mirror of
https://github.com/Unidata/netcdf-c.git
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Merge pull request #2017 from DennisHeimbigner/zarrfillv.dmh
NCZarr is outputting fill value as an array instead of a singleton.
This commit is contained in:
Ward Fisher
GitHub
commit
1ee604a3a7
@ -7,6 +7,7 @@ This file contains a high-level description of this package's evolution. Release
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## 4.8.1 - TBD
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* [Bug Fix] Store NCZarr fillvalue as a singleton instead of a 1-element array. See [Github #2017](https://github.com/Unidata/netcdf-c/issues/2017).
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* [Bug Fixes] The netcdf-c library was incorrectly determining the scope of dimension; similar to the type scope problem. See [Github #2012](https://github.com/Unidata/netcdf-c/pull/2012) for more information.
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* [Bug Fix] Re-enable DAP2 authorization testing. See [Github #2011](https://github.com/Unidata/netcdf-c/issues/2011).
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* [Bug Fix] Fix bug with windows version of mkstemp that causes failure to create more than 26 temp files. See [Github #1998](https://github.com/Unidata/netcdf-c/pull/1998).
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@ -324,8 +324,12 @@ NCZ_stringconvert(nc_type typeid, size_t len, void* data0, NCjson** jdatap)
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/* Create a string valued json object */
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if((stat = NCJnewstringn(NCJ_STRING,len,src,&jdata)))
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goto done;
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} else { /* for all other values, create an array of values */
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if((stat = NCJnew(NCJ_ARRAY,&jdata))) goto done;
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} else { /* all other cases */
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if(len == 0) {stat = NC_EINVAL; goto done;}
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if(len > 1) {
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if((stat = NCJnew(NCJ_ARRAY,&jdata))) goto done;
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} else /* return a singletone */
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jdata = NULL;
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for(i=0;i<len;i++) {
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char* special = NULL;
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double d;
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@ -371,7 +375,10 @@ NCZ_stringconvert(nc_type typeid, size_t len, void* data0, NCjson** jdatap)
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if(special) {nullfree(str); str = strdup(special);}
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jvalue->value = str;
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str = NULL;
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nclistpush(jdata->contents,jvalue);
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if(len == 1)
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jdata = jvalue;
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else
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nclistpush(jdata->contents,jvalue);
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jvalue = NULL;
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src += typelen;
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}
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@ -15,7 +15,7 @@ static int ncz_jsonize_atts(NCindex* attlist, NCjson** jattrsp);
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static int load_jatts(NCZMAP* map, NC_OBJ* container, NCjson** jattrsp, NClist** atypes);
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static int zconvert(nc_type typeid, size_t typelen, void* dst, NCjson* src);
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static int computeattrinfo(const char* name, NClist* atypes, NCjson* values,
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nc_type* typeidp, size_t* lenp, void** datap);
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nc_type* typeidp, size_t* typelenp, size_t* lenp, void** datap);
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static int parse_group_content(NCjson* jcontent, NClist* dimdefs, NClist* varnames, NClist* subgrps);
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static int parse_group_content_pure(NCZ_FILE_INFO_T* zinfo, NC_GRP_INFO_T* grp, NClist* varnames, NClist* subgrps);
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static int define_grp(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp);
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@ -28,7 +28,7 @@ static int locategroup(NC_FILE_INFO_T* file, size_t nsegs, NClist* segments, NC_
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static int createdim(NC_FILE_INFO_T* file, const char* name, size64_t dimlen, NC_DIM_INFO_T** dimp);
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static int parsedimrefs(NC_FILE_INFO_T*, NClist* dimnames, size64_t* shape, NC_DIM_INFO_T** dims, int create);
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static int decodeints(NCjson* jshape, size64_t* shapes);
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static int computeattrdata(nc_type* typeidp, NCjson* values, size_t* lenp, void** datap);
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static int computeattrdata(nc_type* typeidp, NCjson* values, size_t* typelenp, size_t* lenp, void** datap);
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static int inferattrtype(NCjson* values, nc_type* typeidp);
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static int mininttype(unsigned long long u64, int negative);
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static int computedimrefs(NC_FILE_INFO_T* file, NC_VAR_INFO_T* var, int purezarr, int xarray, int ndims, NClist* dimnames, size64_t* shapes, NC_DIM_INFO_T** dims);
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@ -244,6 +244,7 @@ ncz_sync_var(NC_FILE_INFO_T* file, NC_VAR_INFO_T* var)
