@cyanheads/pubchem-mcp-server 0.4.2 → 0.5.0

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Files changed (41) hide show
  1. package/README.md +1 -1
  2. package/dist/mcp-server/resources/definitions/assay.resource.d.ts.map +1 -1
  3. package/dist/mcp-server/resources/definitions/assay.resource.js +1 -1
  4. package/dist/mcp-server/resources/definitions/assay.resource.js.map +1 -1
  5. package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js +1 -1
  6. package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js.map +1 -1
  7. package/dist/mcp-server/resources/definitions/compound-image.resource.js +1 -1
  8. package/dist/mcp-server/resources/definitions/compound-image.resource.js.map +1 -1
  9. package/dist/mcp-server/resources/definitions/compound-safety.resource.js +1 -1
  10. package/dist/mcp-server/resources/definitions/compound-safety.resource.js.map +1 -1
  11. package/dist/mcp-server/resources/definitions/compound-xrefs.resource.js +1 -1
  12. package/dist/mcp-server/resources/definitions/compound-xrefs.resource.js.map +1 -1
  13. package/dist/mcp-server/resources/definitions/compound.resource.js +1 -1
  14. package/dist/mcp-server/resources/definitions/compound.resource.js.map +1 -1
  15. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts +3 -0
  16. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts.map +1 -1
  17. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js +41 -13
  18. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js.map +1 -1
  19. package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js +2 -2
  20. package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js.map +1 -1
  21. package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts.map +1 -1
  22. package/dist/mcp-server/tools/definitions/get-compound-details.tool.js +24 -10
  23. package/dist/mcp-server/tools/definitions/get-compound-details.tool.js.map +1 -1
  24. package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js +3 -3
  25. package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js.map +1 -1
  26. package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts.map +1 -1
  27. package/dist/mcp-server/tools/definitions/get-summary.tool.js +39 -9
  28. package/dist/mcp-server/tools/definitions/get-summary.tool.js.map +1 -1
  29. package/dist/mcp-server/tools/definitions/index.d.ts +5 -1
  30. package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
  31. package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts +2 -1
  32. package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map +1 -1
  33. package/dist/mcp-server/tools/definitions/search-compounds.tool.js +46 -18
  34. package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map +1 -1
  35. package/dist/services/pubchem/pubchem-client.d.ts +26 -4
  36. package/dist/services/pubchem/pubchem-client.d.ts.map +1 -1
  37. package/dist/services/pubchem/pubchem-client.js +43 -15
  38. package/dist/services/pubchem/pubchem-client.js.map +1 -1
  39. package/manifest.json +1 -1
  40. package/package.json +1 -1
  41. package/server.json +3 -3
package/dist/mcp-server/tools/definitions/get-summary.tool.js CHANGED
@@ -28,7 +28,10 @@ const entitySummaryDataSchema = z.object({
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  scientificName: z.string().optional().describe('Scientific name (taxonomy summaries).'),
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  commonName: z.string().optional().describe('Common name (taxonomy summaries).'),
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  rank: z.string().optional().describe('Taxonomic rank (taxonomy summaries).'),
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- lineage: z.array(z.string()).optional().describe('Parent taxonomy lineage (taxonomy summaries).'),
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+ lineage: z
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+ .array(z.string())
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+ .optional()
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+ .describe('Taxonomic lineage ordered from the most inclusive rank to the most specific, e.g. ["Eukaryota", "Metazoa", "Chordata"] (taxonomy summaries). Ranks that do not apply to the entity are omitted.'),
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  });
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  export const getSummary = tool('pubchem_get_summary', {
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  title: 'Get Entity Summary',
@@ -125,12 +128,15 @@ export const getSummary = tool('pubchem_get_summary', {
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  if (Array.isArray(value)) {
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  if (value.length === 0)
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  continue;
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- // synonyms / lineage — upstream free text; escape each element inline.
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+ /**
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+ * synonyms / lineage — upstream free text; escape each element inline.
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+ * Rendered in full: structuredContent carries the whole array, so capping
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+ * here would hide values the structured surface already returned.
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+ * Pipe-separated because synonyms carry their own commas ("Homo sapiens
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+ * Linnaeus, 1758"), which would split one entry into two.
