Code cleanup for relecov_core

relecov_core/admin.py

@@ -1,37 +1,10 @@
+# Generic imports
 from django.contrib import admin
 from django.contrib.auth.admin import UserAdmin
 from django.contrib.auth.models import User
 
-from relecov_core.models import (
-    BioinfoAnalysisValue,
-    BioinfoAnalysisField,
-    Classification,
-    Chromosome,
-    ConfigSetting,
-    Effect,
-    Error,
-    Gene,
-    Filter,
-    LineageFields,
-    LineageValues,
-    LineageInfo,
-    MetadataVisualization,
-    OrganismAnnotation,
-    Profile,
-    PropertyOptions,
-    PublicDatabaseFields,
-    PublicDatabaseValues,
-    PublicDatabaseType,
-    Sample,
-    SampleState,
-    Schema,
-    SchemaProperties,
-    TemporalSampleStorage,
-    Variant,
-    VariantInSample,
-    VariantAnnotation,
-    DateUpdateState,
-)
+# Local imports
+import relecov_core.models
 
 
 def custom_date_format(self):
@@ -41,7 +14,7 @@ def custom_date_format(self):
 
 
 class ProfileInLine(admin.StackedInline):
-    model = Profile
+    model = relecov_core.models.Profile
     can_delete = False
     verbose_name_plural = "Profile"
     fk_name = "user"
@@ -199,30 +172,36 @@ class MetadataVisualizationAdmin(admin.ModelAdmin):
 # Register models
 admin.site.unregister(User)
 admin.site.register(User, CustomUserAdmin)
-admin.site.register(ConfigSetting, ConfigSettingAdmin)
-admin.site.register(Filter, FilterAdmin)
-admin.site.register(Effect, EffectAdmin)
-admin.site.register(Gene, GeneAdmin)
-admin.site.register(Chromosome, ChromosomeAdmin)
-admin.site.register(LineageFields, LineageFieldsAdmin)
-admin.site.register(LineageValues, LineageValuesAdmin)
-admin.site.register(Sample, SampleAdmin)
-admin.site.register(SampleState, SampleStateAdmin)
-admin.site.register(Variant, VariantAdmin)
-admin.site.register(VariantInSample, VariantInSampleAdmin)
-admin.site.register(VariantAnnotation, VariantAnnotationAdmin)
-admin.site.register(Schema, SchemaAdmin)
-admin.site.register(SchemaProperties, SchemaPropertiesAdmin)
-admin.site.register(PropertyOptions, PropertyOptionsAdmin)
-admin.site.register(PublicDatabaseType, PublicDatabaseTypeAdmin)
-admin.site.register(PublicDatabaseFields, PublicDatabaseFieldsAdmin)
-admin.site.register(PublicDatabaseValues, PublicDatabaseValuesAdmin)
-admin.site.register(MetadataVisualization, MetadataVisualizationAdmin)
-admin.site.register(BioinfoAnalysisField, BioinfoAnalysisFielddAdmin)
-admin.site.register(BioinfoAnalysisValue, BioinfoAnalysisValueAdmin)
-admin.site.register(Classification, ClassificationAdmin)
-admin.site.register(TemporalSampleStorage, TemporalSampleStorageAdmin)
-admin.site.register(Error, ErrorAdmin)
-admin.site.register(DateUpdateState, DateUpdateStateAdmin)
-admin.site.register(LineageInfo, LineageInfoAdmin)
-admin.site.register(OrganismAnnotation, OrganismAnnotationAdmin)
+admin.site.register(relecov_core.models.ConfigSetting, ConfigSettingAdmin)
+admin.site.register(relecov_core.models.Filter, FilterAdmin)
+admin.site.register(relecov_core.models.Effect, EffectAdmin)
+admin.site.register(relecov_core.models.Gene, GeneAdmin)
+admin.site.register(relecov_core.models.Chromosome, ChromosomeAdmin)
+admin.site.register(relecov_core.models.LineageFields, LineageFieldsAdmin)
+admin.site.register(relecov_core.models.LineageValues, LineageValuesAdmin)
+admin.site.register(relecov_core.models.Sample, SampleAdmin)
+admin.site.register(relecov_core.models.SampleState, SampleStateAdmin)
+admin.site.register(relecov_core.models.Variant, VariantAdmin)
+admin.site.register(relecov_core.models.VariantInSample, VariantInSampleAdmin)
+admin.site.register(relecov_core.models.VariantAnnotation, VariantAnnotationAdmin)
+admin.site.register(relecov_core.models.Schema, SchemaAdmin)
+admin.site.register(relecov_core.models.SchemaProperties, SchemaPropertiesAdmin)
+admin.site.register(relecov_core.models.PropertyOptions, PropertyOptionsAdmin)
+admin.site.register(relecov_core.models.PublicDatabaseType, PublicDatabaseTypeAdmin)
+admin.site.register(relecov_core.models.PublicDatabaseFields, PublicDatabaseFieldsAdmin)
+admin.site.register(relecov_core.models.PublicDatabaseValues, PublicDatabaseValuesAdmin)
+admin.site.register(
+    relecov_core.models.MetadataVisualization, MetadataVisualizationAdmin
+)
+admin.site.register(
+    relecov_core.models.BioinfoAnalysisField, BioinfoAnalysisFielddAdmin
+)
+admin.site.register(relecov_core.models.BioinfoAnalysisValue, BioinfoAnalysisValueAdmin)
+admin.site.register(relecov_core.models.Classification, ClassificationAdmin)
+admin.site.register(
+    relecov_core.models.TemporalSampleStorage, TemporalSampleStorageAdmin
+)
+admin.site.register(relecov_core.models.Error, ErrorAdmin)
+admin.site.register(relecov_core.models.DateUpdateState, DateUpdateStateAdmin)
+admin.site.register(relecov_core.models.LineageInfo, LineageInfoAdmin)
+admin.site.register(relecov_core.models.OrganismAnnotation, OrganismAnnotationAdmin)

