From 8178a096829794263192e10dfbab0c4e82507637 Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Thu, 2 Jan 2025 16:21:26 -0500 Subject: [PATCH 01/10] Fixed bugs with reports and null values --- .../sedml/testsupport/OmexTestReport.java | 24 ++++++++++--------- 1 file changed, 13 insertions(+), 11 deletions(-) diff --git a/vcell-core/src/main/java/org/vcell/sedml/testsupport/OmexTestReport.java b/vcell-core/src/main/java/org/vcell/sedml/testsupport/OmexTestReport.java index 156538181a..da5311e60f 100644 --- a/vcell-core/src/main/java/org/vcell/sedml/testsupport/OmexTestReport.java +++ b/vcell-core/src/main/java/org/vcell/sedml/testsupport/OmexTestReport.java @@ -8,6 +8,7 @@ import org.apache.logging.log4j.Logger; import org.vcell.util.Pair; +import java.io.File; import java.nio.file.Path; import java.nio.file.Paths; import java.util.*; @@ -55,15 +56,14 @@ public OmexTestReport(List testCases, List execSu if (testCase.known_status != OmexTestCase.Status.FAIL) { continue; } - FailureType failureType = (testCase.known_failure_type != null) ? testCase.known_failure_type : FailureType.UNCATETORIZED_FAULT; - this.historicalFailureTypeCounts.put(failureType, this.historicalFailureTypeCounts.getOrDefault(failureType, 0) + 1); + + this.historicalFailureTypeCounts.put(testCase.known_failure_type, this.historicalFailureTypeCounts.getOrDefault(testCase.known_failure_type, 0) + 1); } for (OmexExecSummary execSummary : execSummaries) { // Collect Failure Types if (execSummary.status == OmexExecSummary.ActualStatus.FAILED){ - FailureType failureType = (execSummary.failure_type != null) ? execSummary.failure_type : FailureType.UNCATETORIZED_FAULT; - this.currentFailureTypeCounts.put(failureType, this.currentFailureTypeCounts.getOrDefault(failureType, 0) + 1); + this.currentFailureTypeCounts.put(execSummary.failure_type , this.currentFailureTypeCounts.getOrDefault(execSummary.failure_type , 0) + 1); } // find matching test case @@ -210,7 +210,9 @@ private static MarkdownTable generateErrorTypeStatistics(Map> pairing = failureTypeList.get(i); - errorTypeStatistics.setRowTitle(i, pairing.one.toString()); + String failureTypeString = pairing.one == null ? "SKIPPED" : pairing.one.toString(); + errorTypeStatistics.setRowTitle(i, failureTypeString); + errorTypeStatistics.setTableValue(i, 0, pairing.two.one); errorTypeStatistics.setTableValue(i, 1, pairing.two.two); } @@ -246,7 +248,7 @@ private static MarkdownTable generateIncomparableStatistics(OmexTestStatistics s nameToIfHistoricalMap.put(testCase.file_path, true); } if (statistics.unmatchedExecutionsCount > 0) for (OmexExecSummary execSummary : unmatchedExecSummaries){ - nameToIfHistoricalMap.put(execSummary.file_path, false); + nameToIfHistoricalMap.put((new File(execSummary.file_path).getName()), false); } List unmatchedNames = new ArrayList<>(nameToIfHistoricalMap.keySet()); unmatchedNames.sort(Comparator.naturalOrder()); @@ -255,8 +257,8 @@ private static MarkdownTable generateIncomparableStatistics(OmexTestStatistics s incomparableStatistics.setRowTitle(i, name); // We want to put a checkmark in the correct column, based on which actually ran the test int matchedColumn = nameToIfHistoricalMap.get(name) ? 0 : 1; - incomparableStatistics.setTableValue(i, matchedColumn, "✔"); - incomparableStatistics.setTableValue(i, 1 - matchedColumn, "❌"); + incomparableStatistics.setTableValue(i, matchedColumn, "yes"); + incomparableStatistics.setTableValue(i, 1 - matchedColumn, "no"); } return incomparableStatistics; } @@ -270,7 +272,7 @@ private static MarkdownTable generateUnmatchedResultStatistics(List" : switch (testCaseChange.original.known_status){ case PASS: yield "PASSED"; case SKIP: @@ -280,13 +282,13 @@ private static MarkdownTable generateUnmatchedResultStatistics(List" : switch (testCaseChange.updated.known_status){ case PASS: yield "PASSED"; case SKIP: yield "SKIPPED"; case FAIL: - yield String.format("FAILED (%s)", testCaseChange.original.known_failure_type.name()); + yield String.format("FAILED (%s)", testCaseChange.updated.known_failure_type.name()); }; unmatchedResultStatistics.setTableValue(i, 1, currentResult); } From 6781d7fe5ad5cf18b0912349dba377acd6846cd4 Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Thu, 2 Jan 2025 16:21:36 -0500 Subject: [PATCH 02/10] Added more failure types --- .../main/java/org/vcell/sedml/testsupport/FailureType.java | 5 ++++- .../org/vcell/sedml/testsupport/OmexTestingDatabase.java | 6 ++++++ 2 files changed, 10 insertions(+), 1 deletion(-) 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 55f8a5c120..cf68da415f 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 @@ -32,6 +32,9 @@ public enum FailureType { UNCATETORIZED_FAULT, UNITS_EXCEPTION, UNKNOWN_IDENTIFIER, - SEDML_NO_SEDMLS_TO_EXECUTE, SEDML_PREPROCESS_FAILURE, UNSUPPORTED_NONSPATIAL_STOCH_HISTOGRAM + SEDML_NO_SEDMLS_TO_EXECUTE, + SEDML_PREPROCESS_FAILURE, + UNSUPPORTED_NONSPATIAL_STOCH_HISTOGRAM, + SOLVER_FAILURE } 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 ced8e4a0af..fe6741d2a7 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 @@ -127,6 +127,12 @@ public static FailureType determineFault(Exception caughtException, List Date: Fri, 3 Jan 2025 13:50:28 -0500 Subject: [PATCH 03/10] Added test cases and fixed CI test --- .../src/main/resources/test_cases.ndjson | 190 +++++++++--------- .../vcell/sedml/testsupport/FailureType.java | 8 +- .../testsupport/OmexTestingDatabase.java | 19 +- 3 files changed, 116 insertions(+), 101 deletions(-) diff --git a/vcell-cli/src/main/resources/test_cases.ndjson b/vcell-cli/src/main/resources/test_cases.ndjson index 0849bd437c..dc13d08bdf 100644 --- a/vcell-cli/src/main/resources/test_cases.ndjson +++ b/vcell-cli/src/main/resources/test_cases.ndjson @@ -6,7 +6,7 @@ {"test_collection":"VCELL_BIOMD","file_path":"BIOMD0000000175.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"MATH_GENERATION_FAILURE","known_failure_desc":"unknown identifier I_Net_E44PPI3K_binding"} {"test_collection":"VCELL_BIOMD","file_path":"BIOMD0000000302.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"MATH_GENERATION_FAILURE","known_failure_desc":"Initial condition for variable 'h_post' references variable 'V_post'"} {"test_collection":"VCELL_BIOMD","file_path":"BIOMD0000000520.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_BIOMD","file_path":"BIOMD0000000561.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"not a dynamic system - can't solve"} +{"test_collection":"VCELL_BIOMD","file_path":"BIOMD0000000561.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"not a dynamic system - can't solve"} {"test_collection":"VCELL_BIOMD","file_path":"BIOMD0000000569.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_BIOMD","file_path":"BIOMD0000000618.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"couldn't find SBase with sid=null in SBMLSymbolMapping"} {"test_collection":"VCELL_BIOMD","file_path":"BIOMD0000000651.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -131,8 +131,8 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000021.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000022.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000023.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000024.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: unsupported SBML element 'delay' in expression"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000025.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: unsupported SBML element 'delay' in expression"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000024.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_DELAY_SBML","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: unsupported SBML element 'delay' in expression"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000025.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_DELAY_SBML","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: unsupported SBML element 'delay' in expression"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000026.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000027.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000028.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -141,13 +141,13 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000031.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000032.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000033.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000034.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: unsupported SBML element 'delay' in expression"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000034.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_DELAY_SBML","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: unsupported SBML element 'delay' in expression"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000035.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000036.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000037.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000038.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000039.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.25' for reactant 'CaER' in reaction 'v1') not handled in VCell at this time"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000040.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-numeric stoichiometry ('f' for product 'Br' in reaction 'Reaction5') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000039.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.25' for reactant 'CaER' in reaction 'v1') not handled in VCell at this time"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000040.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_NUMERIC_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-numeric stoichiometry ('f' for product 'Br' in reaction 'Reaction5') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000041.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000042.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000043.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -166,11 +166,11 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000056.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000057.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000058.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000059.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.01' for reactant 'Ca_cyt' in reaction 'Calcium_cyt_Jerp') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000059.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.01' for reactant 'Ca_cyt' in reaction 'Calcium_cyt_Jerp') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000060.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000061.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000062.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000063.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for reactant 'FDP' in reaction 'Vgol') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000063.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for reactant 'FDP' in reaction 'Vgol') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000064.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000065.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000066.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -188,7 +188,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000078.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000079.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000080.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000081.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('9.967E-4' for reactant 'ATP_C' in reaction 'PIP5kinase') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000081.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('9.967E-4' for reactant 'ATP_C' in reaction 'PIP5kinase') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000082.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000083.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000084.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -244,7 +244,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000134.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000135.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000136.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000137.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000137_BIOMD0000000137_url.sedml_BIOMD0000000137_url' Task 'task1'. java.lang.RuntimeException: Could not execute code: CVODE solver failed : at time 0.01, discontinuity ((x6 + x7 + x8) > 100) evaluated to TRUE, solver assumed FALSE"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000137.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000137_BIOMD0000000137_url.sedml_BIOMD0000000137_url' Task 'task1'. java.lang.RuntimeException: Could not execute code: CVODE solver failed : at time 0.01, discontinuity ((x6 + x7 + x8) > 100) evaluated to TRUE, solver assumed FALSE"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000138.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000139.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000140.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -252,17 +252,17 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000142.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000143.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000144.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000145.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.001' for reactant 'Ca_ER' in reaction 'R9') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000145.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.001' for reactant 'Ca_ER' in reaction 'R9') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000146.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000147.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000148.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000149.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000150.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000151.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for product 'x13' in reaction 'R23') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000151.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for product 'x13' in reaction 'R23') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000152.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000153.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000154.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: unsupported SBML element 'delay' in expression"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000155.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: unsupported SBML element 'delay' in expression"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000154.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_DELAY_SBML","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: unsupported SBML element 'delay' in expression"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000155.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_DELAY_SBML","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: unsupported SBML element 'delay' in expression"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000156.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000157.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000158.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -303,17 +303,17 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000193.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000194.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000195.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000196.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: unsupported SBML element 'delay' in expression"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000196.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_DELAY_SBML","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: unsupported SBML element 'delay' in expression"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000197.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000198.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000199.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for reactant 'NADPH' in reaction 'r4') not handled in VCell at this time"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000199.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for reactant 'NADPH' in reaction 'r4') not handled in VCell at this time"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000200.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000201.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000202.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000203.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000204.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000205.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000206.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.1' for product 's6o' in reaction 'v10') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000206.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.1' for product 's6o' in reaction 'v10') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000207.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000208.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000209.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -339,9 +339,9 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000229.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000230.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000231.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000232.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for reactant 'O2' in reaction 'vresp') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000232.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for reactant 'O2' in reaction 'vresp') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000233.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000234.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"1626.047 seconds - timeout - Failed execution: Model 'BIOMD0000000234_GemcitabineCorrected.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out in SundialsSolverStandalone_x64"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000234.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"1626.047 seconds - timeout - Failed execution: Model 'BIOMD0000000234_GemcitabineCorrected.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out in SundialsSolverStandalone_x64"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000235.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000236.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000237.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -351,9 +351,9 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000241.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000242.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000243.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000244.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for reactant 'FBP' in reaction 'e_Emp') not handled in VCell at this time."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000245.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.978' for product 's_pyr' in reaction 'r1') not handled in VCell at this time."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000246.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.001' for product 'Ca_in' in reaction 'vo') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000244.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for reactant 'FBP' in reaction 'e_Emp') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000245.