agentic-flow 1.9.0 → 1.9.1

package/agentic-flow/examples/crispr-cas13-pipeline/docs/database-schemas.sql

@@ -1,731 +0,0 @@
--- CRISPR-Cas13 Bioinformatics Pipeline - PostgreSQL Database Schema
--- Version: 1.0.0
--- Date: 2025-10-12
--- PostgreSQL 15+ required
--- Extensions: uuid-ossp, pg_trgm (for full-text search)
-
--- Enable required extensions
-CREATE EXTENSION IF NOT EXISTS "uuid-ossp";
-CREATE EXTENSION IF NOT EXISTS "pg_trgm";
-
--- ============================================================================
--- CORE TABLES
--- ============================================================================
-
--- Users table (authentication and authorization)
-CREATE TABLE users (
-    user_id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    email VARCHAR(255) UNIQUE NOT NULL,
-    username VARCHAR(50) UNIQUE NOT NULL CHECK (username ~ '^[a-z0-9_-]{3,20}$'),
-    password_hash VARCHAR(255) NOT NULL,
-    full_name VARCHAR(100),
-    institution VARCHAR(200),
-    role VARCHAR(20) NOT NULL CHECK (role IN ('admin', 'researcher', 'analyst', 'guest')) DEFAULT 'researcher',
-    permissions TEXT[] DEFAULT ARRAY['submit_jobs']::TEXT[],
-    api_key_hash VARCHAR(255),
-    api_key_created_at TIMESTAMP WITH TIME ZONE,
-    last_login TIMESTAMP WITH TIME ZONE,
-    account_status VARCHAR(20) NOT NULL CHECK (account_status IN ('active', 'suspended', 'deleted')) DEFAULT 'active',
-    storage_quota_gb INTEGER DEFAULT 1000,
-    storage_used_gb NUMERIC(10, 2) DEFAULT 0.0,
-    created_at TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP,
-    updated_at TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP,
-
-    CONSTRAINT valid_storage_quota CHECK (storage_quota_gb > 0),
-    CONSTRAINT storage_within_quota CHECK (storage_used_gb <= storage_quota_gb)
-);
-
-CREATE INDEX idx_users_email ON users(email);
-CREATE INDEX idx_users_username ON users(username);
-CREATE INDEX idx_users_role ON users(role);
-CREATE INDEX idx_users_account_status ON users(account_status);
-
--- Reference genomes table
-CREATE TABLE reference_genomes (
-    genome_id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    species VARCHAR(100) NOT NULL,
-    assembly_name VARCHAR(50) NOT NULL,
-    assembly_accession VARCHAR(50),
-    source VARCHAR(20) NOT NULL CHECK (source IN ('NCBI', 'Ensembl', 'UCSC', 'custom')),
-    ensembl_version INTEGER,
-    genome_fasta_uri TEXT NOT NULL,
-    annotation_gtf_uri TEXT NOT NULL,
-    transcriptome_fasta_uri TEXT,
-    star_index_uri TEXT,
-    hisat2_index_uri TEXT,
-    bowtie2_index_uri TEXT,
-    total_genome_size BIGINT,
-    gene_count INTEGER,
-    created_at TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP,
-
-    CONSTRAINT unique_assembly UNIQUE (species, assembly_name, source)
-);
-
-CREATE INDEX idx_reference_genomes_species ON reference_genomes(species);
-CREATE INDEX idx_reference_genomes_assembly ON reference_genomes(assembly_name);
-
--- Experiments table
-CREATE TABLE experiments (
-    experiment_id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    user_id UUID NOT NULL REFERENCES users(user_id) ON DELETE CASCADE,
-    title VARCHAR(200) NOT NULL,
-    description TEXT,
-    species VARCHAR(50) NOT NULL CHECK (species IN ('rhesus_macaque', 'cynomolgus_macaque', 'human_cell_line', 'mouse', 'custom')),
-    ncbi_taxonomy_id INTEGER,
-    tissue_type VARCHAR(50),
-    cas13_variant VARCHAR(10) NOT NULL CHECK (cas13_variant IN ('Cas13a', 'Cas13b', 'Cas13c', 'Cas13d')),
-    delivery_method VARCHAR(50),
-    timepoint_hours INTEGER CHECK (timepoint_hours >= 0),
-    replicate_number INTEGER CHECK (replicate_number >= 1),
-    control_type VARCHAR(50) CHECK (control_type IN ('mock_treated', 'non_targeting_grna', 'untreated', 'positive_control')),
-    experimenter VARCHAR(100),
-    institution VARCHAR(200),
-    iacuc_protocol VARCHAR(50),
-    date_performed TIMESTAMP WITH TIME ZONE NOT NULL,
-    metadata JSONB DEFAULT '{}'::JSONB,
-    created_at TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP,
