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docs: omop investigation (#1919)
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‎CodeListLibrary_project/clinicalcode/migrations/0134_alter_omop_codes_valid_end_date_omoprelationships.py‎

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# Generated by Django 5.1.8 on 2026-02-09 14:32
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import datetime
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import django.contrib.postgres.indexes
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import django.db.models.deletion
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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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('clinicalcode', '0133_omop_codes'),
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]
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operations = [
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migrations.AlterField(
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model_name='omop_codes',
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name='valid_end_date',
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field=models.DateField(blank=True, default=datetime.date(2099, 12, 31)),
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),
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migrations.CreateModel(
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name='OMOPRelationships',
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fields=[
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('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False)),
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('relationship', models.CharField(max_length=64)),
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('valid_start_date', models.DateField(auto_now_add=True)),
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('valid_end_date', models.DateField(blank=True, default=datetime.date(2099, 12, 31))),
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('invalid_reason', models.CharField(blank=True, choices=[('D', 'Deprecated'), ('U', 'Upgraded')], default=None, max_length=1, null=True)),
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('code0', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='source_relationships', to='clinicalcode.omop_codes', to_field='code')),
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('code1', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='destination_relationships', to='clinicalcode.omop_codes', to_field='code')),
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],
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options={
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'indexes': [models.Index(fields=['code0'], name='clinicalcod_code0_i_9f4db1_idx'), models.Index(fields=['code1'], name='clinicalcod_code1_i_fbd524_idx'), models.Index(fields=['code0', 'code1'], name='clinicalcod_code0_i_634ab7_idx'), models.Index(fields=['code0', 'relationship', 'invalid_reason'], name='clinicalcod_code0_i_bea734_idx'), django.contrib.postgres.indexes.GinIndex(fields=['code0'], name='omop_e0_trgm_idx', opclasses=['gin_trgm_ops']), django.contrib.postgres.indexes.GinIndex(fields=['code0', 'relationship', 'invalid_reason'], name='omop_e0t_tgbt_idx', opclasses=['', 'gin_trgm_ops', ''])],
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'unique_together': {('code0', 'code1', 'relationship')},
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},
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),
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]

