API Improvements (#8)

* Lazy load converter from Bioregistry

Depends on biopragmatics/bioregistry#652, helps with #7

* Add function for guessing the version of a parse results

* Use robot merge

* Add function for loading local obo graph json

* Better access to properties

* Inline upgrading

Related to #7

* Update data.tsv

* Update setup.cfg

* Flake

setup.cfg

@@ -54,7 +54,7 @@ keywords =
 
 [options]
 install_requires =
-    bioregistry>=0.5.86
+    bioregistry>=0.6.13
     curies>=0.3.0
     requests
     pydantic

src/bioontologies/__init__.py

@@ -2,10 +2,16 @@
 
 """Tools for biomedical ontologies."""
 
-from .robot import convert_to_obograph, get_obograph_by_iri, get_obograph_by_prefix
+from .robot import (
+    convert_to_obograph,
+    get_obograph_by_iri,
+    get_obograph_by_path,
+    get_obograph_by_prefix,
+)
 
 __all__ = [
     "convert_to_obograph",
     "get_obograph_by_prefix",
     "get_obograph_by_iri",
+    "get_obograph_by_path",
 ]

src/bioontologies/obograph.py

@@ -9,13 +9,11 @@
 from operator import attrgetter
 from typing import Any, Iterable, List, Mapping, Optional, Set, Tuple, Union
 
-from bioregistry import curie_to_str, manager
-from curies import Converter
+from bioregistry import curie_to_str, get_default_converter, manager
 from pydantic import BaseModel, Field
 from tqdm.auto import tqdm
 from typing_extensions import Literal
 
-from . import upgrade
 from .relations import ground_relation
 
 __all__ = [
@@ -40,8 +38,6 @@
 
 MaybeCURIE = Union[Tuple[str, str], Tuple[None, None]]
 
-converter = Converter.from_reverse_prefix_map(manager.get_reverse_prefix_map(include_prefixes=True))
-
 
 class StandardizeMixin:
     """A mixin for classes representing standardizable data."""
@@ -85,6 +81,7 @@ def val_curie(self) -> str:
 
     def standardize(self):
         """Standardize this property."""
+        self.val = self.val.replace("\n", " ")
         self.pred_prefix, self.pred_identifier = _parse_uri_or_curie_or_str(self.pred)
         self.val_prefix, self.val_identifier = _parse_uri_or_curie_or_str(self.val)
         self.standardized = True
@@ -273,6 +270,14 @@ def xrefs(self) -> List[Xref]:
             return self.meta.xrefs
         return []
 
+    @property
+    def properties(self) -> List[Property]:
+        """Get the properties for this node."""
+        if not self.meta or self.meta.basicPropertyValues is None:
+            return []
+        # TODO filter out ones grabbed by other getters
+        return self.meta.basicPropertyValues
+
     @property
     def replaced_by(self) -> Optional[str]:
         """Get the identifier that this node was replaced by."""
@@ -565,13 +570,15 @@ def _parse_obo_rel(s: str, identifier: str) -> Union[Tuple[str, str], Tuple[None
 def _compress_uri_or_curie_or_str(
     s: str, *, debug: bool = False
 ) -> Union[Tuple[str, str], Tuple[None, str]]:
+    from .upgrade import insert, upgrade
+
     s = s.replace(" ", "")
 
-    cv = upgrade.upgrade(s)
+    cv = upgrade(s)
     if cv:
         return cv
 
-    prefix, identifier = converter.parse_uri(s)
+    prefix, identifier = get_default_converter().parse_uri(s)
     if prefix and identifier:
         if prefix == "obo" and "#" in identifier:
             return _parse_obo_rel(s, identifier)
@@ -587,7 +594,7 @@ def _compress_uri_or_curie_or_str(
         if s.startswith(x):
             prefix, identifier = ground_relation(s[len(x) :])
             if prefix and identifier:
-                upgrade.insert(s, prefix, identifier)
+                insert(s, prefix, identifier)
                 return prefix, identifier
             elif s not in WARNED:
                 tqdm.write(f"could not parse legacy RO: {s}")

src/bioontologies/robot.py

@@ -35,6 +35,7 @@
     # Processors
     "get_obograph_by_prefix",
     "get_obograph_by_iri",
+    "get_obograph_by_path",
 ]
 
 logger = logging.getLogger(__name__)
@@ -92,6 +93,15 @@ def guess(self, prefix: str) -> Graph:
             return id_to_graph[CANONICAL[prefix]]
         raise ValueError(f"Several graphs in {prefix}: {sorted(id_to_graph)}")
 
