diff --git a/.gitignore b/.gitignore index 0835549af..1fc2d8ec1 100644 --- a/.gitignore +++ b/.gitignore @@ -18,6 +18,10 @@ deploy_config.json browser/build.env +# Environment configuration (contains local paths and secrets) +.env +.env.fish + # Build outputs browser/dist @@ -36,3 +40,10 @@ hail-*.log # Reads metadata databases reads/*.db + +.grove +.grove-worktrees + +# Binary artifacts for Docker builds +bin/ +resources/ diff --git a/browser/package.json b/browser/package.json index baadd8fa7..a25028452 100644 --- a/browser/package.json +++ b/browser/package.json @@ -21,6 +21,9 @@ "@gnomad/track-transcripts": "4.0.0", "@gnomad/track-variants": "3.0.0", "@gnomad/ui": "^3.0.0", + "@copilotkit/react-core": "^1.10.6", + "@copilotkit/react-ui": "^1.10.6", + "@copilotkit/react-textarea": "^1.10.6", "@visx/axis": "^3.0.0", "@visx/group": "^3.0.0", "@visx/legend": "^3.12.0", diff --git a/browser/src/App.tsx b/browser/src/App.tsx index 3edcd1a6f..f2d55f996 100644 --- a/browser/src/App.tsx +++ b/browser/src/App.tsx @@ -1,6 +1,9 @@ import React, { Suspense, lazy, useEffect, useState } from 'react' import { BrowserRouter as Router, Route, useLocation } from 'react-router-dom' import styled from 'styled-components' +import { CopilotKit } from '@copilotkit/react-core' +import '@copilotkit/react-ui/styles.css' +import './styles/chatComponents.css' import Delayed from './Delayed' import ErrorBoundary from './ErrorBoundary' @@ -8,6 +11,7 @@ import ErrorBoundary from './ErrorBoundary' import Notifications, { showNotification } from './Notifications' import StatusMessage from './StatusMessage' import userPreferences from './userPreferences' +import { GnomadCopilot } from './GnomadCopilot' const NavBar = lazy(() => import('./NavBar')) const Routes = lazy(() => import('./Routes')) @@ -41,7 +45,7 @@ const GoogleAnalytics = () => { const location = useLocation() useEffect(() => { if ((window as any).gtag) { - ;(window as any).gtag('config', (window as any).gaTrackingId, { + ; (window as any).gtag('config', (window as any).gaTrackingId, { page_path: location.pathname, }) } @@ -69,10 +73,12 @@ const Banner = styled.div` } ` + const BANNER_CONTENT = null const App = () => { const [isLoading, setIsLoading] = useState(true) + useEffect(() => { userPreferences.loadPreferences().then( () => { @@ -89,44 +95,49 @@ const App = () => { ) }, []) + const copilotKitUrl = '/api/copilotkit' + return ( - - {/* On any navigation, send event to Google Analytics. */} - - - {/** - * On any navigation, scroll to the anchor specified by location fragment (if any) or to the top of the page. - * If the page's module is already loaded, scrolling is handled by this router's render function. If the page's - * module is loaded by Suspense, scrolling is handled by the useEffect hook in the PageLoading component. - */} - { - scrollToAnchorOrStartOfPage(location) - return null - }} - /> - - - {isLoading ? ( - - Loading - - ) : ( - - - - {BANNER_CONTENT && {BANNER_CONTENT}} - - - - }> - + + + {/* On any navigation, send event to Google Analytics. */} + + + {/** + * On any navigation, scroll to the anchor specified by location fragment (if any) or to the top of the page. + * If the page's module is already loaded, scrolling is handled by this router's render function. If the page's + * module is loaded by Suspense, scrolling is handled by the useEffect hook in the PageLoading component. + */} + { + scrollToAnchorOrStartOfPage(location) + return null + }} + /> + + + {isLoading ? ( + + Loading + + ) : ( + + + + + {BANNER_CONTENT && {BANNER_CONTENT}} + + + }> + + + - - )} - - + )} + + + ) } diff --git a/browser/src/DocumentTitle.ts b/browser/src/DocumentTitle.ts index 651d8ed60..9d783fc8b 100644 --- a/browser/src/DocumentTitle.ts +++ b/browser/src/DocumentTitle.ts @@ -1,20 +1,68 @@ import PropTypes from 'prop-types' import { useEffect } from 'react' +import { useCopilotReadable } from '@copilotkit/react-core' -const DocumentTitle = ({ title }: any) => { +const DocumentTitle = ({ title, pageContext }: any) => { useEffect(() => { const fullTitle = title ? `${title} | gnomAD` : 'gnomAD' document.title = fullTitle }, [title]) + + let contextDescription = 'The current page context' + let contextValue = 'No context is available for the current page.' + + if (pageContext) { + if (pageContext.gene_id && pageContext.symbol) { + contextDescription = 'The currently viewed gene' + const geneContext = { + gene_id: pageContext.gene_id, + symbol: pageContext.symbol, + name: pageContext.name, + reference_genome: pageContext.reference_genome, + } + contextValue = JSON.stringify(geneContext, null, 2) + } else if (pageContext.variant_id) { + contextDescription = 'The currently viewed variant' + const datasetId = new URL(window.location.href).searchParams.get('dataset') + const variantContext = { + variant_id: pageContext.variant_id, + dataset: datasetId, + reference_genome: pageContext.reference_genome, + caid: pageContext.caid, + rsids: pageContext.rsids, + } + contextValue = JSON.stringify(variantContext, null, 2) + } else if (pageContext.chrom && pageContext.start && pageContext.stop) { + contextDescription = 'The currently viewed genomic region' + const regionContext = { + chrom: pageContext.chrom, + start: pageContext.start, + stop: pageContext.stop, + reference_genome: pageContext.reference_genome, + } + contextValue = JSON.stringify(regionContext, null, 2) + } else { + // Fallback for other contexts that might be passed + contextValue = JSON.stringify(pageContext, null, 2) + } + } + + useCopilotReadable({ + description: contextDescription, + value: contextValue, + }) + return null } DocumentTitle.propTypes = { title: PropTypes.string, + pageContext: PropTypes.object, } DocumentTitle.defaultProps = { title: null, + pageContext: null, } export default DocumentTitle diff --git a/browser/src/GenePage/GenePage.tsx b/browser/src/GenePage/GenePage.tsx index f8acc4a15..5e0ff0acf 100644 --- a/browser/src/GenePage/GenePage.tsx +++ b/browser/src/GenePage/GenePage.tsx @@ -362,7 +362,7 @@ const GenePage = ({ datasetId, gene, geneId }: Props) => { return ( - + ` + width: ${(props) => props.width}px; + overflow: hidden; + display: flex; + flex-direction: column; + background: white; + min-width: 300px; + max-width: 80%; +` + +const ResizeHandle = styled.div` + width: 4px; + background-color: #e0e0e0; + cursor: col-resize; + flex-shrink: 0; + transition: background-color 0.2s; + + &:hover { + background-color: #0d79d0; + } + + &:active { + background-color: #0d79d0; + } +` + +const ToggleButton = styled.button` + position: fixed; + bottom: 24px; + right: 24px; + z-index: 1000; + padding: 12px 24px; + border-radius: 8px; + border: 1px solid #ddd; + background-color: #fff; + color: #333; + font-size: 16px; + font-weight: 500; + box-shadow: 0 4px 12px rgba(0, 0, 0, 0.1); + cursor: pointer; + transition: all 0.2s ease-in-out; + + &:hover { + background-color: #f7f7f7; + box-shadow: 0 6px 16px rgba(0, 0, 0, 0.12); + } +` + +const StyledCopilotChat = styled(CopilotChat)` + height: 100%; + --copilot-kit-primary-color: #0d79d0; + --copilot-kit-background-color: white; + --copilot-kit-header-background: #f7f7f7; + + /* Increase font size in the chat input textarea */ + textarea { + font-size: 14px !important; + } + + /* Also apply to any input fields */ + input[type="text"] { + font-size: 14px !important; + } + + /* Style suggestion chips */ + button[data-suggestion] { + font-size: 14px !important; + } +` + + +export function GnomadCopilot({ children }: { children: React.ReactNode }) { + const [isChatOpen, setIsChatOpen] = useState(true) + const [chatWidth, setChatWidth] = useState(window.innerWidth / 3) // Default to 1/3 of screen + const isResizing = useRef(false) + const containerRef = useRef(null) + const history = useHistory() + const location = useLocation() + + // Initialize MCP state rendering (renders inline in chat) + useMCPStateRender() + + // Initialize gnomAD variant actions + useGnomadVariantActions() + + // Initialize Juha API actions + useJuhaActions() + + // Show "interpret this variant" suggestion only on variant pages + const isVariantPage = location.pathname.startsWith('/variant/') + const isGenePage = location.pathname.startsWith('/gene/') + const isRegionPage = location.pathname.startsWith('/region/') + + // Define suggestions based on the current page + const suggestions = useMemo(() => { + if (isVariantPage) { + return [ + { + title: "Display the variant summary", + message: "Please display the variant summary", + }, + { + title: "Interpret this variant", + message: "Can you help me interpret the clinical significance and population frequency of this variant?", + }, + { + title: "Is this variant too common?", + message: "Is this variant's allele frequency too high for it to cause a rare Mendelian disease?", + }, + { + title: "Analyze expression at this location (Pext)", + message: "Analyze the Pext score for this variant's location. Is it in a functionally important region that is expressed across many tissues?", + }, + { + title: "Check in silico predictors", + message: "What do in silico predictors like REVEL and CADD say about this variant?", + }, + { + title: "Find credible sets for variant", + message: "Using the Juha API, find credible sets from GWAS, eQTL, and pQTL studies for this variant.", + }, + { + title: "Check variant for colocalization", + message: "Using the Juha API, find traits that colocalize at this variant's locus.", + }, + ] + } + if (isGenePage) { + return [ + { + title: "Summarize gene constraint", + message: "Summarize this gene's constraint scores, like pLI and missense o/e.", + }, + { + title: "Check tissue expression", + message: "In which tissues is this gene most highly expressed?", + }, + { + title: "Look up Mendelian disease", + message: "Is this gene associated with any Mendelian diseases?", + }, + { + title: "Analyze expression regions (Pext)", + message: "Provide a Pext analysis for this gene to identify functionally important regions.", + }, + { + title: "Find associations in gene region", + message: "Using the Juha API, find GWAS, eQTL, and pQTL credible sets in this gene's region.", + }, + { + title: "Find QTLs for this gene", + message: "Using the Juha API, find QTLs (eQTLs, pQTLs) where this gene is the target.", + }, + { + title: "Find curated disease associations", + message: "Using the Juha API, what diseases are associated with this gene from curated sources like ClinGen and GenCC?", + }, + ] + } + if (isRegionPage) { + return [ + { + title: "Find associations in region", + message: "Using the Juha API, find GWAS, eQTL, and pQTL credible sets that overlap with this genomic region.", + }, + ] + } + return [] + }, [isVariantPage, isGenePage, isRegionPage]) + + useCopilotAction({ + name: 'navigateToVariantPage', + description: 'Navigate to the gnomAD variant page for a given variant ID.', + parameters: [ + { + name: 'variantId', + type: 'string', + description: "The variant ID, such as '1-55516888-G-GA' or an rsID like 'rs527413419'.", + required: true, + }, + { + name: 'datasetId', + type: 'string', + description: `The dataset ID to use, for example 'gnomad_r4'. If not provided, the current dataset will be used.