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Add notebook_required_files to analysis notebook template and result #444

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196 changes: 196 additions & 0 deletions alembic/versions/20251112_151700_4b526a1ded96_add_asset_label_analysis_notebook_.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,196 @@
"""Add asset label analysis_notebook_template

Revision ID: 4b526a1ded96
Revises: a33cdde1ea6a
Create Date: 2025-11-12 15:17:00.381264

"""

from typing import Sequence, Union

from alembic import op
import sqlalchemy as sa
from alembic_postgresql_enum import TableReference

from sqlalchemy import Text
import app.db.types

# revision identifiers, used by Alembic.
revision: str = "4b526a1ded96"
down_revision: Union[str, None] = "a33cdde1ea6a"
branch_labels: Union[str, Sequence[str], None] = None
depends_on: Union[str, Sequence[str], None] = None


def upgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
op.sync_enum_values(
enum_schema="public",
enum_name="contenttype",
new_values=[
"application/json",
"application/swc",
"application/nrrd",
"application/obj",
"application/hoc",
"application/asc",
"application/abf",
"application/nwb",
"application/x-hdf5",
"text/plain",
"application/vnd.directory",
"application/mod",
"application/pdf",
"image/png",
"image/jpeg",
"model/gltf-binary",
"application/gzip",
"image/webp",
"application/x-ipynb+json",
"application/zip",
],
affected_columns=[
TableReference(table_schema="public", table_name="asset", column_name="content_type")
],
enum_values_to_rename=[],
)
op.sync_enum_values(
enum_schema="public",
enum_name="assetlabel",
new_values=[
"morphology",
"morphology_with_spines",
"cell_composition_summary",
"cell_composition_volumes",
"single_neuron_synaptome_config",
"single_neuron_synaptome_simulation_data",
"single_neuron_simulation_data",
"sonata_circuit",
"compressed_sonata_circuit",
"circuit_figures",
"circuit_analysis_data",
"circuit_connectivity_matrices",
"nwb",
"neuron_hoc",
"emodel_optimization_output",
"sonata_simulation_config",
"simulation_generation_config",
"ion_channel_modeling_generation_config",
"custom_node_sets",
"campaign_generation_config",
"campaign_summary",
"replay_spikes",
"voltage_report",
"spike_report",
"neuron_mechanisms",
"brain_atlas_annotation",
"brain_atlas_region_mesh",
"voxel_densities",
"validation_result_figure",
"validation_result_details",
"simulation_designer_image",
"circuit_visualization",
"node_stats",
"network_stats_a",
"network_stats_b",
"cell_surface_mesh",
"jupyter_notebook",
"requirements",
"notebook_required_files",
"ion_channel_model_figure",
"ion_channel_model_figure_summary_json",
"ion_channel_model_thumbnail",
"circuit_extraction_config",
],
affected_columns=[
TableReference(table_schema="public", table_name="asset", column_name="label")
],
enum_values_to_rename=[],
)
# ### end Alembic commands ###


def downgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
op.sync_enum_values(
enum_schema="public",
enum_name="assetlabel",
new_values=[
"morphology",
"morphology_with_spines",
"cell_composition_summary",
"cell_composition_volumes",
"single_neuron_synaptome_config",
"single_neuron_synaptome_simulation_data",
"single_neuron_simulation_data",
"sonata_circuit",
"compressed_sonata_circuit",
"circuit_figures",
"circuit_analysis_data",
"circuit_connectivity_matrices",
"nwb",
"neuron_hoc",
"emodel_optimization_output",
"sonata_simulation_config",
"simulation_generation_config",
"ion_channel_modeling_generation_config",
"custom_node_sets",
"campaign_generation_config",
"campaign_summary",
"replay_spikes",
"voltage_report",
"spike_report",
"neuron_mechanisms",
"brain_atlas_annotation",
"brain_atlas_region_mesh",
"voxel_densities",
"validation_result_figure",
"validation_result_details",
"simulation_designer_image",
"circuit_visualization",
"node_stats",
"network_stats_a",
"network_stats_b",
"cell_surface_mesh",
"jupyter_notebook",
"requirements",
"ion_channel_model_figure",
"ion_channel_model_figure_summary_json",
"ion_channel_model_thumbnail",
"circuit_extraction_config",
],
affected_columns=[
TableReference(table_schema="public", table_name="asset", column_name="label")
],
enum_values_to_rename=[],
)
op.sync_enum_values(
enum_schema="public",
enum_name="contenttype",
new_values=[
"application/json",
"application/swc",
"application/nrrd",
"application/obj",
"application/hoc",
"application/asc",
"application/abf",
"application/nwb",
"application/x-hdf5",
"text/plain",
"application/vnd.directory",
"application/mod",
"application/pdf",
"image/png",
"image/jpeg",
"model/gltf-binary",
"application/gzip",
"image/webp",
"application/x-ipynb+json",
],
affected_columns=[
TableReference(table_schema="public", table_name="asset", column_name="content_type")
],
enum_values_to_rename=[],
)
# ### end Alembic commands ###
4 changes: 3 additions & 1 deletion app/db/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1963,6 +1963,7 @@ class AnalysisNotebookTemplate(Entity, NameDescriptionVectorMixin):
Assets:
- a .ipynb file.
- requirements.txt produced with `pip freeze` if possible.
- an optional zip archive with label `notebook_required_files`.
"""

__tablename__ = EntityType.analysis_notebook_template.value
Expand Down Expand Up @@ -2040,7 +2041,8 @@ class AnalysisNotebookResult(Entity, NameDescriptionVectorMixin):
id (uuid.UUID): Primary key, referencing the entity ID.

Assets:
- a .ipynb file
- a .ipynb file.
- an optional zip archive with label `notebook_required_files`.
"""

__tablename__ = EntityType.analysis_notebook_result.value
Expand Down
11 changes: 10 additions & 1 deletion app/db/types.py
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Original file line number Diff line number Diff line change
Expand Up @@ -379,6 +379,7 @@ class ContentType(StrEnum):
gzip = "application/gzip"
webp = "image/webp"
ipynb = "application/x-ipynb+json"
zip = "application/zip"


class AssetLabel(StrEnum):
Expand Down Expand Up @@ -422,6 +423,7 @@ class AssetLabel(StrEnum):
cell_surface_mesh = auto()
jupyter_notebook = auto()
requirements = auto()
notebook_required_files = auto()
ion_channel_model_figure = auto()
ion_channel_model_figure_summary_json = auto()
ion_channel_model_thumbnail = auto()
Expand Down Expand Up @@ -460,6 +462,7 @@ class LabelRequirements(BaseModel):
),
ContentType.webp: (".webp",),
ContentType.ipynb: (".ipynb",),
ContentType.zip: (".zip",),
}

ALLOWED_ASSET_LABELS_PER_ENTITY: dict[
Expand All @@ -469,6 +472,9 @@ class LabelRequirements(BaseModel):
AssetLabel.jupyter_notebook: [
LabelRequirements(content_type=ContentType.ipynb, is_directory=False)
],
AssetLabel.notebook_required_files: [
LabelRequirements(content_type=ContentType.zip, is_directory=False)
],
AssetLabel.requirements: [
LabelRequirements(content_type=ContentType.text, is_directory=False)
],
Expand All @@ -481,7 +487,10 @@ class LabelRequirements(BaseModel):
EntityType.analysis_notebook_result: {
AssetLabel.jupyter_notebook: [
LabelRequirements(content_type=ContentType.ipynb, is_directory=False)
]
],
AssetLabel.notebook_required_files: [
LabelRequirements(content_type=ContentType.zip, is_directory=False)
],
},
EntityType.brain_atlas: {
AssetLabel.brain_atlas_annotation: [
Expand Down
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