Failure with data import

[sneumann]

Hi, there is a failure in the logs

Unhandled promise error: (converted from warning) ERROR: An error occurred when invoking the ExtendedTask.
Caused by error in `value[[3L]]()`:
! Error in add_qfeatures: sirCat %in% colnames(annotation) is not TRUE

which probably comes from

MetFamily/R/parsePeakAbundanceMatrixQF.R

Line 235 in 6b8e782

stopifnot(sirCat %in% colnames(annotation))

The import does not finish, and there should be better diagnostics for the user.

Yours,
Steffen

[sneumann]

The import can use one of the columns:

siriusFileColumnNames
[1] "NPC class"             "NPC superclass"        "NPC pathway"          
[4] "ClassyFire subclass"   "ClassyFire class"      "ClassyFire superclass"
[7] "ClassyFire kingdom"   

the current SIRIUS *.tsv has the following column names:

> colnames(annotation)
 [1] "SIRIUS_formulaRank"                               
 [2] "SIRIUS_molecularFormula"                          
 [3] "SIRIUS_adduct"                                    
 [4] "SIRIUS_precursorFormula"                          
 [5] "SIRIUS_NPC#pathway"                               
 [6] "SIRIUS_NPC#pathway Probability"                   
 [7] "SIRIUS_NPC#superclass"                            
 [8] "SIRIUS_NPC#superclass Probability"                
 [9] "SIRIUS_NPC#class"                                 
[10] "SIRIUS_NPC#class Probability"                     
[11] "SIRIUS_ClassyFire#superclass"                     
[12] "SIRIUS_ClassyFire#superclass probability"         
[13] "SIRIUS_ClassyFire#class"                          
[14] "SIRIUS_ClassyFire#class Probability"              
[15] "SIRIUS_ClassyFire#subclass"                       
[16] "SIRIUS_ClassyFire#subclass Probability"           
[17] "SIRIUS_ClassyFire#level 5"                        
[18] "SIRIUS_ClassyFire#level 5 Probability"            
[19] "SIRIUS_ClassyFire#most specific class"            
[20] "SIRIUS_ClassyFire#most specific class Probability"
[21] "SIRIUS_ClassyFire#all classifications"            
[22] "SIRIUS_ionMass"                                   
[23] "SIRIUS_retentionTimeInSeconds"                    
[24] "SIRIUS_retentionTimeInMinutes"                    
[25] "SIRIUS_formulaId"                                 
[26] "SIRIUS_alignedFeatureId"                          
[27] "SIRIUS_compoundId"                                
[28] "SIRIUS_mappingFeatureId"                          
[29] "SIRIUS_overallFeatureQuality" 

Note that MetFamily already performs the following operation on the colnames:

MetFamily/R/parsePeakAbundanceMatrixQF.R

Line 234 in 6b8e782

sirCat <- stringr::str_replace(siriusFileColumnName, " ", "#")

[sneumann]

We confirmed the following command fixes import:
sed -i -e s/SIRIUS_//g canopus_structure_summary.tsv

The SIRIUS 6.5.4 has this prefix SIRIUS_ , and the Changelog
https://v6.docs.sirius-ms.io/changelog/#631-2025-09-18
mentions that this prefix is optional.

The addSiriusAnnotations() should accommodate that, possibly by removing the prefix,
or by adding it to older SIRIUS input files.

Yours, Steffen