fix handling of bad URIs in OMEX and bad file names in outputs

Author: moraru

vcell-cli/src/main/java/org/vcell/cli/CLIStandalone.java

@@ -67,7 +67,8 @@ private static void singleExec(String[] args) {
 				SedML sedml = null;
 				sedml = Libsedml.readDocument(completeSedmlPath).getSedMLModel();
 				SolverHandler solverHandler = new SolverHandler();
-				ExternalDocInfo externalDocInfo = new ExternalDocInfo(completeSedmlPath, true);
+				// send the omex file since we do better handling of malformed model URIs in XMLHelper code
+				ExternalDocInfo externalDocInfo = new ExternalDocInfo(new File(inputFile), true);
 				solverHandler.simulateAllTasks(externalDocInfo, sedml, outDirForCurrentSedml);
 			} 
 			// At the end

vcell-cli/src/main/java/org/vcell/cli/SolverHandler.java

@@ -61,33 +61,33 @@ public void simulateAllTasks(ExternalDocInfo externalDocInfo, SedML sedml, File
 				SolverDescription sd = std.getSolverDescription();
 				String kisao = sd.getKisao();
 				if (SolverDescription.CVODE.getKisao().contentEquals(kisao)) {
-					ODESolverResultSet odeSolverResultSet = CVODEHelper.solve(outputDir, sims[i].getDescription(), bioModel);
+					ODESolverResultSet odeSolverResultSet = CVODEHelper.solve(outputDir, sims[i].getDescription().replaceAll("[:\\\\/*?|<>]", "_"), bioModel);
 					System.out.println("Finished: " + docName + ": - task '" + sims[i].getDescription() + "'.");
 				} else if (SolverDescription.StochGibson.getKisao().contentEquals(kisao)) {
-					ODESolverResultSet odeSolverResultSet = StockGibsonHelper.solve(outputDir, sims[i].getDescription(),
+					ODESolverResultSet odeSolverResultSet = StockGibsonHelper.solve(outputDir, sims[i].getDescription().replaceAll("[:\\\\/*?|<>]", "_"),
 							bioModel);
 					System.out.println("Finished: " + docName + ": - task '" + sims[i].getDescription() + "'.");
 				} else if (SolverDescription.IDA.getKisao().contentEquals(kisao)) {
-					ODESolverResultSet odeSolverResultSet = IDAHelper.solve(outputDir, sims[i].getDescription(), bioModel);
+					ODESolverResultSet odeSolverResultSet = IDAHelper.solve(outputDir, sims[i].getDescription().replaceAll("[:\\\\/*?|<>]", "_"), bioModel);
 					System.out.println("Finished: " + docName + ": - task '" + sims[i].getDescription() + "'.");
 				} else if (SolverDescription.RungeKuttaFehlberg.getKisao().contentEquals(kisao)) {
-					ODESolverResultSet odeSolverResultSet = RungeKuttaFelhbergHelper.solve(outputDir, sims[i].getDescription(),
+					ODESolverResultSet odeSolverResultSet = RungeKuttaFelhbergHelper.solve(outputDir, sims[i].getDescription().replaceAll("[:\\\\/*?|<>]", "_"),
 							bioModel);
 					System.out.println("Finished: " + docName + ": - task '" + sims[i].getDescription() + "'.");
 				} else if (SolverDescription.AdamsMoulton.getKisao().contentEquals(kisao)) {
-					ODESolverResultSet odeSolverResultSet = AdamsMoultonHelper.solve(outputDir, sims[i].getDescription(),
+					ODESolverResultSet odeSolverResultSet = AdamsMoultonHelper.solve(outputDir, sims[i].getDescription().replaceAll("[:\\\\/*?|<>]", "_"),
 							bioModel);
 					System.out.println("Finished: " + docName + ": - task '" + sims[i].getDescription() + "'.");
 				} else if (SolverDescription.ForwardEuler.getKisao().contentEquals(kisao)) {
-					ODESolverResultSet odeSolverResultSet = ForwardEulerHelper.solve(outputDir, sims[i].getDescription(),
+					ODESolverResultSet odeSolverResultSet = ForwardEulerHelper.solve(outputDir, sims[i].getDescription().replaceAll("[:\\\\/*?|<>]", "_"),
 							bioModel);
 					System.out.println("Finished: " + docName + ": - task '" + sims[i].getDescription() + "'.");
 				} else if (SolverDescription.RungeKutta2.getKisao().contentEquals(kisao)) {
-					ODESolverResultSet odeSolverResultSet = RungeKutta2Helper.solve(outputDir, sims[i].getDescription(),
+					ODESolverResultSet odeSolverResultSet = RungeKutta2Helper.solve(outputDir, sims[i].getDescription().replaceAll("[:\\\\/*?|<>]", "_"),
 							bioModel);
 					System.out.println("Finished: " + docName + ": - task '" + sims[i].getDescription() + "'.");
 				} else if (SolverDescription.RungeKutta4.getKisao().contentEquals(kisao)) {
-					ODESolverResultSet odeSolverResultSet = RungeKutta4Helper.solve(outputDir, sims[i].getDescription(),
+					ODESolverResultSet odeSolverResultSet = RungeKutta4Helper.solve(outputDir, sims[i].getDescription().replaceAll("[:\\\\/*?|<>]", "_"),
 							bioModel);
 					System.out.println("Finished: " + docName + ": - task '" + sims[i].getDescription() + "'.");
 				} else {