sbol-cli 0.2.1

use std::path::PathBuf;

use clap::{Args, Parser, Subcommand, ValueEnum};

use sbol::{ExternalValidationMode, RdfFormat, Severity};

#[derive(Parser)]
#[command(
    name = "sbol",
    version = env!("SBOL_VERSION_FULL"),
    about = "Command-line tool for SBOL 3 documents",
    propagate_version = true
)]
pub(crate) struct Cli {
    /// When to colorize output. `auto` colorizes the streams that are
    /// TTYs and `NO_COLOR` is unset.
    #[arg(long, value_enum, default_value_t = ColorMode::Auto, global = true)]
    pub(crate) color: ColorMode,

    #[command(subcommand)]
    pub(crate) command: Command,
}

#[derive(Subcommand)]
pub(crate) enum Command {
    /// Validate an SBOL 3 document against the spec.
    Validate(ValidateArgs),
    /// Convert an SBOL 3 document between RDF serializations.
    Convert(ConvertArgs),
    /// Upgrade an SBOL 2 RDF document to SBOL 3.
    Upgrade(UpgradeArgs),
    /// Downgrade an SBOL 3 RDF document to SBOL 2.
    Downgrade(DowngradeArgs),
    /// Import a GenBank file (.gb / .gbk) into SBOL 3.
    ImportGenbank(ImportGenbankArgs),
    /// Import a FASTA file (.fasta / .fa / .fna / .faa) into SBOL 3.
    ImportFasta(ImportFastaArgs),
    /// Inspect the built-in validation rule catalog.
    #[command(subcommand)]
    Rules(RulesCommand),
    /// Manage cached extension ontologies (NCIT and others).
    #[command(subcommand)]
    Ontology(OntologyCommand),
}

#[derive(Subcommand)]
pub(crate) enum RulesCommand {
    /// List validation rules, their implementation status, and spec section.
    List(RulesListArgs),
}

#[derive(Subcommand)]
pub(crate) enum OntologyCommand {
    /// Download and build a named ontology extension into the cache.
    Install(OntologyInstallArgs),
    /// List installed ontology extensions.
    List,
    /// Print the cache directory path.
    Path,
    /// Remove an installed ontology extension.
    Remove(OntologyRemoveArgs),
    /// Re-hash an installed extension's TSV and compare against its
    /// manifest. Errors if the extension is missing or tampered with.
    Verify(OntologyVerifyArgs),
}

#[derive(Args)]
pub(crate) struct OntologyInstallArgs {
    /// Built-in ontology to install. Currently: `ncit`.
    pub(crate) name: String,
    /// Re-download and rebuild even if already installed.
    #[arg(long)]
    pub(crate) force: bool,
}

#[derive(Args)]
pub(crate) struct OntologyRemoveArgs {
    /// Cache entry name (e.g. `ncit`).
    pub(crate) name: String,
}

#[derive(Args)]
pub(crate) struct OntologyVerifyArgs {
    /// Cache entry name to verify. If omitted, every installed
    /// extension is verified.
    pub(crate) name: Option<String>,
}

#[derive(Clone, Copy, Debug, PartialEq, Eq, ValueEnum)]
pub(crate) enum OutputFormat {
    Text,
    Json,
    #[cfg(feature = "sarif")]
    Sarif,
}

#[derive(Clone, Copy, Debug, PartialEq, Eq, ValueEnum)]
pub(crate) enum RulesFormat {
    Text,
    Json,
}

#[derive(Clone, Copy, Debug, PartialEq, Eq, ValueEnum)]
pub(crate) enum ColorMode {
    Auto,
    Always,
    Never,
}

#[derive(Clone, Copy, Debug, PartialEq, Eq, ValueEnum)]
pub(crate) enum RuleStatusFilter {
    Error,
    Warning,
    Configurable,
    MachineUncheckable,
    Unimplemented,
}

#[derive(Clone, Copy, Debug, PartialEq, Eq, ValueEnum)]
pub(crate) enum RdfFormatArg {
    Turtle,
    Rdfxml,
    Jsonld,
    Ntriples,
}

impl From<RdfFormatArg> for RdfFormat {
    fn from(value: RdfFormatArg) -> Self {
        match value {
            RdfFormatArg::Turtle => RdfFormat::Turtle,
            RdfFormatArg::Rdfxml => RdfFormat::RdfXml,
            RdfFormatArg::Jsonld => RdfFormat::JsonLd,
            RdfFormatArg::Ntriples => RdfFormat::NTriples,
        }
    }
}

