README-fnndsc.md

pfdcm (FNNDSC notes)

Notes relevant to starting/using the pfdcm service at the FNNDSC.

Abstract

This document provides some quick and simple notes on starting the pfdcm service at the Fetal Neonatal and Development Science Center.

Preliminaries

pfdcm is deployed on host titan as the chris-local user. To start/reset a deployment, log in to titan with appropriate password (consult the dev team if you need this):

# This only works from within the FNNDSC/BCH local network
ssh chris-local@titan

Once logged in, simply type v to switch to a properly configured fish shell session (some trivia: v denotes the word vis which is fish in Dutch/Afrikaans).

Now, change to the pfdcm source repo and pull any latest changes

cd ~/src/pfdcm
git pull

Build

Build the latest docker image

# Set some vars
set UID (id -u)
export PROXY="http://10.41.13.4:3128"

# Here we build an image called local/pfdcm
# Using --no-cache is a good idea to force the image to build all from scratch
docker build --no-cache --build-arg http_proxy=$PROXY --build-arg UID=$UID -t local/pfdcm .

Build issues

Sometimes the build has been noticed to fail with

WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7fb28ccc79a0>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')': /simple/pip

If this is the case, the simplest resolution is to restart docker services:

sudo service docker restart

Deploy

docker run --name pfdcm  --rm -it -d                                            \
        -p 4005:4005 -p 10402:11113 -p 5555:5555 -p 10502:11113 -p 11113:11113  \
        -v /home/dicom:/home/dicom                                              \
        -v /neuro/users/chris/PACS:/neuro/users/chris/PACS                      \
        local/pfdcm /start-reload.sh

Startup

# Assuming you are currently here
# titan:/home/chris-local/src/pfdcm
cd pfdcm
./pfdcm.sh -u -i --

The prompt will block. Wait a few seconds. On success you'll see a screen full of JSON, typically ending with

{
  {
    { 
        "prior": {
        "status": true,
        "install": {
          "stdout": "",
          "stderr": "",
          "cwd": "/app",
          "cmd": "mv /tmp/dicomlistener /etc/xinetd.d/dicomlistener",
          "returncode": 0
        },
        "prior": {
          "status": true,
          "fileContents": "\n        service dicomlistener\n        {\n            disable             = no\n            socket_type         = stream\n            wait                = no\n            user                = root\n            server              = /usr/local/bin/storescp.sh\n            server_args         = -t /tmp/data -E /usr/local/bin -D /home/dicom -p 11113\n            type                = UNLISTED\n            port                = 10502\n            bind                = 0.0.0.0\n        } ",
          "file": "/tmp/dicomlistener"
        }
      }
    }
  }
}

and the prompt will return.

Test

To check that the service is working properly, run the following query

./pfdcm.sh -u -Q --query -T csv  -- (cat qr.txt)

which will perform a quick PACS Query on the contents of the file qr.txt (note that this file is NOT part of this repo and exists solely in the FNNDSC directory; note also the fish shell conventions).

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