### Initial Project Setup and Run

Source: https://github.com/fnndsc/chris_ultron_backend/blob/master/README.md

Clones the ChRIS Ultron Backend repository and starts the development environment using 'just'. This is the primary command for getting the backend running.

```shell
git clone https://github.com/FNNDSC/ChRIS_ultron_backEnd.git
cd ChRIS_ultron_backEnd
just
```

--------------------------------

### Start Vagrant Environment

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Vagrant-Setup-OSX

Initiates the Vagrant virtual machine, provisioning it with the necessary software and configurations. This process can take a significant amount of time due to software installations.

```shell
<host>$ vagrant up
```

--------------------------------

### Setup Python Environment and Services

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Workflow-notes

Steps to set up the Python virtual environment, activate it, and start the Django and pman services required for the ChRIS Ultron backend.

```bash
export WORKON_HOME=~/src/python-env
source /usr/local/bin/virtualenvwrapper.sh
workon chris_env
cd ~/src/ChRIS_ultron_backend/chris_backend
manage.py runserver localhost:8000
pman --rawmode 1 --http --port 5010 --listeners 12
```

--------------------------------

### Certbot Installation and HTTPS Setup

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Deployment

Installs Certbot and the Apache plugin on Ubuntu, then uses Certbot to automatically obtain SSL certificates and configure Apache for HTTPS.

```bash
# install (on Ubuntu)
sudo apt install certbot python3-certbot-apache
# enable HTTPS using magic. gets certs and write apache configs
sudo certbot --apache
```

--------------------------------

### Start Orthanc Instance

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/PACS-Pull-wokflow

Command to start the Orthanc server. After starting, access the web interface to upload DICOM data.

```shell
~/work/orthancAndPluginsOSX.stable$ ./startOrthanc.command
```

--------------------------------

### CLI API Request Example

Source: https://github.com/fnndsc/chris_ultron_backend/blob/master/README.md

Demonstrates making an HTTP request to the ChRIS API using the 'xh' tool and processing the JSON response with 'jnv'. Requires 'xh' and 'jnv' to be installed.

```shell
xh -a chris:chris1234 :8000/api/v1/ | jnv
```

--------------------------------

### Apache VirtualHost Basic Example

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Deployment

A basic Apache VirtualHost configuration combining reverse proxy for API requests and serving a static front-end SPA from a specified DocumentRoot.

```apache
<VirtualHost *:80>
  ServerName chrisstore.co
  ProxyPass "/api" "http://localhost:8010/api"
  ProxyAddHeaders On  # this is the default anyways
  RequestHeader set "X-Forwarded-Proto" expr=%{REQUEST_SCHEME}
  DocumentRoot /var/src/ChRIS_store_ui/build

  ErrorLog ${APACHE_LOG_DIR}/chrisstore.error.log
  CustomLog ${APACHE_LOG_DIR}/chrisstore.access.log combined
</VirtualHost>
```

--------------------------------

### ChRIS Ultron Backend Setup and Environment Variables

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/2.4.2-ChRIS-FS--DS--DS-plugin-worflow-summary-[moc]

Commands to clone the ChRIS Ultron backend repository, perform initial setup, and set essential environment variables for API interaction.

```bash
git clone https://github.com/FNNDSC/ChRIS_ultron_backEnd
cd ChRIS_ultron_backEnd

*destroy* ; sudo rm -fr CHRIS_REMOTE_FS; rm -fr CHRIS_REMOTE_FS ; *make* -U -I -s

export HOST_IP=$(ip route | grep -v docker | awk '{if(NF==11) print $9}')
export HOST_PORT=8000
```

--------------------------------

### Install Sphinx Dependencies

Source: https://github.com/fnndsc/chris_ultron_backend/blob/master/README.md

Installs Sphinx and the sphinxcontrib-httpdomain package, which is useful for documenting REST APIs within Sphinx documentation. These are prerequisites for building HTML documentation.

```shell
pip install Sphinx
pip install sphinxcontrib-httpdomain
```

--------------------------------

### Start Django Development Server

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Vagrant-Setup-OSX

Starts the Django development server, making the ChRIS-ultron-backend application accessible. It listens on all network interfaces on port 8000.

```shell
<guest>(chris-ultron)$ python manage.py runserver 0.0.0.0:8000
```

