Sped up build time file writing

snijderlab · Oct 23, 2023 · 7b6ebff · 7b6ebff
1 parent a1f9a5a
commit 7b6ebff
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Showing 5 changed files with 50 additions and 47 deletions.
diff --git a/src/build/atomic_masses.rs b/src/build/atomic_masses.rs
@@ -1,4 +1,4 @@
-use std::{ffi::OsString, fs, path::Path};
+use std::{ffi::OsString, io::BufWriter, io::Write, path::Path};
 
 use crate::Element;
 
@@ -107,25 +107,27 @@ pub fn build_atomic_masses(out_dir: &OsString, _debug: bool) -> Result<(), Strin
         });
 
     let dest_path = Path::new(&out_dir).join("elements.rs");
-    fs::write(
-        dest_path,
-        format!(
-            "#[allow(clippy::all, clippy::pedantic, clippy::nursery)]\n/// The data for all the elements (atomic_mass/monoisotopic mass, atomic_weight, isotopes: (num, mass, abundance))\npub const ELEMENTAL_DATA: &[(Option<f64>, Option<f64>, &[(u16, f64, f64)])] = &[
-                {}
-                ];",
-            combined_data.fold(String::new(), |acc, element| format!(
-                "{}\n({:?}, {:?}, &[{}]),",
-                acc,
-                element.0,
-                element.1,
-                element.2.iter().fold(String::new(), |acc, i| format!(
-                    "{}({},{:.1},{:.1}),",
-                    acc, i.0, i.1, i.2
-                ))
-            ))
-        ),
+    let file = std::fs::File::create(dest_path).unwrap();
+    let mut writer = BufWriter::new(file);
+    writeln!(
+        writer,
+        "#[allow(clippy::all, clippy::pedantic, clippy::nursery)]\n/// The data for all the elements (atomic_mass/monoisotopic mass, atomic_weight, isotopes: (num, mass, abundance))\npub const ELEMENTAL_DATA: &[(Option<f64>, Option<f64>, &[(u16, f64, f64)])] = &["
     )
     .unwrap();
+    for element in combined_data {
+        writeln!(
+            writer,
+            "({:?}, {:?}, &[{}]),",
+            element.0,
+            element.1,
+            element.2.iter().fold(String::new(), |acc, i| format!(
+                "{}({},{:.1},{:.1}),",
+                acc, i.0, i.1, i.2
+            ))
+        )
+        .unwrap();
+    }
+    writeln!(writer, "];").unwrap();
 
     Ok(())
 }

diff --git a/src/build/gnome.rs b/src/build/gnome.rs
@@ -1,7 +1,6 @@
-use std::{collections::HashMap, ffi::OsString, io::BufWriter, path::Path};
+use std::{collections::HashMap, ffi::OsString, io::BufWriter, io::Write, path::Path};
 
 use crate::{build::csv::parse_csv, glycan::GlycanStructure};
-use std::io::Write;
 
 use super::obo::OboOntology;
 

diff --git a/src/build/psi_mod.rs b/src/build/psi_mod.rs
@@ -1,4 +1,4 @@
-use std::{ffi::OsString, fs, path::Path};
+use std::{ffi::OsString, io::BufWriter, io::Write, path::Path};
 
 use crate::{formula::MolecularFormula, ELEMENT_PARSE_LIST};
 
@@ -9,18 +9,19 @@ use super::{
 
 pub fn build_psi_mod_ontology(out_dir: &OsString, debug: bool) {
     let mods = parse_psi_mod(debug);
+
     let dest_path = Path::new(&out_dir).join("psi-mod.rs");
-    fs::write(
-        dest_path,
-        format!(
-            "pub const PSI_MOD_ONTOLOGY: &[(usize, &str, Modification)] = &[
-                {}
-                ];",
-            mods.iter()
-                .fold(String::new(), |acc, m| format!("{}\n{},", acc, m.to_code()))
-        ),
+    let file = std::fs::File::create(dest_path).unwrap();
+    let mut writer = BufWriter::new(file);
+    writeln!(
+        writer,
+        "pub const PSI_MOD_ONTOLOGY: &[(usize, &str, Modification)] = &["
     )
     .unwrap();
+    for m in mods {
+        writeln!(writer, "{},", m.to_code()).unwrap();
+    }
+    writeln!(writer, "];").unwrap();
 }
 
 fn parse_psi_mod(_debug: bool) -> Vec<OntologyModification> {

diff --git a/src/build/unimod.rs b/src/build/unimod.rs
@@ -1,4 +1,4 @@
-use std::{ffi::OsString, fs, iter, path::Path};
+use std::{ffi::OsString, io::BufWriter, io::Write, iter, path::Path};
 
 use regex::Regex;
 