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.978' for product 's_pyr' in reaction 'r1') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000246.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.001' for product 'Ca_in' in reaction 'vo') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000247.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000248.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Failed to translate SBML model into BioModel: Error binding global parameter 'ATPase_flux_mM' to model: 'ATPase' is either not found in your model or is not allowed to be used in the current context."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000249.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -383,8 +383,8 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000273.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000274.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000275.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000276.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000276_BIOMD0000000276_url.sedml_BIOMD0000000276_url' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE ERROR] CVode\n The right-hand side routine failed at the first call.\n\nCVODE solver failed : CV_FIRST_RHSFUNC_ERR: The right-hand side routine failed at the first call : FunctionRangeException : FunctionRangeException : Evaluated to infinity in \"(9.8436754999999998006 - ((0.00049463777420084603827 + (0.048942788387963273578 / (1 + ((((1.2549999999999998934 * (__D_B_0 == 1)) + ((1.2549999999999998934 - (0.1817000000000000004 * (1 - exp( - (0.044200000000000003175 * ( - 575 + t)))))) * !((__D_B_0 == 1)))) / (1.2549999999999998934 * (0.16863731981259902359 ^ (1 / (15 + (112.51999999999999602 / (1 + exp( - (1000000 * (1.2161999999999999478 - ((1.2549999999999998934 * (__D_B_0 == 1)) + ((1.2549999999999998934 - (0.1817000000000000004 * (1 - exp( - (0.044200000000000003175 * ( - 575 + t)))))) * !((__D_B_0 == 1)))))))))))))) ^ (15 + (112.51999999999999602 / (1 + exp( - (1000000 * (1.2161999999999999478 - ((1.2549999999999998934 * (__D_B_0 == 1)) + ((1.2549999999999998934 - (0.1817000000000000004 * (1 - exp( - (0.044200000000000003175 * ( - 575 + t)))))) * !((__D_B_0 == 1)))))))))))))) * x1) - (0.012500000000000000694 * x1))\"\n where:\n\t__D_B_0 = 1.000000\n\tt = 0.000000\n\tx1 = 0.000000"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000277.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000277_BIOMD0000000277_url.sedml_BIOMD0000000277_url' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE ERROR] CVode\n The right-hand side routine failed at the first call.\n\nCVODE solver failed : CV_FIRST_RHSFUNC_ERR: The right-hand side routine failed at the first call : FunctionRangeException : FunctionRangeException : Evaluated to infinity in \"(9.8436754999999998006 - ((0.00049463777420084603827 + (0.048942788387963273578 / (1 + ((((1.2199999999999999734 * (__D_B_0 == 1)) + ((1.2199999999999999734 + (0.26240000000000002212 * (1 - exp( - (0.05689999999999999919 * ( - 575 + t)))))) * !((__D_B_0 == 1)))) / (1.2549999999999998934 * (0.16863731981259902359 ^ (1 / (15 + (112.51999999999999602 / (1 + exp( - (1000000 * (1.2161999999999999478 - ((1.2199999999999999734 * (__D_B_0 == 1)) + ((1.2199999999999999734 + (0.26240000000000002212 * (1 - exp( - (0.05689999999999999919 * ( - 575 + t)))))) * !((__D_B_0 == 1)))))))))))))) ^ (15 + (112.51999999999999602 / (1 + exp( - (1000000 * (1.2161999999999999478 - ((1.2199999999999999734 * (__D_B_0 == 1)) + ((1.2199999999999999734 + (0.26240000000000002212 * (1 - exp( - (0.05689999999999999919 * ( - 575 + t)))))) * !((__D_B_0 == 1)))))))))))))) * x1) - (0.012500000000000000694 * x1))\"\n where:\n\t__D_B_0 = 1.000000\n\tt = 0.000000\n\tx1 = 0.000000"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000276.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000276_BIOMD0000000276_url.sedml_BIOMD0000000276_url' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE ERROR] CVode\n The right-hand side routine failed at the first call.\n\nCVODE solver failed : CV_FIRST_RHSFUNC_ERR: The right-hand side routine failed at the first call : FunctionRangeException : FunctionRangeException : Evaluated to infinity in \"(9.8436754999999998006 - ((0.00049463777420084603827 + (0.048942788387963273578 / (1 + ((((1.2549999999999998934 * (__D_B_0 == 1)) + ((1.2549999999999998934 - (0.1817000000000000004 * (1 - exp( - (0.044200000000000003175 * ( - 575 + t)))))) * !((__D_B_0 == 1)))) / (1.2549999999999998934 * (0.16863731981259902359 ^ (1 / (15 + (112.51999999999999602 / (1 + exp( - (1000000 * (1.2161999999999999478 - ((1.2549999999999998934 * (__D_B_0 == 1)) + ((1.2549999999999998934 - (0.1817000000000000004 * (1 - exp( - (0.044200000000000003175 * ( - 575 + t)))))) * !((__D_B_0 == 1)))))))))))))) ^ (15 + (112.51999999999999602 / (1 + exp( - (1000000 * (1.2161999999999999478 - ((1.2549999999999998934 * (__D_B_0 == 1)) + ((1.2549999999999998934 - (0.1817000000000000004 * (1 - exp( - (0.044200000000000003175 * ( - 575 + t)))))) * !((__D_B_0 == 1)))))))))))))) * x1) - (0.012500000000000000694 * x1))\"\n where:\n\t__D_B_0 = 1.000000\n\tt = 0.000000\n\tx1 = 0.000000"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000277.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000277_BIOMD0000000277_url.sedml_BIOMD0000000277_url' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE ERROR] CVode\n The right-hand side routine failed at the first call.\n\nCVODE solver failed : CV_FIRST_RHSFUNC_ERR: The right-hand side routine failed at the first call : FunctionRangeException : FunctionRangeException : Evaluated to infinity in \"(9.8436754999999998006 - ((0.00049463777420084603827 + (0.048942788387963273578 / (1 + ((((1.2199999999999999734 * (__D_B_0 == 1)) + ((1.2199999999999999734 + (0.26240000000000002212 * (1 - exp( - (0.05689999999999999919 * ( - 575 + t)))))) * !((__D_B_0 == 1)))) / (1.2549999999999998934 * (0.16863731981259902359 ^ (1 / (15 + (112.51999999999999602 / (1 + exp( - (1000000 * (1.2161999999999999478 - ((1.2199999999999999734 * (__D_B_0 == 1)) + ((1.2199999999999999734 + (0.26240000000000002212 * (1 - exp( - (0.05689999999999999919 * ( - 575 + t)))))) * !((__D_B_0 == 1)))))))))))))) ^ (15 + (112.51999999999999602 / (1 + exp( - (1000000 * (1.2161999999999999478 - ((1.2199999999999999734 * (__D_B_0 == 1)) + ((1.2199999999999999734 + (0.26240000000000002212 * (1 - exp( - (0.05689999999999999919 * ( - 575 + t)))))) * !((__D_B_0 == 1)))))))))))))) * x1) - (0.012500000000000000694 * x1))\"\n where:\n\t__D_B_0 = 1.000000\n\tt = 0.000000\n\tx1 = 0.000000"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000278.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000279.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000280.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -408,7 +408,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000298.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000299.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000300.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000301.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000301_BIOMD0000000301_url.sedml_BIOMD0000000301_url' Task 'task1'. java.lang.RuntimeException: Could not execute code: CVODE solver failed : at time 0.01, discontinuity (t >= 0.010000000000000000208) evaluated to TRUE, solver assumed FALSE"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000301.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000301_BIOMD0000000301_url.sedml_BIOMD0000000301_url' Task 'task1'. java.lang.RuntimeException: Could not execute code: CVODE solver failed : at time 0.01, discontinuity (t >= 0.010000000000000000208) evaluated to TRUE, solver assumed FALSE"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000302.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"MATH_GENERATION_FAILURE","known_failure_desc":"MappingException occurred: failed to generate math: generated an invalid mathDescription: Initial condition for variable 'h_post' references variable 'V_post'. Initial conditions cannot reference variables"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000303.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000304.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -426,7 +426,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000316.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000317.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000318.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000319.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.02' for product 'gamma' in reaction 'r3') not handled in VCell at this time"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000319.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.02' for product 'gamma' in reaction 'r3') not handled in VCell at this time"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000320.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000321.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000322.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -445,11 +445,11 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000335.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000336.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000337.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000338.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'compartment_1' has constant attribute set to False, not currently supported"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000339.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'compartment_1' has constant attribute set to False, not currently supported"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000338.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'compartment_1' has constant attribute set to False, not currently supported"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000339.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'compartment_1' has constant attribute set to False, not currently supported"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000340.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000341.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000342.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'Vmed' has constant attribute set to False, not currently supported"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000342.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'Vmed' has constant attribute set to False, not currently supported"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000343.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000344.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000345.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -460,9 +460,9 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000350.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000351.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000352.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000353.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('12345.7' for reactant 'cpd_C00369Glc_CS' in reaction 'rn_R02112CS_G2') not handled in VCell at this time"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000354.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'cytosol' has constant attribute set to False, not currently supported"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000355.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'cytosol' has constant attribute set to False, not currently supported"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000353.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('12345.7' for reactant 'cpd_C00369Glc_CS' in reaction 'rn_R02112CS_G2') not handled in VCell at this time"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000354.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'cytosol' has constant attribute set to False, not currently supported"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000355.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'cytosol' has constant attribute set to False, not currently supported"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000356.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000357.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000358.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -490,16 +490,16 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000380.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000381.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000382.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000383.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.5' for product 'PGA' in reaction 'PGA_prod_Vo') not handled in VCell at this time."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000384.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.5' for product 'PGA' in reaction 'PGA_prod_Vo') not handled in VCell at this time."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000385.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.5' for product 'PGA' in reaction 'PGA_prod_Vo') not handled in VCell at this time."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000386.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.5' for product 'PGA' in reaction 'PGA_prod_Vo') not handled in VCell at this time."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000387.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.5' for product 'PGA' in reaction 'PGA_prod_Vo') not handled in VCell at this time."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000388.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.6' for product 'Ru5P' in reaction 'GAP2Ru5P') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000383.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.5' for product 'PGA' in reaction 'PGA_prod_Vo') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000384.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.5' for product 'PGA' in reaction 'PGA_prod_Vo') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000385.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.5' for product 'PGA' in reaction 'PGA_prod_Vo') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000386.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.5' for product 'PGA' in reaction 'PGA_prod_Vo') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000387.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.5' for product 'PGA' in reaction 'PGA_prod_Vo') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000388.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.6' for product 'Ru5P' in reaction 'GAP2Ru5P') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000389.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000390.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000391.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000392.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for reactant 'ATP' in reaction 'RuBisCO_6_O2') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000392.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for reactant 'ATP' in reaction 'RuBisCO_6_O2') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000393.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000394.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000395.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -522,7 +522,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000412.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000413.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000414.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000415.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.574' for product 'species_7' in reaction 'reaction_1') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000415.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.574' for product 'species_7' in reaction 'reaction_1') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000416.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000417.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000418.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -531,12 +531,12 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000421.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000422.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000423.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000424.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'Default' has constant attribute set to False, not currently supported."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000424.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'Default' has constant attribute set to False, not currently supported."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000425.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000426.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.08' for reactant 'species_31' in reaction 'reaction_28') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000426.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.08' for reactant 'species_31' in reaction 'reaction_28') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000427.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000428.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000429.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'compartment_1' has constant attribute set to False, not currently supported."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000429.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'compartment_1' has constant attribute set to False, not currently supported."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000430.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000431.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000432.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -570,17 +570,17 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000460.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: couldn't find SBase with sid=null in SBMLSymbolMapping"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000461.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: couldn't find SBase with sid=null in SBMLSymbolMapping"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000462.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000463.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('8.5' for reactant 'species_14' in reaction 'reaction_11') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000463.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('8.5' for reactant 'species_14' in reaction 'reaction_11') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000464.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000465.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000466.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000467.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000468.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"found more than one SBase match for sid=unitime, matched [org.vcell.sbml.vcell.SBMLSymbolMapping$SBaseWrapper@15c6027d, org.vcell.sbml.vcell.SBMLSymbolMapping$SBaseWrapper@11c88cca]"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000469.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.5' for reactant 's_1372' in reaction 'r_1230') not handled in VCell at this time."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000470.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.5' for reactant 's_1372' in reaction 'r_1230') not handled in VCell at this time."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000471.