Submit VCell <IP_ADDRESS>

id: vcell
version: <IP_ADDRESS>
specificationsUrl: https://github.com/virtualcell/vcell/releases/download/<IP_ADDRESS>/biosimulators.json
specificationsPatch:
version: <IP_ADDRESS>
image:
url: ghcr.io/virtualcell/biosimulators_vcell:<IP_ADDRESS>
digest: "sha256:78ae012e68a32c2d0cb9548079eb5e62b88ab74f0b349cb5fab7580712f7a9e6"
validateImage: true
commitSimulator: false

Thank you @vcdaemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, and validating your Docker image. You have chosen not to submit your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator validation job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (2.7 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log: None

cli.CliDisplaysHelpInline (4.5 s)

Test that a command-line interface provides inline help.
Warnings:
Command-line interfaces should display basic help when no arguments are provided.

The command-line interface displayed the following when no argument was provided:

  docker: Command recieved::<>
  <>
  Default case selected
  VCell shall execute <biosimulations >
   INFO (CLIStandalone:38) - Starting Vcell... []{}
  ERROR (BiosimulationsCommand:112) - null []{}
  java.lang.NullPointerException: null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:51) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Command-line interface should support the `-h` option for displaying help inline.

The command-line interface displayed the following when executed with `-h`:

  docker: Command recieved::<-h>
  <-h>
  Default case selected
  VCell shall execute <biosimulations -h>
   INFO (CLIStandalone:38) - Starting Vcell... []{}
  Usage: CLIStandalone biosimulations [-dhqv] [-i=<ARCHIVE>] [-o=<OUT_DIR>]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    -d, --debug               full application debug mode
    -h, --help                show this help message and exit
    -i, --archive=<ARCHIVE>   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    -o, --out-dir=<OUT_DIR>   Directory to save outputs
    -q, --quiet               suppress all console output
    -v, --version             show program's version number and exit

Command-line interface should support the `--help` option for displaying help inline.

The command-line interface displayed the following when executed with `--help`:

  docker: Command recieved::<--help>
  <--help>
  Default case selected
  VCell shall execute <biosimulations --help>
   INFO (CLIStandalone:38) - Starting Vcell... []{}
  Usage: CLIStandalone biosimulations [-dhqv] [-i=<ARCHIVE>] [-o=<OUT_DIR>]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    -d, --debug               full application debug mode
    -h, --help                show this help message and exit
    -i, --archive=<ARCHIVE>   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    -o, --out-dir=<OUT_DIR>   Directory to save outputs
    -q, --quiet               suppress all console output
    -v, --version             show program's version number and exit

Log: None

docker_image.DeclaresSupportedEnvironmentVariables (0.5 s)

Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log: None

docker_image.HasBioContainersLabels (0.3 s)

Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

Skips
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000263

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log: None

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:
Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000496

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000437

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:
Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorProducesLinear3DPlots (0.4 s)

Test that a simulator produces linear 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.4 s)

Test that a simulator produces logarithmic 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.4 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsComputeModelChanges (23.7 s)

Test that a simulator supports compute model changes
Reason for skip:
Simulator did not produce the following reports:
  - `BIOMD0000000912_sim.sedml/report`

Log:
docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:38) - Starting Vcell... []{}

 INFO (PropertyLoader:577) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{}

 INFO (PropertyLoader:583) - ServerID=<IP_ADDRESS>, SoftwareVersion=<IP_ADDRESS> []{}

 INFO (BiosimulationsCommand:98) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:119) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:507) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (NativeLib:29) - Loading combinej []{}

 INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_c2116e8f-ac00-4cfa-aeea-290705f908555470525652818891965 []{}

 INFO (SedmlJob:107) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:330) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

ERROR (SedmlJob:253) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

 INFO (SedmlJob:273) - Generating outputs...  []{}

 INFO (SedmlJob:361) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:156) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:435) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document.

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:298) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 WARN (SedmlJob:306) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:144) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@4821aa9f []{}

 INFO (NativeLib:29) - Loading jhdf5 []{}

 INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:172) - Omex archive.omex processing completed (5s) []{}

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:38) - Starting Vcell... []{}

 INFO (PropertyLoader:577) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{}

 INFO (PropertyLoader:583) - ServerID=<IP_ADDRESS>, SoftwareVersion=<IP_ADDRESS> []{}

 INFO (BiosimulationsCommand:98) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:119) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:507) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (NativeLib:29) - Loading combinej []{}

 INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_d1d96468-9706-48e6-9f6c-d66f514be698429443898631895116 []{}

 INFO (SedmlJob:107) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:330) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

ERROR (SedmlJob:253) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

 INFO (SedmlJob:273) - Generating outputs...  []{}

 INFO (SedmlJob:361) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:156) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:435) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document.

