feat: Add input CLI arg (bda9ea80) · Commits · Research Enablement / Xylem

lcov.info

+57 −50

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		@@ -112,43 +112,47 @@ FN:16,run
		FNF:1
		FNDA:0,run
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		TN:
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		@@ -288,7 +292,7 @@ FNDA:0,Config::get_environment_variables
		FNDA:1,Config::get_inputs
		FNDA:1,Config::get_module_list
		FNDA:0,Config::prepare_modules
		FNDA:1,Config::read
		FNDA:3,Config::read
		FNDA:1,Config::read_json
		FNDA:1,Config::read_yaml
		FNDA:0,Config::run_workflow
		@@ -296,17 +300,20 @@ FNDA:0,Config::set_environment_variables
		FNDA:0,Config::verify_requirements
		FNDA:0,Config::verify_resources
		FNDA:0,Config::with_options
		FNDA:2,Extension::from_string
		FNDA:3,Extension::from_string
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		TN:
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		@@ -1061,8 +1068,8 @@ FNDA:0,Label::pass
		FNDA:0,Label::read
		FNDA:0,Label::rejected
		FNDA:0,Label::run
		FNDA:2,Label::using
		FNDA:2,Label::fmt_using
		FNDA:4,Label::using
		FNDA:4,Label::fmt_using
		FNDA:1,add_dot_slash
		FNDA:1,add_forward_slash
		FNDA:0,download_binary
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pipe-cli/src/cli.rs

+17 −14

Original line number	Diff line number	Diff line
		@@ -35,25 +35,25 @@ pub enum Commands {
		#[arg(value_name = "PATH", value_hint = clap::ValueHint::DirPath)]
		path: Option<std::path::PathBuf>,
		/// Path to configuration file
		#[arg(short = 'c', long = "config", value_name = "PATH", value_hint = clap::ValueHint::DirPath)]
		#[arg(short, long, value_name = "PATH", value_hint = clap::ValueHint::DirPath)]
		config: Option<std::path::PathBuf>,
		/// Reporter(s) to use to output the results - console (default) and/or json
		#[arg(short = 'r', long = "reporter", value_name = "STRING", num_args=0..=2)]
		#[arg(short, long, value_name = "STRING", num_args=0..=2)]
		reporter: Option<Vec<String>>,
		/// Destination path for reporters that use one
		#[arg(short = 'o', long = "output", value_name = "PATH", value_hint = clap::ValueHint::DirPath)]
		#[arg(short, long, value_name = "PATH", value_hint = clap::ValueHint::DirPath)]
		output: Option<std::path::PathBuf>,
		/// Return all results that pass or fail check conditions
		#[arg(short = 'a', long = "all", value_name = "BOOL")]
		#[arg(short, long, value_name = "BOOL")]
		all: bool,
		/// Only return results that pass their associated check
		#[arg(short = 'p', long = "pass", value_name = "BOOL")]
		#[arg(short, long, value_name = "BOOL")]
		pass: bool,
		/// Report results in minimal format
		#[arg(short = 'm', long = "minimal", value_name = "BOOL")]
		#[arg(short, long, value_name = "BOOL")]
		minimal: bool,
		/// Deduplicate results
		#[arg(short = 'u', long = "unique", value_name = "BOOL")]
		#[arg(short, long, value_name = "BOOL")]
		unique: bool,
		},
		/// Check environment parameters and verify PIPE requirements are met
		@@ -67,10 +67,10 @@ pub enum Commands {
		/// Path to configuration file
		///
		/// Validate PIPE requirements are met for a given configuration
		#[arg(short = 'c', long = "config", value_name = "PATH", value_hint = clap::ValueHint::DirPath)]
		#[arg(short, long, value_name = "PATH", value_hint = clap::ValueHint::DirPath)]
		config: Option<std::path::PathBuf>,
		/// Scan environment and attempt to fix unmet requirements
		#[arg(short = 'f', long = "fix", value_name = "BOOL")]
		#[arg(short, long, value_name = "BOOL")]
		fix: bool,
		},
		/// Run workflow using configuration file
		@@ -84,19 +84,22 @@ pub enum Commands {
		#[clap(verbatim_doc_comment)]
		Run {
		/// Path to configuration file
		#[arg(short = 'c', long = "config", value_name = "PATH", value_hint = clap::ValueHint::DirPath)]
		#[arg(short, long, value_name = "PATH", value_hint = clap::ValueHint::DirPath)]
		config: Option<std::path::PathBuf>,
		/// Reporter(s) to use to output the results - console (default) and/or json
		#[arg(short = 'r', long = "reporter", value_name = "STRING", num_args=0..=2)]
		#[arg(short, long, value_name = "STRING", num_args=0..=2)]
		reporter: Option<Vec<String>>,
		/// Destination path for reporters that use one
		#[arg(short = 'o', long = "output", value_name = "PATH", value_hint = clap::ValueHint::DirPath)]
		#[arg(short, long, value_name = "PATH", value_hint = clap::ValueHint::DirPath)]
		output: Option<std::path::PathBuf>,
		/// Value(s) to use as INPUT variable in workflow
		#[arg(short, long, value_name = "LIST", value_delimiter = ',')]
		input: Option<Vec<String>>,
		/// Execute workflow dry run (do not actually make changes to environment)
		#[arg(short = 'd', long = "dry-run", value_name = "BOOL")]
		#[arg(short, long = "dry-run", value_name = "BOOL")]
		dry_run: bool,
		/// Execute workflow without connection to the internet
		#[arg(long = "offline", value_name = "BOOL")]
		#[arg(long, value_name = "BOOL")]
		offline: bool,
		/// Skip calculating and verifying checksum for downloaded binary files
		#[arg(long = "skip-verify-checksum", value_name = "BOOL")]