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('4.33333333333333' for reactant 's_0056' in reaction 'r_1052') not handled in VCell at this time."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000472.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('4.33333333333333' for reactant 's_0056' in reaction 'r_1052') not handled in VCell at this time."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000473.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.8' for reactant 's_0595' in reaction 'r_1014') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000469.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.5' for reactant 's_1372' in reaction 'r_1230') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000470.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.5' for reactant 's_1372' in reaction 'r_1230') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000471.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('4.33333333333333' for reactant 's_0056' in reaction 'r_1052') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000472.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('4.33333333333333' for reactant 's_0056' in reaction 'r_1052') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000473.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.8' for reactant 's_0595' in reaction 'r_1014') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000474.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"found more than one SBase match for sid=v, matched [org.vcell.sbml.vcell.SBMLSymbolMapping$SBaseWrapper@3ba97962, org.vcell.sbml.vcell.SBMLSymbolMapping$SBaseWrapper@5b5b53c6]"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000475.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000476.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -603,8 +603,8 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000493.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000494.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000495.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000496.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.1358' for reactant 's_0001' in reaction 'r_1812') not handled in VCell at this time."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000497.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.1358' for reactant 's_0001' in reaction 'r_1812') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000496.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.1358' for reactant 's_0001' in reaction 'r_1812') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000497.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.1358' for reactant 's_0001' in reaction 'r_1812') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000498.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Unable to initialize bioModel for the given selection: Cannot invoke \"cbit.vcell.solver.Simulation.getImportedTaskID()\" because \"simulation\" is null"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000499.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_9' 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":"BIOMD0000000500.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Unable to initialize bioModel for the given selection: Cannot invoke \"cbit.vcell.solver.Simulation.getImportedTaskID()\" because \"simulation\" is null"} @@ -638,8 +638,8 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000528.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000529.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000530.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000531.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000531_model.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVDENSE ERROR] CVDense\n A memory request failed.\n\nCVODE solver failed : CV_CONV_FAILURE: convergence test failures occurred too many times during one internal step"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000532.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000532_Vazquez2014.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVDENSE ERROR] CVDense\n A memory request failed.\n\nCVODE solver failed : CV_CONV_FAILURE: convergence test failures occurred too many times during one internal step"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000531.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000531_model.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVDENSE ERROR] CVDense\n A memory request failed.\n\nCVODE solver failed : CV_CONV_FAILURE: convergence test failures occurred too many times during one internal step"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000532.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000532_Vazquez2014.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVDENSE ERROR] CVDense\n A memory request failed.\n\nCVODE solver failed : CV_CONV_FAILURE: convergence test failures occurred too many times during one internal step"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000533.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000534.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_6' 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":"BIOMD0000000535.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_3' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context"} @@ -661,23 +661,23 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000551.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000552.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000553.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000554.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000554_Cloutier2009(final).sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE ERROR] CVode\n The right-hand side routine failed at the first call.\n\nCVODE solver failed : CV_FIRST_RHSFUNC_ERR: The right-hand side routine failed at the first call : FunctionRangeException : FunctionRangeException : Evaluated to infinity in \"(0.01200000000000000025 + (0.005040000000000000209 / (1 + exp( - (4.5918599999999996086 * ( - 199 + t))))) - (0.005040000000000000209 / (1 + exp( - (4.5918599999999996086 * ( - 505 + t))))) - (0.01200000000000000025 * (((42.372881355932207725 * Vv) ^ 2) + (1483.050847457627242 * ((42.372881355932207725 * Vv) ^ - 0.5) * (0.01200000000000000025 + (0.005040000000000000209 / (1 + exp( - (4.5918599999999996086 * ( - 199 + t))))) - (0.005040000000000000209 / (1 + exp( - (4.5918599999999996086 * ( - 505 + t)))))))) / (1 + (17.796610169491525966 * ((42.372881355932207725 * Vv) ^ - 0.5)))))\"\n where:\n\tt = 0.000000\n\tVv = 0.023700"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000555.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000555_Auer2010.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVDENSE ERROR] CVDense\n A memory request failed.\n\nCVODE solver failed : CV_CONV_FAILURE: convergence test failures occurred too many times during one internal step"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000554.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000554_Cloutier2009(final).sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE ERROR] CVode\n The right-hand side routine failed at the first call.\n\nCVODE solver failed : CV_FIRST_RHSFUNC_ERR: The right-hand side routine failed at the first call : FunctionRangeException : FunctionRangeException : Evaluated to infinity in \"(0.01200000000000000025 + (0.005040000000000000209 / (1 + exp( - (4.5918599999999996086 * ( - 199 + t))))) - (0.005040000000000000209 / (1 + exp( - (4.5918599999999996086 * ( - 505 + t))))) - (0.01200000000000000025 * (((42.372881355932207725 * Vv) ^ 2) + (1483.050847457627242 * ((42.372881355932207725 * Vv) ^ - 0.5) * (0.01200000000000000025 + (0.005040000000000000209 / (1 + exp( - (4.5918599999999996086 * ( - 199 + t))))) - (0.005040000000000000209 / (1 + exp( - (4.5918599999999996086 * ( - 505 + t)))))))) / (1 + (17.796610169491525966 * ((42.372881355932207725 * Vv) ^ - 0.5)))))\"\n where:\n\tt = 0.000000\n\tVv = 0.023700"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000555.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000555_Auer2010.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVDENSE ERROR] CVDense\n A memory request failed.\n\nCVODE solver failed : CV_CONV_FAILURE: convergence test failures occurred too many times during one internal step"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000556.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Unable to create and add rate rule to VC model : 'r0.LumpedJ' is either not found in your model or is not allowed to be used in the current context"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000557.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000558.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000559.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000560.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000561.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000561_Martins2013.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVDENSE ERROR] CVDense\n A memory request failed.\n\nCVODE solver failed : CV_CONV_FAILURE: convergence test failures occurred too many times during one internal step"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000561.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000561_Martins2013.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVDENSE ERROR] CVDense\n A memory request failed.\n\nCVODE solver failed : CV_CONV_FAILURE: convergence test failures occurred too many times during one internal step"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000562.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000000562 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000563.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000564.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000565.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000566.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000566_Morris2009.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVDENSE ERROR] CVDense\n A memory request failed.\n\nCVODE solver failed : CV_CONV_FAILURE: convergence test failures occurred too many times during one internal step"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000567.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000567_Morris2008.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVDENSE ERROR] CVDense\n A memory request failed.\n\nCVODE solver failed : CV_CONV_FAILURE: convergence test failures occurred too many times during one internal step"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000566.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000566_Morris2009.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVDENSE ERROR] CVDense\n A memory request failed.\n\nCVODE solver failed : CV_CONV_FAILURE: convergence test failures occurred too many times during one internal step"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000567.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000567_Morris2008.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVDENSE ERROR] CVDense\n A memory request failed.\n\nCVODE solver failed : CV_CONV_FAILURE: convergence test failures occurred too many times during one internal step"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000568.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000569.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000570.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'compartment_4' has constant attribute set to False, not currently supported."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000570.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'compartment_4' has constant attribute set to False, not currently supported."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000571.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000572.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000573.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -703,7 +703,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000593.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000000593 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000594.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000595.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":"timeout > 12 minutes"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000596.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000596.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_XML_NODE_FAILURE","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000597.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000598.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000599.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_1' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context"} @@ -715,7 +715,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000605.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000606.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000607.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000608.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for reactant 'x_18' in reaction 'R_18') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000608.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for reactant 'x_18' in reaction 'R_18') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000609.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000610.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000611.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -727,14 +727,14 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000617.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000618.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error processing model: model2 - couldn't find SBase with sid=null in SBMLSymbolMapping org.vcell.sbml.vcell.SBMLImportException: couldn't find SBase with sid=null in SBMLSymbolMapping"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000619.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000620.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000620_BIOMD0000000620_url.sedml_BIOMD0000000620_url' Task 'task1'. java.lang.RuntimeException: Could not execute code: CVODE solver failed : at time 5.5, discontinuity (t == Anakinra_dose_counter) evaluated to TRUE, solver assumed FALSE"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000621.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000621_BIOMD0000000621_url.sedml_BIOMD0000000621_url' Task 'task1'. java.lang.RuntimeException: Could not execute code: CVODE solver failed : at time 5.5, discontinuity (t == Anakinra_dose_counter) evaluated to TRUE, solver assumed FALSE"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000620.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000620_BIOMD0000000620_url.sedml_BIOMD0000000620_url' Task 'task1'. java.lang.RuntimeException: Could not execute code: CVODE solver failed : at time 5.5, discontinuity (t == Anakinra_dose_counter) evaluated to TRUE, solver assumed FALSE"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000621.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000621_BIOMD0000000621_url.sedml_BIOMD0000000621_url' Task 'task1'. java.lang.RuntimeException: Could not execute code: CVODE solver failed : at time 5.5, discontinuity (t == Anakinra_dose_counter) evaluated to TRUE, solver assumed FALSE"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000622.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000623.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000624.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000625.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000626.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000627.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'venous_balloon' has constant attribute set to False, not currently supported."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000627.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'venous_balloon' has constant attribute set to False, not currently supported."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000628.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_8' 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":"BIOMD0000000629.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000630.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -779,7 +779,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000670.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000671.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000672.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000673.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000673_MODEL1006230054_edited.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVDENSE ERROR] CVDense\n A memory request failed.\n\nCVODE solver failed : CV_CONV_FAILURE: convergence test failures occurred too many times during one internal step"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000673.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000673_MODEL1006230054_edited.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVDENSE ERROR] CVDense\n A memory request failed.\n\nCVODE solver failed : CV_CONV_FAILURE: convergence test failures occurred too many times during one internal step"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000674.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000675.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000676.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -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":"UNCATETORIZED_FAULT","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":"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":"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} @@ -824,7 +824,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000716.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000717.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000718.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000719.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000719_tsai2014.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE ERROR] CVode\n The right-hand side routine failed at the first call.\n\nCVODE solver failed : CV_FIRST_RHSFUNC_ERR: The right-hand side routine failed at the first call : DivideByZeroException : DivideByZeroException : divide by zero in \"( - (1.5 * (APC_C_active - APC_C_total) / (1 + ((0.5 / Plx1_active) ^ 4))) - (0.14999999999999999445 * APC_C_active))\"\n where:\n\tAPC_C_active = 1.000000\n\tAPC_C_total = 1.000000\n\tPlx1_active = 0.000000"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000719.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000719_tsai2014.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE ERROR] CVode\n The right-hand side routine failed at the first call.\n\nCVODE solver failed : CV_FIRST_RHSFUNC_ERR: The right-hand side routine failed at the first call : DivideByZeroException : DivideByZeroException : divide by zero in \"( - (1.5 * (APC_C_active - APC_C_total) / (1 + ((0.5 / Plx1_active) ^ 4))) - (0.14999999999999999445 * APC_C_active))\"\n where:\n\tAPC_C_active = 1.000000\n\tAPC_C_total = 1.000000\n\tPlx1_active = 0.000000"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000720.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000721.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000722.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -837,7 +837,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000729.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000730.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000731.