DPL 950 - NT barcodes import #1453

seenanair · 2023-12-14T10:45:40Z

GeneralReception page update
- New source option "Sequencescape Tubes"
- Print support
  - Displays only when source selected is "Sequencescape Tubes"
  - Displays human barcodes when user enters a valid barcode
  - Printer option selection
  - Support priniting on 'Print' button click
- Fetching labware data from Sequencescape on entering/scanning barcodes
- Import functaionlity modification
SequencescapeTubes added in receptions
sequencescapeUils.js added - all generic functions used between receptions/Sequencescape and receptions/SequenscapeTubes
Unit and e2e test case updates
Resolving import paths

Feature flag removed for Sequencescapr V1 SequencescapeTubes added Common functions moved to sequencescapeUtils.js

…lpers.js)

stevieing

A few things to look at but looking good.

stevieing · 2023-12-15T11:22:40Z

src/lib/receptions/Sequencescape.js

+ *
+ * @returns {Array} Array of attribute keys
+ */
+const getAttributeKeys = () => {


I think you can turn this into a 1 liner
return Object.keys(labwareTypes).flatMap((type) => labwareTypes[type].attributes)

stevieing · 2023-12-15T11:24:17Z

src/lib/receptions/SequencescapeTubes.js

+    ...buildRequestAndSample({ aliquot, study, sample, sample_metadata, requestOptions }),
+  }
+}
+const labwareTypes = {


labwareTypes seem to be the same in both receptions. Maybe we can move it to the utils?

Actually they are different in both -
For Sequencescape it contains both plates and tubes,
const labwareTypes = { plates: { type: 'plates', attributes: 'plates_attributes', transformFunction: transformPlate, }, tubes: { type: 'tubes', attributes: 'tubes_attributes', transformFunction: transformTube, }, }

For SequenceTubes , it contains only tubes
const labwareTypes = { tubes: { type: 'tubes', attributes: 'tubes_attributes', transformFunction: transformTube, }, }

Probably , we can have the default in utils as only having tubes
const labwareTypes = { tubes: { type: 'tubes', attributes: 'tubes_attributes', transformFunction: transformTube, }, }
and in Sequencescape , we can modify this generic type to append the 'plates' as well. But , I am not sure whether it improves much as there are only two of them. Please comment.

Could the default have both plates and tubes and then each reception uses the appropriate one?

That sounds good. I will make the changes 👍

stevieing · 2023-12-15T11:24:52Z

src/lib/receptions/index.js

+    name: 'sequencescape-tubes',
+    text: 'Sequencescape Tubes',
+    value: 'SequencescapeTubes',
+  },
 }

 // TO MODIFY - remove versions once dpl_877_reception_request is enabled by default


I think you can remove this comment now you have removed the flag?

stevieing · 2023-12-15T11:25:49Z

src/lib/receptions/sequencescapeUtils.js

  }
 }

-const labwareTypes = {


As per my previous comment I think we could put this back to remove duplication in the receptions.

stevieing · 2023-12-15T11:26:41Z

src/views/GeneralReception.vue

+    // labwareData is used to store the input barcodes as well as the data fetched from sequencescape which is then imported into traction
+    labwareData: {
+      inputBarcodes: [], // inputBarcodes is used to store the barcodes that the user has inputted
+      foundBarcodes: new Set(), // foundBarcodes is used to store the barcodes that have been found in sequencescape


Nice. Using sets is a great way to prevent duplicates.

stevieing · 2023-12-15T11:27:44Z

src/views/GeneralReception.vue

    showModal(message) {
      this.modalState = { visible: true, message }
    },
-    importFailed({ message }) {
+    //Handler for deleting barcodes from the input field


Not entirey sure what is going on here but you may be able to turn it into a map.

This handler is designed for an edge case that addresses inconsistencies arising when the user enters barcodes and subsequently deletes them using the backspace or delete key. When the user inputs data, we fetch that information upon pressing the enter key, and our labwareData object keeps the necessary details from sequencescape fetch (used for printing or importing).
However, if the user removes the barcode by pressing delete or backspace, the data stored in our state may become inconsistent with what is present in the input barcode field. Therefore, it is essential to delete all information corresponding to the deleted input barcode. Failing to do so could result in printing or importing information related to barcodes that are no longer in the input barcode field.
Hope it make sense.

As we are keeping three different array fields in labwareData for inputBarcodes, foundBarcdes(from SS) and attributes (again from SS for import) I thought forEach is better to make changes for each of them.

Please let me know your thoughts on this.

The alternative solution to completely eliminate this issue and this handler is to inform the user that, after making any changes in input barcode field( whether it is delete or any edit), they should press 'Enter'. This action will ensure that the labwareData state aligns consistently with the barcodes in the input field.

