From edfe91d78fb9fa9eb8222896346f03c4234d2e08 Mon Sep 17 00:00:00 2001 From: jcschaff Date: Sat, 14 Dec 2024 14:13:47 -0500 Subject: [PATCH 1/7] extracted OMEX execution failure categories into shared enum --- .../vcell/cli/testsupport/FailureType.java | 37 ++++++++ .../vcell/cli/run/BSTSBasedOmexExecTest.java | 90 ++++++------------- 2 files changed, 64 insertions(+), 63 deletions(-) create mode 100644 vcell-cli/src/main/java/org/vcell/cli/testsupport/FailureType.java diff --git a/vcell-cli/src/main/java/org/vcell/cli/testsupport/FailureType.java b/vcell-cli/src/main/java/org/vcell/cli/testsupport/FailureType.java new file mode 100644 index 0000000000..4872d5b54e --- /dev/null +++ b/vcell-cli/src/main/java/org/vcell/cli/testsupport/FailureType.java @@ -0,0 +1,37 @@ +package org.vcell.cli.testsupport; + +@SuppressWarnings("unused") +public enum FailureType { + ARRAY_INDEX_OUT_OF_BOUNDS, + BAD_EULER_FORWARD, + DIVIDE_BY_ZERO, + EXPRESSIONS_DIFFERENT, + EXPRESSION_BINDING, + GEOMETRY_SPEC_DIFFERENT, + HDF5_FILE_ALREADY_EXISTS, // reports.h5 file already exists, so action is blocked. Fixed in branch to be merged in. + MATHOVERRIDES_SurfToVol, + MATH_GENERATION_FAILURE, + MATH_OVERRIDES_A_FUNCTION, + MATH_OVERRIDES_INVALID, + NULL_POINTER_EXCEPTION, + OPERATION_NOT_SUPPORTED, // VCell simply doesn't have the necessary features to run this archive. + SBML_IMPORT_FAILURE, + SEDML_DIFF_NUMBER_OF_BIOMODELS, + SEDML_ERRONEOUS_UNIT_SYSTEM, + SEDML_ERROR_CONSTRUCTING_SIMCONTEXT, + SEDML_MATH_OVERRIDE_NAMES_DIFFERENT, + SEDML_MATH_OVERRIDE_NOT_EQUIVALENT, + SEDML_NONSPATIAL_STOCH_HISTOGRAM, + SEDML_NO_MODELS_IN_OMEX, + SEDML_SIMCONTEXT_NOT_FOUND_BY_NAME, + SEDML_SIMULATION_NOT_FOUND_BY_NAME, + SEDML_UNSUPPORTED_ENTITY, + SEDML_UNSUPPORTED_MODEL_REFERENCE, // Model refers to either a non-existent model (invalid SED-ML) or to another model with changes (not supported yet) + SEDML_SBML_LEVEL_CHANGE, // unsupported SBML Level change within the SED-ML + TOO_SLOW, + UNCATETORIZED_FAULT, + UNITS_EXCEPTION, + UNKNOWN_IDENTIFIER, + SEDML_NO_SEDMLS_TO_EXECUTE, SEDML_PREPROCESS_FAILURE, UNSUPPORTED_NONSPATIAL_STOCH_HISTOGRAM + +} diff --git a/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedOmexExecTest.java b/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedOmexExecTest.java index b217dfd192..518f04e34e 100644 --- a/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedOmexExecTest.java +++ b/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedOmexExecTest.java @@ -2,11 +2,9 @@ import cbit.vcell.mapping.MappingException; import cbit.vcell.mongodb.VCMongoMessage; -import cbit.vcell.resource.NativeLib; import cbit.vcell.resource.PropertyLoader; import org.apache.commons.io.FileUtils; import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Tag; import org.junit.jupiter.params.ParameterizedTest; @@ -15,6 +13,7 @@ import org.vcell.cli.CLIPythonManager; import org.vcell.cli.CLIRecordable; import org.vcell.cli.PythonStreamException; +import org.vcell.cli.testsupport.FailureType; import org.vcell.sbml.vcell.SBMLImportException; import org.vcell.trace.Span; import org.vcell.trace.TraceEvent; @@ -53,42 +52,7 @@ public static void teardown() throws Exception { VCellUtilityHub.shutdown(); } - @SuppressWarnings("unused") - public enum FAULT { - ARRAY_INDEX_OUT_OF_BOUNDS, - BAD_EULER_FORWARD, - DIVIDE_BY_ZERO, - EXPRESSIONS_DIFFERENT, - EXPRESSION_BINDING, - GEOMETRY_SPEC_DIFFERENT, - HDF5_FILE_ALREADY_EXISTS, // reports.h5 file already exists, so action is blocked. Fixed in branch to be merged in. - MATHOVERRIDES_SurfToVol, - MATH_GENERATION_FAILURE, - MATH_OVERRIDES_A_FUNCTION, - MATH_OVERRIDES_INVALID, - NULL_POINTER_EXCEPTION, - OPERATION_NOT_SUPPORTED, // VCell simply doesn't have the necessary features to run this archive. - SBML_IMPORT_FAILURE, - SEDML_DIFF_NUMBER_OF_BIOMODELS, - SEDML_ERRONEOUS_UNIT_SYSTEM, - SEDML_ERROR_CONSTRUCTING_SIMCONTEXT, - SEDML_MATH_OVERRIDE_NAMES_DIFFERENT, - SEDML_MATH_OVERRIDE_NOT_EQUIVALENT, - SEDML_NONSPATIAL_STOCH_HISTOGRAM, - SEDML_NO_MODELS_IN_OMEX, - SEDML_SIMCONTEXT_NOT_FOUND_BY_NAME, - SEDML_SIMULATION_NOT_FOUND_BY_NAME, - SEDML_UNSUPPORTED_ENTITY, - SEDML_UNSUPPORTED_MODEL_REFERENCE, // Model refers to either a non-existent model (invalid SED-ML) or to another model with changes (not supported yet) - TOO_SLOW, - UNCATETORIZED_FAULT, - UNITS_EXCEPTION, - UNKNOWN_IDENTIFIER, - SEDML_NO_SEDMLS_TO_EXECUTE, SEDML_PREPROCESS_FAILURE, UNSUPPORTED_NONSPATIAL_STOCH_HISTOGRAM - - } - -// @SuppressWarnings("unused") + // @SuppressWarnings("unused") // static Set needToCurateModels(){ // // These models are skipped by BSTS, and we need to look to see if that was because we don't have a KISAO exact match // HashSet skippedModels = new HashSet<>(); @@ -113,29 +77,29 @@ static Set blacklistedModels(){ return blacklistSet; } - static Map knownFaults() { - HashMap faults = new HashMap<>(); + static Map knownFaults() { + HashMap faults = new HashMap<>(); faults.put("synths/sedml/SimulatorSupportsModelAttributeChanges/1.execute-should-fail.omex", - FAULT.SEDML_ERRONEOUS_UNIT_SYSTEM); + FailureType.SEDML_ERRONEOUS_UNIT_SYSTEM); faults.put("synths/sedml/SimulatorSupportsAddReplaceRemoveModelElementChanges/1.execute-should-fail.omex", - FAULT.SEDML_ERRONEOUS_UNIT_SYSTEM); + FailureType.SEDML_ERRONEOUS_UNIT_SYSTEM); faults.put("synths/sedml/SimulatorSupportsAddReplaceRemoveModelElementChanges/3.execute-should-fail.omex", - FAULT.SEDML_ERRONEOUS_UNIT_SYSTEM); + FailureType.SEDML_ERRONEOUS_UNIT_SYSTEM); //faults.put("misc-projects/BIOMD0000000005.omex", null); // works - faults.put("misc-projects/BIOMD0000000175.omex", FAULT.MATH_GENERATION_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_6652012719407098827omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: MappingException occurred: failed to generate math: Unable to sort, unknown identifier I_Net_E44PPI3K_binding - faults.put("misc-projects/BIOMD0000000302.omex", FAULT.MATH_GENERATION_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_8639905465728503850omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: 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. + faults.put("misc-projects/BIOMD0000000175.omex", FailureType.MATH_GENERATION_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_6652012719407098827omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: MappingException occurred: failed to generate math: Unable to sort, unknown identifier I_Net_E44PPI3K_binding + faults.put("misc-projects/BIOMD0000000302.omex", FailureType.MATH_GENERATION_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_8639905465728503850omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: 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. //faults.put("misc-projects/BIOMD0000000520.omex", null); // works!! - faults.put("misc-projects/BIOMD0000000561.omex", FAULT.UNCATETORIZED_FAULT); // (not a dynamic system - can't solve) | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_4023640363466179720omex) | SIMULATIONS_RUN(runSimulations) | BioModel(BSTS_OmexFile_4023640363466179720omex_Martins2013.sedml_model) | SIMULATION_RUN(task1_task1) | **** Error: Failed execution: Model 'BSTS_OmexFile_4023640363466179720omex_Martins2013.sedml_model' Task 'task1'. + faults.put("misc-projects/BIOMD0000000561.omex", FailureType.UNCATETORIZED_FAULT); // (not a dynamic system - can't solve) | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_4023640363466179720omex) | SIMULATIONS_RUN(runSimulations) | BioModel(BSTS_OmexFile_4023640363466179720omex_Martins2013.sedml_model) | SIMULATION_RUN(task1_task1) | **** Error: Failed execution: Model 'BSTS_OmexFile_4023640363466179720omex_Martins2013.sedml_model' Task 'task1'. //faults.put("misc-projects/BIOMD0000000569.omex", null); // works!! - faults.put("misc-projects/BIOMD0000000618.omex", FAULT.SBML_IMPORT_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_13012177097014737572omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Error processing model: model2 - couldn't find SBase with sid=null in SBMLSymbolMapping + faults.put("misc-projects/BIOMD0000000618.omex", FailureType.SBML_IMPORT_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_13012177097014737572omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Error processing model: model2 - couldn't find SBase with sid=null in SBMLSymbolMapping //faults.put("misc-projects/BIOMD0000000651.omex", null); // works!! //faults.put("misc-projects/BIOMD0000000668.omex", null); // works!! //faults.put("misc-projects/BIOMD0000000669.omex", null); // works!! //faults.put("misc-projects/BIOMD0000000676.omex", null); // works!! //faults.put("misc-projects/BIOMD0000000718.omex", null); // works!! - faults.put("misc-projects/BIOMD0000000731.omex", FAULT.SBML_IMPORT_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_7811157837075929926omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: Failed to translate SBML model into BioModel: 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. Check that you have provided the correct and full name (e.g. Ca_Cytosol). + faults.put("misc-projects/BIOMD0000000731.omex", FailureType.SBML_IMPORT_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_7811157837075929926omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: Failed to translate SBML model into BioModel: 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. Check that you have provided the correct and full name (e.g. Ca_Cytosol). //faults.put("misc-projects/BIOMD0000000842.omex", null); // works!! //faults.put("misc-projects/BIOMD0000000843.omex", null); // works!! //faults.put("misc-projects/BIOMD0000000932.omex", null); // works!! @@ -153,8 +117,8 @@ static Map knownFaults() { //faults.put("misc-projects/BIOMD0000001010.omex", null); // works!! //faults.put("misc-projects/BIOMD0000001014.omex", null); // works!! //faults.put("misc-projects/BIOMD0000001018.omex", null); // works!! - faults.put("misc-projects/BIOMD0000001061.omex", FAULT.SEDML_NO_SEDMLS_TO_EXECUTE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_6151950245083004772omex) | **** Error: writeErrorList(): BSTS_OmexFile_6151950245083004772omex | java.lang.RuntimeException: There are no SED-MLs in the archive to execute - faults.put("misc-projects/BIOMD0000001064.omex", FAULT.SEDML_NO_SEDMLS_TO_EXECUTE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_855930052238018769omex) | **** Error: writeErrorList(): BSTS_OmexFile_855930052238018769omex | java.lang.RuntimeException: There are no SED-MLs in the archive to execute + faults.put("misc-projects/BIOMD0000001061.omex", FailureType.SEDML_NO_SEDMLS_TO_EXECUTE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_6151950245083004772omex) | **** Error: writeErrorList(): BSTS_OmexFile_6151950245083004772omex | java.lang.RuntimeException: There are no SED-MLs in the archive to execute + faults.put("misc-projects/BIOMD0000001064.omex", FailureType.SEDML_NO_SEDMLS_TO_EXECUTE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_855930052238018769omex) | **** Error: writeErrorList(): BSTS_OmexFile_855930052238018769omex | java.lang.RuntimeException: There are no SED-MLs in the archive to execute //faults.put("misc-projects/BIOMD0000001072.omex", null); // works!! //faults.put("misc-projects/BIOMD0000001077.omex", null); // works!! @@ -254,7 +218,7 @@ public void writeImportErrorList(Exception e, String message) { @ParameterizedTest @MethodSource("testCases") public void testBSTSBasedOmex(String testCaseFilename) throws Exception { - FAULT knownFault = knownFaults().get(testCaseFilename); + FailureType knownFault = knownFaults().get(testCaseFilename); try { System.out.println("running test " + testCaseFilename); @@ -277,7 +241,7 @@ public void testBSTSBasedOmex(String testCaseFilename) throws Exception { System.err.println("=========== End Tracer report ==========="); e.printStackTrace(System.err); List errorEvents = Tracer.getErrors(); - FAULT fault = this.determineFault(e, errorEvents); + FailureType fault = this.determineFault(e, errorEvents); if (knownFault != null) { if (knownFault == fault) { System.err.println("Found expected error " + knownFault.name() + ": " + e.getMessage()); @@ -294,7 +258,7 @@ public void testBSTSBasedOmex(String testCaseFilename) throws Exception { } } - private FAULT determineFault(Throwable caughtException, List errorEvents){ // Throwable because Assertion Error + private FailureType determineFault(Throwable caughtException, List errorEvents){ // Throwable because Assertion Error String errorMessage = caughtException.getMessage(); if (errorMessage == null) errorMessage = ""; // Prevent nullptr exception @@ -302,41 +266,41 @@ private FAULT determineFault(Throwable caughtException, List errorEv errorMessage = caughtException.getCause().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 FAULT.SEDML_UNSUPPORTED_MODEL_REFERENCE; + return FailureType.SEDML_UNSUPPORTED_MODEL_REFERENCE; } else if (errorMessage.contains("System IO encountered a fatal error")){ Throwable subException = caughtException.getCause(); //String subMessage = (subException == null) ? "" : subException.getMessage(); if (subException instanceof FileAlreadyExistsException){ - return FAULT.HDF5_FILE_ALREADY_EXISTS; + return FailureType.HDF5_FILE_ALREADY_EXISTS; } } else if (errorMessage.contains("error while processing outputs: null")){ Throwable subException = caughtException.getCause(); if (subException instanceof ArrayIndexOutOfBoundsException){ - return FAULT.ARRAY_INDEX_OUT_OF_BOUNDS; + return FailureType.ARRAY_INDEX_OUT_OF_BOUNDS; } } else if (errorMessage.contains("nconsistent unit system in SBML model") || errorMessage.contains("ust be of type")){ - return FAULT.SEDML_ERRONEOUS_UNIT_SYSTEM; + return FailureType.SEDML_ERRONEOUS_UNIT_SYSTEM; } else if (errorMessage.contains("There are no SED-MLs in the archive to execute")) { - return FAULT.SEDML_NO_SEDMLS_TO_EXECUTE; + return FailureType.SEDML_NO_SEDMLS_TO_EXECUTE; } else if (errorMessage.contains("MappingException occurred: failed to generate math")) { - return FAULT.MATH_GENERATION_FAILURE; + return FailureType.MATH_GENERATION_FAILURE; } // else check Tracer error events for known faults for (TraceEvent event : errorEvents) { if (event.hasException(SBMLImportException.class)) { - return FAULT.SBML_IMPORT_FAILURE; + return FailureType.SBML_IMPORT_FAILURE; } if (event.span.getNestedContextName().contains(Span.ContextType.PROCESSING_SEDML.name()+"(preProcessDoc)")){ - return FAULT.SEDML_PREPROCESS_FAILURE; + return FailureType.SEDML_PREPROCESS_FAILURE; } if (event.hasException(MappingException.class)) { - return FAULT.MATH_GENERATION_FAILURE; + return FailureType.MATH_GENERATION_FAILURE; } } - return FAULT.UNCATETORIZED_FAULT; + return FailureType.UNCATETORIZED_FAULT; } } From 89dcc8604a085843f4460d976ff071790dd32082 Mon Sep 17 00:00:00 2001 From: jcschaff Date: Sat, 14 Dec 2024 14:16:15 -0500 Subject: [PATCH 2/7] WIP: OmexTextCase (ndjson, csv) unifies unit/nightly test reports --- .../vcell/cli/testsupport/OmexTestCase.java | 97 ++ .../cli/testsupport/OmexTestingDatabase.java | 60 + .../src/main/resources/known_problems.csv | 1177 +++++++++++++++++ 3 files changed, 1334 insertions(+) create mode 100644 vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestCase.java create mode 100644 vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java create mode 100644 vcell-cli/src/main/resources/known_problems.csv diff --git a/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestCase.java b/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestCase.java new file mode 100644 index 0000000000..57a3f7af49 --- /dev/null +++ b/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestCase.java @@ -0,0 +1,97 @@ +package org.vcell.cli.testsupport; + +public class OmexTestCase { + + public enum TestDataRepo { + vcell, sysbio + } + public enum TestCollection { + VCELL_BIOMD(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/misc-projects"), + VCELL_BSTS_VCML(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/vcml"), + VCELL_BSTS_SBML_CORE(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/sbml-core"), + VCELL_BSTS_SYNTHS(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/synths"), + SYSBIO_BIOMD(TestDataRepo.sysbio, "omex_files"); + + public final TestDataRepo repo; + public final String pathPrefix; + + TestCollection(TestDataRepo repo, String pathPrefix) { + this.repo = repo; + this.pathPrefix = pathPrefix; + } + } + public enum Status { + PASS, + FAIL, + SKIP + } + + public TestCollection test_collection; + public String file_path; + public Boolean should_fail; + public Status known_status; + public FailureType known_failure_type; + public String known_failure_desc; + + // from csv + public OmexTestCase(String[] csvLine) { + test_collection = TestCollection.valueOf(csvLine[0]); + file_path = csvLine[1]; + should_fail = Boolean.parseBoolean(csvLine[2]); + if (csvLine[3].trim().isEmpty()) { + known_status = null; + } else { + known_status = Status.valueOf(csvLine[3]); + } + if (csvLine[4].trim().isEmpty()) { + known_failure_type = null; + } else { + known_failure_type = FailureType.valueOf(csvLine[4]); + } + known_failure_desc = parseCsvStringField(csvLine[5]); + } + + // to csv + public String[] toCsvLine() { + return new String[] { + test_collection.toString(), + file_path, + should_fail.toString(), + (known_status !=null) ? known_status.toString() : "", + (known_failure_type !=null) ? known_failure_type.toString() : "", + printCsvStringField(known_failure_desc) + }; + } + + @Override + public String toString() { + return "OmexTestCase{" + + "test_collection=" + test_collection + + ", file_path='" + file_path + '\'' + + ", should_fail=" + should_fail + + ", known_status=" + known_status + + ", known_failure_type=" + known_failure_type + + ", known_failure_desc="+((known_failure_desc!=null)?('\'' + known_failure_desc + '\''):null) + + '}'; + } + private String parseCsvStringField(String str) { + str = str.strip(); + // strip leading and trailing double quotes + if (str.startsWith("\"") && str.endsWith("\"")) { + str = str.substring(1, str.length()-1); + } + // strip escaped double quotes + str = str.replace("\"\"", "\""); + if (str.isEmpty()){ + return null; + } + return str; + } + + private String printCsvStringField(String str) { + if (str == null){ + return ""; + } + return "\"" + str.replace("\"", "\"\"") + "\""; + } +} diff --git a/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java b/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java new file mode 100644 index 0000000000..1aa91d5656 --- /dev/null +++ b/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java @@ -0,0 +1,60 @@ +package org.vcell.cli.testsupport; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import java.io.BufferedReader; +import java.io.FileReader; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.stream.Collectors; + +public class OmexTestingDatabase { + + // read a newline-delimited json file into a list of OmexTextCase objects + public static List readOmexTestCasesFromNdjson(String path) throws IOException { + List testCases = new ArrayList<>(); + ObjectMapper objectMapper = new ObjectMapper(); + try (BufferedReader reader = new BufferedReader(new FileReader(path));) { + String line = reader.readLine(); + while (line != null) { + // use jackson objectmapper to read an OmexTestCase object from a json string + OmexTestCase testCase = objectMapper.readValue(line, OmexTestCase.class); + testCases.add(testCase); + } + } + return testCases; + } + + // read a csv file into a list of OmexTextCase objects + public static List readOmexTestCasesFromCsv(String path) throws IOException{ + List testCases = new ArrayList<>(); + try (BufferedReader reader = new BufferedReader(new FileReader(path));) { + String line = reader.readLine(); // read header + line = reader.readLine(); // read first line + while (line != null) { + line = line + " "; // add a space to the end of the line to handle empty fields at the end + line = line.replace(",,",", ,"); // replace empty fields with ", ," + String[] fields = line.split(","); + testCases.add(new OmexTestCase(fields)); + line = reader.readLine(); + } + } + return testCases; + } + + public static void main(String[] args) { + try { + List testCases = readOmexTestCasesFromCsv("/Users/jimschaff/Documents/workspace/vcell/vcell-cli/src/main/resources/known_problems.csv"); + ObjectMapper objectMapper = new ObjectMapper(); + for (OmexTestCase testCase : testCases) { + System.out.println(Arrays.stream(testCase.toCsvLine()).collect(Collectors.joining(","))); + System.out.println(testCase); + System.out.println(objectMapper.writeValueAsString(testCase)); + } + } catch (IOException e) { + e.printStackTrace(); + } + } +} diff --git a/vcell-cli/src/main/resources/known_problems.csv b/vcell-cli/src/main/resources/known_problems.csv new file mode 100644 index 0000000000..6e9693e4f6 --- /dev/null +++ b/vcell-cli/src/main/resources/known_problems.csv @@ -0,0 +1,1177 @@ +test_collection,file_path,should_fail,known_status,known_failure,known_failure_description +VCELL_BIOMD,BIOMD0000000005.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000175.omex,,FAIL,MATH_GENERATION_FAILURE,"unknown identifier I_Net_E44PPI3K_binding" +VCELL_BIOMD,BIOMD0000000302.omex,,FAIL,MATH_GENERATION_FAILURE,"Initial condition for variable 'h_post' references variable 'V_post'" +VCELL_BIOMD,BIOMD0000000520.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000561.omex,,FAIL,UNCATETORIZED_FAULT,"not a dynamic system - can't solve" +VCELL_BIOMD,BIOMD0000000569.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000618.omex,,FAIL,SBML_IMPORT_FAILURE,"couldn't find SBase with sid=null in SBMLSymbolMapping" +VCELL_BIOMD,BIOMD0000000651.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000668.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000669.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000676.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000679.omex,,,, +VCELL_BIOMD,BIOMD0000000680.omex,,,, +VCELL_BIOMD,BIOMD0000000681.omex,,,, +VCELL_BIOMD,BIOMD0000000684.omex,,,, +VCELL_BIOMD,BIOMD0000000718.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000724.omex,,,, +VCELL_BIOMD,BIOMD0000000731.omex,,FAIL,SBML_IMPORT_FAILURE,"Error binding global parameter 'Treg_origin_fraction_CD4' to model" +VCELL_BIOMD,BIOMD0000000842.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000843.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000915.omex,,,, +VCELL_BIOMD,BIOMD0000000932.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000944.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000951.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000957.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000968.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000972.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000973.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000983.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000985.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000989.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000991.omex,,PASS,, +VCELL_BIOMD,BIOMD0000000997.omex,,PASS,, +VCELL_BIOMD,BIOMD0000001010.omex,,PASS,, +VCELL_BIOMD,BIOMD0000001014.omex,,PASS,, +VCELL_BIOMD,BIOMD0000001018.omex,,PASS,, +VCELL_BIOMD,BIOMD0000001061.omex,,FAIL,SEDML_NO_SEDMLS_TO_EXECUTE,"There are no SED-MLs in the archive to execute" +VCELL_BIOMD,BIOMD0000001064.omex,,FAIL,SEDML_NO_SEDMLS_TO_EXECUTE,"There are no SED-MLs in the archive to execute" +VCELL_BIOMD,BIOMD0000001072.omex,,PASS,, +VCELL_BIOMD,BIOMD0000001077.omex,,PASS,, +VCELL_BSTS_VCML,Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength.omex,,,, +VCELL_BSTS_SBML_CORE,Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex,,,, +VCELL_BSTS_SBML_CORE,Parmar-BMC-Syst-Biol-2017-iron-distribution.omex,,,, +VCELL_BSTS_SBML_CORE,Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex,,,, +VCELL_BSTS_SBML_CORE,Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex,,,, +VCELL_BSTS_SBML_CORE,Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex,,,, +VCELL_BSTS_SBML_CORE,Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex,,,, +VCELL_BSTS_SBML_CORE,Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex,,,, +VCELL_BSTS_SBML_CORE,Tomida-EMBO-J-2003-NFAT-translocation.omex,,,, +VCELL_BSTS_SBML_CORE,Vilar-PNAS-2002-minimal-circardian-clock.omex,,,, +VCELL_BSTS_SBML_CORE,Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex,,,, +VCELL_BSTS_SBML_CORE,Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex,,,, +VCELL_BSTS_SBML_CORE,Elowitz-Nature-2000-Repressilator.omex,,,, +VCELL_BSTS_SBML_CORE,Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex,,,, +VCELL_BSTS_SYNTHS,docker_image/SingularityImageExecutesSimulationsSuccessfully/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,results_report/SimulatorGeneratesReportsOfSimulationResults/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,combine_archive/WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,combine_archive/WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,combine_archive/CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,combine_archive/CombineArchiveHasSedDocumentsInNestedDirectories/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,log/SimulatorReportsTheStatusOfTheExecutionOfSedDocuments/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,log/SimulatorReportsTheStatusOfTheExecutionOfSedOutputs/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,log/SimulatorReportsTheStatusOfTheExecutionOfCombineArchives/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,log/SimulatorReportsTheStatusOfTheExecutionOfSedTasks/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsAddReplaceRemoveModelElementChanges/3.execute-should-fail.omex,TRUE,FAIL,SEDML_ERRONEOUS_UNIT_SYSTEM, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsAddReplaceRemoveModelElementChanges/1.execute-should-fail.omex,TRUE,FAIL,SEDML_ERRONEOUS_UNIT_SYSTEM, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsAddReplaceRemoveModelElementChanges/2.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorProducesMultiplePlots/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorProducesMultiplePlots/2.