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mwang87 / MetabolomicsSpectrumResolver

Metabolomics Spectrum Resolver/Displayer
https://metabolomics-usi.ucsd.edu/
MIT License
9 stars 2 forks source link

Support ProForma Natively in Resolver #158

Open mwang87 opened 3 years ago

mwang87 commented 3 years ago

Currently USIs like this:

mzspec:GNPS:TASK-82c0124b6053407fa41ba98f53fd8d89-spectrum_library_mgf_splits/114.mgf:scan:1:[+42.011]-AAAAAAAAAAGAAGGR/1

do not parse because MassIVE does not support it (it should) but we should also translate proforma locally anyway.

benpullman commented 3 years ago

Looking at this I don't think it's a resolution issue from MassIVE, more so, two small bugs here.

The first is an issue with regular expressions: https://github.com/mwang87/MetabolomicsSpectrumResolver/blob/5f772b3df7aeff2a31be88b80faf9399bd4da306/parsing.py#L37, which does not properly separate the annotation from the rest of the USI. (I think it should be r':(.+)?$)

The second is that if this is fixed, the spectrum has to be resolved using the MassIVE USI resolution service (and not the GNPS task resolution service) if there is an annotation given to the USI. Then everything will work properly. Example URL for the above USI if properly handed off to MassIVE.