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/*! \page dap_support DAP Support
\tableofcontents
\section dap_introduction OPeNDAP Introduction
Beginning with netCDF version 4.1, optional support is provided for
accessing data through OPeNDAP servers using the DAP protocol.
Currently, only DAP protocol version 2 is supported; DAP protocol
version 4 support is under development.
DAP support is automatically enabled if a usable curl library can be
set using the LDFLAGS environment variable (similar to the way
that the HDF5 libraries are referenced).
DAP support can forcibly be enabled or disabled using the --enable-dap
flag or the --disable-dap flag, respectively. If enabled,
then DAP2 support requires access to the curl library.
Refer to the installation manual for details
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.
\subsection dap_dap_information OPeNDAP Documentation
See the following pages for more information.
- \subpage dap_accessing_data
- <a href="auth.html">netCDF Authorization Support</a>
- \subpage esg
- \subpage dap_to_netcdf
- \subpage var_dim_trans
- \subpage var_name_trans
\page dap_accessing_data Accessing OPeNDAP Data
\tableofcontents
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 three parts.
- URL - this is a standard form URL such as
http://remotetest.unidata.ucar.edu/dts/test.01
- Constraints - these are suffixed to the URL and take the form
“?\<projections>&\<selections>”. The meaning of the terms projection
and selection is somewhat complicated; and the OPeNDAP web site,
http://www.opendap.org , should be consulted. The interaction of DAP
constraints with netCDF is complex and at the moment requires an
understanding of how DAP is translated to netCDF.
- Client parameters - these may be specified in either of
two ways. The older, deprecated form prefixes text to the
front of the url and is of the the general form [\<name>]
or [\<name>=value]. Examples include [show=fetch] and
[noprefetch]. The newer, preferred form prefixes the
parameters to the end of the url using the semi-standard '#'
format: e.g. http://....#show=fetch&noprefetch.
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.
\code
http://remotetest.unidata.ucar.edu/dts/test.01.dds
http://remotetest.unidata.ucar.edu/dts/test.01.das
\endcode
Then by using the following ncdump command, it is possible to see the
equivalent netCDF Classic translation.
\code
ncdump -h http://remotetest.unidata.ucar.edu/dts/test.01
\endcode
The DDS output from the web server should look like this.
\code
Dataset {
Byte b;
Int32 i32;
UInt32 ui32;
Int16 i16;
UInt16 ui16;
Float32 f32;
Float64 f64;
String s;
Url u;
} SimpleTypes;
\endcode
The DAS output from the web server should look like this.
\code
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'';
}
}
\endcode
The output from ncdump should look like this.
\code
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) ;
}
\endcode
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 used, and the data retrieved using
the following command
\code
ncdump -h http://remotetest.unidata.ucar.edu/dts/test.01.dds#show=dds
\endcode
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.
\code
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 ;
...
}
\endcode
\page dap_to_netcdf DAP to NetCDF Translation Rules
\tableofcontents
Currently only one translation available: DAP 2 Protocol to netCDF-3.
There used to be a DAP 2 Protocol to netCDF-4 translation
but that has been removed until the DAP4 protocol is available.
\section nc3_trans_rules netCDF-3 Translation Rules
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, except that some errors in that older translation have
been fixed.
For illustrative purposes, the following example will be used.
\code
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;
\endcode
\section var_def Variable Definition
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.
\code
f1
S1.f11
S1.FS2.f1
S1.FS2.f2
S2.G1.temp
S2.G2.G2
lat
lon
\endcode
\page var_dim_trans Variable Dimension Translation
\tableofcontents
A variable's rank is determined from three sources.
- The variable has the dimensions associated with the field it
represents (e.g. S1.FS2.f1[3] in the above example).
- The variable inherits the dimensions associated with any containing
structure that has a rank greater than zero. These dimensions precede
those of case 1. Thus, we have in our example, f1[2][3], where the
first dimension comes from the containing Structure FS2[2].
- The variable's set of dimensions are altered if any of its
containers is a DAP DDS Sequence. This is discussed more fully below.
