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Commit 7d0df31d authored by Xiao Gui's avatar Xiao Gui
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chore: cleanup code improve reusability

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deploy/datasets/query.js
+ 125
− 86
View file @ 7d0df31d
......@@ -32,7 +32,7 @@ const fetchDatasetFromKg = async ({ user } = {}) => {
}
const cacheData = ({results, ...rest}) => {
const cacheData = ({ results, ...rest }) => {
cachedData = results
otherQueryResult = rest
return cachedData
......@@ -55,7 +55,7 @@ const getPublicDs = () => Promise.race([
const getDs = ({ user }) => user
? fetchDatasetFromKg({ user }).then(({results}) => results)
? fetchDatasetFromKg({ user }).then(({ results }) => results)
: getPublicDs()
/**
......@@ -78,7 +78,7 @@ const readConfigFile = (filename) => new Promise((resolve, reject) => {
filepath = path.join(__dirname, '..', '..', 'src', 'res', 'ext', filename)
}
fs.readFile(filepath, 'utf-8', (err, data) => {
if(err) reject(err)
if (err) reject(err)
resolve(data)
})
})
......@@ -116,16 +116,16 @@ readConfigFile('waxholmRatV2_0.json')
*/
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))
})
const regex = new RegExp(pr.name.replace(/[-[\]{}()*+?.,\\^$|#\s]/g, '\\$&'), 'i')
return atlasPr.some(aPr => regex.test(aPr.name))
})
: false
const manualFilter = require('./supplements/parcellation')
const filter = (datasets = [], {templateName, parcellationName}) => datasets
.filter(ds => commonSenseDsFilter({ds, templateName, parcellationName }))
const filter = (datasets = [], { templateName, parcellationName }) => datasets
.filter(ds => commonSenseDsFilter({ ds, templateName, parcellationName }))
.filter(ds => {
if (/infant/.test(ds.name))
return false
......@@ -133,20 +133,20 @@ const filter = (datasets = [], {templateName, parcellationName}) => datasets
return ds.referenceSpaces.some(rs => rs.name === templateName)
}
if (parcellationName) {
if (parcellationName === 'Fibre Bundle Atlas - Long Bundle'){
if (parcellationName === 'Fibre Bundle Atlas - Long Bundle') {
return manualFilterDWM(ds)
}
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
)
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
}
......@@ -171,12 +171,12 @@ const filter = (datasets = [], {templateName, parcellationName}) => datasets
exports.init = async () => {
const { getPublicAccessToken: getPublic } = await kgQueryUtil()
getPublicAccessToken = getPublic
const {results = []} = await fetchDatasetFromKg()
const { results = [] } = await fetchDatasetFromKg()
cachedData = results
}
exports.getDatasets = ({ templateName, parcellationName, user }) => getDs({ user })
.then(json => filter(json, {templateName, parcellationName}))
.then(json => filter(json, { templateName, parcellationName }))
exports.getPreview = ({ datasetName, templateSelected }) => getPreviewFile({ datasetName, templateSelected })
......@@ -185,82 +185,121 @@ exports.getPreview = ({ datasetName, templateSelected }) => getPreviewFile({ dat
* change to real spatial query
*/
const cachedMap = new Map()
const fetchSpatialDataFromKg = async ({ templateName, queryArg, user }) => {
try {
const coordsString = queryArg.split('__');
const boundingBoxCorners = coordsString.map(coordString => coordString.split('_'))
if (templateName === 'Waxholm Space rat brain atlas v.2.0') {
const boundingBoxInWaxhomV2VoxelSpace = boundingBoxCorners.map(transformWaxholmV2NmToVoxel)
const spatialData = await fetchSpatialData({boundingBoxInWaxhomV2VoxelSpace, user})
if (spatialData.length) {
return spatialData
} else {
return []
}
/**
* TODO change to URL constructor to improve readability
*/
const spatialQuery = 'https://kg.humanbrainproject.eu/query/neuroglancer/seeg/coordinate/v1.0.0/spatialWithCoordinates/instances?vocab=https%3A%2F%2Fschema.hbp.eu%2FmyQuery%2F'
const getXformFn = (templateSpace) => {
const _ = {}
switch(templateSpace){
case 'Waxholm Space rat brain atlas v.2.0':
_['nmToVoxel'] = transformWaxholmV2NmToVoxel
_['voxelToNm'] = transformWaxholmV2VoxelToNm
break;
default: {
_['nmToVoxel'] = defaultXform
_['voxelToNm'] = defaultXform
}
} catch (e) {
console.log('datasets#query.js#fetchSpatialDataFromKg', 'read file and parse json failed', e)
return []
}
return _
}
exports.getSpatialDatasets = async ({ templateName, queryGeometry, queryArg, user }) => {
return await fetchSpatialDataFromKg({ templateName, queryArg, user })
const getSpatialSearcParam = ({ templateName, queryArg }) => {
let kgSpaceName
const { nmToVoxel } = getXformFn(templateName)
const coordsString = queryArg.split('__');
const boundingBoxCorners = coordsString.map(coordString => coordString.split('_'))
