agentic-flow 1.9.0 → 1.9.2

package/agentic-flow/examples/crispr-cas13-pipeline/docs/data-layer/schema.sql

@@ -1,363 +0,0 @@
--- CRISPR-Cas13 Pipeline Database Schema
--- PostgreSQL 16
--- Version: 1.0.0
--- Last Updated: 2025-10-12
-
--- Enable required extensions
-CREATE EXTENSION IF NOT EXISTS "uuid-ossp";
-CREATE EXTENSION IF NOT EXISTS "pg_stat_statements";
-CREATE EXTENSION IF NOT EXISTS "pg_trgm"; -- For fuzzy text search
-
--- =====================================================
--- USERS & AUTHENTICATION
--- =====================================================
-
-CREATE TABLE users (
-    id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    email VARCHAR(255) UNIQUE NOT NULL,
-    full_name VARCHAR(255) NOT NULL,
-    password_hash VARCHAR(255) NOT NULL,
-    role VARCHAR(50) NOT NULL DEFAULT 'researcher' CHECK (role IN ('guest', 'researcher', 'bioinformatician', 'admin')),
-    institution VARCHAR(255),
-    is_active BOOLEAN DEFAULT TRUE,
-    email_verified BOOLEAN DEFAULT FALSE,
-    created_at TIMESTAMPTZ DEFAULT NOW(),
-    updated_at TIMESTAMPTZ DEFAULT NOW(),
-    last_login_at TIMESTAMPTZ
-);
-
-CREATE INDEX idx_users_email ON users(email);
-CREATE INDEX idx_users_role ON users(role);
-CREATE INDEX idx_users_is_active ON users(is_active);
-
--- =====================================================
--- EXPERIMENTS
--- =====================================================
-
-CREATE TABLE experiments (
-    id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    user_id UUID NOT NULL REFERENCES users(id) ON DELETE CASCADE,
-    name VARCHAR(255) NOT NULL,
-    description TEXT,
-    organism VARCHAR(100) DEFAULT 'Macaca mulatta',
-    target_gene VARCHAR(100),
-    cas13_variant VARCHAR(50) CHECK (cas13_variant IN ('Cas13a', 'Cas13b', 'Cas13d')),
-    guide_rna_sequence TEXT NOT NULL,
-    status VARCHAR(50) DEFAULT 'pending' CHECK (status IN ('pending', 'processing', 'completed', 'failed', 'cancelled')),
-    metadata JSONB DEFAULT '{}',
-    created_at TIMESTAMPTZ DEFAULT NOW(),
-    updated_at TIMESTAMPTZ DEFAULT NOW(),
-    started_at TIMESTAMPTZ,
-    completed_at TIMESTAMPTZ
-);
-
-CREATE INDEX idx_experiments_user_id ON experiments(user_id);
-CREATE INDEX idx_experiments_status ON experiments(status);
-CREATE INDEX idx_experiments_created_at ON experiments(created_at DESC);
-CREATE INDEX idx_experiments_target_gene ON experiments(target_gene) WHERE target_gene IS NOT NULL;
-CREATE INDEX idx_experiments_metadata_gin ON experiments USING gin(metadata jsonb_path_ops);
-
--- =====================================================
--- SAMPLES
--- =====================================================
-
-CREATE TABLE samples (
-    id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    experiment_id UUID NOT NULL REFERENCES experiments(id) ON DELETE CASCADE,
-    sample_name VARCHAR(255) NOT NULL,
-    sample_type VARCHAR(50) CHECK (sample_type IN ('control', 'treatment', 'timepoint_0h', 'timepoint_24h', 'timepoint_48h', 'timepoint_72h')),
-    fastq_r1_path TEXT NOT NULL,
-    fastq_r2_path TEXT,
-    sequencing_platform VARCHAR(100) DEFAULT 'Illumina NovaSeq 6000',
-    read_count BIGINT,
