}, 403)
# 2) Validate user's permission for the bucket
if 'bucket' not in data:
return ({
'error': 'Bad Request',
'message': 'Missing required parameter "bucket"'
}, 400)
session = utils.generate_user_session(token)
fc_auth = utils.generate_user_session(
request.headers['X-Fc-Auth']
) if 'X-Fc-Auth' in request.headers else None
fc_auth_error = (
'Authorized' if fc_auth is not None
or 'cloud-platform' in token_info['scope'] else
'Not Authorized. Repeat request with the "X-Fc-Auth" header containing application-default credentials'
)
if fc_auth is None:
logger.log("Missing backup Firecloud authentication",
token_info=token_info,
authorized=True
if 'cloud-platform' in token_info['scope'] else False,
severity='DEBUG')
read, write = utils.validate_permissions(session, data['bucket'])
if read is None:
# Error, write will contain a message
return ({
'error': 'Cannot Validate Bucket Permissions',
'message': write
}, 400)
if not (read and write):
# User doesn't have full permissions to the bucket
return ({
'error':
'Not Authorized',
'message':
'User lacks read/write permissions to the requested bucket'
}, 403)
# 2.b) Verify that the bucket belongs to this project
if 'namespace' not in data or 'workspace' not in data:
return ({
'error':
'Bad Request',
'message':
'Missing required parameters "namespace" and "workspace"'
}, 400)
core_session = utils.generate_core_session()
result, message = utils.authenticate_bucket(
data['bucket'], data['namespace'], data['workspace'],
fc_auth if fc_auth is not None else session, core_session)
if not result:
return ({
'error': 'Cannot Validate Bucket Signature',
'message': message,
'FC-Auth': fc_auth_error
}, 400)
# 3) Issue worker account
default_session = utils.generate_default_session(
scopes=['https://www.googleapis.com/auth/cloud-platform'])
account_email = utils.ld_acct_in_project(token_info['email'])
response = utils.query_service_account(default_session, account_email)
if response.status_code == 404:
account_name = account_email.split('@')[0]
logger.log('Issuing new pet service account',
user=token_info['email'],
service_account=account_email,
severity='DEBUG')
response = default_session.post(
'https://iam.googleapis.com/v1/projects/{project}/serviceAccounts'
.format(project=os.environ.get('GCP_PROJECT')),
headers={'Content-Type': 'application/json'},
json={
'accountId': account_name,
'serviceAccount': {
'displayName': token_info['email']
}
})
if response.status_code >= 400:
return ({
'error': 'Unable to issue service account',
'message': response.text
}, 400)
elif response.status_code >= 400:
return ({
'error': 'Unable to query service account',
'message': response.text
}, 400)
if response.json()['email'] != account_email:
return ({
'error':
'Service account email did not match expected value',
'message':
response.json()['email'] + ' != ' + account_email
}, 400)
# 4) Update worker bindings
logger.log("Updating service account bindings",
account=account_email,
bindings={
os.environ.get("FUNCTION_IDENTITY"):
'roles/iam.serviceAccountUser',
account_email: 'roles/iam.serviceAccountUser'
})
response = default_session.post(
'https://iam.googleapis.com/v1/projects/{project}/serviceAccounts/{account}:setIamPolicy'
.format(project=os.environ.get('GCP_PROJECT'),
account=account_email),
headers={'Content-Type': 'application/json'},
json={
"policy": {
"bindings": [{
"role":
"roles/iam.serviceAccountUser",
"members": [
# Allows the gcloud functions account to set this pet account on comwell servers
"serviceAccount:{email}".format(
email=os.environ.get("FUNCTION_IDENTITY")),
# Allows the service account to set itself as the compute account on cromwell workers
"serviceAccount:{email}".format(email=account_email
)
]
}]
},
"updateMask": "bindings"
})
if response.status_code != 200:
return ({
'error':
'Unable to update service account bindings',
'message':
'(%d) : %s' % (response.status_code, response.text)
})
# 5) Update project bindings
logger.log("Updating project-wide iam roles",
bindings={
account_email: 'Pet_account',
token_info['email']: 'Lapdog_user'
},
severity="INFO")
status, response = utils.update_iam_policy(
default_session, {
'serviceAccount:' + account_email: 'Pet_account',
'user:'******'email']: 'Lapdog_user'
})
if not status:
return ({
'error':
'Unable to update project IAM policy',
'message':
'(%d) : %s' % (response.status_code, response.text)
}, 400)
# 6) Generate Key
logger.log('Issuing new service account key',
service_account=account_email)
response = default_session.post(
'https://iam.googleapis.com/v1/projects/{project}/serviceAccounts/{email}/keys'
.format(project=os.environ.get('GCP_PROJECT'),
email=quote(account_email)))
if response.status_code >= 400:
return ({
'error': 'Unable to issue service account key',
'message': response.text
}, 400)
# 7) Register with Firecloud
time.sleep(
10
) # New service account keys take a few seconds before they're usable
# Register the user's new pet service account w/ Firecloud
# We authenticate as the service account by using the newly generated key
pet_session = AuthorizedSession(
google.oauth2.service_account.Credentials.
