running example Error: Node Shape_tables.a1 failed to run on host xxx && UnicodeEncodeError

[locta66]

running sudo docker run --rm -ti -v $HOST:$DOCK nipy/mindboggle mindboggle123 $IMAGE --id $ID

error info：

File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/plugins/tools.py", line 72, in report_crash
crash2txt(crashfile, dict(node=node, traceback=traceback))
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/utils/filemanip.py", line 753, in crash2txt
fp.write('Node inputs:\n{}\n'.format(node.inputs))
UnicodeEncodeError: 'ascii' codec can't encode character '\u2019' in position 524657: ordinal not in range(128)
Return code: 1

while output in the start of running it seems I have a correct version. according to #175 , I follow #188 to get image from another docker hub but the same error occurred.

Running nipype version 1.2.3 (latest: 1.2.3)
Running mindboggle version 1.3.7 (latest: 1.3.7)

[jling-NM]

Also having possible regression of #175.

Command list:
docker pull nipy/mindboggle
Running nipype version 1.2.3 (latest: 1.2.3)
Running mindboggle version 1.3.7 (latest: 1.3.7)

HOST=/na/homes/jling
DOCK=/home/jovyan/work
ID=arno
docker run --rm -ti -v $HOST:$DOCK -p 5000:5000 nipy/mindboggle

DOCK=/home/jovyan/work
ID=arno
EXAMPLE=$DOCK/mindboggle_input_example
FREESURFER_SUBJECT=$EXAMPLE/freesurfer/subjects/arno
ANTS_SUBJECT=$EXAMPLE/ants/subjects/arno
OUT=$DOCK/mindboggled

This works without error:
mindboggle $FREESURFER_SUBJECT --out $OUT
--ants $ANTS_SUBJECT/antsBrainSegmentation.nii.gz
--no_surfaces

If I remove the '--no_surfaces' flag i get an error:
root@58643bb86042:~# mindboggle $FREESURFER_SUBJECT --out $OUT --ants $ANTS_SUBJECT/antsBrainSegmentation.nii.gz

Compute area and index-normalized linear FEM Laplace-Beltrami spectrum
249 vertices for label 1032
Compute area and index-normalized linear FEM Laplace-Beltrami spectrum
191014-17:58:13,111 nipype.workflow INFO:
[Node] Finished "Mindboggle.Surface_feature_shapes.Spectra_labels".
191014-17:58:13,112 nipype.workflow INFO:
[Node] Setting-up "Mindboggle.Surface_features.Sulci" in "/home/jovyan/work/mindboggled/working/arno/Mindboggle/Surface_features/_hemi_lh/Sulci".
191014-17:58:15,8 nipype.workflow ERROR:
Node Sulci.a0 failed to run on host 58643bb86042.
191014-17:58:15,10 nipype.workflow ERROR:
Saving crash info to /root/crash-20191014-175815-root-Sulci.a0-a964b9c5-a4d8-42aa-a89b-eb5cd9366acf.txt
Traceback (most recent call last):
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 48, in run
node.run(updatehash=updatehash)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 474, in run
write_node_report(self, is_mapnode=isinstance(self, MapNode))
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py", line 139, in write_node_report
report_file.write_text('\n'.join(lines))
File "/opt/miniconda-latest/envs/mb/lib/python3.6/pathlib.py", line 1216, in write_text
return f.write(data)
UnicodeEncodeError: 'ascii' codec can't encode character '\u2019' in position 495941: ordinal not in range(128)

[locta66]

@jling-NM using the commands you provided, I encountered similar errors, while the first error is occurred by Node Shape_tables.a1 failed to run on host 1760134c2830. , then it goes to save crash file and encountered a Unicode encode error.
It is strange for a software reporting error on example data, there must be something wrong! Do previous versions work well?

