npm - clinicaltrialsgov-mcp-server - Versions diffs - 2.7.0 → 2.7.2 - Mend

clinicaltrialsgov-mcp-server 2.7.0 → 2.7.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (29) hide show

package/README.md CHANGED Viewed

@@ -7,13 +7,13 @@
 <div align="center">
-[![npm](https://img.shields.io/npm/v/clinicaltrialsgov-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/clinicaltrialsgov-mcp-server) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/clinicaltrialsgov-mcp-server) [![Version](https://img.shields.io/badge/Version-2.7.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![npm](https://img.shields.io/npm/v/clinicaltrialsgov-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/clinicaltrialsgov-mcp-server) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/clinicaltrialsgov-mcp-server) [![Version](https://img.shields.io/badge/Version-2.7.2-blue.svg?style=flat-square)](./CHANGELOG.md) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
 </div>
 <div align="center">
-[![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/clinicaltrialsgov-mcp-server/releases/latest/download/clinicaltrialsgov-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=clinicaltrialsgov-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvY2xpbmljYWx0cmlhbHNnb3YtbWNwLXNlcnZlciJdfQ==) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22clinicaltrialsgov-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads/clinicaltrialsgov-mcp-server%22%5D%7D)
+[![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/clinicaltrialsgov-mcp-server/releases/latest/download/clinicaltrialsgov-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=clinicaltrialsgov-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsImNsaW5pY2FsdHJpYWxzZ292LW1jcC1zZXJ2ZXIiXX0=) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22clinicaltrialsgov-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22clinicaltrialsgov-mcp-server%22%5D%7D)
 [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-67E8F9?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)

package/dist/mcp-server/tools/definitions/get-field-definitions.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"get-field-definitions.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-field-definitions.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAmB,MAAM,+BAA+B,CAAC;AAuClF,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EA+M9B~~,CAAC"}
1	+ {"version":3,"file":"get-field-definitions.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-field-definitions.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAmB,MAAM,+BAA+B,CAAC;AAuClF,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2N9B,CAAC"}

package/dist/mcp-server/tools/definitions/get-field-definitions.tool.js CHANGED Viewed

@@ -132,11 +132,19 @@ export const getFieldDefinitions = tool('clinicaltrials_get_field_definitions',
                 if (!input.query) {
                     throw validationError('mode="search" requires `query`. Pass a keyword to search by.');
                 }
-                const matches = await service.searchFieldDefinitions(input.query, input.limit, ctx);
+                const { entries: matches, total } = await service.searchFieldDefinitions(input.query, input.limit, ctx);
                 const fields = matches.map(indexEntryToResult);
-                ctx.log.info('Field search completed', { query: input.query, matchCount: fields.length });
+                ctx.log.info('Field search completed', {
+                    query: input.query,
+                    matchCount: fields.length,
+                    total,
+                });
                 ctx.enrich({ searchQuery: input.query });
-                ctx.enrich.truncated({ shown: fields.length, cap: input.limit });
+                // Disclose truncation only when the match set actually exceeded the cap —
+                // otherwise the "raise the cap" notice misleads when shown < cap.
+                if (total > input.limit) {
+                    ctx.enrich.truncated({ shown: fields.length, cap: input.limit });
+                }
                 if (fields.length === 0) {
                     ctx.enrich.notice(`No fields matched "${input.query}". Try a broader keyword (e.g. "enrollment", "sponsor", "eligibility") or use mode="overview" to see all top-level sections.`);
                 }

package/dist/mcp-server/tools/definitions/get-field-definitions.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/get-field-values.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"get-field-values.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-field-values.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;~~AAIjE~~,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;~~cAwHzB~~,CAAC"}
1	+ {"version":3,"file":"get-field-values.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-field-values.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAKjE,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;cAkIzB,CAAC"}

package/dist/mcp-server/tools/definitions/get-field-values.tool.js CHANGED Viewed

