clinicaltrialsgov-mcp-server 2.6.2 → 2.6.4

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Files changed (26) hide show
  1. package/README.md +1 -9
  2. package/dist/config/server-config.d.ts +0 -15
  3. package/dist/config/server-config.d.ts.map +1 -1
  4. package/dist/config/server-config.js +0 -35
  5. package/dist/config/server-config.js.map +1 -1
  6. package/dist/index.js +1 -20
  7. package/dist/index.js.map +1 -1
  8. package/dist/mcp-server/tools/definitions/find-eligible.tool.js +1 -1
  9. package/dist/mcp-server/tools/definitions/find-eligible.tool.js.map +1 -1
  10. package/dist/services/clinical-trials/clinical-trials-service.d.ts +0 -19
  11. package/dist/services/clinical-trials/clinical-trials-service.d.ts.map +1 -1
  12. package/dist/services/clinical-trials/clinical-trials-service.js +1 -226
  13. package/dist/services/clinical-trials/clinical-trials-service.js.map +1 -1
  14. package/package.json +2 -2
  15. package/dist/services/clinical-trials/mirror/index.d.ts +0 -31
  16. package/dist/services/clinical-trials/mirror/index.d.ts.map +0 -1
  17. package/dist/services/clinical-trials/mirror/index.js +0 -66
  18. package/dist/services/clinical-trials/mirror/index.js.map +0 -1
  19. package/dist/services/clinical-trials/mirror/ingester.d.ts +0 -39
  20. package/dist/services/clinical-trials/mirror/ingester.d.ts.map +0 -1
  21. package/dist/services/clinical-trials/mirror/ingester.js +0 -308
  22. package/dist/services/clinical-trials/mirror/ingester.js.map +0 -1
  23. package/dist/services/clinical-trials/mirror/types.d.ts +0 -68
  24. package/dist/services/clinical-trials/mirror/types.d.ts.map +0 -1
  25. package/dist/services/clinical-trials/mirror/types.js +0 -45
  26. package/dist/services/clinical-trials/mirror/types.js.map +0 -1
package/README.md CHANGED
@@ -7,7 +7,7 @@
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  <div align="center">
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- [![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-2.6.2-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/)
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+ [![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-2.6.4-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/)
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  </div>
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@@ -177,10 +177,6 @@ All configuration is optional — the server works with defaults and no API keys
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  | `CT_API_BASE_URL` | ClinicalTrials.gov API base URL. | `https://clinicaltrials.gov/api/v2` |
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  | `CT_REQUEST_TIMEOUT_MS` | Per-request timeout in milliseconds. | `30000` |
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  | `CT_MAX_PAGE_SIZE` | Maximum page size cap. | `200` |
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- | `CT_MIRROR_ENABLED` | Enable the local SQLite study mirror. | `false` |
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- | `CT_MIRROR_PATH` | Filesystem path for the mirror database. | `./clinical-trials-mirror.db` |
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- | `CT_MIRROR_REFRESH_CRON` | Cron schedule for incremental mirror sync. | `0 3 * * *` (3 AM daily) |
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- | `CT_MIRROR_FALLBACK_LIVE` | Fall back to live API when mirror is not yet bootstrapped. | `true` |
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  | `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http`. | `stdio` |
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  | `MCP_HTTP_PORT` | Port for HTTP server. | `3010` |
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  | `MCP_AUTH_MODE` | Auth mode: `none`, `jwt`, or `oauth`. | `none` |
@@ -188,10 +184,6 @@ All configuration is optional — the server works with defaults and no API keys
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  | `LOGS_DIR` | Directory for log files (Node.js only). | `<project-root>/logs` |
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  | `OTEL_ENABLED` | Enable OpenTelemetry tracing. | `false` |
190
186
 
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- ### Local study mirror (opt-in)
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-
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- Setting `CT_MIRROR_ENABLED=true` activates a self-refreshing SQLite+FTS5 local mirror of the ~577K-study corpus. Search and count queries route to the mirror first, with transparent fallback to the live API when the mirror is not yet ready (`CT_MIRROR_FALLBACK_LIVE=true`, the default). The mirror must be bootstrapped out-of-band before it becomes ready — while enabled but not yet bootstrapped it falls through to the live API identically to the disabled state. Once bootstrapped, the mirror eliminates live-API round-trips for most search and lookup operations. Full-record lookups (`clinicaltrials_get_study_record`), results data, field definitions, and field values remain live-API only.
