diff --git a/.env.schema b/.env.schema index da56f5a4..269a8829 100644 --- a/.env.schema +++ b/.env.schema @@ -14,6 +14,11 @@ NEXT_PUBLIC_ARRANGER_MANIFEST_COLUMNS=fieldName, "fieldName", 'fieldName' ######### DMS NEXT_PUBLIC_SSO_PROVIDERS= +######## Visualizer Apps +NEXT_PUBLIC_JBROWSE_ENABLED=false +NEXT_PUBLIC_IOBIO_ENABLED=false +NEXT_PUBLIC_CBIOPORTAL_ENABLED=false + # ######## Optional features/functionalities NEXT_PUBLIC_DEBUG=true @@ -28,3 +33,9 @@ NEXT_PUBLIC_KEYCLOAK_REALM=myrealm NEXT_PUBLIC_KEYCLOAK_CLIENT_ID=webclient KEYCLOAK_CLIENT_SECRET=client_secret NEXT_PUBLIC_KEYCLOAK_PERMISSION_AUDIENCE=song + +# Score file access is needed for IOBIO and jBrowse components. This variable is not needed in vanilla Stage or Arranger +NEXT_PUBLIC_SCORE_API_URL= + +# Iobio Configuration +NEXT_PUBLIC_IOBIO_API_URL= diff --git a/Jenkinsfile b/Jenkinsfile index 83e36eb2..ee5c5237 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -1,2 +1,2 @@ @Library(value='jenkins-pipeline-library@master', changelog=false) _ -pipelineOVERTUREStage() +pipelineOvertureStage() diff --git a/additional.d.ts b/additional.d.ts index 3b83822d..97d16dd2 100644 --- a/additional.d.ts +++ b/additional.d.ts @@ -1,3 +1,24 @@ +/* + * + * Copyright (c) 2024 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + declare module 'url-join'; declare module 'js-cookie'; declare module 'jsonwebtoken'; diff --git a/components/pages/explorer/BamTable/StatsTable.tsx b/components/pages/explorer/BamTable/StatsTable.tsx new file mode 100644 index 00000000..b1f48f87 --- /dev/null +++ b/components/pages/explorer/BamTable/StatsTable.tsx @@ -0,0 +1,175 @@ +/* + * + * Copyright (c) 2024 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + +import { css, useTheme } from '@emotion/react'; +import { useTableContext } from '@overture-stack/arranger-components'; +import { useState } from 'react'; + +import { type FileTableData } from '../fileTypes'; +import { getTableData } from './tableUtils'; + +export const StatsTable = ({ file, fileId = '' }: { file: FileTableData; fileId?: string }) => { + const [showTable, setShowTable] = useState(true); + const { selectedRows } = useTableContext({ callerName: 'File Metadata Table' }); + const theme = useTheme(); + const { fileAccess, fileDataType, fileDonorId, fileFormat, fileStudy, fileSize, fileStrategy } = getTableData(file); + + return ( + <> +
+ + {selectedRows.length} File{`${selectedRows.length > 1 ? 's' : ''}`} Selected + + +
+ {showTable ? ( + + + + + + + + + + + + + + + + + + + + + + + +
File IDDonor IDStudyData TypeStrategyFormatSizeFile Access
{fileId}{fileDonorId}{fileStudy}{fileDataType}{fileStrategy}{fileFormat}{fileSize}{fileAccess}
+ ) : null} + + ); +}; diff --git a/components/pages/explorer/BamTable/ToggleButtonPanel.tsx b/components/pages/explorer/BamTable/ToggleButtonPanel.tsx new file mode 100644 index 00000000..f7059ade --- /dev/null +++ b/components/pages/explorer/BamTable/ToggleButtonPanel.tsx @@ -0,0 +1,99 @@ +/* + * + * Copyright (c) 2024 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + +import { css, useTheme } from '@emotion/react'; +import { + bamDisplayNames, + bamKeys, + type BamContext, + type BamKey, +} from '@overture-stack/iobio-components/packages/iobio-react-components/'; + +const getActiveButtonStyles = ({ active }: { active: boolean }) => { + const { + colors: { accent, white }, + } = useTheme(); + return ` + background-color: ${active ? white : accent}; + color: ${active ? accent : white}; + `; +}; + +export const ToggleButtonPanel = ({ + bamContext, + onToggle, +}: { + bamContext: BamContext; + onToggle: (key: BamKey, value: boolean) => void; +}) => { + const { + colors: { accent }, + } = useTheme(); + const contextKeys = bamKeys.filter((key) => bamContext.hasOwnProperty(key)); + return ( +
+
+ Show / Hide:{' '} +
+
+ {contextKeys.map((key) => { + const active = !!bamContext[key]; + const toggleButtonStyles = getActiveButtonStyles({ active }); + + return ( + + ); + })} +
+
+ ); +}; diff --git a/components/pages/explorer/BamTable/index.tsx b/components/pages/explorer/BamTable/index.tsx new file mode 100644 index 00000000..a6ba1404 --- /dev/null +++ b/components/pages/explorer/BamTable/index.tsx @@ -0,0 +1,224 @@ +/* + * + * Copyright (c) 2024 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + +'use client'; + +import { css, useTheme } from '@emotion/react'; +import { + histogramKeys, + defaultBamContext as initElementState, + getDefaultBedFileUrl, + IobioCoverageDepth, + IobioDataBroker, + IobioHistogram, + IobioPercentBox, + isOutlierKey, + getFileMetadata, + percentKeys, + IobioLabelInfoButton, + IobioPanel, + fileMetaDataSchema, + type BamContext, + type BamPercentKey, + type BamHistogramKey, + type FileDocument, + type FileMetaData, + type ScoreConfig, +} from '@overture-stack/iobio-components/packages/iobio-react-components/'; +import { useArrangerData } from '@overture-stack/arranger-components'; +import { useEffect, useState } from 'react'; + +import Loader from '@/components/Loader'; +import { getConfig } from '@/global/config'; +import { SCORE_API_DOWNLOAD_PATH } from '@/global/utils/constants'; +import { type FileTableData, isFileResponse } from '../fileTypes'; +import { IobioFileQuery } from './tableUtils'; +import { ToggleButtonPanel } from './ToggleButtonPanel'; +import { StatsTable } from './StatsTable'; + +const BamTable = ({ file }: { file?: FileTableData }) => { + const { apiFetcher } = useArrangerData({ callerName: 'GetindexFile' }); + const theme = useTheme(); + const [elementState, setElementState] = useState(initElementState); + const [indexFileData, setIndexFileData] = useState(undefined); + const [fileMetaData, setFileMetaData] = useState(undefined); + const [loading, setLoading] = useState(true); + + const { NEXT_PUBLIC_IOBIO_API_URL, NEXT_PUBLIC_SCORE_API_URL } = getConfig(); + const fileUrl = fileMetaData?.parts[0]?.url || null; + const fileId = file?.id || fileUrl?.split('/').pop()?.split('?')