#[derive(Clone, Copy, Debug, PartialEq, Eq, ValueEnum)]
pub(crate) enum SeverityArg {
    Warning,
    Error,
}

#[derive(Clone, Copy, Debug, PartialEq, Eq, ValueEnum)]
pub(crate) enum ExternalModeArg {
    Off,
    Provided,
    Allowed,
}

impl From<ExternalModeArg> for ExternalValidationMode {
    fn from(value: ExternalModeArg) -> Self {
        match value {
            ExternalModeArg::Off => ExternalValidationMode::Off,
            ExternalModeArg::Provided => ExternalValidationMode::ProvidedOnly,
            ExternalModeArg::Allowed => ExternalValidationMode::ExternalAllowed,
        }
    }
}

impl From<SeverityArg> for Severity {
    fn from(value: SeverityArg) -> Self {
        match value {
            SeverityArg::Warning => Severity::Warning,
            SeverityArg::Error => Severity::Error,
        }
    }
}

#[derive(Args)]
pub(crate) struct ValidateArgs {
    /// Path to an SBOL 3 document. Format is inferred from the extension —
    /// `.ttl` (Turtle), `.rdf` (RDF/XML), `.jsonld` (JSON-LD), or `.nt`
    /// (N-Triples).
    pub(crate) path: PathBuf,

    /// Output format.
    #[arg(long, value_enum, default_value_t = OutputFormat::Text)]
    pub(crate) format: OutputFormat,

    /// Destination for output. Use `-` for stdout.
    #[arg(long, default_value = "-")]
    pub(crate) output: String,

    /// Suppress diagnostics for these rule IDs (e.g. `--allow sbol3-10502`).
    #[arg(long = "allow", value_name = "RULE_ID")]
    pub(crate) allow: Vec<String>,

    /// Promote these rule IDs to error severity.
    #[arg(long = "deny", value_name = "RULE_ID")]
    pub(crate) deny: Vec<String>,

    /// Demote these rule IDs to warning severity.
    #[arg(long = "warn", value_name = "RULE_ID")]
    pub(crate) warn: Vec<String>,

    /// Floor on the severity of any emitted issue.
    #[arg(long, value_enum)]
    pub(crate) severity_floor: Option<SeverityArg>,

    /// Ceiling on the severity of any emitted issue.
    #[arg(long, value_enum)]
    pub(crate) severity_ceiling: Option<SeverityArg>,

    /// Treat warnings as errors (alias for `--severity-floor error`).
    #[arg(long)]
    pub(crate) treat_warnings_as_errors: bool,

    /// Use `Document::check_complete` semantics: any rule with partial
    /// coverage causes exit code 3.
    #[arg(long)]
    pub(crate) treat_partial_as_errors: bool,

    /// In text output, print a coverage summary after the issues.
    #[arg(long)]
    pub(crate) show_coverage: bool,

    /// Whether to resolve external documents and content.
    #[arg(long, value_enum, default_value_t = ExternalModeArg::Off)]
    pub(crate) external_mode: ExternalModeArg,

    /// Filesystem roots from which external Attachment / Model / TopLevel
    /// references may be resolved.
    #[arg(long = "resolve-documents", value_name = "DIR")]
    pub(crate) resolve_documents: Vec<PathBuf>,

    /// Filesystem roots for Attachment / Model byte content.
    #[arg(long = "resolve-content", value_name = "DIR")]
    pub(crate) resolve_content: Vec<PathBuf>,

    /// Cache directory required by `--external-mode allowed` when the
    /// `http-resolver` feature is built in.
    #[arg(long)]
    pub(crate) cache_dir: Option<PathBuf>,

    /// Layer an installed runtime ontology extension on top of the bundled
    /// facts for this validation run. Pass the cache entry name (e.g.
    /// `--ontology ncit`). Repeatable; later extensions override earlier
    /// ones on conflict.
    #[arg(long = "ontology", value_name = "NAME")]
    pub(crate) ontology: Vec<String>,
}

