@yeyuan98/opencode-bioresearcher-plugin 1.5.0 → 1.5.1

package/README.md

@@ -75,47 +75,47 @@ Parse PubMed XML files to markdown or Excel format. Supports `.xml` and `.xml.gz
 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/).
-
-### OBO Parser
-
-Parse OBO (Open Biological and Biomedical Ontology) files to CSV format. Handles Term, Typedef, and Instance frames.
-
-**Flatten complex ontologies into analysis-ready tables.**
-
-```text
-Parse go.obo file and convert to CSV using parse_obo_file tool.
-```
-
-Reference: [OBO Format](http://owlcollab.github.io/oboformat/doc/obo-syntax.html).
-
-### JSON Tools
-
-Extract, validate, and infer JSON schemas from data.
-
-**Robust JSON handling for LLM workflows.**
-
-```text
-Extract JSON from output.md using jsonExtract tool.
-Validate data.json against schema.json using jsonValidate tool.
-Infer schema from sample.json using jsonInfer tool.
-```
-
-### Database Tools
-
-Query MySQL and MongoDB databases with read-only access.
-
-**Explore your data warehouse without leaving the conversation.**
-
-```text
-List all tables in the database.
-Describe the schema for table users.
-Query orders placed in the last 30 days.
-```
-
-Configuration via `env.jsonc` in working directory. Use the `env-jsonc-setup` skill for guided setup.
-
-## Skills
+Reference: [PubMed Download Data](https://pubmed.ncbi.nlm.nih.gov/download/).
+
+### OBO Parser
+
+Parse OBO (Open Biological and Biomedical Ontology) files to CSV format. Handles Term, Typedef, and Instance frames.
+
+**Flatten complex ontologies into analysis-ready tables.**
+
+```text
+Parse go.obo file and convert to CSV using parse_obo_file tool.
+```
+
+Reference: [OBO Format](http://owlcollab.github.io/oboformat/doc/obo-syntax.html).
+
+### JSON Tools
+
+Extract, validate, and infer JSON schemas from data.
+
+**Robust JSON handling for LLM workflows.**
+
+```text
+Extract JSON from output.md using jsonExtract tool.
+Validate data.json against schema.json using jsonValidate tool.
+Infer schema from sample.json using jsonInfer tool.
+```
+
+### Database Tools
+
+Query MySQL and MongoDB databases with read-only access.
+
+**Explore your data warehouse without leaving the conversation.**
+
+```text
+List all tables in the database.
+Describe the schema for table users.
+Query orders placed in the last 30 days.
+```
+
+Configuration via `env.jsonc` in working directory. Use the `env-jsonc-setup` skill for guided setup.
+
+## Skills
 
 Skills are reusable prompt templates discovered from multiple paths:
 
@@ -128,16 +128,16 @@ Skills are reusable prompt templates discovered from multiple paths:
 
 This plugin provides a skill tool that overrides Opencode's built-in to support plugin-shipped skills.
 
-See [skill-tools/README.md](skill-tools/README.md) for full documentation.
+See README in `tools/skill` for full documentation.
+
+### Supplied skills
 
-### Supplied skills
-
-- `demo-skill`: showcase skill tool mechanisms.
-- `python-setup-uv`: setup python runtime in your working directory with uv.
-- `pubmed-weekly`: automated download of pubmed daily update files over the past one week.
-- `long-table-summary`: batch-process large tables using parallel subagents for summarization.
-- `bioresearcher-core`: core patterns and utilities (retry, JSON tools, subagent waves) for skill development.
-- `env-jsonc-setup`: guided setup for database connection configuration (db-tools).
+- `demo-skill`: showcase skill tool mechanisms.
+- `python-setup-uv`: setup python runtime in your working directory with uv.
+- `pubmed-weekly`: automated download of pubmed daily update files over the past one week.
+- `long-table-summary`: batch-process large tables using parallel subagents for summarization.
+- `bioresearcher-core`: core patterns and utilities (retry, JSON tools, subagent waves) for skill development.
+- `env-jsonc-setup`: guided setup for database connection configuration (db-tools).
 
