netcdf-c/oc2/ocinternal.c
Dennis Heimbigner f3e711e2b8 Add support for setting HDF5 alignment property when creating a file
re: https://github.com/Unidata/netcdf-c/issues/2177
re: https://github.com/Unidata/netcdf-c/pull/2178

Provide get/set functions to store global data alignment
information and apply it when a file is created.

The api is as follows:
````
int nc_set_alignment(int threshold, int alignment);
int nc_get_alignment(int* thresholdp, int* alignmentp);
````

If defined, then for every file created opened after the call to
nc_set_alignment, for every new variable added to the file, the
most recently set threshold and alignment values will be applied
to that variable.

The nc_get_alignment function return the last values set by
nc_set_alignment.  If nc_set_alignment has not been called, then
it returns the value 0 for both threshold and alignment.

The alignment parameters are stored in the NCglobalstate object
(see below) for use as needed. Repeated calls to nc_set_alignment
will overwrite any existing values in NCglobalstate.

The alignment parameters are applied in libhdf5/hdf5create.c
and libhdf5/hdf5open.c

The set/get alignment functions are defined in libsrc4/nc4internal.c.

A test program was added as nc_test4/tst_alignment.c.

## Misc. Changes Unrelated to Alignment

* The NCRCglobalstate type was renamed to NCglobalstate to
  indicate that it represented more general global state than
  just .rc data.  It was also moved to nc4internal.h.  This led
  to a large number of small changes: mostly renaming. The
  global state management functions were moved to nc4internal.c.

* The global chunk cache variables have been moved into
  NCglobalstate.  As warranted, other global state will be moved
  as well.

* Some misc. problems with the nczarr performance tests were corrected.
2022-01-29 15:27:52 -07:00

