Issue regarding the use of "dods:" in DODSNetcdfFile

netCDF-Java/CDM

The netCDF Java library provides an interface for scientific data access. It can be used to read scientific data from a variety of file formats including netCDF, HDF, GRIB, BUFR, and many others. By itself, the netCDF-Java library can only write netCDF-3 files. It can write netCDF-4 files by using JNI to call the netCDF-C library. It also implements Unidata's Common Data Model (CDM) to provide data geolocation capabilities.

For more information about netCDF-Java/CDM, see the netCDF-Java web page at

https://www.unidata.ucar.edu/software/netcdf-java/

and the CDM web page at

https://docs.unidata.ucar.edu/netcdf-java/current/userguide/common_data_model_overview.html

You can obtain a copy of the latest released version of netCDF-Java software from

https://www.unidata.ucar.edu/downloads/netcdf-java/

Contributors

Are you looking to contribute to the netCDF-Java efforts? That's great! Please see our contributors guide for more information!

NetCDF Markup Language (NcML)

NcML is an XML representation of netCDF metadata, it approximates the header information one gets from a netCDF file with the "ncdump -h" command. NcML is similar to the netCDF CDL (network Common data form Description Language), except, of course, it uses XML syntax.

Beyond simply describing a netCDF file, it can also be used to describe changes to existing netCDF files. A limited number of tools, mainly netCDF-Java based tools, support these features of NcML.

For more information about NcML, see the NcML web page at

https://docs.unidata.ucar.edu/netcdf-java/current/userguide/ncml_overview.html

THREDDS Catalogs

THREDDS Catalogs can be thought of as representing logical directories of on-line data resources. They are encoded as XML and provide a place for annotations and other metadata about the data resources. While the THREDDS Data Server (TDS) generates THREDDS Catalogs, THREDDS Catalogs are not limited to those produced by the TDS. These XML documents are how THREDDS-enabled data consumers find out what data is available from data providers.

THREDDS Catalog documentation (including the specification) is available at

https://docs.unidata.ucar.edu/tds/current/userguide/basic_client_catalog.html

Licensing

netCDF-Java is released under the BSD-3 licence, which can be found here.

Furthermore, this project includes code from third-party open-source software components:

ERDDAP: for details, see waterml/README.md
JUnit: for details, see cdm-test-utils/README.md
Edal (The University of Reading): The CDM calendars are implemented using classes from Jon Blower's uk.ac.rdg.resc.edal.time package.

Each of these software components have their own license. Please see third-party-licenses/.

How to use

The latest released and snapshot software artifacts (e.g. .jar files) are available from Unidata's Nexus repository:

https://artifacts.unidata.ucar.edu/#browse/browse:unidata-all

To build netCDF-java from this repository, follow this tutorial.

To use the netCDF-Java library as a dependency using maven or gradle, follow these instructions.

Previous releases

Prior to v5.0.0, the netCDF-Java/CDM library and the THREDDS Data Server (TDS) have been built and released together. Starting with version 5, these two packages have been decoupled, allowing new features or bug fixes to be implemented in each package separately, and released independently. Releases prior to v5.0.0 were managed at https://github.com/unidata/thredds, which holds the combined code based used by v4.6 and earlier.

	// canonicalize name
	String urlName = datasetURL; // actual URL uses http:
	this.location = datasetURL; // canonical name uses "dods:"
	if (datasetURL.startsWith("dods:")) {
	urlName = "http:" + datasetURL.substring(5);
	} else if (datasetURL.startsWith("http:")) {
	this.location = "dods:" + datasetURL.substring(5);
	} else if (datasetURL.startsWith("https:")) {
	this.location = "dods:" + datasetURL.substring(6);
	} else if (datasetURL.startsWith("file:")) {
	this.location = datasetURL;
	} else {
	throw new java.net.MalformedURLException(datasetURL + " must start with dods: or http: or file:");
	}

