netcdf-c/ncgen/genj.c
Dennis Heimbigner 59e04ae071 This PR adds EXPERIMENTAL support for accessing data in the
cloud using a variant of the Zarr protocol and storage
format. This enhancement is generically referred to as "NCZarr".

The data model supported by NCZarr is netcdf-4 minus the user-defined
types and the String type. In this sense it is similar to the CDF-5
data model.

More detailed information about enabling and using NCZarr is
described in the document NUG/nczarr.md and in a
[Unidata Developer's blog entry](https://www.unidata.ucar.edu/blogs/developer/en/entry/overview-of-zarr-support-in).

WARNING: this code has had limited testing, so do use this version
for production work. Also, performance improvements are ongoing.
Note especially the following platform matrix of successful tests:

Platform | Build System | S3 support
------------------------------------
Linux+gcc      | Automake     | yes
Linux+gcc      | CMake        | yes
Visual Studio  | CMake        | no

Additionally, and as a consequence of the addition of NCZarr,
major changes have been made to the Filter API. NOTE: NCZarr
does not yet support filters, but these changes are enablers for
that support in the future.  Note that it is possible
(probable?) that there will be some accidental reversions if the
changes here did not correctly mimic the existing filter testing.

In any case, previously filter ids and parameters were of type
unsigned int. In order to support the more general zarr filter
model, this was all converted to char*.  The old HDF5-specific,
unsigned int operations are still supported but they are
wrappers around the new, char* based nc_filterx_XXX functions.
This entailed at least the following changes:
1. Added the files libdispatch/dfilterx.c and include/ncfilter.h
2. Some filterx utilities have been moved to libdispatch/daux.c
3. A new entry, "filter_actions" was added to the NCDispatch table
   and the version bumped.
4. An overly complex set of structs was created to support funnelling
   all of the filterx operations thru a single dispatch
   "filter_actions" entry.
5. Move common code to from libhdf5 to libsrc4 so that it is accessible
   to nczarr.

Changes directly related to Zarr:
1. Modified CMakeList.txt and configure.ac to support both C and C++
   -- this is in support of S3 support via the awd-sdk libraries.
2. Define a size64_t type to support nczarr.
3. More reworking of libdispatch/dinfermodel.c to
   support zarr and to regularize the structure of the fragments
   section of a URL.

Changes not directly related to Zarr:
1. Make client-side filter registration be conditional, with default off.
2. Hack include/nc4internal.h to make some flags added by Ed be unique:
   e.g. NC_CREAT, NC_INDEF, etc.
3. cleanup include/nchttp.h and libdispatch/dhttp.c.
4. Misc. changes to support compiling under Visual Studio including:
   * Better testing under windows for dirent.h and opendir and closedir.
5. Misc. changes to the oc2 code to support various libcurl CURLOPT flags
   and to centralize error reporting.
6. By default, suppress the vlen tests that have unfixed memory leaks; add option to enable them.
7. Make part of the nc_test/test_byterange.sh test be contingent on remotetest.unidata.ucar.edu being accessible.

Changes Left TO-DO:
1. fix provenance code, it is too HDF5 specific.
2020-06-28 18:02:47 -06:00

