Beginning with NetCDF version 4.1, optional support is provided for accessing data through OPeNDAP servers using the DAP protocol.
DAP support is automatically enabled if a usable curl library can be located using the curl-config program or by the –with-curl-config flag. It can forcibly be enabled or disabled using the –enable-dap flag or the –disable-dap flag, respectively. If enabled, then DAP support requires access to the curl library. Refer to the installation manual for details The NetCDF Installation and Porting Guide.
DAP uses a data model that is different from that supported by netCDF, either classic or enhanced. Generically, the DAP data model is encoded textually in a DDS (Dataset Descriptor Structure). There is a second data model for DAP attributes, which is encoded textually in a DAS (Dataset Attribute Structure). For detailed information about the DAP DDS and DAS, refer to the OPeNDAP web site http://opendap.org.
In order to access an OPeNDAP data source through the netCDF API, the file name normally used is replaced with a URL with a specific format. The URL is composed of four parts.
It is possible to see what the translation does to a particular DAP data source in either of two ways. First, one can examine the DDS source through a web browser and then examine the translation using the ncdump -h command to see the netCDF Classic translation. The ncdump output will actually be the union of the DDS with the DAS, so to see the complete translation, it is necessary to view both.
For example, if a web browser is given the following, the first URL will return the DDS for the specified dataset, and the second URL will return the DAS for the specified dataset.
http://test.opendap.org:8080/dods/dts/test.01.dds http://test.opendap.org:8080/dods/dts/test.01.das
Then by using the following ncdump command, it is possible to see the equivalent netCDF Classic translation.
ncdump -h http://test.opendap.org:8080/dods/dts/test.01
The DDS output from the web server should look like this.
Dataset { Byte b; Int32 i32; UInt32 ui32; Int16 i16; UInt16 ui16; Float32 f32; Float64 f64; String s; Url u; } SimpleTypes;
The DAS output from the web server should look like this.
Attributes { Facility { String PrincipleInvestigator ``Mark Abbott'', ``Ph.D''; String DataCenter ``COAS Environmental Computer Facility''; String DrifterType ``MetOcean WOCE/OCM''; } b { String Description ``A test byte''; String units ``unknown''; } i32 { String Description ``A 32 bit test server int''; String units ``unknown''; } }
The output from ncdump should look like this.
netcdf test { dimensions: stringdim64 = 64 ; variables: byte b ; b:Description = "A test byte" ; b:units = "unknown" ; int i32 ; i32:Description = "A 32 bit test server int" ; i32:units = "unknown" ; int ui32 ; short i16 ; short ui16 ; float f32 ; double f64 ; char s(stringdim64) ; char u(stringdim64) ; }Note that the fields of type String and type URL have suddenly acquired a dimension. This is because strings are translated to arrays of char, which requires adding an extra dimension. The size of the dimension is determined in a variety of ways and can be specified. It defaults to 64 and when read, the underlying string is either padded or truncated to that length.
Also note that the Facility
attributes do not appear
in the translation because they are neither global nor
associated with a variable in the DDS.
Alternately, one can get the text of the DDS as a global attribute by using the client parameters mechanism . In this case, the parameter “[show=dds]” can be prefixed to the URL and the data retrieved using the following command
ncdump -h [show=dds]http://test.opendap.org:8080/dods/dts/test.01.dds
The ncdump -h command will then show both the translation and the original DDS. In the above example, the DDS would appear as the global attribute “_DDS” as follows.
netcdf test { ... variables: :_DDS = "Dataset { Byte b; Int32 i32; UInt32 ui32; Int16 i16; UInt16 ui16; Float32 f32; Float64 f64; Strings; Url u; } SimpleTypes;" byte b ; ... }
Two translations are currently available.
The current default translation code translates the OPeNDAP protocol to netCDF-3 (classic). This netCDF-3 translation converts an OPeNDAP DAP protocol version 2 DDS to netCDF-3 and is designed to mimic as closely as possible the translation provided by the libnc-dap system. In addition, a translation to netCDF-4 (enhanced) is provided that is entirely new.
For illustrative purposes, the following example will be used.
Dataset { Int32 f1; Structure { Int32 f11; Structure { Int32 f1[3]; Int32 f2; } FS2[2]; } S1; Structure { Grid { Array: Float32 temp[lat=2][lon=2]; Maps: Int32 lat[lat=2]; Int32 lon[lon=2]; } G1; } S2; Grid { Array: Float32 G2[lat=2][lon=2]; Maps: Int32 lat[2]; Int32 lon[2]; } G2; Int32 lat[lat=2]; Int32 lon[lon=2]; } D1;
The set of netCDF variables is derived from the fields with primitive base types as they occur in Sequences, Grids, and Structures. The field names are modified to be fully qualified initially. For the above, the set of variables are as follows. The coordinate variables within grids are left out in order to mimic the behavior of libnc-dap.
A variable's rank is determined from three sources.
For dimensions, the rules are as follows.
dimensions: unlimited = UNLIMITED; lat = 2 ; lon = 2 ; S1.FS2.f1_0 = 2 ; S1.FS2.f1_1 = 3 ; S1.FS2.f2_0 = 2 ;
The steps for variable name translation are as follows.
