Access lab comment fields for a given sample

[magnulei]

This is a feature request from @solveigmo

She would like to have the option to review lab comments registered for a sample. This came up today when Solveig wanted to review the reason for sample withdraw from the queue.

I see two options:

Option 1:
A button that activates a function to query the lims using api. Using the api we should be able to traverse the history of that sample and return all comment fields. The comments will be presented to the user in a pop-up window (modal).

Option 2:
Add the comments into the sqlite db. Make each sample row clickable to show a popup modal window with all the comments in it.

Time usage:
Not sure. But not that many hours. I think option 1 is the fastest to implement since I wouldnt have to touch the database structure. Option 2 is probably more robust, but will require a database update.

Another smaller development thing, @karinlag.

[karinlag]

Just a question, these things are then not viewable from the customer view in lablink? I seem to recall way back when that "customers" would be able to view the status in lablink?

[magnulei]

@karinlag , yes - the progress status is made available from both LabLink and ShinyClarity.
Here you see the status fields I have configured in Clarity (snippet from the ShinyClarity):

Most of these statuses are clear. However, I have not been able to cover all possible reasons for sample failure. To remedy this, we have the more generic one called "Removed: Sample withdrawn". If a sample is removed outside of the "Manager Review" process it will get this more generic status (done automatically by cron: https://github.com/NorwegianVeterinaryInstitute/nvi_lims_epps/blob/main/cron-jobs/cron-update-project-status.py).

If we want to figure out what happened, one way is to look at the sample comments left by lab users on step comment fields. These comment fields are not available from ShinyClarity (or LabLink). But then again, both me and Cathrine can easily track this on request using the Clarity sample genealogy feature, so that is probably good enough.

But I think this one is a simple one to implement. At the same time Im not in a hurry to get this done. Just wanted to make a note of it to make sure I dont forget the idea 😄

[karinlag]

Am I correct in interpreting your text here as "we are talking about comments that are only available inside of the lab person version of Clarity"? And that if we want to get to them, we have to either log in as a lab-user or extract via api?

[magnulei]

Am I correct in interpreting your text here as "we are talking about comments that are only available inside of the lab person version of Clarity"? And that if we want to get to them, we have to either log in as a lab-user or extract via api?

Spot on!
And "Comments" are open multi-line text fields to document anything unusual from the lab. Found on most lab steps. And will thus be a comment for the entire step (ie all samples on that step is associated with the comment).

[karinlag]

Thanks for confirming @magnulei !

On a different level: we should figure out how to get "this is important/This is outbreak" etc information that is supplied upon submission passed on to others, most importantly @ajkarloss . Could that be part of this too?

[magnulei]

Thanks for confirming @magnulei !

On a different level: we should figure out how to get "this is important/This is outbreak" etc information that is supplied upon submission passed on to others, most importantly @ajkarloss . Could that be part of this too?

When do we need the info? At sample submission? Or when completed sequencing?

There is a comment field when submitting samples in lablink. The info from there is sent to us via email. So thats one way to get the info.

Else, we could for example find somewhere suitable in LIMS/lablink to input that info and have it trigger an email alert to Jeevan (and others who are interested).

Lets discuss whats needed. Seems easily solvable

[karinlag]

@ajkarloss might have comments on this, but for me I would want to know upon sample submission or not long after that. This so we can ensure smooth handling downstream from the sequencing (aka check things in vigas early for instance, and other things). Could also be in shinylims for instance, so we can look it up.

Let's talk :)

[magnulei]

I have started the foundation for something like what you are asking for @karinlag. I have a UDF on the submitted samples called "Prioritet". Only place to set it now is in the sample submission form, but it is locked and sort of hidden away from view. I could open this up in the submissionform, but that would open it up for all users to judge "Pritoritet"-status for themselves. And I suspect that submitters often would forget setting the correct tag.

So a suggestion to better implement the "Prioritet"-UDF:

1. Wait until we have growth on agar (which will be shortly after submission)
2. When closing the "On Agar/Broth for Extraction" step, Guro and Basma would have to actively select the priority status from a drop down on each sample before being allowed to close the step (can optionally be done in batch - so 1 click for the entire sample set). This updates the UDF "Prioritet".
3. If priority samples, auto-send mail to those interested (hard-coded user list)
4. Also, add a clear indicator in shiny clarity to let us know that priority samples are coming. Could also add a button to retrieve info on all active samples with a priority tag (simple API call).

Will need to run it by Guro, Basma and @ajkarloss

[karinlag]

Another potential thing we could do instead of priority is to basically implement of hensikt? That way we know what the isolates are sequenced for, and then we can do the prioritization out from that? Possible ooptions could then be Utbrudd, Forskning, Oppdrag, possible others?

Pulling in @Camilsek here :)

[magnulei]

I really like that idea. Easy to implement. A simple drop-down list in the sample submission list where submittors must make a selection.

When I have that info and can forward it to the lab view for the lab users (in the step queues). I could add the info into the submission auto-mails (maybe add an exclamation mark in the header). I could also somehow make it easily visible in shiny clarity if that is something we want.