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JasperVanDenBosch / niprov

provenance for neuroimaging data
BSD 3-Clause "New" or "Revised" License
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Mongo db error #171

Closed ktavabi closed 8 years ago

ktavabi commented 8 years ago

So this happened with the handler

/home/ktavabi/Projects/niprov/niprov/fif.py:24: DeprecationWarning: add_eeg_ref defaults to True in 0.13, will default to False in 0.14, and will be removed in 0.15. We recommend to use add_eeg_ref=False and set_eeg_reference() instead. img = self.libs.mne.io.Raw(self.path, allow_maxshield=True) Traceback (most recent call last): File "/home/ktavabi/Projects/shiva/shiva/process.py", line 163, in print_status=True File "/home/ktavabi/Projects/mnefun/mnefun/_mnefun.py", line 594, in do_processing p.on_process(text, func, outs[ii], p) File "/home/ktavabi/Projects/niprov/niprov/mnefunsupport.py", line 70, in handler provenance.log(pcafile, trans, sssfile, provenance=customprov) File "/home/ktavabi/Projects/niprov/niprov/context.py", line 54, in log transient, script, user, provenance, opts, self.deps) File "/home/ktavabi/Projects/niprov/niprov/logging.py", line 88, in log dependencies=dependencies) File "/home/ktavabi/Projects/niprov/niprov/adding.py", line 93, in add repository.update(img) File "/home/ktavabi/Projects/niprov/niprov/mongo.py", line 65, in update self.deflate(image)) File "build/bdist.linux-x86_64/egg/pymongo/collection.py", line 2244, in update File "build/bdist.linux-x86_64/egg/pymongo/collection.py", line 715, in _update File "build/bdist.linux-x86_64/egg/pymongo/pool.py", line 244, in command File "build/bdist.linux-x86_64/egg/pymongo/pool.py", line 372, in _raise_connection_failure bson.errors.InvalidDocument: Cannot encode object: array([ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16])

JasperVanDenBosch commented 8 years ago

Looks like there is an array in the params object that we are not decoding to a list

On Oct 5, 2016 10:51, "Kambiz Tavabi" notifications@github.com wrote:

So this happened with the handler

/home/ktavabi/Projects/niprov/niprov/fif.py:24: DeprecationWarning: add_eeg_ref defaults to True in 0.13, will default to False in 0.14, and will be removed in 0.15. We recommend to use add_eeg_ref=False and set_eeg_reference() instead. img = self.libs.mne.io.Raw(self.path, allow_maxshield=True) Traceback (most recent call last): File "/home/ktavabi/Projects/shiva/shiva/process.py", line 163, in print_status=True File "/home/ktavabi/Projects/mnefun/mnefun/_mnefun.py", line 594, in do_processing p.on_process(text, func, outs[ii], p) File "/home/ktavabi/Projects/niprov/niprov/mnefunsupport.py", line 70, in handler provenance.log(pcafile, trans, sssfile, provenance=customprov) File "/home/ktavabi/Projects/niprov/niprov/context.py", line 54, in log transient, script, user, provenance, opts, self.deps) File "/home/ktavabi/Projects/niprov/niprov/logging.py", line 88, in log dependencies=dependencies) File "/home/ktavabi/Projects/niprov/niprov/adding.py", line 93, in add repository.update(img) File "/home/ktavabi/Projects/niprov/niprov/mongo.py", line 65, in update self.deflate(image)) File "build/bdist.linux-x86_64/egg/pymongo/collection.py", line 2244, in update File "build/bdist.linux-x86_64/egg/pymongo/collection.py", line 715, in _update File "build/bdist.linux-x86_64/egg/pymongo/pool.py", line 244, in command File "build/bdist.linux-x86_64/egg/pymongo/pool.py", line 372, in _raise_connection_failure bson.errors.InvalidDocument: Cannot encode object: array([ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16])

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ktavabi commented 8 years ago

Oh, that must be params.subject_indices

JasperVanDenBosch commented 8 years ago

Which params attribute contains this list of 16 integers? @kambysese

On Oct 5, 2016 11:02, "Jasper van den Bosch" japsai@gmail.com wrote:

Looks like there is an array in the params object that we are not decoding to a list

On Oct 5, 2016 10:51, "Kambiz Tavabi" notifications@github.com wrote:

So this happened with the handler

/home/ktavabi/Projects/niprov/niprov/fif.py:24: DeprecationWarning: add_eeg_ref defaults to True in 0.13, will default to False in 0.14, and will be removed in 0.15. We recommend to use add_eeg_ref=False and set_eeg_reference() instead. img = self.libs.mne.io.Raw(self.path, allow_maxshield=True) Traceback (most recent call last): File "/home/ktavabi/Projects/shiva/shiva/process.py", line 163, in print_status=True File "/home/ktavabi/Projects/mnefun/mnefun/_mnefun.py", line 594, in do_processing p.on_process(text, func, outs[ii], p) File "/home/ktavabi/Projects/niprov/niprov/mnefunsupport.py", line 70, in handler provenance.log(pcafile, trans, sssfile, provenance=customprov) File "/home/ktavabi/Projects/niprov/niprov/context.py", line 54, in log transient, script, user, provenance, opts, self.deps) File "/home/ktavabi/Projects/niprov/niprov/logging.py", line 88, in log dependencies=dependencies) File "/home/ktavabi/Projects/niprov/niprov/adding.py", line 93, in add repository.update(img) File "/home/ktavabi/Projects/niprov/niprov/mongo.py", line 65, in update self.deflate(image)) File "build/bdist.linux-x86_64/egg/pymongo/collection.py", line 2244, in update File "build/bdist.linux-x86_64/egg/pymongo/collection.py", line 715, in _update File "build/bdist.linux-x86_64/egg/pymongo/pool.py", line 244, in command File "build/bdist.linux-x86_64/egg/pymongo/pool.py", line 372, in _raise_connection_failure bson.errors.InvalidDocument: Cannot encode object: array([ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16])

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ktavabi commented 8 years ago

params.subject_indices is always an (N, ) array

JasperVanDenBosch commented 8 years ago

Weird it should be caught by line 41 in mnefunsupport. I'll fix this later today

On Oct 5, 2016 11:15, "Kambiz Tavabi" notifications@github.com wrote:

params.subject_indices is always an (N, ) array

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JasperVanDenBosch commented 8 years ago

I can't replicate this. Is your mnefunsupport altered? Maybe best if we look together sometime

JasperVanDenBosch commented 8 years ago

Think we haven't seen this in a while, right @kambysese? Closing it for now

ktavabi commented 8 years ago

IIRC this was squashed