ucar.nc2.dods

Class DODSNetcdfFile

java.lang.Object

ucar.nc2.NetcdfFile

ucar.nc2.dods.DODSNetcdfFile

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, FileCacheable

@NotThreadSafe
public class DODSNetcdfFile
extends NetcdfFile
implements java.io.Closeable

Access to DODS datasets through the Netcdf API.

See Also:

NetcdfFile

Field Summary

Fields

Modifier and Type	Field and Description
static boolean	debugAttributes
static boolean	debugCached
static boolean	debugCE
static boolean	debugCharArray
static boolean	debugConstruct
static boolean	debugConvertData
static boolean	debugDataResult
static boolean	debugOpenResult
static boolean	debugOpenTime
static boolean	debugPreload
static boolean	debugServerCall
static boolean	debugTime
static boolean	showNCfile

Fields inherited from class ucar.nc2.NetcdfFile

cache, cacheName, debugCompress, debugSPI, dimensions, gattributes, id, IOSP_MESSAGE_ADD_RECORD_STRUCTURE, IOSP_MESSAGE_CONVERT_RECORD_STRUCTURE, IOSP_MESSAGE_RANDOM_ACCESS_FILE, IOSP_MESSAGE_REMOVE_RECORD_STRUCTURE, location, reservedCdl, reservedFullName, reservedSectionSpec, rootGroup, showRequest, spi, title, variables

Constructor Summary

Constructors

Constructor and Description
DODSNetcdfFile(java.lang.String datasetURL) Open a DODS file.
DODSNetcdfFile(java.lang.String datasetURL, CancelTask cancelTask) Open a DODS file, allow user control over preloading string arrays and making structure data available through netcdf API.

Method Summary

Modifier and Type	Method and Description
static java.lang.String	canonicalURL(java.lang.String urlName) Create the canonical form of the URL.
void	close() Close all resources (files, sockets, etc) associated with this file.
protected static Attribute	combineAxesAttrs(Attribute axis1, Attribute axis2) Safely combine the multiple axis attributes without duplication
static int	convertToDODSType(DataType dataType, boolean isUnsigned) Get the DODS data class corresponding to the Netcdf data type.
static DataType	convertToNCType(BaseType dtype) Get the Netcdf data type corresponding to the DODS BaseType class.
static DataType	convertToNCType(int dodsDataType) Get the Netcdf data type corresponding to the DODS data type.
void	getDetailInfo(java.util.Formatter f)
static java.lang.String	getDODSConstraintName(Variable var) Return a variable name suitable for use in a DAP constraint expression.
java.lang.String	getFileTypeDescription() Get a human-readable description for this file type.
java.lang.String	getFileTypeId() Get the file type id for the underlying data source.
static boolean	isUnsigned(BaseType dtype) Get whether this is an unsigned type.
static boolean	isUnsigned(int dodsDataType) Get whether this is an unsigned type.
static void	main(java.lang.String[] arg)
protected int[]	makeShape(DArray dodsArray)
java.util.List<Array>	readArrays(java.util.List<Variable> preloadVariables) Make a single call to the DODS Server to read all the named variable's data in one client/server roundtrip.
protected Array	readData(Variable v, Section section)
Array	readSection(java.lang.String variableSection) Read a variable using the given section specification.
long	readToByteChannel(Variable v, Section section, java.nio.channels.WritableByteChannel channel) Read data from a top level Variable and send data to a WritableByteChannel.
Array	readWithCE(Variable v, java.lang.String CE)
protected void	reGroup() Go thru the variables/structure-variables and their attributes and move to the proper groups.
protected void	reGroupVariable(Group rootgroup, DODSVariable dodsv) Deprecated.
protected void	reGroupVariableAttributes(Group rootgroup, Variable v)
static void	setAllowCompression(boolean b) Set whether to allow messages to be compressed.
static void	setAllowDeflate(boolean b) Deprecated. use setAllowCompression
static void	setAllowSessions(boolean b) Set whether to allow sessions by allowing cookies.
static void	setCoordinateVariablePreloadSize(int size) If preloading, set maximum size of coordinate variables to be preloaded.
static void	setDebugFlags(DebugFlags debugFlag) Debugging flags.
static void	setPreload(boolean b) Set whether small variables are preloaded; only turn off for debugging.

