clinicaltrialsgov-mcp-server 2.4.7 → 2.4.9

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Files changed (32) hide show
  1. package/README.md +2 -2
  2. package/dist/index.js +1 -0
  3. package/dist/index.js.map +1 -1
  4. package/dist/mcp-server/tools/definitions/find-eligible.tool.d.ts.map +1 -1
  5. package/dist/mcp-server/tools/definitions/find-eligible.tool.js +1 -1
  6. package/dist/mcp-server/tools/definitions/find-eligible.tool.js.map +1 -1
  7. package/dist/mcp-server/tools/definitions/get-study-count.tool.d.ts +6 -1
  8. package/dist/mcp-server/tools/definitions/get-study-count.tool.d.ts.map +1 -1
  9. package/dist/mcp-server/tools/definitions/get-study-count.tool.js +17 -5
  10. package/dist/mcp-server/tools/definitions/get-study-count.tool.js.map +1 -1
  11. package/dist/mcp-server/tools/definitions/get-study-results.tool.d.ts.map +1 -1
  12. package/dist/mcp-server/tools/definitions/get-study-results.tool.js +57 -12
  13. package/dist/mcp-server/tools/definitions/get-study-results.tool.js.map +1 -1
  14. package/dist/mcp-server/tools/definitions/get-study.tool.d.ts +14 -0
  15. package/dist/mcp-server/tools/definitions/get-study.tool.d.ts.map +1 -1
  16. package/dist/mcp-server/tools/definitions/get-study.tool.js +110 -15
  17. package/dist/mcp-server/tools/definitions/get-study.tool.js.map +1 -1
  18. package/dist/mcp-server/tools/definitions/search-studies.tool.d.ts +6 -1
  19. package/dist/mcp-server/tools/definitions/search-studies.tool.d.ts.map +1 -1
  20. package/dist/mcp-server/tools/definitions/search-studies.tool.js +26 -8
  21. package/dist/mcp-server/tools/definitions/search-studies.tool.js.map +1 -1
  22. package/dist/mcp-server/tools/utils/recovery-hints.d.ts +1 -0
  23. package/dist/mcp-server/tools/utils/recovery-hints.d.ts.map +1 -1
  24. package/dist/mcp-server/tools/utils/recovery-hints.js +1 -0
  25. package/dist/mcp-server/tools/utils/recovery-hints.js.map +1 -1
  26. package/dist/services/clinical-trials/clinical-trials-service.d.ts +8 -0
  27. package/dist/services/clinical-trials/clinical-trials-service.d.ts.map +1 -1
  28. package/dist/services/clinical-trials/clinical-trials-service.js +75 -3
  29. package/dist/services/clinical-trials/clinical-trials-service.js.map +1 -1
  30. package/dist/services/clinical-trials/types.d.ts +4 -0
  31. package/dist/services/clinical-trials/types.d.ts.map +1 -1
  32. package/package.json +9 -9
package/README.md CHANGED
@@ -10,11 +10,11 @@
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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)
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  [![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)
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- [![Version](https://img.shields.io/badge/Version-2.4.7-blue.svg?style=flat-square)](./CHANGELOG.md)
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+ [![Version](https://img.shields.io/badge/Version-2.4.9-blue.svg?style=flat-square)](./CHANGELOG.md)
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  [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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- [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.28.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
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+ [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
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  [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE)
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  [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/)
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package/dist/index.js CHANGED
@@ -12,6 +12,7 @@ await createApp({
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  tools: allToolDefinitions,
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  resources: allResourceDefinitions,
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  prompts: allPromptDefinitions,
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+ instructions: `Use the clinicaltrials_* tools to access the ClinicalTrials.gov registry — public, read-only, ~577K studies. Studies are addressed by NCT ID (NCT followed by 8 digits). Field names for the fields, advancedFilter, and sort parameters are PascalCase leaves (NCTId, OverallStatus, EnrollmentCount) — call clinicaltrials_get_field_definitions to discover them and clinicaltrials_get_field_values for valid enum values. Typical workflow: clinicaltrials_search_studies (pass fields to trim ~70KB records) → clinicaltrials_get_study_record → clinicaltrials_get_study_results (only when hasResults=true). Use clinicaltrials_get_study_count for cheap breakdowns and clinicaltrials_find_eligible for patient matching.`,