const bbInVoxelSpace = boundingBoxCorners.map(nmToVoxel)
switch (templateName){
case 'Waxholm Space rat brain atlas v.2.0':
kgSpaceName = 'waxholmV2'
break;
default:
kgSpaceName = templateName
}
return {
boundingBox: `${kgSpaceName}:${bbInVoxelSpace.map(v => v.join(',')).join(',')}`
}
}
async function fetchSpatialData({ user, boundingBoxInWaxhomV2VoxelSpace }) {
const { releasedOnly, option } = await getUserKGRequestInfo({ user })
const spatialQuery = 'https://kg.humanbrainproject.eu/query/neuroglancer/seeg/coordinate/v1.0.0/spatialWithCoordinates/instances?vocab=https%3A%2F%2Fschema.hbp.eu%2FmyQuery%2F'
return await new Promise((resolve, reject) => {
// ToDo need too add: "${releasedOnly ? '&databaseScope=RELEASED' : ''}"
request(`${spatialQuery}&boundingBox=waxholmV2:${boundingBoxInWaxhomV2VoxelSpace.map(cornerCoord => cornerCoord.join(',')).join(',')}${releasedOnly ? '&databaseScope=RELEASED' : ''}`, option, (err, resp, body) => {
if (err)
return reject(err)
if (resp.statusCode >= 400) {
return reject(resp.statusCode)
}
const json = JSON.parse(body).results.map(res => {
return {name: res.name,
templateSpace: res['dataset'][0]['name'],
geometry: {
type: "point",
space: "real",
position: transformVoxelToWaxholmV2Nm ([
res['coordinates'][0]['x'],
res['coordinates'][0]['y'],
res['coordinates'][0]['z'],
])}
}
})
return resolve(json)
})
const fetchSpatialDataFromKg = async ({ templateName, queryGeometry, queryArg, user }) => {
const { releasedOnly, option } = await getUserKGRequestInfo({ user })
const _ = getSpatialSearcParam({ templateName, queryGeometry, queryArg })
const url = require('url')
const search = new url.URLSearchParams()
for (let key in _) {
search.append(key, _[key])
}
if (releasedOnly) search.append('databaseScope', 'RELEASED')
const _url = `${spatialQuery}&${search.toString()}`
return await new Promise((resolve, reject) => {
request(_url, option, (err, resp, body) => {
if (err)
return reject(err)
if (resp.statusCode >= 400) {
return reject(resp.statusCode)
}
const json = JSON.parse(body)
const { voxelToNm } = getXformFn(templateName)
const _ = json.results.map(({ name, coordinates}) => {
return {
name,
templateSpace: templateName,
geometry: {
type: 'point',
space: 'real',
position: voxelToNm([
coordinates[0].x,
coordinates[0].y,
coordinates[0].z
])
}
}
})
return resolve(_)
})
})
}
exports.getSpatialDatasets = async ({ templateName, queryGeometry, queryArg, user }) => {
/**
* Local data can be injected here
*/
return await fetchSpatialDataFromKg({ templateName, queryGeometry, queryArg, user })
}
async function getUserKGRequestInfo({ user }) {
const accessToken = user && user.tokenset && user.tokenset.access_token
const releasedOnly = !accessToken
let publicAccessToken
if (!accessToken && getPublicAccessToken) {
publicAccessToken = await getPublicAccessToken()
const accessToken = user && user.tokenset && user.tokenset.access_token
const releasedOnly = !accessToken
let publicAccessToken
if (!accessToken && getPublicAccessToken) {
publicAccessToken = await getPublicAccessToken()
}
const option = accessToken || publicAccessToken || process.env.ACCESS_TOKEN
? {
auth: {
'bearer': accessToken || publicAccessToken || process.env.ACCESS_TOKEN
}
}
const option = accessToken || publicAccessToken || process.env.ACCESS_TOKEN
? {
auth: {
'bearer': accessToken || publicAccessToken || process.env.ACCESS_TOKEN
}
}
: {}
: {}
return {option, releasedOnly}
return {option, releasedOnly}
}
/**
*
* perhaps export the xform fns into a different module
* ideally, in the future, KG can handle xform of voxel to nm
*/
const transformWaxholmV2NmToVoxel = (coord) => {
/**
......@@ -271,19 +310,19 @@ const transformWaxholmV2NmToVoxel = (coord) => {
* atlas viewer applies translation (below in nm) in order to center the brain
* query already translates nm to mm, so the unit of transl should be [mm, mm, mm]
*/
const transl = [-9550781,-24355468,-9707031].map(v => v / 1e6)
const transl = [-9550781, -24355468, -9707031].map(v => v / 1e6)
/**
* mm/voxel
*/
const voxelDim = [0.0390625, 0.0390625, 0.0390625]
return coord.map((v, idx) => (v - transl[idx]) / voxelDim[idx] )
return coord.map((v, idx) => (v - transl[idx]) / voxelDim[idx])
}
const transformVoxelToWaxholmV2Nm = (coord) => {
const transl = [-9550781,-24355468,-9707031].map(v => v / 1e6)
const transformWaxholmV2VoxelToNm = (coord) => {
const transl = [-9550781, -24355468, -9707031].map(v => v / 1e6)
const voxelDim = [0.0390625, 0.0390625, 0.0390625]
return coord.map((v, idx) => (v * voxelDim[idx]) + transl[idx])
}
const defaultXform = (coord) => coord
\ No newline at end of file
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