Annotations endpoints

app/api/annotations/lrs.py

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+#! /usr/bin/env python3
+
+from . import serializers
+from . import models
+
+from django.core.exceptions import ValidationError
+from django.http import HttpResponse, HttpResponseNotFound
+from django.shortcuts import get_object_or_404
+from rest_framework import generics, mixins, permissions, status, viewsets
+from rest_framework.filters import OrderingFilter, SearchFilter
+from rest_framework.response import Response
+from rest_framework.views import APIView
+
+from django_filters import FilterSet, ModelChoiceFilter
+from django_filters import rest_framework as filters
+
+class FeatureTrackDetailView(generics.ListAPIView):
+    """
+    Detail View for a given FeatureTrack
+    """
+    serializer_class = serializers.TrackDetailSerializer
+    permission_classes = [permissions.IsAuthenticatedOrReadOnly]
+    lookup_url_kwarg = 'acc'
+
+    def get_queryset(self):
+        """
+        This view should return a FeatureTrack by UniProt and name
+         Example:
+            /featureTracks/<ACC>/<name>/
+            /featureTracks/P0DTC4/Genomic_Variants_CNCB/
+        """
+        uniprot_acc = self.kwargs['acc']
+        name = self.kwargs['name']
+        return models.FeatureTrack.objects.filter(
+            uniprot_entry__accession=uniprot_acc,
+            name=name)
+
+class TrackDetailView(generics.RetrieveAPIView):
+    """
+    Detail View for a given FeatureTrack
+    """
+    queryset = models.FeatureTrack.objects.all()
+    serializer_class = serializers.TrackDetailSerializer
+    #permission_classes = [permissions.IsAuthenticatedOrReadOnly]
+    filter_backends = (filters.DjangoFilterBackend,
+                       SearchFilter, OrderingFilter)
+    filterset_fields = ['mutationType', 'sourceType', 'mutationEffect']
+    search_fields = ['mutationType']
+    ordering_fields = ['mutationType', 'mutationEffect', 'sourceType']
+    ordering = ['mutationType']
+    lookup_url_kwarg = 'name'
+    multiple_lookup_fields = ['uniprot_entry', 'name']
+
+    def get_object(self):
+        queryset = self.get_queryset()
+        filter = {}
+        for field in self.multiple_lookup_fields:
+            pass #filter[field] = self.kwargs[field]
+
+        obj = get_object_or_404(queryset, **filter)
+        self.check_object_permissions(self.request, obj)
+        return obj

app/api/annotations/migrations/0001_initial.py

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+# Generated by Django 4.2.8 on 2025-06-13 08:17
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='SMARTentity',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('uniprotid', models.CharField(blank=True, default='', max_length=30, null=True)),
+                ('domain', models.CharField(blank=True, default='', max_length=30, null=True)),
+                ('start', models.IntegerField(blank=True, null=True)),
+                ('end', models.IntegerField(blank=True, null=True)),
+                ('evalue', models.CharField(blank=True, default='1', max_length=20, null=True)),
+                ('type', models.CharField(default='', max_length=30, null=True)),
+            ],
+        ),
+    ]

app/api/annotations/migrations/0002_pfamentity.py

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+# Generated by Django 4.2.8 on 2025-06-13 10:46
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('annotations', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='PFAMentity',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('pfamid', models.CharField(blank=True, default='', max_length=30, null=True)),
+            ],
+        ),
+    ]

app/api/annotations/migrations/0003_ensemblannotation.py

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+# Generated by Django 4.2.8 on 2025-06-19 10:11
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('annotations', '0002_pfamentity'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='EnsemblAnnotation',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('geneName', models.CharField(blank=True, default='', max_length=30, null=True)),
+                ('transcriptName', models.CharField(blank=True, default='', max_length=30, null=True)),
+                ('start', models.IntegerField(blank=True, null=True)),
+                ('end', models.IntegerField(blank=True, null=True)),
+                ('type', models.CharField(blank=True, default='', max_length=30, null=True)),
+            ],
+        ),
+    ]

app/api/annotations/migrations/0004_biomutanentries_dbptmentries_dsysmapentries_and_more.py