@@ -5,6 +5,7 @@
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getClinicalTrialsService } from '../../../services/clinical-trials/clinical-trials-service.js';
+import { toArray } from '../utils/query-helpers.js';
 import { RECOVERY_HINTS } from '../utils/recovery-hints.js';
 export const getFieldValues = tool('clinicaltrials_get_field_values', {
     description: `Discover valid values for ClinicalTrials.gov fields with study counts per value. Use to explore available filter options before building a search — e.g., valid OverallStatus, Phase, InterventionType, StudyType, or LeadSponsorClass values.`,
@@ -32,7 +33,10 @@ export const getFieldValues = tool('clinicaltrials_get_field_values', {
         fields: z
             .union([
             z.string().describe('A single PascalCase field name.'),
-            z.array(z.string()).describe('Multiple PascalCase field names.'),
+            z
+                .array(z.string())
+                .min(1)
+                .describe('Multiple PascalCase field names (at least one required).'),
         ])
             .describe(`PascalCase field name(s) to get value statistics for. Examples: OverallStatus, Phase, StudyType, Sex, LeadSponsorClass. Use clinicaltrials_get_field_definitions with a query to find more field names.`),
     }),
@@ -72,7 +76,10 @@ export const getFieldValues = tool('clinicaltrials_get_field_values', {
             .describe('One entry per requested field: canonical path, PascalCase piece name, data type, missing/unique counts, and top values with study counts (or trueCount/falseCount for BOOLEAN fields).'),
     }),
     async handler(input, ctx) {
-        const fields = Array.isArray(input.fields) ? input.fields : [input.fields];
+        const fields = toArray(input.fields);
+        if (fields.length === 0) {
+            throw ctx.fail('field_invalid', 'Provide at least one PascalCase field name (e.g. "OverallStatus").', { ...ctx.recoveryFor('field_invalid') });
+        }
         const service = getClinicalTrialsService();
         const stats = await service.getFieldValues(fields, ctx);
         ctx.log.info('Field values fetched', { fieldCount: stats.length });

package/dist/mcp-server/tools/definitions/get-field-values.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/get-study-count.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"get-study-count.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-study-count.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAKjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EAsLxB~~,CAAC"}
1	+ {"version":3,"file":"get-study-count.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-study-count.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAKjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA4LxB,CAAC"}

package/dist/mcp-server/tools/definitions/get-study-count.tool.js CHANGED Viewed

@@ -101,7 +101,7 @@ export const getStudyCount = tool('clinicaltrials_get_study_count', {
         searchCriteria: z
             .record(z.string(), z.unknown())
             .optional()
-            .describe('Echo of active query/filter criteria applied to this count.'),
+            .describe('Echo of active query/filter criteria applied to this count, including sentinelFilterActive when the default unknown-enrollment exclusion is in effect.'),
         notice: z
             .string()
             .optional()
@@ -156,6 +156,11 @@ export const getStudyCount = tool('clinicaltrials_get_study_count', {
             criteria.phaseFilter = input.phaseFilter;
         if (input.advancedFilter)
             criteria.advancedFilter = input.advancedFilter;
+        // Flag the default unknown-enrollment exclusion (EnrollmentCount=99999999),
+        // mirroring search_studies — otherwise a count silently differs from an
+        // unfiltered /stats total with no signal that a filter was applied.
+        if (!input.includeUnknownEnrollment)
+            criteria.sentinelFilterActive = true;
         if (Object.keys(criteria).length > 0)
             ctx.enrich({ searchCriteria: criteria });
         if (totalCount === 0)

package/dist/mcp-server/tools/definitions/get-study-count.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/get-study-results.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"get-study-results.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-study-results.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqdjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAoP1B,CAAC"}

package/dist/mcp-server/tools/definitions/get-study-results.tool.js CHANGED Viewed

