BI-1910 - Allow Breeder to Upload a Genotype Sample File #343

timparsons · 2023-10-30T15:40:24Z

Description

Story: https://breedinginsight.atlassian.net/browse/BI-1910

Created a new UI component named "Sample Management"

Defined a new import type: Genotype Sample
Defined a new import template
Created a list view of all sample submissions
Created a detailed view of an individual submission
Implemented ability to manual update the status of a submission
Implemented the ability to automatically submit to a vendor and check the status

Dependencies

bi-api/feature/BI-1910
bi-docker-stack/feature/BI-1910

Testing

Testing with germplasm

Create germplasm records in your program
On the Import Data page, go to the "Genotype Samples" tab, and download the template
Populate the template, and make sure to populate the GID column
Upload the sample submission file, and ensure the preview is correct, and confirming succeeds
Navigate to the submission's detail page, and ensure the GID column is populated

Testing with ObsUnitIDs

Create germplasm records in your program
Create an experiment
On the Import Data page, go to the "Genotype Samples" tab, and download the template
Populate the template, and make sure to populate the ObsUnitID column
Upload the sample submission file, and ensure the preview is correct, and confirming succeeds
Navigate to the submission's detail page, and ensure the ObsUnitID and GID columns are populated

Manual Submission

When on the submission detail page, and the submission has not been submitted, click on "Manage Submission" and you should see an option for "Manual Update Submission"
Clicking on "Manual Update Submission" should open a modal window with a dropdown allowing you to change the submissions status
Change the status to "SUBMITTED" and click save, ensure save succeeds and the metadata on the detail page is updated

Automated Submission

Set the BRAPI_VENDOR_SUBMISSION_ENABLED property to true for both bi-web and bi-api and restart
When on the submission detail page, and the submission has not been submitted, click on "Manage Submission" and you should see an option for "Submit to DArT"
Clicking on "Submit to DArT" should open a modal window asking you to confirm this action
Click "Submit"
Ensure the submission was successful and that the metadata on the detail page is updated to show the vendor submission ID and status
Click on "Manage Submission" and you should see an option for "Check Vendor Status".
Click "Check Vendor Status", and a modal should appear with a loading indicator
Ensure there are no errors, and that the "Last Status Check" is updated to the current time

General testing

Ensure that all successful uploads display in the Sample Management table, and show correct status information and metadata
Ensure when viewing a submission detail that the metadata is correct, the table containing the sample information is correct, and the tab containing plate layouts is correct

Checklist:

I have performed a self-review of my own code
I have tested my code and ensured it meets the acceptance criteria of the story
I have create/modified unit tests to cover this change
I have commented my code, particularly in hard-to-understand areas
I have made corresponding changes to documentation
I have run TAF: https://github.com/Breeding-Insight/taf/actions/runs/6765876438

nickpalladino

Did you figure out that issue from the demo where the table didn't display after a certain sequence of menu item selections?

nickpalladino · 2023-11-07T15:01:27Z

src/assets/scss/main.scss

+    z-index: 1;
+    pointer-events: none;
+  }
+  .th-wrap {


Does this affect the display of anything with existing tables?

No, I just restructured the scss to be nested

nickpalladino · 2023-11-07T16:44:16Z

src/components/germplasm/GermplasmLink.vue

+  private loading = true;
+  private germplasm?: Germplasm;
+
+  fetchGermplasm() {


What is the purpose of this, doesn't seem to be actually loading anything.

Nothing anymore. I'll remove that!

sounds good

nickpalladino · 2023-11-09T16:12:44Z

src/views/import/ImportSample.vue

+              </div>
+              <div class="column is-narrow">
+                <div class="has-text-dark has-text-centered is-size-7">
+                  <button class="button is-outlined is-primary" :id="'download-sample-template'" v-on:click="generateTemplate()">Download the Sample Import Template</button>


What was the reason the file was generated rather than hosted on box like the other imports?

Speed of development primarily. Doing this allowed me to quickly make changes to the template as I was receiving feedback from others. I can make a file and put it on Box like the others. It may be worth talking about a static template vs generated template looking to the future.

Moved the template to be served from Box

Sounds good

timparsons · 2023-11-10T14:27:16Z

Did you figure out that issue from the demo where the table didn't display after a certain sequence of menu item selections?

@nickpalladino I did! It was a data loading workflow issue. Once I fixed that workflow, it is now working as expected

davedrp · 2023-11-21T20:25:33Z

Testing. I found a bug.

I imported a sample submission file with a row having the value of lowercase 'c'.
It imported without error and saved the row with a value of lowercase 'c'.
BUT, when retrieving the data from the submission's detail page, I got the error message "Error while trying to load submission details"
- the error seems to occur in SubmissionDetails.vue in the section of code with plateLayout[sample.row.charCodeAt(0) - 'A'.charCodeAt(0)]

timparsons · 2023-11-22T16:51:16Z

Testing. I found a bug.

I imported a sample submission file with a row having the value of lowercase 'c'.

It imported without error and saved the row with a value of lowercase 'c'.

BUT, when retrieving the data from the submission's detail page, I got the error message "Error while trying to load submission details"

the error seems to occur in SubmissionDetails.vue in the section of code with plateLayout[sample.row.charCodeAt(0) - 'A'.charCodeAt(0)]

Good catch @davedrp!! I've fixed this by forcing the row to be uppercase when saving

…eractive Able to interact with the DeltaBreed backend to fetch data. Able to submit submission via BrAPI. Able to manual update a submission's status.

