openalex-research-mcp 0.3.0 → 0.4.1

package/QUICKSTART.md

@@ -69,36 +69,52 @@ Which countries are leading research in renewable energy?
 
 ## Available Tools
 
-The server provides 18 specialized tools:
-
-**Literature Search:**
-- `search_works` - Advanced search for papers
-- `get_work` - Get detailed paper information
-- `get_related_works` - Find similar papers
-- `search_by_topic` - Explore specific research domains
-- `autocomplete_search` - Fast typeahead search
+The server provides 31 specialized tools:
+
+**Literature Search & Discovery:**
+- `search_works` - Advanced search with Boolean operators, venue/institution filters
+- `get_work` - Get complete metadata for a specific work
+- `get_related_works` - Find similar papers based on citations and topics
+- `search_by_topic` - Explore literature in specific research domains
+- `autocomplete_search` - Fast typeahead search for all entity types
+
+**Credibility-Gated Search (Journal & Conference Presets):**
+- `list_journal_presets` - List all available journal/conference and institution group presets
+- `search_in_journal_list` - Search within a named preset (UTD24, FT50, AJG tiers, etc.)
+- `search_works_in_venue` - Search within a specific venue by name, ISSN, or ID
+- `get_top_venues_for_field` - Discover top journals/conferences ranked by h-index
+- `check_venue_quality` - Inspect h-index, impact, and indexing status of any venue
 
 **Citation Analysis:**
-- `get_work_citations` - Who cites this paper
-- `get_work_references` - What this paper cites
-- `get_citation_network` - Complete citation graph
-- `get_top_cited_works` - Most influential papers
-
-**Author & Institutions:**
-- `search_authors` - Find researchers
-- `get_author_works` - Author's publications
-- `get_author_collaborators` - Co-authorship networks
-- `search_institutions` - Find universities/organizations
-
-**Research Trends:**
-- `analyze_topic_trends` - Track research evolution
-- `compare_research_areas` - Compare different fields
-- `get_trending_topics` - Discover emerging areas
-- `analyze_geographic_distribution` - Global research mapping
+- `get_work_citations` - Forward citation analysis (who cites this work)
+- `get_work_references` - Backward citation analysis (what this work cites)
+- `get_citation_network` - Build citation networks (forward + backward)
+- `get_top_cited_works` - Find the most influential papers in a field
+
+**Author & Institution Analysis:**
+- `search_authors` - Find researchers with h-index and citation metrics
+- `search_authors_by_expertise` - Find experts in a topic ranked by h-index
+- `get_author_profile` - Full profile: h-index, i10-index, top works, recent works
+- `get_author_works` - Analyze an author's publication history
+- `get_author_collaborators` - Map co-authorship networks
+- `search_institutions` - Find academic institutions
+
+**High-Value Citation Finding:**
+- `find_review_articles` - Find review papers and meta-analyses
+- `find_seminal_papers` - Find foundational "must-cite" papers
+- `find_open_access_version` - Find freely available versions of papers
+- `batch_resolve_references` - Validate up to 20 DOIs/IDs at once
+
+**Research Landscape & Trends:**
+- `analyze_topic_trends` - Track research evolution over time
+- `compare_research_areas` - Compare activity across different fields
+- `get_trending_topics` - Discover emerging research areas
+- `analyze_geographic_distribution` - Map global research activity
 
 **Entity Lookup:**
-- `get_entity` - Get any OpenAlex entity
-- `search_sources` - Find journals/venues
+- `get_entity` - Get any OpenAlex entity (works, authors, sources, etc.)
+- `search_sources` - Find journals/conferences sorted by h-index
+- `health_check` - Verify server and API connectivity
 
 ## Tips
 

package/README.md

@@ -2,6 +2,19 @@
 
 A Model Context Protocol (MCP) server that provides access to OpenAlex, a comprehensive open catalog of scholarly papers, authors, institutions, and more. Designed to empower AI assistants to conduct literature reviews, analyze research trends, and map the scholarly landscape.
 
