@yeyuan98/opencode-bioresearcher-plugin 1.4.0 → 1.5.0-alpha.0

package/dist/skills/bioresearcher-core/examples/contexts.json

@@ -1,29 +1,29 @@
-[
-  {
-    "file_path": "/absolute/path/to/data.xlsx",
-    "sheet_name": "Sheet1",
-    "batch_number": 1,
-    "row_start": 2,
-    "row_end": 31,
-    "output_file": "./outputs/batch001.md",
-    "instructions_json": "{\n  \"species\": \"Species classification: Tier1/Tier2/NA\",\n  \"topic\": \"Main topic: Oncology/Immunology/General Biology/Others\"\n}"
-  },
-  {
-    "file_path": "/absolute/path/to/data.xlsx",
-    "sheet_name": "Sheet1",
-    "batch_number": 2,
-    "row_start": 32,
-    "row_end": 61,
-    "output_file": "./outputs/batch002.md",
-    "instructions_json": "{\n  \"species\": \"Species classification: Tier1/Tier2/NA\",\n  \"topic\": \"Main topic: Oncology/Immunology/General Biology/Others\"\n}"
-  },
-  {
-    "file_path": "/absolute/path/to/data.xlsx",
-    "sheet_name": "Sheet1",
-    "batch_number": 3,
-    "row_start": 62,
-    "row_end": 91,
-    "output_file": "./outputs/batch003.md",
-    "instructions_json": "{\n  \"species\": \"Species classification: Tier1/Tier2/NA\",\n  \"topic\": \"Main topic: Oncology/Immunology/General Biology/Others\"\n}"
-  }
-]
+[
+  {
+    "file_path": "/absolute/path/to/data.xlsx",
+    "sheet_name": "Sheet1",
+    "batch_number": 1,
+    "row_start": 2,
+    "row_end": 31,
+    "output_file": "./outputs/batch001.md",
+    "instructions_json": "{\n  \"species\": \"Species classification: Tier1/Tier2/NA\",\n  \"topic\": \"Main topic: Oncology/Immunology/General Biology/Others\"\n}"
+  },
+  {
+    "file_path": "/absolute/path/to/data.xlsx",
+    "sheet_name": "Sheet1",
+    "batch_number": 2,
+    "row_start": 32,
+    "row_end": 61,
+    "output_file": "./outputs/batch002.md",
+    "instructions_json": "{\n  \"species\": \"Species classification: Tier1/Tier2/NA\",\n  \"topic\": \"Main topic: Oncology/Immunology/General Biology/Others\"\n}"
+  },
+  {
+    "file_path": "/absolute/path/to/data.xlsx",
+    "sheet_name": "Sheet1",
+    "batch_number": 3,
+    "row_start": 62,
+    "row_end": 91,
+    "output_file": "./outputs/batch003.md",
+    "instructions_json": "{\n  \"species\": \"Species classification: Tier1/Tier2/NA\",\n  \"topic\": \"Main topic: Oncology/Immunology/General Biology/Others\"\n}"
+  }
+]

package/dist/skills/bioresearcher-core/examples/data-exchange-example.md

@@ -1,303 +1,303 @@
-# Data Exchange Example
-
-This example demonstrates the complete main/subagent data exchange workflow.
-
-## Scenario
-
-Main agent needs to process a large table (90 rows) in 3 batches of 30 rows each.
