diff --git a/deploy/datasets/index.js b/deploy/datasets/index.js index 7bc9333b68fd051ed6d73b508a9cd3667e0fccf5..a6f15dd43d6e8754cc7dfbc869b7fc4a19896a7f 100644 --- a/deploy/datasets/index.js +++ b/deploy/datasets/index.js @@ -1,6 +1,6 @@ const express = require('express') const datasetsRouter = express.Router() -const { init, getDatasets } = require('./query') +const { init, getDatasets, getPreview } = require('./query') init().catch(e => { console.warn(`dataset init failed`, e) @@ -22,13 +22,12 @@ datasetsRouter.get('/templateName/:templateName', (req, res, next) => { .catch(error => { next({ code: 500, - error + error, + trace: 'parcellationName' }) }) }) - - datasetsRouter.get('/parcellationName/:parcellationName', (req, res, next) => { const { parcellationName } = req.params const { user } = req @@ -39,7 +38,30 @@ datasetsRouter.get('/parcellationName/:parcellationName', (req, res, next) => { .catch(error => { next({ code: 500, - error + error, + trace: 'parcellationName' + }) + }) +}) + +datasetsRouter.get('/preview/:datasetName', (req, res, next) => { + const { datasetName } = req.params + getPreview({ datasetName }) + .then(preview => { + if (preview) { + res.status(200).send(JSON.stringify(preview)) + } else { + next({ + code: 404, + trace: 'preview' + }) + } + }) + .catch(error => { + next({ + code: 500, + error, + trace: 'preview' }) }) }) diff --git a/deploy/datasets/query.js b/deploy/datasets/query.js index edf455b9b559b31b376010be9b2c16e92f1d3a79..46d7ac3a8727d23eb8180882ee19a1458f419735 100644 --- a/deploy/datasets/query.js +++ b/deploy/datasets/query.js @@ -1,6 +1,7 @@ const fs = require('fs') const request = require('request') const path = require('path') +const { getPreviewFile, hasPreview } = require('./supplements/previewFile') let cachedData = null let otherQueryResult = null @@ -9,10 +10,10 @@ const timeout = process.env.TIMEOUT || 5000 const fetchDatasetFromKg = (arg) => new Promise((resolve, reject) => { const accessToken = arg && arg.user && arg.user.tokenset && arg.user.tokenset.access_token - const option = accessToken + const option = accessToken || process.env.ACCESS_TOKEN ? { auth: { - 'bearer': accessToken + 'bearer': accessToken || process.env.ACCESS_TOKEN } } : {} @@ -101,27 +102,39 @@ const filterByPRs = (prs, atlasPr) => atlasPr }) : false -const filter = (datasets, {templateName, parcellationName}) => datasets.filter(ds => { - if (templateName) { - return ds.referenceSpaces.some(rs => rs.name === templateName) - } - if (parcellationName) { - return ds.parcellationRegion.length > 0 - ? filterByPRs( - ds.parcellationRegion, - parcellationName === 'JuBrain Cytoarchitectonic Atlas' && juBrain && !/infant/.test(ds.name) - ? juBrain - : parcellationName === 'Fibre Bundle Atlas - Long Bundle' && longBundle - ? longBundle - : parcellationName === 'Fibre Bundle Atlas - Short Bundle' && shortBundle - ? shortBundle - : null - ) - : false - } - - return false -}) +const manualFilter = require('./supplements/parcellation') + +const filter = (datasets, {templateName, parcellationName}) => datasets + .filter(ds => { + if (templateName) { + return ds.referenceSpaces.some(rs => rs.name === templateName) + } + if (parcellationName) { + return ds.parcellationRegion.length > 0 + ? filterByPRs( + ds.parcellationRegion, + parcellationName === 'JuBrain Cytoarchitectonic Atlas' && juBrain && !/infant/.test(ds.name) + ? juBrain + : parcellationName === 'Fibre Bundle Atlas - Long Bundle' && longBundle + ? longBundle + : parcellationName === 'Fibre Bundle Atlas - Short Bundle' && shortBundle + ? shortBundle + : null + ) + : manualFilter({ parcellationName, dataset: ds }) + } + + return false + }) + .map(ds => { + return { + ...ds, + ...parcellationName && ds.parcellationRegion.length === 0 + ? { parcellationRegion: [{ name: manualFilter({ parcellationName, dataset: ds }) }] } + : {}, + preview: hasPreview({ datasetName: ds.name }) + } + }) /** * on init, populate the cached data @@ -134,3 +147,4 @@ exports.init = () => fetchDatasetFromKg() exports.getDatasets = ({ templateName, parcellationName, user }) => getDs({ user }) .then(json => filter(json, {templateName, parcellationName})) +exports.getPreview = ({ datasetName }) => getPreviewFile({ datasetName }) \ No newline at end of file diff --git a/deploy/datasets/supplements/.gitignore b/deploy/datasets/supplements/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..16b9d46ca2ab51e9b5f8a9e5ba31f3ef5a906ab6 --- /dev/null +++ b/deploy/datasets/supplements/.gitignore @@ -0,0 +1 @@ +raw diff --git a/deploy/datasets/supplements/data/allen.json b/deploy/datasets/supplements/data/allen.json new file mode 100644 index 0000000000000000000000000000000000000000..58ad544920be956ac5dc0ad5c5f880c04eca0451 --- /dev/null +++ b/deploy/datasets/supplements/data/allen.json @@ -0,0 +1,453 @@ +[ + { + "Dataset name": "3D imaging of the vascular system of the mouse brain.", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus&p=2#Dataset/632636291a6ff5cb30c55821abaa55c4", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Cerebral cortex", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2F3248-7V", + "PLA": "774", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "3D reconstruction of the vascular system of the mouse brain.", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/a3fd14501d8a5c2ffcaee445ac6f8a5e", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Cerebral cortex", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493/3248-7V", + "PLA": "745", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Action potential dependent sIPSCs - from juvenile (P21-30) C57Bl6/J male mice", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/679c1e4beb7b5f8d7097f1835480a76f", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Field CA1", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2FH57G-ZK5", + "PLA": "15", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Arc expression in resting state", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus&p=2#Dataset/6a5980f16d1b3fd1422db723f9e2c6dc", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 4", + "Semantic link(s)": "Cerebrum", + "Coordinate-based": "Landmark-Reg", + "DOI": "https://doi.org/10.25493%2FMDRW-SWQ", + "PLA": "19", + "EMBARGO": "NO", + "Comments:": "right hemisphere" + }, + { + "Dataset name": "Brain-wide distribution of glutamate type 1 transporter protein (GLT1)", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/63bbb845ac6d2f1839f919c2ef0455bc", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Cerebrum", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2FY147-2CE", + "PLA": "167", + "EMBARGO": "NO", + "Comments:": "also in WHS v2" + }, + { + "Dataset name": "Brainwide distribution and variance of amyloid-beta deposits in tg-ArcSwe mice", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/7e972a9c1c1fc2bb493d09512f6550d5", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Cerebrum", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2FG6CQ-D4D", + "PLA": "138", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Ca2+/calmodulin-dependent protein kinase II tetracycline-transactivator expression: coronal sections (case 317.8)", + "Dataset URL": "https://www.humanbrainproject.eu/en/explore-the-brain/search/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/e15e4048955ed04112d2652d5a8ce587", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Cerebrum", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2FW97C-01R", + "PLA": "case 317.8", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Cell density and distribution in the somatosensory cortex of the mouse brain", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/4e3d82a38ec816d970dff814c9fd2689", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Primary somatosensory area, lower limb; Primary motor area", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2F4HFC-6ZX", + "PLA": "", + "EMBARGO": "YES", + "Comments:": "" + }, + { + "Dataset name": "Comparative overview of brain-wide tetracycline-transactivator expression", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus&p=2#Dataset/48cffa543d49f446f0187902734dd631", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 4", + "Semantic link(s)": "Cerebrum", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2FARKS-R7H", + "PLA": "N/A", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Cortical recordings of the Fmr1KO mouse model of Fragile X syndrome during slow wave activity", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/9f11bd320876be5d037164ce696a384f", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Prelimbic area; Primary motor area; Primary somatosensory area; Anteromedial visual area", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2F5VDM-SHH", + "PLA": "", + "EMBARGO": "YES", + "Comments:": "" + }, + { + "Dataset name": "Fluorescence cortical recording of mouse activity after stroke", + "Dataset URL": "https://www.humanbrainproject.eu/en/explore-the-brain/search/?facet_type[0]=Dataset#Dataset/4730b8c4ae603587a04b4c4362869f91", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 4", + "Semantic link(s)": "Anterior area; Anterior cingulate area, dorsal part; Anterolateral visual area; Posteromedial visual area; Primary motor area; Primary somatosensory area, barrel field; Primary somatosensory area, lower limb; Primary somatosensory area, nose; Primary somatosensory area, trunk; Primary somatosensory area, unassigned; Primary somatosensory area, upper limb; Primary visual area; Retrosplenial area, dorsal part; Retrosplenial area, lateral agranular part; Retrosplenial area, ventral part; Rostrolateral area; Secondary motor area", + "Coordinate-based": "Point coordinates", + "DOI": "https://doi.org/10.25493%2FZ9J0-ZZQ", + "PLA": "552", + "EMBARGO": "YES", + "Comments:": "" + }, + { + "Dataset name": "Hippocampal image volume derived from Thy1-GFP-M transgenic mouse", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/8fb1a664ca3390bae960cc1aa11f5827", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Hippocampal region", + "Coordinate-based": "Landmark-Reg", + "DOI": "https://doi.org/10.25493%2FPMDH-FW1", + "PLA": "20", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Neuropsin tetracycline-transactivator expression: coronal sections (case 1952)", + "Dataset URL": "https://www.humanbrainproject.eu/en/explore-the-brain/search/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/e0f992755e391b1dbdaf5b9669ffb49a", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Cerebrum", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2F5H13-1Q0", + "PLA": "case 1952", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Neuropsin tetracycline-transactivator expression: coronal sections (case 2849)", + "Dataset URL": "https://www.humanbrainproject.eu/en/explore-the-brain/search/?facet_type[0]=Dataset#Dataset/cf9866eac157682b8320037236f54aa4", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 4", + "Semantic link(s)": "Cerebrum", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2FWB6K-V72", + "PLA": "case 2849", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Neuropsin tetracycline-transactivator expression: horizontal sections (case 2877)", + "Dataset URL": "https://www.humanbrainproject.eu/en/explore-the-brain/search/?facet_type[0]=Dataset#Dataset/d56b1fe14bb84987a3a2340e21652b2d", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 5", + "Semantic link(s)": "Cerebrum", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2FAYBB-BXV", + "PLA": "case 2877", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Parvalbumin interneruron distribution in the mouse brain", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus&p=2#Dataset/f740e7bb4e7a93647e3a9da50d6d965b", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 4", + "Semantic link(s)": "Cerebellum", + "Coordinate-based": "Landmark-Reg", + "DOI": "https://doi.org/10.25493%2FQSJE-H14", + "PLA": "21", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Pituitary homeobox 3 tetracycline-transactivator expression: coronal sections (case 3435)", + "Dataset URL": "https://www.humanbrainproject.eu/en/explore-the-brain/search/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus&p=2#Dataset/a028609d74b7ab5c66aafafff6ee512a", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 4", + "Semantic link(s)": "Cerebrum", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2FFMGJ-4N3", + "PLA": "case 