Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

(Improve order flow) Remove old microbial validation #4090

Merged
merged 3 commits into from
Jan 15, 2025
Merged

(Improve order flow) Remove old microbial validation #4090

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
29ca54f
Remove old microbial validation
islean Jan 15, 2025
60441c3
Fix fixture
islean Jan 15, 2025
a4b841a
Merge branch 'improve-order-flow-main' into remove-old-microbial-vali…
islean Jan 15, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
43 changes: 0 additions & 43 deletions cg/services/orders/validate_order_services/validate_microbial_order.py
View file
Open in desktop

This file was deleted.

17 changes: 11 additions & 6 deletions tests/fixture_plugins/orders_fixtures/order_to_submit_fixtures.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,13 @@
from cg.services.order_validation_service.workflows.balsamic.models.order import BalsamicOrder
from cg.services.order_validation_service.workflows.fastq.models.order import FastqOrder
from cg.services.order_validation_service.workflows.metagenome.models.order import MetagenomeOrder
from cg.services.order_validation_service.workflows.microbial_fastq.models.order import (
MicrobialFastqOrder,
)
from cg.services.order_validation_service.workflows.microsalt.models.order import MicrosaltOrder
from cg.services.order_validation_service.workflows.mip_dna.models.order import MipDnaOrder
from cg.services.order_validation_service.workflows.mip_rna.models.order import MipRnaOrder
from cg.services.order_validation_service.workflows.mutant.models.order import MutantOrder
from cg.services.order_validation_service.workflows.pacbio_long_read.models.order import PacbioOrder


Expand Down Expand Up @@ -127,6 +132,7 @@ def all_orders_to_submit(
fluffy_order_to_submit: dict,
metagenome_order_to_submit: dict,
microbial_order_to_submit: dict,
microbial_fastq_order_to_submit: dict,
mip_dna_order_to_submit: dict,
mip_rna_order_to_submit: dict,
pacbio_order_to_submit: dict,
Expand All @@ -140,15 +146,14 @@ def all_orders_to_submit(
OrderType.FASTQ: FastqOrder.model_validate(fastq_order_to_submit),
# OrderType.FLUFFY: FluffyOrder.model_validate(rml_order_to_submit),
OrderType.METAGENOME: MetagenomeOrder.model_validate(metagenome_order_to_submit),
# OrderType.MICROSALT: OrderIn.parse_obj(
# microbial_order_to_submit, project=OrderType.MICROSALT
# ),
OrderType.MICROBIAL_FASTQ: MicrobialFastqOrder.model_validate(
microbial_fastq_order_to_submit
),
OrderType.MICROSALT: MicrosaltOrder.model_validate(microbial_order_to_submit),
OrderType.MIP_DNA: MipDnaOrder.model_validate(mip_dna_order_to_submit),
OrderType.MIP_RNA: MipRnaOrder.model_validate(mip_rna_order_to_submit),
OrderType.PACBIO_LONG_READ: PacbioOrder.model_validate(pacbio_order_to_submit),
# OrderType.RML: OrderIn.parse_obj(rml_order_to_submit, project=OrderType.RML),
# OrderType.RNAFUSION: RnaFusionOrder.model_validate(rnafusion_order_to_submit),
# OrderType.SARS_COV_2: OrderIn.parse_obj(
# sarscov2_order_to_submit, project=OrderType.SARS_COV_2
# ),
OrderType.SARS_COV_2: MutantOrder.model_validate(sarscov2_order_to_submit),
}
66 changes: 0 additions & 66 deletions tests/services/orders/test_validate_order_service/test_validate_microbial_order_service.py
View file
Open in desktop

This file was deleted.

Loading