{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_t"},{"status":"SUCCEEDED","id":"data_set_x"},{"status":"SUCCEEDED","id":"data_set_y"},{"status":"SUCCEEDED","id":"data_set_z"}],"duration":0.051716,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_t_x"},{"status":"SUCCEEDED","id":"curve_t_y"},{"status":"SUCCEEDED","id":"curve_t_z"}],"duration":0.191254,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"OpenCOR.SimulationSupport.Simulation.run","key":"method"},{"value":[{"kisaoID":"KISAO_0000467","value":"1.0"},{"kisaoID":"KISAO_0000475","value":"BDF"}],"key":"algorithmParameters"}],"algorithm":"KISAO_0000019","duration":0.666391,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `z` may be invalid.\n  - XPath could not be validated.\n- Variable `y` may be invalid.\n  - XPath could not be validated.\n- Variable `t` may be invalid.\n  - XPath could not be validated.\n- Variable `x` may be invalid.\n  - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n  - The following tasks do not contribute to outputs:\n    - `repeatedTask`\n    - `task1`\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.974719,"output":"  Found 1 tasks and 2 outputs:\n    Tasks:\n      `task`\n    Outputs:\n      `plot`\n      `report`\n  Executing task 1: `task`\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\n    Generating 2 outputs ...\n      Generating output 1: `report` ... \u001b[34msucceeded\u001b[0m\n      Generating output 2: `plot` ... \u001b[34msucceeded\u001b[0m\n\n  Executed 1 tasks and 2 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 2\n      Skipped: 0\n      Failed: 0\n","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"simulation.sedml"}],"duration":1.509885,"output":"\u001b[0;36mThank you for using runBioSimulations!\u001b[0m\n\n\u001b[0;36m================================================ Loading Singularity ================================================\u001b[0m\n\n\u001b[0;36m============================================ Downloading COMBINE archive ============================================\u001b[0m\n  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n                                 Dload  Upload   Total   Spent    Left  Speed\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    463      0 --:--:-- --:--:-- --:--:--   463\n\r100 55449  100 55449    0     0   131k      0 --:--:-- --:--:-- --:--:--  131k\n\n\u001b[0;36m============================================= Executing COMBINE archive =============================================\u001b[0m\nINFO:    Using cached SIF image\nTraceback (most recent call last):\n  File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 247, in <module>\n    if not update_paths(args.path, args.scripts_dir, args.clear_args, args.extra_args):\n  File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 213, in update_paths\n    update_scripts(scripts_dir, new_path, clear_args, extra_args)\n  File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 125, in update_scripts\n    update_script(os.path.join(bin_dir, fn), new_path, clear_args, extra_args)\n  File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 118, in update_script\n    with open(script_filename, 'w') as f:\nOSError: [Errno 30] Read-only file system: '/home/opencor/OpenCOR/bin/../python/bin/biosimulators-utils'\nArchive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\n  simulation.sedml:\n    Tasks (1):\n      task\n    Reports (1):\n      report: 4 data sets\n    Plots (1):\n      plot: 3 curves\n\nExecuting SED-ML file 1: simulation.sedml ...\n\nBundling outputs ...\nCleaning up ...\n\n============= SUMMARY =============\nExecuted 1 SED documents:\n  SED documents (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n  Tasks (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n  Outputs (2):\n    Succeeded: 2\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /simulation.sedml\ncreating dataset /simulation.sedml/plot, shape: (4, 1001), type: float64\ndataset created, uuid: d-afa78625-6ccfdceb-031f-3c9f76-a54e6b, chunk_size: (4, 1001)\ncreating dataset /simulation.sedml/report, shape: (4, 1001), type: float64\ndataset created, uuid: d-afa78625-6ccfdceb-204c-dbb4cf-eaa14f, chunk_size: (4, 1001)\ncreating attribute combineArchiveLocation in /simulation.sedml\ncreating attribute uri in /simulation.sedml\ncreating attribute _type in /simulation.