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Treg_origin_fraction_CD4' to model: 'func_TRegs_Production_from_CD4' is either not found in your model or is not allowed to be used in the current context"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000732.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000732_Kirschner_1998.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 3.5563e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 3.5563e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 3.5563e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 3.5563e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 2.21887e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 2.21887e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 2.21887e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 2.21887e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 1.36968e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 1.36968e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n The above warning has been issued mxhnil times and will not be issued again for this problem.\n\n\n[CVODE ERROR] CVode\n At t = 737.903, mxstep steps taken before reaching tout.\n\nCVODE solver failed : CV_TOO_MUCH_WORK: took mxstep internal steps but could not reach tout.\n\nTry reducing maximum time step."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000732.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000732_Kirschner_1998.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 3.5563e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 3.5563e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 3.5563e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 3.5563e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 2.21887e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 2.21887e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 2.21887e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 2.21887e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 1.36968e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 1.36968e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n The above warning has been issued mxhnil times and will not be issued again for this problem.\n\n\n[CVODE ERROR] CVode\n At t = 737.903, mxstep steps taken before reaching tout.\n\nCVODE solver failed : CV_TOO_MUCH_WORK: took mxstep internal steps but could not reach tout.\n\nTry reducing maximum time step."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000733.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000734.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000735.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -891,7 +891,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000783.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000784.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000785.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000786.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000786.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_XML_NODE_FAILURE","known_failure_desc":"class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000787.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000788.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000789.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -899,7 +899,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000791.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000792.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000793.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000794.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000794.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_XML_NODE_FAILURE","known_failure_desc":"class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000795.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000796.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000797.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -919,7 +919,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000811.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000812.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000813.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000814.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000814_Perez-Garcia19 Computational design of improved standardized chemotherapy protocols for grade 2 oligodendrogliomas.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: CVODE solver failed : at time 28.616, discontinuity ((((t - (28 * ceil((0.035714285714285712303 * t)))) * (((t < 0.0) && 1) || 0.0)) + ((t - (28 * floor((0.035714285714285712303 * t)))) * !((((t < 0.0) && 1) || 0.0)))) == 27) evaluated to FALSE, solver assumed TRUE"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000814.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000814_Perez-Garcia19 Computational design of improved standardized chemotherapy protocols for grade 2 oligodendrogliomas.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: CVODE solver failed : at time 28.616, discontinuity ((((t - (28 * ceil((0.035714285714285712303 * t)))) * (((t < 0.0) && 1) || 0.0)) + ((t - (28 * floor((0.035714285714285712303 * t)))) * !((((t < 0.0) && 1) || 0.0)))) == 27) evaluated to FALSE, solver assumed TRUE"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000815.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000816.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000817.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -932,10 +932,10 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000824.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000825.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000826.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000827.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000827_Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 4.51381e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n The above warning has been issued mxhnil times and will not be issued again for this problem.\n\n\n[CVODE ERROR] CVode\n At t = 78.2588, mxstep steps taken before reaching tout.\n\nCVODE solver failed : CV_TOO_MUCH_WORK: took mxstep internal steps but could not reach tout.\n\nTry reducing maximum time step."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000827.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000827_Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 6.54889e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 78.2588 and h = 4.51381e-15 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n The above warning has been issued mxhnil times and will not be issued again for this problem.\n\n\n[CVODE ERROR] CVode\n At t = 78.2588, mxstep steps taken before reaching tout.\n\nCVODE solver failed : CV_TOO_MUCH_WORK: took mxstep internal steps but could not reach tout.\n\nTry reducing maximum time step."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000828.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000829.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000830.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000830.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_XML_NODE_FAILURE","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000831.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000832.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_4' 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":"BIOMD0000000833.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -946,7 +946,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000838.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000839.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000840.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000841.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: unsupported SBML element 'delay' in expression"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000841.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_DELAY_SBML","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: unsupported SBML element 'delay' in expression"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000842.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000843.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000844.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -954,14 +954,14 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000846.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000847.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"java.lang.NullPointerException: Cannot invoke \"cbit.vcell.solver.Simulation.getImportedTaskID()\" because \"simulation\" is null"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000848.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000849.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000849.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_XML_NODE_FAILURE","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000850.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000851.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000852.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000853.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000854.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000855.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000856.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'tV' has constant attribute set to False, not currently supported."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000856.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'tV' has constant attribute set to False, not currently supported."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000857.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000858.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000859.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -977,7 +977,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000869.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"java.lang.NullPointerException: Cannot invoke \"cbit.vcell.solver.Simulation.getImportedTaskID()\" because \"simulation\" is null"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000870.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"java.lang.NullPointerException: Cannot invoke \"cbit.vcell.solver.Simulation.getImportedTaskID()\" because \"simulation\" is null"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000871.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"java.lang.NullPointerException: Cannot invoke \"cbit.vcell.solver.Simulation.getImportedTaskID()\" because \"simulation\" is null"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000872.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000872.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_XML_NODE_FAILURE","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000873.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000874.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000875.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1004,7 +1004,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000896.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000897.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000898.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000899.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000899.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_XML_NODE_FAILURE","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000900.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000901.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000902.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1030,7 +1030,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000922.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000923.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000924.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000925.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000925.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_XML_NODE_FAILURE","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000926.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000927.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"java.lang.NullPointerException: Cannot invoke \"cbit.vcell.solver.Simulation.getImportedTaskID()\" because \"simulation\" is null"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000928.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1066,11 +1066,11 @@ {"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} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000960.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000961.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000961.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_XML_NODE_FAILURE","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000962.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000963.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000964.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000965.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000965.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_XML_NODE_FAILURE","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000966.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000967.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000968.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1093,7 +1093,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000985.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000986.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000987.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000988.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000988.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_XML_NODE_FAILURE","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000989.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000990.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000991.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1116,7 +1116,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001010.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001011.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001012.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001013.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000001013_Leon-Triana2021 - eqs 1 and 2 - fig 3b.sedml_model15' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b57e146875651314089006626/BIOMD0000001013/Leon-Triana2021 - eqs 1 and 2 - fig 3b.sedml/SimID_1601148481_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b57e146875651314089006626/BIOMD0000001013/Leon-Triana2021 - eqs 1 and 2 - fig 3b.sedml/SimID_1601148481_0_.ida\") "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001013.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000001013_Leon-Triana2021 - eqs 1 and 2 - fig 3b.sedml_model15' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b57e146875651314089006626/BIOMD0000001013/Leon-Triana2021 - eqs 1 and 2 - fig 3b.sedml/SimID_1601148481_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b57e146875651314089006626/BIOMD0000001013/Leon-Triana2021 - eqs 1 and 2 - fig 3b.sedml/SimID_1601148481_0_.ida\") "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001014.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001015.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001016.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1125,29 +1125,29 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001019.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001020.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001021.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_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":"BIOMD0000001022.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000001022_Creemers2021 - Fig 2(B) inset 2.sedml_model6' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b4214e7972318304477051167/BIOMD0000001022/Creemers2021 - Fig 2(B) inset 2.sedml/SimID_1038023516_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b4214e7972318304477051167/BIOMD0000001022/Creemers2021 - Fig 2(B) inset 2.sedml/SimID_1038023516_0_.ida\") "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001022.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000001022_Creemers2021 - Fig 2(B) inset 2.sedml_model6' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b4214e7972318304477051167/BIOMD0000001022/Creemers2021 - Fig 2(B) inset 2.sedml/SimID_1038023516_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b4214e7972318304477051167/BIOMD0000001022/Creemers2021 - Fig 2(B) inset 2.sedml/SimID_1038023516_0_.ida\") "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001023.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001024.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001025.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000001025_Chaudhury2020 Eq 7-9 - Fig 4(B) simulation.sedml_model5' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b43fd52760581088069625327/BIOMD0000001025/Chaudhury2020 Eq 7-9 - Fig 4(B) simulation.sedml/SimID_1974748314_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b43fd52760581088069625327/BIOMD0000001025/Chaudhury2020 Eq 7-9 - Fig 4(B) simulation.sedml/SimID_1974748314_0_.ida\") "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001025.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000001025_Chaudhury2020 Eq 7-9 - Fig 4(B) simulation.sedml_model5' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b43fd52760581088069625327/BIOMD0000001025/Chaudhury2020 Eq 7-9 - Fig 4(B) simulation.sedml/SimID_1974748314_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b43fd52760581088069625327/BIOMD0000001025/Chaudhury2020 Eq 7-9 - Fig 4(B) simulation.sedml/SimID_1974748314_0_.ida\") "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001026.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Summary_flux_to_RBC' to model: 'Vin' is either not found in your model or is not allowed to be used in the current context"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001027.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'Liver' has constant attribute set to False, not currently supported."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001028.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'Liver' has constant attribute set to False, not currently supported."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001029.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'Liver' has constant attribute set to False, not currently supported."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001030.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000001030_Sontag2017 - Fig 1D shifted exponential simulation.sedml_model4' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b42ace2198722070284996283/BIOMD0000001030/Sontag2017 - Fig 1D shifted exponential simulation.sedml/SimID_1085451342_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b42ace2198722070284996283/BIOMD0000001030/Sontag2017 - Fig 1D shifted exponential simulation.sedml/SimID_1085451342_0_.ida\") "} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001031.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000001031_Al-Tuwairqi2020 - Fig2b simulation.sedml_model6' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b4239d16177731767565387322/BIOMD0000001031/Al-Tuwairqi2020 - Fig2b simulation.sedml/SimID_1472540734_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b4239d16177731767565387322/BIOMD0000001031/Al-Tuwairqi2020 - Fig2b simulation.sedml/SimID_1472540734_0_.ida\") "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001027.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'Liver' has constant attribute set to False, not currently supported."