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Merge branch 'master' of https://github.com/MyersResearchGroup/iBioSim.git

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This commit is contained in:
Chris Myers 2022-03-31 15:31:21 -06:00
commit b6aa5bf573
1 changed files with 10 additions and 2 deletions
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12
conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/Converter.java
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@ -105,6 +105,7 @@ public class Converter {
System.err.println("\t-r <url> The specified synbiohub repository the user wants VPR model generator to connect to");
System.err.println("\t -env <SBML environment file> is the complete directory path of the environmental file to instantiate to your model. This only works when VPR model generator is used");
System.err.println("\t-Cello This option is for dynamic modeling of Cello parts and parametrization");
System.err.println("\t-tmID Set the ID of the top SBML model");
System.exit(1);
}
@ -150,6 +151,7 @@ public class Converter {
String version = null; //-v
String urlVPR = ""; //The specified synbiohub repository the user wants VPR model generator to connect to.
String environment ="";
String topModelId = null;
HashSet<String> ref_sbolInputFilePath = new HashSet<String>(); //rsbol
@ -309,6 +311,12 @@ public class Converter {
topEnvir = true;
environment = args[++index];
break;
case "-tmID":
if(index+1 >= args.length || (!args[index+1].isEmpty() && args[index+1].charAt(0)=='-'))
{
usage();
}
topModelId = args[++index];
default:
fullInputFileName = args[index];
}
@ -544,7 +552,7 @@ public class Converter {
SBMLutilities.exportSBMLModels(models, outputDir, outputFileName, noOutput, sbmlOut, singleSBMLOutput);
}
}
/* TODO: PEDRO FIX ME
if (topModelId != null) {
SBMLDocument topModel = SBMLutilities.readSBML(vpr_output+".xml", null, null);
topModel.getModel().setId(topModelId);
@ -563,7 +571,7 @@ public class Converter {
e.printStackTrace();
}
}
*/
if (doVPR) {
if (topEnvir) {
SBMLDocument topEnvironment = SBMLutilities.readSBML(environment, null, null);