{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_H"},{"status":"SUCCEEDED","id":"data_set_ICA"},{"status":"SUCCEEDED","id":"data_set_IK"},{"status":"SUCCEEDED","id":"data_set_INA"},{"status":"SUCCEEDED","id":"data_set_M"},{"status":"SUCCEEDED","id":"data_set_MCA"},{"status":"SUCCEEDED","id":"data_set_N"},{"status":"SUCCEEDED","id":"data_set_V"}],"duration":0.103883,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_1"}],"duration":0.185663,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"euler","key":"meth"},{"value":"20.0","key":"total"},{"value":"0.01","key":"dt"},{"value":"0.0","key":"t0"},{"value":"2","key":"njmp"}],"algorithm":"KISAO_0000030","duration":0.088992,"output":"/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `model` may be invalid.\r\n  - The model file `/tmp/tmpc726ezk2/AP-sim-Ca.ode` has warnings.\r\n    - The XPP file may be not be formulated correctly\r\n      - INA is a duplicate name\r\n      - IK is a duplicate name\r\n      - ICA is a duplicate name\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.485368,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  AP-sim-Ca.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 9 data sets\r\n    Plots (1):\r\n      plot: 1 curves\r\n\r\nExecuting SED-ML file 1: AP-sim-Ca.sedml ...\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n  - Model `model` has warnings.\r\n    - The model file `AP-sim-Ca.ode` has warnings.\r\n      - The XPP file may be not be formulated correctly\r\n        - INA is a duplicate name\r\n        - IK is a duplicate name\r\n        - ICA is a duplicate name\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task`\r\n    Outputs:\r\n      `plot`\r\n      `report`\r\n  Executing task 1: `task`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `report` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"AP-sim-Ca.sedml"}],"duration":0.784873,"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/OMEX 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    472      0 --:--:-- --:--:-- --:--:--   471\r100   139  100   139    0     0    466      0 --:--:-- --:--:-- --:--:--   466\n\r100   99k  100   99k    0     0   243k      0 --:--:-- --:--:-- --:--:--  243k\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mCOMBINE/OMEX archive has warnings.\r\n  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n  - Model `model` has warnings.\r\n    - The model file `AP-sim-Ca.ode` has warnings.\r\n      - The XPP file may be not be formulated correctly\r\n        - INA is a duplicate name\r\n        - IK is a duplicate name\r\n        - ICA is a duplicate name\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n  - The SED-ML file at location `AP-sim-Ca.sedml` has warnings.\r\n    - Model `model` has warnings.\r\n      - The model file `AP-sim-Ca.ode` has warnings.\r\n        - The XPP file may be not be formulated correctly\r\n          - INA is a duplicate name\r\n          - IK is a duplicate name\r\n          - ICA is a duplicate name\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n \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\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 contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/AP-sim-Ca.ode  \n  inflating: contents/Readme.html    \n  inflating: contents/AP-sim-Ca.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/AP-sim-Ca.JPG  \n  inflating: contents/manifest.xml   \nCompleted 1.2 KiB/160.9 KiB (20.8 KiB/s) with 6 file(s) remaining\rupload: contents/AP-sim-Ca.ode to s3://files.biosimulations.org/simulations/621d42a987550e369891ba92/contents/AP-sim-Ca.ode\nCompleted 1.2 KiB/160.9 KiB (20.8 KiB/s) with 5 file(s) remaining\rCompleted 1.9 KiB/160.9 KiB (16.6 KiB/s) with 5 file(s) remaining\rCompleted 7.6 KiB/160.9 KiB (66.2 KiB/s) with 5 file(s) remaining\rupload: contents/AP-sim-Ca.sedml to s3://files.biosimulations.org/simulations/621d42a987550e369891ba92/contents/AP-sim-Ca.sedml\nCompleted 7.6 KiB/160.9 KiB (66.2 KiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42a987550e369891ba92/contents/manifest.xml\nCompleted 7.6 KiB/160.9 KiB (66.2 KiB/s) with 3 file(s) remaining\rCompleted 67.5 KiB/160.9 KiB (462.4 KiB/s) with 3 file(s) remaining\rupload: contents/AP-sim-Ca.JPG to s3://files.biosimulations.org/simulations/621d42a987550e369891ba92/contents/AP-sim-Ca.JPG\nCompleted 