@@ -6,6 +6,7 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getClinicalTrialsService } from '../../../services/clinical-trials/clinical-trials-service.js';
 import { nctIdSchema } from '../utils/_schemas.js';
+import { toArray } from '../utils/query-helpers.js';
 import { RECOVERY_HINTS } from '../utils/recovery-hints.js';
 const VALID_SECTIONS = [
     'outcomes',
@@ -22,6 +23,18 @@ const SECTION_MAP = {
     baseline: 'baselineCharacteristicsModule',
     moreInfo: 'moreInfoModule',
 };
+/**
+ * Resolve a measurement value for the condensed/text channels. The caller's
+ * `!= null` guard drops genuinely-empty cells; the `"NA"`/`"NR"` sentinels are
+ * NOT dropped — for time-to-event MEDIAN measures they encode "median not
+ * reached", and silently dropping them removes an entire arm from the rendered
+ * measure (the comparator then reads as the headline result). Surface that
+ * explicitly for MEDIAN; pass other sentinel-bearing values through unchanged.
+ */
+function displayMeasurementValue(value, paramType) {
+    const v = String(value);
+    return (v === 'NA' || v === 'NR') && paramType === 'MEDIAN' ? 'not reached' : v;
+}
 /**
  * Extract top-line per-group stats from a raw outcome object (full mode).
  * Returns undefined if no measurement values are present.
@@ -38,10 +51,10 @@ function extractTopStats(o) {
         return;
     const groupMap = new Map(groups.map((g) => [g.id, (g.title ?? g.id)]));
     const stats = measurements
-        .filter((m) => m.value != null && m.value !== 'NA' && m.value !== 'NR')
+        .filter((m) => m.value != null)
         .map((m) => ({
         group: groupMap.get(m.groupId) ?? m.groupId,
-        value: m.value,
+        value: displayMeasurementValue(m.value, o.paramType),
         ...(m.spread != null ? { spread: m.spread } : {}),
     }));
     return stats.length ? stats : undefined;
@@ -371,11 +384,11 @@ function formatBaseline(bl, lines) {
                 const prefix = clsTitle ?? catTitle ?? '';
                 const measurements = cat.measurements;
                 const vals = (measurements ?? [])
-                    .filter((v) => v.value != null && v.value !== 'NA' && v.value !== 'NR')
+                    .filter((v) => v.value != null)
                     .map((v) => {
                     const gName = shortGroup(gm.get(v.groupId) ?? v.groupId);
                     const spread = v.spread != null ? ` ±${v.spread}` : '';
-                    return `${gName}: ${v.value}${spread}`;
+                    return `${gName}: ${displayMeasurementValue(v.value, paramType)}${spread}`;
                 })
                     .join(', ');
                 if (vals)
@@ -501,7 +514,7 @@ export const getStudyResults = tool('clinicaltrials_get_study_results', {
             .describe('Studies that could not be fetched.'),
     }),
     async handler(input, ctx) {
-        const nctIds = Array.isArray(input.nctIds) ? input.nctIds : [input.nctIds];
+        const nctIds = toArray(input.nctIds);
         const sections = input.sections
             ? Array.isArray(input.sections)
                 ? input.sections

package/dist/mcp-server/tools/definitions/get-study-results.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/get-study.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"get-study.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-study.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;~~AA+IjE~~,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~cAyfnB~~,CAAC"}
1	+ {"version":3,"file":"get-study.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-study.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAuKjE,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAmgBnB,CAAC"}