 Prompt the following and follow along:
 

package/dist/index.js

@@ -1,12 +1,12 @@
 import { createBioResearcherAgent } from "./agents/bioresearcher/index";
 import { createBioResearcherDRAgent } from "./agents/bioresearcherDR/index";
 import { createBioResearcherDRWorkerAgent } from "./agents/bioresearcherDR_worker/index";
-import { tableTools } from "./table-tools/index";
-import { dbTools } from "./db-tools/index";
-import { blockingTimer, calculator, jsonExtract, jsonValidate, jsonInfer } from "./misc-tools/index";
-import { parse_pubmed_articleSet } from "./parser-tools/pubmed";
-import { parse_obo_file } from "./parser-tools/obo";
-import { SkillTool } from "./skill-tools";
+import { tableTools } from "./tools/table/index";
+import { dbTools } from "./tools/db/index";
+import { blockingTimer, calculator, jsonExtract, jsonValidate, jsonInfer } from "./tools/misc/index";
+import { parse_pubmed_articleSet } from "./tools/parser/pubmed";
+import { parse_obo_file } from "./tools/parser/obo";
+import { SkillTool } from "./tools/skill";
 export const BioResearcherPlugin = async () => {
     return {
         config: async (config) => {

package/dist/skills/bioresearcher-tests/README.md

@@ -0,0 +1,90 @@
+# BioResearcher Tests Skill
+
+Comprehensive test suite for the bioresearcher plugin.
+
+## Quick Start
+
+```
+skill bioresearcher-tests
+```
+
+Then follow the workflow steps in SKILL.md.
+
+## Test Coverage
+
+### Parser Tools
+- `parse_pubmed_articleSet` - PubMed XML parsing (single/excel/individual modes)
+- `parse_obo_file` - OBO ontology parsing
+
+### Table Tools (13 tools)
+- `tableListSheets` - List worksheets
+- `tableGetSheetPreview` - Preview first 6 rows
+- `tableGetHeaders` - Get column headers
+- `tableGetCell` - Get cell by address
+- `tableGetRange` - Get range of cells
+- `tableFilterRows` - Filter with conditions
+- `tableSearch` - Search across cells
+- `tableSummarize` - Statistical summary
+- `tableGroupBy` - Group aggregation
+- `tablePivotSummary` - Pivot tables
+- `tableCreateFile` - Create new file
+- `tableAppendRows` - Append rows
+- `tableUpdateCell` - Update cell
+
+### JSON Tools
+- `jsonExtract` - Extract JSON from files
+- `jsonValidate` - Validate against schema
+- `jsonInfer` - Infer schema from data
+
+### Misc Tools
+- `blockingTimer` - Blocking delays
+- `calculator` - Math expressions
+
+### Skills
+- `demo-skill` - Full execution
+- `bioresearcher-core` - Full execution
+- Other skills - Metadata only (use Question tool)
+
+## Not Tested
+
+### Database Tools
+Require live database connection:
+- `dbQuery`
+- `dbListTables`
+- `dbDescribeTable`
+
+### Interactive Skills
+Use Question tool (user interaction):
+- `python-setup-uv`
+- `long-table-summary`
+- `env-jsonc-setup`
+- `pubmed-weekly`
+
+## Report Output
+
+Tests generate `.bioresearcher-tests/test_report.md` containing:
+- Pass/fail summary by category
+- List of skipped tests with reasons
+- Detailed failure diagnostics
+- Validator results for each test
+
+## File Structure
+
+```
+bioresearcher-tests/
+├── SKILL.md              # Main skill with workflow
+├── README.md             # This file
+├── pyproject.toml        # Python project config
+├── test_runner.py        # Test structure generator
+├── resources/            # Gzipped test inputs
+│   ├── pubmed_sample.xml.gz
+│   ├── obo_sample.obo.gz
+│   ├── table_sample.xlsx.gz
+│   └── json_samples/*.gz
+└── test_cases/           # Test definitions
+    ├── parser_tests.md
+    ├── table_tests.md
+    ├── json_tests.md
+    ├── misc_tests.md
+    └── skill_tests.md
+```

