The outputs of the SED-ML files in a COMBINE archive need to be saved to unique file names.
Currently, executeCombineArchive uses file names equal to the id of the report or plot and the extension .csv or .pdf. When an archive has multiple SED-ML files with outputs that have the same ids, this will result in overwriting output files.
The convention we've adopted for AMICI, BioNetGen, CBMPy, COBRAPy, COPASI, GillesPy2, PySCeS, and VCell is that outputs should be saved to paths equal the concatenation of the following:
the location of the parent SED-ML document within the COMBINE archive
The outputs of the SED-ML files in a COMBINE archive need to be saved to unique file names.
Currently,
executeCombineArchiveuses file names equal to the id of the report or plot and the extension.csvor.pdf. When an archive has multiple SED-ML files with outputs that have the same ids, this will result in overwriting output files.The convention we've adopted for AMICI, BioNetGen, CBMPy, COBRAPy, COPASI, GillesPy2, PySCeS, and VCell is that outputs should be saved to paths equal the concatenation of the following:
.csv,.pdf)This guarantees a unique path for each output.