diff --git a/deploy/datasets/query.js b/deploy/datasets/query.js
index d3cfeec0127dd907522d8b9dd92c8a80781a666c..c1d5da681e63da93eb2758b70961793a585bb7ed 100644
--- a/deploy/datasets/query.js
+++ b/deploy/datasets/query.js
@@ -5,7 +5,6 @@ const path = require('path')
const archiver = require('archiver')
const { commonSenseDsFilter } = require('./supplements/commonSense')
const { getPreviewFile, hasPreview } = require('./supplements/previewFile')
-const { manualFilter: manualFilterDWM, manualMap: manualMapDWM } = require('./supplements/util/mapDwm')
const kgQueryUtil = require('./../auth/util')
@@ -15,7 +14,7 @@ let otherQueryResult = null
const KG_ROOT = process.env.KG_ROOT || `https://kg.humanbrainproject.org`
const KG_PATH = process.env.KG_PATH || `/query/minds/core/dataset/v1.0.0/interactiveViewerKgQuery-v0_1`
const KG_PARAM = {
- size: process.env.KG_SEARCH_SIZE || '450',
+ size: process.env.KG_SEARCH_SIZE || '1000',
vocab: process.env.KG_SEARCH_VOCAB || 'https://schema.hbp.eu/myQuery/'
}
@@ -58,20 +57,29 @@ const cacheData = ({ results, ...rest }) => {
return cachedData
}
-const getPublicDs = () => Promise.race([
- new Promise((rs, rj) => {
- setTimeout(() => {
- if (cachedData) {
- rs(cachedData)
- } else {
- /**
- * cached data not available, have to wait
- */
- }
- }, timeout)
- }),
- fetchDatasetFromKg().then(cacheData)
-])
+let fetchingPublicDataInProgress = false
+let getPublicDsPr
+
+const getPublicDs = async () => {
+
+ /**
+ * every request to public ds will trigger a refresh pull from master KG (throttled pending on resolved request)
+ */
+ if (!fetchingPublicDataInProgress) {
+ fetchingPublicDataInProgress = true
+ getPublicDsPr = fetchDatasetFromKg()
+ .then(_ => {
+ fetchingPublicDataInProgress = false
+ getPublicDsPr = null
+ return _
+ })
+ .then(cacheData)
+ }
+
+ if (cachedData) return Promise.resolve(cachedData)
+ if (getPublicDsPr) return getPublicDsPr
+ throw `cached Data not yet resolved, neither is get public ds defined`
+}
const getDs = ({ user }) => user
@@ -103,46 +111,68 @@ const readConfigFile = (filename) => new Promise((resolve, reject) => {
})
})
-let juBrain = null
-let shortBundle = null
-let longBundle = null
-let waxholm = null
-let allen = null
+const populateSet = (flattenedRegions, set = new Set()) => {
+ if (!(set instanceof Set)) throw `set needs to be an instance of Set`
+ if (!(flattenedRegions instanceof Array)) throw `flattenedRegions needs to be an instance of Array`
+ for (const region of flattenedRegions) {
+ const { name, relatedAreas } = region
+ if (name) set.add(name)
+ if (relatedAreas && relatedAreas instanceof Array && relatedAreas.length > 0) {
+ for (const relatedArea of relatedAreas) {
+ if(typeof relatedArea === 'string') set.add(relatedArea)
+ else console.warn(`related area not an instance of String. skipping`, relatedArea)
+ }
+ }
+ }
+ return set
+}
+
+let juBrainSet = new Set(),
+ shortBundleSet = new Set(),
+ longBundleSet = new Set(),
+ waxholmSet = new Set(),
+ allenSet = new Set()
readConfigFile('colin.json')
.then(data => JSON.parse(data))
.then(json => {
- juBrain = flattenArray(json.parcellations[0].regions)
+ const juBrain = flattenArray(json.parcellations[0].regions)
+ juBrainSet = populateSet(juBrain)
+
})
.catch(console.error)
readConfigFile('MNI152.json')
.then(data => JSON.parse(data))
.then(json => {
- longBundle = flattenArray(json.parcellations[0].regions)
- shortBundle = flattenArray(json.parcellations[1].regions)
+ const longBundle = flattenArray(json.parcellations.find(({ name }) => name === 'Fibre Bundle Atlas - Long Bundle').regions)
+ const shortBundle = flattenArray(json.parcellations.find(({ name }) => name === 'Fibre Bundle Atlas - Short Bundle').regions)
+
+ longBundleSet = populateSet(longBundle)
+ shortBundleSet = populateSet(shortBundle)
})
.catch(console.error)
readConfigFile('waxholmRatV2_0.json')
.then(data => JSON.parse(data))
.then(json => {
- waxholm = flattenArray(json.parcellations[0].regions)
+ const waxholm = flattenArray(json.parcellations[0].regions)
+
+ waxholmSet = populateSet(waxholm)
})
.catch(console.error)
-/**
- * deprecated
- */
-const filterByPRs = (prs, atlasPr) => atlasPr
- ? prs.some(pr => {
- const regex = new RegExp(pr.name.replace(/[-[\]{}()*+?.,\\^$|#\s]/g, '\\$&'), 'i')