If the type of the netCDF variable is char, then an extra string
dimension is added as the last dimension.
\section dim_trans Dimension translation
For dimensions, the rules are as follows.
Fields in dimensioned structures inherit the dimension of the
structure; thus the above list would have the following dimensioned
variables.
\code
S1.FS2.f1 -> S1.FS2.f1[2][3]
S1.FS2.f2 -> S1.FS2.f2[2]
S2.G1.temp -> S2.G1.temp[lat=2][lon=2]
S2.G1.lat -> S2.G1.lat[lat=2]
S2.G1.lon -> S2.G1.lon[lon=2]
S2.G2.G2 -> S2.G2.lon[lat=2][lon=2]
S2.G2.lat -> S2.G2.lat[lat=2]
S2.G2.lon -> S2.G2.lon[lon=2]
lat -> lat[lat=2]
lon -> lon[lon=2]
\endcode
Collect all of the dimension specifications from the DDS, both named
and anonymous (unnamed) For each unique anonymous dimension with value
NN create a netCDF dimension of the form "XX_<i>=NN", where XX is the
fully qualified name of the variable and i is the i'th (inherited)
dimension of the array where the anonymous dimension occurs. For our
example, this would create the following dimensions.
\code
S1.FS2.f1_0 = 2 ;
S1.FS2.f1_1 = 3 ;
S1.FS2.f2_0 = 2 ;
S2.G2.lat_0 = 2 ;
S2.G2.lon_0 = 2 ;
\endcode
If however, the anonymous dimension is the single dimension of a MAP
vector in a Grid then the dimension is given the same name as the map
vector This leads to the following.
\code
S2.G2.lat_0 -> S2.G2.lat
S2.G2.lon_0 -> S2.G2.lon
\endcode
For each unique named dimension "<name>=NN", create a netCDF dimension
of the form "<name>=NN", where name has the qualifications removed. If
this leads to duplicates (i.e. same name and same value), then the
duplicates are ignored. This produces the following.
\code
S2.G2.lat -> lat
S2.G2.lon -> lon
\endcode
Note that this produces duplicates that will be ignored later.
At this point the only dimensions left to process should be named
dimensions with the same name as some dimension from step number 3,
but with a different value. For those dimensions create a dimension of
the form "<name>M=NN" where M is a counter starting at 1. The example
has no instances of this.
Finally and if needed, define a single UNLIMITED dimension named
"unlimited" with value zero. Unlimited will be used to handle certain
kinds of DAP sequences (see below).
This leads to the following set of dimensions.
\code
dimensions:
unlimited = UNLIMITED;
lat = 2 ;
lon = 2 ;
S1.FS2.f1_0 = 2 ;
S1.FS2.f1_1 = 3 ;
S1.FS2.f2_0 = 2 ;
\endcode
\page var_name_trans Variable Name Translation
\tableofcontents
The steps for variable name translation are as follows.
Take the set of variables captured above. Thus for the above DDS, the
following fields would be collected.
\code
f1
S1.f11
S1.FS2.f1
S1.FS2.f2
S2.G1.temp
S2.G2.G2
lat
lon
\endcode
All grid array variables are renamed to be the same as the containing
grid and the grid prefix is removed. In the above DDS, this results in
the following changes.
\code
G1.temp -> G1
G2.G2 -> G2
\endcode
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.
\code
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) ;
}
\endcode
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.
\code
int S1.FS2.f1(lat, lat) ;
\endcode
Note that this is incorrect because it dimensions S1.FS2.f1(2,2)
rather than S1.FS2.f1(2,3).
\section dap_translation Translating DAP DDS Sequences
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.
Let the variable be contained in Sequence Q1, where Q1 is the
innermost containing sequence. If Q1 is itself contained (directly or
indirectly) in a sequence, or Q1 is contained (again directly or
indirectly) in a structure that has rank greater than 0, then the
variable will have an initial UNLIMITED dimension. Further, all
dimensions coming from "above" and including (in the containment
sense) the innermost Sequence, Q1, will be removed and replaced by
that single UNLIMITED dimension. The size associated with that
UNLIMITED is zero, which means that its contents are inaccessible
through the netCDF-3 API. Again, this differs from libnc-dap, which
leaves out such variables. Again, however, this difference is backward
compatible.
