From a076355d8087a2020e6e75bcd74f4d6c2f8d80a4 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@mit.edu>
Date: Mon, 17 Dec 2018 18:08:32 -0500
Subject: [PATCH 1/5] wip: dicom receiver

---
 docker-compose.yml | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 docker-compose.yml

diff --git a/docker-compose.yml b/docker-compose.yml
new file mode 100644
index 0000000..c95c27a
--- /dev/null
+++ b/docker-compose.yml
@@ -0,0 +1,9 @@
+version: '3'
+services:
+  dcm-receiver:
+    image: mgxd/dcmrecv:latest
+    ports:
+      - "8080:8080"
+    volumes:
+      - ./dicoms:/dicoms
+    command: storescp -v --output-directory /dicoms 8080

From b4e285dc60a1a0abd05ad928054c40fe63fbe2fb Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@mit.edu>
Date: Fri, 21 Dec 2018 12:51:02 -0500
Subject: [PATCH 2/5] enh: heudiconv cronjob

---
 .env               |  6 ++++++
 cron/Dockerfile    | 14 ++++++++++++++
 cron/heudiconv.sh  | 28 ++++++++++++++++++++++++++++
 cron/heudicron     |  4 ++++
 cron/start-cron    |  9 +++++++++
 dcmrecv/Dockerfile | 10 ++++++++++
 dcmrecv/README.md  |  4 ++++
 docker-compose.yml | 16 +++++++++++++---
 8 files changed, 88 insertions(+), 3 deletions(-)
 create mode 100644 .env
 create mode 100644 cron/Dockerfile
 create mode 100644 cron/heudiconv.sh
 create mode 100644 cron/heudicron
 create mode 100644 cron/start-cron
 create mode 100644 dcmrecv/Dockerfile
 create mode 100644 dcmrecv/README.md

diff --git a/.env b/.env
new file mode 100644
index 0000000..780fc08
--- /dev/null
+++ b/.env
@@ -0,0 +1,6 @@
+# environment variables for `docker-compose`
+DICOMDIR=./dicoms
+PORT=8080
+HEUDICONV_OUTDIR=./output
+# args used: --files, -f, -o, -b
+HEUDICONV_XARGS=""
diff --git a/cron/Dockerfile b/cron/Dockerfile
new file mode 100644
index 0000000..42581ac
--- /dev/null
+++ b/cron/Dockerfile
@@ -0,0 +1,14 @@
+FROM nipy/heudiconv:latest
+
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends cron \
+    && apt-get clean
+
+COPY heudicron /etc/cron.d/heudicron
+COPY heudiconv.sh start-cron /
+
+RUN chmod +x /heudiconv.sh /start-cron \
+    && chmod 0644 /etc/cron.d/heudicron \
+    && touch /var/log/cron.log
+
+ENTRYPOINT ["/start-cron"]
diff --git a/cron/heudiconv.sh b/cron/heudiconv.sh
new file mode 100644
index 0000000..71cf4b4
--- /dev/null
+++ b/cron/heudiconv.sh
@@ -0,0 +1,28 @@
+#!/bin/bash
+
+HEUDICONV_DICOMDIR="/dicoms"
+HEUDICONV_OUTDIR="/output"
+HEUDICONV_XARGS=${HEUDICONV_XARGS:-""}
+HEUDICONV_HISTORY="${HEUDICONV_OUTDIR}/.heudiconv.history"
+
+set -eu
+
+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 ${HEUDICONV_DICOMDIR}); do
+   if grep "${DICOMS}" ${HEUDICONV_HISTORY} > /dev/null; then
+      # existing conversion was found
+      continue
+   fi
+
+   CMD="heudiconv -f reproin --bids --datalad -o ${HEUDICONV_OUTDIR}/${DICOMS} --files ${HEUDICONV_DICOMDIR}/${DICOMS} ${HEUDICONV_XARGS}"
+   ${CMD}
+done
diff --git a/cron/heudicron b/cron/heudicron
new file mode 100644
index 0000000..8597ce8
--- /dev/null
+++ b/cron/heudicron
@@ -0,0 +1,4 @@
+# key: min (0-59) | hr (0-23) | dom (1-31) | mon (1-12) | dow (0,7=sun) | command
+
+# trigger heudiconv every day at 4am
+2 * * * * /heudiconv.sh >> /var/log/cron.log
diff --git a/cron/start-cron b/cron/start-cron
new file mode 100644
index 0000000..8cde482
--- /dev/null
+++ b/cron/start-cron
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+service cron start
+
+CRONLOG="/var/log/cron.log"
+
+while true; do
+  tail -f /var/log/cron.log
+done
diff --git a/dcmrecv/Dockerfile b/dcmrecv/Dockerfile
new file mode 100644
index 0000000..0ede2c2
--- /dev/null
+++ b/dcmrecv/Dockerfile
@@ -0,0 +1,10 @@
+FROM debian:stretch
+
+ARG DEBIAN_FRONTEND="noninteractive"
+
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends ca-certificates apt-utils dcmtk \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+WORKDIR /dicoms
diff --git a/dcmrecv/README.md b/dcmrecv/README.md
new file mode 100644
index 0000000..6956dce
--- /dev/null
+++ b/dcmrecv/README.md
@@ -0,0 +1,4 @@
+# docker-compose up to start application
+
+# dcm-receiver app will launch docker container running storescp
+# listening for DICOMs on port 8080 and saving to an output directory
diff --git a/docker-compose.yml b/docker-compose.yml
index c95c27a..39909c5 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -3,7 +3,17 @@ services:
   dcm-receiver:
     image: mgxd/dcmrecv:latest
     ports:
-      - "8080:8080"
+      - "${PORT}:${PORT}"
     volumes:
-      - ./dicoms:/dicoms
-    command: storescp -v --output-directory /dicoms 8080
+      - ${DICOMDIR}:/dicoms
+    command: storescp -v -sp --output-directory /dicoms ${PORT}
+
+  heudiconv:
+    build: ./cron
+    volumes:
+      - ${DICOMDIR}:/dicoms:ro
+      - ${HEUDICONV_OUTDIR}:/output
+    depends_on:
+      - dcm-receiver
+    command:
+      - /start-cron

