DPL-812: FluidX tube rack data report #1433

StephenHulme · 2023-10-25T08:40:22Z

Closes ##1439

Changes proposed in this pull request

Add button to the PBMC Plate that generates a report of well contents
Add extensive testing to assist with accurate mocking

Acceptance criteria

Data should include:
- donor
- parent barcode (vacutainer)
- fluidx barcode (tube that it's being transferred in)
- extraction & freeze date (both should be the same) - creation date of the fluidx tube
- which tubes are destined for sequencing vs contingency
- cell count
- viability
- volume
- study (needed for when uploading into Titian)
- collection site

Example CSV Report

Workflow,scRNA Core PBMC Bank

Well name,Donor ID,Stock barcode,FluidX barcode,Extraction and freeze date,Sequencing or contingency,Cell count (cells/ml),Viability (%),Volume (µl),Study name,Collection site
SQPD-9011:B1,,NT13A,SQ16102001,2023-10-16 11:32:16 +0100,Sequencing,2030000,76,135,UAT Study,Sanger
SQPD-9011:C1,,NT13A,SP16102007,2023-10-16 11:32:30 +0100,Contingency,2300000,75,135,UAT Study,Sanger
SQPD-9011:D1,,NT14B,SQ16102002,2023-10-16 11:32:16 +0100,Sequencing,2100000,75,135,UAT Study,Sanger
SQPD-9011:E1,,NT14B,SP16102008,2023-10-16 11:32:30 +0100,Contingency,2280000,75,135,UAT Study,Sanger
SQPD-9011:F1,,NT14B,SP16102009,2023-10-16 11:32:30 +0100,Contingency,2110000,75,135,UAT Study,Sanger
SQPD-9011:G1,,NT15C,SQ16102003,2023-10-16 11:32:16 +0100,Sequencing,2220000,76,135,UAT Study,Sanger
SQPD-9011:H1,,NT15C,SP16102010,2023-10-16 11:32:31 +0100,Contingency,1940000,74,135,UAT Study,Sanger
SQPD-9011:A2,,NT15C,SP16102011,2023-10-16 11:32:31 +0100,Contingency,2030000,75,135,UAT Study,Sanger
SQPD-9011:B2,,NT16D,SQ16102004,2023-10-16 11:32:17 +0100,Sequencing,2030000,76,135,UAT Study,Sanger
SQPD-9011:C2,,NT16D,SP16102012,2023-10-16 11:32:31 +0100,Contingency,2300000,75,135,UAT Study,Sanger

Instructions for Reviewers

[All PRs] - Confirm PR template filled
[Feature Branches] - Review code
[Production Merges to main]
- Check story numbers included
- Check for debug code
- Check version

- includes some styling changes

StephenHulme · 2023-10-25T08:44:41Z

app/sequencescape/sequencescape/api/v2/well.rb

+  def latest_cell_viability
+    latest_qc(key: 'viability', units: '%')
+  end
+


Copied across from DPL-827

KatyTaylor · 2023-10-30T10:14:58Z

app/views/exports/pbmc_bank_tubes_content_report.csv.erb

+  CSV.generate_line [
+                      'Well name',
+                      'Donor ID',
+                      'Parent barcode',


I know this is what it says in the story (my fault, not sure where it came from in the first place), but could we call this "Stock barcode" instead? I think "Parent barcode" is misleading because the LRC Blood Vac tube is not the parent labware of the LRC Bank Seq / Spare tubes. Thanks.

No worries :) Fixed in 7d3868a

app/views/exports/pbmc_bank_tubes_content_report.csv.erb

config/exports/exports.yml

KatyTaylor

I've left you a few comments.

Thanks for spending time improving the test setup. If there are any changes you feel would make the test setup better but you didn't have time for, please raise them, because I think we need to make improvements as it's quite a pain point!

codeclimate · 2023-10-30T15:14:15Z

Code Climate has analyzed commit 613c3bc and detected 0 issues on this pull request.

The test coverage on the diff in this pull request is 100.0% (50% is the threshold).

This pull request will bring the total coverage in the repository to 90.0% (0.0% change).

View more on Code Climate.

