Refactor of database tables and api related core utilities

conf/first_install_tables.json

@@ -141,5 +141,172 @@
         "name": "RelecovManager",
         "permissions": []
     }
+},    {
+    "model": "core.errorname",
+    "pk": 1,
+    "fields": {
+        "error_code": "0",
+        "error_name": "No Error"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 2,
+    "fields": {
+        "error_code": "100",
+        "error_name": "AttributeError: An object attribute is missing or invalid"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 3,
+    "fields": {
+        "error_code": "101",
+        "error_name": "TypeError: An operation or function was applied to an object of inappropriate type"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 4,
+    "fields": {
+        "error_code": "102",
+        "error_name": "ValueError: An operation received an argument with the right type but inappropriate value"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 5,
+    "fields": {
+        "error_code": "103",
+        "error_name": "KeyError: A key was not found in a mapping or dictionary"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 6,
+    "fields": {
+        "error_code": "104",
+        "error_name": "IndexError: A sequence subscript was out of range"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 7,
+    "fields": {
+        "error_code": "105",
+        "error_name": "ImportError: A module or object could not be imported"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 8,
+    "fields": {
+        "error_code": "106",
+        "error_name": "ModuleNotFoundError: A specified module could not be found"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 9,
+    "fields": {
+        "error_code": "107",
+        "error_name": "ZeroDivisionError: Division or modulo by zero"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 10,
+    "fields": {
+        "error_code": "108",
+        "error_name": "FileNotFoundError: A file or directory was requested but does not exist"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 11,
+    "fields": {
+        "error_code": "109",
+        "error_name": "IOError: An input/output operation failed"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 12,
+    "fields": {
+        "error_code": "110",
+        "error_name": "PermissionError: An operation lacked the necessary permissions"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 13,
+    "fields": {
+        "error_code": "111",
+        "error_name": "TimeoutError: An operation exceeded its designated time limit"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 14,
+    "fields": {
+        "error_code": "112",
+        "error_name": "MemoryError: An operation ran out of memory"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 15,
+    "fields": {
+        "error_code": "113",
+        "error_name": "RecursionError: The maximum recursion depth was exceeded"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 16,
+    "fields": {
+        "error_code": "114",
+        "error_name": "NameError: A variable or function name is not defined"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 17,
+    "fields": {
+        "error_code": "115",
+        "error_name": "SyntaxError: Invalid syntax in the code"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 18,
+    "fields": {
+        "error_code": "116",
+        "error_name": "IndentationError: Code indentation is incorrect"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 19,
+    "fields": {
+        "error_code": "117",
+        "error_name": "StopIteration: Iteration has no further items"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 20,
+    "fields": {
+        "error_code": "118",
+        "error_name": "OverflowError: A numerical calculation exceeded a range limit"
+    }
+},
+{
+    "model": "core.errorname",
+    "pk": 21,
+    "fields": {
+        "error_code": "999",
+        "error_name": "Other unspecified error occurred"
+    }
 }
 ]

core/admin.py

@@ -33,13 +33,8 @@ class AnalysisPerformedAdmin(admin.ModelAdmin):
     list_display = ["typeID", "sampleID"]
 
 
-class BioinfoAnalysisFielddAdmin(admin.ModelAdmin):
-    list_display = ["property_name", "label_name"]
-    search_fields = ("property_name__icontains",)
-
-
-class BioinfoAnalysisValueAdmin(admin.ModelAdmin):
-    list_display = ["value", "bioinfo_analysis_fieldID"]
+class MetadataValuesAdmin(admin.ModelAdmin):
+    list_display = ["value", "sample", "schema_property", "analysis_date"]
     search_fields = ("value__icontains",)
 
 
@@ -51,16 +46,26 @@ class ConfigSettingAdmin(admin.ModelAdmin):
     list_display = ["configuration_name", "configuration_value"]
 
 
-class DateUpdateStateAdmin(admin.ModelAdmin):
-    list_display = ["sampleID", "stateID", custom_date_format]
+class SampleStateHistoryAdmin(admin.ModelAdmin):
+    list_display = [
+        "is_current",
+        custom_date_format,
+        "sample_id",
+        "state_id",
+        "error_name_id",
+    ]
 
 
 class EffectAdmin(admin.ModelAdmin):
     list_display = ["effect"]
 