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithChanges/1.execute-should-fail.omex,TRUE,SKIP,SEDML_SBML_LEVEL_CHANGE, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithChanges/2.execution-should-succeed.omex,,SKIP,SEDML_SBML_LEVEL_CHANGE, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsDataGeneratorsWithDifferentShapes/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithFunctionalRanges/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsDataSetsWithDifferentShapes/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithVectorRanges/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsComputeModelChanges/1.execute-should-fail.omex,TRUE,SKIP,SEDML_SBML_LEVEL_CHANGE, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsComputeModelChanges/2.execution-should-succeed.omex,,SKIP,SEDML_SBML_LEVEL_CHANGE, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsMultipleReportsPerSedDocument/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorProducesLogarithmic2DPlots/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorProducesLogarithmic2DPlots/2.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsModelAttributeChanges/1.execute-should-fail.omex,TRUE,FAIL,SEDML_ERRONEOUS_UNIT_SYSTEM, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsModelAttributeChanges/2.execution-should-succeed.omex,,SKIP,SEDML_SBML_LEVEL_CHANGE, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsMultipleTasksPerSedDocument/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsAlgorithmParameters/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/1.execute-should-fail.omex,TRUE,SKIP,SEDML_SBML_LEVEL_CHANGE, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2.execution-should-succeed.omex,,SKIP,SEDML_SBML_LEVEL_CHANGE, +VCELL_BSTS_SYNTHS,sedml/SimulatorProducesLinear2DPlots/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorProducesLinear2DPlots/2.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes/2.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorCanResolveModelSourcesDefinedByUriFragments/1.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsSubstitutingAlgorithms/3.execute-should-fail.omex,TRUE,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsSubstitutingAlgorithms/4.execution-should-succeed.omex,,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsSubstitutingAlgorithms/1.execute-should-fail.omex,TRUE,,, +VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsSubstitutingAlgorithms/2.execution-should-succeed.omex.omex,,,, +SYSBIO_BIOMD,BIOMD0000000001.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000002.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000003.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000004.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000005.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000006.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000007.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000008.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000009.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000010.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000011.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000012.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000013.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000014.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000015.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000016.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000017.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000018.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000019.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000020.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000021.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000022.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000023.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000024.omex,,,, +SYSBIO_BIOMD,BIOMD0000000025.omex,,,, +SYSBIO_BIOMD,BIOMD0000000026.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000027.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000028.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000029.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000030.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000031.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000032.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000033.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000034.omex,,,, +SYSBIO_BIOMD,BIOMD0000000035.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000036.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000037.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000038.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000039.omex,,,, +SYSBIO_BIOMD,BIOMD0000000040.omex,,,, +SYSBIO_BIOMD,BIOMD0000000041.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000042.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000043.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000044.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000045.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000046.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000047.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000048.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000049.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000050.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000051.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000052.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000053.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000054.omex,,,, +SYSBIO_BIOMD,BIOMD0000000055.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000056.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000057.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000058.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000059.omex,,,, +SYSBIO_BIOMD,BIOMD0000000060.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000061.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000062.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000063.omex,,,, +SYSBIO_BIOMD,BIOMD0000000064.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000065.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000066.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000067.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000068.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000069.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000070.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000071.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000072.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000073.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000074.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000075.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000076.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000077.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000078.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000079.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000080.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000081.omex,,,, +SYSBIO_BIOMD,BIOMD0000000082.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000083.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000084.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000085.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000086.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000087.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000088.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000089.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000090.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000091.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000092.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000093.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000094.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000095.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000096.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000097.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000098.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000099.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000100.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000101.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000102.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000103.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000104.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000105.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000106.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000107.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000108.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000109.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000110.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000111.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000112.omex,,,, +SYSBIO_BIOMD,BIOMD0000000113.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000114.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000115.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000116.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000117.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000118.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000119.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000120.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000121.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000122.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000123.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000124.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000125.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000126.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000127.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000128.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000129.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000130.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000131.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000132.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000133.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000134.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000135.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000136.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000137.omex,,,, +SYSBIO_BIOMD,BIOMD0000000138.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000139.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000140.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000141.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000142.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000143.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000144.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000145.omex,,,, +SYSBIO_BIOMD,BIOMD0000000146.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000147.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000148.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000149.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000150.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000151.omex,,,, +SYSBIO_BIOMD,BIOMD0000000152.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000153.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000154.omex,,,, +SYSBIO_BIOMD,BIOMD0000000155.omex,,,, +SYSBIO_BIOMD,BIOMD0000000156.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000157.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000158.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000159.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000160.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000161.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000162.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000163.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000164.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000165.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000166.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000167.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000168.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000169.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000170.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000171.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000172.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000173.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000174.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000175.omex,,,, +SYSBIO_BIOMD,BIOMD0000000176.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000177.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000178.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000179.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000180.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000181.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000182.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000183.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000184.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000185.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000186.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000187.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000188.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000189.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000190.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000191.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000192.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000193.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000194.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000195.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000196.omex,,,, +SYSBIO_BIOMD,BIOMD0000000197.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000198.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000199.omex,,,, +SYSBIO_BIOMD,BIOMD0000000200.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000201.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000202.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000203.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000204.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000205.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000206.omex,,,, +SYSBIO_BIOMD,BIOMD0000000207.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000208.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000209.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000210.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000211.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000212.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000213.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000214.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000215.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000216.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000217.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000218.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000219.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000220.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000221.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000222.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000223.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000224.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000225.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000226.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000227.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000228.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000229.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000230.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000231.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000232.omex,,,, +SYSBIO_BIOMD,BIOMD0000000233.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000234.omex,,,, +SYSBIO_BIOMD,BIOMD0000000235.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000236.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000237.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000238.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000239.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000240.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000241.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000242.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000243.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000244.omex,,,, +SYSBIO_BIOMD,BIOMD0000000245.omex,,,, +SYSBIO_BIOMD,BIOMD0000000246.omex,,,, +SYSBIO_BIOMD,BIOMD0000000247.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000248.omex,,,, +SYSBIO_BIOMD,BIOMD0000000249.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000250.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000251.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000252.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000253.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000254.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000255.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000256.omex,,,, +SYSBIO_BIOMD,BIOMD0000000257.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000258.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000259.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000260.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000261.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000262.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000263.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000264.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000265.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000266.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000267.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000268.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000269.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000270.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000271.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000272.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000273.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000274.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000275.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000276.omex,,,, +SYSBIO_BIOMD,BIOMD0000000277.omex,,,, +SYSBIO_BIOMD,BIOMD0000000278.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000279.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000280.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000281.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000282.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000283.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000284.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000285.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000286.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000287.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000288.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000289.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000290.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000291.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000292.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000293.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000294.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000295.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000296.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000297.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000298.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000299.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000300.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000301.omex,,,, +SYSBIO_BIOMD,BIOMD0000000302.omex,,,, +SYSBIO_BIOMD,BIOMD0000000303.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000304.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000305.omex,,,, +SYSBIO_BIOMD,BIOMD0000000306.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000307.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000308.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000309.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000310.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000311.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000312.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000313.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000314.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000315.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000316.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000317.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000318.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000319.omex,,,, +SYSBIO_BIOMD,BIOMD0000000320.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000321.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000322.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000323.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000324.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000325.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000326.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000327.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000328.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000329.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000330.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000331.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000332.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000333.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000334.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000335.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000336.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000337.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000338.omex,,,, +SYSBIO_BIOMD,BIOMD0000000339.omex,,,, +SYSBIO_BIOMD,BIOMD0000000340.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000341.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000342.omex,,,, +SYSBIO_BIOMD,BIOMD0000000343.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000344.omex,,,, +SYSBIO_BIOMD,BIOMD0000000345.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000346.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000347.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000348.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000349.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000350.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000351.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000352.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000353.omex,,,, +SYSBIO_BIOMD,BIOMD0000000354.omex,,,, +SYSBIO_BIOMD,BIOMD0000000355.omex,,,, +SYSBIO_BIOMD,BIOMD0000000356.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000357.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000358.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000359.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000360.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000361.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000362.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000363.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000364.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000365.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000366.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000367.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000368.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000369.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000370.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000371.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000372.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000373.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000374.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000375.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000376.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000377.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000378.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000379.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000380.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000381.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000382.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000383.omex,,,, +SYSBIO_BIOMD,BIOMD0000000384.omex,,,, +SYSBIO_BIOMD,BIOMD0000000385.omex,,,, +SYSBIO_BIOMD,BIOMD0000000386.omex,,,, +SYSBIO_BIOMD,BIOMD0000000387.omex,,,, +SYSBIO_BIOMD,BIOMD0000000388.omex,,,, +SYSBIO_BIOMD,BIOMD0000000389.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000390.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000391.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000392.omex,,,, +SYSBIO_BIOMD,BIOMD0000000393.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000394.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000395.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000396.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000397.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000398.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000399.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000400.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000401.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000402.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000403.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000404.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000405.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000406.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000407.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000408.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000409.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000410.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000411.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000412.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000413.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000414.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000415.omex,,,, +SYSBIO_BIOMD,BIOMD0000000416.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000417.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000418.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000419.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000420.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000421.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000422.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000423.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000424.omex,,,, +SYSBIO_BIOMD,BIOMD0000000425.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000426.omex,,,, +SYSBIO_BIOMD,BIOMD0000000427.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000428.