-    updated_at TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP
-);
-
-CREATE INDEX idx_experiments_user_id ON experiments(user_id);
-CREATE INDEX idx_experiments_species ON experiments(species);
-CREATE INDEX idx_experiments_cas13_variant ON experiments(cas13_variant);
-CREATE INDEX idx_experiments_date_performed ON experiments(date_performed);
-CREATE INDEX idx_experiments_tissue_type ON experiments(tissue_type);
-CREATE INDEX idx_experiments_metadata ON experiments USING GIN (metadata);
-CREATE INDEX idx_experiments_title_trgm ON experiments USING GIN (title gin_trgm_ops);
-
--- Guide RNA table
-CREATE TABLE guide_rnas (
-    grna_id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    experiment_id UUID NOT NULL REFERENCES experiments(experiment_id) ON DELETE CASCADE,
-    sequence_rna VARCHAR(30) NOT NULL CHECK (sequence_rna ~ '^[ACGTU]{22,30}$'),
-    sequence_dna VARCHAR(30) NOT NULL CHECK (sequence_dna ~ '^[ACGT]{22,30}$'),
-    length INTEGER NOT NULL CHECK (length BETWEEN 22 AND 30),
-    target_gene VARCHAR(50) NOT NULL,
-    target_transcript_id VARCHAR(50),
-    target_transcript_biotype VARCHAR(50),
-    protospacer_chromosome VARCHAR(10),
-    protospacer_start INTEGER,
-    protospacer_end INTEGER,
-    protospacer_strand CHAR(1) CHECK (protospacer_strand IN ('+', '-')),
-    pfs_sequence VARCHAR(6),
-    gc_content NUMERIC(5, 4) CHECK (gc_content BETWEEN 0 AND 1),
-    secondary_structure_dot_bracket TEXT,
-    secondary_structure_mfe NUMERIC(8, 2),
-    off_target_potential VARCHAR(10) CHECK (off_target_potential IN ('low', 'medium', 'high')),
-    design_tool VARCHAR(50),
-    created_at TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP,
-
-    CONSTRAINT unique_grna_per_experiment UNIQUE (experiment_id)
-);
-
-CREATE INDEX idx_guide_rnas_experiment_id ON guide_rnas(experiment_id);
-CREATE INDEX idx_guide_rnas_target_gene ON guide_rnas(target_gene);
-CREATE INDEX idx_guide_rnas_sequence_rna ON guide_rnas(sequence_rna);
-
--- Sequencing runs table
-CREATE TABLE sequencing_runs (
-    run_id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    experiment_id UUID NOT NULL REFERENCES experiments(experiment_id) ON DELETE CASCADE,
-    sample_id VARCHAR(100) NOT NULL,
-    sequencing_platform VARCHAR(100) NOT NULL,
-    library_prep VARCHAR(100),
-    read_type VARCHAR(20) NOT NULL CHECK (read_type IN ('single_end', 'paired_end')),
-    read_length INTEGER CHECK (read_length BETWEEN 50 AND 300),
-    total_reads BIGINT CHECK (total_reads >= 0),
-    flowcell_id VARCHAR(50),
-    lane INTEGER CHECK (lane BETWEEN 1 AND 8),
-    barcode_index VARCHAR(12) CHECK (barcode_index ~ '^[ACGT]+$'),
-    sequencing_date TIMESTAMP WITH TIME ZONE,
-    sequencing_facility VARCHAR(200),
-    created_at TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP,
-
-    CONSTRAINT unique_sample_per_experiment UNIQUE (experiment_id, sample_id)
-);
-
-CREATE INDEX idx_sequencing_runs_experiment_id ON sequencing_runs(experiment_id);
-CREATE INDEX idx_sequencing_runs_sample_id ON sequencing_runs(sample_id);
-CREATE INDEX idx_sequencing_runs_platform ON sequencing_runs(sequencing_platform);
-
--- FASTQ files table
-CREATE TABLE fastq_files (
-    file_id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    sequencing_run_id UUID NOT NULL REFERENCES sequencing_runs(run_id) ON DELETE CASCADE,
-    file_path TEXT NOT NULL,
-    file_name VARCHAR(255) NOT NULL,
-    read_pair VARCHAR(10) NOT NULL CHECK (read_pair IN ('R1', 'R2', 'single')),
-    file_size BIGINT NOT NULL CHECK (file_size > 0),
-    compression VARCHAR(20) NOT NULL CHECK (compression IN ('gzip', 'bzip2', 'uncompressed')) DEFAULT 'gzip',
-    md5_checksum CHAR(32) NOT NULL CHECK (md5_checksum ~ '^[a-f0-9]{32}$'),
-    sha256_checksum CHAR(64) CHECK (sha256_checksum ~ '^[a-f0-9]{64}$'),
-    quality_encoding VARCHAR(20) NOT NULL CHECK (quality_encoding IN ('Phred33', 'Phred64')) DEFAULT 'Phred33',
