lamindb 1.0.5__py3-none-any.whl → 1.1.1__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (80) hide show
  1. lamindb/__init__.py +17 -6
  2. lamindb/_artifact.py +202 -87
  3. lamindb/_can_curate.py +27 -8
  4. lamindb/_collection.py +86 -52
  5. lamindb/_feature.py +177 -41
  6. lamindb/_finish.py +21 -7
  7. lamindb/_from_values.py +83 -98
  8. lamindb/_parents.py +4 -4
  9. lamindb/_query_set.py +78 -18
  10. lamindb/_record.py +170 -53
  11. lamindb/_run.py +4 -4
  12. lamindb/_save.py +42 -11
  13. lamindb/_schema.py +135 -38
  14. lamindb/_storage.py +1 -1
  15. lamindb/_tracked.py +129 -0
  16. lamindb/_transform.py +21 -8
  17. lamindb/_ulabel.py +5 -14
  18. lamindb/base/users.py +1 -4
  19. lamindb/base/validation.py +2 -6
  20. lamindb/core/__init__.py +13 -14
  21. lamindb/core/_context.py +14 -9
  22. lamindb/core/_data.py +29 -25
  23. lamindb/core/_describe.py +1 -1
  24. lamindb/core/_django.py +1 -1
  25. lamindb/core/_feature_manager.py +53 -43
  26. lamindb/core/_label_manager.py +4 -4
  27. lamindb/core/_mapped_collection.py +24 -9
  28. lamindb/core/_track_environment.py +2 -1
  29. lamindb/core/datasets/__init__.py +6 -1
  30. lamindb/core/datasets/_core.py +12 -11
  31. lamindb/core/datasets/_small.py +67 -21
  32. lamindb/core/exceptions.py +1 -90
  33. lamindb/core/loaders.py +21 -15
  34. lamindb/core/relations.py +6 -4
  35. lamindb/core/storage/_anndata_accessor.py +49 -3
  36. lamindb/core/storage/_backed_access.py +12 -7
  37. lamindb/core/storage/_pyarrow_dataset.py +40 -15
  38. lamindb/core/storage/_tiledbsoma.py +56 -12
  39. lamindb/core/storage/paths.py +30 -24
  40. lamindb/core/subsettings/_creation_settings.py +4 -16
  41. lamindb/curators/__init__.py +2193 -846
  42. lamindb/curators/_cellxgene_schemas/__init__.py +26 -0
  43. lamindb/curators/_cellxgene_schemas/schema_versions.yml +104 -0
  44. lamindb/errors.py +96 -0
  45. lamindb/integrations/_vitessce.py +3 -3
  46. lamindb/migrations/0069_squashed.py +76 -75
  47. lamindb/migrations/0075_lamindbv1_part5.py +4 -5
  48. lamindb/migrations/0082_alter_feature_dtype.py +21 -0
  49. lamindb/migrations/0083_alter_feature_is_type_alter_flextable_is_type_and_more.py +94 -0
  50. lamindb/migrations/0084_alter_schemafeature_feature_and_more.py +35 -0
  51. lamindb/migrations/0085_alter_feature_is_type_alter_flextable_is_type_and_more.py +63 -0
  52. lamindb/migrations/0086_various.py +95 -0
  53. lamindb/migrations/0087_rename__schemas_m2m_artifact_feature_sets_and_more.py +41 -0
  54. lamindb/migrations/0088_schema_components.py +273 -0
  55. lamindb/migrations/0088_squashed.py +4372 -0
  56. lamindb/models.py +475 -168
  57. {lamindb-1.0.5.dist-info → lamindb-1.1.1.dist-info}/METADATA +9 -7
  58. lamindb-1.1.1.dist-info/RECORD +95 -0
  59. lamindb/curators/_spatial.py +0 -528
  60. lamindb/migrations/0052_squashed.py +0 -1261
  61. lamindb/migrations/0053_alter_featureset_hash_alter_paramvalue_created_by_and_more.py +0 -57
  62. lamindb/migrations/0054_alter_feature_previous_runs_and_more.py +0 -35
  63. lamindb/migrations/0055_artifact_type_artifactparamvalue_and_more.py +0 -61
  64. lamindb/migrations/0056_rename_ulabel_ref_is_name_artifactulabel_label_ref_is_name_and_more.py +0 -22
  65. lamindb/migrations/0057_link_models_latest_report_and_others.py +0 -356
  66. lamindb/migrations/0058_artifact__actions_collection__actions.py +0 -22
  67. lamindb/migrations/0059_alter_artifact__accessor_alter_artifact__hash_type_and_more.py +0 -31
  68. lamindb/migrations/0060_alter_artifact__actions.py +0 -22
  69. lamindb/migrations/0061_alter_collection_meta_artifact_alter_run_environment_and_more.py +0 -45
  70. lamindb/migrations/0062_add_is_latest_field.py +0 -32
  71. lamindb/migrations/0063_populate_latest_field.py +0 -45
  72. lamindb/migrations/0064_alter_artifact_version_alter_collection_version_and_more.py +0 -33
  73. lamindb/migrations/0065_remove_collection_feature_sets_and_more.py +0 -22
  74. lamindb/migrations/0066_alter_artifact__feature_values_and_more.py +0 -352
  75. lamindb/migrations/0067_alter_featurevalue_unique_together_and_more.py +0 -20
  76. lamindb/migrations/0068_alter_artifactulabel_unique_together_and_more.py +0 -20
  77. lamindb/migrations/0069_alter_artifact__accessor_alter_artifact__hash_type_and_more.py +0 -1294
  78. lamindb-1.0.5.dist-info/RECORD +0 -102
  79. {lamindb-1.0.5.dist-info → lamindb-1.1.1.dist-info}/LICENSE +0 -0
  80. {lamindb-1.0.5.dist-info → lamindb-1.1.1.dist-info}/WHEEL +0 -0
@@ -1,57 +0,0 @@
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- # Generated by Django 5.0.6 on 2024-05-29 08:56
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-
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- import django.db.models.deletion
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- from django.db import migrations, models
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-
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- import lamindb.base.users
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-
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-
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- class Migration(migrations.Migration):
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- dependencies = [
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- ("lamindb", "0052_squashed"),
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- ]
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-
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- operations = [
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- migrations.AlterField(
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- model_name="featureset",
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- name="hash",
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- field=models.CharField(
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- db_index=True, default=None, max_length=20, null=True, unique=True
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- ),
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- ),
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- migrations.AlterField(
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- model_name="paramvalue",
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- name="created_by",
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- field=models.ForeignKey(
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- default=lamindb.base.users.current_user_id,
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- on_delete=django.db.models.deletion.PROTECT,
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- to="lamindb.user",
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- ),
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- ),
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- migrations.AlterField(
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- model_name="run",
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- name="created_by",
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- field=models.ForeignKey(
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- default=lamindb.base.users.current_user_id,
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- on_delete=django.db.models.deletion.CASCADE,
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- to="lamindb.user",
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- ),
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- ),
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- migrations.AlterField(
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- model_name="transform",
