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openMINDS pipeline
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build triggered by submodule version
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Lines changed: 654 additions & 645 deletions

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‎openminds/base.py‎

Lines changed: 15 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -14,6 +14,10 @@
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class Node(metaclass=Registry):
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"""
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Base class for a metadata node
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"""
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@property
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def uuid(self):
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if self.id is not None:
@@ -29,7 +33,7 @@ def has_property(self, name):
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def to_jsonld(self, include_empty_properties=True, embed_linked_nodes=True, with_context=True):
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"""
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docstring goes here
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Return a represention of this metadata node as a dictionary that can be directly serialized to JSON-LD.
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"""
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def value_to_jsonld(value):
@@ -77,7 +81,7 @@ def value_to_jsonld(value):
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@classmethod
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def from_jsonld(cls, data):
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"""
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docstring goes here
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Create a Python object representing a metadata node from a JSON-LD-compatible dictionary
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"""
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data_copy = data.copy()
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context = data_copy.pop("@context", None)
@@ -141,7 +145,7 @@ def links(self):
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class LinkedMetadata(Node):
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"""
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docstring goes here
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A Python representation of a metadata node that should have a unique identifier.
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"""
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def __init__(self, id=None, **properties):
@@ -151,15 +155,15 @@ def __init__(self, id=None, **properties):
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def save(self, file_path, indent=2):
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"""
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docstring goes here
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Save this object to a file in JSON-LD format
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"""
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with open(file_path, "w") as output_file:
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json.dump(self.to_jsonld(), output_file, indent=indent)
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@classmethod
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def load(cls, file_path):
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"""
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docstring goes here
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Create a Python object representing a metadata node from a JSON-LD file
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"""
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with open(file_path, "r") as input_file:
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data = json.load(input_file)
@@ -168,7 +172,8 @@ def load(cls, file_path):
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class EmbeddedMetadata(Node):
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"""
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docstring goes here
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A Python representation of a metadata node that should only be embedded within another node,
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and should not have a unique identifier.
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"""
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def __init__(self, **properties):
@@ -177,6 +182,10 @@ def __init__(self, **properties):
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class IRI:
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"""
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Representation of an Internationalized Resource Identifier
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"""
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180189
def __init__(self, value: Union[str, IRI]):
181190
if isinstance(value, IRI):
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iri = value.value

‎openminds/latest/chemicals/__init__.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
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from .chemical_mixture import ChemicalMixture
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from .product_source import ProductSource
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from .chemical_substance import ChemicalSubstance
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from .product_source import ProductSource
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from .amount_of_chemical import AmountOfChemical

‎openminds/latest/computation/__init__.py‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -1,17 +1,17 @@
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from .workflow_recipe_version import WorkflowRecipeVersion
2-
from .visualization import Visualization
3-
from .software_agent import SoftwareAgent
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from .validation_test import ValidationTest
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from .workflow_recipe import WorkflowRecipe
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from .optimization import Optimization
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from .model_validation import ModelValidation
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from .hardware_system import HardwareSystem
7+
from .launch_configuration import LaunchConfiguration
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from .data_copy import DataCopy
9+
from .software_agent import SoftwareAgent
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from .simulation import Simulation
8-
from .optimization import Optimization
9-
from .validation_test import ValidationTest
10-
from .workflow_execution import WorkflowExecution
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from .visualization import Visualization
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from .local_file import LocalFile
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from .environment import Environment
12-
from .model_validation import ModelValidation
13-
from .generic_computation import GenericComputation
14-
from .data_analysis import DataAnalysis
15-
from .launch_configuration import LaunchConfiguration
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from .workflow_execution import WorkflowExecution
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from .validation_test_version import ValidationTestVersion
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from .local_file import LocalFile
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from .data_analysis import DataAnalysis
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from .generic_computation import GenericComputation

‎openminds/latest/computation/validation_test_version.py‎

Lines changed: 1 addition & 1 deletion
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@@ -4,8 +4,8 @@
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# this file was auto-generated!
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7-
from datetime import date
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from openminds.base import IRI
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from datetime import date
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from openminds.base import LinkedMetadata
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from openminds.properties import Property

