Erreur Python lors de l'exécution de isatab2w4m

Error when running on MTBLS174:

|   Traceback (most recent call last):
|   File "/shared/mfs/data/galaxy/mutable-data/shed_tools/toolshed.g2.bx.psu.edu/repos/prog/isa2w4m/1883d5274962/isa2w4m/isa2w4m.py", line 8, in <module>
|   isatab2w4m.main()
|   File "/shared/mfs/data/galaxy/mutable-data/dependencies/_conda/envs/__isatools@0.10.3/lib/python3.8/site-packages/isatools/convert/isatab2w4m.py", line 569, in main
|   convert(input_dir           = args_dict['input_dir'],
|   File "/shared/mfs/data/galaxy/mutable-data/dependencies/_conda/envs/__isatools@0.10.3/lib/python3.8/site-packages/isatools/convert/isatab2w4m.py", line 548, in convert
|   assays = convert2w4m(input_dir      = input_dir,
|   File "/shared/mfs/data/galaxy/mutable-data/dependencies/_conda/envs/__isatools@0.10.3/lib/python3.8/site-packages/isatools/convert/isatab2w4m.py", line 458, in convert2w4m
|   variable_names = make_variable_names(measures_df)
|   File "/shared/mfs/data/galaxy/mutable-data/dependencies/_conda/envs/__isatools@0.10.3/lib/python3.8/site-packages/isatools/convert/isatab2w4m.py", line 295, in make_variable_names
|   if assay_df.keys().contains(col):
|   AttributeError: 'Index' object has no attribute 'contains'

Je vais essayer de reproduire l'erreur en dehors de Galaxy, mais c'est étrange car cela ressemble à un problème de version de package, ce qui ne devrait pas arriver avec conda.

If it can help in your investigation, here is the packages shipped with isatools==0.10.3

(__isatools@0.10.3) $ conda list
# packages in environment at /shared/ifbstor1/galaxy/mutable-data/dependencies/_conda/envs/__isatools@0.10.3:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                      1_llvm    conda-forge
attrs                     19.3.0                     py_0    conda-forge
beautifulsoup4            4.8.2                    py38_0    conda-forge
biopython                 1.76             py38h516909a_0    conda-forge
ca-certificates           2019.11.28           hecc5488_0    conda-forge
certifi                   2019.11.28       py38h32f6830_1    conda-forge
cffi                      1.14.0           py38hd463f26_0    conda-forge
chardet                   3.0.4           py38h32f6830_1006    conda-forge
cryptography              2.8              py38h766eaa4_2    conda-forge
decorator                 4.4.2                      py_0    conda-forge
et_xmlfile                1.0.1                   py_1001    conda-forge
fastobo                   0.7.0            py38he1b5a44_0    bioconda
frozendict                1.2                        py_2    conda-forge
icu                       64.2                 he1b5a44_1    conda-forge
idna                      2.9                        py_1    conda-forge
importlib-metadata        1.5.0            py38h32f6830_1    conda-forge
importlib_metadata        1.5.0                         1    conda-forge
isatools                  0.10.3                     py_1    bioconda
iso8601                   0.1.12                     py_1    conda-forge
jdcal                     1.4.1                      py_0    conda-forge
jinja2                    2.11.1                     py_0    conda-forge
jsonschema                3.2.0            py38h32f6830_1    conda-forge
ld_impl_linux-64          2.35.1               hea4e1c9_1    conda-forge
libblas                   3.8.0               16_openblas    conda-forge
libcblas                  3.8.0               16_openblas    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_2    conda-forge
libgfortran-ng            7.3.0                hdf63c60_5    conda-forge
libiconv                  1.15              h516909a_1006    conda-forge
liblapack                 3.8.0               16_openblas    conda-forge
libopenblas               0.3.9                h5ec1e0e_0    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_2    conda-forge
libxml2                   2.9.10               hee79883_0    conda-forge
libxslt                   1.1.33               h31b3aaa_0    conda-forge
llvm-openmp               9.0.1                hc9558a2_2    conda-forge
lxml                      4.5.0            py38hbb43d70_1    conda-forge
markupsafe                1.1.1            py38h1e0a361_1    conda-forge
mzml2isa                  0.5.1                      py_1    bioconda
ncurses                   6.1               hf484d3e_1002    conda-forge
networkx                  2.4                        py_1    conda-forge
numpy                     1.18.1           py38h95a1406_0    conda-forge
openpyxl                  3.0.3                      py_0    conda-forge
openssl                   1.1.1e               h516909a_0    conda-forge
pandas                    1.0.3            py38hcb8c335_0    conda-forge
pip                       20.0.2                     py_2    conda-forge
progressbar2              3.50.0                     py_2    conda-forge
pronto                    2.0.1                      py_0    bioconda
pycparser                 2.20                       py_0    conda-forge
pyopenssl                 19.1.0                     py_1    conda-forge
pyrsistent                0.15.7           py38h1e0a361_1    conda-forge
pysocks                   1.7.1            py38h32f6830_1    conda-forge
python                    3.8.2           h9d8adfe_4_cpython    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python-utils              2.4.0                      py_0    conda-forge
python_abi                3.8                      1_cp38    conda-forge
pytz                      2019.3                     py_0    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
requests                  2.23.0             pyh8c360ce_2    conda-forge
setuptools                46.0.0           py38h32f6830_2    conda-forge
six                       1.14.0                     py_1    conda-forge
soupsieve                 1.9.4            py38h32f6830_1    conda-forge
sqlite                    3.30.1               hcee41ef_0    conda-forge
tk                        8.6.10               hed695b0_0    conda-forge
urllib3                   1.25.7           py38h32f6830_1    conda-forge
wheel                     0.34.2                     py_1    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
zipp                      3.1.0                      py_0    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge

Bonjour @pkrog

Avez-vous pu finalement résoudre le problème ou est-ce toujours d'actualité ?

Bonjour,

Pas encore. Je suis en train de mettre à jour vers la version 0.12 d'isatools, en espérant que cela résolve le problème.
Je vous préviens lorsque j'ai mis une nouvelle version de mtbls-dwnld disponible sur le toolshed.

Cordialement,

1 J'aime

Voici la nouvelle version (4.1.5) de mtbls-dwnld à installer :
https://toolshed.g2.bx.psu.edu/repository?repository_id=d6c9bf262e5ee360&changeset_revision=1fd8547867be

1 J'aime

Salut,

C'est en cours d'installation :

mtbls-dwnld 4.1.5 devrait maintenant être disponible sur https://usegalaxy.fr

Merci. Maintenant je mets aussi à jour isa2w4m, et je te préviens quand il est prêt.

1 J'aime