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Make all models available under entitysdk.models (#46)
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9 files changed

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-125
lines changed

9 files changed

+194
-125
lines changed

‎examples/01_searching.ipynb

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@@ -13,14 +13,15 @@
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"\n",
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"from entitysdk.client import Client\n",
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"from entitysdk.common import ProjectContext\n",
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"from entitysdk.models.agent import Organization, Person\n",
17-
"from entitysdk.models.contribution import Role\n",
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"from entitysdk.models.morphology import (\n",
16+
"from entitysdk.models import (\n",
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" MTypeClass,\n",
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" Organization,\n",
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" Person,\n",
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" ReconstructionMorphology,\n",
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" Role,\n",
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" Species,\n",
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" Strain,\n",
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")\n",
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"from entitysdk.models.mtype import MTypeClass\n",
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"\n",
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"entitycore_api_url = \"http://127.0.0.1:8000\"\n",
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"project_context = ProjectContext(\n",

‎examples/02_morphology.ipynb

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@@ -16,7 +16,7 @@
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"\n",
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"from entitysdk.client import Client\n",
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"from entitysdk.common import ProjectContext\n",
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"from entitysdk.models.morphology import (\n",
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"from entitysdk.models import (\n",
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" BrainLocation,\n",
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" BrainRegion,\n",
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" ReconstructionMorphology,\n",

‎examples/03_contribution.ipynb

Lines changed: 1 addition & 3 deletions
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@@ -13,9 +13,7 @@
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"\n",
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"from entitysdk.client import Client\n",
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"from entitysdk.common import ProjectContext\n",
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"from entitysdk.models.agent import Organization\n",
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"from entitysdk.models.contribution import Contribution, Role\n",
18-
"from entitysdk.models.morphology import ReconstructionMorphology\n",
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"from entitysdk.models import Contribution, Organization, ReconstructionMorphology, Role\n",
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"\n",
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"entitycore_api_url = \"http://127.0.0.1:8000\"\n",
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"project_context = ProjectContext(\n",

‎src/entitysdk/models/__init__.py

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@@ -1 +1,31 @@
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"""Models for entitysdk."""
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from entitysdk.models.agent import Organization, Person
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from entitysdk.models.asset import Asset
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from entitysdk.models.brain_location import BrainLocation
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from entitysdk.models.brain_region import BrainRegion
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from entitysdk.models.contribution import Contribution, Role
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from entitysdk.models.entity import Entity
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from entitysdk.models.ion_channel_model import IonChannelModel, NeuronBlock, UseIon
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from entitysdk.models.morphology import ReconstructionMorphology
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from entitysdk.models.mtype import MTypeClass
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from entitysdk.models.taxonomy import Species, Strain, Taxonomy
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__all__ = [
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"Asset",
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"BrainLocation",
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"BrainRegion",
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"Contribution",
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"Entity",
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"IonChannelModel",
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"MTypeClass",
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"NeuronBlock",
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"Organization",
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"Person",
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"ReconstructionMorphology",
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"Role",
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"Species",
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"Strain",
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"Taxonomy",
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"UseIon",
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]

‎src/entitysdk/models/brain_location.py

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@@ -0,0 +1,33 @@
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"""Brain location model."""
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from typing import Annotated
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from pydantic import Field
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from entitysdk.models.core import Struct
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9+
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class BrainLocation(Struct):
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"""BrainLocation model."""
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x: Annotated[
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float,
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Field(
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examples=[1.0, 2.0, 3.0],
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description="The x coordinate of the brain location.",
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),
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]
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y: Annotated[
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float,
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Field(
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examples=[1.0, 2.0, 3.0],
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description="The y coordinate of the brain location.",
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),
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]
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z: Annotated[
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float,
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Field(
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examples=[1.0, 2.0, 3.0],
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description="The z coordinate of the brain location.",
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),
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]

‎src/entitysdk/models/license.py

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@@ -0,0 +1,33 @@
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"""License model."""
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from typing import Annotated
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from pydantic import Field
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from entitysdk.models.entity import Entity
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class License(Entity):
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"""License model."""
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name: Annotated[
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str,
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Field(
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examples=["Apache 2.0"],
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description="The name of the license.",
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),
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]
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description: Annotated[
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str,
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Field(
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examples=["The 2.0 version of the Apache License"],
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description="The description of the license.",
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),
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]
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label: Annotated[
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str,
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Field(
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examples=["Apache 2.0"],
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description="The label of the license.",
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),
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]

‎src/entitysdk/models/morphology.py

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Original file line numberDiff line numberDiff line change
@@ -5,127 +5,13 @@
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from pydantic import Field
66

