Comments (4)
The reason is that in edu.ucsd.sbrg.escher.EscherConverter.parseEscherJson(EscherConverter.java:232)
escherJson.get(0) = null
and escherJson.get(1) = null
from escherconverter.
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.
from escherconverter.
@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.
from escherconverter.
Examples sent.
from escherconverter.
Related Issues (20)
- Documentation
- Live version returns a 403 Forbidden HOT 3
- Going the reverse direction: from standard format to Escher map HOT 2
- WARNING: java.lang.IllegalArgumentException: Invalid label bounds HOT 4
- Connections gone after conversion HOT 23
- ReconMap returns NullPointerException HOT 2
- Converting .json file to .sbml and back returns an IllegalArgumentException HOT 3
- Conversion stops at CreateMultiMarkers if neither BoundingBox nor Curve are set HOT 1
- Setting --gui=false returns JsonParseException HOT 1
- Inability to detect nodes leads to NullPointerException HOT 1
- NullPointerException when inferring compartment boundaries HOT 3
- WriteEscherJson cannot create new files
- Conversion SBML -> Escher creates mistake in file HOT 7
- SBML format convertion into Json file HOT 5
- Update to JSBML 1.5
- Potential security vulnerabilities in third-party library detected
- Problem with parsing BIGG IDs
- Incompatibility with SBGN because of dependency conflict
- Reading input file json file
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from escherconverter.