From 5772751558ac0d9b813a57a109bd15d411b47a9c Mon Sep 17 00:00:00 2001
From: Daviti Gogshelidze <daviti1@mail.com>
Date: Fri, 14 Jun 2019 17:03:03 +0200
Subject: [PATCH] Syncronise spatial search with KG
---
deploy/datasets/query.js | 111 +++++++++++++++++++++++--------
deploy/datasets/spatialRouter.js | 5 +-
2 files changed, 88 insertions(+), 28 deletions(-)
diff --git a/deploy/datasets/query.js b/deploy/datasets/query.js
index 17ee2c7b7..973e47243 100644
--- a/deploy/datasets/query.js
+++ b/deploy/datasets/query.js
@@ -17,21 +17,10 @@ let getPublicAccessToken
const fetchDatasetFromKg = async (arg) => {
- const accessToken = arg && arg.user && arg.user.tokenset && arg.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 userState = getUserToken(arg)
+
return await new Promise((resolve, reject) => {
- request(`${queryUrl}${releasedOnly ? '&databaseScope=RELEASED' : ''}`, option, (err, resp, body) => {
+ request(`${queryUrl}${userState.releasedOnly ? '&databaseScope=RELEASED' : ''}`, userState.option, (err, resp, body) => {
if (err)
return reject(err)
if (resp.statusCode >= 400)
@@ -196,17 +185,15 @@ exports.getPreview = ({ datasetName, templateSelected }) => getPreviewFile({ dat
* change to real spatial query
*/
const cachedMap = new Map()
-const fetchSpatialDataFromKg = async ({ templateName, queryArg }) => {
- // const cachedResult = cachedMap.get(templateName)
- // if (cachedResult)
- // return cachedResult
-
- try {
- const filename = path.join(STORAGE_PATH, templateName + '.json')
+const fetchSpatialDataFromKg = async ({ templateName, queryArg, req }) => {
+ try {
+ // const filename = path.join(STORAGE_PATH, templateName + '.json')
+ const filename = path.join(__dirname + '/data/waxholm-hbp-00937-transformed.json')
const exists = fs.existsSync(filename)
if (!exists)
return []
+
const data = fs.readFileSync(filename, 'utf-8')
const json = JSON.parse(data)
@@ -216,16 +203,39 @@ const fetchSpatialDataFromKg = async ({ templateName, queryArg }) => {
cubeDots.push(element.split('_'))
});
- // cachedMap.set(templateName, json.filter(filterByqueryArg(cubeDots)))
- return json.filter(filterByqueryArg(cubeDots))
- } catch (e) {
+
+ if (templateName !== 'Waxholm Space rat brain atlas v.2.0') {
+ return json.filter(filterByqueryArg(cubeDots))
+ } else {
+ if (user && user.req) {
+ const centerDifference = [-9.550781, -24.355468, -9.707031]
+ let calculatedCubeDots = []
+ cubeDots.forEach((dots, index) => {
+ calculatedCubeDots[index] = cubeDots[index].map((num, idx) => {
+ return +num - centerDifference[idx]
+ })
+ })
+
+ calculatedCubeDots = calculatedCubeDots.map(x => transformToWoxel(x))
+
+ const resultFromKG = await getSpatialSearchOk({calculatedCubeDots, req})
+
+ if (resultFromKG && resultFromKG['total'] && resultFromKG['total'] > 0) {
+ return json.filter(filterByqueryArg(cubeDots))
+ } else {
+ return []
+ }
+ }
+
+ }
+ } catch (e) {
console.log('datasets#query.js#fetchSpatialDataFromKg', 'read file and parse json failed', e)
return []
}
}
-exports.getSpatialDatasets = async ({ templateName, queryGeometry, queryArg }) => {
- return await fetchSpatialDataFromKg({ templateName, queryArg })
+exports.getSpatialDatasets = async ({ templateName, queryGeometry, queryArg, req }) => {
+ return await fetchSpatialDataFromKg({ templateName, queryArg, req })
}
@@ -242,4 +252,53 @@ function filterByqueryArg(cubeDots) {
}
return false;
}
+
+
+async function getSpatialSearchOk(arg) {
+
+ const userState = getUserToken(arg.req)
+ const option = {
+ headers: {
+ 'Authorization': userState.token
+ }
+ }
+
+ const spatialQuery = 'https://kg.humanbrainproject.org/query/minds/core/dataset/v1.0.0/spatialSimple/instances?size=10&boundingBox=waxholmV2:180,750,390,200,780,400'
+
+ return await new Promise((resolve, reject) => {
+ request(`${spatialQuery}${'&boundingBox=waxholmV2:' + arg.calculatedCubeDots[0].concat(arg.calculatedCubeDots[1])}${userState.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)
+ return resolve(json)
+ })
+ })
+}
+
+function getUserToken(arg) {
+ const accessToken = arg && arg.user && arg.user.tokenset && arg.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
+ }
+ }
+ : {}
+
+ return {option, releasedOnly, token: accessToken || publicAccessToken || process.env.ACCESS_TOKEN}
+}
+
+const transformToWoxel = (coord) => {
+ const transl = [-9550781,-24355468,-9707031].map(v => v / 1e6)
+ const voxelDim = [0.0390625, 0.0390625, 0.0390625]
+ return coord.map((v, idx) => (v - transl[idx]) / voxelDim[idx] )
+}
+
diff --git a/deploy/datasets/spatialRouter.js b/deploy/datasets/spatialRouter.js
index 584eae6db..400da2aee 100644
--- a/deploy/datasets/spatialRouter.js
+++ b/deploy/datasets/spatialRouter.js
@@ -24,8 +24,9 @@ router.get('/templateName/:templateName/:queryGeometry/:queryArg', (req, res, ne
error: errorString,
trace: 'dataset#spatialRouter'
})
-
- getSpatialDatasets({ templateName, queryGeometry, queryArg })
+
+
+ getSpatialDatasets({ templateName, queryGeometry, queryArg, req })
.then(arr => res.status(200).json(arr))
.catch(error => {
next({
--
GitLab