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pgleesonpgleeson
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More unifoirmity in listing of generated files by jNeuroML
1 parent 9098898 commit a754d1b

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1 file changed

+42
-26
lines changed

1 file changed

+42
-26
lines changed

‎src/main/java/org/neuroml/JNeuroML.java‎

Lines changed: 42 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -143,6 +143,8 @@ public class JNeuroML
143143

144144
public static final String PNG_FLAG = "-png";
145145

146+
public static final String GENERATED_FILE = ">>> JNML generated file: ";
147+
146148
static String usage = "Usage: \n\n" + " " + JNML_SCRIPT + " LEMSFile.xml\n"
147149
+ " Load LEMSFile.xml using jLEMS, parse it and validate it as LEMS, and execute the model it contains\n\n"
148150

@@ -522,7 +524,11 @@ else if (args[i].equals(OUTPUT_DIR_FLAG))
522524
}
523525
else
524526
{
525-
nw.generateAndRun(nogui, compile, run, false);
527+
List<File> files = nw.generateAndRun(nogui, compile, run, false);
528+
for(File genFile : files)
529+
{
530+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
531+
}
526532
}
527533

528534
}
@@ -535,7 +541,12 @@ else if(args[1].equals(PYNN_EXPORT_FLAG))
535541
boolean runNrn = (args.length==3 && args[2].equals(RUN_PYNN_NEURON_FLAG));
536542

537543
PyNNWriter pw = new PyNNWriter(lems, lemsFile.getParentFile(), nFile);
538-
pw.generateAndRun(false, runNrn);
544+
545+
List<File> files = pw.generateAndRun(false, runNrn);
546+
for(File genFile : files)
547+
{
548+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
549+
}
539550
}
540551
else if(args[1].equals(NETPYNE_EXPORT_FLAG))
541552
{
@@ -581,7 +592,12 @@ else if (args[i].equals(NUMBER_PROCESSORS_FLAG))
581592

582593
String mainFilename = generateFormatFilename(lemsFile, Format.NETPYNE, "_netpyne");
583594
NetPyNEWriter npw = new NetPyNEWriter(lems, outputDir, mainFilename);
584-
npw.generateAndRun(nogui, run, np, json);
595+
List<File> files = npw.generateAndRun(nogui, run, np, json);
596+
597+
for(File genFile : files)
598+
{
599+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
600+
}
585601
}
586602
// Two arguments
587603
else if(args.length == 2)
@@ -647,7 +663,7 @@ else if(args[1].equals(VERTEX_EXPORT_FLAG))
647663
generateFormatFilename(lemsFile, Format.VERTEX, "_run"));
648664
for(File genFile : vw.convert())
649665
{
650-
System.out.println("Writing to: " + genFile.getAbsolutePath());
666+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
651667
}
652668

653669
}
@@ -660,7 +676,7 @@ else if(args[1].equals(SBML_EXPORT_FLAG))
660676
SBMLWriter sbmlw = new SBMLWriter(lems, lemsFile.getParentFile(), generateFormatFilename(lemsFile, Format.SBML, null));
661677
for(File genFile : sbmlw.convert())
662678
{
663-
System.out.println("Writing to: " + genFile.getAbsolutePath());
679+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
664680
}
665681

666682
}
@@ -673,13 +689,13 @@ else if(args[1].equals(SBML_SEDML_EXPORT_FLAG))
673689
SBMLWriter sbmlw = new SBMLWriter(lems, lemsFile.getParentFile(), generateFormatFilename(lemsFile, Format.SBML, null));
674690
for(File genFile : sbmlw.convert())
675691
{
676-
System.out.println("Writing SBML to: " + genFile.getAbsolutePath());
692+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
677693
}
678694

679695
SEDMLWriter sedw = new SEDMLWriter(lems, lemsFile.getParentFile(), generateFormatFilename(lemsFile, Format.SEDML, null), lemsFile.getName(), Format.SBML);
680696
for(File genFile : sedw.convert())
681697
{
682-
System.out.println("Writing SED-ML to: " + genFile.getAbsolutePath());
698+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
683699
}
684700
}
685701
else if(args[1].equals(XPP_EXPORT_FLAG))
@@ -691,7 +707,7 @@ else if(args[1].equals(XPP_EXPORT_FLAG))
691707
XppWriter xppw = new XppWriter(lems, lemsFile.getParentFile(), generateFormatFilename(lemsFile, Format.XPP, null));
692708
for(File genFile : xppw.convert())
693709
{
694-
System.out.println("Writing to: " + genFile.getAbsolutePath());
710+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
695711
}
696712