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000429.omex,,,, +SYSBIO_BIOMD,BIOMD0000000430.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000431.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000432.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000433.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000434.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000435.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000436.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000437.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000438.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000439.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000440.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000441.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000442.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000443.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000444.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000445.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000446.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000447.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000448.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000449.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000450.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000451.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000452.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000453.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000454.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000455.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000456.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000457.omex,,,, +SYSBIO_BIOMD,BIOMD0000000458.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000459.omex,,,, +SYSBIO_BIOMD,BIOMD0000000460.omex,,,, +SYSBIO_BIOMD,BIOMD0000000461.omex,,,, +SYSBIO_BIOMD,BIOMD0000000462.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000463.omex,,,, +SYSBIO_BIOMD,BIOMD0000000464.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000465.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000466.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000467.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000468.omex,,,, +SYSBIO_BIOMD,BIOMD0000000469.omex,,,, +SYSBIO_BIOMD,BIOMD0000000470.omex,,,, +SYSBIO_BIOMD,BIOMD0000000471.omex,,,, +SYSBIO_BIOMD,BIOMD0000000472.omex,,,, +SYSBIO_BIOMD,BIOMD0000000473.omex,,,, +SYSBIO_BIOMD,BIOMD0000000474.omex,,,, +SYSBIO_BIOMD,BIOMD0000000475.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000476.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000477.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000478.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000479.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000480.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000481.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000482.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000483.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000484.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000485.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000486.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000487.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000488.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000489.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000490.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000491.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000492.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000493.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000494.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000495.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000496.omex,,,, +SYSBIO_BIOMD,BIOMD0000000497.omex,,,, +SYSBIO_BIOMD,BIOMD0000000498.omex,,,, +SYSBIO_BIOMD,BIOMD0000000499.omex,,,, +SYSBIO_BIOMD,BIOMD0000000500.omex,,,, +SYSBIO_BIOMD,BIOMD0000000501.omex,,,, +SYSBIO_BIOMD,BIOMD0000000502.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000503.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000504.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000505.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000506.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000507.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000508.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000509.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000510.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000511.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000512.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000513.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000514.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000515.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000516.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000517.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000518.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000519.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000520.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000521.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000522.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000523.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000524.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000525.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000526.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000527.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000528.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000529.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000530.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000531.omex,,,, +SYSBIO_BIOMD,BIOMD0000000532.omex,,,, +SYSBIO_BIOMD,BIOMD0000000533.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000534.omex,,,, +SYSBIO_BIOMD,BIOMD0000000535.omex,,,, +SYSBIO_BIOMD,BIOMD0000000536.omex,,,, +SYSBIO_BIOMD,BIOMD0000000537.omex,,,, +SYSBIO_BIOMD,BIOMD0000000538.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000539.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000540.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000541.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000542.omex,,,, +SYSBIO_BIOMD,BIOMD0000000543.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000544.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000545.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000546.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000547.omex,,,, +SYSBIO_BIOMD,BIOMD0000000548.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000549.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000550.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000551.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000552.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000553.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000554.omex,,,, +SYSBIO_BIOMD,BIOMD0000000555.omex,,,, +SYSBIO_BIOMD,BIOMD0000000556.omex,,,, +SYSBIO_BIOMD,BIOMD0000000557.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000558.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000559.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000560.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000561.omex,,,, +SYSBIO_BIOMD,BIOMD0000000562.omex,,,, +SYSBIO_BIOMD,BIOMD0000000563.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000564.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000565.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000566.omex,,,, +SYSBIO_BIOMD,BIOMD0000000567.omex,,,, +SYSBIO_BIOMD,BIOMD0000000568.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000569.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000570.omex,,,, +SYSBIO_BIOMD,BIOMD0000000571.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000572.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000573.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000574.omex,,,, +SYSBIO_BIOMD,BIOMD0000000575.omex,,,, +SYSBIO_BIOMD,BIOMD0000000576.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000577.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000578.omex,,,, +SYSBIO_BIOMD,BIOMD0000000579.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000580.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000581.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000582.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000583.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000584.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000585.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000586.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000587.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000588.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000589.omex,,,, +SYSBIO_BIOMD,BIOMD0000000590.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000591.omex,,,, +SYSBIO_BIOMD,BIOMD0000000592.omex,,,, +SYSBIO_BIOMD,BIOMD0000000593.omex,,,, +SYSBIO_BIOMD,BIOMD0000000594.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000595.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000596.omex,,,, +SYSBIO_BIOMD,BIOMD0000000597.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000598.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000599.omex,,,, +SYSBIO_BIOMD,BIOMD0000000600.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000601.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000602.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000603.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000604.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000605.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000606.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000607.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000608.omex,,,, +SYSBIO_BIOMD,BIOMD0000000609.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000610.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000611.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000612.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000613.omex,,,, +SYSBIO_BIOMD,BIOMD0000000614.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000615.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000616.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000617.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000618.omex,,,, +SYSBIO_BIOMD,BIOMD0000000619.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000620.omex,,,, +SYSBIO_BIOMD,BIOMD0000000621.omex,,,, +SYSBIO_BIOMD,BIOMD0000000622.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000623.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000624.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000625.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000626.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000627.omex,,,, +SYSBIO_BIOMD,BIOMD0000000628.omex,,,, +SYSBIO_BIOMD,BIOMD0000000629.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000630.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000631.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000632.omex,,,, +SYSBIO_BIOMD,BIOMD0000000633.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000634.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000635.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000636.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000637.omex,,,, +SYSBIO_BIOMD,BIOMD0000000638.omex,,,, +SYSBIO_BIOMD,BIOMD0000000639.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000640.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000641.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000642.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000643.omex,,,, +SYSBIO_BIOMD,BIOMD0000000644.omex,,,, +SYSBIO_BIOMD,BIOMD0000000645.omex,,,, +SYSBIO_BIOMD,BIOMD0000000646.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000647.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000648.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000650.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000651.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000652.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000653.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000654.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000655.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000656.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000657.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000658.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000659.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000660.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000661.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000662.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000663.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000664.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000665.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000666.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000667.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000668.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000669.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000670.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000671.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000672.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000673.omex,,,, +SYSBIO_BIOMD,BIOMD0000000674.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000675.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000676.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000677.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000678.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000679.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000680.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000681.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000682.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000683.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000684.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000685.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000686.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000687.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000688.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000689.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000690.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000691.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000692.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000693.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000695.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000696.omex,,,, +SYSBIO_BIOMD,BIOMD0000000697.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000698.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000699.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000700.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000701.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000702.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000703.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000704.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000705.omex,,,, +SYSBIO_BIOMD,BIOMD0000000706.omex,,,, +SYSBIO_BIOMD,BIOMD0000000707.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000708.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000709.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000710.omex,,,, +SYSBIO_BIOMD,BIOMD0000000711.omex,,,, +SYSBIO_BIOMD,BIOMD0000000712.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000713.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000714.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000715.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000716.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000717.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000718.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000719.omex,,,, +SYSBIO_BIOMD,BIOMD0000000720.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000721.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000722.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000723.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000724.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000725.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000726.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000727.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000728.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000729.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000730.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000731.omex,,,, +SYSBIO_BIOMD,BIOMD0000000732.omex,,,, +SYSBIO_BIOMD,BIOMD0000000733.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000734.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000735.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000736.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000737.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000738.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000739.omex,,,, +SYSBIO_BIOMD,BIOMD0000000740.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000741.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000742.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000743.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000744.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000745.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000746.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000747.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000748.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000749.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000750.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000751.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000752.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000753.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000754.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000755.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000756.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000757.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000758.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000759.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000760.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000761.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000762.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000763.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000764.omex,,,, +SYSBIO_BIOMD,BIOMD0000000765.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000766.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000767.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000768.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000769.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000770.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000771.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000772.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000773.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000774.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000775.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000776.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000777.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000778.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000779.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000780.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000781.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000782.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000783.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000784.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000785.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000786.omex,,,, +SYSBIO_BIOMD,BIOMD0000000787.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000788.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000789.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000790.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000791.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000792.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000793.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000794.omex,,,, +SYSBIO_BIOMD,BIOMD0000000795.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000796.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000797.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000798.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000799.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000800.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000801.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000802.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000803.omex,,,, +SYSBIO_BIOMD,BIOMD0000000804.omex,,,, +SYSBIO_BIOMD,BIOMD0000000805.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000806.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000807.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000808.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000809.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000810.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000811.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000812.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000813.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000814.omex,,,, +SYSBIO_BIOMD,BIOMD0000000815.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000816.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000817.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000818.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000819.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000820.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000821.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000822.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000823.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000824.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000825.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000826.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000827.omex,,,, +SYSBIO_BIOMD,BIOMD0000000828.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000829.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000830.omex,,,, +SYSBIO_BIOMD,BIOMD0000000831.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000832.omex,,,, +SYSBIO_BIOMD,BIOMD0000000833.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000834.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000835.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000836.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000837.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000838.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000839.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000840.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000841.omex,,,, +SYSBIO_BIOMD,BIOMD0000000842.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000843.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000844.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000845.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000846.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000847.omex,,,, +SYSBIO_BIOMD,BIOMD0000000848.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000849.omex,,,, +SYSBIO_BIOMD,BIOMD0000000850.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000851.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000852.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000853.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000854.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000855.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000856.omex,,,, +SYSBIO_BIOMD,BIOMD0000000857.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000858.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000859.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000860.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000861.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000862.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000863.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000864.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000865.omex,,,, +SYSBIO_BIOMD,BIOMD0000000866.omex,,,, +SYSBIO_BIOMD,BIOMD0000000867.omex,,,, +SYSBIO_BIOMD,BIOMD0000000868.omex,,,, +SYSBIO_BIOMD,BIOMD0000000869.omex,,,, +SYSBIO_BIOMD,BIOMD0000000870.omex,,,, +SYSBIO_BIOMD,BIOMD0000000871.omex,,,, +SYSBIO_BIOMD,BIOMD0000000872.omex,,,, +SYSBIO_BIOMD,BIOMD0000000873.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000874.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000875.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000876.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000877.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000878.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000879.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000880.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000881.omex,,,, +SYSBIO_BIOMD,BIOMD0000000882.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000883.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000884.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000885.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000886.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000887.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000888.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000889.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000890.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000891.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000892.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000893.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000894.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000895.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000896.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000897.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000898.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000899.omex,,,, +SYSBIO_BIOMD,BIOMD0000000900.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000901.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000902.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000903.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000904.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000905.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000906.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000907.