715 lines
20 KiB
C

/* Copyright 2018, UCAR/Unidata and OPeNDAP, Inc.
See the COPYRIGHT file for more information. */
#include "config.h"
#include <stdio.h>
#ifdef HAVE_STDINT_H
#include <stdint.h>
#endif
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
#ifdef HAVE_SYS_STAT_H
#include <sys/stat.h>
#endif
#if _MSC_VER
#include <io.h>
#include <direct.h>
#include <process.h>
#endif
#ifdef HAVE_FTW_H
#include <ftw.h>
#endif
#include <errno.h>
#include "nc4internal.h"
#include "ocinternal.h"
#include "ocdebug.h"
#include "occurlfunctions.h"
#include "ochttp.h"
#include "ocread.h"
#include "dapparselex.h"
#include "ncpathmgr.h"
#define DATADDSFILE "datadds"
#define CLBRACE '{'
#define CRBRACE '}'
#define OCBUFFERSIZE "HTTP.READ.BUFFERSIZE"
#define OCKEEPALIVE "HTTP.KEEPALIVE"
#ifdef HAVE_CURLOPT_BUFFERSIZE
#ifndef CURL_MAX_READ_SIZE
#define CURL_MAX_READ_SIZE (512*1024)
#endif
#endif
/*Forward*/
static OCerror ocextractddsinmemory(OCstate*,OCtree*,int);
static OCerror ocextractddsinfile(OCstate*,OCtree*,int);
static OCerror createtempfile(OCstate*,OCtree*);
static int dataError(XXDR* xdrs, OCstate*);
static void ocremovefile(const char* path);
static OCerror ocset_curlproperties(OCstate*);
static OCerror ocget_rcproperties(OCstate*);
extern OCnode* makeunlimiteddimension(void);
int ocdebug = 0;
int ocinitialized = 0;
OCerror
ocinternalinitialize(void)
{
int stat = OC_NOERR;
if(ocinitialized) return OC_NOERR;
ocinitialized = 1;
#if 0
if(sizeof(off_t) != sizeof(void*)) {
fprintf(stderr,"OC xxdr depends on the assumption that sizeof(off_t) == sizeof(void*)\n");
/*
Commenting out for now, as this does not hold true on 32-bit linux systems.
OCASSERT(sizeof(off_t) == sizeof(void*));
*/
}
#endif
/* Compute some xdr related flags */
xxdr_init();
return OCTHROW(stat);
}
/**************************************************/
OCerror
ocopen(OCstate** statep, const char* url)
{
int stat = OC_NOERR;
OCstate * state = NULL;
NCURI* tmpurl = NULL;
CURL* curl = NULL; /* curl handle*/
if(!ocinitialized)
ocinternalinitialize();
if(ncuriparse(url,&tmpurl)) {
OCTHROWCHK(stat=OC_EBADURL);
goto fail;
}
stat = occurlopen(&curl);
if(stat != OC_NOERR) {OCTHROWCHK(stat); goto fail;}
state = (OCstate*)ocmalloc(sizeof(OCstate)); /* ocmalloc zeros memory*/
if(state == NULL) {OCTHROWCHK(stat=OC_ENOMEM); goto fail;}
/* Setup DAP state*/
state->header.magic = OCMAGIC;
state->header.occlass = OC_State;
state->curl = curl;
state->trees = nclistnew();
state->uri = tmpurl;
state->packet = ncbytesnew();
ncbytessetalloc(state->packet,DFALTPACKETSIZE); /*initial reasonable size*/
/* Initialize auth info from rc file */
stat = NC_authsetup(&state->auth, state->uri);
/* Initialize misc info from rc file */
stat = ocget_rcproperties(state);
/* Apply curl properties for this link;
assumes state has been initialized */
stat = ocset_curlproperties(state);
if(stat != OC_NOERR) goto fail;
/* Set the one-time curl flags */
if((stat=ocset_flags_perlink(state))!= OC_NOERR) goto fail;
#if 1 /* temporarily make per-link */
if((stat=ocset_flags_perfetch(state))!= OC_NOERR) goto fail;
#endif
oc_curl_protocols(state);
if(statep) *statep = state;
else {
if(state != NULL) ocfree(state);
}
return OCTHROW(stat);
fail:
ncurifree(tmpurl);
if(state != NULL) ocfree(state);
if(curl != NULL) occurlclose(curl);
return OCTHROW(stat);
}
OCerror
ocfetch(OCstate* state, const char* constraint, OCdxd kind, OCflags flags,
OCnode** rootp)
{
OCtree* tree = NULL;
OCnode* root = NULL;
OCerror stat = OC_NOERR;
tree = (OCtree*)ocmalloc(sizeof(OCtree));
