diff --git a/README.md b/README.md index d43af02..fb4f16f 100644 --- a/README.md +++ b/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"
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). diff --git a/caMicroscope.yml b/caMicroscope.yml index 247920c..86e376b 100644 --- a/caMicroscope.yml +++ b/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: diff --git a/config/login.html b/config/login.html index 8a02921..199272c 100644 --- a/config/login.html +++ b/config/login.html @@ -83,7 +83,7 @@

Please Sign In With Your Google Account

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"; diff --git a/config/pathdbmysql.cnf b/config/pathdbmysql.cnf new file mode 100644 index 0000000..b732df7 --- /dev/null +++ b/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] diff --git a/config/routes.json b/config/routes.json index c3b6cba..e9ef28f 100644 --- a/config/routes.json +++ b/config/routes.json @@ -373,7 +373,7 @@ {"function":"mongoUpdate", "args": ["camic", "freeform"]} ] }, - + { "route":"/data/Configuration/find", "method":"get", diff --git a/kubernetes/README.md b/kubernetes/README.md index f65a5fc..770847c 100644 --- a/kubernetes/README.md +++ b/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. diff --git a/kubernetes/caMicroscope.yml b/kubernetes/caMicroscope.yml index b1592fc..b27c55a 100644 --- a/kubernetes/caMicroscope.yml +++ b/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" diff --git a/kubernetes/camicroscope_add_config.sh b/kubernetes/camicroscope_add_config.sh new file mode 100755 index 0000000..941a488 --- /dev/null +++ b/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 diff --git a/kubernetes/cleanup.sh b/kubernetes/cleanup.sh index 43cd39d..2be2a5e 100755 --- a/kubernetes/cleanup.sh +++ b/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 diff --git a/kubernetes/pathdb_add_config.sh b/kubernetes/pathdb_add_config.sh new file mode 100755 index 0000000..4a12799 --- /dev/null +++ b/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 diff --git a/kubernetes/pv_cleanup.sh b/kubernetes/pv_cleanup.sh new file mode 100755 index 0000000..ecf2b76 --- /dev/null +++ b/kubernetes/pv_cleanup.sh @@ -0,0 +1,3 @@ +#!/bin/bash +kubectl delete --all pvc +kubectl delete --all pv diff --git a/kubernetes/quip-pathdb.yml b/kubernetes/quip-pathdb.yml new file mode 100644 index 0000000..4b7f0dd --- /dev/null +++ b/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 diff --git a/quip-pathdb.yml b/quip-pathdb.yml index 8c1939f..2198416 100644 --- a/quip-pathdb.yml +++ b/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: diff --git a/test/package-lock.json b/test/package-lock.json index 356eb5b..2bf5ca2 100644 --- a/test/package-lock.json +++ b/test/package-lock.json @@ -5,9 +5,9 @@ "requires": true, "dependencies": { "abab": { - "version": "2.0.0", - 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"jsdom": "^11.11.0", + "jsdom": "^16.5.0", "mocha": "^5.1.1", "node-fetch": "^2.6.1", "whatwg-fetch": "^3.0.0"