Merge branch 'main' of https://github.com/cmatKhan/yeastregulatorydb

wq

.dockerignore

@@ -10,3 +10,4 @@
 venv
 .git
 .envs/
+rds_redis_ec2_config.yml

rds_redis_ec2_config.yml

@@ -0,0 +1,153 @@
+AWSTemplateFormatVersion: '2010-09-09'
+Description: CloudFormation template for PostgreSQL RDS, Redis ElastiCache, and Ubuntu EC2 instance.
+
+Resources:
+  MyCustomParameterGroup:
+    Type: AWS::RDS::DBParameterGroup
+    Properties:
+      Description: Custom parameter group for my DB
+      Family: postgres13 # Adjust based on your PostgreSQL version
+      Parameters:
+        max_connections: "200" # Example: Increase max connections
+
+  MyDBInstance:
+    Type: AWS::RDS::DBInstance
+    DependsOn:
+      - MyDBSecurityGroup
+    Properties:
+      DBName: mydatabase
+      AllocatedStorage: 20
+      DBInstanceClass: db.t3.micro
+      Engine: postgres
+      MasterUsername: postgres
+      MasterUserPassword: Jex19UIFCmM2u6ZhRKZd
+      BackupRetentionPeriod: 3
+      VPCSecurityGroups:
+        - !Ref MyDBSecurityGroup
+      DBParameterGroupName: !Ref MyCustomParameterGroup # Associate the custom parameter group
+
+  MyDBProxy:
+    Type: AWS::RDS::DBProxy
+    Properties:
+      DBProxyName: mydbproxy
+      EngineFamily: POSTGRESQL
+      Auth:
+        - AuthScheme: SECRETS
+          IAMAuth: DISABLED
+          SecretArn: !GetAtt MyDBSecret.Arn
+      RoleArn: !GetAtt MyDBProxyRole.Arn
+      VpcSecurityGroupIds:
+        - !Ref MyDBSecurityGroup
+      VpcSubnetIds:
+        - !Ref MySubnet1
+        - !Ref MySubnet2
+      RequireTLS: false
+
+  MyDBProxyRole:
+    Type: AWS::IAM::Role
+    Properties:
+      AssumeRolePolicyDocument:
+        Version: '2012-10-17'
+        Statement:
+          - Effect: Allow
+            Principal:
+              Service: rds.amazonaws.com
+            Action: sts:AssumeRole
+      Policies:
+        - PolicyName: RDSProxyPolicy
+          PolicyDocument:
+            Version: '2012-10-17'
+            Statement:
+              - Effect: Allow
+                Action:
+                  - secretsmanager:GetSecretValue
+                  - secretsmanager:DescribeSecret
+                Resource: '*'
+
+  MyDBSecret:
+    Type: AWS::SecretsManager::Secret
+    Properties:
+      Name: MyDBSecret
+      Description: "RDS database credentials"
+      SecretString: !Sub '{"username":"${MyDBInstance.MasterUsername}","password":"Jex19UIFCmM2u6ZhRKZd","engine":"postgres","host":"${MyDBInstance.Endpoint.Address}","port":"5432","dbClusterIdentifier":"${MyDBInstance.DBInstanceIdentifier}"}'
+
+
+  MyElastiCacheRedis:
+    Type: AWS::ElastiCache::CacheCluster
+    DependsOn:
+      - MyCacheSecurityGroup
+    Properties:
+      CacheNodeType: cache.t2.micro
+      Engine: redis
+      NumCacheNodes: 1
+      VpcSecurityGroupIds:
+        - !Ref MyCacheSecurityGroup
+
+  MyEC2Instance:
+    Type: AWS::EC2::Instance
+    DependsOn:
+      - MyInstanceSecurityGroup
+    Properties:
+      ImageId: ami-05fb0b8c1424f266b
+      InstanceType: t2.micro
+      SecurityGroupIds:
+        - !GetAtt MyInstanceSecurityGroup.GroupId
+      KeyName: general_strides
+
+  MyDBSecurityGroup:
+    Type: AWS::EC2::SecurityGroup
+    DependsOn:
+      - MyInstanceSecurityGroup
+    Properties:
+      GroupDescription: Allow access to PostgreSQL
+      VpcId: vpc-0e2c306eb7a371817
+      SecurityGroupIngress:
+        - IpProtocol: tcp
+          FromPort: 5432
+          ToPort: 5432
+          SourceSecurityGroupId: !Ref MyInstanceSecurityGroup
+
+  MyCacheSecurityGroup:
+    Type: AWS::EC2::SecurityGroup
+    DependsOn: MyInstanceSecurityGroup
+    Properties:
+      GroupDescription: Allow access to Redis
+      VpcId: vpc-0e2c306eb7a371817
+      SecurityGroupIngress:
+        - IpProtocol: tcp
+          FromPort: 6379
+          ToPort: 6379
+          SourceSecurityGroupId: !Ref MyInstanceSecurityGroup
+
+  MyInstanceSecurityGroup:
+    Type: AWS::EC2::SecurityGroup
+    Properties:
+      GroupDescription: Security group for EC2 instance
+      VpcId: vpc-0e2c306eb7a371817
+      SecurityGroupIngress:
+        - IpProtocol: tcp
+          FromPort: 22
+          ToPort: 22
+          CidrIp: 107.200.64.20/32
+        - IpProtocol: tcp
+          FromPort: 80
+          ToPort: 80
+          CidrIp: 0.0.0.0/0
+
+Outputs:
+  RDSInstanceEndpoint:
+    Description: Endpoint of the RDS instance
+    Value: !GetAtt MyDBInstance.Endpoint.Address
+
+  RDSProxyEndpoint:
+    Description: Endpoint of the RDS Proxy
+    Value: !GetAtt MyDBProxy.Endpoint
+
+  RedisEndpoint:
+    Description: Endpoint of the Redis ElastiCache instance
+    Value: !GetAtt MyElastiCacheRedis.RedisEndpoint.Address
+
+  EC2InstancePublicIP:
+    Description: Public IP of the EC2 instance
+    Value: !GetAtt MyEC2Instance.PublicIp
+

