diff --git a/Dockerfile b/Dockerfile index 588e1efca446da79f6d454c1b7c3153522e9117b..08353ee6c4c80b9763017a1aac712714c5048e74 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,6 +6,9 @@ ENV BACKEND_URL=${BACKEND_URL} ARG USE_LOGO ENV USE_LOGO=${USE_LOGO:-hbp} +ARG DATASET_PREVIEW_URL +ENV DATASET_PREVIEW_URL=${DATASET_PREVIEW_URL:-https://hbp-kg-dataset-previewer.apps.hbp.eu/datasetPreview} + COPY . /iv WORKDIR /iv diff --git a/deploy/datasets/query.js b/deploy/datasets/query.js index eb5571d757efd013f5372f0fd50961c147eed5ee..fc97e10e70a590a3fdcb982ddfc893915c9fa140 100644 --- a/deploy/datasets/query.js +++ b/deploy/datasets/query.js @@ -4,26 +4,31 @@ const URL = require('url') const path = require('path') const archiver = require('archiver') const { getPreviewFile, hasPreview } = require('./supplements/previewFile') -const { init: kgQueryUtilInit, getUserKGRequestParam, filterDatasets } = require('./util') +const { constants, init: kgQueryUtilInit, getUserKGRequestParam, filterDatasets } = require('./util') let cachedData = null let otherQueryResult = null -const KG_ROOT = process.env.KG_ROOT || `https://kg.humanbrainproject.eu` -const KG_PATH = process.env.KG_PATH || `/query/minds/core/dataset/v1.0.0/interactiveViewerKgQuery-v0_3` +const { KG_ROOT, KG_SEARCH_VOCAB } = constants + +const KG_DATASET_SEARCH_QUERY_NAME = process.env.KG_DATASET_SEARCH_QUERY_NAME || 'interactiveViewerKgQuery-v0_3' +const KG_DATASET_SEARCH_PATH = process.env.KG_DATASET_SEARCH_PATH || '/minds/core/dataset/v1.0.0' + +const kgDatasetSearchFullString = `${KG_DATASET_SEARCH_PATH}/${KG_DATASET_SEARCH_QUERY_NAME}` + const KG_PARAM = { size: process.env.KG_SEARCH_SIZE || '1000', - vocab: process.env.KG_SEARCH_VOCAB || 'https://schema.hbp.eu/myQuery/' + vocab: KG_SEARCH_VOCAB } -const KG_QUERY_DATASETS_URL = new URL.URL(`${KG_ROOT}${KG_PATH}/instances`) +const KG_QUERY_DATASETS_URL = new URL.URL(`${KG_ROOT}${kgDatasetSearchFullString}/instances`) for (let key in KG_PARAM) { KG_QUERY_DATASETS_URL.searchParams.set(key, KG_PARAM[key]) } const getKgQuerySingleDatasetUrl = ({ kgId }) => { const _newUrl = new URL.URL(KG_QUERY_DATASETS_URL) - _newUrl.pathname = `${KG_PATH}/instances/${kgId}` + _newUrl.pathname = `${_newUrl.pathname}/${kgId}` return _newUrl } diff --git a/deploy/datasets/spatialQuery.js b/deploy/datasets/spatialQuery.js index a93e41cdda0eb157a5b20c103251010041da34bd..11eec98d36a90bb53439f4be2f10b0fd6be95eff 100644 --- a/deploy/datasets/spatialQuery.js +++ b/deploy/datasets/spatialQuery.js @@ -1,12 +1,24 @@ const url = require('url') const request = require('request') -const { getUserKGRequestParam } = require('./util') +const { getUserKGRequestParam, constants } = require('./util') const { transformWaxholmV2NmToVoxel, transformWaxholmV2VoxelToNm } = require('./spatialXform/waxholmRat') /** * TODO change to URL constructor to improve readability */ -const spatialQuery = 'https://kg.humanbrainproject.eu/query/neuroglancer/seeg/coordinate/v1.0.0/spatialWithCoordinatesNG/instances?vocab=https%3A%2F%2Fschema.hbp.eu%2FmyQuery%2F' + +const { KG_ROOT, KG_SEARCH_VOCAB } = constants + +const kgParams = { + vocab: KG_SEARCH_VOCAB +} + +const KG_SPATIAL_DATASET_SEARCH_QUERY_NAME = process.env.KG_SPATIAL_DATASET_SEARCH_QUERY_NAME || 'iav-spatial-query-v2' +const KG_SPATIAL_DATASET_SEARCH_PATH = process.env.KG_SPATIAL_DATASET_SEARCH_PATH || '/neuroglancer/seeg/coordinate/v1.0.0' + +const kgSpatialDatasetSearchFullString = `${KG_SPATIAL_DATASET_SEARCH_PATH}/${KG_SPATIAL_DATASET_SEARCH_QUERY_NAME}` + +const kgQuerySpatialDatasetUrl = new url.URL(`${KG_ROOT}${kgSpatialDatasetSearchFullString}/instances`) const defaultXform = (coord) => coord @@ -51,30 +63,29 @@ const fetchSpatialDataFromKg = async ({ templateName, queryGeometry, queryArg, u const { releasedOnly, option } = await getUserKGRequestParam({ user }) const _ = getSpatialSearcParam({ templateName, queryGeometry, queryArg }) - const search = new url.URLSearchParams() + const _url = new url.URL(kgQuerySpatialDatasetUrl) + + for (const key in kgParams){ + _url.searchParams.append(key, kgParams[key]) + } for (let key in _) { - search.append(key, _[key]) + _url.searchParams.append(key, _[key]) } - if (releasedOnly) search.append('databaseScope', 'RELEASED') - - const _url = `${spatialQuery}&${search.toString()}` + if (releasedOnly) _url.searchParams.append('databaseScope', 'RELEASED') + return await new Promise((resolve, reject) => { request(_url, option, (err, resp, body) => { - if (err) - return reject(err) + 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, dataset}) => { + const _ = json.results.map(({ coordinates, ...rest}) => { return { - name, - templateSpace: templateName, - dataset: dataset.map(ds => ds = {name: ds.name, externalLink: 'https://kg.humanbrainproject.eu/instances/Dataset/' + ds.identifier}), + ...rest, geometry: { type: 'point', space: 'real', diff --git a/deploy/datasets/util.js b/deploy/datasets/util.js index d37ff932fd1b4a3025ec7267039f2736f4c79449..cdc9ca91a3905fc72d14e50222342249b38c7e13 100644 --- a/deploy/datasets/util.js +++ b/deploy/datasets/util.js @@ -296,6 +296,9 @@ const init = async () => { getPublicAccessToken = getPublic } +const KG_ROOT = process.env.KG_ROOT || `https://kg.humanbrainproject.eu/query` +const KG_SEARCH_VOCAB = process.env.KG_SEARCH_VOCAB || 'https://schema.hbp.eu/myQuery/' + module.exports = { getIdFromFullId, populateSet, @@ -318,5 +321,9 @@ module.exports = { allen2015Set, allen2017Set } + }, + constants: { + KG_ROOT, + KG_SEARCH_VOCAB } } \ No newline at end of file diff --git a/package.json b/package.json index 3800114bcea82a892be260eae8e04a33ad1bf79a..fcaa8dff775fc6b1b3e197e6e4c275386e65aee0 100644 --- a/package.json +++ b/package.json @@ -47,6 +47,7 @@ "@typescript-eslint/eslint-plugin": "^2.12.0", "@typescript-eslint/parser": "^2.12.0", "angular2-template-loader": "^0.6.2", + "bootstrap": "^4.4.1", "codelyzer": "^5.0.1", "core-js": "^3.0.1", "css-loader": "^3.2.0", @@ -67,7 +68,7 @@ "karma-jasmine": "^2.0.1", "karma-typescript": "^4.1.1", "karma-webpack": "^3.0.0", - "kg-dataset-previewer": "0.0.8", + "kg-dataset-previewer": "0.0.10", "lodash.merge": "^4.6.2", "mini-css-extract-plugin": "^0.8.0", "ngx-bootstrap": "3.0.1", diff --git a/spec/karma.conf.js b/spec/karma.conf.js index ee43450136d389ae2f97f90dfb94cf09cf2393c8..4f4eb985a36341172d86343a1b95e194e9300bbc 100644 --- a/spec/karma.conf.js +++ b/spec/karma.conf.js @@ -25,7 +25,27 @@ module.exports = function(config) { // list of files / patterns to load in the browser files: [ - './spec/test.ts' + './spec/test.ts', + { + pattern: 'node_modules/bootstrap/dist/css/bootstrap.min.css', + served: true, + included: true + }, + { + pattern: 'node_modules/@angular/material/prebuilt-themes/indigo-pink.css', + served: true, + included: true + }, + { + pattern: './src/util/worker.js', + served: true, + included: false + }, + { + pattern: './src/res/css/extra_styles.css', + served: true, + included: true + } ], diff --git a/spec/util.ts b/spec/util.ts new file mode 100644 index 0000000000000000000000000000000000000000..9925589fefa2a49339b67a696b69eae2ef8476f8 --- /dev/null +++ b/spec/util.ts @@ -0,0 +1,14084 @@ +import { HttpInterceptor, HttpEvent, HttpHandler, HttpRequest, HttpResponse, HttpHeaders } from '@angular/common/http' +import { Injectable } from '@angular/core'; +import { Observable, of } from 'rxjs'; + +@Injectable() +export class HttpMockRequestInterceptor implements HttpInterceptor{ + + intercept(request:HttpRequest<any>, next:HttpHandler):Observable<HttpEvent<any>> { + const test = /\/datasets/.test(request.url) + if (test) { + + const headers = new HttpHeaders() + headers.set('content-type', 'application/json') + + return of(new HttpResponse({ + status: 200, + body: [], + headers + })) + } + return next.handle(request) + } +} + +export const JUBRAIN_COLIN_CH123_LEFT = { + "name": "Ch 123 (Basal Forebrain) - left hemisphere", + "rgb": [ + 124, + 233, + 167 + ], + "labelIndex": 286, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP", + "position": [ + -2339339, + 4405405, + -8804805 + ] +} + +export const JUBRAIN_COLIN_CH123_RIGHT = { + "name": "Ch 123 (Basal Forebrain) - right hemisphere", + "rgb": [ + 124, + 233, + 167 + ], + "ngId": "jubrain colin v18 right", + "labelIndex": 286, + "children": [], + "status": "publicP", + "position": [ + 3240000, + 5153846, + -8347692 + ] +} + +export const COLIN = { + "name": "MNI Colin 27", + "fullId": "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992", + "type": "template", + "species": "Human", + "useTheme": "dark", + "ngId": "colin", + "nehubaConfigURL": "nehubaConfig/colinNehubaConfig", + "parcellations": [ + { + "name": "JuBrain Cytoarchitectonic Atlas", + "ngId": "jubrain colin v18 left", + "auxillaryMeshIndices": [ + 65535 + ], + "hasAdditionalViewMode": [ + "connectivity" + ], + "originDatasets": [ + { + "kgSchema": "minds/core/dataset/v1.0.0", + "kgId": "4ac9f0bc-560d-47e0-8916-7b24da9bb0ce" + } + ], + "properties": { + "version": "1.0", + "description": "This dataset contains the whole-brain parcellation of the JuBrain Cytoarchitectonic Atlas (Amunts and Zilles, 2015) in the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. The parcellation is derived from the individual probability maps (PMs) of the cytoarchitectonic regions released in the JuBrain Atlas, that are further combined into a Maximum Probability Map (MPM). The MPM is calculated by considering for each voxel the probability of all cytoarchitectonic areas released in the atlas, and determining the most probable assignment (Eickhoff 2005). Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.", + "publications": [ + { + "doi": "https://doi.org/10.1038/nrn2776", + "citation": "Zilles K, Amunts K (2010) Centenary of Brodmann’s map – conception and fate. Nature Reviews Neuroscience 11(2): 139-145 " + }, + { + "doi": "https://doi.org/10.1016/j.neuroimage.2007.02.037", + "citation": "Amunts K, Schleicher A, Zilles K (2007) Cytoarchitecture of the cerebral cortex – more than localization. Neuroimage 37: 1061-1065" + }, + { + "doi": "http://dx.doi.org/10.1016/B978-012693019-1/50023-X", + "citation": "Zilles K, Schleicher A, Palomero-Gallagher N, Amunts K (2002) Quantitative analysis of cyto- and receptor architecture of the human brain. In: /Brain Mapping: The Methods/, J. C. Mazziotta and A. Toga (eds.), USA: Elsevier, 2002, p. 573-602." + } + ] + }, + "regions": [ + { + "name": "telencephalon", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "cerebral nuclei", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "basal forebrain", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "magnocellular group within septum", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "Ch 123 (Basal Forebrain)", + "arealabel": "Ch-123", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/7SEP-P2V", + "synonyms": [], + "rgb": [ + 124, + 233, + 167 + ], + "children": [ + { + "name": "Ch 123 (Basal Forebrain) - left hemisphere", + "rgb": [ + 124, + 233, + 167 + ], + "labelIndex": 286, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP", + "position": [ + -2339339, + 4405405, + -8804805 + ] + }, + { + "name": "Ch 123 (Basal Forebrain) - right hemisphere", + "rgb": [ + 124, + 233, + 167 + ], + "ngId": "jubrain colin v18 right", + "labelIndex": 286, + "children": [], + "status": "publicP", + "position": [ + 3240000, + 5153846, + -8347692 + ] + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022" + } + }, + "relatedAreas": [] + } + ] + }, + { + "name": "sublenticular part of basal forebrain", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "Ch 4 (Basal Forebrain)", + "arealabel": "Ch-4", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/VZJ5-8WJ", + "synonyms": [], + "rgb": [ + 116, + 243, + 12 + ], + "children": [ + { + "name": "Ch 4 (Basal Forebrain) - left hemisphere", + "rgb": [ + 116, + 243, + 12 + ], + "labelIndex": 264, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP", + "position": [ + -16053628, + -454259, + -12470032 + ] + }, + { + "name": "Ch 4 (Basal Forebrain) - right hemisphere", + "rgb": [ + 116, + 243, + 12 + ], + "ngId": "jubrain colin v18 right", + "labelIndex": 264, + "children": [], + "status": "publicP", + "position": [ + 17655072, + 263768, + -11539130 + ] + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "a5c9d95f-8e7c-4454-91b6-a790387370fc" + } + }, + "relatedAreas": [] + } + ] + }, + { + "name": "magnocellular group within horizontal limb of diagnoal band", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "Ch 123 (Basal Forebrain)", + "arealabel": "Ch-123", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/7SEP-P2V", + "synonyms": [], + "rgb": [ + 124, + 233, + 167 + ], + "children": [ + { + "name": "Ch 123 (Basal Forebrain) - left hemisphere", + "rgb": [ + 124, + 233, + 167 + ], + "labelIndex": 286, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP", + "position": [ + -2339339, + 4405405, + -8804805 + ] + }, + { + "name": "Ch 123 (Basal Forebrain) - right hemisphere", + "rgb": [ + 124, + 233, + 167 + ], + "ngId": "jubrain colin v18 right", + "labelIndex": 286, + "children": [], + "status": "publicP", + "position": [ + 3240000, + 5153846, + -8347692 + ] + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022" + } + }, + "relatedAreas": [] + } + ] + } + ] + }, + { + "name": "amygdala", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "laterobasal group", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "LB (Amygdala)", + "arealabel": "LB", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/C3X0-NV3", + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "LB (Amygdala) - left hemisphere", + "rgb": null, + "labelIndex": 15, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP" + }, + { + "name": "LB (Amygdala) - right hemisphere", + "rgb": null, + "ngId": "jubrain colin v18 right", + "labelIndex": 15, + "children": [], + "status": "publicP" + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "708df0fa-e9a4-4c23-bd85-8957f6d30faf" + } + }, + "relatedAreas": [] + }, + { + "name": "LB (Amygdala)", + "arealabel": "LB", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/C3X0-NV3", + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "LB (Amygdala) - left hemisphere", + "rgb": null, + "labelIndex": 11, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP" + }, + { + "name": "LB (Amygdala) - right hemisphere", + "rgb": null, + "ngId": "jubrain colin v18 right", + "labelIndex": 11, + "children": [], + "status": "publicP" + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "708df0fa-e9a4-4c23-bd85-8957f6d30faf" + } + }, + "relatedAreas": [] + }, + { + "name": "LB (Amygdala)", + "arealabel": "LB", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/C3X0-NV3", + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "LB (Amygdala) - left hemisphere", + "rgb": null, + "labelIndex": 19, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP" + }, + { + "name": "LB (Amygdala) - right hemisphere", + "rgb": null, + "ngId": "jubrain colin v18 right", + "labelIndex": 19, + "children": [], + "status": "publicP" + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "708df0fa-e9a4-4c23-bd85-8957f6d30faf" + } + }, + "relatedAreas": [] + }, + { + "name": "LB (Amygdala)", + "arealabel": "LB", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/C3X0-NV3", + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "LB (Amygdala) - left hemisphere", + "rgb": null, + "labelIndex": 13, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP", + "position": [ + -25304803, + -1696429, + -23766626 + ] + }, + { + "name": "LB (Amygdala) - right hemisphere", + "rgb": null, + "ngId": "jubrain colin v18 right", + "labelIndex": 13, + "children": [], + "status": "publicP", + "position": [ + 28015494, + -81343, + -24045836 + ] + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "708df0fa-e9a4-4c23-bd85-8957f6d30faf" + } + }, + "relatedAreas": [] + } + ] + }, + { + "name": "superficial group", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "SF (Amygdala)", + "arealabel": "SF", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/WD31-SEA", + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "SF (Amygdala) - 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(Holmes et al., 1998), mapped to fit the MNI305 space. Although not capturing brain variability, it is well established in neuroscience due to its high definition. HBP provides the JuBrain probabilistic cytoarchitectonic atlas (Amunts et al.) in this space." + } +} + +export const JUBRAIN_COLIN = { + "name": "JuBrain Cytoarchitectonic Atlas", + "ngId": "jubrain colin v18 left", + "auxillaryMeshIndices": [ + 65535 + ], + "hasAdditionalViewMode": [ + "connectivity" + ], + "originDatasets": [ + { + "kgSchema": "minds/core/dataset/v1.0.0", + "kgId": "4ac9f0bc-560d-47e0-8916-7b24da9bb0ce" + } + ], + "properties": { + "version": "1.0", + "description": "This dataset contains the whole-brain parcellation of the JuBrain Cytoarchitectonic Atlas (Amunts and Zilles, 2015) in the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. The parcellation is derived from the individual probability maps (PMs) of the cytoarchitectonic regions released in the JuBrain Atlas, that are further combined into a Maximum Probability Map (MPM). The MPM is calculated by considering for each voxel the probability of all cytoarchitectonic areas released in the atlas, and determining the most probable assignment (Eickhoff 2005). Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.", + "publications": [ + { + "doi": "https://doi.org/10.1038/nrn2776", + "citation": "Zilles K, Amunts K (2010) Centenary of Brodmann’s map – conception and fate. Nature Reviews Neuroscience 11(2): 139-145 " + }, + { + "doi": "https://doi.org/10.1016/j.neuroimage.2007.02.037", + "citation": "Amunts K, Schleicher A, Zilles K (2007) Cytoarchitecture of the cerebral cortex – more than localization. Neuroimage 37: 1061-1065" + }, + { + "doi": "http://dx.doi.org/10.1016/B978-012693019-1/50023-X", + "citation": "Zilles K, Schleicher A, Palomero-Gallagher N, Amunts K (2002) Quantitative analysis of cyto- and receptor architecture of the human brain. In: /Brain Mapping: The Methods/, J. C. Mazziotta and A. Toga (eds.), USA: Elsevier, 2002, p. 573-602." + } + ] + }, + "regions": [ + { + "name": "telencephalon", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "cerebral nuclei", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "basal forebrain", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "magnocellular group within septum", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "Ch 123 (Basal Forebrain)", + "arealabel": "Ch-123", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/7SEP-P2V", + "synonyms": [], + "rgb": [ + 124, + 233, + 167 + ], + "children": [ + { + "name": "Ch 123 (Basal Forebrain) - left hemisphere", + "rgb": [ + 124, + 233, + 167 + ], + "labelIndex": 286, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP", + "position": [ + -2339339, + 4405405, + -8804805 + ] + }, + { + "name": "Ch 123 (Basal Forebrain) - 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left hemisphere", + "rgb": [ + 137, + 12, + 73 + ], + "labelIndex": 68, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP", + "position": [ + -13947917, + -9576389, + -18975694 + ] + }, + { + "name": "HATA (Hippocampus) - right hemisphere", + "rgb": [ + 137, + 12, + 73 + ], + "ngId": "jubrain colin v18 right", + "labelIndex": 68, + "children": [], + "status": "publicP", + "position": [ + 15080586, + -8358974, + -17871795 + ] + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "9ec4a423-70fa-43cd-90b3-fbc26a3cbc6c" + } + }, + "relatedAreas": [] + }, + { + "name": "Entorhinal Cortex", + "arealabel": "Entorhinal-Cortex", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/KNXY-B1Z", + "synonyms": [], + "rgb": [ + 35, + 159, + 214 + ], + "children": [ + { + "name": "Entorhinal Cortex - left hemisphere", + "rgb": [ + 35, + 159, + 214 + ], + "labelIndex": 60, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP", + "position": [ + -20926052, + -6082765, + -33357509 + ] + }, + { + "name": "Entorhinal Cortex - right hemisphere", + "rgb": [ + 35, + 159, + 214 + ], + "ngId": "jubrain colin v18 right", + "labelIndex": 60, + "children": [], + "status": "publicP", + "position": [ + 22877203, + -3501469, + -32577556 + ] + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "030827d4-e0d1-4406-b71f-3f58dc2f9cca" + } + }, + "relatedAreas": [] + }, + { + "name": "CA (Hippocampus)", + "arealabel": "CA", + "status": "publicP", + "labelIndex": null, + "relatedAreas": [ + { + "name": "CA1 (Hippocampus)", + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "bfc0beb7-310c-4c57-b810-2adc464bd02c" + } + } + } + ], + "doi": "https://doi.org/10.25493/B85T-D88", + "synonyms": [], + "rgb": [ + 250, + 191, + 217 + ], + "children": [ + { + "name": "CA (Hippocampus) - left hemisphere", + "rgb": [ + 250, + 191, + 217 + ], + "labelIndex": 191, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP", + "position": [ + -27476326, + -26068931, + -11082817 + ] + }, + { + "name": "CA (Hippocampus) - right hemisphere", + "rgb": [ + 250, + 191, + 217 + ], + "ngId": "jubrain colin v18 right", + "labelIndex": 191, + "children": [], + "status": "publicP", + "position": [ + 29426785, + -24801145, + -11142814 + ] + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "a0d14d3e-bc30-41cf-8b28-540067897f80" + } + } + }, + { + "name": "DG (Hippocampus)", + "arealabel": "DG", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/M8JP-XQT", + "synonyms": [], + "rgb": [ + 149, + 55, + 120 + ], + "children": [ + { + "name": "DG (Hippocampus) - left hemisphere", + "rgb": [ + 149, + 55, + 120 + ], + "labelIndex": 61, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP", + "position": [ + -26946498, + -26708171, + -9589494 + ] + }, + { + "name": "DG (Hippocampus) - right hemisphere", + "rgb": [ + 149, + 55, + 120 + ], + "ngId": "jubrain colin v18 right", + "labelIndex": 61, + "children": [], + "status": "publicP", + "position": [ + 28316456, + -24674684, + -10596203 + ] + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "0bea7e03-bfb2-4907-9d45-db9071ce627d" + } + }, + "relatedAreas": [] + }, + { + "name": "Subiculum (Hippocampus)", + "arealabel": "Subiculum", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/QKJH-F45", + "synonyms": [], + "rgb": [ + 111, + 125, + 219 + ], + "children": [ + { + "name": "Subiculum (Hippocampus) - left hemisphere", + "rgb": [ + 111, + 125, + 219 + ], + "labelIndex": 192, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP", + "position": [ + -20352171, + -24057796, + -16326997 + ] + }, + { + "name": "Subiculum (Hippocampus) - right hemisphere", + "rgb": [ + 111, + 125, + 219 + ], + "ngId": "jubrain colin v18 right", + "labelIndex": 192, + "children": [], + "status": "publicP", + "position": [ + 22543982, + -23195614, + -15923499 + ] + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "7e2dab4c-a140-440d-a322-c1679adef2d4" + } + }, + "relatedAreas": [] + } + ] + } + ] + } + ] + } + ] + }, + { + "name": "metencephalon", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "cerebellum", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "cerebellar nuclei", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "globose nucleus", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "Interposed Nucleus (Cerebellum)", + "arealabel": "Interposed-Nucleus", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/8PTB-JDH", + "synonyms": [], + "rgb": [ + 170, + 29, + 10 + ], + "children": [ + { + "name": "Interposed Nucleus (Cerebellum) - left hemisphere", + "rgb": [ + 170, + 29, + 10 + ], + "labelIndex": 251, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP", + "position": [ + -8457921, + -55262376, + -30235149 + ] + }, + { + "name": "Interposed Nucleus (Cerebellum) - right hemisphere", + "rgb": [ + 170, + 29, + 10 + ], + "ngId": "jubrain colin v18 right", + "labelIndex": 251, + "children": [], + "status": "publicP", + "position": [ + 7917989, + -54201058, + -31489418 + ] + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "85e7bb13-4b73-4f6f-8222-3adb7b800788" + } + }, + "relatedAreas": [] + } + ] + }, + { + "name": "dentate nucleus", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "Dorsal Dentate Nucleus (Cerebellum)", + "arealabel": "Dorsal-Dentate-Nucleus", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/M5QG-SHH", + "synonyms": [], + "rgb": [ + 89, + 201, + 99 + ], + "children": [ + { + "name": "Dorsal Dentate Nucleus (Cerebellum) - left hemisphere", + "rgb": [ + 89, + 201, + 99 + ], + "labelIndex": 240, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP", + "position": [ + -16612782, + -56036341, + -36064536 + ] + }, + { + "name": "Dorsal Dentate Nucleus (Cerebellum) - right hemisphere", + "rgb": [ + 89, + 201, + 99 + ], + "ngId": "jubrain colin v18 right", + "labelIndex": 240, + "children": [], + "status": "publicP", + "position": [ + 15388967, + -58303395, + -36586280 + ] + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "58095aef-da69-43d4-887c-009c095cecce" + } + }, + "relatedAreas": [] + }, + { + "name": "Ventral Dentate Nucleus (Cerebellum)", + "arealabel": "Ventral-Dentate-Nucleus", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/FQE5-5QR", + "synonyms": [], + "rgb": [ + 39, + 129, + 9 + ], + "children": [ + { + "name": "Ventral Dentate Nucleus (Cerebellum) - left hemisphere", + "rgb": [ + 39, + 129, + 9 + ], + "labelIndex": 241, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP", + "position": [ + -13112867, + -56176072, + -29957111 + ] + }, + { + "name": "Ventral Dentate Nucleus (Cerebellum) - right hemisphere", + "rgb": [ + 39, + 129, + 9 + ], + "ngId": "jubrain colin v18 right", + "labelIndex": 241, + "children": [], + "status": "publicP", + "position": [ + 