#15 SBML2SBML ACSN

[Anonymous]

I'm attempting to convert the atlas of cancer signalling networks into SMBL L2V4, from here

https://acsn.curie.fr/ACSN2/downloads/XMLs/acsn2_global_master.xml

The online tool returns error 22 and error 23, both with the note:

The conversion could not begin, please check the URL provided

Exception detailsjava.net.ConnectException: Connection timed out

Using the downloadable tool (latest version from SVN) I am able to run the conversion, but it gives a blank file. To get the code to run, I edit LD_LIBRARY_PATH to point to the lib folder where libsbml has been installed (through macports), edit line that run readline (which gives an error on my machine) to manually point to the sbfc install location, and edit the line pointing to the system java location. No errors are returned following the run, but the log file reads;

---

2021-02-16 12:08
sbfConverter.sh: Convertion, using SBML2SBML_L2V4, for 'acsn2_global_master.xml'...

---

java.io.FileNotFoundException: src/org/sbfc/ontology/go.obo (No such file or directory)
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(FileInputStream.java:212)
at java.base/java.io.FileInputStream.<init>(FileInputStream.java:154)
at java.base/java.io.FileInputStream.<init>(FileInputStream.java:109)
at java.base/java.io.FileReader.<init>(FileReader.java:60)
at org.sbfc.ontology.OboOntology.<init>(OboOntology.java:76)
at org.sbfc.converter.biopax2sbml.BioPAX2SBML.<clinit>(BioPAX2SBML.java:170)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:340)
at org.util.classlist.ConverterSearcher.isConverter(ConverterSearcher.java:60)
at org.util.classlist.ConverterSearcher.getConverterFullNameList(ConverterSearcher.java:105)
at org.sbfc.converter.Converter.<clinit>(Converter.java:52)
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/Users/benjamin/src/sbfc-code/lib/jsbml-1.5-with-dependencies.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/Users/benjamin/src/sbfc-code/lib/paxtools/paxtools-5.0.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.apache.logging.slf4j.Log4jLoggerFactory]
Loading the default Identifiers.org registry database from the jar file.
java.lang.ClassNotFoundException: org.sbfc.converter.SBML2SBML
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:602)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:340)
at org.sbfc.converter.Converter.convertFromFile(Converter.java:167)
at org.sbfc.converter.Converter.convertFromFile(Converter.java:138)
at org.sbfc.converter.Converter.main(Converter.java:305)
</clinit></clinit></init></init></init></init>

Please could you advise how to move forward with the conversion?