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- name="created_by",
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- field=models.ForeignKey(
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- default=lamindb.base.users.current_user_id,
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- on_delete=django.db.models.deletion.PROTECT,
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- to="lamindb.user",
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- ),
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- ),
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- migrations.AlterUniqueTogether(
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- name="featurevalue",
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- unique_together={("feature", "value")},
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- ),
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- migrations.AlterUniqueTogether(
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- name="paramvalue",
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- unique_together={("param", "value")},
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- ),
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- ]
@@ -1,35 +0,0 @@
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- # Generated by Django 5.1 on 2024-06-13 10:31
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-
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- from django.db import migrations, models
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-
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-
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- class Migration(migrations.Migration):
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- dependencies = [
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- (
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- "lamindb",
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- "0053_alter_featureset_hash_alter_paramvalue_created_by_and_more",
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- ),
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- ]
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-
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- operations = [
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- migrations.AlterField(
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- model_name="feature",
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- name="previous_runs",
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- field=models.ManyToManyField(related_name="+", to="lamindb.run"),
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- ),
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- migrations.AlterField(
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- model_name="param",
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- name="previous_runs",
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- field=models.ManyToManyField(related_name="+", to="lamindb.run"),
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- ),
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- migrations.AlterField(
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- model_name="storage",
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- name="previous_runs",
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- field=models.ManyToManyField(related_name="+", to="lamindb.run"),
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- ),
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- migrations.AlterField(
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- model_name="ulabel",
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- name="previous_runs",
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- field=models.ManyToManyField(related_name="+", to="lamindb.run"),
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- ),
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- ]
@@ -1,61 +0,0 @@
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- # Generated by Django 5.1 on 2024-06-19 09:56
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-
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- import django.db.models.deletion
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- from django.db import migrations, models
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-
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- import lamindb.models
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-
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-
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- class Migration(migrations.Migration):
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- dependencies = [
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- ("lamindb", "0054_alter_feature_previous_runs_and_more"),
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- ]
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-
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- operations = [
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- migrations.AddField(
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- model_name="artifact",
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- name="type",
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- field=models.CharField(
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- choices=[("dataset", "dataset"), ("model", "model"), ("code", "code")],
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- db_index=True,
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- default=None,
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- max_length=20,
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- null=True,
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- ),
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- ),
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- migrations.CreateModel(
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- name="ArtifactParamValue",
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- fields=[
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- ("id", models.BigAutoField(primary_key=True, serialize=False)),
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- (
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- "artifact",
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- models.ForeignKey(
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- on_delete=django.db.models.deletion.CASCADE,
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- related_name="+",
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- to="lamindb.artifact",
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- ),
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- ),
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- (
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- "paramvalue",
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- models.ForeignKey(
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- on_delete=django.db.models.deletion.PROTECT,
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- related_name="+",
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- to="lamindb.paramvalue",
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- ),
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- ),
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- ],
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- options={
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- "unique_together": {("artifact", "paramvalue")},
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- },
