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X1062 probe hybridisation qc #377

Merged

sabrine33 merged 13 commits into devel from x1062_probe_hybridisation_QC

Aug 31, 2023

Contributor

sabrine33 commented Aug 17, 2023

No description provided.

sabrine33 added 5 commits

August 17, 2023 08:22


          fixes x1062—As a PO (Minal), I want users to record probe hybridisati…

52efa40

…on end time for tracking of Xenium #240


          Merge branch 'devel' of github.com:sanger/stan-client into x1062_prob…

539d46e

…e_hybridisation_QC

# Conflicts:
#	src/types/sdk.ts


          resolving sdk.ts conflicts with devel branch


          fixes x1056 As TS (Katy) I would like the visium concentration unit t…

6141a5f

…o be visible on the visium concentration table for confirmation in the lab #365


          Merge branch 'devel' of github.com:sanger/stan-client into x1062_prob…

165da6b

…e_hybridisation_QC

sabrine33 requested a review from seenanair

August 17, 2023 18:57

seenanair reviewed

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Contributor

seenanair left a comment

Cool, looking good.
Just one question , the story says 'The labware must have had probe hybridisation already recorded on it.'. Of course the core will return terror, but would it be better to let user know as soon as they scan labware?

src/components/AppShell.tsx

+                                    path={'/lab/probe_hybridisation_qc'}
+                                    icon={<LabwareIcon className="flex-shrink-0 h-6 w-6 text-sdb-400" />}
+                                    description={'Recording Probe hybridisation QC completion date and set sample sections comments.'}
+                                  />

Contributor

seenanair Aug 21, 2023

There is a section below to display menu items for smaller screen width. Would you please update this menu item there as well?

src/pages/ProbeHybridisationQC.tsx Outdated

+                labwares: {
+                  '': {
+                    globalComments: [],
+                    completionDateTime: '',

Contributor

seenanair Aug 21, 2023

completionDateTime can be initialised to the current time

src/pages/ProbeHybridisationQC.tsx Outdated

+                      slot.samples.forEach((sample) => {
+                        const sampleAddressId = `${slot.address}-${sample.id}`;
+                        const oldSelected = values.labwares[labware.barcode]?.sampleAddressComments?.[sampleAddressId] || [];
+                        const updatedSelected = [...oldSelected, ...mapCommentOptionsToValues(options)];

Contributor

seenanair Aug 21, 2023

Why we need oldSelected and updateSelected?

Contributor Author

sabrine33 Aug 21, 2023

to cover the use case; where the user selects some options for a specific section and then adds other comments from the global comment

Contributor

seenanair Aug 21, 2023

Ohh, is it supposed to behave like that or is it to override everything by comments from 'apply all' drop down when they change some value in it ? It is better to clarify with Katy.

src/pages/ProbeHybridisationQC.tsx Outdated

+                }, []);
+                const updateSectionCommentsFromGlobal = useCallback(
+                  (options: OptionType[], labware: LabwareFieldsFragment, values, setFieldValue) => {

Contributor

seenanair Aug 21, 2023

It would be good to specify values ad setFieldValue as it defaults to 'any' in typescript which should generally be avoided whenever possible

src/pages/ProbeHybridisationQC.tsx

+                    <AppShell.Main>
+                      <Formik<ProbeHybridisationQCFormValues>
+                        initialValues={formInitialValues}
+                        validationSchema={validationWorkNumber}

Contributor

seenanair Aug 21, 2023

You are not validating time field which is required

Contributor Author

sabrine33 Aug 21, 2023

the validation is done automatically by the input field, as I specified the min/max there

src/pages/ProbeHybridisationQC.tsx Outdated

+                                              />
+                                              <MutedText className="pl-2">
+                                                If not manually selected, the current timestamp will be applied automatically
+                                              </MutedText>

Contributor

seenanair Aug 21, 2023

Please make use of formik error handling capabilities, by including this field in validation schema , so we can avoid using MutedText and validateCompletionDateTime

Contributor Author

sabrine33 Aug 21, 2023

hmmm I am not sure how to include this in the formik errors as the request is still valid, when the completion time is not been selected

Contributor

seenanair Aug 21, 2023 •

edited

Loading

I think the request should not be valid with taht empty field. It can display a default value in the field which is the current time when it opens, and the validation can be based on that time which is the default

seenanair reviewed

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cypress/e2e/pages/ProbeHybridisationQC.cy.ts

+                            }
+                          )
+                        );
+                      });

Contributor

seenanair Aug 21, 2023

Please add a global mock handler for this as we do with all other operations in stan-client

seenanair reviewed

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seenanair left a comment

Story says , 'Probe hybridisation comments (editable on config page)' . i think this need to be added in config page

src/components/Routes.tsx Outdated

+                          key={routeProps.location.key}
+                          dataFetcher={() =>
+                            stanCore.GetComments({
+                              commentCategory: 'section',

Contributor

seenanair Aug 21, 2023

This should not be 'section', but Probe hybridisation comments I hope

Contributor Author

sabrine33 Aug 21, 2023

Good point, as the comments are applied for section, I thought we need to get the section comments?do you think we need tp get the Probe QC comment instead ?

