netcdf-c/NUG/DAP2.dox

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\page dap2 DAP2 Protocol Support

\tableofcontents

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# DAP2 (OPeNDAP) Introduction {#dap2_intro}

Beginning with netCDF version 4.1, optional support is provided for
accessing data through servers supporting the DAP2 protocol.

DAP2 support is enabled if the _--enable-dap__ option
is used with _./configure_. If DAP2 support is enabled, then
a usable version of _libcurl_ must be specified
using the _LDFLAGS_ environment variable (similar to the way
that the _HDF5_ libraries are referenced).
Refer to the installation manual for details.
By default DAP2 support is enabled if _libcurl_ is found.
DAP2 support can be disabled using the _--disable-dap_.

DAP2 uses a data model that is different from that supported by
netCDF, either classic or enhanced. Generically, the DAP2
meta-data is encoded textually in a _DDS_ (Dataset Descriptor
Structure). There is a second textual object, the _DAS_ (Dataset
Attribute Structure), for specifying DAP2 attributes.  . For
detailed information about the DAP2 DDS and DAS, refer to the
OPeNDAP web site http://opendap.org.

# Accessing DAP2 Data {#dap2_accessing_data}

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 DAP2
   constraints with netCDF is complex and at the moment requires an
   understanding of how DAP2 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
DAP2 data source by examining the DDS source through a web
browser and then examining 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 via the
browser.

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://remotetest.unidata.ucar.edu/dts/test.01.dds
     http://remotetest.unidata.ucar.edu/dts/test.01.das
````

Then by using the following ncdump command, it is possible to see the
equivalent netCDF Classic translation.
````
     ncdump -h http://remotetest.unidata.ucar.edu/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 the netCDF model does
not support strings, but DAP2 does support strings.
So, DAP2 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.

# DAP2 to NetCDF Translation Rules {#dap2_to_netcdf}

The netCDF library DAP2 support code translate the DAP2 data model
into the netCDF classic (netCDF-3) data model.

## netCDF-3 Translation Rules {#dap2_nc32_trans_rules}

The netCDF-3 translation is designed to mimic as closely as
possible the translation provided by the now obsolete libnc-dap2
system, except that some errors in that older translation have
been fixed.

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;
````

## Variable Definition {#dap2_var2_def}

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-dap2.
````
    f1
    S1.f11
    S1.FS2.f1
    S1.FS2.f2
    S2.G1.temp
    S2.G2.G2
    lat
    lon
````

## DAP2 Reserved Keywords {#dap2_reserved_keywords}

In the OPeNDAP DAP2 protocol, there are a number of reserved keywords.  These keywords are case insensitive and if you use one as a netCDF variable name, you may encounter odd behavior such as case changes (depending on the client DDS/DAS parser).  The list of reserved keywords as used by the netCDF-C library parser are as follows:

- alias
- array
- attributes
- byte
- dataset
- error
- float32
- float64
- grid
- int16
- int32
- maps
- sequence
- string
- structure
- uint16
- uint32
- url
- code
- message
- program_type
- program


## Variable Dimension Translation {#dap2_var_dim_trans}

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 DAP2 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.

## Dimension translation {#dap2_dim2_trans}

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.
````
        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]
````

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.
````
        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 ;
````

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.
````
        S2.G2.lat_0 -> S2.G2.lat
        S2.G2.lon_0 -> S2.G2.lon
````

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.
````
        S2.G2.lat -> lat
        S2.G2.lon -> lon
````

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 DAP2 sequences (see below).

This leads to the following set of dimensions.
````
dimensions:
  unlimited = UNLIMITED;
  lat = 2 ;
  lon = 2 ;
  S1.FS2.f1_0 = 2 ;
  S1.FS2.f1_1 = 3 ;
  S1.FS2.f2_0 = 2 ;
````

## Variable Name Translation {#dap2_var_name_trans}

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.
````
        f1
        S1.f11
        S1.FS2.f1
        S1.FS2.f2
        S2.G1.temp
        S2.G2.G2
        lat
        lon
````

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.
````
        G1.temp -> G1
        G2.G2 -> G2
````

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 practice, the unlimited dimension is dropped because it is unused.

There are differences with the original libnc-dap2 here because
libnc-dap2 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).

## Translating DAP2 DDS Sequences {#dap2_translation}

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-dap2, 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.
````
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 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-dap2 did essentially the same thing, it can be
assumed that the cost is not prohibitive.

# Caching {#dap2_dap2_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.

# Defined Client Parameters {#dap2_dap2_defined_params}

Currently, a limited set of client parameters is
recognized. Parameters not listed here are ignored, but no error is
signalled. All names are case insensitive.

