Merge pull request #137 from jbernal0019/master

Implement pfcon in-network operation mode

.dockerignore

@@ -9,3 +9,4 @@ Dockerfile
 .git
 LICENSE
 CHRIS_REMOTE_FS
+swift_storage

.gitignore

@@ -16,3 +16,4 @@
 
 dc.out
 CHRIS_REMOTE_FS/
+swift_storage/

README.rst

@@ -87,6 +87,22 @@ Remove pfcon's containers
     $> cd pfcon
     $> ./unmake.sh
 
+Start pfcon's development server and backend containers operating in-network (with Swift storage)
+-------------------------------------------------------------------------------------------------
+
+.. code-block:: bash
+
+    $> cd pfcon
+    $> ./make.sh -N
+
+Remove pfcon's containers operating in-network (with Swift storage)
+-------------------------------------------------------------------
+
+.. code-block:: bash
+
+    $> cd pfcon
+    $> ./unmake.sh -N
+
 Remove the local Docker Swarm cluster if desired
 ------------------------------------------------
 
@@ -132,6 +148,23 @@ Remove pfcon's containers
     $> ./unmake.sh -O kubernetes
 
 
+Start pfcon's development server and backend containers operating in-network (with Swift storage)
+-------------------------------------------------------------------------------------------------
+
+.. code-block:: bash
+
+    $> cd pfcon
+    $> ./make.sh -N -O kubernetes
+
+Remove pfcon's containers operating in-network (with Swift storage)
+-------------------------------------------------------------------
+
+.. code-block:: bash
+
+    $> cd pfcon
+    $> ./unmake.sh -N -O kubernetes
+
+
 **********************
 Production deployments
 **********************

kubernetes/pfcon_dev.yaml

@@ -42,7 +42,7 @@ spec:
           image: busybox:1.32
           command: [ 'sh', '-c', "until wget --spider -S -T 2 http://pman:5010/api/v1/ 2>&1 | grep '200 OK'; do echo waiting for pman; done" ]
       containers:
-        - image: fnndsc/pfcon:dev
+        - image: localhost:5000/fnndsc/pfcon:dev
           name: pfcon
           stdin: true
           tty: true
@@ -119,6 +119,8 @@ spec:
           # (where pfcon shares the data) into the spawned container. This directory is
           # passed in the STOREBASE env variable.
           env:
+            - name: STORAGE_TYPE
+              value: host
             - name: SECRET_KEY
               value: "anysu^l=@pnsf!5piqz6!!5kdcdpo79y6jebbp+2244yjm*#+k"
             - name: STOREBASE

kubernetes/pfcon_dev_innetwork.yaml

@@ -0,0 +1,191 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: pfcon
+  labels:
+    app: pfcon
+    env: development
+spec:
+  type: NodePort
+  selector:
+    app: pfcon
+    env: development
+  ports:
+    - port: 30006
+      targetPort: 5005
+      nodePort: 30006
+
+---
+
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: pfcon
+  labels:
+    app: pfcon
+    env: development
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: pfcon
+      env: development
+  template:
+    metadata:
+      name: pfcon
+      labels:
+        app: pfcon
+        env: development
+    spec:
+      initContainers:
+        - name: init-pfcon
+          image: busybox:1.32
+          command: [ 'sh', '-c', "until wget --spider -S -T 2 http://pman:5010/api/v1/ 2>&1 | grep '200 OK'; do echo waiting for pman; done" ]
+        - name: init-swift
+          image: busybox:1.32
+          command: [ "sh", "-c", "until wget --spider -S -T 2 http://swift:8080/info 2>&1 | grep '200 OK'; do echo waiting for Swift storage; sleep2; done" ]
+      containers:
+        - image: fnndsc/pfcon:dev
+          name: pfcon
+          stdin: true
+          tty: true
+          ports:
+            - containerPort: 5005
+          env:
+            - name: APPLICATION_MODE
+              value: development
+          command: ["python"]
+          args: ["-m", "pfcon"]
+          volumeMounts:
+            - mountPath: "/var/local/storeBase"
+              name: "storebase"
+            - mountPath: "/app/pfcon"
+              name: "pfcon-source"
+            - mountPath: "/app/tests"
+              name: "pfcon-tests"
+      volumes:
+        - name: "storebase"
+          hostPath:
+            path: ${STOREBASE}
+        - name: "pfcon-source"
+          hostPath:
+            path: ${SOURCEDIR}/pfcon
+        - name: "pfcon-tests"
+          hostPath:
+            path: ${SOURCEDIR}/tests
+
+---
+
+apiVersion: v1
+kind: Service
+metadata:
+  name: pman
+  labels:
+    app: pman
+    env: production
+spec:
+  selector:
+    app: pman
+    env: production
+  ports:
+    - port: 5010
+      targetPort: 5010
+
+---
+
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: pman
+  labels:
+    app: pman
+    env: production
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: pman
+      env: production
+  template:
+    metadata:
+      name: pman
+      labels:
+        app: pman
+        env: production
+    spec:
+      containers:
+        - image: fnndsc/pman
+          name: pman
+          ports:
+            - containerPort: 5010
+          # Since pman spins off containers of its own it needs to mount storeBase dir
+          # (where pfcon shares the data) into the spawned container. This directory is
+          # passed in the STOREBASE env variable.
+          env:
+            - name: STORAGE_TYPE
+              value: host
+            - name: SECRET_KEY
+              value: "anysu^l=@pnsf!5piqz6!!5kdcdpo79y6jebbp+2244yjm*#+k"
+            - name: STOREBASE
+              value: ${STOREBASE}
+            - name: CONTAINER_ENV
+              value: kubernetes
+
+---
+
+apiVersion: v1
+kind: Service
+metadata:
+  name: swift
+  labels:
+    app: swift
+    env: production
+spec:
+  type: NodePort
+  selector:
+    app: swift
+    env: production
+  ports:
+    - port: 8080
+      targetPort: 8080
+      nodePort: 30080
+
+---
+
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: swift
+  labels:
+    app: swift
+    env: production
+spec:
+  replicas: 1  # stateful service, so only a single replica must be used
+  selector:
+    matchLabels:
+      app: swift
+      env: production
+  template:
+    metadata:
+      name: swift
+      labels:
+        app: swift
+        env: production
+    spec:
+      containers:
+        - name: swift
+          image: fnndsc/docker-swift-onlyone
+          ports:
+            - containerPort: 8080
+          env:
+            - name: SWIFT_USERNAME
+              value: chris:chris1234
+            - name: SWIFT_KEY
+              value: testing
+          volumeMounts:
+            - name: swiftdb
+              mountPath: "/srv"
+      volumes:
+        - name: swiftdb
+          hostPath:
+            path: ${SOURCEDIR}/swift_storage