`, + required: false, + }, + ], + handler: async ({ variantId, datasetId }) => { + // Get the current dataset from the URL if not provided + const currentUrl = new URL(window.location.href) + const currentDatasetId = currentUrl.searchParams.get('dataset') || 'gnomad_r4' + const targetDatasetId = datasetId || currentDatasetId + + const url = `/variant/${variantId}?dataset=${targetDatasetId}` + console.log(`Navigating to: ${url}`) + history.push(url) + + return { + message: `Navigating to the variant page for ${variantId}.`, + } + }, + }) + + const handleMouseDown = useCallback((e: React.MouseEvent) => { + isResizing.current = true + document.body.style.cursor = 'col-resize' + document.body.style.userSelect = 'none' + }, []) + + const handleMouseMove = useCallback((e: MouseEvent) => { + if (!isResizing.current || !containerRef.current) return + + const containerRect = containerRef.current.getBoundingClientRect() + const newWidth = containerRect.right - e.clientX + + // Ensure width stays within bounds + const minWidth = 300 + const maxWidth = containerRect.width * 0.8 + + if (newWidth >= minWidth && newWidth <= maxWidth) { + setChatWidth(newWidth) + } + }, []) + + const handleMouseUp = useCallback(() => { + isResizing.current = false + document.body.style.cursor = '' + document.body.style.userSelect = '' + }, []) + + React.useEffect(() => { + if (isChatOpen) { + document.addEventListener('mousemove', handleMouseMove) + document.addEventListener('mouseup', handleMouseUp) + + return () => { + document.removeEventListener('mousemove', handleMouseMove) + document.removeEventListener('mouseup', handleMouseUp) + } + } + }, [isChatOpen, handleMouseMove, handleMouseUp]) + + return ( + <> + + {children} + {isChatOpen && ( + <> + + + + + + )} + + + setIsChatOpen(!isChatOpen)}> + {isChatOpen ? 'Close Assistant' : 'Ask gnomAD Assistant'} + + + ) +} diff --git a/browser/src/RegionPage/RegionPage.tsx b/browser/src/RegionPage/RegionPage.tsx index ff7e91016..d828edcd0 100644 --- a/browser/src/RegionPage/RegionPage.tsx +++ b/browser/src/RegionPage/RegionPage.tsx @@ -119,6 +119,7 @@ const RegionPage = ({ datasetId, region }: RegionPageProps) => { } diff --git a/browser/src/VariantPage/VariantPage.tsx b/browser/src/VariantPage/VariantPage.tsx index 40b358e81..d72c2d10f 100644 --- a/browser/src/VariantPage/VariantPage.tsx +++ b/browser/src/VariantPage/VariantPage.tsx @@ -814,10 +814,12 @@ const checkGeneLink = (transcript_consequences: TranscriptConsequence[] | null) const VariantPage = ({ datasetId, variantId }: VariantPageProps) => { const gene = { ensembleId: '' } + const [variantData, setVariantData] = React.useState(null) + return ( // @ts-expect-error TS(2746) FIXME: This JSX tag's 'children' prop expects a single ch... Remove this comment to see the full error message - + { gene.ensembleId = geneData.ensembleId } + // Update variant data for CopilotKit context + if (variantData?.variant_id !== variant.variant_id) { + setVariantData(variant) + } + pageContent = } diff --git a/browser/src/components/Progress.tsx b/browser/src/components/Progress.tsx new file mode 100644 index 000000000..dfa2862dd --- /dev/null +++ b/browser/src/components/Progress.tsx @@ -0,0 +1,97 @@ +"use client"; + +import React from "react"; +import styled from 'styled-components'; + +interface ProgressProps { + logs: string[]; +} + +const ProgressContainer = styled.div` + background: #f8f9fa; + border: 1px solid #e9ecef; + border-radius: 8px; + padding: 16px; + margin-bottom: 16px; +`; + +const ProgressHeader = styled.div` + display: flex; + align-items: center; + gap: 8px; + margin-bottom: 12px; +`; + +const StatusIndicator = styled.div` + width: 8px; + height: 8px; + background: #28a745; + border-radius: 50%; + animation: pulse 1.5s ease-in-out infinite; + + @keyframes pulse { + 0%, 100% { opacity: 1; } + 50% { opacity: 0.5; } + } +`; + +const ProgressTitle = styled.h3` + font-size: 14px; + font-weight: 600; + color: #495057; + margin: 0; +`; + +const LogsContainer = styled.div` + max-height: 256px; + overflow-y: auto; + display: flex; + flex-direction: column; + gap: 8px; +`; + +const LogEntry = styled.div` + font-size: 12px; + color: #6c757d; + font-family: 'SF Mono', 'Monaco', 'Inconsolata', 'Roboto Mono', monospace; + background: white; + padding: 8px; + border-radius: 4px; + border: 1px solid #e9ecef; +`; + +const LogIndex = styled.span` + color: #adb5bd; + margin-right: 8px; +`; + +const EmptyState = styled.p` + font-size: 12px; + color: #6c757d; + font-style: italic; + margin: 0; +`; + +export function Progress({ logs }: ProgressProps) { + return ( + + + + MCP Tool Activity + + + + {logs.map((log, index) => ( + + [{index + 1}] + {log} + + ))} + + + {logs.length === 0 && ( + No tool activity yet... + )} + + ); +} \ No newline at end of file diff --git a/browser/src/gmd/components/JuhaToolsDisplay.tsx b/browser/src/gmd/components/JuhaToolsDisplay.tsx new file mode 100644 index 000000000..7db90cf5a --- /dev/null +++ b/browser/src/gmd/components/JuhaToolsDisplay.tsx @@ -0,0 +1,222 @@ +import React, { forwardRef, memo, useState } from 'react' +import styled from 'styled-components' +import { Grid } from '@gnomad/ui' +import credibleSetTableColumns from './credibleSetTableColumns' +import colocalizationTableColumns from './colocalizationTableColumns' +import geneDiseaseTableColumns from './geneDiseaseTableColumns' +import VariantLoading from './VariantLoading' // Re-using for now, can be specialized + +const DisplayWrapper = styled.div` + width: 100%; + max-width: 100%; + margin: 10px 0; + margin-bottom: 20px; +` + +const ErrorMessage = styled.div` + padding: 20px; + background-color: #ffebee; + border: 1px solid #ffcdd2; + border-radius: 4px; + color: #c62828; +` + +const NoResultsMessage = styled.div` + padding: 20px; + background-color: #f5f5f5; + border: 1px solid #e0e0e0; + border-radius: 4px; + color: #666; + text-align: center; +` + +const TableContainer = styled.div` + height: 500px; + min-height: 500px; + margin-bottom: 40px; + position: relative; +` + +// CredibleSetTable Component +const CredibleSetTable = memo( + forwardRef((props: any, ref) => { + const { columns, variants, sortKey, sortOrder, onRequestSort, ...rest } = props + return ( + `${variant.cs_id}-${variant.chr}-${variant.pos}-${variant.ref}-${variant.alt}-${variant.resource}-${variant.data_type}`} + /> + ) + }) +) + +CredibleSetTable.displayName = 'CredibleSetTable' + +// ColocalizationTable Component +const ColocalizationTable = memo( + forwardRef((props: any, ref) => { + const { columns, variants, sortKey, sortOrder, onRequestSort, ...rest } = props + return ( + `${variant.cs1_id}-${variant.cs2_id}-${variant.chr}`} + /> + ) + }) +) + +ColocalizationTable.displayName = 'ColocalizationTable' + +// GeneDiseaseTable Component +const GeneDiseaseTable = memo( + forwardRef((props: any, ref) => { + const { columns, data, sortKey, sortOrder, onRequestSort, ...rest } = props + return ( + // @ts-expect-error TS(2769) FIXME: No overload matches this call. + `${row.uuid}-${row.gene_symbol}-${row.disease_curie}-${row.submitter}`} + /> + ) + }) +) +GeneDiseaseTable.displayName = 'GeneDiseaseTable' + +// Main Display Component +const JuhaToolsDisplay = ({ data, toolName }: { data: any, toolName: string }) => { + // Debug logging + console.log('[JuhaToolsDisplay] Received data:', data) + console.log('[JuhaToolsDisplay] Data type:', typeof data) + console.log('[JuhaToolsDisplay] Data keys:', data ? Object.keys(data) : 'null') + console.log('[JuhaToolsDisplay] Is array?:', Array.isArray(data)) + + if (data.error) { + return ( + + Error: {data.error} + + ) + } + + const processedData = Array.isArray(data) ? data : data.results || [] + console.log('[JuhaToolsDisplay] Processed data length:', processedData.length) + console.log('[JuhaToolsDisplay] First item:', processedData[0]) + + if (processedData.length === 0) { + return ( + + No results found for {toolName}. + + ) + } + + // Determine which table to render based on data shape + const firstItem = processedData[0] + + // State for sorting + const [sortKey, setSortKey] = useState('') + const [sortOrder, setSortOrder] = useState<'ascending' | 'descending'>('descending') + + const handleRequestSort = (newSortKey: string) => { + if (newSortKey === sortKey) { + setSortOrder(sortOrder === 'ascending' ? 'descending' : 'ascending') + } else { + setSortKey(newSortKey) + setSortOrder('descending') + } + } + + if (firstItem.cs_id) { // Credible Set data + const defaultSortKey = sortKey || 'mlog10p' + return ( + + + + + + ) + } else if (firstItem['PP.H4.abf'] !== undefined || firstItem.cs1_id !== undefined) { // Colocalization data + const defaultSortKey = sortKey || 'PP.H4.abf' + return ( + + + + + + ) + } else if (firstItem.disease_curie) { // Gene-Disease data + const defaultSortKey = sortKey || 'disease_title' + return ( + + + + + + ) + } + + return ( + + + Unknown data format received from tool. + {process.env.NODE_ENV === 'development' && ( +
+ Sample data keys: {firstItem ? JSON.stringify(Object.keys(firstItem)) : 'no data'} +