3435", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Pituitary homeobox 3 tetracycline-transactivator expression: coronal sections (case 6517)", + "Dataset URL": "https://www.humanbrainproject.eu/en/explore-the-brain/search/?facet_type[0]=Dataset#Dataset/e9b51ea64b41dc297b0914f7207bd4fb", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 5", + "Semantic link(s)": "Cerebrum", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2FDTB3-0KP", + "PLA": "case 6517", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Pituitary homeobox 3 tetracycline-transactivator expression: horizontal sections (case 5154)", + "Dataset URL": "https://www.humanbrainproject.eu/en/explore-the-brain/search/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/2fa3662939761472e8488da76fe49085", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Cerebrum", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2F2382-AYM", + "PLA": "case 5154", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Pituitary homeobox 3 tetracycline-transactivator expression: horizontal sections (case 6513)", + "Dataset URL": "https://www.humanbrainproject.eu/en/explore-the-brain/search/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/818289386f50cb9a791aae661a4c2f92", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Cerebrum", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2F1AH7-T1A", + "PLA": "case 6513", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Prion promoter tetracycline-transactivator expression: coronal sections (case 388.12)", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/0715fc5d4958b0b73891cae874c37b29", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Cerebrum", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2FT9P1-WH4", + "PLA": "case 388.12", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Purkinje cell distribution in mouse cerebellum", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus&p=2#Dataset/0d89723452a334fd8e7fbd040ba79376", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 4", + "Semantic link(s)": "Cerebellum", + "Coordinate-based": "Landmark-Reg", + "DOI": "https://doi.org/10.25493%2F76F0-87N", + "PLA": "22", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Purkinje cell protein 2 tetracycline-transactivator expression: coronal sections (case 1261)", + "Dataset URL": "https://www.humanbrainproject.eu/en/explore-the-brain/search/?facet_type[0]=Dataset#Dataset/ca8162a22e5f43fbbe1a1bed22303fdf", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 5", + "Semantic link(s)": "Cerebrum", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2FA2EG-VPR", + "PLA": "case 1261", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Purkinje cell protein 2 tetracycline-transactivator expression: coronal sections (case 4340)", + "Dataset URL": "https://www.humanbrainproject.eu/en/explore-the-brain/search/?facet_type[0]=Dataset#Dataset/03fe9f1fcabedf124d9e6a0e457dca26", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 6", + "Semantic link(s)": "Cerebrum", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2FYCGE-ADC", + "PLA": "case 4340", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Purkinje cell protein 2 tetracycline-transactivator expression: horizontal sections (case 3292)", + "Dataset URL": "https://www.humanbrainproject.eu/en/explore-the-brain/search/?facet_type[0]=Dataset#Dataset/70bdda26f3c38dda1790d2a24209100e", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 7", + "Semantic link(s)": "Cerebrum", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2FD1PR-55A", + "PLA": "case 3292", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Recordings of cerebellar granule cells current-voltage relations", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/40a8ed8caae4989506d69fd290b67a90", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Vermal regions", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2FMDAR-XEB", + "PLA": "810", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Recordings of cerebellar neuronal firing induced by currents steps", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/5e245cf67a42a14a56bc43913f7bf28a", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Vermal regions", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2F4AF6-WSD", + "PLA": "810", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Recordings of excitatory postsynaptic currents from cerebellar neurons", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/a1ba394b5f353a67f9cec3549891d77b", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Vermal regions", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2FF2VK-MB4", + "PLA": "810", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Recordings of excitatory postsynaptic potentials from cerebellar neurons", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/2ea6f32e8dfd644d426b93aac0ae6eec", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Vermal regions", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2FG07Q-K87", + "PLA": "810", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Recordings of passive cellular parameters of cerebellar neurons", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/077778de710a9192795869a8885525ac", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Vermal regions", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2FMVHQ-4YA", + "PLA": "810", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Recordings of spontaneous firing of cerebellar interneurons (Golgi cells)", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/4197a2f5d71432349fb37ff3ad429580", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 3", + "Semantic link(s)": "Vermal regions", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2FJQH3-0A4", + "PLA": "810", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "sIPSCs from juvenile (P21-30) C57B16/J male mice from hippocampal CA1 pyramidal neurons receiving input from PV+ and CCK+ interneurons", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus&p=2#Dataset/fb1dab2cc153f8de099996172ea4d8b8", + "Reference atlas": "Allen Mouse Common Coordinate Framework, version 4", + "Semantic link(s)": "Field CA1", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2FPHA7-5KZ", + "PLA": "12", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "sIPSCs from juvenile (P21-30) C57Bl6/J male mice from CA1 pyramidal neurons receiving input from PV+ interneurons", + "Dataset URL": 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100644 index 0000000000000000000000000000000000000000..8f218a5fed27c5773d39c74ab585adfb7e1f5982 --- /dev/null +++ b/deploy/datasets/supplements/data/receptorPreview.json @@ -0,0 +1 @@ +[["Density measurements of different receptors for Area 4p",[{"name":"Receptor density fingerprint of Area 4p","filename":"fingerprint","mimetype":"application/json","properties":{"description":"**Multireceptor fingerprint for area 4p.** This polar plot shows the mean receptor densities in fmol/mg protein (solid shape) and standard deviation (dashed line) of 16 receptor binding sites in the area 4p. 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protein)","display":true},"elements":{"point":{"radius":0,"hoverRadius":8,"hitRadius":4}}},"colors":[{"borderColor":"rgba(255,255,255,1)","backgroundColor":"rgba(5,198,198,0.2)"},{"borderColor":"rgba(255,255,255,1)"}]}}]]] \ No newline at end of file diff --git a/deploy/datasets/supplements/data/waxholm.json b/deploy/datasets/supplements/data/waxholm.json new file mode 100644 index 0000000000000000000000000000000000000000..db52cc9345128274a7cd4a56bf2d49e7417dfaf1 --- /dev/null +++ b/deploy/datasets/supplements/data/waxholm.json @@ -0,0 +1,112 @@ +[ + { + "Dataset name": "3D high resolution SRXTM image data of cortical vasculature of rat brain.", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Rattus%20norvegicus#Dataset/943484f6f124311f2a60861e29f49b3e", + "Reference atlas": "Waxholm Space atlas of the Sprague Dawley rat brain, version 2", + "Semantic link(s)": "Neocortex", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2FHCPQ-MY8", + "PLA": "18", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Atlas of normal rat brain cyto- and myeloarchitecture", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Rattus%20norvegicus#Dataset/6ce1f96ae210b2335b75a793367e3865", + "Reference atlas": "Waxholm Space atlas of the Sprague Dawley rat brain, version 2", + "Semantic link(s)": "Whole Brain (v2.0)", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2FC63A-FEY", + "PLA": "165", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Brain-wide distribution of glutamate type 1 transporter protein (GLT1)", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Mus%20musculus#Dataset/63bbb845ac6d2f1839f919c2ef0455bc", + "Reference atlas": "Waxholm Space atlas of the Sprague Dawley rat brain, version 2", + "Semantic link(s)": "Whole Brain (v2.0)", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2FY147-2CE", + "PLA": "167", + "EMBARGO": "NO", + "Comments:": "Also in CCF v3" + }, + { + "Dataset name": "Brain-wide distribution of vesicular glutamate transporter type 3 (VGLUT3)", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Rattus%20norvegicus#Dataset/ca2de49ed9e6660242b937c8e9f2e4eb", + "Reference atlas": "Waxholm Space atlas of the Sprague Dawley rat brain, version 2", + "Semantic link(s)": "Whole Brain (v2.0)", + "Coordinate-based": "QuickNII", + "DOI": "https://doi.org/10.25493%2FGP15-1MS", + "PLA": "168", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Graphical representation of rat cortical vasculature reconstructed from high resolution 3D SRXTM data.", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Rattus%20norvegicus#Dataset/fc6865e8670b65aebec05b73f9e795c7", + "Reference atlas": "Waxholm Space atlas of the Sprague Dawley rat brain, version 2", + "Semantic link(s)": "Neocortex", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2FK243-13K", + "PLA": "17", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Large scale multi-channel EEG in rats", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Rattus%20norvegicus#Dataset/c5aab03945700ffb1a2fd2fd83819340", + "Reference atlas": "Waxholm Space atlas of the Sprague Dawley rat brain, version 2", + "Semantic link(s)": "Neocortex", + "Coordinate-based": "Point coordinates", + "DOI": "https://doi.org/10.25493%2F4SPM-V00", + "PLA": "", + "EMBARGO": "YES", + "Comments:": "" + }, + { + "Dataset name": "Loose-cell attached patch-clamp recordings from cerebellar granule cells", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Rattus%20norvegicus#Dataset/430c8508746cbd9f8f5c91b66ae97316", + "Reference atlas": "Waxholm Space atlas of the Sprague Dawley rat brain, version 2", + "Semantic link(s)": "Cerebellum", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2F6R48-E3V", + "PLA": "810", + "EMBARGO": "NO", + "Comments:": "" + }, + { + "Dataset name": "Recordings of cerebellar neuronal firing induced by currents steps", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Rattus%20norvegicus#Dataset/5e245cf67a42a14a56bc43913f7bf28a", + "Reference atlas": "Waxholm Space atlas of the Sprague Dawley rat brain, version 2", + "Semantic link(s)": "Cerebellum", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2F4AF6-WSD", + "PLA": "810", + "EMBARGO": "NO", + "Comments:": "Also in CCF v3" + }, + { + "Dataset name": "Recordings of excitatory postsynaptic currents from cerebellar neurons", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Rattus%20norvegicus#Dataset/a1ba394b5f353a67f9cec3549891d77b", + "Reference atlas": "Waxholm Space atlas of the Sprague Dawley rat brain, version 2", + "Semantic link(s)": "Cerebellum", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2FF2VK-MB4", + "PLA": "810", + "EMBARGO": "NO", + "Comments:": "Also in CCF v3" + }, + { + "Dataset name": "Recordings of excitatory postsynaptic potentials from cerebellar neurons", + "Dataset URL": "https://kg.humanbrainproject.org/webapp/?facet_type[0]=Dataset&facet_Dataset_subjects.children.species[0]=Rattus%20norvegicus#Dataset/2ea6f32e8dfd644d426b93aac0ae6eec", + "Reference atlas": "Waxholm Space atlas of the Sprague Dawley rat brain, version 2", + "Semantic link(s)": "Cerebellum", + "Coordinate-based": "", + "DOI": "https://doi.org/10.25493%2FG07Q-K87", + "PLA": "810", + "EMBARGO": "NO", + "Comments:": "Also