MEMCHECK(tree,OC_ENOMEM);
memset((void*)tree,0,sizeof(OCtree));
tree->dxdclass = kind;
tree->state = state;
tree->constraint = nulldup(constraint);
/* Set per-fetch curl properties */
#if 0 /* temporarily make per-link */
if((stat=ocset_flags_perfetch(state))!= OC_NOERR) goto fail;
#endif
ncbytesclear(state->packet);
switch (kind) {
case OCDAS:
stat = readDAS(state,tree,flags);
if(stat == OC_NOERR) {
tree->text = ncbytesdup(state->packet);
if(tree->text == NULL) stat = OC_EDAS;
}
break;
case OCDDS:
stat = readDDS(state,tree,flags);
if(stat == OC_NOERR) {
tree->text = ncbytesdup(state->packet);
if(tree->text == NULL) stat = OC_EDDS;
}
break;
case OCDATADDS:
if((flags & OCONDISK) != 0) {/* store in file */
/* Create the datadds file immediately
so that DRNO can reference it*/
/* Make the tmp file*/
stat = createtempfile(state,tree);
if(stat) {OCTHROWCHK(stat); goto fail;}
stat = readDATADDS(state,tree,flags);
if(stat == OC_NOERR) {
/* Separate the DDS from data and return the dds;
will modify packet */
stat = ocextractddsinfile(state,tree,flags);
}
} else { /*inmemory*/
stat = readDATADDS(state,tree,flags);
if(stat == OC_NOERR) {
/* Separate the DDS from data and return the dds;
will modify packet */
stat = ocextractddsinmemory(state,tree,flags);
}
}
break;
default:
break;
}/*switch*/
/* Obtain any http code */
state->error.httpcode = ocfetchhttpcode(state->curl);
if(stat != OC_NOERR) {
if(state->error.httpcode >= 400) {
nclog(NCLOGWARN,"oc_open: Could not read url (%s); http error = %l",
ncuribuild(state->uri,NULL,NULL,NCURIALL),state->error.httpcode);
} else {
nclog(NCLOGWARN,"oc_open: Could not read url");
}
goto fail;
}
tree->nodes = NULL;
stat = DAPparse(state,tree,tree->text);
/* Check and report on an error return from the server */
if(stat == OC_EDAPSVC && state->error.code != NULL) {
fprintf(stderr,"oc_open: server error retrieving url: code=%s message=\"%s\"",
state->error.code,
(state->error.message?state->error.message:""));
}
if(stat) {OCTHROWCHK(stat); goto fail;}
root = tree->root;
/* make sure */
tree->root = root;
root->tree = tree;
/* Verify the parse */
switch (kind) {
case OCDAS:
if(root->octype != OC_Attributeset)
{OCTHROWCHK(stat=OC_EDAS); goto fail;}
break;
case OCDDS:
if(root->octype != OC_Dataset)
{OCTHROWCHK(stat=OC_EDDS); goto fail;}
break;
case OCDATADDS:
if(root->octype != OC_Dataset)
{OCTHROWCHK(stat=OC_EDATADDS); goto fail;}
/* Modify the tree kind */
tree->dxdclass = OCDATADDS;
break;
default: return OC_EINVAL;
}
if(kind != OCDAS) {
/* Process ocnodes to mark those that are cacheable */
ocmarkcacheable(state,root);
/* Process ocnodes to handle various semantic issues*/
occomputesemantics(tree->nodes);
}
/* Process ocnodes to compute name info*/
occomputefullnames(tree->root);
if(kind == OCDATADDS) {
if((flags & OCONDISK) != 0) {
tree->data.xdrs = xxdr_filecreate(tree->data.file,tree->data.bod);
} else {
#ifdef OCDEBUG
fprintf(stderr,"ocfetch.datadds.memory: datasize=%lu bod=%lu\n",
(unsigned long)tree->data.datasize,(unsigned long)tree->data.bod);
#endif
/* Switch to zero based memory */
tree->data.xdrs
= xxdr_memcreate(tree->data.memory,tree->data.datasize,tree->data.bod);
}
MEMCHECK(tree->data.xdrs,OC_ENOMEM);
/* Do a quick check to see if server returned an ERROR {}
at the beginning of the data
*/
if(dataError(tree->data.xdrs,state)) {
stat = OC_EDATADDS;
fprintf(stderr,"oc_open: server error retrieving url: code=%s message=\"%s\"",
state->error.code,
(state->error.message?state->error.message:""));
goto fail;
}
/* Compile the data into a more accessible format */
