-
+
Homo sapiens Mus musculus Saccharomyces cerevisiae S288C
-
+
HSP90 KCNQ4 TEM-1 β-lactamase
- Upload Your Data
+ Upload Your Data
- Add an experiment
- Add a score set
@@ -91,15 +91,15 @@
- News
+ News
-
+
Tracks for many score sets are now available on the UCSC Genome Browser.
-
+
Example:
-
track for
@@ -117,7 +117,7 @@
- Citing MaveDB
+ Citing MaveDB
To cite MaveDB, please cite our most recent publication:
@@ -188,11 +188,6 @@ td, th {
vertical-align: top;
}
-ul {
- padding-left: 1em;
- list-style-type: disc;
-}
-
.mave-hgvs-example {
background: #eee;
padding: 0 3px;
diff --git a/src/components/screens/ScoreSetCalibrationsView.vue b/src/components/screens/ScoreSetCalibrationsView.vue
index 06dec8cb..17eb704a 100644
--- a/src/components/screens/ScoreSetCalibrationsView.vue
+++ b/src/components/screens/ScoreSetCalibrationsView.vue
@@ -6,19 +6,16 @@
@@ -493,10 +497,11 @@ export default {
await this.reloadItem()
} catch (error) {
console.error('Error publishing calibration:', error)
+ const errorMessage = axios.isAxiosError(error) && error.response?.data?.detail && (typeof error.response.data.detail === 'string' || error.response.data.detail instanceof String) ? error.response.data.detail : error
this.$toast.add({
severity: 'error',
summary: 'Calibration Not Published',
- detail: `An error occurred while publishing the calibration: ${error}. Please try again later.`,
+ detail: `An error occurred while publishing the calibration: ${errorMessage}. Please try again later.`,
life: 4000
})
}
@@ -520,10 +525,11 @@ export default {
await this.reloadItem()
} catch (error) {
console.error('Error demoting calibration:', error)
+ const errorMessage = axios.isAxiosError(error) && error.response?.data?.detail && (typeof error.response.data.detail === 'string' || error.response.data.detail instanceof String) ? error.response.data.detail : error
this.$toast.add({
severity: 'error',
summary: 'Calibration Not Demoted',
- detail: `An error occurred while demoting the calibration: ${error}. Please try again later.`,
+ detail: `An error occurred while demoting the calibration: ${errorMessage}. Please try again later.`,
life: 4000
})
}
@@ -541,10 +547,11 @@ export default {
await this.reloadItem()
} catch (error) {
console.error('Error promoting calibration:', error)
+ const errorMessage = axios.isAxiosError(error) && error.response?.data?.detail && (typeof error.response.data.detail === 'string' || error.response.data.detail instanceof String) ? error.response.data.detail : error
this.$toast.add({
severity: 'error',
summary: 'Calibration Not Promoted',
- detail: `An error occurred while promoting the calibration: ${error}. Please try again later.`,
+ detail: `An error occurred while promoting the calibration: ${errorMessage}. Please try again later.`,
life: 4000
})
}
@@ -573,10 +580,11 @@ export default {
await this.reloadItem()
} catch (error) {
console.error('Error deleting calibration:', error)
+ const errorMessage = axios.isAxiosError(error) && error.response?.data?.detail && (typeof error.response.data.detail === 'string' || error.response.data.detail instanceof String) ? error.response.data.detail : error
this.$toast.add({
severity: 'error',
summary: 'Calibration Not Deleted',
- detail: `An error occurred while deleting the calibration: ${error}. Please try again later.`,
+ detail: `An error occurred while deleting the calibration: ${errorMessage}. Please try again later.`,
life: 4000
})
}
@@ -603,10 +611,11 @@ export default {
document.body.removeChild(link)
} catch (error) {
console.error('Error downloading calibrations:', error)
+ const errorMessage = axios.isAxiosError(error) && error.response?.data?.detail && (typeof error.response.data.detail === 'string' || error.response.data.detail instanceof String) ? error.response.data.detail : error
this.$toast.add({
severity: 'error',
summary: 'Download Failed',
- detail: `An error occurred while downloading the calibrations: ${error}. Please try again later.`,
+ detail: `An error occurred while downloading the calibrations: ${errorMessage}. Please try again later.`,
life: 4000
})
}
diff --git a/src/components/screens/ScoreSetCreator.vue b/src/components/screens/ScoreSetCreator.vue
index 6e60bdff..79252e49 100644
--- a/src/components/screens/ScoreSetCreator.vue
+++ b/src/components/screens/ScoreSetCreator.vue
@@ -8,19 +8,19 @@
Create a new score set
- Clear
- Cancel
+ Clear
+ Cancel
Parent experiment and context
- Score set information
- Targets
- Target {{ targetIdx + 1 }}
- Score Calibration
- Variant Scores
+ Score set information
+ Targets
+ Target {{ targetIdx + 1 }}
+ Score Calibration
+ Variant Scores
@@ -55,8 +55,8 @@
that you created?
-
-
+
Meta-analyses are score sets derived from data in other score sets that were created by you or
other users. For example:
-
+
a score set that combines data from two other score sets to produce new scores, or
a score set that adds imputed missing values to the scores in another score set.
-
-
+
No experiments found.