-
-## Step 1: Main Agent Creates Prompt Files
-
-### Template (subagent_template.md)
-
-```markdown
-# Batch Processing Task
-
-## Input
-- File: {file_path}
-- Sheet: {sheet_name}
-- Rows: {row_start} to {row_end}
-
-## Output Format
-Write JSON to: {output_file}
-
-```json
-{
-  "batch_number": {batch_number},
-  "row_count": <integer>,
-  "summaries": [
-    {
-      "row_number": <integer>,
-      "status": "<success/failure>",
-      "result": "<string>"
-    }
-  ]
-}
-```
-```
-
-### Generate Prompts
-
-```bash
-uv run python <skill_path>/python/template.py generate-batches \
-  --template subagent_template.md \
-  --contexts batch_contexts.json \
-  --output-dir ./prompts \
-  --filename-pattern "batch{index:03d}.md"
-```
-
-### Contexts (batch_contexts.json)
-
-```json
-[
-  {
-    "file_path": "/data/table.xlsx",
-    "sheet_name": "Data",
-    "batch_number": 1,
-    "row_start": 2,
-    "row_end": 31,
-    "output_file": "./outputs/batch001.md"
-  },
-  {
-    "file_path": "/data/table.xlsx",
-    "sheet_name": "Data",
-    "batch_number": 2,
-    "row_start": 32,
-    "row_end": 61,
-    "output_file": "./outputs/batch002.md"
-  },
-  {
-    "file_path": "/data/table.xlsx",
-    "sheet_name": "Data",
-    "batch_number": 3,
-    "row_start": 62,
-    "row_end": 91,
-    "output_file": "./outputs/batch003.md"
-  }
-]
-```
-
-## Step 2: Main Agent Launches Subagents
-
-### Wave 1 (All 3 batches)
-
-```
-task(
-  subagent_type="general",
-  description="Process batch 001",
-  prompt="Read your prompt from ./prompts/batch001.md and perform the task exactly as written."
-)
-
-task(
-  subagent_type="general",
-  description="Process batch 002",
-  prompt="Read your prompt from ./prompts/batch002.md and perform the task exactly as written."
-)
-
-task(
-  subagent_type="general",
-  description="Process batch 003",
-  prompt="Read your prompt from ./prompts/batch003.md and perform the task exactly as written."
-)
-```
-
-## Step 3: Subagent Processes and Writes Output
-
-### Subagent reads prompt
-```
-Read ./prompts/batch001.md
-```
-
-### Subagent processes data
-```
-tableGetRange(file_path="/data/table.xlsx", sheet_name="Data", range="A2:Z31")
-```
-
-### Subagent writes output (./outputs/batch001.md)
-
-```json
-{
-  "batch_number": 1,
-  "row_count": 30,
-  "summaries": [
-    {"row_number": 2, "status": "success", "result": "Processed OK"},
-    {"row_number": 3, "status": "success", "result": "Processed OK"},
-    {"row_number": 4, "status": "failure", "result": "Missing data"},
-    "..."
-  ]
-}
-```
-
-## Step 4: Main Agent Validates Outputs
-
-### Extract JSON
-
-```
-jsonExtract(file_path="./outputs/batch001.md")
-```
-
-Returns:
-```json
-{
-  "success": true,
-  "data": {
-    "batch_number": 1,
-    "row_count": 30,
-    "summaries": [...]
-  },
-  "metadata": {
-    "method": "object",
-    "dataType": "object"
-  }
-}
-```
-
-### Infer Schema from First Output
-
-```
-jsonInfer(
-  data='{"batch_number": 1, "row_count": 30, "summaries": [{"row_number": 2, "status": "success", "result": "OK"}]}',
-  strict=true
-)
-```
-
-Returns:
-```json
-{
-  "success": true,
-  "data": {
-    "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "type": "object",
-    "properties": {
-      "batch_number": {"type": "integer"},
-      "row_count": {"type": "integer"},
-      "summaries": {
-        "type": "array",
-        "items": {
-          "type": "object",
-          "properties": {
-            "row_number": {"type": "integer"},
-            "status": {"type": "string"},
-            "result": {"type": "string"}
-          },
-          "required": ["row_number", "status", "result"]
-        }
-      }
-    },
-    "required": ["batch_number", "row_count", "summaries"]
-  }
-}
-```
-
-### Validate Other Outputs
-
-```
-jsonValidate(
-  data='{"batch_number": 2, "row_count": 30, "summaries": [...]}',
-  schema='<inferred_schema>'
-)
-```
-
-Returns:
-```json
-{
-  "success": true,
-  "valid": true,
