change ' Raw data file checksum type' to 'Data file checksum type'

ISA-tools / mzml2isa

Parser to get meta information from mzML file and parse relevant information to a ISA-Tab structure

GNU General Public License v3.0

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change ' Raw data file checksum type' to 'Data file checksum type' #39

Closed proccaserra closed 4 years ago

proccaserra commented 4 years ago

in template isa /mzml2isa/templates/i_mzML.txt.

Current template causes a mismatch between declared Parameters in i_Investigation.txt file and Parameters used in a_assay.txt file.

Causes test_msml2isa.py tests too fail.

Tomnl commented 4 years ago

Thanks @proccaserra. All the tests are currently passing on travis (but I need to check if we are properly checking the imzML functionality).

Which test is failing for you? - could you paste the error message please?

proccaserra commented 4 years ago

@Tomnl sorry about being unclear, I was referring to the following tests on the isa-api project itself https://github.com/ISA-tools/isa-api/blob/master/tests/test_mzml2isa.py

2019-07-18 18:28:07,812 [ERROR]: isatab.py(check_protocol_parameter_usage:2878) >> (E) Some protocol parameters referenced in an assay file a_MTBLS267_metabolite_profiling_mass_spectrometry.txt are not declared in the investigation file: ['Data file checksum type'] 2019-07-18 18:28:08,308 [ERROR]: utils.py(assert_tab_content_equal:188) >> Value: 0.006-30.000, does not match: 0.006-30.0121

Tomnl commented 4 years ago

Thanks for the info @proccaserra.

Just to check - where do you get the mzMLs from? Do you get them directly from MetaboLights MTBLS267 (via FTP) or have you got the data saved somewhere?