	Variable v = new Variable(ncfile, null, null, shortName);
	if (datatype == DIFF_PHASE) {
	v.setDataType(DataType.USHORT);
	} else {
	v.setDataType(DataType.UBYTE);
	}

	int dataCount = getGateCount(datatype);
	if (datatype == DIFF_PHASE) {
	short[] data = new short[dataCount];
	raf.readShort(data, 0, dataCount);

	for (int gateIdx : gateRange) {
	if (gateIdx >= dataCount)
	ii.setShortNext(MISSING_DATA);
	else
	ii.setShortNext(data[gateIdx]);
	}
	} else {

	byte[] data = new byte[dataCount];
	raf.readFully(data);
	// short [] ds = convertunsignedByte2Short(data);
	for (int gateIdx : gateRange) {
	if (gateIdx >= dataCount)
	ii.setByteNext(MISSING_DATA);
	else
	ii.setByteNext(data[gateIdx]);
	}

CF	NetCDF Java
point	POINT
profile	PROFILE
timeSeries	STATION
timeSeriesProfile	STATION_PROFILE
trajectory	TRAJECTORY
trajectoryProfile	SECTION

	dbp1 = din.readInt();
	dbp2 = din.readInt();
	dbp3 = din.readInt();
	dbp4 = din.readInt();
	dbp5 = din.readInt();
	dbp6 = din.readInt();
	dbp7 = din.readInt();
	dbp8 = din.readInt();
	dbp9 = din.readInt();

	vcp = getDataBlockValue(din, (short) dbp1, 40);
	int dbpp4 = 0;
	int dbpp5 = 0;
	int dbpp6 = 0;
	int dbpp7 = 0;
	int dbpp8 = 0;
	int dbpp9 = 0;

	if (dbp4 > 0) {
	String tname = getDataBlockStringValue(din, (short) dbp4, 1, 3);
	if (tname.startsWith("REF")) {
	hasHighResREFData = true;
	dbpp4 = dbp4;
	} else if (tname.startsWith("VEL")) {
	hasHighResVELData = true;
	dbpp5 = dbp4;
	} else if (tname.startsWith("SW")) {
	hasHighResSWData = true;
	dbpp6 = dbp4;
	} else if (tname.startsWith("ZDR")) {
	hasHighResZDRData = true;
	dbpp7 = dbp4;
	} else if (tname.startsWith("PHI")) {
	hasHighResPHIData = true;
	dbpp8 = dbp4;
	} else if (tname.startsWith("RHO")) {
	hasHighResRHOData = true;
	dbpp9 = dbp4;
	} else {
	logger.warn("Missing radial product dbp4={} tname={}", dbp4, tname);
	}

	}
	if (dbp5 > 0) {

	String tname = getDataBlockStringValue(din, (short) dbp5, 1, 3);
	if (tname.startsWith("REF")) {
	hasHighResREFData = true;
	dbpp4 = dbp5;
	} else if (tname.startsWith("VEL")) {
	hasHighResVELData = true;
	dbpp5 = dbp5;
	} else if (tname.startsWith("SW")) {
	hasHighResSWData = true;
	dbpp6 = dbp5;
	} else if (tname.startsWith("ZDR")) {
	hasHighResZDRData = true;
	dbpp7 = dbp5;
	} else if (tname.startsWith("PHI")) {
	hasHighResPHIData = true;
	dbpp8 = dbp5;
	} else if (tname.startsWith("RHO")) {
	hasHighResRHOData = true;
	dbpp9 = dbp5;
	} else {
	logger.warn("Missing radial product dbp5={} tname={}", dbp5, tname);
	}
	}
	if (dbp6 > 0) {