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001028.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'Liver' has constant attribute set to False, not currently supported."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001029.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'Liver' has constant attribute set to False, not currently supported."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001030.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000001030_Sontag2017 - Fig 1D shifted exponential simulation.sedml_model4' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b42ace2198722070284996283/BIOMD0000001030/Sontag2017 - Fig 1D shifted exponential simulation.sedml/SimID_1085451342_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b42ace2198722070284996283/BIOMD0000001030/Sontag2017 - Fig 1D shifted exponential simulation.sedml/SimID_1085451342_0_.ida\") "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001031.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000001031_Al-Tuwairqi2020 - Fig2b simulation.sedml_model6' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b4239d16177731767565387322/BIOMD0000001031/Al-Tuwairqi2020 - Fig2b simulation.sedml/SimID_1472540734_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b4239d16177731767565387322/BIOMD0000001031/Al-Tuwairqi2020 - Fig2b simulation.sedml/SimID_1472540734_0_.ida\") "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001032.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001033.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001034.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001035.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000001035_Al-Tuwairqi2020 - Fig7(a) simulation.sedml_model11' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b48bb36616768759896770720/BIOMD0000001035/Al-Tuwairqi2020 - Fig7(a) simulation.sedml/SimID_724140336_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b48bb36616768759896770720/BIOMD0000001035/Al-Tuwairqi2020 - Fig7(a) simulation.sedml/SimID_724140336_0_.ida\") "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001035.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000001035_Al-Tuwairqi2020 - Fig7(a) simulation.sedml_model11' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b48bb36616768759896770720/BIOMD0000001035/Al-Tuwairqi2020 - Fig7(a) simulation.sedml/SimID_724140336_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b48bb36616768759896770720/BIOMD0000001035/Al-Tuwairqi2020 - Fig7(a) simulation.sedml/SimID_724140336_0_.ida\") "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001036.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001037.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001038.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001039.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'Liver' has constant attribute set to False, not currently supported."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001039.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'Liver' has constant attribute set to False, not currently supported."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001040.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Summary_flux_to_RBC' to model: 'Vin' is either not found in your model or is not allowed to be used in the current context"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001041.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001042.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000001042_Makhlouf2020 - Fig1(b).sedml_model1' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193fa3dcefc8848860965362711991/BIOMD0000001042/Makhlouf2020 - Fig1(b).sedml/SimID_1236394790_0_.cvodeInput\" \"/tmp/VCell_CLI_193fa3dcefc8848860965362711991/BIOMD0000001042/Makhlouf2020 - Fig1(b).sedml/SimID_1236394790_0_.ida\") "} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001043.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000001043_Wodarz2001 - Fig3A non-cytotoxic.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b4ce9c2304006454824128300/BIOMD0000001043/Wodarz2001 - Fig3A non-cytotoxic.sedml/SimID_1036516481_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b4ce9c2304006454824128300/BIOMD0000001043/Wodarz2001 - Fig3A non-cytotoxic.sedml/SimID_1036516481_0_.ida\") "} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001044.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001042.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000001042_Makhlouf2020 - Fig1(b).sedml_model1' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193fa3dcefc8848860965362711991/BIOMD0000001042/Makhlouf2020 - Fig1(b).sedml/SimID_1236394790_0_.cvodeInput\" \"/tmp/VCell_CLI_193fa3dcefc8848860965362711991/BIOMD0000001042/Makhlouf2020 - Fig1(b).sedml/SimID_1236394790_0_.ida\") "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001043.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000001043_Wodarz2001 - Fig3A non-cytotoxic.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b4ce9c2304006454824128300/BIOMD0000001043/Wodarz2001 - Fig3A non-cytotoxic.sedml/SimID_1036516481_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b4ce9c2304006454824128300/BIOMD0000001043/Wodarz2001 - Fig3A non-cytotoxic.sedml/SimID_1036516481_0_.ida\") "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001044.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_XML_NODE_FAILURE","known_failure_desc":"java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001045.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001046.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000001046 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001047.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 cf68da415f..9fda0fd72b 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 @@ -35,6 +35,10 @@ public enum FailureType { SEDML_NO_SEDMLS_TO_EXECUTE, SEDML_PREPROCESS_FAILURE, UNSUPPORTED_NONSPATIAL_STOCH_HISTOGRAM, - SOLVER_FAILURE - + UNSUPPORTED_NON_INT_STOCH, + UNSUPPORTED_NON_NUMERIC_STOCH, + SBML_XML_NODE_FAILURE, + SOLVER_FAILURE, + UNSUPPORTED_DELAY_SBML, + UNSUPPORTED_NON_CONSTANT_COMPARTMENTS } 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 fe6741d2a7..fa24ce797c 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 @@ -109,12 +109,23 @@ public static FailureType determineFault(Exception caughtException, List Date: Mon, 6 Jan 2025 10:41:33 -0500 Subject: [PATCH 04/10] Reorganized Failure Assignment system to have fall-backs and reduce code-rewrite --- .../testsupport/OmexTestingDatabase.java | 43 ++++++++++++------- 1 file changed, 27 insertions(+), 16 deletions(-) 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 fa24ce797c..a3f7056699 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 @@ -105,7 +105,31 @@ public static OmexExecSummary summarize(File inputFilePath, Exception exception, } public static FailureType determineFault(Exception caughtException, List errorEvents){ // Throwable because Assertion Error - String errorMessage = caughtException == null ? "" : caughtException.getMessage(); + FailureType determinedFailure; + if (caughtException != null) if ((determinedFailure = determineFault(caughtException)) != null) return determinedFailure; + if (errorEvents == null) return FailureType.UNCATETORIZED_FAULT; + for (TraceEvent errorEvent : errorEvents) if ((determinedFailure = determineFault(errorEvent)) != null) return determinedFailure; + return FailureType.UNCATETORIZED_FAULT; + } + + private static FailureType determineFault(TraceEvent traceEvent){ + if (traceEvent.hasException(SBMLImportException.class)) { + FailureType sbmlFailureType; + return (sbmlFailureType = determineFault(traceEvent.exception)) != null ? sbmlFailureType : FailureType.SBML_IMPORT_FAILURE; + } + if (traceEvent.span.getNestedContextName().contains(Span.ContextType.PROCESSING_SEDML.name()+"(preProcessDoc)")){ + return FailureType.SEDML_PREPROCESS_FAILURE; + } + if (traceEvent.hasException(MappingException.class)) { + return FailureType.MATH_GENERATION_FAILURE; + } + // One last check: + if (traceEvent.exception != null) return determineFault(traceEvent.exception); + return null; + } + + private static FailureType determineFault(Exception caughtException){ + String errorMessage = caughtException.getMessage(); 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; @@ -145,20 +169,7 @@ public static FailureType determineFault(Exception caughtException, List Date: Mon, 6 Jan 2025 10:46:13 -0500 Subject: [PATCH 05/10] Trying to fix poetry bug with version change --- .github/workflows/NightlyBMDB_CLI.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/NightlyBMDB_CLI.yml b/.github/workflows/NightlyBMDB_CLI.yml index 4487a13d4b..9ba2a2087f 100644 --- a/.github/workflows/NightlyBMDB_CLI.yml +++ b/.github/workflows/NightlyBMDB_CLI.yml @@ -6,7 +6,7 @@ on: env: python-version: "3.10" - poetry-version: "1.2.1" + poetry-version: "2.0" jobs: build: From dc62c9c25a05be18642831ccb66a1d7504011051 Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Mon, 6 Jan 2025 10:53:12 -0500 Subject: [PATCH 06/10] Renaming and updating pythonVtk --- pythonVtk/poetry.lock | 903 ++++++----- pythonVtk/pyproject.toml | 2 +- pythonVtk/{ => python_vtk}/__init__.py | 0 pythonVtk/{ => python_vtk}/mypy.ini | 0 .../{ => python_vtk}/vcellvismesh/__init__.py | 0 .../vcellvismesh/constants.py | 0 .../{ => python_vtk}/vcellvismesh/ttypes.py | 0 .../{ => python_vtk}/vtkService/__init__.py | 0 .../vtkService/makeLittleVtk.py | 60 +- .../vtkService/vtkAddData_not_used.py | 82 +- .../{ => python_vtk}/vtkService/vtkService.py | 1320 ++++++++--------- 11 files changed, 1267 insertions(+), 1100 deletions(-) rename pythonVtk/{ => python_vtk}/__init__.py (100%) rename pythonVtk/{ => python_vtk}/mypy.ini (100%) rename pythonVtk/{ => python_vtk}/vcellvismesh/__init__.py (100%) rename pythonVtk/{ => python_vtk}/vcellvismesh/constants.py (100%) rename pythonVtk/{ => python_vtk}/vcellvismesh/ttypes.py (100%) rename pythonVtk/{ => python_vtk}/vtkService/__init__.py (100%) rename pythonVtk/{ => python_vtk}/vtkService/makeLittleVtk.py (96%) rename pythonVtk/{ => python_vtk}/vtkService/vtkAddData_not_used.py (96%) rename pythonVtk/{ => python_vtk}/vtkService/vtkService.py (97%) diff --git a/pythonVtk/poetry.lock b/pythonVtk/poetry.lock index a8f59cb1f9..389db61eb2 100644 --- a/pythonVtk/poetry.lock +++ b/pythonVtk/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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(>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] [metadata] lock-version = "2.0" diff --git a/pythonVtk/pyproject.toml b/pythonVtk/pyproject.toml index 26ae66167c..b9b16e1701 100644 --- a/pythonVtk/pyproject.toml +++ b/pythonVtk/pyproject.toml @@ -1,5 +1,5 @@ [tool.poetry] -name = "pythonvtk" +name = "python_vtk" version = "0.1.0" description = "" authors = ["Jim Schaff "] diff --git a/pythonVtk/__init__.py b/pythonVtk/python_vtk/__init__.py similarity index 100% rename from pythonVtk/__init__.py rename to pythonVtk/python_vtk/__init__.py diff --git a/pythonVtk/mypy.ini b/pythonVtk/python_vtk/mypy.ini similarity index 100% rename from pythonVtk/mypy.ini rename to pythonVtk/python_vtk/mypy.ini diff --git a/pythonVtk/vcellvismesh/__init__.py b/pythonVtk/python_vtk/vcellvismesh/__init__.py similarity index 100% rename from pythonVtk/vcellvismesh/__init__.py rename to pythonVtk/python_vtk/vcellvismesh/__init__.py diff --git a/pythonVtk/vcellvismesh/constants.py b/pythonVtk/python_vtk/vcellvismesh/constants.py similarity index 100% rename from pythonVtk/vcellvismesh/constants.py rename to pythonVtk/python_vtk/vcellvismesh/constants.py diff --git a/pythonVtk/vcellvismesh/ttypes.py b/pythonVtk/python_vtk/vcellvismesh/ttypes.py similarity index 100% rename from pythonVtk/vcellvismesh/ttypes.py rename to pythonVtk/python_vtk/vcellvismesh/ttypes.py diff --git a/pythonVtk/vtkService/__init__.py b/pythonVtk/python_vtk/vtkService/__init__.py similarity index 100% rename from pythonVtk/vtkService/__init__.py rename to pythonVtk/python_vtk/vtkService/__init__.py diff --git a/pythonVtk/vtkService/makeLittleVtk.py b/pythonVtk/python_vtk/vtkService/makeLittleVtk.py similarity index 96% rename from pythonVtk/vtkService/makeLittleVtk.py rename to pythonVtk/python_vtk/vtkService/makeLittleVtk.py index a697d8c162..fb4ff371c6 100644 --- a/pythonVtk/vtkService/makeLittleVtk.py +++ b/pythonVtk/python_vtk/vtkService/makeLittleVtk.py @@ -1,30 +1,30 @@ -import vtk - -import vtkService.vtkService as vtkService - -x = [1, 2, 3, 4] -y = [1, 2, 3, 4] -ugrid = vtk.vtkUnstructuredGrid() -points = vtk.vtkPoints() -points.SetDataTypeToDouble() -xyToNode = [[] for i in range(len(x))] -index = 0 -for i, xCoord in enumerate(x): - for yCoord in y: - points.InsertNextPoint(xCoord, yCoord, 0.0) - xyToNode[i].append(index) - index += 1 -ugrid.SetPoints(points) - -# Add the volume elements -for i, xCoord in enumerate(x[:-1]): - for j, yCoord in enumerate(y[:-1]): - idList = vtk.vtkIdList() - idList.InsertNextId(xyToNode[i][j]) - idList.InsertNextId(xyToNode[i + 1][j]) - idList.InsertNextId(xyToNode[i + 1][j + 1]) - idList.InsertNextId(xyToNode[i][j + 1]) - ugrid.InsertNextCell(vtk.VTK_QUAD, idList) - -vtkService.writevtk(ugrid, "abc.vtu") -vtkService.writeDataArrayToNewVtkFile("abc.vtu", "var", [1., 2., 3., 4., 5., 6., 7., 8., 9.], "abc_var.vtu") +import vtk + +import vtkService.vtkService as vtkService + +x = [1, 2, 3, 4] +y = [1, 2, 3, 4] +ugrid = vtk.vtkUnstructuredGrid() +points = vtk.vtkPoints() +points.SetDataTypeToDouble() +xyToNode = [[] for i in range(len(x))] +index = 0 +for i, xCoord in enumerate(x): + for yCoord in y: + points.InsertNextPoint(xCoord, yCoord, 0.0) + xyToNode[i].append(index) + index += 1 +ugrid.SetPoints(points) + +# Add the volume elements +for i, xCoord in enumerate(x[:-1]): + for j, yCoord in enumerate(y[:-1]): + idList = vtk.vtkIdList() + idList.InsertNextId(xyToNode[i][j]) + idList.InsertNextId(xyToNode[i + 1][j]) + idList.InsertNextId(xyToNode[i + 1][j + 1]) + idList.InsertNextId(xyToNode[i][j + 1]) + ugrid.InsertNextCell(vtk.VTK_QUAD, idList) + +vtkService.writevtk(ugrid, "abc.vtu") +vtkService.writeDataArrayToNewVtkFile("abc.vtu", "var", [1., 2., 3., 4., 5., 6., 7., 8., 9.], "abc_var.vtu") diff --git a/pythonVtk/vtkService/vtkAddData_not_used.py b/pythonVtk/python_vtk/vtkService/vtkAddData_not_used.py similarity index 96% rename from pythonVtk/vtkService/vtkAddData_not_used.py rename to pythonVtk/python_vtk/vtkService/vtkAddData_not_used.py index 1d2407b429..f5cd87c8cd 100644 --- a/pythonVtk/vtkService/vtkAddData_not_used.py +++ b/pythonVtk/python_vtk/vtkService/vtkAddData_not_used.py @@ -1,41 +1,41 @@ -import argparse - -import numpy as np -import vtk - -from vtkService.vtkService import writeDataArrayToNewVtkFile - - -def main(): - # try: - parser = argparse.ArgumentParser() - parser.add_argument("invtkfile", help="filename of input vtk mesh (VTK XML unstructured grid") - parser.add_argument("varname", help="name of cell data variable") - parser.add_argument("outvtkfile", help="filename of output vtk mesh (VTK XML unstructured grid") - args = parser.parse_args() - - # deserialize raw bytes into VarDataAdd - reader = vtk.vtkXMLUnstructuredGridReader() - reader.SetFileName(args.invtkfile) - reader.Update() - mesh = reader.GetOutput() - assert isinstance(mesh, vtk.vtkUnstructuredGrid) - num_cells = mesh.GetCells().GetSize() - - # write 0..N-1 into data - npdata = np.arange(0, num_cells, 0.1) - - writeDataArrayToNewVtkFile(args.invtkfile, args.varname, npdata, args.outvtkfile) - print("done") - - -# except: -# e = sys.exc_info()[0] -# print("exception "+e) -# sys.exit(-1) -# else: -# sys.exit(0) - - -if __name__ == '__main__': - main() +import argparse + +import numpy as np +import vtk + +from vtkService.vtkService import writeDataArrayToNewVtkFile + + +def main(): + # try: + parser = argparse.ArgumentParser() + parser.add_argument("invtkfile", help="filename of input vtk mesh (VTK XML unstructured grid") + parser.add_argument("varname", help="name of cell data variable") + parser.add_argument("outvtkfile", help="filename of output vtk mesh (VTK XML unstructured grid") + args = parser.parse_args() + + # deserialize raw bytes into VarDataAdd + reader = vtk.vtkXMLUnstructuredGridReader() + reader.SetFileName(args.invtkfile) + reader.Update() + mesh = reader.GetOutput() + assert isinstance(mesh, vtk.vtkUnstructuredGrid) + num_cells = mesh.GetCells().GetSize() + + # write 0..N-1 into data + npdata = np.arange(0, num_cells, 0.1) + + writeDataArrayToNewVtkFile(args.invtkfile, args.varname, npdata, args.outvtkfile) + print("done") + + +# except: +# e = sys.exc_info()[0] +# print("exception "+e) +# sys.exit(-1) +# else: +# sys.exit(0) + + +if __name__ == '__main__': + main() diff --git a/pythonVtk/vtkService/vtkService.py b/pythonVtk/python_vtk/vtkService/vtkService.py similarity index 97% rename from pythonVtk/vtkService/vtkService.py rename to pythonVtk/python_vtk/vtkService/vtkService.py index 074a705b60..42c5562a8f 100644 --- a/pythonVtk/vtkService/vtkService.py +++ b/pythonVtk/python_vtk/vtkService/vtkService.py @@ -1,660 +1,660 @@ -import argparse -import copy -import os -import sys -import traceback - -import vtkmodules.all as vtk -from thrift.TSerialization import TBinaryProtocol -from thrift.TSerialization import deserialize -from thrift.TSerialization import serialize - -from vcellvismesh.ttypes import ChomboIndexData -from vcellvismesh.ttypes import FiniteVolumeIndexData -from vcellvismesh.ttypes import MovingBoundaryIndexData -from vcellvismesh.ttypes import PolyhedronFace -from vcellvismesh.ttypes import VisIrregularPolyhedron -from vcellvismesh.ttypes import VisLine -from vcellvismesh.ttypes import VisMesh -from vcellvismesh.ttypes import VisPolygon -from vcellvismesh.ttypes import VisTetrahedron - - -def writeChomboVolumeVtkGridAndIndexData(visMesh: VisMesh, domainname: str, vtkfile, indexfile) -> None: - originalVisMesh = visMesh - correctedVisMesh = originalVisMesh # same mesh if no irregularPolyhedra - if originalVisMesh.irregularPolyhedra is not None: - correctedVisMesh = copy.deepcopy(visMesh) - if correctedVisMesh.tetrahedra is None: - correctedVisMesh.tetrahedra = [] - for irregularPolyhedron in correctedVisMesh.irregularPolyhedra: - tets = createTetrahedra(irregularPolyhedron, correctedVisMesh) - for tet in tets: - correctedVisMesh.tetrahedra.append(tet) - correctedVisMesh.irregularPolyhedra = None - - vtkgrid: vtk.vtkUnstructuredGrid = getVolumeVtkGrid(correctedVisMesh) - writevtk(vtkgrid, vtkfile) - chomboIndexData = ChomboIndexData() - chomboIndexData.chomboVolumeIndices = [] - chomboIndexData.domainName = domainname - if correctedVisMesh.dimension == 2: - if correctedVisMesh.polygons is not None: - for polygon in correctedVisMesh.polygons: - assert isinstance(polygon, VisPolygon) - chomboIndexData.chomboVolumeIndices.append(polygon.chomboVolumeIndex) - if chomboIndexData.chomboVolumeIndices is None: - print("didn't find any indices ... bad") - elif correctedVisMesh.dimension == 3: - if correctedVisMesh.visVoxels is not None: - for voxel in correctedVisMesh.visVoxels: - chomboIndexData.chomboVolumeIndices.append(voxel.chomboVolumeIndex) - if correctedVisMesh.irregularPolyhedra is not None: - raise Exception("unexpected irregular polyhedra in mesh, should have been replaced with tetrahedra") - if correctedVisMesh.tetrahedra is not None: - for tetrahedron in correctedVisMesh.tetrahedra: - assert isinstance(tetrahedron, VisTetrahedron) - chomboIndexData.chomboVolumeIndices.append(tetrahedron.chomboVolumeIndex) - if len(chomboIndexData.chomboVolumeIndices) == 