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+ */
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  const items = value.map((v) => inlineData(String(v)));
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- const display = items.length > 10
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- ? `${items.slice(0, 10).join(', ')} (+${items.length - 10} more)`
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- : items.join(', ');
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- lines.push(` ${formatKey(key)}: ${display}`);
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+ lines.push(` ${formatKey(key)}: ${items.join(' | ')}`);
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  }
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  else if (typeof value === 'string') {
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  lines.push(` ${formatKey(key)}: ${inlineData(value)}`);
@@ -174,6 +180,29 @@ function toStrArr(v) {
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  return [v];
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  return;
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  }
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+ /**
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+ * Ranks of PubChem's `RankedLineage`, ordered most-inclusive-first. The upstream
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+ * object keys run the other way (Species first) and carry empty strings for ranks
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+ * that do not apply, so the flat lineage is rebuilt in this order with blanks dropped.
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+ */
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+ const LINEAGE_RANKS = [
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+ 'Superkingdom',
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+ 'Kingdom',
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+ 'Phylum',
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+ 'Class',
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+ 'Order',
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+ 'Family',
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+ 'Genus',
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+ 'Species',
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+ ];
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+ /** Flatten a `RankedLineage` object into an ordered list of taxon names. */
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+ function toLineage(v) {
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+ if (typeof v !== 'object' || v === null || Array.isArray(v))
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+ return;
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+ const ranked = v;
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+ const names = LINEAGE_RANKS.map((rank) => ranked[rank]).filter((name) => typeof name === 'string' && name.length > 0);
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+ return names.length > 0 ? names : undefined;
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+ }
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  /** Assign `value` to `target[key]` only when defined — keeps unknowns off the output. */
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  function put(target, key, value) {
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  if (value !== undefined)
@@ -187,8 +216,8 @@ function extractSummary(entityType, raw) {
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  put(data, 'name', toStr(raw.Name ?? raw.AssayName));
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  put(data, 'description', toStr(raw.Description));
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  put(data, 'sourceName', toStr(raw.SourceName));
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- put(data, 'numSubstances', toNum(raw.NumberOfSubstances ?? raw.TotalSIDCount));
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- put(data, 'numActive', toNum(raw.ActiveSidCount ?? raw.ActiveCount));
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+ put(data, 'numSubstances', toNum(raw.SIDCountAll));
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+ put(data, 'numActive', toNum(raw.SIDCountActive));
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  return data;
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  case 'gene':
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  put(data, 'geneId', toNum(raw.GeneID));
@@ -211,7 +240,8 @@ function extractSummary(entityType, raw) {
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  put(data, 'scientificName', toStr(raw.ScientificName));
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  put(data, 'commonName', toStr(raw.CommonName));
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  put(data, 'rank', toStr(raw.Rank));
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- put(data, 'lineage', toStrArr(raw.Lineage ?? raw.ParentTaxList));
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+ put(data, 'lineage', toLineage(raw.RankedLineage));
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+ put(data, 'synonyms', toStrArr(raw.Synonym));
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  return data;
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  }
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  }
package/dist/mcp-server/tools/definitions/get-summary.tool.js.map CHANGED
@@ -1 +1 @@
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1
+ 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package/dist/mcp-server/tools/definitions/index.d.ts CHANGED