package/dist/mcp-server/tools/definitions/get-study.tool.js CHANGED Viewed

@@ -21,8 +21,10 @@ function haversineMi(a, b) {
 }
 /**
  * Apply caller-requested filters to the study so structuredContent and format()
- * see the same data. Totals from before filtering are preserved in `meta` and
- * returned alongside the filtered study.
+ * see the same data. A limit (and its corresponding upstream total) is recorded
+ * in `meta` only when it actually reduced the set — reporting a cap that trimmed
+ * nothing would imply a filter was applied when none was. `nearLocation` always
+ * filters (drops non-geo sites, sorts, applies radius), so it is always echoed.
  */
 function applyFilters(study, input) {
     const ps = study.protocolSection;
@@ -33,20 +35,30 @@ function applyFilters(study, input) {
     const origLocations = ps.contactsLocationsModule?.locations;
     const hasLocationFilter = input.nearLocation != null || input.locationLimit != null;
     if (origLocations?.length && hasLocationFilter) {
-        meta.totalLocations = origLocations.length;
         let locations = origLocations;
         if (input.nearLocation) {
             const { lat, lon, radiusMi } = input.nearLocation;
             const withGeo = origLocations.filter((l) => l.geoPoint != null);
-            meta.locationsWithoutGeo = origLocations.length - withGeo.length;
+            const withoutGeo = origLocations.length - withGeo.length;
+            if (withoutGeo > 0)
+                meta.locationsWithoutGeo = withoutGeo;
             locations = withGeo
                 .map((l) => ({ ...l, distanceMi: haversineMi({ lat, lon }, l.geoPoint) }))
                 .filter((l) => l.distanceMi <= radiusMi)
                 .sort((a, b) => a.distanceMi - b.distanceMi);
+            // nearLocation always filters → always echo it.
+            meta.nearLocation = input.nearLocation;
         }
+        const beforeLimit = locations.length;
         if (input.locationLimit != null) {
             locations = locations.slice(0, input.locationLimit);
+            // Echo the limit only when the slice actually trimmed something.
+            if (beforeLimit > input.locationLimit)
+                meta.locationLimit = input.locationLimit;
         }
+        // Record the upstream total only when the returned set is smaller than it.
+        if (locations.length < origLocations.length)
+            meta.totalLocations = origLocations.length;
         nextPs = {
             ...nextPs,
             contactsLocationsModule: {
@@ -59,24 +71,34 @@ function applyFilters(study, input) {
     if (outcomes && input.outcomeLimit != null) {
         const limit = input.outcomeLimit;
         const nextOutcomes = { ...outcomes };
-        if (outcomes.secondaryOutcomes?.length) {
-            meta.totalSecondaryOutcomes = outcomes.secondaryOutcomes.length;
-            nextOutcomes.secondaryOutcomes = outcomes.secondaryOutcomes.slice(0, limit);
+        let trimmed = false;
+        const secondary = outcomes.secondaryOutcomes;
+        if (secondary && secondary.length > limit) {
+            meta.totalSecondaryOutcomes = secondary.length;
+            nextOutcomes.secondaryOutcomes = secondary.slice(0, limit);
+            trimmed = true;
         }
-        if (outcomes.otherOutcomes?.length) {
-            meta.totalOtherOutcomes = outcomes.otherOutcomes.length;
-            nextOutcomes.otherOutcomes = outcomes.otherOutcomes.slice(0, limit);
+        const other = outcomes.otherOutcomes;
+        if (other && other.length > limit) {
+            meta.totalOtherOutcomes = other.length;
+            nextOutcomes.otherOutcomes = other.slice(0, limit);
+            trimmed = true;
+        }
+        if (trimmed) {
+            meta.outcomeLimit = limit;
+            nextPs = { ...nextPs, outcomesModule: nextOutcomes };
         }
-        nextPs = { ...nextPs, outcomesModule: nextOutcomes };
     }
     const refs = ps.referencesModule;
-    if (refs?.references?.length && input.referenceLimit != null) {
+    const referenceLimit = input.referenceLimit;
+    if (refs?.references && referenceLimit != null && refs.references.length > referenceLimit) {
         meta.totalReferences = refs.references.length;
+        meta.referenceLimit = referenceLimit;
         nextPs = {
             ...nextPs,
             referencesModule: {
                 ...refs,
-                references: refs.references.slice(0, input.referenceLimit),
+                references: refs.references.slice(0, referenceLimit),
             },
         };
     }
@@ -109,7 +131,7 @@ function summarizeResults(study) {
     return Object.keys(summary).length > 0 ? summary : undefined;
 }
 export const getStudy = tool('clinicaltrials_get_study_record', {
-    description: 'Fetch a single clinical trial study by NCT ID from ClinicalTrials.gov. Returns the full study record including protocol details, eligibility criteria, outcomes, arms, interventions, contacts, and locations. Optional locationLimit / outcomeLimit / referenceLimit / nearLocation parameters trim locations, outcomes, and references — original totals are preserved in `filtersApplied` whenever a cap is applied.',
+    description: 'Fetch a single clinical trial study by NCT ID from ClinicalTrials.gov. Returns the full study record including protocol details, eligibility criteria, outcomes, arms, interventions, contacts, and locations. Optional locationLimit / outcomeLimit / referenceLimit / nearLocation parameters trim locations, outcomes, and references — original totals are preserved in `filtersApplied` only when a cap actually trims the set.',
