Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

updating tests #1422

Merged
merged 1 commit into from
Jan 17, 2025
+2 −2
Merged

updating tests #1422

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions vcell-cli/src/main/resources/test_cases.ndjson
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -880,7 +880,7 @@
{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000772.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000773.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000774.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000775.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000775.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Unable to initialize bioModel for the given selection: Failed to translate SBML model into BioModel: org.vcell.sbml.vcell.SBMLImportException: error parsing expression '<?xml version='1.0' encoding='UTF-8'?>\n<math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n <apply>\n <csymbol encoding=\"text\" definitionURL=\"http://www.sbml.org/sbml/symbols/rateOf\"> rateOf </csymbol>\n <ci> G </ci>\n </apply>\n</math>': cannot translate csymbol from MathML org.vcell.sbml.vcell.SBMLImportException: Failed to translate SBML model into BioModel: org.vcell.sbml.vcell.SBMLImportException: error parsing expression '<?xml version='1.0' encoding='UTF-8'?>\n<math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n <apply>\n <csymbol encoding=\"text\" definitionURL=\"http://www.sbml.org/sbml/symbols/rateOf\"> rateOf </csymbol>\n <ci> G </ci>\n </apply>\n</math>': cannot translate csymbol from MathML"}
{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000776.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000777.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000778.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
Expand Down Expand Up @@ -1061,7 +1061,7 @@
{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000953.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000954.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000955.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000956.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"BIOMODEL_IMPORT_SEDML_FAILURE","known_failure_desc":"Unable to initialize bioModel for the given selection: expecting vcell var 'Ro_CA' mapped to SBML target 'Ro_CA' to be constant valued org.vcell.sedml.SEDMLImportException: expecting vcell var 'Ro_CA' mapped to SBML target 'Ro_CA' to be constant valued"}
{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000956.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_PREPROCESS_FAILURE","known_failure_desc":"SED-ML processing for /tmp/vcell_temp_f8b36c92-959c-4afc-87b1-1777f13d50a214966175554076948981/Bertozzi2020.sedml failed with error: org.vcell.cli.PythonStreamException: Python error caught: <\nTraceback (most recent call last):\n File \"<stdin>\", line 1, in <module>\n File \"/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/wrapper.py\", line 36, in genSedml2d3d\n cli.gen_sedml_2d_3d(omexFilePath, baseOutPath)\n File \"/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py\", line 95, in gen_sedml_2d_3d\n doc = SedmlSimulationReader().run(content_filename)\n File \"/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.10/lib/python3.10/site-packages/biosimulators_utils/sedml/io.py\", line 1539, in run\n raise ValueError(msg)\nValueError: The SED document is invalid.\n - Model `model` is invalid.\n - The model file `Bertozzi2020.xml` is invalid.\n - SBML component consistency (20623) at line 217, column 6: A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object.\n Reference: L3V2 Section 4.6\n The required attribute 'hasOnlySubstanceUnits' is missing from the <species> with the id 'Infected'.\n \n - SBML component consistency (20623) at line 258, column 6: A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object.\n Reference: L3V2 Section 4.6\n The required attribute 'hasOnlySubstanceUnits' is missing from the <species> with the id 'Recovered'.\n \n - SBML component consistency (20623) at line 299, column 6: A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount', 'initialConcentration', 'substanceUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Species object.\n Reference: L3V2 Section 4.6\n The required attribute 'hasOnlySubstanceUnits' is missing from the <species> with the id 'Susceptible'.\n \n - SBML component consistency (20706) at line 657, column 6: A Parameter object must have the required attributes 'id' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'value' and 'units'. No other attributes from the SBML Level 3 Core namespace are permitted on a Parameter object.\n Reference: L3V2 Section 4.7\n The required attribute 'constant' is missing from the <parameter> with the id 'ModelValue_3'.\n \n - SBML component consistency (20706) at line 662, column 6: A Parameter object must have the required attributes 'id' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'value' and 'units'. No other attributes from the SBML Level 3 Core namespace are permitted on a Parameter object.\n Reference: L3V2 Section 4.7\n The required attribute 'constant' is missing from the <parameter> with the id 'ModelValue_10'.