-
+
Experiment
-
+
{{
validationErrors.experiment
}}
@@ -139,7 +139,7 @@
-
+
Supersedes
-
+
{{
validationErrors.supersededScoreSetUrn
}}
@@ -177,7 +177,7 @@
-
+
Meta-analysis for
-
+
{{
validationErrors.metaAnalyzesScoreSetUrns
}}
@@ -219,7 +219,7 @@
-
+
Some fields were autopopulated based on the selected experiment and should be inspected to ensure
they are still relevant to this score set.
@@ -236,10 +236,10 @@
-
+
Title
-
+
{{ validationErrors.title }}
@@ -255,10 +255,10 @@
-
+
Short description
-
+
{{
validationErrors.shortDescription
}}
@@ -283,10 +283,10 @@
-
+
Abstract
-
+
@@ -309,7 +309,7 @@
May be formatted using
Markdown . Should
include:
-
+
a description of how the scores in this score set were generated from the data in the
@@ -338,10 +338,10 @@
-
+
Methods
-
+
@@ -368,8 +368,8 @@
-
-
+ License
-
+
-
-
+
-
+
Data usage guidelines
-
+
{{
validationErrors.dataUsagePolicy
}}
@@ -434,33 +434,21 @@
Examples: 1111-1111-1111-1111
-
-
+
-
-
-
- {{ slotProps.value.givenName }} {{ slotProps.value.familyName }} ({{
- slotProps.value.orcidId
- }})
-
-
{{ slotProps.value.orcidId }}
-
-
-
-
+ fluid
+ multiple
+ :option-label="(x) => x.givenName || x.familyName ? `${x.givenName} ${x.familyName} (${x.orcidId})` : x.orcidId"
+ :typeahead="false"
+ @blur="updateContributors"
+ @keyup.escape="clearAutoCompleteInput"
+ @keyup.space="updateContributors"
+ @update:model-value="newContributorsAdded"
+ />
Contributors
-
+
{{
validationErrors.contributors
}}
@@ -477,25 +465,20 @@
-
-
+
-
-
-
{{ slotProps.value.identifier }}
-
-
-
-
+ :multiple="true"
+ option-label="identifier"
+ :typeahead="false"
+ @blur="updateDoiIdentifiers"
+ @keyup.escape="clearAutoCompleteInput"
+ @keyup.space="updateDoiIdentifiers"
+ @update:model-value="newDoiIdentifiersAdded"
+ />
DOI identifiers
-
+
{{
validationErrors.doiIdentifiers
}}
@@ -514,27 +497,18 @@
-
-
+
-
-
-
Title: {{ slotProps.option.title }}
@@ -545,7 +519,7 @@
Publication identifiers
-
+
{{
validationErrors.publicationIdentifiers
}}
@@ -556,7 +530,7 @@
Of the above publications, the primary publication that describes the score set.
-
+
Primary publication
-
+
{{
validationErrors.primaryPublicationIdentifiers
}}
@@ -589,7 +563,7 @@
Any additional metadata about the score set, as a JSON file.
-
+
Upload a JSON file here.
-
+
{{
validationErrors.extraMetadata
}}
@@ -643,8 +617,8 @@
accession instead of uploading the target locus sequence as your own target.
-
+
-
+
+
{{
isBaseEditor
@@ -691,8 +665,8 @@
the case, your variants will need to be described explicitly from the target they came from.
-
-
+ How many targets will be included with this score set?
-
+
Targets
-
+
-
+
Copy from an existing target
-
+
@@ -791,16 +765,16 @@
-
+
Target name
-
- {{
- validationErrors[`targetGene.${targetIdx}.name`]
+
+ {{
+ validationErrors[`targetGenes.${targetIdx}.targetGene.name`]
}}
@@ -816,18 +790,18 @@
-
+
Target label
-
+
{{ validationErrors[`targetGene.${targetIdx}.targetSequence.label`] }} {{ validationErrors[`targetGenes.${targetIdx}.targetGene.targetSequence.label`] }}
@@ -837,18 +811,16 @@
The functional category of the target
-
-
-
+
+
- {{
- validationErrors[`targetGene.${targetIdx}.category`]
+ {{
+ validationErrors[`targetGenes.${targetIdx}.targetGene.category`]
}}
@@ -866,8 +838,8 @@
target sequence) in order to match the coordinates in the linked sequence.
-
-
+
-
-
{{ dbName }} identifier
+
+ {{ dbName }} identifier
+
+
{{
+ validationErrors[`targetGenes.${targetIdx}.targetGene.externalIdentifiers.${dbName}.identifier.identifier`]
+ }}
+
+
+ Offset
+
+ {{ validationErrors[`targetGenes.${targetIdx}.targetGene.externalIdentifiers.${dbName}.offset`] }}
-
- Offset
-
{{ validationErrors[`targetGene.${targetIdx}.externalIdentifiers.${dbName}`] }}
- {{
- validationErrors[`targetGene.${targetIdx}.externalIdentifiers.${dbName}.identifier`]
- }}
- {{ validationErrors[`targetGene.${targetIdx}.externalIdentifiers.${dbName}.offset`] }} {{ validationErrors[`targetGenes.${targetIdx}.targetGene.externalIdentifiers.${dbName}`] }}
@@ -942,7 +918,7 @@
-
+
Taxonomy
-
+
{{ validationErrors[`targetGene.${targetIdx}.targetSequence.taxonomy`] }} {{ validationErrors[`targetGenes.${targetIdx}.targetGene.targetSequence.taxonomy`] }}
The sequence type of the target
-
+
+
{{ validationErrors[`targetGene.${targetIdx}.targetSequence.sequenceType`] }} {{ validationErrors[`targetGenes.${targetIdx}.targetGene.targetSequence.sequenceType`] }}
@@ -1002,7 +978,7 @@
-
+
-
+
{{ validationErrors[`targetGene.${targetIdx}.targetSequence.sequence`] }} {{ validationErrors[`targetGenes.${targetIdx}.targetGene.targetSequence.sequence`] }}
@@ -1060,8 +1036,8 @@
describe variants relative to a RefSeq or Ensembl accession representing a gene.