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- bases=(models.Model, lamindb.models.LinkORM),
51
- ),
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- migrations.AddField(
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- model_name="artifact",
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- name="param_values",
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- field=models.ManyToManyField(
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- related_name="artifacts",
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- through="lamindb.ArtifactParamValue",
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- to="lamindb.paramvalue",
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- ),
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- ),
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- ]
@@ -1,22 +0,0 @@
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- # Generated by Django 5.1 on 2024-07-26 12:53
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-
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- from django.db import migrations
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-
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-
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- class Migration(migrations.Migration):
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- dependencies = [
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- ("lamindb", "0055_artifact_type_artifactparamvalue_and_more"),
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- ]
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-
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- operations = [
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- migrations.RenameField(
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- model_name="artifactulabel",
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- old_name="ulabel_ref_is_name",
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- new_name="label_ref_is_name",
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- ),
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- migrations.RenameField(
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- model_name="collectionulabel",
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- old_name="ulabel_ref_is_name",
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- new_name="label_ref_is_name",
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- ),
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- ]
@@ -1,356 +0,0 @@
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- # Generated by Django 5.0.7 on 2024-07-30 12:42
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-
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- import django.db.models.deletion
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- from django.db import migrations, models
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-
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-
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- class Migration(migrations.Migration):
8
- dependencies = [
9
- (
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- "lamindb",
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- "0056_rename_ulabel_ref_is_name_artifactulabel_label_ref_is_name_and_more",
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- ),
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- ]
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-
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- operations = [
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- migrations.RunSQL(
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- sql="""
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- UPDATE lamindb_artifact
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- SET hash = SUBSTR(hash, 1, 22)
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- WHERE length(hash) > 22;
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-
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- UPDATE lamindb_collection
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- SET hash = SUBSTR(hash, 1, 22)
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- WHERE length(hash) > 22;
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-
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- UPDATE lamindb_featureset
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- SET hash = SUBSTR(hash, 1, 22)
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- WHERE length(hash) > 22;
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- """,
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- ),
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- migrations.AlterField(
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- model_name="artifactfeatureset",
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- name="artifact",
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- field=models.ForeignKey(
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- on_delete=django.db.models.deletion.CASCADE,
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- related_name="links_feature_set",
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- to="lamindb.artifact",
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- ),
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- ),
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- migrations.AlterField(
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- model_name="artifactfeatureset",
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- name="featureset",
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- field=models.ForeignKey(
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- on_delete=django.db.models.deletion.PROTECT,
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- related_name="links_artifact",
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- to="lamindb.featureset",
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- ),
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- ),
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- migrations.AlterField(
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- model_name="artifactulabel",
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- name="artifact",
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- field=models.ForeignKey(
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- on_delete=django.db.models.deletion.CASCADE,
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- related_name="links_ulabel",
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- to="lamindb.artifact",
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- ),
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- ),
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- migrations.AlterField(
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- model_name="artifactulabel",
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- name="feature",
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- field=models.ForeignKey(
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- default=None,
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- null=True,
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- on_delete=django.db.models.deletion.PROTECT,
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- related_name="links_artifactulabel",
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- to="lamindb.feature",
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- ),
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- ),
