public CommandLineRunContainer execute(ComputeProperties computeProperties) throws Exception {
Context context = new Context(computeProperties);
String userName = null;
String pass = null;
ComputeDbApiConnection dbApiConnection = null;
ComputeDbApiClient dbApiClient = null;
// check if we are working with database; database default is database=none
if (!computeProperties.database.equalsIgnoreCase(Parameters.DATABASE_DEFAULT)) {
userName = computeProperties.molgenisuser;
pass = computeProperties.molgenispass;
dbApiConnection =
new HttpClientComputeDbApiConnection(
computeProperties.database, computeProperties.port, "/api/v1", userName, pass);
dbApiClient = new ComputeDbApiClient(dbApiConnection);
}
if (computeProperties.showHelp) {
new HelpFormatter()
.printHelp("sh molgenis-compute.sh -p parameters.csv", computeProperties.getOptions());
return commandLineRunContainer;
}
if (computeProperties.create) {
new WorkflowGenerator(computeProperties.createDirName);
return commandLineRunContainer;
} else if (computeProperties.clear) {
File file = new File(Parameters.PROPERTIES);
if (file.delete()) {
LOG.info(file.getName() + " is cleared");
} else {
LOG.info("Fail to clear " + file.getName());
}
return commandLineRunContainer;
} else if (computeProperties.generate) {
String toPrint = computeProperties.workFlow;
LOG.info("Using workflow: " + new File(toPrint).getAbsolutePath());
if (defaultsExists(computeProperties)) {
toPrint = computeProperties.defaults;
LOG.info("Using defaults: " + new File(toPrint).getAbsolutePath());
}
for (int i = 0; i < computeProperties.getParameterFiles().length; i++) {
toPrint = computeProperties.getParameterFiles()[i];
LOG.info("Using parameters: " + new File(toPrint).getAbsolutePath());
}
LOG.info("Using run (output) dir: " + new File(computeProperties.runDir).getAbsolutePath());
LOG.info("Using backend: " + computeProperties.backend);
LOG.info("Using runID: " + computeProperties.runId + "\n\n");
generate(context, computeProperties);
if (Parameters.DATABASE_DEFAULT.equals(
computeProperties.database)) { // if database none (= off), then do following
if (computeProperties.list) {
// list *.sh files in rundir
File[] scripts =
new File(computeProperties.runDir)
.listFiles(
new FilenameFilter() {
@Override
public boolean accept(File dir, String filename) {
return filename.endsWith(".sh");
}
});
LOG.info("Generated jobs that are ready to run:");
if (null == scripts)
System.out.println(
"None. Remark: the run (output) directory '"
+ computeProperties.runDir
+ "' does not exist.");
else if (0 == scripts.length) System.out.println("None.");
else
for (File script : scripts) {
System.out.println("- " + script.getName());
}
}
} else {
String runName = computeProperties.runId;
String backendUrl = computeProperties.backendUrl;
String backendName = computeProperties.backend;
Long pollInterval = Long.parseLong(computeProperties.interval);
Iterable<Task> tasks = context.getTasks();
String submitScript = "none";
if (backendName.equalsIgnoreCase(Parameters.SCHEDULER_PBS)
|| backendName.equalsIgnoreCase(Parameters.SCHEDULER_SLURM)) {
for (Task task : tasks) {
String name = task.getName();
String wrappedScript =
FileUtils.readFileToString(new File(computeProperties.runDir + "/" + name + ".sh"));
task.setScript(wrappedScript);
}
submitScript =
FileUtils.readFileToString(new File(computeProperties.runDir + "/submit.sh"));
}
// TODO The user env is now written to file
// String environment = context.getUserEnvironment();
//
// CreateRunRequest createRunRequest = new CreateRunRequest(runName, backendUrl,
// pollInterval, tasks,
// environment, userName, submitScript);
//
// dbApiClient.createRun(createRunRequest);
System.out.println(
"\n Run "
+ computeProperties.runId
+ " is inserted into database on "
+ computeProperties.database);
}
}
if (computeProperties.execute) {
if (computeProperties.database.equalsIgnoreCase(Parameters.DATABASE_DEFAULT)) {
String runDir = computeProperties.runDir;
SystemCommandExecutorImpl exe = new SystemCommandExecutorImpl();
exe.runCommand("sh " + runDir + "/submit.sh");
String err = exe.getCommandError();
String out = exe.getCommandOutput();
