Description

Refactor Arnold where necessary
Moved Pydantic to version 2 #47

Description

A decision has been reach to continue the development for the collection of pipeline metrics in Arnold, so the functionality developed in Maven will be implemented within Arnold.

for dunamic plots

Description

Currently Arnold resides outside of the mongo-eco-system. We should migrate it into where the other mongo dbs reside.

• check cg_lims that communicates with arnold to have the proper address
• update servers
• update arnold

Description

After an update to the python3.XX-slim base images, Gunicorn has problems creating threads. See issue docker-library/python#835.

Suggested solution

• switch to python3.XX-slim-bullseye as base image

https://cigrid.scilifelab.se/lab-preps/steps

https://arnold-stage.scilifelab.se/docs#/prep/get_step_type_process_udfs_api_v1_step_step_type_process_udfs_get

Description

The trending capabilities should be removed from Arnold since the software should only deal with storing and fetching of data. Trending will be implemented elsewhere, with perhaps different software.

Find field names reused (or have potential to be reused) by all pipelines and fields unique to pipelines

Shared

RD

CANCER

NIPT

COVID

MICROBIAL

https://www.figma.com/file/Gz9eZYmbOfGa0UEezoJP6M/Graph-1%3A-Number-of-samples-received-(and-delivered)%2C-broken-down-per-month?node-id=0%3A1

Target response

[
    { date: "2020/01", datapoints: [{ tag: "WGS", turnaround_time: 80 },
]

[
    { date: "2020/01", datapoints: [{ priority: "low", turnaround_time: 80 },
]

In trending endpoints, some negative values are way off the charts and totally change the look and proportions of graphs

TBD

The cigrid tab for turnaround times is broken due to requests failing against the arnold api

Network Error https://arnold.scilifelab.se/api/v1/turnaround?&date_min=2022-12-01&date_max=2023-12-01&group=tag

Seems like the endpoint is broken.

For example:
https://arnold-stage.scilifelab.se/api/v1/trends/sample_turnaround_times?field=prepped_to_sequenced&year=2022&group=customer

GET https://arnold.scilifelab.se/api/v1/trends/nr_samples?&year=2022&group=customer
returns data of samples received for cust0 and cust124 in December 2022

@annaengstrom reported the bug

https://docs.google.com/document/d/1eRqtCeIIYboYPw2GdyMb6ER4j4C2Z4PyQ9Nf2Otzfl8/edit#

Investigate Number of delivered analyses (ie have a delivered_date set in statusdb)

Secure endpoints of Arnold:

• User collection in db
• Endpoints for user management
• Separate API into internal and external
• Load step data from LIMS via internal API