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🎨 Add blank=True #2

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Nov 17, 2024
Merged

🎨 Add blank=True #2

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eb8e377
🎨 Add blank=True
sunnyosun Nov 15, 2024
6a528df
🚚 Rename CanValidate to CanCurate
sunnyosun Nov 15, 2024
284b414
🎨 Import lamindb
sunnyosun Nov 17, 2024
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2 changes: 2 additions & 0 deletions cellregistry/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,5 +29,7 @@ def __getattr__(name):


if _check_instance_setup():
import lamindb

del __getattr__ # delete so that imports work out
from .models import Cell
2 changes: 1 addition & 1 deletion cellregistry/migrations/0001_initial.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@ class Migration(migrations.Migration):
options={
"abstract": False,
},
bases=(lnschema_core.models.CanValidate, models.Model),
bases=(lnschema_core.models.CanCurate, models.Model),
),
migrations.CreateModel(
name="ArtifactCell",
Expand Down
126 changes: 126 additions & 0 deletions cellregistry/migrations/0002_alter_artifactcell_artifact_alter_artifactcell_cell_and_more.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,126 @@
# Generated by Django 5.2 on 2024-11-15 14:16

import django.db.models.deletion
import lnschema_core.fields
import lnschema_core.ids
import lnschema_core.models
import lnschema_core.users
from django.db import migrations


class Migration(migrations.Migration):
dependencies = [
("cellregistry", "0001_initial"),
(
"lnschema_core",
"0069_alter_artifact__accessor_alter_artifact__hash_type_and_more",
),
]

operations = [
migrations.AlterField(
model_name="artifactcell",
name="artifact",
field=lnschema_core.fields.ForeignKey(
blank=True,
on_delete=django.db.models.deletion.CASCADE,
related_name="links_cell",
to="lnschema_core.artifact",
),
),
migrations.AlterField(
model_name="artifactcell",
name="cell",
field=lnschema_core.fields.ForeignKey(
blank=True,
on_delete=django.db.models.deletion.CASCADE,
related_name="links_artifact",
to="cellregistry.cell",
),
),
migrations.AlterField(
model_name="artifactcell",
name="created_at",
field=lnschema_core.fields.DateTimeField(auto_now_add=True, db_index=True),
),
migrations.AlterField(
model_name="artifactcell",
name="created_by",
field=lnschema_core.fields.ForeignKey(
blank=True,
default=lnschema_core.users.current_user_id,
on_delete=django.db.models.deletion.PROTECT,
related_name="+",
to="lnschema_core.user",
),
),
migrations.AlterField(
model_name="artifactcell",
name="run",
field=lnschema_core.fields.ForeignKey(
blank=True,
default=lnschema_core.models.current_run,
null=True,
on_delete=django.db.models.deletion.PROTECT,
related_name="+",
to="lnschema_core.run",
),
),
migrations.AlterField(
model_name="cell",
name="created_at",
field=lnschema_core.fields.DateTimeField(auto_now_add=True, db_index=True),
),
migrations.AlterField(
model_name="cell",
name="created_by",
field=lnschema_core.fields.ForeignKey(
blank=True,
default=lnschema_core.users.current_user_id,
on_delete=django.db.models.deletion.PROTECT,
related_name="+",
to="lnschema_core.user",
),
),
migrations.AlterField(
model_name="cell",
name="description",
field=lnschema_core.fields.CharField(
blank=True, db_index=True, default=None, max_length=255, null=True
),
),
migrations.AlterField(
model_name="cell",
name="name",
field=lnschema_core.fields.CharField(
blank=True, db_index=True, default=None, max_length=255, unique=True
),
),
migrations.AlterField(
model_name="cell",
name="run",
field=lnschema_core.fields.ForeignKey(
blank=True,
default=lnschema_core.models.current_run,
null=True,
on_delete=django.db.models.deletion.PROTECT,
related_name="+",
to="lnschema_core.run",
),
),
migrations.AlterField(
model_name="cell",
name="uid",
field=lnschema_core.fields.CharField(
blank=True,
default=lnschema_core.ids.base62_20,
max_length=20,
unique=True,
),
),
migrations.AlterField(
model_name="cell",
name="updated_at",
field=lnschema_core.fields.DateTimeField(auto_now=True, db_index=True),
),
]
31 changes: 14 additions & 17 deletions cellregistry/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,10 @@
from django.db import models
from django.db.models import CASCADE, PROTECT
from lnschema_core import ids
from lnschema_core.fields import CharField, ForeignKey
from lnschema_core.models import (
Artifact,
CanValidate,
CanCurate,
Feature,
LinkORM,
Record,
Expand All @@ -16,7 +17,7 @@
)