-  "data": {...}
-}
-```
-
-## Step 5: Main Agent Combines Outputs
-
-### Collect All Summaries
-
-```
-all_rows = []
-
-for batch in [1, 2, 3]:
-    result = jsonExtract(file_path=f"./outputs/batch{batch:03d}.md")
-    if result.success:
-        all_rows.extend(result.data["summaries"])
-```
-
-### Create Combined Excel
-
-```
-tableCreateFile(
-  file_path="./combined_results.xlsx",
-  sheet_name="Results",
-  data=all_rows
-)
-```
-
-## Complete Workflow Summary
-
-1. **Template**: Defines output format with schema
-2. **Contexts**: Provides batch-specific values
-3. **Generation**: Creates prompt files from template + contexts
-4. **Subagents**: Read prompts, process, write JSON outputs
-5. **Extraction**: jsonExtract parses JSON from outputs
-6. **Validation**: jsonValidate ensures schema compliance
-7. **Combination**: tableCreateFile merges all results
-
-## Error Handling Examples
-
-### Missing Output File
-
-```
-jsonExtract(file_path="./outputs/batch002.md")
-```
-
-Returns:
-```json
-{
-  "success": false,
-  "error": {
-    "code": "FILE_NOT_FOUND",
-    "message": "File not found: ./outputs/batch002.md"
-  }
-}
-```
-
-### Invalid JSON in Output
-
-```
-jsonExtract(file_path="./outputs/batch003.md")
-```
-
-Returns:
-```json
-{
-  "success": false,
-  "error": {
-    "code": "NO_JSON_FOUND",
-    "message": "No valid JSON found in file"
-  }
-}
-```
-
-### Schema Validation Failure
-
-```
-jsonValidate(
-  data='{"batch_number": "one", "summaries": []}',
-  schema='{"properties": {"batch_number": {"type": "integer"}}}'
-)
-```
-
-Returns:
-```json
-{
-  "success": true,
-  "valid": false,
-  "errors": [
-    {
-      "path": "batch_number",
-      "message": "Expected number, received string",
-      "code": "invalid_type",
-      "expected": "number",
-      "received": "string"
-    }
-  ]
-}
-```
+# Data Exchange Example
+
+This example demonstrates the complete main/subagent data exchange workflow.
+
+## Scenario
+
+Main agent needs to process a large table (90 rows) in 3 batches of 30 rows each.
+
+## Step 1: Main Agent Creates Prompt Files
+
+### Template (subagent_template.md)
+
+```markdown
+# Batch Processing Task
+
+## Input
+- File: {file_path}
+- Sheet: {sheet_name}
+- Rows: {row_start} to {row_end}
+
+## Output Format
+Write JSON to: {output_file}
+
+```json
+{
+  "batch_number": {batch_number},
+  "row_count": <integer>,
+  "summaries": [
+    {
+      "row_number": <integer>,
+      "status": "<success/failure>",
+      "result": "<string>"
+    }
+  ]
+}
+```
+```
+
+### Generate Prompts
+
+```bash
+uv run python <skill_path>/python/template.py generate-batches \
+  --template subagent_template.md \
+  --contexts batch_contexts.json \
+  --output-dir ./prompts \
+  --filename-pattern "batch{index:03d}.md"
+```
+
+### Contexts (batch_contexts.json)
+
+```json
+[
+  {
+    "file_path": "/data/table.xlsx",
+    "sheet_name": "Data",
+    "batch_number": 1,
+    "row_start": 2,
+    "row_end": 31,
+    "output_file": "./outputs/batch001.md"
+  },
+  {
+    "file_path": "/data/table.xlsx",
+    "sheet_name": "Data",
+    "batch_number": 2,
+    "row_start": 32,
+    "row_end": 61,
+    "output_file": "./outputs/batch002.md"
+  },
+  {
+    "file_path": "/data/table.xlsx",
+    "sheet_name": "Data",
+    "batch_number": 3,
+    "row_start": 62,
+    "row_end": 91,
+    "output_file": "./outputs/batch003.md"
+  }
+]
+```
+
+## Step 2: Main Agent Launches Subagents
+
+### Wave 1 (All 3 batches)
+
+```
+task(
+  subagent_type="general",
+  description="Process batch 001",
+  prompt="Read your prompt from ./prompts/batch001.md and perform the task exactly as written."
+)
+
+task(
+  subagent_type="general",
+  description="Process batch 002",
+  prompt="Read your prompt from ./prompts/batch002.md and perform the task exactly as written."
+)
+
+task(
+  subagent_type="general",
+  description="Process batch 003",
+  prompt="Read your prompt from ./prompts/batch003.md and perform the task exactly as written."