+ )} + + + ) +} + +export default JuhaToolsDisplay + +// Loading Component +export const JuhaToolsLoading: React.FC<{ message: string }> = ({ message }) => { + // We can reuse VariantLoading for simplicity for now. + return +} diff --git a/browser/src/gmd/components/VariantCard.tsx b/browser/src/gmd/components/VariantCard.tsx new file mode 100644 index 000000000..5812b62f6 --- /dev/null +++ b/browser/src/gmd/components/VariantCard.tsx @@ -0,0 +1,337 @@ +import React from 'react' +import styled from 'styled-components' +import { Badge, Button, ExternalLink } from '@gnomad/ui' +import AttributeList, { AttributeListItem } from '../../AttributeList' + +const CardWrapper = styled.div` + background: #ffffff; + border: 1px solid #e0e0e0; + border-radius: 8px; + padding: 20px; + margin: 10px 0; + width: 100%; + box-shadow: 0 1px 3px rgba(0, 0, 0, 0.12); +` + +const CardHeader = styled.div` + display: flex; + align-items: center; + justify-content: space-between; + margin-bottom: 15px; +` + +const VariantTitle = styled.h3` + margin: 0; + font-size: 1.1em; + font-weight: 600; + color: #333; +` + +const VariantSubtitle = styled.div` + color: #666; + font-size: 0.9em; + margin-top: 5px; +` + +const Section = styled.div` + margin-top: 15px; +` + +const SectionTitle = styled.h4` + margin: 0 0 10px 0; + font-size: 0.9em; + font-weight: 600; + color: #666; + text-transform: uppercase; + letter-spacing: 0.05em; +` + +const FrequencyGrid = styled.div` + display: grid; + grid-template-columns: repeat(auto-fit, minmax(150px, 1fr)); + gap: 10px; + margin-top: 10px; +` + +const FrequencyItem = styled.div` + background: #f8f8f8; + padding: 10px; + border-radius: 4px; +` + +const FrequencyLabel = styled.div` + font-size: 0.8em; + color: #666; + margin-bottom: 2px; +` + +const FrequencyValue = styled.div` + font-size: 1.1em; + font-weight: 600; + color: #333; +` + +const ActionBar = styled.div` + display: flex; + gap: 10px; + margin-top: 20px; + padding-top: 15px; + border-top: 1px solid #e0e0e0; +` + +interface VariantData { + variant_id: string + reference_genome?: string + chrom?: string + pos?: number + ref?: string + alt?: string + rsids?: string[] + flags?: string[] + exome?: { + ac: number + an: number + af?: number + homozygote_count: number + hemizygote_count?: number + faf95?: { + popmax: number + popmax_population: string + } + populations?: Array<{ + id: string + ac: number + an: number + homozygote_count: number + }> + } + genome?: { + ac: number + an: number + af?: number + homozygote_count: number + hemizygote_count?: number + faf95?: { + popmax: number + popmax_population: string + } + populations?: Array<{ + id: string + ac: number + an: number + homozygote_count: number + }> + } + transcript_consequences?: Array<{ + gene_id: string + gene_symbol: string + transcript_id: string + consequence_terms: string[] + major_consequence: string + is_canonical: boolean + hgvs?: string + hgvsc?: string + hgvsp?: string + lof?: string + lof_flags?: string + lof_filter?: string + }> + in_silico_predictors?: Array<{ + id: string + value: string + flags?: string[] + }> +} + +interface VariantCardProps { + variant: VariantData + onViewDetails?: () => void + onNavigateToVariant?: () => void +} + +const formatFrequency = (frequency: number): string => { + if (frequency === 0) return '0' + if (frequency < 0.00001) return frequency.toExponential(2) + return frequency.toFixed(5) +} + +const calculateAF = (ac: number, an: number): number => { + return an > 0 ? ac / an : 0 +} + +const VariantCard: React.FC = ({ + variant, + onViewDetails, + onNavigateToVariant +}) => { + console.log('VariantCard received variant:', variant) + console.log('variant.transcript_consequences:', variant.transcript_consequences) + console.log('variant.variant_id:', variant.variant_id) + console.log('variant.variantId:', variant.variantId) + + // Get the first canonical transcript or the first transcript + const canonicalTranscript = variant.transcript_consequences?.find(t => t.is_canonical) || variant.transcript_consequences?.[0] + + // Calculate allele frequencies + const exomeAF = variant.exome ? calculateAF(variant.exome.ac, variant.exome.an) : undefined + const genomeAF = variant.genome ? calculateAF(variant.genome.ac, variant.genome.an) : undefined + + // Determine which frequency data to display + const hasExomeData = variant.exome && variant.exome.an > 0 + const hasGenomeData = variant.genome && variant.genome.an > 0 + + return ( + + +
+ {variant.variant_id} + + {canonicalTranscript?.gene_symbol && ( + <> + {canonicalTranscript.gene_symbol} + {canonicalTranscript.major_consequence && ` • ${canonicalTranscript.major_consequence.replace(/_/g, ' ')}`} + + )} + +
+ {variant.flags && variant.flags.length > 0 && ( +
+ {variant.flags.map((flag) => ( + + {flag} + + ))} +
+ )} + + + + {canonicalTranscript?.hgvsp && ( + + {canonicalTranscript.hgvsp} + + )} + {canonicalTranscript?.hgvsc && ( + + {canonicalTranscript.hgvsc} + + )} + {variant.rsids && variant.rsids.length > 0 && ( + + {variant.rsids.map((rsid, index) => ( + + {index > 0 && ', '} + + {rsid} + + + ))} + + )} + + + {(hasExomeData || hasGenomeData) && ( +
+ Allele Frequency + + {hasExomeData && ( + <> + + Exome AF + {formatFrequency(exomeAF!)} + + + Exome AC/AN + + {variant.exome!.ac} / {variant.exome!.an} + + + {variant.exome!.homozygote_count !== undefined && ( + + Exome Homozygotes + {variant.exome!.homozygote_count} + + )} + + )} + {hasGenomeData && ( + <> + + Genome AF + {formatFrequency(genomeAF!)} + + + Genome AC/AN + + {variant.genome!.ac} / {variant.genome!.an} + + + {variant.genome!.homozygote_count !== undefined && ( + + Genome Homozygotes + {variant.genome!.homozygote_count} + + )} + + )} + + + {/* Display FAF if available */} + {(variant.exome?.faf95 || variant.genome?.faf95) && ( + + {variant.exome?.faf95 && ( + + Exome FAF95 ({variant.exome.faf95.popmax_population}) + {formatFrequency(variant.exome.faf95.popmax)} + + )} + {variant.genome?.faf95 && ( + + Genome FAF95 ({variant.genome.faf95.popmax_population}) + {formatFrequency(variant.genome.faf95.popmax)} + + )} + + )} +
+ )} + + {variant.in_silico_predictors && variant.in_silico_predictors.length > 0 && ( +
+ In Silico Predictors + + {variant.in_silico_predictors.map((predictor) => ( + + {predictor.value} + {predictor.flags && predictor.flags.length > 0 && ( + + {predictor.flags.map((flag) => ( + + {flag} + + ))} + + )} + + ))} + +
+ )} + + + {onNavigateToVariant && ( + + )} + {onViewDetails && ( + + )} + + + ) +} + +export default VariantCard \ No newline at end of file diff --git a/browser/src/gmd/components/VariantDisplay.tsx b/browser/src/gmd/components/VariantDisplay.tsx new file mode 100644 index 000000000..387c6ab70 --- /dev/null +++ b/browser/src/gmd/components/VariantDisplay.tsx @@ -0,0 +1,156 @@ +import React from 'react' +import styled from 'styled-components' +import { useHistory } from 'react-router-dom' +import VariantCard from './VariantCard' + +const DisplayWrapper = styled.div` + width: 100%; + max-width: 600px; +` + +const ErrorMessage = styled.div` + padding: 20px; + background-color: #ffebee; + border: 1px solid #ffcdd2; + border-radius: 4px; + color: #c62828; +` + +const NoResultsMessage = styled.div` + padding: 20px; + background-color: #f5f5f5; + border: 1px solid #e0e0e0; + border-radius: 4px; + color: #666; + text-align: center; +` + +const VariantListHeader = styled.div` + margin-bottom: 10px; + padding: 10px 0; + border-bottom: 1px solid #e0e0e0; +` + +const ResultCount = styled.div` + font-size: 0.9em; + color: #666; + font-weight: 600; +` + +interface VariantDisplayProps { + data: any +} + +const VariantDisplay: React.FC = ({ data }) => { + const history = useHistory() + + console.log('VariantDisplay received data:', data) + console.log('Data type:', typeof data) + console.log('Data keys:', data ? Object.keys(data) : 'no data') + if (data && typeof data === 'object') { + console.log('Data stringified:', JSON.stringify(data, null, 2)) + } + + // Handle error cases + if (!data) { + return ( + + + No data available + + + ) + } + + if (data.error) { + return ( + + + Error: {data.error} + + + ) + } + + // Handle CopilotKit's wrapped response format + let processedData = data + + // If data is an array with text objects (CopilotKit format) + if (Array.isArray(data) && data.length > 0 && data[0].type === 'text' && data[0].text) { + try { + // Extract and parse the JSON from the text + const jsonText = data[0].text + processedData = JSON.parse(jsonText) + console.log('Parsed variant data:', processedData) + } catch (error) { + console.error('Failed to parse variant data:', error) + return ( + + + Error parsing variant data + + + ) + } + } + + // Determine if we have a single variant or multiple variants + const variants = Array.isArray(processedData) ? processedData : (processedData.variants || [processedData]) + console.log('Processed variants:', variants) + + if (variants.length === 0) { + return ( + + + No variants found + + + ) + } + + const handleNavigateToVariant = (variantId: string, referenceGenome?: string) => { + // Navigate to the variant page + // The route structure is typically /variant/{variantId}?dataset={datasetId} + // Map reference genome to dataset ID + let dataset = 'gnomad_r4' + if (referenceGenome === 'GRCh37') { + dataset = 'gnomad_r2_1_1' + } else if (referenceGenome === 'GRCh38') { + dataset = 'gnomad_r4' + } + history.push(`/variant/${variantId}?dataset=${dataset}`) + } + + // Single variant display + if (variants.length === 1) { + const variant = variants[0] + return ( + + handleNavigateToVariant(variant.variant_id || variant.variantId, variant.reference_genome)} + /> + + ) + } + + // Multiple variants display + return ( + + + + Found {variants.length} variant{variants.length !== 1 ? 's' : ''} + + + {variants.map((variant: any, index: number) => ( + handleNavigateToVariant(variant.variant_id || variant.variantId, variant.reference_genome)} + /> + ))} + + ) +} + +export default VariantDisplay \ No newline at end of file diff --git a/browser/src/gmd/components/VariantLoading.tsx b/browser/src/gmd/components/VariantLoading.tsx new file mode 100644 index 000000000..7a107a1d3 --- /dev/null +++ b/browser/src/gmd/components/VariantLoading.tsx @@ -0,0 +1,125 @@ +import React from 'react' +import styled, { keyframes } from 'styled-components' + +const pulse = keyframes` + 0% { + opacity: 1; + } + 50% { + opacity: 0.5; + } + 100% { + opacity: 1; + } +` + +const LoadingWrapper = styled.div` + background: #ffffff; + border: 1px solid #e0e0e0; + border-radius: 8px; + padding: 20px; + margin: 10px 0; + width: 100%; + max-width: 600px; +` + +const SkeletonHeader = styled.div` + display: flex; + align-items: center; + justify-content: space-between; + margin-bottom: 15px; +` + +const SkeletonTitle = styled.div` + height: 24px; + width: 200px; + background-color: #e0e0e0; + border-radius: 4px; + animation: ${pulse} 1.5s ease-in-out infinite; +` + +const SkeletonSubtitle = styled.div` + height: 18px; + width: 150px; + background-color: #e0e0e0; + border-radius: 4px; + margin-top: 8px; + animation: ${pulse} 1.5s ease-in-out infinite; +` + +const SkeletonBadge = styled.div` + height: 24px; + width: 60px; + background-color: #e0e0e0; + border-radius: 4px; + animation: ${pulse} 1.5s ease-in-out infinite; +` + +const SkeletonContent = styled.div` + margin-top: 20px; +` + +const SkeletonLine = styled.div<{ width?: string }>` + height: 16px; + width: ${props => props.width || '100%'}; + background-color: #e0e0e0; + border-radius: 4px; + margin-bottom: 12px; + animation: ${pulse} 1.5s ease-in-out infinite; +` + +const SkeletonGrid = styled.div` + display: grid; + grid-template-columns: repeat(3, 1fr); + gap: 10px; + margin-top: 15px; +` + +const SkeletonBox = styled.div` + height: 60px; + background-color: #f5f5f5; + border-radius: 4px; + padding: 10px; + animation: ${pulse} 1.5s ease-in-out infinite; +` + +const LoadingMessage = styled.div` + text-align: center; + color: #666; + font-size: 0.9em; + margin-top: 15px; +` + +interface VariantLoadingProps { + message?: string +} + +const VariantLoading: React.FC = ({ message = 'Loading variant data...' }) => { + return ( + + +
