build triggered by submodule version

Author: openMINDS pipeline

openminds/collection.py

@@ -193,7 +193,7 @@ def validate(self, ignore=None):
         """
         all_failures = {}
         for node in self:
-            failures = node.validate()
+            failures = node.validate(ignore=ignore)
             if failures:
                 all_failures[node.id] = failures
         return all_failures

openminds/latest/computation/model_validation.py

@@ -5,6 +5,7 @@
 # this file was auto-generated!
 
 from datetime import datetime, time
+from numbers import Real
 
 from openminds.base import LinkedMetadata
 from openminds.properties import Property
@@ -131,7 +132,7 @@ class ModelValidation(LinkedMetadata):
         ),
         Property(
             "score",
-            float,
+            Real,
             "score",
             description="no description available",
             instructions="Enter the numerical score generated by this model validation.",

openminds/latest/controlled_terms/action_status_type.py

@@ -123,21 +123,21 @@ def by_name(cls, name):
     id="https://openminds.ebrains.eu/instances/actionStatusType/active",
     definition="An in-progress action.",
     name="active",
-    preferred_ontology_identifier="https://schema.org/ActiveActionStatus",
+    preferred_ontology_identifier=IRI("https://schema.org/ActiveActionStatus"),
     synonyms=["active action status", "active action"],
 )
 ActionStatusType.completed = ActionStatusType(
     id="https://openminds.ebrains.eu/instances/actionStatusType/completed",
     definition="An action that has already taken place with a successful outcome.",
     name="completed",
-    preferred_ontology_identifier="https://schema.org/CompletedActionStatus",
+    preferred_ontology_identifier=IRI("https://schema.org/CompletedActionStatus"),
     synonyms=["completed action status", "completed action", "finished successfully"],
 )
 ActionStatusType.failed = ActionStatusType(
     id="https://openminds.ebrains.eu/instances/actionStatusType/failed",
     definition="An action that failed to complete or completed but produced an error.",
     name="failed",
-    preferred_ontology_identifier="https://schema.org/FailedActionStatus",
+    preferred_ontology_identifier=IRI("https://schema.org/FailedActionStatus"),
     synonyms=["failed action status", "failed action", "finished unsuccessfully", "error"],
 )
 ActionStatusType.inactive = ActionStatusType(
@@ -162,6 +162,6 @@ def by_name(cls, name):
     id="https://openminds.ebrains.eu/instances/actionStatusType/potential",
     definition="A description of an action that is supported.",
     name="potential",
-    preferred_ontology_identifier="https://schema.org/PotentialActionStatus",
+    preferred_ontology_identifier=IRI("https://schema.org/PotentialActionStatus"),
     synonyms=["potential action type", "potential action"],
 )

