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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>PCGL Data Acquisition Workflow</title>
<script src="https://cdnjs.cloudflare.com/ajax/libs/react/18.2.0/umd/react.production.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/react-dom/18.2.0/umd/react-dom.production.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/babel-standalone/7.23.5/babel.min.js"></script>
<link href="https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600;700;800&display=swap" rel="stylesheet">
<style>
* { box-sizing: border-box; margin: 0; padding: 0; }
body { font-family: 'Inter', -apple-system, BlinkMacSystemFont, sans-serif; }
</style>
</head>
<body>
<div id="root"></div>
<script type="text/babel">
const PCGLDataAcquisitionWorkflow = () => {
const colors = {
discoveryPhase: '#0d9488',
accessPhase: '#7c3aed',
authPhase: '#dc2626',
downloadPhase: '#2563eb',
researcher: '#059669',
dacMember: '#d97706',
dacChair: '#ea580c',
instRep: '#0891b2',
system: '#6366f1',
uiMethod: '#8b5cf6',
apiMethod: '#f59e0b',
cliMethod: '#10b981',
background: '#0f172a',
cardBg: '#1e293b',
cardBgAlt: '#334155',
textPrimary: '#f1f5f9',
textSecondary: '#94a3b8',
textAccent: '#38bdf8',
border: '#475569',
connector: '#64748b',
highlight: '#fbbf24',
success: '#22c55e',
};
const Arrow = ({ direction = 'down', color = colors.connector, size = 24 }) => {
if (direction === 'down') {
return (
<svg width={size} height={size} viewBox="0 0 24 24" fill="none">
<path d="M12 4v16m0 0l-6-6m6 6l6-6" stroke={color} strokeWidth="2" strokeLinecap="round" strokeLinejoin="round"/>
</svg>
);
}
if (direction === 'right') {
return (
<svg width={size} height={size} viewBox="0 0 24 24" fill="none">
<path d="M4 12h16m0 0l-6-6m6 6l-6 6" stroke={color} strokeWidth="2" strokeLinecap="round" strokeLinejoin="round"/>
</svg>
);
}
return null;
};
const Badge = ({ children, color }) => (
<span style={{
display: 'inline-block',
padding: '2px 8px',
borderRadius: '9999px',
fontSize: '10px',
fontWeight: '600',
backgroundColor: color,
color: '#fff',
textTransform: 'uppercase',
letterSpacing: '0.5px',
}}>
{children}
</span>
);
const StepCard = ({ number, title, description, badges = [], tools = [], color, isOptional = false, isFuture = false }) => (
<div style={{
backgroundColor: colors.cardBg,
borderRadius: '12px',
padding: '18px',
border: isFuture ? `2px dashed ${color}` : `2px solid ${color}`,
position: 'relative',
minWidth: '260px',
maxWidth: '300px',
boxShadow: `0 4px 20px ${color}33`,
opacity: isFuture ? 0.7 : 1,
}}>
{isFuture && (
<div style={{
position: 'absolute',
top: '-10px',
right: '10px',
backgroundColor: colors.highlight,
color: colors.background,
padding: '2px 10px',
borderRadius: '4px',
fontSize: '9px',
fontWeight: '700',
textTransform: 'uppercase',
}}>
Future
</div>
)}
<div style={{
display: 'flex',
alignItems: 'center',
gap: '10px',
marginBottom: '10px',
}}>
<div style={{
width: '32px',
height: '32px',
borderRadius: '50%',
backgroundColor: color,
display: 'flex',
alignItems: 'center',
justifyContent: 'center',
fontWeight: '700',
fontSize: '14px',
color: '#fff',
flexShrink: 0,
}}>
{number}
</div>
<h3 style={{
margin: 0,
fontSize: '14px',
fontWeight: '700',
color: colors.textPrimary,
lineHeight: 1.3,
}}>{title}</h3>
</div>
<p style={{
margin: '0 0 10px 0',
fontSize: '12px',
color: colors.textSecondary,
lineHeight: '1.5',
}}>{description}</p>
{badges.length > 0 && (
<div style={{ display: 'flex', gap: '4px', flexWrap: 'wrap', marginBottom: '8px' }}>
{badges.map((badge, i) => (
<Badge key={i} color={badge.color}>{badge.label}</Badge>
))}
</div>
