netcdf-c/libdispatch/nclog.c

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/*********************************************************************
* Copyright 2018, UCAR/Unidata
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* See netcdf/COPYRIGHT file for copying and redistribution conditions.
* $Header$
*********************************************************************/
#include "config.h"
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#ifdef _MSC_VER
#include<io.h>
#endif
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#include <stdlib.h>
#include <stdio.h>
#include <stdarg.h>
#include <string.h>
#include <errno.h>
Primary change: add dap4 support Specific changes: 1. Add dap4 code: libdap4 and dap4_test. Note that until the d4ts server problem is solved, dap4 is turned off. 2. Modify various files to support dap4 flags: configure.ac, Makefile.am, CMakeLists.txt, etc. 3. Add nc_test/test_common.sh. This centralizes the handling of the locations of various things in the build tree: e.g. where is ncgen.exe located. See nc_test/test_common.sh for details. 4. Modify .sh files to use test_common.sh 5. Obsolete separate oc2 by moving it to be part of netcdf-c. This means replacing code with netcdf-c equivalents. 5. Add --with-testserver to configure.ac to allow override of the servers to be used for --enable-dap-remote-tests. 6. There were multiple versions of nctypealignment code. Try to centralize in libdispatch/doffset.c and include/ncoffsets.h 7. Add a unit test for the ncuri code because of its complexity. 8. Move the findserver code out of libdispatch and into a separate, self contained program in ncdap_test and dap4_test. 9. Move the dispatch header files (nc{3,4}dispatch.h) to .../include because they are now shared by modules. 10. Revamp the handling of TOPSRCDIR and TOPBUILDDIR for shell scripts. 11. Make use of MREMAP if available 12. Misc. minor changes e.g. - #include <config.h> -> #include "config.h" - Add some no-install headers to /include - extern -> EXTERNL and vice versa as needed - misc header cleanup - clean up checking for misc. unix vs microsoft functions 13. Change copyright decls in some files to point to LICENSE file. 14. Add notes to RELEASENOTES.md
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#ifdef HAVE_FCNTL_H
#include <fcntl.h>
#endif
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
#ifdef HAVE_EXECINFO_H
#include <execinfo.h>
#endif
#include "netcdf.h"
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#include "nclog.h"
#define PREFIXLEN 8
#define MAXTAGS 256
#define NCTAGDFALT "Log";
Add support for Zarr string type to NCZarr * re: https://github.com/Unidata/netcdf-c/pull/2278 * re: https://github.com/Unidata/netcdf-c/issues/2485 * re: https://github.com/Unidata/netcdf-c/issues/2474 This PR subsumes PR https://github.com/Unidata/netcdf-c/pull/2278. Actually is a bit an omnibus covering several issues. ## PR https://github.com/Unidata/netcdf-c/pull/2278 Add support for the Zarr string type. Zarr strings are restricted currently to be of fixed size. The primary issue to be addressed is to provide a way for user to specify the size of the fixed length strings. This is handled by providing the following new attributes special: 1. **_nczarr_default_maxstrlen** &mdash; This is an attribute of the root group. It specifies the default maximum string length for string types. If not specified, then it has the value of 64 characters. 2. **_nczarr_maxstrlen** &mdash; This is a per-variable attribute. It specifies the maximum string length for the string type associated with the variable. If not specified, then it is assigned the value of **_nczarr_default_maxstrlen**. This PR also requires some hacking to handle the existing netcdf-c NC_CHAR type, which does not exist in zarr. The goal was to choose numpy types for both the netcdf-c NC_STRING type and the netcdf-c NC_CHAR type such that if a pure zarr implementation read them, it would still work and an NC_CHAR type would be handled by zarr as a string of length 1. For writing variables and NCZarr attributes, the type mapping is as follows: * "|S1" for NC_CHAR. * ">S1" for NC_STRING && MAXSTRLEN==1 * ">Sn" for NC_STRING && MAXSTRLEN==n Note that it is a bit of a hack to use endianness, but it should be ok since for string/char, the endianness has no meaning. For reading attributes with pure zarr (i.e. with no nczarr atribute types defined), they will always be interpreted as of type NC_CHAR. ## Issue: https://github.com/Unidata/netcdf-c/issues/2474 This PR partly fixes this issue because it provided more comprehensive support for Zarr attributes that are JSON valued expressions. This PR still does not address the problem in that issue where the _ARRAY_DIMENSION attribute is incorrectly set. Than can only be fixed by the creator of the datasets. ## Issue: https://github.com/Unidata/netcdf-c/issues/2485 This PR also fixes the scalar failure shown in this issue. It generally cleans up scalar handling. It also adds a note to the documentation describing that NCZarr supports scalars while Zarr does not and also how scalar interoperability is achieved. ## Misc. Other Changes 1. Convert the nczarr special attributes and keys to be all lower case. So "_NCZARR_ATTR" now used "_nczarr_attr. Support back compatibility for the upper case names. 2. Cleanup my too-clever-by-half handling of scalars in libnczarr.
