As big of a fan of podman/kubernetes that I am, this is a docker project, not a podman project. I recommend installing docker instead.
sudo install -d -o $USER -g $USER /usr/local/src/issues-chris
git clone [email protected]:team19hackathon2021/issues-chris.git /usr/local/src/issues-chris
cd /usr/local/src/issues-chris
ansible-playbook -K chris_dev_setup.yml
Your mission, should you choose to accept it, is define the ChRIS pman systemd service file. .
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/roles/chris_pman/templates/chris_pman.service
[Unit]
Description=
After=network.service
[Service]
Type=simple
User={{ APP_USER }}
ExecStart=/usr/bin/podman run --name {{ PMAN_NAME }}\{\% if APP_POD_NETWORK is defined \%\} --pod {{ PMAN_POD }}\{\% endif \%\}\{\% if APP_CONTAINER_NETWORK is defined \%\} --network {{ APP_CONTAINER_NETWORK }}\{\% endif \%\} -v {{ PMAN_SRC }}:/home/localuser/pman --rm -e "STOREBASE={{ APP_DATA }}" -e "SECRET_KEY={{ APP_SECRET_KEY }}" -e "CONTAINER_ENV=podman" -e 'PODMAN_IP_ADDRESS={{ PODMAN_IP_ADDRESS }}' {{ PMAN_IMAGE }}:{{ PMAN_VERSION }}
ExecStop=/usr/bin/podman rm {{ PMAN_NAME }} -f
Restart=on-failure
[Install]
WantedBy=multi-user.target
http://www.gnuplot.info/ (python)
(https://deoldify.ai/) (python based)
Help ease-of-use in standing up the ChRIS platform would be to get two core backend components of ChRIS - pman - packaged for and listed in the Red Hat Container Catalog (or some other public container registry if another one is deemed more suitable.) The end goal is making it easier to get ChRIS up and running on OpenShift.
Web browser testing for ChRIS UI on an Android tablet
Your mission, should you choose to accept it, is define the ending Ansible tasks to install ChRIS to podman locally.
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/roles/chris_after/tasks/main.yml
---
# hackathonLabels: ansible,yml
Your mission, should you choose to accept it, is create an Ansible Playbook to setup the pman container locally.
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/chris_pman.yml
---
# define the playbook to run locally
- name: Install the ChRIS containers locally in podman with Ansible
connection: local
hosts: localhost
# Run the chris_defaults role to load the ChRIS related variables.
roles:
- chris_defaults
# Now run the chris_pman role to install the pman container to podman.
- chris_pman
Your mission, should you choose to accept it, is define the ChRIS store systemd service file. .
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/roles/chris_store/templates/chris_store.service
[Unit]
Description=
After=network.service
[Service]
Type=simple
User={{ APP_USER }}
ExecStart=/usr/bin/podman run --name {{ STORE_NAME }}\{\% if APP_POD_NETWORK is defined \%\} --pod {{ STORE_POD }}\{\% endif \%\}\{\% if APP_CONTAINER_NETWORK is defined \%\} --network {{ APP_CONTAINER_NETWORK }}\{\% endif \%\} --rm -e "DJANGO_SETTINGS_MODULE=config.settings.production" -e "DJANGO_DB_MIGRATE=on" -e "DJANGO_ALLOWED_HOSTS=*" -e 'DJANGO_SECRET_KEY={{ APP_SECRET_KEY }}' -e "DJANGO_CORS_ORIGIN_ALLOW_ALL=true" -e "DJANGO_CORS_ORIGIN_WHITELIST=babymri.org" -e "DJANGO_SECURE_PROXY_SSL_HEADER=" -e "DJANGO_USE_X_FORWARDED_HOST=false" -e "DATABASE_HOST={{ STORE_HOSTNAME }}" -e "DATABASE_PORT={{ DEV_DB_PORT }}" -e "SWIFT_AUTH_URL=http://{{ SWIFT_HOSTNAME }}:{{ SWIFT_PORT }}/auth/v1.0" -e "POSTGRES_DB={{ STORE_DB_DATABASE }}" -e "POSTGRES_USER={{ STORE_DB_USER }}" -e "POSTGRES_PASSWORD={{ STORE_DB_PASSWORD }}" -e "SWIFT_USERNAME={{ SWIFT_USERNAME }}" -e "SWIFT_KEY={{ SWIFT_KEY }}" -e "SWIFT_CONTAINER_NAME=store_users" {{ STORE_IMAGE }}:{{ STORE_VERSION }} python manage.py runserver 0.0.0.0:{{ STORE_PORT }}
ExecStop=/usr/bin/podman rm {{ STORE_NAME }} -f
Restart=on-failure
[Install]
WantedBy=multi-user.target
Help ease-of-use in standing up the ChRIS platform would be to get two core backend components of ChRIS - pfcon - packaged for and listed in the Red Hat Container Catalog (or some other public container registry if another one is deemed more suitable.) The end goal is making it easier to get ChRIS up and running on OpenShift.