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- migrations.AlterField(
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- model_name="artifactulabel",
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- name="ulabel",
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- field=models.ForeignKey(
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- on_delete=django.db.models.deletion.PROTECT,
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- related_name="links_artifact",
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- to="lamindb.ulabel",
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- ),
77
- ),
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- migrations.AlterField(
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- model_name="collectionartifact",
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- name="artifact",
81
- field=models.ForeignKey(
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- on_delete=django.db.models.deletion.PROTECT,
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- related_name="links_collection",
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- to="lamindb.artifact",
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- ),
86
- ),
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- migrations.AlterField(
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- model_name="collectionartifact",
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- name="collection",
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- field=models.ForeignKey(
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- on_delete=django.db.models.deletion.CASCADE,
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- related_name="links_artifact",
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- to="lamindb.collection",
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- ),
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- ),
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- migrations.AlterField(
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- model_name="collectionfeatureset",
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- name="collection",
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- field=models.ForeignKey(
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- on_delete=django.db.models.deletion.CASCADE,
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- related_name="links_feature_set",
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- to="lamindb.collection",
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- ),
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- ),
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- migrations.AlterField(
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- model_name="collectionfeatureset",
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- name="featureset",
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- field=models.ForeignKey(
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- on_delete=django.db.models.deletion.PROTECT,
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- related_name="links_collection",
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- to="lamindb.featureset",
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- ),
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- ),
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- migrations.AlterField(
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- model_name="collectionulabel",
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- name="collection",
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- field=models.ForeignKey(
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- on_delete=django.db.models.deletion.CASCADE,
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- related_name="links_ulabel",
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- to="lamindb.collection",
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- ),
122
- ),
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- migrations.AlterField(
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- model_name="collectionulabel",
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- name="feature",
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- field=models.ForeignKey(
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- default=None,
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- null=True,
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- on_delete=django.db.models.deletion.PROTECT,
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- related_name="links_collectionulabel",
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- to="lamindb.feature",
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- ),
133
- ),
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- migrations.AlterField(
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- model_name="collectionulabel",
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- name="ulabel",
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- field=models.ForeignKey(
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- on_delete=django.db.models.deletion.PROTECT,
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- related_name="links_collection",
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- to="lamindb.ulabel",
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- ),
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- ),
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- migrations.RemoveField(
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- model_name="transform",
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- name="latest_report",
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- ),
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- migrations.RenameField(
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- model_name="artifact",
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- old_name="input_of",
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- new_name="input_of_runs",
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- ),
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- migrations.RenameField(
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- model_name="collection",
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- old_name="input_of",
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- new_name="input_of_runs",
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- ),
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- migrations.RenameField(
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- model_name="collection",
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- old_name="unordered_artifacts",
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- new_name="artifacts",
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- ),
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- migrations.RenameField(
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- model_name="collection",
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- old_name="artifact",
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- new_name="meta_artifact",
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- ),
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- migrations.AlterField(
168
- model_name="artifact",
169
- name="type",
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- field=models.CharField(
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- choices=[("dataset", "dataset"), ("model", "model")],
