Add order status service #2965

seallard · 2024-02-20T08:59:02Z

Description

Closes Clinical-Genomics/streamline-delivery#35.

Add service providing the following information for orders

Number of cases
Number of cases with samples in lab prep
Number of cases with samples in sequencing
Number of running analyses
Number of failed analyses
Number of delivered analyses
Number of cancelled analyses

Blocked by https://github.com/Clinical-Genomics/servers/pull/1286

Added

Status summaries to response from /orders

This version is a

MINOR - when you add functionality in a backwards compatible manner

cg/apps/tb/dto/summary_response.py

islean

Looks nice! 🔥

cg/apps/tb/api.py

cg/apps/tb/dto/summary_response.py

cg/server/dto/orders/orders_request.py

cg/services/order_service/utils.py

cg/store/crud/read.py

cg/store/filters/status_order_filters.py

islean · 2024-02-21T13:25:14Z

Might be nice with a test for the summary?

seallard · 2024-02-21T15:56:26Z

Might be nice with a test for the summary?

Yes, I want to add one! I would have to mock the reply from trailblazer. Will look into it, might be too messy due how things are instantiated but would be nice

islean

Looks good! Probably should test performance before merging though

cg/server/dto/orders/orders_request.py

cg/services/orders/order_service/utils.py

cg/services/orders/order_status_service/dto/case_status_summary.py

cg/services/orders/order_status_service/utils.py

cg/store/filters/status_order_filters.py

cg/services/orders/order_status_service/order_status_service.py

Vince-janv

Found one potential bug. Might need a small technical refinement for it

cg/services/orders/order_status_service/utils.py

cg/services/orders/order_service/order_service.py

cg/services/orders/order_service/utils.py

seallard · 2024-02-27T16:15:53Z

Tested in stage. Performance seems OK even when retrieving summaries for 50 orders at a time. Will leave optimization for later.

time curl 'https://cg-statusdb-stage.scilifelab.se/api/v1/orders?includeSummary=true&limit=5' -H 'User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.15; rv:123.0) Gecko/20100101 Firefox/123.0' -H 'Accept: application/json, text/plain, */*' -H 'Accept-Language: en-US,en;q=0.5' -H 'Accept-Encoding: gzip, deflate, br' -H 'Referer: https://cigrid-stage.scilifelab.se/' -H 'Authorization: Bearer token' -H 'Origin: https://cigrid-stage.scilifelab.se' -H 'Connection: keep-alive' -H 'Sec-Fetch-Dest: empty' -H 'Sec-Fetch-Mode: cors' -H 'Sec-Fetch-Site: same-site' -H 'Pragma: no-cache' -H 'Cache-Control: no-cache' -H 'TE: trailers'
{
  "orders": [
    {
      "customer_id": "cust139",
      "order_date": "2024-01-30",
      "order_id": 1,
      "summary": {
        "cancelled": 0,
        "delivered": 0,
        "failed": 0,
        "in_preparation": 1,
        "in_sequencing": 1,
        "order_id": 1,
        "running": 0,
        "total": 1
      },
      "ticket_id": 124515,
      "workflow": "mip-dna"
    },
    {
      "customer_id": "cust002",
      "order_date": "2024-01-30",
      "order_id": 2,
      "summary": {
        "cancelled": 0,
        "delivered": 1,
        "failed": 2,
        "in_preparation": 0,
        "in_sequencing": 0,
        "order_id": 2,
        "running": 0,
        "total": 1
      },
      "ticket_id": 587841,
      "workflow": "balsamic"
    },
    {
      "customer_id": "cust087",
      "order_date": "2024-01-30",
      "order_id": 3,
      "summary": {
        "cancelled": 0,
        "delivered": 1,
        "failed": 0,
        "in_preparation": 0,
        "in_sequencing": 0,
        "order_id": 3,
        "running": 0,
        "total": 1
      },
      "ticket_id": 772082,
      "workflow": "balsamic"
    },
    {
      "customer_id": "cust003",
      "order_date": "2024-01-30",
      "order_id": 4,
      "summary": {
        "cancelled": 0,
        "delivered": 3,
        "failed": 0,
        "in_preparation": 0,
        "in_sequencing": 0,
        "order_id": 4,
        "running": 0,
        "total": 1
      },
      "ticket_id": 512736,
      "workflow": "mip-dna"
    },
    {
      "customer_id": "cust002",
      "order_date": "2024-01-31",
      "order_id": 5,
      "summary": {
        "cancelled": 0,
        "delivered": 0,
        "failed": 0,
        "in_preparation": 0,
        "in_sequencing": 0,
        "order_id": 5,
        "running": 0,
        "total": 1
      },
      "ticket_id": 755205,
      "workflow": "mip-dna"
    }
  ]
}
curl  -H  -H 'Accept: application/json, text/plain, */*' -H  -H  -H  -H  -H    0.02s user 0.01s system 6% cpu 0.392 total