-    quality_score FLOAT CHECK (quality_score >= 0 AND quality_score <= 100),
-    metadata JSONB DEFAULT '{}',
-    created_at TIMESTAMPTZ DEFAULT NOW(),
-    updated_at TIMESTAMPTZ DEFAULT NOW(),
-
-    CONSTRAINT unique_sample_name UNIQUE (experiment_id, sample_name)
-);
-
-CREATE INDEX idx_samples_experiment_id ON samples(experiment_id);
-CREATE INDEX idx_samples_sample_type ON samples(sample_type);
-CREATE INDEX idx_samples_metadata_gin ON samples USING gin(metadata jsonb_path_ops);
-
--- =====================================================
--- ANALYSIS JOBS
--- =====================================================
-
-CREATE TABLE analysis_jobs (
-    id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    experiment_id UUID NOT NULL REFERENCES experiments(id) ON DELETE CASCADE,
-    sample_id UUID REFERENCES samples(id) ON DELETE CASCADE,
-    job_type VARCHAR(50) NOT NULL CHECK (job_type IN ('alignment', 'off_target', 'diff_expr', 'immune_response', 'quality_control')),
-    status VARCHAR(50) DEFAULT 'queued' CHECK (status IN ('queued', 'running', 'completed', 'failed', 'cancelled', 'retrying')),
-    priority INT DEFAULT 5 CHECK (priority BETWEEN 1 AND 10),
-    worker_pod VARCHAR(255),
-    started_at TIMESTAMPTZ,
-    completed_at TIMESTAMPTZ,
-    error_message TEXT,
-    retry_count INT DEFAULT 0,
-    max_retries INT DEFAULT 3,
-    metrics JSONB DEFAULT '{}', -- execution_time_ms, memory_usage_mb, cpu_usage_percent
-    created_at TIMESTAMPTZ DEFAULT NOW(),
-    updated_at TIMESTAMPTZ DEFAULT NOW()
-);
-
-CREATE INDEX idx_jobs_experiment_id ON analysis_jobs(experiment_id);
-CREATE INDEX idx_jobs_sample_id ON analysis_jobs(sample_id) WHERE sample_id IS NOT NULL;
-CREATE INDEX idx_jobs_status ON analysis_jobs(status);
-CREATE INDEX idx_jobs_job_type ON analysis_jobs(job_type);
-CREATE INDEX idx_jobs_priority ON analysis_jobs(priority DESC) WHERE status = 'queued';
-CREATE INDEX idx_jobs_created_at ON analysis_jobs(created_at DESC);
-
--- =====================================================
--- OFF-TARGET PREDICTIONS
--- =====================================================
-
-CREATE TABLE off_targets (
-    id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    job_id UUID NOT NULL REFERENCES analysis_jobs(id) ON DELETE CASCADE,
-    chromosome VARCHAR(50) NOT NULL,
-    position BIGINT NOT NULL CHECK (position > 0),
-    strand CHAR(1) CHECK (strand IN ('+', '-')),
-    target_sequence TEXT NOT NULL,
-    mismatch_count INT NOT NULL CHECK (mismatch_count >= 0),
-    cfd_score FLOAT CHECK (cfd_score >= 0 AND cfd_score <= 1),
-    mit_score FLOAT CHECK (mit_score >= 0 AND mit_score <= 100),
-    gene_symbol VARCHAR(100),
-    gene_id VARCHAR(100),
-    annotation TEXT,
-    distance_to_gene INT,
-    created_at TIMESTAMPTZ DEFAULT NOW()
-);
-
-CREATE INDEX idx_off_targets_job_id ON off_targets(job_id);
-CREATE INDEX idx_off_targets_chromosome ON off_targets(chromosome);
-CREATE INDEX idx_off_targets_position ON off_targets(position);
-CREATE INDEX idx_off_targets_mismatch_count ON off_targets(mismatch_count);
-CREATE INDEX idx_off_targets_cfd_score ON off_targets(cfd_score DESC NULLS LAST);