https://www.datalad.org/ (To enable importing DataLad repos into ChRIS feeds)
(python based)
https://www.statsmodels.org (python based)
We would like to instead of perf testing have folks test setting up the ChRIS platform end-to-end, first with a completely local configuration (running CUBE, ChRIS UI, pfcon, pman, etc. locally), then testing it with a local ChRIS/CUBE configured to use a remote pfcon and pman running on OpenShift. Pre-req will be either ability to stand up a k8s/OpenShift somewhere accessible, or access to a public OpenShift account. We would like volunteers setting these things up to document any missteps / confusion / deficiencies in the documentation so we can improve the setup workflow as well as our docs that support setting these up.
Your mission, should you choose to accept it, is define the default Ansible variables to use.
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/roles/chris_defaults/defaults/main.yml
---
# Define the main application variables.
APP_NAME: ChRIS
APP_POD: "{{ APP_NAME }}_pod"
APP_NETWORK: "ChRIS"
APP_PYTHON: "{{ '/usr/bin/python' if lookup('file', '/usr/bin/python', errors='ignore') else '/usr/bin/python3' }}"
APP_SRC: "/usr/local/src/ChRIS_ultron_backEnd"
APP_OPT: "/opt/{{ APP_NAME }}"
APP_VAR: "/var/{{ APP_NAME }}"
APP_DATA: "{{ APP_VAR }}/data"
APP_DEV_DB_DATA: "{{ APP_SRC }}/chris_dev_db_data"
APP_STORE_DB_DATA: "{{ APP_SRC }}/chris_store_db_data"
APP_SWIFT_DATA: "{{ APP_SRC }}/swift_storage_dev"
APP_QUEUE_DATA: "{{ APP_SRC }}/queue_data"
APP_BACKEND_DATA: "{{ APP_SRC }}/chris_backend"
APP_CONF: "{{ APP_OPT }}/conf/zoo.cfg"
APP_REPO: "https://github.com/FNNDSC/ChRIS_ultron_backEnd.git"
APP_VERSION:
APP_TAG: ""
APP_USER: "root"
APP_SECRET_KEY: "w1kxu^l=@pnsf!5piqz6!!5kdcdpo79y6jebbp+2244yjm*#+k"
APP_SUPER_USER_NAME: rudolph
APP_SUPER_USER_PASSWORD: rudolph1234
APP_SUPER_USER_EMAIL: [email protected]
# Define the pman application variables.
PMAN_NAME: "{{ APP_NAME }}_pman"
PMAN_POD: "{{ APP_NAME }}_pod"
PMAN_HOSTNAME: "localhost"
PMAN_IMAGE: "docker.io/computate/pman"
PMAN_VERSION: "latest"
PMAN_SERVICE: "{{ PMAN_NAME }}"
PMAN_SYSTEMD: "/usr/lib/systemd/system/{{ PMAN_SERVICE }}.service"
PMAN_SRC: "/usr/local/src/pman"
PMAN_REPO: "[email protected]:FNNDSC/pman.git"
PMAN_PORT: "5010"
# Define the pfcon application variables.
PFCON_NAME: "{{ APP_NAME }}_pfcon"
PFCON_POD: "{{ APP_NAME }}_pod"
PFCON_HOSTNAME: "localhost"
PFCON_IMAGE: "fnndsc/pfcon"
PFCON_VERSION: "latest"
PFCON_SERVICE: "{{ PFCON_NAME }}"
PFCON_SYSTEMD: "/usr/lib/systemd/system/{{ PFCON_SERVICE }}.service"
PFCON_SRC: "/usr/local/src/pfcon"
PFCON_REPO: "[email protected]:FNNDSC/pfcon.git"
PFCON_PORT: "30005"
# Define the dev application variables.
DEV_NAME: "{{ APP_NAME }}_dev"
DEV_POD: "{{ APP_NAME }}_pod"
DEV_HOSTNAME: "localhost"
DEV_IMAGE: "fnndsc/chris"
DEV_VERSION: "dev"
DEV_SERVICE: "{{ DEV_NAME }}"
DEV_SYSTEMD: "/usr/lib/systemd/system/{{ DEV_SERVICE }}.service"
DEV_PORT: "8000"