- return atlasPr.some(aPr => regex.test(aPr.name))
+readConfigFile('allenMouse.json')
+ .then(data => JSON.parse(data))
+ .then(json => {
+ const flattenedAllen = flattenArray(json.parcellations[0].regions)
+ allenSet = populateSet(flattenedAllen)
})
- : false
-
-const manualFilter = require('./supplements/parcellation')
+const filterByPRSet = (prs, atlasPrSet = new Set()) => {
+ if (!(atlasPrSet instanceof Set)) throw `atlasPrSet needs to be a set!`
+ return prs.some(({ name }) => atlasPrSet.has(name))
+}
const filter = (datasets = [], { templateName, parcellationName }) => datasets
.filter(ds => commonSenseDsFilter({ ds, templateName, parcellationName }))
@@ -153,34 +183,36 @@ const filter = (datasets = [], { templateName, parcellationName }) => datasets
return ds.referenceSpaces.some(rs => rs.name === templateName)
}
if (parcellationName) {
- if (parcellationName === 'Fibre Bundle Atlas - Long Bundle') {
- return manualFilterDWM(ds)
+ if (ds.parcellationRegion.length === 0) return false
+
+ let useSet
+ switch (parcellationName) {
+ case 'JuBrain Cytoarchitectonic Atlas':
+ useSet = juBrainSet
+ break;
+ case 'Fibre Bundle Atlas - Short Bundle':
+ useSet = shortBundleSet
+ break;
+ case 'Fibre Bundle Atlas - Long Bundle':
+ useSet = longBundleSet
+ break;
+ case 'Waxholm Space rat brain atlas v.2.0':
+ useSet = waxholmSet
+ break;
+ case 'Allen adult mouse brain reference atlas V3 Brain Atlas':
+ useSet = allenSet
+ break;
+ default:
+ useSet = new Set()
}
- return ds.parcellationRegion.length > 0
- ? filterByPRs(
- ds.parcellationRegion,
- parcellationName === 'JuBrain Cytoarchitectonic Atlas' && juBrain
- ? juBrain
- : parcellationName === 'Fibre Bundle Atlas - Short Bundle' && shortBundle
- ? shortBundle
- : parcellationName === 'Waxholm Space rat brain atlas v.2.0'
- ? waxholm
- : null
- )
- : false
+ return filterByPRSet(ds.parcellationRegion, useSet)
}
return false
})
.map(ds => {
- if (parcellationName && parcellationName === 'Fibre Bundle Atlas - Long Bundle') {
- return manualMapDWM(ds)
- }
return {
...ds,
- ...parcellationName && ds.parcellationRegion.length === 0
- ? { parcellationRegion: [{ name: manualFilter({ parcellationName, dataset: ds }) }] }
- : {},
preview: hasPreview({ datasetName: ds.name })
}
})
@@ -191,8 +223,7 @@ const filter = (datasets = [], { templateName, parcellationName }) => datasets
exports.init = async () => {
const { getPublicAccessToken: getPublic } = await kgQueryUtil()
getPublicAccessToken = getPublic
- const { results = [] } = await fetchDatasetFromKg()
- cachedData = results
+ return await getPublicDs()
}
exports.getDatasets = ({ templateName, parcellationName, user }) => getDs({ user })
diff --git a/deploy/datasets/supplements/data/receptorPreview.json b/deploy/datasets/supplements/data/receptorPreview.json
index 535ad50bf3bed721ddb1ae3eba56469784b7e66a..a0d1ee6066719c7ae023dd7147ceaff8d31d42d2 100644
--- a/deploy/datasets/supplements/data/receptorPreview.json
+++ b/deploy/datasets/supplements/data/receptorPreview.json
@@ -1 +1 @@
-[["Density measurements of different receptors for Area 4p",[{"name":"Receptor density fingerprint of Area 4p","filename":"fingerprint","mimetype":"application/json","properties":{"description":"**Multireceptor fingerprint for area 4p.** This polar plot shows the mean receptor densities in fmol/mg protein (solid shape) and standard deviation (dashed line) of 16 receptor binding sites in the area 4p. The data is based on the left and right hemisphere of one female subject (brain id: hg0201, sample ids: ID07 and ID08, age: 77, cause of death: lung edema) and the right hemispheres of two male subjects (brain id: hg0500, sample ids: ID09, age: 72, cause of death: cardiac arrest | brain id: hg0100, sample ids: ID12, age: 77, cause of death: coronary heart disease).","publications":[]},"data":{"chartType":"radar","labels":["AMPA (Glu)","kainate (Glu)","NMDA (Glu)","mGluR2/3 (Glu)","GABAá´€(GABA)","GABAá´ƒ(GABA)","GABAá´€(BZ)","Mâ‚(ACh)","Mâ‚‚(ACh)","M₃(ACh)","α₄β₂(ACh)","αâ‚(NA)","α₂(NA)","5-HTâ‚á´€(5-HT)","5-HTâ‚‚(5-HT)","Dâ‚(DA)"],"datasets":[{"label":"mean","data":["286","286","739","NA","999","1842","1337","245","141","400","69","193","111","162","234","49"]},{"label":"mean_sd","data":["40","35","1","NA","108","10","65","23","27","44","13","7","15","31","2","5"]}],"chartOptions":{"scale":{"ticks":{"showLabelBackdrop":false}},"legend":{"display":true},"title":{"text":"Receptor