)}
{tools.length > 0 && (
<div style={{
marginTop: '10px',
paddingTop: '10px',
borderTop: `1px solid ${colors.border}`,
}}>
<div style={{ fontSize: '9px', color: colors.textSecondary, marginBottom: '4px', textTransform: 'uppercase', letterSpacing: '0.5px' }}>
Tools / APIs
</div>
{tools.map((tool, i) => (
<div key={i} style={{
fontSize: '10px',
color: colors.textAccent,
fontFamily: 'monospace',
backgroundColor: colors.cardBgAlt,
padding: '3px 6px',
borderRadius: '4px',
marginBottom: '3px',
}}>
{tool}
</div>
))}
</div>
)}
</div>
);
const PhaseHeader = ({ title, subtitle, color, icon }) => (
<div style={{
backgroundColor: color,
padding: '12px 20px',
borderRadius: '8px 8px 0 0',
display: 'flex',
alignItems: 'center',
gap: '12px',
}}>
<span style={{ fontSize: '24px' }}>{icon}</span>
<div>
<h2 style={{
margin: 0,
fontSize: '16px',
fontWeight: '700',
color: '#fff',
letterSpacing: '0.5px',
}}>{title}</h2>
{subtitle && (
<p style={{
margin: '2px 0 0 0',
fontSize: '11px',
color: 'rgba(255,255,255,0.8)',
}}>{subtitle}</p>
)}
</div>
</div>
);
const MethodOption = ({ title, description, icon, color, tools = [], isFuture = false }) => (
<div style={{
backgroundColor: colors.cardBgAlt,
borderRadius: '8px',
padding: '14px',
border: isFuture ? `2px dashed ${color}` : `1px solid ${color}`,
flex: 1,
minWidth: '200px',
opacity: isFuture ? 0.7 : 1,
position: 'relative',
}}>
{isFuture && (
<div style={{
position: 'absolute',
top: '-10px',
right: '10px',
backgroundColor: colors.highlight,
color: colors.background,
padding: '2px 10px',
borderRadius: '4px',
fontSize: '9px',
fontWeight: '700',
textTransform: 'uppercase',
}}>
Future
</div>
)}
<div style={{ display: 'flex', alignItems: 'center', gap: '8px', marginBottom: '8px' }}>
<span style={{ fontSize: '18px' }}>{icon}</span>
<span style={{ fontSize: '13px', fontWeight: '600', color: color }}>{title}</span>
</div>
<p style={{ fontSize: '11px', color: colors.textSecondary, margin: '0 0 8px 0' }}>{description}</p>
{tools.map((tool, i) => (
<div key={i} style={{
fontSize: '10px',
color: colors.textAccent,
fontFamily: 'monospace',
backgroundColor: colors.cardBg,
padding: '3px 6px',
borderRadius: '4px',
marginBottom: '2px',
}}>
{tool}
</div>
))}
</div>
);
return (
<div style={{
fontFamily: "'Inter', -apple-system, BlinkMacSystemFont, sans-serif",
backgroundColor: colors.background,
minHeight: '100vh',
padding: '40px',
color: colors.textPrimary,
}}>
{/* Header */}
<div style={{ textAlign: 'center', marginBottom: '36px' }}>
<h1 style={{
fontSize: '30px',
fontWeight: '800',
margin: '0 0 8px 0',
background: 'linear-gradient(135deg, #22d3ee, #a78bfa)',
WebkitBackgroundClip: 'text',
WebkitTextFillColor: 'transparent',
letterSpacing: '-0.5px',
}}>
PCGL Data Acquisition Workflow
</h1>
</div>
{/* Legend */}
<div style={{
display: 'flex',
justifyContent: 'center',
gap: '20px',
marginBottom: '36px',
flexWrap: 'wrap',
}}>
<div style={{ display: 'flex', alignItems: 'center', gap: '6px' }}>
<div style={{ width: '14px', height: '14px', backgroundColor: colors.researcher, borderRadius: '3px' }}/>
<span style={{ fontSize: '11px', color: colors.textSecondary }}>Data Seeker / Researcher</span>
</div>
<div style={{ display: 'flex', alignItems: 'center', gap: '6px' }}>
<div style={{ width: '14px', height: '14px', backgroundColor: colors.instRep, borderRadius: '3px' }}/>
<span style={{ fontSize: '11px', color: colors.textSecondary }}>Institutional Rep</span>
</div>
<div style={{ display: 'flex', alignItems: 'center', gap: '6px' }}>
<div style={{ width: '14px', height: '14px', backgroundColor: colors.dacMember, borderRadius: '3px' }}/>