# Define the dev database application variables.
DEV_DB_NAME: "{{ APP_NAME }}_dev_db"
DEV_DB_POD: "{{ APP_NAME }}_pod"
DEV_DB_HOSTNAME: "localhost"
DEV_DB_IMAGE: "postgres"
DEV_DB_VERSION: "13"
DEV_DB_SERVICE: "{{ DEV_DB_NAME }}"
DEV_DB_SYSTEMD: "/usr/lib/systemd/system/{{ DEV_DB_SERVICE }}.service"
DEV_DB_PORT: "5432"
DEV_DB_DATABASE: "chris_dev"
DEV_DB_USER: "chris"
DEV_DB_PASSWORD: "Chris1234"
DEV_DB_BECOME_USER: "{{ DEV_DB_USER }}"
DEV_DB_BECOME_PASSWORD: "{{ DEV_DB_PASSWORD }}"
# Define the store database application variables.
STORE_DB_DATABASE: "chris_store"
STORE_DB_USER: "chris"
STORE_DB_PASSWORD: "Chris1234"
# Define the swift storage application variables.
SWIFT_NAME: "{{ APP_NAME }}_swift"
SWIFT_POD: "{{ APP_NAME }}_pod"
SWIFT_HOSTNAME: "localhost"
SWIFT_IMAGE: "fnndsc/docker-swift-onlyone"
SWIFT_VERSION: "latest"
SWIFT_SERVICE: "{{ SWIFT_NAME }}"
SWIFT_SYSTEMD: "/usr/lib/systemd/system/{{ SWIFT_SERVICE }}.service"
SWIFT_USERNAME: "chris:chris1234"
SWIFT_KEY: "testing"
SWIFT_PORT: "8080"
# Define the RabbitMQ queue application variables.
QUEUE_NAME: "{{ APP_NAME }}_queue"
QUEUE_POD: "{{ APP_NAME }}_pod"
QUEUE_HOSTNAME: "localhost"
QUEUE_IMAGE: "rabbitmq"
QUEUE_VERSION: "3"
QUEUE_SERVICE: "{{ QUEUE_NAME }}"
QUEUE_SYSTEMD: "/usr/lib/systemd/system/{{ QUEUE_SERVICE }}.service"
# Define the ChRIS store application variables.
STORE_NAME: "{{ APP_NAME }}_store"
STORE_POD: "{{ APP_NAME }}_pod"
STORE_HOSTNAME: "localhost"
STORE_IMAGE: "fnndsc/chris_store"
STORE_VERSION: "latest"
STORE_SERVICE: "{{ STORE_NAME }}"
STORE_SYSTEMD: "/usr/lib/systemd/system/{{ STORE_SERVICE }}.service"
STORE_PORT: "8010"
# Define the scheduler application variables.
SCHEDULER_NAME: "{{ APP_NAME }}_scheduler"
SCHEDULER_POD: "{{ APP_NAME }}_pod"
SCHEDULER_HOSTNAME: "localhost"
SCHEDULER_IMAGE: "fnndsc/chris"
SCHEDULER_VERSION: "dev"
SCHEDULER_SERVICE: "{{ SCHEDULER_NAME }}"
SCHEDULER_SYSTEMD: "/usr/lib/systemd/system/{{ SCHEDULER_SERVICE }}.service"
# Define the worker periodic application variables.
WORKER_PERIODIC_NAME: "{{ APP_NAME }}_worker_periodic"
WORKER_PERIODIC_POD: "{{ APP_NAME }}_pod"
WORKER_PERIODIC_HOSTNAME: "localhost"
WORKER_PERIODIC_IMAGE: "fnndsc/chris"
WORKER_PERIODIC_VERSION: "dev"
WORKER_PERIODIC_SERVICE: "{{ WORKER_PERIODIC_NAME }}"
WORKER_PERIODIC_SYSTEMD: "/usr/lib/systemd/system/{{ WORKER_PERIODIC_SERVICE }}.service"
# Define the worker application variables.
WORKER_NAME: "{{ APP_NAME }}_worker"
WORKER_POD: "{{ APP_NAME }}_pod"
WORKER_HOSTNAME: "localhost"
WORKER_IMAGE: "fnndsc/chris"
WORKER_VERSION: "dev"
WORKER_SERVICE: "{{ WORKER_NAME }}"
WORKER_SYSTEMD: "/usr/lib/systemd/system/{{ WORKER_SERVICE }}.service"