-    upload_date TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP,
-    uploaded_by UUID REFERENCES users(user_id),
-
-    CONSTRAINT unique_file_path UNIQUE (file_path)
-);
-
-CREATE INDEX idx_fastq_files_sequencing_run_id ON fastq_files(sequencing_run_id);
-CREATE INDEX idx_fastq_files_md5 ON fastq_files(md5_checksum);
-
--- Quality control table
-CREATE TABLE quality_control (
-    qc_id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    sequencing_run_id UUID NOT NULL REFERENCES sequencing_runs(run_id) ON DELETE CASCADE,
-    status VARCHAR(10) NOT NULL CHECK (status IN ('pass', 'warn', 'fail')),
-    total_sequences BIGINT,
-    poor_quality_sequences BIGINT,
-    sequence_length_min INTEGER,
-    sequence_length_max INTEGER,
-    sequence_length_mean NUMERIC(8, 2),
-    mean_quality_score NUMERIC(5, 2) CHECK (mean_quality_score BETWEEN 0 AND 42),
-    gc_content NUMERIC(5, 2) CHECK (gc_content BETWEEN 0 AND 100),
-    adapter_content_illumina_universal NUMERIC(5, 2),
-    adapter_content_illumina_small_rna NUMERIC(5, 2),
-    adapter_content_nextera NUMERIC(5, 2),
-    duplication_rate NUMERIC(5, 2) CHECK (duplication_rate BETWEEN 0 AND 100),
-    per_base_quality JSONB,
-    overrepresented_sequences JSONB,
-    report_html_uri TEXT,
-    report_json_uri TEXT,
-    fastqc_version VARCHAR(20),
-    created_at TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP,
-
-    CONSTRAINT unique_qc_per_run UNIQUE (sequencing_run_id)
-);
-
-CREATE INDEX idx_quality_control_sequencing_run_id ON quality_control(sequencing_run_id);
-CREATE INDEX idx_quality_control_status ON quality_control(status);
-
--- Alignments table
-CREATE TABLE alignments (
-    alignment_id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    sequencing_run_id UUID NOT NULL REFERENCES sequencing_runs(run_id) ON DELETE CASCADE,
-    reference_genome_id UUID NOT NULL REFERENCES reference_genomes(genome_id),
-    aligner VARCHAR(20) NOT NULL CHECK (aligner IN ('STAR', 'HISAT2', 'Bowtie2', 'BWA-MEM', 'minimap2')),
-    aligner_version VARCHAR(20) NOT NULL,
-    alignment_parameters JSONB NOT NULL DEFAULT '{}'::JSONB,
-    bam_file_uri TEXT NOT NULL,
-    bai_file_uri TEXT,
-    total_reads BIGINT,
-    mapped_reads BIGINT,
-    uniquely_mapped_reads BIGINT,
-    multi_mapped_reads BIGINT,
-    unmapped_reads BIGINT,
-    alignment_rate NUMERIC(5, 4) CHECK (alignment_rate BETWEEN 0 AND 1),
-    mean_mapping_quality NUMERIC(5, 2) CHECK (mean_mapping_quality BETWEEN 0 AND 60),
-    insert_size_mean NUMERIC(8, 2),
-    insert_size_median NUMERIC(8, 2),
-    insert_size_std_dev NUMERIC(8, 2),
-    mean_coverage NUMERIC(10, 2),
-    median_coverage NUMERIC(10, 2),
-    covered_bases BIGINT,
-    execution_time_seconds INTEGER,
-    peak_memory_gb NUMERIC(8, 2),
-    created_at TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP,
-
-    CONSTRAINT unique_alignment_per_run UNIQUE (sequencing_run_id, reference_genome_id, aligner),
-    CONSTRAINT valid_read_counts CHECK (
-        total_reads = (mapped_reads + unmapped_reads) AND
-        mapped_reads = (uniquely_mapped_reads + multi_mapped_reads)
-    )
-);
-
-CREATE INDEX idx_alignments_sequencing_run_id ON alignments(sequencing_run_id);
-CREATE INDEX idx_alignments_reference_genome_id ON alignments(reference_genome_id);
-CREATE INDEX idx_alignments_aligner ON alignments(aligner);
-
--- Target analysis table (on-target activity)
-CREATE TABLE target_analysis (
-    analysis_id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    experiment_id UUID NOT NULL REFERENCES experiments(experiment_id) ON DELETE CASCADE,
-    alignment_id UUID REFERENCES alignments(alignment_id),
-    target_gene VARCHAR(50) NOT NULL,
-    target_transcript_id VARCHAR(50),
-    control_expression_tpm NUMERIC(12, 4) CHECK (control_expression_tpm >= 0),
-    treated_expression_tpm NUMERIC(12, 4) CHECK (treated_expression_tpm >= 0),
-    fold_change NUMERIC(10, 4),
-    log2_fold_change NUMERIC(10, 4),
-    knockdown_efficiency NUMERIC(5, 4) CHECK (knockdown_efficiency BETWEEN 0 AND 1),