697713
}
@@ -704,7 +720,7 @@ else if(args[1].equals(DNSIM_EXPORT_FLAG))
704720
DNSimWriter dnsimw = new DNSimWriter(lems, lemsFile.getParentFile(), generateFormatFilename(lemsFile, Format.DN_SIM, null));
705721
for(File genFile : dnsimw.convert())
706722
{
707-
System.out.println("Writing to: " + genFile.getAbsolutePath());
723+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
708724
}
709725

710726
}
@@ -720,7 +736,7 @@ else if(args[1].equals(NEST_EXPORT_FLAG))
720736
NestWriter nw = new NestWriter(lems, lemsFile.getParentFile(), nFile);
721737
for(File genFile : nw.convert())
722738
{
723-
System.out.println("Writing to: " + genFile.getAbsolutePath());
739+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
724740
}
725741
}
726742
else if(args[1].equals(MOOSE_EXPORT_FLAG))
@@ -735,7 +751,7 @@ else if(args[1].equals(MOOSE_EXPORT_FLAG))
735751
MooseWriter nw = new MooseWriter(lems, lemsFile.getParentFile(), nFile);
736752
for(File genFile : nw.convert())
737753
{
738-
System.out.println("Writing to: " + genFile.getAbsolutePath());
754+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
739755
}
740756
}
741757
else if(args[1].equals(EDEN_EXPORT_FLAG))
@@ -750,7 +766,7 @@ else if(args[1].equals(EDEN_EXPORT_FLAG))
750766
EDENWriter nw = new EDENWriter(lems, lemsFile, lemsFile.getParentFile(), nFile);
751767
for(File genFile : nw.convert())
752768
{
753-
System.out.println("Writing to: " + genFile.getAbsolutePath());
769+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
754770
}
755771
}
756772

@@ -785,7 +801,7 @@ else if(args[1].equals(SEDML_EXPORT_FLAG) || args[1].equals(SEDML_EXPORT_FLAG2))
785801
SEDMLWriter sedw = new SEDMLWriter(lems, lemsFile.getParentFile(), generateFormatFilename(lemsFile, Format.SEDML, null), lemsFile.getName(), Format.NEUROML2);
786802
for(File genFile : sedw.convert())
787803
{
788-
System.out.println("Writing to: " + genFile.getAbsolutePath());
804+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
789805
}
790806

791807
}
@@ -800,7 +816,7 @@ else if(args[1].equals(CELLML_EXPORT_FLAG))
800816
generateFormatFilename(lemsFile, Format.CELLML, null));
801817
for(File genFile : cellmlw.convert())
802818
{
803-
System.out.println("Writing to: " + genFile.getAbsolutePath());
819+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
804820
}
805821

806822
}
@@ -815,7 +831,7 @@ else if(args[1].equals(NINEML_EXPORT_FLAG) || args[1].equals(SPINEML_EXPORT_FLAG
815831
XineMLWriter xw = new XineMLWriter(lems, v, lemsFile.getParentFile(), lemsFile.getName().replaceAll("." + Format.LEMS.getExtension(), suffix));
816832
for(File genFile : xw.convert())
817833
{
818-
System.out.println("Writing to: " + genFile.getAbsolutePath());
834+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
819835
}
820836

821837
}
@@ -833,7 +849,7 @@ else if(args[1].equals(MATLAB_EXPORT_FLAG)/* || args[1].equals(MATLAB_EULER_EXPO
833849
MatlabWriter matlabw = new MatlabWriter(lems, lemsFile.getParentFile(), filename);
834850
for(File genFile : matlabw.convert())
835851
{
836-
System.out.println("Writing to: " + genFile.getAbsolutePath());
852+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
837853
}
838854

839855
}
@@ -848,7 +864,7 @@ else if(args[1].equals(CVODE_EXPORT_FLAG))
848864
cw.setSolver(CWriter.Solver.CVODE);
849865
for(File genFile : cw.convert())
850866
{
851-
System.out.println("Writing to: " + genFile.getAbsolutePath());
867+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
852868
}
853869

854870
}
@@ -863,7 +879,7 @@ else if(args[1].equals(MODELICA_EXPORT_FLAG))
863879
ModelicaWriter modw = new ModelicaWriter(lems, lemsFile.getParentFile(), mFile);
864880
for(File genFile : modw.convert())
865881
{
866-
System.out.println("Writing to: " + genFile.getAbsolutePath());
882+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
867883
}
868884

