investigation-preparing

name	investigation-preparing
description	Initializes the patent investigation database and imports CSV files. Use this skill to set up the SQLite database (patents.db) before running screening. Supports database initialization and CSV import. Example usage: - "Initialize the patent database and import CSV files from csv/"
context	fork

Patent Investigation Database - Preparing Operations

For External Skills and Agents

WARNING: DO NOT read files from references/instructions/ directory. Those are internal reference files for this skill's internal use only.

To use this skill:

1. Invoke via Skill tool: Skill: investigation-preparing
2. Provide your request with data
3. The skill will handle all SQL operations automatically

Example requests:

• "Initialize the database"
• "Import CSV files from csv/ directory"
• "Execute SQL query: SELECT COUNT(*) FROM screened_patents"

Purpose

Manages database preparation operations for the SQLite database (patents.db) in the working directory, including initialization, data import, and data retrieval.

Internal Reference (For This Skill Only)

The following sections are for the skill's internal operations when processing requests from external agents.

Database Prerequisites

• SQLite3 command must be available
• Workspace root must be writable for database creation

Workspace Path Resolution

CRITICAL: All sqlite3 commands MUST use absolute paths. Before executing any database operation, capture the workspace directory:

WORKSPACE="$(pwd)"

Then use $WORKSPACE/patents.db in all subsequent commands. Never use bare relative paths like sqlite3 patents.db — the working directory may differ from the workspace in forked or containerized environments.

Database Initialization

IMPORTANT: Before executing any database operation, verify that patents.db exists and is properly initialized.

Check Database Status

WORKSPACE="$(pwd)"
if [ ! -f "$WORKSPACE/patents.db" ]; then
    echo "Database not found. Initializing..."
    sqlite3 "$WORKSPACE/patents.db" < "$WORKSPACE/references/sql/initialize-database.sql"
else
    sqlite3 "$WORKSPACE/patents.db" ".tables"
fi

Initialize Database (if needed)

If patents.db does not exist or has an invalid schema:

WORKSPACE="$(pwd)"
sqlite3 "$WORKSPACE/patents.db" < "$WORKSPACE/references/sql/initialize-database.sql"

This command creates all necessary tables (target_patents, screened_patents, claims, elements), views, and triggers.

Internal Operation Mapping (For This Skill Only)

When processing external requests, map them to internal instruction files:

External Request	Internal Reference File
"Initialize database"	SKILL.md → Database Initialization
"Import CSV files..."	references/instructions/import-csv.md

CRITICAL: These reference files are for INTERNAL USE ONLY. External agents should invoke via Skill tool, not read these files.

SQL Execution (Internal Use Only)

When executing SQL operations based on internal reference files:

sqlite3 "$WORKSPACE/patents.db" "<SQL_QUERY>"

For multi-line SQL:

sqlite3 "$WORKSPACE/patents.db" <<EOF
<SQL_QUERY_1>;
<SQL_QUERY_2>;
...
EOF

Output Formats

• JSON output: Use sqlite3 -json for programmatic use
• Text output: Use sqlite3 -column for human-readable format
• CSV output: Use sqlite3 -header -csv for CSV export

Internal Workflows (For This Skill Only)

Workflow 1: Initialize and Import

1. External: "Initialize the database and import CSV files from csv/"
2. Internal: Check database status → Execute import-csv.md instructions

State Management

Initial State

• No patents.db file exists

Final State

• patents.db created with proper schema in working directory
• Data imported from CSV files (if provided)
• Database queries executed successfully

Internal References (For This Skill Only)

These files are for the skill's internal use when processing requests. External agents should NOT read these:

• references/instructions/: Operation-based documentation (SQL queries and operations)
  • import-csv.md: CSV file import with ETL processing
  • execute-sql-with-retry.md: Generic SQL execution with retry logic
• references/sql/: SQL schema and query files
  • initialize-database.sql: Database schema definition
• references/schema.md: Database schema documentation

IMPORTANT: External agents should invoke this skill via the Skill tool, not access these internal files directly.