from_service_account_info(
json.loads(
base64.b64decode(
response.json()
['privateKeyData']).decode())).with_scopes([
'https://www.googleapis.com/auth/userinfo.profile',
'https://www.googleapis.com/auth/userinfo.email'
]))
while True:
try:
response = pet_session.post(
"https://api.firecloud.org/register/profile",
headers={
'User-Agent': 'FISS/0.16.9',
'Content-Type': 'application/json'
},
json={
"firstName": "Service",
"lastName": "Account",
"title": "None",
"contactEmail": token_info['email'],
"institute": "None",
"institutionalProgram": "None",
"programLocationCity": "None",
"programLocationState": "None",
"programLocationCountry": "None",
"pi": "None",
"nonProfitStatus": "false"
},
timeout=10)
break
except google.auth.exceptions.RefreshError:
logger.log_exception("Service account key not ready")
time.sleep(10) # need more time for key to propagate
if response.status_code != 200:
return ({
'error': "Unable to register account with firecloud",
'message': response.text
}, 400)
# 8) Check ProxyGroup
# Either add the new service account to the user's [email protected] group
# Or create the group, if it doesn't exist
fc_session = fc_auth if fc_auth is not None else session
response = fc_session.get('https://api.firecloud.org/api/groups',
headers={'User-Agent': 'FISS/0.16.9'},
timeout=5)
if response.status_code != 200:
return ({
'error': "Unable to enumerate user's groups",
'message': response.text,
'FC-Auth': fc_auth_error
}, 400)
target_group = utils.proxy_group_for_user(token_info['email'])
for group in response.json():
if group['groupName'] == target_group:
# 9) Register Account in Group
response = fc_session.put(
'https://api.firecloud.org/api/groups/{group}/member/{email}'
.format(group=target_group, email=quote(account_email)),
timeout=5)
if response.status_code != 204:
return ({
'error':
'Unable to add pet account to proxy group',
'message':
"Please manually add {email} to {group}".format(
group=target_group, email=quote(account_email)),
'FC-Auth':
fc_auth_error
}, 400)
else:
return (account_email, 200)
# 8.b) Create Group
response = session.post(
'https://api.firecloud.org/api/groups/{group}'.format(
group=target_group),
timeout=5)
if response.status_code >= 400:
return ({
'error': 'Unable to create Firecloud proxy group',
'message': response.text
}, 400)
# 9) Register Account in Group
response = fc_session.put(
'https://api.firecloud.org/api/groups/{group}/member/{email}'.