# Define the ChRIS UI application variables.
UI_NAME: "ChRIS_ui"
UI_REPO: "[email protected]:FNNDSC/ChRIS_ui.git"
UI_SRC: "/usr/local/src/{{ UI_NAME }}"
UI_POD: "{{ APP_NAME }}_pod"
UI_HOSTNAME: "localhost"
UI_IMAGE: "fnndsc/chris_ui"
UI_VERSION: "dev"
UI_SERVICE: "{{ UI_NAME }}"
UI_SYSTEMD: "/usr/lib/systemd/system/{{ UI_SERVICE }}.service"
UI_PORT: "3000"
UI_DATA: "{{ UI_SRC }}"
# Define the Podman TCP related application variables.
##############
# Podman TCP #
##############
PODMAN_TCP_NAME: "podman_tcp"
PODMAN_TCP_SERVICE: "{{ PODMAN_TCP_NAME }}"
PODMAN_TCP_SYSTEMD: "/usr/lib/systemd/system/{{ PODMAN_TCP_SERVICE }}.service"
PODMAN_IP_ADDRESS: "{{ lookup('env', 'HOSTNAME') }}"
PODMAN_TCP_PORT: 5000
# Define other Ansible related application variables.
####################
# Ansible defaults #
####################
# Add to an ansible-vault the username of your user on your computer (echo $HOSTNAME).
USER_NAME: "{{ lookup('env', 'USER') }}"
https://pyscenedetect.readthedocs.io/en/latest/ (python based)
Your mission, should you choose to accept it, is create an Ansible Playbook to setup everything.
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/install_all.yml
---
# Define the playbook to run locally.
- name: Install the ChRIS containers locally in podman with Ansible
connection: local
hosts: localhost
# Call the all the ChRIS Ansible roles.
roles:
- chris_defaults
- chris_before
- chris_dev_db
- chris_pman
- chris_pfcon
- chris_podman_tcp
- chris_queue
- chris_scheduler
- chris_swift
- chris_worker
- chris_worker_periodic
- chris_dev
- chris_ui
- chris_store
- chris_after
- chris_plugins
Your mission, should you choose to accept it, is define the ChRIS dev systemd service file.
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/roles/chris_dev/templates/chris_dev.service
[Unit]
Description=
After=network.service
[Service]
Type=simple
User={{ APP_USER }}
ExecStart=/usr/bin/podman run --name {{ DEV_NAME }}\{\% if APP_POD_NETWORK is defined \%\} --pod {{ DEV_POD }}\{\% endif \%\}\{\% if APP_CONTAINER_NETWORK is defined \%\} --network {{ APP_CONTAINER_NETWORK }}\{\% endif \%\} -v {{ APP_SRC }}/chris_backend:/home/localuser/chris_backend --rm -e "DJANGO_SETTINGS_MODULE=config.settings.local" -e "DJANGO_DB_MIGRATE=on" -e "DJANGO_COLLECTSTATIC=off" -e "SWIFT_HOSTNAME={{ SWIFT_HOSTNAME }}" -e "STORE_HOSTNAME={{ STORE_HOSTNAME }}" -e "PFCON_HOSTNAME={{ PFCON_HOSTNAME }}" -e "QUEUE_HOSTNAME={{ QUEUE_HOSTNAME }}" -e "DEV_DB_HOSTNAME={{ DEV_DB_HOSTNAME }}" {{ DEV_IMAGE }}:{{ DEV_VERSION }} python manage.py runserver 0.0.0.0:{{ DEV_PORT }}
ExecStop=/usr/bin/podman rm {{ DEV_NAME }} -f
Restart=on-failure
[Install]
WantedBy=multi-user.target
Your mission, should you choose to accept it, is define the ChRIS Podman TCP systemd service file.
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/roles/chris_podman_tcp/templates/chris_podman_tcp.service
Description=Podman TCP API Service
After=network.service
StartLimitIntervalSec=0
[Service]
Type=exec
KillMode=process
Environment=LOGGING="--log-level=info"
\{\% if (PODMAN_MAJOR_VERSION | int) > 1 \%\}
ExecStart=/usr/bin/podman $LOGGING system service tcp:{{ PODMAN_IP_ADDRESS }}:{{ PODMAN_TCP_PORT }} -t 0
\{\% else \%\}
ExecStart=/usr/bin/podman varlink tcp:{{ PODMAN_IP_ADDRESS }}:{{ PODMAN_TCP_PORT }} -t 0
\{\% endif \%\}
[Install]
WantedBy=multi-user.target
Your mission, should you choose to accept it, is define the ChRIS RabbitMQ queue systemd service file.