-CREATE INDEX idx_off_targets_mit_score ON off_targets(mit_score DESC NULLS LAST);
-CREATE INDEX idx_off_targets_gene_symbol ON off_targets(gene_symbol) WHERE gene_symbol IS NOT NULL;
-CREATE INDEX idx_off_targets_location ON off_targets(chromosome, position);
-
--- =====================================================
--- DIFFERENTIAL EXPRESSION RESULTS
--- =====================================================
-
-CREATE TABLE differential_expression (
-    id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    job_id UUID NOT NULL REFERENCES analysis_jobs(id) ON DELETE CASCADE,
-    gene_id VARCHAR(100) NOT NULL,
-    gene_symbol VARCHAR(100),
-    gene_name TEXT,
-    base_mean FLOAT CHECK (base_mean >= 0),
-    log2_fold_change FLOAT NOT NULL,
-    lfcse FLOAT CHECK (lfcse >= 0),
-    stat FLOAT,
-    pvalue FLOAT CHECK (pvalue >= 0 AND pvalue <= 1),
-    padj FLOAT CHECK (padj >= 0 AND padj <= 1),
-    significant BOOLEAN GENERATED ALWAYS AS (padj < 0.05 AND padj IS NOT NULL) STORED,
-    created_at TIMESTAMPTZ DEFAULT NOW()
-);
-
-CREATE INDEX idx_diff_expr_job_id ON differential_expression(job_id);
-CREATE INDEX idx_diff_expr_gene_id ON differential_expression(gene_id);
-CREATE INDEX idx_diff_expr_gene_symbol ON differential_expression(gene_symbol) WHERE gene_symbol IS NOT NULL;
-CREATE INDEX idx_diff_expr_padj ON differential_expression(padj ASC NULLS LAST);
-CREATE INDEX idx_diff_expr_log2fc ON differential_expression(log2_fold_change);
-CREATE INDEX idx_diff_expr_significant ON differential_expression(significant) WHERE significant = TRUE;
-
--- =====================================================
--- IMMUNE RESPONSE SIGNATURES
--- =====================================================
-
-CREATE TABLE immune_signatures (
-    id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    job_id UUID NOT NULL REFERENCES analysis_jobs(id) ON DELETE CASCADE,
-    signature_name VARCHAR(255) NOT NULL,
-    signature_source VARCHAR(100) CHECK (signature_source IN ('ImmuneSigDB', 'MSigDB', 'Reactome', 'KEGG', 'GO')),
-    signature_id VARCHAR(100),
-    enrichment_score FLOAT NOT NULL,
-    normalized_enrichment_score FLOAT,
-    pvalue FLOAT CHECK (pvalue >= 0 AND pvalue <= 1),
-    fdr FLOAT CHECK (fdr >= 0 AND fdr <= 1),
-    leading_edge_genes TEXT[], -- Array of gene symbols
-    gene_set_size INT,
-    overlap_size INT,
-    created_at TIMESTAMPTZ DEFAULT NOW()
-);
-
-CREATE INDEX idx_immune_sig_job_id ON immune_signatures(job_id);
-CREATE INDEX idx_immune_sig_name ON immune_signatures(signature_name);
-CREATE INDEX idx_immune_sig_source ON immune_signatures(signature_source);
-CREATE INDEX idx_immune_sig_fdr ON immune_signatures(fdr ASC NULLS LAST);
-CREATE INDEX idx_immune_sig_nes ON immune_signatures(normalized_enrichment_score DESC NULLS LAST);
-
--- =====================================================
--- AUDIT LOG (Partitioned by Month)
--- =====================================================
-
-CREATE TABLE audit_log (
-    id BIGSERIAL,
-    user_id UUID REFERENCES users(id) ON DELETE SET NULL,
-    action VARCHAR(100) NOT NULL,
-    resource_type VARCHAR(100),
-    resource_id UUID,
-    ip_address INET,
-    user_agent TEXT,