--------------------------------

### Install Vagrant Guest Additions Plugin

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Vagrant-Setup-OSX

Installs the `vagrant-vbguest` plugin, which ensures VirtualBox guest additions are installed and updated within the Vagrant VM. This is crucial for proper folder sharing and integration.

```shell
<host>$ vagrant plugin install vagrant-vbguest
```

--------------------------------

### Install HTTPie and Swift Client

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/1.2-ChRIS-FS-plugin-workflow:-upload-files-to-CUBE-and-create-a-new-top-level-feed-(pl-pacscopy)

Installs the httpie and swift command-line tools, which are dependencies for pushing data to CUBE storage.

```bash
pip install httpie
pip install swift
```

--------------------------------

### Install Required Python Packages

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/2.4-ChRIS-FS--DS--DS-plugin-worflow:-simulate-a-FreeSurfer---MPC---heatmap-workflow

Installs the 'httpie' and 'swift' Python packages, which are command-line applications used for interacting with the CUBE API and swift storage respectively.

```bash
pip install httpie
```

```bash
pip install swift
```

--------------------------------

### ChRIS API: GET Homepage

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/0.-ChRIS-preliminary-workflow:-intro

Fetches the root endpoint of the ChRIS API to get general system information and available links. It uses 'pfurl' with authentication and specifies pretty-printing for the JSON output.

```bash
pfurl --auth chris:chris1234 --verb GET --raw --http ${HOST_IP}:8000/api/v1/ \
    --quiet --jsonpprintindent 4
```

```javascript
{
  "collection": {
    "items": [ ],
    "links": [
      { "href": "http://10.17.24.163:8000/api/v1/tags/", "rel": "tags" },
      { "href": "http://10.17.24.163:8000/api/v1/plugins/", "rel": "plugins" }
    ],
    "queries": [
      {
        "data": [
          { "name": "name", "value": "" },
          { "name": "min_id", "value": "" },
          { "name": "max_id", "value": "" },
          { "name": "min_creation_date", "value": "" },
          { "name": "max_creation_date", "value": "" }
        ],
        "href": "http://10.17.24.163:8000/api/v1/search/",
        "rel": "search"
      }
    ],
    "version": "1.0",
    "href": "http://10.17.24.163:8000/api/v1/"
  }
}
```

--------------------------------

### Instantiate CUBE Backend

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/2.4.1-ChRIS-FS--DS--DS-plugin-worflow-summary

Steps to clone the ChRIS_ultron_backEnd repository, navigate to the directory, and prepare the environment by destroying existing configurations and making the system. It emphasizes skipping unit and integration tests.

```bash
git clone https://github.com/FNNDSC/ChRIS_ultron_backEnd
cd ChRIS_ultron_backEnd

*destroy* ; sudo rm -fr CHRIS_REMOTE_FS; rm -fr CHRIS_REMOTE_FS ; *make* -U -I -s
```

--------------------------------

### Monitor Plugin Instance Status with pfurl

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/5.-ChRIS-plugin-geretrieve

This example shows how to poll the status of a plugin instance using pfurl. It retrieves the instance details via a GET request to the API, allowing users to check if a plugin has finished successfully.

```bash
pfurl --auth chris:chris1234 \
      --verb GET --http ${HOST_IP}:8000/api/v1/plugins/instances/1/ \
      --content-type application/vnd.collection+json             \
      --quiet --jsonpprintindent 4
```

--------------------------------

### Clone and Navigate ChRIS Backend

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/2.4-ChRIS-FS--DS--DS-plugin-worflow:-simulate-a-FreeSurfer---MPC---heatmap-workflow

Clones the ChRIS_ultron_backEnd repository from GitHub and navigates into the project directory. This is the initial setup step for working with the CUBE backend.

```bash
git clone https://github.com/FNNDSC/ChRIS_ultron_backEnd
cd ChRIS_ultron_backEnd
```