-    p_value DOUBLE PRECISION CHECK (p_value BETWEEN 0 AND 1),
-    adjusted_p_value DOUBLE PRECISION CHECK (adjusted_p_value BETWEEN 0 AND 1),
-    control_read_count BIGINT,
-    treated_read_count BIGINT,
-    total_library_size_control BIGINT,
-    total_library_size_treated BIGINT,
-    transcript_abundance JSONB,
-    confidence_level VARCHAR(10) CHECK (confidence_level IN ('high', 'medium', 'low')),
-    statistical_method VARCHAR(20) CHECK (statistical_method IN ('DESeq2', 'edgeR', 'limma-voom', 'NOISeq')),
-    created_at TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP,
-
-    CONSTRAINT unique_target_analysis UNIQUE (experiment_id, target_gene)
-);
-
-CREATE INDEX idx_target_analysis_experiment_id ON target_analysis(experiment_id);
-CREATE INDEX idx_target_analysis_target_gene ON target_analysis(target_gene);
-CREATE INDEX idx_target_analysis_p_value ON target_analysis(p_value);
-CREATE INDEX idx_target_analysis_knockdown_efficiency ON target_analysis(knockdown_efficiency);
-
--- Off-target sites table
-CREATE TABLE off_target_sites (
-    offtarget_id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    experiment_id UUID NOT NULL REFERENCES experiments(experiment_id) ON DELETE CASCADE,
-    rank INTEGER NOT NULL CHECK (rank >= 1),
-    confidence_score NUMERIC(5, 4) NOT NULL CHECK (confidence_score BETWEEN 0 AND 1),
-    gene_symbol VARCHAR(50),
-    gene_id VARCHAR(50),
-    transcript_id VARCHAR(50),
-    chromosome VARCHAR(10) NOT NULL,
-    genomic_start INTEGER NOT NULL CHECK (genomic_start > 0),
-    genomic_end INTEGER NOT NULL CHECK (genomic_end > genomic_start),
-    strand CHAR(1) NOT NULL CHECK (strand IN ('+', '-')),
-    aligned_sequence VARCHAR(30) NOT NULL,
-    guide_alignment VARCHAR(30) NOT NULL,
-    target_alignment VARCHAR(30) NOT NULL,
-    alignment_visual VARCHAR(30),
-    mismatch_count INTEGER NOT NULL CHECK (mismatch_count >= 0 AND mismatch_count <= 10),
-    mismatch_positions INTEGER[],
-    seed_mismatches INTEGER CHECK (seed_mismatches >= 0),
-    pam_flanking_sequence VARCHAR(6),
-    sequence_context TEXT,
-    accessibility_score NUMERIC(5, 4) CHECK (accessibility_score BETWEEN 0 AND 1),
-    secondary_structure_dot_bracket TEXT,
-    secondary_structure_mfe NUMERIC(8, 2),
-    expression_level NUMERIC(12, 4) CHECK (expression_level >= 0),
-    observed_cleavage BOOLEAN DEFAULT FALSE,
-    fold_change NUMERIC(10, 4),
-    prediction_method VARCHAR(50) NOT NULL,
-    created_at TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP,
-
-    CONSTRAINT unique_off_target_rank UNIQUE (experiment_id, rank)
-);
-
-CREATE INDEX idx_off_target_sites_experiment_id ON off_target_sites(experiment_id);
-CREATE INDEX idx_off_target_sites_confidence_score ON off_target_sites(confidence_score DESC);
-CREATE INDEX idx_off_target_sites_gene_symbol ON off_target_sites(gene_symbol);
-CREATE INDEX idx_off_target_sites_genomic_location ON off_target_sites(chromosome, genomic_start, genomic_end);
-
--- Immune response analysis table
-CREATE TABLE immune_response (
-    immune_id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    experiment_id UUID NOT NULL REFERENCES experiments(experiment_id) ON DELETE CASCADE,
-    overall_immune_score NUMERIC(8, 4),
-    interferon_score NUMERIC(8, 4),
-    activated_pathways TEXT[],
-    differential_genes JSONB,
-    gene_set_enrichment JSONB,
-    key_cytokines JSONB,
-    pattern_recognition_receptors JSONB,
-    interferon_stimulated_genes JSONB,
-    heatmap_uri TEXT,
-    created_at TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP,
-
-    CONSTRAINT unique_immune_analysis UNIQUE (experiment_id)
-);
-
-CREATE INDEX idx_immune_response_experiment_id ON immune_response(experiment_id);
-CREATE INDEX idx_immune_response_overall_score ON immune_response(overall_immune_score);
-CREATE INDEX idx_immune_response_activated_pathways ON immune_response USING GIN (activated_pathways);
-
--- Processing jobs table