relecov_core/api/apps.py

@@ -1,3 +1,4 @@
+# Generic imports
 from django.apps import AppConfig
 
 

relecov_core/api/serializers.py

@@ -1,86 +1,77 @@
+# Generic imports
 from rest_framework import serializers
 
-from relecov_core.models import (
-    BioinfoAnalysisValue,
-    DateUpdateState,
-    Effect,
-    Filter,
-    LineageValues,
-    Sample,
-    Variant,
-    VariantAnnotation,
-    VariantInSample,
-    PublicDatabaseValues,
-)
+# Local imports
+import relecov_core.models
 
 
 class CreateBioinfoAnalysisValueSerializer(serializers.ModelSerializer):
     class Meta:
-        model = BioinfoAnalysisValue
+        model = relecov_core.models.BioinfoAnalysisValue
         fields = "__all__"
 
 
 class CreateDateAfterChangeStateSerializer(serializers.ModelSerializer):
     class Meta:
-        model = DateUpdateState
+        model = relecov_core.models.DateUpdateState
         fields = "__all__"
 
 
 class CreateSampleSerializer(serializers.ModelSerializer):
     class Meta:
-        model = Sample
+        model = relecov_core.models.Sample
         fields = "__all__"
 
 
 class CreateEffectSerializer(serializers.ModelSerializer):
     class Meta:
-        model = Effect
+        model = relecov_core.models.Effect
         fields = "__all__"
 
 
 class CreateErrorSerializer(serializers.ModelSerializer):
     class Meta:
-        model = Sample
+        model = relecov_core.models.Sample
         fields = "__all__"
 
 
 class CreateVariantInSampleSerializer(serializers.ModelSerializer):
     class Meta:
-        model = VariantInSample
+        model = relecov_core.models.VariantInSample
         fields = "__all__"
 
 
 class CreateVariantAnnotationSerializer(serializers.ModelSerializer):
     class Meta:
-        model = VariantAnnotation
+        model = relecov_core.models.VariantAnnotation
         fields = "__all__"
 
 
 class CreateFilterSerializer(serializers.ModelSerializer):
     class Meta:
-        model = Filter
+        model = relecov_core.models.Filter
         fields = "__all__"
 
 
 class CreateVariantSerializer(serializers.ModelSerializer):
     class Meta:
-        model = Variant
+        model = relecov_core.models.Variant
         fields = "__all__"
 
 
 class CreateLineageValueSerializer(serializers.ModelSerializer):
     class Meta:
-        model = LineageValues
+        model = relecov_core.models.LineageValues
         fields = "__all__"
 
 
 class CreatePublicDatabaseValueSerializer(serializers.ModelSerializer):
     class Meta:
-        model = PublicDatabaseValues
+        model = relecov_core.models.PublicDatabaseValues
         fields = "__all__"
 
 
 class UpdateStateSampleSerializer(serializers.ModelSerializer):
     class Meta:
-        model = Sample
+        model = relecov_core.models.Sample
         fields = "__all__"

relecov_core/api/urls.py

@@ -1,14 +1,27 @@
+# Generic imports
 from django.urls import path
-from relecov_core.api import views
+
+# Local imports
+import relecov_core.api
 
 app_name = "relecov_api"
 
 
 urlpatterns = [
     path(
-        "createBioinfoData", views.create_bioinfo_metadata, name="create_bioinfo_data"
+        "createBioinfoData",
+        relecov_core.api.views.create_bioinfo_metadata,
+        name="create_bioinfo_data",
+    ),
+    path(
+        "createSampleData",
+        relecov_core.api.views.create_sample_data,
+        name="create_sample_data",
+    ),
+    path(
+        "createVariantData",
+        relecov_core.api.views.create_variant_data,
+        name="create_variant_data",
     ),
-    path("createSampleData", views.create_sample_data, name="create_sample_data"),
-    path("createVariantData", views.create_variant_data, name="create_variant_data"),
-    path("updateState", views.update_state, name="update_state"),
+    path("updateState", relecov_core.api.views.update_state, name="update_state"),
 ]

relecov_core/api/utils/bioinfo_metadata_handling.py → relecov_core/api/utils/bioinfo_metadata.py

