search

shalinshah1993 / SBSCL

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.
https://draeger-lab.github.io/SBSCL/
GNU Lesser General Public License v3.0
0 stars 2 forks source link

Example SEDML L1V2 files have errors #37

Closed shalinshah1993 closed 6 years ago

shalinshah1993 commented 6 years ago

Example files from SED-ML L1V2 specification can be found here.

Example 1: The algorithm KIASO ID 0000282 isn't supported by SBSCL.

Example 2: Running this model gives following error:

 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:785) - Some characters cannot be read: 302 Found
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:785) - Some characters cannot be read: 302 Found
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:785) - Some characters cannot be read: 
  The resource was found at 
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:785) - Some characters cannot be read: https://sourceforge.net/p/libsedml/code/119/tree/trunk/Samples/models/oscli.xml?format=raw
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:785) - Some characters cannot be read: ;
you should be redirected automatically.

 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
12.06 13:34:59 WARNS org.simulator.sedml.SedMLSBMLSimulatorExecutor@252: Illegal character (NULL, unicode 0) encountered: not valid in any content
 at [row,col {unknown-source}]: [12,8]
12.06 13:34:59 WARNS org.simulator.sedml.SedMLSBMLSimulatorExecutor@446: Simulation failed during execution: stepper with model: model1
[Fatal Error] :12:8: Content is not allowed in trailing section.
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:785) - Some characters cannot be read: 302 Found
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:785) - Some characters cannot be read: 302 Found
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:785) - Some characters cannot be read: 
  The resource was found at 
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:785) - Some characters cannot be read: https://sourceforge.net/p/libsedml/code/119/tree/trunk/Samples/models/oscli.xml?format=raw
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:785) - Some characters cannot be read: ;
you should be redirected automatically.

 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
12.06 13:34:59 WARNS org.simulator.sedml.SedMLSBMLSimulatorExecutor@252: Illegal character (NULL, unicode 0) encountered: not valid in any content
 at [row,col {unknown-source}]: [12,8]
12.06 13:34:59 WARNS org.simulator.sedml.SedMLSBMLSimulatorExecutor@387: Simulation failed during execution: stepper with model: model1
Exception in thread "main" java.util.NoSuchElementException: No value present
    at java.util.Optional.get(Unknown Source)
    at org.simulator.sedml.SedMLSBMLSimulatorExecutor.run(SedMLSBMLSimulatorExecutor.java:402)
    at org.simulator.examples.SEDMLv2Example.main(SEDMLv2Example.java:45)

Example 3: The model source is E:\Users\fbergmann\Documents\sbml models\borisejb.xml.

Example 4: Running this model gives following error:

WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:785) - Some characters cannot be read: 302 Found
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:785) - Some characters cannot be read: 302 Found
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:785) - Some characters cannot be read: 
  The resource was found at 
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:785) - Some characters cannot be read: https://sourceforge.net/p/libsedml/code/119/tree/trunk/Samples/models/oscli.xml?format=raw
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:785) - Some characters cannot be read: ;
you should be redirected automatically.

 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
12.06 13:36:25 WARNS org.simulator.sedml.SedMLSBMLSimulatorExecutor@215: Illegal character (NULL, unicode 0) encountered: not valid in any content
 at [row,col {unknown-source}]: [12,8]
12.06 13:36:25 WARNS org.simulator.sedml.SedMLSBMLSimulatorExecutor@446: Simulation failed during execution: timecourse1 with model: model1
[Fatal Error] :12:8: Content is not allowed in trailing section.
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:785) - Some characters cannot be read: 302 Found
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:785) - Some characters cannot be read: 302 Found
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:785) - Some characters cannot be read: 
  The resource was found at 
 WARN (SBMLReader.java:1073) - Cannot find a parser for the  namespace
 WARN (SBMLReader.java:785) - Some characters cannot be read: https://sourceforge.net/p/libsedml/code/119/tree/trunk/Samples/models/oscli.xml?format=raw
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:785) - Some characters cannot be read: ;
you should be redirected automatically.

 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
 WARN (SBMLReader.java:1301) - !!! event.isEndElement: there is a problem in your SBML file !!!!
 WARN (SBMLReader.java:1302) - This should never happen, there is probably a problem with the parsers used.
 Try to check if one needed parser is missing or if you are using a parser in development.
12.06 13:36:25 WARNS org.simulator.sedml.SedMLSBMLSimulatorExecutor@215: Illegal character (NULL, unicode 0) encountered: not valid in any content
 at [row,col {unknown-source}]: [12,8]
12.06 13:36:25 WARNS org.simulator.sedml.SedMLSBMLSimulatorExecutor@387: Simulation failed during execution: timecourse1 with model: model1
Exception in thread "main" java.util.NoSuchElementException: No value present
    at java.util.Optional.get(Unknown Source)
    at org.simulator.sedml.SedMLSBMLSimulatorExecutor.run(SedMLSBMLSimulatorExecutor.java:402)
    at org.simulator.examples.SEDMLv2Example.main(SEDMLv2Example.java:45)

Example 5: The model source is E:\Users\fbergmann\Documents\sbml models\borisejb.xml

Please give suggestions as to what changes should we make to these example files. Issue https://github.com/shalinshah1993/SBSCL/issues/17 depends on this.

matthiaskoenig commented 6 years ago

Hi Shalin, yes there are many issues with the L1V2 examples. All these issues have been fixed in the L1V3 examples. I recommend using the L1V3 examples (with exception of the data ones) and just change the level and version from L1V3 to L1V2. L1V2 is subset of L1V3 so these examples will work. https://sed-ml.github.io/examples.html

M

shalinshah1993 commented 6 years ago

Okay! Thanks for adding them and creating test files @matthiaskoenig

@draeger do you know why SBML is giving those errors and what does that mean?

niko-rodrigue commented 6 years ago

If the source is "E:\Users\fbergmann\Documents\sbml models\borisejb.xml" it probably mean that libsedml cannot find it in your system and probably pass a strange String to JSBML which then output these warnings. Let's start from scratch with the L1V3 examples. We will see if we see further warnings/errors then.

shalinshah1993 commented 6 years ago

This issue was moved to draeger-lab/SBSCL#19