in CCF v3" + } +] \ No newline at end of file diff --git a/deploy/datasets/supplements/parcellation.js b/deploy/datasets/supplements/parcellation.js new file mode 100644 index 0000000000000000000000000000000000000000..20527e571c065ddcf70d9a6a7ba9162e95af79b2 --- /dev/null +++ b/deploy/datasets/supplements/parcellation.js @@ -0,0 +1,27 @@ +const fs = require('fs') +const path = require('path') +let waxholm = new Map(), + allen = new Map() + +fs.readFile(path.join(__dirname, 'data', 'allen.json'), 'utf-8', (err, data) => { + if (err) + throw err + const json = JSON.parse(data) + allen = new Map(json.map(item => [item['Dataset name'], item["Semantic link(s)"]])) +}) + + +fs.readFile(path.join(__dirname, 'data', 'waxholm.json'), 'utf-8', (err, data) => { + if (err) + throw err + const json = JSON.parse(data) + waxholm = new Map(json.map(item => [item['Dataset name'], item["Semantic link(s)"]])) +}) + +module.exports = ({ parcellationName, dataset }) => { + return parcellationName === 'Allen adult mouse brain reference atlas V3 Brain Atlas' + ? allen.get(dataset.name) + : parcellationName === 'Whole Brain (v2.0)' + ? waxholm.get(dataset.name) + : false +} \ No newline at end of file diff --git a/deploy/datasets/supplements/previewFile.js b/deploy/datasets/supplements/previewFile.js new file mode 100644 index 0000000000000000000000000000000000000000..a8c7bd90c42342bf56f2cbc83ec6c52e4493750f --- /dev/null +++ b/deploy/datasets/supplements/previewFile.js @@ -0,0 +1,33 @@ +const fs = require('fs') +const path = require('path') + +const DISABLE_RECEPTOR_PREVIEW = process.env.DISABLE_RECEPTOR_PREVIEW +const DISABLE_JUBRAIN_PMAP = process.env.DISABLE_JUBRAIN_PMAP + +let previewMap = new Map(), + previewMapKeySet = new Set() + +const readFile = (filename) => new Promise((resolve) => { + fs.readFile(path.join(__dirname, 'data', filename), 'utf-8', (err, data) => { + if (err) + throw err + resolve(JSON.parse(data)) + }) +}) + +Promise.all([ + DISABLE_RECEPTOR_PREVIEW ? Promise.resolve([]) : readFile('receptorPreview.json'), + DISABLE_JUBRAIN_PMAP ? Promise.resolve([]) : readFile('pmapJubrainPreview.json'), +]) + .then(arrOfA => arrOfA.reduce((acc, item) => acc.concat(item), [])) + .then(iterable => { + previewMap = new Map(iterable) + previewMapKeySet = new Set(previewMap.keys()) + }) + .catch(e => { + console.error('preview file error', e) + }) + +exports.getPreviewFile = ({ datasetName }) => Promise.resolve(previewMap.get(datasetName)) +exports.getAllPreviewDSNames = () => Array.from(previewMap.keys()) +exports.hasPreview = ({ datasetName }) => previewMapKeySet.has(datasetName) \ No newline at end of file diff --git a/deploy/nehubaConfig/index.js b/deploy/nehubaConfig/index.js index 0e716e53fa61864f318cfbb60411ef28e3c2a6fb..9b000cbb9003e4d37e7bc82c7f3eff22199e9f66 100644 --- a/deploy/nehubaConfig/index.js +++ b/deploy/nehubaConfig/index.js @@ -9,7 +9,11 @@ nehubaConfigRouter.get('/:configId', (req, res, next) => { const configFilePath = path.join(__dirname, '..', 'res', `${configId}.json`) fs.readFile(configFilePath, 'utf-8', (error, data) => { if (error) - return next({code: 500, error}) + return next({ + code: 500, + error, + trace: 'fetching config' + }) res.status(200).send(data) }) }) diff --git a/deploy/server.js b/deploy/server.js index 8f3a55817fe845a4336f3296316e318e49f9b6c6..cd6a1da4c2e72ac70be1157b88de454e2e993d7f 100644 --- a/deploy/server.js +++ b/deploy/server.js @@ -4,7 +4,6 @@ const app = express() const session = require('express-session') const MemoryStore = require('memorystore')(session) - app.disable('x-powered-by') if (process.env.NODE_ENV !== 'production') { @@ -44,23 +43,28 @@ const startServer = async (app) => { console.log('error during configureAuth', e) } - const templateRouter = require('./templates') - const nehubaConfigRouter = require('./nehubaConfig') - const datasetRouter = require('./datasets') const catchError = require('./catchError') - + app.use(catchError) + const publicPath = process.env.NODE_ENV === 'production' ? path.join(__dirname, 'public') : path.join(__dirname, '..', 'dist', 'aot') + app.use(express.static(publicPath)) + + app.use((req, res, next) => { + res.set('Content-Type', 'application/json') + next() + }) + + const templateRouter = require('./templates') + const nehubaConfigRouter = require('./nehubaConfig') + const datasetRouter = require('./datasets') + app.use('/templates', templateRouter) app.use('/nehubaConfig', nehubaConfigRouter) app.use('/datasets', datasetRouter) - app.use(catchError) - - app.use(express.static(publicPath)) - const PORT = process.env.PORT || 3000 app.listen(PORT, () => console.log(`listening on port ${PORT}`)) diff --git a/deploy/templates/index.js b/deploy/templates/index.js index e22658cd590a6cc60e565c61e04863779f9e938e..1ed84e544f0754e84ee8f48855d7b30975361de4 100644 --- a/deploy/templates/index.js +++ b/deploy/templates/index.js @@ -13,7 +13,8 @@ router.get('/', (req, res, next) => { }) .catch(error => next({ code: 500, - error + error, + trace: 'getTemplate' })) }) @@ -34,7 +35,8 @@ router.get('/:template', (req, res, next) => { }) .catch(error => next({ code: 500, - error + error, + trace: 'getTemplate/template' })) }) diff --git a/src/atlasViewer/atlasViewer.component.ts b/src/atlasViewer/atlasViewer.component.ts index 94e5ba520d60e42adada9b03c274dab3c5b61374..65db16cfc66501b73c06f4e5ced584eee91733ef 100644 --- a/src/atlasViewer/atlasViewer.component.ts +++ b/src/atlasViewer/atlasViewer.component.ts @@ -6,7 +6,6 @@ import { map, filter, distinctUntilChanged, delay, concatMap, debounceTime } fro import { AtlasViewerDataService } from "./atlasViewer.dataService.service"; import { WidgetServices } from "./widgetUnit/widgetService.service"; import { LayoutMainSide } from "../layouts/mainside/mainside.component"; -import { Chart } from 'chart.js' import { AtlasViewerConstantsServices } from "./atlasViewer.constantService.service"; import { BsModalService } from "ngx-bootstrap/modal"; import { ModalUnit } from "./modalUnit/modalUnit.component"; @@ -229,6 +228,8 @@ export class AtlasViewer implements OnDestroy, OnInit { template.useTheme === 'dark' : false + this.constantsService.darktheme = this.darktheme + /* new viewer should reset the spatial data search */ this.store.dispatch({ type : FETCHED_SPATIAL_DATA, @@ -249,67 +250,6 @@ export class AtlasViewer implements OnDestroy, OnInit { ).subscribe(v => this.layoutMainSide.showSide = isDefined(v)) ) - /** - * Because there is no easy way to display standard deviation natively, use a plugin - * */ - Chart.pluginService.register({ - - /* patching background color fill, so saved images do not look completely white */ - beforeDraw: (chart) => { - const ctx = chart.ctx as CanvasRenderingContext2D; - ctx.fillStyle = this.darktheme ? - `rgba(50,50,50,0.8)` : - `rgba(255,255,255,0.8)` - - if (chart.canvas) ctx.fillRect(0, 0, chart.canvas.width, chart.canvas.height) - - }, - - /* patching standard deviation for polar (potentially also line/bar etc) graph */ - afterInit: (chart) => { - if (chart.config.options && chart.config.options.tooltips) { - - chart.config.options.tooltips.callbacks = { - label: function (tooltipItem, data) { - let sdValue - if (data.datasets && typeof tooltipItem.datasetIndex != 'undefined' && data.datasets[tooltipItem.datasetIndex].label) { - const sdLabel = data.datasets[tooltipItem.datasetIndex].label + '_sd' - const sd = data.datasets.find(dataset => typeof dataset.label != 'undefined' && dataset.label == sdLabel) - if (sd && sd.data && typeof tooltipItem.index != 'undefined' && typeof tooltipItem.yLabel != 'undefined') sdValue = Number(sd.data[tooltipItem.index]) - Number(tooltipItem.yLabel) - } - return `${tooltipItem.yLabel} ${sdValue ? '(' + sdValue + ')' : ''}` - } - } - } - if (chart.data.datasets) { - chart.data.datasets = chart.data.datasets - .map(dataset => { - if (dataset.label && /\_sd$/.test(dataset.label)) { - const originalDS = chart.data.datasets!.find(baseDS => typeof baseDS.label !== 'undefined' && (baseDS.label == dataset.label!.replace(/_sd$/, ''))) - if (originalDS) { - return Object.assign({}, dataset, { - data: (originalDS.data as number[]).map((datapoint, idx) => (Number(datapoint) + Number((dataset.data as number[])[idx]))), - ... this.constantsService.chartSdStyle - }) - } else { - return dataset - } - } else if (dataset.label) { - const sdDS = chart.data.datasets!.find(sdDS => typeof sdDS.label !== 'undefined' && (sdDS.label == dataset.label + '_sd')) - if (sdDS) { - return Object.assign({}, dataset, { - ...this.constantsService.chartBaseStyle - }) - } else { - return dataset - } - } else { - return dataset - } - }) - } - } - }) } /** diff --git a/src/atlasViewer/atlasViewer.constantService.service.ts b/src/atlasViewer/atlasViewer.constantService.service.ts index 575158dbf9f20296fad4f163d83719586f550f13..17c926b6b55ea6b27b9a973ff9e80f693ae81524 100644 --- a/src/atlasViewer/atlasViewer.constantService.service.ts +++ b/src/atlasViewer/atlasViewer.constantService.service.ts @@ -2,8 +2,10 @@ import { Injectable } from "@angular/core"; import { Store } from "@ngrx/store"; import { ViewerStateInterface, Property, FETCHED_METADATA } from "../services/stateStore.service"; import { Subject } from "rxjs"; -import { ACTION_TYPES, ViewerConfiguration, viewerConfigState } from 'src/services/state/viewerConfig.store' -import { User } from "src/services/auth.service"; +import { ACTION_TYPES, ViewerConfiguration } from 'src/services/state/viewerConfig.store' + +export const CM_THRESHOLD = `0.05` +export const CM_MATLAB_JET = `float r;if( x < 0.7 ){r = 4.0 * x - 1.5;} else {r = -4.0 * x + 4.5;}float g;if (x < 0.5) {g = 4.0 * x - 0.5;} else {g = -4.0 * x + 3.5;}float b;if (x < 0.3) {b = 4.0 * x + 0.5;} else {b = -4.0 * x + 2.5;}float a = 1.0;` @Injectable({ providedIn : 'root' @@ -11,9 +13,12 @@ import { User } from "src/services/auth.service"; export class AtlasViewerConstantsServices{ + public darktheme: boolean = false public mobile: boolean public loadExportNehubaPromise : Promise<boolean> + public getActiveColorMapFragmentMain = ():string=>`void main(){float x = toNormalized(getDataValue());${CM_MATLAB_JET}if(x>${CM_THRESHOLD}){emitRGB(vec3(r,g,b));}else{emitTransparent();}}` + public ngLandmarkLayerName = 'spatial landmark layer' public ngUserLandmarkLayerName = 'user landmark layer' @@ -201,6 +206,7 @@ Interactive atlas viewer requires **webgl2.0**, and the \`EXT_color_buffer_float private showHelpPerspectiveMobile = [ ['drag', 'change perspective view'] ] + private showHelpPerspectiveDesktop = [ ['drag', 'change perspective view'] ] @@ -288,4 +294,4 @@ export const SUPPORT_LIBRARY_MAP : Map<string,HTMLElement> = new Map([ ['vue@2.5.16',parseURLToElement('https://cdn.jsdelivr.net/npm/vue@2.5.16/dist/vue.js')], ['preact@8.4.2',parseURLToElement('https://cdn.jsdelivr.net/npm/preact@8.4.2/dist/preact.min.js')], ['d3@5.7.0',parseURLToElement('https://cdnjs.cloudflare.com/ajax/libs/d3/5.7.0/d3.min.js')] -]) +]) \ No newline at end of file diff --git a/src/atlasViewer/atlasViewer.dataService.service.ts b/src/atlasViewer/atlasViewer.dataService.service.ts index 3cc95082cdd71699dd9147928cb7237f60deefbb..182bd824b534c62d1744263c4f25d9a97d9f695b 100644 --- a/src/atlasViewer/atlasViewer.dataService.service.ts +++ b/src/atlasViewer/atlasViewer.dataService.service.ts @@ -1,7 +1,6 @@ import { Injectable, OnDestroy } from "@angular/core"; import { Store, select } from "@ngrx/store"; import { ViewerStateInterface, FETCHED_TEMPLATE, DataEntry, FETCHED_DATAENTRIES, safeFilter, FETCHED_SPATIAL_DATA, UPDATE_SPATIAL_DATA } from "../services/stateStore.service"; -import { map, distinctUntilChanged, debounceTime } from "rxjs/operators"; import { Subscription, combineLatest } from "rxjs"; import { AtlasViewerConstantsServices } from "./atlasViewer.constantService.service"; import { PluginManifest } from "./atlasViewer.pluginService.service"; diff --git a/src/atlasViewer/atlasViewer.urlService.service.ts b/src/atlasViewer/atlasViewer.urlService.service.ts index d33ae8b6789cd0a91aac31fa475fa882eab2aead..7d95d349e7f31115773417278ae9786bce632c60 100644 --- a/src/atlasViewer/atlasViewer.urlService.service.ts +++ b/src/atlasViewer/atlasViewer.urlService.service.ts @@ -4,7 +4,6 @@ import { ViewerStateInterface, isDefined, NEWVIEWER, getLabelIndexMap, SELECT_RE import { PluginInitManifestInterface } from 'src/services/state/pluginState.store' import { Observable,combineLatest } from "rxjs"; import { filter, map, scan, distinctUntilChanged, skipWhile, take } from "rxjs/operators"; -import { getActiveColorMapFragmentMain } from "../ui/nehubaContainer/nehubaContainer.component"; import { PluginServices } from "./atlasViewer.pluginService.service"; import { AtlasViewerConstantsServices } from "./atlasViewer.constantService.service"; import { ToastService } from "src/services/toastService.service"; @@ -175,7 +174,7 @@ export class AtlasViewerURLService{ name : layer, source : `nifti://${layer}`, mixability : 'nonmixable', - shader : getActiveColorMapFragmentMain() + shader : this.constantService.getActiveColorMapFragmentMain() } })) } diff --git a/src/atlasViewer/widgetUnit/widgetUnit.component.ts b/src/atlasViewer/widgetUnit/widgetUnit.component.ts index 2ff33338c8318ae06e750b0389852064e6f0806f..4c0392deb9dbee9b7d284364e82e4913a85f6c36 100644 --- a/src/atlasViewer/widgetUnit/widgetUnit.component.ts +++ b/src/atlasViewer/widgetUnit/widgetUnit.component.ts @@ -81,7 +81,6 @@ export class WidgetUnit { } exit(event?:Event){ - console.log('exit') if(event){ event.stopPropagation() event.preventDefault() diff --git a/src/components/flatTree/flatTree.style.css b/src/components/flatTree/flatTree.style.css index cc5bdf60a95b1ccbf06c3a71bb6fe2ea71d5c2f6..1eb8e5e11f385e08de61989c548ccce1c1d03a0a 100644 --- a/src/components/flatTree/flatTree.style.css +++ b/src/components/flatTree/flatTree.style.css @@ -32,6 +32,7 @@ .render-node-text { + white-space: nowrap; cursor:default; } @@ -185,4 +186,9 @@ span[renderText] .render-node-level-10 > .padding-block-container { left: -10em; +} + +.r-270 +{ + transform: rotate(270deg); } \ No newline at end of file diff --git a/src/components/flatTree/flatTree.template.html b/src/components/flatTree/flatTree.template.html index 2e8cd6192a073b2aa551d947370cc32db50cdbce..5888e601e26ce777aa083e9656f3f94875ff6e1a 100644 --- a/src/components/flatTree/flatTree.template.html +++ b/src/components/flatTree/flatTree.template.html @@ -24,7 +24,7 @@ <span *ngIf = "findChildren(flattenedItem).length > 0; else noChildren" (click) = "$event.stopPropagation(); toggleCollapse(flattenedItem)" > - <i [ngClass] = "isCollapsed(flattenedItem) ? 'fa-chevron-right' : 'fa-chevron-down'" class="fas"></i> + <i [ngClass] = "isCollapsed(flattenedItem) ? '' : 'r-270'" class="fas fa-chevron-down"></i> </span> <ng-template #noChildren> <i class="fas fa-none"> diff --git a/src/res/css/extra_styles.css b/src/res/css/extra_styles.css index e3ac773b276941b2fdb7edf3099fe510c2bb16e9..58d0c8a6a84a04fa15818eac82d72a6d64ae27b4 100644 --- a/src/res/css/extra_styles.css +++ b/src/res/css/extra_styles.css @@ -245,4 +245,9 @@ markdown-dom pre code { background-color: rgba(70, 70 , 70, 1.0); color: rgba(255, 255, 255, 1.0); +} + +.r-90 +{ + transform: rotate(90deg)!important; } \ No newline at end of file diff --git a/src/services/state/dataStore.store.ts b/src/services/state/dataStore.store.ts index 889f1bbdc9f0ec88fb4d61b7838e010292d9f895..1c8999e78981de8af165a4b656da1182172a6ebd 100644 --- a/src/services/state/dataStore.store.ts +++ b/src/services/state/dataStore.store.ts @@ -53,6 +53,8 @@ export interface DataEntry{ publications: Publication[] embargoStatus: string[] + preview?: boolean + /** * TODO typo, should be kgReferences */ @@ -119,7 +121,15 @@ export interface File{ name: string absolutePath: string byteSize: number - contentType: string + contentType: string, +} + +export interface ViewerPreviewFile{ + name: string + filename: string + mimetype: string + url?: string + data?: any } export interface FileSupplementData{ diff --git a/src/ui/databrowserModule/databrowser.module.ts b/src/ui/databrowserModule/databrowser.module.ts index 4f10475c54a3d075875a078d279e20d0ba793924..a360a6c3eaa1c6668b2c0d77e42e4adff1be73fa 100644 --- a/src/ui/databrowserModule/databrowser.module.ts +++ b/src/ui/databrowserModule/databrowser.module.ts @@ -5,25 +5,41 @@ import { DatasetViewerComponent } from "./datasetViewer/datasetViewer.component" import { ComponentsModule } from "src/components/components.module"; import { ModalityPicker } from "./modalityPicker/modalityPicker.component"; import { RegionHierarchy } from "./regionHierachy/regionHierarchy.component"; -import { FilterNameBySearch } from "./filterNameBySearch.pipe"; +import { FilterNameBySearch } from "./util/filterNameBySearch.pipe"; import { FormsModule } from "@angular/forms"; import { DatabrowserService } from "./databrowser.service"; -import { PathToNestedChildren } from "./pathToNestedChildren.pipe"; -import { CopyPropertyPipe } from "./copyProperty.pipe"; -import { FilterDataEntriesbyMethods } from "./filterDataEntriesByMethods.pipe"; -import { FilterDataEntriesByRegion } from "./filterDataEntriesByRegion.pipe"; +import { PathToNestedChildren } from "./util/pathToNestedChildren.pipe"; +import { CopyPropertyPipe } from "./util/copyProperty.pipe"; +import { FilterDataEntriesbyMethods } from "./util/filterDataEntriesByMethods.pipe"; +import { FilterDataEntriesByRegion } from "./util/filterDataEntriesByRegion.pipe"; +import { TooltipModule } from "ngx-bootstrap/tooltip"; +import { PreviewComponent } from "./preview/preview.component"; +import { FileViewer } from "./fileviewer/fileviewer.component"; +import { RadarChart } from "./fileviewer/radar/radar.chart.component"; +import { ChartsModule } from "ng2-charts"; +import { LineChart } from "./fileviewer/line/line.chart.component"; +import { DedicatedViewer } from "./fileviewer/dedicated/dedicated.component"; +import { Chart } from 'chart.js' +import { AtlasViewerConstantsServices } from "src/atlasViewer/atlasViewer.constantService.service"; @NgModule({ imports:[ + ChartsModule, CommonModule, ComponentsModule, - FormsModule + FormsModule, + TooltipModule.forRoot() ], declarations: [ DataBrowser, DatasetViewerComponent, ModalityPicker, RegionHierarchy, + PreviewComponent, + FileViewer, + RadarChart, + LineChart, + DedicatedViewer, /** * pipes @@ -49,5 +65,69 @@ import { FilterDataEntriesByRegion } from "./filterDataEntriesByRegion.pipe"; }) export class DatabrowserModule{ + constructor( + constantsService:AtlasViewerConstantsServices + ){ + /** + * Because there is no easy way to display standard deviation natively, use a plugin + * */ + Chart.pluginService.register({ + + /* patching background color fill, so saved images do not look completely white */ + beforeDraw: (chart) => { + const ctx = chart.ctx as CanvasRenderingContext2D; + ctx.fillStyle = constantsService.darktheme ? + `rgba(50,50,50,0.8)` : + `rgba(255,255,255,0.8)` + + if (chart.canvas) ctx.fillRect(0, 0, chart.canvas.width, chart.canvas.height) + + }, + + /* patching standard deviation for polar (potentially also line/bar etc) graph */ + afterInit: (chart) => { + if (chart.config.options && chart.config.options.tooltips) { + chart.config.options.tooltips.callbacks = { + label: function (tooltipItem, data) { + let sdValue + if (data.datasets && typeof tooltipItem.datasetIndex != 'undefined' && data.datasets[tooltipItem.datasetIndex].label) { + const sdLabel = data.datasets[tooltipItem.datasetIndex].label + '_sd' + const sd = data.datasets.find(dataset => typeof dataset.label != 'undefined' && dataset.label == sdLabel) + if (sd && sd.data && typeof tooltipItem.index != 'undefined' && typeof tooltipItem.yLabel != 'undefined') sdValue = Number(sd.data[tooltipItem.index]) - Number(tooltipItem.yLabel) + } + return `${tooltipItem.yLabel} ${sdValue ? '(' + sdValue + ')' : ''}` + } + } + } + if (chart.data.datasets) { + chart.data.datasets = chart.data.datasets + .map(dataset => { + if (dataset.label && /\_sd$/.test(dataset.label)) { + const originalDS = chart.data.datasets!.find(baseDS => typeof baseDS.label !== 'undefined' && (baseDS.label == dataset.label!.replace(/_sd$/, ''))) + if (originalDS) { + return Object.assign({}, dataset, { + data: (originalDS.data as number[]).map((datapoint, idx) => (Number(datapoint) + Number((dataset.data as number[])[idx]))), + ... constantsService.chartSdStyle + }) + } else { + return dataset + } + } else if (dataset.label) { + const sdDS = chart.data.datasets!.find(sdDS => typeof sdDS.label !== 'undefined' && (sdDS.label == dataset.label + '_sd')) + if (sdDS) { + return Object.assign({}, dataset, { + ...constantsService.chartBaseStyle + }) + } else { + return dataset + } + } else { + return dataset + } + }) + } + } + }) + } } \ No newline at end of file diff --git a/src/ui/databrowserModule/databrowser.service.ts b/src/ui/databrowserModule/databrowser.service.ts index 0a948ff58adc040caedbd33b81463e20e0c37596..65be98caebc16638f21d51d78a1f54469cd716a7 100644 --- a/src/ui/databrowserModule/databrowser.service.ts +++ b/src/ui/databrowserModule/databrowser.service.ts @@ -1,7 +1,7 @@ import { Injectable, ComponentRef, OnDestroy } from "@angular/core"; import { Store, select } from "@ngrx/store"; import { ViewerConfiguration } from "src/services/state/viewerConfig.store"; -import { SELECT_REGIONS, extractLabelIdx, CHANGE_NAVIGATION, DataEntry, File, safeFilter, isDefined, getLabelIndexMap, FETCHED_DATAENTRIES, SELECT_PARCELLATION } from "src/services/stateStore.service"; +import { SELECT_REGIONS, extractLabelIdx, CHANGE_NAVIGATION, DataEntry, File, safeFilter, isDefined, getLabelIndexMap, FETCHED_DATAENTRIES, SELECT_PARCELLATION, ADD_NG_LAYER, NgViewerStateInterface, REMOVE_NG_LAYER } from "src/services/stateStore.service"; import { WidgetServices } from "src/atlasViewer/widgetUnit/widgetService.service"; import { map, distinctUntilChanged, filter, debounceTime } from "rxjs/operators"; import { Subscription, combineLatest, Observable, BehaviorSubject } from "rxjs"; @@ -44,6 +44,14 @@ export class DatabrowserService implements OnDestroy{ private store: Store<ViewerConfiguration>, private widgetService: WidgetServices ){ + + this.subscriptions.push( + this.store.pipe( + select('ngViewerState') + ).subscribe(layersInterface => + this.ngLayers = new Set(layersInterface.layers.map(l => l.source.replace(/^nifti\:\/\//, '')))) + ) + this.selectedRegions$ = this.store.pipe( select('viewerState'), filter(state => isDefined(state) && isDefined(state.regionsSelected)), @@ -82,20 +90,20 @@ export class DatabrowserService implements OnDestroy{ ) this.fetchDataObservable$ = combineLatest( - this.store.pipe( - select('viewerState'), - safeFilter('templateSelected'), - map(({templateSelected})=>(templateSelected.name)), - distinctUntilChanged() - ), - this.store.pipe( - select('viewerState'), - safeFilter('parcellationSelected'), - map(({parcellationSelected})=>(parcellationSelected.name)), - distinctUntilChanged() - ), - this.manualFetchDataset$ - ) + this.store.pipe( + select('viewerState'), + safeFilter('templateSelected'), + map(({templateSelected})=>(templateSelected.name)), + distinctUntilChanged() + ), + this.store.pipe( + select('viewerState'), + safeFilter('parcellationSelected'), + map(({parcellationSelected})=>(parcellationSelected.name)), + distinctUntilChanged() + ), + this.manualFetchDataset$ + ) this.subscriptions.push( this.fetchDataObservable$.pipe( @@ -107,7 +115,7 @@ export class DatabrowserService implements OnDestroy{ ngOnDestroy(){ this.subscriptions.forEach(s => s.unsubscribe()) } - + public updateRegionSelection(regions: any[]) { this.store.dispatch({ type: SELECT_REGIONS, @@ -215,5 +223,43 @@ export class DatabrowserService implements OnDestroy{ }) } + public fetchPreviewData(datasetName: string){ + const encodedDatasetName = encodeURI(datasetName) + return new Promise((resolve, reject) => { + fetch(`${this.constantService.backendUrl}datasets/preview/${encodedDatasetName}`) + .then(res => res.json()) + .then(resolve) + .catch(reject) + }) + } + + /** + * dedicated viewing (nifti heat maps etc) + */ + private niftiLayerName: string = `nifty layer` + public ngLayers : Set<string> = new Set() + public showNewNgLayer({ url }):void{ + + const layer = { + name : url, + source : `nifti://${url}`, + mixability : 'nonmixable', + shader : this.constantService.getActiveColorMapFragmentMain() + } + this.store.dispatch({ + type: ADD_NG_LAYER, + layer + }) + } + + removeNgLayer({ url }) { + this.store.dispatch({ + type : REMOVE_NG_LAYER, + layer : { + name : url + } + }) + } + public temporaryFilterDataentryName = temporaryFilterDataentryName } \ No newline at end of file diff --git a/src/ui/databrowserModule/databrowser/databrowser.component.ts