Merge pull request #78 from miykael/handle_crashes

Catch crashes, instead of flagging `CRASH`

Author: miykael

Dockerfile

@@ -5,7 +5,7 @@
 # pull request on our GitHub repository:
 #     https://github.com/kaczmarj/neurodocker
 #
-# Timestamp: 2018-04-23 18:54:53
+# Timestamp: 2018-05-07 20:43:57
 
 FROM neurodebian:stretch-non-free
 
@@ -143,7 +143,7 @@ RUN mkdir /output && chmod 777 /output && chmod a+s /output
 USER neuro
 
 # User-defined BASH instruction
-RUN bash -c "source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && datalad get -r sub-01/ses-test/anat sub-01/ses-test/func/*fingerfootlips*"
+RUN bash -c "source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && datalad update -r && datalad get -r sub-01/ses-test/anat sub-01/ses-test/func/*fingerfootlips*"
 
 # User-defined BASH instruction
 RUN bash -c "curl -L https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/580705089ad5a101f17944a9 -o /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz && tar xf /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz -C /data/ds000114/derivatives/fmriprep/. && rm /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz && find /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c -type f -not -name ?mm_T1.nii.gz -not -name ?mm_brainmask.nii.gz -not -name ?mm_tpm*.nii.gz -delete"
@@ -249,7 +249,7 @@ RUN echo '{ \
     \n    ], \
     \n    [ \
     \n      "run_bash", \
-    \n      "source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && datalad get -r sub-01/ses-test/anat sub-01/ses-test/func/*fingerfootlips*" \
+    \n      "source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && datalad update -r && datalad get -r sub-01/ses-test/anat sub-01/ses-test/func/*fingerfootlips*" \
     \n    ], \
     \n    [ \
     \n      "run_bash", \
@@ -289,6 +289,6 @@ RUN echo '{ \
     \n      ] \
     \n    ] \
     \n  ], \
-    \n  "generation_timestamp": "2018-04-23 18:54:53", \
+    \n  "generation_timestamp": "2018-05-07 20:43:57", \
     \n  "neurodocker_version": "0.3.2" \
     \n}' > /neurodocker/neurodocker_specs.json

create_dockerfile.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-docker run --rm kaczmarj/neurodocker:master generate -b neurodebian:stretch-non-free -p apt \
+docker run --rm kaczmarj/neurodocker:v0.3.2 generate -b neurodebian:stretch-non-free -p apt \
 --install convert3d ants fsl gcc g++ graphviz tree \
           git-annex-standalone vim emacs-nox nano less ncdu \
           tig git-annex-remote-rclone octave \
@@ -21,7 +21,7 @@ docker run --rm kaczmarj/neurodocker:master generate -b neurodebian:stretch-non-
 --run 'mkdir /data && chmod 777 /data && chmod a+s /data' \
 --run 'mkdir /output && chmod 777 /output && chmod a+s /output' \
 --user=neuro \
---run-bash 'source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && datalad get -r sub-01/ses-test/anat sub-01/ses-test/func/*fingerfootlips*' \
+--run-bash 'source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && datalad update -r && datalad get -r sub-01/ses-test/anat sub-01/ses-test/func/*fingerfootlips*' \
 --run-bash 'curl -L https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/580705089ad5a101f17944a9 -o /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz && tar xf /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz -C /data/ds000114/derivatives/fmriprep/. && rm /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz && find /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c -type f -not -name ?mm_T1.nii.gz -not -name ?mm_brainmask.nii.gz -not -name ?mm_tpm*.nii.gz -delete' \
 --copy . "/home/neuro/nipype_tutorial" \
 --user=root \

notebooks/advanced_create_interfaces.ipynb

@@ -45,7 +45,7 @@
     "      <td style=\"text-align:left\">Do not have inputs/outputs, but expose them from the interfaces wrapped inside</td>\n",
     "    </tr>\n",
     "    <tr>\n",
-    "      <td style=\"text-align:left\">Do not cache results (unless you use [interface caching](http://nipype.readthedocs.io/en/latest/users/caching_tutorial.html))</td>\n",
+    "      <td style=\"text-align:left\">Do not cache results (unless you use [interface caching](advanced_interfaces_caching.ipynb))</td>\n",
     "      <td style=\"text-align:left\">Cache results</td>\n",
     "    </tr>\n",
     "    <tr>\n",
@@ -383,7 +383,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "TransformInfo().cmdline  # This will CRASH"
+    "try:\n",
+    "    TransformInfo().cmdline\n",
+    "\n",
+    "except(ValueError) as err:\n",
+    "    print('It crashed with...')\n",
+    "    print(\"ValueError:\", err)\n",
+    "else:\n",
+    "    raise"
    ]
   },
   {
@@ -399,7 +406,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "my_info_interface.inputs.in_file = 'idontexist.tfm'  # This will CRASH, too"
+    "try:\n",
+    "    my_info_interface.inputs.in_file = 'idontexist.tfm'\n",
+    "\n",
+    "except(Exception) as err:\n",
+    "    print('It crashed with...')\n",
+    "    print(\"TraitError:\", err)\n",
+    "else:\n",
+    "    raise"
    ]
   },
   {
@@ -928,9 +942,23 @@
    "source": [
     "will_fail_at_run = TranslateImage(\n",
     "    in_file='/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz',\n",
-    "    out_file='translated.nii.gz')\n",
+    "    out_file='translated.nii.gz')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "try:\n",
+    "    result = will_fail_at_run.run()\n",
     "\n",
-    "result = will_fail_at_run.run()  # This will CRASH"
+    "except(NotImplementedError) as err:\n",
+    "    print('It crashed with...')\n",
+    "    print(\"NotImplementedError:\", err)\n",
+    "else:\n",
+    "    raise"
    ]
   },
   {
@@ -978,9 +1006,23 @@
    "source": [
     "half_works = TranslateImage(\n",
     "    in_file='/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz',\n",
-    "    out_file='translated_nipype.nii.gz')\n",
+    "    out_file='translated_nipype.nii.gz')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "try:\n",
+    "    result = half_works.run()\n",
     "\n",
-    "result = half_works.run()  # This will CRASH, too"
+    "except(NotImplementedError) as err:\n",
+    "    print('It crashed with...')\n",
+    "    print(\"NotImplementedError:\", err)\n",
+    "else:\n",
+    "    raise"
    ]
   },
   {

test_notebooks.py

@@ -30,7 +30,7 @@ def _notebook_run(path):
             ep.preprocess(nb, {'metadata': {'path': this_file_directory}})
 
         except CellExecutionError as e:
-            if "TAB" in e.traceback or "CRASH" in e.traceback:
+            if "TAB" in e.traceback:
                 print(str(e.traceback).split("\n")[-2])
             else:
                 raise e
@@ -85,9 +85,9 @@ def reduce_notebook_load(path):
 Dir_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), "notebooks")
 
 @pytest.mark.parametrize("notebook",
-                         glob(os.path.join(Dir_path, "introduction_*.ipynb")) +
-                         glob(os.path.join(Dir_path, "basic*.ipynb")) +
-                         glob(os.path.join(Dir_path, "advanced*.ipynb")) +
+                         sorted(glob(os.path.join(Dir_path, "introduction_*.ipynb"))) +
+                         sorted(glob(os.path.join(Dir_path, "basic*.ipynb"))) +
+                         sorted(glob(os.path.join(Dir_path, "advanced*.ipynb"))) +
                          [os.path.join(Dir_path, "example_preprocessing.ipynb"),
                           os.path.join(Dir_path, "example_1stlevel.ipynb"),
                           os.path.join(Dir_path, "example_normalize.ipynb"),