-    metadata JSONB DEFAULT '{}',
-    created_at TIMESTAMPTZ DEFAULT NOW() NOT NULL,
-
-    PRIMARY KEY (id, created_at)
-) PARTITION BY RANGE (created_at);
-
-CREATE INDEX idx_audit_log_user_id ON audit_log(user_id) WHERE user_id IS NOT NULL;
-CREATE INDEX idx_audit_log_action ON audit_log(action);
-CREATE INDEX idx_audit_log_created_at ON audit_log(created_at DESC);
-CREATE INDEX idx_audit_log_resource ON audit_log(resource_type, resource_id) WHERE resource_id IS NOT NULL;
-
--- Create initial partitions (2025)
-CREATE TABLE audit_log_2025_01 PARTITION OF audit_log
-    FOR VALUES FROM ('2025-01-01') TO ('2025-02-01');
-CREATE TABLE audit_log_2025_02 PARTITION OF audit_log
-    FOR VALUES FROM ('2025-02-01') TO ('2025-03-01');
-CREATE TABLE audit_log_2025_03 PARTITION OF audit_log
-    FOR VALUES FROM ('2025-03-01') TO ('2025-04-01');
-CREATE TABLE audit_log_2025_04 PARTITION OF audit_log
-    FOR VALUES FROM ('2025-04-01') TO ('2025-05-01');
-CREATE TABLE audit_log_2025_05 PARTITION OF audit_log
-    FOR VALUES FROM ('2025-05-01') TO ('2025-06-01');
-CREATE TABLE audit_log_2025_06 PARTITION OF audit_log
-    FOR VALUES FROM ('2025-06-01') TO ('2025-07-01');
-CREATE TABLE audit_log_2025_07 PARTITION OF audit_log
-    FOR VALUES FROM ('2025-07-01') TO ('2025-08-01');
-CREATE TABLE audit_log_2025_08 PARTITION OF audit_log
-    FOR VALUES FROM ('2025-08-01') TO ('2025-09-01');
-CREATE TABLE audit_log_2025_09 PARTITION OF audit_log
-    FOR VALUES FROM ('2025-09-01') TO ('2025-10-01');
-CREATE TABLE audit_log_2025_10 PARTITION OF audit_log
-    FOR VALUES FROM ('2025-10-01') TO ('2025-11-01');
-CREATE TABLE audit_log_2025_11 PARTITION OF audit_log
-    FOR VALUES FROM ('2025-11-01') TO ('2025-12-01');
-CREATE TABLE audit_log_2025_12 PARTITION OF audit_log
-    FOR VALUES FROM ('2025-12-01') TO ('2026-01-01');
-
--- =====================================================
--- MATERIALIZED VIEWS
--- =====================================================
-
--- Experiment summary statistics
-CREATE MATERIALIZED VIEW experiment_summary AS
-SELECT
-    e.id,
-    e.name,
-    e.status,
-    COUNT(DISTINCT s.id) AS sample_count,
-    COUNT(DISTINCT aj.id) AS job_count,
-    COUNT(DISTINCT aj.id) FILTER (WHERE aj.status = 'completed') AS completed_jobs,
-    COUNT(DISTINCT aj.id) FILTER (WHERE aj.status = 'failed') AS failed_jobs,
-    e.created_at,
-    e.completed_at
-FROM experiments e
-LEFT JOIN samples s ON e.id = s.experiment_id
-LEFT JOIN analysis_jobs aj ON e.id = aj.experiment_id
-GROUP BY e.id, e.name, e.status, e.created_at, e.completed_at;
-
-CREATE UNIQUE INDEX idx_experiment_summary_id ON experiment_summary(id);
-
--- User activity statistics
-CREATE MATERIALIZED VIEW user_activity_stats AS
-SELECT
-    u.id,
-    u.email,
-    u.full_name,
-    u.role,
-    COUNT(DISTINCT e.id) AS experiment_count,
-    COUNT(DISTINCT aj.id) AS total_jobs,
-    MAX(e.created_at) AS last_experiment_date,
-    MAX(u.last_login_at) AS last_login
-FROM users u
-LEFT JOIN experiments e ON u.id = e.user_id
-LEFT JOIN analysis_jobs aj ON e.id = aj.experiment_id
-GROUP BY u.id, u.email, u.full_name, u.role;
-
-CREATE UNIQUE INDEX idx_user_activity_id ON user_activity_stats(id);