605 lines
16 KiB
C

/*********************************************************************
* Copyright 2018, UCAR/Unidata
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
* $Header: /upc/share/CVS/netcdf-3/ncgen/genj.c,v 1.2 2010/05/17 23:26:44 dmh Exp $
*********************************************************************/
#include "includes.h"
#ifdef ENABLE_JAVA
#undef EXCEPTWRAP
#undef TRACE
/*MNEMONIC*/
#define USEMEMORY 1
extern List* vlenconstants; /* List<Constant*>;*/
/* Forward */
static void genj_definevardata(Symbol* vsym);
static const char* jtypeallcaps(nc_type type);
static const char* jtypecap(nc_type type);
static const char* jtype(nc_type type);
static const char* jarraytype(nc_type type);
static const char* jname(Symbol* sym);
static void genj_defineattr(Symbol* asym);
static void genj_definevardata(Symbol*);
static void genj_write(Generator*,Symbol* sym, Bytebuffer* code,
int rank, size_t* start, size_t* count);
static void genj_writevar(Generator*,Symbol*,Bytebuffer*,int,size_t*,size_t*);
static void genj_writeattr(Generator*,Symbol*,Bytebuffer*,int,size_t*,size_t*);
/*
* Generate code for creating netCDF from in-memory structure.
*/
void
genjava_netcdf(void)
{
int idim, ivar, iatt, maxdims;
int ndims, nvars, natts, ngatts;
const char *filename = rootgroup->file.filename;
ndims = listlength(dimdefs);
nvars = listlength(vardefs);
natts = listlength(attdefs);
ngatts = listlength(gattdefs);
/* Construct the main class */
codeline("import java.util.*;");
codeline("import ucar.ma2.*;");
codeline("import ucar.nc2.*;");
codeline("import ucar.nc2.NetcdfFile.*;");
codeline("");
codepartial("public class ");
codeline(mainname);
codeline("{");
/* Now construct the main procedure*/
codeline("");
codeline("static public void main(String[] argv) throws Exception");
codeline("{");
/* create necessary declarations */
if(ndims > 0) {
codeline("");
codelined(1,"/* dimension lengths */");
for(idim = 0; idim < ndims; idim++) {
Symbol* dsym = (Symbol*)listget(dimdefs,idim);
if(dsym->dim.declsize == NC_UNLIMITED) {
bbprintf0(stmt,"%sfinal int %s_len = 0;\n",
indented(1),jname(dsym));
} else {
bbprintf0(stmt,"%sfinal int %s_len = %lu;\n",
indented(1),
jname(dsym),
(unsigned long) dsym->dim.declsize);
}
codedump(stmt);
}
}
codeflush();
maxdims = 0; /* most dimensions of any variable */
for(ivar = 0; ivar < nvars; ivar++) {
Symbol* vsym = (Symbol*)listget(vardefs,ivar);
if(vsym->typ.dimset.ndims > maxdims)
maxdims = vsym->typ.dimset.ndims;
}
codeline("");
#ifdef EXCEPTWRAP
codelined(1,"try {");
#endif
/* create netCDF file, uses NC_CLOBBER mode */
codeline("");
codelined(1,"/* enter define mode */");
bbprintf0(stmt,
"%sNetcdfFileWriteable ncfile = NetcdfFileWriteable.createNew(\"%s\", %s);\n",
indented(1),filename,(nofill_flag?"false":"true"));
codedump(stmt);
codeflush();
/* define dimensions from info in dims array */
if(ndims > 0) {
codeline("");
codelined(1,"/* define dimensions */");
for(idim = 0; idim < ndims; idim++) {
Symbol* dsym = (Symbol*)listget(dimdefs,idim);
if(dsym->dim.declsize == NC_UNLIMITED) {
bbprintf0(stmt,"%sDimension %s_dim = ncfile.addUnlimitedDimension(\"%s\");\n",
indented(1),jname(dsym),jescapifyname(dsym->name));
} else {
bbprintf0(stmt,"%sDimension %s_dim = ncfile.addDimension(\"%s\", %s_len);\n",
indented(1),jname(dsym),jescapifyname(dsym->name), jname(dsym));
}
codedump(stmt);
}
codeflush();
}
/* define variables from info in vars array */
if(nvars > 0) {
codeline("");
codelined(1,"/* define variables */");
