Add containerization and deployment to k8s

.dockerignore

@@ -0,0 +1,13 @@
+.git/
+deployment/
+data/
+
+.dockerignore
+.gitignore
+
+*.csv
+*.db
+*.md
+
+Dockerfile
+LICENSE

Dockerfile

@@ -0,0 +1,32 @@
+FROM python:3.10-alpine
+
+# upgrade pip
+RUN pip install --upgrade pip
+
+# get curl for healthchecks
+RUN apk add curl
+
+# permissions and nonroot user for tightened security
+RUN adduser -D 1000 -u 1000
+RUN mkdir /home/app/ && chown -R 1000:1000 /home/app
+RUN mkdir -p /var/log/flask-app && touch /var/log/flask-app/flask-app.err.log && touch /var/log/flask-app/flask-app.out.log
+RUN chown -R 1000:1000 /var/log/flask-app
+WORKDIR /home/app
+USER 1000
+
+# copy all the files to the container
+COPY --chown=1000:1000 . .
+
+# venv
+ENV VIRTUAL_ENV=/home/app/venv
+
+# python setup
+RUN python -m venv $VIRTUAL_ENV
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+RUN export FLASK_APP=app.py
+RUN pip install -r requirements.txt
+
+# define the port number the container should expose
+EXPOSE 5000
+
+CMD ["python", "app.py"]

app.py

@@ -2,7 +2,8 @@
 import sqlite3
 
 app = Flask(__name__)
-
+app.config["DB_DRIVER"] = "sqlite3"
+app.config["DB_CONNECTION_STRING"] = "./data/genes.db"
 
 def get_data_values():
     def chromosome_key(chromosome: str) -> int:
@@ -14,11 +15,8 @@ def chromosome_key(chromosome: str) -> int:
                 return 89
             case _:
                 return int(chrtype)
-
-
-    connection = sqlite3.connect('genes.db')
+    connection = sqlite3.connect(app.config["DB_CONNECTION_STRING"])
     cur = connection.cursor()
-
     values = {}
 
     cur.execute('SELECT DISTINCT strand FROM genes')
@@ -47,23 +45,24 @@ def chromosome_key(chromosome: str) -> int:
 @app.route('/get_results')
 def get_results():
     parameters = request.args
-    connection = sqlite3.connect('genes.db')
+    connection = sqlite3.connect(app.config["DB_CONNECTION_STRING"])
     cur = connection.cursor()
 
     conditions = []
-    strand = parameters['strand']
+
+    strand = parameters.get("strand", default="")
     if strand:
         conditions.append(f'strand = "{strand}"')
-    protein_name = parameters['protein_name']
+    protein_name = parameters.get("protein_name", default="")
     if protein_name:
         conditions.append(f'protein_name = "{protein_name}"')
-    chromosome = parameters['chromosome']
+    chromosome = parameters.get("chromosome", default="")
     if chromosome:
         conditions.append(f'chromosome = "{chromosome}"')
-    start_min = parameters['start_min']
-    start_max = parameters['start_max']
-    end_min = parameters['end_min']
-    end_max = parameters['end_max']
+    start_min = parameters.get("start_min", default="")
+    start_max = parameters.get("start_max", default="")
+    end_min = parameters.get("end_min", default="")
+    end_max = parameters.get("end_max", default="")
 
     if start_min:
         conditions.append(f'start >= {start_min}')
@@ -96,4 +95,4 @@ def download_all():
 
 
 if __name__ == '__main__':
-    app.run()
+    app.run(host='0.0.0.0')

