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More Metadata Sections for Hermes (#150)
* genotyping information section done * imputation section done * done with genotyping qc
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2 files changed

+217
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‎cypress/e2e/hermes/hermes-upload.cy.js‎

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Original file line numberDiff line numberDiff line change
@@ -21,6 +21,19 @@ describe('Hermes Upload', {retries: 0}, () => {
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cy.get("#caseDefinition").type("My case definition");
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cy.get("#totalSampleSize").type("989");
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cy.get("#maleProportionCohort").type("1");
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cy.get('#callingAlgorithm').type("You called, algorithm?");
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cy.get('#genotypingArray').type("Array against you");
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cy.get('[data-cy="referenceGenome"]').type('Hg19').type('{enter}');
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cy.get('#imputationSoftware').type('Imputate this software');
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cy.get('#imputationReference').type('Imputation reference');
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cy.get('#numberOfVariantsForImputation').type('47');
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cy.get('#imputationQualityMeasure').type('highest quality');
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cy.get('[data-cy="relatedIndividualsRemoved"]').type('Yes').type('{enter}');
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cy.get('#variantCallRate').type('.22');
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cy.get('#sampleCallRate').type('.2247');
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cy.get('#hwePValue').type('.09121');
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cy.get('#maf').type('1');
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cy.get('#otherFilters').type('My Filters');
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// cy.get("#participants").type('20');
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// cy.get("#sexProportion").type('20');

