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Updating instances of ingest_metadata.metadata and ingest_metadata.fi… #1712

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Updating instances of ingest_metadata.metadata and ingest_metadata.fi… #1712

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7e2e973
Updating instances of ingest_metadata.metadata and ingest_metadata.fi…
maxsibilla Oct 25, 2024
043c5a6
Pulling latest changes from main
maxsibilla Dec 6, 2024
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14 changes: 3 additions & 11 deletions src/components/custom/entities/Metadata.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ function Metadata({data, metadata, mappedMetadata, groups}) {
if (!downloadRef.current) {
return
}

if (!downloadRef.current.href) {
// This is a bit of a hack to lazy download the provenance metadata
try {
Expand Down Expand Up @@ -161,7 +161,7 @@ function Metadata({data, metadata, mappedMetadata, groups}) {
}
// The dataset nav link
} else if (eq(ancestor.entity_type, cache.entities.dataset)) {
if (ancestor.ingest_metadata && Object.keys(ancestor.ingest_metadata).length && 'metadata' in ancestor.ingest_metadata) {
if (ancestor.metadata && Object.keys(ancestor.metadata).length > 0) {
return (
popoverCommon(index, 'dataset', ancestor)
)
Expand Down Expand Up @@ -208,18 +208,10 @@ function Metadata({data, metadata, mappedMetadata, groups}) {
tabPaneCommon('0', index, ancestor, metadata, undefined, groups)
)
}
} else if (!eq(ancestor.entity_type, cache.entities.dataset) && ancestor.metadata && Object.keys(ancestor.metadata).length > 0) {
// Handle mouse source and sample table
// Mice sources and all samples have their metadata inside "metadata"
} else if ( ancestor.metadata && Object.keys(ancestor.metadata).length > 0) {
return (
tabPaneCommon('1', index, ancestor, ancestor.metadata, ancestor.cedar_mapped_metadata)
)
} else if (ancestor.ingest_metadata && Object.keys(ancestor.ingest_metadata).length && 'metadata' in ancestor.ingest_metadata) {
// Handle dataset table
// Datasets have their metadata inside "metadata.metadata"
return (
tabPaneCommon('2', index, ancestor, ancestor.ingest_metadata.metadata, ancestor.cedar_mapped_metadata)
)
}
})}
</Tab.Content>
Expand Down
18 changes: 5 additions & 13 deletions src/components/custom/entities/dataset/FileTreeView.jsx
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Expand Up @@ -15,7 +15,7 @@ import InputGroup from 'react-bootstrap/InputGroup';
import {Tree} from 'primereact/tree';
import 'primeicons/primeicons.css';

export const FileTreeView = ({data, selection = {}, keys = {files: 'ingest_metadata', uuid: 'uuid'},
export const FileTreeView = ({data, selection = {}, keys = {files: 'files', uuid: 'uuid'},
loadDerived = true, treeViewOnly = false, className = '', filesClassName = '',
showQAButton = true, showDataProductButton = true, includeDescription= false,
showDownloadAllButton = false}) => {
Expand Down Expand Up @@ -45,14 +45,6 @@ export const FileTreeView = ({data, selection = {}, keys = {files: 'ingest_metad
return Array.isArray(obj) ? obj.length : Object.keys(obj).length
}

const getFiles = (data) => {
if (keys.files.contains('ingest_metadata')) {
return data?.ingest_metadata?.files
} else {
return data[keys.files]
}
}

useEffect( () => {
async function fetchData() {
await fetch_globus_filepath(data[keys.uuid]).then((globusData) => {
Expand All @@ -64,17 +56,17 @@ export const FileTreeView = ({data, selection = {}, keys = {files: 'ingest_metad
fetchData()

//Default to use files, otherwise wait until derivedDataset is populated
if (getFiles(data) && getLength(getFiles(data))) {
if (data[keys.files] && getLength(data[keys.files])) {
setHasData(true)
buildTree(data[keys.uuid], getFiles(data))
buildTree(data[keys.uuid], data[keys.files])
}
}, [])

useEffect(() => {
if (loadDerived) {
if (isPrimaryDataset && getFiles(derivedDataset) && getLength(getFiles(derivedDataset))) {
if (isPrimaryDataset && derivedDataset[keys.files] && getLength(derivedDataset[keys.files])) {
setHasData(true)
buildTree(derivedDataset[keys.uuid], getFiles(derivedDataset))
buildTree(derivedDataset[keys.uuid], derivedDataset[keys.files])
}
}

