npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.20 → 2.10.22 - Mend

@cyanheads/pubmed-mcp-server 2.10.20 → 2.10.22

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 (110) hide show

package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js CHANGED Viewed

@@ -6,7 +6,7 @@
  * because EPMC's search API doesn't support offset. `max_results`, `limit`, and
  * `maxResults` are accepted as aliases for `pageSize`. A `query` with no search
  * term (`()`, `<b></b>`) or a blank `cursorMark` is rejected before Europe PMC
- * is called.
+ * is called. A lower-case `sources` code is read as its upper-case form.
  * The total hit count rides in `output` so `format()` can state it in the
  * header, and `searchUrl` opens the source-filtered query Europe PMC actually
  * ran.
@@ -25,6 +25,7 @@ import { getEuropePmcService } from '../../../services/europe-pmc/europe-pmc-ser
 import { EUROPEPMC_ALL_SOURCES, EUROPEPMC_DEFAULT_SOURCES, } from '../../../services/europe-pmc/types.js';
 import { toDisplayText } from '../../../services/ncbi/parsing/text-helpers.js';
 import { conceptMeta, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID, SCHEMA_SEARCH_ACTION, } from './_concepts.js';
+import { europePmcSourceInputSchema } from './_schemas.js';
 import { escapeMarkdownInline, sliceCodeUnits } from './_text.js';
 import { hasVisibleText } from './_visible-text.js';
 const SourceEnum = z.enum(['MED', 'PMC', 'PPR', 'PAT', 'AGR']);
@@ -38,7 +39,7 @@ const SourceEnum = z.enum(['MED', 'PMC', 'PPR', 'PAT', 'AGR']);
 const ABSTRACT_SNIPPET_LIMIT = 400;
 // ─── Tool Definition ─────────────────────────────────────────────────────────
 export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
-    description: 'Search Europe PMC, a broad open-access biomedical corpus. Surfaces preprints (`source: PPR`), patents (`source: PAT`), Agricola (`source: AGR`), plus everything in PubMed (`MED`) and PMC. Use when additional coverage is needed — preprints and EPMC-only OA records are the typical recovery. Paginate via `cursorMark`. Defaults to `MED`, `PMC`, and `PPR`; pass `sources` to include `PAT` / `AGR`. Abstracts arrive as a bounded `abstractSnippet` with `abstractTruncated` marking the cut ones — pass a hit’s `source` and `epmcId` to `pubmed_europepmc_fetch` for the complete abstract.',
+    description: 'Search Europe PMC, a broad open-access biomedical corpus. Surfaces preprints (`source: PPR`), patents (`source: PAT`), Agricola (`source: AGR`), plus everything in PubMed (`MED`) and PMC. Use when additional coverage is needed — preprints and EPMC-only OA records are the typical recovery. Paginate via `cursorMark`. Defaults to `MED`, `PMC`, and `PPR`; pass `sources` to include `PAT` / `AGR`. Abstracts arrive as a bounded `abstractSnippet` with `abstractTruncated` marking the cut ones — pass a hit to `pubmed_europepmc_fetch` as `records: [{ source, epmcId }]` for the complete abstract.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SEARCH_ACTION, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts',
@@ -80,7 +81,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
             .default('*')
             .describe("Pagination cursor. Use `*` (default) for the first page; pass the previous response's `nextCursorMark` verbatim for subsequent pages. A whitespace-only cursor, invisible characters included, is rejected before the request, and a cursor Europe PMC cannot read fails with `europepmc_invalid_input` once a retry of it fails again while the first page of the same query is served."),
         sources: z
-            .array(SourceEnum)
+            .array(europePmcSourceInputSchema)
             .min(1)
             .optional()
             .describe(`Filter to specific EPMC sources. Defaults to ${EUROPEPMC_DEFAULT_SOURCES.join(', ')} when omitted. Pass an explicit array including PAT or AGR to broaden coverage. Allowed values: ${EUROPEPMC_ALL_SOURCES.join(', ')}.`),
@@ -91,7 +92,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
         sort: z
             .string()
             .optional()
-            .describe('Optional EPMC sort: `<field> asc|desc`, or several comma-separated keys applied in order (`PUB_YEAR desc, CITED desc`). Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking. Field and direction match case-insensitively. A field outside the documented set may be honored, silently ignored, or rejected, and a sort using one — or a key without `asc`/`desc` — can fail with `europepmc_invalid_input` naming it, even when Europe PMC honors the field. Note: `P_PDATE_D` is ignored for preprint-only (`sources: ["PPR"]`) result sets — preprints have no populated publication date, so use `PUB_YEAR` to order preprints by date.'),