[0]; + const fileFormat = file?.file_type; + const fileStrategy = file?.analysis?.experiment?.experimentalStrategy; + const bedUrl = getDefaultBedFileUrl(fileStrategy); + const indexFileUrl = indexFileData?.parts[0]?.url || null; + + const updateElements = (key: keyof BamContext, value: boolean) => { + const newState = { + ...elementState, + [key]: !value, + }; + setElementState(newState); + }; + + useEffect(() => { + if (!fileUrl && file) { + const loadAndSetFile = async () => { + const iobioFileResponse = await apiFetcher({ + endpointTag: 'GetIobioFileData', + body: { + query: IobioFileQuery, + variables: { + first: 1, + sqon: { + content: [{ op: 'in', content: { fieldName: '_id', value: fileId } }], + op: 'and', + }, + }, + }, + }); + + if (isFileResponse(iobioFileResponse)) { + const fileDocument: FileDocument = iobioFileResponse.data.file.hits.edges[0].node; + const scoreConfig: ScoreConfig = { + scoreApiUrl: NEXT_PUBLIC_SCORE_API_URL, + scoreApiDownloadPath: SCORE_API_DOWNLOAD_PATH, + }; + const { scoreFileMetadata, indexFileMetadata } = await getFileMetadata({ + selectedFile: fileDocument, + scoreConfig, + }); + + if (fileMetaDataSchema.safeParse(scoreFileMetadata).success) { + setFileMetaData(scoreFileMetadata); + setIndexFileData(indexFileMetadata); + } else { + setFileMetaData(undefined); + console.error('Error retrieving Score File Data'); + } + } else { + setFileMetaData(undefined); + console.error('Error retrieving Score File Data'); + } + setLoading(false); + }; + // On page load, file table data is populated, + // but original file url needs to be requested from Score to use for Iobio analysis + loadAndSetFile(); + } else if (file === null) { + // TODO: Add Client Error Handling + console.error('No File Data'); + } + }, [fileUrl, file]); + + return ( + <> +

File Id: {fileId}

+ + {loading || !fileUrl ? ( + + ) : ( + <> + +
+
+ {percentKeys.map( + (key: BamPercentKey) => + elementState[key] && ( +
+ + +
+ ), + )} +
+
+ {elementState['coverage_depth'] && ( +
+ +
+ )} + {histogramKeys.map( + (key: BamHistogramKey) => + elementState[key] && ( +
+ + + + +
+ ), + )} +
+
+ + )} + {file && } + + ); +}; + +export default BamTable; diff --git a/components/pages/explorer/BamTable/tableUtils.tsx b/components/pages/explorer/BamTable/tableUtils.tsx new file mode 100644 index 00000000..3b537a1f --- /dev/null +++ b/components/pages/explorer/BamTable/tableUtils.tsx @@ -0,0 +1,79 @@ +/* + * + * Copyright (c) 2024 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + +import { type FileTableData } from '../fileTypes'; + +const getFileSizeString = (numFileSize: number) => + numFileSize < 10 ** 3 + ? `${numFileSize} bytes` + : numFileSize < 10 ** 6 + ? `${(numFileSize / 10 ** 3).toFixed(2)} KB` + : numFileSize < 10 ** 9 + ? `${(numFileSize / 10 ** 6).toFixed(2)} MB` + : numFileSize < 10 ** 12 + ? `${(numFileSize / 10 ** 9).toFixed(2)} GB` + : `${(numFileSize / 10 ** 12).toFixed(2)} TB`; + +export const getTableData = (file: FileTableData) => { + const fileAccess = file?.file_access; + const fileDataType = file?.data_type; + const fileDonorId = file?.donors?.hits.edges[0].node.submitter_donor_id; + const fileFormat = file?.file_type; + const fileStudy = file?.analysis?.collaborator?.hits.edges[0].node.name; + const fileStrategy = file?.analysis?.experiment?.experimentalStrategy; + const numFileSize = file?.file.size ?? 0; + const fileSize = getFileSizeString(numFileSize); + + return { fileAccess, fileDataType, fileDonorId, fileFormat, fileStudy, fileStrategy, fileSize }; +}; + +export const IobioFileQuery = `query IobioFile ($sqon: JSON) { + file { + hits (filters: $sqon) { + total + edges { + node { + object_id + data_type + file_access + file_type + analysis { + experiment { experimentalStrategy } + } + file { + size + name + data_type + index_file { + object_id + name + file_type + md5sum + data_type + size + dataCategory + } + } + } + } + } + } + }`; diff --git a/components/pages/explorer/HeaderButtons.tsx b/components/pages/explorer/HeaderButtons.tsx new file mode 100644 index 00000000..1ec98071 --- /dev/null +++ b/components/pages/explorer/HeaderButtons.tsx @@ -0,0 +1,147 @@ +/* + * + * Copyright (c) 2025 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + +import { css, useTheme } from '@emotion/react'; +import { ChevronDown, FullScreen, BarGraph } from '../../theme/icons'; +import { tableTypes } from './constants'; + +const getHeaderButtonStyles = ({ active, accent }: { active: boolean; accent: string }) => { + const { + colors: { white }, + } = useTheme(); + return ` + border: 1px solid ${accent}; + border-radius: 0.5rem; + display: inline-flex; + font-size: 14px; + line-height: 1.3rem; + min-width: fit-content; + padding: 0.3rem 0.8rem; + background-color: ${active ? white : accent}; + color: ${active ? accent : white}; + `; +}; + +export const FullScreenButton = ({ + isFullScreen, + setFullScreen, +}: { + isFullScreen: boolean; + setFullScreen: () => void; +}) => { + const { + colors: { accent, white }, + } = useTheme(); + return ( + + ); +}; + +export const VisualizerButton = ({ + iconColor, + disabled, + openModal, +}: { + disabled: boolean; + iconColor: string; + openModal?: () => void; +}) => { + const { + colors: { accent2, grey_1, grey_4 }, + } = useTheme(); + return ( + + ); +}; + +export const FileButton = ({ setTable }: { setTable: (tableName: string) => void }) => { + const { + colors: { accent2, white }, + } = useTheme(); + return ( + + ); +}; diff --git a/components/pages/explorer/Modal/components.tsx b/components/pages/explorer/Modal/components.tsx new file mode 100644 index 00000000..91e5b75a --- /dev/null +++ b/components/pages/explorer/Modal/components.tsx @@ -0,0 +1,322 @@ +/* + * + * Copyright (c) 2025 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + +import { css, useTheme, Theme } from '@emotion/react'; +import urlJoin from 'url-join'; +import { getConfig } from '../../../../global/config'; +import { bamFileExtensions } from '@overture-stack/iobio-components/packages/iobio-react-components/'; +import { tableTypes } from '../constants'; +import { type FileTableData } from '../fileTypes'; +import { type BadgeItem, type VisualizerDetailProps } from './types'; + +const accentBadgeStyle = ({ theme, isDisabled }: { theme: Theme; isDisabled: boolean }) => css` + ${badgeStyle({ theme, isDisabled })} + background-color: #497AA2; + margin-left: 5px; + ${isDisabled ? `background-color: #757575;` : ''} +`; + +const badgeStyle = ({ theme, isDisabled }: { theme: Theme; isDisabled: boolean }) => css` + display: inline-flex; + border: none; + border-radius: 20px; + margin: 5px; + margin-left: 0px; + min-width: fit-content; + padding: 3px 10px; + background-color: ${theme.colors.accent}; + color: ${theme.colors.white}; + + ${isDisabled ? `background-color: #353535;` : ''} +`; + +const optionStyle = ({ theme, isEnabled }: { theme: Theme; isEnabled: boolean }) => css` + background: unset; + border: 1px solid ${theme.colors.grey_5}; + border-radius: 16px; + cursor: pointer; + display: inline-flex; + flex: 1; + font-family: 'Lato', sans-serif; + margin: 0 0.5rem; + padding: 10px; + position: relative; + + ${isEnabled ? '' : `cursor: not-allowed; color: ${theme.colors.grey_6};`} +`; + +export const VisualizerDetail = ({ description, isEnabled, logoImage, previewImage, title }: VisualizerDetailProps) => { + return ( + <> +
+ +
+
+ +

+ {title} +

+
+

+ {description} +

+ + ); +}; + +export const Badges = ({ isEnabled, badges }: { isEnabled: boolean; badges: BadgeItem[] }) => { + const theme = useTheme(); + const badgeGroup = badges.map((badge, index) => { + const badgeCss = badge.isAccent + ? accentBadgeStyle({ theme, isDisabled: !isEnabled }) + : badgeStyle({ theme, isDisabled: !isEnabled }); + return ( +
+ {badge.label} +
+ ); + }); + return <>{badgeGroup}; +}; + +export const VisualizerOption = ({ + badges, + details: { title, description, previewImage, logoImage }, + isEnabled, + onClick, +}: { + badges: BadgeItem[]; + details: VisualizerDetailProps; + isEnabled: boolean; + onClick: () => void; +}) => { + const theme = useTheme(); + return ( + + ); +}; + +const featureFlagError = (appName: string) => + `The ${appName} Visualizer is not enabled. Please update your app configuration.`; +const tooManyFilesError = (count: number) => { + const countText = count > 1 ? `${count} files` : `${count} file`; + return `Too many files are selected. Please select a maximum of ${countText} to launch plugin.`; +}; +const wrongFileTypeError = + 'This app does not support the file type you are using. Please choose a different app or use another file format.'; + +/** + * + * Responsibility is rendering the options available + * ie. read configs, gather data etc then render each option with data + * + */ +export const VisualizerModal = ({ + closeModal, + setTable, + currentFiles, + setErrorMessage, +}: { + closeModal: () => void; + setTable: (tableType: string) => void; + currentFiles: FileTableData[]; + setErrorMessage: (s: string) => void; +}) => { + const { + NEXT_PUBLIC_BASE_PATH, + NEXT_PUBLIC_IOBIO_ENABLED, + NEXT_PUBLIC_JBROWSE_ENABLED, + NEXT_PUBLIC_CBIOPORTAL_ENABLED, + } = getConfig(); + + const isJbrowseEnabled = NEXT_PUBLIC_JBROWSE_ENABLED && currentFiles.length <= 5; + const isCBioEnabled = NEXT_PUBLIC_CBIOPORTAL_ENABLED && currentFiles.length <= 2; + const isIobioEnabled = + NEXT_PUBLIC_IOBIO_ENABLED && + currentFiles.length === 1 && + currentFiles[0].file_type !== undefined && + bamFileExtensions.includes(currentFiles[0].file_type); + + const selectVisualizer = (tableType: string) => { + setTable(tableType); + closeModal(); + }; + + return ( + <> + { + if (isJbrowseEnabled) { + selectVisualizer(tableTypes.JBROWSE_TABLE); + } else { + const errorMessage = !NEXT_PUBLIC_JBROWSE_ENABLED + ? featureFlagError('JBrowse') + : !(currentFiles.length <= 5) + ? tooManyFilesError(5) + : wrongFileTypeError; + setErrorMessage(errorMessage); + } + }} + isEnabled={isJbrowseEnabled} + details={{ + title: 'JBrowse', + description: + 'A fully featured genome browser that is capable of visualizing diverse types of genome-located data.', + previewImage: urlJoin(NEXT_PUBLIC_BASE_PATH, '/images/jBrowse_Preview.png'), + logoImage: urlJoin(NEXT_PUBLIC_BASE_PATH, '/images/jBrowse_Logo.png'), + }} + /> + { + if (isIobioEnabled) { + selectVisualizer(tableTypes.BAM_TABLE); + } else { + const errorMessage = !NEXT_PUBLIC_IOBIO_ENABLED + ? featureFlagError('Iobio') + : !(currentFiles.length === 1) + ? tooManyFilesError(1) + : wrongFileTypeError; + setErrorMessage(errorMessage); + } + }} + isEnabled={!!isIobioEnabled} + details={{ + title: 'IOBIO', + description: 'Examine your sequence alignment file in seconds', + previewImage: urlJoin(NEXT_PUBLIC_BASE_PATH, '/images/IOBIO_Preview.png'), + logoImage: urlJoin(NEXT_PUBLIC_BASE_PATH, '/images/IOBIO_Logo.png'), + }} + /> + { + if (isCBioEnabled) { + selectVisualizer(tableTypes.CBIO_TABLE); + } else { + const errorMessage = !NEXT_PUBLIC_CBIOPORTAL_ENABLED + ? featureFlagError('cBioPortal') + : !(currentFiles.length <= 2) + ? tooManyFilesError(2) + : wrongFileTypeError; + setErrorMessage(errorMessage); + } + }} + /> + + ); +}; diff --git a/components/pages/explorer/Modal/index.tsx b/components/pages/explorer/Modal/index.tsx new file mode 100644 index 00000000..dad8add3 --- /dev/null +++ b/components/pages/explorer/Modal/index.tsx @@ -0,0 +1,148 @@ +/* + * + * Copyright (c) 2025 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + +import { useEffect, ReactNode } from 'react'; +import ReactModal from 'react-modal'; +import { css, useTheme } from '@emotion/react'; +import { Dismiss } from '../../../theme/icons'; + +// Encapsulates the 3rd party component, base layout, and if modal is open +const ModalContainer = ({ + children, + appRootId, + isModalOpen, + closeModal, + errorMessage, +}: { + children: ReactNode; + closeModal: () => void; + appRootId: string; + isModalOpen: boolean; + errorMessage?: string; +}) => { + useEffect(() => { + ReactModal.setAppElement(appRootId); + }, []); + + const theme = useTheme(); + + return ( + +
