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Feature/distinguish linking accession ids #449

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merged 4 commits into from
Sep 8, 2021
Merged

Feature/distinguish linking accession ids #449

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a13e8d6
Add Title to linking accessionIds
hannyle Sep 3, 2021
b111f4c
Make linkingAccessionIds selectable and work with Title
hannyle Sep 6, 2021
d978b20
Make Title as required field in form and update cypress test
hannyle Sep 6, 2021
4ac41fb
Add special case for DAC form
hannyle Sep 7, 2021
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29 changes: 27 additions & 2 deletions cypress/integration/linkingAccessionIds.spec.js
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,8 @@ describe("Linking Accession Ids", function () {
.should("be.visible")
.then($btn => $btn.click())
)
cy.get("input[name='sampleName.taxonId']").type(123)
cy.get("[data-testid='title']").type("Test Sample title")
cy.get("[data-testid='sampleName.taxonId']").type(123)
// Submit Sample form
cy.get("button[type=submit]").contains("Submit").click()
cy.get(".MuiListItem-container", { timeout: 10000 }).should("have.length", 1)
Expand All @@ -66,13 +67,16 @@ describe("Linking Accession Ids", function () {
.should("be.visible")
.then($btn => $btn.click())
)
cy.get("[data-testid='title']").type("Test Experiment title")
cy.get("input[name='studyRef.label']").type("Study Label")

// Select studyAccessionId
cy.get("select[name='studyRef.accessionId']").then($el => {
const studyAccessionId = cy.get("@studyAccessionId")
$el.click()
$el.select(studyAccessionId)
})
cy.get("select[name='studyRef.accessionId']").should("contain", " - Title:")

cy.get("textarea[name='design.designDescription']").type("Design description")
cy.get("select[name='design.sampleDescriptor']").select("Individual Sample")
Expand All @@ -82,6 +86,7 @@ describe("Linking Accession Ids", function () {
const sampleAccessionId = cy.get("@sampleAccessionId")
$el.select(sampleAccessionId)
})
cy.get("select[name='design.sampleDescriptor.accessionId']").should("contain", " - Title:")

cy.get("select[name='design.libraryDescriptor.libraryStrategy']").select("AMPLICON")
cy.get("select[name='design.libraryDescriptor.librarySource']").select("GENOMIC")
Expand All @@ -107,13 +112,15 @@ describe("Linking Accession Ids", function () {
.should("be.visible")
.then($btn => $btn.click())
)
cy.get("[data-testid='title']").type("Test Run title")
cy.get("h2[data-testid='experimentRef']").parent().children("button").click()
cy.get("[data-testid='experimentRef[0].label']").type("Test experiment label ref")
// Select experimentAccessionId
cy.get("select[name='experimentRef[0].accessionId']").then($el => {
const experimentAccessionId = cy.get("@experimentAccessionId")
$el.select(experimentAccessionId)
})
cy.get("select[name='experimentRef[0].accessionId']").should("contain", " - Title:")

// Submit Run form
cy.get("button[type=submit]").contains("Submit").click()
Expand All @@ -136,6 +143,7 @@ describe("Linking Accession Ids", function () {
.should("be.visible")
.then($btn => $btn.click())
)
cy.get("[data-testid='title']").type("Test Analysis title")
cy.get("select[name='analysisType']").select("Reference Alignment")
cy.get("select[name='analysisType.referenceAlignment.assembly']").select("Standard")
cy.get("input[name='analysisType.referenceAlignment.assembly.accessionId']").type("Standard accessionId")
Expand All @@ -144,24 +152,32 @@ describe("Linking Accession Ids", function () {
const studyAccessionId = cy.get("@studyAccessionId")
$el.select(studyAccessionId)
})
cy.get("select[name='studyRef.accessionId']").should("contain", " - Title:")

// Select experimentAccessionId
cy.get("div").contains("Experiment Reference").parent().children("button").click()
cy.get("select[name='experimentRef[0].accessionId']").then($el => {
const experimentAccessionId = cy.get("@experimentAccessionId")
$el.select(experimentAccessionId)
})
cy.get("select[name='experimentRef[0].accessionId']").should("contain", " - Title:")

// Select sampleAccessionId
cy.get("div").contains("Sample Reference").parent().children("button").click()
cy.get("select[name='sampleRef[0].accessionId']").then($el => {
const sampleAccessionId = cy.get("@sampleAccessionId")
$el.select(sampleAccessionId)
})
cy.get("select[name='sampleRef[0].accessionId']").should("contain", " - Title:")

// Select runAccessionId
cy.get("div").contains("Run Reference").parent().children("button").click()
cy.get("select[name='runRef[0].accessionId']").then($el => {
const runAccessionId = cy.get("@runAccessionId")
$el.select(runAccessionId)
})
cy.get("select[name='runRef[0].accessionId']").should("contain", " - Title:")

// Submit Analysis form
cy.get("button[type=submit]").contains("Submit").click()
cy.get(".MuiListItem-container", { timeout: 10000 }).should("have.length", 1)
Expand All @@ -173,6 +189,7 @@ describe("Linking Accession Ids", function () {

// Another Analysis form
cy.get("button[type=button]").contains("New form").click()
cy.get("[data-testid='title']").type("Test Analysis title 2")
cy.get("select[name='analysisType']").select("Reference Alignment")
cy.get("select[name='analysisType.referenceAlignment.assembly']").select("Standard")
cy.get("input[name='analysisType.referenceAlignment.assembly.accessionId']").type("Standard accessionId 2")
Expand All @@ -183,6 +200,7 @@ describe("Linking Accession Ids", function () {
const analysisAccessionId = cy.get("@analysisAccessionId")
$el.select(analysisAccessionId)
})
cy.get("select[name='analysisRef[0].accessionId']").should("contain", " - Title:")