+            .describe('Optional EPMC sort: `<field> asc|desc`, or several comma-separated keys applied in order (`PUB_YEAR desc, CITED desc`). Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year), `FIRST_IDATE_D` (date first indexed in Europe PMC). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking; `relevance` or `relevance desc` is sent as no sort. Field and direction match case-insensitively. Each key must be one field plus `asc` or `desc`: a key without a direction, an empty key, or an extra word fails with `europepmc_invalid_input` before the request. A field outside the documented set may be honored, silently ignored, or refused — a sort Europe PMC refuses fails with `europepmc_invalid_input` naming it, and an empty Europe PMC response to a sort with an undocumented field fails the same way, even when Europe PMC honors the field. Note: `P_PDATE_D` is ignored for preprint-only (`sources: ["PPR"]`) result sets — preprints have no populated publication date, so use `PUB_YEAR desc` to order preprints by date.'),
     }),
     output: z.object({
         hits: z
@@ -100,7 +101,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
             source: SourceEnum.describe('Europe PMC source — `MED` (PubMed), `PMC` (PubMed Central), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola)'),
             epmcId: z
                 .string()
-                .describe("Europe PMC's internal record id. Pass it with this hit's `source` to `pubmed_europepmc_fetch` for the complete record. Europe PMC's `fullTextXML` is keyed on `pmcId`, not on this id, so records without a PMC counterpart have no full text to fetch."),
+                .describe("Europe PMC's internal record id. Pass it with this hit's `source` to `pubmed_europepmc_fetch` as `records: [{ source, epmcId }]` for the complete record. Europe PMC's `fullTextXML` is keyed on `pmcId`, not on this id, so records without a PMC counterpart have no full text to fetch."),
             title: z
                 .string()
                 .optional()
@@ -139,7 +140,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
             abstractTruncated: z
                 .boolean()
                 .optional()
-                .describe('Whether `abstractSnippet` was cut short of the full abstract. Retrieve the complete text with `pubmed_europepmc_fetch` using this record’s `source` and `epmcId`. Present whenever `abstractSnippet` is; omitted when Europe PMC carries no abstract.'),
+                .describe('Whether `abstractSnippet` was cut short of the full abstract. Retrieve the complete text by passing this record to `pubmed_europepmc_fetch` as `records: [{ source, epmcId }]`. Present whenever `abstractSnippet` is; omitted when Europe PMC carries no abstract.'),
             citedByCount: z.number().optional().describe('Citation count reported by Europe PMC'),
             epmcUrl: z.string().describe('Europe PMC article URL'),
         })
@@ -261,7 +262,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
         }
         else if (sortField === 'P_PDATE_D' && isPprOnly) {
             notice =
-                'Europe PMC ignores `P_PDATE_D` sort for preprint-only (PPR) results — preprints have no populated publication date, so records are returned in relevance order, not by date. To order preprints by date, sort by `PUB_YEAR`, or re-rank the returned page by each record’s `firstPublicationDate`.';
+                'Europe PMC ignores `P_PDATE_D` sort for preprint-only (PPR) results — preprints have no populated publication date, so records are returned in relevance order, not by date. To order preprints by date, sort by `PUB_YEAR desc`, or re-rank the returned page by each record’s `firstPublicationDate`.';
         }
         ctx.log.info('pubmed_europepmc_search completed', {
             hitCount: result.hitCount,
@@ -323,7 +324,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
                 if (h.abstractSnippet) {
                     lines.push(`\n${h.abstractSnippet}`);
                     if (h.abstractTruncated) {
-                        lines.push(`_Abstract truncated at ${ABSTRACT_SNIPPET_LIMIT} characters — call \`pubmed_europepmc_fetch\` with this record's \`source\` and \`epmcId\` for the complete text._`);
+                        lines.push(`_Abstract truncated at ${ABSTRACT_SNIPPET_LIMIT} characters — pass this hit to \`pubmed_europepmc_fetch\` as \`records: [{ source, epmcId }]\` for the complete text._`);
                     }
                 }
             }

