Merge branch 'main' into distcheck.dmh

RELEASE_NOTES.md

@@ -7,7 +7,11 @@ This file contains a high-level description of this package's evolution. Release
 
 ## 4.8.2 - TBD
 
+
 * [Bug Fix] Get "make distcheck" to work See [Github #/2343](https://github.com/Unidata/netcdf-c/pull/2343).
+* [Enhancement] Allow the read/write of JSON-valued Zarr attributes to allow
+for domain specific info such as used by GDAL/Zarr. See [Github #????](https://github.com/Unidata/netcdf-c/pull/????).
+* [Enhancement] Turn on the XArray convention for NCZarr files by default. WARNING, this means that the mode should explicitly specify nczarr" or "zarr" even if "xarray" or "noxarray" is specified. See [Github #2257](https://github.com/Unidata/netcdf-c/pull/2257).
 * [Enhancement] Update the documentation to match the current filter capabilities See [Github #2249](https://github.com/Unidata/netcdf-c/pull/2249).
 * [Enhancement] Support installation of pre-built standard filters into user-specified location. See [Github #2318](https://github.com/Unidata/netcdf-c/pull/2318).
 * [Enhancement] Improve filter support. More specifically (1) add nc_inq_filter_avail to check if a filter is available, (2) add the notion of standard filters, (3) cleanup szip support to fix interaction with NCZarr. See [Github #2245](https://github.com/Unidata/netcdf-c/pull/2245).

docs/nczarr.md

@@ -136,16 +136,18 @@ Note that It should be the case that zipping a _file_
 format directory tree will produce a file readable by the
 _zip_ storage format, and vice-versa.
 
-By default, _mode=zarr_ also supports the XArray _\_ARRAY\_DIMENSIONS_ convention. The _noxarray_ mode tells the library to disable the XArray support.
+By default, the XArray convention is supported and used for
+both NCZarr files and pure Zarr files. This
+means that every variable in the root group whose named dimensions
+are also in the root group will have an attribute called
+*\_ARRAY\_DIMENSIONS* that stores those dimension names.
+The _noxarray_ mode tells the library to disable the XArray support.
 
 The netcdf-c library is capable of inferring additional mode flags based on the flags it finds. Currently we have the following inferences.
-
-- _xarray_ => _zarr_
-- _noxarray_ => _zarr_
 - _zarr_ => _nczarr_
 
