[CLOSED] MIA crashes when typing any letter in the filter field

[M40V]

Issue by blemasso Monday May 13, 2019 at 11:50 GMT _Originally opened as https://github.com/populse/populse_mia/issues/84_

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Describe the bug When I type any letter in the filter field MIA is crashing

Generated error gin-e05-laban:populse_mia blemasso$ python3 main.py Populse_MIA in "developer" mode /Users/blemasso/.populse_mia/configuration.yml has been detected. Checking the installed versions of nipype and mia_processes ...

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• mia use already the installed version of nipype and mia_processes (1.1.9 and 1.1.1 respectively) Exception hooking in progress ... Clean up before closing mia done ... Traceback (most recent call last): File "/Users/blemasso/Data_non_synch/Populse/populse_mia/python/populse_mia/data_browser/data_browser.py", line 605, in search_str return_list = [getattr(scan, TAG_FILENAME) for scan in generator] File "/Users/blemasso/Data_non_synch/Populse/populse_mia/python/populse_mia/data_browser/data_browser.py", line 605, in return_list = [getattr(scan, TAG_FILENAME) for scan in generator] File "/Users/blemasso/.local/lib/python3.7/site-packages/populse_db/database.py", line 1510, in filter_documents filter_query = self.__filter_query(collection, filter_query) File "/Users/blemasso/.local/lib/python3.7/site-packages/populse_db/database.py", line 1483, in filter_query tree = populse_db.filter.filter_parser().parse(filter) File "/Users/blemasso/.local/lib/python3.7/site-packages/populse_db/filter.py", line 109, in filter_parser _grammar_parser = Lark(filter_grammar) File "/Users/blemasso/.local/lib/python3.7/site-packages/lark/lark.py", line 221, in init self.parser = self._build_parser() File "/Users/blemasso/.local/lib/python3.7/site-packages/lark/lark.py", line 241, in _build_parser return self.parser_class(self.lexer_conf, parser_conf, options=self.options) File "/Users/blemasso/.local/lib/python3.7/site-packages/lark/parser_frontends.py", line 141, in init__ self._prepare_match(lexer_conf) File "/Users/blemasso/.local/lib/python3.7/site-packages/lark/parser_frontends.py", line 157, in _prepare_match raise ValueError("Dynamic Earley doesn't support weights on terminals", t, t.priority) ValueError: ("Dynamic Earley doesn't support weights on terminals", TerminalDef('KEYWORD_LITERAL', '(?i:(?:(?i:(?:(?i:NULL)|(?i:TRUE)))|(?i:FALSE)))'), 2)

To Reproduce I open MIA, then, when I enter any letter (or number, or symbol) in the filter field, MIA crashes. It happens with or without any project open/

Desktop (please complete the following information):

• MacOs 10.14.4

[M40V]

Comment by servoz Monday May 13, 2019 at 12:16 GMT

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Not sure, but this sounds like an already opened issue in the populse_db, or strongly linked with ?

[M40V]

Comment by blemasso Monday May 13, 2019 at 12:26 GMT

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ok noted

[M40V]

Comment by servoz Monday May 13, 2019 at 12:43 GMT

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Please, can you type in a shell (and give the return): python3 -m pip show lark_parser

[M40V]

Comment by blemasso Monday May 13, 2019 at 12:45 GMT

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nothing...

[M40V]

Comment by servoz Monday May 13, 2019 at 12:54 GMT

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and python3 -m pip list

[M40V]

Comment by blemasso Monday May 13, 2019 at 13:41 GMT

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gin-e05-laban:populse_mia blemasso$ python3 -m pip list Package Version