<span style={{ fontSize: '11px', color: colors.textSecondary }}>DAC Member</span>
</div>
<div style={{ display: 'flex', alignItems: 'center', gap: '6px' }}>
<div style={{ width: '14px', height: '14px', backgroundColor: colors.dacChair, borderRadius: '3px' }}/>
<span style={{ fontSize: '11px', color: colors.textSecondary }}>DAC Chair</span>
</div>
<div style={{ display: 'flex', alignItems: 'center', gap: '6px' }}>
<div style={{ width: '14px', height: '14px', backgroundColor: colors.system, borderRadius: '3px' }}/>
<span style={{ fontSize: '11px', color: colors.textSecondary }}>System / Automated</span>
</div>
</div>
<div style={{ maxWidth: '1300px', margin: '0 auto' }}>
{/* Phase 1: Discovery */}
<div style={{ marginBottom: '28px' }}>
<PhaseHeader
title="PHASE 1: Data Discovery"
subtitle="Explore and identify datasets of interest"
color={colors.discoveryPhase}
icon="🔍"
/>
<div style={{
backgroundColor: colors.cardBg,
borderRadius: '0 0 12px 12px',
padding: '20px',
border: `1px solid ${colors.border}`,
borderTop: 'none',
}}>
<div style={{ marginBottom: '20px' }}>
<div style={{ fontSize: '12px', color: colors.textSecondary, marginBottom: '12px', fontWeight: '600' }}>
Choose Your Discovery Method:
</div>
<div style={{ display: 'flex', gap: '16px', flexWrap: 'wrap' }}>
<MethodOption
title="Research Portal UI"
description="Interactive web interface for browsing and searching datasets with aggregate views."
icon="🖥️"
color={colors.uiMethod}
tools={['Data Catalogue', 'Search & Filter', 'Bilingual Interface']}
/>
<MethodOption
title="Beacon v2 API"
description="Programmatic discovery via GA4GH standard API for integration with external tools."
icon="📡"
color={colors.apiMethod}
tools={['REST API', 'Federated Queries']}
/>
<MethodOption
title="3rd Party Platforms"
description="Discover PCGL data through integrated platforms like EGA, gnomAD, or community tools."
icon="🌐"
color={colors.cliMethod}
tools={['EGA/CGA Discovery', 'Data Access APIs']}
isFuture={true}
/>
</div>
</div>
<div style={{
display: 'flex',
justifyContent: 'center',
gap: '16px',
flexWrap: 'wrap',
alignItems: 'center',
}}>
<StepCard
number="1.1"
title="Browse Aggregate Data"
description="Access fully public aggregate views without login. See dataset counts, study summaries, and basic statistics."
badges={[
{ label: 'Researcher', color: colors.researcher },
]}
tools={['Public Access: No Login Required']}
color={colors.discoveryPhase}
/>
<Arrow direction="right" />
<StepCard
number="1.2"
title="Identify Target Studies"
description="Select specific studies/cohorts of interest and review their data use conditions and DUO codes."
badges={[
{ label: 'Researcher', color: colors.researcher },
]}
tools={['Data Use Ontology (DUO)', 'Study Metadata']}
color={colors.discoveryPhase}
/>
</div>
</div>
</div>
<div style={{ display: 'flex', justifyContent: 'center', margin: '20px 0' }}>
<Arrow direction="down" size={28} color={colors.highlight} />
</div>
{/* Phase 2: Access Request */}
<div style={{ marginBottom: '28px' }}>
<PhaseHeader
title="PHASE 2: Data Access Request"
subtitle="Submit and review access application through DACO"
color={colors.accessPhase}
icon="📝"
/>
<div style={{
backgroundColor: colors.cardBg,
borderRadius: '0 0 12px 12px',
padding: '20px',
border: `1px solid ${colors.border}`,
borderTop: 'none',
}}>
<div style={{
display: 'flex',
justifyContent: 'center',
gap: '16px',
flexWrap: 'wrap',
alignItems: 'center',
}}>
<StepCard
number="2.1"
title="Request Access from Portal"
description="Click 'Request Access' on Research Portal. Routed to DACO with selected studies pre-populated."