@@ -1,18 +1,7 @@
-from relecov_core.models import (
-    BioinfoAnalysisField,
-    BioinfoAnalysisValue,
-    LineageFields,
-    Sample,
-)
-
-from relecov_core.core_config import (
-    ERROR_UNABLE_TO_STORE_IN_DATABASE,
-)
-
-from relecov_core.api.serializers import (
-    CreateBioinfoAnalysisValueSerializer,
-    CreateLineageValueSerializer,
-)
+# Local imports
+import relecov_core.models
+import relecov_core.api.serializers
+import relecov_core.config
 
 
 def split_bioinfo_data(data, schema_obj):
@@ -24,11 +13,11 @@ def split_bioinfo_data(data, schema_obj):
         if field == "sequencing_sample_id":
             split_data["sample"] = value
         # if this field belongs to BioinfoAnalysisField table
-        if BioinfoAnalysisField.objects.filter(
+        if relecov_core.models.BioinfoAnalysisField.objects.filter(
             schemaID=schema_obj, property_name__iexact=field
         ).exists():
             split_data["bioinfo"][field] = value
-        elif LineageFields.objects.filter(
+        elif relecov_core.models.LineageFields.objects.filter(
             schemaID=schema_obj, property_name__iexact=field
         ).exists():
             split_data["lineage"][field] = value
@@ -38,21 +27,21 @@ def split_bioinfo_data(data, schema_obj):
 
 
 def get_analysis_defined(s_obj):
-    return BioinfoAnalysisValue.objects.filter(
+    return relecov_core.models.BioinfoAnalysisValue.objects.filter(
         bioinfo_analysis_fieldID__property_name="analysis_date", sample=s_obj
     ).values_list("value", flat=True)
 
 
 def store_bioinfo_data(s_data, schema_obj):
     """Save the new field data in database"""
     # schema_id = schema_obj.get_schema_id()
-    sample_obj = Sample.objects.filter(
+    sample_obj = relecov_core.models.Sample.objects.filter(
         sequencing_sample_id__iexact=s_data["sample"]
     ).last()
     # field to BioinfoAnalysisField table
     for field, value in s_data["bioinfo"].items():
         field_id = (
-            BioinfoAnalysisField.objects.filter(
+            relecov_core.models.BioinfoAnalysisField.objects.filter(
                 schemaID=schema_obj, property_name__iexact=field
             )
             .last()
@@ -63,26 +52,38 @@ def store_bioinfo_data(s_data, schema_obj):
             "bioinfo_analysis_fieldID": field_id,
         }
 
-        bio_value_serializer = CreateBioinfoAnalysisValueSerializer(data=data)
+        bio_value_serializer = (
+            relecov_core.api.serializers.CreateBioinfoAnalysisValueSerializer(data=data)
+        )
         if not bio_value_serializer.is_valid():
-            return {"ERROR": str(field + " " + ERROR_UNABLE_TO_STORE_IN_DATABASE)}
+            return {
+                "ERROR": str(
+                    field + " " + relecov_core.config.ERROR_UNABLE_TO_STORE_IN_DATABASE
+                )
+            }
         bio_value_obj = bio_value_serializer.save()
         sample_obj.bio_analysis_values.add(bio_value_obj)
 
     # field to LineageFields table
     for field, value in s_data["lineage"].items():
         lineage_id = (
-            LineageFields.objects.filter(
+            relecov_core.models.LineageFields.objects.filter(
                 schemaID=schema_obj, property_name__iexact=field
             )
             .last()
             .get_lineage_field_id()
         )
         data = {"value": value, "lineage_fieldID": lineage_id}
-        lineage_value_serializer = CreateLineageValueSerializer(data=data)
+        lineage_value_serializer = (
+            relecov_core.api.serializers.CreateLineageValueSerializer(data=data)
+        )
 
         if not lineage_value_serializer.is_valid():
-            return {"ERROR": str(field + " " + ERROR_UNABLE_TO_STORE_IN_DATABASE)}
+            return {
+                "ERROR": str(
+                    field + " " + relecov_core.config.ERROR_UNABLE_TO_STORE_IN_DATABASE
+                )
+            }
         lineage_value_obj = lineage_value_serializer.save()
         sample_obj.lineage_values.add(lineage_value_obj)