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-
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  ## Running the Server
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  ### Local Development
package/dist/config/server-config.d.ts CHANGED
@@ -8,23 +8,8 @@ declare const ServerConfigSchema: z.ZodObject<{
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  requestTimeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
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  maxPageSize: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
10
10
  }, z.core.$strip>;
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- /** Mirror-specific configuration parsed separately from the flat env var set. */
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- declare const MirrorConfigSchema: z.ZodObject<{
13
- enabled: z.ZodDefault<z.ZodCoercedBoolean<unknown>>;
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- path: z.ZodDefault<z.ZodString>;
15
- refreshCron: z.ZodDefault<z.ZodString>;
16
- fallbackLive: z.ZodDefault<z.ZodCoercedBoolean<unknown>>;
17
- }, z.core.$strip>;
18
11
  export type ServerConfig = z.infer<typeof ServerConfigSchema>;
19
- export type MirrorConfig = z.infer<typeof MirrorConfigSchema> & {
20
- /** API base URL forwarded from the main config for the mirror ingester. */
21
- apiBaseUrl: string;
22
- /** Per-request timeout forwarded from the main config for the mirror ingester. */
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- requestTimeoutMs: number;
24
- };
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12
  /** Get server configuration (lazy-parsed from env vars). */
26
13
  export declare function getServerConfig(): ServerConfig;
27
- /** Get mirror configuration (lazy-parsed from env vars). */
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- export declare function getMirrorConfig(): MirrorConfig;
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14
  export {};
30
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  //# sourceMappingURL=server-config.d.ts.map
package/dist/config/server-config.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,QAAA,MAAM,kBAAkB;;;;iBAOtB,CAAC;AAEH,iFAAiF;AACjF,QAAA,MAAM,kBAAkB;;;;;iBActB,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAC9D,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,GAAG;IAC9D,2EAA2E;IAC3E,UAAU,EAAE,MAAM,CAAC;IACnB,kFAAkF;IAClF,gBAAgB,EAAE,MAAM,CAAC;CAC1B,CAAC;AAKF,4DAA4D;AAC5D,wBAAgB,eAAe,IAAI,YAAY,CAO9C;AAED,4DAA4D;AAC5D,wBAAgB,eAAe,IAAI,YAAY,CAgB9C"}
1
+ {"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,QAAA,MAAM,kBAAkB;;;;iBAOtB,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,4DAA4D;AAC5D,wBAAgB,eAAe,IAAI,YAAY,CAO9C"}
package/dist/config/server-config.js CHANGED
@@ -12,24 +12,7 @@ const ServerConfigSchema = z.object({
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  requestTimeoutMs: z.coerce.number().default(30_000).describe('Per-request timeout in ms'),
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13
  maxPageSize: z.coerce.number().default(200).describe('Maximum page size cap'),
14
14
  });