+
+ +
+

+ Select Visualization App: +

+

+ Choose the appropriate app to analyze your selected data. +

+
+ {children} +
+

+ {errorMessage && errorMessage?.length > 1 ? errorMessage : ''} +

+
+ + ); +}; + +export default ModalContainer; diff --git a/components/pages/explorer/Modal/types.tsx b/components/pages/explorer/Modal/types.tsx new file mode 100644 index 00000000..e80605c6 --- /dev/null +++ b/components/pages/explorer/Modal/types.tsx @@ -0,0 +1,33 @@ +/* + * + * Copyright (c) 2025 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + +export type BadgeItem = { + label: string; + isAccent: boolean; +}; + +export type VisualizerDetailProps = { + title: string; + description: string; + previewImage: string; + logoImage: string; + isEnabled?: boolean; +}; diff --git a/components/pages/explorer/PageContent.tsx b/components/pages/explorer/PageContent.tsx index af1d060b..26cf4055 100644 --- a/components/pages/explorer/PageContent.tsx +++ b/components/pages/explorer/PageContent.tsx @@ -19,27 +19,42 @@ * */ -import { useEffect, useMemo, useState } from 'react'; import { css, useTheme } from '@emotion/react'; -import { useArrangerData } from '@overture-stack/arranger-components'; +import { useArrangerData, useTableContext } from '@overture-stack/arranger-components'; import { SQONType } from '@overture-stack/arranger-components/dist/DataContext/types.js'; +import { type UseTableContextProps } from '@overture-stack/arranger-components/dist/Table/types'; import stringify from 'fast-json-stable-stringify'; import { isEqual } from 'lodash'; +import { useEffect, useMemo, useRef, useState } from 'react'; import useUrlParamState from '@/global/hooks/useUrlParamsState'; +import BamTable from './BamTable/index'; +import { tableTypes } from './constants'; import Facets from './Facets'; -import RepoTable from './RepoTable'; +import { type FileTableData, rowIsFileData } from './fileTypes'; import QueryBar from './QueryBar'; +import RepoTable from './RepoTable'; +import TableHeader from './TableHeader'; +import ModalContainer from './Modal'; +import { VisualizerModal } from './Modal/components'; const PageContent = () => { const theme = useTheme(); const [showSidebar, setShowSidebar] = useState(true); const sidebarWidth = showSidebar ? theme.dimensions.facets.width : 0; - // TODO: abstract this param handling into an Arranger integration. - const { sqon, setSQON } = useArrangerData({ callerName: 'Explorer-PageContent' }); + const contextProps: Partial = { + callerName: 'Explorer-PageContent', + }; + const arrangerData = useArrangerData(contextProps); + const { sqon, setSQON } = arrangerData; + const tableContext = useTableContext(contextProps); + const { selectedRows, tableData } = tableContext; + const [tableType, setTableType] = useState(tableTypes['REPO_TABLE']); + const [isModalOpen, setModalOpen] = useState(false); const [firstRender, setFirstRender] = useState(true); + const [isFullScreen, setFullscreen] = useState(Boolean(document.fullscreenElement)); const [currentFilters, setCurrentFilters] = useUrlParamState('filters', null, { prepare: (v) => v.replace('"field"', '"fieldName"'), deSerialize: (v) => { @@ -47,6 +62,9 @@ const PageContent = () => { }, serialize: (v) => (v ? stringify(v) : ''), }); + const pageContentRef = useRef(null); + // TODO: Remove 2nd condition here when adding JBrowse & cBio tables + const isFileTableActive = tableType === tableTypes['REPO_TABLE'] || !(tableType === tableTypes['BAM_TABLE']); useEffect(() => { if (firstRender) { @@ -59,14 +77,58 @@ const PageContent = () => { firstRender || isEqual(sqon, currentFilters) || setCurrentFilters(sqon); }, [currentFilters, firstRender, setCurrentFilters, sqon]); + const fileData = tableData.filter(rowIsFileData) as FileTableData[]; + const currentFiles = fileData.filter((row) => selectedRows.includes(row.id)); + + const iconColor = isFileTableActive + ? currentFiles.length + ? theme.colors.accent + : theme.colors.grey_4 + : theme.colors.white; + + const closeModal = () => { + setModalOpen(false); + setErrorMessage(''); + }; + + const openModal = () => { + setModalOpen(true); + }; + + const toggleFullScreen = () => { + if (!isFullScreen && pageContentRef.current) { + pageContentRef.current.requestFullscreen(); + setFullscreen(true); + } else { + document.exitFullscreen(); + setFullscreen(false); + } + }; + + const [errorMessage, setErrorMessage] = useState(''); + return useMemo( () => (
+ + +
{ > Show */} -
), - [], + [tableType, tableContext], ); }; diff --git a/components/pages/explorer/QueryBar.tsx b/components/pages/explorer/QueryBar.tsx index 8f668e63..35f192cf 100644 --- a/components/pages/explorer/QueryBar.tsx +++ b/components/pages/explorer/QueryBar.tsx @@ -71,7 +71,7 @@ const getCurrentSQONStyles = (theme: DMSThemeInterface) => ({ ${theme.typography.label}; &:after { - content: url(data:image/svg+xml,%3Csvg%20width%3D%228%22%20height%3D%228%22%20stroke%3D%22white%22%20stroke-width%3D%222%22%20xmlns%3D%22http%3A//www.w3.org/2000/svg%22%3E%0A%20%20%3Cline%20x1%3D%220%22%20y1%3D%220%22%20x2%3D%228%22%20y2%3D%228%22%20/%3E%0A%20%20%3Cline%20x1%3D%228%22%20y1%3D%220%22%20x2%3D%220%22%20y2%3D%228%22%20/%3E%0A%3C/svg%3E); + content: url('data:image/svg+xml,%3Csvg%20width%3D%228%22%20height%3D%228%22%20stroke%3D%22white%22%20stroke-width%3D%222%22%20xmlns%3D%22http%3A//www.w3.org/2000/svg%22%3E%0A%20%20%3Cline%20x1%3D%220%22%20y1%3D%220%22%20x2%3D%228%22%20y2%3D%228%22%20/%3E%0A%20%20%3Cline%20x1%3D%228%22%20y1%3D%220%22%20x2%3D%220%22%20y2%3D%228%22%20/%3E%0A%3C/svg%3E'); margin-left: 9px; } `, diff --git a/components/pages/explorer/RepoTable.tsx b/components/pages/explorer/RepoTable.tsx index 2e5993bb..e239c214 100644 --- a/components/pages/explorer/RepoTable.tsx +++ b/components/pages/explorer/RepoTable.tsx @@ -19,34 +19,19 @@ * */ -import { useMemo } from 'react'; import { css, useTheme } from '@emotion/react'; import { - Pagination, + CountDisplay, + MaxRowsSelector, + PageSelector, Table, - TableContextProvider, useArrangerTheme, - Toolbar, } from '@overture-stack/arranger-components'; -import { CustomExporterInput } from '@overture-stack/arranger-components/dist/Table/DownloadButton/types'; import { UseThemeContextProps } from '@overture-stack/arranger-components/dist/ThemeContext/types'; -import urlJoin from 'url-join'; - -import { getConfig } from '@/global/config'; -import StyledLink from '@/components/Link'; +import { useMemo } from 'react'; import { DMSThemeInterface } from '@/components/theme'; -import { Download } from '@/components/theme/icons'; -import { INTERNAL_API_PROXY } from '@/global/utils/constants'; -const getTableConfigs = ({ - apiHost, - customExporters, - theme, -}: { - apiHost: string; - customExporters?: CustomExporterInput; - theme: DMSThemeInterface; -}): UseThemeContextProps => ({ +const getTableConfigs = ({ theme }: { theme: DMSThemeInterface }): UseThemeContextProps => ({ callerName: 'RepoTable', components: { Table: { @@ -62,52 +47,8 @@ const getTableConfigs = ({ // Child components CountDisplay: { - fontColor: 'inherit', - }, - DownloadButton: { - customExporters, - downloadUrl: urlJoin(apiHost, 'download'), - label: () => ( - <> - path { - fill: ${theme.colors.grey_5}; - } - `} - />{' '} - Download - - ), - ListWrapper: { - width: '11rem', - }, - }, - DropDown: { - arrowColor: '#151c3d', - arrowTransition: 'all 0s', - background: theme.colors.white, - borderColor: theme.colors.grey_5, - css: css` - ${theme.typography.subheading2} - line-height: 1.3rem; - `, - fontColor: theme.colors.accent_dark, - disabledFontColor: theme.colors.grey_5, - hoverBackground: theme.colors.secondary_light, - - ListWrapper: { - background: theme.colors.white, - css: css` - ${theme.shadow.default} - `, - fontColor: theme.colors.black, - fontSize: '0.7rem', - hoverBackground: theme.colors.secondary_light, - }, + // Table CountDisplay is hidden in order to position CountDisplay with Pagination + fontSize: '0px', }, HeaderRow: { borderColor: theme.colors.grey_3, @@ -141,67 +82,48 @@ const getTableConfigs = ({ }); const RepoTable = () => { - const { NEXT_PUBLIC_ARRANGER_MANIFEST_COLUMNS } = getConfig(); const theme = useTheme(); - const today = new Date().toISOString().slice(0, 10).replace(/-/g, ''); - const manifestColumns = NEXT_PUBLIC_ARRANGER_MANIFEST_COLUMNS.split(',') - .filter((field) => field.trim()) // break it into arrays, and ensure there's no empty field names - .map((fieldName) => fieldName.replace(/['"]+/g, '').trim()); - const customExporters = [ - { label: 'File Table', fileName: `data-explorer-table-export.${today}.tsv` }, // exports a TSV with what is displayed on the table (columns selected, etc.) - { label: 'File Manifest', fileName: `score-manifest.${today}.tsv`, columns: manifestColumns }, // exports a TSV with the manifest columns - { - label: () => ( - - To download files using a file manifest, please follow these - - instructions - - . - - ), - }, - ]; - - useArrangerTheme(getTableConfigs({ apiHost: INTERNAL_API_PROXY.ARRANGER, customExporters, theme })); + useArrangerTheme(tableConfig); return useMemo( () => ( <> -
+
- - - - - - + + + + ), [], diff --git a/components/pages/explorer/TableHeader.tsx b/components/pages/explorer/TableHeader.tsx new file mode 100644 index 00000000..eaad77db --- /dev/null +++ b/components/pages/explorer/TableHeader.tsx @@ -0,0 +1,214 @@ +/* + * + * Copyright (c) 2025 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + +import { type SetStateAction } from 'react'; +import { css, useTheme } from '@emotion/react'; +import { ColumnsSelectButton, DownloadButton, useArrangerTheme } from '@overture-stack/arranger-components'; +import urlJoin from 'url-join'; + +import StyledLink from '@/components/Link'; +import { Download } from '@/components/theme/icons'; +import { getConfig } from '@/global/config'; +import { INTERNAL_API_PROXY } from '@/global/utils/constants'; +import { FileButton, FullScreenButton, VisualizerButton } from './HeaderButtons'; + +const TableHeader = ({ + iconColor, + visualizersEnabled, + isFileTableActive, + isFullScreen, + toggleFullScreen, + setTable, + openModal, +}: { + iconColor: string; + visualizersEnabled: boolean; + isFileTableActive: boolean; + isFullScreen: boolean; + toggleFullScreen: () => void; + setTable: (value: SetStateAction) => void; + openModal: () => void; +}) => { + const { NEXT_PUBLIC_ARRANGER_MANIFEST_COLUMNS } = getConfig(); + const theme = useTheme(); + + const today = new Date().toISOString().slice(0, 10).replace(/-/g, ''); + const manifestColumns = NEXT_PUBLIC_ARRANGER_MANIFEST_COLUMNS.split(',') + .filter((field) => field.trim()) // break it into arrays, and ensure there's no empty field names + .map((fieldName) => fieldName.replace(/['"]+/g, '').trim()); + const customExporters = [ + { label: 'File Table', fileName: `data-explorer-table-export.${today}.tsv` }, // exports a TSV with what is displayed on the table (columns selected, etc.) + { label: 'File Manifest', fileName: `score-manifest.${today}.tsv`, columns: manifestColumns }, // exports a TSV with the manifest columns + { + label: () => ( + + To download files using a file manifest, please follow these + + instructions + + . + + ), + }, + ]; + + const buttonStyles = { + callerName: 'TableHeader', + components: { + Table: { + DownloadButton: { + customExporters, + css: css` + border-radius: 0.5rem; + padding: 0.3rem 0.8rem; + margin-left: 0.5rem; + :hover { + color: ${theme.colors.accent_dark}; + svg { + background-color: ${theme.colors.secondary_light}; + path { + fill: ${theme.colors.accent_dark}; + } + } + } + :disabled { + svg { + background-color: ${theme.colors.secondary_light}; + } + path { + fill: ${theme.colors.grey_5}; + } + } + `, + downloadUrl: urlJoin(INTERNAL_API_PROXY.ARRANGER, 'download'), + label: () => ( + <> + {' '} + Download + + ), + ListWrapper: { + width: '11rem', + }, + }, + DropDown: { + arrowColor: theme.colors.white, + arrowTransition: 'all 0s', + background: theme.colors.accent, + borderColor: theme.colors.grey_5, + css: css` + ${theme.typography.subheading2} + border-radius: 0.5rem; + line-height: 1.3rem; + padding: 0.3rem 0.8rem; + :disabled { + path { + fill: ${theme.colors.grey_5}; + } + } + :hover { + color: ${theme.colors.accent_dark}; + svg { + path { + fill: ${theme.colors.accent_dark}; + } + } + } + `, + disabledFontColor: theme.colors.grey_5, + fontColor: theme.colors.white, + hoverBackground: theme.colors.secondary_light, + + ListWrapper: { + background: theme.colors.white, + css: css` + ${theme.shadow.default} + `, + fontColor: theme.colors.black, + fontSize: '0.7rem', + hoverBackground: theme.colors.secondary_light, + }, + }, + }, + }, + }; + + useArrangerTheme(buttonStyles); + + return ( +