+ + +
+ + + + + + + + + + + + + + + + {message} + + ) +} + +export default VariantLoading \ No newline at end of file diff --git a/browser/src/gmd/components/colocalizationTableColumns.tsx b/browser/src/gmd/components/colocalizationTableColumns.tsx new file mode 100644 index 000000000..725b043c6 --- /dev/null +++ b/browser/src/gmd/components/colocalizationTableColumns.tsx @@ -0,0 +1,36 @@ +import React from 'react' +import { Cell, NumericCell } from '../../tableCells' +import { makeNumericCompareFunction, makeStringCompareFunction } from '../../VariantList/sortUtilities' + +const colocalizationTableColumns = [ + { + key: 'trait1_original', + heading: 'Trait 1', + minWidth: 200, + compareFunction: makeStringCompareFunction('trait1_original'), + render: (row: any) => {row.trait1_original}, + }, + { + key: 'trait2_original', + heading: 'Trait 2', + minWidth: 200, + compareFunction: makeStringCompareFunction('trait2_original'), + render: (row: any) => {row.trait2_original}, + }, + { + key: 'PP.H4.abf', + heading: 'P(H4)', + minWidth: 80, + compareFunction: makeNumericCompareFunction('PP.H4.abf'), + render: (row: any) => {row['PP.H4.abf'].toFixed(3)}, + }, + { + key: 'clpp', + heading: 'CLPP', + minWidth: 80, + compareFunction: makeNumericCompareFunction('clpp'), + render: (row: any) => {row.clpp.toFixed(3)}, + }, +] + +export default colocalizationTableColumns diff --git a/browser/src/gmd/components/credibleSetTableColumns.tsx b/browser/src/gmd/components/credibleSetTableColumns.tsx new file mode 100644 index 000000000..316f935e5 --- /dev/null +++ b/browser/src/gmd/components/credibleSetTableColumns.tsx @@ -0,0 +1,84 @@ +import React from 'react' +import { Cell, NumericCell } from '../../tableCells' +import Link from '../../Link' +import { makeNumericCompareFunction, makeStringCompareFunction } from '../../VariantList/sortUtilities' +import { TooltipAnchor, TooltipHint } from '@gnomad/ui' + +const credibleSetTableColumns = [ + { + key: 'resource', + heading: 'Resource', + minWidth: 100, + compareFunction: makeStringCompareFunction('resource'), + render: (row: any) => {row.resource}, + }, + { + key: 'data_type', + heading: 'Data Type', + minWidth: 80, + compareFunction: makeStringCompareFunction('data_type'), + render: (row: any) => {row.data_type}, + }, + { + key: 'trait', + heading: 'Trait', + minWidth: 200, + compareFunction: makeStringCompareFunction('trait_original'), + render: (row: any) => {row.trait_original}, + }, + { + key: 'variant_id', + heading: 'Variant', + minWidth: 150, + compareFunction: makeNumericCompareFunction('pos'), + render: (row: any) => { + const variantId = `${row.chr}-${row.pos}-${row.ref}-${row.alt}` + return ( + + {variantId} + + ) + }, + }, + { + key: 'mlog10p', + heading: '-log10(p)', + minWidth: 80, + compareFunction: makeNumericCompareFunction('mlog10p'), + render: (row: any) => {row.mlog10p.toFixed(2)}, + }, + { + key: 'beta', + heading: 'Beta', + minWidth: 80, + compareFunction: makeNumericCompareFunction('beta'), + render: (row: any) => {row.beta ? row.beta.toExponential(2) : 'N/A'}, + }, + { + key: 'pip', + heading: ( + + {/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */} + PIP + + ), + minWidth: 80, + compareFunction: makeNumericCompareFunction('pip'), + render: (row: any) => {row.pip ? row.pip.toFixed(3) : 'N/A'}, + }, + { + key: 'gene_most_severe', + heading: 'Gene', + minWidth: 100, + compareFunction: makeStringCompareFunction('gene_most_severe'), + render: (row: any) => ( + + {row.gene_most_severe && ( + {row.gene_most_severe} + )} + + ), + }, +] + +export default credibleSetTableColumns diff --git a/browser/src/gmd/components/geneDiseaseTableColumns.tsx b/browser/src/gmd/components/geneDiseaseTableColumns.tsx new file mode 100644 index 000000000..081c9d1ca --- /dev/null +++ b/browser/src/gmd/components/geneDiseaseTableColumns.tsx @@ -0,0 +1,45 @@ +import React from 'react' +import { Cell } from '../../tableCells' +import { makeStringCompareFunction } from '../../VariantList/sortUtilities' +import { ExternalLink } from '@gnomad/ui' + +const getMondoId = (curie: string) => curie.replace('MONDO:', '') + +const geneDiseaseTableColumns = [ + { + key: 'disease_title', + heading: 'Disease', + minWidth: 250, + compareFunction: makeStringCompareFunction('disease_title'), + render: (row: any) => ( + + + {row.disease_title} + + + ), + }, + { + key: 'classification', + heading: 'Classification', + minWidth: 120, + compareFunction: makeStringCompareFunction('classification'), + render: (row: any) => {row.classification}, + }, + { + key: 'mode_of_inheritance', + heading: 'Inheritance', + minWidth: 120, + compareFunction: makeStringCompareFunction('mode_of_inheritance'), + render: (row: any) => {row.mode_of_inheritance || 'N/A'}, + }, + { + key: 'submitter', + heading: 'Source', + minWidth: 100, + compareFunction: makeStringCompareFunction('submitter'), + render: (row: any) => {row.submitter}, + }, +] + +export default geneDiseaseTableColumns diff --git a/browser/src/gmd/hooks/useGnomadVariantActions.tsx b/browser/src/gmd/hooks/useGnomadVariantActions.tsx new file mode 100644 index 000000000..fc17caefc --- /dev/null +++ b/browser/src/gmd/hooks/useGnomadVariantActions.tsx @@ -0,0 +1,117 @@ +import React from 'react' +import { useCopilotAction } from '@copilotkit/react-core' +import VariantLoading from '../components/VariantLoading' +import VariantDisplay from '../components/VariantDisplay' + +export function useGnomadVariantActions() { + // Action for getting variant summary + useCopilotAction({ + name: 'get_variant_summary', + description: 'Fetch summary information for a genetic variant', + parameters: [ + { + name: 'variant_id', + type: 'string', + description: 'The variant identifier (e.g., "1-55516888-G-A")', + required: true, + }, + { + name: 'dataset', + type: 'string', + description: 'The dataset to query (e.g., "gnomad_r4")', + required: false, + }, + ], + handler: async ({ variant_id, dataset }) => { + // The handler returns the parameters that will be sent to the backend + return { variant_id, dataset } + }, + render: (props) => { + const { status, result } = props + console.log('get_variant_summary render props:', { status, result }) + + if (status === 'executing') { + return + } + + if (status === 'complete' && result) { + console.log('Rendering VariantDisplay with data:', result) + return + } + + return null + }, + }) + + // Action for getting variant details with population frequencies + useCopilotAction({ + name: 'get_variant_details', + description: 'Fetch detailed information for a variant including population frequencies', + parameters: [ + { + name: 'variant_id', + type: 'string', + description: 'The variant identifier', + required: true, + }, + { + name: 'dataset', + type: 'string', + description: 'The dataset to query', + required: false, + }, + ], + handler: async ({ variant_id, dataset }) => { + return { variant_id, dataset } + }, + render: (props) => { + const { status, result } = props + + if (status === 'executing') { + return + } + + if (status === 'complete' && result) { + return + } + + return null + }, + }) + + // Action for getting variant frequencies + useCopilotAction({ + name: 'get_variant_frequencies', + description: 'Fetch allele frequency information for a variant', + parameters: [ + { + name: 'variant_id', + type: 'string', + description: 'The variant identifier', + required: true, + }, + { + name: 'dataset', + type: 'string', + description: 'The dataset to query', + required: false, + }, + ], + handler: async ({ variant_id, dataset }) => { + return { variant_id, dataset } + }, + render: (props) => { + const { status, result } = props + + if (status === 'executing') { + return + } + + if (status === 'complete' && result) { + return + } + + return null + }, + }) +} \ No newline at end of file diff --git a/browser/src/gmd/hooks/useJuhaActions.tsx b/browser/src/gmd/hooks/useJuhaActions.tsx new file mode 100644 index 000000000..4fa5995d8 --- /dev/null +++ b/browser/src/gmd/hooks/useJuhaActions.tsx @@ -0,0 +1,125 @@ +import React from 'react' +import { useCopilotAction } from '@copilotkit/react-core' +import JuhaToolsDisplay, { JuhaToolsLoading } from '../components/JuhaToolsDisplay' + +export function useJuhaActions() { + useCopilotAction({ + name: "get_juha_credible_sets_by_variant", + description: "Fetches GWAS, eQTL, and pQTL credible sets for a specific variant from the Juha API.", + parameters: [ + { name: 'variant_id', type: 'string', required: true, description: "The ID of the variant (e.g., '1-55516888-G-GA')." }, + ], + handler: async (args) => args, + render: (props) => { + const { status, result } = props + if (status === 'executing') return + if (status === 'complete') { + // Debug logging + console.log('[Juha] Credible sets by variant - Full result:', result) + console.log('[Juha] Credible sets by variant - structuredContent:', result?.structuredContent) + console.log('[Juha] Credible sets by variant - result type:', typeof result) + console.log('[Juha] Credible sets by variant - result keys:', result ? Object.keys(result) : 'null') + + // Extract structured content from MCP response + const data = result?.structuredContent || result + return + } + return null + }, + }) + + useCopilotAction({ + name: "get_juha_credible_sets_by_gene", + description: "Fetches