forked from enviPath/enviPy
[Feature] PEPPER in enviPath (#332)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#332
This commit is contained in:
179
epdb/migrations/0016_remove_enviformer_model_status_and_more.py
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179
epdb/migrations/0016_remove_enviformer_model_status_and_more.py
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@ -0,0 +1,179 @@
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# Generated by Django 5.2.7 on 2026-02-12 09:38
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import django.db.models.deletion
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from django.conf import settings
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from django.db import migrations, models
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class Migration(migrations.Migration):
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dependencies = [
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("epdb", "0015_user_is_reviewer"),
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]
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operations = [
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migrations.RemoveField(
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model_name="enviformer",
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name="model_status",
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),
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migrations.RemoveField(
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model_name="mlrelativereasoning",
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name="model_status",
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),
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migrations.RemoveField(
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model_name="rulebasedrelativereasoning",
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name="model_status",
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),
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migrations.AddField(
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model_name="epmodel",
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name="model_status",
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field=models.CharField(
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choices=[
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("INITIAL", "Initial"),
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("INITIALIZING", "Model is initializing."),
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("BUILDING", "Model is building."),
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(
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"BUILT_NOT_EVALUATED",
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"Model is built and can be used for predictions, Model is not evaluated yet.",
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),
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("EVALUATING", "Model is evaluating"),
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("FINISHED", "Model has finished building and evaluation."),
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("ERROR", "Model has failed."),
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],
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default="INITIAL",
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),
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),
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migrations.AlterField(
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model_name="enviformer",
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name="eval_packages",
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field=models.ManyToManyField(
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blank=True,
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related_name="%(app_label)s_%(class)s_eval_packages",
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to=settings.EPDB_PACKAGE_MODEL,
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verbose_name="Evaluation Packages",
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),
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),
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migrations.AlterField(
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model_name="enviformer",
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name="rule_packages",
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field=models.ManyToManyField(
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blank=True,
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related_name="%(app_label)s_%(class)s_rule_packages",
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to=settings.EPDB_PACKAGE_MODEL,
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verbose_name="Rule Packages",
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),
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),
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migrations.AlterField(
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model_name="mlrelativereasoning",
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name="eval_packages",
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field=models.ManyToManyField(
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blank=True,
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related_name="%(app_label)s_%(class)s_eval_packages",
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to=settings.EPDB_PACKAGE_MODEL,
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verbose_name="Evaluation Packages",
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),
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),
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migrations.AlterField(
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model_name="mlrelativereasoning",
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name="rule_packages",
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field=models.ManyToManyField(
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blank=True,
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related_name="%(app_label)s_%(class)s_rule_packages",
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to=settings.EPDB_PACKAGE_MODEL,
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verbose_name="Rule Packages",
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),
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),
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migrations.AlterField(
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model_name="rulebasedrelativereasoning",
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name="eval_packages",
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field=models.ManyToManyField(
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blank=True,
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related_name="%(app_label)s_%(class)s_eval_packages",
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to=settings.EPDB_PACKAGE_MODEL,
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verbose_name="Evaluation Packages",
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),
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),
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migrations.AlterField(
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model_name="rulebasedrelativereasoning",
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name="rule_packages",
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field=models.ManyToManyField(
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blank=True,
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related_name="%(app_label)s_%(class)s_rule_packages",
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to=settings.EPDB_PACKAGE_MODEL,
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verbose_name="Rule Packages",
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),
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),
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migrations.CreateModel(
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name="PropertyPluginModel",
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fields=[
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(
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"epmodel_ptr",
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models.OneToOneField(
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auto_created=True,
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on_delete=django.db.models.deletion.CASCADE,
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parent_link=True,
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primary_key=True,
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serialize=False,
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to="epdb.epmodel",
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),
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),
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("threshold", models.FloatField(default=0.5)),
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("eval_results", models.JSONField(blank=True, default=dict, null=True)),
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("multigen_eval", models.BooleanField(default=False)),
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("plugin_identifier", models.CharField(max_length=255)),
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(
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"app_domain",
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models.ForeignKey(
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blank=True,
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default=None,
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null=True,
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on_delete=django.db.models.deletion.SET_NULL,
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to="epdb.applicabilitydomain",
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),
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),
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(
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"data_packages",