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/roles/chris_queue/templates/chris_queue.service
[Unit]
Description=
After=network.service
[Service]
Type=simple
User={{ APP_USER }}
ExecStart=/usr/bin/podman run --name {{ QUEUE_NAME }}\{\% if APP_POD_NETWORK is defined \%\} --pod {{ QUEUE_POD }}\{\% endif \%\}\{\% if APP_CONTAINER_NETWORK is defined \%\} --network {{ APP_CONTAINER_NETWORK }}\{\% endif \%\} -v {{ APP_QUEUE_DATA }}:/var/lib/rabbitmq --rm {{ QUEUE_IMAGE }}:{{ QUEUE_VERSION }}
ExecStop=/usr/bin/podman rm {{ QUEUE_NAME }} -f
Restart=on-failure
[Install]
WantedBy=multi-user.target
Your mission, should you choose to accept it, is define the Ansible tasks to setup all the main ChRIS plugins.
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/roles/chris_plugins/tasks/main.yml
---
- name: "Add the superuser to the ChRIS store container"
shell: /usr/bin/podman exec {{ STORE_NAME }} python manage.py createsuperuser --noinput --username '{{ APP_SUPER_USER_NAME }}' --email '{{ APP_SUPER_USER_EMAIL }}'
become: true
ignore_errors: true
- name: "Set the superuser password to the ChRIS store container"
shell: /usr/bin/podman exec {{ STORE_NAME }} python manage.py shell -c "from django.contrib.auth.models import User; user=User.objects.get(username='{{ APP_SUPER_USER_NAME }}'); user.set_password('{{ APP_SUPER_USER_PASSWORD }}'); user.save(); "
become: true
- name: "Install ChRIS plugins"
include_role:
name: chris_plugin
loop: "{{ APP_PLUGINS }}"
loop_control:
loop_var: APP_PLUGIN
Your mission, should you choose to accept it, is create an Ansible Playbook to setup the main ChRIS plugins.
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/install_plugins.yml
---
# Define the playbook to run locally.
- name: Install only the ChRIS plugins locally in podman with Ansible
connection: local
hosts: localhost
# Run the chris_plugins role to load the main ChRIS plugins.
roles:
- chris_plugins
Your mission, should you choose to accept it, is define the Ansible tasks to setup the pman application as a container in podman.
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/roles/chris_pman/tasks/main.yml
---
# automate the setup of the ChRIS pman source code repository.
- name: Check for the {{ PMAN_NAME }} README file
stat:
path: "{{ PMAN_SRC }}/README.rst"
register: PMAN_README
- name: Create the {{ PMAN_NAME }} source directory {{ PMAN_SRC }}
file:
name: "{{ PMAN_SRC }}"
state: directory
owner: "{{ USER_NAME }}"
when: not PMAN_README.stat.exists
become: true
- name: Clone the {{ PMAN_REPO }} source code into {{ PMAN_SRC }}
git:
repo: "{{ PMAN_REPO }}"
dest: "{{ PMAN_SRC }}"
when: not PMAN_README.stat.exists
- name: set SELinux permissions on {{ PMAN_SRC }}
sefcontext:
target: "{{ PMAN_SRC }}(/.*)?"
setype: container_file_t
become: true
vars:
ansible_python_interpreter: "{{ APP_PYTHON }}"
- name: reload SELinux policy to ensure that {{ APP_NAME }} is executable
command: "restorecon -irv {{ PMAN_SRC }}"
become: true
# Automate the deployment of ChRIS pman as a Podman container running as a Systemd service.
- name: Create the {{ PMAN_NAME }} systemd service {{ PMAN_SYSTEMD }}.
template:
src: chris_pman.service
dest: "{{ PMAN_SYSTEMD }}"
become: true
when: ansible_pkg_mgr != 'homebrew'
- name: Reload the services.
systemd:
daemon_reload: true
become: true
when: ansible_pkg_mgr != 'homebrew'
- name: Start and enable the {{ PMAN_SERVICE }} service.
service:
name: "{{ PMAN_SERVICE }}"
enabled: true
state: restarted
become: true
Your mission, should you choose to accept it, is define the Ansible tasks to install the pfcon application as a container in podman.
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/roles/chris_pfcon/tasks/main.yml
---
# automate the setup of the ChRIS pfcon source code repository.
- name: Check for the {{ PFCON_NAME }} README file
stat:
path: "{{ PFCON_SRC }}/README.rst"
register: PFCON_README
- name: Create the {{ PFCON_NAME }} source directory {{ PFCON_SRC }}
file:
name: "{{ PFCON_SRC }}"
state: directory
owner: "{{ USER_NAME }}"
when: not PFCON_README.stat.exists
become: true
- name: Clone the {{ PFCON_REPO }} source code into {{ PFCON_SRC }}
git:
repo: "{{ PFCON_REPO }}"
dest: "{{ PFCON_SRC }}"
when: not PFCON_README.stat.exists
- name: set SELinux permissions on {{ PFCON_SRC }}
sefcontext:
target: "{{ PFCON_SRC }}(/.*)?"