It is important to note that this process could produce duplicate variables (i.e. with the same name); in that case they are all assumed to have the same content and the duplicates are ignored. If it turns out that the duplicates have different content, then the translation will not detect this. YOU HAVE BEEN WARNED.
The final netCDF-3 schema (minus attributes) is then as follows.
netcdf t { dimensions: unlimited = UNLIMITED ; lat = 2 ; lon = 2 ; S1.FS2.f1_0 = 2 ; S1.FS2.f1_1 = 3 ; S1.FS2.f2_0 = 2 ; variables: int f1 ; int lat(lat) ; int lon(lon) ; int S1.f11 ; int S1.FS2.f1(S1.FS2.f1_0, S1.FS2.f1_1) ; int S1.FS2.f2(S1_FS2_f2_0) ; float S2.G1(lat, lon) ; float G2(lat, lon) ; }In actuality, the unlimited dimension is dropped because it is unused.
There are differences with the original libnc-dap here because libnc-dap technically was incorrect. The original would have said this, for example.
int S1.FS2.f1(lat, lat) ;Note that this is incorrect because it dimensions S1.FS2.f1(2,2) rather than S1.FS2.f1(2,3).
Any variable (as determined above) that is contained directly or indirectly by a Sequence is subject to revision of its rank using the following rules.
Consider this example.
Dataset { Structure { Sequence { Int32 f1[3]; Int32 f2; } SQ1; } S1[2]; Sequence { Structure { Int32 x1[7]; } S2[5]; } Q2; } D;The corresponding netCDF-3 translation is pretty much as follows (the value for dimension Q2 may differ).
dimensions: unlimited = UNLIMITED ; // (0 currently) S1.SQ1.f1_0 = 2 ; S1.SQ1.f1_1 = 3 ; S1.SQ1.f2_0 = 2 ; Q2.S2.x1_0 = 5 ; Q2.S2.x1_1 = 7 ; Q2 = 5 ; variables: int S1.SQ1.f1(unlimited, S1.SQ1.f1_1) ; int S1.SQ1.f2(unlimited) ; int Q2.S2.x1(Q2, Q2.S2.x1_0, Q2.S2.x1_1) ;Note that for example S1.SQ1.f1_0 is not actually used because it has been folded into the unlimited dimension.
Note that there is a performance cost because the translation code has to walk the data to determine how many records are associated with the sequence. Since libnc-dap did essentially the same thing, it can be assumed that the cost is not prohibitive.
A DAP to netCDF-4 translation also exists, but is not the default and in any case is only available if the "–enable-netcdf-4" option is specified at configure time. This translation includes some elements of the libnc-dap translation, but attempts to provide a simpler (but not, unfortunately, simple) set of translation rules than is used for the netCDF-3 translation. Please note that the translation is still experimental and will change to respond to unforeseen problems or to suggested improvements.
This text will use this running example.
Dataset { Int32 f1[fdim=10]; Structure { Int32 f11; Structure { Int32 f1[3]; Int32 f2; } FS2[2]; } S1; Grid { Array: Float32 temp[lat=2][lon=2]; Maps: Int32 lat[2]; Int32 lon[2]; } G1; Sequence { Float64 depth; } Q1; } D
The rule for choosing variables is relatively simple. Start with the names of the top-level fields of the DDS. The term top-level means that the object is a direct subnode of the Dataset object. In our example, this produces the set [f1, S1, G1, Q1].
The rules for choosing and defining dimensions is as follows.
The rules for choosing user-defined types are as follows.
The types of the fields are the types of the corresponding field of the Structure, Sequence, or Grid. Note that this type might be itself a user-defined type.
From the example, we get the following compound types.
compound FS2_t { int f1(3); int f2; }; compound S1_t { int f11; FS2_t FS2(2); }; compound G1_t { float temp(2,2); int lat(2); int lon(2); } compound Q1_record_t { double depth; };
X_record_t (*) X_tIn our example, this produces the following type.
Q1_record_t (*) Q1_t
T (*) Q.f
The decision about whether to translate to netCDF-3 or netCDF-4 is determined by applying the following rules in order.
In an effort to provide better performance for some access patterns, client-side caching of data is available. The default is no caching, but it may be enabled by prefixing the URL with "[cache]".
Caching operates basically as follows.
In order to decide if you should enable caching, you will need to have some understanding of the access patterns of your program.
Unfortunately, caching is currently an all or nothing proposition, so for more complex access patterns, the decision to cache or not may not have an obvious answer. Probably a good rule of thumb is to avoid caching initially and later turn it on to see its effect on performance.
Currently, a limited set of client parameters is recognized. Parameters not listed here are ignored, but no error is signalled.
The OPeNDAP support makes use of the logging facility of the underlying oc system. Note that this is currently separate from the existing netCDF logging facility. Turning on this logging can sometimes give important information. Logging can be enabled by prefixing the url with the client parameter [log] or [log=filename], where the first case will send log output to standard error and the second will send log output to the specified file.
Users should also be aware that the DAP subsystem creates temporary files of the name dataddsXXXXXX, where XXXXX is some random string. If the program using the DAP subsystem crashes, these files may be left around. It is perfectly safe to delete them. Also, if you are accessing data over an NFS mount, you may see some .nfsxxxxx files; those can be ignored as well.