-CREATE TABLE processing_jobs (
-    job_id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    job_type VARCHAR(50) NOT NULL CHECK (job_type IN ('qc_only', 'alignment', 'full_pipeline', 'off_target_prediction', 'immune_analysis', 'custom')),
-    status VARCHAR(20) NOT NULL CHECK (status IN ('queued', 'running', 'completed', 'failed', 'cancelled')) DEFAULT 'queued',
-    priority VARCHAR(10) NOT NULL CHECK (priority IN ('low', 'normal', 'high', 'urgent')) DEFAULT 'normal',
-    experiment_id UUID REFERENCES experiments(experiment_id) ON DELETE CASCADE,
-    sequencing_run_id UUID REFERENCES sequencing_runs(run_id) ON DELETE CASCADE,
-    reference_genome_id UUID REFERENCES reference_genomes(genome_id),
-    input_files TEXT[],
-    output_files TEXT[],
-    parameters JSONB DEFAULT '{}'::JSONB,
-    progress NUMERIC(5, 4) CHECK (progress BETWEEN 0 AND 1) DEFAULT 0,
-    current_stage VARCHAR(100),
-    eta_seconds INTEGER,
-    started_at TIMESTAMP WITH TIME ZONE,
-    completed_at TIMESTAMP WITH TIME ZONE,
-    execution_time_seconds INTEGER,
-    error_message TEXT,
-    error_code VARCHAR(50),
-    retry_count INTEGER DEFAULT 0,
-    max_retries INTEGER DEFAULT 3,
-    cpu_hours NUMERIC(10, 4),
-    peak_memory_gb NUMERIC(10, 4),
-    disk_io_gb NUMERIC(10, 4),
-    gpu_hours NUMERIC(10, 4),
-    worker_node VARCHAR(100),
-    container_image VARCHAR(200),
-    notification_email VARCHAR(255),
-    created_by UUID NOT NULL REFERENCES users(user_id),
-    created_at TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP,
-
-    CONSTRAINT valid_completion CHECK (
-        (status = 'completed' AND completed_at IS NOT NULL) OR
-        (status != 'completed' AND completed_at IS NULL)
-    ),
-    CONSTRAINT valid_start_time CHECK (
-        (status IN ('running', 'completed', 'failed', 'cancelled') AND started_at IS NOT NULL) OR
-        (status = 'queued' AND started_at IS NULL)
-    )
-);
-
-CREATE INDEX idx_processing_jobs_status ON processing_jobs(status);
-CREATE INDEX idx_processing_jobs_experiment_id ON processing_jobs(experiment_id);
-CREATE INDEX idx_processing_jobs_created_by ON processing_jobs(created_by);
-CREATE INDEX idx_processing_jobs_created_at ON processing_jobs(created_at DESC);
-CREATE INDEX idx_processing_jobs_priority ON processing_jobs(priority);
-
--- Provenance table (W3C PROV-O)
-CREATE TABLE provenance (
-    provenance_id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    entity_id VARCHAR(255) NOT NULL,
-    entity_type VARCHAR(50) NOT NULL CHECK (entity_type IN ('fastq_file', 'bam_file', 'vcf_file', 'expression_matrix', 'qc_report', 'analysis_result')),
-    activity_id VARCHAR(255) NOT NULL,
-    activity_type VARCHAR(50) NOT NULL CHECK (activity_type IN ('quality_control', 'trimming', 'alignment', 'quantification', 'differential_expression', 'off_target_prediction')),
-    agent_id VARCHAR(255) NOT NULL,
-    agent_type VARCHAR(50) NOT NULL CHECK (agent_type IN ('software_tool', 'user', 'automated_pipeline')),
-    tool_name VARCHAR(100),
-    tool_version VARCHAR(50),
-    tool_parameters JSONB,
-    input_entities TEXT[],
-    output_entities TEXT[],
-    started_at TIMESTAMP WITH TIME ZONE NOT NULL,
-    ended_at TIMESTAMP WITH TIME ZONE,
-    execution_environment JSONB,
-    provenance_graph_rdf TEXT,
-    created_at TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP
-);
-
-CREATE INDEX idx_provenance_entity_id ON provenance(entity_id);
-CREATE INDEX idx_provenance_activity_id ON provenance(activity_id);
-CREATE INDEX idx_provenance_agent_id ON provenance(agent_id);
-CREATE INDEX idx_provenance_entity_type ON provenance(entity_type);
-CREATE INDEX idx_provenance_activity_type ON provenance(activity_type);
-
--- Audit log table
-CREATE TABLE audit_log (
-    log_id UUID PRIMARY KEY DEFAULT uuid_generate_v4(),
-    event_type VARCHAR(50) NOT NULL,
-    user_id UUID REFERENCES users(user_id),
-    resource_type VARCHAR(50),
-    resource_id VARCHAR(255),
-    action VARCHAR(20),