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  setup() {
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  initClinicalTrialsService();
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  },
package/dist/index.js.map CHANGED
@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/find-eligible.tool.d.ts.map CHANGED
@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/find-eligible.tool.js CHANGED
@@ -85,7 +85,7 @@ export const findEligible = tool('clinicaltrials_find_eligible', {
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  conditions: z
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  .array(z.string())
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  .min(1)
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- .describe('Medical conditions or diagnoses. E.g., ["Type 2 Diabetes", "Hypertension"].'),
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+ .describe('Medical conditions or diagnoses. E.g., ["Type 2 Diabetes", "Hypertension"]. Plain words only — brackets, parentheses, and commas inside an entry will trip the upstream Essie parser.'),
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  location: z
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  .object({
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  country: z.string().describe('Country name. E.g., "United States".'),
package/dist/mcp-server/tools/definitions/find-eligible.tool.js.map CHANGED
@@ -1 +1 @@
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1
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package/dist/mcp-server/tools/definitions/get-study-count.tool.d.ts CHANGED
@@ -20,8 +20,13 @@ export declare const getStudyCount: import("@cyanheads/mcp-ts-core").ToolDefinit
20
20
  }, z.core.$strip>, readonly [{
21
21
  readonly reason: "field_invalid";
22
22
  readonly code: JsonRpcErrorCode.ValidationError;
23
- readonly when: "A field name in the advanced filter is invalid (often a module name instead of a piece name).";
23
+ readonly when: "A field name in the advanced filter or AREA[] expression is invalid (often a module name instead of a piece name).";
24
24
  readonly recovery: "Call clinicaltrials_get_field_definitions to browse the field tree; use PascalCase piece names like OverallStatus, Phase, or StudyType.";
25
+ }, {
26
+ readonly reason: "query_parse_error";
27
+ readonly code: JsonRpcErrorCode.ValidationError;
28
+ readonly when: "A free-text query or advancedFilter expression uses syntax the upstream Essie parser rejects — typically a reserved character ([, ], (, ), or comma) in a query/conditionQuery/etc. value.";
29
+ readonly recovery: "Field-scoped search uses advancedFilter with AREA[FieldName]value (call clinicaltrials_get_field_definitions to look up the right FieldName); free-text fields (query, conditionQuery, etc.) take plain words plus AND, OR, NOT — brackets, parentheses, and commas are reserved by the upstream parser.";
25
30
  }, {
26
31
  readonly reason: "rate_limited";
27
32
  readonly code: JsonRpcErrorCode.RateLimited;
package/dist/mcp-server/tools/definitions/get-study-count.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
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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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+IxB,CAAC"}
package/dist/mcp-server/tools/definitions/get-study-count.tool.js CHANGED
@@ -18,9 +18,15 @@ export const getStudyCount = tool('clinicaltrials_get_study_count', {
18
18
  {
19
19
  reason: 'field_invalid',
20
20
  code: JsonRpcErrorCode.ValidationError,
21
- when: 'A field name in the advanced filter is invalid (often a module name instead of a piece name).',
21
+ when: 'A field name in the advanced filter or AREA[] expression is invalid (often a module name instead of a piece name).',
22
22
  recovery: RECOVERY_HINTS.field_invalid,
23
23
  },
24
+ {
25
+ reason: 'query_parse_error',
26
+ code: JsonRpcErrorCode.ValidationError,
27
+ when: 'A free-text query or advancedFilter expression uses syntax the upstream Essie parser rejects — typically a reserved character ([, ], (, ), or comma) in a query/conditionQuery/etc. value.',
28
+ recovery: RECOVERY_HINTS.query_parse_error,
29
+ },
24
30
  {
25
31
  reason: 'rate_limited',
26
32
  code: JsonRpcErrorCode.RateLimited,
@@ -30,16 +36,22 @@ export const getStudyCount = tool('clinicaltrials_get_study_count', {
30
36
  },
31
37
  ],
32
38
  input: z.object({
33
- query: z.string().optional().describe('General full-text search across all fields.'),
39
+ query: z
40
+ .string()
41
+ .optional()
42
