Quotes in annotation spreadsheets

[miguelalba]

Currently users need to provide strings and file parameters in the annotation spreadsheet with surrounding quotes. For example:

ID	Value
Input_conc	"conc_inputs3.csv"
Input_EGR	"EGR_inputs3.csv"
Input_ROP	"ROP_inputs3.csv"
Input_r_time	"r_time_inputs3.csv"

These parameters produce the following R script for a simulation:

Input_conc <- "conc_inputs3.csv"
Input_EGR <- "EGR_inputs3.csv"
Input_ROP <- "ROP_inputs3.csv"
Input_r_time <- "r_time_inputs3.csv"

It would be desirable to allow parameter values in the annotation spreadsheet without quotes, so that the importer code would take care of adding the necessary quotes according to the parameter type. E.g. string and file paths.

Nodes affected

Writer node

• Generated SedML needs to omit quotes for so that the extra quotes are not escaped. A SedML parameter in an annotation has a value="<value>". Thus the inner value should not have an extra pair of quotes.
• Generated SBML. Same as with SedML.

Reader node

• Simulations loaded from SedML should ignore extra quotes generated from legacy nodes. (old).
• SBML code is not used still.

Runner node

• Parameters of string and file type need now to be surrounded with quotes before evaluation.

[schuelet]

@miguelalba What is the status here?