Contributor

seenanair Aug 21, 2023

Good point, as the comments are applied for section, I thought we need to get the section comments?do you think we need tp get the Probe QC comment instead ?

I understood it that way which need to be added in configuration page as well. Better to clarify it with Dave or Minal/Katy.

sabrine33 added 4 commits

August 22, 2023 12:59


          validate the labware as soon as the user scans the barcode

a9028b3


          Merge branch 'devel' of github.com:sanger/stan-client into x1062_prob…

dcf5d72

…e_hybridisation_QC


          update cypress ProbeHybridisationQC tests

c0963a3


          update sdk for Probe Hybridisation QC

d996002

seenanair reviewed

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Contributor

seenanair left a comment

It seems like are some unintended changes happened with merge. Please check locally that everything works fine with your page and Xenium Analyser page

src/mocks/handlers/labwareHandlers.ts Outdated

-                    })
-                  );
-                })
+                )

Contributor

seenanair Aug 22, 2023

I think this needs to be in this file

cypress/e2e/pages/ProbeHybridisationQC.cy.ts Outdated

@@ @@ -67,9 +112,20 @@ describe('Probe Hybridisation QC', () => { @@
                 });
                 describe('Submission', () => {
-                  context('when selecting a released labware', () => {
+                  context('when  repeated comment specified for the same section', () => {

Contributor

seenanair Aug 22, 2023

The context name doesn't match with what it does

cypress/e2e/pages/xeniumProbeHybridisationSpec.cy.ts Outdated

@@ @@ -266,7 +266,7 @@ describe('Xenium Probe Hybridisation', () => { @@
                     });
                     it('shows a success message', () => {
-                      cy.findByText('Xenium probe hybridisation recorded on all labware').should('be.visible');
+                      cy.findByText('Xenium probe hubridisation recorded on all labware').should('be.visible');

Contributor

seenanair Aug 22, 2023

Something gone wring with merge it seems. this typo was fixed in the other branch which is again reverted back now. Please change to 'hybridisation'

src/components/AppShell.tsx

-                                    path={'/lab/xenium_analyser'}
-                                    icon={<LabwareIcon className="flex-shrink-0 h-6 w-6 text-sdb-400" />}
-                                    description={'Recording Xenium analyser information'}
+                                    description={'Recording Probe hybridisation for Xenium slides.'}

Contributor

seenanair Aug 22, 2023

Again merge - The previous description was correct 'Recording Xenium analyser information'

Contributor

seenanair Aug 23, 2023

@sabrine33 did you change this? I couldn't see this update in your PR

src/components/AppShell.tsx

		<div className="grid grid-cols-2 ml-2 gap-y-4 gap-x-8">
		<StanMobileNavLink to="/lab/xenium_analyser">Xenium Analyser</StanMobileNavLink>

Contributor

seenanair Aug 22, 2023

This shouldn't be removed

src/components/Table.tsx Outdated

-              };
-              export const TabelCentredCell: React.FC<Props> = ({ children, ...rest }) => {
-                return <div className="flex items-center justify-center">{children}</div>;
-              };

Contributor

seenanair Aug 22, 2023

This as well need to be kept

src/graphql/queries/FindLatestOperation.graphql Outdated

@@ @@ -1,5 +1,5 @@ @@
               query FindLatestOperation($barcode: String!, $operationType: String!) {
                 findLatestOp(barcode: $barcode, operationType: $operationType) {
-                  id
+                  ...OperationFields

Contributor

seenanair Aug 22, 2023

This needs to be id not OperationFields

sabrine33 added 2 commits

August 23, 2023 09:03


          fix merging conflicts

6578cb0


          remove unused variable

139cbf7

seenanair approved these changes

View reviewed changes

src/components/AppShell.tsx

-                                    path={'/lab/xenium_analyser'}
-                                    icon={<LabwareIcon className="flex-shrink-0 h-6 w-6 text-sdb-400" />}
-                                    description={'Recording Xenium analyser information'}
+                                    description={'Recording Probe hybridisation for Xenium slides.'}

Contributor

seenanair Aug 23, 2023

@sabrine33 did you change this? I couldn't see this update in your PR

sabrine33 added 2 commits

August 31, 2023 10:57


          Merge branch 'devel' of github.com:sanger/stan-client into x1062_prob…

82b33e4

…e_hybridisation_QC

# Conflicts:
#	src/components/Routes.tsx
#	src/mocks/repositories/commentRepository.ts
#	src/types/sdk.ts


          merging conflicts

3ef2508

sabrine33 merged commit 07b735c into devel

7 checks passed

sabrine33 deleted the x1062_probe_hybridisation_QC branch

August 31, 2023 11:23

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