@yeyuan98/opencode-bioresearcher-plugin 1.2.1 → 1.2.3

package/README.md

@@ -1,12 +1,19 @@
 # BioResearcher Plugin
 
-OpenCode plugin that adds a `Bioresearcher` agent.
+OpenCode plugin that adds agents and tools for biomedical and pharmaceutical research.
 
 ## Overview
 
-No nonsense and powerful. An agent that just works for your typical biomedical and pharmaceutical research needs.
+No nonsense and powerful. Agents and tools that just work for your typical biomedical and pharmaceutical research needs.
 
-Tab to activate the Bioresearcher Agent and starting asking right away.
+Tab to activate and start asking right away:
+
+- The **Bioresearcher Agent** is jack-of-all-trades.
+- The **BioresearcherDR Agent** is a specialist for biomed/pharma deep research (DR).
+
+## Agents
+
+### BioresearcherDR
 
 By default, it will conduct **highly detailed and in-depth** research, easily surpassing all general purpose LLM applications.
 
@@ -16,7 +23,57 @@ To reduce research depth and make research process faster, start your question w
 light-research Significance of KRAS for cancer?
 ```
 
-Based on fantastic work of the [BioMCP Team](https://biomcp.org/blog/ai-assisted-clinical-trial-search-analysis/).
+To skip the Question-Clarification cycle, prompt your question with `no-interview`:
+
+```text
+no-interview light-research Significance of KRAS for cancer?
+```
+
+## Tools
+
+### Table Tools
+
+Manipulate Excel, CSV, and ODS files with precision and smart parsing for dates, numbers, and data types.
+
+**Enable LLMs to wrangle huge tables WITHOUT overwhelming model context.**
+
+```text
+What are tools for table processing?
+What are column names in XXX.xlsx?
+Analyze XXX.xlsx - group by Y column, and report unique values of Z column.
+```
+
+### Calculator
+
+Evaluate mathematical expressions with full support for brackets, powers, and scientific notation.
+
+**Make your model accurate with numbers. No more 3.11 > 3.9 nor 1+2=5.**
+
+```text
+Use the calculator tool: (3+1.5*6-1/2)^3
+```
+
+### Blocking Timer
+
+Pause execution for testing or pacing operations.
+
+**Respect API rate limits. No more IP bans/blocks.**
+
+```text
+Query XXX API. You MUST include a 0.5 second delay between two API calls with the blockingTimer tool.
+```
+
+### PubMed Parser
+
+Parse PubMed XML files to markdown or Excel format. Supports `.xml` and `.xml.gz` files.
+
+**Analyze years of publication articles in one go. Simple and powerful.**
+
+```text
+Download pubmed article data from https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed26n1340.xml.gz and parse to Excel format.
+```
+
+Reference: [PubMed Download Data](https://pubmed.ncbi.nlm.nih.gov/download/).
 
 ## Installation
 
@@ -52,4 +109,3 @@ BioMCP is absolutely required and might take time to load. You will need to have
 ## License
 
 CC BY-NC-ND 4.0
-

package/dist/parser-tools/pubmed/types.d.ts

@@ -93,7 +93,6 @@ export interface ParsedArticle {
     doi: string | null;
     abstract: string | null;
     keywords: string[];
-    publicationDate?: string;
     error?: string;
 }
 export interface ProcessingStats {
@@ -104,7 +103,6 @@ export interface ProcessingStats {
 export interface ExcelRow {
     PMID: string;
     Title: string;
-    PublicationDate: string;
     Authors: string;
     Journal: string;
     DOI: string;

package/dist/parser-tools/pubmed/utils.d.ts

@@ -8,7 +8,6 @@ export declare function extractJournalInfo(article: PubmedArticle): string;
 export declare function extractDOI(article: PubmedArticle): string | null;
 export declare function extractAbstract(article: PubmedArticle): string | null;
 export declare function extractKeywords(article: PubmedArticle): string[];
-export declare function extractPublicationDate(article: PubmedArticle): string | undefined;
 export declare function extractAllFields(article: PubmedArticle): ParsedArticle;
 export declare function generateArticleMarkdown(data: ParsedArticle): string;
 export declare function generateExcelFile(articles: ParsedArticle[], outputFilePath: string): void;

package/dist/parser-tools/pubmed/utils.js

@@ -53,7 +53,6 @@ export function extractJournalInfo(article) {
     const year = getText(pubDate?.Year) || '';
     const volume = getText(journalIssue?.Volume) || '';
     const issue = getText(journalIssue?.Issue) || '';
-    const pages = getText(article.MedlineCitation?.Article?.Pagination?.MedlinePgn) || '';
     let info = title;
     if (year)
         info += `, ${year}`;
@@ -64,8 +63,6 @@ export function extractJournalInfo(article) {
         if (issue)
             info += `(${issue})`;
     }
-    if (pages)
-        info += `:${pages}`;
     return info;
 }
 export function extractDOI(article) {
@@ -98,26 +95,6 @@ export function extractKeywords(article) {
         .map(kw => getText(kw))
         .filter((kw) => kw !== null && kw.length > 0);
 }
-export function extractPublicationDate(article) {
-    const history = article.PubmedData?.History;
-    if (!history)
-        return undefined;
-    const pubDates = toArray(history.PubMedPubDate);
-    const pubDate = pubDates.find(p => p['@_PubStatus'] === 'pubmed' || p['@_PubStatus'] === 'medline');
-    if (!pubDate)
-        return undefined;
-    const year = getText(pubDate.Year) || '';
-    const month = getText(pubDate.Month) || '';
-    const day = getText(pubDate.Day) || '';
-    let date;
-    if (year)
-        date = year;
-    if (month)
-        date = `${date || ''} ${month}`;
-    if (day)
-        date = `${date || ''} ${day}`;
-    return date || undefined;
-}
 export function extractAllFields(article) {
     return {
         PMID: extractPMID(article),
@@ -126,8 +103,7 @@ export function extractAllFields(article) {
         journal: extractJournalInfo(article),
         doi: extractDOI(article),
         abstract: extractAbstract(article),
-        keywords: extractKeywords(article),
-        publicationDate: extractPublicationDate(article)
+        keywords: extractKeywords(article)
     };
 }
 export function generateArticleMarkdown(data) {
@@ -137,9 +113,6 @@ export function generateArticleMarkdown(data) {
     }
     markdown += `## PMID\n${data.PMID}\n\n`;
     markdown += `## Title\n${data.title}\n\n`;
-    if (data.publicationDate) {
-        markdown += `## Publication Date\n${data.publicationDate}\n\n`;
-    }
     markdown += `## Authors\n`;
     data.authors.forEach(author => {
         markdown += `- ${author}\n`;
@@ -161,7 +134,6 @@ export function generateExcelFile(articles, outputFilePath) {
     const excelRows = articles.map(article => ({
         PMID: article.error ? `[ERROR] ${article.PMID}` : article.PMID,
         Title: article.title,
-        PublicationDate: article.publicationDate || '',
         Authors: article.authors.join(', '),
         Journal: article.journal,
         DOI: article.doi || '',

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@yeyuan98/opencode-bioresearcher-plugin",
-  "version": "1.2.1",
+  "version": "1.2.3",
   "description": "OpenCode plugin that adds a bioresearcher agent",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",