@yeyuan98/opencode-bioresearcher-plugin 1.5.0 → 1.5.2-alpha.2

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

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+# Miscellaneous Tool Tests
+
+## Test: Timer - Short Delay
+- Tool: blockingTimer
+- Input:
+  ```json
+  {"delay": 1}
+  ```
+- Validators:
+  - contains_string("Timer completed")
+  - contains_string("1 seconds")
+- Expected: Timer completed message after 1 second
+
+## Test: Timer - Zero Delay
+- Tool: blockingTimer
+- Input:
+  ```json
+  {"delay": 0}
+  ```
+- Validators:
+  - contains_string("Timer completed")
+- Expected: Immediate completion
+
+## Test: Timer - Max Exceeded
+- Tool: blockingTimer
+- Input:
+  ```json
+  {"delay": 301}
+  ```
+- Validators:
+  - contains_string("300")
+  - contains_string("NOT exceed")
+- Expected: Error about max delay exceeded
+
+## Test: Calculator - Basic Arithmetic
+- Tool: calculator
+- Input:
+  ```json
+  {"formula": "2 + 3 * 4", "precision": 3}
+  ```
+- Validators:
+  - has result
+  - result === 14
+- Expected: 14 (order of operations: 3*4=12, 2+12=14)
+
+## Test: Calculator - Power
+- Tool: calculator
+- Input:
+  ```json
+  {"formula": "2 ^ 10", "precision": 0}
+  ```
+- Validators:
+  - has result
+  - result === 1024
+- Expected: 1024 (2 to power of 10)
+
+## Test: Calculator - Brackets
+- Tool: calculator
+- Input:
+  ```json
+  {"formula": "(2 + 3) * 4", "precision": 3}
+  ```
+- Validators:
+  - has result
+  - result === 20
+- Expected: 20 (brackets first: 5*4=20)
+
+## Test: Calculator - Scientific Notation
+- Tool: calculator
+- Input:
+  ```json
+  {"formula": "1e3 + 500", "precision": 3}
+  ```
+- Validators:
+  - has result
+  - result === 1500
+- Expected: 1500 (1000 + 500)
+
+## Test: Calculator - Division by Zero
+- Tool: calculator
+- Input:
+  ```json
+  {"formula": "1 / 0", "precision": 3}
+  ```
+- Validators:
+  - contains_string("CALCULATOR ERROR")
+- Expected: Error about division by zero
+
+## Test: Calculator - Invalid Syntax
+- Tool: calculator
+- Input:
+  ```json
+  {"formula": "2(3)", "precision": 3}
+  ```
+- Validators:
+  - contains_string("CALCULATOR ERROR")
+  - contains_string("parentheses")
+- Expected: Error about implicit multiplication not allowed
+
+## Test: Calculator - Precision
+- Tool: calculator
+- Input:
+  ```json
+  {"formula": "10 / 3", "precision": 2}
+  ```
+- Validators:
+  - has result
+  - result === 3.33
+- Expected: 3.33 (2 decimal places)
+
+## Test: Timer - Exact Boundary
+- Tool: blockingTimer
+- Input:
+  ```json
+  {"delay": 300}
+  ```
+- Validators:
+  - contains_string("Timer completed")
+- Expected: Timer completes at exact max boundary (300s)
+
+## Test: Calculator - Empty Formula
+- Tool: calculator
+- Input:
+  ```json
+  {"formula": "", "precision": 3}
+  ```
+- Validators:
+  - contains_string("CALCULATOR ERROR")
+  - contains_string("empty")
+- Expected: Error about empty formula
+
+## Test: Calculator - Invalid Characters
+- Tool: calculator
+- Input:
+  ```json
+  {"formula": "2 + abc", "precision": 3}
+  ```
+- Validators:
+  - contains_string("CALCULATOR ERROR")
+  - contains_string("invalid characters")
+- Expected: Error about invalid characters

