Merge pull request #194 from camicroscope/develop

For 3.9.11

README.md

@@ -63,6 +63,8 @@ Running QuIP with PathDB (https://github.com/SBU-BMI/PathDB):
 3) build with, "docker-compose -f quip-pathdb.yml build"<br>
 4) run with, "docker-compose -f quip-pathdb.yml up -d"
 
+The default login for pathdb is `admin` with password `bluecheese2018`. Please change this password before exposing this service to the internet.
+
 ## Support
 Feel free to add any support inquiry as a github issue to this repository. Other feedback can be given via [this form](https://docs.google.com/forms/d/e/1FAIpQLScL91LxrpAZjU88GBZP9gmcdgdf8__uNUwhws2lzU6Lr4qNwA/viewform).
 

caMicroscope.yml

@@ -11,18 +11,11 @@ services:
           max-size: "10m"
     volumes:
       - ./db:/data/db
-    command: bash /config/run_idx.sh
-    logging:
-      options:
-          max-file: "5"
-          max-size: "10m"
-    depends_on:
-      - mongo
   back:
     build:
-      context: "https://github.com/camicroscope/caracal.git#v3.9.10"
+      context: "https://github.com/camicroscope/caracal.git#v3.9.11"
       args:
-        viewer: "v3.9.10"
+        viewer: "v3.9.11"
     depends_on:
       - "mongo"
     ports:
@@ -55,7 +48,7 @@ services:
     volumes:
       - ./images/:/images/
   loader:
-    build: "https://github.com/camicroscope/SlideLoader.git#v3.9.10"
+    build: "https://github.com/camicroscope/SlideLoader.git#v3.9.11"
     container_name: ca-load
     restart: always
     logging:

config/login.html

@@ -83,7 +83,7 @@ <h3>Please Sign In With Your Google Account</h3>
               if (x.hasOwnProperty("token")) {
                 document.cookie = cookie_name + "=" + x.token;
                 let token_data = parseJwt(x.token);
-                window.location = "./apps/landing/landing.html";
+                window.location = "./apps/table.html";
               } else {
                 window.alert("User not added");
                 window.location = "./apps/signup/signup.html";

config/pathdbmysql.cnf

@@ -0,0 +1,32 @@
+[mysqld]
+datadir=/data/pathdb/mysql
+user=mysql
+skip-name-resolve
+symbolic-links=0
+max_connections = 150
+max_user_connections = 150
+key_buffer = 36M
+myisam_sort_buffer_size = 64M
+join_buffer_size = 2M
+read_buffer_size = 2M
+sort_buffer_size = 3M
+table_cache = 1024
+thread_cache_size = 286
+interactive_timeout = 25
+wait_timeout = 1800
+connect_timeout = 10
+max_allowed_packet = 16M
+max_connect_errors = 1000
+query_cache_limit = 1M
+query_cache_size = 0
+query_cache_type = 0
+tmp_table_size = 16M
+
+innodb-flush-log-at-trx-commit=2
+innodb_file_per_table=ON
+innodb_buffer_pool_size = 4G
+innodb_log_file_size=512M
+innodb_stats_on_metadata=0
+innodb_buffer_pool_instances=4
+
+[mysqld_safe]

config/routes.json

@@ -373,7 +373,7 @@
       {"function":"mongoUpdate", "args": ["camic", "freeform"]}
     ]
   },
-  
+
   {
     "route":"/data/Configuration/find",
     "method":"get",

kubernetes/README.md

@@ -1,17 +1,16 @@
 # Kubernetes Version of caMicroscope and quip
 
-## FYI
-- ALL host mounts are ignored, at least as of now.
+Note that the images persistent volume starts empty. Please replace `emptyDir` with an alternate source if required.
 
-## Develop
+## develop and caMicroscope
 run `kubectl apply -f develop.yml` to create, cleanup.sh to remove *everything* when done.
 
-When using minikube, run `minikube tunnel` then `minikube service ca-back --url` to get the url.
+When using minikube, run `minikube tunnel` then `minikube service back --url` to get the url.
 
-
-## caMicroscope
-TODO
+For instances where security is enabled, after generating keys in 'jwt_keys' and confiuring login.html, run `camicroscope_add_config.sh` or some modification thereof as needed for your configuration.
 
