@the-cascade-protocol/cli 0.2.5 → 0.3.1

package/dist/commands/pod/import.js

@@ -0,0 +1,382 @@
+/**
+ * cascade pod import <pod-dir> <files...>
+ *
+ * Import FHIR JSON or Cascade Turtle files into a Cascade Pod.
+ *
+ * Converts FHIR to Cascade Turtle if needed, optionally reconciles multiple
+ * inputs, routes records by type to the correct pod data files, updates type
+ * indexes, and appends ldp:contains references to index.ttl.
+ *
+ * Options:
+ *   --source-system <name>   Tag all records with this system name
+ *   --no-reconcile           Skip reconciliation even with multiple files
+ *   --trust <scores>         Trust scores e.g. hospital=0.95,clinic=0.85
+ *   --dry-run                Preview without writing any files
+ *   --report <file>          Write import report JSON to file
+ *   --passthrough <mode>     Passthrough mode: full|minimal (default: full)
+ */
+import * as fs from 'fs/promises';
+import * as path from 'path';
+import { Parser } from 'n3';
+import { printResult, printError, printVerbose } from '../../lib/output.js';
+import { convert } from '../../lib/fhir-converter/index.js';
+import { quadsToTurtle } from '../../lib/fhir-converter/types.js';
+import { runReconciliation } from '../../lib/reconciler.js';
+import { DATA_TYPES, resolvePodDir, fileExists, } from './helpers.js';
+// ---------------------------------------------------------------------------
+// Turtle parsing helper: returns map from subject URI -> Quad[]
+// ---------------------------------------------------------------------------
+async function parseTurtleToQuads(turtle) {
+    return new Promise((resolve, reject) => {
+        const parser = new Parser({ format: 'Turtle' });
+        const bySubject = new Map();
+        parser.parse(turtle, (error, quad) => {
+            if (error) {
+                reject(error);
+                return;
+            }
+            if (!quad) {
+                resolve(bySubject);
+                return;
+            }
+            const subj = quad.subject.value;
+            if (!bySubject.has(subj))
+                bySubject.set(subj, []);
+            bySubject.get(subj).push(quad);
+        });
+    });
+}
+// ---------------------------------------------------------------------------
+// Route a subject's rdf:type to a DATA_TYPES key
+// ---------------------------------------------------------------------------
+function routeTypeKey(quads) {
+    const rdfTypeIri = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type';
+    const typeQuad = quads.find(q => q.predicate.value === rdfTypeIri);
+    const typeIri = typeQuad?.object.value ?? '';
+    // Exact match first
+    for (const [key, info] of Object.entries(DATA_TYPES)) {
+        if (info.isFhirPassthroughBucket)
+            continue;
+        if (info.rdfTypes.includes(typeIri))
+            return key;
+    }
+    // FHIR passthrough: type starts with http://hl7.org/fhir/
+    if (typeIri.startsWith('http://hl7.org/fhir/'))
+        return 'fhir-passthrough';
+    // Unknown type: fallback to fhir-passthrough
+    return 'fhir-passthrough';
+}
+// ---------------------------------------------------------------------------
+// Shorten a full IRI to a prefixed form for type registrations
+// ---------------------------------------------------------------------------
+const PREFIX_MAP = {
+    'https://ns.cascadeprotocol.org/core/v1#': 'cascade',
+    'https://ns.cascadeprotocol.org/health/v1#': 'health',
+    'https://ns.cascadeprotocol.org/clinical/v1#': 'clinical',
+    'https://ns.cascadeprotocol.org/coverage/v1#': 'coverage',
+    'http://hl7.org/fhir/': 'fhir',
+};
+function shortenForTurtle(iri) {
+    for (const [ns, prefix] of Object.entries(PREFIX_MAP)) {
+        if (iri.startsWith(ns))
+            return `${prefix}:${iri.slice(ns.length)}`;
+    }
+    return `<${iri}>`;
+}
+// ---------------------------------------------------------------------------
+// Build a TypeRegistration block
+// ---------------------------------------------------------------------------
+function buildTypeRegistration(key, info) {
+    const forClass = shortenForTurtle(info.rdfTypes[0]);
+    const instance = `</${info.directory}/${info.filename}>`;
+    return `\n<#${key}> a solid:TypeRegistration ;\n    solid:forClass ${forClass} ;\n    solid:instance ${instance} .\n`;
+}
+// ---------------------------------------------------------------------------
+// Determine which type index a DATA_TYPE entry should register in
