feat: mesh codes

fix!: fix code list regex issue; note the class name changes to elements
SwanseaUniversityMedical · Nov 4, 2024 · 6e47737 · 6e47737
1 parent 386f3c2
commit 6e47737
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Showing 10 changed files with 112 additions and 6 deletions.
diff --git a/...Library_project/clinicalcode/migrations/0117_icd_9_codes_icd9_code_ln_gin_idx_and_more.py b/...Library_project/clinicalcode/migrations/0117_icd_9_codes_icd9_code_ln_gin_idx_and_more.py
@@ -0,0 +1,22 @@
+# Generated by Django 5.1.2 on 2024-10-24 14:23
+
+import django.contrib.postgres.indexes
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('clinicalcode', '0116_ontology_descendants'),
+    ]
+
+    operations = [
+        migrations.AddIndex(
+            model_name='icd_9_codes',
+            index=django.contrib.postgres.indexes.GinIndex(fields=['code'], name='icd9_code_ln_gin_idx', opclasses=['gin_trgm_ops']),
+        ),
+        migrations.AddIndex(
+            model_name='icd_9_codes',
+            index=django.contrib.postgres.indexes.GinIndex(fields=['description'], name='icd9_desc_ln_gin_idx', opclasses=['gin_trgm_ops']),
+        ),
+    ]
diff --git a/CodeListLibrary_project/clinicalcode/migrations/0118_mesh_codes.py b/CodeListLibrary_project/clinicalcode/migrations/0118_mesh_codes.py
@@ -0,0 +1,33 @@
+# Generated by Django 5.1.2 on 2024-11-04 20:13
+
+import datetime
+import django.contrib.postgres.fields
+import django.contrib.postgres.indexes
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('clinicalcode', '0117_icd_9_codes_icd9_code_ln_gin_idx_and_more'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='MESH_CODES',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False)),
+                ('code', models.CharField(blank=True, default='', max_length=10, null=True)),
+                ('description', models.CharField(blank=True, default='', max_length=256, null=True)),
+                ('parent_codes', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), blank=True, null=True, size=None)),
+                ('record_type', models.IntegerField(blank=True, default=0, null=True)),
+                ('record_category', models.IntegerField(blank=True, default=0, null=True)),
+                ('record_modifier', models.IntegerField(blank=True, default=0, null=True)),
+                ('active', models.BooleanField(blank=True, default=True, null=True)),
+                ('effective_time', models.DateField(blank=True, default=datetime.date.today, null=True)),
+            ],
+            options={
+                'indexes': [django.contrib.postgres.indexes.GinIndex(fields=['code'], name='mesh_code_ln_gin_idx', opclasses=['gin_trgm_ops']), django.contrib.postgres.indexes.GinIndex(fields=['description'], name='mesh_desc_ln_gin_idx', opclasses=['gin_trgm_ops'])],
+            },
+        ),
+    ]
diff --git a/CodeListLibrary_project/clinicalcode/models/ICD_9_CODES.py b/CodeListLibrary_project/clinicalcode/models/ICD_9_CODES.py
@@ -1,4 +1,5 @@
 from django.db import models
+from django.contrib.postgres.indexes import GinIndex
 
 class ICD_9_CODES(models.Model):
     code = models.CharField(max_length=50, null=True, blank=True)
@@ -10,3 +11,17 @@ class ICD_9_CODES(models.Model):
     effective_from = models.DateTimeField(null=True, blank=True)
     effective_to = models.DateField(null=True, blank=True)
     avail_from_dt = models.DateField(null=True, blank=True)
+
+    class Meta:
+        indexes = [
+            GinIndex(
+                name='icd9_code_ln_gin_idx',
+                fields=['code'],
+                opclasses=['gin_trgm_ops']
+            ),
+            GinIndex(
+                name='icd9_desc_ln_gin_idx',
+                fields=['description'],
+                opclasses=['gin_trgm_ops']
+            ),
+        ]
diff --git a/CodeListLibrary_project/clinicalcode/models/MESH_CODES.py b/CodeListLibrary_project/clinicalcode/models/MESH_CODES.py
@@ -0,0 +1,35 @@
+from django.db import models
+from django.contrib.postgres.fields import ArrayField
+from django.contrib.postgres.search import SearchVectorField
+from django.contrib.postgres.indexes import GinIndex
+
+import datetime
+
+from ..entity_utils import constants
+
+class MESH_CODES(models.Model):
+    # Top-level
+    id = models.BigAutoField(auto_created=True, primary_key=True)
+    code = models.CharField(max_length=10, null=True, blank=True, unique=False, default='')
+    description = models.CharField(max_length=256, null=True, blank=True, default='')
+    parent_codes = ArrayField(models.TextField(), blank=True, null=True)
+    record_type = models.IntegerField(null=True, blank=True, default=0)
+    record_category = models.IntegerField(null=True, blank=True, default=0)
+    record_modifier = models.IntegerField(null=True, blank=True, default=0)
+    active = models.BooleanField(null=True, blank=True, default=True)
+    effective_time = models.DateField(null=True, blank=True, default=datetime.date.today)
+
+    class Meta:
+        # Index reference
+        indexes = [
+            GinIndex(
+                name='mesh_code_ln_gin_idx',
+                fields=['code'],
+                opclasses=['gin_trgm_ops']
+            ),
+            GinIndex(
+                name='mesh_desc_ln_gin_idx',
+                fields=['description'],
+                opclasses=['gin_trgm_ops']
+            ),
+        ]
diff --git a/CodeListLibrary_project/clinicalcode/models/__init__.py b/CodeListLibrary_project/clinicalcode/models/__init__.py
@@ -38,6 +38,7 @@
 from .GPRD_PRODUCT_CODES import GPRD_PRODUCT_CODES
 from .EMIS_CODES import EMIS_CODES
 from .VISION_CODES import VISION_CODES
+from .MESH_CODES import MESH_CODES
 