15
- /** Mirror-specific configuration parsed separately from the flat env var set. */
16
- const MirrorConfigSchema = z.object({
17
- enabled: z.coerce.boolean().default(false).describe('Enable the local SQLite study mirror'),
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- path: z
19
- .string()
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- .default('./clinical-trials-mirror.db')
21
- .describe('Filesystem path for the mirror SQLite database'),
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- refreshCron: z
23
- .string()
24
- .default('0 3 * * *')
25
- .describe('Cron expression for incremental mirror refresh (default: 3 AM daily)'),
26
- fallbackLive: z.coerce
27
- .boolean()
28
- .default(true)
29
- .describe('Fall back to live API when mirror is not ready'),
30
- });
31
15
  let _config;
32
- let _mirrorConfig;
33
16
  /** Get server configuration (lazy-parsed from env vars). */
34
17
  export function getServerConfig() {
35
18
  _config ??= parseEnvConfig(ServerConfigSchema, {
@@ -39,22 +22,4 @@ export function getServerConfig() {
39
22
  });
40
23
  return _config;
41
24
  }
42
- /** Get mirror configuration (lazy-parsed from env vars). */
43
- export function getMirrorConfig() {
44
- if (!_mirrorConfig) {
45
- const base = parseEnvConfig(MirrorConfigSchema, {
46
- enabled: 'CT_MIRROR_ENABLED',
47
- path: 'CT_MIRROR_PATH',
48
- refreshCron: 'CT_MIRROR_REFRESH_CRON',
49
- fallbackLive: 'CT_MIRROR_FALLBACK_LIVE',
50
- });
51
- const server = getServerConfig();
52
- _mirrorConfig = {
53
- ...base,
54
- apiBaseUrl: server.apiBaseUrl,
55
- requestTimeoutMs: server.requestTimeoutMs,
56
- };
57
- }
58
- return _mirrorConfig;
59
- }
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  //# sourceMappingURL=server-config.js.map
package/dist/config/server-config.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"server-config.js","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,EAAE,cAAc,EAAE,MAAM,+BAA+B,CAAC;AAE/D,MAAM,kBAAkB,GAAG,CAAC,CAAC,MAAM,CAAC;IAClC,UAAU,EAAE,CAAC;SACV,MAAM,EAAE;SACR,OAAO,CAAC,mCAAmC,CAAC;SAC5C,QAAQ,CAAC,iCAAiC,CAAC;IAC9C,gBAAgB,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,2BAA2B,CAAC;IACzF,WAAW,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,uBAAuB,CAAC;CAC9E,CAAC,CAAC;AAEH,iFAAiF;AACjF,MAAM,kBAAkB,GAAG,CAAC,CAAC,MAAM,CAAC;IAClC,OAAO,EAAE,CAAC,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,QAAQ,CAAC,sCAAsC,CAAC;IAC3F,IAAI,EAAE,CAAC;SACJ,MAAM,EAAE;SACR,OAAO,CAAC,6BAA6B,CAAC;SACtC,QAAQ,CAAC,gDAAgD,CAAC;IAC7D,WAAW,EAAE,CAAC;SACX,MAAM,EAAE;SACR,OAAO,CAAC,WAAW,CAAC;SACpB,QAAQ,CAAC,sEAAsE,CAAC;IACnF,YAAY,EAAE,CAAC,CAAC,MAAM;SACnB,OAAO,EAAE;SACT,OAAO,CAAC,IAAI,CAAC;SACb,QAAQ,CAAC,gDAAgD,CAAC;CAC9D,CAAC,CAAC;AAUH,IAAI,OAAiC,CAAC;AACtC,IAAI,aAAuC,CAAC;AAE5C,4DAA4D;AAC5D,MAAM,UAAU,eAAe;IAC7B,OAAO,KAAK,cAAc,CAAC,kBAAkB,EAAE;QAC7C,UAAU,EAAE,iBAAiB;QAC7B,gBAAgB,EAAE,uBAAuB;QACzC,WAAW,EAAE,kBAAkB;KAChC,CAAC,CAAC;IACH,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,4DAA4D;AAC5D,MAAM,UAAU,eAAe;IAC7B,IAAI,CAAC,aAAa,EAAE,CAAC;QACnB,MAAM,IAAI,GAAG,cAAc,CAAC,kBAAkB,EAAE;YAC9C,OAAO,EAAE,mBAAmB;YAC5B,IAAI,EAAE,gBAAgB;YACtB,WAAW,EAAE,wBAAwB;YACrC,YAAY,EAAE,yBAAyB;SACxC,CAAC,CAAC;QACH,MAAM,MAAM,GAAG,eAAe,EAAE,CAAC;QACjC,aAAa,GAAG;YACd,GAAG,IAAI;YACP,UAAU,EAAE,MAAM,CAAC,UAAU;YAC7B,gBAAgB,EAAE,MAAM,CAAC,gBAAgB;SAC1C,CAAC;IACJ,CAAC;IACD,OAAO,aAAa,CAAC;AACvB,CAAC"}