-    ip_address INET,
-    user_agent TEXT,
-    request_method VARCHAR(10),
-    request_path TEXT,
-    response_status INTEGER,
-    details JSONB,
-    timestamp TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP,
-    severity VARCHAR(20) NOT NULL CHECK (severity IN ('info', 'warning', 'error', 'critical')) DEFAULT 'info'
-);
-
-CREATE INDEX idx_audit_log_user_id ON audit_log(user_id);
-CREATE INDEX idx_audit_log_event_type ON audit_log(event_type);
-CREATE INDEX idx_audit_log_timestamp ON audit_log(timestamp DESC);
-CREATE INDEX idx_audit_log_resource ON audit_log(resource_type, resource_id);
-CREATE INDEX idx_audit_log_severity ON audit_log(severity);
-
--- ============================================================================
--- VIEWS
--- ============================================================================
-
--- Complete experiment view (denormalized for easy querying)
-CREATE OR REPLACE VIEW v_experiments_complete AS
-SELECT
-    e.experiment_id,
-    e.title,
-    e.description,
-    e.species,
-    e.tissue_type,
-    e.cas13_variant,
-    e.date_performed,
-    e.experimenter,
-    e.institution,
-    u.username AS created_by_username,
-    g.sequence_rna AS guide_rna_sequence,
-    g.target_gene,
-    g.target_transcript_id,
-    COUNT(DISTINCT sr.run_id) AS sequencing_runs_count,
-    COUNT(DISTINCT pj.job_id) AS jobs_count,
-    COUNT(DISTINCT CASE WHEN pj.status = 'completed' THEN pj.job_id END) AS completed_jobs_count,
-    EXISTS(SELECT 1 FROM target_analysis ta WHERE ta.experiment_id = e.experiment_id) AS has_target_analysis,
-    EXISTS(SELECT 1 FROM off_target_sites ots WHERE ots.experiment_id = e.experiment_id) AS has_offtarget_analysis,
-    EXISTS(SELECT 1 FROM immune_response ir WHERE ir.experiment_id = e.experiment_id) AS has_immune_analysis,
-    e.created_at,
-    e.updated_at
-FROM
-    experiments e
-    INNER JOIN users u ON e.user_id = u.user_id
-    LEFT JOIN guide_rnas g ON e.experiment_id = g.experiment_id
-    LEFT JOIN sequencing_runs sr ON e.experiment_id = sr.experiment_id
-    LEFT JOIN processing_jobs pj ON e.experiment_id = pj.experiment_id
-GROUP BY
-    e.experiment_id, e.title, e.description, e.species, e.tissue_type,
-    e.cas13_variant, e.date_performed, e.experimenter, e.institution,
-    u.username, g.sequence_rna, g.target_gene, g.target_transcript_id,
-    e.created_at, e.updated_at;
-
--- Active jobs view
-CREATE OR REPLACE VIEW v_active_jobs AS
-SELECT
-    pj.job_id,
-    pj.job_type,
-    pj.status,
-    pj.priority,
-    pj.progress,
-    pj.current_stage,
-    pj.eta_seconds,
-    e.title AS experiment_title,
-    e.experiment_id,
-    u.username AS created_by_username,
-    pj.started_at,
-    pj.created_at,
-    EXTRACT(EPOCH FROM (CURRENT_TIMESTAMP - pj.started_at))::INTEGER AS running_time_seconds
-FROM
-    processing_jobs pj
-    INNER JOIN users u ON pj.created_by = u.user_id
-    LEFT JOIN experiments e ON pj.experiment_id = e.experiment_id
-WHERE
-    pj.status IN ('queued', 'running')
-ORDER BY
-    CASE pj.priority
-        WHEN 'urgent' THEN 1
-        WHEN 'high' THEN 2
-        WHEN 'normal' THEN 3
-        WHEN 'low' THEN 4
-    END,
-    pj.created_at;
-
--- User storage summary view
-CREATE OR REPLACE VIEW v_user_storage AS
-SELECT
-    u.user_id,
-    u.username,
-    u.email,
-    u.storage_quota_gb,
-    u.storage_used_gb,
-    ROUND((u.storage_used_gb / u.storage_quota_gb * 100)::NUMERIC, 2) AS storage_used_percent,
-    COUNT(DISTINCT e.experiment_id) AS total_experiments,
-    COUNT(DISTINCT sr.run_id) AS total_sequencing_runs,
-    COUNT(DISTINCT ff.file_id) AS total_files,
-    SUM(ff.file_size) / (1024.0 * 1024 * 1024) AS calculated_storage_gb
-FROM
-    users u
-    LEFT JOIN experiments e ON u.user_id = e.user_id
-    LEFT JOIN sequencing_runs sr ON e.experiment_id = sr.experiment_id
-    LEFT JOIN fastq_files ff ON sr.run_id = ff.sequencing_run_id
-WHERE
-    u.account_status = 'active'
-GROUP BY
