search

virtualcell / vcell

Virtual Cell Framework
http://vcell.org/
Other
66 stars 20 forks source link

Error running in the server but no problem running local (invalid character) #842

Open pmendes opened 1 year ago

pmendes commented 1 year ago

When trying to run the attached VCML file on the server it fails with the error:

DataAccessException-RPC method DbRequestQueue:saveBioModel() failed: response status: 500 reason: internal error invoking DbRequestQueue:saveBioModel(): java.lang.RuntimeException: source document is not well-formedError on line 12023: An invalid XML character (Unicode: 0x13) was found in the element content of the document.

Note that before running you have to change to Adams-Moulton method. With CVODE the file runs but has an error (due to tolerances). When switching to Adams-Moulton and trying to run on the server then I get the above error message. Running it locally works without errors. vonDassow2000_1x4_timecourse1_simulation_xml_model.vcml.zip

ACowan0105 commented 1 year ago

Discussion at software meeting: Pedro suggested may relate to annotations, since this model has flybase annotations and our annotations do not have that yet. Issue #843 requests addition of annotations to flybase.