credible sets within the genomic region of a given gene from the Juha API.", + parameters: [ + { name: 'gene_symbol', type: 'string', required: true, description: "The official symbol of the gene (e.g., 'PCSK9')." }, + ], + handler: async (args) => args, + render: (props) => { + const { status, result } = props + if (status === 'executing') return + if (status === 'complete') { + // Extract structured content from MCP response + const data = result?.structuredContent || result + return + } + return null + }, + }) + + useCopilotAction({ + name: "get_juha_credible_sets_by_region", + description: "Fetches credible sets within a specified genomic region (e.g., 'chr1:1000-2000') from the Juha API.", + parameters: [ + { name: 'region', type: 'string', required: true, description: "The genomic region in the format 'chr:start-end'." }, + ], + handler: async (args) => args, + render: (props) => { + const { status, result } = props + if (status === 'executing') return + if (status === 'complete') { + // Extract structured content from MCP response + const data = result?.structuredContent || result + return + } + return null + }, + }) + + useCopilotAction({ + name: "get_juha_qtls_by_gene", + description: "Fetches genome-wide QTL credible sets where the specified gene is the target from the Juha API.", + parameters: [ + { name: 'gene_symbol', type: 'string', required: true, description: "The official symbol of the gene (e.g., 'APOE')." }, + ], + handler: async (args) => args, + render: (props) => { + const { status, result } = props; + if (status === 'executing') return ; + if (status === 'complete') { + // Extract structured content from MCP response + const data = result?.structuredContent || result + return ; + } + return null; + }, + }); + + useCopilotAction({ + name: "get_juha_colocalization_by_variant", + description: "Fetches colocalization data to see which traits share a causal variant at a variant's locus from the Juha API.", + parameters: [ + { name: 'variant_id', type: 'string', required: true, description: "The ID of the variant (e.g., '1-55516888-G-GA')." }, + ], + handler: async (args) => args, + render: (props) => { + const { status, result } = props; + if (status === 'executing') return ; + if (status === 'complete') { + // Extract structured content from MCP response + const data = result?.structuredContent || result + return ; + } + return null; + }, + }); + + useCopilotAction({ + name: "get_juha_gene_disease_associations", + description: "Fetches curated gene-to-disease associations from the Juha API.", + parameters: [ + { name: 'gene_symbol', type: 'string', required: true, description: "The official symbol of the gene (e.g., 'CFTR')." }, + ], + handler: async (args) => args, + render: (props) => { + const { status, result } = props; + if (status === 'executing') return ; + if (status === 'complete') { + // Extract structured content from MCP response + const data = result?.structuredContent || result + return ; + } + return null; + }, + }); +} diff --git a/browser/src/hooks/useMCPStateRender.tsx b/browser/src/hooks/useMCPStateRender.tsx new file mode 100644 index 000000000..9f4fc2b25 --- /dev/null +++ b/browser/src/hooks/useMCPStateRender.tsx @@ -0,0 +1,231 @@ +import React, { useState } from "react"; +import { useCopilotAction } from "@copilotkit/react-core"; +import styled from 'styled-components'; + +const ToolStateContainer = styled.div<{ isExecuting: boolean }>` + border: 1px solid ${props => props.isExecuting ? '#007bff' : '#28a745'}; + border-radius: 8px; + padding: 16px; + margin: 8px 0; + background: ${props => props.isExecuting ? '#f0f8ff' : '#f8fff8'}; + transition: all 0.3s ease; +`; + +const ToolHeader = styled.div` + display: flex; + align-items: flex-start; + gap: 12px; +`; + +const StatusIcon = styled.div<{ isExecuting: boolean }>` + width: 32px; + height: 32px; + border-radius: 50%; + display: flex; + align-items: center; + justify-content: center; + background: ${props => props.isExecuting ? '#e3f2fd' : '#e8f5e8'}; + margin-top: 4px; +`; + +const StatusIndicator = styled.div` + width: 12px; + height: 12px; + background: #007bff; + border-radius: 50%; + animation: pulse 1.5s ease-in-out infinite; + + @keyframes pulse { + 0%, 100% { opacity: 1; } + 50% { opacity: 0.3; } + } +`; + +const CheckIcon = styled.svg` + width: 16px; + height: 16px; + color: #28a745; +`; + +const ToolContent = styled.div` + flex: 1; +`; + +const ToolTitle = styled.h4<{ isExecuting: boolean }>` + font-size: 14px; + font-weight: 600; + margin: 0 0 8px 0; + color: ${props => props.isExecuting ? '#0056b3' : '#155724'}; +`; + +const StatusLine = styled.div` + display: flex; + align-items: center; + gap: 8px; + font-size: 12px; + color: #6c757d; + margin-bottom: 4px; +`; + +const StatusArrow = styled.span` + color: #adb5bd; +`; + +const StatusText = styled.span` + font-family: 'SF Mono', 'Monaco', 'Inconsolata', 'Roboto Mono', monospace; +`; + +const ParametersToggle = styled.button` + display: flex; + align-items: center; + gap: 8px; + background: none; + border: none; + font-size: 12px; + color: #6c757d; + cursor: pointer; + padding: 4px 0; + font-family: 'SF Mono', 'Monaco', 'Inconsolata', 'Roboto Mono', monospace; + + &:hover { + color: #495057; + } +`; + +const ChevronIcon = styled.svg<{ expanded: boolean }>` + width: 12px; + height: 12px; + transition: transform 0.2s ease; + transform: ${props => props.expanded ? 'rotate(90deg)' : 'rotate(0deg)'}; +`; + +const ParametersContent = styled.pre` + margin: 8px 0 0 24px; + padding: 8px; + background: #f8f9fa; + border-radius: 4px; + font-size: 11px; + overflow-x: auto; + border: 1px solid #e9ecef; +`; + +const ProcessingLine = styled.div` + display: flex; + align-items: center; + gap: 8px; + font-size: 12px; + color: #6c757d; + animation: pulse 1.5s ease-in-out infinite; +`; + +const SuccessLine = styled.div` + display: flex; + align-items: center; + gap: 8px; + font-size: 12px; + color: #28a745; +`; + +const SuccessIcon = styled.span` + color: #28a745; +`; + +interface ToolStateDisplayProps { + name: string; + status: string; + args: any; +} + +function ToolStateDisplay({ name, status, args }: ToolStateDisplayProps) { + const [isExpanded, setIsExpanded] = useState(false); + const isExecuting = status === "executing"; + const isComplete = status === "complete"; + + return ( + + + + {isExecuting ? ( + + ) : ( + + + + )} + + + + Tool: {name} + + + {isExecuting && ( + <> + + › + Calling MCP server... + + + setIsExpanded(!isExpanded)}> + › + Parameters + + + + + + {isExpanded && ( + + {args ? JSON.stringify(args, null, 2) : "No parameters"} + + )} + + › + Processing request... + + + )} + + {isComplete && ( + <> + + ✓ + Tool completed successfully + + + setIsExpanded(!isExpanded)}> + › + Parameters + + + + + + {isExpanded && ( + + {args ? JSON.stringify(args, null, 2) : "No parameters"} + + )} + + )} + + + + ); +} + +export function useMCPStateRender() { + // Catch all tool calls including MCP tools + useCopilotAction({ + name: "*", + description: "Monitor all tool calls", + render: ({ name, status, args }) => { + // Show for both executing and complete status + if (status === "idle") { + return null; + } + + // Render inline tool state + return ; + }, + }); +} \ No newline at end of file diff --git a/browser/src/styles/chatComponents.css b/browser/src/styles/chatComponents.css new file mode 100644 index 000000000..652876218 --- /dev/null +++ b/browser/src/styles/chatComponents.css @@ -0,0 +1,101 @@ +/* Styles for components rendered in the chat sidebar */ +.chat-component-container { + max-width: 100%; + padding: 0.5rem; + background-color: white; + border-radius: 0.5rem; + box-shadow: 0 1px 3px 0 rgba(0, 0, 0, 0.1); + margin-bottom: 1rem; + border: 1px solid #e5e7eb; +} + +/* Make tables scrollable horizontally in the narrow chat pane */ +.chat-component-container table { + display: block; + overflow-x: auto; + white-space: nowrap; + font-size: 0.875rem; + max-width: 100%; +} + +/* Adjust table styling for better readability in compact space */ +.chat-component-container th, +.chat-component-container td { + padding: 0.25rem 0.5rem; + font-size: 0.8125rem; +} + +.chat-component-container th[scope='col'] { + padding-left: 1rem; +} + +.chat-component-container td { + padding-left: 1rem; +} + +/* Ensure badges and other inline elements don't break layout */ +.chat-component-container span { + white-space: nowrap; +} + +/* Adjust heading sizes */ +.chat-component-container h4 { + font-size: 1rem; + font-weight: 600; + color: #1f2937; +} + +/* Warning and info boxes */ +.chat-component-container p { + font-size: 0.875rem; + margin: 0.5rem 0; +} + +/* Ensure tooltips work properly in the chat context */ +.chat-component-container [role="tooltip"] { + z-index: 9999; +} + +/* Variant Card specific styles for chat context */ +.chat-component-container .variant-card { + width: 100%; + box-sizing: border-box; +} + +/* Ensure variant cards don't have excessive margins in chat */ +.chat-component-container > div > div { + margin: 0; +} + +/* Adjust button spacing in variant cards */ +.chat-component-container button { + font-size: 0.875rem; + padding: 0.375rem 0.75rem; +} + +/* Ensure AttributeList renders properly in narrow space */ +.chat-component-container dl { + font-size: 0.875rem; +} + +.chat-component-container dt { + font-weight: 600; + margin-bottom: 0.125rem; +} + +.chat-component-container dd { + margin-left: 0; + margin-bottom: 0.5rem; +} + +/* Grid layout adjustments for frequency data */ +.chat-component-container .frequency-grid { + grid-template-columns: repeat(auto-fit, minmax(120px, 1fr)); +} + +/* Ensure external links are identifiable */ +.chat-component-container a[href^="http"] { + color: #0d79d0; + text-decoration: underline; + word-break: break-word; +} \ No newline at end of file diff --git a/copilotkit-server/README.md b/copilotkit-server/README.md new file mode 100644 index 000000000..af2a8f5c5 --- /dev/null +++ b/copilotkit-server/README.md @@ -0,0 +1,32 @@ +# CopilotKit Server + +**Note:** The CopilotKit server code has been moved into the GraphQL API codebase. + +## Location + +The CopilotKit server is now integrated into the GraphQL API at: +- **Source code:** `graphql-api/src/copilotkit/` +- **Mounted in:** `graphql-api/src/app.ts` + +## Architecture + +The CopilotKit server now runs as part of the same Node.js process as the GraphQL API, mounted at `/api/copilotkit`. This