If the variable is contained in a single Sequence (i.e. not nested)
and all containing structures have rank 0, then the variable will have
an initial dimension whose size is the record count for that
Sequence. The name of the new dimension will be the name of the
Sequence.
Consider this example.
\code
Dataset {
Structure {
Sequence {
Int32 f1[3];
Int32 f2;
} SQ1;
} S1[2];
Sequence {
Structure {
Int32 x1[7];
} S2[5];
} Q2;
} D;
\endcode
The corresponding netCDF-3 translation is pretty much as follows (the
value for dimension Q2 may differ).
\code
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) ;
\endcode
Note that for example S1.SQ1.f1_0 is not actually used because it has
been folded into the unlimited dimension.
Note that for sequences without a leading unlimited dimension, 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.
\section dap_caching Caching
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 the parameter "cache".
Caching operates basically as follows.
When a URL is first accessed using nc_open(), netCDF automatically
does a pre-fetch of selected variables. These include all variables
smaller than a specified (and user definable) size. This allows, for
example, quick access to coordinate variables. This can be suppressed
with the parameter "noprefetch".
Whenever a request is made using some variant of the nc_get_var() API
procedures, the complete variable is fetched and stored in the cache
as a new cache entry. Subsequence requests for any part of that
variable will access the cache entry to obtain the data.
The cache may become too full, either because there are too many
entries or because it is taking up too much disk space. In this case
cache entries are purged until the cache size limits are reached. The
cache purge algorithm is LRU (least recently used) so that variables
that are repeatedly referenced will tend to stay in the cache.
The cache is completely purged when nc_close() is invoked.
In order to decide if you should enable caching, you will need to have
some understanding of the access patterns of your program.
The ncdump program always dumps one or more whole variables so it
turns on caching.
If your program accesses only parts of a number of variables, then
caching should probably not be used since fetching whole variables
will probably slow down your program for no purpose.
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.
\section dap_defined_params Defined Client Parameters
Currently, a limited set of client parameters is
recognized. Parameters not listed here are ignored, but no error is
signalled.
Parameter Name Legal Values Semantics
- "log" | "log=<file>" - Turn on logging and send the log output to
the specified file. If no file is specified, then output is sent to standard
error.
- "show=... das|dds|url" - This causes information to appear as
specific global attributes. The currently recognized tags are "dds"
to display the underlying DDS, "das" similarly, and "url" to display
the url used to retrieve the data. This parameter may be specified
multiple times (e.g. “show=dds&show=url”).
- "show=fetch" - This parameter causes the netCDF code to log a copy
of the complete url for every HTTP get request. If logging is
enabled, then this can be helpful in checking to see the access
behavior of the netCDF code.
- "stringlength=NN" - Specify the default string length to use for
string dimensions. The default is 64.
- "stringlength_<var>=NN" - Specify the default string length to use
for a string dimension for the specified variable. The default is
64.
- "cache" - This enables caching.
- "cachelimit=NN" - Specify the maximum amount of space allowed for
the cache.
- "cachecount=NN" - Specify the maximum number of entries in the
cache.
- "noprefetch" - This disables prefetch of small variables.
\section dap_debug Notes on Debugging OPeNDAP Access
The OPeNDAP support makes use of the logging facility of the
underlying oc system (see http://www.opendap.org/oc).
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
using 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 if one is
accessing data over an NFS mount, one may see some .nfsxxxxx files;
those can be ignored.
\subsection http_config HTTP Configuration.
Limited support for configuring the http connection is provided via
parameters in the “.dodsrc” configuration file. The relevant .dodsrc file is
located by first looking in the current working directory, and if not
found, then looking in the directory specified by the “$HOME”
environment variable.
Entries in the .dodsrc file are of the form:
\code
['['<url>']']<key>=<value>
\endcode
That is, it consists of a key name and value pair and optionally
preceded by a url enclosed in square brackets.
