The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.
@draeger
This PR fixes the issue occured while simulating the OMEX test file (present at src/test/resources/omex) using OMEXExample.java
The error was
Exception in thread "main" java.lang.AssertionError: Simulatation failed: The model could not be resolved from its source reference. (Using uri: ./BIOMD0000000012.xml) at org.junit.Assert.fail(Assert.java:88) at org.simulator.examples.OMEXExample.main(OMEXExample.java:75)
The issue was that while running a temporarily created SED-ML file for simulation, the source file i.e. BIOMD0000000012.xml should also be present in the same directory. So, this PR also creates the source file in the same location where temporary SED-ML file is created.
Also, the deprecated getFile() method in OMEXArchive is replaced with the extractFile() method.
This PR also updates the OMEXExample.java and solves the SED-ML file similar to the how simple SED-ML file is solved (as in SEDMLExample.java).
@draeger This PR fixes the issue occured while simulating the OMEX test file (present at
src/test/resources/omex) usingOMEXExample.javaThe error wasException in thread "main" java.lang.AssertionError: Simulatation failed: The model could not be resolved from its source reference. (Using uri: ./BIOMD0000000012.xml) at org.junit.Assert.fail(Assert.java:88) at org.simulator.examples.OMEXExample.main(OMEXExample.java:75)The issue was that while running a temporarily created SED-ML file for simulation, the source file i.e.
BIOMD0000000012.xmlshould also be present in the same directory. So, this PR also creates the source file in the same location where temporary SED-ML file is created.Also, the deprecated getFile() method in OMEXArchive is replaced with the extractFile() method.
This PR also updates the
OMEXExample.javaand solves the SED-ML file similar to the how simple SED-ML file is solved (as inSEDMLExample.java).