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MyersResearchGroup / iBioSim

iBioSim is a computer-aided design (CAD) tool aimed for the modeling, analysis, and design of genetic circuits. It is capable of importing and exporting models specified using the Systems Biology Markup Language (SBML). iBioSim also supports the Synthetic Biology Open Language (SBOL), an emerging standard for information exchange in synthetic biology.
http://www.async.ece.utah.edu/ibiosim
Apache License 2.0
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Cannot Upload project to SynBioHub. #605

Open buggsley opened 4 years ago

buggsley commented 4 years ago

iBioSim Version 3.0.0

Operating system: Windows 10

Bug reported by: pfontanarrosa@gmail.com

Description: When trying to upload, I get the following error: org.synbiohub.frontend.SynBioHubException: 400 org.sbolstandard.core2.SBOLValidationException: sbol-10809: If a MapsTo is contained by a Module then the remote property of the MapsTo MUST refer to a FunctionalComponent in the ModuleDefinition that is referenced by the definition property of the Module. Reference: SBOL Version 2.3.0 Section 7.7.3 on page 29 :https://synbiohub.org/user/pfontanarrosa/Testingupload/Simulation_Environment_md/C1/YFP/1 at org.sbolstandard.core2.MapsTo.setRemote(MapsTo.java:242) at org.sbolstandard.core2.SBOLDocument.updateReferences(SBOLDocument.java:3122) at org.sbolstandard.core2.SBOLDocument.changeURIPrefixVersion(SBOLDocument.java:3310) at org.synbiohub.PrepareSubmissionJob.execute(PrepareSubmissionJob.java:349) at org.synbiohub.Main$1.run(Main.java:30) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

Fontanapink commented 4 years ago

Here is the project I am trying to upload. UploadProject.zip

cjmyers commented 4 years ago

I imported this OMEX file into a new project and uploaded successfully. Is this still having problems for you? Sorry for the long long delay on this one.