#[derive(Clone, Copy, Debug, PartialEq, Eq, ValueEnum)]
pub(crate) enum UpgradeReportFormat {
    None,
    Text,
    Json,
}

#[derive(Args)]
pub(crate) struct UpgradeArgs {
    /// Path to an SBOL 2 RDF document. Input format is inferred from the
    /// extension — `.ttl` (Turtle), `.rdf` / `.xml` (RDF/XML), `.jsonld`
    /// (JSON-LD), or `.nt` (N-Triples). Use `--from` to override.
    pub(crate) path: PathBuf,

    /// Override the input format inference. Useful for SBOL 2 files
    /// distributed with non-standard extensions.
    #[arg(long, value_enum, value_name = "FORMAT")]
    pub(crate) from: Option<RdfFormatArg>,

    /// Target SBOL 3 RDF serialization. If omitted, inferred from
    /// `--output`'s extension.
    #[arg(long, value_enum, value_name = "FORMAT")]
    pub(crate) to: Option<RdfFormatArg>,

    /// Destination path for the SBOL 3 output. Use `-` (the default) for
    /// stdout; in that case `--to` is required.
    #[arg(long, short = 'o', default_value = "-")]
    pub(crate) output: String,

    /// Default `hasNamespace` value for top-level objects whose namespace
    /// cannot be derived from the input. Without this flag, such objects
    /// fall back to the URL scheme+host or, failing that, omit
    /// `hasNamespace` entirely.
    #[arg(long, value_name = "IRI")]
    pub(crate) namespace: Option<String>,

    /// Where to write the conversion report.
    #[arg(long, value_enum, default_value_t = UpgradeReportFormat::None)]
    pub(crate) report: UpgradeReportFormat,

    /// Exit with status 1 if any conversion warnings were produced.
    #[arg(long)]
    pub(crate) strict: bool,

    /// Run SBOL 3 validation on the converted document and fold the result
    /// into the exit code: code 1 if validation finds errors.
    #[arg(long)]
    pub(crate) validate: bool,
}

#[derive(Args)]
pub(crate) struct DowngradeArgs {
    /// Path to an SBOL 3 RDF document. Input format is inferred from
    /// the extension (`.ttl`, `.rdf` / `.xml`, `.jsonld`, `.nt`).
    pub(crate) path: PathBuf,

    /// Override the input format inference. Useful for SBOL 3 RDF files
    /// distributed with non-standard extensions.
    #[arg(long, value_enum, value_name = "FORMAT")]
    pub(crate) from: Option<RdfFormatArg>,

    /// Target SBOL 2 RDF serialization. If omitted, inferred from
    /// `--output`'s extension.
    #[arg(long, value_enum, value_name = "FORMAT")]
    pub(crate) to: Option<RdfFormatArg>,

    /// Destination path. Use `-` (the default) for stdout; in that
    /// case `--to` is required.
    #[arg(long, short = 'o', default_value = "-")]
    pub(crate) output: String,

    /// Version string assigned to top-level objects whose source
    /// document didn't carry `backport:sbol2version`. Omit to leave
    /// such subjects unversioned (SBOL 2 makes `sbol2:version`
    /// optional); pass `--default-version 1` to match the libSBOLj /
    /// SynBioHub convention of always emitting one.
    #[arg(long, value_name = "VERSION")]
    pub(crate) default_version: Option<String>,

    /// Validate the downgrade by round-tripping the produced SBOL 2
    /// back up through `sbol::upgrade` and running SBOL 3 validation
    /// on the result. There is no native SBOL 2 validator in this
    /// workspace, so this round-trip is the proxy for structural
    /// correctness. Exit code 1 on validation errors.
    #[arg(long)]
    pub(crate) validate: bool,

    /// Exit with status 1 if any downgrade warnings were produced.
    #[arg(long)]
    pub(crate) strict: bool,
}

#[derive(Clone, Copy, Debug, PartialEq, Eq, ValueEnum)]
pub(crate) enum FastaAlphabetArg {
    Dna,
    Rna,
    Protein,
}

impl From<FastaAlphabetArg> for sbol_fasta::Alphabet {
    fn from(value: FastaAlphabetArg) -> Self {
        match value {
            FastaAlphabetArg::Dna => sbol_fasta::Alphabet::Dna,
            FastaAlphabetArg::Rna => sbol_fasta::Alphabet::Rna,
            FastaAlphabetArg::Protein => sbol_fasta::Alphabet::Protein,
        }
    }
}