12107011, + -55974170, + -31385609 + ] + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "57282342-5a75-4e07-bcdc-2d368c517b71" + } + }, + "relatedAreas": [] + } + ] + }, + { + "name": "fastigial nucleus", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "Fastigial Nucleus (Cerebellum)", + "arealabel": "Fastigial-Nucleus", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/3YJ9-S6G", + "synonyms": [], + "rgb": [ + 200, + 100, + 10 + ], + "children": [ + { + "name": "Fastigial Nucleus (Cerebellum) - left hemisphere", + "rgb": [ + 200, + 100, + 10 + ], + "labelIndex": 219, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP", + "position": [ + -3828877, + -53149733, + -29013369 + ] + }, + { + "name": "Fastigial Nucleus (Cerebellum) - right hemisphere", + "rgb": [ + 200, + 100, + 10 + ], + "ngId": "jubrain colin v18 right", + "labelIndex": 219, + "children": [], + "status": "publicP", + "position": [ + 3011287, + -53069977, + -29040632 + ] + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "e8abfe3d-8b64-45c2-8853-314d82873273" + } + }, + "relatedAreas": [] + } + ] + }, + { + "name": "emboliform nucleus", + "status": null, + "labelIndex": null, + "synonyms": [], + "rgb": null, + "children": [ + { + "name": "Interposed Nucleus (Cerebellum)", + "arealabel": "Interposed-Nucleus", + "status": "publicP", + "labelIndex": null, + "doi": "https://doi.org/10.25493/8PTB-JDH", + "synonyms": [], + "rgb": [ + 170, + 29, + 10 + ], + "children": [ + { + "name": "Interposed Nucleus (Cerebellum) - left hemisphere", + "rgb": [ + 170, + 29, + 10 + ], + "labelIndex": 251, + "ngId": "jubrain colin v18 left", + "children": [], + "status": "publicP", + "position": [ + -8457921, + -55262376, + -30235149 + ] + }, + { + "name": "Interposed Nucleus (Cerebellum) - right hemisphere", + "rgb": [ + 170, + 29, + 10 + ], + "ngId": "jubrain colin v18 right", + "labelIndex": 251, + "children": [], + "status": "publicP", + "position": [ + 7917989, + -54201058, + -31489418 + ] + } + ], + "fullId": { + "kg": { + "kgSchema": "minds/core/parcellationregion/v1.0.0", + "kgId": "85e7bb13-4b73-4f6f-8222-3adb7b800788" + } + }, + "relatedAreas": [] + } + ] + } + ] + } + ] + } + ] + } + ] +} diff --git a/src/atlasViewer/atlasViewer.component.ts b/src/atlasViewer/atlasViewer.component.ts index 7b2659e3cfb08e3ecb498db89a99cb0e8502e6a0..3dcb365b3f578d52eb83be5b462fabdc23dfe487 100644 --- a/src/atlasViewer/atlasViewer.component.ts +++ b/src/atlasViewer/atlasViewer.component.ts @@ -41,6 +41,7 @@ import { FixedMouseContextualContainerDirective } from "src/util/directives/Fixe import { getViewer, isSame } from "src/util/fn"; import { NehubaContainer } from "../ui/nehubaContainer/nehubaContainer.component"; import { colorAnimation } from "./atlasViewer.animation" +import { MouseHoverDirective } from "src/util/directives/mouseOver.directive"; /** * TODO @@ -71,6 +72,7 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit { @ViewChild(NehubaContainer) public nehubaContainer: NehubaContainer @ViewChild(FixedMouseContextualContainerDirective) public rClContextualMenu: FixedMouseContextualContainerDirective + @ViewChild(MouseHoverDirective) private mouseOverNehuba: MouseHoverDirective @ViewChild('mobileMenuTabs') public mobileMenuTabs: TabsetComponent @@ -99,6 +101,8 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit { public onhoverSegments$: Observable<string[]> public onhoverLandmark$: Observable<{landmarkName: string, datasets: any} | null> + public onhoverLandmarkForFixed$: Observable<any> + private subscriptions: Subscription[] = [] /* handlers for nglayer */ @@ -119,8 +123,10 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit { private pluginRegionSelectionEnabled$: Observable<boolean> private pluginRegionSelectionEnabled: boolean = false - private persistentStateNotifierTemplate$: Observable<string> - // private pluginRegionSelectionEnabled: boolean = false + public persistentStateNotifierTemplate$: Observable<string> + + private hoveringRegions = [] + public presentDatasetDialogRef: MatDialogRef<any> constructor( private store: Store<IavRootStoreInterface>, @@ -207,6 +213,7 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit { distinctUntilChanged(isSame), ) + // TODO deprecate this.dedicatedView$ = this.store.pipe( select('viewerState'), filter(state => isDefined(state) && typeof state.dedicatedView !== 'undefined'), @@ -214,47 +221,18 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit { distinctUntilChanged(), ) - this.onhoverLandmark$ = combineLatest( - this.store.pipe( - select('uiState'), - map(state => state.mouseOverLandmark), - ), - this.store.pipe( - select('dataStore'), - safeFilter('fetchedSpatialData'), - map(state => state.fetchedSpatialData), - ), - ).pipe( - map(([landmark, spatialDatas]) => { - if (landmark === null) { - return landmark - } - const idx = Number(landmark.replace('label=', '')) - if (isNaN(idx)) { - this.log.warn(`Landmark index could not be parsed as a number: ${landmark}`) - return { - landmarkName: idx, - } - } else { - return { - landmarkName: spatialDatas[idx].name, - } - } - }), - ) - // TODO temporary hack. even though the front octant is hidden, it seems if a mesh is present, hover will select the said mesh - this.onhoverSegments$ = combineLatest( - this.store.pipe( - select('uiState'), - select('mouseOverSegments'), - filter(v => !!v), - distinctUntilChanged((o, n) => o.length === n.length && n.every(segment => o.find(oSegment => oSegment.layer.name === segment.layer.name && oSegment.segment === segment.segment) ) ), - /* cannot filter by state, as the template expects a default value, or it will throw ExpressionChangedAfterItHasBeenCheckedError */ + this.onhoverSegments$ = this.store.pipe( + select('uiState'), + select('mouseOverSegments'), + filter(v => !!v), + distinctUntilChanged((o, n) => o.length === n.length && n.every(segment => o.find(oSegment => oSegment.layer.name === segment.layer.name && oSegment.segment === segment.segment) ) ), + /* cannot filter by state, as the template expects a default value, or it will throw ExpressionChangedAfterItHasBeenCheckedError */ - ), - this.onhoverLandmark$, ).pipe( + withLatestFrom( + this.onhoverLandmark$ || of(null) + ), map(([segments, onhoverLandmark]) => onhoverLandmark ? null : segments ), map(segments => { if (!segments) { return null } @@ -296,10 +274,11 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit { } }), ) - - this.onhoverSegments$.subscribe(hr => { - this.hoveringRegions = hr - }) + this.subscriptions.push( + this.onhoverSegments$.subscribe(hr => { + this.hoveringRegions = hr + }) + ) } private selectedParcellation$: Observable<any> @@ -405,6 +384,10 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit { this.rd.appendChild(document.head, prefecthMainBundle) } + this.onhoverLandmark$ = this.mouseOverNehuba.currentOnHoverObs$.pipe( + select('landmark') + ) + /** * Show Cookie disclaimer if not yet agreed */ @@ -437,21 +420,28 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit { withLatestFrom(this.onhoverSegments$), map(([_flag, onhoverSegments]) => onhoverSegments || []), ) - } - private hoveringRegions = [] + this.onhoverLandmarkForFixed$ = this.rClContextualMenu.onShow.pipe( + withLatestFrom( + this.onhoverLandmark$ || of(null) + ), + map(([_flag, onhoverLandmark]) => onhoverLandmark) + ) + } public mouseDownNehuba(_event) { this.rClContextualMenu.hide() } public mouseClickNehuba(event) { - // if (this.mouseUpLeftPosition === event.pageX && this.mouseUpTopPosition === event.pageY) {} + if (!this.rClContextualMenu) { return } this.rClContextualMenu.mousePos = [ event.clientX, event.clientY, ] + + // TODO what if user is hovering a landmark? if (!this.pluginRegionSelectionEnabled) { this.rClContextualMenu.show() } else { diff --git a/src/atlasViewer/atlasViewer.constantService.service.ts b/src/atlasViewer/atlasViewer.constantService.service.ts index afe18ac8547250f0eda154d075a0e14753c1be37..0f4302f2eb877084511118620c525b0028172365 100644 --- a/src/atlasViewer/atlasViewer.constantService.service.ts +++ b/src/atlasViewer/atlasViewer.constantService.service.ts @@ -1,4 +1,4 @@ -import { HttpClient } from "@angular/common/http"; +import { HttpClient, HttpHeaders } from "@angular/common/http"; import { Injectable, OnDestroy } from "@angular/core"; import { select, Store } from "@ngrx/store"; import { merge, Observable, of, Subscription, throwError, fromEvent, forkJoin } from "rxjs"; @@ -121,18 +121,6 @@ export class AtlasViewerConstantsServices implements OnDestroy { }), ) - /* to be provided by KG in future */ - public templateUrlsPr: Promise<string[]> = new