format(group=target_group, email=quote(account_email)),
timeout=5)
if response.status_code != 204:
return ({
'error':
'Unable to add pet account to proxy group',
'message':
"Please manually add {email} to {group}".format(
group=target_group + '@firecloud.org',
email=quote(account_email)),
'FC-Auth':
fc_auth_error
}, 400)
else:
return (account_email, 200)
except requests.ReadTimeout:
logger.log_exception('Firecloud timeout')
return ({
'error':
'timeout to firecloud',
'message':
'Took longer than 5 seconds for Firecloud to respond. Please try again later'
}, 400)
except:
logger.log_exception()
return ({
'error': 'Unknown Error',
'message': traceback.format_exc()
}, 500)
def new_about():
if not validate_token(request):
return render_template("error_page.html")
user = get_data_by_token(request.cookies.get('token', None))
return render_template("about.html")
def quotas(request):
logger = utils.CloudLogger().log_request(request)
try:
# 1) Validate the token
token = utils.extract_token(request.headers, None)
if token is None:
return ({
'error': 'Bad Request',
'message': 'Token must be provided in header or body'
}, 400)
token_info = utils.get_token_info(token)
if 'error' in token_info:
return ({
'error':
'Invalid Token',
'message':
token_info['error_description'] if 'error_description'
in token_info else 'Google rejected the client token'
}, 401)
if not utils.validate_token(token_info):
return ({
'error':
'Rejected token',
'message':
'Token was valid but did not meet Lapdog security requirements. Token must have email, profile, openid, and devstorage.read_write scopes.'
' Broad users must authenticate via a LapdogToken'
}, 403)
# 2) Check service account
default_session = utils.generate_default_session(
scopes=['https://www.googleapis.com/auth/cloud-platform'])
account_email = utils.ld_acct_in_project(token_info['email'])
response = utils.query_service_account(default_session, account_email)
if response.status_code >= 400:
return ({
'error': 'Unable to query service account',
'message': response.text
}, 400)
if response.json()['email'] != account_email:
return ({
'error':
'Service account email did not match expected value',
'message':
response.json()['email'] + ' != ' + account_email
}, 400)
# 3) Query quota usage
project_usage = default_session.get(
'https://www.googleapis.com/compute/v1/projects/{project}'.format(
project=os.environ.get('GCP_PROJECT')))
if project_usage.status_code != 200:
return ({
'error':
'Invalid response from Google',
'message':
'(%d) : %s' % (project_usage.status_code, project_usage.text)
}, 400)
quotas = [{
**quota,
**{
'percent': ('%0.2f%%' % (100 * quota['usage'] / quota['limit'])) if quota['limit'] > 0 else '0.00%'
}
} for quota in project_usage.json()['quotas']]
for region_name in utils.enabled_regions():
region_usage = default_session.get(
'https://www.googleapis.com/compute/v1/projects/{project}/regions/{region}'
.format(project=os.environ.get('GCP_PROJECT'),
region=region_name))
if region_usage.status_code != 200:
return ({
'error':
'Invalid response from Google',
'message':
'(%d) : %s' % (region_usage.status_code, region_usage.text)
}, 400)
quotas += [{
**quota,
**{
'percent': ('%0.2f%%' % (100 * quota['usage'] / quota['limit'])) if quota['limit'] > 0 else '0.00%',
'metric':
region_name + '.' + quota['metric']
}
} for quota in region_usage.json()['quotas']]
return ({
'raw':
quotas,
'alerts': [
quota for quota in quotas
if quota['limit'] > 0 and quota['usage'] /
quota['limit'] >= 0.5
]
}, 200)
except:
logger.log_exception()
return ({
'error': 'Unknown Error',
'message': traceback.format_exc()
}, 500)
def new_calc():
db = DbClient()
if not validate_token(request):
return render_template("error_page.html")
user = get_data_by_token(request.cookies.get('token', None))