From 6f10f02437b2e47bc0d81fabc11469ec4354dbbb Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@mit.edu>
Date: Mon, 24 Dec 2018 06:04:47 -0500
Subject: [PATCH 3/5] enh+doc: docker-compose listener + converter

---
 .env               | 12 +++++++++++-
 README.md          | 17 +++++++++++++++++
 cron/Dockerfile    | 18 +++++++++++-------
 cron/heudiconv.sh  | 14 ++++++++++++--
 cron/start-cron    |  2 ++
 docker-compose.yml |  4 +---
 6 files changed, 54 insertions(+), 13 deletions(-)

diff --git a/.env b/.env
index 780fc08..c71416f 100644
--- a/.env
+++ b/.env
@@ -1,6 +1,16 @@
-# environment variables for `docker-compose`
+# 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=""
diff --git a/README.md b/README.md
index 899fd6f..cb507b3 100644
--- a/README.md
+++ b/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
diff --git a/cron/Dockerfile b/cron/Dockerfile
index 42581ac..e22192d 100644
--- a/cron/Dockerfile
+++ b/cron/Dockerfile
@@ -1,14 +1,18 @@
 FROM nipy/heudiconv:latest
 
 RUN apt-get update -qq \
-    && apt-get install -y -q --no-install-recommends cron \
+    && apt-get install -y -qq --no-install-recommends cron \
     && apt-get clean
 
-COPY heudicron /etc/cron.d/heudicron
-COPY heudiconv.sh start-cron /
+RUN git config --global user.email "user@heudiconv" \
+    && git config --global user.name "heudiconv-erter"
 
-RUN chmod +x /heudiconv.sh /start-cron \
-    && chmod 0644 /etc/cron.d/heudicron \
-    && touch /var/log/cron.log
+COPY heudiconv.sh /
 
