From 78a5c79887dae8f86290512156518882195c6b9f Mon Sep 17 00:00:00 2001
From: Daviti Gogshelidze <daviti1@mail.com>
Date: Tue, 2 Jul 2019 14:38:03 +0200
Subject: [PATCH] Add spatial search from KG
---
deploy/datasets/query.js | 71 ++++++++++++++++++----------------------
1 file changed, 32 insertions(+), 39 deletions(-)
diff --git a/deploy/datasets/query.js b/deploy/datasets/query.js
index b0df2342c..47a6b446d 100644
--- a/deploy/datasets/query.js
+++ b/deploy/datasets/query.js
@@ -187,25 +187,14 @@ exports.getPreview = ({ datasetName, templateSelected }) => getPreviewFile({ dat
const cachedMap = new Map()
const fetchSpatialDataFromKg = async ({ templateName, queryArg, user }) => {
try {
- const filename = path.join(STORAGE_PATH, templateName + '.json')
- const exists = fs.existsSync(filename)
-
- if (!exists)
- return []
-
-
- const data = fs.readFileSync(filename, 'utf-8')
- const json = JSON.parse(data)
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(boundingBoxCorners))
- } else {
+ if (templateName === 'Waxholm Space rat brain atlas v.2.0') {
const boundingBoxInWaxhomV2VoxelSpace = boundingBoxCorners.map(transformWaxholmV2NmToVoxel)
- const { total = 0 } = await getSpatialSearchOk({boundingBoxInWaxhomV2VoxelSpace, user})
- if (total > 0) {
- return json.filter(filterByqueryArg(boundingBoxCorners))
+ const spatialData = await fetchSpatialData({boundingBoxInWaxhomV2VoxelSpace, user})
+ if (spatialData.length) {
+ return spatialData
} else {
return []
}
@@ -220,35 +209,33 @@ exports.getSpatialDatasets = async ({ templateName, queryGeometry, queryArg, use
return await fetchSpatialDataFromKg({ templateName, queryArg, user })
}
-
-function filterByqueryArg(cubeDots) {
- return function (item) {
- const px = item.geometry.position[0]
- const py = item.geometry.position[1]
- const pz = item.geometry.position[2]
- 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 false
- }
-}
-
-
-async function getSpatialSearchOk({ user, boundingBoxInWaxhomV2VoxelSpace }) {
-
+async function fetchSpatialData({ user, boundingBoxInWaxhomV2VoxelSpace }) {
const { releasedOnly, option } = await getUserKGRequestInfo({ user })
-
- const spatialQuery = 'https://kg.humanbrainproject.org/query/minds/core/dataset/v1.0.0/spatialSimple/instances?size=10'
+ 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)
+ if (resp.statusCode >= 400) {
return reject(resp.statusCode)
- const json = JSON.parse(body)
+ }
+
+ 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)
})
})
@@ -269,7 +256,7 @@ async function getUserKGRequestInfo({ user }) {
}
: {}
- return {option, releasedOnly, token: accessToken || publicAccessToken || process.env.ACCESS_TOKEN}
+ return {option, releasedOnly}
}
/**
@@ -285,7 +272,7 @@ const transformWaxholmV2NmToVoxel = (coord) => {
* 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
*/
@@ -293,4 +280,10 @@ const transformWaxholmV2NmToVoxel = (coord) => {
return coord.map((v, idx) => (v - transl[idx]) / voxelDim[idx] )
}
+const transformVoxelToWaxholmV2Nm = (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])
+}
+
--
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