Clinical-Genomics/cg

Add information on internal negative control for a given sample

Closed this issue · 6 comments

beatrizsavinhas commented

As a production user and cg developer,
I want to be able to easily get information on which internal negative control was used for the prep of a given sample,
So that I don't have to manually search for it in lims.

Acceptance Criteria

  • It is possible to search for a sample and get its internal negative control.

Notes

This functionality would much facilitate QC checks for analyses that require internal controls, which is currently done manually.

Would be an important tool for this project: Improve the comparison and analysis of control samples in production

Suggested solution:

Alternative 1

- Add a Pool table listing pools
- Add a SamplePool table displaying pool and samples relationship
- A pool object includes corresponding sample links
- The tables are populated from lims - relevant lims step: Target Enrichment TWIST

Alternative 1 was decided against so as to not repeat in cg the information that is in LIMS.

Alternative 2

  • Add internal_control field to the Sample model and populate it with the corresponding internal control sample

Implementation plan

  • Work item 1
  • Work item 2
karlnyr commented

We should redefine this so that it would solve " Create a connection between our internal control and related samples of that same prep" in https://github.com/Clinical-Genomics/project-planning/issues/562

karlnyr commented

Discussion

  • Alternative 2 sounds good - we could fetch information from lims of the latest prep and fill up the field of the "LatestInternalControl" (or something similar to that)
beatrizsavinhas commented

After our discussion in Issue Refinement @Clinical-Genomics/sysdev, I decided to clean up this issue to make it more clear! Feel free to change the description if you think something needs to be clarified.

diitaz93 commented

Unfinished technical refinement discussion

  • There is a long-term solution to this and other issues using data analytics tools such as Tableu or Superset (AA)
  • There are two parts of this issue:
    1. Fetching internal negative control for one sample in production's everyday routine
    2. A bulk action to get internal negative controls of several samples, used for example in deviations (more seldomly)
  • The most urgent part of this issue is number 1, as it makes production users lose time almost every day
  • To solve this, CO/VJ proposed adding the negative control in cigrid-ui (also known as trailblazer), in the case view.
    • BSV proposed that it could be a column in the sample table, called Negative control with the sample id, not even a link
    • MOD said that the front end part won't bring any problems
  • the second part of the issue could be solved later
  • CO mentioned that we could include non-cg-database information in the statusDB admin view, for example LIMS information
karlnyr commented

Discussion

diitaz93 commented

Understood, prodbioinfo will handle this. Closing