StephenHulme added 30 commits October 17, 2023 17:03

wip: add initial PBMC Bank Tubes Content Report

028620b

fix: update values

b104b1b

fix: remove duplicate well position

887a488

fix: tidy up code

d120b61

style: lint

35e2caa

fix: update values

487c631

fix: remove debug code and lint

5ec5451

fix: update report with units and additional notes

b1eee38

- includes some styling changes

refactor: rename destination_tube -> child_tube

afc431c

tests: add test for well-aliquot-study fixture

2dc9a9e

fix: remove existing study reference

4c54790

fix: remove existing project reference

2f32679

fix: re-establish relationships

623ee0f

tests: add tests for well-aliquot relationships

4107296

fix: restore relationships

66484c1

tests: add test for order_group

f3047df

tests: add tests to specify study and project

be1573b

tests: add tests to specify study and project at well level

219daee

tests: add tests to specify study and project at plate level

f438a6a

tests: specify study and project at plate level for submission

596ae2c

tests: add tests for same study and project

93c187b

Merge branch 'dpl-812-tests' into dpl-812-fluidx-tube-rack-data-report

8eb2598

tests: update column headings

e383aa6

fix: remove erroneous leading line

4e57dce

tests: refactor and add missing values

6008819

tests: add missing study

0f7de3c

tests: add donor and row-by-row evaluation to tests

b95584b

fix: add extraction-date and study name

15691a5

fix: update barcodes

59e35e6

style: remove development comments

a742683

StephenHulme added 4 commits October 24, 2023 16:48

refactor: rename child_tube -> child_tube_v1

fbc7a10

style: lint

96cc5f5

style: lindt

2b6b796

tests: specify donor_id

cfc6c80

StephenHulme commented Oct 25, 2023

View reviewed changes

StephenHulme requested review from andrewsparkes and KatyTaylor October 25, 2023 09:04

KatyTaylor linked an issue Oct 30, 2023 that may be closed by this pull request

DPL-812 Transfer PBMC bank data to BioResource team #1439

Closed

1 task

KatyTaylor reviewed Oct 30, 2023

View reviewed changes

app/views/exports/pbmc_bank_tubes_content_report.csv.erb Outdated Show resolved Hide resolved

KatyTaylor reviewed Oct 30, 2023

View reviewed changes

app/views/exports/pbmc_bank_tubes_content_report.csv.erb Outdated Show resolved Hide resolved

KatyTaylor reviewed Oct 30, 2023

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config/exports/exports.yml Outdated Show resolved Hide resolved

KatyTaylor requested changes Oct 30, 2023

View reviewed changes

StephenHulme added 5 commits October 30, 2023 13:45

Merge branch 'develop' into dpl-812-fluidx-tube-rack-data-report

451eb64

fix: revert inadvertent debugging changes

f6c477b

fix: rename Parent barcode -> Stock barcode

7d3868a

fix: use purpose name instead of tube name to determine destination

3a4e64d

fix: update dev comment

613c3bc

KatyTaylor approved these changes Oct 30, 2023

View reviewed changes

StephenHulme merged commit e1583b1 into develop Oct 31, 2023
8 checks passed

StephenHulme deleted the dpl-812-fluidx-tube-rack-data-report branch October 31, 2023 09:46

StephenHulme mentioned this pull request Nov 2, 2023

DPL-812.1: FluidX tube rack data report - donor-id fix #1447

Merged

StephenHulme mentioned this pull request Nov 15, 2023

DPL-812.2: repair undefined method 'value' for nil:NilClass #1464

Merged

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DPL-812: FluidX tube rack data report #1433

DPL-812: FluidX tube rack data report #1433

StephenHulme commented Oct 25, 2023 •

edited

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StephenHulme Oct 25, 2023

KatyTaylor Oct 30, 2023

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codeclimate bot commented Oct 30, 2023

DPL-812: FluidX tube rack data report #1433

DPL-812: FluidX tube rack data report #1433

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StephenHulme commented Oct 25, 2023 • edited Loading

Changes proposed in this pull request

Acceptance criteria

Example CSV Report

Instructions for Reviewers

StephenHulme Oct 25, 2023

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StephenHulme commented Oct 25, 2023 •

edited

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