username = db.users.get_user_by_id(user['user_id'])['user']
config_trashold = conf.trash_threshold
present_treshold = conf.trash_threshold
if request.method == 'POST':
if request.form.get('range'):
present_percent = request.form.get('range')
capacity = int(present_percent)
present_treshold = capacity
if request.form.get('trashold'):
result = request.form.get('trashold')
if '%' in result:
threshold = int(result[:-1])
else:
threshold = int(result)
conf.trash_threshold = int(threshold)
capacity = int(conf.trash_threshold)
config_trashold = capacity
present_treshold = capacity
else:
capacity = conf.trash_threshold
pickup_sensors = db.sensors.get_sensor_over_x_capacity(capacity)
if not pickup_sensors:
pickup_sensors = []
remain_sensors = db.sensors.get_sensor_under_x_capacity(capacity)
if not remain_sensors:
remain_sensors = []
threshold = conf.trash_threshold
risk_sensors = []
total_trash_to_pickup = 0
for sensor in remain_sensors:
fill_avg = utils.get_avg_fill_per_sensor(
db.statistics.get_sensor_stat_by_id(sensor['id']))
if int(sensor['capacity']) + fill_avg >= threshold:
risk_sensors.append(sensor)
sensor['fill_avg'] = fill_avg
for sensor in pickup_sensors:
fill_avg = utils.get_avg_fill_per_sensor(
db.statistics.get_sensor_stat_by_id(sensor['id']))
total_trash_to_pickup += sensor['capacity']
sensor['fill_avg'] = fill_avg
calculate_capacity = sensor['capacity']
days_until_full = 0
while calculate_capacity <= capacity:
calculate_capacity += fill_avg
days_until_full += 1
sensor['day_until_full'] = days_until_full
truck_needed = round(total_trash_to_pickup / 1000)
if truck_needed == 0:
truck_needed = 1
return render_template("calc.html",
sensors=pickup_sensors,
capacityint=capacity,
total_to_pickup=len(pickup_sensors),
config_trashold=config_trashold,
present_treshold=present_treshold,
risked=len(risk_sensors),
truck_needed=truck_needed,
unrisked=len(pickup_sensors) + len(remain_sensors) -
len(risk_sensors),
username=username)
def new_stats():
db = DbClient()
if not validate_token(request):
return render_template("error_page.html")
user = get_data_by_token(request.cookies.get('token', None))
return render_template("analytics.html")
def create_submission(request):
logger = utils.CloudLogger().log_request(request)
try:
data = request.get_json()
# 1) Validate the token
if not isinstance(data, dict):
return ({
'error':
"Bad Request",
'message': ("No data was provided" if data is None else
"Expected JSON dictionary in request body")
}, 400)
token = utils.extract_token(request.headers, data)
if token is None:
return ({
'error': 'Bad Request',
'message': 'Token must be provided in header or body'
}, 400)
token_info = utils.get_token_info(token)
if 'error' in token_info:
return ({
'error':
'Invalid Token',
'message':
token_info['error_description'] if 'error_description'
in token_info else 'Google rejected the client token'
}, 401)
if not utils.validate_token(token_info):
return ({
'error':
'Rejected token',
'message':
'Token was valid but did not meet Lapdog security requirements. Token must have email, profile, openid, and devstorage.read_write scopes.'
' Broad users must authenticate via a LapdogToken'
}, 403)
# 1.b) Verify the user has a pet account
response = utils.query_service_account(
utils.generate_default_session(
scopes=['https://www.googleapis.com/auth/cloud-platform']),
utils.ld_acct_in_project(token_info['email']))
if response.status_code != 200:
return ({
'error': 'User has not registered with this Lapdog Engine',
'message': response.text
}, 401)
# 2) Validate user's permission for the bucket
if 'bucket' not in data:
return ({
'error': 'Bad Request',
'message': 'Missing required parameter "bucket"'
}, 400)
session = utils.generate_user_session(token)