Expand Down
2 changes: 1 addition & 1 deletion src/components/custom/vitessce/VignetteList.jsx
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Expand Up @@ -15,7 +15,7 @@ function VignetteList({ publication, ancillaryPublication }) {
const fetchVignettesData = async (uuid) => {
log.debug('==== Fetching vignettes data')
// ancillaryPublication should have a json config file
const fileName = ancillaryPublication.ingest_metadata.files[0].rel_path
const fileName = ancillaryPublication.files[0].rel_path
const path = `${uuid}/${fileName}`
const publicationAncillaryConfig = await getJSONFromAssetsEndpoint(path)

Expand Down
36 changes: 18 additions & 18 deletions src/config/search/metadata.js
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Expand Up @@ -437,60 +437,60 @@ export const SEARCH_METADATA = {
},

// Dataset
'ingest_metadata.metadata.acquisition_instrument_model': {
'metadata.acquisition_instrument_model': {
label: 'Acquisition Instrument Model',
type: 'value',
field: 'ingest_metadata.metadata.acquisition_instrument_model.keyword',
field: 'metadata.acquisition_instrument_model.keyword',
isExpanded: false,
filterType: 'any',
isFilterable: false,
facetType: 'term',
isAggregationActive: doesTermFilterContainValues('entity_type', ['Dataset']),
isFacetVisible: doesAggregationHaveBuckets('ingest_metadata.metadata.acquisition_instrument_model')
isFacetVisible: doesAggregationHaveBuckets('metadata.acquisition_instrument_model')
},
'ingest_metadata.metadata.acquisition_instrument_vendor': {
'metadata.acquisition_instrument_vendor': {
label: 'Acquisition Instrument Vendor',
type: 'value',
field: 'ingest_metadata.metadata.acquisition_instrument_vendor.keyword',
field: 'metadata.acquisition_instrument_vendor.keyword',
isExpanded: false,
filterType: 'any',
isFilterable: false,
facetType: 'term',
isAggregationActive: doesTermFilterContainValues('entity_type', ['Dataset']),
isFacetVisible: doesAggregationHaveBuckets('ingest_metadata.metadata.acquisition_instrument_vendor')
isFacetVisible: doesAggregationHaveBuckets('metadata.acquisition_instrument_vendor')
},
'ingest_metadata.metadata.analyte_class': {
'metadata.analyte_class': {
label: 'Analyte Class',
type: 'value',
field: 'ingest_metadata.metadata.analyte_class.keyword',
field: 'metadata.analyte_class.keyword',
isExpanded: false,
filterType: 'any',
isFilterable: false,
facetType: 'term',
isAggregationActive: doesTermFilterContainValues('entity_type', ['Dataset']),
isFacetVisible: doesAggregationHaveBuckets('ingest_metadata.metadata.analyte_class')
isFacetVisible: doesAggregationHaveBuckets('metadata.analyte_class')
},
'ingest_metadata.metadata.assay_category': {
'metadata.assay_category': {
label: 'Assay Category',
type: 'value',
field: 'ingest_metadata.metadata.assay_category.keyword',
field: 'metadata.assay_category.keyword',
isExpanded: false,
filterType: 'any',
isFilterable: false,
facetType: 'term',
isAggregationActive: doesTermFilterContainValues('entity_type', ['Dataset']),
isFacetVisible: doesAggregationHaveBuckets('ingest_metadata.metadata.assay_category')
isFacetVisible: doesAggregationHaveBuckets('metadata.assay_category')
},
'ingest_metadata.metadata.operator': {
'metadata.operator': {
label: 'Operator',
type: 'value',
field: 'ingest_metadata.metadata.operator.keyword',
field: 'metadata.operator.keyword',
isExpanded: false,
filterType: 'any',
isFilterable: false,
facetType: 'term',
isAggregationActive: doesTermFilterContainValues('entity_type', ['Dataset']),
isFacetVisible: doesAggregationHaveBuckets('ingest_metadata.metadata.operator')
isFacetVisible: doesAggregationHaveBuckets('metadata.operator')
},
},
disjunctiveFacets: [],
Expand Down Expand Up @@ -599,7 +599,7 @@ export const SEARCH_METADATA = {
entityType: 'dataset',
queryString: searchUIQueryString([
{field: 'entity_type', values: ['Dataset'], type: 'any'},
{field: 'ingest_metadata.metadata.analyte_class', values: ['Nucleic acid and protein'], type: 'any'}
{field: 'metadata.analyte_class', values: ['Nucleic acid and protein'], type: 'any'}
])
},
{
Expand All @@ -608,7 +608,7 @@ export const SEARCH_METADATA = {
entityType: 'dataset',
queryString: searchUIQueryString([
{field: 'entity_type', values: ['Dataset'], type: 'any'},
{field: 'ingest_metadata.metadata.analyte_class', values: ['RNA'], type: 'any'}
{field: 'metadata.analyte_class', values: ['RNA'], type: 'any'}
])
},
{
Expand All @@ -617,7 +617,7 @@ export const SEARCH_METADATA = {
entityType: 'dataset',
queryString: searchUIQueryString([
{field: 'entity_type', values: ['Dataset'], type: 'any'},
{field: 'ingest_metadata.metadata.assay_category', values: ['sequence'], type: 'any'}
{field: 'metadata.assay_category', values: ['sequence'], type: 'any'}
])
},
],
Expand Down
6 changes: 3 additions & 3 deletions src/context/DerivedContext.jsx
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Expand Up @@ -149,15 +149,15 @@ export const DerivedProvider = ({children, showVitessceList, setShowVitessceList
if (datasetIs.processed(entity.creation_action)) {
const response = await fetch("/api/find?uuid=" + entity.uuid, getRequestHeaders())
const processed = await response.json()
if (processed.ingest_metadata && processed.ingest_metadata.files && processed.ingest_metadata.files.length) {
let dataProducts = filterFilesForDataProducts(processed.ingest_metadata.files, processed)
if (processed.files && processed.files.length) {
let dataProducts = filterFilesForDataProducts(processed.files, processed)
_files = _files.concat(dataProducts)
}
}
}
setDataProducts(_files)
} else {
_files = data.ingest_metadata?.files || []
_files = data?.files || []
setDataProducts(filterFilesForDataProducts(_files, data))