b/src/ui/databrowserModule/databrowser/databrowser.component.ts index f2ffd83505028f1975369ae5a035ec4981e34789..07890a3b0221645facf01409ebddd9c25b36ad2f 100644 --- a/src/ui/databrowserModule/databrowser/databrowser.component.ts +++ b/src/ui/databrowserModule/databrowser/databrowser.component.ts @@ -1,8 +1,6 @@ -import { Component, OnDestroy, OnInit, Injector, ViewChild } from "@angular/core"; -import { DataEntry, File } from "src/services/stateStore.service"; +import { Component, OnDestroy, OnInit, ViewChild } from "@angular/core"; +import { DataEntry } from "src/services/stateStore.service"; import { Subscription, merge } from "rxjs"; -import { ComponentFactory } from "@angular/core/src/render3"; -import { FileViewer } from "src/ui/fileviewer/fileviewer.component"; import { DatabrowserService } from "../databrowser.service"; import { ModalityPicker } from "../modalityPicker/modalityPicker.component"; @@ -50,7 +48,6 @@ export class DataBrowser implements OnDestroy,OnInit{ public gemoetryFilter: any constructor( - private injector: Injector, private dbService: DatabrowserService ){ @@ -72,6 +69,11 @@ export class DataBrowser implements OnDestroy,OnInit{ this.dbService.fetchDataObservable$ ).subscribe(() => { this.resetCurrentPage() + /** + * Only reset modality picker + * resetting all creates infinite loop + */ + this.modalityPicker.clearAll() }) ) @@ -93,7 +95,7 @@ export class DataBrowser implements OnDestroy,OnInit{ } public showParcellationList: boolean = false - + deselectRegion(region:any){ /** * when user clicks x on region selector @@ -108,34 +110,10 @@ export class DataBrowser implements OnDestroy,OnInit{ this.modalityPicker.toggleModality({name: modality}) } - /** - * TODO - * work around for now. - * service does not have injector, and thus cannot create componentt - */ - private fileViewerComponentFactory: ComponentFactory<FileViewer> - private dataWindowRegistry: Set<string> = new Set() - launchFile({dataset, file}:{dataset:DataEntry, file:File}){ - - if(dataset.formats.findIndex(format => format.toLowerCase() === 'nifti' ) >= 0){ - - // TODO use KG id in future - if(this.dataWindowRegistry.has(file.name)){ - /* already open, will not open again */ - return - } - /* not yet open, add the name to registry */ - this.dataWindowRegistry.add(file.name) - - const component = this.fileViewerComponentFactory.create(this.injector) - component.instance.searchResultFile = file - // const compref = this.dbService.attachFileViewer(component, file) - - /* on destroy, removes name from registry */ - // compref.onDestroy(() => this.dataWindowRegistry.delete(file.name)) - }else{ - /** no mime type */ - } + public filePreviewName: string + onShowPreviewDataset(payload: {datasetName:string, event:MouseEvent}){ + const { datasetName, event } = payload + this.filePreviewName = datasetName } changeParcellation(payload) { @@ -151,8 +129,8 @@ export class DataBrowser implements OnDestroy,OnInit{ this.currentPage = 0 } - resetFilters(event:MouseEvent){ - event.preventDefault() + resetFilters(event?:MouseEvent){ + event && event.preventDefault() this.modalityPicker.clearAll() this.dbService.updateRegionSelection([]) } diff --git a/src/ui/databrowserModule/databrowser/databrowser.style.css b/src/ui/databrowserModule/databrowser/databrowser.style.css index 4060ef62d897f4d7f4e82776d0bf2bf7d82ecc9f..68f83fe7357575becf16ea1fca9ac131ee58c603 100644 --- a/src/ui/databrowserModule/databrowser/databrowser.style.css +++ b/src/ui/databrowserModule/databrowser/databrowser.style.css @@ -185,4 +185,29 @@ modality-picker radio-list { display: block; +} + +/* datawrapper */ +:host > .dataEntryWrapper +{ + white-space: nowrap; + overflow: hidden; + width:200%; + padding: 0; + transition: transform 190ms ease; +} + +.dataEntryWrapper > * +{ + vertical-align: top; + white-space: initial; + width: 50%; + display:inline-block; + padding: 0.5em 1em; +} + +.filePreviewContainer +{ + max-height: 100%; + overflow:auto; } \ No newline at end of file diff --git a/src/ui/databrowserModule/databrowser/databrowser.template.html b/src/ui/databrowserModule/databrowser/databrowser.template.html index 6d86e7f883061e177a6d3b072faea3cc578137a6..4653194a66a2cb74139b1cfe4d2aaf2376a1752a 100644 --- a/src/ui/databrowserModule/databrowser/databrowser.template.html +++ b/src/ui/databrowserModule/databrowser/databrowser.template.html @@ -43,8 +43,8 @@ <div (click)="showParcellationList = !showParcellationList" - class="toggleParcellationBtn btn btn-secondary btn-sm"> - <i [ngClass]="showParcellationList ? 'fa-chevron-down' : 'fa-chevron-left' " class="fas"></i> + class="toggleParcellationBtn btn btn-secondary btn-sm rounded-circle"> + <i [ngClass]="showParcellationList ? '' : 'r-90' " class="fas fa-chevron-down"></i> </div> </div> @@ -89,39 +89,63 @@ </ng-template> <ng-template #showData> - <!-- Data Entries --> - <div> - <i *ngIf="dbService.fetchedDataEntries$ | async"> - {{ (dbService.fetchedDataEntries$ | async).length }} total results. - <span - *ngIf="selectedRegions.length + modalityFilter.length > 0 "> - {{ (dbService.fetchedDataEntries$ | async | filterDataEntriesByMethods : modalityFilter | filterDataEntriesByRegion : selectedRegions).length }} - filtered results. - <a - href="#" - class="btn btn-sm btn-link" - (click)="resetFilters($event)">reset filters - </a> - </span> - </i> - <i *ngIf="!(dbService.fetchedDataEntries$ | async)"> - No results to show. - </i> - </div> - <div *ngIf="dbService.fetchedDataEntries$ | async"> - <dataset-viewer - class="mt-1" - *ngFor="let dataset of dbService.fetchedDataEntries$ | async | filterDataEntriesByMethods : modalityFilter | filterDataEntriesByRegion : selectedRegions | searchResultPagination : currentPage : hitsPerPage" - (launchFileViewer) = "launchFile($event)" - [dataset] = "dataset"> - </dataset-viewer> + <!-- datawrapper --> + <div + [ngStyle]="filePreviewName ? {'transform': 'translateX(-50%)'} : {}" + class="dataEntryWrapper"> + + <!-- dataentries --> + <div class="dataEntry"> + <div> + <i *ngIf="dbService.fetchedDataEntries$ | async"> + {{ (dbService.fetchedDataEntries$ | async).length }} total results. + <span + *ngIf="selectedRegions.length + modalityFilter.length > 0 "> + {{ (dbService.fetchedDataEntries$ | async | filterDataEntriesByMethods : modalityFilter | filterDataEntriesByRegion : selectedRegions).length }} + filtered results. + <a + href="#" + class="btn btn-sm btn-link" + (click)="resetFilters($event)">reset filters + </a> + </span> + </i> + <i *ngIf="!(dbService.fetchedDataEntries$ | async)"> + No results to show. + </i> + </div> + <div *ngIf="dbService.fetchedDataEntries$ | async"> + <dataset-viewer + class="mt-1" + *ngFor="let dataset of dbService.fetchedDataEntries$ | async | filterDataEntriesByMethods : modalityFilter | filterDataEntriesByRegion : selectedRegions | searchResultPagination : currentPage : hitsPerPage" + (showPreviewDataset)="onShowPreviewDataset($event)" + [dataset]="dataset"> + </dataset-viewer> + </div> + + <pagination-component + *ngIf="dbService.fetchedDataEntries$ | async" + (paginationChange)="currentPage = $event" + [hitsPerPage]="hitsPerPage" + [total]="(dbService.fetchedDataEntries$ | async | filterDataEntriesByMethods : modalityFilter | filterDataEntriesByRegion : selectedRegions).length" + [currentPage]="currentPage"> + </pagination-component> + </div> + + <!-- file preview --> + <div + class="filePreview"> + <div class="filePreviewContainer"> + <div (click)="filePreviewName=null" class="rounded-circle btn btn-sm btn-outline-secondary"> + <i class="fas fa-arrow-left"></i> + </div> + <preview-component + *ngIf="filePreviewName" + [datasetName]="filePreviewName"> + + </preview-component> + + </div> + </div> </div> - - <pagination-component - *ngIf="dbService.fetchedDataEntries$ | async" - (paginationChange)="currentPage = $event" - [hitsPerPage]="hitsPerPage" - [total]="(dbService.fetchedDataEntries$ | async | filterDataEntriesByMethods : modalityFilter | filterDataEntriesByRegion : selectedRegions).length" - [currentPage]="currentPage"> - </pagination-component> </ng-template> \ No newline at end of file diff --git a/src/ui/databrowserModule/datasetViewer/datasetViewer.component.ts b/src/ui/databrowserModule/datasetViewer/datasetViewer.component.ts index 4ad17eded8a6ca7422228ad3d0ace7556b959ac1..d042842f54da23ceb81d56a4eca1ee3a9f398a0c 100644 --- a/src/ui/databrowserModule/datasetViewer/datasetViewer.component.ts +++ b/src/ui/databrowserModule/datasetViewer/datasetViewer.component.ts @@ -9,28 +9,17 @@ import { DataEntry } from "src/services/stateStore.service"; export class DatasetViewerComponent{ @Input() dataset : DataEntry - @Output() launchFileViewer : EventEmitter<{dataset:DataEntry, file:any}> = new EventEmitter() + + @Output() showPreviewDataset: EventEmitter<{datasetName:string, event:MouseEvent}> = new EventEmitter() - previewFileClick(ev, el){ - - ev.event.preventDefault() - ev.event.stopPropagation() - if(ev.inputItem.children.length > 0){ - el.toggleCollapse(ev.inputItem) - }else{ - this.launchFileViewer.emit({ - dataset : this.dataset, - file : ev.inputItem - }) - } + previewDataset(event:MouseEvent){ + this.showPreviewDataset.emit({ + event, + datasetName: this.dataset.name + }) } - renderNode(obj){ - return obj.name - ? obj.name - : obj.path - } get methods(): string[]{ return this.dataset.activity.reduce((acc, act) => { diff --git a/src/ui/databrowserModule/datasetViewer/datasetViewer.template.html b/src/ui/databrowserModule/datasetViewer/datasetViewer.template.html index 1dcfe9ebb59ab17670aae44994fdf8ea7423e762..ecd085f7cc7b35b55c4530672645b4de073e3780 100644 --- a/src/ui/databrowserModule/datasetViewer/datasetViewer.template.html +++ b/src/ui/databrowserModule/datasetViewer/datasetViewer.template.html @@ -4,12 +4,26 @@ {{ dataset.name }} </div> - <a - *ngFor="let kgr of kgReference" - target="_blank" - [href]="kgr"> - open in knowledge graph - </a> + <div class="btn-group"> + + <a + *ngFor="let kgr of kgReference" + class="btn btn-sm btn-outline-secondary" + target="_blank" + tooltip="show in knowledge graph" + [href]="kgr"> + <i class="fas fa-brain"></i> + </a> + + <a + *ngIf="dataset.preview" + class="btn btn-sm btn-outline-secondary" + (click)="previewDataset($event)" + tooltip="preview dataset" + href="#"> + <i class="fas fa-chart-pie"></i> + </a> + </div> <!-- <kg-entry-viewer [dataset]="dataset"> </kg-entry-viewer> --> @@ -20,15 +34,6 @@ <h5> Preview Dataset </h5> - <flat-tree-component - #flatTreeNode - *ngFor = "let item of dataset.files | copyProperty : 'filename' : 'path' | pathToNestedChildren" - [childrenExpanded] = "false" - [renderNode] = "renderNode" - [inputItem] = " item " - (treeNodeClick)= "previewFileClick($event, flatTreeNode)"> - - </flat-tree-component> <hr /> </div> </div> diff --git a/src/ui/fileviewer/chart.interface.ts b/src/ui/databrowserModule/fileviewer/chart.interface.ts similarity index 100% rename from src/ui/fileviewer/chart.interface.ts rename to src/ui/databrowserModule/fileviewer/chart.interface.ts diff --git a/src/ui/databrowserModule/fileviewer/dedicated/dedicated.component.ts b/src/ui/databrowserModule/fileviewer/dedicated/dedicated.component.ts new file mode 100644 index 0000000000000000000000000000000000000000..f7ddd748850aef15f3f9a6bc50845cafe3ee4db3 --- /dev/null +++ b/src/ui/databrowserModule/fileviewer/dedicated/dedicated.component.ts @@ -0,0 +1,46 @@ +import { Component, Input } from "@angular/core"; +import { ViewerPreviewFile } from "src/services/state/dataStore.store"; +import { DatabrowserService } from "../../databrowser.service"; + +@Component({ + selector : 'dedicated-viewer', + templateUrl : './dedicated.template.html', + styleUrls : [ + `./dedicated.style.css` + ] +}) + +export class DedicatedViewer{ + @Input() previewFile : ViewerPreviewFile + + constructor( + private dbService:DatabrowserService, + ){ + + } + + get isShowing(){ + return this.dbService.ngLayers.has(this.previewFile.url) + } + + showDedicatedView(){ + this.dbService.showNewNgLayer({ url: this.previewFile.url }) + } + + removeDedicatedView(){ + this.dbService.removeNgLayer({ url: this.previewFile.url }) + } + + click(event:MouseEvent){ + event.preventDefault() + this.isShowing + ? this.removeDedicatedView() + : this.showDedicatedView() + } + + get tooltipText(){ + return this.isShowing + ? 