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(Improve order flow) Remove submitters #4062

Merged
merged 10 commits into from
Jan 10, 2025
Merged

(Improve order flow) Remove submitters #4062

merged 10 commits into from
Jan 10, 2025

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islean
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@islean islean commented Jan 8, 2025 •
edited
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Description

With the storing services reworked, it seems reasonable to remove the submitters as they were wrappers for

  • a validation service, and
  • a storing service
    but are now only wrappers for the storing services.

This PR reworks the submitter registry to a storing service registry. For now, removing the old validation services was deemed out of scope but will be done in future PRs

Added

Changed

  • The OrderSubmitterRegistry is a StoringServiceRegistry
  • The OrderSubmitters are removed
  • The OrdersAPI needs no Store in its init
  • The OrdersAPI needs a StoringServiceRegistry instead of a SubmitterRegistry
  • The OrdersAPI needs an OrderValidationService

Fixed

How to prepare for test

  • Ssh to relevant server (depending on type of change)
  • Use stage: us
  • Paxa the environment: paxa
  • Install on stage (example for Hasta): 
    bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_cg -t cg -b [THIS-BRANCH-NAME] -a

How to test

  • Do ...

Expected test outcome

  • Check that ...
  • Take a screenshot and attach or copy/paste the output.

Review

  • Tests executed by
  • "Merge and deploy" approved by
    Thanks for filling in who performed the code review and the test!

This version is a

  • MAJOR - when you make incompatible API changes
  • MINOR - when you add functionality in a backwards compatible manner
  • PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

  • Document in ...
  • Deploy this branch on ...
  • Inform to ...

@islean islean requested a review from a team as a code owner January 8, 2025 14:59
@clingen-sthlm clingen-sthlm temporarily deployed to stage January 8, 2025 15:10 Inactive
@islean
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islean commented Jan 8, 2025

Tested by submitting an RNAFusion order:

request:

{
	"cases": [
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					"comment": "comment",
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					"concentration_ng_ul": "6",
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					"container": "96 well plate",
					"container_name": "plate1",
					"control": "negative",
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					"region_code": null,
					"require_qc_ok": false,
					"rml_plate_name": null,
					"selection_criteria": null,
					"sex": "unknown",
					"source": "muscle",
					"status": null,
					"subject_id": "miprnasubject9",
					"tissue_block_size": null,
					"tumour": true,
					"tumour_purity": null,
					"verified_organism": null,
					"volume": "28",
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					"well_position_rml": null
				}
			],
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		{
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					"data_delivery": "fastq + analysis",
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					"source": "tissue (fresh frozen)",
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					"subject_id": "miprnasubject20",
					"tissue_block_size": null,
					"tumour": true,
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					"volume": "39",
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				}
			],
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		}
	],
	"comment": null,
	"customer": "cust000",
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	"dataAnalysis": "rnafusion",
	"delivery_type": "fastq-analysis",
	"name": "1508.33.rnafusion",
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}

Response:

{
	"project": {
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		"id": "STG15732",
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	},
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			"comment": null,
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			"customer": {
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			},
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			"internal_id": "elegantfawn",
			"is_compressible": true,
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			"priority": "standard",
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		},
		{
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			"created_at": "Wed, 08 Jan 2025 16:13:10 GMT",
			"customer": {
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			},
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			"internal_id": "neutrallynx",
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		},
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			},
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			"id": 50902,
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		},
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			},
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		},
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			},
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			"id": 50916,
			"internal_id": "integralshiner",
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			"name": "miprnacase15",
			"ordered_at": "Wed, 08 Jan 2025 16:13:10 GMT",
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			"data_analysis": "rnafusion",
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			"id": 50917,
			"internal_id": "leadingprimate",
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			"name": "miprnacase16",
			"ordered_at": "Wed, 08 Jan 2025 16:13:10 GMT",
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			},
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			"data_analysis": "rnafusion",
			"data_delivery": "fastq-analysis",
			"id": 50918,
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			"created_at": "Wed, 08 Jan 2025 16:13:10 GMT",
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				"comment": "240311: Added \"is trusted\" /AG\r\n220606-VW: Added invoicing address and updated also other fields.",
				"data_archive_location": "PDC",
				"delivery_contact_id": 126,
				"id": 1,
				"internal_id": "cust000",
				"invoice_address": "Karolinska Institutet\r\nFakturor\r\nBox 23109\r\n104 35 Stockholm",
				"invoice_contact_id": 1,
				"invoice_reference": "ZZC1VALWIR",
				"is_clinical": false,
				"is_trusted": true,
				"lab_contact_id": null,
				"loqus_upload": false,
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				"organisation_number": "202100-2973",
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				"project_account_ki": "C1 34 101 063",
				"project_account_kth": "80205",
				"return_samples": false,
				"scout_access": true,
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			},
			"customer_id": 1,
			"data_analysis": "rnafusion",
			"data_delivery": "fastq-analysis",
			"id": 50919,
			"internal_id": "exoticanemone",
			"is_compressible": true,
			"name": "miprnacase18",
			"ordered_at": "Wed, 08 Jan 2025 16:13:10 GMT",
			"panels": [],
			"priority": "research",
			"synopsis": null,
			"tickets": "1001927"
		}
	]
}

@islean
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islean commented Jan 8, 2025

Order stored:

image

Cases created:

image

Samples linked:

image

Sample data populated:

image

@islean
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islean commented Jan 8, 2025

In LIMS:

image

@islean
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islean commented Jan 8, 2025

In Freshdesk:

image

diitaz93
diitaz93 approved these changes Jan 9, 2025
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Looks great 💯 I think a simplification of the registry should be done but that is probably out of scope. Also, I suggest some renaming of directories to avoid having imports several lines long, it could improve readability

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Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.2% Duplication on New Code

See analysis details on SonarQube Cloud

Vince-janv
Vince-janv approved these changes Jan 10, 2025
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Looks good 👌

cg/services/orders/store_order_services/storing_service_registry.py Show resolved Hide resolved
@clingen-sthlm clingen-sthlm temporarily deployed to stage January 10, 2025 13:04 Inactive
@islean islean merged commit 653377f into improve-order-flow-main Jan 10, 2025
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@islean islean deleted the remove-submitters branch January 10, 2025 13:10
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@diitaz93 diitaz93 diitaz93 approved these changes

@Vince-janv Vince-janv Vince-janv approved these changes

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@islean @diitaz93 @Vince-janv @clingen-sthlm