12350691447

Committed 16 Dec 2024 10:27AM UTC coverage: 80.864%. First build

Build # 12350691447

Build Type

Pull #3976

github

Committed by

web-flow

Commit Message

Merge f0a779aa9 into e88e10d97

Pull Request Pull Request #3976: Improve order flow storing main

Run Details

114 of 185 new or added lines in 42 files covered. (61.62%)

13611 of 16832 relevant lines covered (80.86%)

1.51 hits per line

Source File
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77.27

/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,
    ) -> 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)
        ticket_number: str | None = self.ticket_handler.parse_ticket_number(order.name)
        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,
41	order_type: OrderType,
42	raw_order: dict,
43	) -> dict:
44	"""Submit a batch of samples.
45
46	Main entry point for the class towards interfaces that implements it.
47	"""
NEW 48	submit_handler: OrderSubmitter = self.submitter_registry.get_order_submitter(order_type)	×
NEW 49	order: Order = submit_handler.order_validation_service.parse_and_validate(raw_order)	×
NEW 50	ticket_number: str \| None = self.ticket_handler.parse_ticket_number(order.name)	×
NEW 51	order.ticket_number = ticket_number	×
NEW 52	return submit_handler.submit_order(order)	×

Clinical-Genomics / cg / 12350691447

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