"""
__license__ = "LGPLv3+"
from flask import request, current_app
from flask_restx._http import HTTPStatus
from flask_restx_patched import Resource
from app.extensions.api import api_v1, Namespace
from app.extensions.auth import token_required, authorization_required
from app.extensions.user_office_link import user_office_link
api = Namespace("User office",
description="User office related namespace",
path="/user_office")
api_v1.add_namespace(api)
@api.route("/sync_all", endpoint="user_office_sync_all")
@api.doc(security="apikey")
class SyncAll(Resource):
"""Sync with user office"""
@token_required
@authorization_required
def post(self):
"""Sync with user office"""
api.logger.info("Sync with uer office")
user_office_link.sync_with_user_office()
from ispyb_ssx.schemas import loaded_sample as loaded_sample_schemas
from ispyb_ssx.schemas import crystal_slurry as crystal_slurry_schemas
from ispyb_ssx.schemas import (
crystal_size_distribution as crystal_size_distribution_schemas, )
from ispyb_ssx.schemas import sample_stock as sample_stock_schemas
from ispyb_ssx.schemas import sample_delivery_device as sample_delivery_device_schemas
from ispyb_ssx.modules import loaded_sample
from ispyb_service_connector import get_ispyb_resource
__license__ = "LGPLv3+"
log = logging.getLogger(__name__)
api = Namespace("Samples",
description="Samples related namespace",
path="/samples")
api_v1.add_namespace(api)
@api.route("", endpoint="loaded_samples")
@api.doc(security="apikey")
class LoadedSample(Resource):
"""Loaded sample resource"""
# @token_required
def get(self):
"""Returns all loaded samples"""
# app.logger.info("Return all data collections")
return loaded_sample.get_loaded_samples(request)
from flask_login import current_user
from flask_restplus_patched import Resource
from flask_restplus_patched._http import HTTPStatus
from app.extensions import db
from app.extensions.api import Namespace, abort
from app.extensions.api.parameters import PaginationParameters
from app.modules.users import permissions
from app.modules.users.models import User
from . import parameters, schemas
from .models import Team, TeamMember
log = logging.getLogger(__name__) # pylint: disable=invalid-name
api = Namespace('teams', description="Teams") # pylint: disable=invalid-name
@api.route('/')
@api.login_required(oauth_scopes=['teams:read'])
class Teams(Resource):
"""
Manipulations with teams.
"""
@api.parameters(PaginationParameters())
@api.response(schemas.BaseTeamSchema(many=True))
def get(self, args):
"""
List of teams.
Returns a list of teams starting from ``offset`` limited by ``limit``
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with py-ispyb. If not, see <http://www.gnu.org/licenses/>.
from flask import request, make_response
from flask_restx_patched import Resource
from app.extensions.api import api_v1, Namespace
from app.extensions import auth_provider
__license__ = "LGPLv3+"
api = Namespace("Authentication",
description="authentication namespace",
path="/auth")
api_v1.add_namespace(api)
@api.route("/login")
class Login(Resource):
"""Login resource"""
def get(self):
authorization = request.authorization
if (not authorization or not authorization.username
or not authorization.password):
if not request.headers.get("username") or not request.headers.get(
"password"):
return make_response(
import logging
from flask_login import current_user # NOQA
from flask_restplus_patched import Resource
from flask_restplus._http import HTTPStatus
from app.extensions import db
from app.extensions.api import Namespace
from app.extensions.api.parameters import PaginationParameters
from app.modules.users import permissions
from . import parameters, schemas
from .models import Collaboration
log = logging.getLogger(__name__) # pylint: disable=invalid-name
api = Namespace('collaborations', description='Collaborations') # pylint: disable=invalid-name
@api.route('/')
@api.login_required(oauth_scopes=['collaborations:read'])
class Collaborations(Resource):
"""
Manipulations with Collaborations.
"""
@api.parameters(PaginationParameters())
@api.response(schemas.BaseCollaborationSchema(many=True))
def get(self, args):
"""
List of Collaboration.