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

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+# Parser Tool Tests
+
+## Test: PubMed XML - Single Mode
+- Tool: parse_pubmed_articleSet
+- Input:
+  ```json
+  {"filePath": ".bioresearcher-tests/workspace/pubmed_sample.xml", "outputMode": "single", "verbose": false}
+  ```
+- Validators:
+  - success_is_true
+  - file_exists
+  - stats.total === 2
+  - stats.successful === 2
+- Expected: Single markdown file with 2 articles
+
+## Test: PubMed XML - Excel Mode
+- Tool: parse_pubmed_articleSet
+- Input:
+  ```json
+  {"filePath": ".bioresearcher-tests/workspace/pubmed_sample.xml", "outputMode": "excel", "outputFileName": "pubmed_test.xlsx", "verbose": false}
+  ```
+- Validators:
+  - success_is_true
+  - file_exists
+  - file ends with .xlsx
+- Expected: Excel file with PMID, Title, Authors, Journal, DOI, Abstract, Keywords columns
+
+## Test: PubMed XML - Individual Mode
+- Tool: parse_pubmed_articleSet
+- Input:
+  ```json
+  {"filePath": ".bioresearcher-tests/workspace/pubmed_sample.xml", "outputMode": "individual", "verbose": false}
+  ```
+- Validators:
+  - success_is_true
+  - directory exists
+- Expected: Directory with individual .md files per article
+
+## Test: OBO - Basic Parsing
+- Tool: parse_obo_file
+- Input:
+  ```json
+  {"filePath": ".bioresearcher-tests/workspace/obo_sample.obo", "outputFileName": "obo_test.csv", "verbose": false}
+  ```
+- Validators:
+  - success_is_true
+  - file_exists
+  - stats.terms >= 3
+- Expected: CSV file with term data
+
+## Test: PubMed - Nonexistent File
+- Tool: parse_pubmed_articleSet
+- Input:
+  ```json
+  {"filePath": ".bioresearcher-tests/workspace/nonexistent.xml", "outputMode": "single"}
+  ```
+- Validators:
+  - contains_string("error")
+- Expected: Error response
+
+## Test: PubMed - Compressed Input
+- Tool: parse_pubmed_articleSet
+- Input:
+  ```json
+  {"filePath": "<skill_path>/resources/pubmed_sample.xml.gz", "outputMode": "single", "verbose": false}
+  ```
+- Validators:
+  - success_is_true
+  - stats.total === 2
+- Expected: Handles .xml.gz compressed files directly
+
+## Test: OBO - Nonexistent File
+- Tool: parse_obo_file
+- Input:
+  ```json
+  {"filePath": ".bioresearcher-tests/workspace/nonexistent.obo", "outputFileName": "test.csv", "verbose": false}
+  ```
+- Validators:
+  - contains_string("error")
+- Expected: Error response for file not found

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

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+# Skill Tests
+
+## Test: Load demo-skill
+- Tool: skill
+- Input:
+  ```json
+  {"name": "demo-skill"}
+  ```
+- Validators:
+  - contains_string("skill_content")
+  - contains_string("demo-skill")
+- Expected: Skill content loaded successfully
+
+## Test: Load bioresearcher-core
+- Tool: skill
+- Input:
+  ```json
+  {"name": "bioresearcher-core"}
+  ```
+- Validators:
+  - contains_string("skill_content")
+  - contains_string("bioresearcher-core")
+  - contains_string("allowed_tools")
+- Expected: Skill content with allowedTools list
+
+## Test: Execute demo-skill Script
+- Tool: Bash
+- Prerequisite: Load skill demo-skill first, extract skill_path
+- Input:
+  ```bash
+  cd <skill_path>/../demo-skill && python demo_script.py
+  ```
+- Validators:
+  - contains_string("Resources resolved")
+- Expected: Demo script executes successfully
+
+## Test: Skill Not Found
+- Tool: skill
+- Input:
+  ```json
+  {"name": "nonexistent-skill-xyz-12345"}
+  ```
+- Validators:
+  - contains_string("not found")
+- Expected: Error with available skills list
+
+---
+
+## Skipped: Skills with User Interaction
+
+The following skills are NOT tested because they use the Question tool
+and require user interaction during execution:
+
+- `python-setup-uv` - Uses Question tool for installer choice and AGENTS.md update
+- `long-table-summary` - Uses Question tool for table location, instructions, batch size
+- `env-jsonc-setup` - Uses Question tool for configuration options
+- `pubmed-weekly` - May use Question tool for download options
+
+These skills are tested for metadata only (loading succeeds, content returned).