Methods inherited from class ucar.nc2.NetcdfFile

addAttribute, addAttribute, addDimension, addGroup, addStringVariable, addVariable, addVariable, addVariableAttribute, canonicalizeUriString, canOpen, empty, findAttribute, findAttValueIgnoreCase, findDimension, findGlobalAttribute, findGlobalAttributeIgnoreCase, findGroup, findVariable, findVariable, findVariableByAttribute, finish, getCacheName, getDetailInfo, getDimensions, getFileTypeVersion, getGlobalAttributes, getId, getIosp, getLastModified, getLocation, getRootGroup, getStructureIterator, getTitle, getUnlimitedDimension, getVariables, hasUnlimitedDimension, iospRegistered, makeFullName, makeFullName, makeFullNameSectionSpec, makeFullNameWithString, makeNameUnescaped, makeRecordStructure, makeRootGroup, makeValidCDLName, makeValidCdmObjectName, makeValidPathName, makeValidSectionSpecName, open, open, open, open, open, open, openInMemory, openInMemory, openInMemory, openInMemory, reacquire, read, readAttributeDouble, readAttributeInteger, readToOutputStream, registerIOProvider, registerIOProvider, registerIOProvider, release, removeDimension, removeRecordStructure, removeVariable, sendIospMessage, setCacheName, setFileCache, setId, setImmutable, setLocation, setProperty, setTitle, showCached, showProxies, syncExtend, toString, toStringDebug, toStringEnd, toStringStart, toStringStart, writeCDL, writeCDL, writeCDL, writeNcML, writeNcML

Methods inherited from class java.lang.Object

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

Field Detail

debugCE

public static boolean debugCE

debugServerCall

public static boolean debugServerCall

debugOpenResult

public static boolean debugOpenResult

debugDataResult

public static boolean debugDataResult

debugCharArray

public static boolean debugCharArray

debugConvertData

public static boolean debugConvertData

debugConstruct

public static boolean debugConstruct

debugPreload

public static boolean debugPreload

debugTime

public static boolean debugTime

showNCfile

public static boolean showNCfile

debugAttributes

public static boolean debugAttributes

debugCached

public static boolean debugCached

debugOpenTime

public static boolean debugOpenTime

Constructor Detail

DODSNetcdfFile

public DODSNetcdfFile(java.lang.String datasetURL)
               throws java.io.IOException

Open a DODS file.

Parameters:

datasetURL - URL of the file. This should start with the protocol "dods:" It may also start with protocol "http:".

Throws:

java.io.IOException - on io error

java.net.MalformedURLException

DODSNetcdfFile

public DODSNetcdfFile(java.lang.String datasetURL,
                      CancelTask cancelTask)
               throws java.io.IOException

Open a DODS file, allow user control over preloading string arrays and making structure data available through netcdf API.

Parameters:

datasetURL - URL of the file. This should start with the protocol "dods:" or "http:".

cancelTask - check if task is cancelled. may be null.

Throws:

java.io.IOException - on io error

java.net.MalformedURLException

Method Detail

setAllowSessions

public static void setAllowSessions(boolean b)

Set whether to allow sessions by allowing cookies. This only affects requests to the TDS. Setting this to true can eliminate consistency problems for datasets that are being updated.

Parameters:

b - true or false. default is false.

setAllowDeflate

public static void setAllowDeflate(boolean b)

Deprecated. use setAllowCompression

Set whether to allow messages to be compressed.

Parameters:

b - true or false.

setAllowCompression

public static void setAllowCompression(boolean b)

Set whether to allow messages to be compressed.

Parameters:

b - true or false.

setDebugFlags

public static void setDebugFlags(DebugFlags debugFlag)

Debugging flags. This is a way to decouple setting flags from particular implementations.

Parameters:

debugFlag - set of debug flags.

setPreload

public static void setPreload(boolean b)

Set whether small variables are preloaded; only turn off for debugging.

Parameters:

b - true if small variables are preloaded (default true)

setCoordinateVariablePreloadSize

public static void setCoordinateVariablePreloadSize(int size)

If preloading, set maximum size of coordinate variables to be preloaded.

Parameters:

size - maximum size of coordinate variables to be preloaded.

canonicalURL

public static java.lang.String canonicalURL(java.lang.String urlName)

Create the canonical form of the URL. If the urlName starts with "http:" or "https:", change it to start with "dods:", otherwise leave it alone.

Parameters:

urlName - the url string

Returns:

canonical form

close

public void close()
           throws java.io.IOException

Description copied from class: NetcdfFile

Close all resources (files, sockets, etc) associated with this file. If the underlying file was acquired, it will be released, otherwise closed. if isClosed() already, nothing will happen

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface FileCacheable

Overrides:

close in class NetcdfFile

Throws:

java.io.IOException - on io error

reGroup

protected void reGroup()
                throws DAP2Exception

Go thru the variables/structure-variables and their attributes and move to the proper groups.

Throws:

DAP2Exception

reGroupVariable

@Deprecated
protected void reGroupVariable(Group rootgroup,
                                           DODSVariable dodsv)
                                    throws DAP2Exception

Deprecated.