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /simulation.sedml/plot\ncreating attribute sedmlDataSetIds in /simulation.sedml/plot\ncreating attribute sedmlDataSetLabels in /simulation.sedml/plot\ncreating attribute sedmlDataSetNames in /simulation.sedml/plot\ncreating attribute sedmlDataSetShapes in /simulation.sedml/plot\ncreating attribute sedmlId in /simulation.sedml/plot\ncreating attribute uri in /simulation.sedml/plot\ncreating attribute _type in /simulation.sedml/report\ncreating attribute sedmlDataSetDataTypes in /simulation.sedml/report\ncreating attribute sedmlDataSetIds in /simulation.sedml/report\ncreating attribute sedmlDataSetLabels in /simulation.sedml/report\ncreating attribute sedmlDataSetNames in /simulation.sedml/report\ncreating attribute sedmlDataSetShapes in /simulation.sedml/report\ncreating attribute sedmlId in /simulation.sedml/report\ncreating attribute uri in /simulation.sedml/report\ncreate_links: /\ngot link: simulation.sedml\ncreate_links: /simulation.sedml\ngot link: plot\ngot link: report\nwrite_dataset src: /simulation.sedml/plot to tgt: /simulation.sedml/plot, shape: (4, 1001), type: float64\niterating over chunks for /simulation.sedml/plot\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /simulation.sedml/plot\nwrite_dataset src: /simulation.sedml/report to tgt: /simulation.sedml/report, shape: (4, 1001), type: float64\niterating over chunks for /simulation.sedml/report\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /simulation.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/61fea492f499ccf25faafc5f\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/simulation.sedml/ (stored 0%)\n  adding: outputs/simulation.sedml/plot.pdf (deflated 11%)\n  adding: outputs/log.yml (deflated 70%)\n  adding: outputs/reports.h5 (deflated 31%)\n  adding: rawLog.txt (deflated 73%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 80.7 KiB/142.1 KiB (1020.5 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/61fea492f499ccf25faafc5f/output.zip\nCompleted 80.7 KiB/142.1 KiB (1020.5 KiB/s) with 3 file(s) remaining\rCompleted 85.6 KiB/142.1 KiB (654.1 KiB/s) with 3 file(s) remaining \rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/61fea492f499ccf25faafc5f/rawLog.txt\nCompleted 85.6 KiB/142.1 KiB (654.1 KiB/s) with 2 file(s) remaining\rCompleted 115.6 KiB/142.1 KiB (848.4 KiB/s) with 2 file(s) remaining\rupload: outputs/simulation.sedml/plot.pdf to s3://files.biosimulations.org/simulations/61fea492f499ccf25faafc5f/outputs/simulation.sedml/plot.pdf\nCompleted 115.6 KiB/142.1 KiB (848.4 KiB/s) with 1 file(s) remaining\rCompleted 142.1 KiB/142.1 KiB (816.0 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/61fea492f499ccf25faafc5f/outputs/plots.zip\nCompleted 74.0 KiB/74.0 KiB (803.3 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/61fea492f499ccf25faafc5f/outputs/reports.h5\nCompleted 3.5 KiB/3.5 KiB (39.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/61fea492f499ccf25faafc5f/outputs/log.yml\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\n\u001b[0;32mProcess and upload the outputs of the simulation run.....Succeeded\nPost the SED-ML file to the API.....Succeeded\nProcess the SED-ML file in the combine archive.....Succeeded\nPost the logs to the API.....Succeeded\nRetrieve the logs of the simulation run.....Succeeded\nPost thumbnails to the API.....Succeeded\nCreate thumbnails from the images specified in the manifest.....Succeeded\nRead the manifest and post the files to the API.....Succeeded\nProcess the manifest file in the combine archive.....Succeeded\nExtract the files in the combine archive.....Succeeded\nPost the Metadata to the API.....Succeeded\nProcess the Metadata in the combine archive.....Succeeded\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","skipReason":null,"exception":null,"status":"SUCCEEDED"}