fc_auth = utils.generate_user_session(
request.headers['X-Fc-Auth']
) if 'X-Fc-Auth' in request.headers else None
if fc_auth is None:
logger.log("Missing backup Firecloud authentication",
token_info=token_info,
authorized=True
if 'cloud-platform' in token_info['scope'] else False,
severity='DEBUG')
read, write = utils.validate_permissions(session, data['bucket'])
if read is None:
# Error, write will contain a message
return ({
'error': 'Cannot Validate Bucket Permissions',
'message': write
}, 400)
if not (read and write):
# User doesn't have full permissions to the bucket
return ({
'error':
'Not Authorized',
'message':
'User lacks read/write permissions to the requested bucket'
}, 403)
# 2.b) Verify that the bucket belongs to this project
if 'namespace' not in data or 'workspace' not in data:
return ({
'error':
'Bad Request',
'message':
'Missing required parameters "namespace" and "workspace"'
}, 400)
core_session = utils.generate_core_session()
result, message = utils.authenticate_bucket(
data['bucket'], data['namespace'], data['workspace'],
fc_auth if fc_auth is not None else session, core_session)
if not result:
return ({
'error':
'Cannot Validate Bucket Signature',
'message':
message,
'FC-Auth':
('Authorized' if fc_auth is not None
or 'cloud-platform' in token_info['scope'] else
'Not Authorized. Repeat request with the "X-Fc-Auth" header containing application-default credentials'
)
}, 400)
# 3) Check that submission.json exists, and is less than 1 Gib
if 'submission_id' not in data:
return ({
'error': 'Bad Request',
'message': 'Missing required parameter "submission_id"'
}, 400)
submission = utils.fetch_submission_blob(session, data['bucket'],
data['submission_id'])
result, message = utils.validate_submission_file(submission)
if not result:
return ({'error': 'Bad Submission', 'message': message}, 400)
# 4) Submit pipelines request
region = 'us-central1'
if 'compute_region' in data:
allowed_regions = utils.enabled_regions()
if data['compute_region'] in allowed_regions:
region = data['compute_region']
else:
return ({
'error':
"Invalid Region",
'message':
"Region not allowed. Enabled regions: " +
repr(allowed_regions)
}, 400)
if 'memory' in data and data['memory'] > 3072:
mtype = 'custom-%d-%d' % (
math.ceil(data['memory'] / 13312) *
2, # Cheapest core:memory ratio
data['memory'])
else:
mtype = 'n1-standard-1'
pipeline = {
'pipeline': {
'actions': [{
'imageUri':
'gcr.io/broad-cga-aarong-gtex/wdl_runner:' +
__CROMWELL_TAG__,
'commands': ['/wdl_runner/wdl_runner.sh'],
'environment': {
'SIGNATURE_ENDPOINT':
'https://{region}-{project}.cloudfunctions.net/signature-{version}'
.format(region=os.environ.get('FUNCTION_REGION'),
project=os.environ.get("GCP_PROJECT"),
version=__API_VERSION__['signature']),
'LAPDOG_PROJECT':
os.environ.get('GCP_PROJECT'),
'WDL':
"gs://{bucket}/lapdog-executions/{submission_id}/method.wdl"
.format(bucket=data['bucket'],
submission_id=data['submission_id']),
'WORKFLOW_INPUTS':
"gs://{bucket}/lapdog-executions/{submission_id}/config.tsv"
.format(bucket=data['bucket'],
submission_id=data['submission_id']),
'WORKFLOW_OPTIONS':
json.dumps(data['options'])
if 'options' in data else '{}',
'LAPDOG_SUBMISSION_ID':
data['submission_id'],
'WORKSPACE':
"gs://{bucket}/lapdog-executions/{submission_id}/workspace/"
.format(bucket=data['bucket'],
submission_id=data['submission_id']),
'OUTPUTS':
"gs://{bucket}/lapdog-executions/{submission_id}/results"
.format(bucket=data['bucket'],
submission_id=data['submission_id']),
'SUBMISSION_DATA_PATH':
"gs://{bucket}/lapdog-executions/{submission_id}/submission.json"
.format(bucket=data['bucket'],
submission_id=data['submission_id']),
'LAPDOG_LOG_PATH':
"gs://{bucket}/lapdog-executions/{submission_id}/logs".
