From 3b1106c648c7d63d5ca39c68c1cf29fabd2a48d7 Mon Sep 17 00:00:00 2001
From: Iago Bonnici <iago.bonnici@umontpellier.fr>
Date: Wed, 24 Jul 2024 13:29:29 +0200
Subject: [PATCH] Resolve file paths relatively to the config file.
---
src/bin/aphid/main.rs | 1 -
src/config.rs | 1 +
src/config/check.rs | 29 +++++++++++++++++++++++++----
3 files changed, 26 insertions(+), 5 deletions(-)
diff --git a/src/bin/aphid/main.rs b/src/bin/aphid/main.rs
index 5603aef..aca3e73 100644
--- a/src/bin/aphid/main.rs
+++ b/src/bin/aphid/main.rs
@@ -29,7 +29,6 @@ use crate::display_tree_analysis::display_geometrical_tree_analysis;
#[command(author, version, about, long_about = None)]
struct Args {
/// Path to the config file.
- #[arg(short, long)]
config: PathBuf,
}
diff --git a/src/config.rs b/src/config.rs
index 5caa52d..88f1932 100644
--- a/src/config.rs
+++ b/src/config.rs
@@ -22,6 +22,7 @@ mod deserialize;
// The final value handed out to user.
pub struct Config {
// Path to the gene trees data file.
+ // If relative: relative to the config file.
pub trees: PathBuf,
// Names of the species of interest.
diff --git a/src/config/check.rs b/src/config/check.rs
index 14e1abc..d97ae99 100644
--- a/src/config/check.rs
+++ b/src/config/check.rs
@@ -60,11 +60,32 @@ impl Config {
);
}
+ let search = (&raw).try_into()?;
+ let taxa = raw.taxa._try_into(interner)?;
+
+ // Resolve relative paths relatively to the config file.
+ let mut trees = raw.taxa.trees;
+ if !trees.is_absolute() {
+ let mut path = path
+ .parent()
+ .unwrap_or_else(|| {
+ panic!(
+ "Config file has been read but its path has no parent: {}",
+ path.to_string_lossy()
+ )
+ })
+ .to_owned();
+ path.push(trees);
+ trees = path
+ .canonicalize()
+ .with_context(|_| CanonicalizeErr { path })?;
+ }
+
// Most checks implemented within `TryFrom` trait.
Ok(Config {
- search: (&raw).try_into()?,
- taxa: raw.taxa._try_into(interner)?,
- trees: raw.taxa.trees,
+ search,
+ taxa,
+ trees,
unresolved_length: raw.unresolved_length,
filters: if let Some(ref raw) = raw.filters {
raw.try_into()?
@@ -640,7 +661,7 @@ pub enum Error {
Config { mess: String },
#[snafu(transparent)]
Optim { source: optim::Error },
- #[snafu(display("Could not canonicalize path: {:?}.", path.to_string_lossy()))]
+ #[snafu(display("Could not canonicalize path: {:?}:\n{source}", path.to_string_lossy()))]
Canonicalize {
source: std::io::Error,
path: PathBuf,
--
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