+## Quick Install
+
+```bash
+npx openalex-research-mcp setup
+```
+
+This auto-detects your Claude Desktop config, prompts for your email and optional API key, writes the config, and verifies connectivity — all in one step. Restart Claude Desktop when done.
+
+**Flags:**
+- `--print` — print the config JSON without writing anything
+- `--config-path` — print the detected config file path and exit
+- `--email you@example.com --api-key YOUR_KEY` — non-interactive / scripted mode
+
 **Features:**
 - ⚡️ **In-memory caching** with TTL for fast repeated requests
 - 🔄 **Retry logic** with exponential backoff for resilient API calls
@@ -428,7 +441,28 @@ MIT
 
 ## Contributing
 
-Contributions are welcome! Please feel free to submit issues or pull requests.
+Contributions are welcome! Here's how to get involved:
+
+### Reporting bugs
+
+- Search [existing issues](https://github.com/oksure/openalex-research-mcp/issues) before opening a new one.
+- Include a clear description of what you expected vs. what happened.
+- If the bug involves an API call, paste the relevant curl command or error message so it can be reproduced quickly (see the [OpenAlex API docs](https://docs.openalex.org) for reference).
+
+### Requesting features
+
+- Open an issue with the `enhancement` label.
+- Describe the use case and, if possible, sketch the desired tool name, input parameters, and example output.
+
+### Submitting pull requests
+
+1. **Fork** the repo and create a branch from `master` (e.g. `fix/my-bug` or `feat/my-feature`).
+2. **Make your changes** following the patterns in [CLAUDE.md](CLAUDE.md) (two-layer architecture, `summarizeWork` for list results, `getFullWorkDetails` for single-work lookups, etc.).
+3. **Add tests** — run `npm test` (vitest) to make sure all 26+ existing tests still pass, and add new tests in `tests/` for any new behaviour.
+4. **Build** with `npm run build` to confirm there are no TypeScript errors.
+5. **Open a PR** against `master` with a clear description of the problem and fix, including any curl-level reproduction steps for API-related bugs.
+
+> **Note on API quirks:** Before adding new filter logic, check the "OpenAlex API Quirks & Common Bugs" section in [CLAUDE.md](CLAUDE.md) — several non-obvious behaviours (date filters, sort suffixes, DOI encoding) are documented there.
 
 ## Resources
 

package/build/config.d.ts

@@ -1,3 +1,4 @@
+export declare function debug(...args: unknown[]): void;
 export declare const CONFIG: {
     API: {
         BASE_URL: string;
@@ -8,6 +9,7 @@ export declare const CONFIG: {
         };
         RETRY: {
             MAX_RETRIES: number;
+            MAX_429_RETRIES: number;
             INITIAL_DELAY_MS: number;
             MAX_DELAY_MS: number;
             BACKOFF_FACTOR: number;

package/build/config.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAAA,eAAO,MAAM,MAAM;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA6BlB,CAAC"}
+{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAEA,wBAAgB,KAAK,CAAC,GAAG,IAAI,EAAE,OAAO,EAAE,GAAG,IAAI,CAE9C;AAED,eAAO,MAAM,MAAM;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA8BlB,CAAC"}

package/build/config.js

@@ -1,3 +1,9 @@
+// Debug logging gated on OPENALEX_DEBUG env var (stderr is safe for MCP stdio servers)
+const DEBUG_ENABLED = process.env.OPENALEX_DEBUG === '1' || process.env.OPENALEX_DEBUG === 'true';
+export function debug(...args) {
+    if (DEBUG_ENABLED)
+        console.error('[openalex]', ...args);
+}
 export const CONFIG = {
     API: {
         BASE_URL: 'https://api.openalex.org',
@@ -8,6 +14,7 @@ export const CONFIG = {
         },
         RETRY: {
             MAX_RETRIES: 3,
+            MAX_429_RETRIES: 3,
             INITIAL_DELAY_MS: 1000,
             MAX_DELAY_MS: 10000,
             BACKOFF_FACTOR: 2,

package/build/config.js.map

@@ -1 +1 @@
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+{"version":3,"file":"config.js","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAAA,uFAAuF;AACvF,MAAM,aAAa,GAAG,OAAO,CAAC,GAAG,CAAC,cAAc,KAAK,GAAG,IAAI,OAAO,CAAC,GAAG,CAAC,cAAc,KAAK,MAAM,CAAC;AAClG,MAAM,UAAU,KAAK,CAAC,GAAG,IAAe;IACtC,IAAI,aAAa;QAAE,OAAO,CAAC,KAAK,CAAC,YAAY,EAAE,GAAG,IAAI,CAAC,CAAC;AAC1D,CAAC;AAED,MAAM,CAAC,MAAM,MAAM,GAAG;IACpB,GAAG,EAAE;QACH,QAAQ,EAAE,0BAA0B;QACpC,OAAO,EAAE,KAAK;QACd,UAAU,EAAE;YACV,mBAAmB,EAAE,EAAE;YACvB,gBAAgB,EAAE,MAAM;SACzB;QACD,KAAK,EAAE;YACL,WAAW,EAAE,CAAC;YACd,eAAe,EAAE,CAAC;YAClB,gBAAgB,EAAE,IAAI;YACtB,YAAY,EAAE,KAAK;YACnB,cAAc,EAAE,CAAC;SAClB;KACF;IACD,KAAK,EAAE;QACL,MAAM,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,EAAE,YAAY;QACnC,QAAQ,EAAE,IAAI;KACf;IACD,GAAG,EAAE;QACH,iBAAiB,EAAE,EAAE;QACrB,aAAa,EAAE,GAAG;QAClB,sBAAsB,EAAE,CAAC;QACzB,mBAAmB,EAAE,GAAG;QACxB,UAAU,EAAE,CAAC;QACb,YAAY,EAAE,EAAE;QAChB,UAAU,EAAE,CAAC;QACb,6BAA6B,EAAE,EAAE;KAClC;CACF,CAAC"}