--------------------------------

### Apache Reverse Proxy Configuration Example

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Deployment

Conceptual setup for Apache to serve ChRIS_store_ui on the root domain and its backend API on the /api/v1/ path, assuming a single server with a specific domain name.

```apache
# Example Apache configuration for ChRIS_store
# Assumes: Backend on http://127.0.0.1:8010/api/v1/
# ChRIS_store_ui cloned to /var/src/ChRIS_store_ui
# Domain name chrisstore.co points to server IP

<VirtualHost *:443>
    ServerName chrisstore.co
    SSLEngine on
    SSLCertificateFile /path/to/your/certificate.crt
    SSLCertificateKeyFile /path/to/your/private.key

    # Serve ChRIS_store_ui (SPA)
    DocumentRoot /var/src/ChRIS_store_ui
    <Directory /var/src/ChRIS_store_ui>
        Options Indexes FollowSymLinks
        AllowOverride All
        Require all granted
        # For SPA routing, rewrite all non-file requests to index.html
        RewriteEngine On
        RewriteCond %{REQUEST_FILENAME} !-f
        RewriteCond %{REQUEST_FILENAME} !-d
        RewriteRule ^(.*)$ /index.html [L]
    </Directory>

    # Proxy API requests to the backend
    ProxyPass /api/v1/ http://127.0.0.1:8010/api/v1/
    ProxyPassReverse /api/v1/ http://127.0.0.1:8010/api/v1/

    ErrorLog ${APACHE_LOG_DIR}/chrisstore.error.log
    CustomLog ${APACHE_LOG_DIR}/chrisstore.access.log combined
</VirtualHost>

# Redirect HTTP to HTTPS
<VirtualHost *:80>
    ServerName chrisstore.co
    Redirect permanent / https://chrisstore.co/
</VirtualHost>
```

--------------------------------

### Create a Plugin via API

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Vagrant-Setup-OSX

Demonstrates creating a new plugin resource using an HTTP POST request to the ChRIS-ultron-backend API. It uses `httpie` for making the request and basic authentication.

```shell
<host>$ brew install httpie
<host>$ http -a chris:Chris1234 POST http://127.0.0.1:8001/api/v1/plugins/ Content-Type:application/vnd.collection+json Accept:application/vnd.collection+json template='{"data":[{"name":"name","value":"Feed1"}, {"name":"plugin","value":1}, {"name":"type","value":"fs"}]}'
```

--------------------------------

### Internal Collection+JSON href Example

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Deployment

An example of the internal Collection+JSON structure, highlighting incorrect and correct href formats for API endpoints. It shows how browsers might block mixed content requests (HTTP AJAX from HTTPS origin).

```json
{
  "collection": {
    "href": "http://cube.example.com/api/v1/",
    "items": [],
    "links": [
      {
        "href": "http://cube.example.com/api/v1/files/",
        "rel": "files"
      },
      {
        "href": "http://cube.example.com/api/v1/computeresources/",
        "rel": "compute_resources"
      }
    ],
    "total": 0,
    "version": "1.0"
  }
}
```

--------------------------------

### HTTP Request and Response Example

Source: https://github.com/fnndsc/chris_ultron_backend/blob/master/docs/source/collections/plugin.rst

Illustrates a typical HTTP GET request to the plugin collection endpoint and its corresponding successful response structure.

```http
GET /api/v1/plugins/ HTTP/1.1
Host: localhost:8000
Accept: application/vnd.collection+json
```

```http
HTTP/1.1 200 OK
Allow: GET
Content-Type: application/vnd.collection+json

{
    "collection": {
        "href": "https://localhost:8000/api/v1/plugins/",
        "items": [
            {
                "data": [
                    {
                        "name": "name",
                        "value": "simpledsapp"
                    },
                    {
                        "name": "type",
                        "value": "ds"
                    }
                ],
                "href": "https://localhost:8000/api/v1/plugins/13/",
                "links": [
                    {
                        "href": "https://localhost:8000/api/v1/plugins/13/parameters/",
                        "rel": "parameters"
                    },
                    {
                        "href": "https://localhost:8000/api/v1/plugins/13/instances/",
                        "rel": "instances"
                    }
                ]
            },
            {
                "data": [
                    {
                        "name": "name",
                        "value": "simplefsapp"
                    },
                    {
                        "name": "type",
                        "value": "fs"
                    }
                ],
                "href": "https://localhost:8000/api/v1/plugins/12/",
                "links": [
                    {
                        "href": "https://localhost:8000/api/v1/plugins/12/parameters/",
                        "rel": "parameters"
                    },
                    {
                        "href": "https://localhost:8000/api/v1/plugins/12/instances/",
                        "rel": "instances"
                    }
                ]
            }
        ],
        "links": [
            {
                "href": "https://localhost:8000/api/v1/",
                "rel": "feeds"
            }
        ],
        "version": "1.0"
    }
}
```