 ## quip
-TODO
-(worried about non-optional config mounts and image mount in particular)
+* Setup required configuration by running `pathdb_add_config.sh`
+* Change the persistent volume configuration in quip-pathdb.yml to match where your slide and other data files are.
+* Run `kubectl apply -f quip-pathdb.yml` to create the pod
+* When using minikube, run `minikube tunnel` then `minikube service pathdb --url` to get the url.

kubernetes/caMicroscope.yml

@@ -1,6 +1,32 @@
 apiVersion: v1
 kind: List
 items:
+ - apiVersion: v1
+   kind: PersistentVolume
+   metadata:
+     name: pv-images
+     labels:
+       type: local
+   spec:
+     storageClassName: manual
+     capacity:
+       storage: 10Gi
+     accessModes:
+       - ReadWriteOnce
+     hostPath:
+       path: /data/images
+ - apiVersion: v1
+   kind: PersistentVolumeClaim
+   metadata:
+     name: pv-images-claim
+   spec:
+     storageClassName: manual
+     volumeName: pv-images
+     accessModes:
+       - ReadWriteOnce
+     resources:
+       requests:
+         storage: 10Gi
  - apiVersion: apps/v1
    kind: Deployment
    metadata:
@@ -25,7 +51,14 @@ items:
            - "ca-back"
          volumes:
            - name: images
-             emptyDir: {}
+             persistentVolumeClaim:
+               claimName: pv-images-claim
+           - name: jwtkeys
+             secret:
+               secretName: camic-jwt-keys
+           - name: loginpage
+             configMap:
+               name: camic-login
          containers:
            - name: mongo
              image: mongo:4.2-bionic
@@ -35,6 +68,11 @@ items:
              image: ghcr.io/camicroscope/caracal:master
              ports:
                - containerPort: 4010
+             volumeMounts:
+             - name: jwtkeys
+               mountPath: /src/keys/
+             - name: loginpage
+               mountPath: /src/static/
              env:
                - name: PORT
                  value: "4010"

kubernetes/camicroscope_add_config.sh

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+kubectl create secret generic camic-jwt-keys --from-file=key=../jwt_keys/key --from-file=key.pub=../jwt_keys/key.pub
+kubectl create configmap camic-login --from-file=login.html=../config/login.html

kubernetes/cleanup.sh

@@ -2,3 +2,5 @@
 kubectl delete --all service
 kubectl delete --all deploy
 kubectl delete --all pod
+kubectl delete --all secret
+kubectl delete --all configmap

kubernetes/pathdb_add_config.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+kubectl create secret generic camic-jwt-keys --from-file=key=../jwt_keys/key --from-file=key.pub=../jwt_keys/key.pub
+kubectl create configmap pathdb-sites --from-file=settings.php=../config/pathdb/settings.php
+kubectl create configmap pathdb-config --from-file=../config/ --from-file=httpd.conf=../config/httpd.conf.template

kubernetes/pv_cleanup.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+kubectl delete --all pvc
+kubectl delete --all pv