‎CodeListLibrary_project/clinicalcode/models/OMOP_CODES.py‎

Lines changed: 180 additions & 102 deletions
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from django.utils.translation import gettext_lazy as _
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from django.contrib.postgres.indexes import GinIndex
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import datetime
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class StandardFlag(models.TextChoices):
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"""
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See `standard_concept` column of `CONCEPT` table found in `OHDSI docs`_.
@@ -11,6 +13,7 @@ class StandardFlag(models.TextChoices):
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STANDARD = 'S', _('Standard Concept')
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CLASSIFICATION = 'C', _('Classification Concept')
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class InvalidFlag(models.TextChoices):
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"""
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See `invalid_reason` column of `CONCEPT` table found in `OHDSI docs`_.
@@ -20,106 +23,181 @@ class InvalidFlag(models.TextChoices):
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DEPRECATED = 'D', _('Deprecated')
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UPGRADED = 'U', _('Upgraded')
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class OMOP_CODES(models.Model):
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"""
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Represents a standardised `OMOP`_ code from its Common Data Model, related to :model:`clinicalcode.CodingSystem`.
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Version
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-------
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Vocabulary version: `v20250827`
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Reference
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---------
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See `OHDSI Single-page docs`_.
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Mapping
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----------
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| Attribute | Table->Column |
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|:---------------------|:---------------------------------|
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| `code` | `CONCEPT->concept_id` |
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| `description` | `CONCEPT->concept_name` |
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| `is_code` | `N/A` |
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| `is_valid` | `N/A` |
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| `standard_concept` | `CONCEPT->standard_concept` |
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| `coding_name` | `N/A` |
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| `coding_system_id` | `N/A` |
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| `domain_name` | `CONCEPT->domain_id` |
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| `class_name` | `CONCEPT->concept_class_id` |
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| `vocabulary_name` | `CONCEPT->vocabulary_id` |
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| `vocabulary_code` | `CONCEPT->concept_code` |
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| `vocabulary_version` | `VOCABULARY->vocabulary_version` |
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| `valid_start_date` | `CONCEPT->valid_start_date` |
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| `valid_end_date` | `CONCEPT->valid_end_date` |
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| `invalid_reason` | `CONCEPT->invalid_reason` |
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| `created` | `N/A` |
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| `modified` | `N/A` |
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.. _OMOP: https://www.ohdsi.org/data-standardization/
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.. _OHDSI Single-page docs: https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:single-page
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"""
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id = models.BigAutoField(auto_created=True, primary_key=True)
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code = models.CharField(max_length=64, null=True, blank=True, unique=True, default='')
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description = models.CharField(max_length=256, null=True, blank=True, default='')
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is_code = models.BooleanField(null=False, default=True)
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is_valid = models.BooleanField(null=False, default=True)
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standard_concept = models.CharField(
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# 'S', 'C' or NULL
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null=True,
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blank=True,
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choices=StandardFlag.choices,
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default=None,
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max_length=1,
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)
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coding_name = models.CharField(max_length=256, null=True, blank=True, default='')
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coding_system = models.ForeignKey(
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'clinicalcode.CodingSystem',
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on_delete=models.SET_NULL,
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null=True,
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blank=True,
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default=None,
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related_name='omop_code'
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)
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domain_name = models.CharField(max_length=256, null=True, blank=True, default='')
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class_name = models.CharField(max_length=256, null=True, blank=True, default='')
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vocabulary_name = models.CharField(max_length=64, null=True, blank=True, default='')
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vocabulary_code = models.CharField(max_length=64, null=True, blank=True, default='')
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vocabulary_version = models.CharField(max_length=256, null=True, blank=True, default='')
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valid_start_date = models.DateField(null=True, blank=True)
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valid_end_date = models.DateField(null=True, blank=True)
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invalid_reason = models.CharField(
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# 'D', 'U' or NULL
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null=True,
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blank=True,
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choices=InvalidFlag.choices,
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default=None,
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max_length=1,
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)
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created = models.DateTimeField(auto_now_add=True, editable=True)
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modified = models.DateTimeField(auto_now_add=True, editable=True)
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class Meta:
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ordering = ('id',)
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indexes = [
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models.Index(fields=['id']),
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models.Index(fields=['created']),
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GinIndex(
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name='omop_cd_trgm_idx',
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fields=['code'],
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opclasses=['gin_trgm_ops']
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),
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GinIndex(
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name='omop_desc_trgm_idx',
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fields=['description'],
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opclasses=['gin_trgm_ops']
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),
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GinIndex(
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name='omop_cs_trgm_idx',
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fields=['coding_name'],
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opclasses=['gin_trgm_ops']
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),
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GinIndex(
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name='omop_vscd_trgm_idx',
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fields=['vocabulary_code'],
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opclasses=['gin_trgm_ops']
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),
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]
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"""
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Represents a standardised `OMOP`_ code from its Common Data Model, related to :model:`clinicalcode.CodingSystem`.
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Version
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-------
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Vocabulary version: `v20250827`
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Reference
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---------
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See `OHDSI Single-page docs`_.
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Mapping
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-------
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| Attribute | Table->Column |
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|:---------------------|:---------------------------------|
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| `code` | `CONCEPT->concept_id` |
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| `description` | `CONCEPT->concept_name` |
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| `is_code` | `N/A` |
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| `is_valid` | `N/A` |
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| `standard_concept` | `CONCEPT->standard_concept` |
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| `coding_name` | `N/A` |
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| `coding_system_id` | `N/A` |
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| `domain_name` | `CONCEPT->domain_id` |
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| `class_name` | `CONCEPT->concept_class_id` |
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| `vocabulary_name` | `CONCEPT->vocabulary_id` |
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| `vocabulary_code` | `CONCEPT->concept_code` |
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| `vocabulary_version` | `VOCABULARY->vocabulary_version` |
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| `valid_start_date` | `CONCEPT->valid_start_date` |
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| `valid_end_date` | `CONCEPT->valid_end_date` |
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| `invalid_reason` | `CONCEPT->invalid_reason` |
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| `created` | `N/A` |
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| `modified` | `N/A` |