data/data.csv

@@ -0,0 +1,20 @@
+chr,start,end,strand,protein_name,seq
+chr7,98881815,98881850,+,AARS,ACTGGTTGTAGGGAACTAGCTATGTGCCTTCTATT
+chr7,98881757,98881792,+,AARS,TGTGTGTATATGCTTGTCAGTGCATGCACGTGTAT
+chr7,77537503,77537574,+,AARS,GCGGCGGGGGGGCCAGCGACCGCAGCCGGGGGGACGCGGGAGGATGGAGCAAGTGGAGATCCTGAGGAAAT
+chr7,139409602,139409655,+,AARS,GGCTGAAACGAAGAGAAGAGAGAGAGAGAGAAGAAAGGGAGAAGCTGAGGAGG
+chr7,100884403,100884485,+,AARS,TTCGCATCCTGGAGCAGGAGGAGGAGGAGGAGCAGGCAGGAAAGCCTGGGGAGCCCAGCAAGAAAGAAGAAGGACGGGCTGG
+chr7,151089904,151089955,+,AARS,AGCCAAGCGGATACAGCCAGGGAGAGTATAGGCCTTCAACAGGAGCCCGCT
+chr7,139412547,139412582,+,AARS,TAGGTCCCGATCACACAGCAAGAATCCAAAAAGGT
+chr7,128794511,128794597,+,AARS,CTGCGGGCTCAGGTGCTGCAGCTGGTGGCAGAACTGGAGGAGACCCGGGAACTGGCAGGGCAGCATGAGGATGACTCCTTGGAGCT
+chr7,151144098,151144180,+,AARS,GAGAGTTGGGGATTTGAGCTGCAGCAGAGAGGGATGAGGGATTTAGCCCTCTGCCCTAAGGTGCCATTGAAAAGGGACAGGA
+chr7,74568835,74568904,+,AARS,CTGGAAGGAGGGAAGGAGATGGCCAGAGAAGGATGTGGGACACAGAGGTGCCGCCATGGATCACCAAGA
+chr7,99364989,99365037,+,AARS,GCGATGGGTTTTGGAGGGAGGGACTGTGAGTTGAGAAGACACAGGCGA
+chr7,158871450,158871499,+,AARS,AGAAGGGCCCGGAAGGAAGAGCTCCGGCAGACCGTGGCCCACCACAACC
+chr7,105014418,105014509,+,AARS,GGTCCTGTGTCCGCAGTGGCTGCTGTCGGGGGGTCGCCTGTTCGCGGAGGTGCGGAGAGACTCCTTGGGGGTCGAGCACATAACGGGGTTC
+chr7,99455908,99455973,+,AARS,TCCCCAGCAGTGGCTCCCCAAGGGAGGGGAGGCTGGGACACTTCTGATGCTGTTCCCTCCCATCT
+chr7,102254792,102254824,+,AARS,TCAGCGTGTACTGAATGCCAGTCTGGCCGGCA
+chr7,75982221,75982287,+,AARS,AGCATTCGCCAGTACGAGCTTGTGGTCCACACCGACATAGATGCGGCCAAGGTGTACATGGGGGAG
+chr7,91992956,91993047,+,AARS,ATGGAAAGTGAGTTGGCTGGGAAGCAGCATGAGATTGAAGAGCTAAACAGAGAGCTGGAAGAAATGAGGGTTACCTATGGGACTGAAGGAC
+chr7,2364368,2364435,+,AARS,CAGAGATGGACAGAGACGTATGTGCGTTGGTCTCCTAAGGGCACCTACCTGGCTACCTTTCATCAAA
+chr7,2379390,2379437,+,AARS,CAGGGGTGGACACTGACGAGCTGGACAGCAACGTGGACGACTGGGAA

deployment/deployment.yaml

@@ -0,0 +1,36 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: rbp-tar
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: rbp-tar
+  template:
+    metadata:
+      labels:
+        app: rbp-tar
+    spec:
+      securityContext:                                                          
+        runAsUser: 1000
+      containers:      
+      - name: rbp-tar
+        image: hub.cerit.io/xrosinec/ncbr/rbp-tar:1.0.1
+        command: ["gunicorn"]
+        args: ["-w 3", "-t 60", "-b 0.0.0.0:5000", "app:app"]
+        ports:
+        resources:
+          requests:
+            cpu: 0.1
+            memory: "100Mi"
+          limits:
+            cpu: 0.25
+            memory: "512Mi"
+        volumeMounts:
+        - mountPath: /home/app/data
+          name: rbp-tar-pvc
+      volumes:
+      - name: rbp-tar-pvc
+        persistentVolumeClaim:
+          claimName: rbp-tar-pvc

deployment/ingress.yaml

@@ -0,0 +1,24 @@
+apiVersion: networking.k8s.io/v1
+kind: Ingress
+metadata:
+  name: rbp-tar-ingress
+  annotations:
+    cert-manager.io/cluster-issuer: letsencrypt-prod
+    kubernetes.io/ingress.class: nginx
+    kubernetes.io/tls-acme: "true"
+spec:
+  tls:
+  - hosts:
+      - rbp-tar.ncbr.dyn.cloud.e-infra.cz
+    secretName: rpb-tar-ncbr-dyn-cloud-e-infra-cz
+  rules:
+  - host: rbp-tar.ncbr.dyn.cloud.e-infra.cz
+    http:
+      paths:
+        - pathType: ImplementationSpecific
+          path: "/"
+          backend:
+            service:
+              name: rbp-tar-svc
+              port: 
+                name: default

deployment/pvc.yaml

@@ -0,0 +1,14 @@
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  labels:
+    app: rbp-tar
+  name: rbp-tar-pvc
+spec:
+  accessModes:
+    - ReadWriteOnce
+  resources:
+    requests:
+      storage: 4Gi
+  storageClassName: nfs-csi
+  volumeMode: Filesystem

deployment/service.yaml

@@ -0,0 +1,13 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: rbp-tar-svc
+spec:
+  type: ClusterIP
+  ports:
+  - name: default                                                 
+    port: 80     
+    protocol: TCP                                                               
+    targetPort: 5000    
+  selector:
+    app: rbp-tar

requirements.txt

@@ -0,0 +1,2 @@
+Flask==2.0.1
+gunicorn==20.1.0