0: - print("didn't find any indices ... bad") - writeChomboIndexData(indexfile, chomboIndexData) - - -def writeChomboMembraneVtkGridAndIndexData(visMesh: VisMesh, domainname: str, vtkfile, indexfile) -> None: - - vtkgrid = getMembraneVtkGrid(visMesh) - writevtk(vtkgrid, vtkfile) - - chomboIndexData = ChomboIndexData() - chomboIndexData.chomboSurfaceIndices = [] - if domainname.upper().endswith("MEMBRANE") is False: - raise Exception("expecting domain name ending with membrane") - chomboIndexData.domainName = domainname - if visMesh.dimension == 3: - if visMesh.surfaceTriangles is not None: - for surfaceTriangle in visMesh.surfaceTriangles: - chomboIndexData.chomboSurfaceIndices.append(surfaceTriangle.chomboSurfaceIndex) - elif visMesh.dimension == 2: - if visMesh.visLines is not None: - for visLine in visMesh.visLines: - assert isinstance(visLine, VisLine) - chomboIndexData.chomboSurfaceIndices.append(visLine.chomboSurfaceIndex) - if len(chomboIndexData.chomboSurfaceIndices) == 0: - print("didn't find any indices ... bad") - writeChomboIndexData(indexfile, chomboIndexData) - - -def writeFiniteVolumeSmoothedVtkGridAndIndexData(visMesh: VisMesh, domainName: str, vtuFile, indexFile) -> None: - vtkgrid = getVolumeVtkGrid(visMesh) - if visMesh.dimension == 3: - vtkgridSmoothed = smoothUnstructuredGridSurface(vtkgrid) - else: - vtkgridSmoothed = vtkgrid - writevtk(vtkgridSmoothed, vtuFile) - finiteVolumeIndexData = FiniteVolumeIndexData() - finiteVolumeIndexData.finiteVolumeIndices = [] - finiteVolumeIndexData.domainName = domainName - if visMesh.dimension == 2: - # if volume - if visMesh.polygons is not None: - for polygon in visMesh.polygons: - finiteVolumeIndexData.finiteVolumeIndices.append(polygon.finiteVolumeIndex) - # if membrane - if visMesh.visLines is not None: - for visLine in visMesh.visLines: - finiteVolumeIndexData.finiteVolumeIndices.append(visLine.finiteVolumeIndex) - elif visMesh.dimension == 3: - # if volume - if visMesh.visVoxels is not None: - for voxel in visMesh.visVoxels: - finiteVolumeIndexData.finiteVolumeIndices.append(voxel.finiteVolumeIndex) - if visMesh.irregularPolyhedra is not None: - raise Exception("unexpected irregular polyhedra in mesh, should have been replaced with tetrahedra") - if visMesh.tetrahedra is not None: - for tetrahedron in visMesh.tetrahedra: - finiteVolumeIndexData.finiteVolumeIndices.append(tetrahedron.finiteVolumeIndex) - # if membrane - if visMesh.polygons is not None: - for polygon in visMesh.polygons: - finiteVolumeIndexData.finiteVolumeIndices.append(polygon.finiteVolumeIndex) - - if finiteVolumeIndexData.finiteVolumeIndices == None or len(finiteVolumeIndexData.finiteVolumeIndices) == 0: - print("didn't find any indices ... bad") - - writeFiniteVolumeIndexData(indexFile, finiteVolumeIndexData) - - -def writeFiniteVolumeIndexData(finiteVolumeIndexFile, finiteVolumeIndexData): - assert isinstance(finiteVolumeIndexData, FiniteVolumeIndexData) - blob = serialize(finiteVolumeIndexData, protocol_factory=TBinaryProtocol.TBinaryProtocolFactory()) - ff = open(finiteVolumeIndexFile,'wb') - ff.write(blob) - ff.close() - print("wrote finitevolume data to file "+str(finiteVolumeIndexFile)) - - -def writeMovingBoundaryVolumeVtkGridAndIndexData(visMesh: VisMesh, domainName: str, vtuFile, indexFile): - vtkgrid = getVolumeVtkGrid(visMesh) - writevtk(vtkgrid, vtuFile) - movingBoundaryIndexData = MovingBoundaryIndexData() - movingBoundaryIndexData.movingBoundaryVolumeIndices = [] - movingBoundaryIndexData.domainName = domainName - movingBoundaryIndexData.timeIndex = 0 - if visMesh.dimension == 2: - # if volume - if visMesh.polygons is not None: - for polygon in visMesh.polygons: - movingBoundaryIndexData.movingBoundaryVolumeIndices.append(polygon.movingBoundaryVolumeIndex) - # if membrane - if visMesh.visLines is not None: - for visLine in visMesh.visLines: - movingBoundaryIndexData.movingBoundarySurfaceIndices.append(visLine.movingBoundarySurfaceIndex) - # elif visMesh.dimension == 3: - # # if volume - # if visMesh.visVoxels is not None: - # for voxel in visMesh.visVoxels: - # movingBoundaryIndexData.finiteVolumeIndices.append(voxel.finiteVolumeIndex) - # if visMesh.irregularPolyhedra is not None: - # raise Exception("unexpected irregular polyhedra in mesh, should have been replaced with tetrahedra") - # if visMesh.tetrahedra is not None: - # for tetrahedron in visMesh.tetrahedra: - # movingBoundaryIndexData.finiteVolumeIndices.append(tetrahedron.finiteVolumeIndex) - # # if membrane - # if visMesh.polygons is not None: - # for polygon in visMesh.polygons: - # movingBoundaryIndexData.finiteVolumeIndices.append(polygon.finiteVolumeIndex) - - if movingBoundaryIndexData.movingBoundaryVolumeIndices == None and movingBoundaryIndexData.movingBoundarySurfaceIndices == None: - print("didn't find any indices ... bad") - - if movingBoundaryIndexData.movingBoundaryVolumeIndices != None and len(movingBoundaryIndexData.movingBoundaryVolumeIndices) == 0: - print("didn't find any indices ... bad") - - if movingBoundaryIndexData.movingBoundarySurfaceIndices != None and len(movingBoundaryIndexData.movingBoundarySurfaceIndices) == 0: - print("didn't find any indices ... bad") - - writeMovingBoundaryIndexData(indexFile, movingBoundaryIndexData) - - -def writeComsolVolumeVtkGridAndIndexData(visMesh, domainName, vtuFile, indexFile): - assert isinstance(visMesh, VisMesh) - vtkgrid = getVolumeVtkGrid(visMesh) - writevtk(vtkgrid, vtuFile) - # movingBoundaryIndexData = MovingBoundaryIndexData() - # movingBoundaryIndexData.movingBoundaryVolumeIndices = [] - # movingBoundaryIndexData.domainName = domainName - # movingBoundaryIndexData.timeIndex = 0 - # if visMesh.dimension == 2: - # # if volume - # if visMesh.polygons is not None: - # for polygon in visMesh.polygons: - # movingBoundaryIndexData.movingBoundaryVolumeIndices.append(polygon.movingBoundaryVolumeIndex) - # # if membrane - # if visMesh.visLines is not None: - # for visLine in visMesh.visLines: - # movingBoundaryIndexData.movingBoundarySurfaceIndices.append(visLine.movingBoundarySurfaceIndex) - # elif visMesh.dimension == 3: - # # if volume - # if visMesh.visVoxels is not None: - # for voxel in visMesh.visVoxels: - # movingBoundaryIndexData.finiteVolumeIndices.append(voxel.finiteVolumeIndex) - # if visMesh.irregularPolyhedra is not None: - # raise Exception("unexpected irregular polyhedra in mesh, should have been replaced with tetrahedra") - # if visMesh.tetrahedra is not None: - # for tetrahedron in visMesh.tetrahedra: - # movingBoundaryIndexData.finiteVolumeIndices.append(tetrahedron.finiteVolumeIndex) - # # if membrane - # if visMesh.polygons is not None: - # for polygon in visMesh.polygons: - # movingBoundaryIndexData.finiteVolumeIndices.append(polygon.finiteVolumeIndex) - - # if movingBoundaryIndexData.movingBoundaryVolumeIndices == None and movingBoundaryIndexData.movingBoundarySurfaceIndices == None: - # print "didn't find any indices ... bad" - # - # if movingBoundaryIndexData.movingBoundaryVolumeIndices != None and len(movingBoundaryIndexData.movingBoundaryVolumeIndices) == 0: - # print "didn't find any indices ... bad" - # - # if movingBoundaryIndexData.movingBoundarySurfaceIndices != None and len(movingBoundaryIndexData.movingBoundarySurfaceIndices) == 0: - # print "didn't find any indices ... bad" - # - #writeMovingBoundaryIndexData(indexFile, None) - - -def writeMovingBoundaryIndexData(movingBoundaryIndexFile, movingBoundaryIndexData): - assert isinstance(movingBoundaryIndexData, MovingBoundaryIndexData) - blob = serialize(movingBoundaryIndexData, protocol_factory=TBinaryProtocol.TBinaryProtocolFactory()) - ff = open(movingBoundaryIndexFile,'wb') - ff.write(blob) - ff.close() - print("wrote movingboundary data to file "+str(movingBoundaryIndexFile)) - - - -def writeChomboIndexData(chomboIndexFile, chomboIndexData): - """ - - Returns: - None: - """ - assert isinstance(chomboIndexData, ChomboIndexData) - blob = serialize(chomboIndexData, protocol_factory=TBinaryProtocol.TBinaryProtocolFactory()) - ff = open(chomboIndexFile,'wb') - ff.write(blob) - ff.close() - print("wrote chomboIndex data to file "+str(chomboIndexFile)) - - -# -# read a vtkUnstructuredGrid from the XML format -# -def readvtk(vtkfile): - if not os.path.isfile(vtkfile): - raise Exception("unstructured grid " + str(vtkfile) + " not found") - - tester = vtk.vtkXMLFileReadTester() - tester.SetFileName(str(vtkfile)) - if tester.TestReadFile() != 1: - raise Exception("expecting XML formatted VTK unstructured grid") - - reader = vtk.vtkXMLUnstructuredGridReader() - reader.SetFileName(vtkfile) - reader.Update() - vtkgrid = reader.GetOutput() - assert isinstance(vtkgrid, vtk.vtkUnstructuredGrid) - print("read from file " + str(vtkfile)) - vtkgrid.BuildLinks() - return vtkgrid - - -# -# write a vtkUnstructuredGrid to the XML format -# -def writevtk(vtkgrid, filename): - writer = vtk.vtkXMLUnstructuredGridWriter() - bASCII = False - if bASCII: - writer.SetDataModeToAscii() - else: - writer.SetCompressorTypeToNone() - writer.SetDataModeToBinary() - try: - writer.SetInputData(vtkgrid) - except AttributeError: - writer.SetInput(vtkgrid) - writer.SetFileName(filename) - writer.Update() - print("wrote to file "+str(filename)) - - -# -# create a single-variable vtu file -# -def writeDataArrayToNewVtkFile(emptyMeshFile, varName, data, newMeshFile): - assert type(emptyMeshFile) is str - assert type(varName) is str - assert type(newMeshFile) is str - try: - #raise ImportError("dummy exception") - import numpy as np - from vtk.util import numpy_support - print("writing varData using numpy") - - data = np.array(data) - vtkgrid = readvtk(emptyMeshFile) - assert isinstance(vtkgrid, vtk.vtkUnstructuredGrid) - - # - # add cell data array to the empty mesh for this variable - # - dataArray = vtk.vtkDoubleArray() - dataArray = numpy_support.numpy_to_vtk(data) - assert isinstance(dataArray, ) - dataArray.SetName(varName) - cellData: vtk.vtkCellData = vtkgrid.GetCellData() - cellData.AddArray(dataArray) - - # - # write mesh and data to the file for that domain and time - # - writevtk(vtkgrid, newMeshFile) - - except ImportError as nonumpy: - import array - print("writing varData using array package") - - print(type(data)) - print(str(data)) - data = array.array('d', data) - vtkgrid = readvtk(emptyMeshFile) - - # - # add cell data array to the empty mesh for this variable - # - dataArray = vtk.vtkDoubleArray() - dataArray.SetVoidArray(data, len(data), 1) - dataArray.SetNumberOfComponents(1) - dataArray.SetName(varName) - cellData: vtk.vtkCellData = vtkgrid.GetCellData() - cellData.AddArray(dataArray) - - # - # write mesh and data to the file for that domain and time - # - writevtk(vtkgrid, newMeshFile) - - -def getMembraneVtkGrid(visMesh: VisMesh) -> vtk.vtkUnstructuredGrid: - vtkpoints = vtk.vtkPoints() - for visPoint in visMesh.surfacePoints: - vtkpoints.InsertNextPoint(visPoint.x,visPoint.y,visPoint.z) - - vtkgrid = vtk.vtkUnstructuredGrid() - vtkgrid.Allocate(len(visMesh.surfacePoints), len(visMesh.surfacePoints)) - vtkgrid.SetPoints(vtkpoints) - - if visMesh.dimension == 2: - vtkline = vtk.vtkLine() - lineType = vtkline.GetCellType() - - for line in visMesh.visLines: - pts = vtk.vtkIdList() - pts.InsertNextId(line.p1) - pts.InsertNextId(line.p2) - vtkgrid.InsertNextCell(lineType, pts) - else: - vtktriangle = vtk.vtkTriangle() - triangleType = vtktriangle.GetCellType() - for surfaceTriangle in visMesh.surfaceTriangles: - pts = vtk.vtkIdList() - for pi in surfaceTriangle.pointIndices: - pts.InsertNextId(pi) - # each triangle is a cell - vtkgrid.InsertNextCell(triangleType, pts) - - vtkgrid.BuildLinks() - return vtkgrid - - -def getVolumeVtkGrid(visMesh: VisMesh) -> vtk.vtkUnstructuredGrid: - bClipPolyhedra = True - - vtkpoints = vtk.vtkPoints() - for visPoint in visMesh.points: - vtkpoints.InsertNextPoint(visPoint.x, visPoint.y, visPoint.z) - - vtkgrid = vtk.vtkUnstructuredGrid() - vtkgrid.Allocate(len(visMesh.points), len(visMesh.points)) - vtkgrid.SetPoints(vtkpoints) - - quadType = vtk.vtkQuad().GetCellType() - # lineType = vtk.vtkLine().GetCellType() - polygonType = vtk.vtkPolygon().GetCellType() - polyhedronType = vtk.vtkPolyhedron().GetCellType() - triangleType = vtk.vtkTriangle().GetCellType() - voxelType = vtk.vtkVoxel().GetCellType() - tetraType = vtk.vtkTetra().GetCellType() - - if visMesh.polygons != None: - for visPolygon in visMesh.polygons: - pts = vtk.vtkIdList() - polygonPoints = visPolygon.pointIndices - for p in polygonPoints: - pts.InsertNextId(p) - - numPoints = len(polygonPoints) - if numPoints == 4: - vtkgrid.InsertNextCell(quadType, pts) - elif numPoints == 3: - vtkgrid.InsertNextCell(triangleType, pts) - else: - vtkgrid.InsertNextCell(polygonType, pts) - # - # replace any VisIrregularPolyhedron with a list of VisTetrahedron - # - if visMesh.visVoxels != None: - for voxel in visMesh.visVoxels: - pts = vtk.vtkIdList() - polyhedronPoints = voxel.pointIndices - for p in polyhedronPoints: - pts.InsertNextId(p) - vtkgrid.InsertNextCell(voxelType, pts) - - if visMesh.tetrahedra != None: - for visTet in visMesh.tetrahedra: - assert isinstance(visTet, VisTetrahedron) - pts = vtk.vtkIdList() - tetPoints = visTet.pointIndices - for p in tetPoints: - pts.InsertNextId(p) - vtkgrid.InsertNextCell(tetraType, pts) - - bInitializedFaces = False - if visMesh.irregularPolyhedra != None: - for clippedPolyhedron in visMesh.irregularPolyhedra: - if bClipPolyhedra == True: - tets = createTetrahedra(clippedPolyhedron, visMesh) - for visTet in tets: - pts = vtk.vtkIdList() - tetPoints = visTet.getPointIndices() - for p in tetPoints: - pts.InsertNextId(p) - vtkgrid.InsertNextCell(tetraType, pts) - else: - faceStreamList = vtk.vtkIdList() - faceStream = getVtkFaceStream(clippedPolyhedron) - for p in faceStream: - faceStreamList.InsertNextId(p) - if bInitializedFaces == False and vtkgrid.GetNumberOfCells() > 0: - vtkgrid.InitializeFacesRepresentation(vtkgrid.GetNumberOfCells()) - bInitializedFaces = True - vtkgrid.InsertNextCell(polyhedronType, faceStreamList) - - vtkgrid.BuildLinks() - # vtkgrid.Squeeze() - return vtkgrid - - -def getVtkFaceStream(irregularPolyhedron: VisIrregularPolyhedron) -> list[int]: - faceStream = [len(irregularPolyhedron.polyhedronFaces), ] - for polyhedronFace in irregularPolyhedron.polyhedronFaces: - faceStream.append(len(polyhedronFace.getVertices())) - for v in polyhedronFace.vertices: - faceStream.append(v) - intFaceStream = [int(v) for v in faceStream] - return intFaceStream - - -def smoothUnstructuredGridSurface(vtkGrid: vtk.vtkUnstructuredGrid) -> vtk.vtkUnstructuredGrid: - ugGeometryFilter = vtk.vtkUnstructuredGridGeometryFilter() - ugGeometryFilter.PassThroughPointIdsOn() - ugGeometryFilter.MergingOff() - try: - ugGeometryFilter.SetInputData(vtkGrid) - except AttributeError: - ugGeometryFilter.SetInput(vtkGrid) - ugGeometryFilter.Update() - surfaceUnstructuredGrid: vtk.vtkUnstructuredGrid = ugGeometryFilter.GetOutput() - originalPointsIdsName = ugGeometryFilter.GetOriginalPointIdsName() - - cellData = surfaceUnstructuredGrid.GetCellData() - numCellArrays = cellData.GetNumberOfArrays() - for i in range(0, numCellArrays): - cellArrayName = cellData.GetArrayName(i) - print("CellArray(" + str(i) + ") '" + cellArrayName + "')") - pointData: vtk.vtkPointData = surfaceUnstructuredGrid.GetPointData() - numPointArrays = pointData.GetNumberOfArrays() - for i in range(0, numPointArrays): - pointArrayName = pointData.GetArrayName(i) - print("PointArray(" + str(i) + ") '" + pointArrayName + "'") - - geometryFilter = vtk.vtkGeometryFilter() - try: - geometryFilter.SetInputData(surfaceUnstructuredGrid) - except AttributeError: - geometryFilter.SetInput(surfaceUnstructuredGrid) - geometryFilter.Update() - polyData: vtk.vtkPolyData = geometryFilter.GetOutput() - - filter = vtk.vtkWindowedSincPolyDataFilter() - try: - filter.SetInputData(polyData) - except AttributeError: - filter.SetInput(polyData) - filter.SetNumberOfIterations(15) - filter.BoundarySmoothingOff() - filter.FeatureEdgeSmoothingOff() - filter.SetFeatureAngle(120.0) - filter.SetPassBand(0.001) - filter.NonManifoldSmoothingOff() - filter.NormalizeCoordinatesOn() - filter.Update() - - smoothedPolydata = filter.GetOutput() - - smoothedPoints: vtk.vtkPoints = smoothedPolydata.GetPoints() - - smoothedPointData: vtk.vtkPointData = smoothedPolydata.GetPointData() - pointIdsArray: vtk.vtkIdTypeArray = smoothedPointData.GetArray(originalPointsIdsName) - pointsIdsArraySize = pointIdsArray.GetSize() - origPoints = vtkGrid.GetPoints() - for i in range(0, pointsIdsArraySize): - pointId = pointIdsArray.GetValue(i) - smoothedPoint = smoothedPoints.GetPoint(i) - origPoints.SetPoint(pointId, smoothedPoint) - - return vtkGrid - - -def getPointIndices(irregularPolyhedron: VisIrregularPolyhedron) -> list[int]: - assert isinstance(irregularPolyhedron, VisIrregularPolyhedron) - pointIndicesSet = set() - for face in irregularPolyhedron.polyhedronFaces: - assert(isinstance(face, PolyhedronFace)) - for pointIndex in face.vertices: - pointIndicesSet.add(pointIndex) - pointArray = [int(x) for x in pointIndicesSet] - return pointArray - - -def createTetrahedra(clippedPolyhedron: VisIrregularPolyhedron, visMesh: VisMesh): - - vtkpolydata = vtk.vtkPolyData() - vtkpoints = vtk.vtkPoints() - polygonType = vtk.vtkPolygon().GetCellType() - uniquePointIndices = getPointIndices(clippedPolyhedron) - for point in uniquePointIndices: - visPoint = visMesh.points[point] - vtkpoints.InsertNextPoint(visPoint.x, visPoint.y, visPoint.z) - vtkpolydata.Allocate(100, 100) - vtkpolydata.SetPoints(vtkpoints) - - for face in clippedPolyhedron.polyhedronFaces: - faceIdList = vtk.vtkIdList() - for visPointIndex in face.vertices: - vtkpointid = -1 - for i in range(0, len(uniquePointIndices)): - if uniquePointIndices[i] == visPointIndex: - vtkpointid = i - faceIdList.InsertNextId(vtkpointid) - vtkpolydata.InsertNextCell(polygonType, faceIdList) - - delaunayFilter = vtk.vtkDelaunay3D() - try: - delaunayFilter.SetInputData(vtkpolydata) - except AttributeError: - delaunayFilter.SetInput(vtkpolydata) - delaunayFilter.Update() - delaunayFilter.SetAlpha(0.1) - vtkgrid2: vtk.vtkUnstructuredGrid = delaunayFilter.GetOutput() - assert isinstance(vtkgrid2, vtk.vtkUnstructuredGrid) # runtime check, remove later - - visTets = [] - numTets = vtkgrid2.GetNumberOfCells() - if numTets < 1: - if len(uniquePointIndices)==4: - visTet = VisTetrahedron(uniquePointIndices) - visTet.chomboVolumeIndex = clippedPolyhedron.chomboVolumeIndex - visTet.finiteVolumeIndex = clippedPolyhedron.finiteVolumeIndex - visTets.append(visTet) - print("made trivial tet ... maybe inside out") - else: - print("found no tets, there are "+str(len(uniquePointIndices))+" unique point indices") - - - # print("numFaces = "+str(vtkpolydata.GetNumberOfCells())+", numTets = "+str(numTets)); - for cellIndex in range(0, numTets): - cell = vtkgrid2.GetCell(cellIndex) - if isinstance(cell, vtk.vtkTetra): - vtkTet: vtk.vtkTetra = cell - tetPointIds: vtk.vtkIdList = vtkTet.GetPointIds() - assert isinstance(tetPointIds, vtk.vtkIdList) - # - # translate from vtkgrid pointids to visMesh point ids - # - numPoints = tetPointIds.GetNumberOfIds() - visPointIds = [] - for p in range(0, numPoints): - visPointIds.append(uniquePointIndices[tetPointIds.GetId(p)]) - visTet = VisTetrahedron(visPointIds) - if clippedPolyhedron.chomboVolumeIndex != None: - visTet.chomboVolumeIndex = clippedPolyhedron.chomboVolumeIndex - if clippedPolyhedron.finiteVolumeIndex != None: - visTet.finiteVolumeIndex = clippedPolyhedron.finiteVolumeIndex - visTets.append(visTet) - else: - print("ChomboMeshMapping.createTetrahedra(): expecting a tet, found a " + cell.