‎openminds/latest/computation/workflow_recipe_version.py‎

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Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@
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# this file was auto-generated!
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7-
from datetime import date
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from openminds.base import IRI
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from datetime import date
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from openminds.base import LinkedMetadata
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from openminds.properties import Property

‎openminds/latest/controlled_terms/__init__.py‎

Lines changed: 66 additions & 66 deletions
Original file line numberDiff line numberDiff line change
@@ -1,78 +1,78 @@
1-
from .annotation_criteria_type import AnnotationCriteriaType
2-
from .stimulation_technique import StimulationTechnique
3-
from .technique import Technique
4-
from .chemical_mixture_type import ChemicalMixtureType
5-
from .biological_process import BiologicalProcess
6-
from .programming_language import ProgrammingLanguage
7-
from .subject_attribute import SubjectAttribute
8-
from .operating_device import OperatingDevice
9-
from .measured_quantity import MeasuredQuantity
10-
from .file_repository_type import FileRepositoryType
11-
from .data_type import DataType
12-
from .species import Species
13-
from .tissue_sample_attribute import TissueSampleAttribute
1+
from .operating_system import OperatingSystem
2+
from .qualitative_overlap import QualitativeOverlap
3+
from .gustatory_stimulus_type import GustatoryStimulusType
144
from .molecular_entity import MolecularEntity
15-
from .uberon_parcellation import UBERONParcellation
16-
from .stimulation_approach import StimulationApproach
5+
from .terminology import Terminology
6+
from .cranial_window_construction_type import CranialWindowConstructionType
7+
from .laterality import Laterality
8+
from .analysis_technique import AnalysisTechnique
9+
from .anatomical_axes_orientation import AnatomicalAxesOrientation
10+
from .optical_stimulus_type import OpticalStimulusType
11+
from .measured_quantity import MeasuredQuantity
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from .disease import Disease
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from .disease_model import DiseaseModel
19-
from .analysis_technique import AnalysisTechnique
20-
from .biological_sex import BiologicalSex
21-
from .genetic_strain_type import GeneticStrainType
22-
from .breeding_type import BreedingType
23-
from .cranial_window_reinforcement_type import CranialWindowReinforcementType
24-
from .action_status_type import ActionStatusType
25-
from .olfactory_stimulus_type import OlfactoryStimulusType
26-
from .handedness import Handedness
27-
from .file_bundle_grouping import FileBundleGrouping
28-
from .qualitative_overlap import QualitativeOverlap
14+
from .atlas_type import AtlasType
15+
from .software_application_category import SoftwareApplicationCategory
16+
from .auditory_stimulus_type import AuditoryStimulusType
17+
from .operating_device import OperatingDevice
18+
from .contribution_type import ContributionType
19+
from .colormap import Colormap
20+
from .type_of_uncertainty import TypeOfUncertainty
21+
from .stimulation_technique import StimulationTechnique
22+
from .unit_of_measurement import UnitOfMeasurement
23+
from .language import Language
24+
from .service import Service
25+
from .difference_measure import DifferenceMeasure
26+
from .data_type import DataType
27+
from .criteria_quality_type import CriteriaQualityType
28+
from .electrical_stimulus_type import ElectricalStimulusType
2929
from .anatomical_identification_type import AnatomicalIdentificationType
30+
from .learning_resource_type import LearningResourceType
31+
from .subcellular_entity import SubcellularEntity
32+
from .preparation_type import PreparationType
33+
from .visual_stimulus_type import VisualStimulusType
34+
from .file_usage_role import FileUsageRole
3035
from .anatomical_plane import AnatomicalPlane
31-
from .patch_clamp_variation import PatchClampVariation
32-
from .software_feature import SoftwareFeature
33-
from .criteria_quality_type import CriteriaQualityType
34-
