Update jupyter notebook.yaml to use node port and get rid of host network

K8/JupyterNotebook/jupyter_notebook_pod_deployment.yaml

@@ -1,21 +1,18 @@
 apiVersion: v1 # Jobs Default K8 API
 kind: Pod # This tells kubernetes what kind of class it is working with
 metadata:
-  name: stimuli-pipeline #
+  name: pipeline-jupyter #
   labels:
-    app: stimuli-pipeline-jupyter # Reference this in your service
+    app: pipeline-jupyter # Reference this in your service
 spec:
   restartPolicy: Never # Options are OnFailure, and Never.
-  hostNetwork: true # This option will allow the pod to use the host network for internet access
   volumes:
   - name: mnt
     hostPath:
       path: /mnt # Directory on the host machine to be mounted
-  imagePullSecrets:
-  - name: docker-credentials
   containers: # Container Level
-  - name: stimuli-pipeline # Container name (Can be set to whatever)
-    image: ninai/stimuli # Docker Image hosted on Docker Hub
+  - name: pipeline # Container name (Can be set to whatever)
+    image: ninai/pipeline:latest # Docker Image hosted on Docker Hub
     ports:
     - containerPort: 8888
     volumeMounts: # Container reference to volumes define above
@@ -47,21 +44,26 @@ spec:
         secretKeyRef:
           name: github-credentials
           key: GITHUB_PASSWORD
+    workingDir: /src
     command: ["/bin/bash"] # Entry point for the container
-    args: ["-c", "pip3 install jupyter \
-    && jupyter notebook --ip='*' --port=8888 --allow-root --no-browser --NotebookApp.token=${GITHUB_PASSWORD}"] # sh commands to clone and run python script
+    # Override the git pull below to pull your own fork, otherwise it clones the default master one from Cajal
+    args: ["-c", "pip3 install jupyter &&\
+    rm -r /data &&\
+    git clone https://$(GITHUB_USERNAME):$(GITHUB_PASSWORD)@github.com/cajal/pipeline.git &&\
+    jupyter notebook --ip='*' --port=8888 --allow-root --no-browser --NotebookApp.token=${GITHUB_PASSWORD}"] 
 
 ---
+
+# This is the node port service. After deployment run kubectl get svc to get the nodeport that was assign to this pod then go do <master-host-name>:<port-number> (should be in the range of 30000-32767)
 kind: Service
 apiVersion: v1
 metadata:
-  name: stimuli-pipeline-jupyter-service
+  name: pipeline-jupyter
 spec:
   type: NodePort
   selector:
-    app: stimuli-pipeline-jupyter
+    app: pipeline-jupyter
   ports:
   - protocol: TCP
-    nodePort: 30000 # Port might be taken so switch it to something else
     port: 8888
     targetPort: 8888