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#define NC_MAX_FRAMES 1024
static int nclogginginitialized = 0;
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static struct NCLOGGLOBAL {
int nclogging;
int tracelevel;
FILE* nclogstream;
int depth;
struct Frame {
const char* fcn;
int level;
int depth;
} frames[NC_MAX_FRAMES];
} nclog_global = {0,-1,NULL};
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.
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static const char* nctagset[] = {"Note","Warning","Error","Debug"};
static const int nctagsize = sizeof(nctagset)/sizeof(char*);
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/* Forward */
static const char* nctagname(int tag);
/*!\defgroup NClog NClog Management
@{*/
/*!\internal
*/
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void
ncloginit(void)
{
const char* envv = NULL;
if(nclogginginitialized)
return;
nclogginginitialized = 1;
memset(&nclog_global,0,sizeof(nclog_global));
nclog_global.tracelevel = -1;
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ncsetlogging(0);
nclog_global.nclogstream = stderr;
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/* Use environment variables to preset nclogging state*/
/* I hope this is portable*/
envv = getenv(NCENVLOGGING);
if(envv != NULL) {
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.
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ncsetlogging(1);
}
envv = getenv(NCENVTRACING);
if(envv != NULL) {
nctracelevel(atoi(envv));
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}
}
/*!
Enable/Disable logging.
\param[in] tf If 1, then turn on logging, if 0, then turn off logging.
\return The previous value of the logging flag.
*/
int
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ncsetlogging(int tf)
{
int was;
if(!nclogginginitialized) ncloginit();
was = nclog_global.nclogging;
nclog_global.nclogging = tf;
if(nclog_global.nclogstream == NULL) nclogopen(NULL);
return was;
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}
int
nclogopen(FILE* stream)
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{
if(!nclogginginitialized) ncloginit();
if(stream == NULL) stream = stderr;
nclog_global.nclogstream = stream;
return 1;
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}
/*!
Send logging messages. This uses a variable
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.
*/
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void
nclog(int tag, const char* fmt, ...)