@@ -11,18 +11,19 @@ use super::{
 
 pub fn build_unimod_ontology(out_dir: &OsString, debug: bool) {
     let mods = parse_unimod(debug);
+
     let dest_path = Path::new(&out_dir).join("unimod.rs");
-    fs::write(
-        dest_path,
-        format!(
-            "pub const UNIMOD_ONTOLOGY: &[(usize, &str, Modification)] = &[
-                {}
-                ];",
-            mods.iter()
-                .fold(String::new(), |acc, m| format!("{}\n{},", acc, m.to_code()))
-        ),
+    let file = std::fs::File::create(dest_path).unwrap();
+    let mut writer = BufWriter::new(file);
+    writeln!(
+        writer,
+        "pub const UNIMOD_ONTOLOGY: &[(usize, &str, Modification)] = &["
     )
     .unwrap();
+    for m in mods {
+        writeln!(writer, "{},", m.to_code()).unwrap();
+    }
+    writeln!(writer, "];").unwrap();
 }
 
 fn parse_unimod(_debug: bool) -> Vec<OntologyModification> {

diff --git a/src/modification.rs b/src/modification.rs
@@ -221,20 +221,20 @@ fn parse_single_modification(
                             .with_long_description("The supplied PSI-MOD accession number is not an existing modification"))
                 }
                 ("u", tail) => find_name_in_ontology(tail, UNIMOD_ONTOLOGY)
-                    .map_err(|_| numerical_mod(tail))
+                    .map_err(|()| numerical_mod(tail))
                     .flat_err()
                     .map(Some)
                     .map_err(|_| basic_error
                         .with_long_description("This modification cannot be read as a Unimod name or numerical modification")),
                 ("m", tail) => find_name_in_ontology(tail, PSI_MOD_ONTOLOGY)
-                    .map_err(|_| numerical_mod(tail))
+                    .map_err(|()| numerical_mod(tail))
                     .flat_err()
                     .map(Some)
                     .map_err(|_| basic_error
                         .with_long_description("This modification cannot be read as a PSI-MOD name or numerical modification")),
                 ("gno", tail) => find_name_in_ontology(tail, GNOME_ONTOLOGY)
                     .map(Some)
-                    .map_err(|_| basic_error
+                    .map_err(|()| basic_error
                         .with_long_description("This modification cannot be read as a GNO name")),
                 ("formula", tail) => Ok(Some(Modification::Formula(
                     parse_molecular_formula_pro_forma(tail).map_err(|e| basic_error
@@ -251,10 +251,10 @@ fn parse_single_modification(
                 ("obs", tail) => numerical_mod(tail).map(Some).map_err(|_| basic_error
                     .with_long_description("This modification cannot be read as a numerical modification")),
                 (_, _tail) => find_name_in_ontology(full.0, UNIMOD_ONTOLOGY)
-                    .map_err(|_| find_name_in_ontology(full.0, PSI_MOD_ONTOLOGY))
+                    .map_err(|()| find_name_in_ontology(full.0, PSI_MOD_ONTOLOGY))
                     .flat_err()
                     .map(Some)
-                    .map_err(|_|
+                    .map_err(|()|
                         CustomError::error(
                             "Invalid modification",
                             "Rustyms does not support these types of modification (yet)",
@@ -265,9 +265,9 @@ fn parse_single_modification(
             Ok(None)
         } else {
             find_name_in_ontology(full.0, UNIMOD_ONTOLOGY)
-                .map_err(|_| find_name_in_ontology(full.0, PSI_MOD_ONTOLOGY))
+                .map_err(|()| find_name_in_ontology(full.0, PSI_MOD_ONTOLOGY))
                 .flat_err()
-                .map_err(|_| numerical_mod(full.0))
+                .map_err(|()| numerical_mod(full.0))
                 .flat_err()
                 .map(Some)
                 .map_err(|_|