package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts CHANGED Viewed

@@ -1,8 +1,8 @@
 /**
- * @fileoverview PubMed spell-check tool. Uses NCBI's ESpell service to correct
- * every misspelled token of a PubMed search query in one call — the recovery
- * step after a zero-hit or thin `pubmed_search_articles` result. `term` is
- * accepted as an alias for `query`.
+ * @fileoverview PubMed spell-check tool. Applies NCBI ESpell's corrections to a
+ * PubMed search query in place, keeping its field tags, operators, spacing, and
+ * gene symbols — the recovery step after a zero-hit or thin
+ * `pubmed_search_articles` result. `term` is accepted as an alias for `query`.
  * @module src/mcp-server/tools/definitions/spell-check.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';

package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"spell-check.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAwEzB,CAAC"}

package/dist/mcp-server/tools/definitions/spell-check.tool.js CHANGED Viewed

@@ -1,8 +1,8 @@
 /**
- * @fileoverview PubMed spell-check tool. Uses NCBI's ESpell service to correct
- * every misspelled token of a PubMed search query in one call — the recovery
- * step after a zero-hit or thin `pubmed_search_articles` result. `term` is
- * accepted as an alias for `query`.
+ * @fileoverview PubMed spell-check tool. Applies NCBI ESpell's corrections to a
+ * PubMed search query in place, keeping its field tags, operators, spacing, and
+ * gene symbols — the recovery step after a zero-hit or thin
+ * `pubmed_search_articles` result. `term` is accepted as an alias for `query`.
  * @module src/mcp-server/tools/definitions/spell-check.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -11,7 +11,7 @@ import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { conceptMeta, SCHEMA_SEARCH_ACTION } from './_concepts.js';
 import { hasVisibleText } from './_visible-text.js';
 export const spellCheckTool = tool('pubmed_spell_check', {
-    description: 'Spell-check a PubMed search query against NCBI ESpell and get the corrected query back. Use after a zero-hit or thin `pubmed_search_articles` result, or when a drug, gene, disease, or author name may be misspelled — every misspelled token is corrected in one call (`alzhiemer diseese treatmnt outcomse` → `alzheimer disease treatment outcomes`), and `hasSuggestion` is false when NCBI has no change to offer. Re-run the search with `corrected`.',
+    description: 'Spell-check a PubMed search query against NCBI ESpell and get the corrected query back. Use after a zero-hit or thin `pubmed_search_articles` result, or when a drug, gene, disease, or author name may be misspelled. Corrections are applied in place, so field tags, operators, spacing, and gene symbols stay as written (`alzhiemer diseese treatmnt outcomse` → `alzheimer disease treatment outcomes`). Words in all capitals, with digits or non-ASCII letters, or differing only in case are never changed, words after a number or symbol ESpell skips are left as written, and `hasSuggestion` is false when no correction was applied. Re-run the search with `corrected`.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SEARCH_ACTION]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/spell-check.tool.ts',
@@ -27,8 +27,12 @@ export const spellCheckTool = tool('pubmed_spell_check', {
     }),
     output: z.object({
         original: z.string().describe('Original query'),
-        corrected: z.string().describe('Corrected query (same as original if no suggestion)'),
-        hasSuggestion: z.boolean().describe('Whether NCBI suggested a correction'),
+        corrected: z
+            .string()
+            .describe("The query with ESpell's accepted corrections applied in place; field tags, operators, spacing, and words in capitals or with digits are kept as written. Same as `original` when `hasSuggestion` is false."),
+        hasSuggestion: z
+            .boolean()
+            .describe('Whether at least one correction was applied to `corrected`'),
     }),
     async handler(input, ctx) {
         ctx.log.info('Executing pubmed_spell_check tool', { query: input.query });
@@ -59,7 +63,7 @@ export const spellCheckTool = tool('pubmed_spell_check', {
         return [
             {
                 type: 'text',
-                text: `No suggestion — query "${result.original}" appears correct as written.`,
+                text: `No correction applied — query "${result.original}" is returned as written.`,
             },
         ];
     },

package/dist/mcp-server/tools/definitions/spell-check.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/error-contracts.d.ts CHANGED Viewed