@@ -145,7 +145,8 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
145
145
  readonly recovery: "Pass a positive integer CID string (e.g. \"2244\"), or set queryType \"smiles\" with a SMILES query.";
146
146
  }], {
147
147
  readonly searchType: import("zod").ZodString;
148
- readonly totalFound: import("zod").ZodNumber;
148
+ readonly totalFound: import("zod").ZodOptional<import("zod").ZodNumber>;
149
+ readonly totalFoundAtLeast: import("zod").ZodOptional<import("zod").ZodNumber>;
149
150
  readonly truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
150
151
  readonly shown: import("zod").ZodOptional<import("zod").ZodNumber>;
151
152
  readonly cap: import("zod").ZodOptional<import("zod").ZodNumber>;
@@ -247,6 +248,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
247
248
  }>>;
248
249
  targetGeneId: import("zod").ZodOptional<import("zod").ZodNumber>;
249
250
  targetAccession: import("zod").ZodOptional<import("zod").ZodString>;
251
+ offset: import("zod").ZodDefault<import("zod").ZodNumber>;
250
252
  maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
251
253
  }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
252
254
  cid: import("zod").ZodNumber;
@@ -270,6 +272,8 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
270
272
  readonly targetFilter: import("zod").ZodOptional<import("zod").ZodString>;
271
273
  readonly filteredCount: import("zod").ZodNumber;
272
274
  readonly returnedCount: import("zod").ZodNumber;
275
+ readonly offset: import("zod").ZodNumber;
276
+ readonly nextOffset: import("zod").ZodOptional<import("zod").ZodNumber>;
273
277
  readonly truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
274
278
  readonly shown: import("zod").ZodOptional<import("zod").ZodNumber>;
275
279
  readonly cap: import("zod").ZodOptional<import("zod").ZodNumber>;
package/dist/mcp-server/tools/definitions/index.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAaH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAW9B,CAAC"}
1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAaH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAW9B,CAAC"}
package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts CHANGED
@@ -60,7 +60,8 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
60
60
  readonly recovery: "Pass a positive integer CID string (e.g. \"2244\"), or set queryType \"smiles\" with a SMILES query.";
61
61
  }], {
62
62
  readonly searchType: z.ZodString;
63
- readonly totalFound: z.ZodNumber;
63
+ readonly totalFound: z.ZodOptional<z.ZodNumber>;
64
+ readonly totalFoundAtLeast: z.ZodOptional<z.ZodNumber>;
64
65
  readonly truncated: z.ZodOptional<z.ZodBoolean>;
65
66
  readonly shown: z.ZodOptional<z.ZodNumber>;
66
67
  readonly cap: z.ZodOptional<z.ZodNumber>;
package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"search-compounds.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-compounds.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwW1B,CAAC"}
1
+ {"version":3,"file":"search-compounds.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-compounds.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA8Y1B,CAAC"}
package/dist/mcp-server/tools/definitions/search-compounds.tool.js CHANGED
@@ -94,11 +94,25 @@ export const searchCompounds = tool('pubchem_search_compounds', {
94
94
  }),
95
95
  // Agent-facing context — search strategy echo, total before cap, and an empty-result
96
96
  // notice. Reaches structuredContent and content[] automatically; not in the domain return.
97
+ //
98
+ // Bounded-total convention: a reported total states only what the server actually
99
+ // observed. `totalFound` carries a true count and appears only when the whole match set
100
+ // was seen. When the upstream request was itself bounded and came back saturated, the
101
+ // exact total is unknowable, so `totalFoundAtLeast` carries a floor in its place rather
102
+ // than a number that reads as a count. Exactly one of the two is populated per call; any
103
+ // other capped output pairs its count field with an `…AtLeast` twin the same way.
97
104
  enrichment: {
98
105
  searchType: z
99
106
  .string()
100
107
  .describe('Search strategy used: identifier, formula, substructure, superstructure, or similarity.'),
101
- totalFound: z.number().describe('Total CIDs found before the maxResults cap.'),
108
+ totalFound: z
109
+ .number()
110
+ .optional()
111
+ .describe('Exact number of matching CIDs, before the maxResults cap. Omitted when a formula, substructure, superstructure, or similarity search filled its page — PubChem returns no match count for those, so totalFoundAtLeast reports a floor instead.'),
112
+ totalFoundAtLeast: z
113
+ .number()
114
+ .optional()
115
+ .describe('Lower bound on matching CIDs, reported in place of totalFound when the exact count is unavailable. At least this many match, and the true total may be higher; raise maxResults to retrieve more.'),
102
116
  truncated: z
103
117
  .boolean()
104
118
  .optional()
@@ -139,6 +153,11 @@ export const searchCompounds = tool('pubchem_search_compounds', {
139
153
  async handler(input, ctx) {
140
154
  const client = getPubChemClient();
141
155
  let allCids = [];
156
+ // Formula and structure searches are bounded server-side. One record past the cap is
157
+ // enough to prove more matches exist without moving the rest of PubChem's match set,
158
+ // which for a common substructure runs to 16.3 MB of CIDs.
159
+ const recordCap = input.maxResults + 1;
160
+ let boundedSearch = false;
142
161
  const identifierMap = new Map();
143
162
  // Identifier-mode resolution tracking (#29): inputs that resolved to no CID, and
144
163
  // CIDs claimed by more than one distinct input (the output row can echo only one).