-ENTRYPOINT ["/start-cron"]
+# 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
diff --git a/cron/heudiconv.sh b/cron/heudiconv.sh
index 71cf4b4..5c78584 100644
--- a/cron/heudiconv.sh
+++ b/cron/heudiconv.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+echo "Running scheduled heudiconv conversion"
+
 HEUDICONV_DICOMDIR="/dicoms"
 HEUDICONV_OUTDIR="/output"
 HEUDICONV_XARGS=${HEUDICONV_XARGS:-""}
@@ -7,6 +9,13 @@ HEUDICONV_HISTORY="${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
@@ -18,11 +27,12 @@ elif [ ! -f ${HEUDICONV_HISTORY} ]; then
 fi
 
 for DICOMS in $(ls ${HEUDICONV_DICOMDIR}); do
-   if grep "${DICOMS}" ${HEUDICONV_HISTORY} > /dev/null; then
+   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 ${HEUDICONV_OUTDIR}/${DICOMS} --files ${HEUDICONV_DICOMDIR}/${DICOMS} ${HEUDICONV_XARGS}"
+   CMD="heudiconv -f reproin --bids --datalad -o ${HEUDICONV_OUTDIR} --files ${HEUDICONV_DICOMDIR}/${DICOMS} ${HEUDICONV_XARGS}"
    ${CMD}
+   printf "${DICOMS}\t$(date)\n" >> ${HEUDICONV_HISTORY}
 done
diff --git a/cron/start-cron b/cron/start-cron
index 8cde482..9019a31 100644
--- a/cron/start-cron
+++ b/cron/start-cron
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+crontab /etc/heudicron
+
 service cron start
 
 CRONLOG="/var/log/cron.log"
diff --git a/docker-compose.yml b/docker-compose.yml
index 39909c5..a92f032 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,7 +1,7 @@
 version: '3'
 services:
   dcm-receiver:
-    image: mgxd/dcmrecv:latest
+    build: ./dcmrecv
     ports:
       - "${PORT}:${PORT}"
     volumes:
@@ -15,5 +15,3 @@ services:
       - ${HEUDICONV_OUTDIR}:/output
     depends_on:
       - dcm-receiver
-    command:
-      - /start-cron

From fec3c2d81311042c211021ef27e651ba08d9a8ab Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@mit.edu>
Date: Sat, 19 Jan 2019 15:24:07 -0500
Subject: [PATCH 4/5] FIX+DOC: cronjob timing, basic documentation

---
 {cron => heudicron}/Dockerfile   | 0
 heudicron/README.md              | 5 +++++
 {cron => heudicron}/heudiconv.sh | 0
 {cron => heudicron}/heudicron    | 4 ++--
 {cron => heudicron}/start-cron   | 0
 5 files changed, 7 insertions(+), 2 deletions(-)
 rename {cron => heudicron}/Dockerfile (100%)
 create mode 100644 heudicron/README.md
 rename {cron => heudicron}/heudiconv.sh (100%)
 rename {cron => heudicron}/heudicron (50%)
 rename {cron => heudicron}/start-cron (100%)

diff --git a/cron/Dockerfile b/heudicron/Dockerfile
similarity index 100%
rename from cron/Dockerfile
rename to heudicron/Dockerfile
diff --git a/heudicron/README.md b/heudicron/README.md
new file mode 100644
index 0000000..745236b
--- /dev/null
+++ b/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.
diff --git a/cron/heudiconv.sh b/heudicron/heudiconv.sh
similarity index 100%
rename from cron/heudiconv.sh
rename to heudicron/heudiconv.sh
diff --git a/cron/heudicron b/heudicron/heudicron
similarity index 50%
rename from cron/heudicron
rename to heudicron/heudicron
index 8597ce8..376e19d 100644
--- a/cron/heudicron
+++ b/heudicron/heudicron
@@ -1,4 +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 4am
-2 * * * * /heudiconv.sh >> /var/log/cron.log
+# trigger heudiconv every day at 3am
+* 3 * * * /heudiconv.sh >> /var/log/cron.log
diff --git a/cron/start-cron b/heudicron/start-cron
similarity index 100%
rename from cron/start-cron
rename to heudicron/start-cron

From a78524a578aabd8ed44cb32d89358b0b8b871ab1 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@mit.edu>
Date: Sat, 19 Jan 2019 15:25:30 -0500
Subject: [PATCH 5/5] FIX: update build path

---
 docker-compose.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker-compose.yml b/docker-compose.yml
index a92f032..b817ec0 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -9,7 +9,7 @@ services:
     command: storescp -v -sp --output-directory /dicoms ${PORT}
 
   heudiconv:
-    build: ./cron
+    build: ./heudicron
     volumes:
       - ${DICOMDIR}:/dicoms:ro
       - ${HEUDICONV_OUTDIR}:/output