from .educational_level import EducationalLevel
36+
from .tissue_sample_type import TissueSampleType
3537
from .cell_culture_type import CellCultureType
38+
from .handedness import Handedness
39+
from .technique import Technique
40+
from .chemical_mixture_type import ChemicalMixtureType
41+
from .organism_system import OrganismSystem
42+
from .experimental_approach import ExperimentalApproach
43+
from .tactile_stimulus_type import TactileStimulusType
3644
from .organ import Organ
37-
from .anatomical_axes_orientation import AnatomicalAxesOrientation
38-
from .type_of_uncertainty import TypeOfUncertainty
39-
from .visual_stimulus_type import VisualStimulusType
40-
from .learning_resource_type import LearningResourceType
45+
from .product_accessibility import ProductAccessibility
46+
from .model_scope import ModelScope
47+
from .subject_attribute import SubjectAttribute
48+
from .device_type import DeviceType
49+
from .cell_type import CellType
50+
from .meta_data_model_type import MetaDataModelType
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from .measured_signal_type import MeasuredSignalType
42-
from .experimental_approach import ExperimentalApproach
43-
from .ethics_assessment import EthicsAssessment
44-
from .gustatory_stimulus_type import GustatoryStimulusType
52+
from .biological_order import BiologicalOrder
53+
from .olfactory_stimulus_type import OlfactoryStimulusType
54+
from .software_feature import SoftwareFeature
55+
from .breeding_type import BreedingType
56+
from .species import Species
57+
from .tissue_sample_attribute import TissueSampleAttribute
4558
from .organism_substance import OrganismSubstance
46-
from .cell_type import CellType
47-
from .subcellular_entity import SubcellularEntity
48-
from .terminology import Terminology
49-
from .organism_system import OrganismSystem
50-
from .unit_of_measurement import UnitOfMeasurement
51-
from .term_suggestion import TermSuggestion
59+
from .biological_process import BiologicalProcess
5260
from .annotation_type import AnnotationType
53-
from .setup_type import SetupType
54-
from .cranial_window_construction_type import CranialWindowConstructionType
55-
from .model_scope import ModelScope
56-
from .laterality import Laterality
57-
from .product_accessibility import ProductAccessibility
58-
from .software_application_category import SoftwareApplicationCategory
59-
from .age_category import AgeCategory
60-
from .service import Service
61-
from .contribution_type import ContributionType
62-
from .meta_data_model_type import MetaDataModelType
63-
from .electrical_stimulus_type import ElectricalStimulusType
6461
from .model_abstraction_level import ModelAbstractionLevel
65-
from .tissue_sample_type import TissueSampleType
66-
from .biological_order import BiologicalOrder
67-
from .operating_system import OperatingSystem
68-
from .device_type import DeviceType
69-
from .difference_measure import DifferenceMeasure
70-
from .file_usage_role import FileUsageRole
71-
from .colormap import Colormap
72-
from .atlas_type import AtlasType
73-
from .preparation_type import PreparationType
62+
from .file_repository_type import FileRepositoryType
7463
from .semantic_data_type import SemanticDataType
75-
from .tactile_stimulus_type import TactileStimulusType
76-
from .auditory_stimulus_type import AuditoryStimulusType
77-
from .language import Language
78-
from .optical_stimulus_type import OpticalStimulusType
64+
from .file_bundle_grouping import FileBundleGrouping
65+
from .term_suggestion import TermSuggestion
66+
from .biological_sex import BiologicalSex
67+
from .educational_level import EducationalLevel
68+
from .ethics_assessment import EthicsAssessment
69+
from .annotation_criteria_type import AnnotationCriteriaType
70+
from .cranial_window_reinforcement_type import CranialWindowReinforcementType
71+
from .patch_clamp_variation import PatchClampVariation
72+
from .genetic_strain_type import GeneticStrainType
73+
from .age_category import AgeCategory
74+
from .uberon_parcellation import UBERONParcellation
75+
from .setup_type import SetupType
76+
from .stimulation_approach import StimulationApproach
77+
from .action_status_type import ActionStatusType
78+
from .programming_language import ProgrammingLanguage

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