@@ -202,7 +221,8 @@ export const searchCompounds = tool('pubchem_search_compounds', {
202
221
  ...ctx.recoveryFor('missing_formula'),
203
222
  });
204
223
  }
205
- allCids = await client.searchByFormula(input.formula, input.allowOtherElements);
224
+ boundedSearch = true;
225
+ allCids = await client.searchByFormula(input.formula, input.allowOtherElements, recordCap);
206
226
  break;
207
227
  }
208
228
  case 'substructure':
@@ -218,21 +238,28 @@ export const searchCompounds = tool('pubchem_search_compounds', {
218
238
  if (input.queryType === 'cid' && !(/^\d+$/.test(input.query) && Number(input.query) > 0)) {
219
239
  throw ctx.fail('invalid_cid_query', `queryType is "cid" but query "${input.query}" is not a positive integer CID.`, { ...ctx.recoveryFor('invalid_cid_query') });
220
240
  }
221
- allCids = await client.searchByStructure(input.searchType, input.query, input.queryType, input.threshold);
241
+ boundedSearch = true;
242
+ allCids = await client.searchByStructure(input.searchType, input.query, input.queryType, input.threshold, recordCap);
222
243
  break;
223
244
  }
224
245
  }
225
246
  // Deduplicate and cap
226
247
  const uniqueCids = [...new Set(allCids)];
227
- const totalFound = uniqueCids.length;
248
+ const observedTotal = uniqueCids.length;
228
249
  const cappedCids = uniqueCids.slice(0, input.maxResults);
250
+ // A bounded search that came back short of its cap returned everything PubChem had, so
251
+ // the count is exact. A saturated one only proves a floor.
252
+ const totalIsExact = !boundedSearch || allCids.length < recordCap;
229
253
  ctx.log.info('Search completed', {
230
254
  searchType: input.searchType,
231
- totalFound,
255
+ observedTotal,
256
+ totalIsExact,
232
257
  returned: cappedCids.length,
233
258
  });
234
259
  // Agent-facing context: search strategy echo, total, and empty-result notice.
235
- ctx.enrich({ searchType: input.searchType, totalFound });
260
+ ctx.enrich(totalIsExact
261
+ ? { searchType: input.searchType, totalFound: observedTotal }
262
+ : { searchType: input.searchType, totalFoundAtLeast: observedTotal });
236
263
  // Identifier-mode signals (#29): name inputs that did not resolve and flag CID
237
264
  // collisions, so a partial miss is never silent. Empty for other search types.
238
265
  const noticeParts = [];
@@ -248,19 +275,20 @@ export const searchCompounds = tool('pubchem_search_compounds', {
248
275
  ? noticeParts.join(' ')
249
276
  : `No compounds matched the ${input.searchType} search. Try a different identifier, broaden the formula, lower the similarity threshold, or verify the SMILES/CID.`);
250
277
  }
251
- else if (totalFound > cappedCids.length) {
278
+ else if (observedTotal > cappedCids.length) {
252
279
  // Truncated: fold any identifier notice into the truncation guidance (notice is
253
- // last-wins, so compose rather than emit two; restate the cap when overriding).
254
- if (noticeParts.length > 0) {
255
- ctx.enrich.truncated({
256
- shown: cappedCids.length,
257
- cap: input.maxResults,
258
- guidance: `${noticeParts.join(' ')} Showing ${cappedCids.length} of ${totalFound} matches — raise maxResults (max 200) for more.`,
259
- });
260
- }
261
- else {
262
- ctx.enrich.truncated({ shown: cappedCids.length, cap: input.maxResults });
263
- }
280
+ // last-wins, so compose rather than emit two). Without an exact total there is no
281
+ // "of N" to quote — say more exist and stop.
282
+ const truncationGuidance = totalIsExact
283
+ ? `Showing ${cappedCids.length} of ${observedTotal} matches — raise maxResults (max 200) for more.`
284
+ : `Showing ${cappedCids.length} matches; more exist, but PubChem reports no match count for a ${input.searchType} search — raise maxResults (max 200) for more.`;
285
+ ctx.enrich.truncated({
286
+ shown: cappedCids.length,
287
+ cap: input.maxResults,
288
+ guidance: noticeParts.length > 0
289
+ ? `${noticeParts.join(' ')} ${truncationGuidance}`
290
+ : truncationGuidance,
291
+ });
264
292
  }
265
293
  else if (noticeParts.length > 0) {
266
294
  ctx.enrich.notice(noticeParts.join(' '));
package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map CHANGED
@@ -1 +1 @@
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package/dist/services/pubchem/pubchem-client.d.ts CHANGED
@@ -19,15 +19,37 @@ export declare class PubChemClient {
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19
  private fetchBinary;
20
20
  /** Fetch a text/plain body (e.g. an SDF record). Non-2xx is classified and thrown. */
21
21
  private fetchText;
22
- /** Fetch CID list, with automatic ListKey polling for async searches */
22
+ /** Fetch CID list, with automatic ListKey polling for async searches.
