Ming Wang issues

Results 105 issues of


                                            Ming Wang

[Bug] Sciex Does not Have Scan Numbers

[WIP] Networking Enrichment Query with MassQL

This should be found: [Viz LInk](http://msql.ucsd.edu//?query=QUERY+scaninfo%28MS1DATA%29+WHERE+MS1MZ%3DX%3ATOLERANCEMZ%3D0.1%3AINTENSITYPERCENT%3D25%3AINTENSITYMATCH%3DY%3AINTENSITYMATCHREFERENCE+AND+%0AMS1MZ%3DX%2B2%3ATOLERANCEMZ%3D0.2%3AINTENSITYMATCH%3DY%2A0.66%3AINTENSITYMATCHPERCENT%3D30+AND+%0AMS1MZ%3DX-2%3ATOLERANCEMZ%3D0.2%3AINTENSITYMATCH%3DY%2A0.66%3AINTENSITYMATCHPERCENT%3D30+AND+MS1MZ%3DX%2B4%3ATOLERANCEMZ%3D0.2%3AINTENSITYMATCH%3DY%2A0.17%3AINTENSITYMATCHPERCENT%3D40+AND+%0AMS1MZ%3DX-4%3ATOLERANCEMZ%3D0.2%3AINTENSITYMATCH%3DY%2A0.17%3AINTENSITYMATCHPERCENT%3D40+AND+%0AMS2PREC%3DX+AND%0AX%3Drange%28min%3D500%2Cmax%3D1000%29+AND%0ARTMIN%3D10&filename=GNPS00002_A3_p.mzML&x_axis=&y_axis=&facet_column=&scan=800&precursor_mz=&x_value=971.443237304688&y_value=0.32&ms1_usi=mzspec%3AGNPS%3ATASK-3290b45278624b9b877bdee60dfbc7b3-f.MSV000084691%2Fccms_peak%2F1810E-II.mzML%3Ascan%3A974&ms2_usi=) But is not found here: https://proteomics2.ucsd.edu/ProteoSAFe/result.jsp?task=747e94f5307d4b0292c323017715636b&view=query_results

[WIP] Caching using Parquet and pre-caching files

Fixes: https://github.com/mwang87/MassQueryLanguage/issues/165 Fixes: https://github.com/mwang87/MassQueryLanguage/issues/164 Fixes: https://github.com/mwang87/MassQueryLanguage/issues/163

[Commandline] Enabling input as cached file rather than full mzML file

[Caching] Using Parquet as caching option

[CommandLine] Enable multiple files and query flag explicit

[Language] Enabling Defect as qualifier

For example ``` QUERY scaninfo(MS2DATA) WHERE MS2PREC=X AND MOBILITY=range(min=X*0.0006775+0.40557, max=X*0.00078231+0.48817) AND X=defect(min=0.9, max=0.99) AND MS2PROD=ANY:DEFECT=defect(min=0.9,max=0.99):INTENSITYPERCENT=10 ```

[Engine] Parallel Query Engine

We have refined using Ray and integrated a bit in the dashboard. However, Ray causes some issues with spillover so likely not going to run it on the cluster.

Ming Wang