public class DataBundles extends Bundles
Modifier and Type | Class and Description |
---|---|
protected static class |
DataBundles.ExtensionIgnoringFilter |
Constructor and Description |
---|
DataBundles() |
Modifier and Type | Method and Description |
---|---|
static void |
createList(Path path) |
static void |
deleteAllExtensions(Path file) |
protected static String |
filenameWithoutExtension(Path entry) |
static ErrorDocument |
getError(Path path) |
static Path |
getInputs(Bundle dataBundle) |
static Path |
getIntermediate(Bundle dataBundle,
UUID uuid) |
static Path |
getIntermediates(Bundle dataBundle) |
static List<Path> |
getList(Path list) |
static Path |
getListItem(Path list,
long position) |
static long |
getListSize(Path list) |
static Path |
getOutputs(Bundle dataBundle) |
static Path |
getPort(Path map,
String portName) |
static NavigableMap<String,Path> |
getPorts(Path path) |
static WorkflowBundleIO |
getWfBundleIO() |
static Path |
getWorkflow(Bundle dataBundle) |
static WorkflowBundle |
getWorkflowBundle(Bundle dataBundle) |
static Path |
getWorkflowDescription(Bundle dataBundle) |
static Path |
getWorkflowRunProvenance(Bundle dataBundle) |
static Path |
getWorkflowRunReport(Bundle dataBundle) |
static com.fasterxml.jackson.databind.JsonNode |
getWorkflowRunReportAsJson(Bundle dataBundle) |
static boolean |
hasInputs(Bundle dataBundle) |
static boolean |
hasOutputs(Bundle dataBundle) |
static boolean |
isError(Path path) |
static boolean |
isList(Path path) |
static boolean |
isMissing(Path item) |
static boolean |
isValue(Path item) |
static Path |
newListItem(Path list) |
static Path |
setError(Path path,
ErrorDocument error) |
static Path |
setError(Path errorPath,
String message,
String trace,
Path... causedBy) |
static Path |
setReference(Path path,
URI reference) |
static void |
setStringValue(Path path,
String string) |
static void |
setWfBundleIO(WorkflowBundleIO wfBundleIO) |
static void |
setWorkflowBundle(Bundle dataBundle,
WorkflowBundle wfBundle) |
static void |
setWorkflowRunReport(Bundle dataBundle,
com.fasterxml.jackson.databind.JsonNode workflowRunReport) |
protected static Path |
withExtension(Path path,
String extension) |
protected static String |
withExtensionFilename(String filename,
String extension) |
closeAndSaveBundle, closeBundle, copyRecursively, createBundle, createBundle, deleteRecursively, getAnnotations, getManifestPath, getMimeType, getReference, getStringValue, isReference, openBundle, openBundle, openBundle, openBundleReadOnly, safeCopy, safeMove, safeMoveOrCopy, setMimeType, uriToBundlePath
public static void createList(Path path) throws IOException
IOException
public static void deleteAllExtensions(Path file) throws IOException
IOException
public static ErrorDocument getError(Path path) throws IOException
IOException
public static Path getInputs(Bundle dataBundle) throws IOException
IOException
public static List<Path> getList(Path list) throws IOException
IOException
public static Path getListItem(Path list, long position) throws IOException
IOException
public static Path getOutputs(Bundle dataBundle) throws IOException
IOException
public static Path getPort(Path map, String portName) throws IOException
IOException
public static NavigableMap<String,Path> getPorts(Path path) throws IOException
IOException
public static boolean hasInputs(Bundle dataBundle)
public static boolean hasOutputs(Bundle dataBundle)
public static boolean isError(Path path)
public static boolean isList(Path path)
public static boolean isMissing(Path item)
public static boolean isValue(Path item)
public static Path newListItem(Path list) throws IOException
IOException
public static Path setError(Path path, ErrorDocument error) throws IOException
IOException
public static Path setError(Path errorPath, String message, String trace, Path... causedBy) throws IOException
IOException
public static Path setReference(Path path, URI reference) throws IOException
IOException
public static void setStringValue(Path path, String string) throws IOException
IOException
protected static String withExtensionFilename(String filename, String extension)
public static com.fasterxml.jackson.databind.JsonNode getWorkflowRunReportAsJson(Bundle dataBundle) throws IOException
IOException
public static void setWorkflowRunReport(Bundle dataBundle, com.fasterxml.jackson.databind.JsonNode workflowRunReport) throws IOException
IOException
public static Path getWorkflow(Bundle dataBundle) throws IOException
IOException
public static Path getWorkflowDescription(Bundle dataBundle) throws IOException
IOException
public static void setWorkflowBundle(Bundle dataBundle, WorkflowBundle wfBundle) throws IOException
IOException
public static WorkflowBundle getWorkflowBundle(Bundle dataBundle) throws ReaderException, IOException
ReaderException
IOException
public static Path getIntermediates(Bundle dataBundle) throws IOException
IOException
public static Path getIntermediate(Bundle dataBundle, UUID uuid) throws IOException
IOException
public static long getListSize(Path list) throws IOException
IOException
public static WorkflowBundleIO getWfBundleIO()
public static void setWfBundleIO(WorkflowBundleIO wfBundleIO)
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