1
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package/dist/index.js CHANGED
@@ -4,13 +4,10 @@
4
4
  * @module index
5
5
  */
6
6
  import { createApp } from '@cyanheads/mcp-ts-core';
7
- import { schedulerService } from '@cyanheads/mcp-ts-core/utils';
8
- import { getMirrorConfig } from './config/server-config.js';
9
7
  import { allPromptDefinitions } from './mcp-server/prompts/definitions/index.js';
10
8
  import { allResourceDefinitions } from './mcp-server/resources/definitions/index.js';
11
9
  import { allToolDefinitions } from './mcp-server/tools/definitions/index.js';
12
10
  import { initClinicalTrialsService } from './services/clinical-trials/clinical-trials-service.js';
13
- import { getClinicalTrialsMirror, initMirror } from './services/clinical-trials/mirror/index.js';
14
11
  await createApp({
15
12
  tools: allToolDefinitions,
16
13
  resources: allResourceDefinitions,
@@ -19,24 +16,8 @@ await createApp({
19
16
  landing: {
20
17
  requireAuth: false,
21
18
  },
22
- async setup({ config }) {
19
+ setup() {
23
20
  initClinicalTrialsService();
24
- const mirrorConfig = getMirrorConfig();
25
- if (mirrorConfig.enabled) {
26
- initMirror(mirrorConfig);
27
- // Schedule incremental refresh on HTTP transport only — stdio operators
28
- // run the server per-request and don't benefit from a persistent cron.
29
- // The full init must be run out-of-band (bootstrap script, CLI, or manual runSync).
30
- if (config.mcpTransportType === 'http') {
31
- const mirror = getClinicalTrialsMirror();
32
- if (mirror) {
33
- await schedulerService.schedule('ct-mirror-refresh', mirrorConfig.refreshCron, async (_ctx) => {
34
- await mirror.runSync({ mode: 'refresh' });
35
- }, 'Incremental ClinicalTrials.gov mirror refresh');
36
- schedulerService.start('ct-mirror-refresh');
37
- }
38
- }
39
- }
40
21
  },
41
22
  });
42
23
  //# sourceMappingURL=index.js.map
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/dist/mcp-server/tools/definitions/find-eligible.tool.js CHANGED
@@ -153,7 +153,7 @@ export const findEligible = tool('clinicaltrials_find_eligible', {
153
153
  input.location.country,
154
154
  ].filter(Boolean);
155
155
  const locationQuery = locationParts.join(', ');
156
- const statusFilter = input.recruitingOnly ? ['RECRUITING', 'NOT_YET_RECRUITING'] : undefined;
156
+ const statusFilter = input.recruitingOnly ? ['RECRUITING'] : undefined;
157
157
  const advancedParts = [
158
158
  `AREA[MinimumAge]RANGE[MIN, ${input.age} years]`,
159
159
  `AREA[MaximumAge]RANGE[${input.age} years, MAX]`,
package/dist/mcp-server/tools/definitions/find-eligible.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/services/clinical-trials/clinical-trials-service.d.ts CHANGED
@@ -1,12 +1,8 @@
1
1
  /**
2
2
  * @fileoverview ClinicalTrials.gov REST API v2 client with retry, rate limiting, and timeout.