stat = occompile(state,tree->root);
if(stat != OC_NOERR)
goto fail;
}
/* Put root into the state->trees list */
nclistpush(state->trees,(void*)root);
if(rootp) *rootp = root;
return stat;
fail:
if(root != NULL)
ocroot_free(root);
else if(tree != NULL)
octree_free(tree);
return OCTHROW(stat);
}
static OCerror
createtempfile(OCstate* state, OCtree* tree)
{
int stat = OC_NOERR;
char* path = NULL;
char* tmppath = NULL;
int len;
NCglobalstate* globalstate = NC_getglobalstate();
len =
strlen(globalstate->tempdir)
+ 1 /* '/' */
+ strlen(DATADDSFILE)
+ 1; /* nul term */
path = (char*)malloc(len);
if(path == NULL) return OC_ENOMEM;
strncpy(path,globalstate->tempdir,len);
strlcat(path,"/",len);
strlcat(path,DATADDSFILE,len);
tmppath = NC_mktmp(path);
free(path);
if(tmppath == NULL) {stat = OC_EACCESS; goto fail;}
#ifdef OCDEBUG
nclog(NCLOGNOTE,"oc_open: creating tmp file: %s",tmppath);
#endif
tree->data.filename = tmppath; /* remember our tmp file name */
tmppath = NULL;
tree->data.file = NCfopen(tree->data.filename,"w+");
if(tree->data.file == NULL) return OC_EOPEN;
/* make the temp file so it will automatically be reclaimed on close */
if(ocdebug == 0)
ocremovefile(tree->data.filename);
return stat;
fail:
if(tmppath != NULL) {
nclog(NCLOGERR,"oc_open: attempt to create tmp file failed: %s",tmppath);
free(tmppath);
} else {
nclog(NCLOGERR,"oc_open: attempt to create tmp file failed: NULL");
}
return OCTHROW(stat);
}
void
occlose(OCstate* state)
{
unsigned int i;
if(state == NULL) return;
/* Warning: ocfreeroot will attempt to remove the root from state->trees */
/* Ok in this case because we are popping the root out of state->trees */
for(i=0;i<nclistlength(state->trees);i++) {
OCnode* root = (OCnode*)nclistpop(state->trees);
ocroot_free(root);
}
nclistfree(state->trees);
ncurifree(state->uri);
ncbytesfree(state->packet);
ocfree(state->error.code);
ocfree(state->error.message);
if(state->curl != NULL) occurlclose(state->curl);
NC_authfree(state->auth);
ocfree(state);
}
static OCerror
ocextractddsinmemory(OCstate* state, OCtree* tree, OCflags flags)
{
OCerror stat = OC_NOERR;
size_t ddslen, bod, bodfound;
/* Read until we find the separator (or EOF)*/
bodfound = ocfindbod(state->packet,&bod,&ddslen);
if(!bodfound) {/* No BOD; pretend */
bod = tree->data.bod;
ddslen = tree->data.datasize;
}
tree->data.bod = bod;
tree->data.ddslen = ddslen;
/* copy out the dds */
if(ddslen > 0) {
tree->text = (char*)ocmalloc(ddslen+1);
memcpy((void*)tree->text,(void*)ncbytescontents(state->packet),ddslen);
tree->text[ddslen] = '\0';
} else
tree->text = NULL;
/* Extract the inmemory contents */
tree->data.memory = ncbytesextract(state->packet);
#ifdef OCIGNORE
/* guarantee the data part is on an 8 byte boundary */
if(tree->data.bod % 8 != 0) {
unsigned long count = tree->data.datasize - tree->data.bod;
memcpy(tree->xdrmemory,tree->xdrmemory+tree->data.bod,count);
tree->data.datasize = count;
tree->data.bod = 0;
tree->data.ddslen = 0;
}
#endif
if(tree->text == NULL) stat = OC_EDATADDS;
return OCTHROW(stat);
}
static OCerror
ocextractddsinfile(OCstate* state, OCtree* tree, OCflags flags)
{
OCerror stat = OC_NOERR;
size_t ddslen, bod, bodfound;
/* Read until we find the separator (or EOF)*/
ncbytesclear(state->packet);
rewind(tree->data.file);
bodfound = 0;
do {
char chunk[1024];
size_t count;
/* read chunks of the file until we find the separator*/
count = fread(chunk,1,sizeof(chunk),tree->data.file);
if(count <= 0) break; /* EOF;*/
ncbytesappendn(state->packet,chunk,count);
bodfound = ocfindbod(state->packet,&bod,&ddslen);
