Merge pull request #209 from mgxd/fix/docker

fail descriptively when cmdline specification is wrong
redo conversion if heuristic has changed

Author: yarikoptic

Dockerfile

@@ -5,7 +5,7 @@
 # pull request on our GitHub repository:
 #     https://github.com/kaczmarj/neurodocker
 #
-# Timestamp: 2018-02-02 16:32:55
+# Timestamp: 2018-05-14 16:30:58
 
 FROM debian:stretch
 
@@ -32,27 +32,48 @@ RUN apt-get update -qq && apt-get install -yq --no-install-recommends  \
     && chmod -R 777 /neurodocker && chmod a+s /neurodocker
 ENTRYPOINT ["/neurodocker/startup.sh"]
 
-RUN apt-get update -qq \
-    && apt-get install -y -q --no-install-recommends git \
-                                                     gcc \
-                                                     pigz \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
 #------------------------
-# Install dcm2niix v1.0.20171215
+# Install dcm2niix v1.0.20180328
 #------------------------
 WORKDIR /tmp
 RUN deps='cmake g++ gcc git make pigz zlib1g-dev' \
     && apt-get update -qq && apt-get install -yq --no-install-recommends $deps \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
     && mkdir dcm2niix \
-    && curl -sSL https://github.com/rordenlab/dcm2niix/tarball/v1.0.20171215 | tar xz -C dcm2niix --strip-components 1 \
+    && curl -sSL https://github.com/rordenlab/dcm2niix/tarball/v1.0.20180328 | tar xz -C dcm2niix --strip-components 1 \
     && mkdir dcm2niix/build && cd dcm2niix/build \
     && cmake .. && make \
     && make install \
-    && rm -rf /tmp/*
+    && rm -rf /tmp/* \
+    && apt-get purge -y --auto-remove $deps
+
+#--------------------------------------------------
+# Add NeuroDebian repository
+# Please note that some packages downloaded through
+# NeuroDebian may have restrictive licenses.
+#--------------------------------------------------
+RUN apt-get update -qq && apt-get install -yq --no-install-recommends dirmngr gnupg \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
+    && curl -sSL http://neuro.debian.net/lists/stretch.us-nh.full \
+    > /etc/apt/sources.list.d/neurodebian.sources.list \
+    && curl -sSL https://dl.dropbox.com/s/zxs209o955q6vkg/neurodebian.gpg \
+    | apt-key add - \
+    && (apt-key adv --refresh-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 || true) \
+    && apt-get update
+
+# Install NeuroDebian packages
+RUN apt-get update -qq && apt-get install -yq --no-install-recommends git-annex-standalone \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends git \
+                                                     gcc \
+                                                     pigz \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 COPY [".", "/src/heudiconv"]
 
@@ -83,26 +104,6 @@ RUN conda create -y -q --name neuro python=2 \
     && sync \
     && sed -i '$isource activate neuro' $ND_ENTRYPOINT
 
-#--------------------------------------------------
-# Add NeuroDebian repository
-# Please note that some packages downloaded through
-# NeuroDebian may have restrictive licenses.
-#--------------------------------------------------
-RUN apt-get update -qq && apt-get install -yq --no-install-recommends dirmngr gnupg \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
-    && curl -sSL http://neuro.debian.net/lists/stretch.us-nh.full \
-    > /etc/apt/sources.list.d/neurodebian.sources.list \
-    && curl -sSL https://dl.dropbox.com/s/zxs209o955q6vkg/neurodebian.gpg \
-    | apt-key add - \
-    && (apt-key adv --refresh-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 || true) \
-    && apt-get update
-
-# Install NeuroDebian packages
-RUN apt-get update -qq && apt-get install -yq --no-install-recommends git-annex-standalone \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
 ENTRYPOINT ["/neurodocker/startup.sh", "heudiconv"]
 
 #--------------------------------------
@@ -117,6 +118,20 @@ RUN echo '{ \
     \n      "debian:stretch" \
     \n    ], \
     \n    [ \
+    \n      "dcm2niix", \
+    \n      { \
+    \n        "version": "v1.0.20180328" \
+    \n      } \
+    \n    ], \
+    \n    [ \
+    \n      "neurodebian", \
+    \n      { \
+    \n        "os_codename": "stretch", \
+    \n        "download_server": "usa-nh", \
+    \n        "pkgs": "git-annex-standalone" \
+    \n      } \
+    \n    ], \
+    \n    [ \
     \n      "install", \
     \n      [ \
     \n        "git", \
@@ -125,12 +140,6 @@ RUN echo '{ \
     \n      ] \
     \n    ], \
     \n    [ \
-    \n      "dcm2niix", \
-    \n      { \
-    \n        "version": "v1.0.20171215" \
-    \n      } \
-    \n    ], \
-    \n    [ \
     \n      "copy", \
     \n      [ \
     \n        ".", \
@@ -142,23 +151,15 @@ RUN echo '{ \
     \n      { \
     \n        "env_name": "neuro", \
     \n        "conda_install": "python=2 traits=4.6.0", \
-    \n        "pip_install": "https://github.com/moloney/dcmstack/tarball/master /src/heudiconv[all]", \
-    \n        "activate": true \
-    \n      } \
-    \n    ], \
-    \n    [ \
-    \n      "neurodebian", \
-    \n      { \
-    \n        "os_codename": "stretch", \
-    \n        "download_server": "usa-nh", \
-    \n        "pkgs": "git-annex-standalone" \
+    \n        "activate": true, \
+    \n        "pip_install": "https://github.com/moloney/dcmstack/tarball/master /src/heudiconv[all]" \
     \n      } \
     \n    ], \
     \n    [ \
     \n      "entrypoint", \
     \n      "/neurodocker/startup.sh heudiconv" \
     \n    ] \
     \n  ], \
-    \n  "generation_timestamp": "2018-02-02 16:32:55", \
+    \n  "generation_timestamp": "2018-05-14 16:30:58", \
     \n  "neurodocker_version": "0.3.2" \
     \n}' > /neurodocker/neurodocker_specs.json

