12276038756

Committed 11 Dec 2024 12:08PM UTC coverage: 84.029%. First build

Build # 12276038756

Build Type

Pull #3936

github

Committed by

web-flow

Commit Message

Merge 4694dc240 into ab9ded5a4

Pull Request Pull Request #3936: (Improve order flow) Minimal implementation FASTQSubmission

Run Details

33 of 53 new or added lines in 11 files covered. (62.26%)

25391 of 30217 relevant lines covered (84.03%)

0.84 hits per line

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62.96

/cg/meta/orders/api.py

"""Unified interface to handle sample submissions.

This interface will update information in Status and/or LIMS as required.

The normal entry for information is through the REST API which will pass a JSON
document with all information about samples in the submission. The input will
be validated and if passing all checks be accepted as new samples.
"""

import logging

from cg.apps.lims import LimsAPI
from cg.meta.orders.ticket_handler import TicketHandler
from cg.models.orders.order import OrderType
from cg.services.order_validation_service.models.order import Order
from cg.services.orders.submitters.order_submitter import OrderSubmitter
from cg.services.orders.submitters.order_submitter_registry import OrderSubmitterRegistry
from cg.store.store import Store

LOG = logging.getLogger(__name__)


class OrdersAPI:
    """Orders API for accepting new samples into the system."""

    def __init__(
        self,
        lims: LimsAPI,
        status: Store,
        ticket_handler: TicketHandler,
        submitter_registry: OrderSubmitterRegistry,
    ):
        super().__init__()
        self.lims = lims
        self.status = status
        self.ticket_handler = ticket_handler
        self.submitter_registry = submitter_registry

    def submit(
        self, order_type: OrderType, raw_order: dict, user_name: str, user_mail: str
    ) -> dict:
        """Submit a batch of samples.

        Main entry point for the class towards interfaces that implements it.
        """
        submit_handler: OrderSubmitter = self.submitter_registry.get_order_submitter(order_type)
        order: Order = submit_handler.order_validation_service.parse_and_validate(raw_order)
        if isinstance(order, dict):
            return order
        # detect manual ticket assignment
        ticket_number: str | None = self.ticket_handler.parse_ticket_number(order.name)
        if not ticket_number:
            ticket_number = self.ticket_handler.create_ticket(
                order=order, user_name=user_name, user_mail=user_mail, order_type=order_type
            )
        else:
            self.ticket_handler.connect_to_ticket(
                order=order,
                user_name=user_name,
                order_type=order_type,
                ticket_number=ticket_number,
            )
        order.ticket_number = ticket_number
        return submit_handler.submit_order(order)

1	"""Unified interface to handle sample submissions.
2
3	This interface will update information in Status and/or LIMS as required.
4
5	The normal entry for information is through the REST API which will pass a JSON
6	document with all information about samples in the submission. The input will
7	be validated and if passing all checks be accepted as new samples.
8	"""
9
10	import logging	1✔
11
12	from cg.apps.lims import LimsAPI	1✔
13	from cg.meta.orders.ticket_handler import TicketHandler	1✔
14	from cg.models.orders.order import OrderType	1✔
15	from cg.services.order_validation_service.models.order import Order	1✔
16	from cg.services.orders.submitters.order_submitter import OrderSubmitter	1✔
17	from cg.services.orders.submitters.order_submitter_registry import OrderSubmitterRegistry	1✔
18	from cg.store.store import Store	1✔
19
20	LOG = logging.getLogger(__name__)	1✔
21
22
23	class OrdersAPI:	1✔
24	"""Orders API for accepting new samples into the system."""
25
26	def __init__(	1✔
27	self,
28	lims: LimsAPI,
29	status: Store,
30	ticket_handler: TicketHandler,
31	submitter_registry: OrderSubmitterRegistry,
32	):
33	super().__init__()	1✔
34	self.lims = lims	1✔
35	self.status = status	1✔
36	self.ticket_handler = ticket_handler	1✔
37	self.submitter_registry = submitter_registry	1✔
38
39	def submit(	1✔
40	self, order_type: OrderType, raw_order: dict, user_name: str, user_mail: str
41	) -> dict:
42	"""Submit a batch of samples.
43
44	Main entry point for the class towards interfaces that implements it.
45	"""
46	submit_handler: OrderSubmitter = self.submitter_registry.get_order_submitter(order_type)	×
47	order: Order = submit_handler.order_validation_service.parse_and_validate(raw_order)	×
NEW 48	if isinstance(order, dict):	×
NEW 49	return order	×
50	# detect manual ticket assignment
51	ticket_number: str \| None = self.ticket_handler.parse_ticket_number(order.name)	×
52	if not ticket_number:	×
53	ticket_number = self.ticket_handler.create_ticket(	×
54	order=order, user_name=user_name, user_mail=user_mail, order_type=order_type
55	)
56	else:
57	self.ticket_handler.connect_to_ticket(	×
58	order=order,
59	user_name=user_name,
60	order_type=order_type,
61	ticket_number=ticket_number,
62	)
63	order.ticket_number = ticket_number	×
64	return submit_handler.submit_order(order)	×

Clinical-Genomics / cg / 12276038756

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