@@ -149,7 +149,7 @@ export declare const EUROPEPMC_SERVICE_ERRORS: readonly [{
 }, {
     readonly reason: 'europepmc_invalid_input';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: 'Europe PMC rejected the request input — an error message in place of results, an empty response to a sort with an undocumented field or no asc/desc direction, or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served).';
+    readonly when: 'Europe PMC rejected the request input — an error message in place of results; a sort it cannot use (one whose keys are not each a field plus asc/desc, rejected before any request; an empty response to a sort with an undocumented field; or a second HTTP 503 to a sorted search when the same query without the sort is served); or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served).';
     readonly recovery: "Fix the rejected input before retrying — the query, the sort, or the cursorMark (pass the previous response's `nextCursorMark` verbatim, or `*` to restart); the same input will most likely be rejected again.";
     readonly retryable: false;
     readonly thrownBy: 'service';

package/dist/services/error-contracts.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/error-contracts.js CHANGED Viewed

@@ -166,7 +166,7 @@ export const EUROPEPMC_SERVICE_ERRORS = [
     {
         reason: 'europepmc_invalid_input',
         code: JsonRpcErrorCode.ValidationError,
-        when: 'Europe PMC rejected the request input — an error message in place of results, an empty response to a sort with an undocumented field or no asc/desc direction, or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served).',
+        when: 'Europe PMC rejected the request input — an error message in place of results; a sort it cannot use (one whose keys are not each a field plus asc/desc, rejected before any request; an empty response to a sort with an undocumented field; or a second HTTP 503 to a sorted search when the same query without the sort is served); or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served).',
         recovery: "Fix the rejected input before retrying — the query, the sort, or the cursorMark (pass the previous response's `nextCursorMark` verbatim, or `*` to restart); the same input will most likely be rejected again.",
         retryable: false,
         thrownBy: 'service',

package/dist/services/error-contracts.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/europe-pmc/api-client.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/europe-pmc/api-client.js CHANGED Viewed

@@ -10,6 +10,7 @@
  */
 import { JsonRpcErrorCode, McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
 import { fetchWithTimeout, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
+import { readBody } from '../fetch-redaction.js';
 import { EUROPEPMC_API_BASE } from './types.js';
 const USER_AGENT = 'pubmed-mcp-server (+https://github.com/cyanheads/pubmed-mcp-server)';
 /**
@@ -73,7 +74,7 @@ export class EuropePmcApiClient {
             const msg = error instanceof Error ? error.message : String(error);
             throw serviceUnavailable(`Europe PMC search request failed: ${msg}`, { reason: 'europepmc_unreachable' }, { cause: error });
         }
-        return response.text();
+        return readBody(response.text());
     }
     /**
      * Fetch the JATS full-text XML for an EPMC record by its internal id.
@@ -112,7 +113,7 @@ export class EuropePmcApiClient {
             const msg = error instanceof Error ? error.message : String(error);
             throw serviceUnavailable(`Europe PMC fullTextXML request failed: ${msg}`, { reason: 'europepmc_unreachable', epmcId }, { cause: error });
         }
-        const xml = await response.text();
+        const xml = await readBody(response.text());
         if (!xml.trim()) {
             logger.debug('Europe PMC returned an empty fullTextXML body.', requestContextService.createRequestContext({
                 operation: 'EuropePmcFullTextXmlEmpty',
@@ -159,7 +160,7 @@ export class EuropePmcApiClient {
             const msg = error instanceof Error ? error.message : String(error);
             throw serviceUnavailable(`Europe PMC links request failed: ${msg}`, { reason: 'europepmc_unreachable' }, { cause: error });
         }
-        return response.text();
+        return readBody(response.text());
     }
     buildSearchUrl(params) {
         const finalParams = {

package/dist/services/europe-pmc/api-client.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/services/europe-pmc/europe-pmc-service.d.ts CHANGED Viewed