+    def guess_version(self, prefix: str) -> Optional[str]:
+        """Guess the version."""
+        try:
+            graph = self.guess(prefix)
+        except ValueError:
+            return None
+        else:
+            return graph.version or graph.version_iri
+
 
 def get_obograph_by_iri(
     iri: str,
@@ -102,6 +112,16 @@ def get_obograph_by_iri(
     return ParseResults(graph_document=graph_document, iri=iri)
 
 
+def get_obograph_by_path(path: Union[str, Path], *, iri: Optional[str] = None) -> ParseResults:
+    """Get an ontology by its OBO Graph JSON file path."""
+    res_json = json.loads(Path(path).resolve().read_text())
+    graph_document = GraphDocument(**res_json)
+    if iri is None:
+        if graph_document.graphs and len(graph_document.graphs) == 1:
+            iri = graph_document.graphs[0].id
+    return ParseResults(graph_document=graph_document, iri=iri)
+
+
 def get_obograph_by_prefix(
     prefix: str,
     *,
@@ -205,6 +225,7 @@ def convert_to_obograph(
     input_is_iri: bool = False,
     extra_args: Optional[List[str]] = None,
     from_iri: Optional[str] = None,
+    merge: bool = True,
 ) -> ParseResults:
     """Convert a local OWL file to a JSON file.
 
@@ -223,6 +244,7 @@ def convert_to_obograph(
     :param extra_args:
         Extra positional arguments to pass in the command line
     :param from_iri: Use this parameter to say what IRI the graph came from
+    :param merge: Use ROBOT's merge command to squash all graphs together
 
     :returns: An object with the parsed OBO Graph JSON and text
         output from the ROBOT conversion program
@@ -243,6 +265,7 @@ def convert_to_obograph(
             output_path=path,
             fmt="json",
             extra_args=extra_args,
+            merge=merge,
         )
         messages = ret.strip().splitlines()
         graph_document_raw = json.loads(path.read_text())
@@ -301,21 +324,31 @@ def convert(
     output_path: Union[str, Path],
     input_flag: Optional[Literal["-i", "-I"]] = None,
     *,
+    merge: bool = True,
     fmt: Optional[str] = None,
     extra_args: Optional[List[str]] = None,
 ) -> str:
     """Convert an OBO file to an OWL file with ROBOT."""
     if input_flag is None:
         input_flag = "-I" if _is_remote(input_path) else "-i"
-    args = [
-        "robot",
-        "convert",
-        input_flag,
-        str(input_path),
-        "-o",
-        str(output_path),
-        *(extra_args or []),
-    ]
+    if merge:
+        args = [
+            "robot",
+            "merge",
+            input_flag,
+            str(input_path),
+            "convert",
+        ]
+    else:
+        args = [
+            "robot",
+            "convert",
+            input_flag,
+            str(input_path),
+        ]
+    args.extend(("-o", str(output_path)))
+    if extra_args:
+        args.extend(extra_args)
     if fmt:
         args.extend(("--format", fmt))
     logger.debug("Running shell command: %s", args)

src/bioontologies/upgrade/data.tsv

@@ -60,6 +60,7 @@ http://purl.obolibrary.org/obo/nbo#has_participant	ro	0000057
 http://purl.obolibrary.org/obo/ncbitaxon#has_rank	debio	0000023
 http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim#has_rank	debio	0000023
 http://purl.obolibrary.org/obo/obo#_PATO_0000047	pato	0000047
+http://purl.obolibrary.org/obo/pato#seeAlso	rdf	seeAlso
 http://purl.obolibrary.org/obo/so#has_origin	debio	0000025
 http://purl.obolibrary.org/obo/uberon/core#conduit_for	ro	0002570
 http://purl.obolibrary.org/obo/uberon/core#existence_starts_and_ends_during	ro	0002491