openminds/latest/controlled_terms/age_category.py

@@ -128,65 +128,65 @@ def by_name(cls, name):
 AgeCategory.adult = AgeCategory(
     id="https://openminds.ebrains.eu/instances/ageCategory/adult",
     definition="'Adult' categorizes the life cycle stage of an animal or human that reached sexual maturity.",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0729043",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0729043"),
     name="adult",
-    preferred_ontology_identifier="http://purl.obolibrary.org/obo/UBERON_0000113",
+    preferred_ontology_identifier=IRI("http://purl.obolibrary.org/obo/UBERON_0000113"),
     synonyms=["adult stage", "post-juvenile adult", "post-juvenile adult stage"],
 )
 AgeCategory.embryo = AgeCategory(
     id="https://openminds.ebrains.eu/instances/ageCategory/embryo",
     definition="'Embryo' categorizes the life cycle stage of an animal or human that starts with fertilitzation and ends with the fully formed embryo.",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0735599",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0735599"),
     name="embryo",
-    preferred_ontology_identifier="http://purl.obolibrary.org/obo/UBERON_0000068",
+    preferred_ontology_identifier=IRI("http://purl.obolibrary.org/obo/UBERON_0000068"),
     synonyms=["embryo stage", "embryonic stage"],
 )
 AgeCategory.infant = AgeCategory(
     id="https://openminds.ebrains.eu/instances/ageCategory/infant",
     definition="'Infant' categorizes the life cycle stage of mammals (animal or human) that follows the neonate stage and ends at weaning.",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0735063",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0735063"),
     name="infant",
-    preferred_ontology_identifier="http://purl.obolibrary.org/obo/UBERON_0034920",
+    preferred_ontology_identifier=IRI("http://purl.obolibrary.org/obo/UBERON_0034920"),
     synonyms=["infant stage"],
 )
 AgeCategory.juvenile = AgeCategory(
     id="https://openminds.ebrains.eu/instances/ageCategory/juvenile",
     definition="'Juvenile' categorizes the life cycle stage of an animal or human that starts with the independence of the nest and/or caregivers and ends with sexual maturity.",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0730395",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0730395"),
     name="juvenile",
-    preferred_ontology_identifier="http://purl.obolibrary.org/obo/UBERON_0034919",
+    preferred_ontology_identifier=IRI("http://purl.obolibrary.org/obo/UBERON_0034919"),
     synonyms=["juvenile stage"],
 )
 AgeCategory.late_adult = AgeCategory(
     id="https://openminds.ebrains.eu/instances/ageCategory/lateAdult",
     definition="'Late adult' categorizes the life cycle stage of an animal or human that follows the prime adult stage.",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0725713",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0725713"),
     name="late adult",
-    preferred_ontology_identifier="http://purl.obolibrary.org/obo/UBERON_0007222",
+    preferred_ontology_identifier=IRI("http://purl.obolibrary.org/obo/UBERON_0007222"),
     synonyms=["elderly", "elderly stage", "geriatric", "geriatric stage", "late adult stage"],
 )
 AgeCategory.neonate = AgeCategory(
     id="https://openminds.ebrains.eu/instances/ageCategory/neonate",
     definition="'Neonate' categorizes the life cycle stage of an animal or human that immediately follows birth.",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0732178",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0732178"),
     name="neonate",
-    preferred_ontology_identifier="http://purl.obolibrary.org/obo/UBERON_0007221",
+    preferred_ontology_identifier=IRI("http://purl.obolibrary.org/obo/UBERON_0007221"),
     synonyms=["neonatal stage", "neonate stage"],
 )
 AgeCategory.perinatal = AgeCategory(
     id="https://openminds.ebrains.eu/instances/ageCategory/perinatal",
     definition="'Perinatal' categorizes the life cycle stage of an animal or human that starts right before birth and ends right after birth.",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0724163",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0724163"),
     name="perinatal",
-    preferred_ontology_identifier="http://purl.obolibrary.org/obo/UBERON_0012101",
+    preferred_ontology_identifier=IRI("http://purl.obolibrary.org/obo/UBERON_0012101"),
     synonyms=["perinatal stage"],
 )
 AgeCategory.prime_adult = AgeCategory(
     id="https://openminds.ebrains.eu/instances/ageCategory/primeAdult",
     definition="'Prime adult' categorizes the life cycle stage of an animal or human that starts at the onset of sexual maturity or the cessation of growth, whichever comes last, and ends before senescence.",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0733125",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0733125"),
     name="prime adult",
-    preferred_ontology_identifier="http://purl.obolibrary.org/obo/UBERON_0018241",
+    preferred_ontology_identifier=IRI("http://purl.obolibrary.org/obo/UBERON_0018241"),
     synonyms=["adulthood stage", "prime adult stage"],
 )
 AgeCategory.young_adult = AgeCategory(