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NCjson* jncvar = NULL;
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NCjson* jdimrefs = NULL;
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NCjson* jtmp = NULL;
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NCjson* jfill = NULL;
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size64_t shape[NC_MAX_VAR_DIMS];
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NCZ_VAR_INFO_T* zvar = var->format_var_info;
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@ -325,7 +326,6 @@ ncz_sync_var(NC_FILE_INFO_T* file, NC_VAR_INFO_T* var)
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if(!var->no_fill) {
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int fillsort;
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int atomictype = var->type_info->hdr.id;
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NCjson* jfill = NULL;
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/* A scalar value providing the default value to use for uninitialized
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portions of the array, or ``null`` if no fill_value is to be used. */
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/* Use the defaults defined in netdf.h */
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@ -339,9 +339,17 @@ ncz_sync_var(NC_FILE_INFO_T* file, NC_VAR_INFO_T* var)
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if((stat = nc4_get_default_fill_value(atomictype,var->fill_value))) goto done;
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}
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/* Convert var->fill_value to a string */
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if((stat = NCZ_stringconvert(atomictype,1,var->fill_value,&jfill)))
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goto done;
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if((stat = NCJinsert(jvar,"fill_value",jfill))) goto done;
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if((stat = NCZ_stringconvert(atomictype,1,var->fill_value,&jfill))) goto done;
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if(jfill->sort == NCJ_ARRAY) { /* stringconvert should prevent this from happening */
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assert(NCJlength(jfill) > 0);
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if((stat = NCJarrayith(jfill,0,&jtmp))) goto done; /* use the 0th element */
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if((stat = NCJclone(jtmp,&jtmp))) goto done; /* clone so we can free it later */
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NCJreclaim(jfill);
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jfill = jtmp;
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jtmp = NULL;
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}
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if((stat = NCJinsert(jvar,"fill_value",jfill))) goto done;
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jfill = NULL;
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}
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/* order key */
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@ -463,6 +471,7 @@ done:
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NCJreclaim(jvar);
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NCJreclaim(jncvar);
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NCJreclaim(jtmp);
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NCJreclaim(jfill);
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return THROW(stat);
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}
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@ -683,6 +692,8 @@ done:
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/**
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@internal Convert a list of attributes to corresponding json.
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Note that this does not push to the file.
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Also note that attributes of length 1 are stored as singletons, not arrays.
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This is to be more consistent with pure zarr.
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@param attlist - [in] the attributes to dictify
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@param jattrsp - [out] the json'ized att list
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@return NC_NOERR
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@ -858,11 +869,11 @@ Extract type and data for an attribute
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*/
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static int
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computeattrinfo(const char* name, NClist* atypes, NCjson* values,
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nc_type* typeidp, size_t* lenp, void** datap)
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nc_type* typeidp, size_t* typelenp, size_t* lenp, void** datap)
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{
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int stat = NC_NOERR;
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int i;
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size_t len;
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size_t len, typelen;
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void* data;
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nc_type typeid;
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@ -880,10 +891,11 @@ computeattrinfo(const char* name, NClist* atypes, NCjson* values,
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}
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if(typeid >= NC_STRING)
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{stat = NC_EINTERNAL; goto done;}
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if((stat = computeattrdata(&typeid, values, &len, &data))) goto done;
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if((stat = computeattrdata(&typeid, values, &typelen, &len, &data))) goto done;
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if(typeidp) *typeidp = typeid;