23
+ *
24
+ * `maxRecords` carries a bounded search's cap into the ListKey retrieval. A search that
25
+ * answers synchronously is already bounded by the `MaxRecords` on its own URL, but that
26
+ * bound lives in the request, not the ListKey — so an async answer would otherwise return
27
+ * the full match set and the caller would read PubChem's ceiling as a real count. Omitted
28
+ * for identifier lookups, which are unbounded by design. */
23
29
  private fetchCids;
24
- /** Poll a PubChem ListKey until results are ready */
30
+ /** Poll a PubChem ListKey until results are ready.
31
+ *
32
+ * `listkey_count` asks PubChem to trim the page; the slice enforces the same bound
33
+ * locally, so the caller's saturation test holds whether or not the parameter is honored. */
25
34
  private pollListKey;
26
35
  searchByName(name: string): Promise<number[]>;
27
36
  searchBySmiles(smiles: string): Promise<number[]>;
28
37
  searchByInchiKey(inchikey: string): Promise<number[]>;
29
- searchByFormula(formula: string, allowOther?: boolean): Promise<number[]>;
30
- searchByStructure(mode: 'substructure' | 'superstructure' | 'similarity', query: string, queryType: 'smiles' | 'cid', threshold?: number): Promise<number[]>;
38
+ /** Formula search, bounded server-side by `maxRecords`.
39
+ *
40
+ * `MaxRecords` is mandatory rather than optional because an unbounded fast search moves
41
+ * PubChem's entire match set: a benzoic-acid substructure query returns 1,000,000 CIDs in
42
+ * 16.3 MB, which is PubChem's own ceiling rather than a real count. Callers ask for the
43
+ * window they will actually use.
44
+ *
45
+ * A response shorter than `maxRecords` is the complete match set; a response of exactly
46
+ * `maxRecords` is saturated, and the true total is not recoverable — PubChem returns the
47
+ * CID list alone, with no match count beside it. Callers that need to distinguish the two
48
+ * compare the returned length against the cap they passed. */
49
+ searchByFormula(formula: string, allowOther: boolean, maxRecords: number): Promise<number[]>;
50
+ /** Substructure, superstructure, and 2D-similarity search, bounded server-side by
51
+ * `maxRecords`. Same cap contract as {@link searchByFormula}. */
52
+ searchByStructure(mode: 'substructure' | 'superstructure' | 'similarity', query: string, queryType: 'smiles' | 'cid', threshold: number | undefined, maxRecords: number): Promise<number[]>;
31
53
  getProperties(cids: number[], properties: string[]): Promise<Array<Record<string, unknown> & {
32
54
  CID: number;
33
55
  }>>;
package/dist/services/pubchem/pubchem-client.d.ts.map CHANGED
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1
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package/dist/services/pubchem/pubchem-client.js CHANGED
@@ -455,12 +455,18 @@ export class PubChemClient {
455
455
  return response.text();
456
456
  }
457
457
  // ── CID Resolution ──────────────────────────────────────────────
458
- /** Fetch CID list, with automatic ListKey polling for async searches */
459
- async fetchCids(url, init) {
458
+ /** Fetch CID list, with automatic ListKey polling for async searches.
459
+ *
460
+ * `maxRecords` carries a bounded search's cap into the ListKey retrieval. A search that
461
+ * answers synchronously is already bounded by the `MaxRecords` on its own URL, but that
462
+ * bound lives in the request, not the ListKey — so an async answer would otherwise return
463
+ * the full match set and the caller would read PubChem's ceiling as a real count. Omitted
464
+ * for identifier lookups, which are unbounded by design. */
465
+ async fetchCids(url, init, maxRecords) {
460
466
  try {
461
467
  const data = await this.fetchJson(url, init);
462
468
  if ('Waiting' in data)
463
- return this.pollListKey(data.Waiting.ListKey);
469
+ return this.pollListKey(data.Waiting.ListKey, maxRecords);
464
470
  return data.IdentifierList.CID;
465
471
  }
466
472
  catch (error) {
@@ -469,16 +475,21 @@ export class PubChemClient {
469
475
  throw error;
470
476
  }
471
477
  }
472
- /** Poll a PubChem ListKey until results are ready */
473
- async pollListKey(listKey, maxAttempts = 20) {
474
- const pollUrl = `${this.pugBase}/compound/listkey/${listKey}/cids/JSON`;
478
+ /** Poll a PubChem ListKey until results are ready.