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:298) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 WARN (SedmlJob:306) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:144) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@1afd72ef []{}

 INFO (NativeLib:29) - Loading jhdf5 []{}

 INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:172) - Omex archive.omex processing completed (5s) []{}

sedml.SimulatorSupportsModelAttributeChanges (23.0 s)

Test that a simulator supports changes to the attributes of model elements
Reason for skip:
Simulator did not produce the following reports:
  - `BIOMD0000000912_sim.sedml/report`

Log:
docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:38) - Starting Vcell... []{}

 INFO (PropertyLoader:577) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{}

 INFO (PropertyLoader:583) - ServerID=<IP_ADDRESS>, SoftwareVersion=<IP_ADDRESS> []{}

 INFO (BiosimulationsCommand:98) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:119) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:507) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (NativeLib:29) - Loading combinej []{}

 INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_c7e87612-aa5a-4c4b-94a2-fb426c1bfe543322166117156827019 []{}

 INFO (SedmlJob:107) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (StringTools:486) - Could not create an integer from the string x []{}

ERROR (SolverHandler:330) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:839) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:838) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

ERROR (SedmlJob:253) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

 []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:839) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:838) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

 INFO (SedmlJob:273) - Generating outputs...  []{}

 INFO (SedmlJob:361) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:156) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:435) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document.

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:298) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 WARN (SedmlJob:306) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

Failure executing the sed document.  []{}

ERROR (ExecutionJob:144) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@1f9d6c7b []{}

 INFO (NativeLib:29) - Loading jhdf5 []{}

 INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:172) - Omex archive.omex processing completed (4s) []{}

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:38) - Starting Vcell... []{}

 INFO (PropertyLoader:577) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{}

 INFO (PropertyLoader:583) - ServerID=<IP_ADDRESS>, SoftwareVersion=<IP_ADDRESS> []{}

 INFO (BiosimulationsCommand:98) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:119) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:507) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (NativeLib:29) - Loading combinej []{}

 INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_844876a4-f480-4fd5-886c-eded6ec20c251452112155771722980 []{}

 INFO (SedmlJob:107) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:330) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

ERROR (SedmlJob:253) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

 INFO (SedmlJob:273) - Generating outputs...  []{}

 INFO (SedmlJob:361) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:156) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:435) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document.

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:298) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.ja ...

The image for your simulator is valid!


[PL-1776] cas overlay build error

Seems like jcifs-ext:0.9.4 was removed from all listed repos.

Can one of the admins verify this patch?

test this please


Failure Management

Disable a subscription after a number of consecutive failures has been reach. Failure defined as not status code 200.

If a webhook callback fails three consecutive times, or the value of the MAXFAILS environment variable, that callback will be disabled. It can only be re-enabled at the database level. This is by design. To do this, the administrator will reset the "failcount" field to 0 and the "active" field to true.


New ram configuration

@artokin

Documentation updated. How we do with the jenkins configuration?

LGTM, please use squashing when mergin in.

Has this been tested with mbed OS 5.6?
I see this has been merged in master instead of the oob branch.


Upgrade gradle version

Hello 👋,
Are there any plans in upgrading the gradle version? It is currently blocking the upgrade of some other packages.
I would be more than happy to help with this.
Thanks!

Thanks, @ Vlad-Adrian, I may not have time to follow up on this issue, feel free to open PR and welcome!

Hi @littleGnAl, I raised a PR for this issue. Can you please check it when you have some time.
Thanks!

The 1.0.1 with the upgrade was published to pub.dev
https://pub.dev/packages/http_proxy_override/versions/1.0.1


tvhebdo.com Canadian epg request

tvhebdo.com Canadian epg request

The guide from tvhebdo.com is now available at this link:
https://iptv-org.github.io/epg/guides/ca/tvhebdo.com.epg.xml

source need ca proxy so how to use proxy with epg-grabber ??

fixed by using http_proxy env before execution.


docker-compse up -d  出现如下 problem

[root@roerpcs11 redmine]# docker-compose up --build
redmine_1     | rm: cannot remove '/home/redmine/redmine/vendor/bundle/ruby/2.3.0/bin': Directory not empty
redmine_1     | rm: cannot remove '/home/redmine/redmine/vendor/bundle/ruby/2.3.0/cache': Directory not empty

You've not given me many details here.  But I'd recommend running docker-compose down and deleting the tmp directory at /srv/docker/redmine/redmine.  I generally see this if I've changed redmine versions.