density fingerprint of Area 4p (fmol/mg protein)","display":true},"elements":{"point":{"radius":0,"hoverRadius":8,"hitRadius":4}}},"colors":[{"borderColor":"rgba(255,255,255,1)","backgroundColor":"rgba(139,71,137,0.2)"},{"borderColor":"rgba(255,255,255,1)"}]}},{"name":"Sample autoradiograph of GABAá´€(BZ) in Area 4p","filename":"GABAá´€(BZ)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2F4p_bm_BZ.jpg"},{"name":"Sample autoradiograph of αâ‚(NA) in Area 4p","filename":"αâ‚(NA)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2F4p_bm_alpha1.jpg"},{"name":"Sample autoradiograph of NMDA (Glu) in Area 4p","filename":"NMDA (Glu)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2F4p_bm_NMDA.jpg"},{"name":"Sample autoradiograph of GABAá´€(GABA) in Area 4p","filename":"GABAá´€(GABA)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2F4p_bm_GABAA.jpg"},{"name":"Sample autoradiograph of α₂(NA) in Area 4p","filename":"α₂(NA)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2F4p_bm_alpha2.jpg"},{"name":"Sample autoradiograph of α₄β₂(ACh) in Area 4p","filename":"α₄β₂(ACh)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2F4p_bm_alpha4beta2.jpg"},{"name":"Sample autoradiograph of Mâ‚(ACh) in Area 4p","filename":"Mâ‚(ACh)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2F4p_bm_M1.jpg"},{"name":"Sample autoradiograph of 5-HTâ‚á´€(5-HT) in Area 4p","filename":"5-HTâ‚á´€(5-HT)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2F4p_bm_5-HT1A.jpg"},{"name":"Sample autoradiograph of kainate (Glu) in Area 4p","filename":"kainate (Glu)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2F4p_bm_kainate.jpg"},{"name":"Sample autoradiograph of Mâ‚‚(ACh) in Area 4p","filename":"Mâ‚‚(ACh)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2F4p_bm_M2.jpg"},{"name":"Sample autoradiograph of AMPA (Glu) in Area 4p","filename":"AMPA (Glu)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2F4p_bm_AMPA.jpg"},{"name":"Sample autoradiograph of Dâ‚(DA) in Area 4p","filename":"Dâ‚(DA)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2F4p_bm_D1.jpg"},{"name":"Sample autoradiograph of M₃(ACh) in Area 4p","filename":"M₃(ACh)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2F4p_bm_M3.jpg"},{"name":"Sample autoradiograph of mGluR2/3 (Glu) in Area 4p","filename":"mGluR2\\/3 (Glu)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2F4p_bm_mGluR2_3.jpg"},{"name":"Sample autoradiograph of 5-HTâ‚‚(5-HT) in Area 4p","filename":"5-HTâ‚‚(5-HT)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2F4p_bm_5-HT2.jpg"},{"name":"Sample autoradiograph of GABAá´ƒ(GABA) in Area 4p","filename":"GABAá´ƒ(GABA)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2F4p_bm_GABAB.jpg"},{"name":"Sample profile of GABAá´€(BZ) in Area 4p","filename":"GABAá´€(BZ)/profile","mimetype":"application/json","properties":{"description":"**Examplary laminar density profile of BZ receptor in area 4p.** This profile plot shows examplary the course of the BZ receptor density (in fmol/mg protein on y axis) from the pial surface (0% on x axis) to the border between layer VI and the white matter (100% on x axis) for area 4p in the left hemisphere of one female subject (brain id: hg0201, sample id: ID07, age: 77, cause of death: lung edema).","publications":[]},"data":{"chartOptions":{"legend":{"display":false},"title":{"display":true,"text":"Example profile of GABAá´€(BZ) in Area 4p"},"scales":{"xAxes":[{"ticks":{"min":0,"max":100,"stepSize":20},"scaleLabel":{"display":true,"labelString":"cortical depth %"}}],"yAxes":[{"ticks":{"beginAtZero":true,"min":0},"scaleLabel":{"display":true,"labelString":"receptor density (fmol/mg protein)"}}]},"elements":{"point":{"radius":0,"hoverRadius":8,"hitRadius":4}}},"chartType":"line","labels":["Example profile of GABAá´€(BZ) in Area 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profile of αâ‚(NA) in Area 4p","filename":"αâ‚(NA)/profile","mimetype":"application/json","properties":{"description":"**Examplary laminar density profile of alpha1 receptor in area 4p.