package/build/filter.d.ts

@@ -0,0 +1,3 @@
+import { FilterOptions } from './openalex-client.js';
+export declare function buildFilter(params: any): FilterOptions;
+//# sourceMappingURL=filter.d.ts.map

package/build/filter.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"filter.d.ts","sourceRoot":"","sources":["../src/filter.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AAIrD,wBAAgB,WAAW,CAAC,MAAM,EAAE,GAAG,GAAG,aAAa,CAwDtD"}

package/build/filter.js

@@ -0,0 +1,61 @@
+// buildFilter — maps MCP tool parameters to OpenAlex API filter format.
+// Exported so it can be unit-tested directly.
+import { INSTITUTION_GROUPS } from './presets.js';
+import { debug } from './config.js';
+export function buildFilter(params) {
+    const filter = {};
+    // Handle publication year range (all tools now use from_year/to_year)
+    const fromYear = params.from_year || params.from_publication_year;
+    const toYear = params.to_year || params.to_publication_year;
+    if (fromYear && toYear) {
+        filter['publication_year'] = `${fromYear}-${toYear}`;
+    }
+    else if (fromYear) {
+        filter['publication_year'] = `>${fromYear - 1}`;
+    }
+    else if (toYear) {
+        filter['publication_year'] = `<${toYear + 1}`;
+    }
+    if (params.cited_by_count) {
+        filter['cited_by_count'] = params.cited_by_count;
+    }
+    if (params.is_oa !== undefined) {
+        filter['is_oa'] = params.is_oa;
+    }
+    if (params.type) {
+        filter['type'] = params.type;
+    }
+    if (params.works_count) {
+        filter['works_count'] = params.works_count;
+    }
+    if (params.country_code) {
+        filter['country_code'] = params.country_code;
+    }
+    if (params.institution) {
+        filter['institutions.display_name'] = params.institution;
+    }
+    if (params.institution_group) {
+        const group = INSTITUTION_GROUPS[params.institution_group];
+        if (group) {
+            filter['authorships.institutions.display_name'] = group.institutions.join('|');
+        }
+    }
+    else if (params.author_institution) {
+        filter['authorships.institutions.display_name'] = params.author_institution;
+    }
+    if (params.source_id) {
+        filter['primary_location.source.id'] = params.source_id;
+    }
+    if (params.source_name) {
+        filter['primary_location.source.display_name.search'] = params.source_name;
+    }
+    if (params.source_issn) {
+        filter['primary_location.source.issn'] = params.source_issn;
+    }
+    if (params.min_citations !== undefined && params.min_citations > 0) {
+        filter['cited_by_count'] = `>${params.min_citations - 1}`;
+    }
+    debug('buildFilter result:', JSON.stringify(filter));
+    return filter;
+}
+//# sourceMappingURL=filter.js.map

package/build/filter.js.map

@@ -0,0 +1 @@
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package/build/formatters.d.ts