when I delete all files  at /srv/docker/redmine/ ，then i execute “docker-compse up -d”
it looks likes as  fellow:
[root@rofckub12 jisd]# docker logs b9aa724da1f9
Initializing logdir...
Initializing datadir...
Generating OpenSSH client keys...
Symlinking dotfiles...
Installing configuration templates...
Configuring redmine...
Configuring redmine::database....
Configuring redmine::unicorn...
Configuring redmine::secret_token...
Generating a session token...
Note:
All old sessions will become invalid.
Please specify the REDMINE_SECRET_TOKEN parameter for persistence.
SHOULD be defined if you have a load-balancing Redmine cluster.
Configuring redmine::max_concurrent_ajax_uploads...
Configuring redmine::sudo_mode...
Configuring redmine::autologin_cookie...
Configuring redmine::backups...
Configuring nginx...
Configuring nginx::redmine...
Migrating database. Please be patient, this could take a while...
redmine_production already exists
rm: cannot remove '/home/redmine/redmine/vendor/bundle/ruby/2.3.0/bin': Directory not empty
rm: cannot remove '/home/redmine/redmine/vendor/bundle/ruby/2.3.0/cache': Directory not empty
rm: cannot remove '/home/redmine/redmine/vendor/bundle/ruby/2.3.0/extensions/x86_64-linux/2.3.0/kgio-2.11.2': Directory not empty
rm: cannot remove '/home/redmine/redmine/vendor/bundle/ruby/2.3.0/extensions/x86_64-linux/2.3.0/mysql2-0.4.10/mysql2': Directory not empty
rm: cannot remove '/home/redmine/redmine/vendor/bundle/ruby/2.3.0/extensions/x86_64-linux/2.3.0/nokogiri-1.8.3/nokogiri': Directory not empty
rm: cannot remove '/home/redmine/redmine/vendor/bundle/ruby/2.3.0/extensions/x86_64-linux/2.3.0/pg-0.18.4': Directory not empty
rm: cannot remove '/home/redmine/redmine/vendor/bundle/ruby/2.3.0/extensions/x86_64-linux/2.3.0/raindrops-0.19.0': Directory not empty
rm: cannot remove '/home/redmine/redmine/vendor/bundle/ruby/2.3.0/extensions/x86_64-linux/2.3.0/redcarpet-3.4.0': Directory not empty
rm: cannot remove '/home/redmine/redmine/vendor/bundle/ruby/2.3.0/extensions/x86_64-linux/2.3.0/rmagick-2.16.0': Directory not empty
rm: cannot remove '/home/redmine/redmine/vendor/bundle/ruby/2.3.0/extensions/x86_64-linux/2.3.0/unicorn-5.4.0': Directory not empty
rm: cannot remove '/home/redmine/redmine/vendor/bundle/ruby/2.3.0/gems/actionmailer-4.2.8/lib/action_mailer': Directory not empty

Did you run docker-compose down?

Closed due to no user input


[WIP] Send email notification after safety comments are changed

Fixes #245
Created a simpler mailer class to send a notification email to the user that edited the safety comments and the Dream (camp) creator.
The email  contents can be edited in : app/views/camp_mailer/safety_comments_updated.html.erb (html)
or app/views/camp_mailer/safety_comments_updated.text.erb (text)
@LioraNaginsky : The email is using the general email layout from app/views/layouts/mailer.{html,text}.erb - In those files there is a line <%= yield %> that inserts the specific mail content (from the above files) and other than that we can edit those files to insert common email content.
@LioraNaginsky @rootux

@enoodle Looks great. Can you specify which tests did you do to make sure this works?

@rootux

Can you specify which tests did you do to make sure this works?

I added two tests: one that makes sure that the controller can render a simple sample mail, sanity check to prevent us from breaking something in the view files. Another is a test in the camps controller spec that makes sure that when the comment file is updated we are calling the email sending function in that controller.


Telemetry points for SQL Database Projects extension

Adds telemetry points for the sql-database-projects extension to cover the following scenarios:

open/create
build
publish
schema compare launch
project item add/delete/exclude/validate
target platform change
sqlproj editing
database references add/remove

Pull Request Test Coverage Report for Build 522053499

45 of 79 (56.96%)  changed or added relevant lines in 7 files are covered.
529 unchanged lines in 14 files lost coverage.
Overall coverage increased (+0.06%) to 43.306%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

extensions/sql-database-projects/src/dialogs/addDatabaseReferenceDialog.ts
2
3
66.67%

extensions/sql-database-projects/src/controllers/projectController.ts
28
61
45.9%