__type__) - - return visTets - - -def main(): - # sys.setrecursionlimit(100000) - - try: - parser = argparse.ArgumentParser() - list_of_meshtypes = ["chombovolume", "chombomembrane", "finitevolume", "movingboundary", "comsolvolume"] - parser.add_argument("meshtype", help="type of visMesh processing required and index file generated", choices=list_of_meshtypes) - parser.add_argument("domainname", help="domain name for output mesh") - parser.add_argument("vismeshfile", help="filename of input visMesh to be processed (thrift serialization via TBinaryProtocol)") - parser.add_argument("vtkfile", help="filename of output vtk mesh (VTK XML unstructured grid") - parser.add_argument("indexfile", help="filename of output ChomboIndexData or FiniteVolumeIndexData (thrift serialization via TBinaryProtocol)") - args = parser.parse_args() - - - f_vismesh = open(args.vismeshfile, "rb") - blob_vismesh = f_vismesh.read() - print("read "+str(len(blob_vismesh))+" bytes from "+args.vismeshfile) - f_vismesh.close() - - visMesh = VisMesh() - protocol_factory = TBinaryProtocol.TBinaryProtocolFactory - # deserialize(visMesh, blob_vismesh, protocol_factory = protocol_factory()) - print("starting deserialization") - deserialize(visMesh, blob_vismesh, protocol_factory=protocol_factory()) - print("done with deserialization") - - if args.meshtype == "chombovolume": - writeChomboVolumeVtkGridAndIndexData(visMesh, args.domainname, args.vtkfile, args.indexfile) - elif args.meshtype == "chombomembrane": - writeChomboMembraneVtkGridAndIndexData(visMesh, args.domainname, args.vtkfile, args.indexfile) - elif args.meshtype == "finitevolume": - writeFiniteVolumeSmoothedVtkGridAndIndexData(visMesh, args.domainname, args.vtkfile, args.indexfile) - elif args.meshtype == "movingboundary": - writeMovingBoundaryVolumeVtkGridAndIndexData(visMesh, args.domainname, args.vtkfile, args.indexfile) - elif args.meshtype == "comsolvolume": - writeComsolVolumeVtkGridAndIndexData(visMesh, args.domainname, args.vtkfile, args.indexfile) - else: - raise Exception("meshtype "+str(args.meshtype)+" not supported") - - except: - e_info = sys.exc_info() - traceback.print_exception(e_info[0], e_info[1], e_info[2], file=sys.stdout) - sys.stderr.write("exception: "+str(e_info[0])+": "+str(e_info[1])+"\n") - sys.stderr.flush() - sys.exit(-1) - else: - sys.exit(0) - - -if __name__ == '__main__': - main() +import argparse +import copy +import os +import sys +import traceback + +import vtkmodules.all as vtk +from thrift.TSerialization import TBinaryProtocol +from thrift.TSerialization import deserialize +from thrift.TSerialization import serialize + +from vcellvismesh.ttypes import ChomboIndexData +from vcellvismesh.ttypes import FiniteVolumeIndexData +from vcellvismesh.ttypes import MovingBoundaryIndexData +from vcellvismesh.ttypes import PolyhedronFace +from vcellvismesh.ttypes import VisIrregularPolyhedron +from vcellvismesh.ttypes import VisLine +from vcellvismesh.ttypes import VisMesh +from vcellvismesh.ttypes import VisPolygon +from vcellvismesh.ttypes import VisTetrahedron + + +def writeChomboVolumeVtkGridAndIndexData(visMesh: VisMesh, domainname: str, vtkfile, indexfile) -> None: + originalVisMesh = visMesh + correctedVisMesh = originalVisMesh # same mesh if no irregularPolyhedra + if originalVisMesh.irregularPolyhedra is not None: + correctedVisMesh = copy.deepcopy(visMesh) + if correctedVisMesh.tetrahedra is None: + correctedVisMesh.tetrahedra = [] + for irregularPolyhedron in correctedVisMesh.irregularPolyhedra: + tets = createTetrahedra(irregularPolyhedron, correctedVisMesh) + for tet in tets: + correctedVisMesh.tetrahedra.append(tet) + correctedVisMesh.irregularPolyhedra = None + + vtkgrid: vtk.vtkUnstructuredGrid = getVolumeVtkGrid(correctedVisMesh) + writevtk(vtkgrid, vtkfile) + chomboIndexData = ChomboIndexData() + chomboIndexData.chomboVolumeIndices = [] + chomboIndexData.domainName = domainname + if correctedVisMesh.dimension == 2: + if correctedVisMesh.polygons is not None: + for polygon in correctedVisMesh.polygons: + assert isinstance(polygon, VisPolygon) + chomboIndexData.chomboVolumeIndices.append(polygon.chomboVolumeIndex) + if chomboIndexData.chomboVolumeIndices is None: + print("didn't find any indices ... bad") + elif correctedVisMesh.dimension == 3: + if correctedVisMesh.visVoxels is not None: + for voxel in correctedVisMesh.visVoxels: + chomboIndexData.chomboVolumeIndices.append(voxel.chomboVolumeIndex) + if correctedVisMesh.irregularPolyhedra is not None: + raise Exception("unexpected irregular polyhedra in mesh, should have been replaced with tetrahedra") + if correctedVisMesh.tetrahedra is not None: + for tetrahedron in correctedVisMesh.tetrahedra: + assert isinstance(tetrahedron, VisTetrahedron) + chomboIndexData.chomboVolumeIndices.append(tetrahedron.chomboVolumeIndex) + if len(chomboIndexData.chomboVolumeIndices) == 0: + print("didn't find any indices ... bad") + writeChomboIndexData(indexfile, chomboIndexData) + + +def writeChomboMembraneVtkGridAndIndexData(visMesh: VisMesh, domainname: str, vtkfile, indexfile) -> None: + + vtkgrid = getMembraneVtkGrid(visMesh) + writevtk(vtkgrid, vtkfile) + + chomboIndexData = ChomboIndexData() + chomboIndexData.chomboSurfaceIndices = [] + if domainname.upper().endswith("MEMBRANE") is False: + raise Exception("expecting domain name ending with membrane") + chomboIndexData.domainName = domainname + if visMesh.dimension == 3: + if visMesh.surfaceTriangles is not None: + for surfaceTriangle in visMesh.surfaceTriangles: + chomboIndexData.chomboSurfaceIndices.append(surfaceTriangle.chomboSurfaceIndex) + elif visMesh.dimension == 2: + if visMesh.visLines is not None: + for visLine in visMesh.visLines: + assert isinstance(visLine, VisLine) + chomboIndexData.chomboSurfaceIndices.append(visLine.chomboSurfaceIndex) + if len(chomboIndexData.chomboSurfaceIndices) == 0: + print("didn't find any indices ... bad") + writeChomboIndexData(indexfile, chomboIndexData) + + +def writeFiniteVolumeSmoothedVtkGridAndIndexData(visMesh: VisMesh, domainName: str, vtuFile, indexFile) -> None: + vtkgrid = getVolumeVtkGrid(visMesh) + if visMesh.dimension == 3: + vtkgridSmoothed = smoothUnstructuredGridSurface(vtkgrid) + else: + vtkgridSmoothed = vtkgrid + writevtk(vtkgridSmoothed, vtuFile) + finiteVolumeIndexData = FiniteVolumeIndexData() + finiteVolumeIndexData.finiteVolumeIndices = [] + finiteVolumeIndexData.domainName = domainName + if visMesh.dimension == 2: + # if volume + if visMesh.polygons is not None: + for polygon in visMesh.polygons: + finiteVolumeIndexData.finiteVolumeIndices.append(polygon.finiteVolumeIndex) + # if membrane + if visMesh.visLines is not None: + for visLine in visMesh.visLines: + finiteVolumeIndexData.finiteVolumeIndices.append(visLine.finiteVolumeIndex) + elif visMesh.dimension == 3: + # if volume + if visMesh.visVoxels is not None: + for voxel in visMesh.visVoxels: + finiteVolumeIndexData.finiteVolumeIndices.append(voxel.finiteVolumeIndex) + if visMesh.irregularPolyhedra is not None: + raise Exception("unexpected irregular polyhedra in mesh, should have been replaced with tetrahedra") + if visMesh.tetrahedra is not None: + for tetrahedron in visMesh.tetrahedra: + finiteVolumeIndexData.finiteVolumeIndices.append(tetrahedron.finiteVolumeIndex) + # if membrane + if visMesh.polygons is not None: + for polygon in visMesh.polygons: + finiteVolumeIndexData.finiteVolumeIndices.append(polygon.finiteVolumeIndex) + + if finiteVolumeIndexData.finiteVolumeIndices == None or len(finiteVolumeIndexData.finiteVolumeIndices) == 0: + print("didn't find any indices ... bad") + + writeFiniteVolumeIndexData(indexFile, finiteVolumeIndexData) + + +def writeFiniteVolumeIndexData(finiteVolumeIndexFile, finiteVolumeIndexData): + assert isinstance(finiteVolumeIndexData, FiniteVolumeIndexData) + blob = serialize(finiteVolumeIndexData, protocol_factory=TBinaryProtocol.TBinaryProtocolFactory()) + ff = open(finiteVolumeIndexFile,'wb') + ff.write(blob) + ff.close() + print("wrote finitevolume data to file "+str(finiteVolumeIndexFile)) + + +def writeMovingBoundaryVolumeVtkGridAndIndexData(visMesh: VisMesh, domainName: str, vtuFile, indexFile): + vtkgrid = getVolumeVtkGrid(visMesh) + writevtk(vtkgrid, vtuFile) + movingBoundaryIndexData = MovingBoundaryIndexData() + movingBoundaryIndexData.movingBoundaryVolumeIndices = [] + movingBoundaryIndexData.domainName = domainName + movingBoundaryIndexData.timeIndex = 0 + if visMesh.dimension == 2: + # if volume + if visMesh.polygons is not None: + for polygon in visMesh.polygons: + movingBoundaryIndexData.movingBoundaryVolumeIndices.append(polygon.movingBoundaryVolumeIndex) + # if membrane + if visMesh.visLines is not None: + for visLine in visMesh.visLines: + movingBoundaryIndexData.movingBoundarySurfaceIndices.append(visLine.movingBoundarySurfaceIndex) + # elif visMesh.dimension == 3: + # # if volume + # if visMesh.visVoxels is not None: + # for voxel in visMesh.visVoxels: + # movingBoundaryIndexData.finiteVolumeIndices.append(voxel.finiteVolumeIndex) + # if visMesh.irregularPolyhedra is not None: + # raise Exception("unexpected irregular polyhedra in mesh, should have been replaced with tetrahedra") + # if visMesh.tetrahedra is not None: + # for tetrahedron in visMesh.tetrahedra: + # movingBoundaryIndexData.finiteVolumeIndices.append(tetrahedron.finiteVolumeIndex) + # # if membrane + # if visMesh.polygons is not None: + # for polygon in visMesh.polygons: + # movingBoundaryIndexData.finiteVolumeIndices.append(polygon.finiteVolumeIndex) + + if movingBoundaryIndexData.movingBoundaryVolumeIndices == None and movingBoundaryIndexData.movingBoundarySurfaceIndices == None: + print("didn't find any indices ... bad") + + if movingBoundaryIndexData.movingBoundaryVolumeIndices != None and len(movingBoundaryIndexData.movingBoundaryVolumeIndices) == 0: + print("didn't find any indices ... bad") + + if movingBoundaryIndexData.movingBoundarySurfaceIndices != None and len(movingBoundaryIndexData.movingBoundarySurfaceIndices) == 0: + print("didn't find any indices ... bad") + + writeMovingBoundaryIndexData(indexFile, movingBoundaryIndexData) + + +def writeComsolVolumeVtkGridAndIndexData(visMesh, domainName, vtuFile, indexFile): + assert isinstance(visMesh, VisMesh) + vtkgrid = getVolumeVtkGrid(visMesh) + writevtk(vtkgrid, vtuFile) + # movingBoundaryIndexData = MovingBoundaryIndexData() + # movingBoundaryIndexData.movingBoundaryVolumeIndices = [] + # movingBoundaryIndexData.domainName = domainName + # movingBoundaryIndexData.timeIndex = 0 + # if visMesh.dimension == 2: + # # if volume + # if visMesh.polygons is not None: + # for polygon in visMesh.polygons: + # movingBoundaryIndexData.movingBoundaryVolumeIndices.append(polygon.movingBoundaryVolumeIndex) + # # if membrane + # if visMesh.visLines is not None: + # for visLine in visMesh.visLines: + # movingBoundaryIndexData.movingBoundarySurfaceIndices.append(visLine.movingBoundarySurfaceIndex) + # elif visMesh.dimension == 3: + # # if volume + # if visMesh.visVoxels is not None: + # for voxel in visMesh.visVoxels: + # movingBoundaryIndexData.finiteVolumeIndices.append(voxel.finiteVolumeIndex) + # if visMesh.irregularPolyhedra is not None: + # raise Exception("unexpected irregular polyhedra in mesh, should have been replaced with tetrahedra") + # if visMesh.tetrahedra is not None: + # for tetrahedron in visMesh.tetrahedra: + # movingBoundaryIndexData.finiteVolumeIndices.append(tetrahedron.finiteVolumeIndex) + # # if membrane + # if visMesh.polygons is not None: + # for polygon in visMesh.polygons: + # movingBoundaryIndexData.finiteVolumeIndices.append(polygon.finiteVolumeIndex) + + # if movingBoundaryIndexData.movingBoundaryVolumeIndices == None and movingBoundaryIndexData.movingBoundarySurfaceIndices == None: + # print "didn't find any indices ... bad" + # + # if movingBoundaryIndexData.movingBoundaryVolumeIndices != None and len(movingBoundaryIndexData.movingBoundaryVolumeIndices) == 0: + # print "didn't find any indices ... bad" + # + # if movingBoundaryIndexData.movingBoundarySurfaceIndices != None and len(movingBoundaryIndexData.movingBoundarySurfaceIndices) == 0: + # print "didn't find any indices ... bad" + # + #writeMovingBoundaryIndexData(indexFile, None) + + +def writeMovingBoundaryIndexData(movingBoundaryIndexFile, movingBoundaryIndexData): + assert isinstance(movingBoundaryIndexData, MovingBoundaryIndexData) + blob = serialize(movingBoundaryIndexData, protocol_factory=TBinaryProtocol.TBinaryProtocolFactory()) + ff = open(movingBoundaryIndexFile,'wb') + ff.write(blob) + ff.close() + print("wrote movingboundary data to file "+str(movingBoundaryIndexFile)) + + + +def writeChomboIndexData(chomboIndexFile, chomboIndexData): + """ + + Returns: + None: + """ + assert isinstance(chomboIndexData, ChomboIndexData) + blob = serialize(chomboIndexData, protocol_factory=TBinaryProtocol.TBinaryProtocolFactory()) + ff = open(chomboIndexFile,'wb') + ff.write(blob) + ff.close() + print("wrote chomboIndex data to file "+str(chomboIndexFile)) + + +# +# read a vtkUnstructuredGrid from the XML format +# +def readvtk(vtkfile): + if not os.path.isfile(vtkfile): + raise Exception("unstructured grid " + str(vtkfile) + " not found") + + tester = vtk.vtkXMLFileReadTester() + tester.SetFileName(str(vtkfile)) + if tester.TestReadFile() != 1: + raise Exception("expecting XML formatted VTK unstructured grid") + + reader = vtk.vtkXMLUnstructuredGridReader() + reader.SetFileName(vtkfile) + reader.Update() + vtkgrid = reader.GetOutput() + assert isinstance(vtkgrid, vtk.vtkUnstructuredGrid) + print("read from file " + str(vtkfile)) + vtkgrid.BuildLinks() + return vtkgrid + + +# +# write a vtkUnstructuredGrid to the XML format +# +def writevtk(vtkgrid, filename): + writer = vtk.vtkXMLUnstructuredGridWriter() + bASCII = False + if bASCII: + writer.SetDataModeToAscii() + else: + writer.SetCompressorTypeToNone() + writer.SetDataModeToBinary() + try: + writer.SetInputData(vtkgrid) + except AttributeError: + writer.SetInput(vtkgrid) + writer.SetFileName(filename) + writer.Update() + print("wrote to file "+str(filename)) + + +# +# create a single-variable vtu file +# +def writeDataArrayToNewVtkFile(emptyMeshFile, varName, data, newMeshFile): + assert type(emptyMeshFile) is str + assert type(varName) is str + assert type(newMeshFile) is str + try: + #raise ImportError("dummy exception") + import numpy as np + from vtk.util import numpy_support + print("writing varData using numpy") + + data = np.array(data) + vtkgrid = readvtk(emptyMeshFile) + assert isinstance(vtkgrid, vtk.vtkUnstructuredGrid) + + # + # add cell data array to the empty mesh for this variable + # + dataArray = vtk.vtkDoubleArray() + dataArray = numpy_support.numpy_to_vtk(data) + assert isinstance(dataArray, ) + dataArray.SetName(varName) + cellData: vtk.vtkCellData = vtkgrid.GetCellData() + cellData.AddArray(dataArray) + + # + # write mesh and data to the file for that domain and time + # + writevtk(vtkgrid, newMeshFile) + + except ImportError as nonumpy: + import array + print("writing varData using array package") + + print(type(data)) + print(str(data)) + data = array.array('d', data) + vtkgrid = readvtk(emptyMeshFile) + + # + # add cell data array to the empty mesh for this variable + # + dataArray = vtk.vtkDoubleArray() + dataArray.SetVoidArray(data, len(data), 1) + dataArray.SetNumberOfComponents(1) + dataArray.SetName(varName) + cellData: vtk.vtkCellData = vtkgrid.GetCellData() + cellData.AddArray(dataArray) + + # + # write mesh and data to the file for that domain and time + # + writevtk(vtkgrid, newMeshFile) + + +def getMembraneVtkGrid(visMesh: VisMesh) -> vtk.vtkUnstructuredGrid: + vtkpoints = vtk.vtkPoints() + for visPoint in visMesh.surfacePoints: + vtkpoints.InsertNextPoint(visPoint.x,visPoint.y,visPoint.z) + + vtkgrid = vtk.vtkUnstructuredGrid() + vtkgrid.Allocate(len(visMesh.surfacePoints), len(visMesh.surfacePoints)) + vtkgrid.SetPoints(vtkpoints) + + if visMesh.dimension == 2: + vtkline = vtk.vtkLine() + lineType = vtkline.GetCellType() + + for line in visMesh.visLines: + pts = vtk.vtkIdList() + pts.InsertNextId(line.p1) + pts.InsertNextId(line.p2) + vtkgrid.InsertNextCell(lineType, pts) + else: + vtktriangle = vtk.vtkTriangle() + triangleType = vtktriangle.GetCellType() + for surfaceTriangle in visMesh.surfaceTriangles: + pts = vtk.vtkIdList() + for pi in surfaceTriangle.pointIndices: + pts.InsertNextId(pi) + # each triangle is a cell + vtkgrid.InsertNextCell(triangleType, pts) + + vtkgrid.BuildLinks() + return vtkgrid + + +def getVolumeVtkGrid(visMesh: VisMesh) -> vtk.vtkUnstructuredGrid: + bClipPolyhedra = True + + vtkpoints = vtk.vtkPoints() + for visPoint in visMesh.points: + vtkpoints.InsertNextPoint(visPoint.x, visPoint.y, visPoint.z) + + vtkgrid = vtk.vtkUnstructuredGrid() + vtkgrid.Allocate(len(visMesh.points), len(visMesh.points)) + vtkgrid.SetPoints(vtkpoints) + + quadType = vtk.vtkQuad().GetCellType() + # lineType = vtk.vtkLine().GetCellType() + polygonType = vtk.vtkPolygon().GetCellType() + polyhedronType = vtk.vtkPolyhedron().GetCellType() + triangleType = vtk.vtkTriangle().GetCellType() + voxelType = vtk.vtkVoxel().GetCellType() + tetraType = vtk.vtkTetra().GetCellType() + + if visMesh.polygons != None: + for visPolygon in visMesh.polygons: + pts = vtk.vtkIdList() + polygonPoints = visPolygon.pointIndices + for p in polygonPoints: + pts.InsertNextId(p) + + numPoints = len(polygonPoints) + if numPoints == 4: + vtkgrid.InsertNextCell(quadType, pts) + elif numPoints == 3: + vtkgrid.InsertNextCell(triangleType, pts) + else: + vtkgrid.InsertNextCell(polygonType, pts) + # + # replace any VisIrregularPolyhedron with a list of VisTetrahedron + # + if visMesh.visVoxels != None: + for voxel in visMesh.visVoxels: + pts = vtk.vtkIdList() + polyhedronPoints = voxel.pointIndices + for p in polyhedronPoints: + pts.InsertNextId(p) + vtkgrid.InsertNextCell(voxelType, pts) + + if visMesh.tetrahedra != None: + for visTet in visMesh.tetrahedra: + assert isinstance(visTet, VisTetrahedron) + pts = vtk.vtkIdList() + tetPoints = visTet.pointIndices + for p in tetPoints: + pts.InsertNextId(p) + vtkgrid.InsertNextCell(tetraType, pts) + + bInitializedFaces = False + if visMesh.irregularPolyhedra != None: + for clippedPolyhedron in visMesh.irregularPolyhedra: + if bClipPolyhedra == True: + tets = createTetrahedra(clippedPolyhedron, visMesh) + for visTet in tets: + pts = vtk.vtkIdList() + tetPoints = visTet.getPointIndices() + for p in tetPoints: + pts.InsertNextId(p) + vtkgrid.InsertNextCell(tetraType, pts) + else: + faceStreamList = vtk.vtkIdList() + faceStream = getVtkFaceStream(clippedPolyhedron) + for p in faceStream: + faceStreamList.InsertNextId(p) + if bInitializedFaces == False and vtkgrid.GetNumberOfCells() > 0: + vtkgrid.InitializeFacesRepresentation(vtkgrid.GetNumberOfCells()) + bInitializedFaces = True + vtkgrid.InsertNextCell(polyhedronType, faceStreamList) + + vtkgrid.BuildLinks() + # vtkgrid.Squeeze() + return vtkgrid + + +def getVtkFaceStream(irregularPolyhedron: VisIrregularPolyhedron) -> list[int]: + faceStream = [len(irregularPolyhedron.polyhedronFaces), ] + for polyhedronFace in irregularPolyhedron.polyhedronFaces: + faceStream.append(len(polyhedronFace.getVertices())) + for v in polyhedronFace.vertices: + faceStream.append(v) + intFaceStream = [int(v) for v in faceStream] + return intFaceStream + + +def smoothUnstructuredGridSurface(vtkGrid: vtk.vtkUnstructuredGrid) -> vtk.vtkUnstructuredGrid: + ugGeometryFilter = vtk.vtkUnstructuredGridGeometryFilter() + ugGeometryFilter.PassThroughPointIdsOn() + ugGeometryFilter.MergingOff() + try: + ugGeometryFilter.SetInputData(vtkGrid) + except