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000908.omex,,,, +SYSBIO_BIOMD,BIOMD0000000909.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000910.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000911.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000912.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000913.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000914.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000915.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000916.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000917.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000918.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000919.omex,,,, +SYSBIO_BIOMD,BIOMD0000000920.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000921.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000922.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000923.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000924.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000925.omex,,,, +SYSBIO_BIOMD,BIOMD0000000926.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000927.omex,,,, +SYSBIO_BIOMD,BIOMD0000000928.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000929.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000930.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000931.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000932.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000933.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000934.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000935.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000936.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000937.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000938.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000939.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000940.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000941.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000942.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000943.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000944.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000945.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000946.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000947.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000948.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000949.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000950.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000951.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000952.omex,,,, +SYSBIO_BIOMD,BIOMD0000000953.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000954.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000955.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000956.omex,,,, +SYSBIO_BIOMD,BIOMD0000000957.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000958.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000959.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000960.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000961.omex,,,, +SYSBIO_BIOMD,BIOMD0000000962.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000963.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000964.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000965.omex,,,, +SYSBIO_BIOMD,BIOMD0000000966.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000967.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000968.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000969.omex,,,, +SYSBIO_BIOMD,BIOMD0000000970.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000971.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000972.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000973.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000974.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000975.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000976.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000977.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000978.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000979.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000980.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000981.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000982.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000983.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000984.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000985.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000986.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000987.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000988.omex,,,, +SYSBIO_BIOMD,BIOMD0000000989.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000990.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000991.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000994.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000995.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000996.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000997.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000998.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000000999.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001000.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001001.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001002.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001003.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001004.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001005.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001006.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001007.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001008.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001009.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001010.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001011.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001012.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001013.omex,,,, +SYSBIO_BIOMD,BIOMD0000001014.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001015.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001016.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001017.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001018.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001019.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001020.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001021.omex,,,, +SYSBIO_BIOMD,BIOMD0000001022.omex,,,, +SYSBIO_BIOMD,BIOMD0000001023.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001024.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001025.omex,,,, +SYSBIO_BIOMD,BIOMD0000001026.omex,,,, +SYSBIO_BIOMD,BIOMD0000001027.omex,,,, +SYSBIO_BIOMD,BIOMD0000001028.omex,,,, +SYSBIO_BIOMD,BIOMD0000001029.omex,,,, +SYSBIO_BIOMD,BIOMD0000001030.omex,,,, +SYSBIO_BIOMD,BIOMD0000001031.omex,,,, +SYSBIO_BIOMD,BIOMD0000001032.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001033.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001034.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001035.omex,,,, +SYSBIO_BIOMD,BIOMD0000001036.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001037.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001038.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001039.omex,,,, +SYSBIO_BIOMD,BIOMD0000001040.omex,,,, +SYSBIO_BIOMD,BIOMD0000001041.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001042.omex,,,, +SYSBIO_BIOMD,BIOMD0000001043.omex,,,, +SYSBIO_BIOMD,BIOMD0000001044.omex,,,, +SYSBIO_BIOMD,BIOMD0000001045.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001046.omex,,,, +SYSBIO_BIOMD,BIOMD0000001047.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001048.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001052.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001053.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001054.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001055.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001056.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001057.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001058.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001059.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001060.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001061.omex,,,, +SYSBIO_BIOMD,BIOMD0000001062.omex,,,, +SYSBIO_BIOMD,BIOMD0000001063.omex,,,, +SYSBIO_BIOMD,BIOMD0000001064.omex,,,, +SYSBIO_BIOMD,BIOMD0000001065.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001066.omex,,,, +SYSBIO_BIOMD,BIOMD0000001067.omex,,,, +SYSBIO_BIOMD,BIOMD0000001068.omex,,,, +SYSBIO_BIOMD,BIOMD0000001069.omex,,,, +SYSBIO_BIOMD,BIOMD0000001070.omex,,,, +SYSBIO_BIOMD,BIOMD0000001071.omex,,,, +SYSBIO_BIOMD,BIOMD0000001072.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001073.omex,,,, +SYSBIO_BIOMD,BIOMD0000001074.omex,,,, +SYSBIO_BIOMD,BIOMD0000001076.omex,,,, +SYSBIO_BIOMD,BIOMD0000001077.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001078.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001079.omex,,PASS,, +SYSBIO_BIOMD,BIOMD0000001080.omex,,PASS,, From 8d2dda0ca58e59cf68f1dad5b76485696208e4e9 Mon Sep 17 00:00:00 2001 From: jcschaff Date: Sun, 15 Dec 2024 19:57:49 -0500 Subject: [PATCH 3/7] drive BSTS testing using OmexTestCases from test_cases.ndjson --- .../vcell/cli/testsupport/OmexTestCase.java | 71 +- .../cli/testsupport/OmexTestingDatabase.java | 78 +- .../src/main/resources/known_problems.csv | 1177 ----------------- .../src/main/resources/test_cases.ndjson | 1176 ++++++++++++++++ .../vcell/cli/run/BSTSBasedOmexExecTest.java | 140 +- .../cli/run/BSTSBasedTestSuiteFiles.java | 139 +- 6 files changed, 1246 insertions(+), 1535 deletions(-) delete mode 100644 vcell-cli/src/main/resources/known_problems.csv create mode 100644 vcell-cli/src/main/resources/test_cases.ndjson diff --git a/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestCase.java b/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestCase.java index 57a3f7af49..6a1f44a3ce 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestCase.java +++ b/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestCase.java @@ -2,67 +2,19 @@ public class OmexTestCase { - public enum TestDataRepo { - vcell, sysbio - } - public enum TestCollection { - VCELL_BIOMD(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/misc-projects"), - VCELL_BSTS_VCML(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/vcml"), - VCELL_BSTS_SBML_CORE(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/sbml-core"), - VCELL_BSTS_SYNTHS(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/synths"), - SYSBIO_BIOMD(TestDataRepo.sysbio, "omex_files"); - - public final TestDataRepo repo; - public final String pathPrefix; - - TestCollection(TestDataRepo repo, String pathPrefix) { - this.repo = repo; - this.pathPrefix = pathPrefix; - } - } public enum Status { PASS, FAIL, SKIP } - public TestCollection test_collection; + public OmexTestingDatabase.TestCollection test_collection; public String file_path; public Boolean should_fail; public Status known_status; public FailureType known_failure_type; public String known_failure_desc; - // from csv - public OmexTestCase(String[] csvLine) { - test_collection = TestCollection.valueOf(csvLine[0]); - file_path = csvLine[1]; - should_fail = Boolean.parseBoolean(csvLine[2]); - if (csvLine[3].trim().isEmpty()) { - known_status = null; - } else { - known_status = Status.valueOf(csvLine[3]); - } - if (csvLine[4].trim().isEmpty()) { - known_failure_type = null; - } else { - known_failure_type = FailureType.valueOf(csvLine[4]); - } - known_failure_desc = parseCsvStringField(csvLine[5]); - } - - // to csv - public String[] toCsvLine() { - return new String[] { - test_collection.toString(), - file_path, - should_fail.toString(), - (known_status !=null) ? known_status.toString() : "", - (known_failure_type !=null) ? known_failure_type.toString() : "", - printCsvStringField(known_failure_desc) - }; - } - @Override public String toString() { return "OmexTestCase{" + @@ -74,24 +26,9 @@ public String toString() { ", known_failure_desc="+((known_failure_desc!=null)?('\'' + known_failure_desc + '\''):null) + '}'; } - private String parseCsvStringField(String str) { - str = str.strip(); - // strip leading and trailing double quotes - if (str.startsWith("\"") && str.endsWith("\"")) { - str = str.substring(1, str.length()-1); - } - // strip escaped double quotes - str = str.replace("\"\"", "\""); - if (str.isEmpty()){ - return null; - } - return str; - } - private String printCsvStringField(String str) { - if (str == null){ - return ""; - } - return "\"" + str.replace("\"", "\"\"") + "\""; + public boolean matchFileSuffix(String path) { + String fullPath = test_collection.pathPrefix + "/" + file_path; + return fullPath.endsWith(path); } } diff --git a/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java b/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java index 1aa91d5656..74f1ff0ff9 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java +++ b/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java @@ -1,60 +1,56 @@ package org.vcell.cli.testsupport; +import com.fasterxml.jackson.databind.MappingIterator; import com.fasterxml.jackson.databind.ObjectMapper; -import java.io.BufferedReader; -import java.io.FileReader; -import java.io.IOException; +import java.io.*; import java.util.ArrayList; -import java.util.Arrays; import java.util.List; -import java.util.stream.Collectors; +import java.util.NoSuchElementException; public class OmexTestingDatabase { - // read a newline-delimited json file into a list of OmexTextCase objects - public static List readOmexTestCasesFromNdjson(String path) throws IOException { - List testCases = new ArrayList<>(); - ObjectMapper objectMapper = new ObjectMapper(); - try (BufferedReader reader = new BufferedReader(new FileReader(path));) { - String line = reader.readLine(); - while (line != null) { - // use jackson objectmapper to read an OmexTestCase object from a json string - OmexTestCase testCase = objectMapper.readValue(line, OmexTestCase.class); - testCases.add(testCase); - } + public enum TestDataRepo { + vcell, sysbio + } + public enum TestCollection { + VCELL_BIOMD(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/misc-projects"), + VCELL_BSTS_VCML(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/vcml"), + VCELL_BSTS_SBML_CORE(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/sbml-core"), + VCELL_BSTS_SYNTHS(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/synths"), + SYSBIO_BIOMD(TestDataRepo.sysbio, "omex_files"); + + public final TestDataRepo repo; + public final String pathPrefix; + + TestCollection(TestDataRepo repo, String pathPrefix) { + this.repo = repo; + this.pathPrefix = pathPrefix; } - return testCases; } - // read a csv file into a list of OmexTextCase objects - public static List readOmexTestCasesFromCsv(String path) throws IOException{ + public static OmexTestCase queryOmexTestCase(List omexTestCases, String path) throws NoSuchElementException { + return omexTestCases.stream().filter(tc -> tc.matchFileSuffix(path)).findFirst().orElseThrow(); + } + + // read a newline-delimited json file into a list of OmexTextCase objects + public static List loadOmexTestCases() throws IOException { List testCases = new ArrayList<>(); - try (BufferedReader reader = new BufferedReader(new FileReader(path));) { - String line = reader.readLine(); // read header - line = reader.readLine(); // read first line - while (line != null) { - line = line + " "; // add a space to the end of the line to handle empty fields at the end - line = line.replace(",,",", ,"); // replace empty fields with ", ," - String[] fields = line.split(","); - testCases.add(new OmexTestCase(fields)); - line = reader.readLine(); + String fileName = "test_cases.ndjson"; + ObjectMapper objectMapper = new ObjectMapper(); + try (InputStream inputStream = OmexTestingDatabase.class.getResourceAsStream("/"+fileName);){ + if (inputStream == null) { + throw new FileNotFoundException("file not found! " + fileName); + } + try (BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream))) { + try (MappingIterator it = objectMapper.readerFor(OmexTestCase.class).readValues(reader)) { + while (it.hasNext()) { + testCases.add(it.next()); + } + } } } return testCases; } - public static void main(String[] args) { - try { - List testCases = readOmexTestCasesFromCsv("/Users/jimschaff/Documents/workspace/vcell/vcell-cli/src/main/resources/known_problems.csv"); - ObjectMapper objectMapper = new ObjectMapper(); - for (OmexTestCase testCase : testCases) { - System.out.println(Arrays.stream(testCase.toCsvLine()).collect(Collectors.joining(","))); - System.out.println(testCase); - System.out.println(objectMapper.writeValueAsString(testCase)); - } - } catch (IOException e) { - e.printStackTrace(); - } - } } diff --git a/vcell-cli/src/main/resources/known_problems.csv b/vcell-cli/src/main/resources/known_problems.csv deleted file mode 100644 index 6e9693e4f6..0000000000 --- a/vcell-cli/src/main/resources/known_problems.csv +++ /dev/null @@ -1,1177 +0,0 @@ -test_collection,file_path,should_fail,known_status,known_failure,known_failure_description -VCELL_BIOMD,BIOMD0000000005.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000175.omex,,FAIL,MATH_GENERATION_FAILURE,"unknown identifier I_Net_E44PPI3K_binding" -VCELL_BIOMD,BIOMD0000000302.omex,,FAIL,MATH_GENERATION_FAILURE,"Initial condition for variable 'h_post' references variable 'V_post'" -VCELL_BIOMD,BIOMD0000000520.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000561.omex,,FAIL,UNCATETORIZED_FAULT,"not a dynamic system - can't solve" -VCELL_BIOMD,BIOMD0000000569.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000618.omex,,FAIL,SBML_IMPORT_FAILURE,"couldn't find SBase with sid=null in SBMLSymbolMapping" -VCELL_BIOMD,BIOMD0000000651.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000668.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000669.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000676.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000679.omex,,,, -VCELL_BIOMD,BIOMD0000000680.omex,,,, -VCELL_BIOMD,BIOMD0000000681.omex,,,, -VCELL_BIOMD,BIOMD0000000684.omex,,,, -VCELL_BIOMD,BIOMD0000000718.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000724.omex,,,, -VCELL_BIOMD,BIOMD0000000731.omex,,FAIL,SBML_IMPORT_FAILURE,"Error binding global parameter 'Treg_origin_fraction_CD4' to model" -VCELL_BIOMD,BIOMD0000000842.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000843.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000915.omex,,,, -VCELL_BIOMD,BIOMD0000000932.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000944.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000951.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000957.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000968.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000972.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000973.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000983.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000985.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000989.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000991.omex,,PASS,, -VCELL_BIOMD,BIOMD0000000997.omex,,PASS,, -VCELL_BIOMD,BIOMD0000001010.omex,,PASS,, -VCELL_BIOMD,BIOMD0000001014.omex,,PASS,, -VCELL_BIOMD,BIOMD0000001018.omex,,PASS,, -VCELL_BIOMD,BIOMD0000001061.omex,,FAIL,SEDML_NO_SEDMLS_TO_EXECUTE,"There are no SED-MLs in the archive to execute" -VCELL_BIOMD,BIOMD0000001064.omex,,FAIL,SEDML_NO_SEDMLS_TO_EXECUTE,"There are no SED-MLs in the archive to execute" -VCELL_BIOMD,BIOMD0000001072.omex,,PASS,, -VCELL_BIOMD,BIOMD0000001077.omex,,PASS,, -VCELL_BSTS_VCML,Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength.omex,,,, -VCELL_BSTS_SBML_CORE,Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex,,,, -VCELL_BSTS_SBML_CORE,Parmar-BMC-Syst-Biol-2017-iron-distribution.omex,,,, -VCELL_BSTS_SBML_CORE,Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex,,,, -VCELL_BSTS_SBML_CORE,Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex,,,, -VCELL_BSTS_SBML_CORE,Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex,,,, -VCELL_BSTS_SBML_CORE,Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex,,,, -VCELL_BSTS_SBML_CORE,Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex,,,, -VCELL_BSTS_SBML_CORE,Tomida-EMBO-J-2003-NFAT-translocation.omex,,,, -VCELL_BSTS_SBML_CORE,Vilar-PNAS-2002-minimal-circardian-clock.omex,,,, -VCELL_BSTS_SBML_CORE,Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex,,,, -VCELL_BSTS_SBML_CORE,Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex,,,, -VCELL_BSTS_SBML_CORE,Elowitz-Nature-2000-Repressilator.omex,,,, -VCELL_BSTS_SBML_CORE,Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex,,,, -VCELL_BSTS_SYNTHS,docker_image/SingularityImageExecutesSimulationsSuccessfully/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,results_report/SimulatorGeneratesReportsOfSimulationResults/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,combine_archive/WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,combine_archive/WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,combine_archive/CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,combine_archive/CombineArchiveHasSedDocumentsInNestedDirectories/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,log/SimulatorReportsTheStatusOfTheExecutionOfSedDocuments/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,log/SimulatorReportsTheStatusOfTheExecutionOfSedOutputs/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,log/SimulatorReportsTheStatusOfTheExecutionOfCombineArchives/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,log/SimulatorReportsTheStatusOfTheExecutionOfSedTasks/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsAddReplaceRemoveModelElementChanges/3.execute-should-fail.omex,TRUE,FAIL,SEDML_ERRONEOUS_UNIT_SYSTEM, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsAddReplaceRemoveModelElementChanges/1.execute-should-fail.omex,TRUE,FAIL,SEDML_ERRONEOUS_UNIT_SYSTEM, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsAddReplaceRemoveModelElementChanges/2.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorProducesMultiplePlots/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorProducesMultiplePlots/2.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithChanges/1.execute-should-fail.omex,TRUE,SKIP,SEDML_SBML_LEVEL_CHANGE, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithChanges/2.execution-should-succeed.omex,,SKIP,SEDML_SBML_LEVEL_CHANGE, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsDataGeneratorsWithDifferentShapes/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithFunctionalRanges/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsDataSetsWithDifferentShapes/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithVectorRanges/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsComputeModelChanges/1.execute-should-fail.omex,TRUE,SKIP,SEDML_SBML_LEVEL_CHANGE, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsComputeModelChanges/2.execution-should-succeed.omex,,SKIP,SEDML_SBML_LEVEL_CHANGE, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsMultipleReportsPerSedDocument/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorProducesLogarithmic2DPlots/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorProducesLogarithmic2DPlots/2.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsModelAttributeChanges/1.execute-should-fail.omex,TRUE,FAIL,SEDML_ERRONEOUS_UNIT_SYSTEM, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsModelAttributeChanges/2.execution-should-succeed.omex,,SKIP,SEDML_SBML_LEVEL_CHANGE, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsMultipleTasksPerSedDocument/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsAlgorithmParameters/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/1.execute-should-fail.omex,TRUE,SKIP,SEDML_SBML_LEVEL_CHANGE, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2.execution-should-succeed.omex,,SKIP,SEDML_SBML_LEVEL_CHANGE, -VCELL_BSTS_SYNTHS,sedml/SimulatorProducesLinear2DPlots/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorProducesLinear2DPlots/2.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes/2.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorCanResolveModelSourcesDefinedByUriFragments/1.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsSubstitutingAlgorithms/3.execute-should-fail.omex,TRUE,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsSubstitutingAlgorithms/4.execution-should-succeed.omex,,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsSubstitutingAlgorithms/1.execute-should-fail.omex,TRUE,,, -VCELL_BSTS_SYNTHS,sedml/SimulatorSupportsSubstitutingAlgorithms/2.execution-should-succeed.omex.omex,,,, -SYSBIO_BIOMD,BIOMD0000000001.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000002.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000003.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000004.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000005.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000006.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000007.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000008.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000009.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000010.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000011.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000012.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000013.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000014.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000015.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000016.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000017.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000018.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000019.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000020.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000021.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000022.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000023.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000024.omex,,,, -SYSBIO_BIOMD,BIOMD0000000025.omex,,,, -SYSBIO_BIOMD,BIOMD0000000026.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000027.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000028.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000029.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000030.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000031.