 
+class ErrorNameAdmin(admin.ModelAdmin):
+    list_display = ["error_name", "error_code", "error_text"]
+
+
 class ErrorAdmin(admin.ModelAdmin):
-    list_display = ["error_name", "display_string"]
+    list_display = ["error_name", "error_code", "erorr_text"]
 
 
 class FilterAdmin(admin.ModelAdmin):
@@ -109,7 +114,6 @@ class SampleAdmin(admin.ModelAdmin):
         "sequencing_sample_id",
         "submitting_lab_sample_id",
         "collecting_lab_sample_id",
-        "state",
     ]
     search_fields = ["sequencing_sample_id__icontains"]
     list_filter = ["created_at"]
@@ -177,6 +181,7 @@ class MetadataVisualizationAdmin(admin.ModelAdmin):
 admin.site.register(core.models.Effect, EffectAdmin)
 admin.site.register(core.models.Gene, GeneAdmin)
 admin.site.register(core.models.Chromosome, ChromosomeAdmin)
+# TODO: Remove the line below when we remove lineage things
 admin.site.register(core.models.LineageFields, LineageFieldsAdmin)
 admin.site.register(core.models.LineageValues, LineageValuesAdmin)
 admin.site.register(core.models.Sample, SampleAdmin)
@@ -191,11 +196,11 @@ class MetadataVisualizationAdmin(admin.ModelAdmin):
 admin.site.register(core.models.PublicDatabaseFields, PublicDatabaseFieldsAdmin)
 admin.site.register(core.models.PublicDatabaseValues, PublicDatabaseValuesAdmin)
 admin.site.register(core.models.MetadataVisualization, MetadataVisualizationAdmin)
-admin.site.register(core.models.BioinfoAnalysisField, BioinfoAnalysisFielddAdmin)
-admin.site.register(core.models.BioinfoAnalysisValue, BioinfoAnalysisValueAdmin)
+admin.site.register(core.models.MetadataValues, MetadataValuesAdmin)
 admin.site.register(core.models.Classification, ClassificationAdmin)
 admin.site.register(core.models.TemporalSampleStorage, TemporalSampleStorageAdmin)
-admin.site.register(core.models.Error, ErrorAdmin)
-admin.site.register(core.models.DateUpdateState, DateUpdateStateAdmin)
+# TODO: Remove the line below when we remove lineage things
 admin.site.register(core.models.LineageInfo, LineageInfoAdmin)
+admin.site.register(core.models.ErrorName, ErrorNameAdmin)
+admin.site.register(core.models.SampleStateHistory, SampleStateHistoryAdmin)
 admin.site.register(core.models.OrganismAnnotation, OrganismAnnotationAdmin)

core/api/serializers.py

@@ -5,15 +5,15 @@
 import core.models
 
 
-class CreateBioinfoAnalysisValueSerializer(serializers.ModelSerializer):
+class CreateMetadataValueSerializer(serializers.ModelSerializer):
     class Meta:
-        model = core.models.BioinfoAnalysisValue
+        model = core.models.MetadataValues
         fields = "__all__"
 
 
-class CreateDateAfterChangeStateSerializer(serializers.ModelSerializer):
+class SampleStateHistorySerializer(serializers.ModelSerializer):
     class Meta:
-        model = core.models.DateUpdateState
+        model = core.models.SampleStateHistory
         fields = "__all__"
 
 
@@ -29,12 +29,6 @@ class Meta:
         fields = "__all__"
 
 
-class CreateErrorSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = core.models.Sample
-        fields = "__all__"
-
-
 class CreateVariantInSampleSerializer(serializers.ModelSerializer):
     class Meta:
         model = core.models.VariantInSample

core/api/urls.py

@@ -10,8 +10,8 @@
 urlpatterns = [
     path(
         "createBioinfoData",
-        core.api.views.create_bioinfo_metadata,
-        name="create_bioinfo_data",
+        core.api.views.create_metadata_value,
+        name="create_metadata_value",
     ),
     path(
         "createSampleData",