For given KEY and URL strings, the value chosen is as follows:
If URL is null, then look for the .dodsrc entry that has no url prefix
and whose key is same as the KEY for which we are looking.
If the URL is not null, then look for all the .dodsrc entries that
have a url, URL1, say, and for which URL1 is a prefix (in the string
sense) of URL. For example, if URL = http//x.y/a, then it will match
entries of the form
\code
1. [http//x.y/a]KEY=VALUE
2. [http//x.y/a/b]KEY=VALUE
\endcode
It will not match an entry of the form
\code
[http//x.y/b]KEY=VALUE
\endcode
because “http://x.y/b” is not a string prefix of
“http://x.y/a”. Finally from the set so constructed, choose the entry
with the longest url prefix: “http//x.y/a/b]KEY=VALUE” in this case.
Currently, the supported set of keys (with descriptions) are as
follows.
<pre>
HTTP.VERBOSE
Type: boolean ("1"/"0")
Description: Produce verbose output, especially using SSL.
Related CURL Flags: CURLOPT_VERBOSE
HTTP.DEFLATE
Type: boolean ("1"/"0")
Description: Allow use of compression by the server.
Related CURL Flags: CURLOPT_ENCODING
HTTP.COOKIEJAR
Type: String representing file path
Description: Specify the name of file into which to store cookies. Defaults to in-memory storage.
Related CURL Flags:CURLOPT_COOKIEJAR
HTTP.CREDENTIALS.USER
Type: String representing user name
Description: Specify the user name for Digest and Basic authentication.
Related CURL Flags:
HTTP.CREDENTIALS.PASSWORD
Type: String representing password
Type: boolean ("1"/"0")
Description: Specify the password for Digest and Basic authentication.
Related CURL Flags:
HTTP.SSL.CERTIFICATE
Type: String representing file path
Description: Path to a file containing a PEM cerficate.
Related CURL Flags: CURLOPT_CERT
HTTP.SSL.KEY
Type: String representing file path
Description: Same as HTTP.SSL.CERTIFICATE, and should usually have the same value.
Related CURL Flags: CURLOPT_SSLKEY
HTTP.SSL.KEYPASSWORD
Type: String representing password
Description: Password for accessing the HTTP.SSL.KEY/HTTP.SSL.CERTIFICATE
Related CURL Flags: CURLOPT_KEYPASSWORD
HTTP.SSL.CAPATH
Type: String representing directory
Description: Path to a directory containing trusted certificates for validating server sertificates.
Related CURL Flags: CURLOPT_CAPATH
HTTP.SSL.VALIDATE
Type: boolean ("1"/"0")
Description: Cause the client to verify the server's presented certificate.
Related CURL Flags: CURLOPT_SSL_VERIFYPEER, CURLOPT_SSL_VERIFYHOST
HTTP.TIMEOUT
Type: String ("dddddd")
Description: Specify the maximum time in seconds that you allow the http transfer operation to take.
Related CURL Flags: CURLOPT_TIMEOUT, CURLOPT_NOSIGNAL
HTTP.PROXY_SERVER
Type: String representing url to access the proxy: (e.g.http://[username:password@]host[:port])
Description: Specify the needed information for accessing a proxy.
Related CURL Flags: CURLOPT_PROXY, CURLOPT_PROXYHOST, CURLOPT_PROXYUSERPWD
</pre>
The related curl flags line indicates the curl flags modified by this
key. See the libcurl documentation of the curl_easy_setopt() function
for more detail (http://curl.haxx.se/libcurl/c/curl_easy_setopt.html).
For ESG client side key support, the following entries must be specified:
\code
HTTP.SSL.VALIDATE
HTTP.COOKIEJAR
HTTP.SSL.CERTIFICATE
HTTP.SSL.KEY
HTTP.SSL.CAPATH
\endcode
Additionally, for ESG, the HTTP.SSL.CERTIFICATE and HTTP.SSL.KEY
entries should have same value, which is the file path for the
certificate produced by MyProxyLogon. The HTTP.SSL.CAPATH entry should
be the path to the "certificates" directory produced by MyProxyLogon.
*/
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