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- db_index=True,
173
- default=None,
174
- max_length=20,
175
- null=True,
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- ),
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- ),
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- migrations.AlterField(
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- model_name="artifact",
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- name="accessor",
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- field=models.CharField(
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- db_column="accessor",
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- db_index=True,
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- default=None,
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- max_length=64,
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- null=True,
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- ),
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- ),
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- migrations.RenameField(
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- model_name="artifact",
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- old_name="accessor",
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- new_name="_accessor",
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- ),
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- migrations.AlterField(
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- model_name="feature",
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- name="name",
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- field=models.CharField(
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- db_index=True, default=None, max_length=150, unique=True
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- ),
200
- ),
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- migrations.RenameField(
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- model_name="transform",
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- old_name="source_code",
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- new_name="_source_code_artifact",
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- ),
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- migrations.AlterField(
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- model_name="transform",
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- name="_source_code_artifact",
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- field=models.ForeignKey(
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- default=None,
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- null=True,
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- on_delete=django.db.models.deletion.PROTECT,
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- related_name="_source_code_of",
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- to="lamindb.artifact",
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- ),
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- ),
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- migrations.AlterField(
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- model_name="artifact",
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- name="type",
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- field=models.CharField(
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- db_index=True, default=None, max_length=20, null=True
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- ),
223
- ),
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- migrations.AlterField(
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- model_name="transform",
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- name="type",
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- field=models.CharField(db_index=True, default="pipeline", max_length=20),
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- ),
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- migrations.RenameField(
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- model_name="artifact",
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- old_name="feature_values",
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- new_name="_feature_values",
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- ),
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- migrations.RenameField(
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- model_name="artifact",
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- old_name="hash_type",
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- new_name="_hash_type",
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- ),
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- migrations.RenameField(
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- model_name="artifact",
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- old_name="key_is_virtual",
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- new_name="_key_is_virtual",
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- ),
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- migrations.RenameField(
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- model_name="artifact",
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- old_name="param_values",
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- new_name="_param_values",
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- ),
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- migrations.RenameField(
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- model_name="run",
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- old_name="param_values",
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- new_name="_param_values",
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- ),
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- migrations.RenameField(
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- model_name="artifact",
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- old_name="previous_runs",
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- new_name="_previous_runs",
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- ),
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- migrations.RenameField(
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- model_name="collection",
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- old_name="previous_runs",
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- new_name="_previous_runs",
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- ),
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- migrations.RenameField(
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- model_name="feature",
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- old_name="previous_runs",
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- new_name="_previous_runs",
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- ),
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- migrations.RenameField(
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- model_name="param",
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- old_name="previous_runs",
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- new_name="_previous_runs",
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- ),
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- migrations.RenameField(
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- model_name="storage",
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- old_name="previous_runs",