** This profile plot shows examplary the course of the alpha1 receptor density (in fmol/mg protein on y axis) from the pial surface (0% on x axis) to the border between layer VI and the white matter (100% on x axis) for area 4p in the left hemisphere of one female subject (brain id: hg0201, sample id: ID07, age: 77, cause of death: lung edema).","publications":[]},"data":{"chartOptions":{"legend":{"display":false},"title":{"display":true,"text":"Example profile of αâ‚(NA) in Area 4p"},"scales":{"xAxes":[{"ticks":{"min":0,"max":100,"stepSize":20},"scaleLabel":{"display":true,"labelString":"cortical depth %"}}],"yAxes":[{"ticks":{"beginAtZero":true,"min":0},"scaleLabel":{"display":true,"labelString":"receptor density (fmol/mg 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protein)","display":true},"elements":{"point":{"radius":0,"hoverRadius":8,"hitRadius":4}}},"colors":[{"borderColor":"rgba(255,255,255,1)","backgroundColor":"rgba(0,100,209,0.2)"},{"borderColor":"rgba(255,255,255,1)"}]}},{"name":"Sample autoradiograph of GABAá´€(BZ) in Area FG1","filename":"GABAá´€(BZ)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2FFG1_bm_BZ.jpg"},{"name":"Sample autoradiograph of αâ‚(NA) in Area FG1","filename":"αâ‚(NA)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2FFG1_bm_alpha1.jpg"},{"name":"Sample autoradiograph of NMDA (Glu) in Area FG1","filename":"NMDA (Glu)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2FFG1_bm_NMDA.jpg"},{"name":"Sample autoradiograph of GABAá´€(GABA) in Area FG1","filename":"GABAá´€(GABA)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2FFG1_bm_GABAA.jpg"},{"name":"Sample autoradiograph of α₂(NA) in Area FG1","filename":"α₂(NA)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2FFG1_bm_alpha2.jpg"},{"name":"Sample autoradiograph of α₄β₂(ACh) in Area FG1","filename":"α₄β₂(ACh)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2FFG1_bm_alpha4beta2.jpg"},{"name":"Sample autoradiograph of Mâ‚(ACh) in Area FG1","filename":"Mâ‚(ACh)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2FFG1_bm_M1.jpg"},{"name":"Sample autoradiograph of 5-HTâ‚á´€(5-HT) in Area FG1","filename":"5-HTâ‚á´€(5-HT)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2FFG1_bm_5-HT1A.jpg"},{"name":"Sample autoradiograph of kainate (Glu) in Area FG1","filename":"kainate (Glu)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2FFG1_bm_kainate.jpg"},{"name":"Sample autoradiograph of Mâ‚‚(ACh) in Area FG1","filename":"Mâ‚‚(ACh)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2FFG1_bm_M2.jpg"},{"name":"Sample autoradiograph of AMPA (Glu) in Area FG1","filename":"AMPA (Glu)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2FFG1_bm_AMPA.jpg"},{"name":"Sample autoradiograph of Dâ‚(DA) in Area FG1","filename":"Dâ‚(DA)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2FFG1_bm_D1.jpg"},{"name":"Sample autoradiograph of M₃(ACh) in Area FG1","filename":"M₃(ACh)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2FFG1_bm_M3.jpg"},{"name":"Sample autoradiograph of 5-HTâ‚‚(5-HT) in Area FG1","filename":"5-HTâ‚‚(5-HT)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2FFG1_bm_5-HT2.jpg"},{"name":"Sample autoradiograph of GABAá´ƒ(GABA) in Area FG1","filename":"GABAá´ƒ(GABA)/autoradiography","mimetype":"image/jpeg","properties":{"description":null,"publications":[]},"data":null,"url":"datasets/previewFile?file=res%2Fimage%2Freceptor%2FFG1_bm_GABAB.jpg"}]],["Density measurements of different receptors for Area PGa",[{"name":"Receptor density fingerprint of Area PGa","filename":"fingerprint","mimetype":"application/json","properties":{"description":null,"publications":[]},"data":{"chartType":"radar","labels":["AMPA (Glu)","kainate (Glu)","NMDA (Glu)","mGluR2/3 (Glu)","GABAá´€(GABA)","GABAá´ƒ(GABA)","GABAá´€(BZ)","Mâ‚(ACh)","Mâ‚‚(ACh)","M₃(ACh)","α₄β₂(ACh)","αâ‚(NA)","α₂(NA)","5-HTâ‚á´€(5-HT)","5-HTâ‚‚(5-HT)","Dâ‚(DA)"],"datasets":[{"label":"mean","data":["463","635","1259","3957","1998","2742","2442","479","172","827","70","361","698","303","441","136"]},{"label":"mean_sd","data":["187","405","278","1655","577","291","876","192","77","348","34","169","mg/mol","123","238","55"]}],"chartOptions":{"scale":{"ticks":{"showLabelBackdrop":false}},"legend":{"display":true},"title":{"text":"Receptor density fingerprint of Area PGa (fmol/mg protein)","display":true},"elements":{"point":{"radius":0,"hoverRadius":8,"hitRadius":4}}},"colors":[{"borderColor":"rgba(255,255,255,1)","backgroundColor":"rgba(5,198,198,0.2)"},{"borderColor":"rgba(255,255,255,1)"}]}}]]]