setype: container_file_t
become: true
vars:
ansible_python_interpreter: "{{ APP_PYTHON }}"
- name: reload SELinux policy to ensure that {{ APP_NAME }} is executable
command: "restorecon -irv {{ PFCON_SRC }}"
become: true
# Automate the deployment of ChRIS pfcon as a Podman container running as a Systemd service.
- name: Create the {{ PFCON_NAME }} systemd service {{ PFCON_SYSTEMD }}.
template:
src: chris_pfcon.service
dest: "{{ PFCON_SYSTEMD }}"
become: true
when: ansible_pkg_mgr != 'homebrew'
- name: Reload the services.
systemd:
daemon_reload: true
become: true
when: ansible_pkg_mgr != 'homebrew'
- name: Start and enable the {{ PFCON_SERVICE }} service.
service:
name: "{{ PFCON_SERVICE }}"
enabled: true
state: restarted
become: true
when: ansible_pkg_mgr != 'homebrew'
https://matplotlib.org/ (python)
Web browser testing for ChRIS UI on an iPhone
Your mission, should you choose to accept it, is define the ChRIS plugin default variables.
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/roles/chris_plugins/defaults/main.yml
---
APP_NAME: ChRIS
DEV_NAME: "{{ APP_NAME }}_dev"
STORE_NAME: "{{ APP_NAME }}_store"
APP_SUPER_USER_NAME: rudolph
APP_SUPER_USER_PASSWORD: rudolph1234
APP_SUPER_USER_EMAIL: [email protected]
PFCON_HOSTNAME: "localhost"
PFCON_PORT: "30005"
APP_PLUGINS:
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-dsdircopy
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-simplefsapp
CONTAINER_ENVIRONMENT: moc
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-simpledsapp
CONTAINER_ENVIRONMENT: moc
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-s3push
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-pfdicom_tagextract
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-pfdicom_tagsub
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-mpcs
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-mpcs
CONTAINER_ENVIRONMENT: moc
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-fshack
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-fastsurfer_inference
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-freesurfer_pp
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-freesurfer_pp
CONTAINER_ENVIRONMENT: moc
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-z2labelmap
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-z2labelmap
CONTAINER_ENVIRONMENT: moc
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-mri10yr06mo01da_normal
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-mri10yr06mo01da_normal
CONTAINER_ENVIRONMENT: moc
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-mgz2lut_report
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-pfdo_mgz2img
- CONTAINER_REPO: jonocameron
CONTAINER_IMAGE: pl-sevstack
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-topologicalcopy
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-brainmgz
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-pfdorun
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-mgz2imageslices
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-multipass
- CONTAINER_REPO: fnndsc
CONTAINER_IMAGE: pl-heatmap
Your mission, should you choose to accept it, is define the ChRIS scheduler systemd service file. .
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/roles/chris_scheduler/templates/chris_scheduler.service
[Unit]
Description=
After=network.service
[Service]
Type=simple
User={{ APP_USER }}
ExecStart=/usr/bin/podman run --name {{ SCHEDULER_NAME }}\{\% if APP_POD_NETWORK is defined \%\} --pod {{ SCHEDULER_POD }}\{\% endif \%\}\{\% if APP_CONTAINER_NETWORK is defined \%\} --network {{ APP_CONTAINER_NETWORK }}\{\% endif \%\} -v {{ APP_BACKEND_DATA }}:/home/localuser/chris_backend --rm -e "DJANGO_SETTINGS_MODULE=config.settings.local" -e "DJANGO_DB_MIGRATE=off" -e "DJANGO_COLLECTSTATIC=off" -e "SWIFT_HOSTNAME={{ SWIFT_HOSTNAME }}" -e "STORE_HOSTNAME={{ STORE_HOSTNAME }}" -e "PFCON_HOSTNAME={{ PFCON_HOSTNAME }}" -e "QUEUE_HOSTNAME={{ QUEUE_HOSTNAME }}" -e "DEV_DB_HOSTNAME={{ DEV_DB_HOSTNAME }}" {{ SCHEDULER_IMAGE }}:{{ SCHEDULER_VERSION }} celery -A core beat -l info --pidfile /home/localuser/celerybeat.pid --scheduler django_celery_beat.schedulers:DatabaseScheduler
ExecStop=/usr/bin/podman rm {{ SCHEDULER_NAME }} -f
Restart=on-failure
[Install]
WantedBy=multi-user.target
Web browser testing for ChRIS UI on an iPad
Your mission, should you choose to accept it, is define the beginning Ansible tasks to install ChRIS to podman locally.