Returns a list of Collaboration starting from ``offset`` limited by ``limit``
from flask_login import current_user
from flask_restplus_patched import Resource
from flask_restplus._http import HTTPStatus
from app.extensions import db
from app.extensions.api import Namespace
from app.extensions.api.parameters import PaginationParameters
from app.modules.users import permissions
from app.modules.users.permissions.types import AccessOperation
from . import parameters, schemas
from .models import Submission
import os
log = logging.getLogger(__name__) # pylint: disable=invalid-name
api = Namespace('submissions', description='Submissions') # pylint: disable=invalid-name
@api.route('/')
@api.login_required(oauth_scopes=['submissions:read'])
class Submissions(Resource):
"""
Manipulations with Submissions.
"""
@api.permission_required(
permissions.ModuleAccessPermission,
kwargs_on_request=lambda kwargs: {
'module': Submission,
'action': AccessOperation.READ,
},
)
import logging
from flask import current_app, request
from flask_restplus_patched import Resource
from flask_restplus._http import HTTPStatus
from app.extensions.api import Namespace
from app.extensions.api import abort
from app.modules.users.models import User
from werkzeug.exceptions import BadRequest
import json
log = logging.getLogger(__name__) # pylint: disable=invalid-name
edm_configuration = Namespace('configuration',
description='(EDM) Configuration') # pylint: disable=invalid-name
edm_configurationDefinition = Namespace(
'configurationDefinition', description='(EDM) Configuration Definition') # pylint: disable=invalid-name
@edm_configuration.route('/')
@edm_configuration.login_required(oauth_scopes=['configuration:read'])
class EDMConfigurationTargets(Resource):
"""
Manipulations with Configuration.
"""
def get(self):
"""
List the possible EDM passthrough targets.
"""
current_app.edm.ensure_initialed()
"""
__license__ = "LGPLv3+"
from flask import request, current_app
from flask_restx._http import HTTPStatus
from flask_restx_patched import Resource
from app.extensions.api import api_v1, Namespace
from app.extensions.auth import token_required, authorization_required
from ispyb_core.schemas import proposal as proposal_schemas
from ispyb_core.modules import proposal
api = Namespace("Proposals",
description="Proposal related namespace",
path="/proposals")
api_v1.add_namespace(api)
@api.route("", endpoint="proposals")
@api.doc(security="apikey")
class Proposals(Resource):
"""Allows to get all proposals"""
@token_required
@authorization_required
def get(self):
"""Returns proposals based on query parameters"""
api.logger.info("Get all proposals")
return proposal.get_proposals(request)
from app.extensions.api import api_v1, Namespace
from app.extensions.auth import token_required, authorization_required
from ispyb_core.schemas import auto_proc as auto_proc_schemas
from ispyb_core.schemas import auto_proc_program as auto_proc_program_schemas
from ispyb_core.schemas import (
auto_proc_program_attachment as auto_proc_program_attachment_schemas, )
from ispyb_core.schemas import (
auto_proc_program_message as auto_proc_program_message_schemas, )
from ispyb_core.schemas import auto_proc_status as auto_proc_status_schemas
from ispyb_core.modules import auto_proc
__license__ = "LGPLv3+"
api = Namespace("Auto processing",
description="Auto processing related namespace",
path="/autoproc")
api_v1.add_namespace(api)
@api.route("", endpoint="auto_procs")
@api.doc(security="apikey")
class AutoProcs(Resource):
"""Allows to get all auto proc entries"""
@token_required
@authorization_required
def get(self):
"""Returns auto proc entries"""
return auto_proc.get_auto_procs(request)
from app.extensions.api import Namespace, abort
from app.modules.users import permissions
from app.extensions.api.parameters import PaginationParameters
from app.modules.auth.models import Code
from .models import Asset
from . import schemas
from PIL import Image
import os
log = logging.getLogger(__name__) # pylint: disable=invalid-name
api = Namespace('assets', description='Assets') # pylint: disable=invalid-name
def process_file_upload(square=False):
FINAL_EXT = '.jpg'
asset_path = current_app.config.get('ASSET_DATABASE_PATH', None)
assert asset_path is not None
assert os.path.exists(asset_path)
allowed_extensions = current_app.config.get('ASSET_ALLOWED_EXTS', [])
upload_file = request.files.get('file', None)
if upload_file is None:
abort(code=HTTPStatus.CONFLICT, message='The file was not uploaded as expected')
import logging
from flask_login import current_user # NOQA
from flask_restplus_patched import Resource
from flask_restplus._http import HTTPStatus
from app.extensions import db
from app.extensions.api import Namespace
from app.extensions.api.parameters import PaginationParameters
from app.modules.users import permissions
from . import parameters, schemas
from .models import Notification
log = logging.getLogger(__name__) # pylint: disable=invalid-name
api = Namespace('notifications', description='Notifications') # pylint: disable=invalid-name
@api.route('/')
@api.login_required(oauth_scopes=['notifications:read'])
class Notifications(Resource):
"""
Manipulations with Notifications.