‎pages/hermes/new.vue‎

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@@ -28,6 +28,7 @@ const formSchema = yup.object({
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cases: yup.number().integer('Cases must be an integer').positive('Cases must be positive')
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.label('Cases').transform(value => (isNaN(value) ? undefined : value)),
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maleProportionCohort: yup.number().min(0).max(1).required()
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.transform(value => (isNaN(value) ? undefined : value))
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.label('Male propoportion (total cohort)'),
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maleProportionCases: yup.number().min(0).max(1).label('Male proportion (cases)').when("cases", {
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is: (value) => value > 0,
@@ -70,7 +71,7 @@ const formSchema = yup.object({
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meanDiagnosisAge: yup.number().positive('Mean diagnosis age must be positive')
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.label('Mean diagnosis age').transform(value => (isNaN(value) ? undefined : value)).when("cases", {
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is: (value) => value > 0,
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then: (schema) => schema.required('You must mean diagnosis age when you specify cases'),
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then: (schema) => schema.required('You must specify mean diagnosis age when you specify cases'),
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otherwise: (schema) => schema,
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}),
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sdDiagnosisAge: yup.number().positive('Standard deviation diagnosis age must be positive')
@@ -79,6 +80,27 @@ const formSchema = yup.object({
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then: (schema) => schema.required('You must mean diagnosis age when you specify cases'),
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otherwise: (schema) => schema,
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}),
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referenceGenome: yup.string().label('Reference Genome').required(),
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genotypingArray: yup.string().label('Genotyping Array').required(),
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callingAlgorithm: yup.string().label('Calling Algorithm').required(),
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imputationSoftware: yup.string().label('Imputation Software').required(),
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imputationReference: yup.string().label('Imputation Reference').required(),
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numberOfVariantsForImputation: yup.number().positive("Number of variants for imputation must be positive")
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.transform(value => (isNaN(value) ? undefined : value))
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.integer("Number of variants should be a whole number")
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.label("Number of Variants for Imputation").required(),
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imputationQualityMeasure: yup.string().label("Imputation Quality Measure").required(),
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relatedIndividualsRemoved: yup.string().label("Related Individuals Removed").required(),
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variantCallRate: yup.number().min(0).max(1).transform(value => (isNaN(value) ? undefined : value))
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.label("Variant Call Rate").required(),
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sampleCallRate: yup.number().min(0).max(1).transform(value => (isNaN(value) ? undefined : value))
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.label("Sample Call Rate").required(),
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hwePValue: yup.number().min(0).max(1).transform(value => (isNaN(value) ? undefined : value))
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.label("HWE p-value").required(),
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maf: yup.number().min(0).max(1).transform(value => (isNaN(value) ? undefined : value))
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.label("MAF").required(),
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otherFilters: yup.string().label("Other QC Filters").required(),
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});
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@@ -112,6 +134,19 @@ const [meanAgeControls] = defineField('meanAgeControls');
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const [sdAgeControls] = defineField('sdAgeControls');
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const [meanDiagnosisAge] = defineField('meanDiagnosisAge');
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const [sdDiagnosisAge] = defineField('sdDiagnosisAge');
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const [referenceGenome] = defineField('referenceGenome');
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const [genotypingArray] = defineField('genotypingArray');
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const [callingAlgorithm] = defineField('callingAlgorithm');
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const [imputationSoftware] = defineField('imputationSoftware');
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const [imputationReference] = defineField('imputationReference');
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const [numberOfVariantsForImputation] = defineField('numberOfVariantsForImputation');
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const [imputationQualityMeasure] = defineField('imputationQualityMeasure');
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const [relatedIndividualsRemoved] = defineField('relatedIndividualsRemoved');
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const [variantCallRate] = defineField('variantCallRate');
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const [sampleCallRate] = defineField('sampleCallRate');
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const [hwePValue] = defineField('hwePValue');
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const [maf] = defineField('maf');
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const [otherFilters] = defineField('otherFilters');
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const store = useDatasetStore();
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const userStore = useUserStore();
@@ -123,11 +158,18 @@ const missingFileError = ref('');
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const missingMappingError = ref('');
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let fileName = null;
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let previousMapping = {};
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const selectedGenomeBuild = ref('');
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const caseAscertainmentOptions = ref([
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{ name: "Electronic Health Records", value: "Electronic Health Records" },
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{ name: "Research Study", value: "Research Study" }
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]);
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const referenceGenomeOptions = ref([
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{ name: "Hg38", value: "Hg38" },
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{ name: "Hg19", value: "Hg19" }
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]);
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const relatedIndividualsRemovedOptions = ref([
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{name: "Yes", value: "Yes"},
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{name: "No", value: "No"},
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]);
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const sexOptions = ref([
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{ name: "Not sex stratified", value: "Not sex stratified" },
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{ name: "Male only", value: "Male only" },
@@ -164,16 +206,8 @@ const analysisSoftware = ref("");
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const statisticalModel = ref("");
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const covariates = ref("");
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const arrayName = ref("");
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const callingAlgorithm = ref("");
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const variantCallRate = ref(null);
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const sampleCallRate = ref(null);
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const hwePValue = ref(null);
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const maf = ref(null);
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const otherQCFilters = ref("");
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const nVariantsForImputation = ref("");
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const prephasingAndImputationSoftware = ref("");
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const imputationReference = ref("");
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const imputationQualityMeasure = ref("");
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const colOptions = ref([]);
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const requiredFields = ref([]);
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const selectedFields = ref({});
@@ -706,6 +740,166 @@ async function uploadSubmit(){
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</Fieldset>
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<Fieldset legend="Genotyping Information">
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<div class="field">
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<label for="reference">Reference Genome</label>
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<Dropdown
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id="referenceGenome"
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v-model="referenceGenome"
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:options="referenceGenomeOptions"
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optionLabel="name"
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optionValue="value"
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placeholder="Select Reference Genome" data-cy="referenceGenome"
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aria-describedby="referenceGenome-help"
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:class="{ 'p-invalid': errors.referenceGenome }"
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/>
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<small id="referenceGenome-help" class="p-error">
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{{ errors.referenceGenome }}
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</small>
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</div>
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<div class="field">
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<label for="genotypingArray">Genotyping Array</label>
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<InputText v-model="genotypingArray" id="genotypingArray" type="text"
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v-tooltip="'The genotyping array name and version used to generate the genetic data (e.g. Illumina Omni2.5)'"
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aria-labelledby="genotypingArray-help"
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:class="{'p-invalid': errors.genotypingArray}"
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/>