     annotations: {
         readOnlyHint: true,
         idempotentHint: true,
@@ -138,21 +160,21 @@ export const getStudy = tool('clinicaltrials_get_study_record', {
             .min(1)
             .max(500)
             .optional()
-            .describe('Optional cap on the number of locations returned. Omit for no cap (full upstream list). Pairs naturally with nearLocation for narrowing a large multi-site trial. Original total preserved in filtersApplied.totalLocations whenever a cap is applied.'),
+            .describe('Optional cap on the number of locations returned. Omit for no cap (full upstream list). Pairs naturally with nearLocation for narrowing a large multi-site trial. Original total preserved in filtersApplied.totalLocations only when the cap trims the list.'),
         outcomeLimit: z
             .number()
             .int()
             .min(1)
             .max(100)
             .optional()
-            .describe('Optional cap on the number of secondary and other outcomes returned. Omit for no cap (full upstream lists). Primary outcomes are never capped. Original totals preserved in filtersApplied.totalSecondaryOutcomes / totalOtherOutcomes whenever a cap is applied.'),
+            .describe('Optional cap on the number of secondary and other outcomes returned. Omit for no cap (full upstream lists). Primary outcomes are never capped. Original totals preserved in filtersApplied.totalSecondaryOutcomes / totalOtherOutcomes only when the cap trims a list.'),
         referenceLimit: z
             .number()
             .int()
             .min(1)
             .max(100)
             .optional()
-            .describe('Optional cap on the number of references returned. Omit for no cap (full upstream list). Original total preserved in filtersApplied.totalReferences whenever a cap is applied. seeAlsoLinks are never capped.'),
+            .describe('Optional cap on the number of references returned. Omit for no cap (full upstream list). Original total preserved in filtersApplied.totalReferences only when the cap trims the list. seeAlsoLinks are never capped.'),
         nearLocation: z
             .object({
             lat: z.number().min(-90).max(90).describe('Latitude in decimal degrees.'),
@@ -160,7 +182,7 @@ export const getStudy = tool('clinicaltrials_get_study_record', {
             radiusMi: z.number().min(1).max(500).default(50).describe('Radius in miles. Default 50.'),
         })
             .optional()
-            .describe('Filter returned locations to those within radius of (lat, lon) and sort by distance. Adds distanceMi to each location. Locations without published coordinates are dropped — most US sites carry them; international sites less reliably so. For broader geographic filtering across studies, use clinicaltrials_search_studies with geoFilter.'),
+            .describe('Filter returned locations to those within radius of (lat, lon) and sort by distance. Adds distanceMi to each location. Locations without published coordinates are dropped — most US sites carry them; international sites less reliably so. Distances reflect ClinicalTrials.gov geocoding granularity — typically city-centroid, not facility-level — so multiple sites in the same city resolve to near-identical distances. For broader geographic filtering across studies, use clinicaltrials_search_studies with geoFilter.'),
     }),
     output: z.object({
         study: z
@@ -193,9 +215,21 @@ export const getStudy = tool('clinicaltrials_get_study_record', {
                 .int()
                 .optional()
                 .describe('Upstream reference count before referenceLimit was applied.'),
-            locationLimit: z.number().int().optional().describe('Echo of the locationLimit input.'),
-            outcomeLimit: z.number().int().optional().describe('Echo of the outcomeLimit input.'),
-            referenceLimit: z.number().int().optional().describe('Echo of the referenceLimit input.'),
+            locationLimit: z
+                .number()
+                .int()
+                .optional()
+                .describe('Echo of the locationLimit input — present only when the cap trimmed the list.'),
+            outcomeLimit: z
+                .number()
+                .int()
+                .optional()
+                .describe('Echo of the outcomeLimit input — present only when the cap trimmed a list.'),
+            referenceLimit: z
+                .number()
+                .int()
+                .optional()
+                .describe('Echo of the referenceLimit input — present only when the cap trimmed the list.'),
             nearLocation: z
                 .object({
                 lat: z.number().describe('Latitude in decimal degrees.'),
@@ -245,13 +279,7 @@ export const getStudy = tool('clinicaltrials_get_study_record', {
         return {
             study: studyOut,
             ...(resultsSummary ? { resultsSummary } : {}),
-            filtersApplied: {
-                ...meta,
-                ...(input.locationLimit != null ? { locationLimit: input.locationLimit } : {}),
-                ...(input.outcomeLimit != null ? { outcomeLimit: input.outcomeLimit } : {}),
-                ...(input.referenceLimit != null ? { referenceLimit: input.referenceLimit } : {}),
-                ...(input.nearLocation ? { nearLocation: input.nearLocation } : {}),
-            },
+            filtersApplied: meta,
         };
     },
     format: (result) => {

package/dist/mcp-server/tools/definitions/get-study.tool.js.map CHANGED Viewed

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package/dist/mcp-server/tools/utils/query-helpers.d.ts CHANGED Viewed

@@ -2,7 +2,18 @@
  * @fileoverview Shared helpers for normalizing tool inputs into API search parameters.
  * @module mcp-server/tools/definitions/query-helpers
  */
-/** Normalize string | string[] to string[]. */
+/**
+ * Normalize `string | string[]` to `string[]`.
+ *
+ * LLM callers intermittently serialize array arguments as JSON strings
+ * (`'["RECRUITING","COMPLETED"]'` rather than `["RECRUITING","COMPLETED"]`). A
+ * `[`-leading string that `JSON.parse`s to an all-string array is unwrapped to
+ * that array. Every legitimate scalar this normalizes (status/phase enums, NCT
+ * IDs, PascalCase field names) starts with a letter, so a `[`-leading string is
+ * always either a stringified array or garbage — and garbage falls through to
+ * the scalar-wrap, preserving the prior behavior.
+ */
+export declare function toArray(v: string | string[]): string[];
 export declare function toArray(v: string | string[] | undefined): string[] | undefined;
 /** Build AREA[] phase filter and combine with user's advancedFilter. */
 export declare function buildAdvancedFilter(phaseFilter?: string[], advancedFilter?: string): string | undefined;

package/dist/mcp-server/tools/utils/query-helpers.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"query-helpers.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/utils/query-helpers.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH~~,+CAA+C~~;~~AAC/C~~,wBAAgB,OAAO,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,SAAS,GAAG,MAAM,EAAE,GAAG,SAAS,~~CAG9E~~;~~AAED~~,wEAAwE;AACxE,wBAAgB,mBAAmB,CACjC,WAAW,CAAC,EAAE,MAAM,EAAE,EACtB,cAAc,CAAC,EAAE,MAAM,GACtB,MAAM,GAAG,SAAS,CAWpB"}
1	+ {"version":3,"file":"query-helpers.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/utils/query-helpers.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH;;;;;;;;;;GAUG;AACH,wBAAgB,OAAO,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,EAAE,CAAC;AACxD,wBAAgB,OAAO,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,SAAS,GAAG,MAAM,EAAE,GAAG,SAAS,CAAC;AAkBhF,wEAAwE;AACxE,wBAAgB,mBAAmB,CACjC,WAAW,CAAC,EAAE,MAAM,EAAE,EACtB,cAAc,CAAC,EAAE,MAAM,GACtB,MAAM,GAAG,SAAS,CAWpB"}