for(ivar = 0; ivar < nvars; ivar++) {
Symbol* vsym = (Symbol*)listget(vardefs,ivar);
Symbol* basetype = vsym->typ.basetype;
Dimset* dimset = &vsym->typ.dimset;
codeline("");
bbprintf0(stmt,"%sArrayList %s_dimlist = new ArrayList();\n",
indented(1),jname(vsym));
codedump(stmt);
if(dimset->ndims > 0) {
for(idim = 0; idim < dimset->ndims; idim++) {
Symbol* dsym = dimset->dimsyms[idim];
bbprintf0(stmt,"%s%s_dimlist.add(%s_dim);\n",
indented(1),jname(vsym),jname(dsym));
codedump(stmt);
}
}
bbprintf0(stmt,
"%sncfile.addVariable(\"%s\", DataType.%s, %s_dimlist);\n",
indented(1),
jescapifyname(vsym->name),
jtypeallcaps(basetype->typ.typecode),
jname(vsym));
codedump(stmt);
}
codeflush();
}
/* Define the global attributes*/
if(ngatts > 0) {
codeline("");
codelined(1,"/* assign global attributes */");
for(iatt = 0; iatt < ngatts; iatt++) {
Symbol* gasym = (Symbol*)listget(gattdefs,iatt);
genj_defineattr(gasym);
}
codeline("");
codeflush();
}
/* Define the variable specific attributes*/
if(natts > 0) {
codeline("");
codelined(1,"/* assign per-variable attributes */");
for(iatt = 0; iatt < natts; iatt++) {
Symbol* asym = (Symbol*)listget(attdefs,iatt);
genj_defineattr(asym);
}
codeline("");
codeflush();
}
codelined(1,"ncfile.create();"); /* equiv to nc_enddef */
if(!header_only) {
/* Load values into those variables with defined data */
if(nvars > 0) {
codeline("");
codelined(1,"/* assign variable data */");
for(ivar = 0; ivar < nvars; ivar++) {
Symbol* vsym = (Symbol*)listget(vardefs,ivar);
if(vsym->data != NULL) genj_definevardata(vsym);
}
codeline("");
}
}
codeflush();
}
void
genjava_close(void)
{
codelined(1,"ncfile.close();");
codeline("");
#ifdef EXCEPTIONWRAP
codelined(1,"} catch(Exception e) {e.printStackTrace();};");
#endif
codelined(1,"}"); /* main */
codeline("}"); /* class Main */
codeflush();
}
const char*
jtypeallcaps(nc_type type)
{
switch (type) {
case NC_CHAR: return "CHAR";
case NC_BYTE: return "BYTE";
case NC_SHORT: return "SHORT";
case NC_INT: return "INT";
case NC_FLOAT: return "FLOAT";
case NC_DOUBLE: return "DOUBLE";
case NC_UBYTE: return "LONG";
case NC_USHORT: return "LONG";
case NC_UINT: return "LONG";
case NC_INT64: return "LONG";
case NC_UINT64: return "LONG";
case NC_STRING: return "STRING";
default: PANIC1("ncctype: bad type code:%d",type);
}
return 0;
}
static const char*
jtypecap(nc_type type)
{
switch (type) {
case NC_CHAR: return "Char";
case NC_BYTE: return "Byte";
case NC_SHORT: return "Short";
case NC_INT: return "Int";
case NC_FLOAT: return "Float";
case NC_DOUBLE: return "Double";
case NC_UBYTE: return "Long";
case NC_USHORT: return "Long";
case NC_UINT: return "Long";
case NC_INT64: return "Long";
case NC_UINT64: return "Long";
case NC_STRING: return "String";
case NC_ENUM: return "Int";
case NC_OPAQUE: return "String";
default: PANIC1("ncctype: bad type code:%d",type);
}
return 0;
}
void
jquotestring(Bytebuffer* databuf, char quote)
{
char* escaped = jescapify(bbContents(databuf),'"',bbLength(databuf));
bbClear(databuf);
bbAppend(databuf,quote);
if(escaped != NULL) bbCat(databuf,escaped);
bbAppend(databuf,quote);
}
/* Compute the name for a given symbol*/
/* Cache in symbol->lname*/
static const char*
jname(Symbol* sym)
{
char* name;
assert (sym->fqn != NULL);
/* convert to language form*/
name = codify(sym->fqn); /* convert to usable form*/
return name;
}
/*
* Return java type name for netCDF type, given type code.
*/
static const char*
jtype(nc_type type)
{
switch (type) {