-
-
+ The assembly for this accession
-
+
- Assembly
-
+
{{ validationErrors[`targetGene.${targetIdx}.targetAccession.assembly`] }} {{ validationErrors[`targetGenes.${targetIdx}.targetGene.targetAccession.assembly`] }}
@@ -1103,8 +1079,8 @@
The gene name for this accession
-
-
+ HGNC Name
-
+
{{ validationErrors[`targetGene.${targetIdx}.targetAccession.gene`] }} {{ validationErrors[`targetGenes.${targetIdx}.targetGene.targetAccession.gene`] }}
@@ -1137,7 +1113,7 @@
-
+
Accession Identifier
-
+
{{ validationErrors[`targetGene.${targetIdx}.targetAccession.accession`] }} {{ validationErrors[`targetGenes.${targetIdx}.targetGene.targetAccession.accession`] }}
The genetic category of the target
-
-
-
+
+
- {{
- validationErrors[`targetGene.${targetIdx}.category`]
+ {{
+ validationErrors[`targetGenes.${targetIdx}.targetGene.category`]
}}
@@ -1215,8 +1189,8 @@
variants.
-
-
+
-
+
Drop a file here.
-
+
{{
validationErrors.scoresFile
}}
@@ -1312,7 +1289,7 @@
-
+
Drop a file here.
-
+
{{
validationErrors.scoreColumnsMetadataFile
}}
@@ -1348,7 +1325,7 @@
-
+
Drop a file here.
-
+
{{
validationErrors.countsFile
}}
@@ -1381,7 +1361,7 @@
-
+
Drop a file here.
-
+
{{
validationErrors.countColumnsMetadataFile
}}
@@ -1436,11 +1416,11 @@ import _ from 'lodash'
import {marked} from 'marked'
import AutoComplete from 'primevue/autocomplete'
import Button from 'primevue/button'
-import Chips from 'primevue/chips'
-import Dropdown from 'primevue/dropdown'
+import Select from 'primevue/select'
import FileUpload from 'primevue/fileupload'
+import FloatLabel from 'primevue/floatlabel'
import InputNumber from 'primevue/inputnumber'
-import InputSwitch from 'primevue/inputswitch'
+import ToggleSwitch from 'primevue/toggleswitch'
import InputText from 'primevue/inputtext'
import Message from 'primevue/message'
import Multiselect from 'primevue/multiselect'
@@ -1512,13 +1492,13 @@ export default {
AutoComplete,
Button,
CalibrationEditor,
- Chips,
DefaultLayout,
- Dropdown,
+ Select,
EmailPrompt,
FileUpload,
+ FloatLabel,
InputNumber,
- InputSwitch,
+ ToggleSwitch,
InputText,
Message,
Multiselect,
@@ -1658,45 +1638,56 @@ export default {
externalGeneDatabases,
validationErrors: {},
+ // File upload states - reactive replacements for refs
+ scoresFileCount: 0,
+ countsFileCount: 0,
+ scoreColumnsMetadataFileCount: 0,
+ countColumnsMetadataFileCount: 0,
+
isTargetSequence: true,
isBaseEditor: false,
isMultiTarget: false,
investigatorIsProvidingScoreCalibrations: false,
- // track this separately, since it is a pain to reconstruct steps from target paths (targetGenes.**step**.rest.of.error.path)
- minTargetGeneStepWithError: Infinity,
-
/** The currently active step. */
activeWizardStep: 1,
/** The highest step that the user has entered. This can be used to prevent the user from jumping ahead. */
maxWizardStepEntered: 1,
-
- stepFields: [
- ['experiment', 'supersededScoreSetUrn', 'metaAnalyzesScoreSetUrns'],
- [
- 'title',
- 'shortDescription',
- 'methodText',
- 'abstractText',
- 'publicationIdentifiers',
- 'primaryPublicationIdentifiers',
- 'extraMetadata',
- 'dataUsagePolicy'
- ],
- ['targets'],
- ['targetGene'],
- ['scoreCalibrations'],
- ['scoresFile', 'countsFile', 'scoreColumnsMetadataFile', 'countColumnsMetadataFile']
- ]
}),
computed: {
+ numSteps: function() {
+ return 5 + this.numTargets
+ },
+
+ stepFields: function() {
+ const fields = {
+ 1: ['experiment', 'supersededScoreSetUrn', 'metaAnalyzesScoreSetUrns'],
+ 2: [
+ 'title',
+ 'shortDescription',
+ 'methodText',
+ 'abstractText',
+ 'publicationIdentifiers',
+ 'primaryPublicationIdentifiers',
+ 'extraMetadata',
+ 'dataUsagePolicy'
+ ],
+ 3: ['targets']
+ }
+ for (let i = 0; i < this.numTargets; i++) {
+ fields[4 + i] = [`targetGenes.${i}.targetGene`]
+ }
+ fields[4 + this.numTargets] = ['scoreCalibrations']
+ fields[5 + this.numTargets] = ['scoresFile', 'countsFile', 'scoreColumnsMetadataFile', 'countColumnsMetadataFile']
+ return fields
+ },
+
maxWizardStepValidated: function () {
- const numSteps = 5 + this.numTargets
- // This yields the index of the maximum step validated, -1 if step 0 is not valid, and -2 if all steps are valid.
