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birmbirm
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Merge pull request #194 from camicroscope/develop
For 3.9.11
2 parents 361d11e + 3fcfc16 commit 928f40c

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-289
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‎README.md

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@@ -63,6 +63,8 @@ Running QuIP with PathDB (https://github.com/SBU-BMI/PathDB):
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3) build with, "docker-compose -f quip-pathdb.yml build"<br>
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4) run with, "docker-compose -f quip-pathdb.yml up -d"
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The default login for pathdb is `admin` with password `bluecheese2018`. Please change this password before exposing this service to the internet.
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## Support
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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).
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‎caMicroscope.yml

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

‎config/login.html

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

‎config/pathdbmysql.cnf

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

‎config/routes.json

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

‎kubernetes/README.md

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

‎kubernetes/caMicroscope.yml

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

‎kubernetes/camicroscope_add_config.sh

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

‎kubernetes/cleanup.sh

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

‎kubernetes/pathdb_add_config.sh

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

‎kubernetes/pv_cleanup.sh

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#!/bin/bash
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kubectl delete --all pvc
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kubectl delete --all pv

‎kubernetes/quip-pathdb.yml

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

‎quip-pathdb.yml

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

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