case NC_CHAR: return "char";
case NC_BYTE: return "byte";
case NC_SHORT: return "short";
case NC_INT: return "int";
case NC_FLOAT: return "float";
case NC_DOUBLE: return "double";
case NC_UBYTE: return "long";
case NC_USHORT: return "long";
case NC_UINT: return "long";
case NC_INT64: return "long";
case NC_UINT64: return "long";
case NC_STRING: return "String";
case NC_ENUM: return "int";
case NC_OPAQUE: return "String";
default: PANIC1("ncctype: bad type code:%d",type);
}
return 0;
}
/*
* Return a type name and dimensions for constant arrays
* for netCDF type, given type code.
*/
static const char*
jarraytype(nc_type type)
{
switch (type) {
case NC_CHAR:
return "String";
case NC_BYTE:
return "byte";
case NC_SHORT:
return "short";
case NC_INT:
return "int";
case NC_FLOAT:
return "float";
case NC_DOUBLE:
return "double";
case NC_UBYTE:
return "long";
case NC_USHORT:
return "long";
case NC_UINT:
return "long";
case NC_INT64:
return "long";
case NC_UINT64:
return "long";
case NC_STRING:
return "String";
case NC_ENUM:
return "int";
case NC_OPAQUE:
return "String";
default:
PANIC1("ncctype: bad type code:%d",type);
}
return 0;
}
/*
* Return netcdf interface type name for netCDF type suffix, given type code.
*/
const char*
jstype(nc_type nctype)
{
switch (nctype) {
case NC_CHAR:
return "text";
case NC_BYTE:
return "schar";
case NC_SHORT:
return "short";
case NC_INT:
return "int";
case NC_FLOAT:
return "float";
case NC_DOUBLE:
return "double";
case NC_UBYTE:
return "ubyte";
case NC_USHORT:
return "ushort";
case NC_UINT:
return "uint";
case NC_INT64:
return "longlong";
case NC_UINT64:
return "ulonglong";
case NC_STRING:
return "string";
case NC_OPAQUE:
return "opaque";
case NC_ENUM:
return "enum";
default:
derror("ncstype: bad type code: %d",nctype);
return 0;
}
}
static void
genj_defineattr(Symbol* asym)
{
Bytebuffer* code; /* capture so we can dump vlens first */
ASSERT(asym->data != NULL);
code = bbNew();
generator_reset(j_generator,NULL);
generate_attrdata(asym,j_generator,(Writer)genj_write,code);
bbFree(code);
}
static void
genj_definevardata(Symbol* vsym)
{
Bytebuffer* code; /* capture so we can dump vlens first */
if(vsym->data == NULL) return;
code = bbNew();
generator_reset(j_generator,NULL);
generate_vardata(vsym,j_generator,(Writer)genj_write,code);
bbFree(code);
}
static void
genj_write(Generator* generator, Symbol* sym, Bytebuffer* code,
int rank, size_t* start, size_t* count)
{
if(sym->objectclass == NC_ATT)
genj_writeattr(generator,sym,code,rank,start,count);
else if(sym->objectclass == NC_VAR)
genj_writevar(generator,sym,code,rank,start,count);
else
PANIC("illegal symbol for genj_write");
}
static void
genj_writevar(Generator* generator, Symbol* vsym, Bytebuffer* code,
int rank, size_t* start, size_t* count)
{
Dimset* dimset = &vsym->typ.dimset;
int typecode = vsym->typ.basetype->typ.typecode;
int i;
codeline("");
codelined(1,"{"); /* Enclose in {...} for scoping */
if(rank == 0) {
bbprintf0(stmt,"%sArray%s.D0 data = new Array%s.D0();\n",
indented(1),jtypecap(typecode), jtypecap(typecode));
codedump(stmt);
if(typecode == NC_CHAR) {
/* Construct the data Array */
jquotestring(code,'\'');
bbprintf0(stmt,"%sdata.set((char)%s);\n",
indented(1),bbContents(code));
} else {
commify(code);
bbprintf0(stmt,"%sdata.set((%s)%s);\n",
indented(1),jtype(typecode),bbContents(code));
}
codedump(stmt);
/* do the actual write */
bbprintf0(stmt,"%sncfile.write(\"%s\",data);\n",
indented(1),jescapifyname(vsym->name));
codedump(stmt);