colocation provides several benefits: + +- **Better performance:** MCP server calls GraphQL API via localhost +- **Simplified deployment:** Single container for both services +- **Easier development:** Shared dependencies and TypeScript configuration + +## Local Development + +For local standalone testing of the CopilotKit functionality, you can still run it separately: + +```bash +cd copilotkit-server +./start.sh +``` + +This will use the standalone server script that imports from the GraphQL API codebase. + +## Production + +In production, the CopilotKit endpoint is automatically available at `/api/copilotkit` as part of the GraphQL API deployment. No separate deployment is needed. diff --git a/copilotkit-server/package.json b/copilotkit-server/package.json new file mode 100644 index 000000000..66775f66f --- /dev/null +++ b/copilotkit-server/package.json @@ -0,0 +1,15 @@ +{ + "name": "@gnomad/copilotkit-server", + "version": "1.0.0", + "private": true, + "dependencies": { + "@copilotkit/runtime": "^1.10.3", + "@google/generative-ai": "^0.21.0", + "@modelcontextprotocol/sdk": "^1.17.4", + "@types/cors": "^2.8.13", + "@types/express": "^4.17.17", + "cors": "^2.8.5", + "express": "^4.20.0", + "typescript": "^5.0.4" + } +} \ No newline at end of file diff --git a/copilotkit-server/src/mcp-client.ts b/copilotkit-server/src/mcp-client.ts new file mode 100644 index 000000000..48adaeef5 --- /dev/null +++ b/copilotkit-server/src/mcp-client.ts @@ -0,0 +1,98 @@ +import { Client } from "@modelcontextprotocol/sdk/client/index.js"; +import { StdioClientTransport } from "@modelcontextprotocol/sdk/client/stdio.js"; +import { MCPClient, MCPTool } from "@copilotkit/runtime"; + +export class LocalMCPClient implements MCPClient { + private client!: Client; + private connected = false; + + constructor(private config: { command: string; args: string[]; env?: Record }) { } + + async connect(): Promise { + // Build environment variables, filtering out undefined values + const env: Record = {}; + + // Add process.env values, filtering undefined + for (const [key, value] of Object.entries(process.env)) { + if (value !== undefined) { + env[key] = value; + } + } + + // Add config env values, overriding process.env + if (this.config.env) { + Object.assign(env, this.config.env); + } + + const transport = new StdioClientTransport({ + command: this.config.command, + args: this.config.args, + env, + }); + + this.client = new Client( + { + name: "copilotkit-client", + version: "1.0.0", + }, + { + capabilities: {}, + } + ); + + await this.client.connect(transport); + this.connected = true; + } + + async tools(): Promise> { + if (!this.connected) { + await this.connect(); + } + + const response = await this.client.listTools(); + const toolsMap: Record = {}; + + for (const tool of response.tools) { + // Convert MCP tool schema to CopilotKit MCPTool schema format + const schema = tool.inputSchema ? { + parameters: { + properties: (tool.inputSchema as any).properties || {}, + required: (tool.inputSchema as any).required || [], + jsonSchema: tool.inputSchema + } + } : undefined; + + toolsMap[tool.name] = { + description: tool.description, + schema, + execute: async (args: any) => { + const result = await this.client.callTool({ + name: tool.name, + arguments: args, + }); + + // Return the full result including structuredContent if present + // Check both result.structuredContent and result._meta.structuredContent + const structuredContent = (result as any).structuredContent || result._meta?.structuredContent; + + if (structuredContent) { + return { + content: result.content, + structuredContent + }; + } + return result.content; + }, + }; + } + + return toolsMap; + } + + async close(): Promise { + if (this.connected) { + await this.client.close(); + this.connected = false; + } + } +} diff --git a/copilotkit-server/src/server.ts b/copilotkit-server/src/server.ts new file mode 100644 index 000000000..0ffd73bc7 --- /dev/null +++ b/copilotkit-server/src/server.ts @@ -0,0 +1,84 @@ +import express, { Application } from 'express'; +import cors from 'cors'; +import { + CopilotRuntime, + GoogleGenerativeAIAdapter, + copilotRuntimeNodeHttpEndpoint, +} from '@copilotkit/runtime'; +import { LocalMCPClient } from './mcp-client'; + +// This function will be imported by the main graphql-api server +export function mountCopilotKit(app: Application) { + const serviceAdapter = new GoogleGenerativeAIAdapter({ + model: 'gemini-2.5-flash', + apiKey: process.env.GOOGLE_GENERATIVE_AI_API_KEY || '', + }); + + // Use an environment variable for the gmd command path, defaulting to 'gmd' for production. + const gmdCommand = process.env.GMD_COMMAND_PATH || 'gmd'; + // Configure the MCP server command. + // Since the MCP server is colocalized with the GraphQL API, it can call it locally + const mcpConfig = { + command: gmdCommand, + args: ['mcp', 'serve'], + env: { + GNOMAD_API_URL: process.env.GNOMAD_API_URL || 'http://localhost:8000/api', + }, + }; + + // Create runtime with MCP support + const runtime = new CopilotRuntime({ + // Function to create MCP clients based on configuration + createMCPClient: async (config) => { + // For local MCP servers, use the stdio client + if (config.endpoint === 'local://gnomad') { + const client = new LocalMCPClient(mcpConfig); + await client.connect(); + return client; + } + throw new Error(`Unsupported MCP endpoint: ${config.endpoint}`); + }, + + // Configure which MCP servers are available + mcpServers: [ + { + endpoint: 'local://gnomad', + apiKey: undefined, // Not needed for local servers + }, + ], + }); + + const handler = copilotRuntimeNodeHttpEndpoint({ + endpoint: '/api/copilotkit', + runtime, + serviceAdapter, + }); + + // Define CORS options for the CopilotKit endpoint + const corsOptions = { + origin: [ + 'http://localhost:8008', // local browser dev + 'http://localhost:8010', // local api dev + 'https://gnomad.broadinstitute.org', // production + ], + credentials: true, + }; + + // Mount the handler on the provided Express app with its own CORS middleware + app.use('/api/copilotkit', cors(corsOptions), (req, res, next) => { + (async () => handler(req, res))().catch(next); + }); + + console.log('CopilotKit server mounted on /api/copilotkit'); +} + +// For local development, allow running as a standalone server +if (require.main === module) { + const app = express(); + mountCopilotKit(app); + + const PORT = process.env.COPILOTKIT_PORT || 4001; + app.listen(PORT, () => { + console.log(`CopilotKit server listening on http://localhost:${PORT}/api/copilotkit`); + }); +} diff --git a/copilotkit-server/start.sh b/copilotkit-server/start.sh new file mode 100755 index 000000000..b890f5238 --- /dev/null +++ b/copilotkit-server/start.sh @@ -0,0 +1,19 @@ +#!/bin/bash + +# This script runs the CopilotKit server standalone for local development/testing +# Note: The CopilotKit server code has been moved to graphql-api/src/copilotkit/ + +export GMD_COMMAND_PATH=${HOME}/.grove/bin/gmd +export MENDELIAN_TSV_PATH=/Users/msolomon/code/browser-ecosystem/gmd-api/data/gene-disease-table_8_13_2025.tsv +export GNOMAD_API_URL=${GNOMAD_API_URL:-http://localhost:8010/api} + +export NODE_ENV=${NODE_ENV:-development} + +if [[ $NODE_ENV == "development" ]]; then + npx ts-node ../graphql-api/src/copilotkit/server.ts +else + echo "ERROR: Production mode not supported for standalone copilotkit-server" + echo "The CopilotKit server is now integrated into the GraphQL API." + echo "For production, deploy the graphql-api which includes CopilotKit." + exit 1 +fi diff --git a/deploy/dockerfiles/browser/api.dockerfile b/deploy/dockerfiles/browser/api.dockerfile index 5a0ee2d8e..6d877c947 100644 --- a/deploy/dockerfiles/browser/api.dockerfile +++ b/deploy/dockerfiles/browser/api.dockerfile @@ -19,11 +19,17 @@ RUN pnpm install --production --frozen-lockfile # Copy source COPY --chown=node:node dataset-metadata /app/dataset-metadata COPY --chown=node:node graphql-api/src /app/graphql-api/src -COPY --chown=node:node tsconfig.json /app/graphql-api/tsconfig.json -COPY --chown=node:node tsconfig.build.json /app/graphql-api/tsconfig.build.json +COPY --chown=node:node browser/src/missingContent.ts /app/browser/src/missingContent.ts +COPY --chown=node:node tsconfig.json /app/tsconfig.json +COPY --chown=node:node tsconfig.build.json /app/tsconfig.build.json # Build JS from TS source -RUN pnpm tsc -p /app/graphql-api/tsconfig.build.json +RUN pnpm tsc -p /app/tsconfig.build.json + +# Copy external artifacts and set permissions +COPY --chown=node:node bin/gmd /usr/local/bin/gmd +RUN chmod +x /usr/local/bin/gmd +COPY --chown=node:node resources/gene-disease-table.tsv /app/resources/gene-disease-table.tsv # Copy static data into place COPY --chown=node:node graphql-api/static_data /app/static_data diff --git a/deploy/dockerfiles/browser/api.dockerfile.dockerignore b/deploy/dockerfiles/browser/api.dockerfile.dockerignore index 779200d8f..205756af2 100644 --- a/deploy/dockerfiles/browser/api.dockerfile.dockerignore +++ b/deploy/dockerfiles/browser/api.dockerfile.dockerignore @@ -1,10 +1,14 @@ * !dataset-metadata +dataset-metadata/**/*.js !graphql-api/package.json !graphql-api/src +!browser/src/missingContent.ts !tsconfig.json !tsconfig.build.json !pnpm-lock.yaml !pnpm-workspace-api-docker.yaml !package.json !graphql-api/static_data +!bin +!resources diff --git a/deploy/dockerfiles/browser/browser.nginx.conf b/deploy/dockerfiles/browser/browser.nginx.conf index ef6ee880f..845c488fe 100644 --- a/deploy/dockerfiles/browser/browser.nginx.conf +++ b/deploy/dockerfiles/browser/browser.nginx.conf @@ -47,6 +47,14 @@ server { # GraphQL API # ############### + # CopilotKit endpoint - no caching for AI chat + location /api/copilotkit { + proxy_pass $API_URL; + proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; + proxy_no_cache 1; + proxy_cache_bypass 1; + } + location /api/ { # Proxy requests to api container # $API_URL is replaced at runtime with the API_URL environment variable. diff --git a/deploy/docs/Deployment.md b/deploy/docs/Deployment.md index ca39575b2..64e39e02e 100644 --- a/deploy/docs/Deployment.md +++ b/deploy/docs/Deployment.md @@ -136,6 +136,60 @@ Before deploying a new version of the browser, either a demo, or to production: - `kubectl config get-contexts` to see your configs cluster - `kubectl config use-context ` to set your configs cluster +7. **Configure and prepare CopilotKit build artifacts** (required for