479
+ *
480
+ * `listkey_count` asks PubChem to trim the page; the slice enforces the same bound
481
+ * locally, so the caller's saturation test holds whether or not the parameter is honored. */
482
+ async pollListKey(listKey, maxRecords, maxAttempts = 20) {
483
+ const query = maxRecords === undefined ? '' : `?listkey_count=${maxRecords}`;
484
+ const pollUrl = `${this.pugBase}/compound/listkey/${listKey}/cids/JSON${query}`;
475
485
  for (let attempt = 0; attempt < maxAttempts; attempt++) {
476
486
  await sleep(1500);
477
487
  try {
478
488
  const data = await this.fetchJson(pollUrl);
479
489
  if ('Waiting' in data)
480
490
  continue;
481
- return data.IdentifierList.CID;
491
+ const cids = data.IdentifierList.CID;
492
+ return maxRecords === undefined ? cids : cids.slice(0, maxRecords);
482
493
  }
483
494
  catch (error) {
484
495
  if (isNotFound(error))
@@ -501,27 +512,44 @@ export class PubChemClient {
501
512
  searchByInchiKey(inchikey) {
502
513
  return this.fetchCids(`${this.pugBase}/compound/inchikey/${encodeURIComponent(inchikey)}/cids/JSON`);
503
514
  }
504
- searchByFormula(formula, allowOther = false) {
505
- const params = allowOther ? '?AllowOtherElements=true' : '';
506
- return this.fetchCids(`${this.pugBase}/compound/fastformula/${encodeURIComponent(formula)}/cids/JSON${params}`);
515
+ /** Formula search, bounded server-side by `maxRecords`.
516
+ *
517
+ * `MaxRecords` is mandatory rather than optional because an unbounded fast search moves
518
+ * PubChem's entire match set: a benzoic-acid substructure query returns 1,000,000 CIDs in
519
+ * 16.3 MB, which is PubChem's own ceiling rather than a real count. Callers ask for the
520
+ * window they will actually use.
521
+ *
522
+ * A response shorter than `maxRecords` is the complete match set; a response of exactly
523
+ * `maxRecords` is saturated, and the true total is not recoverable — PubChem returns the
524
+ * CID list alone, with no match count beside it. Callers that need to distinguish the two
525
+ * compare the returned length against the cap they passed. */
526
+ searchByFormula(formula, allowOther, maxRecords) {
527
+ const params = new URLSearchParams({ MaxRecords: String(maxRecords) });
528
+ if (allowOther)
529
+ params.set('AllowOtherElements', 'true');
530
+ return this.fetchCids(`${this.pugBase}/compound/fastformula/${encodeURIComponent(formula)}/cids/JSON?${params}`, undefined, maxRecords);
507
531
  }
508
- searchByStructure(mode, query, queryType, threshold) {
532
+ /** Substructure, superstructure, and 2D-similarity search, bounded server-side by
533
+ * `maxRecords`. Same cap contract as {@link searchByFormula}. */
534
+ searchByStructure(mode, query, queryType, threshold, maxRecords) {
509
535
  const endpoint = mode === 'similarity'
510
536
  ? 'fastsimilarity_2d'
511
537
  : mode === 'substructure'
512
538
  ? 'fastsubstructure'
513
539
  : 'fastsuperstructure';
514
- const thresholdParam = mode === 'similarity' ? `?Threshold=${threshold ?? 90}` : '';
540
+ const params = new URLSearchParams({ MaxRecords: String(maxRecords) });
541
+ if (mode === 'similarity')
542
+ params.set('Threshold', String(threshold ?? 90));
515
543
  if (queryType === 'cid') {
516
- return this.fetchCids(`${this.pugBase}/compound/${endpoint}/cid/${query}/cids/JSON${thresholdParam}`);
544
+ return this.fetchCids(`${this.pugBase}/compound/${endpoint}/cid/${query}/cids/JSON?${params}`, undefined, maxRecords);
517
545
  }
518
546
  // POST for SMILES to avoid encoding issues
519
- const url = `${this.pugBase}/compound/${endpoint}/smiles/cids/JSON${thresholdParam}`;
547
+ const url = `${this.pugBase}/compound/${endpoint}/smiles/cids/JSON?${params}`;
520
548
  return this.fetchCids(url, {
521
549
  method: 'POST',
522
550
  headers: { 'Content-Type': 'application/x-www-form-urlencoded' },
523
551
  body: new URLSearchParams({ smiles: query }).toString(),
524
- });
552
+ }, maxRecords);
525
553
  }
526
554
  // ── Compound Data ───────────────────────────────────────────────
527
555
  async getProperties(cids, properties) {