AttributeError: + ugGeometryFilter.SetInput(vtkGrid) + ugGeometryFilter.Update() + surfaceUnstructuredGrid: vtk.vtkUnstructuredGrid = ugGeometryFilter.GetOutput() + originalPointsIdsName = ugGeometryFilter.GetOriginalPointIdsName() + + cellData = surfaceUnstructuredGrid.GetCellData() + numCellArrays = cellData.GetNumberOfArrays() + for i in range(0, numCellArrays): + cellArrayName = cellData.GetArrayName(i) + print("CellArray(" + str(i) + ") '" + cellArrayName + "')") + pointData: vtk.vtkPointData = surfaceUnstructuredGrid.GetPointData() + numPointArrays = pointData.GetNumberOfArrays() + for i in range(0, numPointArrays): + pointArrayName = pointData.GetArrayName(i) + print("PointArray(" + str(i) + ") '" + pointArrayName + "'") + + geometryFilter = vtk.vtkGeometryFilter() + try: + geometryFilter.SetInputData(surfaceUnstructuredGrid) + except AttributeError: + geometryFilter.SetInput(surfaceUnstructuredGrid) + geometryFilter.Update() + polyData: vtk.vtkPolyData = geometryFilter.GetOutput() + + filter = vtk.vtkWindowedSincPolyDataFilter() + try: + filter.SetInputData(polyData) + except AttributeError: + filter.SetInput(polyData) + filter.SetNumberOfIterations(15) + filter.BoundarySmoothingOff() + filter.FeatureEdgeSmoothingOff() + filter.SetFeatureAngle(120.0) + filter.SetPassBand(0.001) + filter.NonManifoldSmoothingOff() + filter.NormalizeCoordinatesOn() + filter.Update() + + smoothedPolydata = filter.GetOutput() + + smoothedPoints: vtk.vtkPoints = smoothedPolydata.GetPoints() + + smoothedPointData: vtk.vtkPointData = smoothedPolydata.GetPointData() + pointIdsArray: vtk.vtkIdTypeArray = smoothedPointData.GetArray(originalPointsIdsName) + pointsIdsArraySize = pointIdsArray.GetSize() + origPoints = vtkGrid.GetPoints() + for i in range(0, pointsIdsArraySize): + pointId = pointIdsArray.GetValue(i) + smoothedPoint = smoothedPoints.GetPoint(i) + origPoints.SetPoint(pointId, smoothedPoint) + + return vtkGrid + + +def getPointIndices(irregularPolyhedron: VisIrregularPolyhedron) -> list[int]: + assert isinstance(irregularPolyhedron, VisIrregularPolyhedron) + pointIndicesSet = set() + for face in irregularPolyhedron.polyhedronFaces: + assert(isinstance(face, PolyhedronFace)) + for pointIndex in face.vertices: + pointIndicesSet.add(pointIndex) + pointArray = [int(x) for x in pointIndicesSet] + return pointArray + + +def createTetrahedra(clippedPolyhedron: VisIrregularPolyhedron, visMesh: VisMesh): + + vtkpolydata = vtk.vtkPolyData() + vtkpoints = vtk.vtkPoints() + polygonType = vtk.vtkPolygon().GetCellType() + uniquePointIndices = getPointIndices(clippedPolyhedron) + for point in uniquePointIndices: + visPoint = visMesh.points[point] + vtkpoints.InsertNextPoint(visPoint.x, visPoint.y, visPoint.z) + vtkpolydata.Allocate(100, 100) + vtkpolydata.SetPoints(vtkpoints) + + for face in clippedPolyhedron.polyhedronFaces: + faceIdList = vtk.vtkIdList() + for visPointIndex in face.vertices: + vtkpointid = -1 + for i in range(0, len(uniquePointIndices)): + if uniquePointIndices[i] == visPointIndex: + vtkpointid = i + faceIdList.InsertNextId(vtkpointid) + vtkpolydata.InsertNextCell(polygonType, faceIdList) + + delaunayFilter = vtk.vtkDelaunay3D() + try: + delaunayFilter.SetInputData(vtkpolydata) + except AttributeError: + delaunayFilter.SetInput(vtkpolydata) + delaunayFilter.Update() + delaunayFilter.SetAlpha(0.1) + vtkgrid2: vtk.vtkUnstructuredGrid = delaunayFilter.GetOutput() + assert isinstance(vtkgrid2, vtk.vtkUnstructuredGrid) # runtime check, remove later + + visTets = [] + numTets = vtkgrid2.GetNumberOfCells() + if numTets < 1: + if len(uniquePointIndices)==4: + visTet = VisTetrahedron(uniquePointIndices) + visTet.chomboVolumeIndex = clippedPolyhedron.chomboVolumeIndex + visTet.finiteVolumeIndex = clippedPolyhedron.finiteVolumeIndex + visTets.append(visTet) + print("made trivial tet ... maybe inside out") + else: + print("found no tets, there are "+str(len(uniquePointIndices))+" unique point indices") + + + # print("numFaces = "+str(vtkpolydata.GetNumberOfCells())+", numTets = "+str(numTets)); + for cellIndex in range(0, numTets): + cell = vtkgrid2.GetCell(cellIndex) + if isinstance(cell, vtk.vtkTetra): + vtkTet: vtk.vtkTetra = cell + tetPointIds: vtk.vtkIdList = vtkTet.GetPointIds() + assert isinstance(tetPointIds, vtk.vtkIdList) + # + # translate from vtkgrid pointids to visMesh point ids + # + numPoints = tetPointIds.GetNumberOfIds() + visPointIds = [] + for p in range(0, numPoints): + visPointIds.append(uniquePointIndices[tetPointIds.GetId(p)]) + visTet = VisTetrahedron(visPointIds) + if clippedPolyhedron.chomboVolumeIndex != None: + visTet.chomboVolumeIndex = clippedPolyhedron.chomboVolumeIndex + if clippedPolyhedron.finiteVolumeIndex != None: + visTet.finiteVolumeIndex = clippedPolyhedron.finiteVolumeIndex + visTets.append(visTet) + else: + print("ChomboMeshMapping.createTetrahedra(): expecting a tet, found a " + cell.__type__) + + return visTets + + +def main(): + # sys.setrecursionlimit(100000) + + try: + parser = argparse.ArgumentParser() + list_of_meshtypes = ["chombovolume", "chombomembrane", "finitevolume", "movingboundary", "comsolvolume"] + parser.add_argument("meshtype", help="type of visMesh processing required and index file generated", choices=list_of_meshtypes) + parser.add_argument("domainname", help="domain name for output mesh") + parser.add_argument("vismeshfile", help="filename of input visMesh to be processed (thrift serialization via TBinaryProtocol)") + parser.add_argument("vtkfile", help="filename of output vtk mesh (VTK XML unstructured grid") + parser.add_argument("indexfile", help="filename of output ChomboIndexData or FiniteVolumeIndexData (thrift serialization via TBinaryProtocol)") + args = parser.parse_args() + + + f_vismesh = open(args.vismeshfile, "rb") + blob_vismesh = f_vismesh.read() + print("read "+str(len(blob_vismesh))+" bytes from "+args.vismeshfile) + f_vismesh.close() + + visMesh = VisMesh() + protocol_factory = TBinaryProtocol.TBinaryProtocolFactory + # deserialize(visMesh, blob_vismesh, protocol_factory = protocol_factory()) + print("starting deserialization") + deserialize(visMesh, blob_vismesh, protocol_factory=protocol_factory()) + print("done with deserialization") + + if args.meshtype == "chombovolume": + writeChomboVolumeVtkGridAndIndexData(visMesh, args.domainname, args.vtkfile, args.indexfile) + elif args.meshtype == "chombomembrane": + writeChomboMembraneVtkGridAndIndexData(visMesh, args.domainname, args.vtkfile, args.indexfile) + elif args.meshtype == "finitevolume": + writeFiniteVolumeSmoothedVtkGridAndIndexData(visMesh, args.domainname, args.vtkfile, args.indexfile) + elif args.meshtype == "movingboundary": + writeMovingBoundaryVolumeVtkGridAndIndexData(visMesh, args.domainname, args.vtkfile, args.indexfile) + elif args.meshtype == "comsolvolume": + writeComsolVolumeVtkGridAndIndexData(visMesh, args.domainname, args.vtkfile, args.indexfile) + else: + raise Exception("meshtype "+str(args.meshtype)+" not supported") + + except: + e_info = sys.exc_info() + traceback.print_exception(e_info[0], e_info[1], e_info[2], file=sys.stdout) + sys.stderr.write("exception: "+str(e_info[0])+": "+str(e_info[1])+"\n") + sys.stderr.flush() + sys.exit(-1) + else: + sys.exit(0) + + +if __name__ == '__main__': + main() From 0ca4bedd381167177d9380e2ff038f15958d7336 Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Mon, 6 Jan 2025 12:52:15 -0500 Subject: [PATCH 07/10] Updating and expanding test cases --- vcell-cli/src/main/resources/test_cases.ndjson | 4 ++-- .../main/java/org/vcell/sedml/testsupport/FailureType.java | 4 +++- .../org/vcell/sedml/testsupport/OmexTestingDatabase.java | 5 +++++ 3 files changed, 10 insertions(+), 3 deletions(-) diff --git a/vcell-cli/src/main/resources/test_cases.ndjson b/vcell-cli/src/main/resources/test_cases.ndjson index dc13d08bdf..89f755796d 100644 --- a/vcell-cli/src/main/resources/test_cases.ndjson +++ b/vcell-cli/src/main/resources/test_cases.ndjson @@ -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":"UNCATETORIZED_FAULT","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":"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":"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} @@ -1165,7 +1165,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001062.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000001062 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001063.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000001063 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001064.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000001064 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001065.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000001065_vonDassow2000_1x4.timecourse1.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE ERROR] CVode\n At t = 660.5repeated recoverable right-hand side function errors.\n\nCVODE solver failed : CV_REPTD_RHSFUNC_ERR: repeated recoverable right-hand side function errors : FunctionDomainException : FunctionDomainException : pow(u,v) and u=-0.000000<0 and v=2.619640 not an integer in \"((0.052821806954783216692 * ((0.00030494421841729539872 / (0.00030494421841729539872 + (EN_0_0 ^ 2.6196399999999999686))) ^ 9.6309500000000003439) / (5.7617237886031359827e-23 + (0.4000000000000000222 * ((0.00030494421841729539872 / (0.00030494421841729539872 + (EN_0_0 ^ 2.6196399999999999686))) ^ 9.6309500000000003439)))) - (0.13205451738695803132 * ci_0_0))\"\n where:\n\tEN_0_0 = -0.000000\n\tci_0_0 = 1.000000\n\n\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/VCell_CLI_193f9f93f2012192791967497390908/BIOMD0000001065/vonDassow2000_1x4.timecourse1.sedml/SimID_1545840175_0_.cvodeInput /tmp/VCell_CLI_193f9f93f2012192791967497390908/BIOMD0000001065/vonDassow2000_1x4.timecourse1.sedml/SimID_1545840175_0_.ida) "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001065.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000001065_vonDassow2000_1x4.timecourse1.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE ERROR] CVode\n At t = 660.5repeated recoverable right-hand side function errors.\n\nCVODE solver failed : CV_REPTD_RHSFUNC_ERR: repeated recoverable right-hand side function errors : FunctionDomainException : FunctionDomainException : pow(u,v) and u=-0.000000<0 and v=2.619640 not an integer in \"((0.052821806954783216692 * ((0.00030494421841729539872 / (0.00030494421841729539872 + (EN_0_0 ^ 2.6196399999999999686))) ^ 9.6309500000000003439) / (5.7617237886031359827e-23 + (0.4000000000000000222 * ((0.00030494421841729539872 / (0.00030494421841729539872 + (EN_0_0 ^ 2.6196399999999999686))) ^ 9.6309500000000003439)))) - (0.13205451738695803132 * ci_0_0))\"\n where:\n\tEN_0_0 = -0.000000\n\tci_0_0 = 1.000000\n\n\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/VCell_CLI_193f9f93f2012192791967497390908/BIOMD0000001065/vonDassow2000_1x4.timecourse1.sedml/SimID_1545840175_0_.cvodeInput /tmp/VCell_CLI_193f9f93f2012192791967497390908/BIOMD0000001065/vonDassow2000_1x4.timecourse1.sedml/SimID_1545840175_0_.ida) "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001066.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000001066 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001067.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000001067 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001068.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000001068 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"} 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 9fda0fd72b..c5e9c9ce59 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 @@ -16,6 +16,7 @@ public enum FailureType { NULL_POINTER_EXCEPTION, OPERATION_NOT_SUPPORTED, // VCell simply doesn't have the necessary features to run this archive. SBML_IMPORT_FAILURE, + SEDML_IMPORT_FAILURE, SEDML_DIFF_NUMBER_OF_BIOMODELS, SEDML_ERRONEOUS_UNIT_SYSTEM, SEDML_ERROR_CONSTRUCTING_SIMCONTEXT, @@ -40,5 +41,6 @@ public enum FailureType { SBML_XML_NODE_FAILURE, SOLVER_FAILURE, UNSUPPORTED_DELAY_SBML, - UNSUPPORTED_NON_CONSTANT_COMPARTMENTS + UNSUPPORTED_NON_CONSTANT_COMPARTMENTS, + BIOMODEL_IMPORT_SEDML_FAILURE } 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 a3f7056699..5990a79eb9 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 @@ -4,6 +4,7 @@ import com.fasterxml.jackson.databind.MappingIterator; import com.fasterxml.jackson.databind.ObjectMapper; import org.vcell.sbml.vcell.SBMLImportException; +import org.vcell.sedml.SEDMLImportException; import org.vcell.trace.Span; import org.vcell.trace.TraceEvent; @@ -117,6 +118,10 @@ private static FailureType determineFault(TraceEvent traceEvent){ FailureType sbmlFailureType; return (sbmlFailureType = determineFault(traceEvent.exception)) != null ? sbmlFailureType : FailureType.SBML_IMPORT_FAILURE; } + if (traceEvent.hasException(SEDMLImportException.class)){ + String errMsg = traceEvent.exception.getMessage() == null ? "" : traceEvent.exception.getMessage(); + return (errMsg.contains("expecting vcell var") && errMsg.contains("to be constant valued")) ? FailureType.BIOMODEL_IMPORT_SEDML_FAILURE : FailureType.SEDML_IMPORT_FAILURE; + } if (traceEvent.span.getNestedContextName().contains(Span.ContextType.PROCESSING_SEDML.name()+"(preProcessDoc)")){ return FailureType.SEDML_PREPROCESS_FAILURE; } From ae225202c20d00586c9086758746221636da9e20 Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Mon, 6 Jan 2025 12:52:33 -0500 Subject: [PATCH 08/10] Adding alarm if we have execution result mismatch --- .github/workflows/NightlyBMDB_CLI.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/workflows/NightlyBMDB_CLI.yml b/.github/workflows/NightlyBMDB_CLI.yml index 9ba2a2087f..ce81d9535b 100644 --- a/.github/workflows/NightlyBMDB_CLI.yml +++ b/.github/workflows/NightlyBMDB_CLI.yml @@ -379,5 +379,11 @@ jobs: - name: Post results to slack part 3 (report.md from exec-report CLI command) run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="$(cat ${GITHUB_WORKSPACE}/report.md)" https://slack.com/api/chat.postMessage - - name: Post results to slack part 4 + - name: Post results to slack part 4 (sound alarm if changed results) + run: | + if grep -q "Unmatched Results Statistics" "$(cat ${GITHUB_WORKSPACE}/report.md)"; then + run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="@here BMDB Nightly Testing has reported a change in execution results!! Please Investigate" https://slack.com/api/chat.postMessage + fi + + - name: Post results to slack part 5 run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="To see detailed logs of the BMDB results, see - ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}. Go see what happened!" https://slack.com/api/chat.postMessage From 88da4b8b4d47c4af0db32c6097f07bd6d10833ee Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Tue, 7 Jan 2025 14:21:01 -0500 Subject: [PATCH 09/10] Removing blocking repository from pom --- .github/workflows/NightlyBMDB_CLI.yml | 2 +- pom.xml | 7 ------- 2 files changed, 1 insertion(+), 8 deletions(-) diff --git a/.github/workflows/NightlyBMDB_CLI.yml b/.github/workflows/NightlyBMDB_CLI.yml index ce81d9535b..e98cd802d2 100644 --- a/.github/workflows/NightlyBMDB_CLI.yml +++ b/.github/workflows/NightlyBMDB_CLI.yml @@ -382,7 +382,7 @@ jobs: - name: Post results to slack part 4 (sound alarm if changed results) run: | if grep -q "Unmatched Results Statistics" "$(cat ${GITHUB_WORKSPACE}/report.md)"; then - run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="@here BMDB Nightly Testing has reported a change in execution results!! Please Investigate" https://slack.com/api/chat.postMessage + curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="@here BMDB Nightly Testing has reported a change in execution results!! Please Investigate" https://slack.com/api/chat.postMessage fi - name: Post results to slack part 5 diff --git a/pom.xml b/pom.xml index 58b84ed970..7ed69a4d12 100644 --- a/pom.xml +++ b/pom.xml @@ -194,13 +194,6 @@ - - - com.springsource.repository.bundles.external - SpringSource Enterprise Bundle Repository - External Bundle Releases - https://repository.springsource.com/maven/bundles/external - - com.alfresco.repository.public From 0eb0c7d381d17549da8cb5a8a18550700a566637 Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Tue, 7 Jan 2025 15:33:23 -0500 Subject: [PATCH 10/10] Added new (and missing) python-vtk prefix --- .../python_vtk/vtkService/makeLittleVtk.py | 2 +- .../vtkService/vtkAddData_not_used.py | 2 +- pythonVtk/python_vtk/vtkService/vtkService.py | 18 +++++++++--------- .../org/vcell/vis/vtk/VtkServicePython.java | 2 +- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/pythonVtk/python_vtk/vtkService/makeLittleVtk.py b/pythonVtk/python_vtk/vtkService/makeLittleVtk.py index fb4ff371c6..57ba15ba67 100644 --- a/pythonVtk/python_vtk/vtkService/makeLittleVtk.py +++ b/pythonVtk/python_vtk/vtkService/makeLittleVtk.py @@ -1,6 +1,6 @@ import vtk -import vtkService.vtkService as vtkService +import python_vtk.vtkService.vtkService as vtkService x = [1, 2, 3, 4] y = [1, 2, 3, 4] diff --git a/pythonVtk/python_vtk/vtkService/vtkAddData_not_used.py b/pythonVtk/python_vtk/vtkService/vtkAddData_not_used.py index f5cd87c8cd..d0067e8be8 100644 --- a/pythonVtk/python_vtk/vtkService/vtkAddData_not_used.py +++ b/pythonVtk/python_vtk/vtkService/vtkAddData_not_used.py @@ -3,7 +3,7 @@ import numpy as np import vtk -from vtkService.vtkService import writeDataArrayToNewVtkFile +from python_vtk.vtkService.vtkService import writeDataArrayToNewVtkFile def main(): diff --git a/pythonVtk/python_vtk/vtkService/vtkService.py b/pythonVtk/python_vtk/vtkService/vtkService.py index 42c5562a8f..b63485fbd2 100644 --- a/pythonVtk/python_vtk/vtkService/vtkService.py +++ b/pythonVtk/python_vtk/vtkService/vtkService.py @@ -9,15 +9,15 @@ from thrift.TSerialization import deserialize from thrift.TSerialization import serialize -from vcellvismesh.ttypes import ChomboIndexData -from vcellvismesh.ttypes import FiniteVolumeIndexData -from vcellvismesh.ttypes import MovingBoundaryIndexData -from vcellvismesh.ttypes import PolyhedronFace -from vcellvismesh.ttypes import VisIrregularPolyhedron -from vcellvismesh.ttypes import VisLine -from vcellvismesh.ttypes import VisMesh -from vcellvismesh.ttypes import VisPolygon -from vcellvismesh.ttypes import VisTetrahedron +from python_vtk.vcellvismesh.ttypes import ChomboIndexData +from python_vtk.vcellvismesh.ttypes import FiniteVolumeIndexData +from python_vtk.vcellvismesh.ttypes import MovingBoundaryIndexData +from python_vtk.vcellvismesh.ttypes import PolyhedronFace +from python_vtk.vcellvismesh.ttypes import VisIrregularPolyhedron +from python_vtk.vcellvismesh.ttypes import VisLine +from python_vtk.vcellvismesh.ttypes import VisMesh +from python_vtk.vcellvismesh.ttypes import VisPolygon +from python_vtk.vcellvismesh.ttypes import VisTetrahedron def writeChomboVolumeVtkGridAndIndexData(visMesh: VisMesh, domainname: str, vtkfile, indexfile) -> None: diff --git a/vcell-core/src/main/java/org/vcell/vis/vtk/VtkServicePython.java b/vcell-core/src/main/java/org/vcell/vis/vtk/VtkServicePython.java index 91f913022b..f08116d1c7 100644 --- a/vcell-core/src/main/java/org/vcell/vis/vtk/VtkServicePython.java +++ b/vcell-core/src/main/java/org/vcell/vis/vtk/VtkServicePython.java @@ -62,7 +62,7 @@ private void callVtkPython(MeshType meshtype, String domainName, Path visMeshFil String.valueOf(visMeshFile.toAbsolutePath()), String.valueOf(vtkFile.toAbsolutePath()), String.valueOf(indexFile.toAbsolutePath()) }; - PythonUtils.callPoetryModule(vtkPythonDir, "vtkService.vtkService", commands); + PythonUtils.callPoetryModule(vtkPythonDir, "python_vtk.vtkService.vtkService", commands); } }