91015-05:13:17,473 nipype.workflow INFO:
[Node] Finished "Mindboggle.Vertex_table".
191015-05:13:17,475 nipype.workflow INFO:
[Node] Setting-up "Mindboggle.Shape_tables" in "/home/jovyan/work/mindboggled/working/arno/Mindboggle/_hemi_rh/Shape_tables".
191015-05:13:19,538 nipype.workflow ERROR:
Node Shape_tables.a1 failed to run on host 1760134c2830.
191015-05:13:19,540 nipype.workflow ERROR:
Saving crash info to /opt/crash-20191015-051319-root-Shape_tables.a1-12564d9b-63ed-4e58-803c-1ba5d026fcab.txt
Traceback (most recent call last):
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py", line 77, in save_hashfile
save_json(hashfile, hashed_inputs)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/utils/filemanip.py", line 673, in save_json
json.dump(data, fp, sort_keys=True, indent=4)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/init.py", line 298, in dump
for chunk in iterable:
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 684, in _iterencode
for chunk in _iterencode_list(o, _current_indent_level):
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 531, in _iterencode_list
for chunk in chunks:
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 531, in _iterencode_list
for chunk in chunks:
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 531, in _iterencode_list
for chunk in chunks:
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 716, in _iterencode
o = _default(o)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 273, in default
o.class.name)
TypeError: Object of type int64 is not JSON serializable
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 48, in run
node.run(updatehash=updatehash)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
_save_hashfile(hashfile_unfinished, self._hashed_inputs)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py", line 85, in save_hashfile
fd.writelines(str(hashed_inputs))
UnicodeEncodeError: 'ascii' codec can't encode character '\u2019' in position 0: ordinal not in range(128)

[jling-NM]

@locta66
I have not tried that. Interesting, however, that your error appears different than mine. Of course the UnicodeEncodeError that comes later is similar.

[binarybottle]

@locta66 and @jling-NM -- Thank you very much for alerting me to the errors you are receiving! I have reinstalled the newest version of Mindboggle and am running the same commands that both of you tried to see if I can replicate the error. I will get back to you with an update soon...

[binarybottle]

Indeed, I received the UnicodeEncodeError as well -- how strange! Let me look into this...

[binarybottle]

I am finding that I get an error when extracting sulci and when writing to the output shape tables.

Error when extracting sulci:
mindboggle $FREESURFER_SUBJECT --out $OUT --no_shapes

[Node] Setting-up "Mindboggle.Surface_features.Sulci" in "/home/jovyan/work/mindboggled/working/arno/Mindboggle/Surface_features/_hemi_rh/Sulci".
191022-02:14:07,127 nipype.workflow ERROR:
Node Sulci.a1 failed to run on host 7a2d47ca2e18.
191022-02:14:07,128 nipype.workflow ERROR:
Saving crash info to /opt/crash-20191022-021407-root-Sulci.a1-4a25c13c-1740-4fe9-a78a-d5a5f1d73bbd.txt
Traceback (most recent call last):
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 48, in run
node.run(updatehash=updatehash)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 474, in run
write_node_report(self, is_mapnode=isinstance(self, MapNode))
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py", line 139, in write_node_report
report_file.write_text('\n'.join(lines))
File "/opt/miniconda-latest/envs/mb/lib/python3.6/pathlib.py", line 1216, in write_text
return f.write(data)
UnicodeEncodeError: 'ascii' codec can't encode character '\u2019' in position 503044: ordinal not in range(128)

Error when writing to shape tables:
mindboggle $FREESURFER_SUBJECT --out $OUT --no_sulci