67.5 KiB/160.9 KiB (462.4 KiB/s) with 2 file(s) remaining\rCompleted 69.7 KiB/160.9 KiB (446.7 KiB/s) with 2 file(s) remaining\rupload: contents/Readme.html to s3://files.biosimulations.org/simulations/621d42a987550e369891ba92/contents/Readme.html\nCompleted 69.7 KiB/160.9 KiB (446.7 KiB/s) with 1 file(s) remaining\rCompleted 160.9 KiB/160.9 KiB (755.7 KiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42a987550e369891ba92/contents/metadata.rdf\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /AP-sim-Ca.sedml\ncreating dataset /AP-sim-Ca.sedml/plot, shape: (2, 1001), type: float64\ndataset created, uuid: d-dcd7fe5e-ece57e40-a574-0632d6-e95829, chunk_size: (2, 1001)\ncreating dataset /AP-sim-Ca.sedml/report, shape: (9, 1001), type: float64\ndataset created, uuid: d-dcd7fe5e-ece57e40-0e5e-e178aa-f61196, chunk_size: (9, 1001)\ncreating attribute combineArchiveLocation in /AP-sim-Ca.sedml\ncreating attribute uri in /AP-sim-Ca.sedml\ncreating attribute _type in /AP-sim-Ca.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /AP-sim-Ca.sedml/plot\ncreating attribute sedmlDataSetIds in /AP-sim-Ca.sedml/plot\ncreating attribute sedmlDataSetLabels in /AP-sim-Ca.sedml/plot\ncreating attribute sedmlDataSetNames in /AP-sim-Ca.sedml/plot\ncreating attribute sedmlDataSetShapes in /AP-sim-Ca.sedml/plot\ncreating attribute sedmlId in /AP-sim-Ca.sedml/plot\ncreating attribute uri in /AP-sim-Ca.sedml/plot\ncreating attribute _type in /AP-sim-Ca.sedml/report\ncreating attribute sedmlDataSetDataTypes in /AP-sim-Ca.sedml/report\ncreating attribute sedmlDataSetIds in /AP-sim-Ca.sedml/report\ncreating attribute sedmlDataSetLabels in /AP-sim-Ca.sedml/report\ncreating attribute sedmlDataSetNames in /AP-sim-Ca.sedml/report\ncreating attribute sedmlDataSetShapes in /AP-sim-Ca.sedml/report\ncreating attribute sedmlId in /AP-sim-Ca.sedml/report\ncreating attribute sedmlName in /AP-sim-Ca.sedml/report\ncreating attribute uri in /AP-sim-Ca.sedml/report\ncreate_links: /\ngot link: AP-sim-Ca.sedml\ncreate_links: /AP-sim-Ca.sedml\ngot link: plot\ngot link: report\nwrite_dataset src: /AP-sim-Ca.sedml/plot to tgt: /AP-sim-Ca.sedml/plot, shape: (2, 1001), type: float64\niterating over chunks for /AP-sim-Ca.sedml/plot\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /AP-sim-Ca.sedml/plot\nwrite_dataset src: /AP-sim-Ca.sedml/report to tgt: /AP-sim-Ca.sedml/report, shape: (9, 1001), type: float64\niterating over chunks for /AP-sim-Ca.sedml/report\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /AP-sim-Ca.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42a987550e369891ba92\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 76%)\n  adding: outputs/AP-sim-Ca.sedml/ (stored 0%)\n  adding: outputs/AP-sim-Ca.sedml/plot.pdf (deflated 34%)\n  adding: outputs/reports.h5 (deflated 24%)\n  adding: rawLog.txt (deflated 78%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 79.2 KiB/98.3 KiB (1.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42a987550e369891ba92/output.zip\nCompleted 79.2 KiB/98.3 KiB (1.0 MiB/s) with 3 file(s) remaining\rCompleted 83.8 KiB/98.3 KiB (904.5 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/621d42a987550e369891ba92/outputs/plots.zip\nCompleted 83.8 KiB/98.3 KiB (904.5 KiB/s) with 2 file(s) remaining\rCompleted 91.0 KiB/98.3 KiB (955.0 KiB/s) with 2 file(s) remaining\rupload: outputs/AP-sim-Ca.sedml/plot.pdf to s3://files.biosimulations.org/simulations/621d42a987550e369891ba92/outputs/AP-sim-Ca.sedml/plot.pdf\nCompleted 91.0 KiB/98.3 KiB (955.0 KiB/s) with 1 file(s) remaining\rCompleted 98.3 KiB/98.3 KiB (699.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42a987550e369891ba92/rawLog.txt\nCompleted 93.0 KiB/93.0 KiB (1020.1 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42a987550e369891ba92/outputs/reports.h5\nCompleted 4.4 KiB/4.4 KiB (81.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42a987550e369891ba92/outputs/log.yml\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess the manifest file in the COMBINE archive ... succeeded.\nRead the manifest and post the files to the API ... succeeded.\nCreate thumbnails from the images specified in the manifest ... succeeded.\nPost thumbnails to the API ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","skipReason":null,"exception":null,"status":"SUCCEEDED"}