sanger / sm_workflow_lims

A small LIMS to assist with managing workflows

Sample Management Workflow

Description

This README would normally document whatever steps are necessary to get the application up and running.

Things you may want to cover:

• Ruby version

• System dependencies

• Configuration

• Database creation

• Database initialization

• How to run the test suite

• Services (job queues, cache servers, search engines, etc.)

• Deployment instructions

• ...

sm_workflow_lims's Issues

DPL-767 [BUG] smwf Memory leak

Describe the bug
There is a memory leak on sm workflow lims that makes it run out of memory. This is the times when the event happened in the past:

[Thu May 20 06:24:27 2021] Out of memory: Kill process 22210 (ruby) score 398 or sacrifice child
[Tue Aug 31 15:28:10 2021] Out of memory: Kill process 22146 (ruby) score 359 or sacrifice child
[Fri Dec 10 14:58:39 2021] Out of memory: Kill process 22226 (ruby) score 324 or sacrifice child
[Mon Jun 27 16:42:17 2022] Out of memory: Kill process 23246 (ruby) score 418 or sacrifice child
[Fri Jul  1 11:48:50 2022] Out of memory: Kill process 23242 (ruby) score 293 or sacrifice child
[Fri Jul  1 12:01:48 2022] Out of memory: Kill process 23248 (ruby) score 323 or sacrifice child
[Mon Jul  4 15:49:07 2022] Out of memory: Kill process 3878 (ruby) score 390 or sacrifice child
[Fri Sep  9 11:05:51 2022] Out of memory: Kill process 26120 (ruby) score 334 or sacrifice child
[Thu Sep 15 19:53:00 2022] Out of memory: Kill process 26123 (ruby) score 313 or sacrifice child
[Fri Oct 21 09:04:02 2022] Out of memory: Kill process 26125 (ruby) score 267 or sacrifice child
[Mon Nov 28 18:29:36 2022] Out of memory: Kill process 19847 (ruby) score 276 or sacrifice child
[Thu Mar  2 17:23:47 2023] Out of memory: Kill process 26122 (ruby) score 314 or sacrifice child
[Thu May 11 09:48:23 2023] Out of memory: Kill process 1651 (ruby) score 416 or sacrifice child

Labwhere do have a similar issue which it has been handled by restarting the server when memory goes too high. We could adopt the same solution in here https://github.com/sanger/deployment/blob/master/roles/deploy_labwhere/templates/puma_monit_memory_check.j2

RT Ticket Number
If applicable

To Reproduce
Steps to reproduce the behaviour:

1. Go to page '...'
2. Click on button '...'
3. See error

Expected behaviour
What was expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• Windows or Mac?
• Browser Chrome, Firefox, Safari or other?
• Browser version (use 'About' to look up)?

Additional context
Add any other context about the problem here.

GPL-307 Add buttons to top of page because

User Story
As a Sample Management user I would like the buttons in Mini LIMS to be at the top of the page as well as the bottom to avoid scrolling.

Who the primary contacts are for this story
Danni Weldon

Acceptance Criteria
Buttons should be added on following pages:

• In Progress
• Volume Check
• Quant
• Report Required
• and any others that seem similar

DPL-245 - Additional 'tab' created within mini LIMS - Fuidigm - to QC [C=?,V=3]

User story

Currently when sample management complete the Fluidigm process, they tick off the completed plates which move to "Report required" when they still require QC. The addition of an intermediate step reflects the workflow better and will let the SSR know when the Fluidigm results are ready to be reported. This would also require and additional "tickable" section in the Admin tab to direct selected workflows to the "Fluidigm in QC" tab. Please could the list of workflows in the Admin tab also be presented in alphabetical order as it can be difficult to find the required workflow.

Who are the primary contacts for this story
James / Danni

Acceptance criteria
To be considered successful the solution must allow:

• A new tab is created called Fluidigm in QC
• Any workflow with "Fluidigm" ticked in the Admin section moves to the Fluidigm in QC tab
• Plates ticked as complete in the "Fludigm in QC" tab then move to report required.
• No other workflows are affected by the new additional tab
• Workflows are presented in alphabetical order in the Admin tab.

Dependencies
This story is blocked by the following dependencies:

• #<issue_no.>
• sanger/#<issue_no.>

References
This story has a non-blocking relationship with:

• #<issue_no.>
• sanger/#<issue_no.>

Additional context
Add any other context or screenshots about the feature request here.

DPL-412 Research - publish to Events Warehouse from Mini LIMS

User story
As a DNAP team lead looking into turn-around times I would like to be able to include time points from Mini LIMS (=SM Workflow LIMS) in my existing reports, which run off the Events Warehouse. This is of particular interest as the biggest time window is currently between when labware is first scanned into LabWhere, and when library prep is started, but there is no detail in between to help determine what's causing the delay. The most important time points to start off with are:

• When first scanned into Mini LIMS
• When reaches 'Report Required' tab

This story is to scope out the work needed to make this happen.