format(bucket=data['bucket'],
submission_id=data['submission_id']),
'PRIVATE_ACCESS':
'true' if
('no_ip' in data and data['no_ip']) else 'false',
'SUBMISSION_ZONES':
" ".join('{}-{}'.format(region, zone)
for zone in GCP_ZONES[region]),
'DUMP_PATH':
(("gs://{bucket}/lapdog-call-cache.sql".format(
bucket=data['bucket']))
if 'callcache' in data and data['callcache'] else "")
}
}],
'resources': {
'regions': [region],
'virtualMachine': {
'machineType':
mtype,
'preemptible':
False,
'labels': {
'lapdog-execution-role': 'cromwell',
'lapdog-submission-id': data['submission_id']
},
'serviceAccount': {
'email':
utils.ld_acct_in_project(token_info['email']),
'scopes': [
"https://www.googleapis.com/auth/cloud-platform",
"https://www.googleapis.com/auth/compute",
"https://www.googleapis.com/auth/devstorage.read_write",
"https://www.googleapis.com/auth/genomics"
]
},
'bootDiskSizeGb':
20 + (max(0, data['cache_size'] -
10) if 'cache_size' in data else 0),
'network': {
'network':
'default',
'usePrivateAddress': ('no_ip' in data
and data['no_ip'])
}
}
},
}
}
papi_url = 'https://lifesciences.googleapis.com/v2beta/projects/{}/locations/{}/pipelines:run'.format(
os.environ.get('GCP_PROJECT'), region)
logger.log("Launching LifeSciences v2Beta pipeline",
pipeline=pipeline['pipeline'],
url=papi_url,
severity='NOTICE')
response = utils.generate_default_session([
"https://www.googleapis.com/auth/cloud-platform",
"https://www.googleapis.com/auth/compute",
"https://www.googleapis.com/auth/genomics"
]).post(papi_url,
headers={'Content-Type': 'application/json'},
json=pipeline)
try:
if response.status_code == 200:
operation = response.json()['name']
# 5) Sign the operation
logger.log("Generating new signature",
data=(data['submission_id'] + operation))
utils.sign_object(
(data['submission_id'] + operation).encode(),
utils.getblob(
'gs://{bucket}/lapdog-executions/{submission_id}/signature'
.format(bucket=data['bucket'],
submission_id=data['submission_id']),
credentials=session.credentials),
core_session.credentials)
return operation, 200
except:
logger.log_exception('PAPIv2 request failed')
return ({
'error': 'Unable to start submission',
'message': traceback.format_exc()
}, 500)
return ({
'error':
'Unable to start submission',
'message':
'Google rejected the pipeline request (%d) : %s' %
(response.status_code, response.text)
}, 400)
except:
logger.log_exception()
return ({
'error': 'Unknown Error',
'message': traceback.format_exc()
}, 500)
def main():
db = DbClient()
try:
if not validate_token(request):
return render_template(
"error_page.html",
error_msg=
"You are not login, please enter to login page to access to the system"
)
user = get_data_by_token(request.cookies.get('token', None))
if request.method == 'POST':
sensors_low = []
sensors_mid = []
sensors_full = []
sensors, checked_list = utils.get_sensors_by_main_filters(request)
for sensor in sensors:
sensor = [
sensor,
]
if int(sensor[0][2]) < 25:
sensors_low = sensors_low + sensor
elif int(sensor[0][2]) < 75:
sensors_mid = sensors_mid + sensor
else:
sensors_full = sensors_full + sensor
else:
sensors = []
sensors_low = db.sensors.get_sensor_between_capacity(0, 25)
if sensors_low:
sensors += sensors_low
sensors_mid = db.sensors.get_sensor_between_capacity(26, 75)
if sensors_mid:
sensors += sensors_mid
sensors_full = db.sensors.get_sensor_between_capacity(76, 100)
if sensors_full:
sensors += sensors_full
sensors = [tuple(sensor.values()) for sensor in sensors]
utils.write_sensors_to_csv(sensors)
sensors = [[x[1], x[4], x[5], x[3], x[2], x[0]] for x in sensors]
return render_template("index.html",
sensors=sensors,
persent_count=len(sensors),
total_count=len(sensors))
utils.write_sensors_to_csv(sensors)
sensor_count = db.sensors.get_count_sensors()['count(*)']
sensors = [[x[1], x[4], x[5], x[3], x[2], x[0]] for x in sensors]
return render_template("index.html",
sensors=sensors,
capacity_empty=checked_list[0],
capacity_mid=checked_list[1],
capacity_full=checked_list[2],
over_trashold=checked_list[3],
below_trashold=checked_list[4],
ConnectedBins=checked_list[5],
FailedBins=checked_list[6],
persent_count=len(sensors),
total_count=sensor_count)
except Exception as e:
print(traceback.format_exc())
print(e)
def abort_submission(request):
logger = utils.CloudLogger().log_request(request)
try:
data = request.get_json()
# 1) Validate the token
if not isinstance(data, dict):
return ({
'error':
"Bad Request",
'message': ("No data was provided" if data is None else
"Expected JSON dictionary in request body")
}, 400)
token = utils.extract_token(request.headers, data)
if token is None:
return ({
'error': 'Bad Request',
'message': 'Token must be provided in header or body'
}, 400)
token_info = utils.get_token_info(token)
if 'error' in token_info:
return ({
'error':
'Invalid Token',
'message':
token_info['error_description'] if 'error_description'
in token_info else 'Google rejected the client token'
}, 401)
if not utils.validate_token(token_info):
return ({
'error':
'Rejected token',
'message':
'Token was valid but did not meet Lapdog security requirements. Token must have email, profile, openid, and devstorage.read_write scopes.'
