@the-cascade-protocol/cli 0.2.5 → 0.3.1

package/dist/commands/convert.d.ts

@@ -5,11 +5,14 @@
  * Supports FHIR R4, Cascade Protocol Turtle, and JSON-LD.
  *
  * Options:
- *   --from <format>     Source format (fhir|cascade|c-cda)
- *   --to <format>       Target format (turtle|jsonld|fhir|cascade)
- *   --format <output>   Output serialization format (turtle|jsonld) [default: turtle]
- *   --json              Output results as JSON envelope (machine-readable)
- *   --verbose           Show detailed conversion information
+ *   --from <format>        Source format (fhir|cascade|c-cda)
+ *   --to <format>          Target format (turtle|jsonld|fhir|cascade)
+ *   --format <output>      Output serialization format (turtle|jsonld) [default: turtle]
+ *   --passthrough <mode>   Passthrough mode for unmapped FHIR types (full|minimal) [default: full]
+ *                          full: stores original FHIR JSON for lossless round-trip
+ *                          minimal: omits fhirJson; smaller output, no round-trip support
+ *   --json                 Output results as JSON envelope (machine-readable)
+ *   --verbose              Show detailed conversion information
  *
  * Supports stdin piping:
  *   cat patient.json | cascade convert --from fhir --to cascade

package/dist/commands/convert.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../../src/commands/convert.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;GAoBG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAqBpC,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAiL7D"}

package/dist/commands/convert.js

@@ -5,20 +5,26 @@
  * Supports FHIR R4, Cascade Protocol Turtle, and JSON-LD.
  *
  * Options:
- *   --from <format>     Source format (fhir|cascade|c-cda)
- *   --to <format>       Target format (turtle|jsonld|fhir|cascade)
- *   --format <output>   Output serialization format (turtle|jsonld) [default: turtle]
- *   --json              Output results as JSON envelope (machine-readable)
- *   --verbose           Show detailed conversion information
+ *   --from <format>        Source format (fhir|cascade|c-cda)
+ *   --to <format>          Target format (turtle|jsonld|fhir|cascade)
+ *   --format <output>      Output serialization format (turtle|jsonld) [default: turtle]
+ *   --passthrough <mode>   Passthrough mode for unmapped FHIR types (full|minimal) [default: full]
+ *                          full: stores original FHIR JSON for lossless round-trip
+ *                          minimal: omits fhirJson; smaller output, no round-trip support
+ *   --json                 Output results as JSON envelope (machine-readable)
+ *   --verbose              Show detailed conversion information
  *
  * Supports stdin piping:
  *   cat patient.json | cascade convert --from fhir --to cascade
  *
  * Zero network calls. All conversion is local.
  */
-import { readFileSync } from 'node:fs';
+import { readFileSync, writeFileSync } from 'node:fs';
+import { dirname, basename, join } from 'node:path';
 import { printResult, printError, printVerbose } from '../lib/output.js';
 import { convert, detectFormat } from '../lib/fhir-converter/index.js';
+import { buildImportManifest } from '../lib/fhir-converter/import-manifest.js';
+import { EXCLUDED_TYPES } from '../lib/fhir-converter/converters-passthrough.js';
 /**
  * Read input from file or stdin.
  * If file is provided, reads from disk.
@@ -40,6 +46,8 @@ export function registerConvertCommand(program) {
         .requiredOption('--to <format>', 'Target format (turtle|jsonld|fhir|cascade)')
         .option('--format <output>', 'Output serialization format (turtle|jsonld)', 'turtle')
         .option('--source-system <name>', 'Tag all records with a source system name (adds cascade:sourceSystem for reconciliation)')
+        .option('--passthrough <mode>', 'Passthrough mode for unmapped FHIR types: full (store fhirJson, round-trip supported) or minimal (omit fhirJson, smaller output)', 'full')
+        .option('--manifest [file]', 'Write import manifest JSON alongside output (default: {input}-manifest.json). Only applies when --from fhir.')
         .action(async (file, options) => {
         const globalOpts = program.opts();
         printVerbose(`Converting from ${options.from} to ${options.to}`, globalOpts);
@@ -88,7 +96,11 @@ export function registerConvertCommand(program) {
         }
         // 4. Run conversion
         const outputSerialization = (options.format === 'jsonld' ? 'jsonld' : 'turtle');
-        const result = await convert(input, options.from, options.to, outputSerialization, options.sourceSystem);
+        const passthroughMinimal = options.passthrough === 'minimal';
+        if (passthroughMinimal) {
+            printVerbose('Passthrough mode: minimal (cascade:fhirJson omitted, round-trip export disabled)', globalOpts);
+        }
+        const result = await convert(input, options.from, options.to, outputSerialization, options.sourceSystem, passthroughMinimal);
         // 5. Output
         if (!result.success) {
             for (const err of result.errors) {
@@ -133,6 +145,38 @@ export function registerConvertCommand(program) {
                 console.error(`${result.warnings.length} warning${result.warnings.length > 1 ? 's' : ''}`);
             }
         }
+        // Write import manifest if requested (FHIR -> Cascade only)
+        if (options.manifest !== undefined && options.from === 'fhir' && result.success) {
+            // Count excluded types from the source bundle
+            const excludedCounts = {};
+            try {
+                const parsed = JSON.parse(input);
+                const resources = parsed.resourceType === 'Bundle'
+                    ? (parsed.entry ?? []).map((e) => e.resource).filter(Boolean)
+                    : [parsed];
+                for (const res of resources) {
+                    if (res?.resourceType && EXCLUDED_TYPES.has(res.resourceType)) {
+                        excludedCounts[res.resourceType] = (excludedCounts[res.resourceType] ?? 0) + 1;
+                    }
+                }
+            }
+            catch {
+                // Input already validated as parseable JSON above; this should not fail
+            }
+            const manifest = buildImportManifest(result, file ?? '<stdin>', options.sourceSystem ?? '', excludedCounts);
+            let manifestPath;
+            if (typeof options.manifest === 'string') {
+                manifestPath = options.manifest;
+            }
+            else if (file) {
+                manifestPath = join(dirname(file), `${basename(file, '.json')}-manifest.json`);
+            }
+            else {
+                manifestPath = 'fhir-import-manifest.json';
+            }
+            writeFileSync(manifestPath, JSON.stringify(manifest, null, 2));
+            console.error(`Import manifest written to: ${manifestPath}`);
+        }
     });
 }
 //# sourceMappingURL=convert.js.map

