From 7d0df31dec827eb31be74ee173fed9a91c0cd2fb Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Wed, 3 Jul 2019 11:23:27 +0200
Subject: [PATCH] chore: cleanup code improve reusability
---
deploy/datasets/query.js | 211 +++++++++++++++++++++++----------------
1 file changed, 125 insertions(+), 86 deletions(-)
diff --git a/deploy/datasets/query.js b/deploy/datasets/query.js
index 47a6b446d..55caaf309 100644
--- a/deploy/datasets/query.js
+++ b/deploy/datasets/query.js
@@ -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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