"""
@api.parameters(PaginationParameters())
@api.response(schemas.BaseNotificationSchema(many=True))
def get(self, args):
"""
List of Notification.
Returns a list of Notification starting from ``offset`` limited by ``limit``
from flask import request
from flask_restx._http import HTTPStatus
from flask_restx_patched import Resource
from app.extensions.auth import token_required, authorization_required
from app.extensions.api import api_v1, Namespace
from ispyb_core.modules import shipping
from ispyb_core.schemas import shipping as shipping_schemas
import logging
__license__ = "LGPLv3+"
log = logging.getLogger(__name__)
api = Namespace("Shipments",
description="Shipment related namespace",
path="/shipments")
api_v1.add_namespace(api)
@api.route("", endpoint="shipments")
@api.doc(security="apikey")
class Shipments(Resource):
"""Allows to get all shipments"""
@token_required
@authorization_required
def get(self):
"""Returns list of shipments"""
return shipping.get_shipments(request), HTTPStatus.OK
@api.expect(shipping_schemas.f_schema)
import logging
from flask_login import current_user
from flask_restplus_patched import Resource
from flask_restplus._http import HTTPStatus
from app.extensions import db
from app.extensions.api import Namespace, abort
from app.modules.users import permissions
from ..related_jira_util.commands import find_related_tickets
from . import parameters, schemas
log = logging.getLogger(__name__) # pylint: disable=invalid-name
api = Namespace('related-jira-finder', description="Related JIRA Finder") # pylint: disable=invalid-name
@api.route('/')
class RelatedJira(Resource):
"""
Use related jira form helpers.
"""
@api.parameters(parameters.RelatedJiraParameters())
def get(self, args):
"""
Get Related JIRA.
This endpoint must be used in order to get a server reCAPTCHA public key which
must be used to receive a reCAPTCHA secret key for POST /users/ form.
"""
import logging
from flask_login import current_user
from flask_restplus_patched import Resource
from flask_restplus._http import HTTPStatus
from app.extensions.api import abort
from app.extensions.api import Namespace
from . import permissions, schemas, parameters
from .models import db, User
log = logging.getLogger(__name__)
api = Namespace('users', description='Users')
@api.route('/')
class Users(Resource):
"""
Manipulations with users.
"""
@api.login_required(oauth_scopes=['users:read'])
@api.permission_required(permissions.StaffRolePermission())
@api.response(schemas.BaseUserSchema(many=True))
@api.paginate(parameters.ListUserParameters())
def get(self, args):
"""
List of users.
