diff --git a/vcell-cli/src/main/resources/test_cases.ndjson b/vcell-cli/src/main/resources/test_cases.ndjson index cf1c4f9ac2..70e1d1738c 100644 --- a/vcell-cli/src/main/resources/test_cases.ndjson +++ b/vcell-cli/src/main/resources/test_cases.ndjson @@ -816,7 +816,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000708.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000709.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000710.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_0_0' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000711.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"TOO_SLOW","known_failure_desc":"> 5 minutes - Failed execution: Model 'BIOMD0000000711_Hancioglu2007 - Human Immune Response to Influenza A virus.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000711.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":"> 5 minutes - Failed execution: Model 'BIOMD0000000711_Hancioglu2007 - Human Immune Response to Influenza A virus.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000712.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000713.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000714.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} diff --git a/vcell-core/src/main/java/org/vcell/sedml/testsupport/FailureType.java b/vcell-core/src/main/java/org/vcell/sedml/testsupport/FailureType.java index 50a90aa8b9..78a9b26a51 100644 --- a/vcell-core/src/main/java/org/vcell/sedml/testsupport/FailureType.java +++ b/vcell-core/src/main/java/org/vcell/sedml/testsupport/FailureType.java @@ -31,7 +31,6 @@ public enum FailureType { SEDML_UNSUPPORTED_MODEL_REFERENCE, // Model refers to either a non-existent model (invalid SED-ML) or to another model with changes (not supported yet) SEDML_NON_UTC_SIMULATION_FOUND, SEDML_SBML_LEVEL_CHANGE, // unsupported SBML Level change within the SED-ML - TOO_SLOW, UNCATEGORIZED_FAULT, UNITS_EXCEPTION, UNKNOWN_IDENTIFIER, diff --git a/vcell-core/src/main/java/org/vcell/sedml/testsupport/OmexTestingDatabase.java b/vcell-core/src/main/java/org/vcell/sedml/testsupport/OmexTestingDatabase.java index 8f9f904476..588f44651c 100644 --- a/vcell-core/src/main/java/org/vcell/sedml/testsupport/OmexTestingDatabase.java +++ b/vcell-core/src/main/java/org/vcell/sedml/testsupport/OmexTestingDatabase.java @@ -152,7 +152,7 @@ private static FailureType determineFault(TraceEvent traceEvent){ private static FailureType determineFault(Exception caughtException){ String errorMessage = caughtException.getMessage(); - if (caughtException instanceof TimeoutException) { + if (caughtException instanceof TimeoutException || errorMessage.contains("Process timed out")) { return FailureType.TIMEOUT_ENCOUNTERED; } else if (errorMessage.contains("refers to either a non-existent model")) { //"refers to either a non-existent model (invalid SED-ML) or to another model with changes (not supported yet)" return FailureType.SEDML_UNSUPPORTED_MODEL_REFERENCE; @@ -189,8 +189,6 @@ private static FailureType determineFault(Exception caughtException){ return FailureType.UNSUPPORTED_DELAY_SBML; } else if (errorMessage.contains("are in unnamed module of loader")){ return FailureType.SBML_IMPORT_FAILURE; - } else if (errorMessage.contains("Process timed out")) { - return FailureType.TOO_SLOW; } return null; }