\n \n - SBML component consistency (20706) at line 667, column 6: A Parameter object must have the required attributes 'id' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'value' and 'units'. No other attributes from the SBML Level 3 Core namespace are permitted on a Parameter object.\n Reference: L3V2 Section 4.7\n The required attribute 'constant' is missing from the <parameter> with the id 'ModelValue_16'.\n \n - SBML component consistency (20706) at line 672, column 6: A Parameter object must have the required attributes 'id' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'value' and 'units'. No other attributes from the SBML Level 3 Core namespace are permitted on a Parameter object.\n Reference: L3V2 Section 4.7\n The required attribute 'constant' is missing from the <parameter> with the id 'ModelValue_15'.\n \n - SBML component consistency (20706) at line 677, column 6: A Parameter object must have the required attributes 'id' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'value' and 'units'. No other attributes from the SBML Level 3 Core namespace are permitted on a Parameter object.\n Reference: L3V2 Section 4.7\n The required attribute 'constant' is missing from the <parameter> with the id 'ModelValue_18'.\n \n - SBML component consistency (20706) at line 682, column 6: A Parameter object must have the required attributes 'id' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'value' and 'units'. No other attributes from the SBML Level 3 Core namespace are permitted on a Parameter object.\n Reference: L3V2 Section 4.7\n The required attribute 'constant' is missing from the <parameter> with the id 'ModelValue_17'.\n \n - SBML component consistency (20706) at line 687, column 6: A Parameter object must have the required attributes 'id' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'value' and 'units'. No other attributes from the SBML Level 3 Core namespace are permitted on a Parameter object.\n Reference: L3V2 Section 4.7\n The required attribute 'constant' is missing from the <parameter> with the id 'ModelValue_0'.\n \n - SBML component consistency (20706) at line 692, column 6: A Parameter object must have the required attributes 'id' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'value' and 'units'. No other attributes from the SBML Level 3 Core namespace are permitted on a Parameter object.\n Reference: L3V2 Section 4.7\n The required attribute 'constant' is missing from the <parameter> with the id 'ModelValue_7'.\n \n - SBML component consistency (20706) at line 697, column 6: A Parameter object must have the required attributes 'id' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'value' and 'units'. No other attributes from the SBML Level 3 Core namespace are permitted on a Parameter object.\n Reference: L3V2 Section 4.7\n The required attribute 'constant' is missing from the <parameter> with the id 'ModelValue_1'.\n \n - SBML component consistency (20706) at line 702, column 6: A Parameter object must have the required attributes 'id' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'value' and 'units'. No other attributes from the SBML Level 3 Core namespace are permitted on a Parameter object.\n Reference: L3V2 Section 4.7\n The required attribute 'constant' is missing from the <parameter> with the id 'ModelValue_8'.\n \n - SBML component consistency (20706) at line 707, column 6: A Parameter object must have the required attributes 'id' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'value' and 'units'. No other attributes from the SBML Level 3 Core namespace are permitted on a Parameter object.\n Reference: L3V2 Section 4.7\n The required attribute 'constant' is missing from the <parameter> with the id 'ModelValue_5'.\n \n - SBML component consistency (20706) at line 712, column 6: A Parameter object must have the required attributes 'id' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'value' and 'units'. No other attributes from the SBML Level 3 Core namespace are permitted on a Parameter object.\n Reference: L3V2 Section 4.7\n The required attribute 'constant' is missing from the <parameter> with the id 'ModelValue_14'.\n \n - SBML component consistency (20706) at line 717, column 6: A Parameter object must have the required attributes 'id' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'value' and 'units'. No other attributes from the SBML Level 3 Core namespace are permitted on a Parameter object.\n Reference: L3V2 Section 4.7\n The required attribute 'constant' is missing from the <parameter> with the id 'ModelValue_6'.\n \n - SBML component consistency (20706) at line 722, column 6: A Parameter object must have the required attributes 'id' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'value' and 'units'. No other attributes from the SBML Level 3 Core namespace are permitted on a Parameter object.\n Reference: L3V2 Section 4.7\n The required attribute 'constant' is missing from the <parameter> with the id 'ModelValue_2'.