-    u.user_id, u.username, u.email, u.storage_quota_gb, u.storage_used_gb;
-
--- ============================================================================
--- FUNCTIONS
--- ============================================================================
-
--- Function to automatically update 'updated_at' timestamp
-CREATE OR REPLACE FUNCTION update_updated_at_column()
-RETURNS TRIGGER AS $$
-BEGIN
-    NEW.updated_at = CURRENT_TIMESTAMP;
-    RETURN NEW;
-END;
-$$ LANGUAGE plpgsql;
-
--- Trigger for experiments table
-CREATE TRIGGER trigger_experiments_updated_at
-BEFORE UPDATE ON experiments
-FOR EACH ROW
-EXECUTE FUNCTION update_updated_at_column();
-
--- Trigger for users table
-CREATE TRIGGER trigger_users_updated_at
-BEFORE UPDATE ON users
-FOR EACH ROW
-EXECUTE FUNCTION update_updated_at_column();
-
--- Function to validate guide RNA sequence (DNA/RNA conversion)
-CREATE OR REPLACE FUNCTION validate_guide_rna()
-RETURNS TRIGGER AS $$
-BEGIN
-    -- Convert RNA to DNA by replacing U with T
-    NEW.sequence_dna = REPLACE(NEW.sequence_rna, 'U', 'T');
-
-    -- Calculate length
-    NEW.length = LENGTH(NEW.sequence_rna);
-
-    -- Calculate GC content
-    NEW.gc_content = (
-        (LENGTH(NEW.sequence_dna) - LENGTH(REPLACE(REPLACE(NEW.sequence_dna, 'G', ''), 'C', '')))::NUMERIC /
-        LENGTH(NEW.sequence_dna)::NUMERIC
-    );
-
-    RETURN NEW;
-END;
-$$ LANGUAGE plpgsql;
-
-CREATE TRIGGER trigger_validate_guide_rna
-BEFORE INSERT OR UPDATE ON guide_rnas
-FOR EACH ROW
-EXECUTE FUNCTION validate_guide_rna();
-
--- Function to update user storage usage
-CREATE OR REPLACE FUNCTION update_user_storage()
-RETURNS TRIGGER AS $$
-DECLARE
-    v_user_id UUID;
-    v_total_storage NUMERIC;
-BEGIN
-    -- Get user_id from experiment chain
-    SELECT e.user_id INTO v_user_id
-    FROM sequencing_runs sr
-    INNER JOIN experiments e ON sr.experiment_id = e.experiment_id
-    WHERE sr.run_id = NEW.sequencing_run_id;
-
-    -- Calculate total storage for user
-    SELECT SUM(ff.file_size) / (1024.0 * 1024 * 1024) INTO v_total_storage
-    FROM fastq_files ff
-    INNER JOIN sequencing_runs sr ON ff.sequencing_run_id = sr.run_id
-    INNER JOIN experiments e ON sr.experiment_id = e.experiment_id
-    WHERE e.user_id = v_user_id;
-
-    -- Update user storage
-    UPDATE users SET storage_used_gb = COALESCE(v_total_storage, 0)
-    WHERE user_id = v_user_id;
-
-    RETURN NEW;
-END;
-$$ LANGUAGE plpgsql;
-
-CREATE TRIGGER trigger_update_user_storage
-AFTER INSERT ON fastq_files
-FOR EACH ROW
-EXECUTE FUNCTION update_user_storage();
-
--- Function to automatically set job execution time
-CREATE OR REPLACE FUNCTION set_job_execution_time()
-RETURNS TRIGGER AS $$
-BEGIN
-    IF NEW.status IN ('completed', 'failed', 'cancelled') AND NEW.started_at IS NOT NULL THEN
-        NEW.execution_time_seconds = EXTRACT(EPOCH FROM (NEW.completed_at - NEW.started_at))::INTEGER;
-    END IF;
-
-    RETURN NEW;
-END;
-$$ LANGUAGE plpgsql;
-
-CREATE TRIGGER trigger_set_job_execution_time
-BEFORE UPDATE ON processing_jobs
-FOR EACH ROW
-WHEN (NEW.status IN ('completed', 'failed', 'cancelled') AND OLD.status != NEW.status)
-EXECUTE FUNCTION set_job_execution_time();
-
--- ============================================================================
--- PARTITIONING (for large-scale deployments)
--- ============================================================================
-
--- Partition audit_log by month for better performance
--- Uncomment if expecting >1M audit log entries
-
--- CREATE TABLE audit_log_template (LIKE audit_log INCLUDING ALL);
---
--- CREATE TABLE audit_log_2025_10 PARTITION OF audit_log_template
--- FOR VALUES FROM ('2025-10-01') TO ('2025-11-01');
---
--- -- Create partitions for future months as needed
-
--- ============================================================================
--- INITIAL DATA
--- ============================================================================
-
--- Insert default admin user (change password immediately!)