+// ---------------------------------------------------------------------------
+function typeIndexForInfo(info) {
+    return info.directory === 'clinical' ? 'publicTypeIndex.ttl' : 'privateTypeIndex.ttl';
+}
+// ---------------------------------------------------------------------------
+// Append to type index file (string manipulation to preserve comments)
+// ---------------------------------------------------------------------------
+async function appendTypeRegistration(indexPath, key, info, dryRun) {
+    const content = await fs.readFile(indexPath, 'utf-8');
+    // Check if already registered (by key name)
+    if (content.includes(`<#${key}>`) || content.includes(`/${info.filename}`)) {
+        return false; // already present
+    }
+    const block = buildTypeRegistration(key, info);
+    if (!dryRun) {
+        await fs.appendFile(indexPath, block, 'utf-8');
+    }
+    return true;
+}
+// ---------------------------------------------------------------------------
+// Append ldp:contains reference to index.ttl
+// ---------------------------------------------------------------------------
+async function appendIndexContains(indexPath, relPath, dryRun) {
+    const content = await fs.readFile(indexPath, 'utf-8');
+    if (content.includes(relPath)) {
+        return false; // already present
+    }
+    // Append a simple ldp:contains statement
+    const line = `\n<> <http://www.w3.org/ns/ldp#contains> <${relPath}> .\n`;
+    if (!dryRun) {
+        await fs.appendFile(indexPath, line, 'utf-8');
+    }
+    return true;
+}
+// ---------------------------------------------------------------------------
+// Command registration
+// ---------------------------------------------------------------------------
+export function registerImportSubcommand(pod, program) {
+    pod
+        .command('import')
+        .description('Import FHIR JSON or Cascade Turtle files into a pod')
+        .argument('<pod-dir>', 'Path to the Cascade Pod directory')
+        .argument('<files...>', 'FHIR JSON or Cascade Turtle files to import')
+        .option('--source-system <name>', 'Tag all imported records with this system name')
+        .option('--no-reconcile', 'Skip reconciliation even when importing multiple files')
+        .option('--trust <scores>', 'Trust scores e.g. hospital=0.95,clinic=0.85')
+        .option('--dry-run', 'Preview the import without writing any files')
+        .option('--report <file>', 'Write import report JSON to this file')
+        .option('--passthrough <mode>', 'Passthrough mode: full or minimal (default: full)', 'full')
+        .action(async (podDirArg, files, options) => {
+        const globalOpts = program.opts();
+        const podDir = resolvePodDir(podDirArg);
+        const dryRun = options.dryRun ?? false;
+        const passthroughMinimal = options.passthrough === 'minimal';
+        // --- Step 1: Validate pod dir ---
+        const indexTtlPath = path.join(podDir, 'index.ttl');
+        if (!(await fileExists(indexTtlPath))) {
+            printError(`Pod not found at ${podDir} (no index.ttl). Run 'cascade pod init' first.`, globalOpts);
+            process.exitCode = 1;
+            return;
+        }
+        if (dryRun) {
+            printVerbose('Dry-run mode: no files will be written.', globalOpts);
+        }
+        // Parse trust scores
+        const trustScores = {};
+        if (options.trust) {
+            for (const pair of options.trust.split(',')) {
+                const [sys, score] = pair.split('=');
+                if (sys && score)
+                    trustScores[sys] = parseFloat(score);
+            }
+        }
+        // --- Step 2: Convert / collect inputs ---
+        const reconcilerInputs = [];
+        const sourceReport = [];
+        const allWarnings = [];
+        for (const filePath of files) {
+            const absPath = path.resolve(process.cwd(), filePath);
+            let content;
+            try {
+                content = await fs.readFile(absPath, 'utf-8');
+            }
+            catch {
+                printError(`Cannot read file: ${absPath}`, globalOpts);
+                process.exitCode = 1;
+                return;
+            }
+            const systemName = options.sourceSystem ?? path.basename(filePath, path.extname(filePath));
+            const trimmed = content.trim();
+            const warnings = [];
+            let turtleContent;
+            let resourceCount = 0;
+            // Detect FHIR JSON vs Turtle