[Node] Setting-up "Mindboggle.Shape_tables" in "/home/jovyan/work/mindboggled/working/arno/Mindboggle/_hemi_rh/Shape_tables".
191022-01:52:09,463 nipype.workflow ERROR:
Node Shape_tables.a1 failed to run on host 7a2d47ca2e18.
191022-01:52:09,465 nipype.workflow ERROR:
Saving crash info to /opt/crash-20191022-015209-root-Shape_tables.a1-be269986-5126-4514-8005-9b11ceded8b0.txt
Traceback (most recent call last):
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py", line 77, in save_hashfile
save_json(hashfile, hashed_inputs)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/utils/filemanip.py", line 673, in save_json
json.dump(data, fp, sort_keys=True, indent=4)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/init.py", line 298, in dump
for chunk in iterable:
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 684, in _iterencode
for chunk in _iterencode_list(o, _current_indent_level):
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 531, in _iterencode_list
for chunk in chunks:
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 531, in _iterencode_list
for chunk in chunks:
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 531, in _iterencode_list
for chunk in chunks:
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 716, in _iterencode
o = _default(o)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 273, in default
o.class.name)
TypeError: Object of type int64 is not JSON serializable

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 48, in run
node.run(updatehash=updatehash)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
_save_hashfile(hashfile_unfinished, self._hashed_inputs)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py", line 85, in save_hashfile
fd.writelines(str(hashed_inputs))
UnicodeEncodeError: 'ascii' codec can't encode character '\u2019' in position 0: ordinal not in range(128)

@satra -- I am having trouble locating the underlying bug in Mindboggle. Usually such a UnicodeEncodeError is the result of an inappropriate str() call of an unicode object, but I'm not finding that in the code. The crash lines above point to non-mindboggle code. Do you have any suggestions?

[locta66]

I am finding that I get an error when extracting sulci and when writing to the output shape tables.

Error when extracting sulci:
mindboggle $FREESURFER_SUBJECT --out $OUT --no_shapes

[Node] Setting-up "Mindboggle.Surface_features.Sulci" in "/home/jovyan/work/mindboggled/working/arno/Mindboggle/Surface_features/_hemi_rh/Sulci".
191022-02:14:07,127 nipype.workflow ERROR:
Node Sulci.a1 failed to run on host 7a2d47ca2e18.
191022-02:14:07,128 nipype.workflow ERROR:
Saving crash info to /opt/crash-20191022-021407-root-Sulci.a1-4a25c13c-1740-4fe9-a78a-d5a5f1d73bbd.txt
Traceback (most recent call last):
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 48, in run
node.run(updatehash=updatehash)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 474, in run
write_node_report(self, is_mapnode=isinstance(self, MapNode))
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py", line 139, in write_node_report
report_file.write_text('\n'.join(lines))
File "/opt/miniconda-latest/envs/mb/lib/python3.6/pathlib.py", line 1216, in write_text
return f.write(data)
UnicodeEncodeError: 'ascii' codec can't encode character '\u2019' in position 503044: ordinal not in range(128)

Error when writing to shape tables:
mindboggle $FREESURFER_SUBJECT --out $OUT --no_sulci

[Node] Setting-up "Mindboggle.Shape_tables" in "/home/jovyan/work/mindboggled/working/arno/Mindboggle/_hemi_rh/Shape_tables".
191022-01:52:09,463 nipype.workflow ERROR:
Node Shape_tables.a1 failed to run on host 7a2d47ca2e18.
191022-01:52:09,465 nipype.workflow ERROR:
Saving crash info to /opt/crash-20191022-015209-root-Shape_tables.a1-be269986-5126-4514-8005-9b11ceded8b0.txt
Traceback (most recent call last):
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py", line 77, in save_hashfile
save_json(hashfile, hashed_inputs)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/utils/filemanip.py", line 673, in save_json
json.dump(data, fp, sort_keys=True, indent=4)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/init.py", line 298, in dump
for chunk in iterable:
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 684, in _iterencode
for chunk in _iterencode_list(o, _current_indent_level):
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 531, in _iterencode_list
for chunk in chunks:
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 531, in _iterencode_list
for chunk in chunks:
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 531, in _iterencode_list
for chunk in chunks:
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 716, in _iterencode
o = _default(o)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/simplejson/encoder.py", line 273, in default
o.class.name)
TypeError: Object of type int64 is not JSON serializable
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 48, in run
node.run(updatehash=updatehash)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
_save_hashfile(hashfile_unfinished, self._hashed_inputs)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py", line 85, in save_hashfile
fd.writelines(str(hashed_inputs))
UnicodeEncodeError: 'ascii' codec can't encode character '\u2019' in position 0: ordinal not in range(128)

@satra -- I am having trouble locating the underlying bug in Mindboggle. Usually such a UnicodeEncodeError is the result of an inappropriate str() call of an unicode object, but I'm not finding that in the code. The crash lines above point to non-mindboggle code. Do you have any suggestions?