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if(lenp) *lenp = len;
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if(typelenp) *typelenp = typelen;
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if(datap) {*datap = data; data = NULL;}
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done:
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@ -895,7 +907,7 @@ done:
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Extract data for an attribute
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*/
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static int
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computeattrdata(nc_type* typeidp, NCjson* values, size_t* lenp, void** datap)
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computeattrdata(nc_type* typeidp, NCjson* values, size_t* typelenp, size_t* lenp, void** datap)
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{
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int stat = NC_NOERR;
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size_t datalen;
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@ -911,7 +923,7 @@ computeattrdata(nc_type* typeidp, NCjson* values, size_t* lenp, void** datap)
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/* Collect the length of the attribute; might be a singleton */
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switch (values->sort) {
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case NCJ_DICT: stat = NC_EINTERNAL; goto done;
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case NCJ_DICT: stat = NC_ENCZARR; goto done;
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case NCJ_ARRAY:
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datalen = nclistlength(values->contents);
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break;
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@ -923,21 +935,22 @@ computeattrdata(nc_type* typeidp, NCjson* values, size_t* lenp, void** datap)
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break;
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}
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/* Allocate data space */
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if((stat = NC4_inq_atomic_type(typeid, NULL, &typelen)))
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goto done;
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if(typeid == NC_CHAR)
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data = malloc(typelen*(datalen+1));
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else
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data = malloc(typelen*datalen);
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if(data == NULL)
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{stat = NC_ENOMEM; goto done;}
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/* convert to target type */
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if((stat = zconvert(typeid, typelen, data, values)))
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goto done;
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if(datalen > 0) {
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/* Allocate data space */
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if((stat = NC4_inq_atomic_type(typeid, NULL, &typelen)))
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goto done;
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if(typeid == NC_CHAR)
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data = malloc(typelen*(datalen+1));
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else
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data = malloc(typelen*datalen);
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if(data == NULL)
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{stat = NC_ENOMEM; goto done;}
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/* convert to target type */
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if((stat = zconvert(typeid, typelen, data, values)))
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goto done;
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}
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if(lenp) *lenp = datalen;
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if(typelenp) *typelenp = typelen;
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if(datap) {*datap = data; data = NULL;}
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if(typeidp) *typeidp = typeid; /* return possibly inferred type */
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@ -982,7 +995,7 @@ inferattrtype(NCjson* value, nc_type* typeidp)
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typeid = NC_CHAR;
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break;
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default:
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return NC_EINTERNAL;
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return NC_ENCZARR;
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}
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if(typeidp) *typeidp = typeid;
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return NC_NOERR;
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@ -1203,7 +1216,7 @@ ncz_read_atts(NC_FILE_INFO_T* file, NC_OBJ* container)
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/* Create the attribute */
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/* Collect the attribute's type and value */
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if((stat = computeattrinfo(key->value,atypes,value,
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&typeid,&len,&data)))
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&typeid,NULL,&len,&data)))
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goto done;
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if((stat = ncz_makeattr(container,attlist,key->value,typeid,len,data,&att)))
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goto done;
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@ -1430,9 +1443,10 @@ define_vars(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp, NClist* varnames)
