ENH: Docker-compose

.env

@@ -0,0 +1,16 @@
+# configurable options for `docker-compose`
+# Description (service-name)
+
+# Directory to store DICOM files (dcm-receiver)
+DICOMDIR=./dicoms
+
+# Port to listen for DICOM transfer (dcm-receiver)
+PORT=8080
+
+# Directory for conversion output (heudiconv)
+HEUDICONV_OUTDIR=./output
+
+
+# ADVANCED: additional heudiconv arguments to use (heudiconv)
+# args used: --files, -f, -o, -b
+HEUDICONV_XARGS=""

README.md

@@ -125,6 +125,23 @@ tools, any environment providing them would suffice, such as
 other Debian-based systems with NeuroDebian repositories configured,
 which would provide all necessary for ReproIn setup components.
 
+
+## `docker-compose` + usage
+
+This repository provides a `docker-compose` file that includes (2) services:
+- DICOM receiver ([dcmtk](https://dicom.offis.de/dcmtk) `storescp`)
+  listening and ready to receive through a port.
+- `reproin` (`heudiconv`) converter set to process all folders in the DICOM
+  directory through a cron job (default is set to everyday at 4am).
+
+Refer to the `.env` file - many options above are configurable within it.
+
+To spin up the reproin service, run `docker-compose up` in the project root -
+ this will route all logs to the console. If you wish to run it in the service
+ in the background, append the `--detach` flag, and use `docker-compose logs`
+ to monitor. Since this is a new feature, it may not behave as intended. If you
+ encounter any errors, please open an issue and let us know.
+
 ## TODOs/WiP/Related
 
 - [ ] add a pre-configured DICOM receiver for fully turnkey deployments

dcmrecv/Dockerfile

@@ -0,0 +1,10 @@
+FROM debian:stretch
+
+ARG DEBIAN_FRONTEND="noninteractive"
+
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends ca-certificates apt-utils dcmtk \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+WORKDIR /dicoms

dcmrecv/README.md

@@ -0,0 +1,4 @@
+# docker-compose up to start application
+
+# dcm-receiver app will launch docker container running storescp
+# listening for DICOMs on port 8080 and saving to an output directory

docker-compose.yml

@@ -0,0 +1,17 @@
+version: '3'
+services:
+  dcm-receiver:
+    build: ./dcmrecv
+    ports:
+      - "${PORT}:${PORT}"
+    volumes:
+      - ${DICOMDIR}:/dicoms
+    command: storescp -v -sp --output-directory /dicoms ${PORT}
+
+  heudiconv:
+    build: ./heudicron
+    volumes:
+      - ${DICOMDIR}:/dicoms:ro
+      - ${HEUDICONV_OUTDIR}:/output
+    depends_on:
+      - dcm-receiver

heudicron/Dockerfile

@@ -0,0 +1,18 @@
+FROM nipy/heudiconv:latest
+
+RUN apt-get update -qq \
+    && apt-get install -y -qq --no-install-recommends cron \
+    && apt-get clean
+
+RUN git config --global user.email "user@heudiconv" \
+    && git config --global user.name "heudiconv-erter"
+
+COPY heudiconv.sh /
+
+# save copy of current PATH to be used in cron job (hacky)
+RUN echo ${PATH} > /opt/heudiconv.path
+
+RUN chmod +x /heudiconv.sh \
+    && (crontab -l; echo "* 4 * * * /heudiconv.sh > /proc/1/fd/1 2>/proc/1/fd/2") | crontab
+
+ENTRYPOINT cron -f

heudicron/README.md

@@ -0,0 +1,5 @@
+# heudicron
+
+Automate received DICOMs through heudiconv's reproin conversion. Users are able
+ to alter automation schedule via the `heudicron` script. By default, `heudiconv`
+ conversions will trigger every day at 3am.

heudicron/heudiconv.sh

@@ -0,0 +1,38 @@
+#!/bin/bash
+
+echo "Running scheduled heudiconv conversion"
+
+HEUDICONV_DICOMDIR="/dicoms"
+HEUDICONV_OUTDIR="/output"
+HEUDICONV_XARGS=${HEUDICONV_XARGS:-""}
+HEUDICONV_HISTORY="${HEUDICONV_OUTDIR}/.heudiconv.history"
+
+set -eu
+
+# cron uses strip down PATH
+# pull container creation PATH variable
+if [ -f /opt/heudiconv.path ]; then
+  echo "Setting heudiconv PATHs"
+  export PATH=$(cat /opt/heudiconv.path)
+fi
+
+if [ ! -d ${HEUDICONV_DICOMDIR} ]; then
+    echo "DICOM directory ${HEUDICONV_DICOMDIR} not properly set or mounted"
+    exit 1
+elif [ ! -d ${HEUDICONV_OUTDIR} ]; then
+    echo "Output directory ${HEUDICONV_OUTDIR} not properly set or mounted"
+    exit 1
+elif [ ! -f ${HEUDICONV_HISTORY} ]; then
+    touch ${HEUDICONV_HISTORY}
+fi
+
+for DICOMS in $(ls ${HEUDICONV_DICOMDIR}); do
+   if cat ${HEUDICONV_HISTORY} | awk '{print $1}' | grep "${DICOMS}" > /dev/null; then
+      # existing conversion was found
+      continue
+   fi
+
+   CMD="heudiconv -f reproin --bids --datalad -o ${HEUDICONV_OUTDIR} --files ${HEUDICONV_DICOMDIR}/${DICOMS} ${HEUDICONV_XARGS}"
+   ${CMD}
+   printf "${DICOMS}\t$(date)\n" >> ${HEUDICONV_HISTORY}
+done

heudicron/heudicron

@@ -0,0 +1,4 @@
+# key: min (0-59) | hr (0-23) | dom (1-31) | mon (1-12) | dow (0,7=sun) | command
+
+# trigger heudiconv every day at 3am
+* 3 * * * /heudiconv.sh >> /var/log/cron.log

heudicron/start-cron

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+crontab /etc/heudicron
+
+service cron start
+
+CRONLOG="/var/log/cron.log"
+
+while true; do
+  tail -f /var/log/cron.log
+done