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jcschaffjcschaff
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bump to 0.0.6, record instantiating jsbml classes using reflection
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+50
-4
lines changed

2 files changed

+50
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lines changed

‎pyproject.toml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
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[tool.poetry]
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name = "libvcell"
7-
version = "0.0.5"
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version = "0.0.6"
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description = "This is a python package which wraps a subset of VCell Java code as a native python package."
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authors = ["Jim Schaff <[email protected]>", "Ezequiel Valencia <[email protected]>"]
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repository = "https://github.com/virtualcell/libvcell"

‎vcell-native/src/main/java/org/vcell/libvcell/MainRecorder.java‎

Lines changed: 49 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -24,21 +24,67 @@ public static void main(String[] args) {
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PropertyLoader.setProperty(PropertyLoader.vcellServerIDProperty, "none");
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PropertyLoader.setProperty(PropertyLoader.mongodbDatabase, "none");
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// exercise the sbmlToFiniteVolumeInput and vcmlToFiniteVolumeInput methods
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try (FileInputStream f_sbml = new FileInputStream(sbml_file)) {
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byte[] data = f_sbml.readAllBytes();
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logger.info("Read " + data.length + " bytes from " + sbml_file.getAbsolutePath());
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String sbml_str = new String(data);
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sbmlToFiniteVolumeInput(sbml_str, output_dir);
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//vcmlToFiniteVolumeInput(vcml_str, sim_name, new File(args[1]));
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}
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// read sbml_file and create a string object
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try (FileInputStream f_vcml = new FileInputStream(vcml_file)) {
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byte[] data = f_vcml.readAllBytes();
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logger.info("Read " + data.length + " bytes from " + vcml_file.getAbsolutePath());
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String vcml_str = new String(data);
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vcmlToFiniteVolumeInput(vcml_str, vcml_sim_name, output_dir);
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}
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// use reflection to load jsbml classes and call their default constructors
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Class.forName("org.sbml.jsbml.AlgebraicRule").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.Annotation").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.AssignmentRule").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.Compartment").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.CompartmentType").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.Constraint").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.Delay").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.Event").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.EventAssignment").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.FunctionDefinition").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.InitialAssignment").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.KineticLaw").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.ListOf").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.LocalParameter").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.Model").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.ModifierSpeciesReference").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.Parameter").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.Priority").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.RateRule").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.Reaction").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.Species").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.SpeciesReference").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.SpeciesType").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.StoichiometryMath").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.Trigger").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.Unit").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.UnitDefinition").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.ArraysParser").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.CompParser").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.DistribParser").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.DynParser").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.FBCParser").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.GroupsParser").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.L3LayoutParser").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.LayoutParser").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.MathMLStaxParser").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.MultiParser").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.QualParser").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.RenderParser").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.ReqParser").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.SBMLCoreParser").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.SBMLLevel1Rule").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.SpatialParser").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader").getDeclaredConstructor().newInstance();
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Class.forName("org.sbml.jsbml.xml.parsers.XMLNodeReader").getDeclaredConstructor().newInstance();
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} catch (Exception e) {
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System.out.println(e.getMessage());
4490
logger.error("Error processing spatial model", e);

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