class Cell(Record, CanValidate, TracksRun, TracksUpdates):
class Cell(Record, CanCurate, TracksRun, TracksUpdates):
"""Single cells.

Example:
Expand All @@ -30,11 +31,9 @@ class Meta(Record.Meta, TracksRun.Meta, TracksUpdates.Meta):

id: int = models.BigAutoField(primary_key=True)
"""Internal id, valid only in one DB instance."""
uid: str = models.CharField(unique=True, max_length=20, default=ids.base62_20)
uid: str = CharField(unique=True, max_length=20, default=ids.base62_20)
"""Universal id, valid across DB instances."""
name: str = models.CharField(
max_length=255, default=None, unique=True, db_index=True
)
name: str = CharField(max_length=255, default=None, unique=True, db_index=True)
"""A unique name for the cell.

It's typically the barcode combined with an identifier for the dataset that
Expand All @@ -47,9 +46,7 @@ class Meta(Record.Meta, TracksRun.Meta, TracksUpdates.Meta):
Pan_T7935494_ATCATGGTCTACCTGC

"""
description: str = models.CharField(
max_length=255, db_index=True, null=True, default=None
)
description: str = CharField(max_length=255, db_index=True, null=True, default=None)
"""A description."""
# ulabels: ULabel = models.ManyToManyField(
# ULabel, through="CellULabel", related_name="cells"
Expand All @@ -67,24 +64,24 @@ class Meta(Record.Meta, TracksRun.Meta, TracksUpdates.Meta):

class ArtifactCell(Record, LinkORM, TracksRun):
id: int = models.BigAutoField(primary_key=True)
artifact: Artifact = models.ForeignKey(Artifact, CASCADE, related_name="links_cell")
cell: Cell = models.ForeignKey(Cell, CASCADE, related_name="links_artifact")
artifact: Artifact = ForeignKey(Artifact, CASCADE, related_name="links_cell")
cell: Cell = ForeignKey(Cell, CASCADE, related_name="links_artifact")


class CellCellType:
id: int = models.BigAutoField(primary_key=True)
cell: Cell = models.ForeignKey(Cell, CASCADE, related_name="links_cell_type")
cell: Cell = ForeignKey(Cell, CASCADE, related_name="links_cell_type")
# follow the .lower() convention in link models
celltype: CellType = models.ForeignKey(CellType, PROTECT, related_name="links_cell")
feature: Feature = models.ForeignKey(
celltype: CellType = ForeignKey(CellType, PROTECT, related_name="links_cell")
feature: Feature = ForeignKey(
Feature, PROTECT, null=True, default=None, related_name="links_cellcelltype"
)


class CellULabel:
id: int = models.BigAutoField(primary_key=True)
cell: Cell = models.ForeignKey(Cell, CASCADE, related_name="links_ulabel")
ulabel: ULabel = models.ForeignKey(ULabel, PROTECT, related_name="links_cell")
feature: Feature = models.ForeignKey(
cell: Cell = ForeignKey(Cell, CASCADE, related_name="links_ulabel")
ulabel: ULabel = ForeignKey(ULabel, PROTECT, related_name="links_cell")
feature: Feature = ForeignKey(
Feature, PROTECT, null=True, default=None, related_name="links_cellulabel"
)
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