A case is in lab preparation if any sample still has not been prepared. A case is in sequencing if all samples have been prepared and at least one sample has not been sequenced yet.

Vince-janv

My previous concern has been addressed ⭐

cg/services/orders/order_status_service/utils.py

islean · 2024-02-28T13:57:46Z

Tested in stage. Performance seems OK even when retrieving summaries for 50 orders at a time. Will leave optimization for later.

time curl 'https://cg-statusdb-stage.scilifelab.se/api/v1/orders?includeSummary=true&limit=5' -H 'User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.15; rv:123.0) Gecko/20100101 Firefox/123.0' -H 'Accept: application/json, text/plain, */*' -H 'Accept-Language: en-US,en;q=0.5' -H 'Accept-Encoding: gzip, deflate, br' -H 'Referer: https://cigrid-stage.scilifelab.se/' -H 'Authorization: Bearer token' -H 'Origin: https://cigrid-stage.scilifelab.se' -H 'Connection: keep-alive' -H 'Sec-Fetch-Dest: empty' -H 'Sec-Fetch-Mode: cors' -H 'Sec-Fetch-Site: same-site' -H 'Pragma: no-cache' -H 'Cache-Control: no-cache' -H 'TE: trailers'
{
  "orders": [
    {
      "customer_id": "cust139",
      "order_date": "2024-01-30",
      "order_id": 1,
      "summary": {
        "cancelled": 0,
        "delivered": 0,
        "failed": 0,
        "in_preparation": 1,
        "in_sequencing": 1,
        "order_id": 1,
        "running": 0,
        "total": 1
      },
      "ticket_id": 124515,
      "workflow": "mip-dna"
    },
    {
      "customer_id": "cust002",
      "order_date": "2024-01-30",
      "order_id": 2,
      "summary": {
        "cancelled": 0,
        "delivered": 1,
        "failed": 2,
        "in_preparation": 0,
        "in_sequencing": 0,
        "order_id": 2,
        "running": 0,
        "total": 1
      },
      "ticket_id": 587841,
      "workflow": "balsamic"
    },
    {
      "customer_id": "cust087",
      "order_date": "2024-01-30",
      "order_id": 3,
      "summary": {
        "cancelled": 0,
        "delivered": 1,
        "failed": 0,
        "in_preparation": 0,
        "in_sequencing": 0,
        "order_id": 3,
        "running": 0,
        "total": 1
      },
      "ticket_id": 772082,
      "workflow": "balsamic"
    },
    {
      "customer_id": "cust003",
      "order_date": "2024-01-30",
      "order_id": 4,
      "summary": {
        "cancelled": 0,
        "delivered": 3,
        "failed": 0,
        "in_preparation": 0,
        "in_sequencing": 0,
        "order_id": 4,
        "running": 0,
        "total": 1
      },
      "ticket_id": 512736,
      "workflow": "mip-dna"
    },
    {
      "customer_id": "cust002",
      "order_date": "2024-01-31",
      "order_id": 5,
      "summary": {
        "cancelled": 0,
        "delivered": 0,
        "failed": 0,
        "in_preparation": 0,
        "in_sequencing": 0,
        "order_id": 5,
        "running": 0,
        "total": 1
      },
      "ticket_id": 755205,
      "workflow": "mip-dna"
    }
  ]
}
curl  -H  -H 'Accept: application/json, text/plain, */*' -H  -H  -H  -H  -H    0.02s user 0.01s system 6% cpu 0.392 total