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+# Generated by Django 4.2.8 on 2025-06-23 10:44
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('annotations', '0003_ensemblannotation'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='biomutanentries',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('proteinID', models.CharField(blank=True, default='', max_length=255, null=True)),
+                ('data', models.TextField(blank=True, default='')),
+                ('created_at', models.DateTimeField(default=None)),
+                ('updated_at', models.DateTimeField(default=None)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='dbptmentries',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('proteinID', models.CharField(blank=True, default='', max_length=255, null=True)),
+                ('data', models.TextField(blank=True, default='')),
+                ('created_at', models.DateTimeField(default=None)),
+                ('updated_at', models.DateTimeField(default=None)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='dsysmapentries',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('proteinID', models.CharField(blank=True, default='', max_length=255, null=True)),
+                ('data', models.TextField(blank=True, default='')),
+                ('created_at', models.DateTimeField(default=None)),
+                ('updated_at', models.DateTimeField(default=None)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='ebifeaturesentries',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('proteinID', models.CharField(blank=True, default='', max_length=255, null=True)),
+                ('data', models.TextField(blank=True, default='')),
+                ('created_at', models.DateTimeField(default=None)),
+                ('updated_at', models.DateTimeField(default=None)),
+                ('features_type', models.CharField(blank=True, default='', max_length=255, null=True)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='EnsemblVariantEntry',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('geneID', models.CharField(blank=True, default='', max_length=255, null=True)),
+                ('data', models.TextField(blank=True, default='')),
+                ('created_at', models.DateTimeField(default=None)),
+                ('updated_at', models.DateTimeField(default=None)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='intrproentries',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('proteinID', models.CharField(blank=True, default='', max_length=255, null=True)),
+                ('data', models.TextField(blank=True, default='')),
+                ('created_at', models.DateTimeField(default=None)),
+                ('updated_at', models.DateTimeField(default=None)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='mobientries',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('proteinID', models.CharField(blank=True, default='', max_length=255, null=True)),
+                ('data', models.TextField(blank=True, default='')),
+                ('created_at', models.DateTimeField(default=None)),
+                ('updated_at', models.DateTimeField(default=None)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='molprobityentries',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('PDBID', models.CharField(blank=True, default='', max_length=255, null=True)),
+                ('data', models.TextField(blank=True, default='')),
+                ('created_at', models.DateTimeField(default=None)),
+                ('updated_at', models.DateTimeField(default=None)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='PDBEntry',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('PDBID', models.CharField(blank=True, default='', max_length=255, null=True)),
+                ('data', models.TextField(blank=True, default='')),
+                ('created_at', models.DateTimeField(default=None)),
+                ('updated_at', models.DateTimeField(default=None)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='PDBRedoEntry',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('PDBID', models.CharField(blank=True, default='', max_length=255, null=True)),
+                ('data', models.TextField(blank=True, default='')),
+                ('created_at', models.DateTimeField(default=None)),
+                ('updated_at', models.DateTimeField(default=None)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='PhosphoEntries',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('proteinID', models.CharField(blank=True, default='', max_length=255, null=True)),
+                ('data', models.TextField(blank=True, default='')),
+                ('created_at', models.DateTimeField(default=None)),
+                ('updated_at', models.DateTimeField(default=None)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='swissvarentries',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('uniprotid', models.CharField(blank=True, default='', max_length=30, null=True)),
+                ('domain', models.CharField(blank=True, default='', max_length=30, null=True)),
+                ('start', models.IntegerField(blank=True, null=True)),
+                ('end', models.IntegerField(blank=True, null=True)),
+                ('evalue', models.CharField(blank=True, default='1', max_length=20, null=True)),
+                ('type', models.CharField(default='', max_length=30, null=True)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='uniprotmappingentries',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('uniprotid', models.CharField(blank=True, default='', max_length=30, null=True)),
+                ('domain', models.CharField(blank=True, default='', max_length=30, null=True)),
+                ('gene', models.TextField(default=None, null=True)),
+                ('transcript', models.TextField(default=None, null=True)),
+                ('start', models.IntegerField(blank=True, null=True)),
+                ('end', models.IntegerField(blank=True, null=True)),
+                ('evalue', models.CharField(blank=True, default='1', max_length=20, null=True)),
+                ('type', models.CharField(default='', max_length=30, null=True)),
+            ],
+        ),
+        migrations.RemoveField(
+            model_name='pfamentity',
+            name='pfamid',
+        ),
+        migrations.AddField(
+            model_name='pfamentity',
+            name='created_at',
+            field=models.DateTimeField(default=None),
+        ),
+        migrations.AddField(
+            model_name='pfamentity',
+            name='data',
+            field=models.TextField(blank=True, default=''),
+        ),
+        migrations.AddField(
+            model_name='pfamentity',
+            name='proteinID',
+            field=models.CharField(blank=True, default='', max_length=255, null=True),
+        ),
+        migrations.AddField(
+            model_name='pfamentity',
+            name='updated_at',
+            field=models.DateTimeField(default=None),
+        ),
+    ]

app/api/annotations/migrations/0005_delete_biomutanentries_delete_dbptmentries_and_more.py

@@ -0,0 +1,73 @@
+# Generated by Django 4.2.8 on 2025-06-27 08:11
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('annotations', '0004_biomutanentries_dbptmentries_dsysmapentries_and_more'),
+    ]
+
+    operations = [
+        migrations.DeleteModel(
+            name='biomutanentries',
+        ),
+        migrations.DeleteModel(
+            name='dbptmentries',
+        ),
+        migrations.DeleteModel(
+            name='dsysmapentries',
+        ),
+        migrations.DeleteModel(
+            name='ebifeaturesentries',
+        ),
+        migrations.DeleteModel(
+            name='EnsemblVariantEntry',
+        ),
+        migrations.DeleteModel(
+            name='intrproentries',
+        ),
+        migrations.DeleteModel(
+            name='mobientries',
+        ),
+        migrations.DeleteModel(
+            name='molprobityentries',
+        ),
+        migrations.DeleteModel(
+            name='PDBEntry',
+        ),
+        migrations.DeleteModel(
+            name='PDBRedoEntry',
+        ),
+        migrations.DeleteModel(
+            name='PhosphoEntries',
+        ),
+        migrations.DeleteModel(
+            name='swissvarentries',
+        ),
+        migrations.DeleteModel(
+            name='uniprotmappingentries',
+        ),
+        migrations.RemoveField(
+            model_name='pfamentity',
+            name='created_at',
+        ),
+        migrations.RemoveField(
+            model_name='pfamentity',
+            name='data',
+        ),
+        migrations.RemoveField(
+            model_name='pfamentity',
+            name='proteinID',
+        ),
+        migrations.RemoveField(
+            model_name='pfamentity',
+            name='updated_at',
+        ),
+        migrations.AddField(
+            model_name='pfamentity',
+            name='pfamid',
+            field=models.CharField(blank=True, default='', max_length=30, null=True),
+        ),
+    ]