Files with Coverage Reduction
New Missed Lines
%

extensions/resource-deployment/src/interfaces.ts
1
95.88%

extensions/sql-database-projects/src/dialogs/addDatabaseReferenceDialog.ts
1
61.44%

extensions/sql-database-projects/src/projectProvider/projectProvider.ts
1
37.5%

extensions/resource-deployment/src/main.ts
7
0%

extensions/sql-database-projects/src/controllers/projectController.ts
7
59.4%

extensions/resource-deployment/src/common/utils.ts
8
64.38%

extensions/arc/src/providers/arcControllersOptionsSourceProvider.ts
10
0%

extensions/resource-deployment/src/ui/notebookWizard/notebookWizardModel.ts
16
7.69%

extensions/resource-deployment/src/ui/resourceTypeWizard.ts
36
8.47%

src/sql/workbench/browser/modelComponents/viewBase.ts
37
1.49%

Totals

Change from base Build 516588758:
0.06%

Covered Lines:
24664

Relevant Lines:
52153

💛  - Coveralls

Pull Request Test Coverage Report for Build 522053499

45 of 79 (56.96%)  changed or added relevant lines in 7 files are covered.
529 unchanged lines in 14 files lost coverage.
Overall coverage increased (+0.06%) to 43.306%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

extensions/sql-database-projects/src/dialogs/addDatabaseReferenceDialog.ts
2
3
66.67%

extensions/sql-database-projects/src/controllers/projectController.ts
28
61
45.9%

Files with Coverage Reduction
New Missed Lines
%

extensions/resource-deployment/src/interfaces.ts
1
95.88%

extensions/sql-database-projects/src/dialogs/addDatabaseReferenceDialog.ts
1
61.44%

extensions/sql-database-projects/src/projectProvider/projectProvider.ts
1
37.5%

extensions/resource-deployment/src/main.ts
7
0%

extensions/sql-database-projects/src/controllers/projectController.ts
7
59.4%

extensions/resource-deployment/src/common/utils.ts
8
64.38%

extensions/arc/src/providers/arcControllersOptionsSourceProvider.ts
10
0%

extensions/resource-deployment/src/ui/notebookWizard/notebookWizardModel.ts
16
7.69%

extensions/resource-deployment/src/ui/resourceTypeWizard.ts
36
8.47%

src/sql/workbench/browser/modelComponents/viewBase.ts
37
1.49%

Totals

Change from base Build 516588758:
0.06%

Covered Lines:
24664

Relevant Lines:
52153

💛  - Coveralls


Fix bad arithmetic expression with overflow

Description
There are spurious crashes in production due to this arithmetic expression. It seems like the issue is caused by an overflow when multiplying a uint64_t by 8.
[] It needs and includes Unit Tests
Changes in Client or Server public APIs
Not needed.
[] It includes documentation for these changes in /doc.

This issue was finally fixed by #1359


Cloning

Includes #200; adds one commit: f8551c72048afee57e2a12deb690d6b3e0ca702d
Fixes CMap blueprint Clone method & refactor cloning.

CMap now requires types to implement Clone.
Clone methods now all take non-pointer receivers as this shaves a couple of lines off their implementations. (Remember, methods defined on non-pointer receivers are also defined on their pointer receivers; calling them on pointers implies an in-memory copy being made prior to the method being called.)
Clone methods added to many types so each one is shorter.

I suspect the test coverage will be stable, but maybe these should have their own tests...

Current coverage is 59.84% (diff: 89.23%)

Merging #201 into master will increase coverage by 0.22%

@@             master       #201   diff @@
==========================================
  Files           120        119     -1
  Lines          6401       6427    +26
  Methods           0          0
  Messages          0          0
  Branches          0          0
==========================================
+ Hits           3816       3846    +30
+ Misses         2254       2249     -5
- Partials        331        332     +1

Powered by Codecov. Last update a45902d...f8551c7


DCOS-38238: Temporarily disable tests that are failing due to Mesos Fetcher regression.

https://issues.apache.org/jira/browse/MESOS-9008

We also need to ensure that we track enabling the tests again.

We also need to ensure that we track enabling the tests again.

I created a ticket to track that: https://jira.mesosphere.com/browse/DCOS-38370


[AS-4497] Add flow to tapped buy now

The type of this PR is: Feature

This PR resolves EMI-1829
Description

PR Checklist (tick all before merging)

[ ] If I've added a new file to the tree I've exported it from the common index.ts
[ ] I've added comments with examples for any new interfaces and ensured that they're in the docs
[ ] No platform-specific terminology has been used outside of click and tap (platform is inferred by the DB storing events)

:rocket: PR was released in v4.175.0 :rocket:


schedule job to sweep stale sessions

Context

Sessions are now server side and therefore need pruning once stale

Changes proposed in this pull request

Prune any stale sessions last updated over 15 days ago

Guidance to review

none

If you end up with more jobs, perhaps it would be worth looking at the way R&P handles cron jobs with delayed_job. It's probably easier to track when it's handled inside application, rather than on another platform (github actions in this case).

I took a look at cron-esque things for delayed job but thought they were all mediocre at best. They all rely on enqueuing the next job after a job has completed which seems brittle to me. Which it why I opted for the workflow as I see that as far less likely to fail.