kubernetes/quip-pathdb.yml

@@ -0,0 +1,190 @@
+apiVersion: v1
+kind: List
+items:
+ - apiVersion: v1
+   kind: PersistentVolume
+   metadata:
+     name: pv-images
+     labels:
+       type: local
+   spec:
+     storageClassName: manual
+     capacity:
+       storage: 10Gi
+     accessModes:
+       - ReadWriteOnce
+     hostPath:
+       path: /data/images
+ - apiVersion: v1
+   kind: PersistentVolume
+   metadata:
+     name: pv-data
+     labels:
+       type: local
+   spec:
+     storageClassName: manual
+     capacity:
+       storage: 10Gi
+     accessModes:
+       - ReadWriteOnce
+     hostPath:
+       path: /data
+ - apiVersion: v1
+   kind: PersistentVolumeClaim
+   metadata:
+     name: pv-data-claim
+   spec:
+     storageClassName: manual
+     volumeName: pv-data
+     accessModes:
+       - ReadWriteOnce
+     resources:
+       requests:
+         storage: 10Gi
+ - apiVersion: v1
+   kind: PersistentVolumeClaim
+   metadata:
+     name: pv-images-claim
+   spec:
+     storageClassName: manual
+     volumeName: pv-images
+     accessModes:
+       - ReadWriteOnce
+     resources:
+       requests:
+         storage: 10Gi
+ - apiVersion: apps/v1
+   kind: Deployment
+   metadata:
+     name: pathdb
+     labels:
+       service: pathdb
+   spec:
+     selector:
+       matchLabels:
+         service: pathdb
+     template:
+       metadata:
+         labels:
+           service: pathdb
+       spec:
+         hostAliases:
+         - ip: "127.0.0.1"
+           hostnames:
+           - "quip-pathdb"
+           - "quip-imageloader"
+           - "quip-segloader"
+           - "quip-hmloader"
+           - "ca-iip"
+           - "ca-mongo"
+           - "ca-back"
+           - "ca-security"
+         volumes:
+           - name: images
+             persistentVolumeClaim:
+               claimName: pv-images-claim
+           - name: data
+             persistentVolumeClaim:
+               claimName: pv-data-claim
+           - name: pathdb-files
+             emptyDir: {}
+           - name: jwtkeys
+             secret:
+               secretName: camic-jwt-keys
+           - name: pathdb-sites
+             configMap:
+               name: pathdb-sites
+           - name: pathdb-config
+             configMap:
+               name: pathdb-config
+         containers:
+           - name: mongo
+             image: mongo:4.2-bionic
+             ports:
+               - containerPort: 27017
+           - name: back
+             image: ghcr.io/camicroscope/caracal:master
+             ports:
+               - containerPort: 4010
+             volumeMounts:
+             - name: jwtkeys
+               mountPath: /src/keys/
+             env:
+               - name: PORT
+                 value: "4010"
+               - name: JWK_URL
+                 value: "https://www.googleapis.com/oauth2/v3/certs"
+               - name: IIP_PATH
+                 value: "http://localhost:8080/fcgi-bin/iipsrv.fcgi"
+               - name: MONGO_URI
+                 value: "mongodb://localhost"
+               - name: GENERATE_KEY_IF_MISSING
+                 value: "true"
+               - name: "DEFAULT_USER_TYPE"
+                 value: "Editor"
+               - name: "DISABLE_SEC"
+                 value: "true"
+               - name: "DISABLE_CSP"
+                 value: "true"
+           - name: iip
+             image: camicroscope/iipimage:latest
+             ports:
+               - containerPort: 8080
+             volumeMounts:
+             - name: images
+               mountPath: /data/images/
+           - name: imageloader
+             image: camicroscope/pathdb-imageloader:latest
+             volumeMounts:
+             - name: data
+               mountPath: /data/
+             - name: images
+               mountPath: /data/images/
+           - name: heatmaploader
+             image: camicroscope/pathdb-heatmaploader:latest
+             volumeMounts:
+             - name: data
+               mountPath: /mnt/data/
+             env:
+               - name: "TZ"
+                 value: "America/New_York"
+               - name: "DEBIAN_FRONTEND"
+                 value: "noninteractive"
+           - name: pathdb
+             image: camicroscope/pathdb:latest
+             ports:
+               - containerPort: 443
+               - containerPort: 80
+             volumeMounts:
+             - name: data
+               mountPath: /data/
+             - name: images
+               mountPath: /data/pathdb/files/wsi
+             - name: pathdb-sites
+               mountPath: /quip/web/sites/default/
+             - name: pathdb-files
+               mountPath: /quip/web/sites/default/files/
+             - name: pathdb-config
+               mountPath: /config/
+             - name: jwtkeys
+               mountPath: /keys/
+ - apiVersion: v1
+   kind: Service
+   metadata:
+     name: pathdb
+     labels:
+       service: pathdb
+   spec:
+     type: NodePort
+     selector:
+       service: pathdb
+     ports:
+       - name: "443"
+         port: 443
+         targetPort: 443
+         nodePort: 30443
+       - name: "80"
+         port: 80
+         targetPort: 80
+         nodePort: 30180
+     type: LoadBalancer

quip-pathdb.yml

@@ -15,9 +15,9 @@ services:
       - ./images/:/data/images/
   back:
     build:
-      context: "https://github.com/camicroscope/caracal.git#v3.9.10"
+      context: "https://github.com/camicroscope/caracal.git#v3.9.11"
       args:
-        viewer: "v3.9.10"
+        viewer: "v3.9.11"
     depends_on:
       - "mongo"
     ports: