Use numbers.Real in place of float in fields where openMINDS specifie…

…s type "number" (fixes #60)
HumanBrainProject · Nov 19, 2024 · 3e6c8b6 · 3e6c8b6
1 parent 8158639
commit 3e6c8b6
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Showing 7 changed files with 22 additions and 12 deletions.
diff --git a/builder/update_openminds.py b/builder/update_openminds.py
@@ -557,6 +557,7 @@ def get_controlled_terms_table(type_):
 preamble = {
     "File": """import os
 import mimetypes
+from numbers import Real
 from pathlib import Path
 from urllib.request import urlretrieve
 from urllib.parse import quote, urlparse, urlunparse
@@ -612,7 +613,7 @@ def get_type(prop):
             type_map = {
                 "string": "str",
                 "integer": "int",
-                "number": "float",
+                "number": "Real",
                 "date": "date",
                 "date-time": "datetime",
                 "time": "time",

diff --git a/fairgraph/openminds/computation/model_validation.py b/fairgraph/openminds/computation/model_validation.py
@@ -9,6 +9,7 @@
 
 
 from datetime import datetime, time
+from numbers import Real
 
 
 class ModelValidation(KGObject):
@@ -94,7 +95,7 @@ class ModelValidation(KGObject):
             multiple=True,
             doc="no description available",
         ),
-        Property("score", float, "vocab:score", doc="no description available"),
+        Property("score", Real, "vocab:score", doc="no description available"),
         Property("start_time", [datetime, time], "vocab:startTime", required=True, doc="no description available"),
         Property(
             "started_by",

diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value.py b/fairgraph/openminds/core/miscellaneous/quantitative_value.py
@@ -7,6 +7,8 @@
 from fairgraph import EmbeddedMetadata, IRI
 from fairgraph.properties import Property
 
+from numbers import Real
+
 
 class QuantitativeValue(EmbeddedMetadata):
     """
@@ -30,7 +32,7 @@ class QuantitativeValue(EmbeddedMetadata):
         ),
         Property(
             "uncertainties",
-            float,
+            Real,
             "vocab:uncertainty",
             multiple=True,
             doc="Quantitative value range defining the uncertainty of a measurement.",
@@ -41,7 +43,7 @@ class QuantitativeValue(EmbeddedMetadata):
             "vocab:unit",
             doc="Determinate quantity adopted as a standard of measurement.",
         ),
-        Property("value", float, "vocab:value", required=True, doc="Entry for a property."),
+        Property("value", Real, "vocab:value", required=True, doc="Entry for a property."),
     ]
     reverse_properties = []
 

diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py b/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py
@@ -7,6 +7,8 @@
 from fairgraph import KGObject, IRI
 from fairgraph.properties import Property
 
+from numbers import Real
+
 
 class QuantitativeValueArray(KGObject):
     """
@@ -25,14 +27,14 @@ class QuantitativeValueArray(KGObject):
     properties = [
         Property(
             "negative_uncertainties",
-            float,
+            Real,
             "vocab:negativeUncertainties",
             multiple=True,
             doc="no description available",
         ),
         Property(
             "positive_uncertainties",
-            float,
+            Real,
             "vocab:positiveUncertainties",
             multiple=True,
             doc="no description available",
@@ -49,7 +51,7 @@ class QuantitativeValueArray(KGObject):
             "vocab:unit",
             doc="Determinate quantity adopted as a standard of measurement.",
         ),
-        Property("values", float, "vocab:values", multiple=True, required=True, doc="no description available"),
+        Property("values", Real, "vocab:values", multiple=True, required=True, doc="no description available"),
     ]
     reverse_properties = []
     existence_query_properties = ("values",)

diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py b/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py
@@ -7,6 +7,8 @@
 from fairgraph import EmbeddedMetadata, IRI
 from fairgraph.properties import Property
 
+from numbers import Real
+
 
 class QuantitativeValueRange(EmbeddedMetadata):
     """
@@ -22,14 +24,14 @@ class QuantitativeValueRange(EmbeddedMetadata):
         "core": "https://openminds.ebrains.eu/core/",
     }
     properties = [
-        Property("max_value", float, "vocab:maxValue", required=True, doc="Greatest quantity attained or allowed."),
+        Property("max_value", Real, "vocab:maxValue", required=True, doc="Greatest quantity attained or allowed."),
         Property(
             "max_value_unit",
             "openminds.controlled_terms.UnitOfMeasurement",
             "vocab:maxValueUnit",
             doc="no description available",
         ),
-        Property("min_value", float, "vocab:minValue", required=True, doc="Smallest quantity attained or allowed."),
+        Property("min_value", Real, "vocab:minValue", required=True, doc="Smallest quantity attained or allowed."),
         Property(
             "min_value_unit",
             "openminds.controlled_terms.UnitOfMeasurement",

diff --git a/fairgraph/properties.py b/fairgraph/properties.py
@@ -18,6 +18,7 @@
 
 from __future__ import annotations
 import logging
+import numbers
 from datetime import date, datetime
 from collections.abc import Iterable, Mapping
 from typing import Any, Dict, List, Optional, Tuple, TYPE_CHECKING, Union
@@ -249,7 +250,7 @@ def serialize(self, value: Any, follow_links: bool = False):
         """
 
         def serialize_single(value):
-            if isinstance(value, (str, int, float, dict)):
+            if isinstance(value, (str, numbers.Real, dict)):
                 return value
             elif isinstance(value, EmbeddedMetadata):
                 return value.to_jsonld(follow_links=follow_links)
@@ -457,7 +458,7 @@ def get_query_filter_property(self, filter: Any) -> QueryProperty:
             filter_obj = None
         else:
             # we have a filter value for this property
-            if self.types[0] in (int, float, bool, datetime, date):
+            if self.types[0] in (int, float, numbers.Real, bool, datetime, date):
                 op = "EQUALS"
             else:
                 op = "CONTAINS"

diff --git a/test/test_base.py b/test/test_base.py
@@ -4,6 +4,7 @@
 """
 
 from datetime import date, datetime
+from numbers import Real
 from fairgraph.embedded import EmbeddedMetadata
 from fairgraph.kgobject import KGObject
 from fairgraph.kgproxy import KGProxy
@@ -37,7 +38,7 @@ class MockEmbeddedObject(EmbeddedMetadata):
         ),
         Property(
             "a_number",
-            float,
+            Real,
             "https://openminds.ebrains.eu/vocab/aNumber",
             multiple=False,
             required=True,