-So for example: ````...#mode=noxarray,zip```` is equivalent to this.
-````...#mode=nczarr,zarr,noxarray,zip
+So for example: ````...#mode=zarr,zip```` is equivalent to this.
+````...#mode=nczarr,zarr,zip
 ````
 <!--
 - log=&lt;output-stream&gt;: this control turns on logging output,
@@ -434,10 +436,13 @@ The value of this attribute is a list of dimension names (strings).
 An example might be ````["time", "lon", "lat"]````.
 It is essentially equivalent to the ````_NCZARR_ARRAY "dimrefs" list````, except that the latter uses fully qualified names so the referenced dimensions can be anywhere in the dataset.
 
-As of _netcdf-c_ version 4.8.1, The Xarray ''_ARRAY_DIMENSIONS'' attribute is supported.
-This attribute will be read/written by default, but can be suppressed if the mode value "noxarray" is specified.
+As of _netcdf-c_ version 4.8.2, The Xarray ''_ARRAY_DIMENSIONS'' attribute is supported for both NCZarr and pure Zarr.
+If possible, this attribute will be read/written by default,
+but can be suppressed if the mode value "noxarray" is specified.
 If detected, then these dimension names are used to define shared dimensions.
-Note that "noxarray" or "xarray" implies pure zarr format.
+The following conditions will cause ''_ARRAY_DIMENSIONS'' to not be written.
+* The variable is not in the root group,
+* Any dimension referenced by the variable is not in the root group.
 
 # Examples {#nczarr_examples}
 

docs/static-pages/software.html

@@ -940,7 +940,7 @@ <h2><a id="gliderscope" name="gliderscope">Gliderccope</a></h2>
  Dr L. Mun Woo <mun.woo@uwa.edu.au>
  at ANFOG (Australian National Facility for Ocean Gliders)
  has developed
- <a href="http://imos.org.au/facilities/oceangliders/glider-data/gliderscope/">Gliderscope</a>.
+ <a href="https://imos.org.au/gliderscope">Gliderscope</a>.
  Gliderscope is an IMOS (Integrated Marine Observing System)
  oceanographic software package allowing users quick easy visualisation
  of ocean glider data, via a convenient graphical user interface.
@@ -2008,7 +2008,7 @@ <h2><a id="netcdf_ninja" name="netcdf_ninja">NetCDF Ninja</a></h2>
  <p>
  Dr L. Mun Woo of University of Western Australia <mun.woo@uwa.edu.au>
  has developed
- <a href="http://imos.org.au/facilities/oceangliders/glider-data/netcdfninja/">NetCDF Ninja</a>,
+ <a href="https://imos.org.au/netcdfninja">NetCDF Ninja</a>,
  a graphical user interface that allows users to browse all
  the metadata contained in netCDF files, scrutinise the data using an
  interactive graphical plot and even make small alterations or export

include/ncjson.h

@@ -56,9 +56,12 @@ struct NCJconst {int bval; long long ival; double dval; char* sval;};
 extern "C" {
 #endif
 
-/* Parse a JSON string */
+/* Parse a string to NCjson*/
 DLLEXPORT int NCJparse(const char* text, unsigned flags, NCjson** jsonp);
 
+/* Parse a counted string to NCjson*/
+DLLEXPORT int NCJparsen(size_t len, const char* text, unsigned flags, NCjson** jsonp);
+
 /* Reclaim a JSON tree */
 DLLEXPORT extern void NCJreclaim(NCjson* json);
 

libdispatch/dinfermodel.c

@@ -137,9 +137,9 @@ static const struct MACRODEF {
 {"dap4","mode",{"dap4",NULL}},
 {"s3","mode",{"s3","nczarr",NULL}},
 {"bytes","mode",{"bytes",NULL}},
-{"xarray","mode",{"nczarr","zarr","xarray",NULL}},
-{"noxarray","mode",{"nczarr","zarr","noxarray",NULL}},
-{"zarr","mode",{"nczarr","zarr","xarray",NULL}},
+{"xarray","mode",{"zarr", NULL}},
+{"noxarray","mode",{"nczarr", "noxarray", NULL}},
+{"zarr","mode",{"nczarr","zarr", NULL}},
 {NULL,NULL,{NULL}}
 };
 
@@ -149,9 +149,8 @@ static const struct MODEINFER {
  char* inference;
 } modeinferences[] = {
 {"zarr","nczarr"},
-{"zarr","xarray"},
 {"xarray","zarr"},
-{"noxarray","zarr"},
+{"noxarray","nczarr"},
 {NULL,NULL}
 };
 

libdispatch/ncjson.c

@@ -94,6 +94,7 @@ static int NCJyytext(NCJparser*, char* start, size_t pdlen);
 static void NCJreclaimArray(struct NCjlist*);
 static void NCJreclaimDict(struct NCjlist*);
 static int NCJunescape(NCJparser* parser);
+static int unescape1(int c);