Promise((resolve, reject) => { - fetch(`${this.backendUrl}templates`, this.getFetchOption()) - .then(res => res.json()) - .then(arr => { - this.templateUrls = arr - return arr - }) - .then(resolve) - .catch(reject) - }) - public templateUrls = Array(100) /* to be provided by KG in future */ @@ -221,6 +209,12 @@ Interactive atlas viewer requires **webgl2.0**, and the \`EXT_color_buffer_float return url.toString() } + public getHttpHeader(): HttpHeaders { + const header = new HttpHeaders() + header.set('referrer', this.getScopedReferer()) + return header + } + public getFetchOption(): RequestInit { return { referrer: this.getScopedReferer(), diff --git a/src/atlasViewer/atlasViewer.style.css b/src/atlasViewer/atlasViewer.style.css index 1782ffbc74ce60ba5ae6cfe459947a26df9cf47b..3a18311b9864ca06db18b3f15e58e74534222216 100644 --- a/src/atlasViewer/atlasViewer.style.css +++ b/src/atlasViewer/atlasViewer.style.css @@ -65,6 +65,7 @@ mat-sidenav { margin: 40px 0 0 5px; } +landmark-ui, region-menu { display:inline-block; diff --git a/src/atlasViewer/atlasViewer.template.html b/src/atlasViewer/atlasViewer.template.html index dfa7199be935d6cf46f9a577e0f4004a3229b99d..d1a50e4f9da121741ad3bb98718dbdaabdc9cd9a 100644 --- a/src/atlasViewer/atlasViewer.template.html +++ b/src/atlasViewer/atlasViewer.template.html @@ -42,12 +42,14 @@ <ng-template #viewerBody> <div class="atlas-container" (drag-drop)="localFileService.handleFileDrop($event)"> - <ui-nehuba-container iav-mouse-hover #iavMouseHoverEl="iavMouseHover" - [currentOnHoverObs$]="iavMouseHoverEl.currentOnHoverObs$" - [currentOnHover]="iavMouseHoverEl.currentOnHoverObs$ | async" - iav-captureClickListenerDirective - (iav-captureClickListenerDirective-onMousedown)="mouseDownNehuba($event)" - (iav-captureClickListenerDirective-onClick)="mouseClickNehuba($event)"> + <ui-nehuba-container + iav-mouse-hover + #iavMouseHoverEl="iavMouseHover" + [currentOnHoverObs$]="iavMouseHoverEl.currentOnHoverObs$" + [currentOnHover]="iavMouseHoverEl.currentOnHoverObs$ | async" + iav-captureClickListenerDirective + (iav-captureClickListenerDirective-onMousedown)="mouseDownNehuba($event)" + (iav-captureClickListenerDirective-onClick)="mouseClickNehuba($event)"> </ui-nehuba-container> <div class="z-index-10 position-absolute pe-none w-100 h-100"> @@ -115,26 +117,28 @@ <div floatingMouseContextualContainerDirective> - <div *ngIf="!ismobile" + <div *ngIf="!ismobile && !presentDatasetDialogRef" class="d-inline-block" iav-mouse-hover - #iavMouseHoverConetxtualBlock="iavMouseHover" + #iavMouseHoverContextualBlock="iavMouseHover" contextualBlock> <ng-container - *ngFor="let labelText of iavMouseHoverConetxtualBlock.currentOnHoverObs$ | async | mouseOverTextPipe : selectedParcellation"> + *ngFor="let labelText of iavMouseHoverContextualBlock.currentOnHoverObs$ | async | mouseOverTextPipe : selectedParcellation"> <mat-list dense> <mat-list-item class="h-auto"> - <mat-icon [fontSet]="(labelText.label | mouseOverIconPipe).fontSet" - [fontIcon]="(labelText.label | mouseOverIconPipe).fontIcon" mat-list-icon> + <mat-icon + [fontSet]="(labelText.label | mouseOverIconPipe).fontSet" + [fontIcon]="(labelText.label | mouseOverIconPipe).fontIcon" + mat-list-icon> </mat-icon> - <div matLine *ngFor="let text of labelText.text" [innerHTML]="text"> - </div> + <div matLine *ngFor="let text of labelText.text" [innerHTML]="text"></div> + </mat-list-item> </mat-list> </ng-container> @@ -142,25 +146,42 @@ <!-- TODO Potentially implementing plugin contextual info --> </div> - <div fixedMouseContextualContainerDirective> + <div fixedMouseContextualContainerDirective + #fixedContainer="iavFixedMouseCtxContainer"> + + <!-- on click segment menu --> <ng-container *ngIf="(onhoverSegmentsForFixed$ | async) as onHoverSegments"> <ng-container *ngFor="let onHoverRegion of onHoverSegments; let first = first"> <!-- ToDo it should change - we should get information about connectivity existence from API--> <div class="d-flex flex-column"> <region-menu - class="pe-all" - [region]="onHoverRegion" - [isSelected]="selectedRegions$ | async | includes : onHoverRegion : compareFn" - [hasConnectivity]="selectedParcellation - && selectedParcellation.hasAdditionalViewMode - && selectedParcellation.hasAdditionalViewMode.includes('connectivity')" - (closeRegionMenu)="rClContextualMenu.hide()"> + class="pe-all" + [region]="onHoverRegion" + [isSelected]="selectedRegions$ | async | includes : onHoverRegion : compareFn" + [hasConnectivity]="selectedParcellation + && selectedParcellation.hasAdditionalViewMode + && selectedParcellation.hasAdditionalViewMode.includes('connectivity')" + (closeRegionMenu)="rClContextualMenu.hide()"> </region-menu> </div> </ng-container> </ng-container> + + <!-- on click landmark menu --> + <ng-container *ngIf="onhoverLandmarkForFixed$ | async as onHoverLandmark"> + + <landmark-ui + class="pe-all" + (relayout)="fixedContainer.recalculatePosition()" + [fullId]="onHoverLandmark.fullId" + [name]="onHoverLandmark.name" + [datasets]="onHoverLandmark.dataset"> + + </landmark-ui> + </ng-container> </div> + </layout-floating-container> <!-- required for manufacturing plugin templates --> diff --git a/src/res/css/extra_styles.css b/src/res/css/extra_styles.css index 0ff2cabc49fc76b7c7bbed5c19ac95d6c91f7eda..0639b9179922f9bcb336ed1fa5611d91939bea53 100644 --- a/src/res/css/extra_styles.css +++ b/src/res/css/extra_styles.css @@ -697,4 +697,22 @@ body::after .o-0 { opacity: 0.0!important; -} \ No newline at end of file +} + +kg-dataset-previewer > img +{ + max-width: 100%; + width: 100%; +} + +/* + TODO, this really should be in searchSideNav.style.css. But karma tests does not seem to like to include style.css + figure out why +*/ +/* exactly 1.5 line height */ + +.h-117px +{ + min-height:117px!important; + flex-basis: 117px!important; +} diff --git a/src/ui/databrowserModule/databrowser.service.ts b/src/ui/databrowserModule/databrowser.service.ts index 533d5c7d09112178813064591c76e6bd8155cd91..b9e069839ecd0308f483643a3a9b4ab559688641 100644 --- a/src/ui/databrowserModule/databrowser.service.ts +++ b/src/ui/databrowserModule/databrowser.service.ts @@ -224,6 +224,7 @@ export class DatabrowserService implements OnDestroy { }) } + // TODO deprecate public fetchPreviewData(datasetName: string) { const encodedDatasetName = encodeURIComponent(datasetName) return new Promise((resolve, reject) => { @@ -246,19 +247,25 @@ export class DatabrowserService implements OnDestroy { public fetchingFlag: boolean = false private mostRecentFetchToken: any - private lowLevelQuery(templateName: string, parcellationName: string) { + private lowLevelQuery(templateName: string, parcellationName: string): Promise<IDataEntry[]> { const encodedTemplateName = encodeURIComponent(templateName) const encodedParcellationName = encodeURIComponent(parcellationName) - return fetch(`${this.constantService.backendUrl}datasets//templateNameParcellationName/${encodedTemplateName}/${encodedParcellationName}`, this.constantService.getFetchOption()) - .then(res => res.json()) - /** - * remove duplicates - */ - .then(arr => arr.reduce((acc, item) => { - const newMap = new Map(acc) - return newMap.set(item.name, item) - }, new Map())) - .then(map => Array.from(map.values() as IDataEntry[])) + + return this.http.get( + `${this.constantService.backendUrl}datasets//templateNameParcellationName/${encodedTemplateName}/${encodedParcellationName}`, + { + headers: this.constantService.getHttpHeader(), + responseType: 'json' + } + ).pipe( + map((arr: any[]) => { + const map = arr.reduce((acc, item) => { + const newMap = new Map(acc) + return newMap.set(item.name, item) + }, new Map()) + return Array.from(map.values() as IDataEntry[]) + }) + ).toPromise() } private fetchData(templateName: string, parcellationName: string) { diff --git a/src/ui/databrowserModule/singleDataset/datasetPreviews/datasetPreviewsList/datasetPreviewList.component.ts b/src/ui/databrowserModule/singleDataset/datasetPreviews/datasetPreviewsList/datasetPreviewList.component.ts index e7844a95db69d0df4e9d2b6307d7cae6704c4ba7..7fcdb4ae1b2419b9e664f476654973ee0ffeae9b 100644 --- a/src/ui/databrowserModule/singleDataset/datasetPreviews/datasetPreviewsList/datasetPreviewList.component.ts +++ b/src/ui/databrowserModule/singleDataset/datasetPreviews/datasetPreviewsList/datasetPreviewList.component.ts @@ -3,6 +3,7 @@ import { ViewerPreviewFile } from "src/services/state/dataStore.store"; import { Store, select } from "@ngrx/store"; import { IavRootStoreInterface } from "src/services/stateStore.service"; import { Observable } from "rxjs"; +import { DS_PREVIEW_URL } from 