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fix(cli): correctly deprecate input args
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 - Add error message for removed `--input-virus-properties`, `--input-root-seq`, `--reference`, `--input-gene-map`, `--genemap`
 - Deduplicate error messages text.
 - Group deprecated args in one place
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@ivan-aksamentov
ivan-aksamentov committed Oct 12, 2023
1 parent 71d3a59 commit 847eaa1
Showing 1 changed file with 69 additions and 70 deletions.
139 changes: 69 additions & 70 deletions packages_rs/nextclade-cli/src/cli/nextclade_cli.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -328,15 +328,10 @@ pub struct NextcladeRunInputArgs {
/// Overrides path to `reference.fasta` in the dataset (`--input-dataset`).
///
/// Supports the following compression formats: "gz", "bz2", "xz", "zst". Use "-" to read uncompressed data from standard input (stdin).
#[clap(long, short = 'r', visible_alias("reference"))]
#[clap(long, short = 'r')]
#[clap(value_hint = ValueHint::FilePath)]
pub input_ref: Option<PathBuf>,

/// REMOVED. Use --input-ref instead
#[clap(long)]
#[clap(hide_long_help = true, hide_short_help = true)]
pub input_root_seq: Option<String>,

/// Path to Auspice JSON v2 file containing reference tree.
///
/// See https://nextstrain.org/docs/bioinformatics/data-formats.
Expand All @@ -348,26 +343,14 @@ pub struct NextcladeRunInputArgs {
#[clap(value_hint = ValueHint::FilePath)]
pub input_tree: Option<PathBuf>,

/// REMOVED. The qc.json file have been merged into pathogen.json, see `--input-pathogen-json`
#[clap(long, short = 'Q')]
#[clap(value_hint = ValueHint::FilePath)]
#[clap(hide_long_help = true, hide_short_help = true)]
pub input_qc_config: Option<PathBuf>,

/// Path to a JSON file containing configuration and data specific to a pathogen.
///
/// Overrides path to `pathogen.json` in the dataset (`--input-dataset`).
///
/// Supports the following compression formats: "gz", "bz2", "xz", "zst". Use "-" to read uncompressed data from standard input (stdin).
#[clap(long, short = 'R')]
#[clap(value_hint = ValueHint::FilePath)]
pub input_pathogen_json: Option<PathBuf>,

/// REMOVED. Merged into pathogen.json, see `--input-pathogen`
#[clap(long, short = 'p')]
#[clap(value_hint = ValueHint::FilePath)]
#[clap(hide_long_help = true, hide_short_help = true)]
pub input_pcr_primers: Option<PathBuf>,
pub input_pathogen_json: Option<PathBuf>,

/// Path to a GFF3 file containing (genome annotation).
///
Expand All @@ -383,7 +366,7 @@ pub struct NextcladeRunInputArgs {
/// https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md
///
/// Supports the following compression formats: "gz", "bz2", "xz", "zst". Use "-" to read uncompressed data from standard input (stdin).
#[clap(long, short = 'm', alias = "genemap")]
#[clap(long, short = 'm')]
#[clap(value_hint = ValueHint::FilePath)]
pub input_annotation: Option<PathBuf>,

Expand All @@ -408,6 +391,41 @@ pub struct NextcladeRunInputArgs {
#[clap(value_hint = ValueHint::Url)]
#[clap(default_value_t = Url::from_str(DATA_FULL_DOMAIN).expect("Invalid URL"))]
pub server: Url,

// Deprecated arguments. Kept in oder to detect usage and print error messages.
/// REMOVED. Use --input-ref instead
#[clap(long)]
#[clap(hide_long_help = true, hide_short_help = true)]
pub input_root_seq: Option<String>,

#[clap(long)]
#[clap(hide_long_help = true, hide_short_help = true)]
pub reference: Option<String>,

/// REMOVED. The qc.json file have been merged into pathogen.json, see `--input-pathogen-json`
#[clap(long, short = 'Q')]
#[clap(hide_long_help = true, hide_short_help = true)]
pub input_qc_config: Option<String>,

/// REMOVED. The virus_properties.json file have been merged into pathogen.json, see `--input-pathogen-json`
#[clap(long, short = 'R')]
#[clap(hide_long_help = true, hide_short_help = true)]
pub input_virus_properties: Option<String>,