- const maxStepValidated = _.findIndex(_.range(0, numSteps), (step) => !this.validateWizardStep(step)) - 1
- return maxStepValidated == -2 ? numSteps - 1 : maxStepValidated + 1
+ // This yields the value of maximum step validated, 0 if step 1 is not valid.
+ const firstUnvalidatedStep = _.find(_.range(1, this.numSteps + 1), (step) => !this.validateWizardStep(step))
+ return firstUnvalidatedStep ? firstUnvalidatedStep - 1 : this.numSteps
},
targetGeneIdentifierSuggestionsList: function () {
@@ -1765,20 +1756,6 @@ export default {
}
}
},
- 'targetGene.externalIdentifiers': {
- deep: true,
- handler: function (newValue) {
- if (!newValue) {
- return
- }
- // If an identifier has been set, set the offset to 0 by default.
- for (const dbName of externalGeneDatabases) {
- if (newValue[dbName]?.identifier?.identifier != null && newValue[dbName]?.offset == null) {
- this.targetGene.externalIdentifiers[dbName].offset = 0
- }
- }
- }
- },
existingTargetGene: {
immediate: true,
handler: function () {
@@ -1824,8 +1801,16 @@ export default {
handler: function (newValue, oldValue) {
if (newValue.length == 1) {
this.primaryPublicationIdentifiers = newValue
- } else if (newValue.length == 0 || (newValue.length > 1 && oldValue.length == 1)) {
- // Clear primary publication if we have just added a second ID, or if we have deleted all IDs.
+ } else if (
+ newValue.length == 0 ||
+ (newValue.length > 1 && oldValue.length == 1) ||
+ (this.primaryPublicationIdentifiers.length > 0 &&
+ !newValue
+ .map((pi) => pi.identifier)
+ .includes(this.primaryPublicationIdentifiers[0].identifier))
+ ) {
+ // Clear primary publication if we have just added a second ID, or if we have deleted all IDs,
+ // or if the primary publication is no longer in the list of publications.
this.primaryPublicationIdentifiers = []
}
}
@@ -1857,11 +1842,11 @@ export default {
if (this.createdTargetGenes.length < this.numTargets) {
for (let i = this.createdTargetGenes.length; i < this.numTargets; i++) {
this.createdTargetGenes.push(emptyTargetGeneWizardObj())
- this.stepFields.splice(3, 0, ['targetGene'])
+ // this.stepFields.splice(3, 0, ['targetGene'])
}
} else if (this.createdTargetGenes.length > this.numTargets) {
this.createdTargetGenes = this.createdTargetGenes.slice(0, this.numTargets)
- this.stepFields.splice(3, oldValue - newValue)
+ // this.stepFields.splice(3, oldValue - newValue)
}
}
}
@@ -1872,16 +1857,16 @@ export default {
},
methods: {
+ clearAutoCompleteInput: function(event) {
+ if (event.target) {
+ event.target.value = ''
+ }
+ },
+
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// Contributors
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////
- clearContributorSearch: function () {
- // This could change with a new PrimeVue version.
- const input = this.$refs.contributorsInput
- input.$refs.input.value = ''
- },
-
lookupOrcidUser: async function (orcidId) {
let orcidUser = null
try {
@@ -1892,8 +1877,20 @@ export default {
return orcidUser
},
- newContributorsAdded: async function (event) {
- const newContributors = event.value
+ updateContributors: function (event) {
+ const currentValue = event.target?.value
+ if (currentValue && currentValue.trim() != '') {
+ this.contributors.push(currentValue.trim())
+ this.newContributorsAdded()
+
+ // clear the input field
+ event.target.value = ''
+ }
+ },
+
+ newContributorsAdded: async function () {
+ // new contributor values are those that are strings rather than objects
+ const newContributors = this.contributors.filter(_.isString)
// Convert any strings to ORCID users without names. Remove whitespace from new entries.
this.contributors = this.contributors.map((c) => (_.isString(c) ? {orcidId: c.trim()} : c))
@@ -1941,7 +1938,7 @@ export default {
validateWizardStep: function (step) {
// Later, this may depend on server-side validation.
switch (true) {
- case step == 0: {
+ case step == 1: {
// Step 0 is valid if
// - The score set is a meta-analysis and at least one meta-analyzed score set has been chosen..
// - The score set is a superseding score set, and the superseded score set has been chosen.