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alabaster 0.7.12
anaconda-client 1.7.2
anaconda-navigator 1.9.7
anaconda-project 0.8.2
appnope 0.1.0
appscript 1.0.1
asn1crypto 0.24.0
astroid 2.2.5
astropy 3.1.2
atomicwrites 1.3.0
attrs 19.1.0
Babel 2.6.0
backcall 0.1.0
backports.os 0.1.1
backports.shutil-get-terminal-size 1.0.0
beautifulsoup4 4.7.1
bitarray 0.8.3
bkcharts 0.2
bleach 3.1.0
bokeh 1.0.4
boto 2.49.0
Bottleneck 1.2.1
capsul 2.2.1
certifi 2019.3.9
cffi 1.12.2
chardet 3.0.4
Click 7.0
cloudpickle 0.8.0
clyent 1.2.2
colorama 0.4.1
conda 4.6.14
conda-build 3.17.8
conda-verify 3.1.1
contextlib2 0.5.5
cryptography 2.6.1
cycler 0.10.0
Cython 0.29.6
cytoolz 0.9.0.1
dask 1.1.4
decorator 4.4.0
defusedxml 0.5.0
distributed 1.26.0
docutils 0.14
entrypoints 0.3
et-xmlfile 1.0.1
fastcache 1.0.2
filelock 3.0.10
Flask 1.0.2
funcsigs 1.0.2
future 0.17.1
gevent 1.4.0
glob2 0.6
gmpy2 2.0.8
greenlet 0.4.15
h5py 2.9.0
heapdict 1.0.0
html5lib 1.0.1
idna 2.8
imageio 2.5.0
imagesize 1.1.0
importlib-metadata 0.0.0
ipykernel 5.1.0
ipython 7.4.0
ipython-genutils 0.2.0
ipywidgets 7.4.2
isodate 0.6.0
isort 4.3.16
itsdangerous 1.1.0
jdcal 1.4
jedi 0.13.3
Jinja2 2.10
jsonschema 3.0.1
jupyter 1.0.0
jupyter-client 5.2.4
jupyter-console 6.0.0
jupyter-core 4.4.0
jupyterlab 0.35.4
jupyterlab-server 0.2.0
keyring 18.0.0
kiwisolver 1.0.1
lark-parser 0.7.1
lazy-object-proxy 1.3.1
libarchive-c 2.8
lief 0.9.0
llvmlite 0.28.0
locket 0.2.0
lxml 4.3.2
MarkupSafe 1.1.1
matplotlib 3.0.3
mccabe 0.6.1
mia-processes 1.1.1
mistune 0.8.4
mkl-fft 1.0.10
mkl-random 1.0.2
more-itertools 6.0.0
mpmath 1.1.0
msgpack 0.6.1
multipledispatch 0.6.0
navigator-updater 0.2.1
nbconvert 5.4.1
nbformat 4.4.0
networkx 2.2
neurdflib 5.0.0.post1 nibabel 2.4.0
nipype 1.1.9
nltk 3.4
nose 1.3.7
notebook 5.7.8
numba 0.43.1
numexpr 2.6.9
numpy 1.16.2
numpydoc 0.8.0
olefile 0.46
openpyxl 2.6.1
packaging 19.0
pandas 0.24.2
pandocfilters 1.4.2
parso 0.3.4
partd 0.3.10
path.py 11.5.0
pathlib2 2.3.3
patsy 0.5.1
pep8 1.7.1
pexpect 4.6.0
pickleshare 0.7.5
Pillow 5.4.1
pip 19.0.3
pkginfo 1.5.0.1
pluggy 0.9.0
ply 3.11
populse-db 1.0.1
populse-mia 1.1.1
prometheus-client 0.6.0
prompt-toolkit 2.0.9
prov 1.5.3
psutil 5.6.1
ptyprocess 0.6.0
py 1.8.0
pycodestyle 2.5.0
pycosat 0.6.3
pycparser 2.19
pycrypto 2.6.1
pycurl 7.43.0.2
pydot 1.4.1
pydotplus 2.0.2
pyflakes 2.1.1
Pygments 2.3.1
pylint 2.3.1
pyodbc 4.0.26
pyOpenSSL 19.0.0
pyparsing 2.3.1
PyQt5 5.12.2
PyQt5-sip 4.19.17
pyrsistent 0.14.11
PySocks 1.6.8
pytest 4.3.1
pytest-arraydiff 0.3
pytest-astropy 0.5.0
pytest-doctestplus 0.3.0
pytest-openfiles 0.3.2
pytest-remotedata 0.3.1
python-dateutil 2.8.0
pytz 2018.9
PyWavelets 1.0.2
PyYAML 5.1
pyzmq 18.0.0
QtAwesome 0.5.7
qtconsole 4.4.3
QtPy 1.7.0
rdflib 4.2.2
requests 2.21.0
rope 0.12.0
ruamel-yaml 0.15.46
scikit-image 0.14.2
scikit-learn 0.20.3
scipy 1.2.1
seaborn 0.9.0
Send2Trash 1.5.0
setuptools 40.8.0
simplegeneric 0.8.1
simplejson 3.16.0
singledispatch 3.4.0.3
sip 4.19.8
six 1.12.0
snakeviz 2.0.0
snowballstemmer 1.2.1
soma-base 4.6.4
soma-workflow 3.0.0
sortedcollections 1.1.2
sortedcontainers 2.1.0
soupsieve 1.8
Sphinx 1.8.5
sphinxcontrib-websupport 1.1.0
spyder 3.3.3
spyder-kernels 0.4.2
SQLAlchemy 1.3.1
statsmodels 0.9.0
sympy 1.3
tables 3.5.1
tblib 1.3.2
terminado 0.8.1
testpath 0.4.2
toolz 0.9.0
tornado 6.0.2
tqdm 4.31.1
traitlets 4.3.2
traits 5.1.1
unicodecsv 0.14.1
urllib3 1.24.1
wcwidth 0.1.7
webencodings 0.5.1
Werkzeug 0.14.1
wheel 0.33.1
widgetsnbextension 3.4.2
wrapt 1.11.1
wurlitzer 1.0.2
xlrd 1.2.0
XlsxWriter 1.1.5
xlwings 0.15.4
xlwt 1.3.0
zict 0.1.4
zipp 0.3.3

[M40V]

Comment by servoz Monday May 13, 2019 at 13:45 GMT

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Please, run in a terminal: python3 -m pip show lark-parser

[M40V]

Comment by blemasso Monday May 13, 2019 at 13:46 GMT

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(base) gin-e05-laban:~ blemasso$ python3 -m pip show lark-parser Name: lark-parser Version: 0.7.1 Summary: a modern parsing library Home-page: https://github.com/erezsh/lark Author: Erez Shinan Author-email: erezshin@gmail.com License: MIT Location: /Users/blemasso/.local/lib/python3.7/site-packages Requires: Required-by: populse-mia, populse-db

[M40V]

Comment by servoz Monday May 13, 2019 at 13:49 GMT

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Please, run in a terminal: python3 -m pip install -I "lark-parser<0.7.0 --user" Then: python3 -c "import lark; print(lark.__version__)"

[M40V]

Comment by servoz Monday May 13, 2019 at 13:52 GMT

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This is the minimal hack, before really fix the already opened issue in the populse_db. Let us know if it is ok for you now

[M40V]

Comment by blemasso Monday May 13, 2019 at 14:35 GMT

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I downgraded lark-parser from 0.7.1 to 0.6.7 on my Conda environment

python3 -c "import lark; print(lark.version)" 0.6.7

And now it is working!