 from .Template import Template
 from .GenericEntity import GenericEntity

diff --git a/CodeListLibrary_project/cll/static/js/clinicalcode/forms/clinical/conceptCreator.js b/CodeListLibrary_project/cll/static/js/clinicalcode/forms/clinical/conceptCreator.js
@@ -1974,7 +1974,7 @@ export default class ConceptCreator {
       let caseSensitive = input.parentNode.parentNode.querySelector('input[name="search-sensitive"]:checked');
       caseSensitive = !isNullOrUndefined(caseSensitive);
 
-      let useDesc = input.parentNode.parentNode.querySelector('input[type="radio"]:checked');
+      let useDesc = input.parentNode.parentNode.querySelector('input[x-item="search-by"]:checked');
       useDesc = !isNullOrUndefined(useDesc) ? useDesc.getAttribute('x-target') : CONCEPT_CREATOR_SEARCH_METHODS.CODES;
       useDesc = useDesc !== CONCEPT_CREATOR_SEARCH_METHODS.CODES;
 

diff --git a/CodeListLibrary_project/cll/templates/components/create/inputs/clinical/concept.html b/CodeListLibrary_project/cll/templates/components/create/inputs/clinical/concept.html
@@ -219,12 +219,12 @@ <h3 class="detailed-input-group__title sm">Searchterm Rule</h3>
           <fieldset class="search-options justify-content-end align-items-center">
             <div class="search-options__container">
               <p class="search-options__title"><strong>Fields:</strong></p>
-              <input class="search-options__input" aria-label="Search by Codes" type="radio" id="search-codes-${id}" name="search-by-option-${id}" x-target="codes" ${used_code}>
+              <input class="search-options__input" aria-label="Search by Codes" type="radio" id="search-codes-${id}" name="search-by-option-${id}" x-item="search-by" x-target="codes" ${used_code}>
               <label class="search-options__label" role="button" tabindex="0" for="search-codes-${id}">
                 <span class="search-options__label-icon"></span>
                 Code
               </label>
-              <input class="search-options__input" aria-label="Search by Description" type="radio" id="search-desc-${id}" name="search-by-option-${id}" x-target="description" ${used_description}>
+              <input class="search-options__input" aria-label="Search by Description" type="radio" id="search-desc-${id}" name="search-by-option-${id}" x-item="search-by" x-target="description" ${used_description}>
               <label class="search-options__label" role="button" tabindex="0" for="search-desc-${id}">
                 <span class="search-options__label-icon"></span>
                 Description

diff --git a/docker/development/env/web/dev.compose.env b/docker/development/env/web/dev.compose.env
@@ -86,7 +86,7 @@ CELERY_BACKEND=redis://redis:6379/0
 
 ## 2. Database settings
 ##  - Settings used by the `postgres` service
-POSTGRES_HOST="localhost"
+POSTGRES_HOST="postgres"
 POSTGRES_DB="concept_library"
 POSTGRES_USER="clluser"
 POSTGRES_PASSWORD="password"

diff --git a/docker/development/env/web/live.compose.env b/docker/development/env/web/live.compose.env
@@ -86,7 +86,7 @@ CELERY_BACKEND=redis://redis:6379/0
 
 ## 2. Database settings
 ##  - Settings used by the `postgres` service
-POSTGRES_HOST="localhost"
+POSTGRES_HOST="postgres"
 POSTGRES_DB="concept_library"
 POSTGRES_USER="clluser"
 POSTGRES_PASSWORD="password"

diff --git a/docker/development/env/web/test.compose.env b/docker/development/env/web/test.compose.env
@@ -86,7 +86,7 @@ CELERY_BACKEND=redis://redis:6379/0
 
 ## 2. Database settings
 ##  - Settings used by the `postgres` service
-POSTGRES_HOST="localhost"
+POSTGRES_HOST="postgres"
 POSTGRES_DB="concept_library"
 POSTGRES_USER="clluser"
 POSTGRES_PASSWORD="password"