{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_B"},{"status":"SUCCEEDED","id":"data_set_Y"},{"status":"SUCCEEDED","id":"data_set_Z"}],"duration":0.096894,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_1"}],"duration":0.189465,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"euler","key":"meth"},{"value":"20.0","key":"total"},{"value":"0.005","key":"dt"},{"value":"0.0","key":"t0"},{"value":"4","key":"njmp"}],"algorithm":"KISAO_0000030","duration":0.079664,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.460768,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  Ca_Oscill.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 4 data sets\r\n    Plots (1):\r\n      plot: 1 curves\r\n\r\nExecuting SED-ML file 1: Ca_Oscill.sedml ...\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":"Ca_Oscill.sedml"}],"duration":0.773778,"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    494      0 --:--:-- --:--:-- --:--:--   494\n\r 96 97855   96 94584    0     0   228k      0 --:--:-- --:--:-- --:--:--  228k\r100 97855  100 97855    0     0   234k      0 --:--:-- --:--:-- --:--:-- 1064k\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 \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/readme.html    \n  inflating: contents/Ca_Oscill.ode  \n  inflating: contents/Ca_Oscill.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/Ca_Oscill.JPG  \n  inflating: contents/manifest.xml   \nCompleted 714 Bytes/200.5 KiB (8.4 KiB/s) with 6 file(s) remaining\rupload: contents/Ca_Oscill.ode to s3://files.biosimulations.org/simulations/621d4299d8a14a834cbf3da6/contents/Ca_Oscill.ode\nCompleted 714 Bytes/200.5 KiB (8.4 KiB/s) with 5 file(s) remaining\rCompleted 77.6 KiB/200.5 KiB (630.5 KiB/s) with 5 file(s) remaining\rupload: contents/Ca_Oscill.JPG to s3://files.biosimulations.org/simulations/621d4299d8a14a834cbf3da6/contents/Ca_Oscill.JPG\nCompleted 77.6 KiB/200.5 KiB (630.5 KiB/s) with 4 file(s) remaining\rCompleted 78.3 KiB/200.5 KiB (624.7 KiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d4299d8a14a834cbf3da6/contents/manifest.xml\nCompleted 78.3 KiB/200.5 KiB (624.7 KiB/s) with 3 file(s) remaining\rCompleted 81.8 KiB/200.5 KiB (562.1 KiB/s) with 3 file(s) remaining\rupload: contents/Ca_Oscill.sedml to s3://files.biosimulations.org/simulations/621d4299d8a14a834cbf3da6/contents/Ca_Oscill.sedml\nCompleted 81.8 KiB/200.5 KiB (562.1 KiB/s) with 2 file(s) remaining\rCompleted 198.0 KiB/200.5 KiB (1.3 MiB/s) with 2 file(s) remaining \rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d4299d8a14a834cbf3da6/contents/metadata.rdf\nCompleted 198.0 KiB/200.5 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 200.5 KiB/200.5 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: contents/readme.html to s3://files.biosimulations.org/simulations/621d4299d8a14a834cbf3da6/contents/readme.html\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Ca_Oscill.sedml\ncreating dataset /Ca_Oscill.sedml/plot, shape: (2, 1001), type: float64\ndataset created, uuid: d-e0eedf56-e7f3e3fa-5aea-850d21-577c64, chunk_size: (2, 1001)\ncreating dataset /Ca_Oscill.sedml/report, shape: (4, 1001), type: float64\ndataset created, uuid: d-e0eedf56-e7f3e3fa-11f8-f4dba5-644e46, chunk_size: (4, 1001)\ncreating attribute combineArchiveLocation in /Ca_Oscill.sedml\ncreating attribute uri in /Ca_Oscill.sedml\ncreating attribute _type in /Ca_Oscill.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /Ca_Oscill.sedml/plot\ncreating attribute sedmlDataSetIds in /Ca_Oscill.sedml/plot\ncreating attribute sedmlDataSetLabels in /Ca_Oscill.sedml/plot\ncreating attribute sedmlDataSetNames in /Ca_Oscill.sedml/plot\ncreating attribute sedmlDataSetShapes in /Ca_Oscill.sedml/plot\ncreating attribute sedmlId in /Ca_Oscill.sedml/plot\ncreating attribute uri in /Ca_Oscill.sedml/plot\ncreating attribute _type in /Ca_Oscill.sedml/report\ncreating attribute sedmlDataSetDataTypes in /Ca_Oscill.sedml/report\ncreating attribute sedmlDataSetIds in /Ca_Oscill.sedml/report\ncreating attribute sedmlDataSetLabels in /Ca_Oscill.sedml/report\ncreating attribute sedmlDataSetNames in /Ca_Oscill.sedml/report\ncreating attribute sedmlDataSetShapes in /Ca_Oscill.sedml/report\ncreating attribute sedmlId in /Ca_Oscill.sedml/report\ncreating attribute sedmlName in /Ca_Oscill.sedml/report\ncreating attribute uri in /Ca_Oscill.sedml/report\ncreate_links: /\ngot link: Ca_Oscill.sedml\ncreate_links: /Ca_Oscill.sedml\ngot link: plot\ngot link: report\nwrite_dataset src: /Ca_Oscill.sedml/plot to tgt: /Ca_Oscill.sedml/plot, shape: (2, 1001), type: float64\niterating over chunks for /Ca_Oscill.sedml/plot\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /Ca_Oscill.sedml/plot\nwrite_dataset src: /Ca_Oscill.sedml/report to tgt: /Ca_Oscill.sedml/report, shape: (4, 1001), type: float64\niterating over chunks for /Ca_Oscill.sedml/report\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /Ca_Oscill.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d4299d8a14a834cbf3da6\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 64%)\n  adding: outputs/Ca_Oscill.sedml/ (stored 0%)\n  adding: outputs/Ca_Oscill.sedml/plot.pdf (deflated 28%)\n  adding: outputs/reports.h5 (deflated 40%)\n  adding: rawLog.txt (deflated 77%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 42.8 KiB/63.2 KiB (520.9 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d4299d8a14a834cbf3da6/output.zip\nCompleted 42.8 KiB/63.2 KiB (520.9 KiB/s) with 3 file(s) remaining\rCompleted 48.6 KiB/63.2 KiB (540.9 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/621d4299d8a14a834cbf3da6/outputs/plots.zip\nCompleted 48.6 KiB/63.2 KiB (540.9 KiB/s) with 2 file(s) remaining\rCompleted 56.9 KiB/63.2 KiB (595.4 KiB/s) with 2 file(s) remaining\rupload: outputs/Ca_Oscill.sedml/plot.pdf to s3://files.biosimulations.org/simulations/621d4299d8a14a834cbf3da6/outputs/Ca_Oscill.sedml/plot.pdf\nCompleted 56.9 KiB/63.2 KiB (595.4 KiB/s) with 1 file(s) remaining\rCompleted 63.2 KiB/63.2 KiB (332.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d4299d8a14a834cbf3da6/rawLog.txt\nCompleted 55.8 KiB/55.8 KiB (453.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d4299d8a14a834cbf3da6/outputs/reports.h5\nCompleted 2.1 KiB/2.1 KiB (35.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d4299d8a14a834cbf3da6/outputs/log.yml\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess and upload the outputs of the simulation run ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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"}