API image builds) + + The gnomAD API now includes the CopilotKit assistant server, which requires two external artifacts to be included in the Docker image: + + - The `gmd` binary + - The Mendelian disease TSV file + + **First-time setup:** + + Create a `.env` file in the repository root with your local paths: + + ``` + cp .env.example .env + ``` + + Edit `.env` and set the following variables: + + ```bash + GMD_BINARY_PATH=/path/to/your/gmd/binary + MENDELIAN_TSV_PATH=/path/to/gene-disease-table.tsv + ``` + + For example: + ```bash + GMD_BINARY_PATH=/Users/yourname/.grove/bin/gmd + MENDELIAN_TSV_PATH=/Users/yourname/data/gene-disease-table.tsv + ``` + + **Before each Docker build:** + + Run the preparation script to copy artifacts into the build context: + + ``` + ./deploy/scripts/prepare-copilotkit-artifacts.sh + ``` + + This will create `bin/gmd` and `resources/gene-disease-table.tsv` from the paths configured in your `.env` file. + + Note: The `.env`, `bin/`, and `resources/` files are in `.gitignore` and should not be committed to the repository. + +8. **Ensure Google AI API Key secret exists in Kubernetes** (one-time setup) + + The CopilotKit server requires a Google Generative AI API key. Create the secret if it doesn't exist: + + ``` + kubectl create secret generic google-generative-ai-api-key \ + --from-literal=api_key=YOUR_GOOGLE_AI_API_KEY + ``` + + To verify the secret exists: + ``` + kubectl get secret google-generative-ai-api-key + ``` + ## Create Demo Browser Deployment Demo deployments are staging environments independently that let stakeholders preview and approve features before the features go to production. diff --git a/deploy/manifests/browser/base/api.deployment.yaml b/deploy/manifests/browser/base/api.deployment.yaml index 95866fc67..42e96fe06 100644 --- a/deploy/manifests/browser/base/api.deployment.yaml +++ b/deploy/manifests/browser/base/api.deployment.yaml @@ -61,6 +61,21 @@ spec: value: 'true' - name: NODE_OPTIONS value: '--max-old-space-size=10240' + - name: MENDELIAN_TSV_PATH + value: '/app/resources/gene-disease-table.tsv' + # HOME is required for gmd to initialize correctly if it needs to write to a home directory. + - name: HOME + value: '/app' + # The Google AI API key must be provided via a Kubernetes secret. + - name: GOOGLE_GENERATIVE_AI_API_KEY + valueFrom: + secretKeyRef: + # This secret must be created in the cluster manually. + name: google-generative-ai-api-key + key: api_key + # MCP server calls the GraphQL API locally since they're colocalized + - name: GNOMAD_API_URL + value: 'http://localhost:8000/api' ports: - name: http containerPort: 8000 diff --git a/deploy/scripts/prepare-copilotkit-artifacts.sh b/deploy/scripts/prepare-copilotkit-artifacts.sh new file mode 100755 index 000000000..9fe62ea2b --- /dev/null +++ b/deploy/scripts/prepare-copilotkit-artifacts.sh @@ -0,0 +1,116 @@ +#!/bin/bash + +# Prepare CopilotKit artifacts for Docker build +# This script copies the required gmd binary and Mendelian TSV file +# into the repository structure for inclusion in the API Docker image +# +# Configuration is read from a .env file in the repository root. +# See .env.example for required variables. + +set -e + +REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/../.." && pwd)" +cd "$REPO_ROOT" + +# Load environment variables from .env file +if [ ! -f ".env" ] && [ ! -f ".env.fish" ]; then + echo "ERROR: .env or .env.fish file not found" + echo + echo "Please create an environment file in the repository root with the required configuration." + echo "You can copy .env.example as a starting point:" + echo + echo " For bash/zsh: cp .env.example .env" + echo " For fish shell: cp .env.example .env.fish (and convert to fish syntax)" + echo + echo "Then edit your env file and set the following variables:" + echo " - GMD_BINARY_PATH: Path to the gmd binary on your build machine" + echo " - MENDELIAN_TSV_PATH: Path to the Mendelian disease TSV file" + echo + exit 1 +fi + +if [ -f ".env" ]; then + echo "Loading configuration from .env..." + # Export variables from .env, ignoring comments and empty lines + set -a + source .env + set +a + echo +else + echo "NOTE: Using .env.fish - ensure variables are exported before running this script" + echo " Run: source .env.fish" + echo +fi + +# Validate required variables +MISSING_VARS=() + +if [ -z "$GMD_BINARY_PATH" ]; then + MISSING_VARS+=("GMD_BINARY_PATH") +fi + +if [ -z "$MENDELIAN_TSV_PATH" ]; then + MISSING_VARS+=("MENDELIAN_TSV_PATH") +fi + +if [ ${#MISSING_VARS[@]} -gt 0 ]; then + echo "ERROR: Required environment variables are not set in .env:" + for var in "${MISSING_VARS[@]}"; do + echo " - $var" + done + echo + echo "Please edit your .env file and set these variables." + echo "See .env.example for reference." + exit 1 +fi + +echo "Preparing CopilotKit build artifacts..." +echo + +# Create directories +echo "Creating bin/ and resources/ directories..." +mkdir -p bin resources + +# Build gmd binary for Linux AMD64 +echo "Building gmd binary for Linux AMD64..." +GMD_SOURCE_DIR="$(dirname "$GMD_BINARY_PATH")/../.." +if [ ! -d "$GMD_SOURCE_DIR" ]; then + echo "ERROR: Cannot find gmd source directory at: $GMD_SOURCE_DIR" + echo + echo "Please check the GMD_BINARY_PATH in your .env file." + exit 1 +fi + +(cd "$GMD_SOURCE_DIR" && GOOS=linux GOARCH=amd64 go build -o "$REPO_ROOT/bin/gmd" .) +if [ $? -ne 0 ]; then + echo "ERROR: Failed to build gmd binary" + exit 1 +fi + +chmod +x bin/gmd +echo "✓ gmd binary built for linux/amd64 at bin/gmd" +echo + +# Copy Mendelian TSV file +if [ ! -f "$MENDELIAN_TSV_PATH" ]; then + echo "ERROR: Mendelian TSV file not found at: $MENDELIAN_TSV_PATH" + echo + echo "Please check the MENDELIAN_TSV_PATH in your .env file." + exit 1 +fi + +echo "Copying Mendelian TSV from $MENDELIAN_TSV_PATH..." +cp "$MENDELIAN_TSV_PATH" resources/gene-disease-table.tsv +echo "✓ Mendelian TSV copied to resources/gene-disease-table.tsv" +echo + +# Verify artifacts +echo "Verification:" +echo " gmd binary: $(ls -lh bin/gmd | awk '{print $5}')" +echo " Mendelian TSV: $(ls -lh resources/gene-disease-table.tsv | awk '{print $5}')" +echo + +echo "✓ CopilotKit artifacts are ready for Docker build" +echo +echo "You can now build the API Docker image with:" +echo " ./deployctl images build --push" diff --git a/graphql-api/package.json b/graphql-api/package.json index 525d8e2f0..01973ba86 100644 --- a/graphql-api/package.json +++ b/graphql-api/package.json @@ -3,13 +3,16 @@ "version": "2.0.0", "private": true, "dependencies": { + "@copilotkit/runtime": "^1.10.6", "@elastic/elasticsearch": "6", "@gnomad/dataset-metadata": "*", "@gnomad/identifiers": "3.0.0", "@google-cloud/storage": "^7.7.0", + "@google/generative-ai": "^0.21.0", "@graphql-tools/load-files": "^6.0.12", "@graphql-tools/merge": "^6.0.12", "@graphql-tools/schema": "^6.0.12", + "@modelcontextprotocol/sdk": "^1.17.4", "@types/compression": "^1.7.2", "@types/cors": "^2.8.13", "@types/express": "^4.17.17", @@ -22,7 +25,7 @@ "cors": "^2.8.5", "express": "^4.20.0", "express-graphql": "^0.12.0", - "graphql": "^15.3.0", + "graphql": "^16.8.1", "graphql-query-complexity": "^0.7.2", "http-errors": "1.8.0", "ioredis": "^5.3.2", diff --git a/graphql-api/src/app.ts b/graphql-api/src/app.ts index f48a45f41..92be99710 100644 --- a/graphql-api/src/app.ts +++ b/graphql-api/src/app.ts @@ -81,6 +81,18 @@ loadWhitelist() const context = { esClient } +// Import and mount the CopilotKit endpoint (if API key is available) +import { mountCopilotKit } from './copilotkit/server' +if (process.env.GOOGLE_GENERATIVE_AI_API_KEY) { + try { + mountCopilotKit(app) + } catch (error) { + logger.error(error) + } +} else { + logger.info('CopilotKit endpoint not mounted (GOOGLE_GENERATIVE_AI_API_KEY not set)') +} + app.use('/api/', graphQLApi({ context })) app.listen(config.PORT) diff --git a/graphql-api/src/copilotkit/mcp-client.ts b/graphql-api/src/copilotkit/mcp-client.ts new file mode 100644 index 000000000..9166bc02c --- /dev/null +++ b/graphql-api/src/copilotkit/mcp-client.ts @@ -0,0 +1,144 @@ +import { Client } from "@modelcontextprotocol/sdk/client/index.js"; +import { StdioClientTransport } from "@modelcontextprotocol/sdk/client/stdio.js"; +import { MCPClient, MCPTool } from "@copilotkit/runtime"; +import logger from '../logger'; + +export class LocalMCPClient implements MCPClient { + private client!: Client; + private connected = false; + + constructor(private config: { command: string; args: string[]; env?: Record }) {} + + async connect(): Promise { + logger.info({ + message: 'MCP client connecting', + command: this.config.command, + args: this.config.args, + }); + + // Build environment variables, filtering out undefined values + const env: Record = {}; + + // Add process.env values, filtering undefined + for (const [key, value] of Object.entries(process.env)) { + if (value !== undefined) { + env[key] = value; + } + } + + // Add config env values, overriding process.env + if (this.config.env) { + Object.assign(env, this.config.env); + } + + const transport = new StdioClientTransport({ + command: this.config.command, + args: this.config.args, + env, + }); + + this.client = new Client( + { + name: "copilotkit-client", + version: "1.0.0", + }, + { + capabilities: {}, + } + ); + + await this.client.connect(transport); + this.connected = true; + logger.info('MCP client connected successfully'); + } + + async tools(): Promise> { + if (!this.connected) { + await this.connect(); + } + + const response = await this.client.listTools(); + const toolsMap: Record = {}; + + logger.info({ + message: 'MCP tools loaded', + toolCount: response.tools.length, + tools: response.tools.map(t => t.name), + }); + + for (const tool of response.tools) { + // Convert MCP tool schema to CopilotKit MCPTool schema format + const schema = tool.inputSchema ? { + parameters: { + properties: (tool.inputSchema as any).properties || {}, + required: (tool.inputSchema as any).required || [], + jsonSchema: tool.inputSchema + } + } : undefined; + + toolsMap[tool.name] = { + description: tool.description, + schema, + execute: async (args: any) => { + const startTime = Date.now(); + logger.info({ + message: 'MCP tool execution started', + tool: tool.name, + args, + }); + + try { + const result = await this.client.callTool({ + name: tool.name, + arguments: args, + }); + const duration = Date.now() - startTime; + + logger.info({ + message: 'MCP tool execution completed', + tool: tool.name, + duration: `${duration}ms`, + hasStructuredContent: !!