badges={[
{ label: 'Researcher', color: colors.researcher },
]}
tools={['Research Portal → DACO Link']}
color={colors.accessPhase}
/>
<Arrow direction="right" />
<StepCard
number="2.2"
title="Complete DACO Application"
description="Fill application with data use description, ethics approval, intended research, collaborators, and institution details."
badges={[
{ label: 'Researcher', color: colors.researcher },
]}
tools={['DACO Portal', 'Ethics Documentation']}
color={colors.accessPhase}
/>
<Arrow direction="right" />
<StepCard
number="2.3"
title="Institutional Review"
description="Institution representative reviews and endorses the application, confirming researcher affiliation and compliance."
badges={[
{ label: 'Inst. Rep', color: colors.instRep },
]}
tools={['DACO Portal']}
color={colors.accessPhase}
/>
<Arrow direction="right" />
<StepCard
number="2.4"
title="DAC Review & Decision"
description="DAC members review application and leave feedback. DAC Chair collates reviews and makes final approve/reject decision."
badges={[
{ label: 'DAC Member', color: colors.dacMember },
{ label: 'DAC Chair', color: colors.dacChair },
]}
tools={['DACO Portal', 'Application Dashboard']}
color={colors.accessPhase}
/>
</div>
<div style={{
marginTop: '16px',
padding: '12px',
backgroundColor: `${colors.accessPhase}15`,
borderRadius: '8px',
border: `1px solid ${colors.accessPhase}`,
}}>
<div style={{ fontSize: '11px', color: colors.accessPhase, fontWeight: '600', marginBottom: '4px' }}>
📋 DACO Portal Features
</div>
<div style={{ fontSize: '10px', color: colors.textSecondary, display: 'flex', gap: '20px', flexWrap: 'wrap' }}>
<span>• Multiple study selection</span>
<span>• Application history & status tracking</span>
<span>• Multi-DAC support</span>
<span>• Collaborator management</span>
<span>• Bilingual (EN/FR)</span>
</div>
</div>
</div>
</div>
<div style={{ display: 'flex', justifyContent: 'center', margin: '20px 0' }}>
<Arrow direction="down" size={28} color={colors.highlight} />
</div>
{/* Phase 3: Authorization */}
<div style={{ marginBottom: '28px' }}>
<PhaseHeader
title="PHASE 3: Authorization & Token Generation"
subtitle="System grants permissions and user obtains credentials"
color={colors.authPhase}
icon="🔐"
/>
<div style={{
backgroundColor: colors.cardBg,
borderRadius: '0 0 12px 12px',
padding: '20px',
border: `1px solid ${colors.border}`,
borderTop: 'none',
}}>
<div style={{
display: 'flex',
justifyContent: 'center',
gap: '16px',
flexWrap: 'wrap',
alignItems: 'center',
}}>
<StepCard
number="3.1"
title="Authorization Granted"
description="Upon DAC approval, AuthZ service automatically records permissions at study/dataset level using GA4GH standards."
badges={[
{ label: 'System', color: colors.system },
]}
tools={['AuthZ Service', 'GA4GH AAI Passports', 'DUO Permissions']}
color={colors.authPhase}
/>
<Arrow direction="right" />
<StepCard
number="3.2"
title="Generate API Token"
description="Researcher logs into token generation page via CILogon to obtain API access token for data download."
badges={[
{ label: 'Researcher', color: colors.researcher },
]}
tools={['CILogon Login', 'Token Generation Page']}
color={colors.authPhase}
/>
<Arrow direction="right" />
<StepCard
number="3.3"
title="Configure CLI Tool"
description="Configure the CLI download tool with storage URL and API token. Same tool used for submission also handles downloads."