@@ -1952,14 +1949,14 @@ export default {
!!((!this.isMetaAnalysis && !this.isSupersedingScoreSet && this.experiment) || this.experimentUrn)
)
}
- case step == 1: {
+ case step == 2: {
return this.title && this.shortDescription && this.abstractText && this.methodText
}
- case step == 2: {
+ case step == 3: {
return this.numTargets > 0
}
- case step > 2 && step < 3 + this.numTargets: {
- const currentTargetGene = this.createdTargetGenes[step - 3].targetGene
+ case step > 3 && step <= (3 + this.numTargets): {
+ const currentTargetGene = this.createdTargetGenes[step - 4].targetGene
if (this.isTargetSequence) {
return (
currentTargetGene.name &&
@@ -1978,7 +1975,7 @@ export default {
)
}
}
- case step == 3 + this.numTargets: {
+ case step == 4 + this.numTargets: {
if (!this.investigatorIsProvidingScoreCalibrations) {
return true
}
@@ -2007,23 +2004,15 @@ export default {
},
minStepWithError: function () {
- const numSteps = this.stepFields.length
- for (let i = 0; i < numSteps; i++) {
+ for (let i = 1; i <= this.numSteps; i++) {
if (this.wizardStepHasError(i)) {
- // errors in the target creation step
- if (i > 2 && i < 3 + this.numTargets) {
- return this.minTargetGeneStepWithError + 3
- }
return i
}
}
- return numSteps - 1
+ return this.numSteps
},
wizardStepHasError: function (step) {
- if (step >= this.stepFields.length) {
- return false
- }
return !this.stepFields[step].every((field) => {
for (const v of Object.keys(this.validationErrors)) {
if (v.startsWith(field)) {
@@ -2245,7 +2234,18 @@ export default {
this.externalIdentifierTextToObject(dbName, targetIdx, event)
},
- acceptNewDoiIdentifier: function () {
+ updateDoiIdentifiers: function (event) {
+ const currentValue = event.target?.value
+ if (currentValue && currentValue.trim() != '') {
+ this.doiIdentifiers.push(currentValue.trim())
+ this.newDoiIdentifiersAdded()
+
+ // clear the input field
+ event.target.value = ''
+ }
+ },
+
+ newDoiIdentifiersAdded: function () {
// Remove new string item from the model and add new structured item in its place if it validates and is not a duplicate.
const idx = this.doiIdentifiers.findIndex((item) => typeof item === 'string' || item instanceof String)
if (idx == -1) {
@@ -2286,19 +2286,6 @@ export default {
}
},
- removePublicationIdentifier: function (value) {
- const removedIdentifier = value.identifier
- const publicationIdx = this.publicationIdentifiers.findIndex((pub) => pub.identifier == removedIdentifier)
- if (publicationIdx != -1) {
- this.publicationIdentifiers.splice(publicationIdx, 1)
- }
- // If we are removing a primary publication identifier, also remove it from that list.
- const primaryIdx = this.primaryPublicationIdentifiers.findIndex((pub) => pub.identifier == removedIdentifier)
- if (primaryIdx != -1) {
- this.primaryPublicationIdentifiers.splice(primaryIdx, 1)
- }
- },
-
removeContributor: function (contributor) {
const index = this.contributors.findIndex(c => c.orcidId === contributor.orcidId)
if (index !== -1) {
@@ -2312,12 +2299,6 @@ export default {
}
},
- clearPublicationIdentifierSearch: function () {
- // This could change with a new Primevue version.
- const input = this.$refs.publicationIdentifiersInput
- input.$refs.focusInput.value = ''
- },
-
searchPublicationIdentifiers: function (event) {
const searchText = (event.query || '').trim()
if (searchText.length > 0) {
@@ -2405,6 +2386,9 @@ export default {
},
fileCleared: function (inputName) {
+ // Update reactive file counts
+ this.updateFileCount(inputName, 0)
+
if (inputName == 'extraMetadataFile') {
this.extraMetadata = null
delete this.clientSideValidationErrors.extraMetadata
@@ -2421,6 +2405,23 @@ export default {
this.mergeValidationErrors()
},
+ updateFileCount: function (inputName, count) {
+ switch (inputName) {
+ case 'scoresFile':
+ this.scoresFileCount = count
+ break
+ case 'countsFile':
+ this.countsFileCount = count
+ break
+ case 'scoreColumnsMetadataFile':
+ this.scoreColumnsMetadataFileCount = count
+ break
+ case 'countColumnsMetadataFile':
+ this.countColumnsMetadataFileCount = count
+ break
+ }
+ },
+
validateJsonObject: function (data, fieldName) {
if (!_.isObject(data) || _.isArray(data)) {
this.clientSideValidationErrors[fieldName] =
@@ -2432,6 +2433,10 @@ export default {
fileSelected: async function (inputName, event, targetIdx) {
const file = event.files[0]
+
+ // Update reactive file counts
+ this.updateFileCount(inputName, event.files.length)
+
if (file) {
const text = await file.text()
switch (inputName) {
@@ -2487,19 +2492,19 @@ export default {
}))
if (fastaData.length == 0) {
this.createdTargetGenes[targetIdx].targetGene.targetSequence.sequence = null
- this.clientSideValidationErrors['targetGene.targetSequence.sequence'] =
+ this.clientSideValidationErrors[`targetGenes.${targetIdx}.targetGene.targetSequence.sequence`] =
'The FASTA file contains no sequences.'
} else if (fastaData.length > 1) {
this.createdTargetGenes[targetIdx].targetGene.targetSequence.sequence = null
- this.clientSideValidationErrors['targetGene.targetSequence.sequence'] =
+ this.clientSideValidationErrors[`targetGenes.${targetIdx}.targetGene.targetSequence.sequence`] =
'The FASTA file contains more than one sequence.'
} else {
this.createdTargetGenes[targetIdx].targetGene.targetSequence.sequence = fastaData[0].sequence
- delete this.clientSideValidationErrors['targetGene.targetSequence.sequence']
+ delete this.clientSideValidationErrors[`targetGenes.${targetIdx}.targetGene.targetSequence.sequence`]
}
} catch (e) {
this.createdTargetGenes[targetIdx].targetGene.targetSequence.sequence = null
- this.clientSideValidationErrors['targetGene.targetSequence.sequence'] =
+ this.clientSideValidationErrors[`targetGenes.${targetIdx}.targetGene.targetSequence.sequence`] =
'The file was not a valid FASTA file.'
console.log('Reference sequence file was not a valid FASTA file.')