} while(!bodfound);
if(!bodfound) {/* No BOD; pretend */
bod = tree->data.bod;
ddslen = tree->data.datasize;
#ifdef OCDEBUG
fprintf(stderr,"missing bod: ddslen=%lu bod=%lu\n",
(unsigned long)ddslen,(unsigned long)bod);
#endif
}
tree->data.bod = bod;
tree->data.ddslen = ddslen;
/* copy out the dds */
if(ddslen > 0) {
tree->text = (char*)ocmalloc(ddslen+1);
memcpy((void*)tree->text,(void*)ncbytescontents(state->packet),ddslen);
tree->text[ddslen] = '\0';
} else
tree->text = NULL;
/* reset the position of the tmp file*/
if(fseek(tree->data.file,(long)tree->data.bod,SEEK_SET) < 0
|| tree->text == NULL)
stat = OC_EDATADDS;
return OCTHROW(stat);
}
OCerror
ocupdatelastmodifieddata(OCstate* state, OCflags ocflags)
{
OCerror status = OC_NOERR;
long lastmodified;
char* base = NULL;
int flags = 0;
if(ocflags & OCENCODEPATH) flags |= NCURIENCODEPATH;
if(ocflags & OCENCODEQUERY) flags |= NCURIENCODEQUERY;
base = ncuribuild(state->uri,NULL,NULL,flags);
status = ocfetchlastmodified(state->curl, base, &lastmodified);
free(base);
if(status == OC_NOERR) {
state->datalastmodified = lastmodified;
}
return OCTHROW(status);
}
/*
Extract state values from .rc file
*/
static OCerror
ocget_rcproperties(OCstate* state)
{
OCerror ocerr = OC_NOERR;
char* option = NULL;
#ifdef HAVE_CURLOPT_BUFFERSIZE
option = NC_rclookup(OCBUFFERSIZE,state->uri->uri,NULL);
if(option != NULL && strlen(option) != 0) {
long bufsize;
if(strcasecmp(option,"max")==0)
bufsize = CURL_MAX_READ_SIZE;
else if(sscanf(option,"%ld",&bufsize) != 1 || bufsize <= 0)
fprintf(stderr,"Illegal %s size\n",OCBUFFERSIZE);
state->curlbuffersize = bufsize;
}
#endif
#ifdef HAVE_CURLOPT_KEEPALIVE
option = NC_rclookup(OCKEEPALIVE,state->uri->uri,NULL);
if(option != NULL && strlen(option) != 0) {
/* The keepalive value is of the form 0 or n/m,
where n is the idle time and m is the interval time;
setting either to zero will prevent that field being set. */
if(strcasecmp(option,"on")==0) {
state->curlkeepalive.active = 1;
} else {
unsigned long idle=0;
unsigned long interval=0;
if(sscanf(option,"%lu/%lu",&idle,&interval) != 2)
fprintf(stderr,"Illegal KEEPALIVE VALUE: %s\n",option);
state->curlkeepalive.idle = idle;
state->curlkeepalive.interval = interval;
state->curlkeepalive.active = 1;
}
}
#endif
return ocerr;
}
/*
Set curl properties for link based on fields in the state.
*/
static OCerror
ocset_curlproperties(OCstate* state)
{
OCerror stat = OC_NOERR;
NCglobalstate* globalstate = NC_getglobalstate();
if(state->auth->curlflags.useragent == NULL) {
size_t len = strlen(DFALTUSERAGENT) + strlen(VERSION) + 1;
char* agent = (char*)malloc(len);
strncpy(agent,DFALTUSERAGENT,len);
strlcat(agent,VERSION,len);
state->auth->curlflags.useragent = agent;
agent = NULL;
}
/* Some servers (e.g. thredds and columbia) appear to require a place
to put cookies in order for some security functions to work
*/
if(state->auth->curlflags.cookiejar != NULL
&& strlen(state->auth->curlflags.cookiejar) == 0) {
free(state->auth->curlflags.cookiejar);
state->auth->curlflags.cookiejar = NULL;
}
if (state->auth->curlflags.cookiejar == NULL) {
/* If no cookie file was defined, define a default */
int stat = NC_NOERR;
char* path = NULL;
char* tmppath = NULL;
int len;
errno = 0;
/* Create the unique cookie file name */
len =
strlen(globalstate->tempdir)
+ 1 /* '/' */
+ strlen("occookies")
+ 1;
path = (char*)calloc(1, len);
if (path == NULL) return OC_ENOMEM;
strncpy(path,globalstate->tempdir,len);
strlcat(path,"/",len);
strlcat(path,"occookies",len);
tmppath = NC_mktmp(path);
if(tmppath == NULL) {