\ No newline at end of file
diff --git a/deploy/datasets/supplements/parcellation.js b/deploy/datasets/supplements/parcellation.js
deleted file mode 100644
index 20527e571c065ddcf70d9a6a7ba9162e95af79b2..0000000000000000000000000000000000000000
--- a/deploy/datasets/supplements/parcellation.js
+++ /dev/null
@@ -1,27 +0,0 @@
-const fs = require('fs')
-const path = require('path')
-let waxholm = new Map(),
- allen = new Map()
-
-fs.readFile(path.join(__dirname, 'data', 'allen.json'), 'utf-8', (err, data) => {
- if (err)
- throw err
- const json = JSON.parse(data)
- allen = new Map(json.map(item => [item['Dataset name'], item["Semantic link(s)"]]))
-})
-
-
-fs.readFile(path.join(__dirname, 'data', 'waxholm.json'), 'utf-8', (err, data) => {
- if (err)
- throw err
- const json = JSON.parse(data)
- waxholm = new Map(json.map(item => [item['Dataset name'], item["Semantic link(s)"]]))
-})
-
-module.exports = ({ parcellationName, dataset }) => {
- return parcellationName === 'Allen adult mouse brain reference atlas V3 Brain Atlas'
- ? allen.get(dataset.name)
- : parcellationName === 'Whole Brain (v2.0)'
- ? waxholm.get(dataset.name)
- : false
-}
\ No newline at end of file
diff --git a/deploy/datasets/supplements/util/mapDwm.js b/deploy/datasets/supplements/util/mapDwm.js
deleted file mode 100644
index b9cda2f1143970a66397c5572c7fbf991ddb96bd..0000000000000000000000000000000000000000
--- a/deploy/datasets/supplements/util/mapDwm.js
+++ /dev/null
@@ -1,69 +0,0 @@
-exports.manualFilter = (dataset) => dataset
- && dataset.project
- && dataset.project instanceof Array
- && dataset.project.some(p => p === 'Atlas of deep white matter fibre bundles, version 2018')
-
-const dict = [ [ 'Probabilistic map of the anterior segment of the left arcuate fasciculus (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/Arcuate_Anterior - Left' ],
-[ 'Probabilistic map of the direct segment of the left arcuate fasciculus (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/Arcuate - Left' ],
-[ 'Probabilistic map of the posterior segment of the left arcuate fasciculus (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/Arcuate_Posterior - Left' ],
-[ 'Probabilistic map of the left long cingulate fibres (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/Cingulum_Long - Left' ],
-[ 'Probabilistic map of the left short cingulate fibres (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/Cingulum_Short - Left' ],
-[ 'Probabilistic map of the left temporal cingulate fibres (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/Cingulum_Temporal - Left' ],
-[ 'Probabilistic map of the left corticospinal tract (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/CorticoSpinalTract - Left' ],
-[ 'Probabilistic map of the left fornix (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/Fornix - Left' ],
-[ 'Probabilistic map of the left inferior fronto-occipital fasciculus (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/InferiorFrontoOccipital - Left' ],
-[ 'Probabilistic map of the left inferior longitudinal fasciculus (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/InferiorLongitudinal - Left' ],
-[ 'Probabilistic map of the left uncinate fasciculus (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/Uncinate - Left' ],
-[ 'Probabilistic map of the anterior segment of the right arcuate fasciculus (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/Arcuate_Anterior - Right' ],
-[ 'Probabilistic map of the posterior segment of the right arcuate fasciculus (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/Arcuate_Posterior - Right' ],
-[ 'Probabilistic map of the posterior segment of the right arcuate fasciculus (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/Arcuate - Right' ],
-[ 'Probabilistic map of the right long cingulate fibres (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/Cingulum_Long - Right' ],
-[ 'Probabilistic map of the right short cingulate fibres (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/Cingulum_Short - Right' ],
-[ 'Probabilistic map of the right temporal cingulate fibres (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/Cingulum_Temporal - Right' ],