+            if (trimmed.startsWith('{') || trimmed.startsWith('[')) {
+                // FHIR JSON
+                printVerbose(`Converting FHIR JSON: ${filePath}`, globalOpts);
+                const result = await convert(content, 'fhir', 'cascade', 'turtle', systemName, passthroughMinimal);
+                if (!result.success) {
+                    printError(`Failed to convert ${filePath}: ${result.errors.join(', ')}`, globalOpts);
+                    process.exitCode = 1;
+                    return;
+                }
+                turtleContent = result.output;
+                resourceCount = result.resourceCount;
+                warnings.push(...result.warnings);
+                allWarnings.push(...result.warnings.map(w => `${filePath}: ${w}`));
+            }
+            else {
+                // Assume Turtle
+                printVerbose(`Reading Turtle: ${filePath}`, globalOpts);
+                turtleContent = content;
+                // Count subjects as rough resource count
+                try {
+                    const quadsMap = await parseTurtleToQuads(turtleContent);
+                    resourceCount = quadsMap.size;
+                }
+                catch {
+                    resourceCount = 0;
+                }
+            }
+            reconcilerInputs.push({ content: turtleContent, systemName });
+            sourceReport.push({ file: filePath, system: systemName, resourceCount, warnings });
+        }
+        // --- Step 3: Reconcile or concatenate ---
+        let mergedTurtle;
+        let reconciliationSummary;
+        const shouldReconcile = options.reconcile !== false && reconcilerInputs.length > 1;
+        if (shouldReconcile) {
+            printVerbose(`Reconciling ${reconcilerInputs.length} inputs...`, globalOpts);
+            const reconcileResult = await runReconciliation(reconcilerInputs, {
+                trustScores,
+                labTolerance: 0.05,
+            });
+            mergedTurtle = reconcileResult.turtle;
+            reconciliationSummary = reconcileResult.report.summary;
+            printVerbose(`Reconciliation complete. Final records: ${reconcileResult.report.summary.finalRecordCount}`, globalOpts);
+        }
+        else {
+            mergedTurtle = reconcilerInputs.map(i => i.content).join('\n\n');
+        }
+        // --- Step 4: Parse merged Turtle into quads grouped by subject ---
+        let subjectQuads;
+        try {
+            subjectQuads = await parseTurtleToQuads(mergedTurtle);
+        }
+        catch (err) {
+            const msg = err instanceof Error ? err.message : String(err);
+            printError(`Failed to parse merged Turtle: ${msg}`, globalOpts);
+            process.exitCode = 1;
+            return;
+        }
+        // --- Step 5: Route subjects to DATA_TYPES buckets ---
+        const buckets = new Map(); // key -> list of subject quad arrays
+        for (const [, quads] of subjectQuads) {
+            const key = routeTypeKey(quads);
+            if (!buckets.has(key))
+                buckets.set(key, []);
+            buckets.get(key).push(quads);
+        }
+        // --- Step 6 & 7: For each bucket, serialize and merge into pod files ---
+        const filesWritten = [];
+        const typeCounts = {};
+        const newFiles = []; // relative paths (for index.ttl updates)
+        for (const [typeKey, subjectQArrays] of buckets) {
+            const info = DATA_TYPES[typeKey];
+            if (!info) {
+                allWarnings.push(`Unknown type key: ${typeKey} — skipping`);
+                continue;
+            }
+            const targetFile = path.join(podDir, info.directory, info.filename);
+            const relPath = `${info.directory}/${info.filename}`;
+            // Serialize new quads
+            const allNewQuads = subjectQArrays.flat();
+            const newTurtle = await quadsToTurtle(allNewQuads);
+            let finalTurtle;
+            let recordsAdded = subjectQArrays.length;
+            let isNewFile = true;
+            if (await fileExists(targetFile)) {
+                isNewFile = false;
+                // Merge: parse existing, combine unique subjects
+                let existingQuads;
+                try {
+                    const existing = await fs.readFile(targetFile, 'utf-8');
+                    existingQuads = await parseTurtleToQuads(existing);
+                }
+                catch {
+                    existingQuads = new Map();
+                }