badges={[
{ label: 'Researcher', color: colors.researcher },
]}
tools={['PCGL CLI Tool', 'Storage URL Config']}
color={colors.authPhase}
/>
</div>
</div>
</div>
<div style={{ display: 'flex', justifyContent: 'center', margin: '20px 0' }}>
<Arrow direction="down" size={28} color={colors.highlight} />
</div>
{/* Phase 4: Data Access */}
<div style={{ marginBottom: '28px' }}>
<PhaseHeader
title="PHASE 4: Data Access"
subtitle="Retrieve or explore approved datasets"
color={colors.downloadPhase}
icon="💾"
/>
<div style={{
backgroundColor: colors.cardBg,
borderRadius: '0 0 12px 12px',
padding: '20px',
border: `1px solid ${colors.border}`,
borderTop: 'none',
}}>
{/* Two Paths Label */}
<div style={{
textAlign: 'center',
marginBottom: '16px',
}}>
<span style={{
backgroundColor: colors.highlight,
color: colors.background,
padding: '4px 16px',
borderRadius: '16px',
fontSize: '11px',
fontWeight: '700',
textTransform: 'uppercase',
letterSpacing: '1px',
}}>
ACCESS PATHS
</span>
</div>
{/* Two parallel paths */}
<div style={{
display: 'flex',
gap: '24px',
flexWrap: 'wrap',
justifyContent: 'center',
alignItems: 'stretch',
}}>
{/* Path A: Data Download */}
<div style={{
flex: '1 1 45%',
minWidth: '320px',
maxWidth: '600px',
backgroundColor: `${colors.downloadPhase}15`,
borderRadius: '12px',
padding: '20px',
border: `2px solid ${colors.downloadPhase}`,
display: 'flex',
flexDirection: 'column',
}}>
<div style={{
display: 'flex',
alignItems: 'center',
gap: '8px',
marginBottom: '16px',
}}>
<div style={{
width: '8px',
height: '24px',
backgroundColor: colors.downloadPhase,
borderRadius: '4px',
}}/>
<h3 style={{ margin: 0, fontSize: '14px', color: colors.downloadPhase, fontWeight: '700' }}>
PATH A: Data Download
</h3>
</div>
{/* Download Steps */}
<div style={{ fontSize: '11px', color: colors.textSecondary, marginBottom: '10px', fontWeight: '600' }}>
Steps:
</div>
<div style={{
display: 'flex',
flexDirection: 'column',
gap: '12px',
alignItems: 'center',
justifyContent: 'center',
marginBottom: '16px',
}}>
<StepCard
number="4A.1"
title="Generate Download Manifest"
description="Create manifest file specifying the files to download from your approved datasets."
badges={[
{ label: 'Researcher', color: colors.researcher },
]}
tools={['Research Portal', 'File Selection']}
color={colors.downloadPhase}
/>
<Arrow direction="down" />
<StepCard
number="4A.2"
title="Download Data Files"
description="Execute CLI download using manifest. Molecular data from SD4H Object Store."
badges={[
{ label: 'Researcher', color: colors.researcher },
]}
tools={['CLI Tool', 'SD4H Object Store']}
color={colors.downloadPhase}
/>
</div>
{/* Download Methods */}
<div style={{ fontSize: '11px', color: colors.textSecondary, marginBottom: '10px', fontWeight: '600' }}>
Download Methods:
</div>
<div style={{ display: 'flex', gap: '10px', flexWrap: 'wrap' }}>
<MethodOption
title="CLI Download (Primary)"
description="Download molecular data using manifest files."
icon="⬇️"
color={colors.cliMethod}
tools={['Manifest File', 'CLI Tool', 'SD4H Object Store']}
/>
<MethodOption
title="GA4GH APIs"
description="Programmatic access via standard APIs."
icon="🔗"
color={colors.apiMethod}
tools={['GA4GH DRS', 'htsget API']}
isFuture={true}
/>
<MethodOption
title="Globus Transfer"
description="Managed transfer for large datasets."