--------------------------------

### Instantiate CUBE Backend

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/2.4-ChRIS-FS--DS--DS-plugin-worflow:-simulate-a-FreeSurfer---MPC---heatmap-workflow

Commands to instantiate the CUBE backend. The first command performs a full build with tests, while the second skips tests and intro for a faster setup. Both commands clean up previous instances.

```bash
*unmake* ; sudo rm -fr CHRIS_REMOTE_FS; rm -fr CHRIS_REMOTE_FS ; *make*
```

```bash
*destroy* ; sudo rm -fr CHRIS_REMOTE_FS; rm -fr CHRIS_REMOTE_FS ; *make* -U -I -s
```

--------------------------------

### Setup Environment Variables and Aliases

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/MICCAI-Work-Flow-(WIP)

Sets up essential environment variables for host IP and port, and creates a Docker alias for the pfurl command-line tool.

```shell
export HOST_IP=$(ip route | grep -v docker | awk '{if(NF==11) print $9}')
export HOST_PORT=8000

alias pfurl='docker run --rm --name pfurl fnndsc/pfurl'
```

--------------------------------

### Minimal Setup for Fedora 32 (Moby)

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Fedora-32-Support-for-Docker

Installs Moby engine and docker-compose on Fedora 32, configures the kernel for cgroup v1 compatibility, enables the Docker service, and reboots the system.

```shell
sudo dnf install -y moby-engine docker-compose
sudo grubby --update-kernel=ALL --args="systemd.unified_cgroup_hierarchy=0"
sudo systemctl enable docker
sudo systemctl reboot
```

--------------------------------

### Workflow Step 1: Call simplefs Plugin

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Workflow-notes

Initiates a 'simplefs' plugin execution by sending a POST request with directory input.

```bash
# 1. Call a 'simplefs' plugin
purl    --auth chris:chris1234                                  \
        --content-type application/vnd.collection+json          \
        --verb POST                                             \
        --raw --jsonwrapper template                            \
        --http 10.17.24.163:8000/api/v1/plugins/1/instances/    \
        --msg \
        '{ 
            "data": [{  "name":     "dir",                
                        "value":    "/home"}] 
         }' --quiet  | underscore print --color
```

--------------------------------

### Retrieve Plugin Collection via API

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Vagrant-Setup-OSX

Fetches a list of all available plugins from the ChRIS-ultron-backend API using an HTTP GET request. It authenticates with the 'ubuntu' user credentials.

```shell
<host>$ http -a ubuntu:chrisultron  http://127.0.0.1:8001/api/v1/plugins
```

--------------------------------

### Create Plugin Instance (simplefsapp)

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Chris-workflow

Demonstrates a POST request to create an instance of the 'simplefsapp' plugin. It uses basic authentication and specifies the content type and template data for the new instance.

```http
http -a bob:bob-pass POST http://127.0.0.1:8000/api/v1/plugins/6/instances/ Content-Type:application/vnd.collection+json Accept:application/vnd.collection+json template:='{"data":[{"name":"prefix","value":"myprefix"}]}'
```

```json
{
    "collection": {
        "href": "http://127.0.0.1:8000/api/v1/plugins/6/instances/",
        "items": [
            {
                "data": [
                    {
                        "name": "id",
                        "value": 37
                    },
                    {
                        "name": "plugin_name",
                        "value": "simplefsapp"
                    },
                    {
                        "name": "owner",
                        "value": "bob"
                    }
                ],
                "href": "http://127.0.0.1:8000/api/v1/plugins/instances/37/",
                "links": [
                    {
                        "href": "http://127.0.0.1:8000/api/v1/20/",
                        "rel": "feed"
                    },
                    {
                        "href": "http://127.0.0.1:8000/api/v1/plugins/6/",
                        "rel": "plugin"
                    },
                    {
                        "href": "http://127.0.0.1:8000/api/v1/plugins/string-parameter/36/",
                        "rel": "string_param"
                    }
                ]
            }
        ],
        "links": [],
        "version": "1.0"
    }
}
```

--------------------------------

### Prepare Vagrant Working Directory

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Vagrant-Setup-OSX

Creates the necessary directory structure for Vagrant to manage the ChRIS-ultron-backend environment. This directory will house configuration files.

```shell
<host>$ mkdir -p ~/work/vagrant/chris-ultron
```