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if(jvalue == NULL)
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var->no_fill = 1;
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else {
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size_t fvlen;
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typeid = var->type_info->hdr.id;
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var->no_fill = 0;
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if((stat = computeattrdata(&typeid, jvalue, NULL, &var->fill_value)))
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if((stat = computeattrdata(&typeid, jvalue, NULL, &fvlen, &var->fill_value)))
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goto done;
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assert(typeid == var->type_info->hdr.id);
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/* Note that we do not create the _FillValue
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@ -27,10 +27,11 @@
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/*
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Synopsis
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pathcvt [-u|-w|-m|-c] [-e] PATH
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pathcvt [-u|-w|-m|-c] [-e] [-d <driveletter>] PATH
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Options
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-e add backslash escapes to '\' and ' '
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-d <driveletter> use driveletter when needed; defaults to 'c'
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Output type options:
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-u convert to Unix form of path
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-w convert to Windows form of path
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@ -45,7 +46,8 @@ Default is to convert to the format used by the platform.
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struct Options {
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int target;
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int escape;
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int escapes;
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int drive;
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int debug;
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} cvtoptions;
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@ -60,11 +62,13 @@ main(int argc, char** argv)
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char* inpath;
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memset((void*)&cvtoptions,0,sizeof(cvtoptions));
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cvtoptions.drive = 'c';
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while ((c = getopt(argc, argv, "cD:ehmuw")) != EOF) {
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while ((c = getopt(argc, argv, "cD:d:ehmuw")) != EOF) {
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switch(c) {
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case 'c': cvtoptions.target = NCPD_CYGWIN; break;
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case 'e': cvtoptions.escape = 1; break;
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case 'd': cvtoptions.drive = optarg[0]; break;
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case 'e': cvtoptions.escapes = 1; break;
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case 'h': usage(NULL); break;
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case 'm': cvtoptions.target = NCPD_MSYS; break;
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case 'u': cvtoptions.target = NCPD_NIX; break;
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@ -90,8 +94,8 @@ main(int argc, char** argv)
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if(cvtoptions.target == NCPD_UNKNOWN)
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cvtpath = NCpathcvt(inpath);
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else
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cvtpath = NCpathcvt_test(inpath,cvtoptions.target,'c');
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if(cvtpath && cvtoptions.escape) {
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cvtpath = NCpathcvt_test(inpath,cvtoptions.target,(char)cvtoptions.drive);
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if(cvtpath && cvtoptions.escapes) {
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char* path = cvtpath; cvtpath = NULL;
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cvtpath = escape(path);
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free(path);
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@ -116,20 +120,16 @@ escape(const char* path)
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const char* p;
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char* q;
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char* epath = NULL;
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const char* escapes = " \\";
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epath = (char*)malloc((2*slen) + 1);
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if(epath == NULL) usage("out of memtory");
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p = path;
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q = epath;
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for(;*p;p++) {
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switch (*p) {
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case '\\': case ' ':
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if(strchr(escapes,*p) != NULL)
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*q++ = '\\';
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/* fall thru */
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default:
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*q++ = *p;
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break;
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}
|
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*q++ = *p;
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}
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*q = '\0';
