Merge pull request #62 from anergictcell/release/0.10.0

Release/0.10.0

CHANGELOG.md

@@ -4,20 +4,28 @@ All notable changes to this project will be documented in this file.
 
 ## Unreleased
 
+## [0.10.0]
+
 ### Feature
 
 - Add Orphante diseases (`OrphaDisease`) to Ontology
 - Filter gene and disease annotations in subontology based on association with phenotypes
 - Add binary version 3
 - Add new example ontology
 
+### Documentation
+
+- Change orders of methods in `Ontology` to clean up the documentation.
+
 ### Refactor
 
+- Improve the OBO parser with better error handling
 - [**breaking**] Add `Disease` trait that is needed to work with `OmimDisease` and `OrphaDisease`
 - Update example ontology
 - Update unit- and doctests to align with updated example ontology
 
-## [0.9.0] - 2024-03-27
+
+## [0.9.1] - 2024-03-30
 
 ### Bugfix
 

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "hpo"
-version = "0.9.1"
+version = "0.10.0"
 edition = "2021"
 authors = ["Jonas Marcello <jonas.marcello@esbme.com>"]
 description = "Human Phenotype Ontology Similarity"
@@ -15,7 +15,6 @@ categories = ["science", "data-structures", "parser-implementations"]
 [dependencies]
 thiserror = "1.0"
 aquamarine = "0" # used in Docs
-statrs = "0.16.0"
 tracing = "0.1"
 smallvec = "1"
 

examples/compare_ontologies.rs

@@ -17,7 +17,7 @@ fn ontology(path_arg: &str) -> Ontology {
     }
 }
 
-fn ontology2(path_arg: &str) -> Ontology {
+fn ontology_transitive(path_arg: &str) -> Ontology {
     let path = Path::new(path_arg);
 
     match path.is_file() {
@@ -226,17 +226,21 @@ fn print_replacement_diff(replacements: Option<(Option<HpoTermId>, Option<HpoTer
 fn main() {
     let mut args = std::env::args();
 
-    if args.len() != 3 {
+    if args.len() < 2 {
         println!("Compare two Ontologies to each other and print the differences\n\n");
-        println!("Usage:\ncompare_ontologies </PATH/TO/ONTOLOGY> </PATH/TO/OTHER-ONTOLOGY>");
+        println!("Usage:\ncompare_ontologies </PATH/TO/ONTOLOGY> [</PATH/TO/OTHER-ONTOLOGY>]");
         println!("e.g.:\ncompare_ontologies tests/ontology.hpo tests/ontology_v2.hpo:\n");
+        println!("Alternatively compare transitive vs non-transitive:\ncompare_ontologies tests/ontology.hpo\n");
         process::exit(1)
     }
     let arg_old = args.nth(1).unwrap();
-    let arg_new = args.next().unwrap();
-
     let lhs = ontology(&arg_old);
-    let rhs = ontology2(&arg_new);
+
+    let rhs = if let Some(arg_new) = args.next() {
+        ontology(&arg_new)
+    } else {
+        ontology_transitive(&arg_old)
+    };
 
     let diffs = lhs.compare(&rhs);
 

src/annotations/gene.rs

@@ -119,11 +119,6 @@ impl Gene {
         &self.name
     }
 
-    /// Connect another [HPO term](`crate::HpoTerm`) to the gene
-    pub fn add_term<I: Into<HpoTermId>>(&mut self, term_id: I) -> bool {
-        self.hpos.insert(term_id)
-    }
-
     /// The set of connected HPO terms
     pub fn hpo_terms(&self) -> &HpoGroup {
         &self.hpos
@@ -193,6 +188,16 @@ impl Gene {
     pub fn to_hpo_set<'a>(&self, ontology: &'a Ontology) -> HpoSet<'a> {
         HpoSet::new(ontology, self.hpos.clone())
     }
+
+    /// Connect another [HPO term](`crate::HpoTerm`) to the gene
+    ///
+    /// # Note
+    ///
+    /// This method does **not** add the [`Gene`] to the [HPO term](`crate::HpoTerm`).
+    /// Clients should not use this method, unless they are creating their own Ontology.
+    pub fn add_term<I: Into<HpoTermId>>(&mut self, term_id: I) -> bool {
+        self.hpos.insert(term_id)
+    }
 }
 
 impl PartialEq for Gene {

src/annotations/omim_disease.rs

@@ -6,8 +6,7 @@ use std::hash::Hash;
 use crate::annotations::disease::DiseaseIterator;
 use crate::annotations::{AnnotationId, Disease};
 use crate::term::HpoGroup;
-use crate::HpoError;
-use crate::HpoTermId;
+use crate::{HpoError, HpoSet, HpoTermId, Ontology};
 