\n \n - SBML component consistency (20706) at line 727, column 6: A Parameter object must have the required attributes 'id' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name', 'value' and 'units'. No other attributes from the SBML Level 3 Core namespace are permitted on a Parameter object.\n Reference: L3V2 Section 4.7\n The required attribute 'constant' is missing from the <parameter> with the id 'ModelValue_9'.\n \n - SBML component consistency (21116) at line 953, column 10: A <speciesReference> object must have the required attributes 'species' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name' 'id' and 'stoichiometry'. No other attributes from the SBML Level 3 Core namespace are permitted on a <speciesReference> object.\n Reference: L3V2 Section 4.11\n The required attribute 'constant' is missing from the <speciesReference> from the <reaction> with the id 'Susceptible_to_Infected'.\n \n - SBML component consistency (21116) at line 956, column 10: A <speciesReference> object must have the required attributes 'species' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name' 'id' and 'stoichiometry'. No other attributes from the SBML Level 3 Core namespace are permitted on a <speciesReference> object.\n Reference: L3V2 Section 4.11\n The required attribute 'constant' is missing from the <speciesReference> from the <reaction> with the id 'Susceptible_to_Infected'.\n \n - SBML component consistency (21116) at line 1015, column 10: A <speciesReference> object must have the required attributes 'species' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name' 'id' and 'stoichiometry'. No other attributes from the SBML Level 3 Core namespace are permitted on a <speciesReference> object.\n Reference: L3V2 Section 4.11\n The required attribute 'constant' is missing from the <speciesReference> from the <reaction> with the id 'Infected_to_Recovered'.\n \n - SBML component consistency (21116) at line 1018, column 10: A <speciesReference> object must have the required attributes 'species' and 'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name' 'id' and 'stoichiometry'. No other attributes from the SBML Level 3 Core namespace are permitted on a <speciesReference> object.\n Reference: L3V2 Section 4.11\n The required attribute 'constant' is missing from the <speciesReference> from the <reaction> with the id 'Infected_to_Recovered'.\n \n - SBML component consistency (21226) at line 1047, column 14: A Trigger object must have the required attributes 'persistent' and 'initialValue', and in addition, may have the optional attributes 'metaid' and 'sboTerm'. No other attributes from the SBML Level 3 Core namespace are permitted on a Trigger object.\n Reference: L3V2 Section 4.12\n The required attribute 'initialValue' is missing.\n \n - SBML component consistency (21226) at line 1047, column 14: A Trigger object must have the required attributes 'persistent' and 'initialValue', and in addition, may have the optional attributes 'metaid' and 'sboTerm'. No other attributes from the SBML Level 3 Core namespace are permitted on a Trigger object.\n Reference: L3V2 Section 4.12\n The required attribute 'persistent' is missing.\n \n - SBML component consistency (21226) at line 1116, column 14: A Trigger object must have the required attributes 'persistent' and 'initialValue', and in addition, may have the optional attributes 'metaid' and 'sboTerm'. No other attributes from the SBML Level 3 Core namespace are permitted on a Trigger object.\n Reference: L3V2 Section 4.12\n The required attribute 'initialValue' is missing.\n \n - SBML component consistency (21226) at line 1116, column 14: A Trigger object must have the required attributes 'persistent' and 'initialValue', and in addition, may have the optional attributes 'metaid' and 'sboTerm'. No other attributes from the SBML Level 3 Core namespace are permitted on a Trigger object.\n Reference: L3V2 Section 4.12\n The required attribute 'persistent' is missing.\n \n - SBML component consistency (21226) at line 1177, column 14: A Trigger object must have the required attributes 'persistent' and 'initialValue', and in addition, may have the optional attributes 'metaid' and 'sboTerm'. No other attributes from the SBML Level 3 Core namespace are permitted on a Trigger object.\n Reference: L3V2 Section 4.12\n The required attribute 'initialValue' is missing.\n \n - SBML component consistency (21226) at line 1177, column 14: A Trigger object must have the required attributes 'persistent' and 'initialValue', and in addition, may have the optional attributes 'metaid' and 'sboTerm'. No other attributes from the SBML Level 3 Core namespace are permitted on a Trigger object.\n Reference: L3V2 Section 4.12\n The required attribute 'persistent' is missing.\n \nname: Bertozzi2020\nsedml_name: Bertozzi2020\ncontent.location: Bertozzi2020.sedml\ncontent_filename: /tmp/VCell_CLI_1946dfe0cc36283838915361190536/BIOMD0000000956/temp/Bertozzi2020.sedml\n\n>\nResult: Failed generating SED-ML for plot2d and 3D \n\n"}
{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000957.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000958.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000959.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
Expand Down