(result as any).structuredContent, + }); + + // Return structured content if available + const structuredContent = (result as any).structuredContent; + if (structuredContent) { + logger.info({ + message: 'MCP tool returned structured content', + tool: tool.name, + structuredContentKeys: Object.keys(structuredContent), + }); + return { + content: result.content, + structuredContent, + }; + } + + return result.content; + } catch (error: any) { + const duration = Date.now() - startTime; + logger.error({ + message: 'MCP tool execution failed', + tool: tool.name, + duration: `${duration}ms`, + error: error.message, + }); + throw error; + } + }, + }; + } + + return toolsMap; + } + + async close(): Promise { + if (this.connected) { + logger.info('MCP client closing'); + await this.client.close(); + this.connected = false; + logger.info('MCP client closed'); + } + } +} \ No newline at end of file diff --git a/graphql-api/src/copilotkit/server.ts b/graphql-api/src/copilotkit/server.ts new file mode 100644 index 000000000..9092d56c7 --- /dev/null +++ b/graphql-api/src/copilotkit/server.ts @@ -0,0 +1,137 @@ +import express, { Application } from 'express'; +import cors from 'cors'; +import { + CopilotRuntime, + GoogleGenerativeAIAdapter, + copilotRuntimeNodeHttpEndpoint, +} from '@copilotkit/runtime'; +import { LocalMCPClient } from './mcp-client'; +import logger from '../logger'; + +// This function will be imported by the main graphql-api server +export function mountCopilotKit(app: Application) { + const serviceAdapter = new GoogleGenerativeAIAdapter({ + model: 'gemini-2.5-flash', + apiKey: process.env.GOOGLE_GENERATIVE_AI_API_KEY || '', + }); + + // Use an environment variable for the gmd command path, defaulting to 'gmd' for production. + const gmdCommand = process.env.GMD_COMMAND_PATH || 'gmd'; + // Configure the MCP server command. + // Since the MCP server is colocalized with the GraphQL API, it can call it locally + const mcpConfig = { + command: gmdCommand, + args: ['mcp', 'serve'], + env: { + GNOMAD_API_URL: process.env.GNOMAD_API_URL || 'http://localhost:8000/api', + }, + }; + + // Create a single shared MCP client instance + let sharedMCPClient: LocalMCPClient | null = null; + + // Create runtime with MCP support + const runtime = new CopilotRuntime({ + // Function to create MCP clients based on configuration + createMCPClient: async (config) => { + // For local MCP servers, use the stdio client + if (config.endpoint === 'local://gnomad') { + // Reuse the same client instance across all requests + if (!sharedMCPClient) { + sharedMCPClient = new LocalMCPClient(mcpConfig); + await sharedMCPClient.connect(); + } + return sharedMCPClient; + } + throw new Error(`Unsupported MCP endpoint: ${config.endpoint}`); + }, + + // Configure which MCP servers are available + mcpServers: [ + { + endpoint: 'local://gnomad', + apiKey: undefined, // Not needed for local servers + }, + ], + }); + + const handler = copilotRuntimeNodeHttpEndpoint({ + endpoint: '/api/copilotkit', + runtime, + serviceAdapter, + }); + + // Define CORS options for the CopilotKit endpoint + const corsOptions = { + origin: [ + 'http://localhost:8008', // local browser dev + 'http://localhost:8010', // local api dev + 'https://gnomad.broadinstitute.org', // production + ], + credentials: true, + }; + + // Mount the handler on the provided Express app with its own CORS middleware + app.use('/api/copilotkit', cors(corsOptions), (req, res, next) => { + const startTime = Date.now(); + const requestId = Math.random().toString(36).substring(7); + + // Log the request with more detail about the conversation + let threadId, messageCount; + try { + const body = req.body || {}; + threadId = body.threadId; + messageCount = body.messages?.length || 0; + } catch (e) { + // ignore parsing errors + } + + logger.info({ + message: 'CopilotKit request', + requestId, + threadId, + messageCount, + method: req.method, + path: req.path, + userAgent: req.headers['user-agent'], + }); + + // Wrap the response to log completion + const originalSend = res.send; + res.send = function(data) { + const duration = Date.now() - startTime; + logger.info({ + message: 'CopilotKit response', + method: req.method, + path: req.path, + statusCode: res.statusCode, + duration: `${duration}ms`, + }); + return originalSend.call(this, data); + }; + + (async () => handler(req, res))().catch((error) => { + logger.error({ + message: 'CopilotKit error', + error: error.message, + stack: error.stack, + method: req.method, + path: req.path, + }); + next(error); + }); + }); + + logger.info('CopilotKit server mounted on /api/copilotkit'); +} + +// For local development, allow running as a standalone server +if (require.main === module) { + const app = express(); + mountCopilotKit(app); + + const PORT = process.env.COPILOTKIT_PORT || 4001; + app.listen(PORT, () => { + console.log(`CopilotKit server listening on http://localhost:${PORT}/api/copilotkit`); + }); +} diff --git a/graphql-api/src/queries/clinvar-variant-queries.ts b/graphql-api/src/queries/clinvar-variant-queries.ts index 97922efc4..d79bfba3c 100644 --- a/graphql-api/src/queries/clinvar-variant-queries.ts +++ b/graphql-api/src/queries/clinvar-variant-queries.ts @@ -25,7 +25,7 @@ const _fetchClinvarReleaseDate = async (esClient: any) => { fetchIndexMetadata(esClient, CLINVAR_VARIANT_INDICES.GRCh38), ]) - const releaseDates = metadata.map((m) => m.table_globals.clinvar_release_date) + const releaseDates = metadata.map((m: any) => m.table_globals.clinvar_release_date) if (releaseDates[0] !== releaseDates[1]) { logger.error({ diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 0237e55e4..6c3ed3351 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -147,6 +147,15 @@ importers: browser: dependencies: + '@copilotkit/react-core': + specifier: ^1.10.6 + version: 1.10.6(@types/react@18.3.21)(react-dom@18.3.1)(react@18.3.1) + '@copilotkit/react-textarea': + specifier: ^1.10.6 + version: 1.10.6(@types/react-dom@18.3.7)(@types/react@18.3.21)(react-dom@18.3.1)(react@18.3.1) + '@copilotkit/react-ui': + specifier: ^1.10.6 + version: 1.10.6(@types/react@18.3.21)(react-dom@18.3.1)(react@18.3.1) '@fortawesome/fontawesome-free': specifier: ^5.8.1 version: 5.15.4 @@ -362,10 +371,40 @@ importers: specifier: ^5.2.1 version: 5.2.1(webpack-cli@5.1.4)(webpack@5.94.0) + copilotkit-server: + dependencies: + '@copilotkit/runtime': + specifier: ^1.10.3 + version: 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false + /uuid@10.0.0: + resolution: {integrity: sha512-8XkAphELsDnEGrDxUOHB3RGvXz6TeuYSGEZBOjtTtPm2lwhGBjLgOzLHB63IUWfBpNucQjND6d3AOudO+H3RWQ==} + hasBin: true + dev: false + + /uuid@11.1.0: + resolution: {integrity: sha512-0/A9rDy9P7cJ+8w1c9WD9V//9Wj15Ce2MPz8Ri6032usz+NfePxx5AcN3bN+r6ZL6jEo066/yNYB3tn4pQEx+A==} + hasBin: true + dev: false + /uuid@2.0.3: resolution: {integrity: sha512-FULf7fayPdpASncVy4DLh3xydlXEJJpvIELjYjNeQWYUZ9pclcpvCZSr2gkmN2FrrGcI7G/cJsIEwk5/8vfXpg==} deprecated: Please upgrade to version 7 or higher. Older versions may use Math.random() in certain circumstances, which is known to be problematic. See https://v8.dev/blog/math-random for details. @@ -13879,6 +20000,17 @@ packages: hasBin: true dev: false + /uvu@0.5.6: + resolution: {integrity: sha512-+g8ENReyr8YsOc6fv/NVJs2vFdHBnBNdfE49rshrTzDWOlUx4Gq7KOS2GD8eqhy2j+Ejq29+SbKH8yjkAqXqoA==} + engines: {node: '>=8'} + hasBin: true + dependencies: + dequal: 2.0.3 + diff: 5.2.0 + kleur: 4.1.5 + sade: 1.8.1 + dev: false + /v8-compile-cache-lib@3.0.1: resolution: {integrity: sha512-wa7YjyUGfNZngI/vtK0UHAN+lgDCxBPCylVXGp0zu59Fz5aiGtNXaq3DhIov063MorB+VfufLh3JlF2KdTK3xg==} dev: true @@ -13902,6 +20034,11 @@ packages: spdx-expression-parse: 3.0.1 dev: true + /validator@13.15.23: + resolution: {integrity: sha512-4yoz1kEWqUjzi5zsPbAS/903QXSYp0UOtHsPpp7p9rHAw/W+dkInskAE386Fat3oKRROwO98d9ZB0G4cObgUyw==} + engines: {node: '>= 0.10'} + dev: false + /value-equal@1.0.1: resolution: {integrity: sha512-NOJ6JZCAWr0zlxZt+xqCHNTEKOsrks2HQd4MqhP1qy4z1SkbEP467eNx6TgDKXMvUOb+OENfJCZwM+16n7fRfw==} dev: false @@ -13919,6 +20056,13 @@ packages: resolution: {integrity: sha512-sSFdyCP3G6Ka0CEmN83A2YCMKIieHx0EDaj5IDP4g1pa5ZJ4FJDvpO0WODLxo4LUX4oe52gmSCK7Jw4SBghqxA==} dev: false + /vfile-location@5.0.3: + resolution: {integrity: sha512-5yXvWDEgqeiYiBe1lbxYF7UMAIm/IcopxMHrMQDq3nvKcjPKIhZklUKL+AE7J7uApI4kwe2snsK+eI6UTj9EHg==} + dependencies: + '@types/unist': 3.0.0 + vfile: 6.0.3 + dev: false + /vfile-message@1.1.1: resolution: {integrity: sha512-1WmsopSGhWt5laNir+633LszXvZ+Z/lxveBf6yhGsqnQIhlhzooZae7zV6YVM1Sdkw68dtAW3ow0pOdPANugvA==} dependencies: @@ -13932,6 +20076,13 @@ packages: unist-util-stringify-position: 2.0.3 dev: true + /vfile-message@3.1.4: + resolution: {integrity: sha512-fa0Z6P8HUrQN4BZaX05SIVXic+7kE3b05PWAtPuYP9QLHsLKYR7/AlLW3NtOrpXRLeawpDLMsVkmk5DG0NXgWw==} + dependencies: + '@types/unist': 2.0.8 + unist-util-stringify-position: 3.0.3 + dev: false + /vfile-message@4.0.2: resolution: {integrity: sha512-jRDZ1IMLttGj41KcZvlrYAaI3CfqpLpfpf+Mfig13viT6NKvRzWZ+lXz0Y5D60w6uJIBAOGq9mSHf0gktF0duw==} dependencies: @@ -13957,6 +20108,22 @@ packages: vfile-message: 2.0.4 dev: true + /vfile@5.3.7: + resolution: {integrity: sha512-r7qlzkgErKjobAmyNIkkSpizsFPYiUPuJb5pNW1RB4JcYVZhs4lIbVqk8XPk033CV/1z8ss5pkax8SuhGpcG8g==} + dependencies: + '@types/unist': 2.0.8 + is-buffer: 2.0.5 + unist-util-stringify-position: 3.0.3 + vfile-message: 3.1.4 + dev: false + + /vfile@6.0.3: + resolution: {integrity: sha512-KzIbH/9tXat2u30jf+smMwFCsno4wHVdNmzFyL+T/L3UGqqk6JKfVqOFOZEpZSHADH1k40ab6NUIXZq422ov3Q==} + dependencies: + '@types/unist': 3.0.0 + vfile-message: 4.0.2 + dev: false + /w3c-xmlserializer@4.0.0: resolution: {integrity: sha512-d+BFHzbiCx6zGfz0HyQ6Rg69w9k19nviJspaj4yNscGjrHu94sVP+aRm75yEbCh+r2/yR+7q6hux9LVtbuTGBw==} engines: {node: '>=14'} @@ -13988,6 +20155,36 @@ packages: dependencies: minimalistic-assert: 1.0.1 + /weaviate-client@3.9.0: + resolution: {integrity: sha512-7qwg7YONAaT4zWnohLrFdzky+rZegVe76J+Tky/+7tuyvjFpdKgSrdqI/wPDh8aji0ZGZrL4DdGwGfFnZ+uV4w==} + engines: {node: '>=18.0.0'} + dependencies: + abort-controller-x: 0.4.3 + graphql: 16.12.0 + graphql-request: 6.1.0(graphql@16.12.0) + long: 5.3.2 + nice-grpc: 2.1.14 + nice-grpc-client-middleware-retry: 3.1.13 + nice-grpc-common: 2.0.2 + uuid: 9.0.1 + transitivePeerDependencies: + - 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