Mismatch version in WEB UI

Hi,
When starting InfluxDB 2.0.6, the version displayed in WEB UI is 2.0.5
Tested with InfluxDB sources and docker image (docker run -p 8086:8086 influxdb:2.0.6)

Duplicate of influxdata/influxdata-docker#484
See the explanation there. I'll leave this one open for others to find.

Closed by #21564


Is there a way to prevent maids from taking damage from players in the game?

everytime my maid gets in front of me they take damage, including other players i'm playing with can hurt/kill my maid and vise versa with theirs, i was wondering if there's a way to keep them from taking any damage from players playing in the game.

Domestication Innovation

Or look for other versions of the mod
ps: my English is not very good, so I used this translator

Suggest Domestication Innovation Mod


Provide more detailed instructions for image file storage when using django-storages

Provide a subsection of Custom image models, "Custom image storage"
Pertinent section of the Wagtail docs
https://docs.wagtail.org/en/stable/advanced_topics/images/custom_image_model.html#custom-image-model
Details
I'm new to wagtail, so this would be for someone else trying to make the image portion of the tutorial work using django-storages. This was much more challenging to figure out than I expected.
I don't want it to be overly specific, but I could not understand what was happening, so hopefully this helps someone else. Happy to take feedback here or if suggested, I'll generate a PR to iterate from.
Custom image paths
When images are saved, wagtail stores the original image along with one or more renditions.
To affect the path of the original image storage and the path of the storage of the renditions, you'll need to first specify custom classes inheriting from AbstractImage and AbstractRendition as explained in Custom image models.
You will also need to override the get_upload_to method:
class CustomWagtailImage(Image):
    def get_upload_to(self, filename):
        return os.path.join(settings.WAGTAIL_BLOG_IMAGES_PATH, filename)

    admin_form_fields = Image.admin_form_fields + ()

To handle the rendition paths, you'll need to set the WAGTAILIMAGES_RENDITION_STORAGE variable in settings.py.  This should refer to a storage backend.
[as a callout]
Note: If you're using django-storages and have subclassed a storage backend for the rest of your site, you can refer to that or create a second class specific to wagtail image storage.  For example, if your storage backend class is:
class WagtailImagesPublicMediaStorage(S3Boto3Storage):  # noqa
    location = '/my/custom/wagtail/image/path'
    default_acl = 'public-read'
    file_overwrite = True

You would want to settings.py to include:
WAGTAILIMAGES_RENDITION_STORAGE = 'cos_django.storage_backends.WagtailImagesPublicMediaStorage'

'remote: Permission to wagtail/wagtail.git denied to shindodkar.
fatal: unable to access 'https://github.com/wagtail/wagtail.git/': The requested URL returned error: 403'
this error is showing every time I try to make PR @lb- how to solve it ...?

@banagale Is the issue still open? I would like to give it a go...

@kituuu Feel free to just go for it if you feel confident with it. You'll need to be able to understand the use case and package usage.

Now that #11749 is merged, any new documentation about this should advise using an alias from STORAGES as WAGTAILIMAGES_RENDITION_STORAGE, rather than a dotted path.


Adding Temp Sensor and Different modes as well as silent button

Adding support for the temperature sensor as a temp sensor and different modes such as sleep, auto etc and support for the silent button make everything a button including oscillating

Temperature, assuming it's returned by the api, should be an easy add. HomeKit, surprisingly, does not support different modes so that's not possible in a way done well.

Based on my review of the HA code, temperature does seem to be returned by the api. I'll take a look and see if I can get it added to this one via a PR.

The websocket connection reports the temperature sensor state so that should be feasible to implement. I agree with @alvst that the modes would be difficult to implement in a clean way. Though I could add a toggle to the config to just permanently mute the fan if that's something people would be interested in.

The reason I didn't initially implement the temp sensor is because I've found it to be inaccurate.

Yes that makes sense. I find the temp sensor in my dreo to be 2-3 degrees, sometimes more, higher than my other temperature sensors say.

maybe adjust it down by 2-3 degrees or asking the user in home bridge setup optionally the difference in temp then adding it later?

Took me a while because I forgot about this but I've created a pull request with the temperature sensor added as well as the offset and ability to show/hide the temperatures sensors. for simplicity, if you have multiple fans, you can't show/hide individual temperature sensors, but you can always hide those within the home app.

Thank You!

Version 3.2 with Temp sensor is off significantly in homekit compared to what it is in the Dreo app.   So my Deep app is reading 68 degrees F and Homekit is reading 154 degrees F

Version 3.2 with Temp sensor is off significantly in homekit compared to what it is in the Dreo app. So my Deep app is reading 68 degrees F and Homekit is reading 154 degrees F

I’m having a similar issue. My Dreo fan temp sensor is showing 100 degrees Fahrenheit higher than the actual reading in the Dreo app. This is new behavior in 3.2.