-
--- =====================================================
--- FUNCTIONS & TRIGGERS
--- =====================================================
-
--- Function to update updated_at timestamp
-CREATE OR REPLACE FUNCTION update_updated_at_column()
-RETURNS TRIGGER AS $$
-BEGIN
-    NEW.updated_at = NOW();
-    RETURN NEW;
-END;
-$$ language 'plpgsql';
-
--- Apply updated_at trigger to tables
-CREATE TRIGGER update_users_updated_at BEFORE UPDATE ON users
-    FOR EACH ROW EXECUTE FUNCTION update_updated_at_column();
-
-CREATE TRIGGER update_experiments_updated_at BEFORE UPDATE ON experiments
-    FOR EACH ROW EXECUTE FUNCTION update_updated_at_column();
-
-CREATE TRIGGER update_samples_updated_at BEFORE UPDATE ON samples
-    FOR EACH ROW EXECUTE FUNCTION update_updated_at_column();
-
-CREATE TRIGGER update_jobs_updated_at BEFORE UPDATE ON analysis_jobs
-    FOR EACH ROW EXECUTE FUNCTION update_updated_at_column();
-
--- Function to create audit log entries
-CREATE OR REPLACE FUNCTION audit_log_trigger()
-RETURNS TRIGGER AS $$
-BEGIN
-    IF (TG_OP = 'INSERT') THEN
-        INSERT INTO audit_log (user_id, action, resource_type, resource_id, metadata)
-        VALUES (NEW.user_id, TG_OP, TG_TABLE_NAME, NEW.id, row_to_json(NEW)::jsonb);
-        RETURN NEW;
-    ELSIF (TG_OP = 'UPDATE') THEN
-        INSERT INTO audit_log (user_id, action, resource_type, resource_id, metadata)
-        VALUES (NEW.user_id, TG_OP, TG_TABLE_NAME, NEW.id, jsonb_build_object('old', row_to_json(OLD), 'new', row_to_json(NEW)));
-        RETURN NEW;
-    ELSIF (TG_OP = 'DELETE') THEN
-        INSERT INTO audit_log (user_id, action, resource_type, resource_id, metadata)
-        VALUES (OLD.user_id, TG_OP, TG_TABLE_NAME, OLD.id, row_to_json(OLD)::jsonb);
-        RETURN OLD;
-    END IF;
-    RETURN NULL;
-END;
-$$ LANGUAGE plpgsql;
-
--- Apply audit trigger to experiments
-CREATE TRIGGER audit_experiments AFTER INSERT OR UPDATE OR DELETE ON experiments
-    FOR EACH ROW EXECUTE FUNCTION audit_log_trigger();
-
--- =====================================================
--- SAMPLE DATA (for development/testing)
--- =====================================================
-
--- Insert admin user
-INSERT INTO users (email, full_name, password_hash, role, email_verified)
-VALUES ('admin@example.com', 'Admin User', '$2b$12$LQv3c1yqBWVHxkd0LHAkCOYz6TtxMQJqhN8/LewY5GyYIwNoK8JW2', 'admin', TRUE);
-
--- Insert researcher user
-INSERT INTO users (email, full_name, password_hash, role, email_verified)
-VALUES ('researcher@example.com', 'Research Scientist', '$2b$12$LQv3c1yqBWVHxkd0LHAkCOYz6TtxMQJqhN8/LewY5GyYIwNoK8JW2', 'researcher', TRUE);
-
--- =====================================================
--- GRANTS & PERMISSIONS
--- =====================================================
-
--- Create application role
-CREATE ROLE crispr_app;
-
--- Grant permissions
-GRANT SELECT, INSERT, UPDATE, DELETE ON ALL TABLES IN SCHEMA public TO crispr_app;
-GRANT USAGE, SELECT ON ALL SEQUENCES IN SCHEMA public TO crispr_app;
-GRANT EXECUTE ON ALL FUNCTIONS IN SCHEMA public TO crispr_app;
-
--- Grant user to application role
-GRANT crispr_app TO crispr_user;