structured_format.pattern-style permissible value creation eg for MIxS (

#785)

* crude MIXS style permissible value illustration

* not comitting expanded schema

* --pv-syntax

* imports order fixed by ruff

* remove experiemtnatil files from root

* test including exec()

* use linkml_runtime.utils.compile_python not exec()

* meaningful test function name

src/oaklib/utilities/subsets/value_set_expander.py

@@ -2,7 +2,7 @@
 from abc import ABC
 from dataclasses import dataclass, field
 from pathlib import Path
-from typing import Iterator, List, Union
+from typing import Iterator, List, Optional, Union
 
 import click
 from linkml_runtime.dumpers import json_dumper
@@ -43,6 +43,7 @@ def expand_value_set(
         value_set: Union[EnumDefinition, AnonymousEnumExpression],
         schema: SchemaDefinition = None,
         source_enum_definition: EnumDefinition = None,
+        pv_syntax: Optional[str] = None,
     ) -> Iterator[PermissibleValue]:
         """
         Expand a value set definition into a list of curies
@@ -71,22 +72,31 @@ def expand_value_set(
                 vset = schema.enums[inherited]
                 pvs.extend(
                     self.expand_value_set(
-                        vset, schema=schema, source_enum_definition=source_enum_definition
+                        vset,
+                        schema=schema,
+                        source_enum_definition=source_enum_definition,
+                        pv_syntax=pv_syntax,
                     )
                 )
         if value_set.include:
             for include in value_set.include:
                 if isinstance(include, AnonymousEnumExpression):
                     pvs.extend(
                         self.expand_value_set(
-                            include, schema=schema, source_enum_definition=source_enum_definition
+                            include,
+                            schema=schema,
+                            source_enum_definition=source_enum_definition,
+                            pv_syntax=pv_syntax,
                         )
                     )
                 else:
                     raise ValueError(f"Unexpected type for include: {type(include)}")
                 pvs.extend(
                     self.expand_value_set(
-                        include, schema=schema, source_enum_definition=source_enum_definition
+                        include,
+                        schema=schema,
+                        source_enum_definition=source_enum_definition,
+                        pv_syntax=pv_syntax,
                     )
                 )
         if value_set.concepts:
@@ -136,7 +146,11 @@ def expand_value_set(
                             rq.source_nodes, predicates=predicates, reflexive=rq.include_self
                         )
                 for curie in results:
-                    pvs.append(self._generate_permissible_value(curie, oi, source_enum_definition))
+                    pvs.append(
+                        self._generate_permissible_value(
+                            curie, oi, source_enum_definition, pv_syntax=pv_syntax
+                        )
+                    )
             else:
                 raise NotImplementedError(f"Must be an OboGraphInterface: {type(oi)}")
         if value_set.minus:
@@ -145,7 +159,10 @@ def expand_value_set(
                     minus_vs, AnonymousEnumExpression
                 ):
                     for pv in self.expand_value_set(
-                        minus_vs, schema=schema, source_enum_definition=source_enum_definition
+                        minus_vs,
+                        schema=schema,
+                        source_enum_definition=source_enum_definition,
+                        pv_syntax=pv_syntax,
                     ):
                         if pv in pvs:
                             pvs.remove(pv)
@@ -181,14 +198,17 @@ def _generate_permissible_value(
         curie: CURIE,
         oi: BasicOntologyInterface,
         enum_definition: EnumDefinition = None,
+        pv_syntax: Optional[str] = None,
     ) -> PermissibleValue:
         definition = oi.definition(curie)
         # \n can break some downstream tooling like LinkML's gen-pydantic (v1.6.6)
         if definition is not None:
             definition = definition.replace("\n", " ")
         label = oi.label(curie)
         pv_formula = enum_definition.pv_formula if enum_definition else None
-        if str(pv_formula) == "CURIE":
+        if pv_syntax is not None:
+            text = pv_syntax.format(id=curie, label=label, definition=definition)
+        elif str(pv_formula) == "CURIE":
             text = curie
         elif str(pv_formula) == "LABEL":
             # not all ontologies will have text for every element
@@ -209,6 +229,7 @@ def expand_in_place(
         schema_path: Union[str, Path],
         value_set_names: List[str] = None,
         output_path: Union[str, Path] = None,
+        pv_syntax: Optional[str] = None,
     ) -> SchemaDefinition:
         """
         Expand value sets in place
@@ -231,7 +252,7 @@ def expand_in_place(
             if value_set_name not in schema.enums:
                 raise ValueError(f"Unknown value set: {value_set_name}")
             value_set = schema.enums[value_set_name]
-            pvs = list(self.expand_value_set(value_set, schema=schema))
+            pvs = list(self.expand_value_set(value_set, schema=schema, pv_syntax=pv_syntax))
             yaml_obj["enums"][value_set_name]["permissible_values"] = {
                 str(pv.text): json_dumper.to_dict(pv) for pv in pvs
             }
@@ -259,8 +280,11 @@ def main(verbose: int, quiet: bool):
 @click.option("-c", "--config", type=click.Path(exists=True))
 @click.option("-s", "--schema", type=click.Path(exists=True))
 @click.option("-o", "--output", type=click.Path())
+@click.option("--pv-syntax", help="Enter a LinkML structured_pattern.syntax-style string ")
+# # add a boolean click option with --mixs-style and (default) --no-mixs-style options
+# @click.option("-m", "--mixs-style", is_flag=True, default=False)
 @click.argument("value_set_names", nargs=-1)
-def expand(config: str, schema: str, value_set_names: List[str], output: str):
+def expand(config: str, schema: str, value_set_names: List[str], output: str, pv_syntax: str):
     """
     Expand a value set. EXPERIMENTAL.
 