// Submit Analysis form
cy.get("button[type=submit]").contains("Submit").click()
Expand Down Expand Up @@ -229,11 +247,14 @@ describe("Linking Accession Ids", function () {
.should("be.visible")
.then($btn => $btn.click())
)
cy.get("[data-testid='title']").type("Test Policy title")
cy.get("input[name='dacRef.label']").type("Test DAC")
cy.get("select[name='dacRef.accessionId']").then($el => {
const dacAccessionId = cy.get("@dacAccessionId")
$el.select(dacAccessionId)
})
cy.get("select[name='dacRef.accessionId']").should("contain", " - Main Contact:")

cy.get("select[name='policy']").select("Policy Text")
cy.get("textarea[name='policy.policyText']").type("Test policy text")
// Submit Policy form
Expand All @@ -257,7 +278,7 @@ describe("Linking Accession Ids", function () {
.then($btn => $btn.click())
)

cy.get("input[name='title']").type("Dataset title")
cy.get("[data-testid='title']").type("Test Dataset title")
cy.get("textarea[name='description']").type("Dataset description")
cy.get("input[name='datasetType']").first().check()

Expand All @@ -266,20 +287,24 @@ describe("Linking Accession Ids", function () {
const policyAccessionId = cy.get("@policyAccessionId")
$el.select(policyAccessionId)
})
cy.get("select[name='policyRef.accessionId']").should("contain", " - Title:")

// Select runAccessionId
cy.get("div").contains("Run Reference").parent().children("button").click()
cy.get("select[name='runRef[0].accessionId']").then($el => {
const runAccessionId = cy.get("@runAccessionId")
$el.select(runAccessionId)
})
cy.get("select[name='runRef[0].accessionId']").should("contain", " - Title:")

// Select analysisAccessionId
cy.get("div").contains("Analysis Reference").parent().children("button").click()
cy.get("select[name='analysisRef[0].accessionId']").then($el => {
const analysisAccessionId = cy.get("@analysisAccessionId")
$el.select(analysisAccessionId)
})
cy.get("select[name='analysisRef[0].accessionId']").should("contain", " - Title:")

// Submit Dataset form
cy.get("button[type=submit]").contains("Submit").click()
cy.get(".MuiListItem-container", { timeout: 10000 }).should("have.length", 1)
Expand Down
7 changes: 6 additions & 1 deletion src/components/NewDraftWizard/WizardForms/WizardFillObjectDetailsForm.js
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -488,7 +488,12 @@ const WizardFillObjectDetailsForm = (): React$Element<typeof Container> => {

const getAccessionIds = (objectType: string) => {
const submissions = metadataObjects?.filter(obj => obj.schema.toLowerCase() === objectType)
const accessionIds = submissions?.map(obj => obj.accessionId)
// Add "- Title: " to accessionId, special case DAC form: add "- Main Contact:"
const accessionIds = submissions?.map(obj =>
obj.schema === ObjectTypes.dac
? `${obj.accessionId} - Main Contact: ${obj.tags?.displayTitle}`
: `${obj.accessionId} - Title: ${obj.tags?.displayTitle}`
)
return accessionIds
}

Expand Down
68 changes: 42 additions & 26 deletions src/components/NewDraftWizard/WizardForms/WizardJSONSchemaParser.js
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Original file line number Diff line number Diff line change
Expand Up @@ -228,6 +228,9 @@ const traverseFields = (
let required = object?.else?.required ?? object.required
let requireFirstItem = false

if (path.length === 0 && propertyKey === "title" && !object.title.includes("DAC - Data Access Committee")) {
requireFirstItem = true
}
// Require first field of section if parent section is a required property
if (
requireFirst ||
Expand Down Expand Up @@ -816,32 +819,45 @@ const FormSelectField = ({
<Controller
name={name}
control={control}
render={({ field, fieldState: { error } }) => (
<div className={classes.divBaseline}>
<ValidationSelectField
{...field}
label={label}
value={field.value || ""}
error={!!error}
helperText={error?.message}
required={required}
select
SelectProps={{ native: true }}
>
<option aria-label="None" value="" disabled />
{options.map(option => (
<option key={`${name}-${option}`} value={option}>
{option}
</option>
))}
</ValidationSelectField>
{description && (
<FieldTooltip title={description} placement="top" arrow>
<HelpOutlineIcon className={classes.fieldTip} />
</FieldTooltip>
)}
</div>
)}
render={({ field, fieldState: { error } }) => {
return (
<div className={classes.divBaseline}>
<ValidationSelectField
{...field}
label={label}
value={field.value || ""}
error={!!error}
helperText={error?.message}
required={required}
select
SelectProps={{ native: true }}
onChange={e =>
field.onChange(() => {
const val = e.target.value
// Case: linkingAccessionIds which include "AccessionId + Form's title", we need to return only accessionId as value
if (val?.includes("Title")) {
const hyphenIndex = val.indexOf("-")
return val.slice(0, hyphenIndex - 1)
}
return val
})
}
>
<option aria-label="None" value="" disabled />
{options.map(option => (
<option key={`${name}-${option}`} value={option}>
{option}
</option>
))}
</ValidationSelectField>
{description && (
<FieldTooltip title={description} placement="top" arrow>
<HelpOutlineIcon className={classes.fieldTip} />
</FieldTooltip>
)}
</div>
)
}}
/>
)
}}
Expand Down