 static int listappend(struct NCjlist* list, NCjson* element);
 
 #ifndef NETCDF_JSON_H
@@ -109,24 +110,28 @@ static int bytesappendc(NCJbuf* bufp, const char c);
 
 int
 NCJparse(const char* text, unsigned flags, NCjson** jsonp)
+{
+ return NCJparsen(strlen(text),text,flags,jsonp);
+}
+
+int
+NCJparsen(size_t len, const char* text, unsigned flags, NCjson** jsonp)
 {
  int stat = NCJ_OK;
- size_t len;
  NCJparser* parser = NULL;
  NCjson* json = NULL;
 
  /* Need at least 1 character of input */
- if(text == NULL || text[0] == '\0')
+ if(len == 0 || text == NULL)
  {stat = NCJTHROW(NCJ_ERR); goto done;}
  if(jsonp == NULL) goto done;
  parser = calloc(1,sizeof(NCJparser));
  if(parser == NULL)
  {stat = NCJTHROW(NCJ_ERR); goto done;}
- len = strlen(text);
  parser->text = (char*)malloc(len+1+1);
  if(parser->text == NULL)
  {stat = NCJTHROW(NCJ_ERR); goto done;}
- strcpy(parser->text,text);
+ memcpy(parser->text,text,len);
  parser->text[len] = '\0';
  parser->text[len+1] = '\0';
  parser->pos = &parser->text[0];
@@ -334,16 +339,21 @@ NCJlex(NCJparser* parser)
  c = *parser->pos;
  if(c == '\0') {
  token = NCJ_EOF;
- } else if(c <= ' ' || c == '\177') {
+ } else if(c <= ' ' || c == '\177') {/* ignore whitespace */
+ parser->pos++;
+ continue;
+ } else if(c == NCJ_ESCAPE) {
  parser->pos++;
- continue; /* ignore whitespace */
+ c = *parser->pos;
+ *parser->pos = unescape1(c);
+ continue;
  } else if(strchr(JSON_WORD, c) != NULL) {
  start = parser->pos;
  for(;;) {
  c = *parser->pos++;
  if(c == '\0' || strchr(JSON_WORD,c) == NULL) break; /* end of word */
  }
- /* Pushback c if not whitespace */
+ /* Pushback c */
  parser->pos--;
  count = ((parser->pos) - start);
  if(NCJyytext(parser,start,count)) goto done;
@@ -604,6 +614,21 @@ NCJunescape(NCJparser* parser)
  return NCJTHROW(NCJ_OK); 
 }
 
+/* Unescape a single character */
+static int
+unescape1(int c)
+{
+ switch (c) {
+ case 'b': c = '\b'; break;
+ case 'f': c = '\f'; break;
+ case 'n': c = '\n'; break;
+ case 'r': c = '\r'; break;
+ case 't': c = '\t'; break;
+ default: c = c; break;/* technically not Json conformant */
+ }
+ return c;
+}
+
 #ifdef NCJDEBUG
 static char*
 tokenname(int token)
@@ -896,7 +921,7 @@ NCJunparseR(const NCjson* json, NCJbuf* buf, unsigned flags)
  if(json->list.len > 0 && json->list.contents != NULL) {
  int shortlist = 0;
  for(i=0;!shortlist && i < json->list.len;i+=2) {
- if(i > 0) bytesappendc(buf,NCJ_COMMA);
+ if(i > 0) {bytesappendc(buf,NCJ_COMMA);bytesappendc(buf,' ');};
  NCJunparseR(json->list.contents[i],buf,flags); /* key */
  bytesappendc(buf,NCJ_COLON);
  bytesappendc(buf,' ');
@@ -945,7 +970,7 @@ escape(const char* text, NCJbuf* buf)
  case '\n': replace = 'n'; break;
  case '\r': replace = 'r'; break;
  case '\t': replace = 't'; break;
- case NCJ_QUOTE: replace = '\''; break;
+ case NCJ_QUOTE: replace = '\"'; break;
  case NCJ_ESCAPE: replace = '\\'; break;
  default: break;
  }

libnczarr/zarr.c

@@ -384,14 +384,15 @@ applycontrols(NCZ_FILE_INFO_T* zinfo)
  }
  /* Process the modelist first */
  zinfo->controls.mapimpl = NCZM_DEFAULT;
+ zinfo->controls.flags |= FLAG_XARRAYDIMS; /* Always support XArray convention where possible */
  for(i=0;i<nclistlength(modelist);i++) {
  const char* p = nclistget(modelist,i);
- if(strcasecmp(p,PUREZARRCONTROL)==0) zinfo->controls.flags |= (FLAG_PUREZARR|FLAG_XARRAYDIMS);
- else if(strcasecmp(p,XARRAYCONTROL)==0) zinfo->controls.flags |= (FLAG_XARRAYDIMS|FLAG_PUREZARR); /*xarray=>zarr*/
- else if(strcasecmp(p,NOXARRAYCONTROL)==0) {
+ if(strcasecmp(p,PUREZARRCONTROL)==0)
+ zinfo->controls.flags |= (FLAG_PUREZARR);
+ else if(strcasecmp(p,XARRAYCONTROL)==0)
+ zinfo->controls.flags |= FLAG_PUREZARR;
+ else if(strcasecmp(p,NOXARRAYCONTROL)==0)
  noflags |= FLAG_XARRAYDIMS;
- zinfo->controls.flags |= FLAG_PUREZARR; /*noxarray=>zarr*/
- }
  else if(strcasecmp(p,"zip")==0) zinfo->controls.mapimpl = NCZM_ZIP;
  else if(strcasecmp(p,"file")==0) zinfo->controls.mapimpl = NCZM_FILE;
  else if(strcasecmp(p,"s3")==0) zinfo->controls.mapimpl = NCZM_S3;