' Broad users must authenticate via a LapdogToken'
}, 403)
# 2) Validate user's permission for the bucket
if 'bucket' not in data:
return ({
'error': 'Bad Request',
'message': 'Missing required parameter "bucket"'
}, 400)
session = utils.generate_user_session(token)
read, write = utils.validate_permissions(session, data['bucket'])
if read is None:
# Error, write will contain a message
return ({
'error': 'Cannot Validate Bucket Permissions',
'message': write
}, 400)
if not (read and write):
# User doesn't have full permissions to the bucket
return ({
'error':
'Not Authorized',
'message':
'User lacks read/write permissions to the requested bucket'
}, 401)
# 3) Check that submission.json exists, and is less than 1 Gib
if 'submission_id' not in data:
return ({
'error': 'Bad Request',
'message': 'Missing required parameter "submission_id"'
}, 400)
submission = utils.fetch_submission_blob(session, data['bucket'],
data['submission_id'])
result, message = utils.validate_submission_file(submission)
if not result:
return ({'error': 'Bad Submission', 'message': message}, 400)
# 4) Download submission and parse operation
try:
submission = json.loads(submission.download_as_string().decode())
except:
return ({
'error': 'Invalid Submission',
'message': 'Submission was not valid JSON'
}, 400)
if 'operation' not in submission:
return ({
'error': 'Invalid Submission',
'message': 'Submission contained no operation metadata'
}, 400)
signature_blob = utils.getblob(
'gs://{bucket}/lapdog-executions/{submission_id}/signature'.format(
bucket=data['bucket'], submission_id=data['submission_id']),
credentials=session.credentials)
if not signature_blob.exists():
return ({
'error':
'No Signature',
'message':
'The submission signature could not be found. Refusing to abort job'
}, 403)
if not utils.verify_signature(
signature_blob,
(data['submission_id'] + submission['operation']).encode()):
return ({
'error':
'Invalid Signature',
'message':
'Could not validate submission signature. Refusing to abort job'
}, 403)
core_session = utils.generate_core_session()
# 5) Generate abort key
logger.log("Generating new signature", data=data['submission_id'])
utils.sign_object(
data['submission_id'].encode(),
utils.getblob(
'gs://{bucket}/lapdog-executions/{submission_id}/abort-key'.
format(bucket=data['bucket'],
submission_id=data['submission_id']),
credentials=session.credentials), core_session.credentials)
if 'hard' in data and data['hard']:
# 6) Abort operation
logger.log("Hard-aborting submission",
submission_id=data['submission_id'],
operation_id=submission['operation'],
severity='NOTICE')
response = core_session.post(
"https://genomics.googleapis.com/v2alpha1/{operation}:cancel".
format(operation=quote(
submission['operation']) # Do not quote slashes here
))
return response.text, response.status_code
return ({
'status':
'Aborting',
'message':
'A soft-abort request has been sent.'
