Merge remote-tracking branch 'origin/main'

# Conflicts: # Cargo.toml
ontology-tools · Sep 30, 2024 · 2688885 · 2688885
2 parents 2172c8a + 7c85ad6
commit 2688885
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Showing 21 changed files with 366 additions and 21 deletions.
diff --git a/gen_pyi.py b/gen_pyi.py
@@ -1,4 +1,5 @@
 import glob
+import inspect
 import os
 import re
 import typing
@@ -24,7 +25,8 @@
     f.write(", ".join([f'"{n}"' for n in pyhornedowl_members]))
     f.write("]\n")
 
-implemented_magic = [f"__{x}__" for x in ["invert", "and", "or", "invert"]]
+implemented_magic = [f"__{x}__" for x in
+                     ["invert", "and", "or", "invert", "iter", "getitem", "setitem", "contains", "len", "delitem"]]
 
 with open("pyhornedowl/__init__.pyi", "w") as f:
     f.write("import typing\n")
@@ -67,7 +69,10 @@
                         for line in doc.splitlines():
                             f.write(f"    {line}\n")
                         f.write("    \"\"\"\n")
-                elif hasattr(member, "__doc__"):
+
+                    continue
+
+                if hasattr(member, "__doc__"):
                     doc = member.__doc__
                     if doc is not None:
                         lines = doc.splitlines()
@@ -87,6 +92,13 @@
                                 f.write(f"    {sign}\n")
                                 doc = "\n".join([f"    {l}" for l in lines[annotations_end+2:]])
                                 f.write(f'    """\n{doc}\n    """\n\n')
+
+                            continue
+
+                if callable(member):
+                    f.write(f"    def {member_name}{inspect.signature(member)}:\n        ...\n\n")
+
+                    continue
 
 
             f.write("\n")

diff --git a/pyhornedowl/__init__.pyi b/pyhornedowl/__init__.pyi
@@ -4,6 +4,7 @@ from typing_extensions import deprecated
 
 import model
 
+
 class PyIndexedOntology:
     """
     Represents a loaded ontology.
@@ -305,6 +306,24 @@ class IndexCreationStrategy:
     """
 
 class PrefixMapping:
+    def __iter__(self, /):
+        ...
+
+    def __len__(self, /):
+        ...
+
+    def __getitem__(self, key, /):
+        ...
+
+    def __setitem__(self, key, value, /):
+        ...
+
+    def __delitem__(self, key, /):
+        ...
+
+    def __contains__(self, key, /):
+        ...
+
     def add_default_prefix_names(self) -> None:
         """
         Adds the prefix for rdf, rdfs, xsd, and owl
@@ -329,7 +348,7 @@ class PrefixMapping:
         """
         ...
 
-    def shring_iri(self, iri: str) -> str:
+    def shrink_iri(self, iri: str) -> str:
         """
         Shrinks an absolute IRI to a CURIE. Throws a ValueError on failure
         """

diff --git a/src/prefix_mapping.rs b/src/prefix_mapping.rs
@@ -26,8 +26,35 @@ impl From<PrefixMapping> for curie::PrefixMapping {
     }
 }
 
+#[pyclass]
+struct Iter {
+    inner: std::vec::IntoIter<(String, String)>
+}
+
+#[pymethods]
+impl Iter {
+    fn __iter__(slf: PyRef<'_, Self>) -> PyRef<'_, Self> {
+        slf
+    }
+
+    fn __next__(mut slf: PyRefMut<'_, Self>) -> Option<(String, String)> {
+        slf.inner.next()
+    }
+}
+
 #[pymethods]
 impl PrefixMapping {
+
+    /// __iter__(self) -> typing.Iterable[typing.Tuple[str, str]]
+    ///
+    /// Get an iterator over all prefixes
+    fn __iter__(slf: PyRef<'_, Self>) -> PyResult<Py<Iter>> {
+        let iter = Iter {
+            inner: slf.0.mappings().map(|(x,y)| ((x.clone(), y.clone()))).collect::<Vec<(String, String)>>().into_iter(),
+        };
+        Py::new(slf.py(), iter)
+    }
+
     pub fn __getitem__(&self, key: &str) -> PyResult<String> {
         self.0
             .expand_curie(&curie::Curie::new(Some(key), ""))
@@ -102,7 +129,7 @@ impl PrefixMapping {
             .map_err(to_py_err!("Invalid or unknown prefix"))
     }
 