import importlib
from flask import current_app
from flask_restx_patched import Resource, HTTPStatus
from app.extensions.api import api_v1, Namespace
# from app.extensions.auth import token_required
from ispyb_core import schemas
__license__ = "LGPLv3+"
api = Namespace("Schemas",
description="Schemas related namespace",
path="/schemas")
api_v1.add_namespace(api)
@api.route("/available_names", endpoint="available_schemas_names")
class SchemasList(Resource):
# @token_required
def get(self):
"""Returns list of available schemas
Returns:
list: list of names
"""
current_app.logger.info("Get all schemas")
from flask import request
from flask_restx_patched import Resource, HTTPStatus
from app.extensions.api import api_v1, Namespace
from app.extensions.auth import token_required, authorization_required
from ispyb_core.schemas import container as container_schemas
from ispyb_core.modules import container
__license__ = "LGPLv3+"
api = Namespace(
"Containers", description="Container related namespace", path="/containers"
)
api_v1.add_namespace(api)
@api.route("", endpoint="containers")
@api.doc(security="apikey")
class Containers(Resource):
"""Containers resource"""
@token_required
@authorization_required
def get(self):
"""Returns all container items"""
return container.get_containers(request)
from datetime import datetime
from flask import request
from flask_restx_patched import Resource, HTTPStatus, abort
from app.extensions.api import api_v1, Namespace
from app.extensions.auth import token_required, authorization_required
from ispyb_core.schemas import session as session_schemas
from ispyb_core.modules import session
__license__ = "LGPLv3+"
log = logging.getLogger(__name__)
api = Namespace("Sessions",
description="Session related namespace",
path="/sessions")
api_v1.add_namespace(api)
@api.route("", endpoint="sessions")
@api.doc(security="apikey")
class Sessions(Resource):
"""Allows to get all sessions and insert a new one"""
@token_required
@authorization_required
def get(self):
"""Returns list of sessions"""
return session.get_sessions(request)
@api.expect(session_schemas.f_schema)
along with py-ispyb. If not, see <http://www.gnu.org/licenses/>.
"""
from flask import request
from flask_restx_patched import Resource, HTTPStatus
from app.extensions.api import api_v1, Namespace
from app.extensions.auth import token_required, authorization_required
from ispyb_core.schemas import dewar as dewar_schemas
from ispyb_core.modules import dewar
__license__ = "LGPLv3+"
api = Namespace("Dewars",
description="Dewar related namespace",
path="/dewars")
api_v1.add_namespace(api)
@api.route("", endpoint="dewars")
@api.doc(security="apikey")
class Dewars(Resource):
"""Dewars resource"""
@token_required
@authorization_required
def get(self):
"""Returns all dewars items"""
return dewar.get_dewars(request)
@token_required
import logging
from flask_restplus_patched import Resource
from flask_restplus._http import HTTPStatus
from app.extensions import db
from app.extensions.api import Namespace
from app.extensions.api.parameters import PaginationParameters
from app.modules.users import permissions
from . import parameters, schemas
from .models import Sighting
log = logging.getLogger(__name__) # pylint: disable=invalid-name
api = Namespace('sightings', description='Sightings') # pylint: disable=invalid-name
@api.route('/')
@api.login_required(oauth_scopes=['sightings:read'])
class Sightings(Resource):
"""
Manipulations with Sightings.
"""
@api.parameters(PaginationParameters())
@api.response(schemas.BaseSightingSchema(many=True))
def get(self, args):
"""
List of Sighting.
Returns a list of Sighting starting from ``offset`` limited by ``limit``
"""
import logging
from flask_login import current_user
from flask_restplus_patched import Resource
from flask_restplus_patched._http import HTTPStatus
from app.extensions.api import Namespace
from app.extensions.api.parameters import PaginationParameters
from . import permissions, schemas, parameters
from .models import db, User
log = logging.getLogger(__name__)
api = Namespace('users', description="Users")
@api.route('/')
class Users(Resource):
"""
Manipulations with users.
"""
@api.login_required(oauth_scopes=['users:read'])
@api.permission_required(permissions.AdminRolePermission())
@api.parameters(PaginationParameters())
@api.response(schemas.BaseUserSchema(many=True))
def get(self, args):
"""
List of users.