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/roles/chris_before/tasks/main.yml
---
# Automate the installation of ChRIS dependencies.
- name: "Setup podman Linux virtual machine on MacOS"
shell: "podman machine init"
when: ansible_pkg_mgr == 'homebrew'
- name: "Start the podman Linux virtual machine on MacOS"
shell: "podman machine start"
when: ansible_pkg_mgr == 'homebrew'
- name: "install podman dependency"
package:
name:
- python3
- python3-pip
- libselinux-python
- libsemanage-python
- podman
state: present
become: true
when: ansible_pkg_mgr != 'homebrew' and APP_PYTHON == '/usr/bin/python'
vars:
ansible_python_interpreter: "{{ APP_PYTHON }}"
- name: "install podman dependency"
package:
name:
- python3
- python3-pip
- python3-libselinux
- python3-libsemanage
- podman
state: present
become: true
when: ansible_pkg_mgr != 'homebrew' and APP_PYTHON == '/usr/bin/python3'
vars:
ansible_python_interpreter: "{{ APP_PYTHON }}"
- name: "install python pip dependencies"
pip:
name: psycopg2-binary
state: present
become: true
when: ansible_pkg_mgr != 'homebrew' and APP_PYTHON == '/usr/bin/python3'
vars:
ansible_python_interpreter: "{{ APP_PYTHON }}"
- name: "install podman dependency"
package:
name:
- python3
- python3-pip
- python3-libselinux
- python3-libsemanage
- podman
state: present
become: true
when: ansible_pkg_mgr != 'homebrew' and APP_PYTHON == '/usr/bin/python3'
vars:
ansible_python_interpreter: "{{ APP_PYTHON }}"
# Check the system podman version to determine network settings.
- name: Check podman version
shell: "podman -v | cut -d ' ' -f3 | cut -d '.' -f1"
register: PODMAN_MAJOR_VERSION_SHELL
- name: Set podman major version
set_fact:
PODMAN_MAJOR_VERSION: "{{ PODMAN_MAJOR_VERSION_SHELL.stdout }}"
- debug:
var: PODMAN_MAJOR_VERSION
- name: Set network vars
set_fact:
APP_POD_NETWORK: "{{ (APP_NETWORK if (PODMAN_MAJOR_VERSION | int) > 1) | default(omit) }}"
APP_CONTAINER_NETWORK: "{{ ('host' if (PODMAN_MAJOR_VERSION | int) <= 1) | default(omit) }}"
- debug:
var: APP_POD_NETWORK
- debug:
var: APP_CONTAINER_NETWORK
- name: Create a podman network {{ APP_NETWORK }}
containers.podman.podman_network:
name: "{{ APP_NETWORK }}"
state: present
become: true
when: APP_POD_NETWORK is defined
ignore_errors: true
# Allow Podman to run containers as systemd services for better logging, starting, stopping and enabling services.
- name: Set container_manage_cgroup flag on to run podman containers as systemd services and keep it persistent across reboots
ansible.posix.seboolean:
name: container_manage_cgroup
state: true
persistent: true
become: true
vars:
ansible_python_interpreter: "{{ APP_PYTHON }}"
# Automate the deployment of a shared podman pod for the ChRIS applications on a shared network.
- name: Create a podman pod {{ APP_POD }} with network {{ APP_POD_NETWORK }}
containers.podman.podman_pod:
name: "{{ APP_POD }}"
network: "{{ APP_POD_NETWORK }}"
publish:
- "{{ PFCON_PORT }}:30005"
- "{{ PMAN_PORT }}:5010"
- "{{ DEV_DB_PORT }}:5432"
- "{{ SWIFT_PORT }}:8080"
- "{{ DEV_PORT }}:8000"
- "{{ STORE_PORT }}:8010"
- "{{ UI_PORT }}:3000"
- "6900-6905:6900-6905"
state: started
become: true
when: APP_POD_NETWORK is defined
# Setup the ChRIS data directory.
- name: Create the {{ APP_NAME }} data directory {{ APP_DATA }}.
file:
name: "{{ APP_DATA }}"
state: directory
owner: "{{ APP_USER }}"
mode: 0777
become: true
- name: set SELinux permissions on {{ APP_DATA }}
sefcontext:
target: "{{ APP_DATA }}(/.*)?"
setype: container_file_t
become: true
vars:
ansible_python_interpreter: "{{ APP_PYTHON }}"
- name: reload SELinux policy to ensure that {{ APP_NAME }} is executable
command: "restorecon -irv {{ APP_DATA }}"
become: true
Create pl-gc-retrieve for Google Cloud.