869885
}
@@ -876,7 +892,7 @@ else if(args[1].equals(DLEMS_EXPORT_FLAG))
876892
DLemsWriter dlemsw = new DLemsWriter(lems, lemsFile.getParentFile(), generateFormatFilename(lemsFile, Format.DLEMS, null), null);
877893
for(File genFile : dlemsw.convert())
878894
{
879-
System.out.println("Writing to: " + genFile.getAbsolutePath());
895+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
880896
}
881897

882898
}
@@ -900,7 +916,7 @@ else if(args[1].equals(BRIAN_EXPORT_FLAG) || args[1].equals(BRIAN2_EXPORT_FLAG))
900916

901917
for(File genFile : bw.convert())
902918
{
903-
System.out.println("Writing to: " + genFile.getAbsolutePath());
919+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
904920
}
905921
}
906922
else if(args[1].equals(OLD_GRAPH_FLAG) || args[1].equals(LEMS_GRAPH_FLAG))
@@ -911,7 +927,7 @@ else if(args[1].equals(OLD_GRAPH_FLAG) || args[1].equals(LEMS_GRAPH_FLAG))
911927
GraphWriter gw = new GraphWriter(lems, lemsFile.getParentFile(), generateFormatFilename(lemsFile, Format.GRAPH_VIZ, null));
912928
List<File> outputFiles = gw.convert();
913929
File gvFile = outputFiles.get(0);
914-
System.out.println("Writing to: " + gvFile.getAbsolutePath());
930+
System.out.println(GENERATED_FILE + gvFile.getAbsolutePath());
915931

916932
String imgFile = gvFile.getAbsolutePath().replace("." + Format.GRAPH_VIZ.getExtension(), "." + Format.PNG.getExtension());
917933
String cmd = "dot -Tpng " + gvFile.getAbsolutePath() + " -o " + imgFile;
@@ -965,7 +981,7 @@ else if(args[1].equals(SVG_FLAG))
965981
SVGWriter svgw = new SVGWriter(nmlDocument, nmlFile.getParentFile(), nmlFile.getName().replaceAll("." + Format.NEUROML2.getExtension(), "." + Format.SVG.getExtension()));
966982
for(File genFile : svgw.convert())
967983
{
968-
System.out.println("Writing to: " + genFile.getAbsolutePath());
984+
System.out.println(GENERATED_FILE + genFile.getAbsolutePath());
969985
}
970986
}
971987
else if(args[1].equals(PNG_FLAG))
@@ -979,7 +995,7 @@ else if(args[1].equals(PNG_FLAG))
979995
SVGWriter svgw = new SVGWriter(nmlDocument, nmlFile.getParentFile(), pngFileName);
980996

981997
svgw.convertToPng(pngFile);
982-
System.out.println("Writing to: " + pngFile.getAbsolutePath());
998+
System.out.println(GENERATED_FILE + pngFile.getAbsolutePath());
983999

9841000
}
9851001
else
@@ -1008,15 +1024,15 @@ else if(args.length == 3)
10081024
String val = entry.getValue();
10091025
File vwFile = new File(lemsFile.getParentFile(), "/" + key + ".vhdl");
10101026
FileUtil.writeStringToFile(val, vwFile);
1011-
System.out.println("Writing to: "+vwFile.getAbsolutePath());
1027+
System.out.println(GENERATED_FILE+vwFile.getAbsolutePath());
10121028
}
10131029

10141030
/*File vwFile = new File(lemsFile.getParentFile(), "/testbench.vhdl");
10151031
FileUtil.writeStringToFile(testbenchScript, vwFile);
10161032
System.out.println("Writing to: "+vwFile.getAbsolutePath());*/
10171033
File vwFile = new File(lemsFile.getParentFile(), "/testbench.prj");
10181034
FileUtil.writeStringToFile(prjScript, vwFile);
1019-
System.out.println("Writing to: "+vwFile.getAbsolutePath());
1035+
System.out.println(GENERATED_FILE+vwFile.getAbsolutePath());
10201036

10211037
}
10221038
}
@@ -1048,7 +1064,7 @@ else if(args.length == 4)
10481064

10491065
File lemsFile = SBMLImporter.convertSBMLToLEMSFile(sbmlFile, duration, dt, true);
10501066

1051-
System.out.println("Written to: " + lemsFile.getAbsolutePath());
1067+
System.out.println(GENERATED_FILE + lemsFile.getAbsolutePath());
10521068

10531069
}
10541070
else

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