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Merged latest from trunk.

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This commit is contained in:
Ward Fisher 2013-03-18 16:58:50 +00:00
commit 0d37707254
15 changed files with 238 additions and 30 deletions
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2
cf
View File

@ -8,7 +8,7 @@ fi
HDF5=1
DAP=1
PNETCDF=1
#PNETCDF=1
#RPC=1
#PGI=1
#M32=1

8
libdap2/Make0
View File

@ -2,12 +2,12 @@ NCLIB=../liblib/.libs/libnetcdf.a
NCINCL=-I ../liblib
#CYGWIN
LFLAG=-L/usr/local/lib
#LFLAG=-L/usr/local/lib
#HDF5LIB=/usr/local/lib/libhdf5_hl.a /usr/local/lib/libhdf5.a
#!CYGWIN
#LFLAG=-L/upc/share/ed/local/${HOST}/lib
#HDF5LIB=/share/ed/local/${HOST}/lib/libhdf5_hl.a /share/ed/local/${HOST}/lib/libhdf5.a
LFLAG=-L/upc/share/ed/local/${HOST}/lib
HDF5LIB=/share/ed/local/${HOST}/lib/libhdf5_hl.a /share/ed/local/${HOST}/lib/libhdf5.a
CURLLIB=-lcurl
ZLIB=-lz
@ -258,7 +258,7 @@ fix::
done
##################################################
T=civ
T=civ2
v::
cc -g -c ${T}.c ${INCL}

18
libdap2/ncdap3.c
View File

@ -79,9 +79,6 @@ NCD3_open(const char * path, int mode,
NCDAPCOMMON* dapcomm = NULL;
const char* value;
/* We will use a fake file descriptor as our internal in-memory filename */
char tmpname[32];
if(!nc3dinitialized) nc3dinitialize();
if(path == NULL)
@ -137,11 +134,18 @@ NCD3_open(const char * path, int mode,
}
/* Use libsrc code for storing metadata */
{
char tmpname[32];
snprintf(tmpname,sizeof(tmpname),"%d",drno->int_ncid);
/* Now, use the file to create the netcdf file; always 64 bit */
ncstat = nc_create(tmpname,NC_DISKLESS|NC_64BIT_OFFSET,&drno->substrate);
if(ncstat != NC_NOERR) {THROWCHK(ncstat); goto done;}
/* Create fake file name: exact name must be unique,
but is otherwise irrelevant because we are using NC_DISKLESS
*/
snprintf(tmpname,sizeof(tmpname),"%d",drno->int_ncid);
/* Now, use the file to create the netcdf file; force classic. */
ncstat = nc_create(tmpname,NC_DISKLESS|NC_CLASSIC_MODEL,&drno->substrate);
if(ncstat != NC_NOERR) {THROWCHK(ncstat); goto done;}
}
/* Avoid fill */
nc_set_fill(drno->substrate,NC_NOFILL,NULL);

2
libdispatch/dfile.c
View File

@ -1446,6 +1446,8 @@ NC_create(const char *path, int cmode, size_t initialsz,
if(model == 0) {
if(cmode & NC_NETCDF4 || cmode & NC_PNETCDF)
model = NC_DISPATCH_NC4;
else if(cmode & NC_CLASSIC_MODEL)
model = NC_DISPATCH_NC3;
}
if(model == 0) {

4
libdispatch/dvarget.c
View File

@ -1383,6 +1383,10 @@ atomic type; it will not read user defined types. For this
function, the type of the data in memory must match the type
of the variable - no data conversion is done.
Use of this family of functions is discouraged, although not
formally deprecated. The reason is the complexity of the
algorithm makes its use difficult for users to properly use.
\param ncid NetCDF or group ID, from a previous call to nc_open(),
nc_create(), nc_def_grp(), or associated inquiry functions such as
nc_inq_ncid().

