use super::{
Cli, Command, FastaCommand, KindArg, PackageCommand, PaddingArg, SeqCommand, TokenizerCommand,
TokenizerProfileArg,
};
use crate::cli::{
build_doctor_report, run_batch_command, run_debug, run_diff, run_pipeline, run_workflow,
};
use crate::errors::{classify_validation_code, classify_verification_code, CliError};
use crate::input::{
open_fasta_input, read_fixture_observations, read_package_manifest, read_tokenizer_config,
};
use crate::output::print_success;
use biors_core::{
model_input::{build_model_inputs_checked, ModelInputPolicy},
package::{inspect_package_manifest, plan_runtime_bridge, validate_package_manifest_artifacts},
sequence::validate_fasta_reader_with_kind_and_hash,
tokenizer::{
inspect_protein_tokenizer_config, protein_tokenizer_config_for_profile,
summarize_fasta_records_reader, tokenize_fasta_records_reader,
tokenize_fasta_records_reader_with_config, ProteinTokenizerConfig,
},
verification::verify_package_outputs_with_observation_base,
};
use clap::CommandFactory;
use std::path::PathBuf;
pub fn run(command: Command) -> Result<(), CliError> {
match command {
Command::Batch { command } => run_batch_command(command),
Command::Completions { shell } => run_completions(shell),
Command::Debug { max_length, path } => run_debug(max_length, path),
Command::Diff { expected, observed } => run_diff(expected, observed),
Command::Doctor => run_doctor(),
Command::Fasta { command } => run_fasta_command(command),
Command::Inspect { path } => run_inspect(path),
Command::ModelInput {
max_length,
pad_token_id,
padding,
path,
} => run_model_input(max_length, pad_token_id, padding, path),
Command::Package { command } => run_package_command(command),
Command::Pipeline {
config,
dry_run,
explain_plan,
max_length,
pad_token_id,
padding,
path,
} => run_pipeline(
config,
dry_run,
explain_plan,
max_length,
pad_token_id,
padding,
path,
),
Command::Seq { command } => run_seq_command(command),
Command::Tokenize {
profile,
config,
path,
} => run_tokenize(profile, config, path),
Command::Tokenizer { command } => run_tokenizer_command(command),
Command::Workflow {
max_length,
pad_token_id,
padding,
path,
} => run_workflow(max_length, pad_token_id, padding, path),
}
}
fn run_completions(shell: clap_complete::Shell) -> Result<(), CliError> {
let mut command = Cli::command();
let name = command.get_name().to_string();
clap_complete::generate(shell, &mut command, name, &mut std::io::stdout());
Ok(())
}
fn run_doctor() -> Result<(), CliError> {
print_success(None, build_doctor_report())
}
fn run_fasta_command(command: FastaCommand) -> Result<(), CliError> {
match command {
FastaCommand::Validate { kind, path } => run_fasta_validate(kind, path),
}
}
fn run_seq_command(command: SeqCommand) -> Result<(), CliError> {
match command {
SeqCommand::Validate { kind, path } => run_seq_validate(kind, path),
}
}
fn run_fasta_validate(kind: KindArg, path: PathBuf) -> Result<(), CliError> {
run_sequence_validation(path, kind)
}
fn run_seq_validate(kind: KindArg, path: PathBuf) -> Result<(), CliError> {
run_sequence_validation(path, kind)
}
fn run_inspect(path: PathBuf) -> Result<(), CliError> {
let reader = open_fasta_input(&path)?;
let output = summarize_fasta_records_reader(reader)
.map_err(|error| CliError::from_fasta_read(path, error))?;
print_success(Some(output.input_hash), output.summary)
}
fn run_model_input(
max_length: usize,
pad_token_id: u8,
padding: PaddingArg,
path: PathBuf,
) -> Result<(), CliError> {
let reader = open_fasta_input(&path)?;
let output = tokenize_fasta_records_reader(reader)
.map_err(|error| CliError::from_fasta_read(path, error))?;
let model_input = build_model_inputs_checked(