/// REMOVED. The pcr_primers.csv file have been merged into pathogen.json, see `--input-pathogen-json`
#[clap(long)]
#[clap(hide_long_help = true, hide_short_help = true)]
pub input_pcr_primers: Option<String>,

/// RENAMED to `--input-annotation`
#[clap(long)]
#[clap(hide_long_help = true, hide_short_help = true)]
pub input_gene_map: Option<String>,

/// RENAMED to `--input-annotation`
#[clap(long)]
#[clap(hide_long_help = true, hide_short_help = true)]
pub genemap: Option<String>,
}

#[allow(clippy::struct_excessive_bools)]
Expand Down Expand Up @@ -899,69 +917,42 @@ Try:
one or multiple positional arguments
with paths to input fasta files
When positional arguments are not provided, nextclade will read input fasta from standard input.
For more information, type:
When positional arguments are not provided, nextclade will read input fasta from standard input."#;

nextclade run --help"#;
const ERROR_MSG_INPUT_ROOT_SEQ_REMOVED: &str =
r#"The argument `--input-root-seq` (alias `--reference`) is removed in favor of `--input-ref`."#;

const ERROR_MSG_INPUT_ROOT_SEQ_REMOVED: &str = r#"The argument `--input-root-seq` is removed in favor of `--input-ref`.
For more information, type
nextclade run --help"#;
const ERROR_MSG_INPUT_GENE_MAP_RENAMED: &str = r#"The argument `--input-gene-map` (alias `--genemap`) is renamed to `--input-annotation`."#;

const ERROR_MSG_OUTPUT_DIR_REMOVED: &str = r#"The argument `--output-dir` is removed in favor of `--output-all`.
When provided, `--output-all` allows to write all possible outputs into a directory.
The defaut base name of the files can be overriden with `--output-basename` argument.
The set of output files can be restricted with `--output-selection` argument.
For more information, type
nextclade run --help"#;

const ERROR_MSG_INPUT_QC_CONFIG_REMOVED: &str = r#"The argument `--input-qc-config` is removed in favor of `--input-pathogen-json`.
Since Nextclade v3, the `pathogen.json` file is an extended version of file known as `virus_properties.json` in Nextclade v2. The Nextclade v2 files `qc.json`, `primers.csv` and `tag.json` are now merged into `pathogen.json`.
For more information, type
nextclade run --help
Read Nextclade documentation at:
https://docs.nextstrain.org/projects/nextclade/en/stable"#;
The set of output files can be restricted with `--output-selection` argument."#;

const ERROR_MSG_INPUT_PCR_PRIMERS_REMOVED: &str = r#"The argument `--input-pcr-primers` is removed in favor of `--input-pathogen-json`.
const ERROR_MSG_INPUT_VIRUS_PROPERTIES_REMOVED: &str = r#"The argument `--input-virus-properties` (alias `-R`) is removed in favor of `--input-pathogen-json`.
Since Nextclade v3, the `pathogen.json` file is an extended version of file known as `virus_properties.json` in Nextclade v2. The Nextclade v2 files `qc.json`, `primers.csv` and `tag.json` are now merged into `pathogen.json`.
Since version 3 Nextclade uses single file `pathogen.json` rather than a set of files `qc.json`, `primers.csv`, `virus_properties.json` and `tag.json` used in Nextclade v2."#;

For more information, type
const ERROR_MSG_INPUT_QC_CONFIG_REMOVED: &str = r#"The argument `--input-qc-config` (alias `-Q`) is removed in favor of `--input-pathogen-json`.
nextclade run --help
Since version 3 Nextclade uses single file `pathogen.json` rather than a set of files `qc.json`, `primers.csv`, `virus_properties.json` and `tag.json` used in Nextclade v2."#;

Read Nextclade documentation at:
const ERROR_MSG_INPUT_PCR_PRIMERS_REMOVED: &str = r#"The argument `--input-pcr-primers` (alias `-p`) is removed in favor of `--input-pathogen-json`.
https://docs.nextstrain.org/projects/nextclade/en/stable"#;
Since version 3 Nextclade uses single file `pathogen.json` rather than a set of files `qc.json`, `primers.csv`, `virus_properties.json` and `tag.json` used in Nextclade v2."#;