tmppath = NC_mktmp(path);
}
free(path);
state->auth->curlflags.cookiejar = tmppath;
state->auth->curlflags.cookiejarcreated = 1;
if (stat != OC_NOERR && errno != EEXIST) {
fprintf(stderr, "Cannot create cookie file\n");
goto fail;
}
errno = 0;
}
OCASSERT(state->auth->curlflags.cookiejar != NULL);
/* Make sure the cookie jar exists and can be read and written */
{
FILE* f = NULL;
char* fname = state->auth->curlflags.cookiejar;
/* See if the file exists already */
f = NCfopen(fname,"r");
if(f == NULL) {
/* Ok, create it */
f = NCfopen(fname,"w+");
if(f == NULL) {
fprintf(stderr,"Cookie file cannot be read and written: %s\n",fname);
{stat = OC_EPERM; goto fail;}
}
} else { /* test if file can be written */
fclose(f);
f = NCfopen(fname,"r+");
if(f == NULL) {
fprintf(stderr,"Cookie file is cannot be written: %s\n",fname);
{stat = OC_EPERM; goto fail;}
}
}
if(f != NULL) fclose(f);
}
#if 0
/* Create a netrc file if specified and required,
where required => >1 NETRC triples exist */
if(ocrc_netrc_required(state)) {
/* WARNING: it appears that a user+pwd was specified specifically, then
the netrc file will be completely disabled. */
if(state->auth->creds.userpwd != NULL) {
nclog(NCLOGWARN,"The rc file specifies both netrc and user+pwd; this will cause curl to ignore the netrc file");
}
stat = oc_build_netrc(state);
}
#endif
return stat;
fail:
return OCTHROW(stat);
}
static const char* ERROR_TAG = "Error ";
static int
dataError(XXDR* xdrs, OCstate* state)
{
int depth=0;
int errfound = 0;
off_t ckp=0,avail=0;
int i=0;
char* errmsg = NULL;
char errortext[16]; /* bigger than |ERROR_TAG|*/
avail = xxdr_getavail(xdrs);
if(avail < strlen(ERROR_TAG))
goto done; /* assume it is ok */
ckp = xxdr_getpos(xdrs);
/* Read enough characters to test for 'ERROR ' */
errortext[0] = '\0';
xxdr_getbytes(xdrs,errortext,(off_t)strlen(ERROR_TAG));
if(ocstrncmp(errortext,ERROR_TAG,strlen(ERROR_TAG)) != 0)
goto done; /* not an immediate error */
/* Try to locate the whole error body */
xxdr_setpos(xdrs,ckp);
for(depth=0,i=0;i<avail;i++) {
xxdr_getbytes(xdrs,errortext,(off_t)1);
if(errortext[0] == CLBRACE) depth++;
else if(errortext[0] == CRBRACE) {
depth--;
if(depth == 0) {i++; break;}
}
}
errmsg = (char*)malloc((size_t)i+1);
if(errmsg == NULL) {errfound = 1; goto done;}
xxdr_setpos(xdrs,ckp);
xxdr_getbytes(xdrs,errmsg,(off_t)i);
errmsg[i] = '\0';
state->error.message = errmsg;
state->error.code = strdup("?");
state->error.httpcode = 404;
xxdr_setpos(xdrs,ckp);
errfound = 1;
done:
xxdr_setpos(xdrs,ckp);
return errfound;
}
/**************************************************/
/* Curl option functions */
/*
Note that if we set the option in curlflags,
then we need to also invoke the ocset_curlopt
to update the curl flags in libcurl.
*/
OCerror
ocset_useragent(OCstate* state, const char* agent)
{
OCerror stat = OC_NOERR;
if(state->auth->curlflags.useragent != NULL)
free(state->auth->curlflags.useragent);
state->auth->curlflags.useragent = strdup(agent);
if(state->auth->curlflags.useragent == NULL)
return OCTHROW(OC_ENOMEM);
stat = ocset_curlflag(state,CURLOPT_USERAGENT);
return stat;
}
OCerror
ocset_netrc(OCstate* state, const char* path)
{
OCerror stat = OC_NOERR;
if(state->auth->curlflags.netrc != NULL)
free(state->auth->curlflags.netrc);
state->auth->curlflags.netrc = strdup(path);
if(state->auth->curlflags.netrc == NULL)
return OCTHROW(OC_ENOMEM);
stat = ocset_curlflag(state,CURLOPT_NETRC);
return stat;
}
static void
ocremovefile(const char* path)
{
#ifdef _MSC_VER
DeleteFile(path);
#else
remove(path);
#endif
}