3
- * Routes search and count operations to the local mirror when enabled and ready,
4
- * falling back to the live API when the mirror is unavailable or the query requires
5
- * features the mirror cannot answer (geo filters, complex AREA[] expressions).
6
3
  * @module services/clinical-trials/clinical-trials-service
7
4
  */
8
5
  import type { Context } from '@cyanheads/mcp-ts-core';
9
- import type { MirrorStatus } from '@cyanheads/mcp-ts-core/mirror';
10
6
  import { type ServerConfig } from '../../config/server-config.js';
11
7
  import { type FieldIndexEntry } from './field-search.js';
12
8
  import type { FieldNode, FieldValueStats, PagedStudiesResponse, SearchParams, Study } from './types.js';
@@ -39,27 +35,12 @@ export declare class ClinicalTrialsService {
39
35
  getStudy(nctId: string, ctx: Context): Promise<Study>;
40
36
  /** Fetch multiple studies by NCT IDs in a single request. Returns identification and results section data. */
41
37
  getStudiesBatch(nctIds: string[], ctx: Context): Promise<Study[]>;
42
- /**
43
- * Return current mirror status, or `undefined` when the mirror is disabled.
44
- * Exposed so tools can surface mirror state to agents when useful.
45
- */
46
- mirrorStatus(): Promise<MirrorStatus | undefined>;
47
38
  /** Get field definitions (metadata tree) from the data model. */
48
39
  getMetadata(includeIndexedOnly: boolean, ctx: Context): Promise<FieldNode[]>;
49
40
  /** Get field value statistics for the specified fields. */
50
41
  getFieldValues(fields: string[], ctx: Context): Promise<FieldValueStats[]>;
51
42
  /** Search the field model by keyword, returning ranked matches with paths and types. */
52
43
  searchFieldDefinitions(query: string, limit: number, ctx: Context): Promise<FieldIndexEntry[]>;
53
- /**
54
- * Attempt to serve a `searchStudies` call from the local mirror.
55
- *
56
- * Returns `null` when the mirror is not ready, or when the query uses
57
- * features the mirror cannot answer (geo filters, complex AREA[] advanced
58
- * filters, field selection beyond the metadata tier, or pageToken
59
- * continuation from a previous live-API page). In all of those cases the
60
- * caller falls through to the live API.
61
- */
62
- private tryMirrorSearch;
63
44
  /** Lazy-load and memoize the flattened field index from /studies/metadata. */
64
45
  private getFieldIndex;
65
46
  /**
package/dist/services/clinical-trials/clinical-trials-service.d.ts.map CHANGED
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package/dist/services/clinical-trials/clinical-trials-service.js CHANGED
@@ -1,15 +1,11 @@
1
1
  /**
2
2
  * @fileoverview ClinicalTrials.gov REST API v2 client with retry, rate limiting, and timeout.
3
- * Routes search and count operations to the local mirror when enabled and ready,
4
- * falling back to the live API when the mirror is unavailable or the query requires
5
- * features the mirror cannot answer (geo filters, complex AREA[] expressions).
6
3
  * @module services/clinical-trials/clinical-trials-service
7
4
  */
8
5
  import { JsonRpcErrorCode, McpError, notFound, rateLimited, serviceUnavailable, validationError, } from '@cyanheads/mcp-ts-core/errors';
9
6
  import { httpErrorFromResponse } from '@cyanheads/mcp-ts-core/utils';
10
- import { getMirrorConfig, getServerConfig } from '../../config/server-config.js';
7
+ import { getServerConfig } from '../../config/server-config.js';
11
8
  import { flattenMetadata, nearestPieces, searchFields, } from './field-search.js';
12
- import { getClinicalTrialsMirror } from './mirror/index.js';
13
9
  const DEFAULT_MAX_RETRIES = 3;
14
10
  const DEFAULT_BASE_BACKOFF_MS = 1000;
15
11
  const DEFAULT_MAX_BACKOFF_MS = 30_000;
@@ -55,13 +51,6 @@ export class ClinicalTrialsService {
55
51
  }
56
52
  /** Search studies with query, filters, pagination, and field selection. */
57
53
  async searchStudies(params, ctx) {
58
- // Route to the local mirror when it is ready and the query is mirrorable.