openminds/latest/controlled_terms/atlas_type.py

@@ -127,9 +127,9 @@ def by_name(cls, name):
 AtlasType.parcellation_scheme = AtlasType(
     id="https://openminds.ebrains.eu/instances/atlasType/parcellationScheme",
     definition="A 'parcellation scheme' is a set of parcels occupying a part or all of an anatomical entity that has been delineated or annotated using a common approach or set of criteria.",
-    interlex_identifier="http://uri.interlex.org/ilx_0108526",
+    interlex_identifier=IRI("http://uri.interlex.org/ilx_0108526"),
     name="parcellation scheme",
-    preferred_ontology_identifier="http://uri.neuinfo.org/nif/nifstd/nlx_144019",
+    preferred_ontology_identifier=IRI("http://uri.neuinfo.org/nif/nifstd/nlx_144019"),
     synonyms=["partition scheme"],
 )
 AtlasType.probabilistic_atlas = AtlasType(

openminds/latest/controlled_terms/biological_order.py

@@ -122,17 +122,17 @@ def by_name(cls, name):
 BiologicalOrder.carnivora = BiologicalOrder(
     id="https://openminds.ebrains.eu/instances/biologicalOrder/carnivora",
     definition="The biological order *Carnivora* (carnivore) belongs to the class *Mammalia* (mammals).",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0101675",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0101675"),
     name="Carnivora",
-    preferred_ontology_identifier="http://purl.obolibrary.org/obo/NCBITaxon_33554",
+    preferred_ontology_identifier=IRI("http://purl.obolibrary.org/obo/NCBITaxon_33554"),
     synonyms=["carnivore"],
 )
 BiologicalOrder.cypriniformes = BiologicalOrder(
     id="https://openminds.ebrains.eu/instances/biologicalOrder/cypriniformes",
     definition="The biological order *Cypriniformes* belongs to the class *Actinopterygii* (ray-finned fishes).",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0737279",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0737279"),
     name="Cypriniformes",
-    preferred_ontology_identifier="http://id.nlm.nih.gov/mesh/2018/M0005508",
+    preferred_ontology_identifier=IRI("http://id.nlm.nih.gov/mesh/2018/M0005508"),
 )
 BiologicalOrder.didelphimorphia = BiologicalOrder(
     id="https://openminds.ebrains.eu/instances/biologicalOrder/didelphimorphia",
@@ -143,23 +143,23 @@ def by_name(cls, name):
 BiologicalOrder.nudibranchia = BiologicalOrder(
     id="https://openminds.ebrains.eu/instances/biologicalOrder/nudibranchia",
     definition="The biological order *Nudibranchia* (nudibranchs) belongs to the class *Gastropoda* (gastropods).",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0107805",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0107805"),
     name="Nudibranchia",
-    preferred_ontology_identifier="http://purl.obolibrary.org/obo/NCBITaxon_70849",
+    preferred_ontology_identifier=IRI("http://purl.obolibrary.org/obo/NCBITaxon_70849"),
     synonyms=["nudibranchs"],
 )
 BiologicalOrder.primates = BiologicalOrder(
     id="https://openminds.ebrains.eu/instances/biologicalOrder/primates",
     definition="The biological order *Primates* belongs to the class *Mammalia* (mammals).",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0486298",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0486298"),
     name="Primates",
-    preferred_ontology_identifier="http://id.nlm.nih.gov/mesh/2018/M0017579",
+    preferred_ontology_identifier=IRI("http://id.nlm.nih.gov/mesh/2018/M0017579"),
 )
 BiologicalOrder.rodentia = BiologicalOrder(
     id="https://openminds.ebrains.eu/instances/biologicalOrder/rodentia",
     definition="The biological order *Rodentia* (rodents) belongs to the class *Mammalia* (mammals).",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0110175",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0110175"),
     name="Rodentia",
-    preferred_ontology_identifier="http://purl.obolibrary.org/obo/NCBITaxon_9989",
+    preferred_ontology_identifier=IRI("http://purl.obolibrary.org/obo/NCBITaxon_9989"),
     synonyms=["rodents"],
 )