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<small id="genotypingArray-help" class="p-error">
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{{ errors.genotypingArray }}
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</small>
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</div>
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<div class="field">
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<label for="callingAlgorithm">Calling Algorithm</label>
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<InputText v-model="callingAlgorithm" id="callingAlgorithm" type="text"
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v-tooltip="'The calling algorithm used (e.g. GATK HaplotypeCaller v4.1)'"
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aria-labelledby="callingAlgorithm-help"
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:class="{'p-invalid': errors.callingAlgorithm}"
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/>
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<small id="callingAlgorithm-help" class="p-error">
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{{ errors.callingAlgorithm }}
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</small>
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</div>
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</Fieldset>
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<Fieldset legend="Imputation Information">
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<div class="field">
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<label for="imputationSoftware">Imputation Software</label>
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<InputText v-model="imputationSoftware" id="imputationSoftware" type="text"
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v-tooltip="'The prephasing and imputation software and version used in the GWAS analysis (e.g. IMPUTE2 v2.3.2)'"
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aria-labelledby="imputationSoftware-help"
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:class="{'p-invalid': errors.imputationSoftware}"
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/>
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<small id="imputationSoftware-help" class="p-error">
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{{ errors.imputationSoftware }}
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</small>
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</div>
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<div class="field">
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<label for="imputationReference">Imputation Reference</label>
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<InputText v-model="imputationReference" id="imputationReference" type="text"
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v-tooltip="'The imputation reference used (e.g. HRCr1.1)'"
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aria-labelledby="imputationReference-help"
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:class="{'p-invalid': errors.imputationReference}"
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/>
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<small id="imputationReference-help" class="p-error">
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{{ errors.imputationReference }}
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</small>
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</div>
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<div class="field">
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<label for="numberOfVariantsForImputation">Number of Variants for Imputation</label>
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<InputText v-model="numberOfVariantsForImputation" id="numberOfVariantsForImputation" type="number"
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v-tooltip="'The number of variants used for imputation (e.g. 10,000)'"
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aria-labelledby="numberOfVariantsForImputation-help"
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:class="{'p-invalid': errors.numberOfVariantsForImputation}"
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/>
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<small id="numberOfVariantsForImputation-help" class="p-error">
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{{ errors.numberOfVariantsForImputation }}
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</small>
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</div>
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<div class="field">
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<label for="imputationQualityMeasure">Imputation Quality Measure</label>
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<InputText v-model="imputationQualityMeasure" id="imputationQualityMeasure" type="text"
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v-tooltip="'The imputation quality measure used and any threshold applied (e.g. INFO > 0.98 / R^2 > 0.85 / MACH R^2 > 0.92)'"
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aria-labelledby="imputationQualityMeasure-help"
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:class="{'p-invalid': errors.imputationQualityMeasure}"
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/>
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<small id="imputationQualityMeasure-help" class="p-error">
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{{ errors.imputationQualityMeasure }}
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</small>
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</div>
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</Fieldset>
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<Fieldset legend="Genotyping Quality Control">
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<div class="field">
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<label for="relatedIndividualsRemoved">Related Individuals Removed?</label>
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<Dropdown
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id="relatedIndividualsRemoved"
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v-model="relatedIndividualsRemoved"
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:options="relatedIndividualsRemovedOptions"
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optionLabel="name"
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optionValue="value"
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placeholder="Related Individuals Removed?" data-cy="relatedIndividualsRemoved"
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aria-describedby="relatedIndividualsRemoved-help"
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:class="{ 'p-invalid': errors.relatedIndividualsRemoved }"
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/>
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<small id="relatedIndividualsRemoved-help" class="p-error">
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{{ errors.relatedIndividualsRemoved }}
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</small>
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</div>
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<div class="field">
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<label for="variantCallRate">Variant Call Rate</label>
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<InputText v-model="variantCallRate" id="variantCallRate" type="number" min="0" max="1"
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v-tooltip="'The variant call rate threshold used (e.g. 0.95)'"
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aria-labelledby="variantCallRate-help"
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:class="{'p-invalid': errors.variantCallRate}"
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/>
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<small id="variantCallRate-help" class="p-error">
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{{ errors.variantCallRate }}
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</small>
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</div>
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<div class="field">
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<label for="sampleCallRate">Sample Call Rate</label>
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<InputText v-model="sampleCallRate" id="sampleCallRate" type="number" min="0" max="1"
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v-tooltip="'The sample call rate threshold used (e.g. 0.97)'"
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aria-labelledby="sampleCallRate-help"
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:class="{'p-invalid': errors.sampleCallRate}"
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/>
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<small id="sampleCallRate-help" class="p-error">
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{{ errors.sampleCallRate }}
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</small>
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</div>
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<div class="field">
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<label for="hwePValue">HWE p-value</label>
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<InputText v-model="hwePValue" id="hwePValue" type="number" min="0" max="1"
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v-tooltip="'The Hardy-Weinberg Equilibrium p-value threshold used (e.g. 0.05)'"
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aria-labelledby="hwePValue-help"
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:class="{'p-invalid': errors.hwePValue}"
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/>
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<small id="hwePValue-help" class="p-error">
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{{ errors.hwePValue }}
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</small>
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</div>
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<div class="field">
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<label for="maf">MAF Threshold</label>
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<InputText v-model="maf" id="maf" type="number" min="0" max="1"
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v-tooltip="'The minor allele frequency threshold used (e.g. 0.01)'"
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aria-labelledby="maf-help"
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:class="{'p-invalid': errors.maf}"
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/>
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<small id="maf-help" class="p-error">
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{{ errors.maf }}
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</small>
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</div>
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<div class="field">
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<label for="otherFilters">Other QC Filters</label>
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<InputText v-model="otherFilters" id="otherFilters" type="text"
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v-tooltip="'Other quality control filters that may have been implemented'"
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aria-labelledby="otherFilters-help"
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:class="{'p-invalid': errors.otherFilters}"
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/>
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<small id="otherFilters-help" class="p-error">
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{{ errors.otherFilters }}
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</small>
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</div>
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</Fieldset>
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</div>

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