'Remove this file in the viewer' + : 'View this file in the viewer' + } +} \ No newline at end of file diff --git a/src/ui/databrowserModule/fileviewer/dedicated/dedicated.style.css b/src/ui/databrowserModule/fileviewer/dedicated/dedicated.style.css new file mode 100644 index 0000000000000000000000000000000000000000..c1ee41eefe5349674cd7d350e80275c86bea4843 --- /dev/null +++ b/src/ui/databrowserModule/fileviewer/dedicated/dedicated.style.css @@ -0,0 +1,5 @@ +a +{ + margin: 0 1em; + transition: all 200ms ease; +} \ No newline at end of file diff --git a/src/ui/databrowserModule/fileviewer/dedicated/dedicated.template.html b/src/ui/databrowserModule/fileviewer/dedicated/dedicated.template.html new file mode 100644 index 0000000000000000000000000000000000000000..3517468edf64042507f0768dead716797805adfe --- /dev/null +++ b/src/ui/databrowserModule/fileviewer/dedicated/dedicated.template.html @@ -0,0 +1,13 @@ +<div class="alert"> + You can directly preview this nifti file overlaying the atlas viewer. +</div> + +<a + href="#" + [tooltip]="tooltipText" + container="body" + class="btn btn-sm rounded-circle" + [ngClass]="isShowing ? 'btn-primary' : 'btn-outline-secondary'" + (click)="click($event)"> + <i class="far fa-eye"></i> +</a> \ No newline at end of file diff --git a/src/ui/fileviewer/fileviewer.component.ts b/src/ui/databrowserModule/fileviewer/fileviewer.component.ts similarity index 75% rename from src/ui/fileviewer/fileviewer.component.ts rename to src/ui/databrowserModule/fileviewer/fileviewer.component.ts index 8de2dc462d592923183553960514a4c21574e843..a044db495e675dfcfc22a264c06c9e0109b365e2 100644 --- a/src/ui/fileviewer/fileviewer.component.ts +++ b/src/ui/databrowserModule/fileviewer/fileviewer.component.ts @@ -1,9 +1,9 @@ import { Component, Input, OnChanges, OnDestroy, ViewChild, ElementRef, OnInit, Output, EventEmitter } from '@angular/core' import { DomSanitizer } from '@angular/platform-browser'; -import { File, FileSupplementData } from '../../services/stateStore.service'; import { interval,from } from 'rxjs'; import { switchMap,take,retry } from 'rxjs/operators' +import { ViewerPreviewFile } from 'src/services/state/dataStore.store'; @Component({ selector : 'file-viewer', @@ -17,11 +17,7 @@ export class FileViewer implements OnChanges,OnDestroy,OnInit{ /** * fetched directly from KG */ - @Input() searchResultFile : File - /** - * currently going to have to be application specific - */ - @Input() fileSupplement: FileSupplementData + @Input() previewFile : ViewerPreviewFile @ViewChild('childChart') childChart : ChartComponentInterface @@ -46,11 +42,7 @@ export class FileViewer implements OnChanges,OnDestroy,OnInit{ } get downloadUrl(){ - return this.searchResultFile.absolutePath ? - this.searchResultFile.absolutePath : - this._downloadUrl ? - this.sanitizer.bypassSecurityTrustResourceUrl(this._downloadUrl) : - null + return this.previewFile.url } /* TODO require better way to check if a chart exists */ @@ -60,8 +52,9 @@ export class FileViewer implements OnChanges,OnDestroy,OnInit{ const timerSet$ = timer$.pipe( switchMap(()=>from(new Promise((rs,rj)=>{ if(!this.childChart) - rj('chart not defined after 500ms') + return rj('chart not defined after 500ms') + debugger this.childChart.canvas.nativeElement.toBlob((blob)=>{ blob ? rs(blob) : rj('blob is undefined') @@ -76,8 +69,8 @@ export class FileViewer implements OnChanges,OnDestroy,OnInit{ },(err)=>console.warn('warning',err)) - if(!this.searchResultFile.absolutePath && this.fileSupplement.data){ - const stringJson = JSON.stringify(this.fileSupplement.data) + if(!this.previewFile.url && this.previewFile.data){ + const stringJson = JSON.stringify(this.previewFile.data) const newBlob = new Blob([stringJson],{type:'application/octet-stream'}) this._downloadUrl = URL.createObjectURL(newBlob) } @@ -86,14 +79,16 @@ export class FileViewer implements OnChanges,OnDestroy,OnInit{ private revokeUrls(){ if(this._downloadUrl){ URL.revokeObjectURL(this._downloadUrl) + this._downloadUrl = null } if(this._pngDownloadUrl){ URL.revokeObjectURL(this._pngDownloadUrl) + this._pngDownloadUrl = null } } get downloadName(){ - return this.searchResultFile.name + return this.previewFile.name } get downloadPng(){ diff --git a/src/ui/fileviewer/fileviewer.style.css b/src/ui/databrowserModule/fileviewer/fileviewer.style.css similarity index 100% rename from src/ui/fileviewer/fileviewer.style.css rename to src/ui/databrowserModule/fileviewer/fileviewer.style.css diff --git a/src/ui/databrowserModule/fileviewer/fileviewer.template.html b/src/ui/databrowserModule/fileviewer/fileviewer.template.html new file mode 100644 index 0000000000000000000000000000000000000000..033ed3a4521d45d2ef0a8803a1023bb2c6416667 --- /dev/null +++ b/src/ui/databrowserModule/fileviewer/fileviewer.template.html @@ -0,0 +1,112 @@ +<div *ngIf = "!previewFile"> + previewFile as an input is required for this component to work... +</div> + +<!-- KG Entry Viewer --> +<!-- <kg-entry-viewer *ngIf = "previewFile.kgID && false" [dataset] = "previewFile"> +</kg-entry-viewer> --> + +<!-- citation --> +<!-- <citations-component + citationContainer + *ngIf = "previewFile && !previewFile.kgID" + [properties] = "previewFile.datasetProperties"> +</citations-component> --> + +<!-- file viewer --> +<div + *ngIf = "previewFile" + [ngSwitch]="previewFile.mimetype"> + + <div emptyRow *ngSwitchCase = "'application/octet-stream'"> + <!-- downloadable data --> + </div> + + <!-- image --> + <div *ngSwitchCase="'image/jpeg'" > + <!-- TODO figure out a more elegant way of dealing with draggable img --> + <img draggable = "false" [src] = "previewFile.url" /> + </div> + + <!-- data container --> + <div [ngSwitch]="previewFile.data.chartType" *ngSwitchCase="'application/json'"> + <radar-chart + #childChart + [colors] = "previewFile.data.colors" + [options] = "previewFile.data.chartOptions" + [labels]="previewFile.data.labels" + [radarDatasets]="previewFile.data.datasets" + *ngSwitchCase="'radar'"> + + </radar-chart> + <line-chart + #childChart + [colors] = "previewFile.data.colors" + [options] = "previewFile.data.chartOptions" + [lineDatasets] = "previewFile.data.datasets" + *ngSwitchCase = "'line'"> + + </line-chart> + <div *ngSwitchDefault> + The json file is not a chart. I mean, we could dump the json, but would it really help? + </div> + </div> + <div *ngSwitchCase = "'application/hibop'"> + <div mimetypeTextContainer> + You will need to install the HiBoP software on your computer, click the 'Download File' button and open the .hibop file. + </div> + </div> + <div *ngSwitchCase = "'application/nifti'"> + <dedicated-viewer + [previewFile] = "previewFile"> + </dedicated-viewer> + </div> + <div *ngSwitchCase = "'application/nehuba-layer'"> + APPLICATION NEHUBA LAYER - NOT YET IMPLEMENTED + <!-- <dedicated-view-controller + [dedicatedViewString]="'nehuba-layer://'+previewFile.url" + [dedicatedViewNehubaLayerObject]="previewFile.data"> + + </dedicated-view-controller> --> + </div> + <div *ngSwitchDefault> + <div mimetypeTextContainer> + The selected file with the mimetype {{ previewFile.mimetype }} could not be displayed. + </div> + </div> +</div> + +<!-- caption --> +<!-- <readmore-component *ngIf = "previewFile.properties && previewFile.properties.description"> + <small id = "captions"> + {{ previewFile.properties.description }} + </small> +</readmore-component> --> + +<div + anchorContainer + *ngIf="downloadUrl"> + <a + class="btn btn-sm btn-outline-secondary rounded-circle" + tooltip="Download file" + container="body" + [href]="downloadUrl" + target="_blank" + download> + <i class="far fa-arrow-alt-circle-down"></i> + </a> +</div> + +<div + anchorContainer + *ngIf="downloadPng"> + <a + class="btn btn-sm btn-outline-secondary rounded-circle" + tooltip="Download chart as an image" + container="body" + [href]="downloadPng" + target="_blank" + download> + <i class="far fa-image"></i> + </a> +</div> diff --git a/src/ui/fileviewer/line/line.chart.component.ts b/src/ui/databrowserModule/fileviewer/line/line.chart.component.ts similarity index 100% rename from src/ui/fileviewer/line/line.chart.component.ts rename to src/ui/databrowserModule/fileviewer/line/line.chart.component.ts diff --git a/src/ui/fileviewer/line/line.chart.style.css b/src/ui/databrowserModule/fileviewer/line/line.chart.style.css similarity index 100% rename from src/ui/fileviewer/line/line.chart.style.css rename to src/ui/databrowserModule/fileviewer/line/line.chart.style.css diff --git a/src/ui/databrowserModule/fileviewer/line/line.chart.template.html b/src/ui/databrowserModule/fileviewer/line/line.chart.template.html new file mode 100644 index 0000000000000000000000000000000000000000..b3882ceae471095800bf33ff36a652f1090d5fa6 --- /dev/null +++ b/src/ui/databrowserModule/fileviewer/line/line.chart.template.html @@ -0,0 +1,26 @@ +<canvas + *ngIf="shapedLineChartDatasets" + (mousewheel)="mousescroll($event)" + width='100%' + height='100%' + baseChart + chartType="line" + [options]="chartOption" + [colors]="colors" + [datasets]="shapedLineChartDatasets" + [labels]="chartDataset.labels" + #canvas> +</canvas> +<a + [download]="csvTitle" + [href]="csvDataUrl" + tooltip="Download line graph as csv" + container="body" + class="btn btn-sm btn-outline-secondary rounded-circle" + *ngIf="shapedLineChartDatasets"> + <i class="fas fa-file-csv"></i> +</a> +<span + *ngIf="!shapedLineChartDatasets"> + datasets are required to display linear graph +</span> \ No newline at end of file diff --git a/src/ui/fileviewer/radar/radar.chart.component.ts b/src/ui/databrowserModule/fileviewer/radar/radar.chart.component.ts similarity index 100% rename from src/ui/fileviewer/radar/radar.chart.component.ts rename to src/ui/databrowserModule/fileviewer/radar/radar.chart.component.ts diff --git a/src/ui/fileviewer/radar/radar.chart.style.css b/src/ui/databrowserModule/fileviewer/radar/radar.chart.style.css similarity index 100% rename from src/ui/fileviewer/radar/radar.chart.style.css rename to src/ui/databrowserModule/fileviewer/radar/radar.chart.style.css diff --git a/src/ui/fileviewer/radar/radar.chart.template.html b/src/ui/databrowserModule/fileviewer/radar/radar.chart.template.html similarity index 100% rename from src/ui/fileviewer/radar/radar.chart.template.html rename to src/ui/databrowserModule/fileviewer/radar/radar.chart.template.html diff --git a/src/ui/databrowserModule/preview/preview.component.ts b/src/ui/databrowserModule/preview/preview.component.ts new file mode 100644 index 0000000000000000000000000000000000000000..46f8884070da9c2112b569d662caf2db495732a7 --- /dev/null +++ b/src/ui/databrowserModule/preview/preview.component.ts @@ -0,0 +1,63 @@ +import { Component, Input, OnInit } from "@angular/core"; +import { DatabrowserService } from "../databrowser.service"; +import { ViewerPreviewFile } from "src/services/state/dataStore.store"; + +@Component({ + selector: 'preview-component', + templateUrl: './preview.template.html', + styleUrls: [ + './preview.style.css' + ] +}) + +export class PreviewComponent implements OnInit{ + @Input() datasetName: string + + public previewFiles: ViewerPreviewFile[] = [] + public activeFile: ViewerPreviewFile + private error: string + + constructor( + private dbrService:DatabrowserService + ){ + + } + + previewFileClick(ev, el){ + + ev.event.preventDefault() + ev.event.stopPropagation() + + if(ev.inputItem.children.length > 0){ + el.toggleCollapse(ev.inputItem) + }else{ + this.activeFile = ev.inputItem + // this.launchFileViewer.emit({ + // dataset : this.dataset, + // file : ev.inputItem + // }) + } + } + + renderNode(obj){ + return obj.name + ? this.activeFile.name === obj.name + ? `<span class="text-warning">${obj.name}</span>` + : obj.name + : obj.path + } + + ngOnInit(){ + if (this.datasetName) { + this.dbrService.fetchPreviewData(this.datasetName) + .then(json => { + this.previewFiles = json as ViewerPreviewFile[] + if (this.previewFiles.length > 0) + this.activeFile = this.previewFiles[0] + }) + .catch(e => { + this.error = JSON.stringify(e) + }) + } + } +} \ No newline at end of file diff --git a/src/ui/databrowserModule/preview/preview.style.css b/src/ui/databrowserModule/preview/preview.style.css new file mode 100644 index 0000000000000000000000000000000000000000..8436fcf81836cdf3f29fede1eec12101907eb36f --- /dev/null +++ b/src/ui/databrowserModule/preview/preview.style.css @@ -0,0 +1,14 @@ +:host +{ + display: block; + width: 100%; +} + +.readmore-wrapper +{ + width: 100%; + overflow-y: auto; + overflow-x: hidden; + font-size: 80%; + max-height: 25em; +} \ No newline at end of file diff --git a/src/ui/databrowserModule/preview/preview.template.html b/src/ui/databrowserModule/preview/preview.template.html new file mode 100644 index 0000000000000000000000000000000000000000..67f1676bc1cd90ddcd5f77ad248b73bd6046a89f --- /dev/null +++ b/src/ui/databrowserModule/preview/preview.template.html @@ -0,0 +1,26 @@ +<div *ngIf="activeFile"> + {{ activeFile.name }} +</div> +<file-viewer + *ngIf="activeFile" + [previewFile]="activeFile"> + +</file-viewer> + +<hr /> +<readmore-component + [collapsedHeight]="65"> + + <div class="readmore-wrapper"> + + <flat-tree-component + #flatTreeNode + *ngFor="let item of previewFiles | copyProperty : 'filename' : 'path' | pathToNestedChildren" + [childrenExpanded]="false" + [renderNode]="renderNode.bind(this)" + [inputItem]="item" + (treeNodeClick)="previewFileClick($event, flatTreeNode)"> + + </flat-tree-component> + </div> +</readmore-component> \ No newline at end of file diff --git a/src/ui/databrowserModule/regionHierachy/regionHierarchy.component.ts b/src/ui/databrowserModule/regionHierachy/regionHierarchy.component.ts index a05d88aa39a1d9c3e5986ef8663f0ba5fd4c0978..085a519a66837113b2a70608fcd20dd16daef301 100644 --- a/src/ui/databrowserModule/regionHierachy/regionHierarchy.component.ts +++ b/src/ui/databrowserModule/regionHierachy/regionHierarchy.component.ts @@ -1,7 +1,7 @@ import { EventEmitter, Component, ElementRef, ViewChild, HostListener, OnInit, ChangeDetectionStrategy, ChangeDetectorRef, Input, Output } from "@angular/core"; import { Subscription, Subject } from "rxjs"; import { buffer, debounceTime } from "rxjs/operators"; -import { FilterNameBySearch } from "../filterNameBySearch.pipe"; +import { FilterNameBySearch } from "../util/filterNameBySearch.pipe"; import { DatabrowserService } from "../databrowser.service"; @Component({ diff --git a/src/ui/databrowserModule/copyProperty.pipe.spec.ts b/src/ui/databrowserModule/util/copyProperty.pipe.spec.ts similarity index 100% rename from src/ui/databrowserModule/copyProperty.pipe.spec.ts rename to src/ui/databrowserModule/util/copyProperty.pipe.spec.ts diff --git a/src/ui/databrowserModule/copyProperty.pipe.ts b/src/ui/databrowserModule/util/copyProperty.pipe.ts similarity index 100% rename from src/ui/databrowserModule/copyProperty.pipe.ts rename to src/ui/databrowserModule/util/copyProperty.pipe.ts diff --git a/src/ui/databrowserModule/filterDataEntriesByMethods.pipe.ts b/src/ui/databrowserModule/util/filterDataEntriesByMethods.pipe.ts similarity index 79% rename from src/ui/databrowserModule/filterDataEntriesByMethods.pipe.ts rename to src/ui/databrowserModule/util/filterDataEntriesByMethods.pipe.ts index 7c3d190dce76779c43e643b2c862dfed15bcf68e..3e010621c216d8ec9846f8273b127beedc40e5c0 100644 --- a/src/ui/databrowserModule/filterDataEntriesByMethods.pipe.ts +++ b/src/ui/databrowserModule/util/filterDataEntriesByMethods.pipe.ts @@ -1,6 +1,6 @@ import { PipeTransform, Pipe } from "@angular/core"; -import { DataEntry } from "../../services/stateStore.service"; -import { temporaryFilterDataentryName } from './databrowser.service' +import { DataEntry } from "src/services/stateStore.service"; +import { temporaryFilterDataentryName } from '../databrowser.service' @Pipe({ name : 'filterDataEntriesByMethods' diff --git a/src/ui/databrowserModule/filterDataEntriesByRegion.pipe.ts b/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts similarity index 100% rename from src/ui/databrowserModule/filterDataEntriesByRegion.pipe.ts rename to src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts diff --git a/src/ui/databrowserModule/filterNameBySearch.pipe.ts b/src/ui/databrowserModule/util/filterNameBySearch.pipe.ts similarity index 100% rename from src/ui/databrowserModule/filterNameBySearch.pipe.ts rename to src/ui/databrowserModule/util/filterNameBySearch.pipe.ts diff --git a/src/ui/databrowserModule/pathToNestedChildren.pipe.spec.ts b/src/ui/databrowserModule/util/pathToNestedChildren.pipe.spec.ts similarity index 100% rename from src/ui/databrowserModule/pathToNestedChildren.pipe.spec.ts rename to src/ui/databrowserModule/util/pathToNestedChildren.pipe.spec.ts diff --git a/src/ui/databrowserModule/pathToNestedChildren.pipe.ts b/src/ui/databrowserModule/util/pathToNestedChildren.pipe.ts similarity index 100% rename from src/ui/databrowserModule/pathToNestedChildren.pipe.ts rename to src/ui/databrowserModule/util/pathToNestedChildren.pipe.ts diff --git a/src/ui/fileviewer/dedicated/dedicated.component.ts b/src/ui/fileviewer/dedicated/dedicated.component.ts deleted file mode 100644 index 94af64024b27b384de6e528744ba90f20ad76f28..0000000000000000000000000000000000000000 --- a/src/ui/fileviewer/dedicated/dedicated.component.ts +++ /dev/null @@ -1,72 +0,0 @@ -import { Component, OnDestroy, Input } from "@angular/core"; -import { Store, select } from "@ngrx/store"; -import { DedicatedViewState, File, ADD_NG_LAYER, REMOVE_NG_LAYER, NgViewerStateInterface } from "../../../services/stateStore.service"; -import { Observable, Subscription } from "rxjs"; -import { getActiveColorMapFragmentMain } from "../../nehubaContainer/nehubaContainer.component"; -import { ToastService } from "../../../services/toastService.service"; - -/** - * TODO maybe obsolete - */ - -@Component({ - selector : 'dedicated-viewer', - templateUrl : './dedicated.template.html', - styleUrls : [ - `./dedicated.style.css` - ] -}) - -export class DedicatedViewer implements OnDestroy{ - @Input() searchResultFile : File - - private ngLayers$ : Observable<NgViewerStateInterface> - private ngLayersSubscription : Subscription - private ngLayers : Set<string> = new Set() - - constructor( - private toastService:ToastService, - private store:Store<DedicatedViewState> - ){ - this.ngLayers$ = this.store.pipe( - select('ngViewerState') - ) - - this.ngLayersSubscription = this.ngLayers$.subscribe(layersInterface => this.ngLayers = new Set(layersInterface.layers.map(l => l.source))) - } - - get isShowing(){ - return this.ngLayers.has(`nifti://${this.searchResultFile.absolutePath}`) - } - - ngOnDestroy(){ - this.ngLayersSubscription.unsubscribe() - } - - showDedicatedView(){ - this.store.dispatch({ - type : ADD_NG_LAYER, - layer : { - name : this.searchResultFile.absolutePath, - source : `nifti://${this.searchResultFile.absolutePath}`, - mixability : 'nonmixable', - shader : getActiveColorMapFragmentMain() - } - }) - setTimeout(() => { - if(this.isShowing) - this.toastService.showToast('nifti showing') - else - this.toastService.showToast('nifti cannot be shown until current nifti layer is cleared') - }, 128) - } - - removeDedicatedView(){ - this.store.dispatch({ - type : REMOVE_NG_LAYER, - layer : { - name : this.searchResultFile.absolutePath - } - }) - } -} \ No newline at end of file diff --git a/src/ui/fileviewer/dedicated/dedicated.style.css b/src/ui/fileviewer/dedicated/dedicated.style.css deleted file mode 100644 index 8f54fa6f02a82636b5735c6a65a1a35b80cdfb1e..0000000000000000000000000000000000000000 --- a/src/ui/fileviewer/dedicated/dedicated.style.css +++ /dev/null @@ -1,4 +0,0 @@ -a -{ - margin: 0 1em; -} \ No newline at end of file diff --git a/src/ui/fileviewer/dedicated/dedicated.template.html b/src/ui/fileviewer/dedicated/dedicated.template.html deleted file mode 100644 index f1481940c1fd4127bd67908d9b89bc9d3e5d16a4..0000000000000000000000000000000000000000 --- a/src/ui/fileviewer/dedicated/dedicated.template.html +++ /dev/null @@ -1,14 +0,0 @@ -<a - href = "#" - (click) = "$event.preventDefault();showDedicatedView()" - *ngIf = "!isShowing"> - - show this dataset in the viewer -</a> -<a - href = "#" - (click) = "$event.preventDefault();removeDedicatedView()" - *ngIf = "isShowing"> - - clear this dataset from the viewer -</a> \ No newline at end of file diff --git a/src/ui/fileviewer/fileviewer.template.html b/src/ui/fileviewer/fileviewer.template.html deleted file mode 100644 index c99d9346670984df61250ba1a7fcc65df96820b0..0000000000000000000000000000000000000000 --- a/src/ui/fileviewer/fileviewer.template.html +++ /dev/null @@ -1,92 +0,0 @@ -<div *ngIf = "!searchResultFile"> - searchResultFile as an input is required for this component to work... -</div> - -<!-- KG Entry Viewer --> -<!-- <kg-entry-viewer *ngIf = "searchResultFile.kgID && false" [dataset] = "searchResultFile"> -</kg-entry-viewer> --> - -<!-- citation --> -<!-- <citations-component - citationContainer - *ngIf = "searchResultFile && !searchResultFile.kgID" - [properties] = "searchResultFile.datasetProperties"> -</citations-component> --> - -<!-- file viewer --> -<div - *ngIf = "searchResultFile" - [ngSwitch]="searchResultFile.mimetype"> - - <div emptyRow *ngSwitchCase = "'application/octet-stream'"> - <!-- downloadable data --> - </div> - - <!-- image --> - <div *ngSwitchCase="'image/jpeg'" > - <!-- TODO figure out a more elegant way of dealing with draggable img --> - <img draggable = "false" [src] = "searchResultFile.url" /> - </div> - - <!-- data container --> - <div [ngSwitch]="searchResultFile.data.chartType" *ngSwitchCase="'application/json'"> - <radar-chart - #childChart - [colors] = "searchResultFile.data.colors" - [options] = "searchResultFile.data.chartOptions" - [labels]="searchResultFile.data.labels" - [radarDatasets]="searchResultFile.data.datasets" - *ngSwitchCase="'radar'"> - - </radar-chart> - <line-chart - #childChart - [colors] = "searchResultFile.data.colors" - [options] = "searchResultFile.data.chartOptions" - [lineDatasets] = "searchResultFile.data.datasets" - *ngSwitchCase = "'line'"> - - </line-chart> - <div *ngSwitchDefault> - The json file is not a chart. I mean, we could dump the json, but would it really help? - </div> - </div> - <div *ngSwitchCase = "'application/hibop'"> - <div mimetypeTextContainer> - You will need to install the HiBoP software on your computer, click the 'Download File' button and open the .hibop file. - </div> - </div> - <div *ngSwitchCase = "'application/nifti'"> - <dedicated-viewer - [searchResultFile] = "searchResultFile"> - </dedicated-viewer> - </div> - <div *ngSwitchCase = "'application/nehuba-layer'"> - APPLICATION NEHUBA LAYER - NOT YET IMPLEMENTED - <!-- <dedicated-view-controller - [dedicatedViewString]="'nehuba-layer://'+searchResultFile.url" - [dedicatedViewNehubaLayerObject]="searchResultFile.data"> - - </dedicated-view-controller> --> - </div> - <div *ngSwitchDefault> - <div mimetypeTextContainer> - The selected file with the mimetype {{ searchResultFile.mimetype }} could not be displayed. - </div> - </div> -</div> - -<!-- caption --> -<!-- <readmore-component *ngIf = "searchResultFile.properties && searchResultFile.properties.description"> - <small id = "captions"> - {{ searchResultFile.properties.description }} - </small> -</readmore-component> --> - -<div anchorContainer *ngIf = "downloadUrl"> - <a [href]="downloadUrl" target = "_blank" download>Download File</a> -</div> - -<div anchorContainer *ngIf = "downloadPng"> - <a [href] = "downloadPng" target = "_blank" download>Download Chart as Image</a> -</div> diff --git a/src/ui/fileviewer/line/line.chart.template.html b/src/ui/fileviewer/line/line.chart.template.html deleted file mode 100644 index a4026c30ce351a3d0d2bd08de257bc7deecc62f8..0000000000000000000000000000000000000000 --- a/src/ui/fileviewer/line/line.chart.template.html +++ /dev/null @@ -1,20 +0,0 @@ -<canvas - *ngIf = "shapedLineChartDatasets" - (mousewheel)="mousescroll($event)" - width = '100%' - height = '100%' - baseChart - chartType="line" - [options]="chartOption" - [colors]="colors" - [datasets]="shapedLineChartDatasets" - [labels]="chartDataset.labels" - #canvas> -</canvas> -<a [download] = "csvTitle" [href] = "csvDataUrl" *ngIf = "shapedLineChartDatasets"> - download line graph as csv -</a> -<span - *ngIf = "!shapedLineChartDatasets"> - datasets are required to display linear graph -</span> \ No newline at end of file diff --git a/src/ui/layerbrowser/layerbrowser.component.ts b/src/ui/layerbrowser/layerbrowser.component.ts index 5de054dc184ff7b15058974344c54513e4105183..4e419c1150791f615013ad7f5a6c827b4c2b4cf2 100644 --- a/src/ui/layerbrowser/layerbrowser.component.ts +++ b/src/ui/layerbrowser/layerbrowser.component.ts @@ -21,6 +21,10 @@ export class LayerBrowser implements OnDestroy{ public forceShowSegmentCurrentState : boolean | null = null public forceShowSegment$ : Observable<boolean|null> + + public ngLayers$: Observable<any> + public advancedMode: boolean = false + private subscriptions : Subscription[] = [] private disposeHandler : any @@ -29,6 +33,19 @@ export class LayerBrowser implements OnDestroy{ constructor(private store : Store<ViewerStateInterface>){ + this.ngLayers$ = store.pipe( + select('viewerState'), + select('templateSelected'), + map(templateSelected => (templateSelected && !this.advancedMode && [ + templateSelected.ngId, + ...templateSelected.parcellations.map(p => p.ngId) + ]) || []) + ) + + /** + * TODO + * this is no longer populated + */ this.fetchedDataEntries$ = this.store.pipe( select('dataStore'), safeFilter('fetchedDataEntries'), @@ -49,6 +66,11 @@ export class LayerBrowser implements OnDestroy{ delay(0) ).subscribe((lockedLayerNames:string[]) => { + /** + * TODO + * if layerbrowser is init before nehuba + * window['viewer'] will return undefined + */ this.lockedLayers = lockedLayerNames this.ngLayersChangeHandler() diff --git a/src/ui/layerbrowser/layerbrowser.style.css b/src/ui/layerbrowser/layerbrowser.style.css index d9b0b2bfbd3eab6d6de2f1f694e7326ff76b5e1a..dc597ad085a5b4f8f21dc3d786a49086a97a5dc5 100644 --- a/src/ui/layerbrowser/layerbrowser.style.css +++ b/src/ui/layerbrowser/layerbrowser.style.css @@ -43,3 +43,7 @@ div[body] color: red; } +.noLayerPlaceHolder +{ + padding: 0.5em 1em; +} \ No newline at end of file diff --git a/src/ui/layerbrowser/layerbrowser.template.html b/src/ui/layerbrowser/layerbrowser.template.html index 652d01cf70fcd1e456248d215b9e89896a28d720..0dd64f021ac5757ccf2bdb99c1fb93557e5066d8 100644 --- a/src/ui/layerbrowser/layerbrowser.template.html +++ b/src/ui/layerbrowser/layerbrowser.template.html @@ -1,51 +1,61 @@ -<div - class="layerContainer" - *ngFor = "let ngLayer of ngLayers"> - - <div> - <i - container = "body" - placement = "bottom" - [tooltip] = "checkLocked(ngLayer) ? 