4
libdispatch/dvarput.c
View File

@ -1305,6 +1305,10 @@ atomic type; it will not write user defined types. For this
function, the type of the data in memory must match the type
of the variable - no data conversion is done.
Use of this family of functions is discouraged, although not
formally deprecated. The reason is the complexity of the
algorithm makes its use difficult for users to properly use.
\param ncid NetCDF or group ID, from a previous call to nc_open(),
nc_create(), nc_def_grp(), or associated inquiry functions such as
nc_inq_ncid().

2
ncdap_test/testdata3/synth9.das
View File

@ -4,4 +4,4 @@ Attributes {
Int32 a1 32;
}
}
}
}

7
ncdap_test/testdata3/synth9.dods
View File

@ -0,0 +1,7 @@
Dataset {
Sequence {
Sequence {
Float32 v4;
} Q2;
} Q1;
} SYNTH8;

8
oc2/daplex.c
View File

@ -300,8 +300,10 @@ dapsetwordchars(DAPlexstate* lexstate, int kind)
void
daplexinit(char* input, DAPlexstate** lexstatep)
{
DAPlexstate* lexstate = (DAPlexstate*)malloc(sizeof(DAPlexstate));
if(lexstatep) *lexstatep = lexstate;
DAPlexstate* lexstate;
if(lexstatep == NULL) return; /* no point in building it */
lexstate = (DAPlexstate*)malloc(sizeof(DAPlexstate));
*lexstatep = lexstate;
if(lexstate == NULL) return;
memset((void*)lexstate,0,sizeof(DAPlexstate));
lexstate->input = strdup(input);
@ -309,8 +311,6 @@ daplexinit(char* input, DAPlexstate** lexstatep)
lexstate->yytext = ocbytesnew();
lexstate->reclaim = oclistnew();
dapsetwordchars(lexstate,0); /* Assume DDS */
if(!lexstatep)
free(lexstate);
}
void