The conversion between Celsius and Fahrenheit is off. I submitted a fix yesterday waiting on approval.


llama3 tokenizer compatibility of DPOTrainer

I see annotations in build_tokenized_answer of DPOTrainer regarding llama tokenizer compatibility.
"""
Llama tokenizer does satisfy enc(a + b) = enc(a) + enc(b).
It does ensure enc(a + b) = enc(a) + enc(a + b)[len(enc(a)):].
Reference:
https://github.com/EleutherAI/lm-evaluation-harness/pull/531#issuecomment-1595586257
"""
I'm confused because it says on top that enc(a+b)=enc(a)+enc(b) is guarantted and also it says
"        # On some tokenizers, like Llama-2 tokenizer, there are occasions where tokens
# can be merged together when tokenizing prompt+answer. This could result
# on the last token from the prompt being different when tokenized on its own
# vs when done as prompt+answer.
"
I might be misunderstood but they seem conflicted.
However I believe the contributors must have covered any possible issues with llama2 tokenizers.
My question is, is this also the case with llama3?
Because I don't see any comments regarding llama3 tokenizer.

I understand your question. This will change with #2209, as we will tokenize prompt and completion separately.
Feel free to take a look at the corresponding section in the PR description.


Mavenization of the hammer and raw pcap streaming support.

There are some things left to do, like define some run profiles for meet.jit.si, beta.meet.jit.si, etc.

This PR is being reworked.


Fix python lint errors.

tox lint is suddenly complaining about binary operators at the end
of the line.  Change pfs_middleware/tox.ini to ignore that warning.
A regular expression in pfs_middleware/pfs_middleware/utils.py used
double quotes for the RE without escaping \d.  Change it to use
a raw string.

This does seem to fix the problem!


docs: update to badge

Description
update to badge
Release required?

[x] No release
[ ] Patch release (x.x.X)
[ ] Minor release (x.X.x)
[ ] Major release (X.x.x)

Release notes content

Run the pipeline
If the CI pipeline doesn't run when you create the PR, the PR requires a user with GitHub collaborators access to run the pipeline.
Run the CI pipeline when the PR is ready for review and you expect tests to pass. Add a comment to the PR with the following text:
/run pipeline

Checklist for reviewers

[ ] If relevant, a test for the change is included or updated with this PR.
[ ] If relevant, documentation for the change is included or updated with this PR.

For mergers

Use a conventional commit message to set the release level. Follow the guidelines.
Include information that users need to know about the PR in the commit message. The commit message becomes part of the GitHub release notes.
Use the Squash and merge option.

@vburckhardt @SirSpidey Do you have any thoughts on the badge for the security approved modules?
Let me know your thoughts and post that will run the pipeline.

As I understand it based on the slack conversation, we'll take a different path to show certified modules.

Now I have updated as per our slack conversation back to graduated.

/run pipeline

:tada: This PR is included in version 2.4.1 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


Update README.md to remove extra spaces in installation command

Made installation command a single line to avoid extra spaces.

@shyiko feel free to merge or if a new version is coming soon you could do that in the same PR (removing extra spaces)


Create, rename and delete a local space

Create new space

Settings

Not visible when base space is selected

Delete

Note: we may want to iterate on/improve the space deletion flow to seek confirmation in a stricter way (type in space name).

Note: UI tests have not yet been added - I tried to write some but our Redux implementation needs a little work before it's ready for quality testing of components that are linked to Redux.

(I rebased this to get the changes for the string-to-single-object PR that merged before it)


Feature: A possibility to set any mesh as the global audio listener

Hey all,
This is my first contribution, so let me start by saying how amazing BabylonJS is, and thanks to all working on this project.
Regarding this feature: currently, the only possible listener for any spatial sounds in the scene is the active camera. This is fine in all cases where the active camera is actually "you".
The problem:
In my game, the camera is positioned always at the Vector3(0, 105, 105) and follows the player around. If the player encounters door for example, that has sound attached to it with spatial distance of 60, the camera will not be able to hear that sound (simply because it's too far away). Right now I am solving this by creating all sounds in the same distance of it's mesh as the camera is from player (so the sound position is mesh.position + Vector3(0, 105, 105)). This works, if the camera is static and is not rotating with the player object.
The solution:
Maybe I am naive, but by reverse engineering the audio engine, I realised the solution should be very simple.
In the file https://github.com/BabylonJS/Babylon.js/blob/d7827d78296faf574984a370dbe25a0a7b93d63f/src/Audio/audioSceneComponent.ts on line 387 we have the _afterRender function that determines the camera's global position and set's the listener position.
 private _afterRender() {
        const scene = this.scene;
        if (!this._audioEnabled || !scene._mainSoundTrack || !scene.soundTracks || (scene._mainSoundTrack.soundCollection.length === 0 && scene.soundTracks.length === 1)) {
            return;
        }

        var listeningCamera: Nullable<Camera>;
        var audioEngine = Engine.audioEngine;

        if (scene.activeCameras.length > 0) {
            listeningCamera = scene.activeCameras[0];
        } else {
            listeningCamera = scene.activeCamera;
        }

        if (listeningCamera && audioEngine.audioContext) {
            audioEngine.audioContext.listener.setPosition(listeningCamera.globalPosition.x, listeningCamera.globalPosition.y, listeningCamera.globalPosition.z);
        ...