System.out.println("\nScripts are executed/submitted on " + computeProperties.backend);
System.out.println(out);
System.out.println(err);
} else {
String backendUserName = computeProperties.backenduser;
String backendPass = computeProperties.backendpass;
if ((backendPass == null) || (backendUserName == null)) {
LOG.info("\nPlease specify username and password for computational back-end");
LOG.info("Use --backenduser[-bu] and --backendpassword[-bp] for this");
return commandLineRunContainer;
}
StartRunRequest startRunRequest =
new StartRunRequest(computeProperties.runId, backendUserName, backendPass);
dbApiClient.start(startRunRequest);
LOG.info(
"\n"
+ computeProperties.runId
+ "is submitted for execution "
+ computeProperties.backend
+ " by user "
+ backendUserName);
}
}
return commandLineRunContainer;
}
/**
* Generate {@link Parameters} and {@link Task}s. After generate is complete, bash scripts will be
* available to submit to the cluster
*
* @param context
* @param computeProperties
* @throws Exception
*/
private void generate(Context context, ComputeProperties computeProperties) throws Exception {
// Create a list of parameter files
List<File> parameterFiles = new ArrayList<File>();
// Add files from the computeProperties parameter String array to the list of parameterFiles
for (String parameterFile : computeProperties.getParameterFiles()) {
parameterFiles.add(new File(parameterFile));
}
// Add default property file if it exists
if (defaultsExists(computeProperties)) {
parameterFiles.add(new File(computeProperties.defaults));
}
// Parse all parameters
CsvParameterParserImpl parser = new CsvParameterParserImpl(computeProperties.stringStore);
// This run ID will be passed to the TupleUtils "to solve" method
parser.setRunID(computeProperties.runId);
if (computeProperties.hasParametersToOverwrite()) {
parser.setParametersToOverwrite(computeProperties.getParametersToOverwrite());
}
// Fold parameters
FoldParametersImpl foldParameters = new FoldParametersImpl(parameterFiles, computeProperties);
// TODO set number of files, only used to check size
context.setFoldParameters(foldParameters);
context.setParameters(parser.parse(parameterFiles, computeProperties));
// Batch the compute job if there is a batch option available
if (computeProperties.batchOption != null) {
context.createBatchAnalyser(computeProperties.batchVariable, computeProperties.batchSize);
}
File outputDirectory = new File(computeProperties.runDir);
computeProperties.runDir = outputDirectory.getCanonicalPath();
outputDirectory.mkdirs();
// Parse workflow
LOG.info("Parsing workflow");
WorkflowImpl workflowImpl =
new WorkflowCsvParserImpl().parse(computeProperties.workFlow, computeProperties);
context.setWorkflow(workflowImpl);
// Create environment.txt with user parameters that are used in at least one of the steps
LOG.info("Creating user.env file");
new EnvironmentGenerator(computeProperties.stringStore)
.generate(context, computeProperties.runDir);
// Create a ScriptGenerator object. This object creates the header, footer, and submit template
// on
// initialization. The object can then be used to create scripts for every generated task.
LOG.info("Generating header and footer templates");
ScriptGenerator scriptGenerator = new ScriptGenerator(computeProperties);
// Create a TaskGenerator object with the current context object
TaskGenerator taskGenerator =
new TaskGenerator(context, scriptGenerator, computeProperties.stringStore);
// Analyze lists in workflow protocols.
// We need to know if list inputs are coming from the same or from a different parameter file to
// combine lists
// or leave them separated
if (foldParameters.getParameters().size() >= 2) {
determineCombineLists(workflowImpl);
}
// Generate tasks, store task names and previous steps in a list of TaskInfo objects
LOG.info("Generating tasks");
List<TaskInfo> taskInfos = taskGenerator.generate();
// Generate submit script with the TaskInfo objects
LOG.info("Generating submit scripts");
scriptGenerator.generateSubmitScript(taskInfos);
LOG.info("All scripts have been generated");
LOG.info("You can find them in: " + outputDirectory);
}