-
Notifications
You must be signed in to change notification settings - Fork 20
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'master' into repair-nightly-testing
- Loading branch information
Showing
76 changed files
with
3,204 additions
and
1,241 deletions.
There are no files selected for viewing
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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); | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
132 changes: 132 additions & 0 deletions
132
vcell-cli/src/main/java/org/vcell/cli/run/ExecuteOmexCommand.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,132 @@ | ||
| 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 a single .omex file and log into exec_summary.json and tracer.json") | ||
| public class ExecuteOmexCommand implements Callable<Integer> { | ||
|
|
||
| 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); | ||
| 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, "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, "tracer.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"); | ||
| } | ||
| } | ||
| } |
Oops, something went wrong.