import logging
import io
from flask import request, jsonify, make_response, Response
from flask_restplus_patched import Resource
from app.extensions.api import Namespace, abort
from app.library import jwt
from mind.manager import img_store_manager
import numpy as np
from PIL import Image
log = logging.getLogger(__name__) # pylint: disable=invalid-name
api = Namespace('image', description="Image") # pylint: disable=invalid-name
@api.route("/upload")
class ImgUpload(Resource):
@jwt.required
def post(self):
try:
file = request.files['image']
img_bytes = file.read()
image_pil = Image.open(io.BytesIO(img_bytes))
uid = img_store_manager.save_image(image_pil)
except Exception as e:
res = {"message": str(e), "image_name": ""}
scode = 500
else:
res = {"message": "upload success.", "image_name": uid}
from flask_login import current_user # NOQA
from flask_restplus_patched import Resource
from flask_restplus._http import HTTPStatus
from app.extensions import db
from app.extensions.api import Namespace
from app.extensions.api.parameters import PaginationParameters
from app.modules.users import permissions
from . import parameters, schemas
from .models import Encounter
log = logging.getLogger(__name__) # pylint: disable=invalid-name
api = Namespace('encounters', description='Encounters') # pylint: disable=invalid-name
@api.route('/')
@api.login_required(oauth_scopes=['encounters:read'])
class Encounters(Resource):
"""
Manipulations with Encounters.
"""
@api.parameters(PaginationParameters())
@api.response(schemas.BaseEncounterSchema(many=True))
def get(self, args):
"""
List of Encounter.
from flask import request
from flask_restx_patched import Resource, HTTPStatus
from app.extensions.api import api_v1, Namespace
from app.extensions.auth import token_required, authorization_required
from ispyb_core.schemas import data_collection as data_collection_schemas
from ispyb_core.modules import data_collection
__license__ = "LGPLv3+"
api = Namespace(
"Data collections",
description="Data collection related namespace",
path="/data_collections",
)
api_v1.add_namespace(api)
@api.route("")
@api.doc(security="apikey")
class DataColletions(Resource):
"""Allows to get all data_collections"""
# @api.marshal_list_with(data_collection_schemas.data_collection_f_schema, skip_none=True, code=HTTPStatus.OK)
# TODO Define model with JSON Schema
@token_required
@authorization_required
def get(self):
"""
import logging
import glob
import os
from flask import current_app
from flask_login import current_user # NOQA
from flask_restplus_patched import Resource
from app.extensions.api import Namespace
import datetime
log = logging.getLogger(__name__) # pylint: disable=invalid-name
api = Namespace('frontends', description='Frontends') # pylint: disable=invalid-name
DATETIME_FMTSTR = '%Y%m%d-%H%M%S'
def parse_frontend_versions():
static_root = current_app.config.get('STATIC_ROOT')
frontend_dist_list = glob.glob(os.path.join(static_root, 'dist-*/'))
frontend_dist_latest = glob.glob(os.path.join(static_root, 'dist-latest/'))
assert len(frontend_dist_latest) == 1
frontend_dist_latest = frontend_dist_latest[0]
assert frontend_dist_latest in frontend_dist_list
frontend_dist_list.remove(frontend_dist_latest)
frontend_link_latest = os.path.realpath(frontend_dist_latest)
--------------------------
"""
import logging
from flask_login import current_user
from flask_restplus_patched import Resource
from werkzeug import security
from app.extensions.api import Namespace, http_exceptions
from . import schemas, parameters
from .models import db, OAuth2Client
log = logging.getLogger(__name__)
api = Namespace('auth', description="Authentication")
@api.route('/oauth2_clients/')
@api.login_required(oauth_scopes=['auth:read'])
class OAuth2Clients(Resource):
"""
Manipulations with OAuth2 clients.
"""
@api.parameters(parameters.ListOAuth2ClientsParameters())
@api.response(schemas.BaseOAuth2ClientSchema(many=True))
def get(self, args):
"""
List of OAuth2 Clients.
Returns a list of OAuth2 Clients starting from ``offset`` limited by
RESTful API Passthroughs resources
--------------------------
"""
import logging
from flask import current_app, request
from flask_restplus_patched import Resource
from app.extensions.api import Namespace
from werkzeug.exceptions import BadRequest
import json
log = logging.getLogger(__name__) # pylint: disable=invalid-name
edm_pass = Namespace('passthroughs/edm', description='EDM Passthroughs') # pylint: disable=invalid-name
acm_pass = Namespace('passthroughs/acm', description='ACM Passthroughs') # pylint: disable=invalid-name
@edm_pass.route('/')
@edm_pass.login_required(oauth_scopes=['passthroughs:read'])
class EDMPassthroughTargets(Resource):
"""
Manipulations with Passthroughs.