}
Expand Down
10 changes: 5 additions & 5 deletions src/pages/dataset.jsx
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Expand Up @@ -108,8 +108,8 @@ function ViewDataset() {
setCitationData(citation)

for (const ancestor of ancestry.ancestors) {
log.debug(ancestor)
if ((ancestor.metadata && Object.keys(ancestor.metadata).length) || (ancestor.ingest_metadata && Object.keys(ancestor.ingest_metadata) && 'metadata' in ancestor.ingest_metadata)) {
console.log(ancestor)
if ((ancestor.metadata && Object.keys(ancestor.metadata).length)) {
setAncestorHasMetadata(true)
break
}
Expand Down Expand Up @@ -202,7 +202,7 @@ function ViewDataset() {
data-bs-parent="#sidebar">Provenance</a>
</li>

{!!((data.ingest_metadata && Object.keys(data.ingest_metadata).length && 'metadata' in data.ingest_metadata) || ancestorHasMetadata) &&
{!!((data.metadata && Object.keys(data.metadata).length || ancestorHasMetadata)) &&
<li className="nav-item">
<a href="#Metadata"
className="nav-link"
Expand Down Expand Up @@ -275,10 +275,10 @@ function ViewDataset() {

{/*Metadata*/}
{/*Datasets have their metadata inside "metadata.metadata"*/}
{!!((data.ingest_metadata && Object.keys(data.ingest_metadata).length && 'metadata' in data.ingest_metadata) || ancestorHasMetadata) &&
{!!((data.metadata && Object.keys(data.metadata).length) || ancestorHasMetadata) &&
<Metadata
data={data}
metadata={data?.ingest_metadata?.metadata}
metadata={data?.metadata}
mappedMetadata={data?.cedar_mapped_metadata}
/>
}
Expand Down
4 changes: 2 additions & 2 deletions src/pages/publication.jsx
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Expand Up @@ -57,10 +57,10 @@ function ViewPublication() {
// get the most recent ancillary publication
ancillaryPublication = _data.descendants
.sort((a, b) => new Date(b.last_modified_timestamp) - new Date(a.last_modified_timestamp))
.find(d => d.dataset_type === 'Publication [ancillary]' && d.ingest_metadata?.files[0]?.rel_path)
.find(d => d.dataset_type === 'Publication [ancillary]' && d?.files[0]?.rel_path)
} else {
ancillaryPublication = _data.descendants
.find(d => d.dataset_type === 'Publication [ancillary]' && d.ingest_metadata?.files[0]?.rel_path)
.find(d => d.dataset_type === 'Publication [ancillary]' && d?.files[0]?.rel_path)
}

setAncillaryPublicationData(ancillaryPublication || {})
Expand Down