-    /// shring_iri(self, iri: str) -> str
+    /// shrink_iri(self, iri: str) -> str
     ///
     /// Shrinks an absolute IRI to a CURIE. Throws a ValueError on failure
     pub fn shrink_iri(&self, iri: &str) -> PyResult<String> {

diff --git a/test/resources/gen.sh b/test/resources/gen.sh
@@ -2,11 +2,25 @@
 
 SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
 
+FILES=("simple" "prefix")
+
+EMPTY_PREFIX="https://example.com/"
+
+for f in "${FILES[@]}"; do
+  robot convert -i "$SCRIPT_DIR/$f.omn" -o "$SCRIPT_DIR/$f.ofn"
+  sed -i "1iPrefix(:=<$EMPTY_PREFIX>)" "$SCRIPT_DIR/$f.ofn"
+
+  robot convert -i "$SCRIPT_DIR/$f.omn" -o "$SCRIPT_DIR/$f.owx"
+  sed -i "10i    <Prefix name=\"\" IRI=\"$EMPTY_PREFIX\"/>" "$SCRIPT_DIR/$f.owx"
+
+  robot convert -i "$SCRIPT_DIR/$f.omn" -o "$SCRIPT_DIR/$f.owl"
+  # no empty prefix in rdf/xml?
+
+  ln -f "$SCRIPT_DIR/$f.omn" "$SCRIPT_DIR/$f.omn.raw"
+  ln -f "$SCRIPT_DIR/$f.ofn" "$SCRIPT_DIR/$f.ofn.raw"
+  ln -f "$SCRIPT_DIR/$f.owx" "$SCRIPT_DIR/$f.owx.raw"
+  ln -f "$SCRIPT_DIR/$f.owl" "$SCRIPT_DIR/$f.owl.raw"
+done
+
+
 