package/dist/skills/bioresearcher-tests/SKILL.md

@@ -0,0 +1,255 @@
+---
+name: bioresearcher-tests
+description: Comprehensive tests for bioresearcher plugin tools and skills
+allowedTools:
+  - Bash
+  - Read
+  - Write
+  - jsonExtract
+  - jsonValidate
+  - jsonInfer
+  - tableListSheets
+  - tableGetSheetPreview
+  - tableGetHeaders
+  - tableGetRange
+  - tableGetCell
+  - tableFilterRows
+  - tableSearch
+  - tableSummarize
+  - tableGroupBy
+  - tablePivotSummary
+  - tableAppendRows
+  - tableUpdateCell
+  - tableCreateFile
+  - blockingTimer
+  - calculator
+  - parse_pubmed_articleSet
+  - parse_obo_file
+  - skill
+  - Question
+---
+
+# BioResearcher Plugin Tests
+
+Comprehensive test suite for bioresearcher plugin tools and skills.
+
+## Test Scope
+
+| Category | Tools | Status |
+|----------|-------|--------|
+| Parser | `parse_pubmed_articleSet`, `parse_obo_file` | Full tests |
+| Table | All 13 `table*` tools | Full tests + negative tests |
+| JSON | `jsonExtract`, `jsonValidate`, `jsonInfer` | Full tests |
+| Misc | `blockingTimer`, `calculator` | Full tests |
+| Skills | `demo-skill` | Full execution |
+| Skills | `bioresearcher-core` | Metadata only |
+| Skills | With Question tool | Metadata only |
+| **Database** | `dbQuery`, `dbListTables`, `dbDescribeTable` | **NOT TESTED** |
+
+> **Note:** Database tools are not tested because they require a live database connection configured via `env.jsonc`. These tools should be tested separately with a proper database environment.
+
+## Workflow
+
+### Step 1: Extract Skill Path
+
+After loading this skill, extract `<skill_path>` from the `<skill_files>` section. Use this path in subsequent steps.
+
+### Step 2: Prepare Test Workspace
+
+Create workspace and extract all gzipped resources using Python (cross-platform):
+
+```python
+python -c "
+import gzip, shutil
+from pathlib import Path
+resources = Path('<skill_path>/resources')
+workspace = Path('.bioresearcher-tests/workspace')
+(workspace / 'json_samples').mkdir(parents=True, exist_ok=True)
+files = [
+    ('pubmed_sample.xml.gz', 'pubmed_sample.xml'),
+    ('obo_sample.obo.gz', 'obo_sample.obo'),
+    ('table_sample.xlsx.gz', 'table_sample.xlsx'),
+    ('json_samples/simple_object.json.gz', 'json_samples/simple_object.json'),
+    ('json_samples/simple_array.json.gz', 'json_samples/simple_array.json'),
+    ('json_samples/nested_object.json.gz', 'json_samples/nested_object.json'),
+    ('json_samples/in_markdown.md.gz', 'json_samples/in_markdown.md'),
+    ('json_samples/schema_draft7.json.gz', 'json_samples/schema_draft7.json'),
+]
+for src, dst in files:
+    with gzip.open(resources / src, 'rb') as f_in:
+        with open(workspace / dst, 'wb') as f_out:
+            shutil.copyfileobj(f_in, f_out)
+print('Workspace prepared successfully')
+"
+```
+
+### Step 3: Run Parser Tests
+
+Execute tests from `<skill_path>/test_cases/parser_tests.md`:
+
+1. **PubMed XML - Single Mode**: Call `parse_pubmed_articleSet` with `filePath`, `outputMode: "single"`
+2. **PubMed XML - Excel Mode**: Call with `outputMode: "excel"`
+3. **PubMed XML - Individual Mode**: Call with `outputMode: "individual"`
+4. **OBO - Basic Parsing**: Call `parse_obo_file` with sample OBO
+5. **PubMed - Nonexistent File**: Test error handling
+
+Record pass/fail for each test.
+
+### Step 4: Run Table Tests
+
+Execute tests from `<skill_path>/test_cases/table_tests.md`:
+
+1. `tableListSheets` - List sheets in sample Excel
+2. `tableGetSheetPreview` - Get first 6 rows
+3. `tableGetHeaders` - Get column headers
+4. `tableGetCell` - Get specific cell value
+5. `tableGetRange` - Get A1:C3 range
+6. `tableFilterRows` - Filter by Age > 25
+7. `tableSearch` - Search for "test"
+8. `tableSummarize` - Get stats for numeric columns