}
@@ -2600,6 +2605,8 @@ export default {
)
)
+ console.log('Preparing to save target genes:', this.createdTargetGenes)
+
const editedFields = {
experimentUrn: this.experimentUrn ? this.experimentUrn : this.experiment?.urn,
title: this.title,
@@ -2621,7 +2628,7 @@ export default {
scoreCalibrations: this.investigatorIsProvidingScoreCalibrations ? [this.calibrationCreateDraft.value] : [],
- targetGenes: this.createdTargetGenes.map((target) => {
+ targetGenes: _.cloneDeep(this.createdTargetGenes).map((target) => {
const targetGene = {
name: target.targetGene.name,
category: target.targetGene.category,
@@ -2631,8 +2638,13 @@ export default {
}
for (const [db, linked] of Object.entries(target.linkedAccessions)) {
+ console.log('Processing linked accession:', db, linked)
if (linked) {
- targetGene.externalIdentifiers.push(target.targetGene.externalIdentifiers[db])
+ const targetGeneExternalIdentifier = _.clone(target.targetGene.externalIdentifiers[db])
+ if (!targetGeneExternalIdentifier.identifier) {
+ targetGeneExternalIdentifier.identifier = {dbName: db}
+ }
+ targetGene.externalIdentifiers.push(targetGeneExternalIdentifier)
}
}
@@ -2684,7 +2696,7 @@ export default {
path = path.slice(1)
}
- let customPath = error.ctx.error.custom_loc
+ let customPath = error.ctx?.error?.custom_loc
if (customPath) {
if (customPath[0] == 'body') {
customPath = customPath.slice(1)
@@ -2695,9 +2707,7 @@ export default {
path = path.concat(customPath)
}
- if (_.isEqual(_.slice(path, 0, 1), ['targetGene'])) {
- this.minTargetGeneStepWithError = Math.min(this.minTargetGeneStepWithError, path[1])
-
+ if (_.isEqual(_.first(path), 'targetGenes') && path.length >= 2) {
// Map errors on indexed external gene identifiers to inputs named for the identifier's database.
if (_.isEqual(_.slice(path, 2, 3), ['externalIdentifiers'])) {
const identifierIndex = path[3]
@@ -2706,12 +2716,14 @@ export default {
// preferable to not displaying the error.
path.splice(
3,
- 2,
+ 1,
identifierOffset?.identifier?.dbName
? identifierOffset.identifier.dbName
: this.externalGeneDatabases[identifierIndex]
)
}
+ // insert 'targetGene' after the targetGenes index to match the form's data structure
+ path.splice(2, 0, 'targetGene')
}
// Add calibration errors to a separate object which is consumed by the calibration sub-component.
@@ -2734,12 +2746,12 @@ export default {
},
uploadData: async function (scoreSet) {
- if (this.$refs.scoresFileUpload.files.length != 1) {
+ if (this.scoresFileCount !== 1) {
this.validationErrors = {scores: 'Required'}
} else {
const formData = new FormData()
formData.append('scores_file', this.$refs.scoresFileUpload.files[0])
- if (this.$refs.countsFileUpload.files.length == 1) {
+ if (this.countsFileCount === 1) {
formData.append('counts_file', this.$refs.countsFileUpload.files[0])
}
if (this.scoreColumnsMetadata) {
@@ -2780,8 +2792,8 @@ export default {
validateAndSave: async function () {
this.clientSideValidationErrors = {}
- const hasScoresFile = this.$refs.scoresFileUpload.files.length == 1
- const hasCountsFile = this.$refs.countsFileUpload.files.length == 1
+ const hasScoresFile = this.scoresFileCount === 1
+ const hasCountsFile = this.countsFileCount === 1
if (hasCountsFile && !hasScoresFile) {
this.clientSideValidationErrors.scoresFile = 'Required'
}
@@ -2920,7 +2932,7 @@ export default {
}
/* Switches */
-.p-inputswitch {
+.p-ToggleSwitch {
margin: 10px 0;
vertical-align: middle;
}
diff --git a/src/components/screens/ScoreSetEditor.vue b/src/components/screens/ScoreSetEditor.vue
index 53a601c7..f83785f2 100644
--- a/src/components/screens/ScoreSetEditor.vue
+++ b/src/components/screens/ScoreSetEditor.vue
@@ -11,8 +11,8 @@
Edit score set {{ item.urn }}
Save changes
- Reset
- Cancel
+ Reset
+ Cancel
-
-
+ Experiment
-
+
{{
validationErrors.experiment
}}
@@ -62,17 +62,17 @@
Score set information
-
+
Title
-
+
{{ validationErrors.title }}
-
+
Short description
-
+
{{
validationErrors.shortDescription
}}
@@ -85,10 +85,10 @@
-
+
Abstract
-
+
@@ -108,10 +108,10 @@
-
+
Methods
-
+
@@ -124,38 +124,29 @@
}}
-
-
+
-
-
-
- {{ slotProps.value.givenName }} {{ slotProps.value.familyName }} ({{
- slotProps.value.orcidId
- }})
-
-
{{ slotProps.value.orcidId }}
-
-
+ fluid
+ multiple
+ :option-label="(x) => x.givenName || x.familyName ? `${x.givenName} ${x.familyName} (${x.orcidId})` : x.orcidId"
+ :typeahead="false"
+ @blur="updateContributors"
+ @keyup.escape="clearAutoCompleteInput"
+ @keyup.space="updateContributors"
+ @update:model-value="newContributorsAdded"
+ />
Contributors
-
+
{{
validationErrors.contributors
}}
-
-
+ License
-
+
{{
validationErrors.licenseId
}}
@@ -183,53 +174,38 @@
-
-
+
-
-
-
{{ slotProps.value.identifier }}
-
-
-
-
+ :multiple="true"
+ option-label="identifier"
+ :typeahead="false"
+ @blur="updateDoiIdentifiers"
+ @keyup.escape="clearAutoCompleteInput"
+ @keyup.space="updateDoiIdentifiers"
+ @update:model-value="newDoiIdentifiersAdded"
+ />
DOIs
-
+
{{
validationErrors.doiIdentifiers
}}
-
+
-
-
-
Title: {{ slotProps.option.title }}
@@ -240,16 +216,15 @@
Publication identifiers
-
+
{{
validationErrors.publicationIdentifiers
}}
-
+
Primary publication
-
+
{{
validationErrors.primaryPublicationIdentifiers
}}
-
- Some fields were autopopulated based on the selected experiment and should be inspected to ensure they
- are still relevant to this score set.