146
oc2/oc.c
View File

@ -539,7 +539,7 @@ Obtain a dds node by name from a dds structure or dataset node.
\param[in] link The link through which the server is accessed.
\param[in] ddsnode The container node of interest.
\param[in] name The name of the field to return.
\param[out] fieldnodep A pointer into which the name'th field node is stored.
\param[out] fieldp A pointer into which the name'th field node is stored.
\retval OC_NOERR The procedure executed normally.
\retval OC_EINDEX No field with the given name was found.
@ -836,7 +836,7 @@ oc_das_attr(OCobject link, OCobject dasnode, size_t index, OCtype* atomtypep, ch
/**@}*/
/**************************************************/
/*! Node Interconnection Management */
/*!\defgroup Interconnection Node Interconnection Management */
/**@{*/
@ -875,7 +875,7 @@ oc_merge_das(OCobject link, OCobject dasroot, OCobject ddsroot)
/**************************************************/
/*! Data Management */
/*!\defgroup Data Data Management */
/**@{*/
/*!
@ -963,8 +963,14 @@ OCerror
oc_data_fieldbyname(OCobject link, OCobject datanode, const char* name, OCobject* fieldp)
{
OCerror err = OC_NOERR;
OCstate* state;
OCdata* data;
size_t count,i;
OCobject ddsnode;
OCVERIFY(OC_State,link);
OCDEREF(OCstate*,state,link);
OCVERIFY(OC_Data,datanode);
OCDEREF(OCdata*,data,datanode);
/* Get the dds node for this datanode */
err = oc_data_ddsnode(link,datanode,&ddsnode);
@ -1492,11 +1498,140 @@ oc_data_readn(OCobject link, OCobject datanode,
}
/*!
This procedure has the same semantics as oc_data_read.
However, it takes an OCddsnode as argument.
The limitation is that the DDS node must be a top-level,
atomic variable.
Top-level means that it is not nested in a Sequence or a
dimensioned Structure; being in a Grid is ok as is being in
a scalar structure.
\param[in] link The link through which the server is accessed.
\param[in] ddsnode The dds node instance of interest.
\param[in] start A vector of indices specifying the starting element
to return.
\param[in] edges A vector of indices specifying the count in each dimension
of the number of elements to return.
\param[in] memsize The size (in bytes) of the memory argument.
\param[out] memory User allocated memory into which the extracted
data is to be stored. The caller is responsible for allocating and free'ing
this argument.
\retval OC_NOERR The procedure executed normally.
\retval OC_EINVAL The memsize argument is too small to hold
the specified data.
\retval OC_EINVALCOORDS The start and/or edges argument is outside
the range of legal indices.
\retval OC_EDATADDS The data retrieved from the server was malformed
and the read request cannot be completed.
*/
OCerror
oc_dds_read(OCobject link, OCobject ddsnode,
size_t* start, size_t* edges,
size_t memsize, void* memory)
{
OCdata* data;
OCnode* dds;
OCVERIFY(OC_Node,ddsnode);
OCDEREF(OCnode*,dds,ddsnode);
/* Get the data associated with this top-level node */
data = dds->data;
if(data == NULL) return OC_EINVAL;
return oc_data_read(link,data,start,edges,memsize,memory);
}
/*!
This procedure is a variant of oc_data_read for reading a single scalar.
This procedure has the same semantics as oc_data_readscalar.
However, it takes an OCddsnode as argument.
The limitation is that the DDS node must be a top-level, atomic variable.
Top-level means that it is not nested in a Sequence or a
dimensioned Structure; being in a Grid is ok as is being in
a scalar structure.
\param[in] link The link through which the server is accessed.
\param[in] ddsnode The dds node instance of interest.
\param[in] memsize The size (in bytes) of the memory argument.
\param[out] memory User allocated memory into which the extracted
data is to be stored. The caller is responsible for allocating and free'ing
this argument.
\retval OC_NOERR The procedure executed normally.
\retval OC_EINVAL The memsize argument is too small to hold
the specified data.
\retval OC_ESCALAR The data instance is not a scalar.
\retval OC_EDATADDS The data retrieved from the server was malformed
and the read request cannot be completed.
\retval OC_EINVAL One of the arguments (link, etc.) was invalid.
*/
OCerror
oc_dds_readscalar(OCobject link, OCobject ddsnode,
size_t memsize, void* memory)
{
return oc_dds_readn(link,ddsnode,NULL,0,memsize,memory);
}
/*!
This procedure is a variant of oc_dds_read for reading
nelements of values starting at a given index position.
If the variable is a scalar, then the
index vector and count will be ignored.
This procedure has the same semantics as oc_data_readn.
However, it takes an OCddsnode as argument.
The limitation is that the DDS node must be a top-level, atomic variable.
Top-level means that it is not nested in a Sequence or a
dimensioned Structure; being in a Grid is ok as is being in
a scalar structure.
\param[in] link The link through which the server is accessed.
\param[in] ddsnode The dds node instance of interest.
\param[in] start A vector of indices specifying the starting element
to return.
\param[in] N The number of elements to read. Reading is assumed
to use row-major order.
\param[in] memsize The size (in bytes) of the memory argument.
\param[out] memory User allocated memory into which the extracted
data is to be stored. The caller is responsible for allocating and free'ing
this argument.
\retval OC_NOERR The procedure executed normally.
\retval OC_EINVAL The memsize argument is too small to hold
the specified data.
\retval OC_EINVALCOORDS The start and/or count argument is outside
the range of legal indices.
\retval OC_EDATADDS The data retrieved from the server was malformed
and the read request cannot be completed.
\retval OC_EINVAL One of the arguments (link, etc.) was invalid.
*/
OCerror
oc_dds_readn(OCobject link, OCobject ddsnode,
size_t* start, size_t N,
size_t memsize, void* memory)
{
OCdata* data;
OCnode* dds;
OCVERIFY(OC_Node,ddsnode);
OCDEREF(OCnode*,dds,ddsnode);
/* Get the data associated with this top-level node */
data = dds->data;
if(data == NULL) return OC_EINVAL;
return oc_data_readn(link,data,start,N,memsize,memory);
}
/**@}*/
/**************************************************/
/* OCtype Management */
/*!\defgroup OCtype OCtype Management
@{*/
@ -1775,6 +1910,7 @@ oc_ping(const char* url)
/*!
Set the user agent field.
\param[in] link The link through which the server is accessed.
\param[in] agent The user agent string
\retval OC_NOERR if the request succeeded.

