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Conversion from JSON to SBML stays at Reading input file #52

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MariaHei opened this issue Jul 29, 2019 · 4 comments
Open

Conversion from JSON to SBML stays at Reading input file #52

MariaHei opened this issue Jul 29, 2019 · 4 comments
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@MariaHei
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Converting some json files to SBML leads to the conversion getting stuck at reading input file in the gui or to a NullPointerException 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

Exception in thread "main" java.lang.NullPointerException
        at com.fasterxml.jackson.databind.ObjectMapper.treeToValue(ObjectMapper.java:1899)
        at edu.ucsd.sbrg.escher.EscherConverter.parseEscherJson(EscherConverter.java:232)
        at edu.ucsd.sbrg.escher.EscherConverter.parseEscherJson(EscherConverter.java:208)
        at edu.ucsd.sbrg.escher.EscherConverter.convert(EscherConverter.java:195)
        at edu.ucsd.sbrg.escher.EscherConverter.convert(EscherConverter.java:450)
        at edu.ucsd.sbrg.escher.EscherConverter.batchProcess(EscherConverter.java:327)
        at edu.ucsd.sbrg.escher.EscherConverter.commandLineMode(EscherConverter.java:384)
        at de.zbit.Launcher.launchCommandLineMode(Launcher.java:725)
        at de.zbit.Launcher.run(Launcher.java:862)
        at de.zbit.Launcher.<init>(Launcher.java:211)
        at edu.ucsd.sbrg.escher.EscherConverter.<init>(EscherConverter.java:263)
        at edu.ucsd.sbrg.escher.EscherConverter.main(EscherConverter.java:253)
@MariaHei MariaHei added the bug label Jul 29, 2019
@MariaHei
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The reason is that in edu.ucsd.sbrg.escher.EscherConverter.parseEscherJson(EscherConverter.java:232) escherJson.get(0) = null and escherJson.get(1) = null

DEVetter pushed a commit to DEVetter/EscherConverter that referenced this issue Oct 10, 2019
Towards issue draeger-lab#52
f615780 
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?
@DEVetter DEVetter mentioned this issue Dec 17, 2019
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@rmtfleming
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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.

@draeger
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draeger commented Dec 27, 2020

@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.

@rmtfleming
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Examples sent.

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@draeger @rmtfleming @MariaHei