+ .describe('General free-text search across all fields. Plain words plus AND, OR, NOT only — brackets, parentheses, and commas are reserved by the upstream Essie parser and will fail. For field-scoped searches, use the dedicated *Query parameters (conditionQuery, interventionQuery, etc.) or advancedFilter with AREA[FieldName]value.'),
34
43
  conditionQuery: z
35
44
  .string()
36
45
  .optional()
37
- .describe('Condition/disease-specific search. E.g., "Type 2 Diabetes", "non-small cell lung cancer".'),
46
+ .describe('Condition/disease-specific search. E.g., "Type 2 Diabetes", "non-small cell lung cancer". Plain words plus AND/OR/NOT only — reserved chars: [ ] ( ) ,'),
38
47
  interventionQuery: z
39
48
  .string()
40
49
  .optional()
41
- .describe('Intervention/treatment search. E.g., "pembrolizumab", "cognitive behavioral therapy".'),
42
- sponsorQuery: z.string().optional().describe('Sponsor/collaborator name search.'),
50
+ .describe('Intervention/treatment search. E.g., "pembrolizumab", "cognitive behavioral therapy". Plain words plus AND/OR/NOT only — reserved chars: [ ] ( ) ,'),
51
+ sponsorQuery: z
52
+ .string()
53
+ .optional()
54
+ .describe('Sponsor/collaborator name search. Plain words plus AND/OR/NOT only — reserved chars: [ ] ( ) ,'),
43
55
  statusFilter: z
44
56
  .union([
45
57
  z.string().describe('A single status value.'),
package/dist/mcp-server/tools/definitions/get-study-count.tool.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/dist/mcp-server/tools/definitions/get-study-results.tool.d.ts.map CHANGED
@@ -1 +1 @@
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;AA4SjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAiP1B,CAAC"}
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;AAwVjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAiP1B,CAAC"}
package/dist/mcp-server/tools/definitions/get-study-results.tool.js CHANGED
@@ -39,11 +39,42 @@ function extractTopStats(o) {
39
39
  }));
40
40
  return stats.length ? stats : undefined;
41
41
  }
42
+ /**
43
+ * Extract topline statistical analysis from a raw outcome object. Returns the
44
+ * first analysis (typically the primary one), keeping only present fields so
45
+ * the summary stays compact.
46
+ */
47
+ function extractTopAnalysis(o) {
48
+ const analyses = o.analyses;
49
+ const a = analyses?.[0];
50
+ if (!a)
51
+ return;
52
+ const keys = [
53
+ 'statisticalMethod',
54
+ 'pValue',
55
+ 'pValueComment',
56
+ 'paramType',
57
+ 'paramValue',
58
+ 'ciPctValue',
59
+ 'ciNumSides',
60
+ 'ciLowerLimit',
61
+ 'ciUpperLimit',
62
+ 'nonInferiorityType',
63
+ 'estimateComment',
64
+ 'groupIds',
65
+ ];
66
+ const out = {};
67
+ for (const k of keys)
68
+ if (a[k] != null)
69
+ out[k] = a[k];
70
+ return Object.keys(out).length > 0 ? out : undefined;
71
+ }
42
72
  /** Condense a full outcome measure to its essential metadata plus top-line per-group stats. */
43
73
  function summarizeOutcome(o) {
44
74
  const groups = o.groups;
45
75
  const classes = o.classes;
46
76
  const topStats = extractTopStats(o);
77
+ const topAnalysis = extractTopAnalysis(o);
47
78
  return {
48
79
  type: o.type,
49
80
  title: o.title,
@@ -54,6 +85,7 @@ function summarizeOutcome(o) {
54
85
  groupCount: groups?.length,
55
86
  classCount: classes?.length,
56
87
  ...(topStats ? { topStats } : {}),
88
+ ...(topAnalysis ? { topAnalysis } : {}),
57
89
  };
58
90
  }
59
91
  /** Condense the adverse events module to counts. */
@@ -100,6 +132,19 @@ function groupMap(obj) {
100
132
  function shortGroup(title, max = 40) {
101
133
  return title.length <= max ? title : `${title.slice(0, max - 1)}…`;
102
134
  }
135
+ /** Render one analysis (summary or full) as a single-line bullet. */
136
+ function formatAnalysisLine(a) {
137
+ const parts = [
138
+ a.statisticalMethod ? `Method: ${a.statisticalMethod}` : '',
139
+ a.pValue ? `p=${a.pValue}` : '',
140
+ a.paramValue ? `${a.paramType ?? 'estimate'}=${a.paramValue}` : '',
141
+ a.ciLowerLimit != null && a.ciUpperLimit != null
142
+ ? `${a.ciPctValue ?? 95}% CI [${a.ciLowerLimit}, ${a.ciUpperLimit}]`
143
+ : '',
144
+ a.nonInferiorityType ? `(${a.nonInferiorityType})` : '',
145
+ ].filter(Boolean);
146
+ return parts.length ? ` Analysis: ${parts.join(', ')}` : '';
147
+ }
103
148
  function formatOutcomes(outcomes, lines) {
104
149
  lines.push(`\n### Outcomes (${outcomes.length} measures)`);
105
150
  for (const o of outcomes) {
@@ -120,20 +165,20 @@ function formatOutcomes(outcomes, lines) {
120
165
  if (topStats?.length) {
121
166
  lines.push(` ${topStats.map((s) => `${s.group}: ${s.value}${s.spread ? ` ±${s.spread}` : ''}`).join(' | ')}`);
122
167
  }
123
- // Full mode: render analyses if present
168
+ // Summary mode: single condensed analysis lifted from analyses[0].