'src/util/constants' @Component({ selector: 'dataset-preview-list', @@ -30,6 +31,8 @@ export class DatasetPreviewList{ @Input() kgId: string + public DS_PREVIEW_URL = DS_PREVIEW_URL + handleKgDsPrvUpdated(event: CustomEvent){ const { detail } = event const { datasetFiles, loadingFlag } = detail diff --git a/src/ui/databrowserModule/singleDataset/datasetPreviews/datasetPreviewsList/datasetPreviewList.template.html b/src/ui/databrowserModule/singleDataset/datasetPreviews/datasetPreviewsList/datasetPreviewList.template.html index a92572cd75eb656dc60f388d0f4bd22c807402c3..25afd1d18921e98c59b6f1c41ecd2449cfeafc6d 100644 --- a/src/ui/databrowserModule/singleDataset/datasetPreviews/datasetPreviewsList/datasetPreviewList.template.html +++ b/src/ui/databrowserModule/singleDataset/datasetPreviews/datasetPreviewsList/datasetPreviewList.template.html @@ -1,4 +1,5 @@ <kg-dataset-list + [backendUrl]="DS_PREVIEW_URL" (kgDsPrvUpdated)="handleKgDsPrvUpdated($event)" class="d-none" [kgId]="kgId"> diff --git a/src/ui/databrowserModule/singleDataset/detailedView/singleDataset.template.html b/src/ui/databrowserModule/singleDataset/detailedView/singleDataset.template.html index 5871fdd9f58deb3fb43dc4f541c53448a060d2cf..88c2c63deec0ea99fca33a3c5c581ce577c61436 100644 --- a/src/ui/databrowserModule/singleDataset/detailedView/singleDataset.template.html +++ b/src/ui/databrowserModule/singleDataset/detailedView/singleDataset.template.html @@ -109,7 +109,7 @@ <!-- download --> - <a *ngIf="files.length > 0" + <a *ngIf="files && files.length > 0" [href]="dlFromKgHref" target="_blank"> <button @@ -135,6 +135,7 @@ </span> <i class="ml-1 far fa-eye"></i> </button> + </mat-card-actions> <mat-card-footer></mat-card-footer> diff --git a/src/ui/databrowserModule/singleDataset/singleDataset.base.ts b/src/ui/databrowserModule/singleDataset/singleDataset.base.ts index 510232f2495fd069c13e931b2938773603e981e1..3ca5b426c11bbea6527dfe33d4da476c12a2a56a 100644 --- a/src/ui/databrowserModule/singleDataset/singleDataset.base.ts +++ b/src/ui/databrowserModule/singleDataset/singleDataset.base.ts @@ -6,6 +6,8 @@ import { HumanReadableFileSizePipe } from "src/util/pipes/humanReadableFileSize. import { DatabrowserService } from "../databrowser.service"; import { KgSingleDatasetService } from "../kgSingleDatasetService.service"; +import { DS_PREVIEW_URL } from 'src/util/constants' + export { DatabrowserService, KgSingleDatasetService, @@ -34,6 +36,8 @@ export class SingleDatasetBase implements OnInit { public preview: boolean = false private humanReadableFileSizePipe: HumanReadableFileSizePipe = new HumanReadableFileSizePipe() + public DS_PREVIEW_URL = DS_PREVIEW_URL + /** * sic! */ diff --git a/src/ui/landmarkUI/landmarkUI.component.ts b/src/ui/landmarkUI/landmarkUI.component.ts new file mode 100644 index 0000000000000000000000000000000000000000..f76b1cac444c86645d95e001ec01fbe9cbba6ce9 --- /dev/null +++ b/src/ui/landmarkUI/landmarkUI.component.ts @@ -0,0 +1,71 @@ +import { Component, Input, OnChanges, Output, EventEmitter, ChangeDetectionStrategy, ChangeDetectorRef, AfterContentChecked } from "@angular/core"; +import { IDataEntry } from "src/services/stateStore.service"; +import { GetKgSchemaIdFromFullIdPipe } from 'src/ui/databrowserModule/util/getKgSchemaIdFromFullId.pipe' +import { AtlasViewerConstantsServices } from "../databrowserModule/singleDataset/singleDataset.base"; +import { Observable } from "rxjs"; +import { DS_PREVIEW_URL } from 'src/util/constants' + +@Component({ + selector: 'landmark-ui', + templateUrl: './landmarkUI.template.html', + styleUrls: [ + './landmarkUI.style.css' + ], + changeDetection: ChangeDetectionStrategy.OnPush +}) + +export class LandmarkUIComponent implements OnChanges, AfterContentChecked{ + @Input() name: string + @Input() fullId: string + @Input() datasets: Partial<IDataEntry>[] + + @Output() relayout: EventEmitter<any> = new EventEmitter() + + private pipe = new GetKgSchemaIdFromFullIdPipe() + + public DS_PREVIEW_URL = DS_PREVIEW_URL + + public previewFilesMap: Map<string, any[]> = new Map() + public previewFiles: any[] = [] + + handleKgDsPrvUpdate(event: CustomEvent, datasetKgId: string){ + const { detail } = event + const { datasetFiles } = detail + + this.previewFilesMap.set(datasetKgId, datasetFiles) + + this.previewFiles = [] + + for (const [datasetKgId, previewFiles] of Array.from(this.previewFilesMap)){ + for (const singlePreviewFile of previewFiles){ + this.previewFiles.push({ + ...singlePreviewFile, + datasetKgId + }) + } + } + this.cdr.markForCheck() + } + + public filterCriteria: string + ngOnChanges(){ + this.filterCriteria = null + if (!this.fullId) return + const [kgSchema, kgId] = this.pipe.transform(this.fullId) + this.filterCriteria = JSON.stringify([ `${kgSchema}/${kgId}` ]) + } + + // TODO need to optimise this. This calls way too frequently. + ngAfterContentChecked(){ + this.relayout.emit() + } + + public darktheme$: Observable<boolean> + + constructor( + constantService: AtlasViewerConstantsServices, + private cdr: ChangeDetectorRef + ){ + this.darktheme$ = constantService.darktheme$ + } +} \ No newline at end of file diff --git a/src/ui/landmarkUI/landmarkUI.style.css b/src/ui/landmarkUI/landmarkUI.style.css new file mode 100644 index 0000000000000000000000000000000000000000..757b1a7bcba50d2da823755e085849b453bff61a --- /dev/null +++ b/src/ui/landmarkUI/landmarkUI.style.css @@ -0,0 +1,21 @@ +kg-dataset-previewer +{ + height: 20em; + width: 30em; +} +.scroll-snap-container +{ + scroll-snap-type: x mandatory; + scroll-padding-left: 1em; + scroll-padding-right: 1em; +} + +.scroll-snap-container > .scroll-snap-child +{ + scroll-snap-align: center; +} + +.w-30em +{ + width:30em!important; +} \ No newline at end of file diff --git a/src/ui/landmarkUI/landmarkUI.template.html b/src/ui/landmarkUI/landmarkUI.template.html new file mode 100644 index 0000000000000000000000000000000000000000..46085769ecdd1ea45a56ef7cc7f05a6bf690744f --- /dev/null +++ b/src/ui/landmarkUI/landmarkUI.template.html @@ -0,0 +1,67 @@ +<mat-card> + <mat-card-title> + + {{ name }} + </mat-card-title> + <mat-card-subtitle> + + <i class="fas fa-map-marker-alt"></i> + <span> + spatial landmark + </span> + </mat-card-subtitle> + + <div class="scroll-snap-container w-100 d-flex flex-row w-30em overflow-auto" mat-card-image> + <div *ngFor="let dsPreview of previewFiles" + class="scroll-snap-child w-30em"> + <kg-dataset-previewer + [darkmode]="darktheme$ | async" + [filename]="dsPreview.filename" + [kgId]="dsPreview.datasetKgId" + [backendUrl]="DS_PREVIEW_URL"> + </kg-dataset-previewer> + </div> + + </div> + <mat-card-content> + + <!-- preview --> + <div> + <small class="text-muted"> + Dataset preview + </small> + + <ng-container *ngFor="let dataset of datasets; let index = index"> + <kg-dataset-list + class="d-none" + [backendUrl]="DS_PREVIEW_URL" + [filterCriteriaProp]="filterCriteria" + *ngIf="dataset.fullId | getKgSchemaIdFromFullIdPipe as kgSchemaId" + (kgDsPrvUpdated)="handleKgDsPrvUpdate($event, kgSchemaId[1])" + [kgId]="kgSchemaId[1]"> + + </kg-dataset-list> + </ng-container> + </div> + + <hr class="text-muted"> + <!-- associated datasets --> + <div> + <small class="text-muted"> + Associated datasets + </small> + <div> + <ng-container *ngFor="let dataset of datasets"> + + <single-dataset-list-view + *ngIf="dataset.fullId | getKgSchemaIdFromFullIdPipe as kgSchemaId" + [ripple]="true" + [kgSchema]="kgSchemaId[0]" + [kgId]="kgSchemaId[1]"> + + </single-dataset-list-view> + </ng-container> + </div> + </div> + </mat-card-content> +</mat-card> diff --git a/src/ui/layerbrowser/layerbrowser.component.ts b/src/ui/layerbrowser/layerbrowser.component.ts index 04be9fc5b65aee96d07894c0339076be6b735afa..ff5df6f6f90b7eb7f13ff242dcfa52fa4c261073 100644 --- a/src/ui/layerbrowser/layerbrowser.component.ts +++ b/src/ui/layerbrowser/layerbrowser.component.ts @@ -48,6 +48,8 @@ export class LayerBrowser implements OnInit, OnDestroy { public darktheme$: Observable<boolean> + private customNgLayers: string[] = ['spatial landmark layer'] + constructor( private store: Store<ViewerStateInterface>, private constantsService: AtlasViewerConstantsServices, @@ -65,6 +67,7 @@ export class LayerBrowser implements OnInit, OnDestroy { return [ ngId, + ...this.customNgLayers, ...otherNgIds, ...templateSelected.parcellations.reduce((acc, curr) => { return acc.concat([ diff --git a/src/ui/nehubaContainer/nehubaContainer.component.ts b/src/ui/nehubaContainer/nehubaContainer.component.ts index 1c0935bda9d33a2c5b4ebb24a68867300f1c5b44..57f033a841748584ad4fa859fc88c1be5c166f40 100644 --- a/src/ui/nehubaContainer/nehubaContainer.component.ts +++ b/src/ui/nehubaContainer/nehubaContainer.component.ts @@ -1090,7 +1090,7 @@ export class NehubaContainer implements OnInit, OnChanges, OnDestroy { this.nehubaViewerSubscriptions.push( this.nehubaViewer.mouseoverLandmarkEmitter.pipe( - throttleTime(100), + distinctUntilChanged() ).subscribe(label => { this.store.dispatch({ type : MOUSE_OVER_LANDMARK, diff --git a/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts b/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts index 1cb264cde6a2c183fdf807ac0f26a5053dce9b81..4b1b28cc730e31742909b20108e8096257690382 100644 --- a/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts +++ b/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts @@ -781,6 +781,7 @@ export class NehubaViewerUnit implements OnInit, OnDestroy { }) }) + // TODO bug: mouseoverlandmarkemitter does not emit empty for VTK layer when user mouse click this.ondestroySubscriptions.push( this.nehubaViewer.mouseOver.layer .filter(obj => obj.layer.name === this.constantService.ngLandmarkLayerName) diff --git a/src/ui/parcellationRegion/regionMenu/regionMenu.style.css b/src/ui/parcellationRegion/regionMenu/regionMenu.style.css index c9f10ea89767c6d94d967b6486d350e0f13f1910..e9a48a372933a13d21d572ccdc4d8cbf1120fa6b 100644 --- a/src/ui/parcellationRegion/regionMenu/regionMenu.style.css +++ b/src/ui/parcellationRegion/regionMenu/regionMenu.style.css @@ -8,13 +8,3 @@ max-height: 310px; transition: max-height 0.25s ease-in; } - -[fixedMouseContextualContainerDirective] -{ - width: 15rem; -} - -[fixedMouseContextualContainerDirective] div[body] -{ - overflow: hidden; -} diff --git a/src/ui/parcellationRegion/regionMenu/regionMenu.template.html b/src/ui/parcellationRegion/regionMenu/regionMenu.template.html index 68f7925fd672d87b5ce1b8e33d320f5dfd51902e..b3271e18f5c696351a1a65dbcf5b33c76f357bc1 100644 --- a/src/ui/parcellationRegion/regionMenu/regionMenu.template.html +++ b/src/ui/parcellationRegion/regionMenu/regionMenu.template.html @@ -1,6 +1,12 @@ <mat-card> - <mat-card-subtitle> + <mat-card-title> {{ region.name }} + </mat-card-title> + <mat-card-subtitle> + <i class="fas fa-brain"></i> + <span> + Brain region + </span> </mat-card-subtitle> <mat-card-content> {{ region.description }} diff --git a/src/ui/searchSideNav/searchSideNav.component.spec.ts b/src/ui/searchSideNav/searchSideNav.component.spec.ts new file mode 100644 index 0000000000000000000000000000000000000000..d080ecbcbd11f57c2de8c9747324a095ad84a8ed --- /dev/null +++ b/src/ui/searchSideNav/searchSideNav.component.spec.ts @@ -0,0 +1,93 @@ +import { async, TestBed } from '@angular/core/testing' +import {} from 'jasmine' +import { AngularMaterialModule } from '../../ui/sharedModules/angularMaterial.module' +import { UIModule } from '../ui.module' +import { SearchSideNav } from './searchSideNav.component' +import { provideMockStore } from '@ngrx/store/testing' +import { defaultRootState } from 'src/services/stateStore.service' +import { By } from '@angular/platform-browser' +import { CdkFixedSizeVirtualScroll } from '@angular/cdk/scrolling' +import { COLIN, JUBRAIN_COLIN_CH123_LEFT, JUBRAIN_COLIN_CH123_RIGHT, JUBRAIN_COLIN, HttpMockRequestInterceptor } from 'spec/util' +import { HTTP_INTERCEPTORS } from '@angular/common/http' +import { ViewerStateController } from '../viewerStateController/viewerStateCFull/viewerState.component' + +describe('SearchSideNav component', () => { + beforeEach(async(() => { + TestBed.configureTestingModule({ + imports: [ + AngularMaterialModule, + UIModule + ], + providers: [ + provideMockStore({ initialState: { + ...defaultRootState, + uiState: { + ...defaultRootState.uiState, + sidePanelExploreCurrentViewIsOpen: true + }, + viewerState: { + ...defaultRootState.viewerState, + templateSelected: COLIN, + parcellationSelected: JUBRAIN_COLIN, + regionsSelected:[ JUBRAIN_COLIN_CH123_LEFT, JUBRAIN_COLIN_CH123_RIGHT ] + } + }}), + { + provide: HTTP_INTERCEPTORS, + useClass: HttpMockRequestInterceptor, + multi: true + } + + ] + }).compileComponents() + })) + it('should create component', () => { + + const fixture = TestBed.createComponent(SearchSideNav); + const app = fixture.debugElement.componentInstance; + + expect(app).toBeTruthy(); + + }) + + it('viewerStateController should be visible', async () => { + + const fixture = TestBed.createComponent(SearchSideNav); + + const vsController = fixture.debugElement.query(By.directive(ViewerStateController)) + expect(vsController).toBeTruthy(); + }) + + it('when parent size is defined, child component should be of the same size', () => { + const fixture = TestBed.createComponent(SearchSideNav) + + fixture.nativeElement.style.width = '1000px' + fixture.nativeElement.style.height = '1000px' + + fixture.debugElement.nativeElement.classList.add('h-100', 'w-100', 'd-block', 'overflow-visible') + + fixture.detectChanges() + + expect(fixture.debugElement.nativeElement.style.width).toEqual('1000px') + expect(fixture.debugElement.nativeElement.style.height).toEqual('1000px') + }) + + it('when multiple regions are selected, cdk should be visible', () => { + + const fixture = TestBed.createComponent(SearchSideNav); + fixture.nativeElement.style.width = '1000px' + fixture.nativeElement.style.height = '1000px' + + fixture.debugElement.nativeElement.classList.add('h-100', 'd-block', 'overflow-visible') + fixture.detectChanges() + + expect(fixture.debugElement.nativeElement.clientWidth).toBeGreaterThan(100) + expect(fixture.debugElement.nativeElement.clientHeight).toBeGreaterThan(100) + + const cdkViewPort = fixture.debugElement.query(By.directive(CdkFixedSizeVirtualScroll)) + expect(cdkViewPort).toBeTruthy() + + expect(cdkViewPort.nativeElement.clientWidth).toBeGreaterThan(80) + expect(cdkViewPort.nativeElement.clientHeight).toBeGreaterThan(80) + }) +}) diff --git a/src/ui/searchSideNav/searchSideNav.component.ts b/src/ui/searchSideNav/searchSideNav.component.ts index 8fdddeea8da25117a0a4e48940bbde47976a3fe0..2bbacbb6e0e8ede1e19f55d4e7102ae237301fcd 100644 --- a/src/ui/searchSideNav/searchSideNav.component.ts +++ b/src/ui/searchSideNav/searchSideNav.component.ts @@ -14,6 +14,7 @@ import { IavRootStoreInterface, SELECT_REGIONS } from "src/services/stateStore.s import { LayerBrowser } from "../layerbrowser/layerbrowser.component"; import { trackRegionBy } from '../viewerStateController/regionHierachy/regionHierarchy.component' import { determinePreviewFileType, PREVIEW_FILE_TYPES } from "../databrowserModule/preview/previewFileIcon.pipe"; +import { DS_PREVIEW_URL } from 'src/util/constants' @Component({ selector: 'search-side-nav', @@ -41,6 +42,8 @@ export class SearchSideNav implements OnDestroy { public darktheme$: Observable<boolean> + public DS_PREVIEW_URL = DS_PREVIEW_URL + constructor( public dialog: MatDialog, private store$: Store<IavRootStoreInterface>, diff --git a/src/ui/searchSideNav/searchSideNav.style.css b/src/ui/searchSideNav/searchSideNav.style.css index f8d38603b6c77b036449a644636964d8ce64d176..40287116012a17025cc03415606ed3a3b6fcaaf6 100644 --- a/src/ui/searchSideNav/searchSideNav.style.css +++ b/src/ui/searchSideNav/searchSideNav.style.css @@ -3,14 +3,6 @@ height: 55px; } -/* exactly 1.5 line height */ - -.h-117px -{ - min-height:117px!important; - flex-basis: 117px!important; -} - .mat-divider-full-width { margin-right:-1.5rem; diff --git a/src/ui/searchSideNav/searchSideNav.template.html b/src/ui/searchSideNav/searchSideNav.template.html index 5628e3aaf482e4d4017bec3d0e8924c969316e29..223de4c5cabc39966f89dbb477513dad065072ce 100644 --- a/src/ui/searchSideNav/searchSideNav.template.html +++ b/src/ui/searchSideNav/searchSideNav.template.html @@ -86,7 +86,7 @@ </div> <!-- show when regions are selected --> - <div *ngIf="regionsSelected.length > 0" class="h-100 d-flex flex-column"> + <div *ngIf="regionsSelected.length > 0" class="flex-grow-1 d-flex flex-column"> <!-- header --> <div class="flex-grow-0 flex-shrink-0"> @@ -95,7 +95,7 @@ </div> <!-- body (region descriptor or multi region list) --> - <div class="flex-grow-1 flex-shrink-1"> + <div class="flex-grow-1 flex-shrink-1 d-flex flex-column"> <ng-container *ngTemplateOutlet="body"> </ng-container> </div> @@ -125,6 +125,9 @@ </ng-template> <ng-template #body> + + <!-- TODO bug in browser? unless using d-flex here and flex-grow-1 in child, child cannot fille parent, even with h-100 --> + <!-- single region --> <ng-template [ngIf]="regionsSelected.length === 1" [ngIfElse]="multiRegionTemplate"> @@ -139,9 +142,10 @@ </region-list-simple-view> </ng-template> + <!