package/dist/commands/convert.js.map

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package/dist/commands/pod/helpers.d.ts

@@ -13,6 +13,8 @@ export interface DataTypeInfo {
     rdfTypes: string[];
     directory: 'clinical' | 'wellness';
     filename: string;
+    /** If true, type detection uses prefix-matching instead of exact IRI matching */
+    isFhirPassthroughBucket?: boolean;
 }
 export declare const DATA_TYPES: Record<string, DataTypeInfo>;
 export { CASCADE_NAMESPACES };

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

@@ -1 +1 @@
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package/dist/commands/pod/helpers.js

@@ -46,7 +46,7 @@ export const DATA_TYPES = {
     },
     insurance: {
         label: 'Insurance',
-        rdfTypes: [CASCADE_NAMESPACES.clinical + 'CoverageRecord'],
+        rdfTypes: [CASCADE_NAMESPACES.coverage + 'InsurancePlan'],
         directory: 'clinical',
         filename: 'insurance.ttl',
     },
@@ -89,6 +89,67 @@ export const DATA_TYPES = {
         directory: 'wellness',
         filename: 'supplements.ttl',
     },
+    procedures: {
+        label: 'Procedures',
+        rdfTypes: [CASCADE_NAMESPACES.clinical + 'Procedure'],
+        directory: 'clinical',
+        filename: 'procedures.ttl',
+    },
+    encounters: {
+        label: 'Encounters',
+        rdfTypes: [CASCADE_NAMESPACES.clinical + 'Encounter'],
+        directory: 'clinical',
+        filename: 'encounters.ttl',
+    },
+    documents: {
+        label: 'Clinical Documents',
+        rdfTypes: [CASCADE_NAMESPACES.clinical + 'ClinicalDocument'],
+        directory: 'clinical',
+        filename: 'documents.ttl',
+    },
+    'lab-reports': {
+        label: 'Lab Reports',
+        rdfTypes: [CASCADE_NAMESPACES.clinical + 'LaboratoryReport'],
+        directory: 'clinical',
+        filename: 'lab-reports.ttl',
+    },
+    'medication-administrations': {
+        label: 'Medication Administrations',
+        rdfTypes: [CASCADE_NAMESPACES.clinical + 'MedicationAdministration'],
+        directory: 'clinical',
+        filename: 'medication-administrations.ttl',
+    },
+    devices: {
+        label: 'Implanted Devices',
+        rdfTypes: [CASCADE_NAMESPACES.clinical + 'ImplantedDevice'],
+        directory: 'clinical',
+        filename: 'devices.ttl',
+    },
+    imaging: {
+        label: 'Imaging Studies',
+        rdfTypes: [CASCADE_NAMESPACES.clinical + 'ImagingStudy'],
+        directory: 'clinical',
+        filename: 'imaging.ttl',
+    },
+    claims: {
+        label: 'Claims',
+        rdfTypes: ['https://ns.cascadeprotocol.org/coverage/v1#ClaimRecord'],
+        directory: 'clinical',
+        filename: 'claims.ttl',
+    },
+    benefits: {
+        label: 'Benefit Statements',
+        rdfTypes: ['https://ns.cascadeprotocol.org/coverage/v1#BenefitStatement'],
+        directory: 'clinical',
+        filename: 'benefits.ttl',
+    },
+    'fhir-passthrough': {
+        label: 'FHIR Passthrough',
+        rdfTypes: ['http://hl7.org/fhir/'],
+        directory: 'clinical',
+        filename: 'fhir-passthrough.ttl',
+        isFhirPassthroughBucket: true,
+    },
 };
 // Re-export CASCADE_NAMESPACES for convenience
 export { CASCADE_NAMESPACES };

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

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package/dist/commands/pod/import.d.ts

@@ -0,0 +1,20 @@
+/**
+ * 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 type { Command } from 'commander';
+export declare function registerImportSubcommand(pod: Command, program: Command): void;
+//# sourceMappingURL=import.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"import.d.ts","sourceRoot":"","sources":["../../../src/commands/pod/import.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAiKzC,wBAAgB,wBAAwB,CAAC,GAAG,EAAE,OAAO,EAAE,OAAO,EAAE,OAAO,GAAG,IAAI,CAyR7E"}