 /// A set of OMIM diseases
 ///
@@ -93,15 +92,83 @@ impl Disease for OmimDisease {
         &self.name
     }
 
-    /// Connect another [HPO term](`crate::HpoTerm`) to the disease
-    fn add_term<I: Into<HpoTermId>>(&mut self, term_id: I) -> bool {
-        self.hpos.insert(term_id)
-    }
-
     /// The set of connected HPO terms
     fn hpo_terms(&self) -> &HpoGroup {
         &self.hpos
     }
+
+    /// Returns a binary representation of the `OmimDisease`
+    ///
+    /// The binary layout is defined as:
+    ///
+    /// | Byte offset | Number of bytes | Description |
+    /// | --- | --- | --- |
+    /// | 0 | 4 | The total length of the binary data blob as big-endian `u32` |
+    /// | 4 | 4 | The `OmimDiseaseId` as big-endian `u32` |
+    /// | 8 | 4 | The length of the `OmimDisease` Name as big-endian `u32` |
+    /// | 12 | n | The `OmimDisease` name as u8 vector |
+    /// | 12 + n | 4 | The number of associated HPO terms as big-endian `u32` |
+    /// | 16 + n | x * 4 | The [`HpoTermId`]s of the associated terms, each encoded as big-endian `u32` |
+    ///
+    /// # Examples
+    ///
+    /// ```
+    /// use hpo::annotations::{Disease, OmimDisease};
+    ///
+    /// let mut disease = OmimDisease::new(123.into(), "FooBar");
+    /// let bytes = disease.as_bytes();
+    ///
+    /// assert_eq!(bytes.len(), 4 + 4 + 4 + 6 + 4);
+    /// assert_eq!(bytes[4..8], [0u8, 0u8, 0u8, 123u8]); // ID of disease => 123
+    /// assert_eq!(bytes[8..12], [0u8, 0u8, 0u8, 6u8]); // Length of Name => 6
+    /// ```
+    fn as_bytes(&self) -> Vec<u8> {
+        fn usize_to_u32(n: usize) -> u32 {
+            n.try_into().expect("unable to convert {n} to u32")
+        }
+        let name = self.name().as_bytes();
+        let name_length = name.len();
+        let size = 4 + 4 + 4 + name_length + 4 + self.hpos.len() * 4;
+
+        let mut res = Vec::new();
+
+        // 4 bytes for total length
+        res.append(&mut usize_to_u32(size).to_be_bytes().to_vec());
+
+        // 4 bytes for OMIM Disease-ID
+        res.append(&mut self.id.to_be_bytes().to_vec());
+
+        // 4 bytes for Length of OMIM Disease Name
+        res.append(&mut usize_to_u32(name_length).to_be_bytes().to_vec());
+
+        // OMIM Disease name (n bytes)
+        for c in name {
+            res.push(*c);
+        }
+
+        // 4 bytes for number of HPO terms
+        res.append(&mut usize_to_u32(self.hpos.len()).to_be_bytes().to_vec());
+
+        // HPO terms
+        res.append(&mut self.hpos.as_bytes());
+
+        res
+    }
+
+    /// Returns an [`HpoSet`] from the `OmimDisease`
+    fn to_hpo_set<'a>(&self, ontology: &'a Ontology) -> HpoSet<'a> {
+        HpoSet::new(ontology, self.hpos.clone())
+    }
+
+    /// Connect another [HPO term](`crate::HpoTerm`) to the disease
+    ///
+    /// # Note
+    ///
+    /// This method does **not** add the [`OmimDisease`] to the [HPO term](`crate::HpoTerm`).
+    /// Clients should not use this method, unless they are creating their own Ontology.
+    fn add_term<I: Into<HpoTermId>>(&mut self, term_id: I) -> bool {
+        self.hpos.insert(term_id)
+    }
 }
 
 impl PartialEq for OmimDisease {

src/lib.rs

@@ -21,6 +21,7 @@ pub mod utils;
 pub use ontology::comparison;
 pub use ontology::Ontology;
 pub use set::HpoSet;
+#[doc(inline)]
 pub use term::{HpoTerm, HpoTermId};
 
 const DEFAULT_NUM_PARENTS: usize = 10;
@@ -59,6 +60,9 @@ pub enum HpoError {
     /// Failed to convert an integer to a float
     #[error("cannot convert int to float")]
     TryFromIntError(#[from] std::num::TryFromIntError),
+    /// Failed to parse a line of input data from the JAX obo
+    #[error("invalid input data: {0}")]
+    InvalidInput(String),
 }
 
 impl From<ParseIntError> for HpoError {