{
if(fmt != NULL) {
va_list args;
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va_start(args, fmt);
ncvlog(tag,fmt,args);
va_end(args);
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}
}
int
ncvlog(int tag, const char* fmt, va_list ap)
{
const char* prefix;
int was = -1;
if(!nclogginginitialized) ncloginit();
if(tag == NCLOGERR) was = ncsetlogging(1);
if(!nclog_global.nclogging || nclog_global.nclogstream == NULL) return was;
prefix = nctagname(tag);
Improve S3 Documentation and Support ## Improvements to S3 Documentation * Create a new document *quickstart_paths.md* that give a summary of the legal path formats used by netcdf-c. This includes both file paths and URL paths. * Modify *nczarr.md* to remove most of the S3 related text. * Move the S3 text from *nczarr.md* to a new document *cloud.md*. * Add some S3-related text to the *byterange.md* document. Hopefully, this will make it easier for users to find the information they want. ## Rebuild NCZarr Testing In order to avoid problems with running make check in parallel, two changes were made: 1. The *nczarr_test* test system was rebuilt. Now, for each test. any generated files are kept in a test-specific directory, isolated from all other test executions. 2. Similarly, since the S3 test bucket is shared, any generated S3 objects are isolated using a test-specific key path. ## Other S3 Related Changes * Add code to ensure that files created on S3 are reclaimed at end of testing. * Used the bash "trap" command to ensure S3 cleanup even if the test fails. * Cleanup the S3 related configure.ac flag set since S3 is used in several places. So now one should use the option *--enable-s3* instead of *--enable-nczarr-s3*, although the latter is still kept as a deprecated alias for the former. * Get some of the github actions yml to work with S3; required fixing various test scripts adding a secret to access the Unidata S3 bucket. * Cleanup S3 portion of libnetcdf.settings.in and netcdf_meta.h.in and test_common.in. * Merge partial S3 support into dhttp.c. * Create an experimental s3 access library especially for use with Windows. It is enabled by using the options *--enable-s3-internal* (automake) or *-DENABLE_S3_INTERNAL=ON* (CMake). Also add a unit-test for it. * Move some definitions from ncrc.h to ncs3sdk.h ## Other Changes * Provide a default implementation of strlcpy and move this and similar defaults into *dmissing.c*.
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fprintf(nclog_global.nclogstream,"%s: ",prefix);
if(fmt != NULL) {
vfprintf(nclog_global.nclogstream, fmt, ap);
}
fprintf(nclog_global.nclogstream, "\n" );
fflush(nclog_global.nclogstream);
return was;
}
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void
nclogtext(int tag, const char* text)
{
nclogtextn(tag,text,strlen(text));
}
/*!
Send arbitrarily long text as a logging message.
Each line will be sent using nclog 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.
*/
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void
nclogtextn(int tag, const char* text, size_t count)
{
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NC_UNUSED(tag);
if(!nclog_global.nclogging || nclog_global.nclogstream == NULL) return;
fwrite(text,1,count,nclog_global.nclogstream);
fflush(nclog_global.nclogstream);
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}
static const char*
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nctagname(int tag)
{
if(tag < 0 || tag >= nctagsize)
return "unknown";
return nctagset[tag];
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}
/*!
Send trace messages.
\param[in] level Indicate the level of trace
\param[in] format Format specification as with printf.
*/
int
nctracelevel(int level)
{
int oldlevel;
if(!nclogginginitialized) ncloginit();
oldlevel = nclog_global.tracelevel;
if(level < 0) {
nclog_global.tracelevel = level;
ncsetlogging(0);
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} else { /*(level >= 0)*/
nclog_global.tracelevel = level;
ncsetlogging(1);
nclogopen(NULL); /* use stderr */
}
return oldlevel;
}
void
nctrace(int level, const char* fcn, const char* fmt, ...)
{
va_list args;
va_start(args, fmt);
ncvtrace(level,fcn,fmt,args);
va_end(args);
}
void
nctracemore(int level, const char* fmt, ...)
{
va_list args;
va_start(args, fmt);
ncvtrace(level,NULL,fmt,args);
va_end(args);
}
void
ncvtrace(int level, const char* fcn, const char* fmt, va_list ap)
{
struct Frame* frame;
if(!nclogginginitialized) ncloginit();
if(nclog_global.tracelevel < 0) ncsetlogging(0);
if(fcn != NULL) {
frame = &nclog_global.frames[nclog_global.depth];
frame->fcn = fcn;
frame->level = level;
frame->depth = nclog_global.depth;
}
if(level <= nclog_global.tracelevel) {
if(fcn != NULL)
fprintf(nclog_global.nclogstream,"%s: (%d): %s:","Enter",level,fcn);
if(fmt != NULL)
vfprintf(nclog_global.nclogstream, fmt, ap);
fprintf(nclog_global.nclogstream, "\n" );
fflush(nclog_global.nclogstream);
}
if(fcn != NULL) nclog_global.depth++;
}
int
ncuntrace(const char* fcn, int err, const char* fmt, ...)