-
-
+
Extra metadata
@@ -314,16 +287,16 @@
Drop a JSON file here.
-
+
{{
validationErrors.extraMetadata
}}
-
+
Data usage policy
-
+
{{
validationErrors.dataUsagePolicy
}}
@@ -347,7 +320,7 @@
-
+
Copy from an existing target gene
-
+
-
+
Target name
-
+
-
+
Target label (only required when providing multiple targets)
-
+
-
+
+
-
+
{{ dbName }} identifier
-
+
-
+
Offset
-
+
-
+
Taxonomy
-
+
{{
validationErrors['targetGene.targetSequence.taxonomy']
}}
-
+
Drop a FASTA file here.
-
+
-
+
+
@@ -508,30 +480,30 @@
-
+
Target gene name
-
+
-
+
- Assembly
-
+
-
-
+ HGNC Name
-
+
-
- Autocomplete By:
+
+ Autocomplete By:
+
+
Accession/Transcript Identifier
-
+
-
+
+
@@ -761,8 +730,8 @@
-
-
+
+ {{
isBaseEditor
? 'This score set represents base editor data.'
@@ -796,7 +765,7 @@
Load a scores file and an optional counts file:
-
+
Drop a file here.
-
+
{{
validationErrors.scoresFile
}}
-
+
Scores column metadata
@@ -854,13 +825,13 @@
Drop a JSON file here.
-
+
{{
validationErrors.scoreColumnsMetadataFile
}}
-
+
Drop a file here.
-
+
{{
validationErrors.countsFile
}}
-
+
Counts column metadata
@@ -918,7 +891,7 @@
Drop a JSON file here.
-
+
{{
validationErrors.countColumnsMetadataFile
}}
@@ -952,14 +925,14 @@ import {marked} from 'marked'
import AutoComplete from 'primevue/autocomplete'
import Button from 'primevue/button'
import Card from 'primevue/card'
-import Chips from 'primevue/chips'
import Column from 'primevue/column'
import DataTable from 'primevue/datatable'
-import Dropdown from 'primevue/dropdown'
+import Select from 'primevue/select'
import FileUpload from 'primevue/fileupload'
+import FloatLabel from 'primevue/floatlabel'
import InputNumber from 'primevue/inputnumber'
import InputText from 'primevue/inputtext'
-import InputSwitch from 'primevue/inputswitch'
+import ToggleSwitch from 'primevue/toggleswitch'
import Message from 'primevue/message'
import Multiselect from 'primevue/multiselect'
import ProgressSpinner from 'primevue/progressspinner'
@@ -1015,17 +988,17 @@ export default {
AutoComplete,
Button,
Card,
- Chips,
Column,
DataTable,
DefaultLayout,
- Dropdown,
+ Select,
EmailPrompt,
EntityLink,
FileUpload,
+ FloatLabel,
InputNumber,
InputText,
- InputSwitch,
+ ToggleSwitch,
Message,
Multiselect,
ProgressSpinner,
@@ -1307,6 +1280,17 @@ export default {
this.assemblySuggestions = await this.fetchTargetAccessionsByAssembly(this.assemblyDropdownValue)
}
}
+ },
+ publicationIdentifiers: function () {
+ // If the primary publication is no longer in the list of publications, clear it.
+ if (
+ this.primaryPublicationIdentifiers.length > 0 &&
+ !this.publicationIdentifiers
+ .map((pi) => pi.identifier)
+ .includes(this.primaryPublicationIdentifiers[0].identifier)
+ ) {
+ this.primaryPublicationIdentifiers = []
+ }
}
},
@@ -1315,16 +1299,16 @@ export default {
},
methods: {
+ clearAutoCompleteInput: function(event) {
+ if (event.target) {
+ event.target.value = ''
+ }
+ },
+
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// Contributors
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////
- clearContributorSearch: function () {
- // This could change with a new PrimeVue version.