	String tname = getDataBlockStringValue(din, (short) dbp6, 1, 3);
	if (tname.startsWith("REF")) {
	hasHighResREFData = true;
	dbpp4 = dbp6;
	} else if (tname.startsWith("VEL")) {
	hasHighResVELData = true;
	dbpp5 = dbp6;
	} else if (tname.startsWith("SW")) {
	hasHighResSWData = true;
	dbpp6 = dbp6;
	} else if (tname.startsWith("ZDR")) {
	hasHighResZDRData = true;
	dbpp7 = dbp6;
	} else if (tname.startsWith("PHI")) {
	hasHighResPHIData = true;
	dbpp8 = dbp6;
	} else if (tname.startsWith("RHO")) {
	hasHighResRHOData = true;
	dbpp9 = dbp6;
	} else {
	logger.warn("Missing radial product dbp6={} tname={}", dbp6, tname);
	}
	}

	if (dbp7 > 0) {

	String tname = getDataBlockStringValue(din, (short) dbp7, 1, 3);
	if (tname.startsWith("REF")) {
	hasHighResREFData = true;
	dbpp4 = dbp7;
	} else if (tname.startsWith("VEL")) {
	hasHighResVELData = true;
	dbpp5 = dbp7;
	} else if (tname.startsWith("SW")) {
	hasHighResSWData = true;
	dbpp6 = dbp7;
	} else if (tname.startsWith("ZDR")) {
	hasHighResZDRData = true;
	dbpp7 = dbp7;
	} else if (tname.startsWith("PHI")) {
	hasHighResPHIData = true;
	dbpp8 = dbp7;
	} else if (tname.startsWith("RHO")) {
	hasHighResRHOData = true;
	dbpp9 = dbp7;
	} else {
	logger.warn("Missing radial product dbp7={} tname={}", dbp7, tname);
	}
	}

	if (dbp8 > 0) {

	String tname = getDataBlockStringValue(din, (short) dbp8, 1, 3);
	if (tname.startsWith("REF")) {
	hasHighResREFData = true;
	dbpp4 = dbp8;
	} else if (tname.startsWith("VEL")) {
	hasHighResVELData = true;
	dbpp5 = dbp8;
	} else if (tname.startsWith("SW")) {
	hasHighResSWData = true;
	dbpp6 = dbp8;
	} else if (tname.startsWith("ZDR")) {
	hasHighResZDRData = true;
	dbpp7 = dbp8;
	} else if (tname.startsWith("PHI")) {
	hasHighResPHIData = true;
	dbpp8 = dbp8;
	} else if (tname.startsWith("RHO")) {
	hasHighResRHOData = true;
	dbpp9 = dbp8;
	} else {
	logger.warn("Missing radial product dbp8={} tname={}", dbp8, tname);
	}
	}

	if (dbp9 > 0) {

	String tname = getDataBlockStringValue(din, (short) dbp9, 1, 3);
	if (tname.startsWith("REF")) {
	hasHighResREFData = true;
	dbpp4 = dbp9;
	} else if (tname.startsWith("VEL")) {
	hasHighResVELData = true;
	dbpp5 = dbp9;
	} else if (tname.startsWith("SW")) {
	hasHighResSWData = true;
	dbpp6 = dbp9;
	} else if (tname.startsWith("ZDR")) {
	hasHighResZDRData = true;
	dbpp7 = dbp9;
	} else if (tname.startsWith("PHI")) {
	hasHighResPHIData = true;
	dbpp8 = dbp9;
	} else if (tname.startsWith("RHO")) {
	hasHighResRHOData = true;
	dbpp9 = dbp9;
	} else {
	logger.warn("Missing radial product dbp9={} tname={}", dbp9, tname);
	}
	}
	// hasHighResREFData = (dbp4 > 0);

	if (hasHighResREFData) {
	reflectHR_gate_count = getDataBlockValue(din, (short) dbpp4, 8);
	reflectHR_first_gate = getDataBlockValue(din, (short) dbpp4, 10);
	reflectHR_gate_size = getDataBlockValue(din, (short) dbpp4, 12);
	ref_rf_threshold = getDataBlockValue(din, (short) dbpp4, 14);
	ref_snr_threshold = getDataBlockValue(din, (short) dbpp4, 16);
	reflectHR_scale = getDataBlockValue1(din, (short) dbpp4, 20);
	reflectHR_addoffset = getDataBlockValue1(din, (short) dbpp4, 24);
	reflectHR_offset = (short) (dbpp4 + 28);