+9. `tableGroupBy` - Group by Category
+10. `tableCreateFile` - Create new Excel file
+11. `tableAppendRows` - Append row to file
+12. `tableUpdateCell` - Update cell A1
+13. `tablePivotSummary` - Create pivot table
+
+Record pass/fail for each test.
+
+### Step 5: Run JSON Tests
+
+Execute tests from `<skill_path>/test_cases/json_tests.md`:
+
+1. `jsonExtract` - Simple object
+2. `jsonExtract` - Array
+3. `jsonExtract` - Nested object
+4. `jsonExtract` - JSON in markdown code block
+5. `jsonExtract` - Return all mode
+6. `jsonExtract` - File not found error
+7. `jsonValidate` - Valid data
+8. `jsonValidate` - Invalid data
+9. `jsonValidate` - Schema from file
+10. `jsonInfer` - Object inference
+11. `jsonInfer` - Array inference
+12. `jsonInfer` - Strict mode
+
+Record pass/fail for each test.
+
+### Step 6: Run Misc Tests
+
+Execute tests from `<skill_path>/test_cases/misc_tests.md`:
+
+1. `blockingTimer` - 1 second delay
+2. `blockingTimer` - Zero delay
+3. `calculator` - Basic arithmetic (2 + 3 * 4)
+4. `calculator` - Power (2 ^ 10)
+5. `calculator` - Brackets ((2 + 3) * 4)
+6. `calculator` - Scientific notation (1e3 + 500)
+7. `calculator` - Division by zero
+8. `calculator` - Invalid syntax (2(3))
+9. `calculator` - Precision (10 / 3 with precision 2)
+
+Record pass/fail for each test.
+
+### Step 7: Run Skill Tests
+
+Execute tests from `<skill_path>/test_cases/skill_tests.md`:
+
+1. Load `demo-skill` - Verify content returned
+2. Load `bioresearcher-core` - Verify allowedTools present
+3. Execute demo-skill script (no Question tool)
+4. Test nonexistent skill error
+
+**Skip these skills (use Question tool):**
+- `python-setup-uv`
+- `long-table-summary`
+- `env-jsonc-setup`
+- `pubmed-weekly`
+
+### Step 8: Generate Report
+
+Create `.bioresearcher-tests/test_report.md` with:
+
+```markdown
+# BioResearcher Plugin Test Report
+
+**Run Date:** <timestamp>
+**Total Tests:** <count>
+**Passed:** <count>
+**Failed:** <count>
+
+## Summary by Category
+
+| Category | Passed | Failed |
+|----------|--------|--------|
+| Parser   | X/Y    | Z      |
+| Table    | X/Y    | Z      |
+| JSON     | X/Y    | Z      |
+| Misc     | X/Y    | Z      |
+| Skills   | X/Y    | Z      |
+
+## Skipped Tests
+
+### Database Tools (Not Tested)
+- `dbQuery` - Requires live database connection
+- `dbListTables` - Requires live database connection
+- `dbDescribeTable` - Requires live database connection
+
+### Skills with User Interaction (Metadata Only)
+- `python-setup-uv` - Uses Question tool
+- `long-table-summary` - Uses Question tool
+- `env-jsonc-setup` - Uses Question tool
+- `pubmed-weekly` - Uses Question tool
+
+## Failed Tests
+
+<For each failed test:>
+### <Category>: <Test Name>
+- **Tool:** `<tool_name>`
+- **Expected:** <expected>
+- **Actual:** <actual>
+- **Error:** <error if any>
+
+## Detailed Results
+
+| Test | Tool | Status |
+|------|------|--------|
+| <name> | `<tool>` | PASS/FAIL |
+```
+
+## Test Case Format
+
+Each test case follows this format:
+
+```markdown
+## Test: <test_name>
+- Tool: <tool_name>
+- Input:
+  ```json
+  {<input_params>}
+  ```
+- Validators:
+  - <validation_rule>
+- Expected: <expected_outcome>
+```
+
+## Validation Rules
+
+| Rule | Description |
+|------|-------------|
+| `success_is_true` | Result has `success: true` |
+| `success_is_false` | Result has `success: false` |
+| `file_exists` | Output file exists |
+| `json_valid` | Output is valid JSON |
+| `stats.total === N` | Stats total equals N |
+| `array_length >= N` | Array has at least N items |
+| `contains_string("x")` | Output contains string |
+| `error.code === "X"` | Error has specific code |
+| `result === N` | Result equals N |
+
+### Step 9: Cleanup (Optional)
+
+Remove test workspace:
+
+```bash
+rm -rf .bioresearcher-tests/
+```