59
- const mirror = getClinicalTrialsMirror();
60
- if (mirror) {
61
- const mirrorResult = await this.tryMirrorSearch(params, mirror, ctx);
62
- if (mirrorResult !== null)
63
- return mirrorResult;
64
- }
65
54
  if (this.validateFieldsLocally && params.fields?.length) {
66
55
  const normalized = await this.normalizeFields(params.fields, ctx);
67
56
  await this.validateFields(normalized, ctx);
@@ -79,16 +68,6 @@ export class ClinicalTrialsService {
79
68
  /** Fetch multiple studies by NCT IDs in a single request. Returns identification and results section data. */
80
69
  async getStudiesBatch(nctIds, ctx) {
81
70
  ctx.log.debug('getStudiesBatch', { count: nctIds.length });
82
- // Route to mirror for ID-targeted lookups when mirror is ready.
83
- const mirror = getClinicalTrialsMirror();
84
- if (mirror && (await mirror.ready())) {
85
- const rows = await mirror.getByIds(nctIds);
86
- if (rows.length > 0) {
87
- ctx.log.debug('getStudiesBatch served from mirror', { count: rows.length });
88
- return rows.map(mirrorRowToStudy);
89
- }
90
- // Mirror has no rows for these IDs → fall through to live API.
91
- }
92
71
  const response = await this.searchStudies({
93
72
  filterIds: nctIds,
94
73
  fields: ['NCTId', 'BriefTitle', 'HasResults', 'ResultsSection'],
@@ -98,16 +77,6 @@ export class ClinicalTrialsService {
98
77
  }, ctx);
99
78
  return response.studies;
100
79
  }
101
- /**
102
- * Return current mirror status, or `undefined` when the mirror is disabled.
103
- * Exposed so tools can surface mirror state to agents when useful.
104
- */
105
- async mirrorStatus() {
106
- const mirror = getClinicalTrialsMirror();
107
- if (!mirror)
108
- return;
109
- return await mirror.status();
110
- }
111
80
  /** Get field definitions (metadata tree) from the data model. */
112
81
  getMetadata(includeIndexedOnly, ctx) {
113
82
  ctx.log.debug('getMetadata', { includeIndexedOnly });
@@ -153,106 +122,6 @@ export class ClinicalTrialsService {
153
122
  return searchFields(query, entries, limit);
154
123
  }
155
124
  /* ------------------------------------------------------------------ */
156
- /* Mirror routing */
157
- /* ------------------------------------------------------------------ */
158
- /**
159
- * Attempt to serve a `searchStudies` call from the local mirror.
160
- *
161
- * Returns `null` when the mirror is not ready, or when the query uses
162
- * features the mirror cannot answer (geo filters, complex AREA[] advanced
163
- * filters, field selection beyond the metadata tier, or pageToken
164
- * continuation from a previous live-API page). In all of those cases the
165
- * caller falls through to the live API.
166
- */
167
- async tryMirrorSearch(params, mirror, ctx) {
168
- // Only serve from mirror when a full sync has ever completed.
169
- const ready = await mirror.ready();
170
- if (!ready) {
171
- const fallback = getMirrorConfig().fallbackLive;
172
- if (!fallback) {
173
- throw serviceUnavailable('Clinical-trials mirror is not ready and CT_MIRROR_FALLBACK_LIVE is disabled.', { hint: 'Run the mirror init script to bootstrap the local database.' });
174
- }
175
- ctx.log.debug('Mirror not ready — falling back to live API');
176
- return null;
177
- }
178
- // Mirror cannot handle: geo filters, advanced AREA[] expressions, or
179
- // pageToken continuation (tokens belong to the live API's pagination state).