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000032.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000033.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000034.omex,,,, -SYSBIO_BIOMD,BIOMD0000000035.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000036.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000037.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000038.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000039.omex,,,, -SYSBIO_BIOMD,BIOMD0000000040.omex,,,, -SYSBIO_BIOMD,BIOMD0000000041.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000042.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000043.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000044.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000045.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000046.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000047.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000048.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000049.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000050.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000051.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000052.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000053.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000054.omex,,,, -SYSBIO_BIOMD,BIOMD0000000055.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000056.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000057.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000058.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000059.omex,,,, -SYSBIO_BIOMD,BIOMD0000000060.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000061.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000062.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000063.omex,,,, -SYSBIO_BIOMD,BIOMD0000000064.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000065.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000066.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000067.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000068.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000069.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000070.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000071.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000072.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000073.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000074.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000075.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000076.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000077.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000078.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000079.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000080.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000081.omex,,,, -SYSBIO_BIOMD,BIOMD0000000082.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000083.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000084.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000085.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000086.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000087.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000088.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000089.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000090.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000091.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000092.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000093.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000094.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000095.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000096.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000097.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000098.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000099.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000100.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000101.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000102.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000103.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000104.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000105.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000106.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000107.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000108.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000109.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000110.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000111.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000112.omex,,,, -SYSBIO_BIOMD,BIOMD0000000113.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000114.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000115.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000116.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000117.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000118.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000119.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000120.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000121.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000122.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000123.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000124.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000125.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000126.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000127.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000128.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000129.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000130.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000131.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000132.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000133.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000134.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000135.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000136.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000137.omex,,,, -SYSBIO_BIOMD,BIOMD0000000138.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000139.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000140.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000141.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000142.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000143.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000144.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000145.omex,,,, -SYSBIO_BIOMD,BIOMD0000000146.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000147.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000148.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000149.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000150.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000151.omex,,,, -SYSBIO_BIOMD,BIOMD0000000152.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000153.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000154.omex,,,, -SYSBIO_BIOMD,BIOMD0000000155.omex,,,, -SYSBIO_BIOMD,BIOMD0000000156.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000157.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000158.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000159.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000160.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000161.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000162.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000163.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000164.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000165.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000166.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000167.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000168.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000169.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000170.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000171.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000172.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000173.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000174.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000175.omex,,,, -SYSBIO_BIOMD,BIOMD0000000176.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000177.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000178.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000179.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000180.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000181.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000182.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000183.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000184.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000185.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000186.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000187.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000188.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000189.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000190.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000191.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000192.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000193.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000194.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000195.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000196.omex,,,, -SYSBIO_BIOMD,BIOMD0000000197.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000198.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000199.omex,,,, -SYSBIO_BIOMD,BIOMD0000000200.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000201.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000202.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000203.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000204.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000205.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000206.omex,,,, -SYSBIO_BIOMD,BIOMD0000000207.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000208.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000209.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000210.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000211.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000212.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000213.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000214.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000215.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000216.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000217.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000218.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000219.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000220.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000221.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000222.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000223.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000224.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000225.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000226.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000227.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000228.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000229.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000230.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000231.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000232.omex,,,, -SYSBIO_BIOMD,BIOMD0000000233.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000234.omex,,,, -SYSBIO_BIOMD,BIOMD0000000235.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000236.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000237.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000238.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000239.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000240.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000241.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000242.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000243.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000244.omex,,,, -SYSBIO_BIOMD,BIOMD0000000245.omex,,,, -SYSBIO_BIOMD,BIOMD0000000246.omex,,,, -SYSBIO_BIOMD,BIOMD0000000247.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000248.omex,,,, -SYSBIO_BIOMD,BIOMD0000000249.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000250.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000251.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000252.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000253.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000254.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000255.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000256.omex,,,, -SYSBIO_BIOMD,BIOMD0000000257.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000258.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000259.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000260.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000261.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000262.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000263.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000264.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000265.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000266.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000267.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000268.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000269.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000270.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000271.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000272.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000273.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000274.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000275.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000276.omex,,,, -SYSBIO_BIOMD,BIOMD0000000277.omex,,,, -SYSBIO_BIOMD,BIOMD0000000278.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000279.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000280.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000281.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000282.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000283.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000284.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000285.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000286.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000287.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000288.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000289.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000290.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000291.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000292.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000293.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000294.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000295.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000296.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000297.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000298.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000299.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000300.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000301.omex,,,, -SYSBIO_BIOMD,BIOMD0000000302.omex,,,, -SYSBIO_BIOMD,BIOMD0000000303.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000304.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000305.omex,,,, -SYSBIO_BIOMD,BIOMD0000000306.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000307.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000308.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000309.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000310.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000311.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000312.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000313.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000314.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000315.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000316.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000317.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000318.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000319.omex,,,, -SYSBIO_BIOMD,BIOMD0000000320.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000321.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000322.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000323.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000324.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000325.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000326.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000327.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000328.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000329.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000330.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000331.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000332.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000333.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000334.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000335.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000336.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000337.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000338.omex,,,, -SYSBIO_BIOMD,BIOMD0000000339.omex,,,, -SYSBIO_BIOMD,BIOMD0000000340.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000341.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000342.omex,,,, -SYSBIO_BIOMD,BIOMD0000000343.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000344.omex,,,, -SYSBIO_BIOMD,BIOMD0000000345.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000346.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000347.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000348.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000349.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000350.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000351.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000352.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000353.omex,,,, -SYSBIO_BIOMD,BIOMD0000000354.omex,,,, -SYSBIO_BIOMD,BIOMD0000000355.omex,,,, -SYSBIO_BIOMD,BIOMD0000000356.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000357.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000358.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000359.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000360.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000361.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000362.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000363.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000364.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000365.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000366.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000367.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000368.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000369.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000370.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000371.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000372.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000373.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000374.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000375.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000376.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000377.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000378.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000379.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000380.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000381.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000382.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000383.omex,,,, -SYSBIO_BIOMD,BIOMD0000000384.omex,,,, -SYSBIO_BIOMD,BIOMD0000000385.omex,,,, -SYSBIO_BIOMD,BIOMD0000000386.omex,,,, -SYSBIO_BIOMD,BIOMD0000000387.omex,,,, -SYSBIO_BIOMD,BIOMD0000000388.omex,,,, -SYSBIO_BIOMD,BIOMD0000000389.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000390.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000391.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000392.omex,,,, -SYSBIO_BIOMD,BIOMD0000000393.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000394.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000395.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000396.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000397.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000398.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000399.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000400.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000401.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000402.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000403.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000404.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000405.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000406.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000407.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000408.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000409.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000410.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000411.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000412.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000413.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000414.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000415.omex,,,, -SYSBIO_BIOMD,BIOMD0000000416.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000417.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000418.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000419.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000420.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000421.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000422.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000423.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000424.omex,,,, -SYSBIO_BIOMD,BIOMD0000000425.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000426.omex,,,, -SYSBIO_BIOMD,BIOMD0000000427.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000428.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000429.omex,,,, -SYSBIO_BIOMD,BIOMD0000000430.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000431.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000432.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000433.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000434.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000435.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000436.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000437.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000438.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000439.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000440.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000441.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000442.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000443.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000444.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000445.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000446.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000447.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000448.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000449.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000450.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000451.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000452.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000453.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000454.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000455.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000456.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000457.omex,,,, -SYSBIO_BIOMD,BIOMD0000000458.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000459.omex,,,, -SYSBIO_BIOMD,BIOMD0000000460.omex,,,, -SYSBIO_BIOMD,BIOMD0000000461.omex,,,, -SYSBIO_BIOMD,BIOMD0000000462.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000463.omex,,,, -SYSBIO_BIOMD,BIOMD0000000464.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000465.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000466.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000467.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000468.omex,,,, -SYSBIO_BIOMD,BIOMD0000000469.omex,,,, -SYSBIO_BIOMD,BIOMD0000000470.omex,,,, -SYSBIO_BIOMD,BIOMD0000000471.omex,,,, -SYSBIO_BIOMD,BIOMD0000000472.omex,,,, -SYSBIO_BIOMD,BIOMD0000000473.omex,,,, -SYSBIO_BIOMD,BIOMD0000000474.omex,,,, -SYSBIO_BIOMD,BIOMD0000000475.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000476.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000477.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000478.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000479.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000480.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000481.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000482.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000483.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000484.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000485.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000486.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000487.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000488.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000489.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000490.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000491.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000492.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000493.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000494.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000495.