-INSERT INTO users (email, username, password_hash, full_name, role, permissions)
-VALUES (
-    'admin@crispr-pipeline.org',
-    'admin',
-    '$2b$12$LQv3c1yqBWVHxkd0LHAkCOYz6TtxMQJqhN8/LewY5oPxZ8l4RMVeC',  -- bcrypt hash of 'changeme123'
-    'System Administrator',
-    'admin',
-    ARRAY['submit_jobs', 'view_all_experiments', 'delete_data', 'manage_users', 'modify_settings']::TEXT[]
-);
-
--- Insert common reference genomes
-INSERT INTO reference_genomes (species, assembly_name, assembly_accession, source, genome_fasta_uri, annotation_gtf_uri, transcriptome_fasta_uri, total_genome_size, gene_count)
-VALUES
-    (
-        'Macaca mulatta',
-        'rheMac10',
-        'GCF_003339765.1',
-        'NCBI',
-        's3://reference-genomes/rheMac10/genome.fa.gz',
-        's3://reference-genomes/rheMac10/genes.gtf.gz',
-        's3://reference-genomes/rheMac10/transcriptome.fa.gz',
-        2971321462,
-        21156
-    ),
-    (
-        'Macaca fascicularis',
-        'macFas5',
-        'GCF_000364345.1',
-        'NCBI',
-        's3://reference-genomes/macFas5/genome.fa.gz',
-        's3://reference-genomes/macFas5/genes.gtf.gz',
-        's3://reference-genomes/macFas5/transcriptome.fa.gz',
-        2887435523,
-        20317
-    ),
-    (
-        'Homo sapiens',
-        'GRCh38',
-        'GCA_000001405.29',
-        'Ensembl',
-        's3://reference-genomes/GRCh38/genome.fa.gz',
-        's3://reference-genomes/GRCh38/genes.gtf.gz',
-        's3://reference-genomes/GRCh38/transcriptome.fa.gz',
-        3099750718,
-        20449
-    );
-
--- ============================================================================
--- GRANTS (adjust based on your security model)
--- ============================================================================
-
--- Create application database user
--- CREATE USER crispr_app WITH PASSWORD 'your_secure_password';
-
--- Grant permissions
--- GRANT CONNECT ON DATABASE crispr_pipeline TO crispr_app;
--- GRANT USAGE ON SCHEMA public TO crispr_app;
--- 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;
-
--- Create read-only analyst role
--- CREATE USER crispr_analyst WITH PASSWORD 'analyst_password';
--- GRANT CONNECT ON DATABASE crispr_pipeline TO crispr_analyst;
--- GRANT USAGE ON SCHEMA public TO crispr_analyst;
--- GRANT SELECT ON ALL TABLES IN SCHEMA public TO crispr_analyst;
-
--- ============================================================================
--- COMMENTS (for documentation)
--- ============================================================================
-
-COMMENT ON TABLE experiments IS 'Core experiment metadata including CRISPR-Cas13 design parameters';
-COMMENT ON TABLE guide_rnas IS 'Guide RNA sequences and target information';
-COMMENT ON TABLE sequencing_runs IS 'Sequencing run metadata linking FASTQ files to experiments';
-COMMENT ON TABLE quality_control IS 'FastQC quality metrics for sequencing data';
-COMMENT ON TABLE alignments IS 'Read alignment results against reference transcriptome';
-COMMENT ON TABLE target_analysis IS 'On-target knockdown efficiency and statistical analysis';
-COMMENT ON TABLE off_target_sites IS 'Predicted and observed off-target cleavage sites';
-COMMENT ON TABLE immune_response IS 'Innate immune pathway activation analysis';
-COMMENT ON TABLE processing_jobs IS 'Asynchronous bioinformatics pipeline jobs';
-COMMENT ON TABLE provenance IS 'W3C PROV-O compliant provenance tracking';
-COMMENT ON TABLE audit_log IS 'System audit trail for security and compliance';
-
--- ============================================================================
--- VACUUM AND ANALYZE
--- ============================================================================
-
-VACUUM ANALYZE;