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CCMS-UCSD / GNPS_Workflows

Public Workflows at GNPS
https://gnps.ucsd.edu/
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MolNetEnhancer - scores output in graphml from GNPS are all empty for nodes with classifications #57

Open justinjjvanderhooft opened 5 years ago

justinjjvanderhooft commented 5 years ago

Using the notebook the correct scores are displayed in the resulting graphml file; when running GNPS-MolNetEnhancer, the scores are not present in the graphml file for classified nodes.

irinakoester commented 5 years ago

@mwang87 and @justinjjvanderhooft This is still a problem. I looked through all output files and the scores are not documented in any file resulting from the GNPS workflow. So as it is right now the MolNetEnhancer GNPS workflow is not functional.

justinjjvanderhooft commented 5 years ago

Thanks for notifying @irinakoester. @madeleineernst did we ever get to the bottom of this? If you are currently highly interested in the scores, you can get them through the MolNetEnhancer notebooks that produce graphml files with the chemical classes and scores. See info and a tutorial with example data here: https://github.com/madeleineernst/pyMolNetEnhancer - the GNPS output does show chemical classes okay.

madeleineernst commented 5 years ago

@mwang87, I create a PR #254, which should fix this issue.

mwang87 commented 5 years ago

Merged, will deploy and test later today