icon="📦"
color={colors.uiMethod}
tools={['Globus Endpoint']}
isFuture={true}
/>
</div>
</div>
{/* Path B: Fine-Grained Exploration */}
<div style={{
flex: '1 1 45%',
minWidth: '320px',
maxWidth: '600px',
backgroundColor: `${colors.discoveryPhase}15`,
borderRadius: '12px',
padding: '20px',
border: `2px solid ${colors.discoveryPhase}`,
display: 'flex',
flexDirection: 'column',
}}>
<div style={{
display: 'flex',
alignItems: 'center',
gap: '8px',
marginBottom: '16px',
}}>
<div style={{
width: '8px',
height: '24px',
backgroundColor: colors.discoveryPhase,
borderRadius: '4px',
}}/>
<h3 style={{ margin: 0, fontSize: '14px', color: colors.discoveryPhase, fontWeight: '700' }}>
PATH B: Fine-Grained Exploration
</h3>
</div>
{/* Exploration Steps */}
<div style={{ fontSize: '11px', color: colors.textSecondary, marginBottom: '10px', fontWeight: '600' }}>
Steps:
</div>
<div style={{
display: 'flex',
flexDirection: 'column',
gap: '12px',
alignItems: 'center',
justifyContent: 'center',
marginBottom: '16px',
}}>
<StepCard
number="4B.1"
title="Access Research Portal"
description="Return to Research Portal with your authorized credentials to access detailed views."
badges={[
{ label: 'Researcher', color: colors.researcher },
]}
tools={['Research Portal', 'CILogon Auth']}
color={colors.discoveryPhase}
/>
<Arrow direction="down" />
<StepCard
number="4B.2"
title="Explore Fine-Grained Data"
description="View individual-level data, detailed metadata, and row-level exploration for authorized datasets."
badges={[
{ label: 'Researcher', color: colors.researcher },
]}
tools={['Data Exploration UI', 'Authorized Dataset Views']}
color={colors.discoveryPhase}
/>
</div>
{/* TRE Option */}
<div style={{ fontSize: '11px', color: colors.textSecondary, marginBottom: '10px', fontWeight: '600' }}>
Advanced Analysis:
</div>
<div style={{ display: 'flex', justifyContent: 'center' }}>
<StepCard
number="4B.3"
title="TRE Analysis"
description="Analyze data within the Trusted Research Environment on SD4H. Avoids full dataset transfers."
badges={[
{ label: 'Researcher', color: colors.researcher },
]}
tools={['TRE / White Tower', 'Jupyter Hub', 'Elastic HPC with SLURM Cluster']}
color={colors.discoveryPhase}
isFuture={true}
/>
</div>
</div>
</div>
{/* Data Types Note */}
<div style={{
marginTop: '20px',
display: 'flex',
gap: '12px',
flexWrap: 'wrap',
}}>
<div style={{
flex: 1,
minWidth: '200px',
padding: '12px',
backgroundColor: colors.cardBgAlt,
borderRadius: '8px',
}}>
<div style={{ fontSize: '11px', color: '#22d3ee', fontWeight: '600', marginBottom: '4px' }}>
🧬 Molecular Data
</div>
<div style={{ fontSize: '10px', color: colors.textSecondary }}>
BAM, CRAM, VCF files downloaded via CLI from SD4H Object Store
</div>
</div>
<div style={{
flex: 1,
minWidth: '200px',
padding: '12px',
backgroundColor: colors.cardBgAlt,
borderRadius: '8px',
}}>
<div style={{ fontSize: '11px', color: '#a78bfa', fontWeight: '600', marginBottom: '4px' }}>
📋 Clinical Data
</div>
<div style={{ fontSize: '10px', color: colors.textSecondary }}>
Phenotype, diagnosis, treatment data available via Research Portal APIs or fine-grained exploration
</div>
</div>
</div>
</div>
</div>
{/* Key Components Summary */}
<div style={{ marginTop: '40px' }}>
<h2 style={{
fontSize: '18px',
fontWeight: '700',
color: colors.textPrimary,
textAlign: 'center',
marginBottom: '20px',
}}>
Key System Components
</h2>
<div style={{
display: 'grid',
gridTemplateColumns: 'repeat(auto-fit, minmax(220px, 1fr))',
gap: '16px',
}}>
<div style={{
backgroundColor: colors.cardBg,
borderRadius: '10px',
padding: '16px',