openminds/latest/controlled_terms/biological_sex.py

@@ -123,26 +123,26 @@ def by_name(cls, name):
     id="https://openminds.ebrains.eu/instances/biologicalSex/female",
     definition="Biological sex that produces egg cells (ova).",
     description="A female organism typically has the capacity to produce relatively large, usually immobile gametes (reproductive cells), called egg cells (or ova). In the process of fertilization, an egg cell (ovum) fuses with a smaller, usually mobile male gametes, called sperm cells (or spermatozoa).",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0104150",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0104150"),
     name="female",
-    preferred_ontology_identifier="http://purl.obolibrary.org/obo/PATO_0000383",
+    preferred_ontology_identifier=IRI("http://purl.obolibrary.org/obo/PATO_0000383"),
 )
 BiologicalSex.hermaphrodite = BiologicalSex(
     id="https://openminds.ebrains.eu/instances/biologicalSex/hermaphrodite",
     definition="Biological sex with both male and female reproductive organs.",
     description="A hermaphrodite is an animal or plant that can produce gametes (reproductive cells) of both, male and female sexes. In sexually dimorphic organisms, hermaphroditism may occur because of variations in the genetic code. The term *hermaphrodite* is considered to be misleading, stigmatizing, and scientifically specious in reference to humans. For this reason, in humans the term *intersex* is typically used.",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0104963",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0104963"),
     name="hermaphrodite",
-    preferred_ontology_identifier="http://purl.obolibrary.org/obo/PATO_0001340",
+    preferred_ontology_identifier=IRI("http://purl.obolibrary.org/obo/PATO_0001340"),
     synonyms=["intersex"],
 )
 BiologicalSex.male = BiologicalSex(
     id="https://openminds.ebrains.eu/instances/biologicalSex/male",
     definition="Biological sex that produces sperm cells (spermatozoa).",
     description="A male organism typically has the capacity to produce relatively small, usually mobile gametes (reproductive cells), called sperm cells (or spermatozoa). In the process of fertilization, these sperm cells fuse with a larger, usually immobile female gamete, called egg cell (or ovum).",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0106489",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0106489"),
     name="male",
-    preferred_ontology_identifier="http://purl.obolibrary.org/obo/PATO_0000384",
+    preferred_ontology_identifier=IRI("http://purl.obolibrary.org/obo/PATO_0000384"),
 )
 BiologicalSex.not_detectable = BiologicalSex(
     id="https://openminds.ebrains.eu/instances/biologicalSex/notDetectable",

openminds/latest/controlled_terms/cell_culture_type.py

@@ -122,14 +122,14 @@ def by_name(cls, name):
 CellCultureType.primary = CellCultureType(
     id="https://openminds.ebrains.eu/instances/cellCultureType/primary",
     definition="A cell culture comprised of primary cultured cells and the media in which they are being actively propagated or quiescently stored.",
-    interlex_identifier="http://uri.interlex.org/base/ilx_0490188",
+    interlex_identifier=IRI("http://uri.interlex.org/base/ilx_0490188"),
     name="primary cell culture",
-    preferred_ontology_identifier="http://id.nlm.nih.gov/mesh/2018/M0452904",
+    preferred_ontology_identifier=IRI("http://id.nlm.nih.gov/mesh/2018/M0452904"),
 )
 CellCultureType.secondary = CellCultureType(
     id="https://openminds.ebrains.eu/instances/cellCultureType/secondary",
     definition="A cultured cell population that is derived through one or more passages in culture.",
-    interlex_identifier="http://uri.interlex.org/ilx_0782434",
+    interlex_identifier=IRI("http://uri.interlex.org/ilx_0782434"),
     name="secondary cell culture",
-    preferred_ontology_identifier="http://purl.obolibrary.org/obo/OBI_0001905",
+    preferred_ontology_identifier=IRI("http://purl.obolibrary.org/obo/OBI_0001905"),
 )