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000496.omex,,,, -SYSBIO_BIOMD,BIOMD0000000497.omex,,,, -SYSBIO_BIOMD,BIOMD0000000498.omex,,,, -SYSBIO_BIOMD,BIOMD0000000499.omex,,,, -SYSBIO_BIOMD,BIOMD0000000500.omex,,,, -SYSBIO_BIOMD,BIOMD0000000501.omex,,,, -SYSBIO_BIOMD,BIOMD0000000502.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000503.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000504.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000505.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000506.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000507.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000508.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000509.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000510.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000511.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000512.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000513.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000514.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000515.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000516.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000517.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000518.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000519.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000520.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000521.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000522.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000523.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000524.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000525.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000526.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000527.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000528.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000529.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000530.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000531.omex,,,, -SYSBIO_BIOMD,BIOMD0000000532.omex,,,, -SYSBIO_BIOMD,BIOMD0000000533.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000534.omex,,,, -SYSBIO_BIOMD,BIOMD0000000535.omex,,,, -SYSBIO_BIOMD,BIOMD0000000536.omex,,,, -SYSBIO_BIOMD,BIOMD0000000537.omex,,,, -SYSBIO_BIOMD,BIOMD0000000538.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000539.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000540.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000541.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000542.omex,,,, -SYSBIO_BIOMD,BIOMD0000000543.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000544.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000545.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000546.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000547.omex,,,, -SYSBIO_BIOMD,BIOMD0000000548.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000549.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000550.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000551.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000552.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000553.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000554.omex,,,, -SYSBIO_BIOMD,BIOMD0000000555.omex,,,, -SYSBIO_BIOMD,BIOMD0000000556.omex,,,, -SYSBIO_BIOMD,BIOMD0000000557.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000558.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000559.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000560.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000561.omex,,,, -SYSBIO_BIOMD,BIOMD0000000562.omex,,,, -SYSBIO_BIOMD,BIOMD0000000563.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000564.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000565.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000566.omex,,,, -SYSBIO_BIOMD,BIOMD0000000567.omex,,,, -SYSBIO_BIOMD,BIOMD0000000568.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000569.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000570.omex,,,, -SYSBIO_BIOMD,BIOMD0000000571.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000572.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000573.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000574.omex,,,, -SYSBIO_BIOMD,BIOMD0000000575.omex,,,, -SYSBIO_BIOMD,BIOMD0000000576.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000577.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000578.omex,,,, -SYSBIO_BIOMD,BIOMD0000000579.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000580.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000581.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000582.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000583.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000584.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000585.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000586.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000587.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000588.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000589.omex,,,, -SYSBIO_BIOMD,BIOMD0000000590.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000591.omex,,,, -SYSBIO_BIOMD,BIOMD0000000592.omex,,,, -SYSBIO_BIOMD,BIOMD0000000593.omex,,,, -SYSBIO_BIOMD,BIOMD0000000594.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000595.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000596.omex,,,, -SYSBIO_BIOMD,BIOMD0000000597.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000598.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000599.omex,,,, -SYSBIO_BIOMD,BIOMD0000000600.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000601.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000602.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000603.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000604.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000605.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000606.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000607.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000608.omex,,,, -SYSBIO_BIOMD,BIOMD0000000609.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000610.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000611.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000612.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000613.omex,,,, -SYSBIO_BIOMD,BIOMD0000000614.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000615.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000616.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000617.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000618.omex,,,, -SYSBIO_BIOMD,BIOMD0000000619.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000620.omex,,,, -SYSBIO_BIOMD,BIOMD0000000621.omex,,,, -SYSBIO_BIOMD,BIOMD0000000622.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000623.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000624.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000625.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000626.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000627.omex,,,, -SYSBIO_BIOMD,BIOMD0000000628.omex,,,, -SYSBIO_BIOMD,BIOMD0000000629.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000630.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000631.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000632.omex,,,, -SYSBIO_BIOMD,BIOMD0000000633.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000634.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000635.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000636.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000637.omex,,,, -SYSBIO_BIOMD,BIOMD0000000638.omex,,,, -SYSBIO_BIOMD,BIOMD0000000639.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000640.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000641.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000642.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000643.omex,,,, -SYSBIO_BIOMD,BIOMD0000000644.omex,,,, -SYSBIO_BIOMD,BIOMD0000000645.omex,,,, -SYSBIO_BIOMD,BIOMD0000000646.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000647.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000648.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000650.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000651.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000652.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000653.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000654.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000655.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000656.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000657.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000658.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000659.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000660.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000661.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000662.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000663.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000664.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000665.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000666.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000667.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000668.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000669.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000670.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000671.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000672.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000673.omex,,,, -SYSBIO_BIOMD,BIOMD0000000674.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000675.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000676.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000677.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000678.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000679.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000680.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000681.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000682.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000683.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000684.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000685.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000686.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000687.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000688.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000689.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000690.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000691.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000692.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000693.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000695.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000696.omex,,,, -SYSBIO_BIOMD,BIOMD0000000697.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000698.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000699.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000700.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000701.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000702.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000703.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000704.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000705.omex,,,, -SYSBIO_BIOMD,BIOMD0000000706.omex,,,, -SYSBIO_BIOMD,BIOMD0000000707.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000708.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000709.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000710.omex,,,, -SYSBIO_BIOMD,BIOMD0000000711.omex,,,, -SYSBIO_BIOMD,BIOMD0000000712.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000713.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000714.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000715.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000716.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000717.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000718.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000719.omex,,,, -SYSBIO_BIOMD,BIOMD0000000720.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000721.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000722.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000723.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000724.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000725.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000726.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000727.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000728.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000729.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000730.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000731.omex,,,, -SYSBIO_BIOMD,BIOMD0000000732.omex,,,, -SYSBIO_BIOMD,BIOMD0000000733.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000734.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000735.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000736.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000737.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000738.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000739.omex,,,, -SYSBIO_BIOMD,BIOMD0000000740.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000741.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000742.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000743.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000744.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000745.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000746.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000747.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000748.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000749.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000750.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000751.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000752.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000753.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000754.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000755.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000756.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000757.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000758.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000759.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000760.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000761.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000762.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000763.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000764.omex,,,, -SYSBIO_BIOMD,BIOMD0000000765.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000766.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000767.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000768.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000769.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000770.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000771.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000772.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000773.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000774.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000775.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000776.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000777.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000778.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000779.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000780.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000781.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000782.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000783.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000784.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000785.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000786.omex,,,, -SYSBIO_BIOMD,BIOMD0000000787.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000788.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000789.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000790.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000791.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000792.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000793.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000794.omex,,,, -SYSBIO_BIOMD,BIOMD0000000795.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000796.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000797.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000798.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000799.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000800.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000801.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000802.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000803.omex,,,, -SYSBIO_BIOMD,BIOMD0000000804.omex,,,, -SYSBIO_BIOMD,BIOMD0000000805.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000806.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000807.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000808.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000809.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000810.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000811.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000812.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000813.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000814.omex,,,, -SYSBIO_BIOMD,BIOMD0000000815.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000816.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000817.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000818.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000819.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000820.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000821.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000822.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000823.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000824.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000825.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000826.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000827.omex,,,, -SYSBIO_BIOMD,BIOMD0000000828.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000829.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000830.omex,,,, -SYSBIO_BIOMD,BIOMD0000000831.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000832.omex,,,, -SYSBIO_BIOMD,BIOMD0000000833.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000834.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000835.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000836.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000837.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000838.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000839.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000840.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000841.omex,,,, -SYSBIO_BIOMD,BIOMD0000000842.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000843.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000844.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000845.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000846.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000847.omex,,,, -SYSBIO_BIOMD,BIOMD0000000848.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000849.omex,,,, -SYSBIO_BIOMD,BIOMD0000000850.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000851.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000852.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000853.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000854.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000855.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000856.omex,,,, -SYSBIO_BIOMD,BIOMD0000000857.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000858.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000859.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000860.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000861.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000862.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000863.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000864.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000865.omex,,,, -SYSBIO_BIOMD,BIOMD0000000866.omex,,,, -SYSBIO_BIOMD,BIOMD0000000867.omex,,,, -SYSBIO_BIOMD,BIOMD0000000868.omex,,,, -SYSBIO_BIOMD,BIOMD0000000869.omex,,,, -SYSBIO_BIOMD,BIOMD0000000870.omex,,,, -SYSBIO_BIOMD,BIOMD0000000871.omex,,,, -SYSBIO_BIOMD,BIOMD0000000872.omex,,,, -SYSBIO_BIOMD,BIOMD0000000873.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000874.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000875.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000876.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000877.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000878.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000879.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000880.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000881.omex,,,, -SYSBIO_BIOMD,BIOMD0000000882.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000883.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000884.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000885.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000886.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000887.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000888.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000889.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000890.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000891.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000892.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000893.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000894.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000895.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000896.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000897.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000898.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000899.omex,,,, -SYSBIO_BIOMD,BIOMD0000000900.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000901.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000902.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000903.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000904.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000905.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000906.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000907.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000908.omex,,,, -SYSBIO_BIOMD,BIOMD0000000909.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000910.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000911.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000912.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000913.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000914.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000915.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000916.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000917.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000918.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000919.omex,,,, -SYSBIO_BIOMD,BIOMD0000000920.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000921.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000922.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000923.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000924.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000925.omex,,,, -SYSBIO_BIOMD,BIOMD0000000926.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000927.omex,,,, -SYSBIO_BIOMD,BIOMD0000000928.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000929.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000930.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000931.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000932.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000933.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000934.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000935.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000936.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000937.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000938.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000939.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000940.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000941.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000942.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000943.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000944.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000945.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000946.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000947.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000948.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000949.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000950.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000951.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000952.omex,,,, -SYSBIO_BIOMD,BIOMD0000000953.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000954.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000955.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000956.omex,,,, -SYSBIO_BIOMD,BIOMD0000000957.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000958.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000959.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000960.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000961.omex,,,, -SYSBIO_BIOMD,BIOMD0000000962.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000963.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000964.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000965.omex,,,, -SYSBIO_BIOMD,BIOMD0000000966.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000967.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000968.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000969.omex,,,, -SYSBIO_BIOMD,BIOMD0000000970.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000971.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000972.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000973.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000974.