package/dist/skills/bioresearcher-tests/pyproject.toml

@@ -0,0 +1,6 @@
+[project]
+name = "bioresearcher-tests"
+version = "1.0.0"
+description = "Test runner for bioresearcher plugin"
+requires-python = ">=3.10"
+dependencies = []

package/dist/skills/bioresearcher-tests/test_cases/json_tests.md

@@ -0,0 +1,137 @@
+# JSON Tool Tests
+
+## Test: Extract - Simple Object
+- Tool: jsonExtract
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/json_samples/simple_object.json", "return_all": false}
+  ```
+- Validators:
+  - success_is_true
+  - has data object
+  - data.name === "test"
+  - data.value === 42
+- Expected: Parsed JSON object with name="test", value=42
+
+## Test: Extract - Array
+- Tool: jsonExtract
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/json_samples/simple_array.json", "return_all": false}
+  ```
+- Validators:
+  - success_is_true
+  - isArray(data)
+  - array_length >= 3
+- Expected: Parsed JSON array [1, 2, 3]
+
+## Test: Extract - Nested Object
+- Tool: jsonExtract
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/json_samples/nested_object.json", "return_all": false}
+  ```
+- Validators:
+  - success_is_true
+  - has data.nested
+- Expected: Nested object parsed with data.nested.deep
+
+## Test: Extract - From Markdown
+- Tool: jsonExtract
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/json_samples/in_markdown.md", "return_all": false}
+  ```
+- Validators:
+  - success_is_true
+  - data.embedded === "true"
+  - method === "json_code_block"
+- Expected: JSON extracted from markdown code block
+
+## Test: Extract - Return All
+- Tool: jsonExtract
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/json_samples/simple_array.json", "return_all": true}
+  ```
+- Validators:
+  - success_is_true
+  - has count
+- Expected: Array with count metadata
+
+## Test: Extract - File Not Found
+- Tool: jsonExtract
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/nonexistent.json", "return_all": false}
+  ```
+- Validators:
+  - success_is_false
+  - error.code === "FILE_NOT_FOUND"
+- Expected: File not found error
+
+## Test: Validate - Valid Data
+- Tool: jsonValidate
+- Input:
+  ```json
+  {"data": "{\"name\": \"test\", \"value\": 42}", "schema": "{\"type\": \"object\", \"properties\": {\"name\": {\"type\": \"string\"}, \"value\": {\"type\": \"number\"}}, \"required\": [\"name\"]}"}
+  ```
+- Validators:
+  - success_is_true
+  - valid === true OR has data
+- Expected: Validation passes
+
+## Test: Validate - Invalid Data
+- Tool: jsonValidate
+- Input:
+  ```json
+  {"data": "{\"name\": 123}", "schema": "{\"type\": \"object\", \"properties\": {\"name\": {\"type\": \"string\"}}, \"required\": [\"name\"]}"}
+  ```
+- Validators:
+  - success_is_true
+  - has errors
+- Expected: Validation errors (name should be string)
+
+## Test: Validate - From Schema File
+- Tool: jsonValidate
+- Input:
+  ```json
+  {"data": "{\"name\": \"test\", \"value\": 42}", "schema": ".bioresearcher-tests/workspace/json_samples/schema_draft7.json"}
+  ```
+- Validators:
+  - success_is_true
+- Expected: Schema loaded from file and validation passes
+
+## Test: Infer - Object
+- Tool: jsonInfer
+- Input:
+  ```json
+  {"data": "{\"name\": \"test\", \"count\": 5, \"active\": true}", "strict": false}
+  ```
+- Validators:
+  - success_is_true
+  - has data object
+  - inferredType === "object"
+- Expected: JSON Schema inferred for object
+
+## Test: Infer - Array
+- Tool: jsonInfer
+- Input:
+  ```json
+  {"data": "[1, 2, 3, 4, 5]", "strict": false}
+  ```
+- Validators:
+  - success_is_true
+  - inferredType === "array"
+- Expected: Array schema inferred
+
+## Test: Infer - Strict Mode
+- Tool: jsonInfer
+- Input:
+  ```json
+  {"data": "{\"name\": \"test\"}", "strict": true}
+  ```
+- Validators:
+  - success_is_true
+  - strictMode === "true"
+- Expected: Schema with required fields