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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,16 +1,16 @@ | ||
| """.. Ignore pydocstyle D400. | ||
| ================================ | ||
| Mutations Base App Configuration | ||
| ================================ | ||
| =============================== | ||
| Variants Base App Configuration | ||
| =============================== | ||
| """ | ||
| from django.apps import AppConfig | ||
|
|
||
|
|
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| class MutationsConfig(AppConfig): | ||
| class VariantsConfig(AppConfig): | ||
| """App configuration.""" | ||
|
|
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| name = "resolwe_bio.mutations" | ||
| label = "resolwe_bio_mutations" | ||
| verbose_name = "Resolwe Bioinformatics Mutations Base" | ||
| name = "resolwe_bio.variants" | ||
| label = "resolwe_bio_variants" | ||
| verbose_name = "Resolwe Bioinformatics Variants Base" |
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| @@ -0,0 +1,192 @@ | ||
| # Generated by Django 4.2.11 on 2024-03-25 10:07 | ||
|
|
||
| from django.conf import settings | ||
| import django.contrib.postgres.fields | ||
| from django.db import migrations, models | ||
| import django.db.models.deletion | ||
|
|
||
|
|
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| class Migration(migrations.Migration): | ||
|
|
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| initial = True | ||
|
|
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| dependencies = [ | ||
| migrations.swappable_dependency(settings.AUTH_USER_MODEL), | ||
| ("flow", "0021_annotationvalue_modified"), | ||
| ] | ||
|
|
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| operations = [ | ||
| migrations.CreateModel( | ||
| name="Variant", | ||
| fields=[ | ||
| ( | ||
| "id", | ||
| models.AutoField( | ||
| auto_created=True, | ||
| primary_key=True, | ||
| serialize=False, | ||
| verbose_name="ID", | ||
| ), | ||
| ), | ||
| ("species", models.CharField(max_length=50)), | ||
| ("genome_assembly", models.CharField(max_length=20)), | ||
| ("chromosome", models.CharField(max_length=20)), | ||
| ("position", models.PositiveBigIntegerField()), | ||
| ("reference", models.CharField(max_length=100)), | ||
| ("alternative", models.CharField(max_length=100)), | ||
| ], | ||
| ), | ||
| migrations.CreateModel( | ||
| name="VariantExperiment", | ||
| fields=[ | ||
| ( | ||
| "id", | ||
| models.AutoField( | ||
| auto_created=True, | ||
| primary_key=True, | ||
| serialize=False, | ||
| verbose_name="ID", | ||
| ), | ||
| ), | ||
| ("variant_data_source", models.CharField(max_length=100)), | ||
| ("date", models.DateTimeField(auto_now_add=True, db_index=True)), | ||
| ( | ||
| "contributor", | ||
| models.ForeignKey( | ||
| on_delete=django.db.models.deletion.PROTECT, | ||
| to=settings.AUTH_USER_MODEL, | ||
| ), | ||
| ), | ||
| ], | ||
| ), | ||
| migrations.CreateModel( | ||
| name="VariantCall", | ||
| fields=[ | ||
| ( | ||
| "id", | ||
| models.AutoField( | ||
| auto_created=True, | ||
| primary_key=True, | ||
| serialize=False, | ||
| verbose_name="ID", | ||
| ), | ||
| ), | ||
| ("quality", models.FloatField()), | ||
| ("depth", models.PositiveIntegerField()), | ||
| ("filter", models.CharField(max_length=20)), | ||
| ("genotype", models.CharField(blank=True, max_length=100, null=True)), | ||
| ( | ||
| "data", | ||
| models.ForeignKey( | ||
| blank=True, | ||
| null=True, | ||
| on_delete=django.db.models.deletion.CASCADE, | ||
| related_name="variant_calls", | ||
| to="flow.data", | ||
| ), | ||
| ), | ||
| ( | ||
| "experiment", | ||
| models.ForeignKey( | ||
| blank=True, | ||
| null=True, | ||
| on_delete=django.db.models.deletion.CASCADE, | ||
| related_name="variant_calls", | ||
| to="resolwe_bio_variants.variantexperiment", | ||
| ), | ||
| ), | ||
| ( | ||
| "sample", | ||
| models.ForeignKey( | ||
| blank=True, | ||
| null=True, | ||
| on_delete=django.db.models.deletion.CASCADE, | ||
| related_name="variant_calls", | ||
| to="flow.entity", | ||
| ), | ||
| ), | ||
| ( | ||
| "variant", | ||
| models.ForeignKey( | ||
| blank=True, | ||
| null=True, | ||
| on_delete=django.db.models.deletion.CASCADE, | ||
| related_name="variant_calls", | ||
| to="resolwe_bio_variants.variant", | ||
| ), | ||
| ), | ||
| ], | ||
| ), | ||
| migrations.CreateModel( | ||
| name="VariantAnnotation", | ||
| fields=[ | ||
| ( | ||
| "id", | ||
| models.AutoField( | ||
| auto_created=True, | ||
| primary_key=True, | ||
| serialize=False, | ||
| verbose_name="ID", | ||
| ), | ||
| ), | ||
| ("type", models.CharField(blank=True, max_length=100, null=True)), | ||
| ("annotation", models.CharField(max_length=200)), | ||
| ("annotation_impact", models.CharField(max_length=20)), | ||
| ("gene", models.CharField(max_length=100)), | ||
| ("protein_impact", models.CharField(max_length=100)), | ||
| ( | ||
| "feature_id", | ||
| django.contrib.postgres.fields.ArrayField( | ||
| base_field=models.CharField(max_length=200), | ||
| default=list, | ||
| size=None, | ||
| ), | ||
| ), | ||
| ( | ||
| "clinical_diagnosis", | ||
| models.CharField(blank=True, max_length=200, null=True), | ||
| ), | ||
| ( | ||
| "clinical_significance", | ||
| models.CharField(blank=True, max_length=100, null=True), | ||
| ), | ||
| ("dbsnp_id", models.CharField(blank=True, max_length=20, null=True)), | ||
| ( | ||
| "clinical_var_id", | ||
| models.CharField(blank=True, max_length=20, null=True), | ||
| ), | ||
| ( | ||
| "data", | ||
| models.ForeignKey( | ||
| blank=True, | ||
| null=True, | ||
| on_delete=django.db.models.deletion.CASCADE, | ||
| related_name="variant_annotations", | ||
| to="flow.data", | ||
| ), | ||
| ), | ||
| ( | ||
| "variant", | ||
| models.OneToOneField( | ||
| on_delete=django.db.models.deletion.CASCADE, | ||
| related_name="annotation", | ||
| to="resolwe_bio_variants.variant", | ||
| ), | ||
| ), | ||
| ], | ||
| ), | ||
| migrations.AddConstraint( | ||
| model_name="variant", | ||
| constraint=models.UniqueConstraint( | ||
| fields=( | ||
| "species", | ||
| "genome_assembly", | ||
| "chromosome", | ||
| "position", | ||
| "reference", | ||
| "alternative", | ||
| ), | ||
| name="uniq_composite_key_variants", | ||
| ), | ||
| ), | ||
| ] |
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