const ERROR_MSG_OUTPUT_INSERTIONS_REMOVED: &str = r#"The argument `--output-insertions` have been removed in favor of `--output-csv` and `--output-tsv`.
In Nextclade v3 the separate arguments `--output-insertions` and `--output-errors` are removed. Please use `--output-csv` (for semicolon-separated table) and `--output-tsv` (for tab-separated table) arguments instead. These tables contain, among others, all the columns from the output insertions table (`--output-insertions`) as well as from the output errors table (`--output-errors`).
For more information, type
nextclade run --help
Read Nextclade documentation at:
https://docs.nextstrain.org/projects/nextclade/en/stable"#;
In Nextclade v3 the separate arguments `--output-insertions` and `--output-errors` are removed. Please use `--output-csv` (for semicolon-separated table) and `--output-tsv` (for tab-separated table) arguments instead. These tables contain, among others, all the columns from the output insertions table (`--output-insertions`) as well as from the output errors table (`--output-errors`)."#;

const ERROR_MSG_OUTPUT_ERRORS_REMOVED: &str = r#"The argument `--output-errors` have been removed in favor of `--output-csv` and `--output-tsv`.
In Nextclade v3 the separate arguments `--output-insertions` and `--output-errors` are removed. Please use `--output-csv` (for semicolon-separated table) and `--output-tsv` (for tab-separated table) arguments instead. These tables contain, among others, all the columns from the output insertions table (`--output-insertions`) as well as from the output errors table (`--output-errors`).
In Nextclade v3 the separate arguments `--output-insertions` and `--output-errors` are removed. Please use `--output-csv` (for semicolon-separated table) and `--output-tsv` (for tab-separated table) arguments instead. These tables contain, among others, all the columns from the output insertions table (`--output-insertions`) as well as from the output errors table (`--output-errors`)."#;

const MSG_READ_DOCS: &str = r#"
For more information, type
Expand All @@ -973,31 +964,39 @@ Read Nextclade documentation at:

pub fn nextclade_check_removed_args(run_args: &NextcladeRunArgs) -> Result<(), Report> {
if run_args.inputs.input_fasta.is_some() {
return make_error!("{ERROR_MSG_INPUT_FASTA_REMOVED}");
return make_error!("{ERROR_MSG_INPUT_FASTA_REMOVED}{MSG_READ_DOCS}");
}

if run_args.inputs.input_root_seq.is_some() || run_args.inputs.reference.is_some() {
return make_error!("{ERROR_MSG_INPUT_ROOT_SEQ_REMOVED}{MSG_READ_DOCS}");
}

if run_args.inputs.input_gene_map.is_some() || run_args.inputs.genemap.is_some() {
return make_error!("{ERROR_MSG_INPUT_GENE_MAP_RENAMED}{MSG_READ_DOCS}");
}

if run_args.inputs.input_root_seq.is_some() {
return make_error!("{ERROR_MSG_INPUT_ROOT_SEQ_REMOVED}");
if run_args.inputs.input_virus_properties.is_some() {
return make_error!("{ERROR_MSG_INPUT_VIRUS_PROPERTIES_REMOVED}{MSG_READ_DOCS}");
}

if run_args.inputs.input_qc_config.is_some() {
return make_error!("{ERROR_MSG_INPUT_QC_CONFIG_REMOVED}");
return make_error!("{ERROR_MSG_INPUT_QC_CONFIG_REMOVED}{MSG_READ_DOCS}");
}

if run_args.inputs.input_pcr_primers.is_some() {
return make_error!("{ERROR_MSG_INPUT_PCR_PRIMERS_REMOVED}");
return make_error!("{ERROR_MSG_INPUT_PCR_PRIMERS_REMOVED}{MSG_READ_DOCS}");
}

if run_args.outputs.output_dir.is_some() {
return make_error!("{ERROR_MSG_OUTPUT_DIR_REMOVED}");
return make_error!("{ERROR_MSG_OUTPUT_DIR_REMOVED}{MSG_READ_DOCS}");
}

if run_args.outputs.output_insertions.is_some() {
return make_error!("{ERROR_MSG_OUTPUT_INSERTIONS_REMOVED}");
return make_error!("{ERROR_MSG_OUTPUT_INSERTIONS_REMOVED}{MSG_READ_DOCS}");
}

if run_args.outputs.output_errors.is_some() {
return make_error!("{ERROR_MSG_OUTPUT_ERRORS_REMOVED}");
return make_error!("{ERROR_MSG_OUTPUT_ERRORS_REMOVED}{MSG_READ_DOCS}");
}

Ok(())
Expand Down

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