Thank you for your attention!
I try to use 'try except' to wrap all the code where occured UnicodeEncodeError and just print out the
error message. It can now output all the tables and I can see some Error information now.
mindboggle $FREESURFER_SUBJECT --out $OUT > error_info.txt

By the way, could you provide a docker image as a temporary solution via dropbox or google? We really need the tools.

[binarybottle]

@locta66 -- Thank you! If you could point me to the specific lines of code that you pinpointed are causing this error, I would be more than happy to fix and push to docker hub!

[binarybottle]

@locta66 and @jling-NM -- All of my doctests seem to be running fine, except where there was a change in nipype. The circleci tests began to break at the same time that nipype switched from 1.2.2 to 1.2.3. I am rebuilding the docker image now using nipype 1.2.2 to test whether this is the culprit...

[binarybottle]

Unfortunately, rebuilding with an earlier version of nipype didn't fix the issue.

[locta66]

Thank you! @binarybottle
I could only print out all the information to a TXT file. For that I am not familiar with mindboggle and the error message, I can not locate the error lines. I wonder if the file would contain any useful information.
https://drive.google.com/open?id=1eWki7-loP2qphh6zTgVwqzQOVBVVyD5j

[binarybottle]

@satra -- I'm confused. When I run the following command in the mindboggle docker container:

mindboggle $FREESURFER_SUBJECT --out $OUT --no_shapes

mindboggle successfully saves a sulcus file but generates the following error related to the sulcus node:

191103-17:38:15,806 nipype.workflow ERROR:
Node Sulci.a1 failed to run on host 7a2d47ca2e18.
191103-17:38:15,807 nipype.workflow ERROR:
Saving crash info to /opt/mindboggle/crash-20191103-173815-root-Sulci.a1-1a4bcbf3-132f-4038-8d4e-e4db39c82760.txt
Traceback (most recent call last):
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 48, in run
node.run(updatehash=updatehash)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 493, in run
write_node_report(self, result=result, is_mapnode=isinstance(self, MapNode))
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py", line 214, in write_node_report
report_file.write_text('\n'.join(lines))
File "/opt/miniconda-latest/envs/mb/lib/python3.6/pathlib.py", line 1216, in write_text
return f.write(data)
UnicodeEncodeError: 'ascii' codec can't encode character '\u2019' in position 503044: ordinal not in range(128)

Traceback (most recent call last):
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 48, in run
node.run(updatehash=updatehash)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 493, in run
write_node_report(self, result=result, is_mapnode=isinstance(self, MapNode))
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py", line 214, in write_node_report
report_file.write_text('\n'.join(lines))
File "/opt/miniconda-latest/envs/mb/lib/python3.6/pathlib.py", line 1216, in write_text
return f.write(data)
UnicodeEncodeError: 'ascii' codec can't encode character '\u2019' in position 503044: ordinal not in range(128)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/opt/miniconda-latest/envs/mb/bin/mindboggle", line 2412, in
mbFlow.run(plugin=args.plugin)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py", line 599, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 53, in run
crashfile = report_crash(node)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/plugins/tools.py", line 72, in report_crash
crash2txt(crashfile, dict(node=node, traceback=traceback))
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/utils/filemanip.py", line 753, in crash2txt
fp.write('Node inputs:\n{}\n'.format(node.inputs))
UnicodeEncodeError: 'ascii' codec can't encode character '\u2019' in position 502867: ordinal not in range(128)

Can you help me figure out what might be going wrong?