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000975.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000976.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000977.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000978.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000979.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000980.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000981.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000982.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000983.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000984.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000985.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000986.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000987.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000988.omex,,,, -SYSBIO_BIOMD,BIOMD0000000989.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000990.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000991.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000994.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000995.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000996.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000997.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000998.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000000999.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001000.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001001.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001002.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001003.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001004.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001005.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001006.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001007.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001008.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001009.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001010.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001011.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001012.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001013.omex,,,, -SYSBIO_BIOMD,BIOMD0000001014.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001015.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001016.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001017.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001018.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001019.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001020.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001021.omex,,,, -SYSBIO_BIOMD,BIOMD0000001022.omex,,,, -SYSBIO_BIOMD,BIOMD0000001023.omex,,PASS,, -SYSBIO_BIOMD,BIOMD0000001024.omex,,PASS,, 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+{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001058.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001059.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001060.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001061.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001062.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001063.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001064.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001065.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001066.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001067.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001068.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001069.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001070.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001071.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001072.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001073.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001074.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001076.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001077.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001078.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001079.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001080.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} diff --git a/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedOmexExecTest.java b/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedOmexExecTest.java index 518f04e34e..9b1e67d1b8 100644 --- a/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedOmexExecTest.java +++ b/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedOmexExecTest.java @@ -14,6 +14,8 @@ import org.vcell.cli.CLIRecordable; import org.vcell.cli.PythonStreamException; import org.vcell.cli.testsupport.FailureType; +import org.vcell.cli.testsupport.OmexTestCase; +import org.vcell.cli.testsupport.OmexTestingDatabase; import org.vcell.sbml.vcell.SBMLImportException; import org.vcell.trace.Span; import org.vcell.trace.TraceEvent; @@ -34,6 +36,7 @@ @Tag("BSTS_IT") public class BSTSBasedOmexExecTest { + static List omexTestCases; @BeforeAll public static void setup() throws PythonStreamException, IOException { @@ -44,6 +47,7 @@ public static void setup() throws PythonStreamException, IOException { VCMongoMessage.enabled = false; CLIPythonManager.getInstance().instantiatePythonProcess(); + omexTestCases = OmexTestingDatabase.loadOmexTestCases(); } @AfterAll @@ -52,129 +56,9 @@ public static void teardown() throws Exception { VCellUtilityHub.shutdown(); } - // @SuppressWarnings("unused") -// static Set needToCurateModels(){ -// // These models are skipped by BSTS, and we need to look to see if that was because we don't have a KISAO exact match -// HashSet skippedModels = new HashSet<>(); -// skippedModels.add("sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex"); -// skippedModels.add("sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex"); -// skippedModels.add("sbml-core/Tomida-EMBO-J-2003-NFAT-translocation.omex"); -// skippedModels.add("sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex"); -// skippedModels.add("sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex"); -// return skippedModels; -// } - - static Set blacklistedModels(){ - HashSet blacklistSet = new HashSet<>(); - // We don't support the following tests because they require a model change for SBML Level - blacklistSet.add("synths/sedml/SimulatorSupportsRepeatedTasksWithChanges/2.execution-should-succeed.omex"); - blacklistSet.add("synths/sedml/SimulatorSupportsComputeModelChanges/1.execute-should-fail.omex"); - blacklistSet.add("synths/sedml/SimulatorSupportsComputeModelChanges/2.execution-should-succeed.omex"); - blacklistSet.add("synths/sedml/SimulatorSupportsModelAttributeChanges/2.execution-should-succeed.omex"); - blacklistSet.add("synths/sedml/SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/1.execute-should-fail.omex"); - blacklistSet.add("synths/sedml/SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2.execution-should-succeed.omex"); - blacklistSet.add("synths/sedml/SimulatorSupportsRepeatedTasksWithChanges/1.execute-should-fail.omex"); - return blacklistSet; - } - - static Map knownFaults() { - HashMap faults = new HashMap<>(); - faults.put("synths/sedml/SimulatorSupportsModelAttributeChanges/1.execute-should-fail.omex", - FailureType.SEDML_ERRONEOUS_UNIT_SYSTEM); - faults.put("synths/sedml/SimulatorSupportsAddReplaceRemoveModelElementChanges/1.execute-should-fail.omex", - FailureType.SEDML_ERRONEOUS_UNIT_SYSTEM); - faults.put("synths/sedml/SimulatorSupportsAddReplaceRemoveModelElementChanges/3.execute-should-fail.omex", - FailureType.SEDML_ERRONEOUS_UNIT_SYSTEM); - - - //faults.put("misc-projects/BIOMD0000000005.omex", null); // works - faults.put("misc-projects/BIOMD0000000175.omex", FailureType.MATH_GENERATION_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_6652012719407098827omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: MappingException occurred: failed to generate math: Unable to sort, unknown identifier I_Net_E44PPI3K_binding - faults.put("misc-projects/BIOMD0000000302.omex", FailureType.MATH_GENERATION_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_8639905465728503850omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: 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. - //faults.put("misc-projects/BIOMD0000000520.omex", null); // works!! - faults.put("misc-projects/BIOMD0000000561.omex", FailureType.UNCATETORIZED_FAULT); // (not a dynamic system - can't solve) | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_4023640363466179720omex) | SIMULATIONS_RUN(runSimulations) | BioModel(BSTS_OmexFile_4023640363466179720omex_Martins2013.sedml_model) | SIMULATION_RUN(task1_task1) | **** Error: Failed execution: Model 'BSTS_OmexFile_4023640363466179720omex_Martins2013.sedml_model' Task 'task1'. - //faults.put("misc-projects/BIOMD0000000569.omex", null); // works!! - faults.put("misc-projects/BIOMD0000000618.omex", FailureType.SBML_IMPORT_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_13012177097014737572omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Error processing model: model2 - couldn't find SBase with sid=null in SBMLSymbolMapping - //faults.put("misc-projects/BIOMD0000000651.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000668.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000669.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000676.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000718.omex", null); // works!! - faults.put("misc-projects/BIOMD0000000731.omex", FailureType.SBML_IMPORT_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_7811157837075929926omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: Failed to translate SBML model into BioModel: 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. Check that you have provided the correct and full name (e.g. Ca_Cytosol). - //faults.put("misc-projects/BIOMD0000000842.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000843.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000932.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000944.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000951.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000957.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000968.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000972.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000973.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000983.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000985.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000989.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000991.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000000997.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000001010.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000001014.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000001018.omex", null); // works!! - faults.put("misc-projects/BIOMD0000001061.omex", FailureType.SEDML_NO_SEDMLS_TO_EXECUTE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_6151950245083004772omex) | **** Error: writeErrorList(): BSTS_OmexFile_6151950245083004772omex | java.lang.RuntimeException: There are no SED-MLs in the archive to execute - faults.put("misc-projects/BIOMD0000001064.omex", FailureType.SEDML_NO_SEDMLS_TO_EXECUTE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_855930052238018769omex) | **** Error: writeErrorList(): BSTS_OmexFile_855930052238018769omex | java.lang.RuntimeException: There are no SED-MLs in the archive to execute - //faults.put("misc-projects/BIOMD0000001072.omex", null); // works!! - //faults.put("misc-projects/BIOMD0000001077.omex", null); // works!! - - return faults; - } - - public static Collection testCases() { - Set modelsToFilter = new HashSet<>(); - Predicate filter; - -// modelsToFilter.addAll(needToCurateModels()); // Comment out if checking that current version will satisfy BSTS - modelsToFilter.addAll(blacklistedModels()); - filter = (t) -> !modelsToFilter.contains(t); - + public static Collection testCases() throws IOException { + Predicate filter = (t) -> !OmexTestCase.Status.SKIP.equals(t.known_status); return Arrays.stream(BSTSBasedTestSuiteFiles.getBSTSTestCases()).filter(filter).collect(Collectors.toList()); -// return Arrays.asList( -// "misc-projects/BIOMD0000000561.omex", -// "misc-projects/BIOMD0000000679.omex", -// "misc-projects/BIOMD0000000680.omex", -// "misc-projects/BIOMD0000000681.omex", -// "misc-projects/BIOMD0000000684.omex", -// "misc-projects/BIOMD0000000724.omex", -// "misc-projects/BIOMD0000000915.omex" -// "misc-projects/BIOMD0000000302.omex", -// "misc-projects/BIOMD0000000175.omex", -// "misc-projects/BIOMD0000000618.omex", -// "misc-projects/BIOMD0000000569.omex", -// "misc-projects/BIOMD0000000973.omex", -// "misc-projects/BIOMD0000000520.omex", -// "misc-projects/BIOMD0000000731.omex", -// "misc-projects/BIOMD0000001061.omex", -// "misc-projects/BIOMD0000001064.omex", -// "misc-projects/BIOMD0000000651.omex", -// "misc-projects/BIOMD0000000668.omex", -// "misc-projects/BIOMD0000000669.omex", -// "misc-projects/BIOMD0000000676.omex", -// "misc-projects/BIOMD0000000718.omex", -// "misc-projects/BIOMD0000000842.omex", -// "misc-projects/BIOMD0000000843.omex", -// "misc-projects/BIOMD0000000932.omex", -// "misc-projects/BIOMD0000000944.omex", -// "misc-projects/BIOMD0000000951.omex", -// "misc-projects/BIOMD0000000957.omex", -// "misc-projects/BIOMD0000000968.omex", -// "misc-projects/BIOMD0000000972.omex", -// "misc-projects/BIOMD0000000983.omex", -// "misc-projects/BIOMD0000000985.omex", -// "misc-projects/BIOMD0000000989.omex", -// "misc-projects/BIOMD0000000991.omex", -// "misc-projects/BIOMD0000000997.omex", -// "misc-projects/BIOMD0000001010.omex", -// "misc-projects/BIOMD0000001014.omex", -// "misc-projects/BIOMD0000001018.omex", -// "misc-projects/BIOMD0000001072.omex", -// "misc-projects/BIOMD0000001077.omex" -// ); } static class TestRecorder implements CLIRecordable { @@ -217,13 +101,13 @@ public void writeImportErrorList(Exception e, String message) { @ParameterizedTest @MethodSource("testCases") - public void testBSTSBasedOmex(String testCaseFilename) throws Exception { - FailureType knownFault = knownFaults().get(testCaseFilename); + public void testBSTSBasedOmex(OmexTestCase testCase) throws Exception { + FailureType knownFault = testCase.known_failure_type; try { - System.out.println("running test " + testCaseFilename); + System.out.println("running testCase " + testCase.test_collection + " " + testCase.file_path); Path outdirPath = Files.createTempDirectory("BSTS_OmexExecTest"); - InputStream omexInputStream = BSTSBasedTestSuiteFiles.getBSTSTestCase(testCaseFilename); + InputStream omexInputStream = BSTSBasedTestSuiteFiles.getBSTSTestCase(testCase); Path omexFile = Files.createTempFile("BSTS_OmexFile_", "omex"); FileUtils.copyInputStreamToFile(omexInputStream, omexFile.toFile()); @@ -251,10 +135,10 @@ public void testBSTSBasedOmex(String testCaseFilename) throws Exception { return; } } else { - fail("unexpected error, add FAULT." + fault.name() + " to " + testCaseFilename); + fail("unexpected error, add FAULT." + fault.name() + " to " + testCase.test_collection + " in knownFaults()"); } - throw new Exception("Test error: " + testCaseFilename + " failed improperly", e); + throw new Exception("Test error: " + testCase + " failed improperly", e); } } diff --git a/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedTestSuiteFiles.java b/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedTestSuiteFiles.java index a04f127e16..57cb164e61 100644 --- a/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedTestSuiteFiles.java +++ b/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedTestSuiteFiles.java @@ -3,142 +3,36 @@ import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Tag; import org.junit.jupiter.api.Test; +import org.vcell.cli.testsupport.OmexTestCase; +import org.vcell.cli.testsupport.OmexTestingDatabase; import java.io.FileNotFoundException; +import java.io.IOException; import java.io.InputStream; -import java.util.Arrays; +import java.util.List; import java.util.function.Predicate; @Tag("Fast") public class BSTSBasedTestSuiteFiles { - private final static String[] allTestFiles = new String[]{ - "misc-projects/BIOMD0000000005.omex", - "misc-projects/BIOMD0000000175.omex", - "misc-projects/BIOMD0000000302.omex", - "misc-projects/BIOMD0000000520.omex", - "misc-projects/BIOMD0000000561.omex", - "misc-projects/BIOMD0000000569.omex", - "misc-projects/BIOMD0000000618.omex", - "misc-projects/BIOMD0000000651.omex", - "misc-projects/BIOMD0000000668.omex", - "misc-projects/BIOMD0000000669.omex", - "misc-projects/BIOMD0000000676.omex", - "misc-projects/BIOMD0000000679.omex", - "misc-projects/BIOMD0000000680.omex", - "misc-projects/BIOMD0000000681.omex", - "misc-projects/BIOMD0000000684.omex", - "misc-projects/BIOMD0000000718.omex", - "misc-projects/BIOMD0000000724.omex", - "misc-projects/BIOMD0000000731.omex", - "misc-projects/BIOMD0000000842.omex", - "misc-projects/BIOMD0000000843.omex", - "misc-projects/BIOMD0000000915.omex", - "misc-projects/BIOMD0000000932.omex", - "misc-projects/BIOMD0000000944.omex", - "misc-projects/BIOMD0000000951.omex", - "misc-projects/BIOMD0000000957.omex", - "misc-projects/BIOMD0000000968.omex", - "misc-projects/BIOMD0000000972.omex", - "misc-projects/BIOMD0000000973.omex", - "misc-projects/BIOMD0000000983.omex", - "misc-projects/BIOMD0000000985.omex", - "misc-projects/BIOMD0000000989.omex", - "misc-projects/BIOMD0000000991.omex", - "misc-projects/BIOMD0000000997.omex", - "misc-projects/BIOMD0000001010.omex", - "misc-projects/BIOMD0000001014.omex", - "misc-projects/BIOMD0000001018.omex", - "misc-projects/BIOMD0000001061.omex", - "misc-projects/BIOMD0000001064.omex", - "misc-projects/BIOMD0000001072.omex", - "misc-projects/BIOMD0000001077.omex", - "vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength.omex", - "sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex", - "sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex", - "sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex", - "sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex", - "sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex", - "sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex", - "sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex", - "sbml-core/Tomida-EMBO-J-2003-NFAT-translocation.omex", - "sbml-core/Vilar-PNAS-2002-minimal-circardian-clock.omex", - "sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex", - "sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex", - "sbml-core/Elowitz-Nature-2000-Repressilator.omex", - "sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex", - "synths/docker_image/SingularityImageExecutesSimulationsSuccessfully/1.execution-should-succeed.omex", - "synths/results_report/SimulatorGeneratesReportsOfSimulationResults/1.execution-should-succeed.omex", - "synths/combine_archive/WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile/1.execution-should-succeed.omex", - "synths/combine_archive/WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments/1.execution-should-succeed.omex", - "synths/combine_archive/CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories/1.execution-should-succeed.omex", - "synths/combine_archive/CombineArchiveHasSedDocumentsInNestedDirectories/1.execution-should-succeed.omex", - "synths/log/SimulatorReportsTheStatusOfTheExecutionOfSedDocuments/1.execution-should-succeed.omex", - "synths/log/SimulatorReportsTheStatusOfTheExecutionOfSedOutputs/1.execution-should-succeed.omex", - "synths/log/SimulatorReportsTheStatusOfTheExecutionOfCombineArchives/1.execution-should-succeed.omex", - "synths/log/SimulatorReportsTheStatusOfTheExecutionOfSedTasks/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsAddReplaceRemoveModelElementChanges/3.execute-should-fail.omex", - "synths/sedml/SimulatorSupportsAddReplaceRemoveModelElementChanges/1.execute-should-fail.omex", - "synths/sedml/SimulatorSupportsAddReplaceRemoveModelElementChanges/2.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1.execution-should-succeed.omex", - "synths/sedml/SimulatorProducesMultiplePlots/1.execution-should-succeed.omex", - "synths/sedml/SimulatorProducesMultiplePlots/2.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsRepeatedTasksWithChanges/1.execute-should-fail.omex", - "synths/sedml/SimulatorSupportsRepeatedTasksWithChanges/2.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsDataGeneratorsWithDifferentShapes/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsRepeatedTasksWithFunctionalRanges/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsDataSetsWithDifferentShapes/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsRepeatedTasksWithVectorRanges/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsComputeModelChanges/1.execute-should-fail.omex", - "synths/sedml/SimulatorSupportsComputeModelChanges/2.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsMultipleReportsPerSedDocument/1.execution-should-succeed.omex", - "synths/sedml/SimulatorProducesLogarithmic2DPlots/1.execution-should-succeed.omex", - "synths/sedml/SimulatorProducesLogarithmic2DPlots/2.execution-should-succeed.omex", - "synths/sedml/SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsModelAttributeChanges/1.execute-should-fail.omex", - "synths/sedml/SimulatorSupportsModelAttributeChanges/2.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsMultipleTasksPerSedDocument/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsAlgorithmParameters/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/1.execute-should-fail.omex", - "synths/sedml/SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2.execution-should-succeed.omex", - "synths/sedml/SimulatorProducesLinear2DPlots/1.execution-should-succeed.omex", - "synths/sedml/SimulatorProducesLinear2DPlots/2.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes/2.execution-should-succeed.omex", - "synths/sedml/SimulatorCanResolveModelSourcesDefinedByUriFragments/1.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsSubstitutingAlgorithms/3.execute-should-fail.omex", - "synths/sedml/SimulatorSupportsSubstitutingAlgorithms/4.execution-should-succeed.omex", - "synths/sedml/SimulatorSupportsSubstitutingAlgorithms/1.execute-should-fail.omex", - "synths/sedml/SimulatorSupportsSubstitutingAlgorithms/2.execution-should-succeed.omex" - }; - public static String[] getBSTSTestCases() { - Predicate testFilter = t -> true; + public static OmexTestCase[] getBSTSTestCases() throws IOException { + List allTestCases = OmexTestingDatabase.loadOmexTestCases(); + Predicate testFilter = t -> t.test_collection.repo == OmexTestingDatabase.TestDataRepo.vcell; - return Arrays.stream(allTestFiles).filter(testFilter).toArray(String[]::new); + return allTestCases.stream().filter(testFilter).toArray(OmexTestCase[]::new); } - public static InputStream getBSTSTestCase(String testFile) { - if (!Arrays.stream(allTestFiles).anyMatch(file -> file.equals(testFile))) { - throw new RuntimeException("file not found for VCell Published Test Suite test "+testFile); - } - try { - return getFileFromResourceAsStream(testFile); - }catch (FileNotFoundException e){ - throw new RuntimeException("failed to find test case file '"+testFile+"': " + e.getMessage(), e); - } + public static InputStream getBSTSTestCase(OmexTestCase testCase) throws FileNotFoundException { + String fullPath = testCase.test_collection.pathPrefix + "/" + testCase.file_path; + // keep the path starting with "/bsts-omex" + String path = fullPath.substring(fullPath.indexOf("/bsts-omex")); + return getFileFromResourceAsStream(path); } private static InputStream getFileFromResourceAsStream(String fileName) throws FileNotFoundException { - InputStream inputStream = BSTSBasedTestSuiteFiles.class.getResourceAsStream("/bsts-omex/"+fileName); + InputStream inputStream = BSTSBasedTestSuiteFiles.class.getResourceAsStream(fileName); if (inputStream == null) { throw new FileNotFoundException("file not found! " + fileName); } else { @@ -147,8 +41,9 @@ private static InputStream getFileFromResourceAsStream(String fileName) throws F } @Test - public void test_read_BSTS_omex_file() { - InputStream inputStream = getBSTSTestCase(allTestFiles[0]); + public void test_read_BSTS_omex_file() throws IOException { + List allTestCases = OmexTestingDatabase.loadOmexTestCases(); + InputStream inputStream = getBSTSTestCase(allTestCases.get(0)); Assertions.assertTrue(inputStream != null); } From 6cffa13106563746595cc939aaaca3ea0a28b695 Mon Sep 17 00:00:00 2001 From: jcschaff Date: Sun, 15 Dec 2024 20:16:15 -0500 Subject: [PATCH 4/7] correct typo in test case filename in test_cases.ndjson --- vcell-cli/src/main/resources/test_cases.ndjson | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vcell-cli/src/main/resources/test_cases.ndjson b/vcell-cli/src/main/resources/test_cases.ndjson index dcb527b794..23267b18ab 100644 --- a/vcell-cli/src/main/resources/test_cases.ndjson +++ b/vcell-cli/src/main/resources/test_cases.ndjson @@ -101,7 +101,7 @@ {"test_collection":"VCELL_BSTS_SYNTHS","file_path":"sedml/SimulatorSupportsSubstitutingAlgorithms/3.execute-should-fail.omex","should_fail":true,"known_status":null,"known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_BSTS_SYNTHS","file_path":"sedml/SimulatorSupportsSubstitutingAlgorithms/4.execution-should-succeed.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_BSTS_SYNTHS","file_path":"sedml/SimulatorSupportsSubstitutingAlgorithms/1.execute-should-fail.omex","should_fail":true,"known_status":null,"known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_BSTS_SYNTHS","file_path":"sedml/SimulatorSupportsSubstitutingAlgorithms/2.execution-should-succeed.omex.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"VCELL_BSTS_SYNTHS","file_path":"sedml/SimulatorSupportsSubstitutingAlgorithms/2.execution-should-succeed.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000001.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000002.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000003.