private void reportOnWorkflow(
String workflowAccession, WorkflowRunStatus status, Date earlyDate, Date lateDate)
throws IOException {
String title = "";
if (workflowAccession != null) {
title = "workflow_" + workflowAccession;
}
if (status != null) {
title += "status_" + status.name();
}
if (earlyDate != null) {
title += "from" + dateFormat.format(earlyDate);
}
if (lateDate != null) {
title += "to" + dateFormat.format(lateDate);
}
initWriter(title);
String report;
try {
Integer workflowParameter = null;
if (workflowAccession != null) {
workflowParameter = Integer.parseInt(workflowAccession);
}
report = metadata.getWorkflowRunReport(workflowParameter, status, earlyDate, lateDate);
} catch (RuntimeException e) {
Log.fatal("Workflow not found", e);
ret = new ReturnValue(ReturnValue.INVALIDPARAMETERS);
return;
}
if (options.has("human")) {
writer.write(TabExpansionUtil.expansion(report));
return;
}
writer.write(report);
}
/** Constructor for WorkflowRunReporter. */
public WorkflowRunReporter() {
super();
parser
.acceptsAll(Arrays.asList("workflow-run-accession", "wra"), "The SWID of the workflow run")
.withRequiredArg();
parser
.acceptsAll(
Arrays.asList("workflow-accession", "wa"),
"The SWID of "
+ "a workflow. All the workflow runs for that workflow will be "
+ "retrieved.")
.withRequiredArg();
parser
.acceptsAll(
Arrays.asList("time-period", "t"),
"Dates to check for "
+ "workflow runs. Dates are in format YYYY-MM-DD. If one date is "
+ "provided, from that point to the present is checked. If two, "
+ "separated by hyphen YYYY-MM-DDL:YYYY-MM-DD then it checks "
+ "that range")
.withRequiredArg();
parser
.acceptsAll(Arrays.asList("output-filename", "o"), "Optional: The output filename")
.withRequiredArg();
parser.acceptsAll(Arrays.asList("stdout"), "Prints to standard out instead of to a file");
parser.acceptsAll(
Arrays.asList(WRSTDOUT),
"Optional: will print the stdout of the workflow run, must specify the --workflow-run-accession");
parser.acceptsAll(
Arrays.asList(WRSTDERR),
"Optional: will print the stderr of the workflow run, must specify the --workflow-run-accession");
this.statusSpec =
parser
.accepts(
"status",
"Optional: Specify a particular status to restrict workflow runs that will be returned, status is one of "
+ Arrays.toString(WorkflowRunStatus.values()))
.withRequiredArg()
.ofType(WorkflowRunStatus.class);
parser.acceptsAll(
Arrays.asList("human"), "Optional: will print output in expanded human friendly format");
ret.setExitStatus(ReturnValue.SUCCESS);
}