My proposal is - Add new method setListener, that would set an internal property this.customListener`. Then simply check if customListener is set and use its absolutePosition, if it's not set, use the camera.
 private _afterRender() {
        const scene = this.scene;
        if (!this._audioEnabled || !scene._mainSoundTrack || !scene.soundTracks || (scene._mainSoundTrack.soundCollection.length === 0 && scene.soundTracks.length === 1)) {
            return;
        }

        var listener: Nullable<Camera | Mesh | AbstractMesh>;
        var listenerPositionKey: 'globalPosition' | 'absolutePosition' = 'globalPosition';
        var audioEngine = Engine.audioEngine;

        if (this.customListener && !this.customListener.isDisposed() && this.customListener.isEnabled()) {
            listener = this.customListener;
            listenerPositionKey = 'absolutePosition'
        }
       else if (scene.activeCameras.length > 0) {
            listener = scene.activeCameras[0];
        } else {
            listener = scene.activeCamera;
        }

        if (listeningCamera && audioEngine.audioContext) {
            audioEngine.audioContext.listener.setPosition(listener[listenerPositionKey].x, listeningCamera[listenerPositionKey].y, listeningCamera[listenerPositionKey].z);
        ...

I am very happy to implement this if you decide to move forward. I do not have a VR headset so I will not be able to test the code that follows this regarding cameras in VR, so a help would be needed unfortunately.
Thanks!

Another possibility how to solve this would be to open the setPosition method to the public, and if the user decides use their own position, do not set the position automatically within the _afterRender method.

I would prefer option B. If setPosition was called we simply use it. Else we use camera.globalPosition
Thanks a ton for your interest and you can definitely go ahead with a PR
Welcome in the family :D

Update @deltakosh :
It seems that the _afterRender function of AudioSceneComponent runs before any custom onAfterRenderObservable calls, which makes it impossible to detect if the user has already set the listener position themselves (unless they'd do it in onBeforeRender...).
One way this could be done, which would have minimum impact on the Babylon code base would be to introduce a new flag on the scene object called something like useCustomListenerPosition, where we would not set the listener position automatically and the user would have to do it themselves (either in the render cycle or statically).
This would have minimal code implications, and there would be no "magic" under the hood.
Although, I am not sure how to handle this part of code
            var i: number;
            for (i = 0; i < scene.mainSoundTrack.soundCollection.length; i++) {
                var sound = scene.mainSoundTrack.soundCollection[i];
                if (sound.useCustomAttenuation) {
                    sound.updateDistanceFromListener();
                }
            }
            if (scene.soundTracks) {
                for (i = 0; i < scene.soundTracks.length; i++) {
                    for (var j = 0; j < scene.soundTracks[i].soundCollection.length; j++) {
                        sound = scene.soundTracks[i].soundCollection[j];
                        if (sound.useCustomAttenuation) {
                            sound.updateDistanceFromListener();
                        }
                    }
                }
            }

in which all the sounds with custom attenuation are updated to reflect the new listener position.
If we were able to make sure the _afterRender function runs after user defined after render calls, we could do this by simply checking if a listener position has been set for this frame.

Other option: we define scene.getAudioListener position as a () => Vector3. So users can provide it and it will be called automatically when we need it.
Not sure to understand why there is a problem with the code you mentioned. As soon as the audio is set up with the new listener position we are all set and nothing else should change

@deltakosh You mean that the user would define it as
scene.getAudioListenerPosition = () => {
    return myMesh.absolutePosition;
}

and then we would call this function in the _afterRender function ?

correct :) this way we have an easy implementation while being really flexible for the user


M.IM8x - review APIs and mark those as obsolete the ones we want to remove in 9x.

We don't have replacements yet, we will have to obsolete the delegates in next major release.


How to localize Active Storage forms?

I am using locales inside the gem to provide a localized Admin experience.
However, I seem to be unable to find what i18n keys are used to translate the Active Storage upload forms. This is how my interface looks like at the moment:

I need to localize the Browse text and the No file selected help textblock.
Any ideas of what those i18n keys are?