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

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+# Table Tool Tests
+
+## Test: List Sheets
+- Tool: tableListSheets
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/table_sample.xlsx"}
+  ```
+- Validators:
+  - has sheets array
+  - array_length >= 1
+- Expected: List of sheet names
+
+## Test: Get Sheet Preview
+- Tool: tableGetSheetPreview
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/table_sample.xlsx"}
+  ```
+- Validators:
+  - has preview array
+  - has total_rows
+- Expected: First 6 rows preview
+
+## Test: Get Headers
+- Tool: tableGetHeaders
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/table_sample.xlsx"}
+  ```
+- Validators:
+  - has headers array
+  - headers includes "Name"
+- Expected: Column headers
+
+## Test: Get Cell
+- Tool: tableGetCell
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/table_sample.xlsx", "cell_address": "A1"}
+  ```
+- Validators:
+  - has value
+  - has type
+- Expected: Cell A1 value
+
+## Test: Get Range
+- Tool: tableGetRange
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/table_sample.xlsx", "range": "A1:C3"}
+  ```
+- Validators:
+  - has data array
+  - rows === 3
+  - columns === 3
+- Expected: 3x3 data array
+
+## Test: Filter Rows
+- Tool: tableFilterRows
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/table_sample.xlsx", "column": "Age", "operator": ">", "value": 25, "max_results": 100}
+  ```
+- Validators:
+  - has matched_rows
+  - has total_matches
+- Expected: Filtered rows where Age > 25
+
+## Test: Search
+- Tool: tableSearch
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/table_sample.xlsx", "search_term": "Active", "max_results": 50}
+  ```
+- Validators:
+  - has results array
+  - has total_found
+- Expected: Cells containing "Active"
+
+## Test: Summarize
+- Tool: tableSummarize
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/table_sample.xlsx", "columns": ["Age", "Score"]}
+  ```
+- Validators:
+  - has summaries object
+- Expected: Statistical summary with sum, avg, min, max, std_dev
+
+## Test: Group By
+- Tool: tableGroupBy
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/table_sample.xlsx", "group_column": "Category", "agg_column": "Score", "agg_type": "avg"}
+  ```
+- Validators:
+  - has groups object
+- Expected: Grouped averages by Category
+
+## Test: Create File
+- Tool: tableCreateFile
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/output_created.xlsx", "sheet_name": "TestData", "data": [{"Name": "Alice", "Age": 30}, {"Name": "Bob", "Age": 25}]}
+  ```
+- Validators:
+  - success_is_true
+  - rows_created === 2
+- Expected: New Excel file created with 2 rows
+
+## Test: Append Rows
+- Tool: tableAppendRows
+- Prerequisite: Test "Create File" must pass first
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/output_created.xlsx", "rows": [{"Name": "Charlie", "Age": 35}]}
+  ```
+- Validators:
+  - success_is_true
+  - rows_appended === 1
+- Expected: Row appended to existing file
+
+## Test: Update Cell
+- Tool: tableUpdateCell
+- Prerequisite: Test "Create File" must pass first
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/output_created.xlsx", "cell_address": "A1", "value": "UpdatedName"}
+  ```
+- Validators:
+  - success_is_true
+- Expected: Cell A1 updated to "UpdatedName"
+
+## Test: Pivot Summary
+- Tool: tablePivotSummary
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/table_sample.xlsx", "row_field": "Category", "col_field": "Status", "value_field": "Score", "agg": "sum"}
+  ```
+- Validators:
+  - has pivot object
+  - has columns array
+- Expected: Pivot table with Category rows, Status columns, Score sums
+
+## Test: Nonexistent File
+- Tool: tableListSheets
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/nonexistent.xlsx"}
+  ```
+- Validators:
+  - contains_string("Error")
+- Expected: Error response for file not found
+
+## Test: Invalid Cell Address
+- Tool: tableGetCell
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/table_sample.xlsx", "cell_address": "INVALID"}
+  ```
+- Validators:
+  - contains_string("Error")
+- Expected: Error response for invalid address
+
+## Test: Invalid Filter Operator
+- Tool: tableFilterRows
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/table_sample.xlsx", "column": "Age", "operator": "INVALID", "value": 25, "max_results": 100}
+  ```
+- Validators:
+  - contains_string("Error")
+- Expected: Error response for invalid operator
+
+## Test: Nonexistent Column
+- Tool: tableSummarize
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/table_sample.xlsx", "columns": ["NonexistentColumn"]}
+  ```
+- Validators:
+  - has summaries object
+- Expected: Empty summaries (graceful handling)
+
+## Test: Out of Bounds Range
+- Tool: tableGetRange
+- Input:
+  ```json
+  {"file_path": ".bioresearcher-tests/workspace/table_sample.xlsx", "range": "Z999:ZZ999"}
+  ```
+- Validators:
+  - has data array
+- Expected: Empty data array (out of bounds handled)