diff --git a/changelog.md b/changelog.md index 176c55f2..d5ad21c2 100644 --- a/changelog.md +++ b/changelog.md @@ -1,5 +1,22 @@ # Changelog +## Release 2.6 (unreleased) +Brief summary of what's in this release: +- combined the filter trees into one +- added clinical data filters +- reorganized the filters (put into filter categories) +- added primary adjudicated category to participant report +- added tooltips to the filter pills to help disambiguate new filters +- removed units from labels in participant report since values will now include the units +- updated endpoints + +### Breaking changes +Breaking changes include any database updates needed, if we need to edit any files on system (like .env or certs, etc). Things that are outside of the code itself that need changed for the system to work. +- This will not work with previous versions of pegasus-data since the graphql endpoints have changed name and structure + +---- + + ## Release 2.5 (10/3/2024) Brief summary of what's in this release: - Segmentation data viewer diff --git a/package-lock.json b/package-lock.json index 3f88c65a..60063788 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "hubble-web", - "version": "2.3.0", + "version": "2.6.0", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "hubble-web", - "version": "2.3.0", + "version": "2.6.0", "dependencies": { "@apollo/client": "3.3.7", "@devexpress/dx-react-core": "3.0.0", @@ -20,6 +20,7 @@ "@fortawesome/free-regular-svg-icons": "6.0.0", "@fortawesome/free-solid-svg-icons": "6.0.0", "@fortawesome/react-fontawesome": "0.2.0", + "@hms-dbmi/viv": "0.16.1", "antd": "5.9.3", "autoprefixer": "10.4.4", "axios": "0.24.0", @@ -28,8 +29,9 @@ "history": "5.1.0", "immutability-helper": "3.1.1", "isomorphic-unfetch": "3.1.0", - 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@@ -4771,6 +4837,7 @@ "version": "5.3.12", "resolved": "https://registry.npmjs.org/@pixi/filter-blur/-/filter-blur-5.3.12.tgz", "integrity": "sha512-8zuOmztmuXCl1pXQpycKTS8HmXPtkmMe6xM93Q1gT7CRLzyS97H3pQAh4YuaGOrJslOKBNDrGVzLVY95fxjcTQ==", + "license": "MIT", "peer": true, "dependencies": { "@pixi/core": "5.3.12", @@ -4781,6 +4848,7 @@ "version": "5.3.12", "resolved": "https://registry.npmjs.org/@pixi/filter-color-matrix/-/filter-color-matrix-5.3.12.tgz", "integrity": "sha512-CblKOry/TvFm7L7iangxYtvQgO3a9n5MsmxDUue68DWZa/iI4r/3TSnsvA+Iijr590e9GsWxy3mj9P4HBMOGTA==", + "license": "MIT", "peer": true, "dependencies": { "@pixi/core": "5.3.12" @@ -4790,6 +4858,7 @@ "version": "5.3.12", "resolved": "https://registry.npmjs.org/@pixi/filter-displacement/-/filter-displacement-5.3.12.tgz", "integrity": "sha512-D/LpJxnGi85wHB6VeBpw0FQAN0mzHHUYNxCADwUhknY+SKfP5RhaYOlk79zqOuakBfQTzL3lPgMNH2EC85EJPw==", + "license": "MIT", "peer": true, "dependencies": { "@pixi/core": "5.3.12", @@ -4800,6 +4869,7 @@ 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"version": "2.5.0", + "version": "2.6.0", "private": true, "homepage": "/spatial-viewer", "baseURL": "/spatial-viewer", @@ -26,7 +26,7 @@ "@hms-dbmi/viv": "0.16.1", "immutability-helper": "3.1.1", "isomorphic-unfetch": "3.1.0", - "kpmp-common-components": "1.2.14", + "kpmp-common-components": "1.2.16", "kpmp-common-styles": "1.0.13", "mathjs": "13.1.0", "react": "17.0.2", diff --git a/src/App.js b/src/App.js index ffe5889d..434a11a7 100755 --- a/src/App.js +++ b/src/App.js @@ -53,24 +53,58 @@ store.subscribe(saveState); const connector = new AppSearchAPIConnector({ searchKey: process.env.REACT_APP_SEARCH_KEY, engineName: "spatial-viewer", - endpointBase: "/spatial-viewer/search", + endpointBase: process.env.REACT_APP_SEARCH_ENDPOINT, cacheResponses: false }) const searchConfig = { apiConnector: connector, searchQuery: { - disjunctiveFacets: ["sex", "age", "redcapid", "tissuetype", "imagetype", "datatype", "configtype", "level", "releaseversion"], + disjunctiveFacets: [ + "sex", + "age", + "redcapid", + "enrollmentcategory", + "imagetype", + "datatype", + "configtype", + "level", + "releaseversion", + "race", + "proteinuria", + "hypertensionhistory", + "hypertensionduration", + "onraasblockade", + "diabetesduration", + "diabeteshistory", + "kdigostage", + "a1c", + "albuminuria", + "baselineegfr", + "primaryadjudicatedcategory", + ], facets: { - sex: { type: "value", size: 100}, - age: { type: "value", size: 100}, - redcapid: { type: "value", size: 500 }, - tissuetype: { type: "value", size: 100}, - imagetype: { type: "value", size: 100}, - datatype: { type: "value", size: 100 }, - configtype: { type: "value", size: 100}, - level: { type: "value", size: 100}, - releaseversion: {type: "value", size: 250} + sex: { type: "value", sort: {"value": "asc"}, size: 100}, + age: { type: "value", sort: {"value": "asc"}, size: 100}, + redcapid: { type: "value", sort: {"value": "asc"}, size: 500 }, + enrollmentcategory: { type: "value", sort: {"value": "asc"}, size: 100}, + imagetype: { type: "value", sort: {"value": "asc"}, size: 100}, + datatype: { type: "value", sort: {"value": "asc"}, size: 100 }, + configtype: { type: "value", sort: {"value": "asc"}, size: 100}, + level: { type: "value", sort: {"value": "asc"}, size: 100}, + releaseversion: {type: "value", sort: {"value": "asc"}, size: 250}, + race: {type: "value", sort: {"value": "asc"}, size: 250}, + proteinuria: {type: "value", sort: {"value": "asc"}, size: 250}, + hypertensionhistory: {type: "value", sort: {"value": "asc"}, size: 250}, + hypertensionduration: {type: "value", sort: {"value": "asc"}, size: 250}, + onraasblockade:{type: "value", sort: {"value": "asc"}, size: 250}, + diabetesduration: {type: "value", sort: {"value": "asc"}, size: 250}, + diabeteshistory: {type: "value", sort: {"value": "asc"}, size: 250}, + kdigostage: {type: "value", sort: {"value": "asc"}, size: 250}, + a1c: {type: "value", sort: {"value": "asc"}, size: 250}, + albuminuria: {type: "value", sort: {"value": "asc"}, size: 250}, + baselineegfr: {type: "value", sort: {"value": "asc"}, size: 250}, + primaryadjudicatedcategory: {type: "value", sort: {"value": "asc"}, size: 250}, } }, initialState: { diff --git a/src/actions/Clinical/clinicalDatasetAction.js b/src/actions/Clinical/clinicalDatasetAction.js index 914f2de6..977bb587 100755 --- a/src/actions/Clinical/clinicalDatasetAction.js +++ b/src/actions/Clinical/clinicalDatasetAction.js @@ -13,9 +13,6 @@ export const fetchAndSetSummaryDatasets = (participant_id) => { export const fetchAndSetClinicalDatasets = (participant_id) => { return async (dispatch) => { let clinicalDatasets = await fetchParticipantClinicalDataset(participant_id); - if (clinicalDatasets) { - clinicalDatasets = JSON.parse(clinicalDatasets.clinicalData); - } clinicalDatasets = mapClinicalKeysToPresentationStyle(clinicalDatasets); dispatch(setClinicalDatasets(clinicalDatasets)); } diff --git a/src/components/ReportCard/ReportCard.js b/src/components/ReportCard/ReportCard.js index e0497d71..bb6b9fe2 100644 --- a/src/components/ReportCard/ReportCard.js +++ b/src/components/ReportCard/ReportCard.js @@ -17,7 +17,7 @@ class ReportCard extends Component { getDefaultColumnWidths = () => { return [ { columnName: 'key', width: 215 }, - { columnName: 'value', width: 180 }, + { columnName: 'value', width: 200 }, ] }; getDefaultLinkColumnWidths = () => { diff --git a/src/components/SpatialViewer/Facets/AllFacets.js b/src/components/SpatialViewer/Facets/AllFacets.js new file mode 100644 index 00000000..005b000f --- /dev/null +++ b/src/components/SpatialViewer/Facets/AllFacets.js @@ -0,0 +1,277 @@ +import React, { Component } from 'react'; +import { Facet } from "@elastic/react-search-ui"; +import { MultiCheckboxFacet } from "@elastic/react-search-ui-views"; +import { Col, Container, Row, UncontrolledAccordion, AccordionItem, AccordionHeader, AccordionBody } from "reactstrap"; + +class AllFacets extends Component { + + constructor(props) { + super(props); + this.state = {}; + + } + + render() { + return ( + + + + + + + + + + + Participant metadata + + + + + + Participant ID + + + + + } /> + + + + + + + Age + + + + + + + + + + + + Enrollment Category + + + + + + + + + + + + Primary Adjudicated Category + + + + + + + + + + + + Race + + + + + + + + + + + + Sex + + + + + + + + + + + + + + + Clinical metadata + + + + + + A1c + + + + + + + + + + + Albuminuria + + + + + + + + + + + Baseline eGFR + + + + + + + + + + + Diabetes Duration + + + + + + + + + + + Diabetes History + + + + + + + + + + + Hypertension Duration + + + + + + + + + + + Hypertension History + + + + + + + + + + + KDIGO Stage + + + + + + + + + + + RAAS Blockade + + + + + + + + + + + Proteinuria + + + + + + + + + + + + + + + Dataset metadata + + + + + + Experimental Strategy + + + + + + + + + + + + Image Type + + + + + + + + + + + + + + + ); + } +} + + +export default AllFacets; diff --git a/src/components/SpatialViewer/Facets/FileFacet.js b/src/components/SpatialViewer/Facets/FileFacet.js deleted file mode 100644 index 9db5fb87..00000000 --- a/src/components/SpatialViewer/Facets/FileFacet.js +++ /dev/null @@ -1,42 +0,0 @@ -import React, {Component} from 'react'; -import {Facet, MultiCheckboxFacet} from "@elastic/react-search-ui"; -import {Col, Container, Row, UncontrolledAccordion, AccordionItem, AccordionHeader, AccordionBody} from "reactstrap"; - -class FileFacet extends Component { - render() { - return ( - - - - - - Experimental Strategy - - - - - - - - - - - - Image Type - - - - - - - - - - - - - ); - } -} - -export default FileFacet; \ No newline at end of file diff --git a/src/components/SpatialViewer/Facets/ParticipantFacet.js b/src/components/SpatialViewer/Facets/ParticipantFacet.js deleted file mode 100644 index a19a8f17..00000000 --- a/src/components/SpatialViewer/Facets/ParticipantFacet.js +++ /dev/null @@ -1,80 +0,0 @@ -import React, {Component} from 'react'; -import {Facet} from "@elastic/react-search-ui"; -import {MultiCheckboxFacet} from "@elastic/react-search-ui-views"; -import {Col, Container, Row, UncontrolledAccordion, AccordionItem, AccordionHeader, AccordionBody} from "reactstrap"; - -class ParticipantFacet extends Component { - - constructor(props) { - super(props); - this.state = {}; - - } - - render() { - return ( - - - - - - Participant ID - - - - - }/> - - - - - - - Sex - - - - - - - - - - - - Age - - - - - - - - - - - - Enrollment Category - - - - - - - - - - - - - ); - } -} - - -export default ParticipantFacet; \ No newline at end of file diff --git a/src/components/SpatialViewer/ImageDatasetList.js b/src/components/SpatialViewer/ImageDatasetList.js index f19f2cd2..67e147c2 100755 --- a/src/components/SpatialViewer/ImageDatasetList.js +++ b/src/components/SpatialViewer/ImageDatasetList.js @@ -1,7 +1,7 @@ import React, { Component } from 'react'; import { DndProvider } from 'react-dnd' import { HTML5Backend } from 'react-dnd-html5-backend' -import {Col, Container, Row, Spinner} from "reactstrap"; +import {Col, Container, Row, Spinner, UncontrolledTooltip} from "reactstrap"; import { resultConverter } from "../../helpers/dataHelper"; import { getImageTypeTooltipCopy } from "./viewConfigHelper"; import { faXmark, faAnglesRight, faAnglesLeft, faTrashCan } from "@fortawesome/free-solid-svg-icons"; @@ -32,8 +32,7 @@ import { Pagination } from './Plugins/pagination.js'; import "@elastic/react-search-ui-views/lib/styles/styles.css"; import ReportCard from "../ReportCard/ReportCard"; -import ParticipantFacet from './Facets/ParticipantFacet.js'; -import FileFacet from './Facets/FileFacet.js'; +import AllFacets from './Facets/AllFacets.js'; class ImageDatasetList extends Component { @@ -45,7 +44,6 @@ class ImageDatasetList extends Component { const defaultHiddenColumns = this.getDefaultHiddenColumnNames(this.getColumns()) this.state = { - activeFilterTab: 'DATASET', tableData: [], cards: this.props.tableSettings.cards || columnCards, currentPage: this.props.tableSettings.currentPage, @@ -217,33 +215,59 @@ class ImageDatasetList extends Component { }; getFilterPills = (filters) => { - return filters.map( - filter => { - return filter.values.map(value => { - return ( -
- {value} - { - this.props.removeFilter(filter.field, value) - }} - className="close-button fas fa-xmark ms-2" - icon={faXmark} /> - -
) - }) - }) + const filterDisplayNames = { + sex: "Sex", + age: "Age", + redcapid: "Participant ID", + enrollmentcategory: "Enrollment Category", + imagetype: "Image Type", + datatype: "Data Type", + configtype: "Config Type", + level: "Level", + releaseversion: "Release Version", + race: "Race", + proteinuria: "Proteinuria", + hypertensionhistory: "Hypertension History", + hypertensionduration: "Hypertension Duration", + onraasblockade: "RAAS Blockade", + diabetesduration: "Diabetes Duration", + diabeteshistory: "Diabetes History", + kdigostage: "KDIGO Stage", + a1c: "A1c", + albuminuria: "Albuminuria", + baselineegfr: "Baseline eGFR", + primaryadjudicatedcategory: "Primary Adjudicated Category" + }; + + return filters.map(filter => { + return filter.values.map(value => { + const sanitizedId = `${filter.field.toString()}-${value.toString()}`.replace(/[^a-zA-Z0-9-_]/g, '_'); + return ( +
+ {value} + + {filterDisplayNames[filter.field] || filter.field} + + { + this.props.removeFilter(filter.field, value); + }} + className="close-button fas fa-xmark ms-2" + icon={faXmark} + /> + +
+ ); + }); + }); }; render() { - const tabEnum = { - DATASET: 'DATASET', - PARTICIPANT: 'PARTICIPANT', - }; - const { columnWidths, sorting } = this.props.tableSettings; const summaryDataset = this.props.summaryDatasets const experimentalDataCounts = this.props.experimentalDataCounts @@ -261,12 +285,7 @@ class ImageDatasetList extends Component {
-
-
{this.props.setActiveFilterTab(tabEnum.DATASET)}} - className={`filter-tab ${this.props.activeFilterTab === tabEnum.DATASET ? 'active' : ''} rounded border`}>DATASET
-
{this.props.setActiveFilterTab(tabEnum.PARTICIPANT)}} - className={`filter-tab ${this.props.activeFilterTab === tabEnum.PARTICIPANT ? 'active' : ''} rounded border`}>PARTICIPANT
- +
{this.props.toggleFilterTab()}}> @@ -274,13 +293,7 @@ class ImageDatasetList extends Component { className="fas fa-angles-left " icon={faAnglesLeft} />
- - {this.props.activeFilterTab === tabEnum.DATASET && - - }{this.props.activeFilterTab === tabEnum.PARTICIPANT && - - } - +
diff --git a/src/components/SpatialViewer/SpatialViewer.js b/src/components/SpatialViewer/SpatialViewer.js index 8755b5bb..01d38f75 100644 --- a/src/components/SpatialViewer/SpatialViewer.js +++ b/src/components/SpatialViewer/SpatialViewer.js @@ -73,7 +73,7 @@ class SpatialViewer extends Component {
{`${this.props.selectedImageDataset["datatype"]} - for ${this.props.selectedImageDataset["tissuetype"]} + for ${this.props.selectedImageDataset["enrollmentcategory"]} sample ${this.props.selectedImageDataset["spectracksampleid"]} (participant `}