	}
	// hasHighResVELData = (dbp5 > 0);
	if (hasHighResVELData) {
	velocityHR_gate_count = getDataBlockValue(din, (short) dbpp5, 8);
	velocityHR_first_gate = getDataBlockValue(din, (short) dbpp5, 10);
	velocityHR_gate_size = getDataBlockValue(din, (short) dbpp5, 12);
	vel_rf_threshold = getDataBlockValue(din, (short) dbpp5, 14);
	vel_snr_threshold = getDataBlockValue(din, (short) dbpp5, 16);
	velocityHR_scale = getDataBlockValue1(din, (short) dbpp5, 20);
	velocityHR_addoffset = getDataBlockValue1(din, (short) dbpp5, 24);
	velocityHR_offset = (short) (dbpp5 + 28);

	}
	// hasHighResSWData = (dbp6 > 0);
	if (hasHighResSWData) {
	spectrumHR_gate_count = getDataBlockValue(din, (short) dbpp6, 8);
	spectrumHR_first_gate = getDataBlockValue(din, (short) dbpp6, 10);
	spectrumHR_gate_size = getDataBlockValue(din, (short) dbpp6, 12);
	sw_rf_threshold = getDataBlockValue(din, (short) dbpp6, 14);
	sw_snr_threshold = getDataBlockValue(din, (short) dbpp6, 16);
	spectrumHR_scale = getDataBlockValue1(din, (short) dbpp6, 20);
	spectrumHR_addoffset = getDataBlockValue1(din, (short) dbpp6, 24);
	spectrumHR_offset = (short) (dbpp6 + 28);

	}
	// hasHighResZDRData = (dbp7 > 0);
	if (hasHighResZDRData) {
	zdrHR_gate_count = getDataBlockValue(din, (short) dbpp7, 8);
	zdrHR_first_gate = getDataBlockValue(din, (short) dbpp7, 10);
	zdrHR_gate_size = getDataBlockValue(din, (short) dbpp7, 12);
	zdrHR_rf_threshold = getDataBlockValue(din, (short) dbpp7, 14);
	zdrHR_snr_threshold = getDataBlockValue(din, (short) dbpp7, 16);
	zdrHR_scale = getDataBlockValue1(din, (short) dbpp7, 20);
	zdrHR_addoffset = getDataBlockValue1(din, (short) dbpp7, 24);
	zdrHR_offset = (short) (dbpp7 + 28);
	}
	// hasHighResPHIData = (dbp8 > 0);
	if (hasHighResPHIData) {
	phiHR_gate_count = getDataBlockValue(din, (short) dbpp8, 8);
	phiHR_first_gate = getDataBlockValue(din, (short) dbpp8, 10);
	phiHR_gate_size = getDataBlockValue(din, (short) dbpp8, 12);
	phiHR_rf_threshold = getDataBlockValue(din, (short) dbpp8, 14);
	phiHR_snr_threshold = getDataBlockValue(din, (short) dbpp8, 16);
	phiHR_scale = getDataBlockValue1(din, (short) dbpp8, 20);
	phiHR_addoffset = getDataBlockValue1(din, (short) dbpp8, 24);
	phiHR_offset = (short) (dbpp8 + 28);
	}
	// hasHighResRHOData = (dbp9 > 0);
	if (hasHighResRHOData) {
	rhoHR_gate_count = getDataBlockValue(din, (short) dbpp9, 8);
	rhoHR_first_gate = getDataBlockValue(din, (short) dbpp9, 10);
	rhoHR_gate_size = getDataBlockValue(din, (short) dbpp9, 12);
	rhoHR_rf_threshold = getDataBlockValue(din, (short) dbpp9, 14);
	rhoHR_snr_threshold = getDataBlockValue(din, (short) dbpp9, 16);
	rhoHR_scale = getDataBlockValue1(din, (short) dbpp9, 20);
	rhoHR_addoffset = getDataBlockValue1(din, (short) dbpp9, 24);
	rhoHR_offset = (short) (dbpp9 + 28);
	}

	NetcdfFile ncfile = createNetcdfFile(filepath, null);
	NetcdfDataset ncd = new NetcdfDataset(ncfile, ENHANCEMENT);

	public String getUnitsString() {
	return "N/A";
	}

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