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models.ManyToManyField(
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blank=True,
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related_name="%(app_label)s_%(class)s_data_packages",
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to=settings.EPDB_PACKAGE_MODEL,
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verbose_name="Data Packages",
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),
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),
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(
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"eval_packages",
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models.ManyToManyField(
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blank=True,
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related_name="%(app_label)s_%(class)s_eval_packages",
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to=settings.EPDB_PACKAGE_MODEL,
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verbose_name="Evaluation Packages",
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),
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),
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(
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"rule_packages",
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models.ManyToManyField(
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blank=True,
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related_name="%(app_label)s_%(class)s_rule_packages",
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to=settings.EPDB_PACKAGE_MODEL,
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verbose_name="Rule Packages",
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),
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),
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],
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options={
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"abstract": False,
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},
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bases=("epdb.epmodel",),
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),
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migrations.AddField(
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model_name="setting",
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name="property_models",
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field=models.ManyToManyField(
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blank=True,
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related_name="settings",
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to="epdb.propertypluginmodel",
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verbose_name="Setting Property Models",
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),
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),
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migrations.DeleteModel(
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name="PluginModel",
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),
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]
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93
epdb/migrations/0017_additionalinformation.py
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93
epdb/migrations/0017_additionalinformation.py
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@ -0,0 +1,93 @@
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# Generated by Django 5.2.7 on 2026-02-20 12:02
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import django.db.models.deletion
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import uuid
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from django.conf import settings
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from django.db import migrations, models
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class Migration(migrations.Migration):
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dependencies = [
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("contenttypes", "0002_remove_content_type_name"),
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("epdb", "0016_remove_enviformer_model_status_and_more"),
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]
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operations = [
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migrations.CreateModel(
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name="AdditionalInformation",
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fields=[
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(
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"id",
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models.BigAutoField(
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auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
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),
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),
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("uuid", models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
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("url", models.TextField(null=True, unique=True, verbose_name="URL")),
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("kv", models.JSONField(blank=True, default=dict, null=True)),
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("type", models.TextField(verbose_name="Additional Information Type")),
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("data", models.JSONField(blank=True, default=dict, null=True)),
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("object_id", models.PositiveBigIntegerField(blank=True, null=True)),
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(
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"content_type",
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models.ForeignKey(
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blank=True,
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null=True,
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on_delete=django.db.models.deletion.CASCADE,
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to="contenttypes.contenttype",
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),
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),
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(
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"package",
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models.ForeignKey(
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on_delete=django.db.models.deletion.CASCADE,
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to=settings.EPDB_PACKAGE_MODEL,
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verbose_name="Package",
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),
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),
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(
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"scenario",
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models.ForeignKey(
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blank=True,
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null=True,
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on_delete=django.db.models.deletion.CASCADE,
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related_name="scenario_additional_information",
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to="epdb.scenario",
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),
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),
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],
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options={
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"indexes": [
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models.Index(fields=["type"], name="epdb_additi_type_394349_idx"),
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models.Index(
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fields=["scenario", "type"], name="epdb_additi_scenari_a59edf_idx"
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),
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models.Index(
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fields=["content_type", "object_id"], name="epdb_additi_content_44d4b4_idx"
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),
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models.Index(
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fields=["scenario", "content_type", "object_id"],
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name="epdb_additi_scenari_ef2bf5_idx",
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),
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],
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"constraints": [
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models.CheckConstraint(
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condition=models.Q(
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models.Q(("content_type__isnull", True), ("object_id__isnull", True)),
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models.Q(("content_type__isnull", False), ("object_id__isnull", False)),
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_connector="OR",
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),
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name="ck_addinfo_gfk_pair",
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),
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models.CheckConstraint(
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condition=models.Q(
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("scenario__isnull", False),
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("content_type__isnull", False),
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_connector="OR",
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),
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name="ck_addinfo_not_both_null",
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),
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],
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},
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),