{
va_list args;
struct Frame* frame;
va_start(args, fmt);
if(nclog_global.depth == 0) {
fprintf(nclog_global.nclogstream,"*** Unmatched untrace: %s: depth==0\n",fcn);
goto done;
}
nclog_global.depth--;
frame = &nclog_global.frames[nclog_global.depth];
if(frame->depth != nclog_global.depth || strcmp(frame->fcn,fcn) != 0) {
fprintf(nclog_global.nclogstream,"*** Unmatched untrace: fcn=%s expected=%s\n",frame->fcn,fcn);
goto done;
}
if(frame->level <= nclog_global.tracelevel) {
fprintf(nclog_global.nclogstream,"%s: (%d): %s: ","Exit",frame->level,frame->fcn);
if(err)
fprintf(nclog_global.nclogstream,"err=(%d) '%s':",err,nc_strerror(err));
if(fmt != NULL)
vfprintf(nclog_global.nclogstream, fmt, args);
fprintf(nclog_global.nclogstream, "\n" );
fflush(nclog_global.nclogstream);
#ifdef HAVE_EXECINFO_H
if(err != 0)
ncbacktrace();
#endif
}
done:
va_end(args);
if(err != 0)
return ncbreakpoint(err);
else
return err;
}
Support MSYS2/Mingw platform re: The current netcdf-c release has some problems with the mingw platform on windows. Mostly they are path issues. Changes to support mingw+msys2: ------------------------------- * Enable option of looking into the windows registry to find the mingw root path. In aid of proper path handling. * Add mingw+msys as a specific platform in configure.ac and move testing of the platform to the front so it is available early. * Handle mingw X libncpoco (dynamic loader) properly even though mingw does not yet support it. * Handle mingw X plugins properly even though mingw does not yet support it. * Alias pwd='pwd -W' to better handle paths in shell scripts. * Plus a number of other minor compile irritations. * Disallow the use of multiple nc_open's on the same file for windows (and mingw) because windows does not seem to handle these properly. Not sure why we did not catch this earlier. * Add mountpoint info to dpathmgr.c to help support mingw. * Cleanup dpathmgr conversions. Known problems: --------------- * I have not been able to get shared libraries to work, so plugins/filters must be disabled. * There is some kind of problem with libcurl that I have not solved, so all uses of libcurl (currently DAP+Byterange) must be disabled. Misc. other fixes: ------------------ * Cleanup the relationship between ENABLE_PLUGINS and various other flags in CMakeLists.txt and configure.ac. * Re-arrange the TESTDIRS order in Makefile.am. * Add pseudo-breakpoint to nclog.[ch] for debugging. * Improve the documentation of the path manager code in ncpathmgr.h * Add better support for relative paths in dpathmgr.c * Default the mode args to NCfopen to include "b" (binary) for windows. * Add optional debugging output in various places. * Make sure that everything builds with plugins disabled. * Fix numerous (s)printf inconsistencies betweenb the format spec and the arguments.
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int
ncthrow(int err,const char* file,int line)
{
if(err == 0) return err;
return ncbreakpoint(err);
}
int
ncbreakpoint(int err)
{
return err;
}
#ifdef HAVE_EXECINFO_H
#define MAXSTACKDEPTH 100
void
ncbacktrace(void)
{
int j, nptrs;
void* buffer[MAXSTACKDEPTH];
char **strings;
if(getenv("NCBACKTRACE") == NULL) return;
nptrs = backtrace(buffer, MAXSTACKDEPTH);
strings = backtrace_symbols(buffer, nptrs);
if (strings == NULL) {
perror("backtrace_symbols");
errno = 0;
return;
}
fprintf(stderr,"Backtrace:\n");
for(j = 0; j < nptrs; j++)
fprintf(stderr,"%s\n", strings[j]);
free(strings);
}
#endif
/**@}*/