Package util

Class URITools

java.lang.Object

util.URITools

public class URITools
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static int	cloudThreads
static String	s3Region
static boolean	useS3CredentialsRead
static boolean	useS3CredentialsWrite

Constructor Summary

Constructors

Constructor	Description
URITools()

Method Summary

Modifier and Type	Method	Description
static String	appendName(URI uri, String name)
static void	copy(org.janelia.saalfeldlab.n5.KeyValueAccess kva, String relativeSrc, String relativeDst)
static void	copyFile(File inputFile, File outputFile)
static String	detectS3Region(URI uri)	Attempts to detect the AWS region of an S3 bucket without any credentials.
static String	fromURI(URI uri)
static String	getFileName(URI uri)
static org.janelia.saalfeldlab.n5.KeyValueAccess	getKeyValueAccess(URI uri)	A little hack to get a generic KeyValueAccess for a cloud store
static URI	getParentURI(URI uri)
static URI	getParentURINoEx(URI uri)
static org.janelia.saalfeldlab.n5.N5Reader	instantiateN5Reader(org.janelia.saalfeldlab.n5.universe.StorageFormat format, URI uri)
static org.janelia.saalfeldlab.n5.N5Writer	instantiateN5Writer(org.janelia.saalfeldlab.n5.universe.StorageFormat format, URI uri)
static boolean	isFile(URI uri)
static boolean	isGC(URI uri)
static boolean	isKnownScheme(URI uri)
static boolean	isS3(URI uri)
static SpimData2	loadSpimData(URI xmlURI, XmlIoSpimData2 io)
static void	main(String[] args)
static BufferedReader	openFileReadCloudReader(org.janelia.saalfeldlab.n5.KeyValueAccess kva, URI uri)
static InputStream	openFileReadCloudStream(org.janelia.saalfeldlab.n5.KeyValueAccess kva, URI uri)
static OutputStream	openFileWriteCloudStream(org.janelia.saalfeldlab.n5.KeyValueAccess kva, URI uri)
static PrintWriter	openFileWriteCloudWriter(org.janelia.saalfeldlab.n5.KeyValueAccess kva, URI uri)
static boolean	prefetch(mpicbg.spim.data.generic.sequence.BasicImgLoader loader, int threads)
static void	saveSpimData(SpimData2 data, URI xmlURI, XmlIoSpimData2 io)
static boolean	setNumFetcherThreads(mpicbg.spim.data.generic.sequence.BasicImgLoader loader, int threads)
static URI	toURI(String uriString)
static URI	xmlFilenameToFullPath(mpicbg.spim.data.generic.AbstractSpimData<?> data, String xmlFileName)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

cloudThreads

public static int cloudThreads

s3Region

public static String s3Region

useS3CredentialsWrite

public static boolean useS3CredentialsWrite

useS3CredentialsRead

public static boolean useS3CredentialsRead

Constructor Details

URITools

public URITools()

Method Details

getParentURINoEx

public static URI getParentURINoEx(URI uri)

getParentURI

public static URI getParentURI(URI uri)
                        throws mpicbg.spim.data.SpimDataIOException

Throws:

mpicbg.spim.data.SpimDataIOException

getKeyValueAccess

public static org.janelia.saalfeldlab.n5.KeyValueAccess getKeyValueAccess(URI uri)

A little hack to get a generic KeyValueAccess for a cloud store

Parameters:

uri - - the full URI (even though only scheme and host/bucket will be used)

Returns:

the KeyValueStore

saveSpimData

public static void saveSpimData(SpimData2 data,
 URI xmlURI,
 XmlIoSpimData2 io)
                         throws mpicbg.spim.data.SpimDataException

Throws:

mpicbg.spim.data.SpimDataException

instantiateN5Writer

public static org.janelia.saalfeldlab.n5.N5Writer instantiateN5Writer(org.janelia.saalfeldlab.n5.universe.StorageFormat format,
 URI uri)

instantiateN5Reader

public static org.janelia.saalfeldlab.n5.N5Reader instantiateN5Reader(org.janelia.saalfeldlab.n5.universe.StorageFormat format,
 URI uri)

detectS3Region

public static String detectS3Region(URI uri)

Attempts to detect the AWS region of an S3 bucket without any credentials. Issues an unauthenticated HTTP HEAD request (path-style) against the global S3 endpoint and reads the x-amz-bucket-region response header, which S3 returns even for 301/403 responses. Path-style against s3.amazonaws.com is used so that bucket names containing dots are handled and TLS still validates.

Parameters:

uri - an s3:// URI; the bucket is taken from the host component

Returns:

the region string (e.g. "us-west-2"), or null if it could not be determined

loadSpimData

public static SpimData2 loadSpimData(URI xmlURI,
 XmlIoSpimData2 io)
                              throws mpicbg.spim.data.SpimDataException

Throws:

mpicbg.spim.data.SpimDataException

setNumFetcherThreads

public static boolean setNumFetcherThreads(mpicbg.spim.data.generic.sequence.BasicImgLoader loader,
 int threads)

prefetch

public static boolean prefetch(mpicbg.spim.data.generic.sequence.BasicImgLoader loader,
 int threads)

openFileReadCloudReader

public static BufferedReader openFileReadCloudReader(org.janelia.saalfeldlab.n5.KeyValueAccess kva,
 URI uri)
                                              throws IOException

Throws:

IOException

openFileReadCloudStream

public static InputStream openFileReadCloudStream(org.janelia.saalfeldlab.n5.KeyValueAccess kva,
 URI uri)
                                           throws IOException

Throws:

IOException

openFileWriteCloudWriter

public static PrintWriter openFileWriteCloudWriter(org.janelia.saalfeldlab.n5.KeyValueAccess kva,
 URI uri)
                                            throws IOException

Throws:

IOException

openFileWriteCloudStream

public static OutputStream openFileWriteCloudStream(org.janelia.saalfeldlab.n5.KeyValueAccess kva,
 URI uri)
                                             throws IOException

Throws:

IOException

copy

public static void copy(org.janelia.saalfeldlab.n5.KeyValueAccess kva,
 String relativeSrc,
 String relativeDst)
                 throws IOException

Throws:

IOException

isKnownScheme

public static boolean isKnownScheme(URI uri)

isGC

public static boolean isGC(URI uri)

isS3

public static boolean isS3(URI uri)

isFile

public static boolean isFile(URI uri)

toURI

public static URI toURI(String uriString)

Parameters:

uriString - - if relative we assume it's a local path and file:/ scheme will be added

Returns:

the URI of the String

fromURI

public static String fromURI(URI uri)

Parameters:

uri - a URI

Returns:

a String representation of a URI, if it starts with file:/ it will be removed

getFileName

public static String getFileName(URI uri)

appendName

public static String appendName(URI uri,
 String name)

xmlFilenameToFullPath

public static URI xmlFilenameToFullPath(mpicbg.spim.data.generic.AbstractSpimData<?> data,
 String xmlFileName)

copyFile

public static void copyFile(File inputFile,
 File outputFile)
                     throws IOException

Throws:

IOException

main

public static void main(String[] args)
                 throws mpicbg.spim.data.SpimDataException,
IOException,
URISyntaxException

Throws:

mpicbg.spim.data.SpimDataException

IOException

URISyntaxException