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 log 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. The name "maxstrlen" is an
  alias for "stringlength".
- "stringlength_\<var\>=NN" - Specify the default string length to use
  for a string dimension for the specified variable. The default is
  64. The name "maxstrlen_\<var\>" is an alias for "stringlength_\<var\>".
- "cache" - This enables caching.
- "nocache" - This disbles caching.
- "cachelimit=NN" - Specify the maximum amount of space allowed for
  the cache.
- "cachecount=NN" - Specify the maximum number of entries in the
  cache.
- "prefetch" - This enables prefetch of small variables (default).
- "noprefetch" - This disables prefetch of small variables.
- "fillmismatch" - This enables _FillValue/Variable type mismatch.
- "nofillmismatch" - This disables _FillValue/Variable type mismatch (default).

# Notes on Debugging OPeNDAP Access {#dap2_dap2_debug}

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.

## HTTP Configuration. {#dap2_http2_config}

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:
````
     ['['<url>']']<key>=<value>
````

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 has the same host and port
as URL. All parts of the url's except host and port are ignored.
For example, if URL = http//x.y/a, then it will match
entries of the form
_[http//x.y/a]KEY=VALUE_ or _[http//x.y/b]KEY=VALUE_.
It will not match an entry of the form _[http//x.y:8080]KEY=VALUE
because the second has a port number (8080) different than the URL.
Finally from the set so constructed, choose the first matching entry.

Currently, the supported set of keys (with descriptions) are as
follows.

1. HTTP.VERBOSE  
        Type: boolean ("1"/"0")  
        Description: Produce verbose output, especially using SSL.  
        Related CURL Flags: CURLOPT_VERBOSE  
1. HTTP.DEFLATE  
        Type: boolean ("1"/"0")  
        Description: Allow use of compression by the server.  
        Related CURL Flags: CURLOPT_ENCODING  
1. 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  
1. HTTP.CREDENTIALS.USER  
        Type: String representing user name  
        Description: Specify the user name for Digest and Basic authentication.  
        Related CURL Flags:  
1. HTTP.CREDENTIALS.PASSWORD  
        Type: String representing password  
        Type: boolean ("1"/"0")  
        Description: Specify the password for Digest and Basic authentication.  
        Related CURL Flags:  
1. HTTP.SSL.CERTIFICATE  
        Type: String representing file path  
        Description: Path to a file containing a PEM cerficate.  
        Related CURL Flags: CURLOPT_CERT  
1. 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  
1. HTTP.SSL.KEYPASSWORD  
        Type: String representing password  
        Description: Password for accessing the HTTP.SSL.KEY/HTTP.SSL.CERTIFICATE  
        Related CURL Flags: CURLOPT_KEYPASSWORD  
1. HTTP.SSL.CAPATH  
        Type: String representing directory  
        Description: Path to a directory containing trusted certificates for validating server certificates.  
        Related CURL Flags: CURLOPT_CAPATH  
1. HTTP.SSL.VERIFYPEER
        Type: integer
        Description: Set certificate checking on the server.
        Related CURL Flags: CURLOPT_SSL_VERIFYHOST  
1. HTTP.SSL.VERIFYPEER
        Type: integer
        Description: Set host validation for the server.
        Related CURL Flags: CURLOPT_SSL_VERIFYPEER
1. HTTP.SSL.VALIDATE  
        Type: boolean ("1"/"0")  
        Description: Alias for VERIFYPEER=1 and VERIFYHOST=2
        Related CURL Flags: CURLOPT_SSL_VERIFYPEER, CURLOPT_SSL_VERIFYHOST  
1. 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, CURLOPT_CONNECTIONTIMEOUT
1. 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  
1. HTTP.READ.BUFFERSIZE  
        Type: String ("dddddd")  
        Description: Specify the the internal buffer size for curl reads.  
        Related CURL Flags: CURLOPT_BUFFERSIZE, CURL_MAX_WRITE_SIZE (16kB),  
                            CURL_MAX_READ_SIZE (512kB).  
1. HTTP.KEEPALIVE  
        Type: String ("on|n/m")  
        Description: Specify that TCP KEEPALIVE should be enabled and that the associated idle wait time is n and that the associated repeat interval is m. If the value is of the form is the string "on", then turn on keepalive, but do not set idle or interval.  
        Related CURL Flags: CURLOPT_TCP_KEEPALIVE, CURLOPT_TCP_KEEPIDLE,  
                            CURLOPT_TCP_KEEPINTVL.  
1. HTTP.CONNECTIONTIMEOUT  
        Type: String ("dddddd")  
        Description: Specify the maximum time in seconds that you allow the http connection to complete.
        Related CURL Flags: CURLOPT_TIMEOUT, CURLOPT_NOSIGNAL  

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:
````
HTTP.SSL.VALIDATE
HTTP.COOKIEJAR
HTTP.SSL.CERTIFICATE
HTTP.SSL.KEY
HTTP.SSL.CAPATH
````

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.

# Point of Contact {#dap2_poc}

__Author__: Dennis Heimbigner<br>
__Email__: dmh at ucar dot edu<br>
__Initial Version__: 3/26/2009<br>
__Last Revised__: 9/25/2018

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