&output.records,
ModelInputPolicy {
max_length,
pad_token_id,
padding: padding.into(),
},
)?;
print_success(Some(output.input_hash), model_input)
}
fn run_package_command(command: PackageCommand) -> Result<(), CliError> {
match command {
PackageCommand::Bridge { path } => run_package_bridge(path),
PackageCommand::Inspect { path } => run_package_inspect(path),
PackageCommand::Validate { path } => run_package_validate(path),
PackageCommand::Verify {
manifest,
observations,
} => run_package_verify(manifest, observations),
}
}
fn run_package_bridge(path: PathBuf) -> Result<(), CliError> {
let (manifest, manifest_base_dir) = read_package_manifest(path)?;
let report = plan_runtime_bridge(&manifest);
let validation = validate_package_manifest_artifacts(&manifest, &manifest_base_dir);
if !validation.valid || !report.ready {
return Err(CliError::Validation {
code: "package.bridge_not_ready",
message: format!(
"{:?}",
validation
.issues
.iter()
.chain(report.blocking_issues.iter())
.collect::<Vec<_>>()
),
location: Some("manifest".to_string()),
});
}
print_success(None, report)
}
fn run_package_inspect(path: PathBuf) -> Result<(), CliError> {
let (manifest, _) = read_package_manifest(path)?;
let summary = inspect_package_manifest(&manifest);
print_success(None, summary)
}
fn run_package_validate(path: PathBuf) -> Result<(), CliError> {
let (manifest, manifest_base_dir) = read_package_manifest(path)?;
let report = validate_package_manifest_artifacts(&manifest, &manifest_base_dir);
if !report.valid {
return Err(CliError::Validation {
code: classify_validation_code(&report),
message: format!("{:?}", report.issues),
location: Some("manifest".to_string()),
});
}
print_success(None, report)
}
fn run_package_verify(manifest: PathBuf, observations: PathBuf) -> Result<(), CliError> {
let (manifest, manifest_base_dir) = read_package_manifest(manifest)?;
let (observations, observations_base_dir) = read_fixture_observations(observations)?;
let report = verify_package_outputs_with_observation_base(
&manifest,
&observations,
&manifest_base_dir,
&observations_base_dir,
);
if report.failed > 0 {
return Err(CliError::Validation {
code: classify_verification_code(&report),
message: format!(
"{:?}",
report
.results
.iter()
.filter_map(|result| result.issue.as_ref())
.collect::<Vec<_>>()
),
location: Some("fixtures".to_string()),
});
}
print_success(None, report)
}
fn run_tokenize(
profile: TokenizerProfileArg,
config: Option<PathBuf>,
path: PathBuf,
) -> Result<(), CliError> {
let config = resolve_tokenizer_config(profile, config)?;
let reader = open_fasta_input(&path)?;
let output = tokenize_fasta_records_reader_with_config(reader, &config)
.map_err(|error| CliError::from_fasta_read(path, error))?;
print_success(Some(output.input_hash), output.records)
}
fn run_tokenizer_command(command: TokenizerCommand) -> Result<(), CliError> {
match command {
TokenizerCommand::Inspect { profile, config } => {
let config = resolve_tokenizer_config(profile, config)?;
print_success(None, inspect_protein_tokenizer_config(&config))
}
}
}
fn resolve_tokenizer_config(
profile: TokenizerProfileArg,
config: Option<PathBuf>,
) -> Result<ProteinTokenizerConfig, CliError> {
match config {
Some(path) => read_tokenizer_config(path),
None => Ok(protein_tokenizer_config_for_profile(profile.into())),
}
}
fn run_sequence_validation(path: PathBuf, kind: KindArg) -> Result<(), CliError> {
let reader = open_fasta_input(&path)?;
let output = validate_fasta_reader_with_kind_and_hash(reader, kind.into())
.map_err(|error| CliError::from_fasta_read(path, error))?;
print_success(Some(output.input_hash), output.report)
}