Maybe worth a call about this? Function seems to work fine but looks like there could be room for simplifying.

Yes sure. Do you have some time tomorrow after 10.30 , for a quick call?

- Removed feature flag comment - Code enhancements

BenTopping

Looking good, couple comments.

BenTopping · 2024-01-02T11:37:05Z

.env.production

Can unstage this if its not intentional.

BenTopping · 2024-01-02T11:39:32Z

src/lib/receptions/SequencescapeTubes.js

+  include: 'receptacles.aliquots.sample.sample_metadata,receptacles.aliquots.study',
+  fields: {
+    tubes: 'labware_barcode,receptacles',
+    wells: 'position,aliquots',


Dont think we need to fetch wells as this is only for tubes.

BenTopping · 2024-01-02T11:55:55Z

src/views/GeneralReception.vue

    showModal(message) {
      this.modalState = { visible: true, message }
    },
-    importFailed({ message }) {
+    //Handler for deleting barcodes from the input field


Maybe worth a call about this? Function seems to work fine but looks like there could be room for simplifying.

…lication

- labwareTypes, transformTube, transformPlate moved to utils

BenTopping · 2024-01-05T10:22:52Z

src/views/GeneralReception.vue

@@ -272,6 +272,7 @@ export default {
      attributes: [], // attributes is used to store the attributes that have been found in sequencescape
    },
    printerName: '',
+    debounceTimer: 1000, // debounce timer for barcode deletion


I think this should be set to null by default since its not the time its the timer itself. I think thats my mistake when we went over it.

@BenTopping
No, you helped a lot. It's bit stupid of me that I didn't realise that it's a timerId returned by setTimeout and not a timer value.
Updated to null now 👍

- debounceTimer set to null - Fixed console warning for TractionBadge.spec.js

seenanair added 10 commits December 1, 2023 20:32

Feature flag removal, SequencescapeTubes,

7c4b853

Feature flag removed for Sequencescapr V1 SequencescapeTubes added Common functions moved to sequencescapeUtils.js

Updates

795eebe

Updates

0661ecd

Refactoring update

72e9935

Test case updates

60cd4e5

Updating import paths extensions

fdb3cf3

Update GeneralReception.vue

08f0b9f

Update GeneralReception.vue

675ca7f

Merge branch 'develop' into dpl-950-import-NT-barcodes

8c39d5f

Prettier runs

57a3781

seenanair requested review from stevieing and BenTopping December 14, 2023 11:36

seenanair added 4 commits December 14, 2023 15:43

Update GeneralReception.vue

d44a607

printerOptions updated using createLabelsFromBarcodes(LabelPrintingHe…

349a5e3

…lpers.js)

Update GeneralReception.vue

37217ea

Merge branch 'develop' into dpl-950-import-NT-barcodes

5cc537a

stevieing requested changes Dec 15, 2023

View reviewed changes

Review comment updates - 1

5c3702d

- Removed feature flag comment - Code enhancements

BenTopping reviewed Jan 2, 2024

View reviewed changes

Review comment update - Added labwareTypes to utils file to avoid dup…

88a7e93

…lication

BenTopping mentioned this pull request Jan 3, 2024

Update vue 3.3.9 → 3.4.3 (minor) #1461

Closed

seenanair added 2 commits January 4, 2024 13:22

Review comments update

f565250

- labwareTypes, transformTube, transformPlate moved to utils

Debounce for barcode deletion - review update

02a074d

stevieing linked an issue Jan 4, 2024 that may be closed by this pull request

DPL-950 - As a Long Read Samples Extraction user (Hermione) I would like to be able to import NT barcodes directly into Traction without using Samples Extraction to remove a dependency and save time #1376

Closed

5 tasks

seenanair requested review from BenTopping and stevieing January 4, 2024 16:27

BenTopping previously approved these changes Jan 5, 2024

View reviewed changes

Updates

198f461

- debounceTimer set to null - Fixed console warning for TractionBadge.spec.js

seenanair dismissed BenTopping’s stale review via 198f461 January 5, 2024 11:23

seenanair requested a review from BenTopping January 5, 2024 11:34

BenTopping approved these changes Jan 5, 2024

View reviewed changes

Merge branch 'develop' into dpl-950-import-NT-barcodes

b32dce2

stevieing approved these changes Jan 10, 2024

View reviewed changes

stevieing merged commit f52a71d into develop Jan 10, 2024
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stevieing deleted the dpl-950-import-NT-barcodes branch January 10, 2024 15:41

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DPL 950 - NT barcodes import #1453

DPL 950 - NT barcodes import #1453

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DPL 950 - NT barcodes import #1453

DPL 950 - NT barcodes import #1453

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seenanair commented Dec 14, 2023 • edited Loading

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seenanair commented Dec 14, 2023 •

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