heudiconv/cli/run.py

@@ -99,6 +99,11 @@ def process_extra_commands(outdir, args):
 def main(argv=None):
     parser = get_parser()
     args = parser.parse_args(argv)
+    # exit if nothing to be done
+    if not args.files and not args.dicom_dir_template and not args.command:
+        lgr.warning("Nothing to be done - displaying usage help")
+        parser.print_help()
+        sys.exit(1)
     # To be done asap so anything random is deterministic
     if args.random_seed is not None:
         import random
@@ -237,6 +242,9 @@ def process_args(args):
     #
     # Load heuristic -- better do it asap to make sure it loads correctly
     #
+    if not args.heuristic:
+        raise RuntimeError("No heuristic specified - add to arguments and rerun")
+
     heuristic = load_heuristic(args.heuristic)
 
     study_sessions = get_study_sessions(args.dicom_dir_template, args.files,

heudiconv/convert.py

@@ -115,6 +115,7 @@ def prep_conversion(sid, dicoms, outdir, heuristic, converter, anon_sid,
 
     # if conversion table(s) do not exist -- we need to prepare them
     # (the *prepare* stage in https://github.com/nipy/heudiconv/issues/134)
+    # if overwrite - recalculate this anyways
     reuse_conversion_table = op.exists(edit_file)
     # We also might need to redo it if changes in the heuristic file
     # detected
@@ -125,17 +126,15 @@ def prep_conversion(sid, dicoms, outdir, heuristic, converter, anon_sid,
     #  1. add a test
     #  2. possibly extract into a dedicated function for easier logic flow here
     #     and a dedicated unittest
-    if not reuse_conversion_table and \
-        op.exists(target_heuristic_filename) and \
-        file_md5sum(target_heuristic_filename) != file_md5sum(heuristic.filename):
+    if (op.exists(target_heuristic_filename) and
+        file_md5sum(target_heuristic_filename) != file_md5sum(heuristic.filename)):
+        # remake conversion table
         reuse_conversion_table = False
         lgr.info(
             "Will not reuse existing conversion table files because heuristic "
             "has changed"
         )
 
-    # MG - maybe add an option to force rerun?
-    # related issue : https://github.com/nipy/heudiconv/issues/84
     if reuse_conversion_table:
         lgr.info("Reloading existing filegroup.json "
                  "because %s exists", edit_file)

heudiconv/external/pydicom.py

@@ -4,8 +4,8 @@
 
 # 1.0.0 of pydicom renamed module from dicom to pydicom
 try:
-    # for pydicom < 1.0
-    import dicom as dcm
-except ImportError:
     # pydicom >= 1.0
     import pydicom as dcm
+except ImportError:
+    # for pydicom < 1.0
+    import dicom as dcm

tests/test_heuristics.py

@@ -24,12 +24,17 @@
 
 # this will fail if not in project's root directory
 def test_smoke_convertall(tmpdir):
-    runner(
-        ("-f convertall -c dcm2niix -o %s -b --datalad "
-         "-s fmap_acq-3mm -d %s/{subject}/*"
-         % (tmpdir, TESTS_DATA_PATH)
-        ).split(' ')
-    )
+    args = ("-c dcm2niix -o %s -b --datalad "
+     "-s fmap_acq-3mm -d %s/{subject}/*"
+     % (tmpdir, TESTS_DATA_PATH)
+    ).split(' ')
+
+    # complain if no heurisitic
+    with pytest.raises(RuntimeError):
+        runner(args)
+
+    args.extend(['-f', 'convertall'])
+    runner(args)
 
 
 @pytest.mark.parametrize('heuristic', ['reproin', 'convertall'])

utils/gen-docker-image.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+set -eu
+
+VER=$(grep -Po '(?<=^__version__ = ).*' ../heudiconv/info.py | sed 's/"//g')
+
+docker run --rm kaczmarj/neurodocker:v0.3.2 generate -b debian:stretch -p apt \
+    --dcm2niix version=v1.0.20180328 \
+    --neurodebian os_codename=stretch download_server=usa-nh pkgs=git-annex-standalone \
+    --install git gcc pigz \
+    --copy . /src/heudiconv \
+    --miniconda env_name=neuro conda_install="python=2 traits=4.6.0" activate=True \
+      pip_install="https://github.com/moloney/dcmstack/tarball/master /src/heudiconv[all]" \
+    --entrypoint "/neurodocker/startup.sh heudiconv" \
+> ../Dockerfile