@@ -0,0 +1,118 @@
+export declare function reconstructAbstract(invertedIndex: any): string;
+export declare function summarizeWork(work: any): {
+    id: any;
+    doi: any;
+    title: any;
+    publication_year: any;
+    publication_date: any;
+    cited_by_count: any;
+    type: any;
+    authors: any;
+    authors_truncated: boolean;
+    primary_topic: {
+        display_name: any;
+        field: any;
+        subfield: any;
+    } | null;
+    open_access: {
+        is_oa: any;
+        oa_status: any;
+        oa_url: any;
+    };
+    landing_page_url: any;
+    pdf_url: any;
+    source: any;
+    source_id: any;
+    source_issn_l: any;
+    source_type: any;
+    fwci: any;
+    abstract: string | null;
+};
+export declare function summarizeAuthor(author: any): {
+    id: any;
+    name: any;
+    orcid: any;
+    works_count: any;
+    cited_by_count: any;
+    h_index: any;
+    i10_index: any;
+    two_year_mean_citedness: any;
+    last_known_institutions: any;
+    top_topics: any;
+};
+export declare function summarizeSource(source: any): {
+    id: any;
+    display_name: any;
+    issn_l: any;
+    issn: any;
+    type: any;
+    h_index: any;
+    two_year_mean_citedness: any;
+    works_count: any;
+    cited_by_count: any;
+    is_oa: any;
+    is_in_doaj: any;
+    homepage_url: any;
+    host_organization: any;
+    topics: any;
+};
+export declare function summarizeWorksList(response: any): {
+    meta: {
+        count: any;
+        page: any;
+        per_page: any;
+    };
+    results: any;
+};
+export declare function getFullWorkDetails(work: any): {
+    id: any;
+    doi: any;
+    title: any;
+    publication_year: any;
+    publication_date: any;
+    cited_by_count: any;
+    type: any;
+    authors: any;
+    primary_topic: {
+        id: any;
+        display_name: any;
+        score: any;
+        field: any;
+        subfield: any;
+        domain: any;
+    } | null;
+    topics: any;
+    open_access: {
+        is_oa: any;
+        oa_status: any;
+        oa_url: any;
+        any_repository_has_fulltext: any;
+    };
+    landing_page_url: any;
+    pdf_url: any;
+    primary_location: {
+        is_oa: any;
+        landing_page_url: any;
+        pdf_url: any;
+        source: {
+            id: any;
+            display_name: any;
+            issn_l: any;
+            issn: any;
+            type: any;
+            host_organization: any;
+        } | null;
+        license: any;
+        version: any;
+    } | null;
+    abstract: string | null;
+    biblio: any;
+    referenced_works_count: any;
+    cited_by_percentile_year: any;
+    fwci: any;
+    keywords: any;
+    grants: any;
+    referenced_works: any;
+    related_works: any;
+};
+//# sourceMappingURL=formatters.d.ts.map

package/build/formatters.d.ts.map

@@ -0,0 +1 @@
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package/build/formatters.js