@@ -14,10 +14,13 @@
  * A search's retry boundary covers fetch and response classification, so
  * Europe PMC's intermittent empty `{ version }` envelope is retried like an
  * HTTP outage; only a sort or cursor that explains it is reported as bad input.
- * Europe PMC answers an unreadable cursor with the HTTP 503 it uses for an
- * outage, so a 503 on a caller-supplied cursor is checked against the first
- * page of the same query, and the cursor is blamed only when a retry draws
- * the 503 again while that first page was served.
+ * A `relevance` sort is sent as none, and a sort whose keys are not each one
+ * field plus `asc`/`desc` fails before the request. Europe PMC answers an
+ * unreadable cursor, and a sort it cannot use, with the HTTP 503 it uses for an
+ * outage, so a 503 on a caller-supplied cursor or a sort is checked against the
+ * first page of the same query — with the sort for the cursor, without it for
+ * the sort — and the input is blamed only when a retry draws the 503 again
+ * while that first page was served.
  * A search reports the effective query Europe PMC echoes back, or — with no
  * echo — the source-filtered query it sent.
  *
@@ -56,14 +59,29 @@ export declare class EuropePmcService {
      * together, so an empty envelope retries like any other transient failure
      * rather than surfacing after the loop has already returned. (#159)
      *
-     * The first HTTP 503 on a caller-supplied cursor draws one probe of the same
-     * query's first page, and the cursor is retried either way: one 503 is not
-     * enough to tell a bad cursor from a transient outage. A later 503 fails the
-     * search at once as non-retryable input only when that probe was served;
-     * otherwise it goes on through the ordinary retry path. A 503 with no retry
-     * left is never probed, since nothing could use the answer. (#180)
+     * The sort is resolved before any request (see {@link effectiveSort}): a
+     * `relevance` sort is dropped, and a malformed one fails with no request.
+     *
+     * Europe PMC answers both an unreadable cursor and a sort it cannot use with
+     * the HTTP 503 it uses for an outage. The first 503 on a search carrying a
+     * caller-supplied cursor or a sort draws probes of the same query's first
+     * page, and the search is retried either way: one 503 is not enough to tell
+     * bad input from a transient outage. With a cursor, the first page with the
+     * sort is probed first (#180); when it is served, the cursor is the suspect.
+     * Otherwise, with a sort, the first page without the sort is probed — never
+     * with the caller's cursor, which Europe PMC binds to the sort that issued
+     * it — and when that is served, the sort is the suspect (#239). A later 503
+     * fails the search at once as non-retryable input naming the suspect; with
+     * no suspect it goes on through the ordinary retry path. A 503 with no retry
+     * left is never probed, since nothing could use the answer.
      */
     search(params: EuropePmcSearchParams): Promise<EuropePmcSearchResult>;
+    /**
+     * Which input, if any, explains a 503 on `request`: the caller's cursor when
+     * the first page with the same sort is served, the sort when the first page
+     * without it is served, otherwise neither.
+     */
+    private diagnose503;
     /**
      * Whether Europe PMC serves the first page of the search in `params`: one
      * request (`cursorMark: '*'`, `pageSize: 1`), paced like any other, with no
@@ -136,7 +154,9 @@ export declare class EuropePmcService {
      *
      * Throws `SerializationError` only for fundamentally invalid XML; an
      * article-free but well-formed body returns `undefined` so callers can
-     * surface a `no-epmc-fulltext` outcome without a hard failure.
+     * surface a `no-epmc-fulltext` outcome without a hard failure. Invisible
+     * characters a deposit carries inside words are dropped before parsing, as
+     * on the PMC EFetch tier. (#224)
      */
     parseFullTextXml(xml: string): JatsNode | undefined;
     /**

package/dist/services/europe-pmc/europe-pmc-service.d.ts.map CHANGED Viewed

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