' If the submission does not abort soon, abort it with hard=True to force-kill the cromwell server'
}, 200)
except:
logger.log_exception()
return ({
'error': 'Unknown Error',
'message': traceback.format_exc()
}, 500)
IGNORE_FILES)
zip_file = open(CHALLENGE_ZIP_FILE_PATH, 'rb')
file = {"zip_configuration": zip_file}
data = {"GITHUB_REPOSITORY": GITHUB_REPOSITORY}
try:
response = requests.post(url, data=data, headers=headers, files=file)
if response.status_code != http.HTTPStatus.OK and response.status_code != http.HTTPStatus.CREATED:
response.raise_for_status()
else:
print("\n" + response.json()["Success"])
except requests.exceptions.HTTPError as err:
if response.status_code in EVALAI_ERROR_CODES:
is_token_valid = validate_token(response.json())
if is_token_valid:
error = response.json()["error"]
error_message = "\nFollowing errors occurred while validating the challenge config:\n{}".format(
error)
print(error_message)
os.environ["CHALLENGE_ERRORS"] = error_message
else:
print(
"\nFollowing errors occurred while validating the challenge config: {}"
.format(err))
os.environ["CHALLENGE_ERRORS"] = str(err)
except Exception as e:
if VALIDATION_STEP == "True":
error_message = "\nFollowing errors occurred while validating the challenge config: {}".format(
e)
def insert_resolution(request):
"""
This function is unique. It is not deployed into each project.
It is deployed once into my personal project which serves as a centralized
database.
"""
logger = utils.CloudLogger().log_request(request)
try:
data = request.get_json()
if not isinstance(data, dict):
return (
{
'error': "Bad Request",
'message': ("No data was provided" if data is None else "Expected JSON dictionary in request body")
},
400
)
token = utils.extract_token(request.headers, data)
token_info = utils.get_token_info(token)
if 'error' in token_info:
return (
{
'error': 'Invalid Token',
'message': token_info['error_description'] if 'error_description' in token_info else 'Google rejected the client token'
},
401
)
if not utils.validate_token(token_info):
return (
{
'error': 'Rejected token',
'message': 'Token was valid but did not meet Lapdog security requirements. Token must have email, profile, openid, and devstorage.read_write scopes.'
' Broad users must authenticate via a LapdogToken'
},
403
)
if 'namespace' not in data:
return (
{
'error': 'Missing Parameters',
'message': "Missing required parameter \"namespace\""
},
400
)
user_session = utils.generate_user_session(token)
while True:
response = user_session.get(
'https://api.firecloud.org/api/profile/billing'
)
if response.status_code == 200:
break
print(response.status_code, response.text, file=sys.stderr)
if response.status_code == 404:
return (
{
'error': "User not found",
'message': "You are not registered yet with firecloud"
},
404
)
time.sleep(5)
projects = {proj['projectName']:proj for proj in response.json()}
if data['namespace'] not in projects:
return (
{
'error': "Bad Namespace",
'message': 'The provided namespace "%s" could not be found' % data['namespace']
},
400
)
if projects[data['namespace']]['role'] not in {'Owner', 'Admin', 'Administrator'}:
return (
{
'error': "Insufficient Permissions",
'message': "The user lacks Owner/Admin privilages on the provided namespace"
},
401
)
if 'project' not in data:
return (
{
'error': "Missing parameters",
'message': "Missing required parameter \"project\""
},
400
)
response = user_session.post(
'https://cloudresourcemanager.googleapis.com/v1/projects/{project}:getIamPolicy'.format(
project=data['project']
)
)
if response.status_code == 403:
return (
{
'error': 'Unauthorized',
'message': "User lacks permissions on the provided project"
},
401
)
if response.status_code != 200:
return (
{
'error': 'Unexpected response from Googla API',
'message': '(%d) : %s' % (response.status_code, response.text)
},
400
)
for policy in response.json()['bindings']:
if policy['role'] == 'roles/owner':
if ('user:'******'email']) in policy['members']:
blob = utils.getblob(
'gs://lapdog-resolutions/%s' % sha512(data['namespace'].encode()).hexdigest(),
credentials=utils.generate_default_session().credentials
)
if blob.exists():
return (
{
'error': "Already Exists",
'message': "A resolution for this namespace is already in place"
},
409
)
logger.log(
"Adding new resolution",
namespace=data['namespace'],
project_id=data['project'],
admin=token_info['email'],
severity='NOTICE'
)
blob.upload_from_string(
data['project'].encode()
)
return (
'gs://lapdog-resolutions/%s' % sha512(data['namespace'].encode()).hexdigest(),
200
)
return (
{
'error': "Unauthorized",
'message': "User lacks ownership of the provided project"
},
400
)
except:
logger.log_exception()
return (
{
'error': "Unknown Error",
'message': traceback.format_exc()
},
500
)