#[derive(Args)]
pub(crate) struct ImportFastaArgs {
    /// Path to a FASTA file (`.fasta` / `.fa` / `.fna` / `.faa`).
    pub(crate) path: PathBuf,

    /// Namespace IRI under which the resulting SBOL 3 top-level
    /// objects will be rooted. Required because FASTA carries no
    /// namespace concept.
    #[arg(long, short = 'n', value_name = "IRI")]
    pub(crate) namespace: String,

    /// Override alphabet auto-detection. Pass when the sequence text
    /// is ambiguous (e.g. a short peptide composed only of A/C/G/T
    /// letters that would otherwise be misclassified as DNA).
    #[arg(long, value_enum, value_name = "ALPHABET")]
    pub(crate) alphabet: Option<FastaAlphabetArg>,

    /// Target SBOL 3 RDF serialization. If omitted, inferred from
    /// `--output`'s extension.
    #[arg(long, value_enum, value_name = "FORMAT")]
    pub(crate) to: Option<RdfFormatArg>,

    /// Destination path. Use `-` (the default) for stdout; in that
    /// case `--to` is required.
    #[arg(long, short = 'o', default_value = "-")]
    pub(crate) output: String,

    /// Run SBOL 3 validation on the converted document and fold the
    /// result into the exit code: code 1 if validation finds errors.
    #[arg(long)]
    pub(crate) validate: bool,

    /// Exit with status 1 if any import warnings were produced.
    #[arg(long)]
    pub(crate) strict: bool,
}

#[derive(Args)]
pub(crate) struct ImportGenbankArgs {
    /// Path to a GenBank flat-file (`.gb` / `.gbk`). Mixed-case month
    /// names in the LOCUS line (as emitted by SynBioHub) are tolerated.
    pub(crate) path: PathBuf,

    /// Namespace IRI under which the resulting SBOL 3 top-level
    /// objects will be rooted. Required because GenBank carries no
    /// namespace concept.
    #[arg(long, short = 'n', value_name = "IRI")]
    pub(crate) namespace: String,

    /// Target SBOL 3 RDF serialization. If omitted, inferred from
    /// `--output`'s extension.
    #[arg(long, value_enum, value_name = "FORMAT")]
    pub(crate) to: Option<RdfFormatArg>,

    /// Destination path. Use `-` (the default) for stdout; in that
    /// case `--to` is required.
    #[arg(long, short = 'o', default_value = "-")]
    pub(crate) output: String,

    /// Run SBOL 3 validation on the converted document and fold the
    /// result into the exit code: code 1 if validation finds errors.
    #[arg(long)]
    pub(crate) validate: bool,

    /// Exit with status 1 if any import warnings were produced.
    #[arg(long)]
    pub(crate) strict: bool,
}

#[derive(Args)]
pub(crate) struct ConvertArgs {
    /// Path to an SBOL 3 document. Input format is inferred from the
    /// extension — `.ttl` (Turtle), `.rdf` (RDF/XML), `.jsonld` (JSON-LD),
    /// or `.nt` (N-Triples).
    pub(crate) path: PathBuf,

    /// Target serialization. If omitted, inferred from `--output`'s
    /// extension.
    #[arg(long, value_enum, value_name = "FORMAT")]
    pub(crate) to: Option<RdfFormatArg>,

    /// Destination path. Use `-` (the default) for stdout; in that case
    /// `--to` is required.
    #[arg(long, short = 'o', default_value = "-")]
    pub(crate) output: String,
}

#[derive(Args)]
pub(crate) struct RulesListArgs {
    /// Output format.
    #[arg(long, value_enum, default_value_t = RulesFormat::Text)]
    pub(crate) format: RulesFormat,

    /// Only show rules with this implementation status.
    #[arg(long, value_enum, value_name = "STATUS")]
    pub(crate) status: Option<RuleStatusFilter>,

    /// Show full notes instead of truncating to fit one line per rule.
    #[arg(long)]
    pub(crate) full: bool,
}