--------------------------------

### Apache Reverse Proxy Configuration

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Deployment

Configures Apache to proxy API requests to a backend service. It forwards requests starting with '/api' to 'http://localhost:8010/api' and sets the X-Forwarded-Proto header.

```apache
ProxyPass "/api" "http://localhost:8010/api"
ProxyAddHeaders On  # this is the default anyways
RequestHeader set "X-Forwarded-Proto" expr=%{REQUEST_SCHEME}
```

--------------------------------

### PACS Server Move-SCU Request Log

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/PACS-Pull-wokflow

An example log message from the PACS Server indicating that a Move-SCU request has been received for the CHRIS-ULTRON-LIS Application Entity. This confirms the server is processing the retrieval request.

```log
W0123 10:03:05.789730 OrthancMoveRequestHandler.cpp:175] Move-SCU request received for AET "CHRIS-ULTRON-LIS"
```

--------------------------------

### Setup Django Database Migrations

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Vagrant-Setup-OSX

Connects to the Vagrant VM via SSH and runs Django's database migration commands. This initializes the database schema required by the ChRIS-ultron-backend application.

```shell
<host>$ vagrant ssh
<guest>(chris-ultron)$ cd ~/chris-ultron-backend/chris_backend
<guest>(chris-ultron)$ python manage.py migrate
```

--------------------------------

### Clone ChRIS-ultron-backend Repository

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Vagrant-Setup-OSX

Clones the ChRIS_ultron_backEnd project from GitHub into a specified directory. This is the first step to obtain the project's source code.

```shell
<host>$ mkdir -p ~/work/gitroot
<host>$ cd ~/work/gitroot
<host>$ git clone https://github.com/FNNDSC/ChRIS_ultron_backEnd.git chris-ultron-backend
```

--------------------------------

### Pause CUBE Execution for Debugging

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Debugging-CUBE-Containerized-Services

Starts the CUBE system with the '-p' flag to pause execution after initial container setup but before full instantiation. This allows for manual restarting of ancillary services for log monitoring or debugging.

```bash
./make.sh -p
```

--------------------------------

### Apache VirtualHost Full Example with SSL

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Deployment

A comprehensive Apache VirtualHost configuration for HTTPS, including a redirect from HTTP, reverse proxy for API, SPA serving, and detailed SSL/TLS settings for security.

```apache
<VirtualHost *:80>
  ServerName chrisstore.co
  RewriteEngine on
  RewriteCond %{SERVER_NAME} =chrisstore.co
  RewriteRule ^ https://%{SERVER_NAME}%{REQUEST_URI} [END,NE,R=permanent]
</VirtualHost>

<VirtualHost *:443>
  ServerName chrisstore.co

  ProxyPass "/api" "http://localhost:8010/api"
  ProxyAddHeaders On  # this is the default anyways
  RequestHeader set "X-Forwarded-Proto" expr=%{REQUEST_SCHEME}

  DocumentRoot /var/www/ChRIS_store_ui/build

  ErrorLog ${APACHE_LOG_DIR}/chrisstore.error.log
  CustomLog ${APACHE_LOG_DIR}/chrisstore.access.log combined

  SSLEngine on
  SSLCertificateFile /etc/letsencrypt/live/chrisstore.co/fullchain.pem
  SSLCertificateKeyFile /etc/letsencrypt/live/chrisstore.co/privkey.pem
  SSLProtocol             all -SSLv2 -SSLv3
  SSLCipherSuite          ECDHE-ECDSA-CHACHA20-POLY1305:ECDHE-RSA-CHACHA20-POLY1305:ECDHE-ECDSA-AES128-GCM-SHA256:ECDHE-RSA-AES128-GCM-SHA256:ECDHE-ECDSA-AES256-GCM-SHA384:ECDHE-RSA-AES256-GCM-SHA384:DHE-RSA-AES128-GCM-SHA256:DHE-RSA-AES256-GCM-SHA384:ECDHE-ECDSA-AES128-SHA256:ECDHE-RSA-AES128-SHA256:ECDHE-ECDSA-AES128-SHA:ECDHE-RSA-AES256-SHA384:ECDHE-RSA-AES128-SHA:ECDHE-ECDSA-AES256-SHA384:ECDHE-ECDSA-AES256-SHA:ECDHE-RSA-AES256-SHA:DHE-RSA-AES128-SHA256:DHE-RSA-AES128-SHA:DHE-RSA-AES256-SHA256:DHE-RSA-AES256-SHA:ECDHE-ECDSA-DES-CBC3-SHA:ECDHE-RSA-DES-CBC3-SHA:EDH-RSA-DES-CBC3-SHA:AES128-GCM-SHA256:AES256-GCM-SHA384:AES128-SHA256:AES256-SHA256:AES128-SHA:AES256-SHA:DES-CBC3-SHA:!DSS
  SSLHonorCipherOrder     on
  SSLCompression          off
  SSLOptions +StrictRequire
</VirtualHost>
```