@@ -281,17 +305,19 @@ def expand(config: str, schema: str, value_set_names: List[str], output: str):
     such as BioPortal or Wikidata. However, note that not all backends are capable of being able to
     render all value sets.
 
-    Example:
+    Examples:
     -------
         vskit expand -c config.yaml -s schema.yaml -o expanded.yaml my_value_set1 my_value_set2
 
+        vskit expand -s schema.yaml -o expanded.yaml --pv-syntax '{label} [{id}] my_value_set1
+
     """
     value_set_names = None if not value_set_names else value_set_names
     expander = ValueSetExpander()
     if config:
         expander.configuration = yaml_loader.load(config, target_class=ValueSetConfiguration)
     expander.expand_in_place(
-        schema_path=schema, value_set_names=value_set_names, output_path=output
+        schema_path=schema, value_set_names=value_set_names, output_path=output, pv_syntax=pv_syntax
     )
 
 

tests/test_pv_syntax_expander.py

@@ -0,0 +1,96 @@
+import contextlib
+import tempfile
+
+from linkml.generators import PythonGenerator
+from linkml_runtime import SchemaView
+from linkml_runtime.dumpers import yaml_dumper
+from linkml_runtime.loaders import yaml_loader
+from linkml_runtime.utils.compile_python import compile_python
+
+from src.oaklib.utilities.subsets.value_set_expander import ValueSetExpander
+
+SCHEMA_STRING = """
+name: label_id_schema
+id: http://example.com/label_id_schema
+imports:
+  - linkml:types
+prefixes:
+  label_id_schema: http://example.com/label_id_schema/
+  linkml: https://w3id.org/linkml/
+  ENVO: http://purl.obolibrary.org/obo/ENVO_
+default_prefix: label_id_schema
+enums:
+  TerrestrialBiomeEnum:
+    minus:
+      - reachable_from:
+          source_ontology: obo:envo
+          source_nodes:
+            - ENVO:00002030
+          relationship_types:
+            - rdfs:subClassOf
+          is_direct: false
+    reachable_from:
+      source_ontology: obo:envo
+      source_nodes:
+        - ENVO:00000428
+      relationship_types:
+        - rdfs:subClassOf
+      is_direct: false
+slots:
+  name:
+    range: string
+  id:
+    range: string
+    required: true
+  biome:
+    range: TerrestrialBiomeEnum
+classes:
+  NamedThing:
+    slots:
+      - name
+      - id
+  Sample:
+    is_a: NamedThing
+    slots:
+      - biome
+"""
+
+DATA_STRING = """
+name: Sample-1
+id: sample_1
+biome: tundra biome [ENVO:01000180]
+"""
+
+
+def test_pv_syntax_expander():
+    view = SchemaView(SCHEMA_STRING)
+
+    with contextlib.ExitStack() as stack:
+        temp_dynamic = stack.enter_context(tempfile.NamedTemporaryFile(mode="w+t", delete=False))
+        temp_expanded = stack.enter_context(tempfile.NamedTemporaryFile(mode="w+t", delete=False))
+
+        yaml_dumper.dump(view.schema, temp_dynamic.name)
+
+        expander = ValueSetExpander()
+
+        expander.expand_in_place(
+            schema_path=temp_dynamic.name,
+            pv_syntax="{label} [{id}]",
+            output_path=temp_expanded.name,
+        )
+
+        expanded_view = SchemaView(temp_expanded.name)
+
+        generator = PythonGenerator(expanded_view.schema)
+
+        python_code = generator.serialize()
+
+        module_name = "test_module"
+
+        module = compile_python(python_code, module_name)
+
+        Sample = module.Sample
+
+        sample_1 = yaml_loader.loads(source=DATA_STRING, target_class=Sample)
+
+        assert sample_1 is not None