Merge pull request #179 from camicroscope/develop

For 3.9.8

caMicroscope.yml

@@ -27,9 +27,9 @@ services:
       - mongo
   back:
     build:
-      context: "https://github.com/camicroscope/caracal.git#v3.9.7"
+      context: "https://github.com/camicroscope/caracal.git#v3.9.8"
       args:
-        viewer: "v3.9.6"
+        viewer: "v3.9.8"
     depends_on:
       - "mongo"
     ports:
@@ -61,7 +61,7 @@ services:
     volumes:
       - ./images/:/images/
   loader:
-    build: "https://github.com/camicroscope/SlideLoader.git#v3.9.4"
+    build: "https://github.com/camicroscope/SlideLoader.git#v3.9.8"
     container_name: ca-load
     restart: always
     logging:

config/contentSecurityPolicy.json

@@ -45,6 +45,7 @@
 ],
 "frameSrc": [
  "'self'",
- "accounts.google.com"
+ "accounts.google.com",
+ "www.youtube-nocookie.com"
 ]
 }

openshift/build_config/quip-back-img.yaml

@@ -0,0 +1,39 @@
+apiVersion: v1
+items:
+- apiVersion: image.openshift.io/v1
+  kind: ImageStream
+  metadata:
+    annotations:
+      openshift.io/generated-by: OpenShiftNewBuild
+    labels:
+      build: quip-back-img
+    name: back
+  spec:
+    lookupPolicy:
+      local: false
+- apiVersion: build.openshift.io/v1
+  kind: BuildConfig
+  metadata:
+    annotations:
+      openshift.io/generated-by: OpenShiftNewBuild
+    labels:
+      build: quip-back-img
+    name: back
+  spec:
+    nodeSelector: null
+    output:
+      to:
+        kind: ImageStreamTag
+        name: back:latest
+    postCommit: {}
+    resources: {}
+    source:
+      git:
+        ref: prism
+        uri: https://github.com/SBU-BMI/caracal.git
+      type: Git
+    strategy:
+      dockerStrategy:
+      type: Docker
+kind: List
+metadata: {}

openshift/build_config/quip-featuredb-img.yaml

@@ -0,0 +1,38 @@
+apiVersion: v1
+items:
+- apiVersion: image.openshift.io/v1
+  kind: ImageStream
+  metadata:
+    annotations:
+      openshift.io/generated-by: OpenShiftNewBuild
+    labels:
+      build: quip-featuredb-img
+    name: featuredb
+  spec:
+    lookupPolicy:
+      local: false
+- apiVersion: build.openshift.io/v1
+  kind: BuildConfig
+  metadata:
+    annotations:
+      openshift.io/generated-by: OpenShiftNewBuild
+    labels:
+      build: quip-featuredb-img
+    name: featuredb 
+  spec:
+    output:
+      to:
+        kind: ImageStreamTag
+        name: featuredb:latest
+    postCommit: {}
+    resources: {}
+    source:
+      git:
+        ref: prism
+        uri: https://github.com/SBU-BMI/quip_featuredb.git
+      type: Git
+    strategy:
+      dockerStrategy:
+      type: Docker
+kind: List
+metadata: {}

openshift/build_config/quip-heatmaploader-img.yaml

@@ -0,0 +1,38 @@
+apiVersion: v1
+items:
+- apiVersion: image.openshift.io/v1
+  kind: ImageStream
+  metadata:
+    annotations:
+      openshift.io/generated-by: OpenShiftNewBuild
+    labels:
+      build: quip-heatmaploader-img
+    name: heatmaploader
+  spec:
+    lookupPolicy:
+      local: false
+- apiVersion: build.openshift.io/v1
+  kind: BuildConfig
+  metadata:
+    annotations:
+      openshift.io/generated-by: OpenShiftNewBuild
+    labels:
+      build: quip-heatmaploader-img
+    name: heatmaploader
+  spec:
+    output:
+      to:
+        kind: ImageStreamTag
+        name: heatmaploader:latest
+    postCommit: {}
+    resources: {}
+    source:
+      git:
+        ref: prism
+        uri: https://github.com/SBU-BMI/uploadHeatmaps.git
+      type: Git
+    strategy:
+      dockerStrategy:
+      type: Docker
+kind: List
+metadata: {}

openshift/build_config/quip-iip-img.yaml

@@ -0,0 +1,37 @@
+apiVersion: v1
+items:
+- apiVersion: image.openshift.io/v1
+  kind: ImageStream
+  metadata:
+    annotations:
+      openshift.io/generated-by: OpenShiftNewBuild
+    labels:
+      build: quip-iip-img
+    name: iip
+  spec:
+    lookupPolicy:
+      local: false
+- apiVersion: build.openshift.io/v1
+  kind: BuildConfig
+  metadata:
+    annotations:
+      openshift.io/generated-by: OpenShiftNewBuild
+    labels:
+      build: quip-iip-img
+    name: iip
+  spec:
+    output:
+      to:
+        kind: ImageStreamTag
+        name: iip:latest
+    postCommit: {}
+    source:
+      git:
+        ref: prism
+        uri: https://github.com/SBU-BMI/iipImage.git
+      type: Git
+    strategy:
+      dockerStrategy:
+      type: Docker
+kind: List
+metadata: {}