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} From b369a80a02eb70d4dc7135ad922656785f2d7699 Mon Sep 17 00:00:00 2001 From: jcschaff Date: Mon, 16 Dec 2024 15:51:20 -0500 Subject: [PATCH 5/7] WIP: introducing OmexExecSummary to unify reporting of errors --- .../java/org/vcell/cli/CLIStandalone.java | 2 + .../main/java/org/vcell/cli/CliTracer.java | 31 +++++ .../java/org/vcell/cli/run/ExecuteImpl.java | 1 - .../org/vcell/cli/run/ExecuteOmexCommand.java | 127 ++++++++++++++++++ .../java/org/vcell/cli/run/ExecutionJob.java | 4 +- .../cli/testsupport/OmexExecSummary.java | 24 ++++ .../cli/testsupport/OmexTestingDatabase.java | 93 ++++++++++++- .../vcell/cli/run/BSTSBasedOmexExecTest.java | 67 ++------- .../testsupport/TestOmexTestingDatabase.java | 63 +++++++++ 9 files changed, 348 insertions(+), 64 deletions(-) create mode 100644 vcell-cli/src/main/java/org/vcell/cli/CliTracer.java create mode 100644 vcell-cli/src/main/java/org/vcell/cli/run/ExecuteOmexCommand.java create mode 100644 vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexExecSummary.java create mode 100644 vcell-cli/src/test/java/org/vcell/cli/testsupport/TestOmexTestingDatabase.java diff --git a/vcell-cli/src/main/java/org/vcell/cli/CLIStandalone.java b/vcell-cli/src/main/java/org/vcell/cli/CLIStandalone.java index 0059febcf0..05d2fc8e2e 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/CLIStandalone.java +++ b/vcell-cli/src/main/java/org/vcell/cli/CLIStandalone.java @@ -2,6 +2,7 @@ import org.vcell.cli.biosimulation.BiosimulationsCommand; import org.vcell.cli.run.ExecuteCommand; +import org.vcell.cli.run.ExecuteOmexCommand; import org.vcell.cli.sbml.ModelCommand; import org.vcell.cli.vcml.*; @@ -22,6 +23,7 @@ ExportOmexBatchCommand.class, ImportOmexCommand.class, ImportOmexBatchCommand.class, + ExecuteOmexCommand.class, ExecuteCommand.class, VersionCommand.class, ModelCommand.class, diff --git a/vcell-cli/src/main/java/org/vcell/cli/CliTracer.java b/vcell-cli/src/main/java/org/vcell/cli/CliTracer.java new file mode 100644 index 0000000000..da0d6d6046 --- /dev/null +++ b/vcell-cli/src/main/java/org/vcell/cli/CliTracer.java @@ -0,0 +1,31 @@ +package org.vcell.cli; + +import org.vcell.trace.Tracer; + +public class CliTracer implements CLIRecordable { + + @Override + public void writeDetailedErrorList(Exception e, String message) { + Tracer.failure(e, "writeDetailedErrorList(): "+message); + } + @Override + public void writeFullSuccessList(String message) { + Tracer.success("writeFullSuccessList(): " + message); + } + @Override + public void writeErrorList(Exception e, String message) { + Tracer.failure(e, "writeErrorList(): " + message); + } + @Override + public void writeDetailedResultList(String message) { + Tracer.log("writeDetailedResultList(): "+message); + } + @Override + public void writeSpatialList(String message) { + Tracer.log("writeSpatialList(): "+message); + } + @Override + public void writeImportErrorList(Exception e, String message) { + Tracer.failure(e, "writeImportErrorList(): " + message); + } +} diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteImpl.java b/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteImpl.java index 9e08a57d14..1774e4131d 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteImpl.java +++ b/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteImpl.java @@ -4,7 +4,6 @@ import cbit.vcell.solver.ode.ODESolverResultSet; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; -import org.jlibsedml.XMLException; import org.vcell.cli.CLIRecordable; import org.vcell.cli.PythonStreamException; import org.vcell.cli.exceptions.ExecutionException; diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteOmexCommand.java b/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteOmexCommand.java new file mode 100644 index 0000000000..36485a5660 --- /dev/null +++ b/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteOmexCommand.java @@ -0,0 +1,127 @@ +package org.vcell.cli.run; + +import com.fasterxml.jackson.databind.ObjectMapper; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.core.LoggerContext; +import org.vcell.cli.CLIPythonManager; +import org.vcell.cli.CLIRecordable; +import org.vcell.cli.CliTracer; +import org.vcell.cli.testsupport.OmexExecSummary; +import org.vcell.cli.testsupport.OmexTestingDatabase; +import org.vcell.trace.Tracer; +import org.vcell.util.FileUtils; +import org.vcell.util.exe.Executable; +import picocli.CommandLine.Command; +import picocli.CommandLine.Option; + +import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import java.util.Date; +import java.util.concurrent.Callable; + +@Command(name = "execute-omex", description = "run .vcml or .omex files via Python API") +public class ExecuteOmexCommand implements Callable { + + private final static Logger logger = LogManager.getLogger(ExecuteOmexCommand.class); + + @Option(names = { "-i", "--inputFilePath" }, required = true, description = "Path to a COMBINE/OMEX archive file") + private File inputFilePath; + + @Option(names = { "-o", "--outputFilePath"}, required = true, description = "Directory to save outputs") + private File outputFilePath; + + @Option(names = {"--keepTempFiles"}, defaultValue = "false") + private boolean bKeepTempFiles = false; + + @Option(names = {"--exactMatchOnly"}, defaultValue = "false") + private boolean bExactMatchOnly = false; + + @Option(names = "--small-mesh", defaultValue = "false", description = "force spatial simulations to have a very small mesh to make execution faster") + private boolean bSmallMeshOverride = false; + + @Option(names = {"--encapsulateOutput"}, defaultValue = "true", description = + "VCell will encapsulate output results in a sub directory when executing with a single input archive; has no effect when providing an input directory") + private boolean bEncapsulateOutput = true; + + @Option(names = {"--timeout_ms"}, defaultValue = "600000", description = "executable wall clock timeout in milliseconds") + // timeout for compiled solver running long jobs; default 10 minutes + private long EXECUTABLE_MAX_WALLCLOCK_MILLIS = 10 * 60 * 1000; + + @Option(names = {"-h", "--help"}, description = "show this help message and exit", usageHelp = true) + private boolean help = false; + + @Option(names = {"-d", "--debug"}, description = "full application debug mode") + private boolean bDebug = false; + + @Option(names = {"-q", "--quiet"}, description = "suppress all console output") + private boolean bQuiet = false; + + + public Integer call() { + + CLIRecordable cliTracer = new CliTracer(); + try { + if (bDebug && bQuiet) { + System.err.println("cannot specify both debug and quiet, try --help for usage"); + return 1; + } + Level logLevel; + if (!bQuiet && bDebug) { + logLevel = Level.DEBUG; + } else if (bQuiet) { + logLevel = Level.OFF; + } else { + logLevel = logger.getLevel(); + } + + if (this.inputFilePath.exists() && !this.inputFilePath.isFile()) { + System.err.println("Input path must be a file"); + return 1; + } + if (this.outputFilePath.exists() && !this.outputFilePath.isDirectory()) { + System.err.println("Output path must be a directory"); + return 1; + } + + LoggerContext config = (LoggerContext)(LogManager.getContext(false)); + config.getConfiguration().getLoggerConfig(LogManager.getLogger("org.vcell").getName()).setLevel(logLevel); + config.getConfiguration().getLoggerConfig(LogManager.getLogger("cbit").getName()).setLevel(logLevel); + config.updateLoggers(); + + + CLIPythonManager.getInstance().instantiatePythonProcess(); + + Executable.setGlobalTimeoutMS(EXECUTABLE_MAX_WALLCLOCK_MILLIS); + logger.info("Beginning execution"); + File tmpDir = Files.createTempDirectory("VCell_CLI_" + Long.toHexString(new Date().getTime())).toFile(); + + Tracer.clearTraceEvents(); + ExecuteImpl.singleMode(inputFilePath, tmpDir, cliTracer, bKeepTempFiles, bExactMatchOnly, + bEncapsulateOutput, bSmallMeshOverride); + CLIPythonManager.getInstance().closePythonProcess(); + // WARNING: Python needs re-instantiation once the above line is called! + FileUtils.copyDirectoryContents(tmpDir, outputFilePath, true, null); + OmexExecSummary omexExecSummary = new OmexExecSummary(); + omexExecSummary.file_path = String.valueOf(inputFilePath); + omexExecSummary.status = OmexExecSummary.ActualStatus.PASSED; + new ObjectMapper().writeValue(new File(outputFilePath, "exec_summary.json"), omexExecSummary); + new ObjectMapper().writeValue(new File(outputFilePath, "logs.json"), Tracer.getTraceEvents()); + return 0; + } catch (Exception e) { ///TODO: Break apart into specific exceptions to maximize logging. + LogManager.getLogger(this.getClass()).error(e.getMessage(), e); + OmexExecSummary omexExecSummary = OmexTestingDatabase.summarize(inputFilePath,e,Tracer.getErrors()); + try { + new ObjectMapper().writeValue(new File(outputFilePath, "exec_summary.json"), omexExecSummary); + new ObjectMapper().writeValue(new File(outputFilePath, "logs.json"), Tracer.getTraceEvents()); + } catch (IOException ex) { + logger.error("Failed to write exec summary and structured logs", ex); + } + return 1; + } finally { + logger.debug("Completed all execution"); + } + } +} diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java b/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java index 2585dfe1f3..459b9d7114 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java +++ b/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java @@ -6,19 +6,17 @@ import org.vcell.cli.PythonStreamException; import org.vcell.cli.exceptions.ExecutionException; import org.vcell.cli.run.hdf5.BiosimulationsHdf5Writer; +import org.vcell.cli.run.hdf5.BiosimulationsHdfWriterException; import org.vcell.cli.run.hdf5.HDF5ExecutionResults; import org.vcell.sedml.log.BiosimulationLog; import org.vcell.util.FileUtils; import java.io.File; import java.io.IOException; -import java.math.BigDecimal; import java.nio.file.Path; import java.nio.file.Paths; import java.util.List; -import org.vcell.cli.run.hdf5.BiosimulationsHdfWriterException; - /** * Contains the code necessary to execute an Omex archive in VCell */ diff --git a/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexExecSummary.java b/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexExecSummary.java new file mode 100644 index 0000000000..d8a8053fc4 --- /dev/null +++ b/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexExecSummary.java @@ -0,0 +1,24 @@ +package org.vcell.cli.testsupport; + +public class OmexExecSummary { + + public enum ActualStatus { + PASSED, + FAILED + } + + public String file_path; + public ActualStatus status; + public FailureType failure_type; + public String failure_desc; + + @Override + public String toString() { + return "OmexExecSummary{" + + ", file_path='" + file_path + '\'' + + ", status=" + status + + ", failure_type=" + failure_type + + ", failure_desc="+((failure_desc!=null)?('\'' + failure_desc + '\''):null) + + '}'; + } +} diff --git a/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java b/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java index 74f1ff0ff9..07f63ea64f 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java +++ b/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java @@ -1,12 +1,18 @@ package org.vcell.cli.testsupport; +import cbit.vcell.mapping.MappingException; import com.fasterxml.jackson.databind.MappingIterator; import com.fasterxml.jackson.databind.ObjectMapper; +import org.vcell.sbml.vcell.SBMLImportException; +import org.vcell.trace.Span; +import org.vcell.trace.TraceEvent; +import org.vcell.trace.Tracer; import java.io.*; +import java.nio.file.FileAlreadyExistsException; +import java.nio.file.Path; import java.util.ArrayList; import java.util.List; -import java.util.NoSuchElementException; public class OmexTestingDatabase { @@ -29,10 +35,30 @@ public enum TestCollection { } } - public static OmexTestCase queryOmexTestCase(List omexTestCases, String path) throws NoSuchElementException { - return omexTestCases.stream().filter(tc -> tc.matchFileSuffix(path)).findFirst().orElseThrow(); + public static List queryOmexTestCase(List omexTestCases, String path) { + return omexTestCases.stream().filter(tc -> tc.matchFileSuffix(path)).toList(); } + public String generateReport(List omexTestCases, List execSummaries) { + StringBuilder report = new StringBuilder(); + for (OmexTestCase testCase : omexTestCases) { + report.append(testCase.toString()).append("\n"); + } + return report.toString(); + } + + public static List loadOmexExecSummaries(String execSummariesNdjson) throws IOException { + List execSummaries = new ArrayList<>(); + ObjectMapper objectMapper = new ObjectMapper(); + try (MappingIterator it = objectMapper.readerFor(OmexExecSummary.class).readValues(execSummariesNdjson)) { + while (it.hasNext()) { + execSummaries.add(it.next()); + } + } + return execSummaries; + } + + // read a newline-delimited json file into a list of OmexTextCase objects public static List loadOmexTestCases() throws IOException { List testCases = new ArrayList<>(); @@ -53,4 +79,65 @@ public static List loadOmexTestCases() throws IOException { return testCases; } + public static OmexExecSummary summarize(File inputFilePath, Exception exception, List errorEvents) { + OmexExecSummary execSummary = new OmexExecSummary(); + execSummary.file_path = inputFilePath.toString(); + execSummary.status = OmexExecSummary.ActualStatus.PASSED; + if (exception != null || !errorEvents.isEmpty()) { + execSummary.failure_type = determineFault(exception, errorEvents); + execSummary.failure_desc = null; + if (exception != null) { + execSummary.failure_desc = exception.getMessage(); + } + if (!errorEvents.isEmpty()) { + execSummary.failure_desc = errorEvents.get(0).message + " " + errorEvents.get(0).exception; + } + } + return execSummary; + } + + public static FailureType determineFault(Exception caughtException, List errorEvents){ // Throwable because Assertion Error + String errorMessage = ""; + if (caughtException != null) { + 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; + } else if (errorMessage.contains("System IO encountered a fatal error")){ + Throwable subException = caughtException.getCause(); + //String subMessage = (subException == null) ? "" : subException.getMessage(); + if (subException instanceof FileAlreadyExistsException){ + return FailureType.HDF5_FILE_ALREADY_EXISTS; + } + } else if (errorMessage.contains("error while processing outputs: null")){ + Throwable subException = caughtException.getCause(); + if (subException instanceof ArrayIndexOutOfBoundsException){ + return FailureType.ARRAY_INDEX_OUT_OF_BOUNDS; + } + } else if (errorMessage.contains("nconsistent unit system in SBML model") || + errorMessage.contains("ust be of type")){ + return FailureType.SEDML_ERRONEOUS_UNIT_SYSTEM; + } else if (errorMessage.contains("There are no SED-MLs in the archive to execute")) { + return FailureType.SEDML_NO_SEDMLS_TO_EXECUTE; + } else if (errorMessage.contains("MappingException occurred: failed to generate math")) { + return FailureType.MATH_GENERATION_FAILURE; + } + + // else check Tracer error events for known faults + for (TraceEvent event : errorEvents) { + if (event.hasException(SBMLImportException.class)) { + return FailureType.SBML_IMPORT_FAILURE; + } + if (event.span.getNestedContextName().contains(Span.ContextType.PROCESSING_SEDML.name()+"(preProcessDoc)")){ + return FailureType.SEDML_PREPROCESS_FAILURE; + } + if (event.hasException(MappingException.class)) { + return FailureType.MATH_GENERATION_FAILURE; + } + } + + return FailureType.UNCATETORIZED_FAULT; + } + } diff --git a/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedOmexExecTest.java b/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedOmexExecTest.java index 9b1e67d1b8..80e9132304 100644 --- a/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedOmexExecTest.java +++ b/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedOmexExecTest.java @@ -1,6 +1,5 @@ package org.vcell.cli.run; -import cbit.vcell.mapping.MappingException; import cbit.vcell.mongodb.VCMongoMessage; import cbit.vcell.resource.PropertyLoader; import org.apache.commons.io.FileUtils; @@ -9,15 +8,12 @@ import org.junit.jupiter.api.Tag; import org.junit.jupiter.params.ParameterizedTest; import org.junit.jupiter.params.provider.MethodSource; -import org.opentest4j.AssertionFailedError; import org.vcell.cli.CLIPythonManager; import org.vcell.cli.CLIRecordable; import org.vcell.cli.PythonStreamException; import org.vcell.cli.testsupport.FailureType; import org.vcell.cli.testsupport.OmexTestCase; import org.vcell.cli.testsupport.OmexTestingDatabase; -import org.vcell.sbml.vcell.SBMLImportException; -import org.vcell.trace.Span; import org.vcell.trace.TraceEvent; import org.vcell.trace.Tracer; import org.vcell.util.VCellUtilityHub; @@ -25,14 +21,15 @@ import java.io.File; import java.io.IOException; import java.io.InputStream; -import java.nio.file.FileAlreadyExistsException; import java.nio.file.Files; import java.nio.file.Path; -import java.util.*; +import java.util.Arrays; +import java.util.Collection; +import java.util.List; import java.util.function.Predicate; import java.util.stream.Collectors; -import static org.junit.jupiter.api.Assertions.*; +import static org.junit.jupiter.api.Assertions.fail; @Tag("BSTS_IT") public class BSTSBasedOmexExecTest { @@ -115,17 +112,19 @@ public void testBSTSBasedOmex(OmexTestCase testCase) throws Exception { ExecuteImpl.singleMode(omexFile.toFile(), outdirPath.toFile(), cliRecorder); List errorEvents = Tracer.getErrors(); String errorMessages = (errorEvents.isEmpty()) ? "" : errorEvents.get(0).message + " " + errorEvents.get(0).exception; - assertTrue(errorEvents.isEmpty(), "failure: '" + errorMessages + "'"); + if (!errorEvents.isEmpty()){ + throw new RuntimeException("failure: '" + errorMessages + "'"); + } if (knownFault != null) { - fail("Expected error " + knownFault.name() + " but found no error"); + throw new RuntimeException("Expected error " + knownFault.name() + " but found no error"); } - } catch (Exception | AssertionFailedError e){ + } catch (Exception e){ System.err.println("========== Begin Tracer report =========="); Tracer.reportErrors(true); System.err.println("=========== End Tracer report ==========="); e.printStackTrace(System.err); List errorEvents = Tracer.getErrors(); - FailureType fault = this.determineFault(e, errorEvents); + FailureType fault = OmexTestingDatabase.determineFault(e, errorEvents); if (knownFault != null) { if (knownFault == fault) { System.err.println("Found expected error " + knownFault.name() + ": " + e.getMessage()); @@ -141,50 +140,4 @@ public void testBSTSBasedOmex(OmexTestCase testCase) throws Exception { throw new Exception("Test error: " + testCase + " failed improperly", e); } } - - private FailureType determineFault(Throwable caughtException, List errorEvents){ // Throwable because Assertion Error - String errorMessage = caughtException.getMessage(); - if (errorMessage == null) errorMessage = ""; // Prevent nullptr exception - - if (caughtException instanceof Error && caughtException.getCause() != null) - errorMessage = caughtException.getCause().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; - } else if (errorMessage.contains("System IO encountered a fatal error")){ - Throwable subException = caughtException.getCause(); - //String subMessage = (subException == null) ? "" : subException.getMessage(); - if (subException instanceof FileAlreadyExistsException){ - return FailureType.HDF5_FILE_ALREADY_EXISTS; - } - } else if (errorMessage.contains("error while processing outputs: null")){ - Throwable subException = caughtException.getCause(); - if (subException instanceof ArrayIndexOutOfBoundsException){ - return FailureType.ARRAY_INDEX_OUT_OF_BOUNDS; - } - } else if (errorMessage.contains("nconsistent unit system in SBML model") || - errorMessage.contains("ust be of type")){ - return FailureType.SEDML_ERRONEOUS_UNIT_SYSTEM; - } else if (errorMessage.contains("There are no SED-MLs in the archive to execute")) { - return FailureType.SEDML_NO_SEDMLS_TO_EXECUTE; - } else if (errorMessage.contains("MappingException occurred: failed to generate math")) { - return FailureType.MATH_GENERATION_FAILURE; - } - - // else check Tracer error events for known faults - for (TraceEvent event : errorEvents) { - if (event.hasException(SBMLImportException.class)) { - return FailureType.SBML_IMPORT_FAILURE; - } - if (event.span.getNestedContextName().contains(Span.ContextType.PROCESSING_SEDML.name()+"(preProcessDoc)")){ - return FailureType.SEDML_PREPROCESS_FAILURE; - } - if (event.hasException(MappingException.class)) { - return FailureType.MATH_GENERATION_FAILURE; - } - } - - return FailureType.UNCATETORIZED_FAULT; - } - } diff --git a/vcell-cli/src/test/java/org/vcell/cli/testsupport/TestOmexTestingDatabase.java b/vcell-cli/src/test/java/org/vcell/cli/testsupport/TestOmexTestingDatabase.java new file mode 100644 index 0000000000..6e16ed9fe7 --- /dev/null +++ b/vcell-cli/src/test/java/org/vcell/cli/testsupport/TestOmexTestingDatabase.java @@ -0,0 +1,63 @@ +package org.vcell.cli.testsupport; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +import java.io.IOException; +import java.util.List; + + +public class TestOmexTestingDatabase { + + @Test + void omexTestCasesLoad() throws IOException { + List allTestCases = OmexTestingDatabase.loadOmexTestCases(); + Assertions.assertFalse(allTestCases.isEmpty()); + } + + @Test + void execSummariesLoad() throws IOException { + String omexExecSummaryJson = + """ + {"file_path": "test1.omex", "status": "PASSED"} + {"file_path": "test2.omex", "status": "PASSED", "failure_type": null, "failure_desc": null} + {"file_path": "aaa.omex", "status": "FAILED", "failure_type": "SBML_IMPORT_FAILURE", "failure_desc": "bad stuff"} + """; + + List allExecSummaries = OmexTestingDatabase.loadOmexExecSummaries(omexExecSummaryJson); + Assertions.assertEquals(3, allExecSummaries.size()); + } + + @Test + void queryOmexTestCase() throws IOException { + String[] shouldFindUnique = { + "sedml/SimulatorSupportsAddReplaceRemoveModelElementChanges/2.execution-should-succeed.omex", + "bsts-omex/misc-projects/BIOMD0000000842.omex", + "omex_files/BIOMD0000000842.omex" + }; + String[] shouldFindMany = { + "11.omex", + "BIOMD0000000842.omex", + "2.execution-should-succeed.omex" + }; + String[] shouldNotFind = { + "11111.omex", + "2.execution-should-succeed", + "sedml/SimulatorSupportsAddReplaceRemoveModelElementChanges" + }; + List allTestCases = OmexTestingDatabase.loadOmexTestCases(); + for (String path : shouldFindUnique) { + List omexTestCase = OmexTestingDatabase.queryOmexTestCase(allTestCases, path); + Assertions.assertEquals(1, omexTestCase.size()); + } + for (String path : shouldFindMany) { + List omexTestCase = OmexTestingDatabase.queryOmexTestCase(allTestCases, path); + Assertions.assertTrue(omexTestCase.size() > 1); + } + for (String path : shouldNotFind) { + List omexTestCase = OmexTestingDatabase.queryOmexTestCase(allTestCases, path); + Assertions.assertTrue(omexTestCase.isEmpty()); + } + } + +} From 91869d8de7934d295171048365469cf1dd7ccce3 Mon Sep 17 00:00:00 2001 From: jcschaff Date: Mon, 16 Dec 2024 17:05:20 -0500 Subject: [PATCH 6/7] fixed 'execute-omex' generation of exec_summary.json for single run --- .../org/vcell/cli/run/ExecuteOmexCommand.java | 15 ++++++++++----- .../cli/testsupport/OmexTestingDatabase.java | 2 +- 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteOmexCommand.java b/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteOmexCommand.java index 36485a5660..f49f4753b7 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteOmexCommand.java +++ b/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteOmexCommand.java @@ -104,18 +104,23 @@ public Integer call() { CLIPythonManager.getInstance().closePythonProcess(); // WARNING: Python needs re-instantiation once the above line is called! FileUtils.copyDirectoryContents(tmpDir, outputFilePath, true, null); - OmexExecSummary omexExecSummary = new OmexExecSummary(); - omexExecSummary.file_path = String.valueOf(inputFilePath); - omexExecSummary.status = OmexExecSummary.ActualStatus.PASSED; + final OmexExecSummary omexExecSummary; + if (Tracer.hasErrors()){ + omexExecSummary = OmexTestingDatabase.summarize(inputFilePath,(Exception)null,Tracer.getErrors()); + } else { + omexExecSummary = new OmexExecSummary(); + omexExecSummary.file_path = String.valueOf(inputFilePath); + omexExecSummary.status = OmexExecSummary.ActualStatus.PASSED; + } new ObjectMapper().writeValue(new File(outputFilePath, "exec_summary.json"), omexExecSummary); - new ObjectMapper().writeValue(new File(outputFilePath, "logs.json"), Tracer.getTraceEvents()); + new ObjectMapper().writeValue(new File(outputFilePath, "tracer.json"), Tracer.getTraceEvents()); return 0; } catch (Exception e) { ///TODO: Break apart into specific exceptions to maximize logging. LogManager.getLogger(this.getClass()).error(e.getMessage(), e); OmexExecSummary omexExecSummary = OmexTestingDatabase.summarize(inputFilePath,e,Tracer.getErrors()); try { new ObjectMapper().writeValue(new File(outputFilePath, "exec_summary.json"), omexExecSummary); - new ObjectMapper().writeValue(new File(outputFilePath, "logs.json"), Tracer.getTraceEvents()); + new ObjectMapper().writeValue(new File(outputFilePath, "tracer.json"), Tracer.getTraceEvents()); } catch (IOException ex) { logger.error("Failed to write exec summary and structured logs", ex); } diff --git a/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java b/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java index 07f63ea64f..d11c3840b5 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java +++ b/vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java @@ -82,7 +82,7 @@ public static List loadOmexTestCases() throws IOException { public static OmexExecSummary summarize(File inputFilePath, Exception exception, List errorEvents) { OmexExecSummary execSummary = new OmexExecSummary(); execSummary.file_path = inputFilePath.toString(); - execSummary.status = OmexExecSummary.ActualStatus.PASSED; + execSummary.status = OmexExecSummary.ActualStatus.FAILED; if (exception != null || !errorEvents.isEmpty()) { execSummary.failure_type = determineFault(exception, errorEvents); execSummary.failure_desc = null; From 1b61b0e144e2bc36724a3e40f296f6e7b847c3bd Mon Sep 17 00:00:00 2001 From: jcschaff Date: Mon, 16 Dec 2024 17:48:08 -0500 Subject: [PATCH 7/7] fix description for execute-omex --- .../src/main/java/org/vcell/cli/run/ExecuteOmexCommand.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteOmexCommand.java b/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteOmexCommand.java index f49f4753b7..2b946e89bb 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteOmexCommand.java +++ b/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteOmexCommand.java @@ -22,7 +22,7 @@ import java.util.Date; import java.util.concurrent.Callable; -@Command(name = "execute-omex", description = "run .vcml or .omex files via Python API") +@Command(name = "execute-omex", description = "run a single .omex file and log into exec_summary.json and tracer.json") public class ExecuteOmexCommand implements Callable { private final static Logger logger = LogManager.getLogger(ExecuteOmexCommand.class);