Welp, I just learned that the localization of these forms depends entirely on the System Language of the user (not even the Browser's language). Therefore, all of this is moot. The thing will be localized perfectly for each user.


Update guessTheNumber.cc.lua

Moved {{ dbDel 0 "NR" }} to after the embed message.  Database value was being deleted prior to message being created, and was always returning 0.

Ill pr the v2 no need to merge joe

Superseded by #69.

Thank you both. Didn't know v2 was in the works.


[docs] supported tags list is unclear on file comment supported tags

at https://typedoc.org/guides/doccomments/#supported-tags , I think the @module and @packageDocumentation tags should also be listed.
If this is acceptable, I can work on this. Do those two make the list of supported tags fully exhaustive? including all conditional tags?

Wow... that page is even more out of date than I thought! It still talks about Highlight.JS, which was switched out for Shiki in 0.20.
Off the top of my head, that list is missing @private, @protected, and @public, which do what you'd expect (though are arguably a bad thing...) It should also mention that @template is a synonym for @typeParam
A PR fixing this would be great!

... and of course the TS-in-JS tags! I had some other updates to do, so I went ahead and updated the site. https://typedoc.org/guides/doccomments/#%40packagedocumentation


Fix for APK gen exception: com.android.dex.DexException

Set dexOptions.jumboMode = true; to mitigate an exception that
might be encountered when trying to generate a (signed?) APK:
"com.android.dex.DexException: Cannot merge new index 65536 into a non-jumbo instruction!"
Solution was taken from this stack overflow article:
https://stackoverflow.com/questions/26093664/dexexception-cannot-merge-new-index-65536-into-a-non-jumbo-instruction

Waiting for Travis, will merge after that


encode data-uuid passed to CKEditor

Pre-Flight checklist

[x] Testing

[x] Code is tested
[x] Changes have been manually tested

What are the relevant tickets? #1059
Really for #1015; fixes a bug introduced in #1036
What's this PR do?
In https://github.com/mitodl/ocw-studio/pull/1036 we began encoding the data-uuid argument for < resource_link > shortcodes. The encoding / decoding worked fine for converting between HTML and Markdown.
But in that PR I forgot to encode the data we passed to CKEditor when creating new links.
How should this be manually tested?
Go to a page within a course

add new links
embed new resources
save and reopen. Everything should look good.

Codecov Report

Merging #1063 (1c058b0) into master (8ae62d6) will increase coverage by 4.32%.
The diff coverage is 70.00%.

@@            Coverage Diff             @@
##           master    #1063      +/-   ##
==========================================
+ Coverage   91.12%   95.44%   +4.32%
==========================================
  Files         201       97     -104
  Lines        7705     2658    -5047
  Branches     1336      547     -789
==========================================
- Hits         7021     2537    -4484
+ Misses        597      121     -476
+ Partials       87        0      -87

Impacted Files
Coverage Δ

static/js/lib/ckeditor/CKEditor.ts
91.17% <57.14%> (-8.83%)
:arrow_down:

static/js/components/widgets/MarkdownEditor.tsx
94.33% <100.00%> (+11.64%)
:arrow_up:

static/js/test_util.ts
100.00% <100.00%> (ø)

...s/management/commands/markdown_cleaning/cleaner.py

videos/youtube.py

content_sync/serializers.py

content_sync/utils.py

main/tasks.py

repl.py

ocw_import/tasks.py

... and 98 more

Continue to review full report at Codecov.

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include overlay to go/packages

This should enable non saved imports to be auto completed :)

@marwan-at-work, does this actually fix the problem for you? I'd imagine the fix should actually be naming the empty variable in ParseFile "data".

@stamblerre tl;dr I didn't notice the empty variable and things did work.
Looking at go/packages we definitely need to pass data as part of the Config.Overlay...I'm not sure if we actually should or shouldn't shadow the data variable through the empty variable. Let me know and I'll update the pr!

oh you're totally right, the file contents wouldn't actually change. sorry about that - thanks for doing this!


[DEVEL]

Description
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Your Environment
[replace this line with basic information about your environment, such as your operating system and the versions of any relevant tools you are using (e.g. Go, Docker)]
Basic Information
[replace this line with basic information about the issue you are experiencing, including but not limited to the names of the files you are working with and any relevant error messages]
Steps to Reproduce
[replace this line with detailed steps to reproduce the issue you are experiencing]
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help this coin


Grpc args doxygen

Fixes #7458

LGTM

Fyi @nicolasnoble this needs to go into the v1.0.x branch so that the generated API references contain this grouping.

Please don't commit doc/ref to the repository
On Mon, Jul 18, 2016, 7:08 PM Kailash Sethuraman<EMAIL_ADDRESS>wrote:

LGTM
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@ctiller Yes, it's been fixed (you may need to reload).

@hsaliak the PR against the v1.0.x branch is at #7470