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MariaHei avatar MariaHei commented on August 20, 2024

The reason is that in edu.ucsd.sbrg.escher.EscherConverter.parseEscherJson(EscherConverter.java:232) escherJson.get(0) = null and escherJson.get(1) = null

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rmtfleming avatar rmtfleming commented on August 20, 2024

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=false

EscherConverter version 1.2.1
Copyright © 2015-2019 University of Tübingen
Systems Biology Research Group.
This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome
to redistribute it under certain conditions.
See http://www.opensource.org/licenses/mit-license.php.

05-Nov-2020 00:38:56 de.zbit.Launcher launchCommandLineMode --- INFO: Launching command-line mode of EscherConverter.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.EscherConverter batchProcess --- INFO: AutoDetect: Escher JSON file found
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.EscherConverter convert --- WARNING: Validating document
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.EscherConverter validateInput --- INFO: Validation: Escher JSON Schema version 1.0.0
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.EscherConverter convert --- WARNING: Validation failed
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.EscherConverter convert --- WARNING: Ignoring unsuccessful validation and moving forward
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.EscherConverter parseEscherJson --- INFO: Reading input file /home/rfleming/work/sbgCloud/programExperimental/projects/tracerBased/results/iDopaConservedMoieties/fol/iDopa_fol.json.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '34'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '12'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '26'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '31'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '1'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '5'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '5'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '10'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '27'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '15'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '2'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '1'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '1'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '1'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '1'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '16'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '0'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '9'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '7'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '44'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '10'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '25'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '1'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '44'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '35'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '1'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '56'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '12'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '51'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '6'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '29'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '26'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '2'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '28'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '19'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '1'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '46'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '38'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '21'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '39'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '32'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '14'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '9'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '28'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '33'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '5'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '32'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '18'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '14'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '60'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '21'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '2'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '35'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '58'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '65'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '1'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '15'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '25'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '45'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '1'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '6'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '28'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '7'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '61'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '43'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '19'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '51'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '31'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '0'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '1'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.model.EscherCompartment setId --- WARNING: Invalid compartment identifier '3'.
05-Nov-2020 00:38:56 edu.ucsd.sbrg.escher.EscherConverter parseEscherJson --- INFO: Finished reading.

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draeger avatar draeger commented on August 20, 2024

@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.

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rmtfleming avatar rmtfleming commented on August 20, 2024

Examples sent.

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