Added feature flag for BrAPI vendor submission

…y to parent DataForm

davedrp · 2023-11-29T14:38:15Z

developer test PASSED

davedrp

I have left some recommendations in the comments, but they are not essential.

davedrp · 2023-11-29T15:35:49Z

src/views/sample-mgmt/SubmissionDetails.vue

+  private activeTab = 'details';
+  private submissionLoading: boolean = true;
+  private submissionDetailsLoading: boolean = true;
+  private downloadModalActive: boolean = false;


downloadModalActive is never used

davedrp · 2023-11-29T15:35:59Z

src/views/sample-mgmt/SubmissionDetails.vue

+import StatusEnum = VendorOrderStatusResponseResult.StatusEnum;
+import {Plate} from "@/breeding-insight/brapi/model/geno/plate";
+import * as XLSX from "xlsx";
+import {WorkBook, WorkSheet} from "xlsx";


WorkSheet is never used.

davedrp · 2023-11-29T15:37:04Z

src/views/sample-mgmt/SubmissionDetails.vue

+  private downloadModalActive: boolean = false;
+  private paginationController: PaginationController = new PaginationController();
+  private submission?: SampleSubmission;
+  private germNameOptions?: Array<String> = [];


Contents of collection 'germNameOptions' are updated, but never queried

davedrp · 2023-11-29T15:45:44Z

src/breeding-insight/dao/SampleSubmissionDAO.ts

+
+import * as api from '@/util/api';
+import { BiResponse, Response } from '@/breeding-insight/model/BiResponse';
+import { BreedingMethod } from '@/breeding-insight/model/BreedingMethod';


'BreedingMethod' imported but not used

davedrp · 2023-11-29T15:46:32Z

src/breeding-insight/dao/SampleSubmissionDAO.ts

+import {Result, ResultGenerator} from "@/breeding-insight/model/Result";
+import {SampleSubmission} from "@/breeding-insight/model/SampleSubmission";
+import {VendorOrderSubmission} from "@/breeding-insight/brapi/model/geno/vendorOrderSubmission";
+import {BrAPIDAOUtil} from "@/breeding-insight/dao/BrAPIDAOUtil";


'BrAPIDAOUtil' imported but not used

github-actions bot added the feature label Oct 30, 2023

timparsons mentioned this pull request Oct 30, 2023

BI-1910 - Allow Breeder to Upload a Genotype Sample File Breeding-Insight/bi-api#306

Merged

7 tasks

timparsons force-pushed the feature/BI-1910 branch from 89ae69f to 88db9be Compare November 6, 2023 02:34

timparsons requested review from davedrp and nickpalladino November 6, 2023 15:35

timparsons assigned davedrp Nov 6, 2023

timparsons marked this pull request as ready for review November 6, 2023 15:35

nickpalladino reviewed Nov 9, 2023

View reviewed changes

timparsons force-pushed the feature/BI-1910 branch from 7681cd7 to c647841 Compare November 10, 2023 19:10

timparsons requested a review from nickpalladino November 10, 2023 19:11

nickpalladino approved these changes Nov 15, 2023

View reviewed changes

timparsons added 11 commits November 22, 2023 11:53

[BI-1910] Creating views for importing and viewing sample submissions

a52f7c7

[BI-1910] updating sample management interfaces to be dynamic and int…

43108d5

…eractive Able to interact with the DeltaBreed backend to fetch data. Able to submit submission via BrAPI. Able to manual update a submission's status.

[BI-1910] cleanup

715e8de

[BI-1910] cleanup

763dd5e

[BI-1910] Adding ability to download a plate layout

51452b9

Added feature flag for BrAPI vendor submission

[BI-1910] Fixing display bug after call to check vendor status

0fd3247

[BI-1910] refactoring NewDataForm/EditDataForm to pass record directl…

2e3cf20

…y to parent DataForm

[BI-1910] cleanup

1529666

[BI-1910] moving import template to be served from Box

9338521

[BI-1910] Genotype Sample tab was accidentally commented out

435dff7

[BI=1910] reverting ProgramConfiguration.vue

0a04076

timparsons force-pushed the feature/BI-1910 branch from 6f917ec to 0a04076 Compare November 22, 2023 16:53

davedrp approved these changes Nov 29, 2023

View reviewed changes

[BI-1910] cleanup

0eb1cb5

timparsons merged commit 4323a59 into develop Nov 29, 2023
1 check passed

timparsons deleted the feature/BI-1910 branch November 29, 2023 19:50

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BI-1910 - Allow Breeder to Upload a Genotype Sample File #343

BI-1910 - Allow Breeder to Upload a Genotype Sample File #343

timparsons commented Oct 30, 2023 •

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BI-1910 - Allow Breeder to Upload a Genotype Sample File #343

BI-1910 - Allow Breeder to Upload a Genotype Sample File #343

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timparsons commented Oct 30, 2023 • edited Loading

Description

Dependencies

Testing

Testing with germplasm

Testing with ObsUnitIDs

Manual Submission

Automated Submission

General testing

Checklist:

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timparsons commented Nov 10, 2023

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timparsons commented Nov 22, 2023

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timparsons commented Oct 30, 2023 •

edited

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