Throws:

DAP2Exception

reGroupVariableAttributes

protected void reGroupVariableAttributes(Group rootgroup,
                                         Variable v)
                                  throws DAP2Exception

Throws:

DAP2Exception

combineAxesAttrs

protected static Attribute combineAxesAttrs(Attribute axis1,
                                            Attribute axis2)

Safely combine the multiple axis attributes without duplication

Parameters:

axis1 - axis attribute 1

axis2 - axis attribute 2

Returns:

the combined axis attribute

makeShape

protected int[] makeShape(DArray dodsArray)

getDODSConstraintName

public static java.lang.String getDODSConstraintName(Variable var)

Return a variable name suitable for use in a DAP constraint expression. [Original code seemed wrong because structures can be nested and hence would have to use the full name just like non-structures]

Parameters:

var - The variable whose name will appear in the CE

Returns:

The name in a form suitable for use in a cE

convertToDODSType

public static int convertToDODSType(DataType dataType,
                                    boolean isUnsigned)

Get the DODS data class corresponding to the Netcdf data type. This is the inverse of convertToNCType().

Parameters:

dataType - Netcdf data type.

isUnsigned - if its unsigned

Returns:

the corresponding DODS type enum, from opendap.dap.Attribute.XXXX.

convertToNCType

public static DataType convertToNCType(int dodsDataType)

Get the Netcdf data type corresponding to the DODS data type. This is the inverse of convertToDODSType().

Parameters:

dodsDataType - DODS type enum, from dods.dap.Attribute.XXXX.

Returns:

the corresponding netcdf DataType.

See Also:

isUnsigned(int)

isUnsigned

public static boolean isUnsigned(int dodsDataType)

Get whether this is an unsigned type.

Parameters:

dodsDataType - DODS type enum, from dods.dap.Attribute.XXXX.

Returns:

true if unsigned

convertToNCType

public static DataType convertToNCType(BaseType dtype)

Get the Netcdf data type corresponding to the DODS BaseType class. This is the inverse of convertToDODSType().

Parameters:

dtype - DODS BaseType.

Returns:

the corresponding netcdf DataType.

See Also:

isUnsigned(int)

isUnsigned

public static boolean isUnsigned(BaseType dtype)

Get whether this is an unsigned type.

Parameters:

dtype - DODS BaseType.

Returns:

true if unsigned

readArrays

public java.util.List<Array> readArrays(java.util.List<Variable> preloadVariables)
                                 throws java.io.IOException

Make a single call to the DODS Server to read all the named variable's data in one client/server roundtrip.

Overrides:

readArrays in class NetcdfFile

Parameters:

preloadVariables - list of type Variable

Returns:

list of type Array, contains the data

Throws:

java.io.IOException - on error

readSection

public Array readSection(java.lang.String variableSection)
                  throws java.io.IOException,
                         InvalidRangeException

Description copied from class: NetcdfFile

Read a variable using the given section specification. The result is always an array of the type of the innermost variable. Its shape is the accumulation of all the shapes of its parent structures.

Overrides:

readSection in class NetcdfFile

Parameters:

variableSection - the constraint expression.

Returns:

data requested

Throws:

java.io.IOException - if error

InvalidRangeException - if variableSection is invalid

See Also:

SectionSpecification

readData

protected Array readData(Variable v,
                         Section section)
                  throws java.io.IOException,
                         InvalidRangeException

Overrides:

readData in class NetcdfFile

Throws:

java.io.IOException

InvalidRangeException

readToByteChannel

public long readToByteChannel(Variable v,
                              Section section,
                              java.nio.channels.WritableByteChannel channel)
                       throws java.io.IOException,
                              InvalidRangeException

Description copied from class: NetcdfFile

Read data from a top level Variable and send data to a WritableByteChannel. Experimental.

Overrides:

readToByteChannel in class NetcdfFile

Parameters:

v - a top-level Variable

section - the section of data to read. There must be a Range for each Dimension in the variable, in order. Note: no nulls allowed. IOSP may not modify.

channel - write data to this WritableByteChannel

Returns:

the number of bytes written to the channel

Throws:

java.io.IOException - if read error

InvalidRangeException - if invalid section

readWithCE

public Array readWithCE(Variable v,
                        java.lang.String CE)
                 throws java.io.IOException

Throws:

java.io.IOException

getDetailInfo

public void getDetailInfo(java.util.Formatter f)

Overrides:

getDetailInfo in class NetcdfFile

getFileTypeId

public java.lang.String getFileTypeId()

Description copied from class: NetcdfFile

Get the file type id for the underlying data source.

Overrides:

getFileTypeId in class NetcdfFile

Returns:

registered id of the file type

See Also:

"https://www.unidata.ucar.edu/software/netcdf-java/formats/FileTypes.html"

getFileTypeDescription

public java.lang.String getFileTypeDescription()

Description copied from class: NetcdfFile

Get a human-readable description for this file type.

Overrides:

getFileTypeDescription in class NetcdfFile

Returns:

description of the file type

See Also:

"https://www.unidata.ucar.edu/software/netcdf-java/formats/FileTypes.html"

main

public static void main(java.lang.String[] arg)