From 795764ad8d9fb6ed3b320f793107fe370e3d9b7f Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Wed, 19 Jun 2019 10:50:49 +0200
Subject: [PATCH] chore: cleanup code, rename var, fix typos
---
deploy/datasets/query.js | 73 ++++++++++++++++----------------
deploy/datasets/spatialRouter.js | 3 +-
2 files changed, 38 insertions(+), 38 deletions(-)
diff --git a/deploy/datasets/query.js b/deploy/datasets/query.js
index 9d5332445..b0df2342c 100644
--- a/deploy/datasets/query.js
+++ b/deploy/datasets/query.js
@@ -15,12 +15,12 @@ const STORAGE_PATH = process.env.STORAGE_PATH || path.join(__dirname, 'data')
let getPublicAccessToken
-const fetchDatasetFromKg = async (arg) => {
+const fetchDatasetFromKg = async ({ user } = {}) => {
- const userState = await getUserKGRequestInfo(arg)
+ const { releasedOnly, option } = await getUserKGRequestInfo({ user })
return await new Promise((resolve, reject) => {
- request(`${queryUrl}${userState.releasedOnly ? '&databaseScope=RELEASED' : ''}`, userState.option, (err, resp, body) => {
+ request(`${queryUrl}${releasedOnly ? '&databaseScope=RELEASED' : ''}`, option, (err, resp, body) => {
if (err)
return reject(err)
if (resp.statusCode >= 400)
@@ -185,7 +185,7 @@ exports.getPreview = ({ datasetName, templateSelected }) => getPreviewFile({ dat
* change to real spatial query
*/
const cachedMap = new Map()
-const fetchSpatialDataFromKg = async ({ templateName, queryArg, req }) => {
+const fetchSpatialDataFromKg = async ({ templateName, queryArg, user }) => {
try {
const filename = path.join(STORAGE_PATH, templateName + '.json')
const exists = fs.existsSync(filename)
@@ -196,27 +196,16 @@ const fetchSpatialDataFromKg = async ({ templateName, queryArg, req }) => {
const data = fs.readFileSync(filename, 'utf-8')
const json = JSON.parse(data)
- var splitQueryArg = queryArg.split('__');
- const cubeDots = []
- splitQueryArg.forEach(element => {
- cubeDots.push(element.split('_'))
- });
-
+ const coordsString = queryArg.split('__');
+ const boundingBoxCorners = coordsString.map(coordString => coordString.split('_'))
if (templateName !== 'Waxholm Space rat brain atlas v.2.0') {
- return json.filter(filterByqueryArg(cubeDots))
+ return json.filter(filterByqueryArg(boundingBoxCorners))
} else {
- 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))
+ const boundingBoxInWaxhomV2VoxelSpace = boundingBoxCorners.map(transformWaxholmV2NmToVoxel)
+ const { total = 0 } = await getSpatialSearchOk({boundingBoxInWaxhomV2VoxelSpace, user})
+ if (total > 0) {
+ return json.filter(filterByqueryArg(boundingBoxCorners))
} else {
return []
}
@@ -227,8 +216,8 @@ const fetchSpatialDataFromKg = async ({ templateName, queryArg, req }) => {
}
}
-exports.getSpatialDatasets = async ({ templateName, queryGeometry, queryArg, req }) => {
- return await fetchSpatialDataFromKg({ templateName, queryArg, req })
+exports.getSpatialDatasets = async ({ templateName, queryGeometry, queryArg, user }) => {
+ return await fetchSpatialDataFromKg({ templateName, queryArg, user })
}
@@ -240,26 +229,21 @@ function filterByqueryArg(cubeDots) {
if (cubeDots[0][0] <= px && px <= cubeDots[1][0]
&& cubeDots[0][1] <= py && py <= cubeDots[1][1]
&& cubeDots[0][2] <= pz && pz <= cubeDots[1][2]) {
- return true;
+ return true
}
+ return false
}
- return false;
}
-async function getSpatialSearchOk(arg) {
+async function getSpatialSearchOk({ user, boundingBoxInWaxhomV2VoxelSpace }) {
- const userState = await getUserKGRequestInfo(arg.req)
- const option = {
- headers: {
- 'Authorization': userState.token
- }
- }
+ const { releasedOnly, option } = await getUserKGRequestInfo({ user })
const spatialQuery = 'https://kg.humanbrainproject.org/query/minds/core/dataset/v1.0.0/spatialSimple/instances?size=10'
return await new Promise((resolve, reject) => {
- request(`${spatialQuery}${'&boundingBox=waxholmV2:' + arg.calculatedCubeDots[0].concat(arg.calculatedCubeDots[1])}${userState.releasedOnly ? '&databaseScope=RELEASED' : ''}`, option, (err, resp, body) => {
+ request(`${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)
@@ -270,8 +254,8 @@ async function getSpatialSearchOk(arg) {
})
}
-async function getUserKGRequestInfo(arg) {
- const accessToken = arg && arg.user && arg.user.tokenset && arg.user.tokenset.access_token
+async function getUserKGRequestInfo({ user }) {
+ const accessToken = user && user.tokenset && user.tokenset.access_token
const releasedOnly = !accessToken
let publicAccessToken
if (!accessToken && getPublicAccessToken) {
@@ -288,8 +272,23 @@ async function getUserKGRequestInfo(arg) {
return {option, releasedOnly, token: accessToken || publicAccessToken || process.env.ACCESS_TOKEN}
}
-const transformToWoxel = (coord) => {
+/**
+ *
+ */
+const transformWaxholmV2NmToVoxel = (coord) => {
+ /**
+ * as waxholm is already in RAS, does not need to swap axis
+ */
+
+ /**
+ * 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)
+
+ /**
+ * mm/voxel
+ */
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 400da2aee..ef6574fc6 100644
--- a/deploy/datasets/spatialRouter.js
+++ b/deploy/datasets/spatialRouter.js
@@ -25,8 +25,9 @@ router.get('/templateName/:templateName/:queryGeometry/:queryArg', (req, res, ne
trace: 'dataset#spatialRouter'
})
+ const { user } = req
- getSpatialDatasets({ templateName, queryGeometry, queryArg, req })
+ getSpatialDatasets({ templateName, queryGeometry, queryArg, user })
.then(arr => res.status(200).json(arr))
.catch(error => {
next({
--
GitLab