} else { /* array */
Bytebuffer* dimbuf = bbNew();
/* Construct the dimension set*/
bbCat(dimbuf,"new int[]{");
for(i=0;i<rank;i++) {
Symbol* dsym = dimset->dimsyms[i];
char tmp[32];
nprintf(tmp,sizeof(tmp),"%lu",dsym->dim.declsize);
if(i>0) {bbCat(dimbuf,", ");}
bbCat(dimbuf,tmp);
}
bbCat(dimbuf,"}");
/* Construct the data array and capture its index */
if(typecode == NC_CHAR) {
jquotestring(code,'"');
bbprintf0(stmt,"%sString contents = ",
indented(1));
} else {
bbprintf0(stmt,"%s%s[] contents = new %s[] {",
indented(1),jtype(typecode),jtype(typecode));
commify(code);
}
codedump(stmt);
codedump(code);
if(typecode != NC_CHAR) codepartial("}");
codeline(";");
bbprintf0(stmt,"%sArray%s data = new Array%s(%s);\n",
indented(1),
jtypecap(typecode),
jtypecap(typecode),
bbContents(dimbuf));
codedump(stmt);
codelined(1,"IndexIterator iter = data.getIndexIterator();");
codelined(1,"int count = 0;");
codelined(1,"while(iter.hasNext())");
if(typecode == NC_CHAR)
bbprintf0(stmt,
"%siter.setCharNext(contents.charAt(count++));\n",indented(2));
else
bbprintf0(stmt,"%siter.set%sNext(contents[count++]);\n",
indented(2),jtypecap(typecode));
codedump(stmt);
bbFree(dimbuf);
/* Construct the origin set from the start set */
bbprintf0(stmt,"%sint[] origin = new int[]{",indented(1));
for(i=0;i<rank;i++) {
bbprintf(stmt,"%s%lu",(i>0?", ":""),start[i]);
}
bbCat(stmt,"};\n");
codedump(stmt);
/* do the actual write */
bbprintf0(stmt,"%sncfile.write(\"%s\",origin,data);\n",
indented(1),jescapifyname(vsym->name));
codedump(stmt);
}
codelined(1,"}"); /* Enclose in {...} for scoping */
codeflush();
}
static void
genj_writeattr(Generator* generator, Symbol* asym, Bytebuffer* code,
int rank, size_t* start, size_t* count)
{
Symbol* basetype = asym->typ.basetype;
nc_type typecode = basetype->typ.typecode;
/* default assumption */
size_t len = asym->data == NULL?0:asym->data->length;
codeprintf("%s/* attribute: %s */\n",indented(1),asym->name);
/* Handle NC_CHAR specially */
if(typecode == NC_CHAR) {
/* revise the length count */
len = bbLength(code);
if(len == 0) {
bbAppend(code,'\0'); len++;
bbClear(code);
bbCat(code,"\"\"");
len++;
} else
jquotestring(code,'"');
bbNull(code);
} else { /* not NC_CHAR*/
char* code2;
commify(code);
/* Convert to constant */
code2 = bbDup(code);
bbClear(code);
bbprintf0(stmt,"new %s[]",
jarraytype(typecode));
bbCatbuf(code,stmt);
bbCat(code,"{");
bbCat(code,code2);
bbCat(code,"}");
efree(code2);
}
switch (typecode) {
case NC_BYTE:
case NC_SHORT:
case NC_INT:
case NC_FLOAT:
case NC_DOUBLE:
codelined(1,"{");
bbprintf0(stmt,"%sArray data = Array.factory(%s.class, new int[]{%lu}, ",
indented(1),
jtype(basetype->typ.typecode),
len);
codedump(stmt);
codedump(code);
codeline(");");
if(asym->att.var == NULL) {
bbprintf0(stmt,"%sncfile.addGlobalAttribute(\"%s\",data);\n",
indented(1),jescapifyname(asym->name));
} else {
bbprintf0(stmt,"%sncfile.addVariableAttribute(\"%s\",\"%s\",data);\n",
indented(1),
jescapifyname(asym->att.var->name),
jescapifyname(asym->name));
}
codedump(stmt);
codelined(1,"}");
codeflush();
break;
case NC_CHAR:
if(asym->att.var == NULL) {
bbprintf0(stmt,"%sncfile.addGlobalAttribute(\"%s\",%s);\n",
indented(1),
jescapifyname(asym->name),
bbContents(code));
} else {
bbprintf0(stmt,"%sncfile.addVariableAttribute(\"%s\",\"%s\",%s);\n",
indented(1),
jescapifyname(asym->att.var->name),
jescapifyname(asym->name),
bbContents(code));
}
codedump(stmt);
codeflush();
break;
default: break;
}
codeflush();
}
#endif /*ENABLE_JAVA*/