Who are the primary contacts for this story
Danni, Liz E, Katy, Andrew

Acceptance criteria
To be considered successful the solution must allow:

• Create sized stories to send events to the warehouse for time points mentioned above.

Additional context
It looks like Mini LIMS has an internal 'events' table - these events might already be created at the time points we need - so we could add the RabbitMQ / Warehouse integration to the same points.

Danni has a Tableau report (made / maintained by Matt F) that has a 'created date' in it of interest, which is what prompted them to ask for this feature. It looks like this probably runs purely off the Mini LIMS database, but it might be worth talking to Matt to investigate:

• Whether adding new information into this report would be a useful stop-gap.
• The queries behind this report.

BUG - Mini LIMS doesn't accept tube rack barcodes

From Danni:

I tested putting these plates into miniLIMS and have come across an issue. When I created a new batch I must enter the plate barcode ID (this will be rack ID), miniLIMs does not like have letters in the plate ID box. The issue with is, this prefix can change as it is chosen by the manufacturer and after speaking to Rich C he believes the SSR’s do need this prefix information.

GPL-307 Remove unused Mini LIMS workflows because

User story
As a Sample Management user I would like the list of workflows in mini LIMS (SM Workflow) to be up to date, so that the view isn't cluttered.

Who the primary contacts are for this story
Danni Weldon

Acceptance criteria
To be considered successful the solution must allow:
1 - Find out which workflows aren't needed any more
2 - Remove them
3 - Don't remove any historical data

Housekeeping - Update rails versions

Describe the Housekeeping
The app is currently on Rails 4, and should ideally be updated to the latest version. Rails 4 is preventing us updating both ruby and bundler versions.

Blocking issues

• This is mostly a blocker, rather than blocked.

Additional context
Add any other context about the problem here.

GPL-815 Migration off travis

This represents the sm_workflow_lims work required for sanger/General-Backlog-Items#109

Original issue:

Background

Travis are have changed their open-source free tier, which places heavy restrictions on our needs. We are currently on a paid plan, but are looking to migrate off.

I have made notes about the changes made to migrate Sequencescape here:
https://github.com/JamesGlover/travis_to_gh_actions

Migrated

• Sequencescape
• Warren

Still on travis, but some actions

These may already have all their actions migrated, although I think its mostly docker build files.
They should have all actions migrated, and be removed from travis

• Baracoda
• lighthouse-ui
• samples_extraction
• print_my_barcode

Repo to migrate

• Traction
• Asset Audits
• Traction-ui
• Quanthub
• Sm_workflow_lims
• sprint
• eln_pmb_bridge [Can't see on travis.com]
• mixtio
• gatekeeper
• baracoda
• traction-service-automated-releases ? (What is this?)
• traction-service
• event_warehouse_ukbb
• sanger_barcode_format
• event_warehouse
• unified_warehouse
• limber
• pmb-client
• labwhere

Probably don't migrate

• json_api_client
  This is a fork of another gem, which brings in some fixes. We should focus of migrating to the latest version, rather than maintaining a fork.

Repos without CI

These repos currently have no CI solution. In some cases its because one probably isn't warranted.

CI needed?

• sequencescape-client-api
• sprint_client
• hca-print-tool
• ftpcmd
• warehouse_two

CI probably not needed

• storelight-sql
• config
• .github
• beckman-robot-scripts
• deployment
• provision
• usg_scripts
• ss_cherrypicking (Empty repo)
• plate_barcode [ Migrate to baracoda instead ]
• General backlog items
• axlsx [Migrate to community fork instead of maintaining our own]
• label_printer [Yana's tool, mostly replaced by steve's recent stuff, not sure how you'd ci the tests]
• sequencescape_search [I don't think we use this?]
• sanger_barcode [Legacy barcode printing]
• irods_reader [Not using functionality]
• psd_logger [No longer used?]

Repos already on GH actions

These repos either never used travis, or were migrated a while ago. I'm judging this by the presence of a .github/workflows folder

• Record Loader(Never used travis)
• Crawler
• storelight
• lighthouse
• wrangler
• stan-client
• stan-core
• automanual

GPL-313 Undo a completed activity, from Report Required tab becuase

Description
Research into what would be involved to undo a complete step for a batch (removing row from Report Required tab), as batches are sometimes completed by mistake

Users
Danni Weldon

GPL-312 Check Report creation fields becuase

Description
Check what fields would you like to see on Admin/Report creation. Is there a current Tableau report in use? Currently study/project/costcode and asset count as column headers.

URL: http://training.sm-workflow.psd.sanger.ac.uk/admin

Users
Danni Weldon