The total seems very off here

sonarqubecloud · 2024-02-28T15:10:52Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

seallard added 4 commits February 20, 2024 09:58

Add query param

81b7a25

Restructure

1cced92

Retrieve summaries from trailblazer

e4a3feb

Clean up response dtos

dcbd8a7

seallard changed the title ~~Add query param~~ Add summary to orders Feb 20, 2024

seallard force-pushed the add-order-summary branch from d4eed0f to dcbd8a7 Compare February 20, 2024 13:49

seallard added 10 commits February 20, 2024 15:02

Formatting

feef77e

Fix model

8b6b17d

Move order service to ext module

102a3eb

Set env vars

c8e5fa9

Fix tests

40c0fe2

Restore old test

9f1d178

Fix dockerfile

66df963

Merge

f9bfcf9

Formatting

6c77a94

Formatting

4898c81

Clinical-Genomics deleted a comment from sonarqubecloud bot Feb 21, 2024

seallard marked this pull request as ready for review February 21, 2024 11:57

seallard requested a review from a team as a code owner February 21, 2024 11:57

seallard added 3 commits February 21, 2024 12:57

Fix optional parameters

4d5de3f

Fix query

5693e60

Fix type

06c504a

seallard commented Feb 21, 2024

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islean approved these changes Feb 21, 2024

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seallard added 2 commits February 23, 2024 12:51

Change param

dcf6450

Merge master

73046ae

seallard force-pushed the add-order-summary branch from 44ac14d to 73046ae Compare February 23, 2024 12:20

Make total count the case count

e937731

seallard changed the title ~~Add summary to orders~~ Add order status summary service Feb 26, 2024

Fix comments

da54c47

seallard changed the title ~~Add order status summary service~~ Add order status service Feb 27, 2024

islean approved these changes Feb 27, 2024

View reviewed changes

seallard added 2 commits February 27, 2024 15:04

Fix comments

cdca79c

Merge branch 'master' into add-order-summary

fa15766

seallard commented Feb 27, 2024

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Naming

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Vince-janv requested changes Feb 27, 2024

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clingen-sthlm temporarily deployed to stage February 27, 2024 15:43 Inactive

Fix endpoint name

b4df1eb

clingen-sthlm temporarily deployed to stage February 27, 2024 16:03 Inactive

Fix trailblazer call

9787703

clingen-sthlm temporarily deployed to stage February 27, 2024 16:12 Inactive

seallard added 2 commits February 28, 2024 10:49

Fix logic for case status

5ba1b2c

A case is in lab preparation if any sample still has not been prepared. A case is in sequencing if all samples have been prepared and at least one sample has not been sequenced yet.

Fix missing import

c86c245

seallard requested a review from Vince-janv February 28, 2024 09:52

Vince-janv approved these changes Feb 28, 2024

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seallard added 2 commits February 28, 2024 14:58

Merge master

a80640b

Fix naming

6058142

clingen-sthlm temporarily deployed to stage February 28, 2024 14:16 Inactive

Cleanup

d52c6a0

clingen-sthlm temporarily deployed to stage February 28, 2024 15:02 Inactive

seallard added 2 commits February 28, 2024 16:06

Fix summary

1fd4aaf

Fix typing

336479a

seallard merged commit b91c2cc into master Feb 28, 2024
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seallard deleted the add-order-summary branch February 28, 2024 15:09

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Add order status service #2965

Add order status service #2965

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Add order status service #2965

Add order status service #2965

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Description

Added

This version is a

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