A ChRIS ds app to retrieve data of interest from Amazon S3 service. Test https://github.com/FNNDSC/pl-s3retrieve (needed for enabling Serratus which uses S3) to make sure it works to pull data down from S3 into ChRIS storage.
maybe a deep learning model based OCR?
Your mission, should you choose to accept it, is define the ChRIS dev database systemd service file.
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/roles/chris_dev_db/templates/chris_dev_db.service
[Unit]
Description=
After=network.service
[Service]
Type=simple
User={{ APP_USER }}
ExecStart=/usr/bin/podman run --name {{ DEV_DB_NAME }}\{\% if APP_POD_NETWORK is defined \%\} --pod {{ DEV_DB_POD }}\{\% endif \%\}\{\% if APP_CONTAINER_NETWORK is defined \%\} --network {{ APP_CONTAINER_NETWORK }}\{\% endif \%\} -v {{ APP_DEV_DB_DATA }}:/var/lib/postgresql/data --rm -e "POSTGRES_DB={{ DEV_DB_DATABASE }}" -e "POSTGRES_USER={{ DEV_DB_BECOME_USER }}" -e "POSTGRES_PASSWORD={{ DEV_DB_BECOME_PASSWORD }}" {{ DEV_DB_IMAGE }}:{{ DEV_DB_VERSION }}
ExecStop=/usr/bin/podman rm {{ DEV_DB_NAME }} -f
Restart=on-failure
[Install]
WantedBy=multi-user.target
Web browser testing for ChRIS UI on an Android phone
Your mission, should you choose to accept it, is define the playbook to run locally.
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service
developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/team19-hackathon-2021
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/chris_pfcon.yml
---
# define the playbook to run locally
- name: Install the ChRIS containers locally in podman with Ansible
connection: local
hosts: localhost
# Run the chris_defaults role to load the ChRIS related variables.
roles:
- chris_defaults
# Now run the chris_pfcon role to install the pfcon container to podman.
- chris_pfcon
Your mission, should you choose to accept it, is define the ChRIS pfcon systemd service file. .
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/roles/chris_pfcon/templates/chris_pfcon.service
[Unit]
Description=
After=network.service
[Service]
Type=simple
User={{ APP_USER }}
ExecStart=/usr/bin/podman run --name {{ PFCON_NAME }}\{\% if APP_POD_NETWORK is defined \%\} --pod {{ PFCON_POD }}\{\% endif \%\}\{\% if APP_CONTAINER_NETWORK is defined \%\} --network {{ APP_CONTAINER_NETWORK }}\{\% endif \%\} -v {{ APP_DATA }}:/home/localuser/storeBase:Z -v {{ PFCON_SRC }}:/home/localuser/pfcon --rm -e "SECRET_KEY={{ APP_SECRET_KEY }}" -e "COMPUTE_SERVICE_URL=http://{{ PMAN_HOSTNAME }}:5010/api/v1/" {{ PFCON_IMAGE }}:{{ PFCON_VERSION }} gunicorn -w 5 -b 0.0.0.0:30005 -t 200 pfcon.wsgi:application
ExecStop=/usr/bin/podman rm {{ PFCON_NAME }} -f
Restart=on-failure
[Install]
WantedBy=multi-user.target
Your mission, should you choose to accept it, is create an Ansible Playbook to setup the initial ChRIS prerequisites.
You will have 4 hours to complete your mission.
ChRIS is a pervasively open source platform that utilizes cloud technologies to democratize medical analytics application development. It enables healthcare organizations to keep owning their data while benefiting from public cloud processing capabilities. ChRIS is developed as part of a collaborative effort between Boston Children’s Hospital, Red Hat, Boston University, and the Mass Open Cloud (MOC). ChRIS allows researchers the ability to simply deploy their applications in a cloud infrastructure with access to more data, more compute, and more collaboration to drive medical innovation. ChRIS uses leading open source technologies to standardize cloud-based healthcare application development, taking care of the infrastructure so medical researchers can focus on their data.
of all Red Hatters for this mission, who will be at your service developing the code and automating the deployment to OpenShift.
Follow the instructions here to setup the project: https://github.com/team19hackathon2021/ChRIS_ultron_backEnd/tree/master/ansible
Create a new file: /usr/local/src/ChRIS_ultron_backEnd/ansible/chris_before.yml
---
# Define the playbook to run locally.
- name: Install the ChRIS containers locally in podman with Ansible
connection: local
hosts: localhost
# Run the chris_defaults role to load the ChRIS related variables.
roles:
- chris_defaults
# Now run the chris_before role to do the prerequisite steps to installing the other applications.
- chris_before
React
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Some thing interesting about visualization, use data art
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