77
from entitysdk.mixin import HasAssets
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from entitysdk.models.brain_location import BrainLocation
89
from entitysdk.models.brain_region import BrainRegion
910
from entitysdk.models.contribution import Contribution
10-
from entitysdk.models.core import Struct
1111
from entitysdk.models.entity import Entity
12+
from entitysdk.models.license import License
1213
from entitysdk.models.mtype import MTypeClass
13-
from entitysdk.typedef import ID
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class License(Entity):
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"""License model."""
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name: Annotated[
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str,
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Field(
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examples=["Apache 2.0"],
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description="The name of the license.",
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),
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]
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description: Annotated[
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str,
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Field(
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examples=["The 2.0 version of the Apache License"],
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description="The description of the license.",
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),
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]
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label: Annotated[
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str,
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Field(
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examples=["Apache 2.0"],
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description="The label of the license.",
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),
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]
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class BrainLocation(Struct):
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"""BrainLocation model."""
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x: Annotated[
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float,
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Field(
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examples=[1.0, 2.0, 3.0],
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description="The x coordinate of the brain location.",
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),
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]
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y: Annotated[
53-
float,
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Field(
55-
examples=[1.0, 2.0, 3.0],
56-
description="The y coordinate of the brain location.",
57-
),
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]
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z: Annotated[
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float,
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Field(
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examples=[1.0, 2.0, 3.0],
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description="The z coordinate of the brain location.",
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),
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]
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class Taxonomy(Entity):
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"""Taxonomy model."""
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name: Annotated[
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str,
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Field(
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examples=["Homo sapiens"],
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description="The name of the taxonomy.",
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),
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]
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pref_label: Annotated[
79-
str,
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Field(
81-
examples=["Homo sapiens"],
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description="The preferred label of the taxonomy.",
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),
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]
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87-
class Species(Entity):
88-
"""Species model."""
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name: Annotated[
91-
str,
92-
Field(
93-
examples=["Mus musculus"],
94-
description="The name of the species.",
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),
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]
97-
taxonomy_id: Annotated[
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str,
99-
Field(
100-
examples=["1"],
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description="The taxonomy id of the species.",
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),
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]
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class Strain(Entity):
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"""Strain model."""
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name: Annotated[
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str,
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Field(
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examples=["C57BL/6J"],
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description="The name of the strain.",
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),
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]
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taxonomy_id: Annotated[
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str,
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Field(
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examples=["1"],
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description="The taxonomy id of the strain.",
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),
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]
123-
species_id: Annotated[
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ID,
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Field(
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description="The species id of the strain.",
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),
128-
]
14+
from entitysdk.models.taxonomy import Species, Strain
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13117
class ReconstructionMorphology(HasAssets, Entity):

‎src/entitysdk/models/taxonomy.py

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"""License model."""
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from typing import Annotated
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from pydantic import Field
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7+
from entitysdk.models.entity import Entity
8+
from entitysdk.typedef import ID
9+
10+
11+
class Species(Entity):
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"""Species model."""
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name: Annotated[
15+
str,
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Field(
17+
examples=["Mus musculus"],
18+
description="The name of the species.",
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),
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]
21+
taxonomy_id: Annotated[
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str,
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Field(
24+
examples=["1"],
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description="The taxonomy id of the species.",
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),
27+
]
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class Strain(Entity):
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"""Strain model."""
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name: Annotated[
34+
str,
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Field(
36+
examples=["C57BL/6J"],
37+
description="The name of the strain.",
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),
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]
40+
taxonomy_id: Annotated[
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str,
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Field(
43+
examples=["1"],
44+
description="The taxonomy id of the strain.",
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),
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]
47+
species_id: Annotated[
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ID,
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Field(
50+
description="The species id of the strain.",
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),
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]
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class Taxonomy(Entity):
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"""Taxonomy model."""
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name: Annotated[
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str,
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Field(
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examples=["Homo sapiens"],
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description="The name of the taxonomy.",
63+
),
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]
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pref_label: Annotated[
66+
str,
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Field(
68+
examples=["Homo sapiens"],
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description="The preferred label of the taxonomy.",
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),
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]

‎tests/unit/models/test_init.py

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import inspect
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from entitysdk import models
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def test_models_all():
7+
"""Ensure that the models imported in enttysdk.models.__init__.py are consistent with __all__"""
8+
imported_names = sorted(
9+
name for name, element in inspect.getmembers(models) if inspect.isclass(element)
10+
)
11+
all_dict_names = sorted(models.__all__)
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assert imported_names == all_dict_names, (
14+
"Imported classes and __all__ in entitysdk.models.__init__.py are not consistent.\n"
15+
f"Imported models : {imported_names}\n"
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f"Names in __all__:"
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)

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