-robot convert -i "$SCRIPT_DIR/simple.omn" -o "$SCRIPT_DIR/simple.ofn"
-robot convert -i "$SCRIPT_DIR/simple.omn" -o "$SCRIPT_DIR/simple.owx"
-robot convert -i "$SCRIPT_DIR/simple.omn" -o "$SCRIPT_DIR/simple.owl"
-ln -f "$SCRIPT_DIR/simple.omn" "$SCRIPT_DIR/simple.omn.raw"
-ln -f "$SCRIPT_DIR/simple.ofn" "$SCRIPT_DIR/simple.ofn.raw"
-ln -f "$SCRIPT_DIR/simple.owx" "$SCRIPT_DIR/simple.owx.raw"
-ln -f "$SCRIPT_DIR/simple.owl" "$SCRIPT_DIR/simple.owl.raw"
diff --git a/test/resources/prefix.ofn b/test/resources/prefix.ofn
@@ -0,0 +1,18 @@
+Prefix(:=<https://example.com/>)
+Prefix(ex1:=<https://example.com/1>)
+Prefix(ex2:=<https://example.com/2>)
+Prefix(ex3:=<https://example.com/3>)
+Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
+Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+
+
+Ontology(
+Declaration(Class(<https://example.com/A>))
+Declaration(Class(ex1:A))
+Declaration(Class(ex2:A))
+Declaration(Class(ex3:A))
+
+)
diff --git a/test/resources/prefix.ofn.raw b/test/resources/prefix.ofn.raw
@@ -0,0 +1,18 @@
+Prefix(:=<https://example.com/>)
+Prefix(ex1:=<https://example.com/1>)
+Prefix(ex2:=<https://example.com/2>)
+Prefix(ex3:=<https://example.com/3>)
+Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
+Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+
+
+Ontology(
+Declaration(Class(<https://example.com/A>))
+Declaration(Class(ex1:A))
+Declaration(Class(ex2:A))
+Declaration(Class(ex3:A))
+
+)
diff --git a/test/resources/prefix.omn b/test/resources/prefix.omn
@@ -0,0 +1,10 @@
+Prefix: : <https://example.com/>
+Prefix: ex1: <https://example.com/1>
+Prefix: ex2: <https://example.com/2>
+Prefix: ex3: <https://example.com/3>
+Ontology:
+    Class: ex1:A
+    Class: ex2:A
+    Class: ex3:A
+    Class: A
+
diff --git a/test/resources/prefix.omn.raw b/test/resources/prefix.omn.raw
@@ -0,0 +1,10 @@
+Prefix: : <https://example.com/>
+Prefix: ex1: <https://example.com/1>
+Prefix: ex2: <https://example.com/2>
+Prefix: ex3: <https://example.com/3>
+Ontology:
+    Class: ex1:A
+    Class: ex2:A
+    Class: ex3:A
+    Class: A
+
diff --git a/test/resources/prefix.owl b/test/resources/prefix.owl
@@ -0,0 +1,53 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://www.w3.org/2002/07/owl#"
+     xml:base="http://www.w3.org/2002/07/owl"
+     xmlns:ex1="https://example.com/1"
+     xmlns:ex2="https://example.com/2"
+     xmlns:ex3="https://example.com/3"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+    <Ontology/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- https://example.com/A -->
+
+    <Class rdf:about="https://example.com/A"/>
+
+
+
+    <!-- https://example.com/1A -->
+
+    <Class rdf:about="https://example.com/1A"/>
+
+
+
+    <!-- https://example.com/2A -->
+
+    <Class rdf:about="https://example.com/2A"/>
+
+
+
+    <!-- https://example.com/3A -->
+
+    <Class rdf:about="https://example.com/3A"/>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->
+
diff --git a/test/resources/prefix.owl.raw b/test/resources/prefix.owl.raw
@@ -0,0 +1,53 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://www.w3.org/2002/07/owl#"
+     xml:base="http://www.w3.org/2002/07/owl"
+     xmlns:ex1="https://example.com/1"
+     xmlns:ex2="https://example.com/2"
+     xmlns:ex3="https://example.com/3"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+    <Ontology/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- https://example.com/A -->
+
+    <Class rdf:about="https://example.com/A"/>
+
+
+
+    <!-- https://example.com/1A -->
+
+    <Class rdf:about="https://example.com/1A"/>
+
+
+
+    <!-- https://example.com/2A -->
+
+    <Class rdf:about="https://example.com/2A"/>
+
+
+
+    <!-- https://example.com/3A -->
+
+    <Class rdf:about="https://example.com/3A"/>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->
+
diff --git a/test/resources/prefix.owx b/test/resources/prefix.owx
@@ -0,0 +1,34 @@
+<?xml version="1.0"?>
+<Ontology xmlns="http://www.w3.org/2002/07/owl#"
+     xml:base="http://www.w3.org/2002/07/owl#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+    <Prefix name="ex1" IRI="https://example.com/1"/>
+    <Prefix name="ex2" IRI="https://example.com/2"/>
+<Prefix name="" IRI="https://example.com/"/>
+    <Prefix name="ex3" IRI="https://example.com/3"/>
+    <Prefix name="owl" IRI="http://www.w3.org/2002/07/owl#"/>
+    <Prefix name="rdf" IRI="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/>
+    <Prefix name="xml" IRI="http://www.w3.org/XML/1998/namespace"/>
+    <Prefix name="xsd" IRI="http://www.w3.org/2001/XMLSchema#"/>
+    <Prefix name="rdfs" IRI="http://www.w3.org/2000/01/rdf-schema#"/>
+    <Declaration>
+        <Class IRI="https://example.com/A"/>
+    </Declaration>
+    <Declaration>
+        <Class abbreviatedIRI="ex1:A"/>
+    </Declaration>
+    <Declaration>
+        <Class abbreviatedIRI="ex2:A"/>
+    </Declaration>
+    <Declaration>
+        <Class abbreviatedIRI="ex3:A"/>
+    </Declaration>
+</Ontology>
+
+
+
+<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->
+