Error when trying to convert Metabolights study MTBLS174 to W4M format with "ISA to W4M" tool:
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'
I see the isatools version is 0.10.3 in the error message, and I have some error with pandas when running this version on my computer. Version 0.12.2 solves this issue and I can extract correctly study 174.
Checking now study 719.
I don't know if this error is from isatools package or from the study content, so I've posted an issue on isatools GitHub repos.
In the meantime I will push a new version of isa2w4m tool so it works at least with MTBLS174.
@yguitton I let you answer about the urgency level.
Could you tell me where does come from the MTBLS719 study? Have you the possibility to check with Metabolights if the study is well written? The error is :
ValueError: ('Could not resolve Protocol parameter from Parameter Value ', 'Extraction Method')
Regarding delays would be cool to have the solution before May 24
For MTBLS719, it's a study from imperial college I can try to reach them (I know a bit one of the team members) and in parallel I can ask Metabolights for support (@pkrog do you have a direct contact there?)