- const input = this.$refs.contributorsInput
- input.$refs.input.value = ''
- },
-
lookupOrcidUser: async function (orcidId) {
let orcidUser = null
try {
@@ -1335,8 +1319,20 @@ export default {
return orcidUser
},
- newContributorsAdded: async function (event) {
- const newContributors = event.value
+ updateContributors: function (event) {
+ const currentValue = event.target?.value
+ if (currentValue && currentValue.trim() != '') {
+ this.contributors.push(currentValue.trim())
+ this.newContributorsAdded()
+
+ // clear the input field
+ event.target.value = ''
+ }
+ },
+
+ newContributorsAdded: async function () {
+ // new contributor values are those that are strings rather than objects
+ const newContributors = this.contributors.filter(_.isString)
// Convert any strings to ORCID users without names. Remove whitespace from new entries.
this.contributors = this.contributors.map((c) => (_.isString(c) ? {orcidId: c.trim()} : c))
@@ -1539,7 +1535,18 @@ export default {
})
},
- acceptNewDoiIdentifier: function () {
+ updateDoiIdentifiers: function (event) {
+ const currentValue = event.target?.value
+ if (currentValue && currentValue.trim() != '') {
+ this.doiIdentifiers.push(currentValue.trim())
+ this.newDoiIdentifiersAdded()
+
+ // clear the input field
+ event.target.value = ''
+ }
+ },
+
+ newDoiIdentifiersAdded: function () {
// Remove new string item from the model and add new structured item in its place if it validates and is not a duplicate.
const idx = this.doiIdentifiers.findIndex((item) => typeof item === 'string' || item instanceof String)
if (idx == -1) {
@@ -1593,19 +1600,6 @@ export default {
}
},
- removePublicationIdentifier: function (value) {
- const removedIdentifier = value.identifier
- const publicationIdx = this.publicationIdentifiers.findIndex((pub) => pub.identifier == removedIdentifier)
- if (publicationIdx != -1) {
- this.publicationIdentifiers.splice(publicationIdx, 1)
- }
- // If we are removing a primary publication identifier, also remove it from that list.
- const primaryIdx = this.primaryPublicationIdentifiers.findIndex((pub) => pub.identifier == removedIdentifier)
- if (primaryIdx != -1) {
- this.primaryPublicationIdentifiers.splice(primaryIdx, 1)
- }
- },
-
clearPublicationIdentifierSearch: function () {
// This could change with a new Primevue version.
const input = this.$refs.publicationIdentifiersInput
diff --git a/src/components/screens/ScoreSetView.vue b/src/components/screens/ScoreSetView.vue
index 692b0b3a..ca7a5949 100644
--- a/src/components/screens/ScoreSetView.vue
+++ b/src/components/screens/ScoreSetView.vue
@@ -17,26 +17,26 @@
Add calibration
- Edit
- Publish
- Edit
+ Publish
+ Delete
- Edit
+ Edit
@@ -44,7 +44,7 @@
Download files and/or charts
-
Scores
+
Scores
- Counts
+ Counts
- Metadata
+ Metadata
-
Mapped Variants
+
Mapped Variants
-
Histogram
+
Histogram
- Heatmap
+ Heatmap
-
Custom Data
+
Custom Data
{{ dataOption.label }}
- Download
- Cancel
+ Cancel
@@ -225,11 +226,11 @@
Send files to
Galaxy
-
Scores
+
Scores
- Counts
+ Counts
-
Mapped Variants Mapped Variants
@@ -304,7 +305,7 @@
External identifier
DOI:
-
+
{{ doi.identifier }}
@@ -313,7 +314,7 @@
No associated DOIs
Raw reads:
-
-
+
@@ -419,12 +420,13 @@ import AutoComplete from 'primevue/autocomplete'
import Button from 'primevue/button'
import Checkbox from 'primevue/checkbox'
import Dialog from 'primevue/dialog'
+import FloatLabel from 'primevue/floatlabel'
import ToggleSwitch from 'primevue/toggleswitch'
import ProgressSpinner from 'primevue/progressspinner'
import ProgressBar from 'primevue/progressbar'
import PrimeDialog from 'primevue/dialog'
import ScrollPanel from 'primevue/scrollpanel'
-import Sidebar from 'primevue/sidebar'
+import Drawer from 'primevue/drawer'
import SplitButton from 'primevue/splitbutton'
import {ref} from 'vue'
import {mapState} from 'vuex'
@@ -473,6 +475,7 @@ export default {
CollectionBadge,
DefaultLayout,
Dialog,
+ FloatLabel,
ToggleSwitch,
ItemNotFound,
PageLoading,
@@ -486,7 +489,7 @@ export default {
ScoreSetProcessingStatus,
ScoreSetSecondaryMetadata,
ScrollPanel,
- Sidebar,
+ Drawer,
SplitButton,
TargetGene
},
@@ -1248,11 +1251,6 @@ export default {
column-gap: 0.5em;
}
-.p-float-label {
- display: flex;
- width: 100%;
-}
-
/* Histogram */
.mavedb-score-set-histogram-pane {
@@ -1336,29 +1334,6 @@ export default {
content: '';
clear: both;
}
-
-.mavedb-help-tooltip-button {
- height: 0.5rem !important;
- width: 0.5rem !important;
- vertical-align: middle;
- /* Remove extra vertical margin/padding if any. */
- margin-top: 0;
- margin-bottom: 0;
- /* Ensure that button is inline with text. */
- display: inline-flex;
- align-items: center;
- background: none;
-}
-
-.mavedb-help-tooltip-button:focus,
-.mavedb-help-tooltip-button:active,
-.mavedb-help-tooltip-button.p-focus {
- background: none;
-}
-
-.mavedb-help-tooltip-button:deep(.p-button-icon) {
- font-size: 0.5rem;
-}
{{ admin.firstName }} {{ admin.lastName }}