From 33ebfab205420318163460e9ed15d16b086eee64 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Fri, 19 Aug 2016 16:56:38 -0700
Subject: [PATCH] validation and strace based provenance

---
 Dockerfile                           | 43 ++++++++++++++++++++--------
 run.py                               |  2 +-
 validation_and_provenance_wrapper.sh | 13 +++++++++
 3 files changed, 45 insertions(+), 13 deletions(-)
 create mode 100644 validation_and_provenance_wrapper.sh

diff --git a/Dockerfile b/Dockerfile
index a8c9fd6..5141409 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,16 +1,37 @@
 FROM ubuntu:16.04
 
-# Enable NeuroDebian repository (if needed)
+# Common for all BIDS Apps
+
+## Install the validator
+RUN apt-get update && apt-get install -y curl
+RUN curl -sL https://deb.nodesource.com/setup_4.x | bash -
+RUN apt-get install -y nodejs
+RUN npm install -g bids-validator
+
+## Install strace
+RUN apt-get install -y build-essential wget
+RUN  wget "http://downloads.sourceforge.net/project/strace/strace/4.13/strace-4.13.tar.xz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fstrace%2F&ts=1471646564&use_mirror=pilotfiber" -O strace.tar.xz && \
+	tar xvf strace.tar.xz && \
+	cd strace-4.13 && \
+	./configure &&\
+	make &&\
+	make install &&\
+	rm -rf \strace-4.13
+
+## Create copy the validation_and_provenance_wrapper wrapper
+RUN mkdir -p /code
+COPY validation_and_provenance_wrapper.sh /code/validation_and_provenance_wrapper.sh
+
+# Specific to each BIDS App
+## Install FSL
 RUN apt-get update \
     && DEBIAN_FRONTEND=noninteractive \
        NEURODEBIAN_ENABLE=yes NEURODEBIAN_MIRROR=origin NEURODEBIAN_FLAVOR=full NEURODEBIAN_UPDATE=0 \
        apt-get install -y neurodebian
-
-# Run apt-get calls
 RUN apt-get update \
     && apt-get install -y fsl-5.0-core
 
-# Configure environment
+## Configure FSL
 ENV FSLDIR=/usr/share/fsl/5.0
 ENV FSLOUTPUTTYPE=NIFTI_GZ
 ENV PATH=/usr/lib/fsl/5.0:$PATH
@@ -21,15 +42,13 @@ ENV FSLTCLSH=/usr/bin/tclsh
 ENV FSLWISH=/usr/bin/wish
 ENV FSLOUTPUTTYPE=NIFTI_GZ
 
-RUN apt-get install -y python3
-RUN apt-get install -y python3-pip
+## Isntall nibabel
+RUN apt-get install -y python3 python3-pip
 RUN pip3 install nibabel
-RUN mkdir -p /code
 
-RUN mkdir /oasis
-RUN mkdir /projects
-RUN mkdir /scratch
-RUN mkdir /local-scratch
+## Copy your entrypoint script
 COPY run.py /code/run.py
+RUN chmod +x /code/run.py
 
-ENTRYPOINT ["/code/run.py"]
+## Define
+ENTRYPOINT ["/code/validation_and_provenance_wrapper.sh", "/code/run.py"]
diff --git a/run.py b/run.py
index d148663..1b50f75 100755
--- a/run.py
+++ b/run.py
@@ -43,7 +43,7 @@
         for T1_file in glob(os.path.join(args.bids_dir, "sub-%s"%subject_label,
                                          "anat", "*_T1w.nii*")) + glob(os.path.join(args.bids_dir,"sub-%s"%subject_label,"ses-*","anat", "*_T1w.nii*")):
             out_file = os.path.split(T1_file)[-1].replace("_T1w.", "_brain.")
-            cmd = "bet %s %s"%(T1_file, os.path.join(args.output_dir, out_file))
+            cmd = "bet %s %s -f 0.7"%(T1_file, os.path.join(args.output_dir, out_file))
             print(cmd)
             subprocess.run(cmd, shell=True, check=True)
 
diff --git a/validation_and_provenance_wrapper.sh b/validation_and_provenance_wrapper.sh
new file mode 100644
index 0000000..88ac70a
--- /dev/null
+++ b/validation_and_provenance_wrapper.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+set -e
+if [ "$#" -ge 4 ]; then
+    bids-validator $2
+		strace -r -s4096 -e trace=execve -fto $3/provenance.txt $1 ${@:2}
+		#reprozip trace -d $3/provenance $1 ${@:2}
+		#reprounzip graph -d $3/provenance --json $3/provenance/graph.json
+		#reprounzip graph -d $3/provenance --dot $3/provenance/graph.dot
+		#reprounzip graph -d $3/provenance --packages drop --otherfiles io --processes run --dot $3/provenance/graph_simplified.dot
+		#dot -Tpng $3/provenance/graph_simplified.dot -o $3/provenance/graph_simplified.png
+	else
+		$1 ${@:2}
+fi