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return epath;
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@ -1,45 +1,36 @@
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path: /xxx/a/b
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/xxx/a/b
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/cygdrive/c/xxx/a/b
|
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/c/xxx/a/b
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c:\\xxx\\a\\b
|
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path: d:/x/y
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/d/x/y
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/cygdrive/d/x/y
|
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/d/x/y
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d:\\x\\y
|
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path: /cygdrive/d/x/y
|
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/d/x/y
|
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/cygdrive/d/x/y
|
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/d/x/y
|
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d:\\x\\y
|
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path: /d/x/y
|
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/d/x/y
|
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/cygdrive/d/x/y
|
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/d/x/y
|
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d:\\x\\y
|
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path: /cygdrive/d
|
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/d
|
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/cygdrive/d
|
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/d
|
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d:
|
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path: /d
|
||||
/d
|
||||
/cygdrive/d
|
||||
/d
|
||||
d:
|
||||
path: /cygdrive/d/git/netcdf-c/dap4_test/test_anon_dim.2.syn
|
||||
/d/git/netcdf-c/dap4_test/test_anon_dim.2.syn
|
||||
/cygdrive/d/git/netcdf-c/dap4_test/test_anon_dim.2.syn
|
||||
/d/git/netcdf-c/dap4_test/test_anon_dim.2.syn
|
||||
d:\\git\\netcdf-c\\dap4_test\\test_anon_dim.2.syn
|
||||
path: d:\x\y
|
||||
/d/x/y
|
||||
/cygdrive/d/x/y
|
||||
/d/x/y
|
||||
d:\\x\\y
|
||||
path: d:\x\y w\z
|
||||
/d/x/y w/z
|
||||
/cygdrive/d/x/y w/z
|
||||
/d/x/y w/z
|
||||
d:\\x\\y\\ w\\z
|
||||
path: -u: |/xxx/x/y| => |/xxx/x/y|
|
||||
path: -c: |/xxx/x/y| => |/cygdrive/c/xxx/x/y|
|
||||
path: -m: |/xxx/x/y| => |/c/xxx/x/y|
|
||||
path: -w: |/xxx/x/y| => |c:\\xxx\\x\\y|
|
||||
path: -u: |d:/x/y| => |/d/x/y|
|
||||
path: -c: |d:/x/y| => |/cygdrive/d/x/y|
|
||||
path: -m: |d:/x/y| => |/d/x/y|
|
||||
path: -w: |d:/x/y| => |d:\\x\\y|
|
||||
path: -u: |/cygdrive/d/x/y| => |/d/x/y|
|
||||
path: -c: |/cygdrive/d/x/y| => |/cygdrive/d/x/y|
|
||||
path: -m: |/cygdrive/d/x/y| => |/d/x/y|
|
||||
path: -w: |/cygdrive/d/x/y| => |d:\\x\\y|
|
||||
path: -u: |/d/x/y| => |/d/x/y|
|
||||
path: -c: |/d/x/y| => |/cygdrive/d/x/y|
|
||||
path: -m: |/d/x/y| => |/d/x/y|
|
||||
path: -w: |/d/x/y| => |d:\\x\\y|
|
||||
path: -u: |/cygdrive/d| => |/d|
|
||||
path: -c: |/cygdrive/d| => |/cygdrive/d|
|
||||
path: -m: |/cygdrive/d| => |/d|
|
||||
path: -w: |/cygdrive/d| => |d:|
|
||||
path: -u: |/d| => |/d|
|
||||
path: -c: |/d| => |/cygdrive/d|
|
||||
path: -m: |/d| => |/d|
|
||||
path: -w: |/d| => |d:|
|
||||
path: -u: |/cygdrive/d/git/netcdf-c/dap4_test/test_anon_dim.2.syn| => |/d/git/netcdf-c/dap4_test/test_anon_dim.2.syn|
|
||||
path: -c: |/cygdrive/d/git/netcdf-c/dap4_test/test_anon_dim.2.syn| => |/cygdrive/d/git/netcdf-c/dap4_test/test_anon_dim.2.syn|
|
||||
path: -m: |/cygdrive/d/git/netcdf-c/dap4_test/test_anon_dim.2.syn| => |/d/git/netcdf-c/dap4_test/test_anon_dim.2.syn|
|
||||
path: -w: |/cygdrive/d/git/netcdf-c/dap4_test/test_anon_dim.2.syn| => |d:\\git\\netcdf-c\\dap4_test\\test_anon_dim.2.syn|
|
||||
path: -u: |d:\x\y| => |/d/x/y|
|
||||
path: -c: |d:\x\y| => |/cygdrive/d/x/y|
|
||||
path: -m: |d:\x\y| => |/d/x/y|
|
||||
path: -w: |d:\x\y| => |d:\\x\\y|
|
||||
path: -u: |d:\x\y w\z| => |/d/x/y\ w/z|
|
||||
path: -c: |d:\x\y w\z| => |/cygdrive/d/x/y\ w/z|
|
||||
path: -m: |d:\x\y w\z| => |/d/x/y\ w/z|
|
||||
path: -w: |d:\x\y w\z| => |d:\\x\\y\ w\\z|
|
||||
|
||||
@ -41,7 +41,7 @@ LOCALRCFILES="$WD/.dodsrc $WD/.daprc $WD/.ncrc $WD/$NETRC $WD/$NETRCIMP"
|
||||
HOMERCFILES="$HOME/.dodsrc $HOME/.daprc $HOME/.ncrc $HOME/$NETRC $HOME/$NETRCIMP"
|
||||
NETRCFILE=$WD/$NETRC
|
||||
DAPRCFILE=$WD/$RC
|
||||
if test "x$FP_ISMSVC" = x1 ; then
|
||||
if test "x$FP_ISMSVC" != x ; then
|
||||
LOCALRCFILES=`${execdir}/pathcvt "$LOCALRCFILES"`
|
||||
HOMERCFILES=`${execdir}/pathcvt "$HOMERCFILES"`
|
||||
NETRCFILE=`${execdir}/pathcvt "$NETRCFILE"`
|
||||
|
||||
@ -8,31 +8,31 @@ set -e
|
||||
testcase1() {
|
||||
T="$1"
|
||||
P="$2"
|
||||
C=`${execdir}/pathcvt $T "$P"`
|
||||
echo " $C"
|
||||
echo -n "path: $T: |$P| => |" >>tmp_pathcvt.txt
|
||||
${execdir}/pathcvt "$T" -e "$P" >>tmp_pathcvt.txt
|
||||
echo "|" >> tmp_pathcvt.txt
|
||||
}
|
||||
|
||||
testcase() {
|
||||
#X=`echo -n "$1" | sed -e 's/\\\/\\\\\\\/g'`
|
||||
X="$1"
|
||||
echo "path:" "$X"
|
||||
testcase1 "-u" "$1"
|
||||
testcase1 "-c" "$1"
|
||||
testcase1 "-m" "$1"
|
||||
testcase1 "-ew" "$1" | sed -e 's/\\/\\\\/g'
|
||||
testcase1 "-w" "$1"
|
||||
}
|
||||
|
||||
rm -f tmp_pathcvt.txt
|
||||
|
||||
testcase "/xxx/a/b" >> tmp_pathcvt.txt
|
||||
testcase "d:/x/y" >> tmp_pathcvt.txt
|
||||
testcase "/cygdrive/d/x/y" >> tmp_pathcvt.txt
|
||||
testcase "/d/x/y" >> tmp_pathcvt.txt
|
||||
testcase "/cygdrive/d" >> tmp_pathcvt.txt
|
||||
testcase "/d" >> tmp_pathcvt.txt
|
||||
testcase "/cygdrive/d/git/netcdf-c/dap4_test/test_anon_dim.2.syn" >> tmp_pathcvt.txt
|
||||
testcase "d:\\x\\y" >> tmp_pathcvt.txt
|
||||
testcase "d:\\x\\y w\\z" >> tmp_pathcvt.txt
|
||||
set -x
|
||||
|
||||
testcase "/xxx/x/y"
|
||||
testcase "d:/x/y"
|
||||
testcase "/cygdrive/d/x/y"
|
||||
testcase "/d/x/y"
|
||||
testcase "/cygdrive/d"
|
||||
testcase "/d"
|
||||
testcase "/cygdrive/d/git/netcdf-c/dap4_test/test_anon_dim.2.syn"
|
||||
testcase "d:\\x\\y"
|
||||
testcase "d:\\x\\y w\\z"
|
||||
|
||||
diff -w ${srcdir}/ref_pathcvt.txt ./tmp_pathcvt.txt
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user