-- multi region --> <ng-template #multiRegionTemplate> - <div class="h-100 d-flex flex-column"> + <div class="flex-grow-1 d-flex flex-row"> <cdk-virtual-scroll-viewport class="flex-grow-1 flex-shrink-1" @@ -175,7 +179,7 @@ [darkmode]="darktheme$ | async" [filename]="previewFilename" [kgId]="previewKgId" - kg-ds-prv-backend-url="https://hbp-kg-dataset-previewer.apps.hbp.eu/datasetPreview"> + [backendUrl]="DS_PREVIEW_URL"> </kg-dataset-previewer> </ng-template> \ No newline at end of file diff --git a/src/ui/ui.module.ts b/src/ui/ui.module.ts index a1d181273ac1515fadb388021f196ba5134b0d37..214785c6dc9f92040438010f2fa4c7d04e6b2974 100644 --- a/src/ui/ui.module.ts +++ b/src/ui/ui.module.ts @@ -78,6 +78,7 @@ import {ConnectivityBrowserComponent} from "src/ui/connectivityBrowser/connectiv import { RegionMenuComponent } from 'src/ui/parcellationRegion/regionMenu/regionMenu.component' import { RegionListSimpleViewComponent } from "./parcellationRegion/regionListSimpleView/regionListSimpleView.component"; import { SimpleRegionComponent } from "./parcellationRegion/regionSimple/regionSimple.component"; +import { LandmarkUIComponent } from "./landmarkUI/landmarkUI.component"; @NgModule({ imports : [ @@ -129,6 +130,7 @@ import { SimpleRegionComponent } from "./parcellationRegion/regionSimple/regionS ConnectivityBrowserComponent, SimpleRegionComponent, RegionListSimpleViewComponent, + LandmarkUIComponent, /* pipes */ GroupDatasetByRegion, @@ -193,6 +195,7 @@ import { SimpleRegionComponent } from "./parcellationRegion/regionSimple/regionS ViewerStateMini, RegionMenuComponent, FixedMouseContextualContainerDirective, + LandmarkUIComponent ], schemas: [ CUSTOM_ELEMENTS_SCHEMA, diff --git a/src/util/constants.ts b/src/util/constants.ts index d43935864e7a384045bc4163bd4518ffc10d6ec0..e9d16f04d6a432b054b425702525bfbcf6304342 100644 --- a/src/util/constants.ts +++ b/src/util/constants.ts @@ -11,3 +11,4 @@ export const LOCAL_STORAGE_CONST = { export const COOKIE_VERSION = '0.3.0' export const KG_TOS_VERSION = '0.3.0' +export const DS_PREVIEW_URL = DATASET_PREVIEW_URL \ No newline at end of file diff --git a/src/util/directives/FixedMouseContextualContainerDirective.directive.ts b/src/util/directives/FixedMouseContextualContainerDirective.directive.ts index d12fdc160d4d1600531fa4fe9b71d7168c557974..113bc0650d13bbea99dbf3527a979a35b966df91 100644 --- a/src/util/directives/FixedMouseContextualContainerDirective.directive.ts +++ b/src/util/directives/FixedMouseContextualContainerDirective.directive.ts @@ -2,6 +2,7 @@ import { Directive, ElementRef, EventEmitter, HostBinding, Input, Output } from @Directive({ selector: '[fixedMouseContextualContainerDirective]', + exportAs: 'iavFixedMouseCtxContainer' }) export class FixedMouseContextualContainerDirective { @@ -21,21 +22,27 @@ export class FixedMouseContextualContainerDirective { constructor( private el: ElementRef, ) { - } - public show() { - setTimeout(() => { - if (window.innerHeight - this.mousePos[1] < this.el.nativeElement.clientHeight) { - this.mousePos[1] = window.innerHeight - this.el.nativeElement.clientHeight - } + public recalculatePosition(){ + const clientWidth = this.el.nativeElement.clientWidth + const clientHeight = this.el.nativeElement.clientHeight + + const windowInnerWidth = window.innerWidth + const windowInnerHeight = window.innerHeight + if (windowInnerHeight - this.mousePos[1] < clientHeight) { + this.mousePos[1] = windowInnerHeight - clientHeight + } - if ((window.innerWidth - this.mousePos[0]) < this.el.nativeElement.clientWidth) { - this.mousePos[0] = window.innerWidth - this.el.nativeElement.clientWidth - } + if ((windowInnerWidth - this.mousePos[0]) < clientWidth) { + this.mousePos[0] = windowInnerWidth - clientWidth + } - this.transform = `translate(${this.mousePos.map(v => v.toString() + 'px').join(', ')})` - }) + this.transform = `translate(${this.mousePos.map(v => v.toString() + 'px').join(', ')})` + } + + public show() { + setTimeout(() => this.recalculatePosition()) this.styleDisplay = 'inline-block' this.isShown = true this.onShow.emit() diff --git a/src/util/directives/mouseOver.directive.spec.ts b/src/util/directives/mouseOver.directive.spec.ts index 3a7a26b9d20ee44cedc4fc80f1db579070308456..613d78ee825f93026770c06378d28e1b9464de9c 100644 --- a/src/util/directives/mouseOver.directive.spec.ts +++ b/src/util/directives/mouseOver.directive.spec.ts @@ -4,7 +4,7 @@ import { scan, skip, take } from 'rxjs/operators'; import { temporalPositveScanFn } from './mouseOver.directive' const segmentsPositive = { segments: [{ hello: 'world' }] } as {segments: any} -const segmentsNegative = { segments: null } +const segmentsNegative = { segments: [] } const userLandmarkPostive = { userLandmark: true } const userLandmarkNegative = { userLandmark: null } diff --git a/src/util/directives/mouseOver.directive.ts b/src/util/directives/mouseOver.directive.ts index 53dc7dadb23e306e57556f010f30f606b1bb2e90..56402863cc100ac51df759bf4a1529752de5d110 100644 --- a/src/util/directives/mouseOver.directive.ts +++ b/src/util/directives/mouseOver.directive.ts @@ -21,7 +21,12 @@ import { getNgIdLabelIndexFromId, IavRootStoreInterface } from "src/services/sta export const temporalPositveScanFn = (acc: Array<{segments: any, landmark: any, userLandmark: any}>, curr: {segments: any, landmark: any, userLandmark: any}) => { const keys = Object.keys(curr) - const isPositive = keys.some(key => !!curr[key]) + + // empty array is truthy + const isPositive = keys.some(key => Array.isArray(curr[key]) + ? curr[key].length > 0 + : !!curr[key] + ) return isPositive ? [curr, ...(acc.filter(item => !keys.some(key => !!item[key])))] as Array<{segments?: any, landmark?: any, userLandmark?: any}> @@ -43,15 +48,18 @@ export class MouseHoverDirective { private log: LoggingService, ) { + // TODO consider moving these into a single obs serviced by a DI service + // can potentially net better performance + const onHoverUserLandmark$ = this.store$.pipe( select('uiState'), - map(state => state.mouseOverUserLandmark), + select('mouseOverUserLandmark'), ) const onHoverLandmark$ = combineLatest( this.store$.pipe( select('uiState'), - map(state => state.mouseOverLandmark), + select('mouseOverLandmark'), ), this.store$.pipe( select('dataStore'), @@ -163,8 +171,17 @@ export class MouseOverTextPipe implements PipeTransform { private renderText = ({ label, obj }): SafeHtml[] => { switch (label) { - case 'landmark': - return [this.sanitizer.sanitize(SecurityContext.HTML, obj.landmarkName)] + case 'landmark': { + const { dataset = [] } = obj + return [ + this.sanitizer.sanitize(SecurityContext.HTML, obj.landmarkName), + ...(dataset.map(ds => this.sanitizer.bypassSecurityTrustHtml(` +<span class="text-muted"> + ${this.sanitizer.sanitize(SecurityContext.HTML, ds.name)} +</span> +`))) + ] + } case 'segments': return obj.map(({ segment }) => this.transformOnHoverSegmentPipe.transform(segment)) case 'userLandmark': @@ -186,7 +203,7 @@ export class MouseOverTextPipe implements PipeTransform { .map(key => { return { label: key, - text: this.renderText({ label: key, obj: inc[key] }), + text: this.renderText({ label: key, obj: inc[key] }) } }) } diff --git a/typings/index.d.ts b/typings/index.d.ts index 8c0461449380840d0bbbcdaf7ee5183a6b08b7bc..cf1b4e30fca132c62ee8261a800088f789b392e1 100644 --- a/typings/index.d.ts +++ b/typings/index.d.ts @@ -14,3 +14,4 @@ declare var VERSION : string declare var PRODUCTION: boolean declare var BACKEND_URL: string declare var USE_LOGO: string +declare var DATASET_PREVIEW_URL: string diff --git a/webpack.common.js b/webpack.common.js index b432b1d516e6e026f7ea57cb6207a13507866848..52e987bddbf7f90d2b16f55ff9b4a16b0b221953 100644 --- a/webpack.common.js +++ b/webpack.common.js @@ -32,7 +32,8 @@ module.exports = { alias : { "third_party" : path.resolve(__dirname,'third_party'), "src" : path.resolve(__dirname,'src'), - "common": path.resolve(__dirname, 'common') + "common": path.resolve(__dirname, 'common'), + "spec": path.resolve(__dirname, 'spec') } }, } \ No newline at end of file diff --git a/webpack.staticassets.js b/webpack.staticassets.js index 5732303b88538bc26c52a14a36737dca17560735..eb5271a3c176e8783ed3107745f8531ab31097f8 100644 --- a/webpack.staticassets.js +++ b/webpack.staticassets.js @@ -70,7 +70,8 @@ module.exports = { ? true : false, BACKEND_URL: (process.env.BACKEND_URL && JSON.stringify(process.env.BACKEND_URL)) || 'null', - USE_LOGO: JSON.stringify(process.env.USE_LOGO || 'hbp' || 'ebrains' ) + USE_LOGO: JSON.stringify(process.env.USE_LOGO || 'hbp' || 'ebrains' ), + DATASET_PREVIEW_URL: JSON.stringify(process.env.DATASET_PREVIEW_URL || 'https://hbp-kg-dataset-previewer.apps.hbp.eu/datasetPreview') }) ], resolve: {