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- new_name="_previous_runs",
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- ),
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- migrations.RenameField(
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- model_name="ulabel",
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- old_name="previous_runs",
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- new_name="_previous_runs",
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- ),
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- migrations.AlterField(
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- model_name="artifact",
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- name="_hash_type",
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- field=models.CharField(
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- db_column="hash_type",
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- db_index=True,
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- default=None,
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- max_length=30,
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- null=True,
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- ),
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- ),
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- migrations.AlterField(
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- model_name="artifact",
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- name="_key_is_virtual",
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- field=models.BooleanField(db_column="key_is_virtual"),
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- ),
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- migrations.AlterField(
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- model_name="artifact",
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- name="hash",
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- field=models.CharField(
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- db_index=True, default=None, max_length=22, null=True
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- ),
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- ),
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- migrations.AlterField(
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- model_name="collection",
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- name="hash",
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- field=models.CharField(
311
- db_index=True, default=None, max_length=22, null=True
312
- ),
313
- ),
314
- migrations.AlterField(
315
- model_name="featureset",
316
- name="hash",
317
- field=models.CharField(
318
- db_index=True, default=None, max_length=22, null=True, unique=True
319
- ),
320
- ),
321
- migrations.AddField(
322
- model_name="transform",
323
- name="hash",
324
- field=models.CharField(
325
- db_index=True, default=None, max_length=22, null=True
326
- ),
327
- ),
328
- migrations.AddField(
329
- model_name="transform",
330
- name="source_code",
331
- field=models.TextField(default=None, null=True),
332
- ),
333
- migrations.AddField(
334
- model_name="run",
335
- name="parent",
336
- field=models.ForeignKey(
337
- default=None,
338
- null=True,
339
- on_delete=django.db.models.deletion.CASCADE,
340
- related_name="children",
341
- to="lamindb.run",
342
- ),
343
- ),
344
- migrations.RenameField(
345
- model_name="transform",
346
- old_name="parents",
347
- new_name="predecessors",
348
- ),
349
- migrations.AlterField(
350
- model_name="transform",
351
- name="predecessors",
352
- field=models.ManyToManyField(
353
- related_name="successors", to="lamindb.transform"
354
- ),
355
- ),
356
- ]
@@ -1,22 +0,0 @@
1
- # Generated by Django 5.2 on 2024-08-02 08:03
2
-
3
- from django.db import migrations, models
4
-
5
-
6
- class Migration(migrations.Migration):
7
- dependencies = [
8
- ("lamindb", "0057_link_models_latest_report_and_others"),
9
- ]
10
-
11
- operations = [
12
- migrations.AddField(
13
- model_name="artifact",
14
- name="_actions",
15
- field=models.ManyToManyField(related_name="+", to="lamindb.artifact"),
16
- ),
17
- migrations.AddField(
18
- model_name="collection",
19
- name="_actions",
20
- field=models.ManyToManyField(related_name="+", to="lamindb.artifact"),
21
- ),
22
- ]
@@ -1,31 +0,0 @@
1
- # Generated by Django 5.2 on 2024-08-02 15:03
2
-
3
- from django.db import migrations, models
4
-
5
-
6
- class Migration(migrations.Migration):
7
- dependencies = [
8
- ("lamindb", "0058_artifact__actions_collection__actions"),
9
- ]
10
-
11
- operations = [
12
- migrations.AlterField(
13
- model_name="artifact",
14
- name="_accessor",
15
- field=models.CharField(
16
- db_index=True, default=None, max_length=64, null=True
17
- ),
18
- ),
19
- migrations.AlterField(
20
- model_name="artifact",
21
- name="_hash_type",
22
- field=models.CharField(
23
- db_index=True, default=None, max_length=30, null=True
24
- ),
25
- ),
26
- migrations.AlterField(
27
- model_name="artifact",
28
- name="_key_is_virtual",
29
- field=models.BooleanField(),
30
- ),
31
- ]
@@ -1,22 +0,0 @@
1
- # Generated by Django 5.2 on 2024-08-07 19:51
2
-
3
- from django.db import migrations, models
4
-
5
-
6
- class Migration(migrations.Migration):
7
- dependencies = [
8
- (
9
- "lamindb",
10
- "0059_alter_artifact__accessor_alter_artifact__hash_type_and_more",
11
- ),
12
- ]
13
-
14
- operations = [
15
- migrations.AlterField(
16
- model_name="artifact",
17
- name="_actions",
18
- field=models.ManyToManyField(
19
- related_name="_action_targets", to="lamindb.artifact"
20
- ),
21
- ),
22
- ]
@@ -1,45 +0,0 @@
1
- # Generated by Django 5.2 on 2024-08-08 11:33
2
-
3
- import django.db.models.deletion
4
- from django.db import migrations, models
5
-
6
-
7
- class Migration(migrations.Migration):
8
- dependencies = [
9
- ("lamindb", "0060_alter_artifact__actions"),
10
- ]
11
-
12
- operations = [
13
- migrations.AlterField(
14
- model_name="collection",
15
- name="meta_artifact",
16
- field=models.OneToOneField(
17
- null=True,
18
- on_delete=django.db.models.deletion.PROTECT,
19
- related_name="_meta_of_collection",
20
- to="lamindb.artifact",
21
- ),
22
- ),
23
- migrations.AlterField(
24
- model_name="run",
25
- name="environment",
26
- field=models.ForeignKey(
27
- default=None,
28
- null=True,
29
- on_delete=django.db.models.deletion.PROTECT,
30
- related_name="_environment_of",
31
- to="lamindb.artifact",
32
- ),
33
- ),
34
- migrations.AlterField(
35
- model_name="run",
36
- name="report",
37
- field=models.ForeignKey(
38
- default=None,
39
- null=True,
40
- on_delete=django.db.models.deletion.PROTECT,
41
- related_name="_report_of",
42
- to="lamindb.artifact",
43
- ),
44
- ),
45
- ]
@@ -1,32 +0,0 @@
1
- # Generated by Django 5.2 on 2024-08-12 07:46
2
-
3
- from django.db import migrations, models
4
-
5
-
6
- # data migration comes in the next migration due to pending triggers
7
- class Migration(migrations.Migration):
8
- dependencies = [
9
- (
10
- "lamindb",
11
- "0061_alter_collection_meta_artifact_alter_run_environment_and_more",
12
- ),
13
- ]
14
-
15
- operations = [
16
- # add the field
17
- migrations.AddField(
18
- model_name="artifact",
19
- name="is_latest",
20
- field=models.BooleanField(db_index=True, default=True),
21
- ),
22
- migrations.AddField(
23
- model_name="collection",
24
- name="is_latest",
25
- field=models.BooleanField(db_index=True, default=True),
26
- ),
27
- migrations.AddField(
28
- model_name="transform",
29
- name="is_latest",
30
- field=models.BooleanField(db_index=True, default=True),
31
- ),
32
- ]