diff --git a/deploy/app.js b/deploy/app.js
index c7ba75d362271c3b12c00a720a0371daf03487ce..9011e1f21e674569e26a6a606519a05fbc623b39 100644
--- a/deploy/app.js
+++ b/deploy/app.js
@@ -37,6 +37,8 @@ app.use(session({
* async function, but can start server without
*/
configureAuth(app)
+ .then(() => console.log('configure auth properly'))
+ .catch(e => console.error('configure auth failed', e))
const publicPath = process.env.NODE_ENV === 'production'
? path.join(__dirname, 'public')
diff --git a/deploy/datasets/query.js b/deploy/datasets/query.js
index 22428ab08bb0fbcd8f1ae7e5df8e8af7f35d5906..dbc2bc1fdeeb52d3577ee27ad8e815ac9084c043 100644
--- a/deploy/datasets/query.js
+++ b/deploy/datasets/query.js
@@ -16,13 +16,10 @@ 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) {
- try {
- publicAccessToken = await getPublicAccessToken()
- } catch (e) {
- console.log('getPublicAccessToken Error', e)
- }
+ publicAccessToken = await getPublicAccessToken()
}
const option = accessToken || publicAccessToken || process.env.ACCESS_TOKEN
? {
@@ -32,7 +29,7 @@ const fetchDatasetFromKg = async (arg) => {
}
: {}
return await new Promise((resolve, reject) => {
- request(queryUrl, option, (err, resp, body) => {
+ request(`${queryUrl}${releasedOnly ? '&databaseScope=RELEASED' : ''}`, option, (err, resp, body) => {
if (err)
return reject(err)
if (resp.statusCode >= 400)
@@ -132,7 +129,7 @@ const filterByPRs = (prs, atlasPr) => atlasPr
const manualFilter = require('./supplements/parcellation')
-const filter = (datasets, {templateName, parcellationName}) => datasets
+const filter = (datasets = [], {templateName, parcellationName}) => datasets
.filter(ds => {
if (/infant/.test(ds.name))
return false
@@ -149,7 +146,7 @@ const filter = (datasets, {templateName, parcellationName}) => datasets
? longBundle
: parcellationName === 'Fibre Bundle Atlas - Short Bundle' && shortBundle
? shortBundle
- : parcellationName === 'Whole Brain (v2.0)'
+ : parcellationName === 'Waxholm Space rat brain atlas v.2.0'
? waxholm
: null
)
@@ -174,7 +171,8 @@ const filter = (datasets, {templateName, parcellationName}) => datasets
exports.init = async () => {
const { getPublicAccessToken: getPublic } = await kgQueryUtil()
getPublicAccessToken = getPublic
- cachedData = await fetchDatasetFromKg()
+ const {results = []} = await fetchDatasetFromKg()
+ cacheData = results
}
exports.getDatasets = ({ templateName, parcellationName, user }) => getDs({ user })
diff --git a/src/res/ext/waxholmRatV2_0.json b/src/res/ext/waxholmRatV2_0.json
index b2a9ac54a23901fc46192b979a780236a9e04b04..c4cf6171da1c2200dc096d378f59dea0ac2e1e49 100644
--- a/src/res/ext/waxholmRatV2_0.json
+++ b/src/res/ext/waxholmRatV2_0.json
@@ -1 +1 @@
-{"name":"Waxholm Space rat brain atlas v.2.0","type":"template","species":"Rat","useTheme":"dark","nehubaConfigURL":"nehubaConfig/waxholmRatV2_0NehubaConfig","parcellations":[{"ngId":"whole","type":"parcellation","name":"Whole Brain (v2.0)","ngData":null,"regions":[{"name":"White matter","description":null,"parent_name":null,"synonyms":[""],"acronyms":[""],"labelIndex":null,"rgb":null,"children":[{"name":"corpus callosum and associated subcortical white matter","description":null,"parent_name":"White matter","synonyms":[""],"acronyms":[""],"labelIndex":67,"rgb":[255,110,0],"children":null},{"name":"Anterior commissure","description":null,"parent_name":"White matter","synonyms":[""],"acronyms":[""],"labelIndex":null,"rgb":null,"children":[{"name":"anterior commissure, anterior part","description":null,"parent_name":"Anterior commissure","synonyms":[""],"acronyms":[""],"labelIndex":36,"rgb":[124,252,0],"children":null},{"name":"anterior commissure, posterior 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Spatial reference is provided by the Waxholm Space coordinate system."}}
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diff --git a/src/ui/databrowserModule/databrowser/databrowser.component.ts b/src/ui/databrowserModule/databrowser/databrowser.component.ts
index b314df6c4b69af7f38bfa12d3f83dc70f08b86b9..603340f20805e3fc0772890280ee38fa49e5e229 100644
--- a/src/ui/databrowserModule/databrowser/databrowser.component.ts
+++ b/src/ui/databrowserModule/databrowser/databrowser.component.ts
@@ -1,7 +1,7 @@
import { Component, OnDestroy, OnInit, ViewChild } from "@angular/core";
-import { DataEntry, DataStateInterface } from "src/services/stateStore.service";
+import { DataEntry } from "src/services/stateStore.service";
import { Subscription, merge } from "rxjs";
-import { DatabrowserService, CountedDataModality, getModalityFromDE } from "../databrowser.service";
+import { DatabrowserService, CountedDataModality } from "../databrowser.service";
import { ModalityPicker } from "../modalityPicker/modalityPicker.component";
@Component({
diff --git a/src/ui/databrowserModule/util/filterDataEntriesByMethods.pipe.ts b/src/ui/databrowserModule/util/filterDataEntriesByMethods.pipe.ts
index 103f57404094a57e33234daf4d49fb655a9e6f8e..3c3db25513fe1663c8c9e8bc7308d85a9a290583 100644
--- a/src/ui/databrowserModule/util/filterDataEntriesByMethods.pipe.ts
+++ b/src/ui/databrowserModule/util/filterDataEntriesByMethods.pipe.ts
@@ -14,11 +14,9 @@ export class FilterDataEntriesbyMethods implements PipeTransform{
const includeEmpty = dataModalities.some(d => d.name === noMethodDisplayName)
return dataEntries && dataModalities && dataModalities.length > 0
? dataEntries.filter(dataEntry => {
- return dataEntry.activity.some(a =>
- includeEmpty
- ? a.methods.length === 0
- : a.methods.some(m =>
- dataModalities.findIndex(dm => dm.name === temporaryFilterDataentryName(m)) >= 0))
+ return includeEmpty && dataEntry.methods.length === 0
+ || dataEntry.methods.some(m =>
+ dataModalities.findIndex(dm => dm.name === temporaryFilterDataentryName(m)) >= 0)
})
: dataEntries
}