-
Notifications
You must be signed in to change notification settings - Fork 10
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Conversion from JSON to SBML stays at Reading input file #52
Comments
The reason is that in |
The file seems to be malformatted: it is missing meta-info and canvas-information: Added a Log-entry to inform the user (in GUI too) and an IOException with a corresponding message. Should malformatted files like this be parsed in any additional way?
I think I see this issue also, using the 1.2.1 binary. In this example, it seems to not progress beyond reading. Is it fixed in the new binary? rfleming@hex1:~/work/sbgCloud/code/fork-cobratoolbox/binary/all$ java -jar -Xms8G -Xmx8G -Duser.language=en /home/rfleming/work/sbgCloud/code/fork-cobratoolbox/binary/all/EscherConverter-1.2.1.jar --input=/home/rfleming/work/sbgCloud/programExperimental/projects/tracerBased/results/iDopaConservedMoieties/fol/iDopa_fol.json --format=SBML --output=/home/rfleming/work/sbgCloud/programExperimental/projects/tracerBased/results/iDopaConservedMoieties/fol/iDopa_fol_SBML_tmp.xml --gui=falseEscherConverter version 1.2.1
|
@rmtfleming Would you mind providing an example file (e.g., via direct e-mail)? I'd like to test it and see how to fix it. Also, with your file there seems a problem with compartment identifiers that we could fix automatically. |
Examples sent. |
Converting some json files to SBML leads to the conversion getting stuck at
reading input file
in the gui or to aNullPointerException
in the command line:java -jar -Xms8G -Xmx8G -Duser.language=en EscherConverter-1.2.1.jar --input=e_coli_core.escher.json --format=SBML --output=ecoli.sbml --gui=false
The text was updated successfully, but these errors were encountered: