Running Kheops on a Mac OS host

This post discusses how to run Kheops from the OsiriX-Foundation on Mac OS, with Docker.

$ git clone git@github.com:OsiriX-Foundation/kheopsDocker.git

$ cd kheopsDocker/

$ sh script_run_docker.sh

Install newman

$ sudo npm install -g newman

/usr/local/bin/newman -> /usr/local/lib/node_modules/newman/bin/newman.js

+ newman@4.5.6

added 160 packages from 196 contributors in 5.481s

   ╭────────────────────────────────────────────────────────────────╮

   │                                                                │

   │       New minor version of npm available! 6.9.0 → 6.13.2       │

   │   Changelog: https://github.com/npm/cli/releases/tag/v6.13.2   │

   │               Run npm install -g npm to update!                │

   │                                                                │

   ╰────────────────────────────────────────────────────────────────╯

Replace line 10 in script_run_docker.sh

with

newman run postman/kheops-Get_tokens.json -e postman/kheops_localhost.postman_environment.json -g postman/Workspace.postman_globals.json --export-globals postman/Workspace.postman_globals.json

Save the file.

If you are using Docker for Mac, you may encounter the error listed in https://github.com/docker/for-mac/issues/2396

Creating pacsldap ... error

Creating db       ...

ERROR: for pacsldap  Cannot start service ldap: b'Mounts denied: \r\nThe paths /etc/localtime and /usr/share/zoneinfo/Europe/Zurich\r\nare not shared from OS X and are not known to Docker.\r\nYou can configure shared paths from Docker -> Preferences... -> File Sharing.\r\Creating db       ... done

ERROR: for ldap  Cannot start service ldap: b'Mounts denied: \r\nThe paths /etc/localtime and /usr/share/zoneinfo/Europe/Zurich\r\nare not shared from OS X and are not known to Docker.\r\nYou can configure shared paths from Docker -> Preferences... -> File Sharing.\r\nSee https://docs.docker.com/docker-for-mac/osxfs/#namespaces for more info.\r\n.'

ERROR: Encountered errors while bringing up the project.

As a work-around, remove all the occurrences of the below line from kheops/docker-compose.yml.

      - /etc/localtime:/etc/localtime:ro

$ sudo mkdir /dcm4chee-arc

$ sudo chmod 777 /dcm4chee-arc

Share /usr/share/zoneinfo/Europe/ and /dcm4chee-arc from the Preferences of Docker Desktop in your Mac host machine.

Save the file and then re-run

$ sh script_run_docker.sh

$ sh script_run_docker.sh

Stopping db       ... done

Stopping pacsldap ... done

Removing pacsarc  ... done

Removing db       ... done

Removing pacsldap ... done

Removing network kheops_default

Removing volume kheops_dcm4chee-ldap-ldap

Removing volume kheops_dcm4chee-ldap-slapdd

Removing volume kheops_dcm4chee-db-data

Removing volume kheops_dcm4chee-arc-wildfly

Removing volume kheops_kheops-db-data

Creating network "kheops_default" with the default driver

Creating volume "kheops_dcm4chee-ldap-ldap" with default driver

Creating volume "kheops_dcm4chee-ldap-slapdd" with default driver

Creating volume "kheops_dcm4chee-db-data" with default driver

Creating volume "kheops_dcm4chee-arc-wildfly" with default driver

Creating volume "kheops_kheops-db-data" with default driver

Creating db       ... done

Creating pacsldap ... done

Creating pacsarc  ... done

Creating kheopszipper           ... done

Creating kheopsauthorization    ... done

Creating pacsauthorizationproxy ... done

Creating kheopsui               ... done

Creating kheopsdicomwebproxy    ... done

Creating kheopsreverseproxy     ... done

CONTAINER ID        IMAGE                                              COMMAND                  CREATED             STATUS              PORTS                                                                                                                                              NAMES

d5caa14fac54        osirixfoundation/kheops-reverse-proxy:ci-test      "./etc/nginx/conf.d/…"   47 seconds ago      Up 45 seconds       0.0.0.0:80->80/tcp, 0.0.0.0:443->443/tcp, 0.0.0.0:8042->8042/tcp, 0.0.0.0:8048->8048/tcp                                                           kheopsreverseproxy

67552e9c9469        osirixfoundation/kheops-dicomweb-proxy:master      "./replaceSecretsAnd…"   48 seconds ago      Up 46 seconds       0.0.0.0:8049->8080/tcp                                                                                                                             kheopsdicomwebproxy

92710a77dd25        osirixfoundation/kheops-ui:master                  "./docker-entrypoint…"   48 seconds ago      Up 46 seconds       80/tcp, 3000/tcp                                                                                                                                   kheopsui

c9fa33eb693d        osirixfoundation/kheops-authorization:dev          "./replaceSecretsAnd…"   50 seconds ago      Up 47 seconds       8080/tcp                                                                                                                                           kheopsauthorization