+                // Add new subjects (dedup by subject URI)
+                let addedCount = 0;
+                for (const [subjectUri, quads] of subjectQuads) {
+                    if (routeTypeKey(quads) === typeKey && !existingQuads.has(subjectUri)) {
+                        existingQuads.set(subjectUri, quads);
+                        addedCount++;
+                    }
+                }
+                recordsAdded = addedCount;
+                const mergedQuads = Array.from(existingQuads.values()).flat();
+                finalTurtle = await quadsToTurtle(mergedQuads);
+            }
+            else {
+                finalTurtle = newTurtle;
+            }
+            if (!dryRun) {
+                await fs.mkdir(path.dirname(targetFile), { recursive: true });
+                await fs.writeFile(targetFile, finalTurtle, 'utf-8');
+            }
+            typeCounts[typeKey] = (typeCounts[typeKey] ?? 0) + recordsAdded;
+            filesWritten.push({ path: targetFile, recordsAdded, type: typeKey });
+            if (isNewFile) {
+                newFiles.push(relPath);
+            }
+            printVerbose(`  ${dryRun ? '[dry-run] ' : ''}${isNewFile ? 'Created' : 'Updated'} ${relPath} (+${recordsAdded} records)`, globalOpts);
+        }
+        // --- Step 8: Update type indexes ---
+        const settingsDir = path.join(podDir, 'settings');
+        const publicIndexPath = path.join(settingsDir, 'publicTypeIndex.ttl');
+        const privateIndexPath = path.join(settingsDir, 'privateTypeIndex.ttl');
+        for (const [typeKey] of buckets) {
+            const info = DATA_TYPES[typeKey];
+            if (!info)
+                continue;
+            const indexFile = typeIndexForInfo(info);
+            const indexPath = indexFile === 'publicTypeIndex.ttl' ? publicIndexPath : privateIndexPath;
+            if (await fileExists(indexPath)) {
+                const appended = await appendTypeRegistration(indexPath, typeKey, info, dryRun);
+                if (appended) {
+                    printVerbose(`  ${dryRun ? '[dry-run] ' : ''}Added type registration for ${typeKey} to ${indexFile}`, globalOpts);
+                }
+            }
+        }
+        // --- Step 9: Update index.ttl for new files ---
+        for (const relPath of newFiles) {
+            if (await fileExists(indexTtlPath)) {
+                const appended = await appendIndexContains(indexTtlPath, relPath, dryRun);
+                if (appended) {
+                    printVerbose(`  ${dryRun ? '[dry-run] ' : ''}Added ${relPath} to index.ttl`, globalOpts);
+                }
+            }
+        }
+        // --- Step 10: Summary and report ---
+        const totalRecordsImported = Object.values(typeCounts).reduce((a, b) => a + b, 0);
+        const importReport = {
+            importedAt: new Date().toISOString(),
+            podDir,
+            sources: sourceReport,
+            reconciliation: shouldReconcile
+                ? { enabled: true, summary: reconciliationSummary }
+                : { enabled: false },
+            filesWritten,
+            typeCounts,
+            totalRecordsImported,
+            warnings: allWarnings,
+            dryRun,
+        };
+        if (options.report && !dryRun) {
+            await fs.writeFile(options.report, JSON.stringify(importReport, null, 2), 'utf-8');
+            printVerbose(`Import report written to: ${options.report}`, globalOpts);
+        }
+        if (globalOpts.json) {
+            printResult(importReport, globalOpts);
+        }
+        else {
+            if (dryRun) {
+                console.log(`\n[dry-run] Import preview for pod: ${podDir}`);
+            }
+            else {
+                console.log(`\nImport complete: ${podDir}`);
+            }
+            console.log(`  Sources:          ${sourceReport.length} file(s)`);
+            console.log(`  Records imported: ${totalRecordsImported}`);
+            console.log(`  Files written:    ${filesWritten.length}`);
+            if (allWarnings.length > 0) {
+                console.log(`  Warnings:         ${allWarnings.length}`);
+                for (const w of allWarnings) {
+                    console.log(`    - ${w}`);
+                }
+            }
+            for (const [type, count] of Object.entries(typeCounts)) {
+                if (count > 0)
+                    console.log(`  ${type}: +${count}`);
+            }
+        }
+    });
+}
+//# sourceMappingURL=import.js.map