+)
+```
+
+## Step 3: Subagent Processes and Writes Output
+
+### Subagent reads prompt
+```
+Read ./prompts/batch001.md
+```
+
+### Subagent processes data
+```
+tableGetRange(file_path="/data/table.xlsx", sheet_name="Data", range="A2:Z31")
+```
+
+### Subagent writes output (./outputs/batch001.md)
+
+```json
+{
+  "batch_number": 1,
+  "row_count": 30,
+  "summaries": [
+    {"row_number": 2, "status": "success", "result": "Processed OK"},
+    {"row_number": 3, "status": "success", "result": "Processed OK"},
+    {"row_number": 4, "status": "failure", "result": "Missing data"},
+    "..."
+  ]
+}
+```
+
+## Step 4: Main Agent Validates Outputs
+
+### Extract JSON
+
+```
+jsonExtract(file_path="./outputs/batch001.md")
+```
+
+Returns:
+```json
+{
+  "success": true,
+  "data": {
+    "batch_number": 1,
+    "row_count": 30,
+    "summaries": [...]
+  },
+  "metadata": {
+    "method": "object",
+    "dataType": "object"
+  }
+}
+```
+
+### Infer Schema from First Output
+
+```
+jsonInfer(
+  data='{"batch_number": 1, "row_count": 30, "summaries": [{"row_number": 2, "status": "success", "result": "OK"}]}',
+  strict=true
+)
+```
+
+Returns:
+```json
+{
+  "success": true,
+  "data": {
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "type": "object",
+    "properties": {
+      "batch_number": {"type": "integer"},
+      "row_count": {"type": "integer"},
+      "summaries": {
+        "type": "array",
+        "items": {
+          "type": "object",
+          "properties": {
+            "row_number": {"type": "integer"},
+            "status": {"type": "string"},
+            "result": {"type": "string"}
+          },
+          "required": ["row_number", "status", "result"]
+        }
+      }
+    },
+    "required": ["batch_number", "row_count", "summaries"]
+  }
+}
+```
+
+### Validate Other Outputs
+
+```
+jsonValidate(
+  data='{"batch_number": 2, "row_count": 30, "summaries": [...]}',
+  schema='<inferred_schema>'
+)
+```
+
+Returns:
+```json
+{
+  "success": true,
+  "valid": true,
+  "data": {...}
+}
+```
+
+## Step 5: Main Agent Combines Outputs
+
+### Collect All Summaries
+
+```
+all_rows = []
+
+for batch in [1, 2, 3]:
+    result = jsonExtract(file_path=f"./outputs/batch{batch:03d}.md")
+    if result.success:
+        all_rows.extend(result.data["summaries"])
+```
+
+### Create Combined Excel
+
+```
+tableCreateFile(
+  file_path="./combined_results.xlsx",
+  sheet_name="Results",
+  data=all_rows
+)
+```
+
+## Complete Workflow Summary
+
+1. **Template**: Defines output format with schema
+2. **Contexts**: Provides batch-specific values
+3. **Generation**: Creates prompt files from template + contexts
+4. **Subagents**: Read prompts, process, write JSON outputs
+5. **Extraction**: jsonExtract parses JSON from outputs
+6. **Validation**: jsonValidate ensures schema compliance
+7. **Combination**: tableCreateFile merges all results
+
+## Error Handling Examples
+
+### Missing Output File
+
+```
+jsonExtract(file_path="./outputs/batch002.md")
+```
+
+Returns:
+```json
+{
+  "success": false,
+  "error": {
+    "code": "FILE_NOT_FOUND",
+    "message": "File not found: ./outputs/batch002.md"
+  }
+}
+```
+
+### Invalid JSON in Output
+
+```
+jsonExtract(file_path="./outputs/batch003.md")
+```
+
+Returns:
+```json
+{
+  "success": false,
+  "error": {
+    "code": "NO_JSON_FOUND",
+    "message": "No valid JSON found in file"
+  }
+}
+```
+
+### Schema Validation Failure
+
+```
+jsonValidate(
+  data='{"batch_number": "one", "summaries": []}',
+  schema='{"properties": {"batch_number": {"type": "integer"}}}'
+)
+```
+
+Returns:
+```json
+{
+  "success": true,
+  "valid": false,
+  "errors": [
+    {
+      "path": "batch_number",
+      "message": "Expected number, received string",
+      "code": "invalid_type",
+      "expected": "number",
+      "received": "string"
+    }
+  ]
+}
+```