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Display biolucida images in gallery based on scicrunch #152

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merged 4 commits into from
Jul 10, 2024
Merged

Display biolucida images in gallery based on scicrunch #152

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8bc6013
Filter invalid biolucida images
ddjnw1yu Jul 2, 2024
4577e57
Minor update
ddjnw1yu Jul 3, 2024
9de0ca3
Minor update and add comment
ddjnw1yu Jul 4, 2024
5529917
Use Scicrunch data to create thumbnail gallery items
ddjnw1yu Jul 9, 2024
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56 changes: 23 additions & 33 deletions components/ImagesGallery/ImagesGallery.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,6 @@ import { baseName, extractSection, extractS3BucketName } from '@/utils/common'
* @param {Number} datasetId
*/
const getThumbnailData = async (datasetDoi, datasetId, datasetVersion, datasetFacetsData) => {
let biolucidaImageData = {}
let scicrunchData = {}
let scicrunch_response = []
let biolucida_response = []
Expand All @@ -59,19 +58,15 @@ const getThumbnailData = async (datasetDoi, datasetId, datasetVersion, datasetFa
biolucida_response = response
})

if (biolucida_response.status === 'success') {
const scicrunchData = pathOr([], ['data','result'], scicrunch_response)
biolucidaImageData = biolucida_response
biolucidaImageData['discover_dataset_version'] = datasetVersion
biolucidaImageData['dataset_info'] = scicrunchData.length > 0 ? scicrunchData[0] : {}
}

if (scicrunch_response.data.result.length > 0) {
scicrunchData = scicrunch_response.data.result[0]
scicrunchData.discover_dataset = {
id: Number(datasetId),
version: datasetVersion
}
if (biolucida_response.status === 'success') {
scicrunchData['dataset_images'] = pathOr([], ['dataset_images'], biolucida_response)
}
// Check for flatmap data
if (scicrunchData.organs) {
let flatmapData = []
Expand Down Expand Up @@ -133,13 +128,11 @@ const getThumbnailData = async (datasetDoi, datasetId, datasetVersion, datasetFa
e
)
return {
biolucidaImageData: {},
scicrunchData: {},
hasError: true
}
}
return {
biolucidaImageData,
scicrunchData,
hasError: false
}
Expand Down Expand Up @@ -213,7 +206,6 @@ export default {
timeseriesItems: [],
timeseriesData: [],
datasetScicrunch: {},
datasetBiolucida: {},
}
},
computed: {
Expand Down Expand Up @@ -259,13 +251,12 @@ export default {
},
async created() {
this.loading = true
const { biolucidaImageData, scicrunchData, hasError } = await getThumbnailData(
const { scicrunchData, hasError } = await getThumbnailData(
this.datasetInfo.doi,
this.datasetId,
this.datasetInfo.version,
this.datasetFacetsData
)
this.datasetBiolucida = biolucidaImageData
this.datasetScicrunch = scicrunchData
this.hasError = hasError

Expand Down Expand Up @@ -324,6 +315,7 @@ export default {
immediate: true,
handler: function(scicrunchData) {
let items = []
let bItems = []
const baseRoute = this.$router.options.base || '/'
let datasetId = -1
let datasetVersion = -1
Expand Down Expand Up @@ -510,31 +502,29 @@ export default {
)
}
this.scicrunchItems = items
}
},
datasetBiolucida: {
deep: true,
immediate: true,
handler: function(biolucidaData) {
const biolucida2DItems = pathOr([], ['dataset_info','biolucida-2d'], biolucidaData)
let items = []
const baseRoute = this.$router.options.base || '/'
if ('dataset_images' in biolucidaData) {
items.push(
...Array.from(biolucidaData.dataset_images.filter((obj, index) => {
return index === biolucidaData.dataset_images.findIndex(o => obj.image_id === o.image_id);
}), dataset_image => {

if ('dataset_images' in scicrunchData && ('biolucida-2d' in scicrunchData || 'biolucida-3d' in scicrunchData)) {
const biolucida2DItems = pathOr([],['biolucida-2d'], scicrunchData)
// Images need to exist in both Scicrunch and Biolucida
const biolucidaItems = biolucida2DItems.concat(pathOr([],['biolucida-3d'], scicrunchData)).filter((bObject) => {
return scicrunchData['dataset_images'].some(image => image.image_id == pathOr("", ['biolucida','identifier'], bObject))
})
bItems.push(
...Array.from(biolucidaItems, biolucida_item => {
let filePath = ""
const dataset_image = scicrunchData['dataset_images'].find((image) => {
return image.image_id == pathOr("", ['biolucida','identifier'], biolucida_item)
})
biolucida2DItems.forEach(biolucida2DItem => {
if (pathOr("", ['biolucida','identifier'], biolucida2DItem) == dataset_image.image_id) {
filePath = "files/" + pathOr("", ['dataset','path'], biolucida2DItem)
}
})
this.getThumbnailFromBiolucida(items, {
this.getThumbnailFromBiolucida(bItems, {
id: dataset_image.image_id,
fetchAttempts: 0
})
this.getImageInfoFromBiolucida(items, {
this.getImageInfoFromBiolucida(bItems, {
id: dataset_image.image_id,
fetchAttempts: 0
})
Expand All @@ -545,16 +535,16 @@ export default {
// If we can naviagte directly to the file path then do it, otherwise we have to redirect from the datasets/biolucida page
let linkUrl = filePath != "" ?
baseRoute +
`datasets/file/${biolucidaData.discover_dataset_id}/${biolucidaData.discover_dataset_version}?path=${filePath}` :
`datasets/file/${datasetId}/${datasetVersion}?path=${filePath}` :
baseRoute +
'datasets/biolucidaviewer/' +
dataset_image.image_id +
'?view=' +
viewEncoding +
'&dataset_version=' +
biolucidaData.discover_dataset_version +
datasetVersion +
'&dataset_id=' +
biolucidaData.discover_dataset_id +
datasetId +
'&item_id=' +
dataset_image.sourcepkg_id

Expand All @@ -568,7 +558,7 @@ export default {
})
)
}
this.biolucidaItems = items
this.biolucidaItems = bItems
}
}
},
Expand Down
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