/artifice

ARTIC Real Time Integrated Field Informatics Control Engine

Primary LanguageJavaScript

ARTIFICE

ARTIC Real Time Integrated Field Informatics Control Engine

This is work in progress and doesn't actually do much at the moment

Installing

git clone https://github.com/rambaut/artifice.git
cd artifice
npm install

Running

First start the demon process:

node artificed.js

In a separate shell, use the command line program to control the demon:

./artifice.js --help
./artifice.js status

Command line interface

Create a project:

./artifice.js new-project my_project \
    --title "This is my new sequencing project" \
    --protocol "ARTIC_EBOV_v1.0" \
    --start-date 2019-07-10 \
    --description "A description of the project"

Creating a project automatically enters it (i.e., makes it the current project). This can also be done retrospectively:

./artifice.js enter-project my_project

Start a new run:

./artifice.js new-run todays_run \
    --title "MinION run on Thursday" \
    --start-date 2019-07-10 \
    --description "A description of the run"

Add samples descriptions with barcode allocations:

./artifice.js add-sample patient_001 \
    --barcodes NB01,NB02 \
    --collection-date 2019-05-04 
./artifice.js add-sample patient_002 \
    --barcodes NB03 \
    --collection-date 2019-05-05 
./artifice.js add-sample patient_003 \
    --barcodes NB04 \
    --collection-date 2019-05-06
    .
    .
    . 

Command line help

Usage: artifice [options] [command]
   
ARTIFICE command line interface

Options:
  -V, --version                      output the version number
  -h, --help                         output usage information

Commands:
  new-project|np [options] <name>    Create a new project
  list-projects|lp [options]         List current projects
  get-projects|gp                    Get current projects in JSON format
  enter-project|ep <name>            Enter a project (make it current)
  exit-project|xp                    Exit currently selected project
  close-project|cp [options] <name>  Close a project (cannot be further modified, unless reopened)
  reopen-project|rp <name>           Re-open a closed project
  new-run|nr [options] <name>        Create a new run within the current project
  list-runs|lr [options]             List runs within the current project
  enter-run|er <name>                Enter a run (make it current)
  exit-run|xr                        Exit the current run
  end-run|er [options] <name>        End a run (cannot be further modified, unless restarted)
  restart-run|rr <name>              Re-start an ended run
  add-sample|ns [options] <name>     Add a new sample within the current run
  list-samples|ls [options]          List samples within the current project
  status|st [options]                Provide information about the current status of ARTIFICE
  get-documents|gd                   Get all documents within the datastore in JSON format