package/dist/commands/pod/import.js.map

@@ -0,0 +1 @@
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package/dist/commands/pod/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/commands/pod/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAMpC,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAOzD"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/commands/pod/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAOpC,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAQzD"}

package/dist/commands/pod/index.js

@@ -19,11 +19,13 @@ import { registerInitSubcommand } from './init.js';
 import { registerQuerySubcommand } from './query.js';
 import { registerExportSubcommand } from './export.js';
 import { registerInfoSubcommand } from './info.js';
+import { registerImportSubcommand } from './import.js';
 export function registerPodCommand(program) {
     const pod = program.command('pod').description('Manage Cascade Pod structures');
     registerInitSubcommand(pod, program);
     registerQuerySubcommand(pod, program);
     registerExportSubcommand(pod, program);
     registerInfoSubcommand(pod, program);
+    registerImportSubcommand(pod, program);
 }
 //# sourceMappingURL=index.js.map

package/dist/commands/pod/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/commands/pod/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAGH,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAC;AACnD,OAAO,EAAE,uBAAuB,EAAE,MAAM,YAAY,CAAC;AACrD,OAAO,EAAE,wBAAwB,EAAE,MAAM,aAAa,CAAC;AACvD,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAC;AAEnD,MAAM,UAAU,kBAAkB,CAAC,OAAgB;IACjD,MAAM,GAAG,GAAG,OAAO,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,+BAA+B,CAAC,CAAC;IAEhF,sBAAsB,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;IACrC,uBAAuB,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;IACtC,wBAAwB,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;IACvC,sBAAsB,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;AACvC,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/commands/pod/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAGH,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAC;AACnD,OAAO,EAAE,uBAAuB,EAAE,MAAM,YAAY,CAAC;AACrD,OAAO,EAAE,wBAAwB,EAAE,MAAM,aAAa,CAAC;AACvD,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAC;AACnD,OAAO,EAAE,wBAAwB,EAAE,MAAM,aAAa,CAAC;AAEvD,MAAM,UAAU,kBAAkB,CAAC,OAAgB;IACjD,MAAM,GAAG,GAAG,OAAO,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,+BAA+B,CAAC,CAAC;IAEhF,sBAAsB,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;IACrC,uBAAuB,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;IACtC,wBAAwB,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;IACvC,sBAAsB,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;IACrC,wBAAwB,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;AACzC,CAAC"}

package/dist/commands/pod/query.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"query.d.ts","sourceRoot":"","sources":["../../../src/commands/pod/query.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAczC,wBAAgB,uBAAuB,CAAC,GAAG,EAAE,OAAO,EAAE,OAAO,EAAE,OAAO,GAAG,IAAI,CA0M5E"}
+{"version":3,"file":"query.d.ts","sourceRoot":"","sources":["../../../src/commands/pod/query.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAczC,wBAAgB,uBAAuB,CAAC,GAAG,EAAE,OAAO,EAAE,OAAO,EAAE,OAAO,GAAG,IAAI,CA2O5E"}

package/dist/commands/pod/query.js

@@ -19,6 +19,17 @@ export function registerQuerySubcommand(pod, program) {
         .option('--immunizations', 'Query immunizations')
         .option('--vital-signs', 'Query vital signs')
         .option('--supplements', 'Query supplements')
+        .option('--insurance', 'Query insurance / coverage plans')
+        .option('--procedures', 'Query procedures')
+        .option('--encounters', 'Query encounters')
+        .option('--documents', 'Query clinical documents')
+        .option('--lab-reports', 'Query laboratory reports (DiagnosticReport)')
+        .option('--medication-administrations', 'Query medication administrations')
+        .option('--devices', 'Query implanted devices')
+        .option('--imaging', 'Query imaging studies')
+        .option('--claims', 'Query insurance claims')
+        .option('--benefits', 'Query explanation of benefits')
+        .option('--fhir-passthrough', 'Query FHIR passthrough records (unmapped types)')
         .option('--all', 'Query all data')
         .action(async (podDir, options) => {
         const globalOpts = program.opts();
@@ -54,9 +65,31 @@ export function registerQuerySubcommand(pod, program) {
                     requestedTypes.push('vital-signs');
                 if (options.supplements)
                     requestedTypes.push('supplements');
+                if (options.insurance)
+                    requestedTypes.push('insurance');
+                if (options.procedures)
+                    requestedTypes.push('procedures');
+                if (options.encounters)
+                    requestedTypes.push('encounters');
+                if (options.documents)
+                    requestedTypes.push('documents');
+                if (options.labReports)
+                    requestedTypes.push('lab-reports');
+                if (options.medicationAdministrations)
+                    requestedTypes.push('medication-administrations');
+                if (options.devices)
+                    requestedTypes.push('devices');
+                if (options.imaging)
+                    requestedTypes.push('imaging');
+                if (options.claims)
+                    requestedTypes.push('claims');
+                if (options.benefits)
+                    requestedTypes.push('benefits');
+                if (options.fhirPassthrough)
+                    requestedTypes.push('fhir-passthrough');
             }
             if (requestedTypes.length === 0) {
-                printError('No query filter specified. Use --medications, --conditions, --all, etc.', globalOpts);
+                printError('No query filter specified. Use --medications, --conditions, --procedures, --all, etc.', globalOpts);
                 process.exitCode = 1;
                 return;
             }

package/dist/commands/pod/query.js.map

@@ -1 +1 @@
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package/dist/commands/reconcile.d.ts.map

@@ -1 +1 @@
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