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.. _OMOP: https://www.ohdsi.org/data-standardization/
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.. _OHDSI Single-page docs: https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:single-page
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"""
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id = models.BigAutoField(auto_created=True, primary_key=True)
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code = models.CharField(max_length=64, null=True, blank=True, unique=True, default='')
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description = models.CharField(max_length=256, null=True, blank=True, default='')
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is_code = models.BooleanField(null=False, default=True)
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is_valid = models.BooleanField(null=False, default=True)
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standard_concept = models.CharField(
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# 'S', 'C' or NULL
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null=True,
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blank=True,
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choices=StandardFlag.choices,
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default=None,
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max_length=1,
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)
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coding_name = models.CharField(max_length=256, null=True, blank=True, default='')
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coding_system = models.ForeignKey(
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'clinicalcode.CodingSystem',
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on_delete=models.SET_NULL,
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null=True,
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blank=True,
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default=None,
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related_name='omop_code'
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)
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domain_name = models.CharField(max_length=256, null=True, blank=True, default='')
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class_name = models.CharField(max_length=256, null=True, blank=True, default='')
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vocabulary_name = models.CharField(max_length=64, null=True, blank=True, default='')
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vocabulary_code = models.CharField(max_length=64, null=True, blank=True, default='')
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vocabulary_version = models.CharField(max_length=256, null=True, blank=True, default='')
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valid_start_date = models.DateField(blank=True, null=True)
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valid_end_date = models.DateField(blank=True, default=datetime.date(2099,12,31))
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invalid_reason = models.CharField(
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# 'D', 'U' or NULL
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null=True,
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blank=True,
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choices=InvalidFlag.choices,
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default=None,
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max_length=1,
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)
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created = models.DateTimeField(auto_now_add=True, editable=True)
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modified = models.DateTimeField(auto_now_add=True, editable=True)
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class Meta:
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ordering = ('id',)
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indexes = [
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models.Index(fields=['id']),
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models.Index(fields=['created']),
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GinIndex(
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name='omop_cd_trgm_idx',
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fields=['code'],
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opclasses=['gin_trgm_ops']
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),
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GinIndex(
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name='omop_desc_trgm_idx',
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fields=['description'],
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opclasses=['gin_trgm_ops']
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),
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GinIndex(
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name='omop_cs_trgm_idx',
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fields=['coding_name'],
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opclasses=['gin_trgm_ops']
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),
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GinIndex(
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name='omop_vscd_trgm_idx',
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fields=['vocabulary_code'],
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opclasses=['gin_trgm_ops']
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),
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]
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class OMOPRelationships(models.Model):
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"""
134+
Represents the edges, or `relationships`_, between OMOP concepts stored in :model:`clinicalcode.OMOP_CODES`.
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Version
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-------
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Vocabulary version: `v20250827`
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Reference
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---------
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See:
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- `Concept Relationship Data Model Conventions`_.
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- `CONCEPT_RELATIONSHIP table`_.
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Mapping
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-------
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| Attribute | Table->Column |
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|:---------------------|:-----------------------------------------|
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| `code0_id` | `CONCEPT_RELATIONSHIP->concept_id_1` |
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| `code1_id` | `CONCEPT_RELATIONSHIP->concept_id_2` |
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| `relationship` | `CONCEPT_RELATIONSHIP->relationship_id` |
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| `valid_start_date` | `CONCEPT_RELATIONSHIP->valid_start_date` |
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| `valid_end_date` | `CONCEPT_RELATIONSHIP->valid_end_date` |
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| `invalid_reason` | `CONCEPT_RELATIONSHIP->invalid_reason` |
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.. _relationships: https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:concept_relationship
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.. _Concept Relationship Data Model Conventions: https://ohdsi.github.io/CommonDataModel/dataModelConventions.html#Concept_Relationships
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.. _CONCEPT_RELATIONSHIP table: https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:concept_relationship
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"""
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id = models.BigAutoField(auto_created=True, primary_key=True)
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code0 = models.ForeignKey(
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to='OMOP_CODES',
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to_field='code',
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related_name=f'source_relationships',
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on_delete=models.CASCADE,
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)
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code1 = models.ForeignKey(
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to='OMOP_CODES',
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to_field='code',
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related_name=f'destination_relationships',
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on_delete=models.CASCADE,
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)
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relationship = models.CharField(max_length=64)
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valid_start_date = models.DateField(blank=True, auto_now_add=True)
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valid_end_date = models.DateField(blank=True, default=datetime.date(2099,12,31))
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invalid_reason = models.CharField(
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# 'D', 'U' or NULL
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null=True,
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blank=True,
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choices=InvalidFlag.choices,
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default=None,
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max_length=1,
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)
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class Meta:
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unique_together = ('code0', 'code1', 'relationship',)
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indexes = [
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models.Index(fields=['code0']),
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models.Index(fields=['code1']),
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models.Index(fields=['code0', 'code1']),
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models.Index(fields=['code0', 'relationship', 'invalid_reason']),
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GinIndex(
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name='omop_e0_trgm_idx',
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fields=['code0'],
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opclasses=['gin_trgm_ops']
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),
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GinIndex(
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name='omop_e0t_tgbt_idx',
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fields=['code0', 'relationship', 'invalid_reason'],
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opclasses=['', 'gin_trgm_ops', '']
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),
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]

‎CodeListLibrary_project/clinicalcode/models/__init__.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -56,7 +56,7 @@
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from .ATCDDD_CODES import ATCDDD_CODES
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from .ICD10CA_CODES import ICD10CA_CODES
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from .ICD10CM_CODES import ICD10CM_CODES
59-
from .OMOP_CODES import OMOP_CODES
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from .OMOP_CODES import OMOP_CODES, OMOPRelationships
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# need to restore EMIS/Vision when deploy. to prod.
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#from .EMIS_CODES import EMIS_CODES

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