openshift/build_config/quip-imageloader-img.yaml

@@ -0,0 +1,38 @@
+apiVersion: v1
+items:
+- apiVersion: image.openshift.io/v1
+  kind: ImageStream
+  metadata:
+    annotations:
+      openshift.io/generated-by: OpenShiftNewBuild
+    labels:
+      build: quip-imageloader-img
+    name: imageloader
+  spec:
+    lookupPolicy:
+      local: false
+- apiVersion: build.openshift.io/v1
+  kind: BuildConfig
+  metadata:
+    annotations:
+      openshift.io/generated-by: OpenShiftNewBuild
+    labels:
+      build: quip-imageloader-img
+    name: imageloader
+  spec:
+    output:
+      to:
+        kind: ImageStreamTag
+        name: imageloader:latest
+    postCommit: {}
+    resources: {}
+    source:
+      git:
+        ref: prism
+        uri: https://github.com/SBU-BMI/ImageLoader.git
+      type: Git
+    strategy:
+      dockerStrategy:
+      type: Docker
+kind: List
+metadata: {}

openshift/build_config/quip-pathdb-img.yaml

@@ -0,0 +1,38 @@
+apiVersion: v1
+items:
+- apiVersion: image.openshift.io/v1
+  kind: ImageStream
+  metadata:
+    annotations:
+      openshift.io/generated-by: OpenShiftNewBuild
+    labels:
+      build: quip-pathdb-img
+    name: pathdb
+  spec:
+    lookupPolicy:
+      local: false
+- apiVersion: build.openshift.io/v1
+  kind: BuildConfig
+  metadata:
+    annotations:
+      openshift.io/generated-by: OpenShiftNewBuild
+    labels:
+      build: quip-pathdb-img
+    name: pathdb
+  spec:
+    output:
+      to:
+        kind: ImageStreamTag
+        name: pathdb:latest
+    postCommit: {}
+    resources: {}
+    source:
+      git:
+        ref: prism
+        uri: https://github.com/SBU-BMI/PathDB.git
+      type: Git
+    strategy:
+      dockerStrategy:
+      type: Docker
+kind: List
+metadata: {}

openshift/build_config/quip-segloader-img.yaml

@@ -0,0 +1,38 @@
+apiVersion: v1
+items:
+- apiVersion: image.openshift.io/v1
+  kind: ImageStream
+  metadata:
+    annotations:
+      openshift.io/generated-by: OpenShiftNewBuild
+    labels:
+      build: quip-segloader-img
+    name: segloader
+  spec:
+    lookupPolicy:
+      local: false
+- apiVersion: build.openshift.io/v1
+  kind: BuildConfig
+  metadata:
+    annotations:
+      openshift.io/generated-by: OpenShiftNewBuild
+    labels:
+      build: quip-segloader-img
+    name: segloader
+  spec:
+    output:
+      to:
+        kind: ImageStreamTag
+        name: segloader:latest
+    postCommit: {}
+    resources: {}
+    source:
+      git:
+        ref: prism
+        uri: https://github.com/SBU-BMI/SegmentationLoader.git
+      type: Git
+    strategy:
+      dockerStrategy:
+      type: Docker
+kind: List
+metadata: {}

openshift/deployment/back-deployment.yaml

@@ -0,0 +1,52 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  annotations:
+    kompose.cmd: kompose convert -f quip-pathdb.yml.PRISM -o openshift2
+    kompose.version: 1.21.0 (992df58d8)
+  creationTimestamp: null
+  labels:
+    io.kompose.service: back
+  name: back
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      io.kompose.service: back
+  template:
+    metadata:
+      annotations:
+        kompose.cmd: kompose convert -f quip-pathdb.yml.PRISM -o openshift2
+        kompose.version: 1.21.0 (992df58d8)
+      creationTimestamp: null
+      labels:
+        io.kompose.service: back
+    spec:
+      containers:
+      - env:
+        - name: DEFAULT_USER_TYPE
+          value: Editor
+        - name: DISABLE_SEC
+          value: "true"
+        - name: IIP_PATH
+          value: http://ca-iip:8080/fcgi-bin/iipsrv.fcgi
+        - name: JWK_URL
+          value: https://www.googleapis.com/oauth2/v3/certs
+        - name: MONGO_URI
+          value: mongodb://ca-mongo
+        image: back:latest
+        imagePullPolicy: ""
+        name: ca-security
+        ports:
+        - containerPort: 4010
+        resources: {}
+        volumeMounts:
+        - mountPath: /root/src/keys/
+          name: keys
+      restartPolicy: Always
+      serviceAccountName: ""
+      volumes:
+      - name: keys
+        persistentVolumeClaim:
+          claimName: keys
+status: {}

openshift/deployment/back-service.yaml

@@ -0,0 +1,19 @@
+apiVersion: v1
+kind: Service
+metadata:
+  annotations:
+    kompose.cmd: kompose convert -f quip-pathdb.yml.PRISM -o openshift2
+    kompose.version: 1.21.0 (992df58d8)
+  creationTimestamp: null
+  labels:
+    io.kompose.service: back
+  name: ca-security
+spec:
+  ports:
+  - name: "4010"
+    port: 4010
+    targetPort: 4010
+  selector:
+    io.kompose.service: back
+status:
+  loadBalancer: {}

openshift/deployment/data-persistentvolumeclaim.yaml

@@ -0,0 +1,14 @@
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  creationTimestamp: null
+  labels:
+    io.kompose.service: data
+  name: data
+spec:
+  accessModes:
+  - ReadWriteOnce
+  resources:
+    requests:
+      storage: 50Gi
+status: {}