19
oc2/oc.h
View File

@ -400,12 +400,14 @@ extern OCerror oc_data_recordcount(OClink, OCdatanode, size_t*);
If scalar, then index and count are ignored.
Caller is responsible for allocating memory(of proper size)
and free'ing it.
See also oc_dds_read().
*/
extern OCerror oc_data_read(OClink, OCdatanode, size_t*, size_t*, size_t, void*);
/* Like oc_data_read, but for reading a scalar.
Caller is responsible for allocating memory(of proper size)
and free'ing it.
See also oc_dds_readscalar().
*/
extern OCerror oc_data_readscalar(OClink, OCdatanode, size_t, void*);
@ -413,6 +415,7 @@ extern OCerror oc_data_readscalar(OClink, OCdatanode, size_t, void*);
and count of the number of elements to read.
Caller is responsible for allocating memory(of proper size)
and free'ing it.
See also oc_dds_readn().
*/
extern OCerror oc_data_readn(OClink, OCdatanode, size_t*, size_t, size_t, void*);
@ -446,6 +449,22 @@ extern int oc_data_indexed(OClink, OCdatanode);
*/
extern int oc_data_indexable(OClink, OCdatanode);
/**************************************************/
/*
For top-level, atomic variables, it is possible to directly
read the associated data without having to use the oc_data_XXX
procedures. Provide special procedures to support this.
*/
/* See oc_data_read for semantics */
extern OCerror oc_dds_read(OClink, OCddsnode, size_t*, size_t*, size_t, void*);
/* See oc_data_readscalar for semantics */
extern OCerror oc_dds_readscalar(OClink, OCddsnode, size_t, void*);
/* See oc_data_readn for semantics */
extern OCerror oc_dds_readn(OClink, OCddsnode, size_t*, size_t, size_t, void*);
/**************************************************/
/* Misc. OCtype-related functions */