@@ -0,0 +1,180 @@
+// Response formatting helpers — pure functions for summarizing OpenAlex API responses.
+// Two-tier strategy: summarized results for list operations, full details for single-work lookups.
+export function reconstructAbstract(invertedIndex) {
+    const words = {};
+    for (const [word, positions] of Object.entries(invertedIndex)) {
+        if (Array.isArray(positions)) {
+            positions.forEach((pos) => {
+                words[pos] = word;
+            });
+        }
+    }
+    const sortedPositions = Object.keys(words).map(Number).sort((a, b) => a - b);
+    return sortedPositions.map(pos => words[pos]).join(' ');
+}
+export function summarizeWork(work) {
+    return {
+        id: work.id,
+        doi: work.doi,
+        title: work.title || work.display_name,
+        publication_year: work.publication_year,
+        publication_date: work.publication_date,
+        cited_by_count: work.cited_by_count,
+        type: work.type,
+        authors: work.authorships?.slice(0, 5).map((a) => ({
+            name: a.author?.display_name,
+            institutions: a.institutions?.slice(0, 2).map((i) => i.display_name)
+        })) || [],
+        authors_truncated: work.authorships?.length > 5,
+        primary_topic: work.primary_topic ? {
+            display_name: work.primary_topic.display_name,
+            field: work.primary_topic.field?.display_name,
+            subfield: work.primary_topic.subfield?.display_name
+        } : null,
+        open_access: {
+            is_oa: work.open_access?.is_oa,
+            oa_status: work.open_access?.oa_status,
+            oa_url: work.open_access?.oa_url
+        },
+        landing_page_url: work.primary_location?.landing_page_url,
+        pdf_url: work.best_oa_location?.pdf_url,
+        source: work.primary_location?.source?.display_name,
+        source_id: work.primary_location?.source?.id,
+        source_issn_l: work.primary_location?.source?.issn_l,
+        source_type: work.primary_location?.source?.type,
+        fwci: work.fwci ?? null,
+        abstract: work.abstract_inverted_index ?
+            reconstructAbstract(work.abstract_inverted_index).substring(0, 600) : null
+    };
+}
+export function summarizeAuthor(author) {
+    return {
+        id: author.id,
+        name: author.display_name,
+        orcid: author.orcid,
+        works_count: author.works_count,
+        cited_by_count: author.cited_by_count,
+        h_index: author.summary_stats?.h_index ?? null,
+        i10_index: author.summary_stats?.i10_index ?? null,
+        two_year_mean_citedness: author.summary_stats?.['2yr_mean_citedness'] ?? null,
+        last_known_institutions: author.last_known_institutions?.slice(0, 2).map((i) => ({
+            display_name: i.display_name,
+            country_code: i.country_code,
+            type: i.type
+        })) || [],
+        top_topics: author.topics?.slice(0, 4).map((t) => ({
+            name: t.display_name,
+            count: t.count
+        })) || []
+    };
+}
+export function summarizeSource(source) {
+    return {
+        id: source.id,
+        display_name: source.display_name,
+        issn_l: source.issn_l,
+        issn: source.issn,
+        type: source.type,
+        h_index: source.summary_stats?.h_index ?? null,
+        two_year_mean_citedness: source.summary_stats?.['2yr_mean_citedness'] ?? null,
+        works_count: source.works_count,
+        cited_by_count: source.cited_by_count,
+        is_oa: source.is_oa,
+        is_in_doaj: source.is_in_doaj,
+        homepage_url: source.homepage_url,
+        host_organization: source.host_organization_name,
+        topics: source.topics?.slice(0, 4).map((t) => t.display_name) || []
+    };
+}
+export function summarizeWorksList(response) {
+    return {
+        meta: {
+            count: response.meta?.count,
+            page: response.meta?.page,
+            per_page: response.meta?.per_page
+        },
+        results: response.results?.map(summarizeWork) || []
+    };
+}
+export function getFullWorkDetails(work) {
+    return {
+        id: work.id,
+        doi: work.doi,
+        title: work.title || work.display_name,
+        publication_year: work.publication_year,
+        publication_date: work.publication_date,
+        cited_by_count: work.cited_by_count,
+        type: work.type,
+        authors: work.authorships?.map((a, index) => ({
+            position: index === 0 ? 'first' : index === work.authorships.length - 1 ? 'last' : 'middle',
+            author_position: a.author_position,
+            name: a.author?.display_name,
+            id: a.author?.id,
+            orcid: a.author?.orcid,
+            institutions: a.institutions?.map((i) => ({
+                id: i.id,
+                display_name: i.display_name,
+                ror: i.ror,
+                country_code: i.country_code,
+                type: i.type
+            })) || [],
+            countries: a.countries || [],
+            is_corresponding: a.is_corresponding,
+            raw_affiliation_strings: a.raw_affiliation_strings || []
+        })) || [],
+        primary_topic: work.primary_topic ? {
+            id: work.primary_topic.id,
+            display_name: work.primary_topic.display_name,
+            score: work.primary_topic.score,
+            field: work.primary_topic.field?.display_name,
+            subfield: work.primary_topic.subfield?.display_name,
+            domain: work.primary_topic.domain?.display_name
+        } : null,
+        topics: work.topics?.slice(0, 5).map((t) => ({
+            id: t.id,
+            display_name: t.display_name,
+            score: t.score
+        })) || [],
+        open_access: {
+            is_oa: work.open_access?.is_oa,
+            oa_status: work.open_access?.oa_status,
+            oa_url: work.open_access?.oa_url,
+            any_repository_has_fulltext: work.open_access?.any_repository_has_fulltext
+        },
+        landing_page_url: work.primary_location?.landing_page_url,
+        pdf_url: work.best_oa_location?.pdf_url,
+        primary_location: work.primary_location ? {
+            is_oa: work.primary_location.is_oa,
+            landing_page_url: work.primary_location.landing_page_url,
+            pdf_url: work.primary_location.pdf_url,
+            source: work.primary_location.source ? {
+                id: work.primary_location.source.id,
+                display_name: work.primary_location.source.display_name,
+                issn_l: work.primary_location.source.issn_l,
+                issn: work.primary_location.source.issn,
+                type: work.primary_location.source.type,
+                host_organization: work.primary_location.source.host_organization_name
+            } : null,
+            license: work.primary_location.license,
+            version: work.primary_location.version
+        } : null,
+        abstract: work.abstract_inverted_index ?
+            reconstructAbstract(work.abstract_inverted_index) : null,
+        biblio: work.biblio,
+        referenced_works_count: work.referenced_works_count,
+        cited_by_percentile_year: work.cited_by_percentile_year,
+        fwci: work.fwci,
+        keywords: work.keywords?.slice(0, 10).map((k) => ({
+            keyword: k.keyword || k.display_name,
+            score: k.score
+        })) || [],
+        grants: work.grants?.slice(0, 5).map((g) => ({
+            funder: g.funder,
+            funder_display_name: g.funder_display_name,
+            award_id: g.award_id
+        })) || [],
+        referenced_works: work.referenced_works || [],
+        related_works: work.related_works || []
+    };
+}
+//# sourceMappingURL=formatters.js.map

package/build/formatters.js.map

@@ -0,0 +1 @@
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