169
+ const topAnalysis = o.topAnalysis;
170
+ if (topAnalysis) {
171
+ const line = formatAnalysisLine(topAnalysis);
172
+ if (line)
173
+ lines.push(line);
174
+ }
175
+ // Full mode: render every analysis on the measure.
124
176
  const analyses = o.analyses;
125
177
  if (analyses?.length) {
126
178
  for (const a of analyses) {
127
- const parts = [
128
- a.statisticalMethod ? `Method: ${a.statisticalMethod}` : '',
129
- a.pValue ? `p=${a.pValue}` : '',
130
- a.paramValue ? `${a.paramType ?? 'estimate'}=${a.paramValue}` : '',
131
- a.ciLowerLimit != null && a.ciUpperLimit != null
132
- ? `${a.ciPctValue ?? 95}% CI [${a.ciLowerLimit}, ${a.ciUpperLimit}]`
133
- : '',
134
- ].filter(Boolean);
135
- if (parts.length)
136
- lines.push(` Analysis: ${parts.join(', ')}`);
179
+ const line = formatAnalysisLine(a);
180
+ if (line)
181
+ lines.push(line);
137
182
  }
138
183
  }
139
184
  }
@@ -332,7 +377,7 @@ export const getStudyResults = tool('clinicaltrials_get_study_results', {
332
377
  outcomes: z
333
378
  .array(z.record(z.string(), z.unknown()))
334
379
  .optional()
335
- .describe('Outcome measures with per-group statistics. Summary mode (compact): type, title, timeFrame, paramType, unitOfMeasure, group/class counts, plus topStats per group when available. Full mode (default): adds raw groups, classes, categories, measurements, and analyses arrays.'),
380
+ .describe('Outcome measures with per-group statistics. Summary mode (compact): type, title, timeFrame, paramType, unitOfMeasure, group/class counts, plus topStats (per-group measurements) and topAnalysis (statisticalMethod, pValue, paramType/Value, ciPctValue/Lower/Upper, nonInferiorityType, groupIds — lifted from analyses[0]) when present. Full mode (default): adds raw groups, classes, categories, measurements, and analyses arrays.'),
336
381
  adverseEvents: z
337
382
  .record(z.string(), z.unknown())
338
383
  .optional()
package/dist/mcp-server/tools/definitions/get-study-results.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/mcp-server/tools/definitions/get-study.tool.d.ts CHANGED
@@ -7,8 +7,22 @@ import { z } from '@cyanheads/mcp-ts-core';
7
7
  import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
8
8
  export declare const getStudy: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
9
9
  nctId: z.ZodString;
10
+ locationLimit: z.ZodDefault<z.ZodNumber>;
11
+ outcomeLimit: z.ZodDefault<z.ZodNumber>;
12
+ nearLocation: z.ZodOptional<z.ZodObject<{
13
+ lat: z.ZodNumber;
14
+ lon: z.ZodNumber;
15
+ radiusMi: z.ZodDefault<z.ZodNumber>;
16
+ }, z.core.$strip>>;
10
17
  }, z.core.$strip>, z.ZodObject<{
11
18
  study: z.ZodRecord<z.ZodString, z.ZodUnknown>;
19
+ locationLimit: z.ZodOptional<z.ZodNumber>;
20
+ outcomeLimit: z.ZodOptional<z.ZodNumber>;
21
+ nearLocation: z.ZodOptional<z.ZodObject<{
22
+ lat: z.ZodNumber;
23
+ lon: z.ZodNumber;
24
+ radiusMi: z.ZodNumber;
25
+ }, z.core.$strip>>;
12
26
  }, z.core.$strip>, readonly [{
13
27
  readonly reason: "study_not_found";
14
28
  readonly code: JsonRpcErrorCode.NotFound;
package/dist/mcp-server/tools/definitions/get-study.tool.d.ts.map CHANGED
@@ -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;AAMjE,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;GAoVnB,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;AAmBjE,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAybnB,CAAC"}