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]
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132
epdb/migrations/0018_auto_20260220_1203.py
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132
epdb/migrations/0018_auto_20260220_1203.py
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@ -0,0 +1,132 @@
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# Generated by Django 5.2.7 on 2026-02-20 12:03
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from django.db import migrations
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def get_additional_information(scenario):
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from envipy_additional_information import registry
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from envipy_additional_information.parsers import TypeOfAerationParser
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for k, vals in scenario.additional_information.items():
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if k == "enzyme":
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continue
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if k == "SpikeConentration":
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k = "SpikeConcentration"
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if k == "AerationType":
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k = "TypeOfAeration"
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for v in vals:
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# Per default additional fields are ignored
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MAPPING = {c.__name__: c for c in registry.list_models().values()}
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try:
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inst = MAPPING[k](**v)
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except Exception:
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if k == "TypeOfAeration":
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toa = TypeOfAerationParser()
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inst = toa.from_string(v["type"])
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# Add uuid to uniquely identify objects for manipulation
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if "uuid" in v:
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inst.__dict__["uuid"] = v["uuid"]
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yield inst
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def forward_func(apps, schema_editor):
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Scenario = apps.get_model("epdb", "Scenario")
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ContentType = apps.get_model("contenttypes", "ContentType")
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AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
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bulk = []
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related = []
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ctype = {o.model: o for o in ContentType.objects.all()}
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parents = Scenario.objects.prefetch_related(
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"compound_set",
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"compoundstructure_set",
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"reaction_set",
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"rule_set",
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"pathway_set",
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"node_set",
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"edge_set",
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).filter(parent__isnull=True)
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for i, scenario in enumerate(parents):
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print(f"{i + 1}/{len(parents)}", end="\r")
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if scenario.parent is not None:
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related.append(scenario.parent)
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continue
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for ai in get_additional_information(scenario):
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bulk.append(
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AdditionalInformation(
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package=scenario.package,
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scenario=scenario,
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type=ai.__class__.__name__,
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data=ai.model_dump(mode="json"),
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)
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)
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print("\n", len(bulk))
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related = Scenario.objects.prefetch_related(
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"compound_set",
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"compoundstructure_set",
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"reaction_set",
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"rule_set",
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"pathway_set",
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"node_set",
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"edge_set",
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).filter(parent__isnull=False)
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for i, scenario in enumerate(related):
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print(f"{i + 1}/{len(related)}", end="\r")
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parent = scenario.parent
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# Check to which objects this scenario is attached to
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for ai in get_additional_information(scenario):
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rel_objs = [
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"compound",
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"compoundstructure",
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"reaction",
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"rule",
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"pathway",
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"node",
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"edge",
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]
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for rel_obj in rel_objs:
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for o in getattr(scenario, f"{rel_obj}_set").all():
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bulk.append(
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AdditionalInformation(
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package=scenario.package,
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scenario=parent,
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type=ai.__class__.__name__,
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data=ai.model_dump(mode="json"),
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content_type=ctype[rel_obj],
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object_id=o.pk,
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)
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)
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print("Start creating additional information objects...")
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AdditionalInformation.objects.bulk_create(bulk)
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print("Done!")
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print(len(bulk))
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Scenario.objects.filter(parent__isnull=False).delete()
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# Call ai save to fix urls
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ais = AdditionalInformation.objects.all()
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total = ais.count()
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for i, ai in enumerate(ais):
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print(f"{i + 1}/{total}", end="\r")
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ai.save()
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class Migration(migrations.Migration):
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dependencies = [
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("epdb", "0017_additionalinformation"),
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]
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operations = [
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migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
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]
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@ -0,0 +1,20 @@
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# Generated by Django 5.2.7 on 2026-02-23 08:45
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from django.db import migrations
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class Migration(migrations.Migration):
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dependencies = [
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("epdb", "0018_auto_20260220_1203"),
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]
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operations = [
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migrations.RemoveField(
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model_name="scenario",
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name="additional_information",
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),
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migrations.RemoveField(
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model_name="scenario",
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name="parent",
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),
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]
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Reference in New Issue
Block a user