yeastregulatorydb/regulatory_data/api/views/CallingCardsBackgroundViewSet.py

@@ -18,7 +18,7 @@ class CallingCardsBackgroundViewSet(UpdateModifiedMixin, viewsets.ModelViewSet):
     A viewset for viewing and editing CallingCardsBackground instances.
     """
 
-    queryset = CallingCardsBackground.objects.select_related("uploader", "fileformat").all()
+    queryset = CallingCardsBackground.objects.select_related("uploader", "fileformat").all().order_by("-id")
     authentication_classes = [SessionAuthentication, TokenAuthentication]
     permission_classes = [IsAuthenticated]
     serializer_class = CallingCardsBackgroundSerializer

yeastregulatorydb/regulatory_data/api/views/ChrMapViewSet.py

@@ -13,7 +13,7 @@ class ChrMapViewSet(UpdateModifiedMixin, viewsets.ModelViewSet):
     A viewset for viewing and editing ChrMap instances.
     """
 
-    queryset = ChrMap.objects.select_related("uploader").all()
+    queryset = ChrMap.objects.select_related("uploader").all().order_by("id")
     authentication_classes = [SessionAuthentication, TokenAuthentication]
     permission_classes = [IsAuthenticated]
     serializer_class = ChrMapSerializer

yeastregulatorydb/regulatory_data/api/views/DataSourceViewSet.py

@@ -14,7 +14,7 @@ class DataSourceViewSet(UpdateModifiedMixin, ExportTableAsGzipFileMixin, viewset
     A viewset for viewing and editing DataSource instances.
     """
 
-    queryset = DataSource.objects.select_related("uploader", "fileformat").all()
+    queryset = DataSource.objects.select_related("uploader", "fileformat").all().order_by("id")
     authentication_classes = [SessionAuthentication, TokenAuthentication]
     permission_classes = [IsAuthenticated]
     serializer_class = DataSourceSerializer

yeastregulatorydb/regulatory_data/api/views/ExpressionManualQCViewSet.py

@@ -21,7 +21,7 @@ class ExpressionManualQCViewSet(UpdateModifiedMixin, viewsets.ModelViewSet):
         "expression__regulator__genomicfeature",
         "expression__source",
         "expression__source__fileformat",
-    ).all()
+    ).all().order_by("-id")
     authentication_classes = [SessionAuthentication, TokenAuthentication]
     permission_classes = [IsAuthenticated]
     serializer_class = ExpressionManualQCSerializer

yeastregulatorydb/regulatory_data/api/views/ExpressionViewSet.py

@@ -26,7 +26,7 @@ class ExpressionViewSet(
 
     queryset = Expression.objects.select_related(
         "uploader", "regulator", "regulator__genomicfeature", "source", "source__fileformat"
-    ).all()
+    ).all().order_by("-id")
     authentication_classes = [SessionAuthentication, TokenAuthentication]
     permission_classes = [IsAuthenticated]
     serializer_class = ExpressionSerializer

yeastregulatorydb/regulatory_data/api/views/FileFormatViewSet.py

@@ -14,7 +14,7 @@ class FileFormatViewSet(UpdateModifiedMixin, ExportTableAsGzipFileMixin, viewset
     A viewset for viewing and editing FileFormat instances.
     """
 
-    queryset = FileFormat.objects.select_related("uploader").all()
+    queryset = FileFormat.objects.select_related("uploader").all().order_by("id")
     authentication_classes = [SessionAuthentication, TokenAuthentication]
     permission_classes = [IsAuthenticated]
     serializer_class = FileFormatSerializer

yeastregulatorydb/regulatory_data/api/views/PromoterSetViewSet.py

@@ -19,7 +19,7 @@ class PromoterSetViewSet(UpdateModifiedMixin, viewsets.ModelViewSet):
     A viewset for viewing and editing PromoterSet instances.
     """
 
-    queryset = PromoterSet.objects.select_related("uploader").all()
+    queryset = PromoterSet.objects.select_related("uploader").all().order_by("id")
     authentication_classes = [SessionAuthentication, TokenAuthentication]
     permission_classes = [IsAuthenticated]
     serializer_class = PromoterSetSerializer

yeastregulatorydb/regulatory_data/api/views/RegulatorViewSet.py

@@ -14,7 +14,7 @@ class RegulatorViewSet(UpdateModifiedMixin, ExportTableAsGzipFileMixin, viewsets
     A viewset for viewing and editing Regulator instances.
     """
 
-    queryset = Regulator.objects.annotated().all()
+    queryset = Regulator.objects.annotated().all().order_by("id")
     authentication_classes = [SessionAuthentication, TokenAuthentication]
     permission_classes = [IsAuthenticated]
     serializer_class = RegulatorSerializer