pipe-cli/src/commands/run/mod.rs

+11 −4

Original line number	Diff line number	Diff line
		@@ -17,6 +17,7 @@ pub fn run(
		config: &Option<PathBuf>,
		_reporter: &Option<Vec<String>>,
		_output: &Option<PathBuf>,
		cli_input: &Option<Vec<String>>,
		cli_dry_run: bool,
		cli_offline: bool,
		cli_skip_verify_checksum: bool,
		@@ -80,10 +81,16 @@ pub fn run(
		info!(value, "=> {} Configuration with input", Label::using());
		config.clone().run_workflow(Some(value.to_string()), &options);
		}),
		\| Some(_) \| None => match cli_input {
		\| Some(values) if !values.is_empty() => values.par_iter().for_each(\|value\| {
		info!(value, "=> {} CLI input", Label::using());
		config.clone().run_workflow(Some(value.to_string()), &options);
		}),
		\| Some(_) \| None => {
		info!("=> {} Configuration with {}", Label::using(), Label::fmt_not_found("NO INPUTS"));
		config.run_workflow(None, &options);
		}
		},
		};
		}
		\| None => error!("=> {} Could not import configuration", Label::fail()),

pipe-cli/src/main.rs

+2 −0

Original line number	Diff line number	Diff line
		@@ -70,6 +70,7 @@ fn main() -> Void {
		config,
		reporter,
		output,
		input,
		dry_run,
		offline,
		skip_verify_checksum,
		@@ -80,6 +81,7 @@ fn main() -> Void {
		config,
		reporter,
		output,
		input,
		*dry_run,
		*offline,
		*skip_verify_checksum,

pipe-lib/src/config.rs

+14 −14

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		@@ -117,21 +117,21 @@ pub struct Rule {
		}
		impl Config {
		pub fn get_environment_variables(self, module: Option<Module>, input: Option<String>) -> HashMap<String, String> {
		match input {
		\| Some(value) => {
		let config_vars = self.variables.clone().unwrap_or_default();
		let module_vars = module.unwrap().variables.clone().unwrap_or_default();
		let mut envs = EnvironmentValue::get_from_serde(&config_vars);
		let parent = PathBuf::from(input.clone().unwrap_or_default())
		.file_name()
		.unwrap()
		.to_str()
		.unwrap()
		.to_string();
		let parent = PathBuf::from(value.clone()).file_name().unwrap().to_str().unwrap().to_string();
		envs.extend(EnvironmentValue::get_from_serde(&module_vars));
		envs.insert("INPUT".to_string(), input.unwrap_or_default());
		envs.insert("INPUT".to_string(), value);
		envs.insert("PARENT_DIRECTORY".to_string(), parent);
		println!("Envs: {:#?}", envs);
		debug!("=> {} Environment variables: {:#?}", Label::using(), envs.dimmed());
		envs
		}
		\| None => HashMap::new(),
		}
		}
		/// Get inputs from input attribute for concurrent workflow execution
		///
		/// See [InputAttribute](crate::InputAttribute) for more details