180
- if (params.filterGeo || params.filterAdvanced || params.pageToken) {
181
- ctx.log.debug('Query not mirrorable — falling back to live API', {
182
- reason: params.filterGeo
183
- ? 'geo_filter'
184
- : params.filterAdvanced
185
- ? 'advanced_filter'
186
- : 'page_token',
187
- });
188
- return null;
189
- }
190
- // Build FTS match string from free-text query parameters.
191
- const ftsTerms = [];
192
- if (params.queryTerm)
193
- ftsTerms.push(sanitizeFts(params.queryTerm));
194
- if (params.queryCond)
195
- ftsTerms.push(sanitizeFts(params.queryCond));
196
- if (params.queryIntr)
197
- ftsTerms.push(sanitizeFts(params.queryIntr));
198
- if (params.querySpons)
199
- ftsTerms.push(sanitizeFts(params.querySpons));
200
- if (params.queryTitles)
201
- ftsTerms.push(sanitizeFts(params.queryTitles));
202
- // queryLocn and queryOutc are not in the FTS index — fall through to live.
203
- if (params.queryLocn || params.queryOutc) {
204
- ctx.log.debug('Query uses non-indexed fields — falling back to live API', {
205
- reason: params.queryLocn ? 'location_query' : 'outcome_query',
206
- });
207
- return null;
208
- }
209
- const match = ftsTerms.join(' ') || undefined;
210
- // Build structured filters for indexed columns.
211
- const filters = [];
212
- if (params.filterOverallStatus?.length === 1) {
213
- filters.push({
214
- column: 'overall_status',
215
- op: 'eq',
216
- value: params.filterOverallStatus[0],
217
- });
218
- }
219
- else if (params.filterOverallStatus?.length) {
220
- filters.push({ column: 'overall_status', op: 'in', value: params.filterOverallStatus });
221
- }
222
- // ID filter — if filterIds set, use getByIds for O(1) lookup.
223
- if (params.filterIds?.length) {
224
- const rows = await mirror.getByIds(params.filterIds);
225
- ctx.log.debug('Mirror ID lookup', { requested: params.filterIds.length, found: rows.length });
226
- const studies = rows.map(mirrorRowToStudy);
227
- return {
228
- studies,
229
- totalCount: studies.length,
230
- };
231
- }
232
- const limit = Math.min(params.pageSize ?? 10, this.maxPageSize);
233
- const offset = 0; // pageToken-based continuation not supported for mirror
234
- const result = await mirror.query({
235
- match,
236
- filters,
237
- sort: match ? 'relevance' : undefined,
238
- limit,
239
- offset,
240
- });
241
- ctx.log.debug('Mirror search', {
242
- match,
243
- filters: filters.length,
244
- total: result.total,
245
- returned: result.rows.length,
246
- });
247
- const studies = result.rows.map(mirrorRowToStudy);
248
- return {
249
- studies,
250
- // countTotal support: return total when params.countTotal !== false (default true)
251
- ...(params.countTotal !== false ? { totalCount: result.total } : {}),
252
- // No nextPageToken — mirror queries don't use cursor pagination
253
- };
254
- }
255
- /* ------------------------------------------------------------------ */
256
125
  /* Internal */
257
126
  /* ------------------------------------------------------------------ */
258
127
  /** Lazy-load and memoize the flattened field index from /studies/metadata. */
@@ -580,100 +449,6 @@ export class ClinicalTrialsService {
580
449
  }
581
450
  }
582
451
  /* ------------------------------------------------------------------ */
583
- /* Mirror helpers */
584
- /* ------------------------------------------------------------------ */
585
- /**
586
- * Convert a mirror row back to the nested study shape that tool handlers expect.