--------------------------------

### Start ChRIS Ultron Backend System

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/0.-ChRIS-preliminary-workflow:-intro

Initiates the ChRIS Ultron Backend (CUBE) system. This command is typically executed from the root of the CUBE source repository.

```bash
make
```

--------------------------------

### API: Fetch API Root and Plugin List

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Chris-workflow

Demonstrates fetching the API root to discover available resources and then retrieving the list of registered plugins. Uses httpie with basic authentication.

```shell
http -a bob:bob-pass http://127.0.0.1:8000/api/v1/
```

```APIDOC
HTTP/1.0 200 OK
Allow: GET, HEAD, OPTIONS
Content-Type: application/vnd.collection+json
Date: Tue, 09 Aug 2016 20:22:04 GMT
Server: WSGIServer/0.2 CPython/3.5.1+
Vary: Accept, Cookie
X-Frame-Options: SAMEORIGIN

{
    "collection": {
        "href": "http://127.0.0.1:8000/api/v1/",
        "items": [],
        "links": [
            {
                "href": "http://127.0.0.1:8000/api/v1/plugins/",
                "rel": "plugins"
            }
        ],
        "version": "1.0"
    }
}
```

```shell
http -a bob:bob-pass http://127.0.0.1:8000/api/v1/plugins/
```

```APIDOC
HTTP/1.0 200 OK
Allow: GET, HEAD, OPTIONS
Content-Type: application/vnd.collection+json
Date: Tue, 09 Aug 2016 20:23:18 GMT
Server: WSGIServer/0.2 CPython/3.5.1+
Vary: Accept, Cookie
X-Frame-Options: SAMEORIGIN

{
    "collection": {
        "href": "http://127.0.0.1:8000/api/v1/plugins/",
        "items": [
            {
                "data": [
                    {
                        "name": "name",
                        "value": "simpledsapp"
                    },
                    {
                        "name": "type",
                        "value": "ds"
                    }
                ],
                "href": "http://127.0.0.1:8000/api/v1/plugins/7/",
                "links": [
                    {
                        "href": "http://127.0.0.1:8000/api/v1/plugins/7/parameters/",
                        "rel": "parameters"
                    },
                    {
                        "href": "http://127.0.0.1:8000/api/v1/plugins/7/instances/",
                        "rel": "instances"
                    }
                ]
            },
            {
                "data": [
                    {
                        "name": "name",
                        "value": "simplefsapp"
                    },
                    {
                        "name": "type",
                        "value": "fs"
                    }
                ],
                "href": "http://127.0.0.1:8000/api/v1/plugins/6/",
                "links": [
                    {
                        "href": "http://127.0.0.1:8000/api/v1/plugins/6/parameters/",
                        "rel": "parameters"
                    },
                    {
                        "href": "http://127.0.0.1:8000/api/v1/plugins/6/instances/",
                        "rel": "instances"
                    }
                ]
            }
        ],
        "links": [
            {
                "href": "http://127.0.0.1:8000/api/v1/",
                "rel": "feeds"
            }
        ],
        "version": "1.0"
    }
}
```

--------------------------------

### Query Job State with pfurl

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/5.-ChRIS-plugin-geretrieve

This snippet shows how to query the state of a job or plugin instance using its ID. It performs a GET request to the specific instance endpoint, allowing for monitoring of the job's progress and status.

```bash
pfurl --auth chris:chris1234 \
      --verb GET \
      --http ${HOST_IP}:8000/api/v1/plugins/instances/2/ \
      --content-type application/vnd.collection+json \
      --quiet --jsonpprintindent 4
```

--------------------------------

### Instantiate CUBE from Source

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/1.2-ChRIS-FS-plugin-workflow:-upload-files-to-CUBE-and-create-a-new-top-level-feed-(pl-pacscopy)