border: `1px solid ${colors.discoveryPhase}`,
}}>
<div style={{ fontSize: '20px', marginBottom: '8px' }}>🔬</div>
<div style={{ fontSize: '13px', fontWeight: '600', color: colors.discoveryPhase, marginBottom: '4px' }}>
Research Portal (Bento)
</div>
<div style={{ fontSize: '10px', color: colors.textSecondary }}>
Data discovery, catalogue browsing, aggregate views, Beacon v2 API, bilingual interface
</div>
</div>
<div style={{
backgroundColor: colors.cardBg,
borderRadius: '10px',
padding: '16px',
border: `1px solid ${colors.accessPhase}`,
}}>
<div style={{ fontSize: '20px', marginBottom: '8px' }}>📋</div>
<div style={{ fontSize: '13px', fontWeight: '600', color: colors.accessPhase, marginBottom: '4px' }}>
DACO Portal
</div>
<div style={{ fontSize: '10px', color: colors.textSecondary }}>
Data access applications, DAC review workflow, approval tracking, multi-DAC support
</div>
</div>
<div style={{
backgroundColor: colors.cardBg,
borderRadius: '10px',
padding: '16px',
border: `1px solid ${colors.authPhase}`,
}}>
<div style={{ fontSize: '20px', marginBottom: '8px' }}>🔑</div>
<div style={{ fontSize: '13px', fontWeight: '600', color: colors.authPhase, marginBottom: '4px' }}>
AuthZ + CILogon
</div>
<div style={{ fontSize: '10px', color: colors.textSecondary }}>
GA4GH AAI standards, institutional identity, permissions management, API tokens
</div>
</div>
<div style={{
backgroundColor: colors.cardBg,
borderRadius: '10px',
padding: '16px',
border: `1px solid ${colors.downloadPhase}`,
}}>
<div style={{ fontSize: '20px', marginBottom: '8px' }}>☁️</div>
<div style={{ fontSize: '13px', fontWeight: '600', color: colors.downloadPhase, marginBottom: '4px' }}>
SD4H Infrastructure
</div>
<div style={{ fontSize: '10px', color: colors.textSecondary }}>
Object storage, TRE environment, secure compute, data archival, Globus endpoint
</div>
</div>
</div>
</div>
{/* Key Notes */}
<div style={{
marginTop: '32px',
padding: '20px',
backgroundColor: colors.cardBg,
borderRadius: '12px',
border: `1px solid ${colors.border}`,
}}>
<h3 style={{ margin: '0 0 12px 0', fontSize: '14px', color: colors.textPrimary }}>
📌 Important Notes
</h3>
<div style={{
display: 'grid',
gridTemplateColumns: 'repeat(auto-fit, minmax(260px, 1fr))',
gap: '12px',
}}>
<div style={{ fontSize: '11px', color: colors.textSecondary }}>
<strong style={{ color: colors.highlight }}>GA4GH Standards:</strong> PCGL uses GA4GH AAI (Passports/Visas), DUO, Beacon v2, DRS, and htsget for international interoperability.
</div>
<div style={{ fontSize: '11px', color: colors.textSecondary }}>
<strong style={{ color: colors.highlight }}>Data Download Policy:</strong> Data download is currently allowed and is the primary access method. TRE-only access is planned for future phases.
</div>
<div style={{ fontSize: '11px', color: colors.textSecondary }}>
<strong style={{ color: colors.highlight }}>Federation:</strong> Federated PCGL nodes are discoverable via Beacon Network but data download requires access through the source node.
</div>
<div style={{ fontSize: '11px', color: colors.textSecondary }}>
<strong style={{ color: colors.highlight }}>Support:</strong> Contact helpdesk@genomelibrary.ca for assistance with data access requests or download issues.
</div>
</div>
</div>
{/* Footer */}
<div style={{
marginTop: '32px',
textAlign: 'center',
fontSize: '10px',
color: colors.textSecondary,
}}>
<p>Source: PCGL Architecture Documentation & WG2 Meeting Minutes (2025)</p>
</div>
</div>
</div>
);
};
ReactDOM.render(<PCGLDataAcquisitionWorkflow />, document.getElementById('root'));
</script>
</body>
</html>