package/dist/mcp-server/tools/utils/query-helpers.js CHANGED Viewed

@@ -2,11 +2,24 @@
  * @fileoverview Shared helpers for normalizing tool inputs into API search parameters.
  * @module mcp-server/tools/definitions/query-helpers
  */
-/** Normalize string | string[] to string[]. */
 export function toArray(v) {
     if (v === undefined)
         return;
-    return Array.isArray(v) ? v : [v];
+    if (Array.isArray(v))
+        return v;
+    const trimmed = v.trim();
+    if (trimmed.startsWith('[')) {
+        try {
+            const parsed = JSON.parse(trimmed);
+            if (Array.isArray(parsed) && parsed.every((x) => typeof x === 'string')) {
+                return parsed;
+            }
+        }
+        catch {
+            // Not valid JSON — fall through to the scalar-wrap (unchanged behavior).
+        }
+    }
+    return [v];
 }
 /** Build AREA[] phase filter and combine with user's advancedFilter. */
 export function buildAdvancedFilter(phaseFilter, advancedFilter) {

package/dist/mcp-server/tools/utils/query-helpers.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/clinical-trials/clinical-trials-service.d.ts CHANGED Viewed

@@ -39,8 +39,14 @@ export declare class ClinicalTrialsService {
     getMetadata(includeIndexedOnly: boolean, ctx: Context): Promise<FieldNode[]>;
     /** Get field value statistics for the specified fields. */
     getFieldValues(fields: string[], ctx: Context): Promise<FieldValueStats[]>;
-    /** Search the field model by keyword, returning ranked matches with paths and types. */
-    searchFieldDefinitions(query: string, limit: number, ctx: Context): Promise<FieldIndexEntry[]>;
+    /**
+     * Search the field model by keyword, returning ranked matches with paths and
+     * types plus the pre-cap match total for accurate truncation disclosure.
+     */
+    searchFieldDefinitions(query: string, limit: number, ctx: Context): Promise<{
+        entries: FieldIndexEntry[];
+        total: number;
+    }>;
     /** Lazy-load and memoize the flattened field index from /studies/metadata. */
     private getFieldIndex;
     /**

package/dist/services/clinical-trials/clinical-trials-service.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/clinical-trials/clinical-trials-service.js CHANGED Viewed

@@ -123,7 +123,10 @@ export class ClinicalTrialsService {
             throw err;
         }
     }
-    /** Search the field model by keyword, returning ranked matches with paths and types. */
+    /**
+     * Search the field model by keyword, returning ranked matches with paths and
+     * types plus the pre-cap match total for accurate truncation disclosure.
+     */
     async searchFieldDefinitions(query, limit, ctx) {
         ctx.log.debug('searchFieldDefinitions', { query, limit });
         const { entries } = await this.getFieldIndex(ctx);

package/dist/services/clinical-trials/clinical-trials-service.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/services/clinical-trials/field-search.d.ts CHANGED Viewed

@@ -25,8 +25,15 @@ export interface FieldIndexEntry {
 }
 /** Walk the metadata tree and emit one entry per node that has a `piece` name. */
 export declare function flattenMetadata(tree: FieldNode[]): FieldIndexEntry[];
-/** Rank entries by relevance to query and return the top `limit`. */
-export declare function searchFields(query: string, entries: FieldIndexEntry[], limit: number): FieldIndexEntry[];
+/**
+ * Rank entries by relevance to query and return the top `limit` along with the
+ * pre-cap match total, so callers can disclose truncation accurately — the slice
+ * alone can't distinguish "exactly `limit` matched" from "more than `limit`".
+ */
+export declare function searchFields(query: string, entries: FieldIndexEntry[], limit: number): {
+    entries: FieldIndexEntry[];
+    total: number;
+};
 /**
  * Suggest the closest valid `piece` names to an invalid input. Uses the same
  * keyword scoring first, falls back to Levenshtein distance for typos that