-[ 'Probabilistic map of the right corticospinal tract (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/CorticoSpinalTract - Right' ],
-[ 'Probabilistic map of the right fornix (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/Fornix - Right' ],
-[ 'Probabilistic map of the right inferior fronto-occipital fasciculus (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/InferiorFrontoOccipital - Right' ],
-[ 'Probabilistic map of the right inferior longitudinal fasciculus (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/InferiorLongitudinal - Right' ],
-[ 'Probabilistic map of the right uncinate fasciculus (atlas of deep white matter fibre bundles, version 2018)',
-'Fibre Bundle Atlas - Long Bundle/Uncinate - Right' ] ]
-
-const dsNameToIdMap = new Map(dict)
-const getIdFromDataset = (dataset) => {
- const id = dsNameToIdMap.get(dataset.name)
- if (id) return id
- return null
-}
-
-exports.manualMap = (dataset) => {
- return {
- preview: !process.env.DISABLE_DWM_PMAP,
- ...dataset,
- parcellationRegion: dataset.parcellationRegion.map(r => {
- return {
- ...r,
- id: getIdFromDataset(dataset)
- }
- })
- }
-}
\ No newline at end of file
diff --git a/src/res/ext/MNI152.json b/src/res/ext/MNI152.json
index 92dd39191c05148ccfcf53949aca8f4ee8c067ef..50de3d7b1eebc47657b8311afb5da0ceff441c5d 100644
--- a/src/res/ext/MNI152.json
+++ b/src/res/ext/MNI152.json
@@ -839,6 +839,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area 7A"
+ ],
"rgb": [
38,
204,
@@ -1179,6 +1182,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas": [
+ "Area 3b"
+ ],
"rgb": [
239,
246,
@@ -1326,6 +1332,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area PFm"
+ ],
"rgb": [
53,
76,
@@ -1372,6 +1381,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area PFop"
+ ],
"rgb": [
146,
153,
@@ -1418,6 +1430,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area PF"
+ ],
"rgb": [
226,
211,
@@ -1464,6 +1479,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area PGp"
+ ],
"rgb": [
92,
116,
@@ -1510,6 +1528,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area PGa"
+ ],
"rgb": [
42,
236,
@@ -1556,6 +1577,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area PFt"
+ ],
"rgb": [
120,
135,
@@ -1602,6 +1626,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area PFcm"
+ ],
"rgb": [
98,
128,
@@ -2392,6 +2419,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area hOc1"
+ ],
"rgb": [
190,
132,
@@ -2888,6 +2918,10 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area 44v",
+ "Area 44d"
+ ],
"rgb": [
54,
74,
@@ -2934,6 +2968,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas": [
+ "Area 45"
+ ],
"rgb": [
167,
103,
@@ -3301,6 +3338,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area 4p"
+ ],
"rgb": [
116,
92,
@@ -4568,6 +4608,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area Te1"
+ ],
"rgb": [
252,
84,
@@ -4623,6 +4666,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area FG1"
+ ],
"rgb": [
131,
183,
@@ -4761,6 +4807,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area FG2"
+ ],
"rgb": [
67,
94,
@@ -5699,62 +5748,98 @@
{
"name": "Arcuate - Left",
"children": [],
- "labelIndex": "1"
+ "labelIndex": "1",
+ "relatedAreas": [
+ "Direct segment of the left arcuate fasciculus"
+ ]
},
{
"name": "Arcuate - Right",
"children": [],
- "labelIndex": "31"
+ "labelIndex": "31",
+ "relatedAreas": [
+ "Direct segment of the right arcuate fasciculus"
+ ]
},
{
"name": "Arcuate_Anterior - Left",
"children": [],
- "labelIndex": "2"
+ "labelIndex": "2",
+ "relatedAreas": [
+ "Anterior segment of the left arcuate fasciculus"
+ ]
},
{
"name": "Arcuate_Anterior - Right",
"children": [],
- "labelIndex": "32"
+ "labelIndex": "32",
+ "relatedAreas": [
+ "Anterior segment of the right arcuate fasciculus"
+ ]
},
{
"name": "Arcuate_Posterior - Left",
"children": [],
- "labelIndex": "3"
+ "labelIndex": "3",
+ "relatedAreas": [
+ "Posterior segment of the left arcuate fasciculus"
+ ]
},
{
"name": "Arcuate_Posterior - Right",
"children": [],
- "labelIndex": "33"
+ "labelIndex": "33",
+ "relatedAreas": [
+ "Posterior segment of the right arcuate fasciculus"
+ ]
},
{
"name": "Cingulum_Long - Left",
"children": [],
- "labelIndex": "4"
+ "labelIndex": "4",
+ "relatedAreas": [
+ "Left long cingulate fibres"
+ ]
},
{
"name": "Cingulum_Long - Right",
"children": [],