42
oc2/occompile.c
View File

@ -12,14 +12,18 @@
#include "ocdebug.h"
#include "ocdump.h"
/* Mnemonic */
#define TOPLEVEL 1
/* Forward */
static OCdata* newocdata(OCnode* template);
static size_t ocxdrsize(OCtype etype,int isscalar);
static OCerror occompile1(OCstate*, OCnode*, XXDR*, OCdata**);
static OCerror occompilerecord(OCstate*, OCnode*, XXDR*, OCdata**);
static OCerror occompilefields(OCstate*, OCdata*, XXDR*);
static OCerror occompilefields(OCstate*, OCdata*, XXDR*, int istoplevel);
static OCerror occompileatomic(OCstate*, OCdata*, XXDR*);
static int ocerrorstring(XXDR* xdrs);
static int istoplevel(OCnode* node);
/* Sequence tag constant */
const char StartOfSequence = '\x5A';
@ -86,13 +90,13 @@ occompile1(OCstate* state, OCnode* xnode, XXDR* xxdrs, OCdata** datap)
case OC_Dataset:
case OC_Grid: /* Always scalars */
ocstat = occompilefields(state,data,xxdrs);
ocstat = occompilefields(state,data,xxdrs,istoplevel(xnode));
if(ocstat != OC_NOERR) goto fail;
break;
case OC_Structure:
if(xnode->array.rank == 0) {/* scalar */
ocstat = occompilefields(state,data,xxdrs);
ocstat = occompilefields(state,data,xxdrs,istoplevel(xnode));
if(ocstat != OC_NOERR) goto fail;
} else { /* dimensioned structure */
unsigned int xdrcount;
@ -124,7 +128,7 @@ occompile1(OCstate* state, OCnode* xnode, XXDR* xxdrs, OCdata** datap)
/* capture the current instance position */
instance->xdroffset = xxdr_getpos(xxdrs);
/* Now compile the fields of this instance */
ocstat = occompilefields(state,instance,xxdrs);
ocstat = occompilefields(state,instance,xxdrs,!TOPLEVEL);
if(ocstat != OC_NOERR) {goto fail;}
}
}
@ -210,7 +214,7 @@ occompilerecord(OCstate* state, OCnode* xnode, XXDR* xxdrs, OCdata** recordp)
/* capture the current record position */
record->xdroffset = xxdr_getpos(xxdrs);
/* Compile the fields of this record */
ocstat = OCTHROW(occompilefields(state,record,xxdrs));
ocstat = OCTHROW(occompilefields(state,record,xxdrs,!TOPLEVEL));
if(ocstat == OC_NOERR) {
if(recordp) *recordp = record;
}
@ -218,7 +222,7 @@ occompilerecord(OCstate* state, OCnode* xnode, XXDR* xxdrs, OCdata** recordp)
}
static OCerror
occompilefields(OCstate* state, OCdata* data, XXDR* xxdrs)
occompilefields(OCstate* state, OCdata* data, XXDR* xxdrs, int istoplevel)
{
int i;
OCerror ocstat = OC_NOERR;
@ -246,6 +250,15 @@ occompilefields(OCstate* state, OCdata* data, XXDR* xxdrs)
fieldinstance->index = i;
}
/* If top-level, then link the OCnode to the OCdata directly */
if(istoplevel) {
for(i=0;i<nelements;i++) {
OCnode* fieldnode = (OCnode*)oclistget(xnode->subnodes,i);
OCdata* fieldinstance = data->instances[i];
fieldnode->data = fieldinstance;
}
}
done:
return OCTHROW(ocstat);
@ -373,6 +386,23 @@ newocdata(OCnode* template)
return data;
}
static int
istoplevel(OCnode* node)
{
if(node == NULL)
return 1; /* base case */
if(!istoplevel(node->container))
return 0;
switch (node->octype) {
case OC_Dataset: case OC_Grid: case OC_Atomic: return 1;
case OC_Structure:
return (node->array.rank == 0 ? 1 : 0); /* Toplevel if scalar */
case OC_Sequence: default: return 0;
}
return 1;
}
/* XDR representation size depends on if this is scalar or not */
static size_t
ocxdrsize(OCtype etype, int isscalar)

1
oc2/ocinternal.h
View File

@ -205,5 +205,4 @@ extern int ocinternalinitialize(void);
extern OCerror ocsetuseragent(OCstate* state, const char* agent);
#endif /*COMMON_H*/

4
oc2/oclog.c
View File

@ -152,7 +152,7 @@ number of arguments and operates like the stdio
printf function.
\param[in] tag Indicate the kind of this log message.
\param[in] format Format specification as with printf.
\param[in] fmt Format specification as with printf.
*/
void
@ -186,8 +186,10 @@ oclogtext(int tag, const char* text)
/*!
Send arbitrarily long text as a logging message.
Each line will be sent using oclog with the specified tag.
\param[in] tag Indicate the kind of this log message.
\param[in] text Arbitrary text to send as a logging message.
\param[in] count Maximum ength of the text to write.
*/
void

1
oc2/ocnode.h
View File

@ -57,6 +57,7 @@ struct OCnode {
OClist* subnodes; /*oclist<OCnode*>*/
/*int attributed;*/ /* 1 if merge was done*/
OClist* attributes; /* oclist<OCattribute*>*/
OCdata* data; /* Defined only if this node is a top-level atomic variable*/
};
#if SIZEOF_SIZE_T == 4