Commands to start CUBE from its repository source directory. Includes options for removing volume containers and necessary sudo commands for filesystem cleanup.

```bash
*destroy* ; sudo rm -fr CHRIS_REMOTE_FS; rm -fr CHRIS_REMOTE_FS ; *make*
```

--------------------------------

### Vagrant Setup for Docker on Fedora

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Fedora-32-Support-for-Docker

This example demonstrates how to set up a Vagrant virtual machine using a Debian Buster image to run Docker. It includes cloning the ChRIS_ultron_backend repository, configuring the Vagrantfile with memory and port forwarding, and provisioning the VM with Docker and docker-compose.

```bash
git clone https://github.com/FNNDSC/ChRIS_ultron_backEnd.git
cd ChRIS_ultron_backEnd
cat > Vagrantfile << EOF
Vagrant.configure("2") do |config|
  config.vm.box = "debian/buster64"
  config.vm.provider "virtualbox" do |vb|
    vb.memory = "8096"
  end
  config.vm.network "forwarded_port", guest: 8000, host: 8000 # cube
  config.vm.network "forwarded_port", guest: 8010, host: 8010 # store
  config.vm.network "forwarded_port", guest: 5005, host: 5005 # pfcon
  config.vm.network "forwarded_port", guest: 5010, host: 5010 # pman
  config.vm.network "forwarded_port", guest: 5055, host: 5055 # pfioh
  config.vm.provision "shell", inline: <<-SHELL
    wget -qO /usr/local/bin/docker-compose "https://github.com/docker/compose/releases/download/1.26.2/docker-compose-$(uname -s)-$(uname -m)"
    chmod +x /usr/local/bin/docker-compose
    wget -qO /tmp/get-docker.sh https://get.docker.com
    sh /tmp/get-docker.sh > /dev/null 2>&1
    systemctl enable --now docker
  SHELL
end
EOF
vagrant up
vagrant ssh -c 'cd /vagrant && sudo ./make.sh'
```

--------------------------------

### Caddy Reverse Proxy Configuration

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Deployment

Example Caddyfile configuration for routing traffic to ChRIS backend services (CUBE, store) and serving ChRIS UI applications. It demonstrates automatic HTTPS with Let's Encrypt and header injection for SSL.

```caddyfile
cube.chris.example.com {
  reverse_proxy localhost:8000 {
    header_up X-Forwarded-Proto {http.request.scheme}
  }
  log
}

api.store.chris.example.com {
  reverse_proxy localhost:8010 {
    header_up X-Forwarded-Proto {http.request.scheme}
  }
  log
}

chris.example.com {
  root * /srv/ChRIS_ui/build
  file_server
  try_files {path} /index.html
}

store.chris.example.com {
  root * /srv/ChRIS_store_ui/build
  file_server
  try_files {path} /index.html
}

# optional but very awesome monitoring app
# https://github.com/netdata/netdata
netdata.chris.example.com {
  reverse_proxy localhost:19999
}
```

--------------------------------

### API: Fetch Plugin Instances and Create Instance

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/Chris-workflow

Demonstrates fetching the instances list for a specific plugin (e.g., 'fs' type) and then performing a POST request to create a new instance. The POST request includes data payload based on the template provided by the API.

```shell
http -a bob:bob-pass http://127.0.0.1:8000/api/v1/plugins/6/instances/
```

```APIDOC
HTTP/1.0 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/vnd.collection+json
Date: Tue, 09 Aug 2016 20:27:29 GMT
Server: WSGIServer/0.2 CPython/3.5.1+
Vary: Accept, Cookie
X-Frame-Options: SAMEORIGIN

{
    "collection": {
        "href": "http://127.0.0.1:8000/api/v1/plugins/6/instances/",
        "items": [],
        "links": [
            {
                "href": "http://127.0.0.1:8000/api/v1/plugins/6/",
                "rel": "plugin"
            }
        ],
        "template": {
            "data": [
                {
                    "name": "previous",
                    "value": ""
                },
                {
                    "name": "dir",
                    "value": ""
                }
            ]
        },
        "version": "1.0"
    }
}
```

```shell
http -a bob:bob-pass POST http://127.0.0.1:8000/api/v1/plugins/6/instances/ Content-Type:application/vnd.collection+json Accept:application/vnd.collection+json template:='{"data":[{"name":"dir","value":"./"}, {"name":"previous","value":""}]}'
```

```APIDOC
HTTP/1.0 201 Created
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/vnd.collection+json
Date: Tue, 09 Aug 2016 20:33:09 GMT
Location: http://127.0.0.1:8000/api/v1/plugins/instances/37/
Server: WSGIServer/0.2 CPython/3.5.1+
Vary: Accept, Cookie
X-Frame-Options: SAMEORIGIN

{
    "collection": {
        "href": "http://127.0.0.1:8000/api/v1/plugins/6/instances/",
        "items": [
            {
                "data": [
                    {
                        "name": "previous",
                        "value": ""
                    },
                    {
                        "name": "dir",
                        "value": "./"
                    }
                ],
                "href": "http://127.0.0.1:8000/api/v1/plugins/instances/37/"
            }
        ],
        "links": [
            {
                "href": "http://127.0.0.1:8000/api/v1/plugins/6/",
                "rel": "plugin"
            }
        ],
        "version": "1.0"
    }
}
```