+ {isFileTableActive ? ( + <> + +
+ + +
+ + ) : ( + <> + + + + )} +
+ ); +}; + +export default TableHeader; diff --git a/components/pages/explorer/constants.ts b/components/pages/explorer/constants.ts new file mode 100644 index 00000000..bb70f0eb --- /dev/null +++ b/components/pages/explorer/constants.ts @@ -0,0 +1,33 @@ +/* + * + * Copyright (c) 2024 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + +import { bamFileExtensions } from '@overture-stack/iobio-components/packages/iobio-react-components/'; + +const vcfFileExtension = 'VCF'; + +export const JBrowseFileExtensions = [vcfFileExtension, ...bamFileExtensions]; + +export const tableTypes = { + REPO_TABLE: 'repoTable', + BAM_TABLE: 'bamTable', + JBROWSE_TABLE: 'jbrowseTable', + CBIO_TABLE: 'cbioTable', +}; diff --git a/components/pages/explorer/fileTypes.ts b/components/pages/explorer/fileTypes.ts new file mode 100644 index 00000000..d8496057 --- /dev/null +++ b/components/pages/explorer/fileTypes.ts @@ -0,0 +1,81 @@ +/* + * + * Copyright (c) 2024 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + +import { JBrowseFileExtensions } from './constants'; +import { type FileDocument } from '@overture-stack/iobio-components/packages/iobio-react-components/'; + +export type FileTableData = { + id: string; + analysis?: { + collaborator?: { + hits: { + edges: [ + { + node: { + name: string; + }; + }, + ]; + }; + }; + experiment?: { experimentalStrategy: string; platform: string }; + }; + data_type?: string; + donors?: { + hits: { + edges: [ + { + node: { + submitter_donor_id: string; + }; + }, + ]; + }; + }; + file_access?: string; + file_type?: string; + file: { size: number }; +}; + +export type FileNode = { + node: FileDocument; +}; + +export type FileResponse = { + data: { + file: { + hits: { + edges: FileNode[]; + total: number; + }; + }; + }; +}; + +// Type Check for Table Data unknown[] +export const rowIsFileData = (row: unknown): row is FileTableData => { + const rowData = row as FileTableData; + return Boolean(rowData?.id && rowData?.file_type && JBrowseFileExtensions.includes(rowData?.file_type)); +}; + +export const isFileResponse = (response: unknown): response is FileResponse => { + return typeof (response as FileResponse)?.data?.file.hits === 'object'; +}; diff --git a/components/pages/explorer/getConfigError.tsx b/components/pages/explorer/getConfigError.tsx index b67d6b40..6a026dfd 100644 --- a/components/pages/explorer/getConfigError.tsx +++ b/components/pages/explorer/getConfigError.tsx @@ -25,15 +25,7 @@ import { css, useTheme } from '@emotion/react'; import { GenericHelpMessage } from '../../DMSAdminContact'; import { Checkmark, Warning } from '../../theme/icons'; -const ListItem = ({ - Icon, - value, - fieldName, -}: { - Icon?: ReactNode; - value: string; - fieldName: string; -}) => { +const ListItem = ({ Icon, value, fieldName }: { Icon?: ReactNode; value: string; fieldName: string }) => { const theme = useTheme(); return ( @@ -82,15 +74,15 @@ const getConfigError = ({ index && documentType ? ( !hasConfig && ( - No active configurations for the platform were found. Please make sure the index and GraphQL - document type are correctly configured. + No active configurations for the platform were found. Please make sure the index and GraphQL document type are + correctly configured. ) ) : ( - One or more of the following values required by the platform do not exist. Please make sure - these values are specified in your platform configuration. + One or more of the following values required by the platform do not exist. Please make sure these values are + specified in your platform configuration.
    { const theme = useTheme(); - const { - NEXT_PUBLIC_ARRANGER_API, - NEXT_PUBLIC_ARRANGER_DOCUMENT_TYPE, - NEXT_PUBLIC_ARRANGER_INDEX, - } = getConfig(); + const { NEXT_PUBLIC_ARRANGER_API, NEXT_PUBLIC_ARRANGER_DOCUMENT_TYPE, NEXT_PUBLIC_ARRANGER_INDEX } = getConfig(); const [arrangerHasConfig, setArrangerHasConfig] = useState(false); const [loadingArrangerConfig, setLoadingArrangerConfig] = useState(true); @@ -149,7 +145,9 @@ const RepositoryPage = () => { }, }} > - + + + )} diff --git a/components/theme/icons/barGraph.tsx b/components/theme/icons/barGraph.tsx new file mode 100644 index 00000000..9c0aa236 --- /dev/null +++ b/components/theme/icons/barGraph.tsx @@ -0,0 +1,266 @@ +/* + * + * Copyright (c) 2025 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + +import { css } from '@emotion/react'; + +import { IconProps } from './types'; + +const BarGraph = ({ width, height, style }: IconProps) => ( + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +); + +export default BarGraph; diff --git a/components/theme/icons/file.tsx b/components/theme/icons/file.tsx new file mode 100644 index 00000000..2edf7a03 --- /dev/null +++ b/components/theme/icons/file.tsx @@ -0,0 +1,47 @@ +/* + * + * Copyright (c) 2024 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + +import { css } from '@emotion/react'; + +import { IconProps } from './types'; + +const File = ({ fill = '#003055', width = 12, height, style }: IconProps) => { + return ( + + + + ); +}; + +export default File; diff --git a/components/theme/icons/fullScreen.tsx b/components/theme/icons/fullScreen.tsx new file mode 100644 index 00000000..a9114582 --- /dev/null +++ b/components/theme/icons/fullScreen.tsx @@ -0,0 +1,44 @@ +/* + * + * Copyright (c) 2025 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + +import { css } from '@emotion/react'; + +import { IconProps } from './types'; + +const FullScreen = ({ width, height, style }: IconProps) => ( + + + +); + +export default FullScreen; diff --git a/components/theme/icons/index.tsx b/components/theme/icons/index.tsx index fa8c5795..44402404 100644 --- a/components/theme/icons/index.tsx +++ b/components/theme/icons/index.tsx @@ -19,40 +19,50 @@ * */ -import GoogleLogo from './google'; +import Avatar from './avatar'; +import BarGraph from './barGraph'; +import Checkmark from './checkmark'; +import ChevronDown from './chevron_down'; +import Dismiss from './dismiss'; +import Download from './download'; +import Error from './error'; import FacebookLogo from './facebook'; +import File from './file'; +import FullScreen from './fullScreen'; import GitHubLogo from './github'; +import GoogleLogo from './google'; +import Illustration from './illustration'; +import KeycloakLogo from './keycloak'; import LinkedInLogo from './linkedin'; import OrcidLogo from './orcid'; -import KeycloakLogo from './keycloak'; -import Illustration from './illustration'; -import Avatar from './avatar'; -import ChevronDown from './chevron_down'; -import Download from './download'; import OvertureLogo from './overture_logo'; import OvertureLogoWithText from './overture_logo_with_text'; import OvertureUser from './overture_user'; -import Checkmark from './checkmark'; +import Screen from './screen'; import Spinner from './spinner'; -import Error from './error'; import Warning from './warning'; export { - GoogleLogo, + Avatar, + BarGraph, + Checkmark, + ChevronDown, + Dismiss, + Download, + Error, FacebookLogo, + File, + FullScreen, GitHubLogo, + GoogleLogo, + Illustration, + KeycloakLogo, LinkedInLogo, OrcidLogo, - KeycloakLogo, - Illustration, - Avatar, - ChevronDown, - Download, OvertureLogo, OvertureLogoWithText, OvertureUser, - Checkmark, + Screen, Spinner, - Error, Warning, }; diff --git a/components/theme/icons/screen.tsx b/components/theme/icons/screen.tsx new file mode 100644 index 00000000..3e599824 --- /dev/null +++ b/components/theme/icons/screen.tsx @@ -0,0 +1,46 @@ +/* + * + * Copyright (c) 2024 The Ontario Institute for Cancer Research. All rights reserved + * + * This program and the accompanying materials are made available under the terms of + * the GNU Affero General Public License v3.0. You should have received a copy of the + * GNU Affero General Public License along with this program. + * If not, see . + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER + * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + +import { css } from '@emotion/react'; +import { IconProps } from './types'; + +const Screen = ({ fill = 'white', height, width = 16, style }: IconProps) => { + return ( + + + + ); +}; + +export default Screen; diff --git a/global/config.ts b/global/config.ts index 2a7f25ea..c5615ed7 100644 --- a/global/config.ts +++ b/global/config.ts @@ -42,12 +42,16 @@ export const getConfig = () => { `-----BEGIN PUBLIC KEY-----\r\nMIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEA0lOqMuPLCVusc6szklNXQL1FHhSkEgR7An+8BllBqTsRHM4bRYosseGFCbYPn8r8FsWuMDtxp0CwTyMQR2PCbJ740DdpbE1KC6jAfZxqcBete7gP0tooJtbvnA6X4vNpG4ukhtUoN9DzNOO0eqMU0Rgyy5HjERdYEWkwTNB30i9I+nHFOSj4MGLBSxNlnuo3keeomCRgtimCx+L/K3HNo0QHTG1J7RzLVAchfQT0lu3pUJ8kB+UM6/6NG+fVyysJyRZ9gadsr4gvHHckw8oUBp2tHvqBEkEdY+rt1Mf5jppt7JUV7HAPLB/qR5jhALY2FX/8MN+lPLmb/nLQQichVQIDAQAB\r\n-----END PUBLIC KEY-----`, NEXT_PUBLIC_KEYCLOAK_CLIENT_ID: publicConfig.NEXT_PUBLIC_KEYCLOAK_CLIENT_ID || '', NEXT_PUBLIC_KEYCLOAK_HOST: publicConfig.NEXT_PUBLIC_KEYCLOAK_HOST || '', - NEXT_PUBLIC_KEYCLOAK_PERMISSION_AUDIENCE: - publicConfig.NEXT_PUBLIC_KEYCLOAK_PERMISSION_AUDIENCE || '', + NEXT_PUBLIC_KEYCLOAK_PERMISSION_AUDIENCE: publicConfig.NEXT_PUBLIC_KEYCLOAK_PERMISSION_AUDIENCE || '', NEXT_PUBLIC_KEYCLOAK_REALM: publicConfig.NEXT_PUBLIC_KEYCLOAK_REALM || '', NEXT_PUBLIC_LAB_NAME: publicConfig.NEXT_PUBLIC_LAB_NAME || 'Overture Stage UI', NEXT_PUBLIC_LOGO_FILENAME: publicConfig.NEXT_PUBLIC_LOGO_FILENAME, + NEXT_PUBLIC_SCORE_API_URL: publicConfig.NEXT_PUBLIC_SCORE_API_URL, + NEXT_PUBLIC_IOBIO_API_URL: publicConfig.NEXT_PUBLIC_IOBIO_API_URL, NEXT_PUBLIC_SSO_PROVIDERS: publicConfig.NEXT_PUBLIC_SSO_PROVIDERS || '', + NEXT_PUBLIC_JBROWSE_ENABLED: publicConfig.NEXT_PUBLIC_JBROWSE_ENABLED === 'true', + NEXT_PUBLIC_IOBIO_ENABLED: publicConfig.NEXT_PUBLIC_IOBIO_ENABLED === 'true', + NEXT_PUBLIC_CBIOPORTAL_ENABLED: publicConfig.NEXT_PUBLIC_CBIOPORTAL_ENABLED === 'true', NEXT_PUBLIC_UI_VERSION: publicConfig.NEXT_PUBLIC_UI_VERSION || '', SESSION_ENCRYPTION_SECRET: process.env.SESSION_ENCRYPTION_SECRET || '', } as { @@ -70,7 +74,12 @@ export const getConfig = () => { NEXT_PUBLIC_KEYCLOAK_REALM: string; NEXT_PUBLIC_LAB_NAME: string; NEXT_PUBLIC_LOGO_FILENAME: string; + NEXT_PUBLIC_SCORE_API_URL: string; + NEXT_PUBLIC_IOBIO_API_URL: string; NEXT_PUBLIC_SSO_PROVIDERS: string; + NEXT_PUBLIC_JBROWSE_ENABLED: boolean; + NEXT_PUBLIC_IOBIO_ENABLED: boolean; + NEXT_PUBLIC_CBIOPORTAL_ENABLED: boolean; NEXT_PUBLIC_UI_VERSION: string; SESSION_ENCRYPTION_SECRET: string; }; diff --git a/global/utils/constants.ts b/global/utils/constants.ts index d003c98c..bca084ac 100644 --- a/global/utils/constants.ts +++ b/global/utils/constants.ts @@ -35,9 +35,11 @@ export const USER_PATH = '/user'; export const LOGIN_PATH = '/login'; // external docs links -export const HELP_URL = 'https://github.com/overture-stack/stage/issues/new/choose' +export const HELP_URL = 'https://github.com/overture-stack/stage/issues/new/choose'; export const EMAIL_SETTING_URL = 'admin@example.com'; +export const SCORE_API_DOWNLOAD_PATH = '/download'; + // keycloak export const KEYCLOAK_URL_ISSUER = urlJoin( NEXT_PUBLIC_KEYCLOAK_HOST, diff --git a/next.config.js b/next.config.js index 92854a2e..0e800653 100644 --- a/next.config.js +++ b/next.config.js @@ -6,15 +6,31 @@ const withPlugins = require('next-compose-plugins'); const { patchWebpackConfig: patchForGlobalCSS } = require('next-global-css'); const withTranspileModules = require('next-transpile-modules')([]); const ExtraWatchWebpackPlugin = require('extra-watch-webpack-plugin'); +const jsdom = require('jsdom'); + /** * @type {import('next').NextConfig} **/ module.exports = withPlugins([withTranspileModules], { webpack: (config, options) => { - // These 'react' related configs are added to enable linking packages in development - // (e.g. Arranger), and not get the "broken Hooks" warning. - // https://reactjs.org/warnings/invalid-hook-call-warning.html#duplicate-react if (options.isServer) { + // Adaptors for Browser APIs used in iobio-charts web components + const { JSDOM } = jsdom; + const dom = new JSDOM('', { url: 'http://localhost/' }); + + // @ts-ignore + global.window = dom.window; + + global.customElements = global.window.customElements; + global.HTMLElement = global.window.HTMLElement; + global.document = global.window.document; + global.Element = global.window.Element; + global.localStorage = global.window.localStorage; + global.navigator = global.window.navigator; + + // These 'react' related configs are added to enable linking packages in development + // (e.g. Arranger), and not get the "broken Hooks" warning. + // https://reactjs.org/warnings/invalid-hook-call-warning.html#duplicate-react config.externals = ['react', ...config.externals]; } else { options.dev && @@ -26,12 +42,11 @@ module.exports = withPlugins([withTranspileModules], { ); } - config.resolve.alias['@emotion/react'] = path.resolve( - __dirname, - '.', - 'node_modules', - '@emotion/react', - ); + config.experiments = { + ...config.experiments, + topLevelAwait: true, + }; + config.resolve.alias['@emotion/react'] = path.resolve(__dirname, '.', 'node_modules', '@emotion/react'); config.resolve.alias['react'] = path.resolve(__dirname, '.', 'node_modules', 'react'); process.env.NODE_ENV === 'development' && (config.optimization.minimize = false); @@ -58,7 +73,12 @@ module.exports = withPlugins([withTranspileModules], { NEXT_PUBLIC_KEYCLOAK_PERMISSION_AUDIENCE: process.env.NEXT_PUBLIC_KEYCLOAK_PERMISSION_AUDIENCE, NEXT_PUBLIC_LAB_NAME: process.env.NEXT_PUBLIC_LAB_NAME, NEXT_PUBLIC_LOGO_FILENAME: process.env.NEXT_PUBLIC_LOGO_FILENAME, + NEXT_PUBLIC_SCORE_API_URL: process.env.NEXT_PUBLIC_SCORE_API_URL, + NEXT_PUBLIC_IOBIO_API_URL: process.env.NEXT_PUBLIC_IOBIO_API_URL, NEXT_PUBLIC_SSO_PROVIDERS: process.env.NEXT_PUBLIC_SSO_PROVIDERS, + NEXT_PUBLIC_JBROWSE_ENABLED: process.env.NEXT_PUBLIC_JBROWSE_ENABLED, + NEXT_PUBLIC_IOBIO_ENABLED: process.env.NEXT_PUBLIC_IOBIO_ENABLED, + NEXT_PUBLIC_CBIOPORTAL_ENABLED: process.env.NEXT_PUBLIC_CBIOPORTAL_ENABLED, NEXT_PUBLIC_UI_VERSION: process.env.npm_package_version, }, assetPrefix: process.env.ASSET_PREFIX || '', diff --git a/package-lock.json b/package-lock.json index dcb8b54f..332610b5 100644 --- a/package-lock.json +++ b/package-lock.json @@ -11,9 +11,11 @@ "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", "@overture-stack/arranger-components": "^3.0.0-beta.34", + "@overture-stack/iobio-components": "^0.0.7", "axios": "^0.27.2", "cryptr": "^6.3.0", "http-proxy": "^1.18.1", + "jsdom": "^24.1.1", "jsonwebtoken": "^8.5.1", "jwt-decode": "^3.1.2", "lodash": "^4.17.21", @@ -26,6 +28,7 @@ "react": "^17.0.2", "react-dom": "^17.0.2", "react-grid-system": "^7.1.1", + "react-modal": "^3.16.3", "react-tippy": "^1.4.0", "url-join": "^5.0.0" }, @@ -35,8 +38,9 @@ "@types/http-proxy": "^1.17.11", "@types/lodash": "^4.14.182", "@types/node": "^17.0.35", - "@types/react": "^17.0.62", + "@types/react": "^17.0.80", "@types/react-dom": "^17.0.20", + "@types/react-modal": "^3.16.3", "@types/url-join": "^4.0.1", "extra-watch-webpack-plugin": "^1.0.3", "fork-ts-checker-webpack-plugin": "^8.0.0", @@ -62,11 +66,12 @@ } }, "node_modules/@babel/code-frame": { - "version": "7.18.6", - "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.18.6.tgz", - "integrity": "sha512-TDCmlK5eOvH+eH7cdAFlNXeVJqWIQ7gW9tY1GJIpUtFb6CmjVyq2VM3u71bOyR8CRihcCgMUYoDNyLXao3+70Q==", + "version": "7.24.7", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.24.7.tgz", + "integrity": "sha512-BcYH1CVJBO9tvyIZ2jVeXgSIMvGZ2FDRvDdOIVQyuklNKSsx+eppDEBq/g47Ayw+RqNFE+URvOShmf+f/qwAlA==", "dependencies": { - "@babel/highlight": "^7.18.6" + "@babel/highlight": "^7.24.7", + "picocolors": "^1.0.0" }, "engines": { "node": ">=6.9.0" @@ -112,14 +117,14 @@ } }, "node_modules/@babel/generator": { - "version": "7.21.3", - "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.21.3.tgz", - "integrity": "sha512-QS3iR1GYC/YGUnW7IdggFeN5c1poPUurnGttOV/bZgPGV+izC/D8HnD6DLwod0fsatNyVn1G3EVWMYIF0nHbeA==", + "version": "7.25.0", + "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.25.0.tgz", + "integrity": "sha512-3LEEcj3PVW8pW2R1SR1M89g/qrYk/m/mB/tLqn7dn4sbBUQyTqnlod+II2U4dqiGtUmkcnAmkMDralTFZttRiw==", "dev": true, "dependencies": { - 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"https://registry.npmjs.org/@babel/parser/-/parser-7.21.3.tgz", - "integrity": "sha512-lobG0d7aOfQRXh8AyklEAgZGvA4FShxo6xQbUrrT/cNBPUdIDojlokwJsQyCC/eKia7ifqM0yP+2DRZ4WKw2RQ==", + "version": "7.25.0", + "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.25.0.tgz", + "integrity": "sha512-CzdIU9jdP0dg7HdyB+bHvDJGagUv+qtzZt5rYCWwW6tITNqV9odjp6Qu41gkG0ca5UfdDUWrKkiAnHHdGRnOrA==", "dev": true, "bin": { "parser": "bin/babel-parser.js" @@ -601,34 +595,31 @@ } }, "node_modules/@babel/template": { - "version": "7.20.7", - "resolved": "https://registry.npmjs.org/@babel/template/-/template-7.20.7.tgz", - "integrity": "sha512-8SegXApWe6VoNw0r9JHpSteLKTpTiLZ4rMlGIm9JQ18KiCtyQiAMEazujAHrUS5flrcqYZa75ukev3P6QmUwUw==", + "version": "7.25.0", + "resolved": "https://registry.npmjs.org/@babel/template/-/template-7.25.0.tgz", + "integrity": "sha512-aOOgh1/5XzKvg1jvVz7AVrx2piJ2XBi227DHmbY6y+bM9H2FlN+IfecYu4Xl0cNiiVejlsCri89LUsbj8vJD9Q==", "dev": true, "dependencies": { - "@babel/code-frame": 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