587
- * Only metadata-tier fields are populated; fields not stored in the mirror
588
- * (e.g., full eligibility details, derived MeSH terms, results section) are
589
- * omitted. Callers that need the full ~70KB record must use the live API.
590
- */
591
- function mirrorRowToStudy(rawRow) {
592
- const row = rawRow;
593
- return {
594
- protocolSection: {
595
- identificationModule: {
596
- ...(row.nct_id && { nctId: row.nct_id }),
597
- ...(row.brief_title && { briefTitle: row.brief_title }),
598
- ...(row.official_title && { officialTitle: row.official_title }),
599
- },
600
- statusModule: {
601
- ...(row.overall_status && { overallStatus: row.overall_status }),
602
- ...(row.start_date && { startDateStruct: { date: row.start_date } }),
603
- ...(row.primary_completion_date && {
604
- primaryCompletionDateStruct: { date: row.primary_completion_date },
605
- }),
606
- ...(row.last_update_post_date && {
607
- lastUpdatePostDateStruct: { date: row.last_update_post_date },
608
- }),
609
- },
610
- designModule: {
611
- ...(row.study_type && { studyType: row.study_type }),
612
- ...(row.phases && { phases: row.phases.split('|').filter(Boolean) }),
613
- ...(row.enrollment_count != null && {
614
- enrollmentInfo: { count: row.enrollment_count },
615
- }),
616
- },
617
- sponsorCollaboratorsModule: {
618
- ...(row.lead_sponsor_name || row.lead_sponsor_class
619
- ? {
620
- leadSponsor: {
621
- ...(row.lead_sponsor_name && { name: row.lead_sponsor_name }),
622
- ...(row.lead_sponsor_class && { class: row.lead_sponsor_class }),
623
- },
624
- }
625
- : {}),
626
- },
627
- conditionsModule: {
628
- ...(row.conditions && { conditions: row.conditions.split('|').filter(Boolean) }),
629
- },
630
- armsInterventionsModule: {
631
- ...(row.interventions && {
632
- interventions: row.interventions
633
- .split('|')
634
- .filter(Boolean)
635
- .map((name) => ({ name })),
636
- }),
637
- },
638
- eligibilityModule: {
639
- ...(row.eligibility_criteria && { eligibilityCriteria: row.eligibility_criteria }),
640
- ...(row.minimum_age && { minimumAge: row.minimum_age }),
641
- ...(row.maximum_age && { maximumAge: row.maximum_age }),
642
- ...(row.sex && { sex: row.sex }),
643
- ...(row.std_ages && { stdAges: row.std_ages.split('|').filter(Boolean) }),
644
- ...(row.healthy_volunteers != null && {
645
- healthyVolunteers: row.healthy_volunteers === 1,
646
- }),
647
- },
648
- contactsLocationsModule: {
649
- ...(row.locations && {
650
- locations: row.locations
651
- .split('|')
652
- .filter(Boolean)
653
- .map((loc) => {
654
- const [city, state, country] = loc.split(', ');
655
- return {
656
- ...(city && { city }),
657
- ...(state && { state }),
658
- ...(country && { country }),
659
- };
660
- }),
661
- }),
662
- },
663
- },
664
- ...(row.has_results != null && { hasResults: row.has_results === 1 }),
665
- };
666
- }
667
- /**
668
- * Sanitize a free-text query for FTS5 MATCH syntax.
669
- * Strips characters that FTS5 treats as special operators unless the caller
670
- * intentionally uses them. Preserves AND/OR/NOT boolean operators.
671
- */
672
- function sanitizeFts(query) {
673
- // Remove characters that break FTS5 MATCH parsing.
674
- return query.replace(/["*^()[\]]/g, ' ').trim();
675
- }
676
- /* ------------------------------------------------------------------ */
677
452
  /* Init / Accessor */
678
453
  /* ------------------------------------------------------------------ */
679
454
  let _service;