"""
def get(self):
"""
List the possible EDM passthrough targets.
"""
current_app.edm.ensure_initialed()
targets = list(current_app.edm.targets)
import logging
from flask_login import current_user # NOQA
from flask_restplus_patched import Resource
from flask_restplus._http import HTTPStatus
from app.extensions import db
from app.extensions.api import Namespace
from app.extensions.api.parameters import PaginationParameters
from app.modules.users import permissions
from . import parameters, schemas
from .models import Organization
log = logging.getLogger(__name__) # pylint: disable=invalid-name
api = Namespace('organizations', description='Organizations') # pylint: disable=invalid-name
@api.route('/')
@api.login_required(oauth_scopes=['organizations:read'])
class Organizations(Resource):
"""
Manipulations with Organizations.
"""
@api.parameters(PaginationParameters())
@api.response(schemas.BaseOrganizationSchema(many=True))
def get(self, args):
"""
List of Organization.
Returns a list of Organization starting from ``offset`` limited by ``limit``
import logging
from flask_restplus_patched import Resource
from flask_restplus._http import HTTPStatus
from flask_login import current_user # NOQA
from app.extensions import db
from app.extensions.api import Namespace
from app.extensions.api.parameters import PaginationParameters
from app.modules.users import permissions
from app.modules.users.permissions.types import AccessOperation
from . import parameters, schemas
from .models import Project
log = logging.getLogger(__name__) # pylint: disable=invalid-name
api = Namespace('projects', description='Projects') # pylint: disable=invalid-name
@api.route('/')
@api.login_required(oauth_scopes=['projects:read'])
class Projects(Resource):
"""
Manipulations with Projects.
"""
@api.permission_required(
permissions.ModuleAccessPermission,
kwargs_on_request=lambda kwargs: {
'module': Project,
'action': AccessOperation.READ,
},
)
import logging
from flask_login import current_user
from flask_restplus_patched import Resource
from flask_restplus._http import HTTPStatus
from app.extensions import db
from app.extensions.api import Namespace, abort
from app.extensions.api.parameters import PaginationParameters
from . import parameters, schemas
from .models import Payment
log = logging.getLogger(__name__) # pylint: disable=invalid-name
api = Namespace('payments', description="Payments") # pylint: disable=invalid-name
@api.route('/')
class Payments(Resource):
"""
Manipulations with Payments.
"""
@api.parameters(PaginationParameters())
@api.response(schemas.BasePaymentSchema(many=True))
def get(self, args):
"""
List of Payment.
Returns a list of Payment starting from ``offset`` limited by ``limit``
parameter.
from . import parameters, schemas
from .models import CharacterAnalysis as CA_Model
from .models import AnalysisReport as AR_Model
from .models import MindMatch as MCM_Model
from .models import MindSpecMatch as MSM_Model
from .models import AI_USER_INFOModel as User_Model
from mind.manager import img_store_manager
from cv.align import get_points, warpImage
from cv.utils import *
from mock import object as mock_obj
log = logging.getLogger(__name__) # pylint: disable=invalid-name
api = Namespace('analysis', description="analysis") # pylint: disable=invalid-name
# bussmodel = api.model('BussModel', {
# 'source_id': fields.Integer(required=True, description='The task unique identifier'),
# 'request_type': fields.String(required=True, description='The task details'),
# 'image': fields.String(required=True, description='The task details'),
# 'sub_type': fields.String(required=True, description='The task details'),
# 'content_id': fields.String(required=True, description='The task details'),
# 'content_type': fields.String(required=True, description='The task details'),
# 'content_text': fields.String(required=True, description='The task details'),
# })
login_dict = {}
Fields_mapping = {
10: {