0f267500942f        osirixfoundation/kheops-zipper:master              "./replaceSecretsAnd…"   50 seconds ago      Up 48 seconds       8080/tcp                                                                                                                                           kheopszipper

c95c6e4380c6        osirixfoundation/pacs-authorization-proxy:master   "/bin/sh -c '. $NGIN…"   50 seconds ago      Up 48 seconds       0.0.0.0:82->80/tcp                                                                                                                                 pacsauthorizationproxy

89c52e69534a        osirixfoundation/kheops-dcm4chee-arc-psql:latest   "/script_entrypoint.…"   51 seconds ago      Up 49 seconds       0.0.0.0:2575->2575/tcp, 0.0.0.0:8080->8080/tcp, 0.0.0.0:8443->8443/tcp, 0.0.0.0:8787->8787/tcp, 0.0.0.0:9990->9990/tcp, 0.0.0.0:11112->11112/tcp   pacsarc

78bf11251bf7        dcm4che/slapd-dcm4chee:2.4.44-15.0                 "/docker-entrypoint.…"   52 seconds ago      Up 50 seconds       389/tcp                                                                                                                                            pacsldap

f4628a1a1c44        osirixfoundation/kheops-database:demo              "verify-secret-env-v…"   52 seconds ago      Up 50 seconds       5432/tcp                                                                                                                                           db

newman

kheops-Get_tokens

→ well-known

  GET https://keycloak.kheops.online/auth/realms/travis/.well-known/openid-configuration [200 OK, 2.62KB, 657ms]

→ get token user 1 (titi)

  POST https://keycloak.kheops.online/auth/realms/travis/protocol/openid-connect/token [200 OK, 2.01KB, 325ms]

→ get token user 2 (toto)

  POST https://keycloak.kheops.online/auth/realms/travis/protocol/openid-connect/token [200 OK, 2.01KB, 314ms]

→ get token user 3 (tata)

  POST https://keycloak.kheops.online/auth/realms/travis/protocol/openid-connect/token [200 OK, 2.01KB, 332ms]

┌─────────────────────────┬─────────────────────┬────────────────────┐

│                         │            executed │             failed │

├─────────────────────────┼─────────────────────┼────────────────────┤

│              iterations │                   1 │                  0 │

├─────────────────────────┼─────────────────────┼────────────────────┤

│                requests │                   4 │                  0 │

├─────────────────────────┼─────────────────────┼────────────────────┤

│            test-scripts │                   4 │                  0 │

├─────────────────────────┼─────────────────────┼────────────────────┤

│      prerequest-scripts │                   0 │                  0 │

├─────────────────────────┼─────────────────────┼────────────────────┤

│              assertions │                   0 │                  0 │

├─────────────────────────┴─────────────────────┴────────────────────┤

│ total run duration: 1790ms                                         │

├────────────────────────────────────────────────────────────────────┤

│ total data received: 7.53KB (approx)                               │

├────────────────────────────────────────────────────────────────────┤

│ average response time: 407ms [min: 314ms, max: 657ms, s.d.: 144ms] │

└────────────────────────────────────────────────────────────────────┘

Then go to http://localhost:8042 from your favorite browser.

Register yourself when it redirects to a page such as https://keycloak.kheops.online/auth/realms/travis/protocol/openid-connect/auth?client_id=loginConnect&redirect_uri=.........

It will take you back to http://localhost:8042/inbox after the registration. Now Kheops is ready to use!

Kheops Web UI

I can even tweet from the Kheops Web UI with a link to the created album!
"My KHEOPS shared album. http://localhost/view/ttuArLPrFv834JQ88KaQGY #KHEOPS"

Apparently, the link is broken. It should be: http://localhost:8042/view/ttuArLPrFv834JQ88KaQGY
But I see the parallels with the concept of Óbidos (MEDIator) replicasets in the given UUID ttuArLPrFv834JQ88KaQGY.

One can also create a sharing URL with upload/edit/delete capabilities (again, the port is not correctly used. But that is a front-end bug they can fix. For our purposes, we just need to add the port in the shared URL).

I can also view the images that I uploaded from OHIF viewer directly, by clicking that link. It uses their cloud hosted instance of the OHIF viewer to view the image stored locally, as can be seen from the URL.







We also observe the Docker containers initialized by this integrated project are - 1) db, 2) pacsldap, 3) pacsarc, 4) pacsauthorizationproxy, 5) kheopszipper, 6) kheopsauthorization, 7) kheopsdicomwebproxy, 8) kheopsui, and 9) kheopsreverseproxy. This system uses the managed Keycloak instance in the cloud for its authorization.