--------------------------------

### Instantiate CUBE Environment

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/1.1-ChRIS-FS-plugin-workflow:-upload-files-to-CUBE-and-create-a-new-top-level-feed-(pl-dircopy)

Prepares and starts the ChRIS Ultron Back End (CUBE) environment. This involves cleaning up previous instances and then making a new one, ensuring a fresh state.

```bash
*unmake* ; sudo rm -fr CHRIS_REMOTE_FS; rm -fr CHRIS_REMOTE_FS ; *make*
```

--------------------------------

### ChRIS API: Get Plugin Parameters

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/5.-ChRIS-plugin-geretrieve

This API documentation describes how to fetch the parameter definitions for a specific ChRIS plugin using its ID. It outlines the endpoint for retrieving parameter information and the structure of the returned parameter data, including type, optionality, and help text.

```APIDOC
GET /api/v1/plugins/<id>/parameters/
  Description: Retrieves the parameter definitions for a specific plugin.
  Authentication: Requires user credentials (e.g., chris:chris1234).
  Parameters:
    --auth <user>:<password>: Authentication credentials.
    --http <HOST_IP>:8000: The base URL of the CUBE backend.
    <id>: The unique identifier of the plugin.
    --quiet: Suppresses verbose output.
    --jsonpprintindent 4: Formats the JSON output with an indent of 4 spaces for readability.
  Example Call:
    pfurl --auth chris:chris1234 --http ${HOST_IP}:8000/api/v1/plugins/9/parameters/ --quiet --jsonpprintindent 4
  Response Structure (Example):
    {
      "collection": {
        "href": "http://<host>:<port>/api/v1/plugins/9/parameters/",
        "items": [
          {
            "href": "http://<host>:<port>/api/v1/plugins/parameters/<param_id>/",
            "data": [
              {"name": "name", "value": "parameter_name"},
              {"name": "type", "value": "string"},
              {"name": "optional", "value": true},
              {"name": "default", "value": ""},
              {"name": "help", "value": "Description of the parameter."}
            ]
          }
        ]
      }
    }
  Related Actions:
    - Fetching specific plugin details.
    - Running plugin instances.
```

--------------------------------

### Execute Shell Commands in CUBE Container

Source: https://github.com/fnndsc/chris_ultron_backend/wiki/5.-ChRIS-plugin-geretrieve

Provides a bash function `dke` to execute commands within a specified Docker container by its name. It also shows an example of using `ls` to list files in a directory after entering the container, demonstrating file system inspection.

```bash
dke () {
    NAME=$1;
    ID=$(dkl | grep $NAME | head -n 1 | awk '{print $1}');
    docker exec -ti $ID /bin/bash
}
```

```bash
dke chris_dev_backend
root@10bd34cb1dc2:/usr/src/chris_backend# cd /usr/users/chris/feed_1/simplefsapp_1/geretrieve_2/data/demo-upload/data/1033/
root@10bd34cb1dc2:/usr/users/chris/feed_1/simplefsapp_1/geretrieve_2/data/demo-upload/data/1033# ls
Axial_FLAIR-33_months-5  Axial_T2-33_months-4  Coronal_T2-33_months-6  Sagittal_T1-33_months-12
root@10bd34cb1dc2:/usr/users/chris/feed_1/simplefsapp_1/geretrieve_2/data/demo-upload/data/1033#
```