- "labelIndex": "34"
+ "labelIndex": "34",
+ "relatedAreas": [
+ "Right long cingulate fibres"
+ ]
},
{
"name": "Cingulum_Short - Left",
"children": [],
- "labelIndex": "5"
+ "labelIndex": "5",
+ "relatedAreas": [
+ "Left short cingulate fibres"
+ ]
},
{
"name": "Cingulum_Short - Right",
"children": [],
- "labelIndex": "35"
+ "labelIndex": "35",
+ "relatedAreas": [
+ "Right short cingulate fibres"
+ ]
},
{
"name": "Cingulum_Temporal - Left",
"children": [],
- "labelIndex": "6"
+ "labelIndex": "6",
+ "relatedAreas": [
+ "Left temporal cingulate fibres"
+ ]
},
{
"name": "Cingulum_Temporal - Right",
"children": [],
- "labelIndex": "36"
+ "labelIndex": "36",
+ "relatedAreas": [
+ "Right temporal cingulate fibres"
+ ]
},
{
"name": "CorpusCallosum_Body",
@@ -5779,12 +5864,18 @@
{
"name": "CorticoSpinalTract - Left",
"children": [],
- "labelIndex": "11"
+ "labelIndex": "11",
+ "relatedAreas": [
+ "Left corticospinal tract"
+ ]
},
{
"name": "CorticoSpinalTract - Right",
"children": [],
- "labelIndex": "41"
+ "labelIndex": "41",
+ "relatedAreas": [
+ "Right corticospinal tract"
+ ]
},
{
"name": "ExternalCapsule - Left",
@@ -5799,32 +5890,50 @@
{
"name": "Fornix - Left",
"children": [],
- "labelIndex": "13"
+ "labelIndex": "13",
+ "relatedAreas": [
+ "Left fornix"
+ ]
},
{
"name": "Fornix - Right",
"children": [],
- "labelIndex": "43"
+ "labelIndex": "43",
+ "relatedAreas": [
+ "Right fornix"
+ ]
},
{
"name": "InferiorFrontoOccipital - Left",
"children": [],
- "labelIndex": "14"
+ "labelIndex": "14",
+ "relatedAreas": [
+ "Left inferior fronto-occipital fasciculus"
+ ]
},
{
"name": "InferiorFrontoOccipital - Right",
"children": [],
- "labelIndex": "44"
+ "labelIndex": "44",
+ "relatedAreas": [
+ "Right inferior fronto-occipital fasciculus"
+ ]
},
{
"name": "InferiorLongitudinal - Left",
"children": [],
- "labelIndex": "15"
+ "labelIndex": "15",
+ "relatedAreas": [
+ "Left inferior longitudinal fasciculus"
+ ]
},
{
"name": "InferiorLongitudinal - Right",
"children": [],
- "labelIndex": "45"
+ "labelIndex": "45",
+ "relatedAreas": [
+ "Right inferior longitudinal fasciculus"
+ ]
},
{
"name": "InferiorLongitudinal_Lateral - Left",
@@ -5879,12 +5988,18 @@
{
"name": "Uncinate - Left",
"children": [],
- "labelIndex": "21"
+ "labelIndex": "21",
+ "relatedAreas": [
+ "Left uncinate fasciculus"
+ ]
},
{
"name": "Uncinate - Right",
"children": [],
- "labelIndex": "51"
+ "labelIndex": "51",
+ "relatedAreas": [
+ "Right uncinate fasciculus"
+ ]
}
]
},
diff --git a/src/res/ext/colin.json b/src/res/ext/colin.json
index beb97256a249d7d24646d029876bf5abe8e4f68b..6c1c35b3ccb425a2d98864ccab76a12926886cef 100644
--- a/src/res/ext/colin.json
+++ b/src/res/ext/colin.json
@@ -839,6 +839,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area 7A"
+ ],
"rgb": [
38,
204,
@@ -1179,6 +1182,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas": [
+ "Area 3b"
+ ],
"rgb": [
239,
246,
@@ -1326,6 +1332,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area PFm"
+ ],
"rgb": [
53,
76,
@@ -1372,6 +1381,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area PFop"
+ ],
"rgb": [
146,
153,
@@ -1418,6 +1430,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area PF"
+ ],
"rgb": [
226,
211,
@@ -1464,6 +1479,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area PGp"
+ ],
"rgb": [
92,
116,
@@ -1510,6 +1528,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area PGa"
+ ],
"rgb": [
42,
236,
@@ -1556,6 +1577,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area PFt"
+ ],
"rgb": [
120,
135,
@@ -1602,6 +1626,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area PFcm"
+ ],
"rgb": [
98,
128,
@@ -2392,6 +2419,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area hOc1"
+ ],
"rgb": [
190,
132,
@@ -2888,6 +2918,10 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area 44v",
+ "Area 44d"
+ ],
"rgb": [
54,
74,
@@ -2902,6 +2936,7 @@
75
],
"labelIndex": 2,
+
"ngId": "jubrain colin v17 left",
"children": [],
"position": [
@@ -2934,6 +2969,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas": [
+ "Area 45"
+ ],
"rgb": [
167,
103,
@@ -3301,6 +3339,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area 4p"
+ ],
"rgb": [
116,
92,
@@ -4568,6 +4609,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area Te1"
+ ],
"rgb": [
252,
84,
@@ -4623,6 +4667,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area FG1"
+ ],
"rgb": [
131,
183,
@@ -4761,6 +4808,9 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
+ "relatedAreas":[
+ "Area FG2"
+ ],
"rgb": [
67,
94,
diff --git a/src/res/images/MNI152.png b/src/res/images/MNI152ICBM2009cNonlinearAsymmetric.png
similarity index 100%
rename from src/res/images/MNI152.png
rename to src/res/images/MNI152ICBM2009cNonlinearAsymmetric.png
diff --git a/src/ui/databrowserModule/databrowser/databrowser.component.ts b/src/ui/databrowserModule/databrowser/databrowser.component.ts
index e9ca1b1e011606c13cf5c31b1dea9c5e9e0af942..b3568e039e3be5c046e2571e2d014ed1cac1877d 100644
--- a/src/ui/databrowserModule/databrowser/databrowser.component.ts
+++ b/src/ui/databrowserModule/databrowser/databrowser.component.ts
@@ -74,7 +74,6 @@ export class DataBrowser implements OnDestroy,OnInit{
this.dbService.getDataByRegion({ regions, parcellation, template })
.then(de => {
this.dataentries = de
- this.fetchingFlag = false
return de
})
.then(this.dbService.getModalityFromDE)
@@ -83,9 +82,11 @@ export class DataBrowser implements OnDestroy,OnInit{
})
.catch(e => {
console.error(e)
- this.fetchingFlag = false
this.fetchError = true
})
+ .finally(() => {
+ this.fetchingFlag = false
+ })
this.subscriptions.push(
merge(
diff --git a/src/ui/databrowserModule/singleDataset/singleDataset.component.ts b/src/ui/databrowserModule/singleDataset/singleDataset.component.ts
index 997ed303fdfca77f1d6abce2241bf38837945e48..20f58c6675a3476797a7cd26efafe5ca63ff6561 100644
--- a/src/ui/databrowserModule/singleDataset/singleDataset.component.ts
+++ b/src/ui/databrowserModule/singleDataset/singleDataset.component.ts
@@ -27,7 +27,7 @@ export class SingleDatasetView implements OnInit {
* sic!
*/
private kgReference: string[] = []
- private files: File[] = []
+ public files: File[] = []
private methods: string[] = []
/**
* sic!
diff --git a/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts b/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts
index 3f45fa9d105f4a34e47dd2d1e1f428670467aa13..4efe62a4c80a893f1020279d9ce080467ed9f1dd 100644
--- a/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts
+++ b/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts
@@ -24,21 +24,13 @@ export class FilterDataEntriesByRegion implements PipeTransform{
*/
const newParcellationRegion = de.parcellationRegion.map(({name, id, ...rest}) => {
- /**
- * TODO: temporary hack, some dataset region name is not exactly the same as region
- */
- /* https://stackoverflow.com/a/9310752/6059235 */
- const regex = new RegExp(name.replace(/[-[\]{}()*+?.,\\^$|#\s]/g, '\\$&'), 'i')
-
const found = flattenedAllRegions.find(r => {
/**
* TODO replace pseudo id with real uuid
*/
- return (r.id && id && r.id === id) || regex.test(r.name)
- /**
- * more correct, but probably should use UUID in the future
- */
- return r.name === name
+ return (r.id && id && r.id === id)
+ || r.name === name
+ || r.relatedAreas && r.relatedAreas.length && r.relatedAreas.some(syn => syn === name)
})
return found
? { name, id, ...rest, ...found }
diff --git a/src/ui/nehubaContainer/nehubaContainer.component.ts b/src/ui/nehubaContainer/nehubaContainer.component.ts
index 74849c89679efbafd7a776c58dabed4306d8f5b6..b002afb1163107168b3d97c33dbdb6303e6323a3 100644
--- a/src/ui/nehubaContainer/nehubaContainer.component.ts
+++ b/src/ui/nehubaContainer/nehubaContainer.component.ts
@@ -1090,7 +1090,8 @@ export class NehubaContainer implements OnInit, OnDestroy{
*/
Object.keys(_navigation).forEach(key => (!_navigation[key]) && delete _navigation[key])
- if( animation ){
+ const { animation: globalAnimationFlag } = this.viewerConfig
+ if( globalAnimationFlag && animation ){
/* animated */
const gen = timedValues()
diff --git a/src/ui/signinBanner/signinBanner.components.ts b/src/ui/signinBanner/signinBanner.components.ts
index 93c18c3f7bec8f44f1d82403524ad24f052c64fd..ae687ba8d2d8811279faa9585f34a4bef174ad5c 100644
--- a/src/ui/signinBanner/signinBanner.components.ts
+++ b/src/ui/signinBanner/signinBanner.components.ts
@@ -203,7 +203,8 @@ export class SigninBanner implements OnInit, OnDestroy{
this.store.dispatch({
type: CHANGE_NAVIGATION,
navigation: {
- position: region.position
+ position: region.position,
+ animation: {}
}
})
} else {