'base layer cannot be hidden' : 'toggle visibility'" +<ng-container *ngIf="ngLayers$ | async | filterNgLayer : ngLayers as filteredNgLayers; else noLayerPlaceHolder"> + <ng-container *ngIf="filteredNgLayers.length > 0; else noLayerPlaceHolder"> + <div + class="layerContainer" + *ngFor = "let ngLayer of filteredNgLayers"> + + <div (click) = "checkLocked(ngLayer) ? null : toggleVisibility(ngLayer)" - class = "fas" - [ngClass] = "checkLocked(ngLayer) ? 'fa-lock muted' :ngLayer.visible ? 'fa-eye-open' : 'fa-eye-close'"> - - </i> - </div> - <div> - <i - container = "body" - placement = "bottom" - [tooltip] = "ngLayer.type === 'segmentation' ? segmentationTooltip() : 'only segmentation layer can hide/show segments'" + class="btn btn-sm btn-outline-secondary rounded-circle"> + <i + container = "body" + placement = "bottom" + [tooltip] = "checkLocked(ngLayer) ? 'base layer cannot be hidden' : 'toggle visibility'" + [ngClass] = "checkLocked(ngLayer) ? 'fas fa-lock muted' :ngLayer.visible ? 'far fa-eye' : 'far fa-eye-slash'"> + + </i> + </div> + <div *ngIf="advancedMode" (click) = "forceSegment.hide();toggleForceShowSegment(ngLayer)" - class = "fas" - #forceSegment = "bs-tooltip" - [ngClass] = "ngLayer.type === 'segmentation' ? ('fa-th-large ' + segmentationAdditionalClass) : 'fa-lock muted' "> - - </i> - </div> - <div> - <i - (click) = "removeLayer(ngLayer)" - container = "body" - placement = "bottom" - [tooltip] = "checkLocked(ngLayer) ? 'base layers cannot be removed' : 'remove layer'" - class = "fas" - [ngClass] = "checkLocked(ngLayer) ? 'fa-lock muted' : 'fa-remove-circle'"> - - </i> - </div> - - <panel-component - [ngClass] = "{'muted-text muted' : !classVisible(ngLayer)}"> - - <div heading> - {{ ngLayer.name | getLayerNameFromDatasets : (fetchedDataEntries$ | async) }} : {{ ngLayer.type }} + class="btn btn-sm btn-outline-secondary rounded-circle"> + <i + container = "body" + placement = "bottom" + [tooltip] = "ngLayer.type === 'segmentation' ? segmentationTooltip() : 'only segmentation layer can hide/show segments'" + class = "fas" + #forceSegment = "bs-tooltip" + [ngClass] = "ngLayer.type === 'segmentation' ? ('fa-th-large ' + segmentationAdditionalClass) : 'fa-lock muted' "> + + </i> + </div> + <div + (click) = "removeLayer(ngLayer)" + class="btn btn-sm btn-outline-secondary rounded-circle"> + <i + container = "body" + placement = "bottom" + [tooltip] = "checkLocked(ngLayer) ? 'base layers cannot be removed' : 'remove layer'" + [ngClass] = "checkLocked(ngLayer) ? 'fas fa-lock muted' : 'far fa-times-circle'"> + + </i> + </div> + <panel-component + [ngClass] = "{'muted-text muted' : !classVisible(ngLayer)}"> + + <div heading> + {{ ngLayer.name | getLayerNameFromDatasets : (fetchedDataEntries$ | async) }} : {{ ngLayer.type }} + </div> + + <div bodyy> + {{ ngLayer.source }} + </div> + </panel-component> </div> + </ng-container> +</ng-container> - <div bodyy> - {{ ngLayer.source }} - </div> - </panel-component> -</div> \ No newline at end of file +<ng-template #noLayerPlaceHolder> + <h5 class="noLayerPlaceHolder text-muted"> + No additional layers added. + </h5> +</ng-template> \ No newline at end of file diff --git a/src/ui/menuicons/menuicons.component.ts b/src/ui/menuicons/menuicons.component.ts index 4d31100bf9c8720b7dae2863b72e357b9135f3c8..45a8a671c96b7fae1508c0dba3a38881503418f2 100644 --- a/src/ui/menuicons/menuicons.component.ts +++ b/src/ui/menuicons/menuicons.component.ts @@ -4,7 +4,6 @@ import { WidgetServices } from "src/atlasViewer/widgetUnit/widgetService.service import { WidgetUnit } from "src/atlasViewer/widgetUnit/widgetUnit.component"; import { LayerBrowser } from "src/ui/layerbrowser/layerbrowser.component"; import { DataBrowser } from "src/ui/databrowserModule/databrowser/databrowser.component"; -import { FileViewer } from "../fileviewer/fileviewer.component"; @Component({ selector: 'menu-icons', @@ -23,10 +22,6 @@ export class MenuIconsBar{ dataBrowser: ComponentRef<DataBrowser> = null dbWidget: ComponentRef<WidgetUnit> = null - /** - * file viewer - */ - fcf: ComponentFactory<FileViewer> /** * layerBrowser @@ -42,7 +37,6 @@ export class MenuIconsBar{ ){ this.dbcf = cfr.resolveComponentFactory(DataBrowser) this.lbcf = cfr.resolveComponentFactory(LayerBrowser) - this.fcf = cfr.resolveComponentFactory(FileViewer) } public clickSearch(event: MouseEvent){ if (this.dbWidget) { @@ -59,32 +53,6 @@ export class MenuIconsBar{ titleHTML: `<i class="fas fa-search"></i> ${this.dataBrowserTitle}` }) - - const dataWindowRegistry: Set<string> = new Set() - - // const sub = this.dataBrowser.instance.launchFile.subscribe(payload => { - // const { dataset, file } = payload - // if(dataset.formats.findIndex(format => format.toLowerCase() === 'nifti' ) >= 0){ - - // // TODO use KG id in future - // if(dataWindowRegistry.has(file.name)){ - // /* already open, will not open again */ - // return - // } - // /* not yet open, add the name to registry */ - // dataWindowRegistry.add(file.name) - - // const component = this.fcf.create(this.injector) - // component.instance.searchResultFile = file - // const compref = this.widgetServices.addNewWidget(component,{title:file.name,exitable:true,state:'floating'}) - - // /* on destroy, removes name from registry */ - // compref.onDestroy(() => dataWindowRegistry.delete(file.name)) - // }else{ - // /** no mime type */ - // } - // }) - this.dbWidget.onDestroy(() => { // sub.unsubscribe() this.dataBrowser = null diff --git a/src/ui/nehubaContainer/nehubaContainer.component.ts b/src/ui/nehubaContainer/nehubaContainer.component.ts index 135b23f0085be1b9870d08d907917a68aa06fc3e..b9215eadfef0737d0e0ccf48594e784f212350ae 100644 --- a/src/ui/nehubaContainer/nehubaContainer.component.ts +++ b/src/ui/nehubaContainer/nehubaContainer.component.ts @@ -1,4 +1,4 @@ -import { Component, ViewChild, ViewContainerRef, ComponentFactoryResolver, ComponentFactory, ComponentRef, OnInit, OnDestroy, ElementRef, HostListener } from "@angular/core"; +import { Component, ViewChild, ViewContainerRef, ComponentFactoryResolver, ComponentFactory, ComponentRef, OnInit, OnDestroy, ElementRef } from "@angular/core"; import { NehubaViewerUnit } from "./nehubaViewer/nehubaViewer.component"; import { Store, select } from "@ngrx/store"; import { ViewerStateInterface, safeFilter, SELECT_REGIONS, getLabelIndexMap, CHANGE_NAVIGATION, isDefined, MOUSE_OVER_SEGMENT, USER_LANDMARKS, ADD_NG_LAYER, REMOVE_NG_LAYER, NgViewerStateInterface, MOUSE_OVER_LANDMARK, SELECT_LANDMARKS, Landmark, PointLandmarkGeometry, PlaneLandmarkGeometry, OtherLandmarkGeometry } from "../../services/stateStore.service"; @@ -1096,11 +1096,6 @@ export const takeOnePipe = [ take(1) ] -export const CM_THRESHOLD = `0.05` -export const CM_MATLAB_JET = `float r;if( x < 0.7 ){r = 4.0 * x - 1.5;} else {r = -4.0 * x + 4.5;}float g;if (x < 0.5) {g = 4.0 * x - 0.5;} else {g = -4.0 * x + 3.5;}float b;if (x < 0.3) {b = 4.0 * x + 0.5;} else {b = -4.0 * x + 2.5;}float a = 1.0;` -export const getActiveColorMapFragmentMain = ():string=>`void main(){float x = toNormalized(getDataValue());${CM_MATLAB_JET}if(x>${CM_THRESHOLD}){emitRGB(vec3(r,g,b));}else{emitTransparent();}}` - - export const singleLmUnchanged = (lm:{id:string,position:[number,number,number]}, map: Map<string,[number,number,number]>) => map.has(lm.id) && map.get(lm.id).every((value,idx) => value === lm.position[idx]) diff --git a/src/ui/ui.module.ts b/src/ui/ui.module.ts index fa00936bf6b5e1c2d35913e3e46c2d06abc4682c..e24e6ac310d315cadea1dc1234b3bfab5b45e826 100644 --- a/src/ui/ui.module.ts +++ b/src/ui/ui.module.ts @@ -10,16 +10,11 @@ import { FormsModule } from "@angular/forms"; import { GroupDatasetByRegion } from "../util/pipes/groupDataEntriesByRegion.pipe"; import { filterRegionDataEntries } from "../util/pipes/filterRegionDataEntries.pipe"; -import { FileViewer } from "./fileviewer/fileviewer.component"; import { MenuIconsBar } from './menuicons/menuicons.component' -import { ChartsModule } from 'ng2-charts' -import { RadarChart } from "./fileviewer/radar/radar.chart.component"; -import { LineChart } from "./fileviewer/line/line.chart.component"; import { GetPropMapPipe } from "../util/pipes/getPropMap.pipe"; import { GetUniquePipe } from "src/util/pipes/getUnique.pipe"; -import { DedicatedViewer } from "./fileviewer/dedicated/dedicated.component"; import { LandmarkUnit } from "./nehubaContainer/landmarkUnit/landmarkUnit.component"; import { SafeStylePipe } from "../util/pipes/safeStyle.pipe"; import { PluginBannerUI } from "./pluginBanner/pluginBanner.component"; @@ -45,11 +40,11 @@ import { PopoverModule } from 'ngx-bootstrap/popover' import { DatabrowserModule } from "./databrowserModule/databrowser.module"; import { SigninBanner } from "./signinBanner/signinBanner.components"; import { SigninModal } from "./signinModal/signinModal.component"; +import { FilterNgLayer } from "src/util/pipes/filterNgLayer.pipe"; @NgModule({ imports : [ - ChartsModule, FormsModule, BrowserModule, LayoutModule, @@ -63,10 +58,6 @@ import { SigninModal } from "./signinModal/signinModal.component"; NehubaContainer, NehubaViewerUnit, SplashScreen, - FileViewer, - RadarChart, - LineChart, - DedicatedViewer, LandmarkUnit, PluginBannerUI, CitationsContainer, @@ -93,6 +84,7 @@ import { SigninModal } from "./signinModal/signinModal.component"; SortDataEntriesToRegion, SpatialLandmarksToDataBrowserItemPipe, FilterNullPipe, + FilterNgLayer, /* directive */ DownloadDirective, @@ -102,7 +94,6 @@ import { SigninModal } from "./signinModal/signinModal.component"; /* dynamically created components needs to be declared here */ NehubaViewerUnit, - FileViewer, LayerBrowser, ], exports : [ @@ -113,7 +104,6 @@ import { SigninModal } from "./signinModal/signinModal.component"; NehubaContainer, NehubaViewerUnit, LayerBrowser, - FileViewer, LogoContainer, TemplateParcellationCitationsContainer, MobileOverlay, diff --git a/src/util/pipes/filterNgLayer.pipe.ts b/src/util/pipes/filterNgLayer.pipe.ts new file mode 100644 index 0000000000000000000000000000000000000000..ab14b3ab8556bcd85d6153119cc2667fb7f72132 --- /dev/null +++ b/src/util/pipes/filterNgLayer.pipe.ts @@ -0,0 +1,13 @@ +import { Pipe, PipeTransform } from "@angular/core"; +import { NgLayerInterface } from "src/atlasViewer/atlasViewer.component"; + +@Pipe({ + name: 'filterNgLayer' +}) + +export class FilterNgLayer implements PipeTransform{ + public transform(excludedLayers: string[] = [], ngLayers: NgLayerInterface[]): NgLayerInterface[] { + const set = new Set(excludedLayers) + return ngLayers.filter(l => !set.has(l.name)) + } +} \ No newline at end of file