package/dist/services/clinical-trials/field-search.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"field-search.d.ts","sourceRoot":"","sources":["../../../src/services/clinical-trials/field-search.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAE5C,4EAA4E;AAC5E,MAAM,WAAW,eAAe;IAC9B,6CAA6C;IAC7C,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,oCAAoC;IACpC,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,2BAA2B;IAC3B,IAAI,EAAE,MAAM,CAAC;IACb,kDAAkD;IAClD,IAAI,EAAE,MAAM,CAAC;IACb,+EAA+E;IAC/E,KAAK,EAAE,MAAM,CAAC;IACd,gDAAgD;IAChD,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,8DAA8D;IAC9D,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,kFAAkF;AAClF,wBAAgB,eAAe,CAAC,IAAI,EAAE,SAAS,EAAE,GAAG,eAAe,EAAE,CAkBpE;AA2FD~~,qEAAqE~~;~~AACrE~~,wBAAgB,YAAY,CAC1B,KAAK,EAAE,MAAM,EACb,OAAO,EAAE,eAAe,EAAE,EAC1B,KAAK,EAAE,MAAM,GACZ,eAAe,EAAE,~~CAInB~~;AAED;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,EAAE,eAAe,EAAE,EAAE,CAAC,SAAI,GAAG,MAAM,EAAE,CAc1F"}
1	+ {"version":3,"file":"field-search.d.ts","sourceRoot":"","sources":["../../../src/services/clinical-trials/field-search.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAE5C,4EAA4E;AAC5E,MAAM,WAAW,eAAe;IAC9B,6CAA6C;IAC7C,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,oCAAoC;IACpC,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,2BAA2B;IAC3B,IAAI,EAAE,MAAM,CAAC;IACb,kDAAkD;IAClD,IAAI,EAAE,MAAM,CAAC;IACb,+EAA+E;IAC/E,KAAK,EAAE,MAAM,CAAC;IACd,gDAAgD;IAChD,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,8DAA8D;IAC9D,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,kFAAkF;AAClF,wBAAgB,eAAe,CAAC,IAAI,EAAE,SAAS,EAAE,GAAG,eAAe,EAAE,CAkBpE;AA2FD;;;;GAIG;AACH,wBAAgB,YAAY,CAC1B,KAAK,EAAE,MAAM,EACb,OAAO,EAAE,eAAe,EAAE,EAC1B,KAAK,EAAE,MAAM,GACZ;IAAE,OAAO,EAAE,eAAe,EAAE,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,CAI/C;AAED;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,EAAE,eAAe,EAAE,EAAE,CAAC,SAAI,GAAG,MAAM,EAAE,CAc1F"}

package/dist/services/clinical-trials/field-search.js CHANGED Viewed

@@ -120,11 +120,15 @@ function scoreEntry(query, entry) {
     const denom = Math.max(1, qSet.size);
     return Math.round((pieceHits * 200 + pieceCoverage * 300 + pathHits * 60 + descHits * 30) / denom);
 }
-/** Rank entries by relevance to query and return the top `limit`. */
+/**
+ * Rank entries by relevance to query and return the top `limit` along with the
+ * pre-cap match total, so callers can disclose truncation accurately — the slice
+ * alone can't distinguish "exactly `limit` matched" from "more than `limit`".
+ */
 export function searchFields(query, entries, limit) {
     const scored = entries.map((e) => ({ e, s: scoreEntry(query, e) })).filter((x) => x.s > 0);
     scored.sort((a, b) => b.s - a.s);
-    return scored.slice(0, Math.max(1, limit)).map((x) => x.e);
+    return { entries: scored.slice(0, Math.max(1, limit)).map((x) => x.e), total: scored.length };
 }
 /**
  * Suggest the closest valid `piece` names to an invalid input. Uses the same

package/dist/services/clinical-trials/field-search.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "clinicaltrialsgov-mcp-server",
-  "version": "2.7.0",
+  "version": "2.7.2",
   "mcpName": "io.github.cyanheads/clinicaltrialsgov-mcp-server",
   "description": "Search ClinicalTrials.gov trials, retrieve study details and results, and match patients to eligible trials via MCP. STDIO or Streamable HTTP.",
   "main": "dist/index.js",
@@ -106,8 +106,8 @@
     "zod": "^4.4.3"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.4.16",
-    "@cloudflare/workers-types": "4.20260611.1",
+    "@biomejs/biome": "^2.5.0",
+    "@cloudflare/workers-types": "4.20260613.1",
     "@types/bun": "^1.3.14",
     "@types/node": "25.9.3",
     "@vitest/coverage-istanbul": "^4.1.8",