netcdf-c/test_common.in
Dennis Heimbigner 231ae96c4b 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** —
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** —
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.
2022-08-27 20:21:13 -06:00

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# Copyright 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014,
# 2015, 2016, 2017, 2018
# University Corporation for Atmospheric Research/Unidata.
# See netcdf-c/COPYRIGHT file for more info.
# Load only once
if test "x$TEST_COMMON_SH" = x ; then
export TEST_COMMON_SH=1
# Define location of execution
TOPSRCDIR='@abs_top_srcdir@'
TOPBUILDDIR='@abs_top_builddir@'
FP_ISCMAKE=@ISCMAKE@
FP_ISMSVC=@ISMSVC@
FP_WINVERMAJOR=@WINVERMAJOR@
FP_WINVERBUILD=@WINVERBUILD@
FP_ISCYGWIN=@ISCYGWIN@
FP_ISMINGW=@ISMINGW@
FP_ISMSYS=@ISMSYS@
FP_ISOSX=@ISOSX@
FP_ISREGEDIT=@ISREGEDIT@
FP_USEPLUGINS=@USEPLUGINS@
# Feature flags
FEATURE_HDF5=@HAS_HDF5@
FEATURE_PARALLEL=@HAS_PARALLEL@
# Define selected features of the build
FEATURE_HDF5=@HAS_HDF5@
FEATURE_NCZARR=@HAS_NCZARR@
FEATURE_S3TESTS=@DO_NCZARR_S3_TESTS@
FEATURE_NCZARR_ZIP=@DO_NCZARR_ZIP_TESTS@
FEATURE_FILTERTESTS=@DO_FILTER_TESTS@
FEATURE_PLUGIN_INSTALL_DIR=@PLUGIN_INSTALL_DIR@
# Thredds-test server is currently disabled
#FEATURE_THREDDSTEST=1
set -e
# Figure out various locations in the src/build tree.
# This is relatively fragile code and is essentially
# specific to netcdf-c. It does, however, have the virtue
# of isolating all this nonsense into one place.
# This will get somewhat simplified (I hope) when
# we move to a separate test_utilities directory
# This code is intended to provide constants
# for accessing various objects in the src/build
# tree(s) across multiple ways of building netcdf-c.
# Currently, the following build situations are supported.
# 1. Autoconf with make check: the src and build trees are the same
# 2. Autoconf with make distcheck: the src and build trees are distinct
# 3. Cmake on a *nix platform using e.g. gcc:
# the src and build trees are distinct.
# 4. Cmake on windows using cygwin or msys.
# The src and build trees are distinct.
#
# For now, an explicit build using the Visual C(++) compiler
# is not supported. The big issue is the handling of executables
# and the notion of a VS configuration/build type like Debug or Release.
# When using VS, executables are placed in a subdirectory of the
# build directory. That subdirectory is named by the configuration type.
# Thus one finds ncdump.exe in $top_builddir/ncdump/Debug instead of
# $top_builddir/ncdump. An additional issue is the extension of an
# executable: .exe vs nothing. This code attempts to figure out which is used.
#
# For possible future fixes, a placeholder is left in place in the
# following code named VS. If it were set to the build type, then,
# in theory, this code would work with Visual C. It is disabled for now.
#
# The goal, then, of this common code is to set up some useful
#constants for use in test shell scripts.
# 1. srcdir - absolute path to the source dir (e.g. ${top_srcdir}/ncgen)
# 2. top_srcdir - absolute path to the root of the source
# 3. top_builddir - absolute path to the root of the build directory;
# may be same as top_srcdir (e.g. #1).
# 4. builddir - absolute path of th the directory into which generated
# stuff (.nc, .cdl, etc) is stored.
# 5. execdir - absolute path of the directory into which executables are
# placed. For all but the VS case, execdir == builddir.
#
# The following are defined to support inter-directory references.
# 6. NCDUMP - absolute path to the ncdump.exe executable
# 7. NCCOPY - absolute path to the nccopy.exe executable
# 8. NCGEN - absolute path to ncgen.exe
# 9. NCGEN3 - absolute path to ncgen3.exe
#10. NCPATHCVT - absolute path to ncpathcvt.exe
# Allow global set -x mechanism for debugging.
if test "x$SETX" = x1 ; then set -x ; fi
# On MINGW, bash and other POSIX utilities use a mounted root directory,
# but executables compiled for Windows do not recognise the mount point.
# Here we ensure that Windows paths are used in tests of Windows executables.
system=`uname`
if test "x${system##MINGW*}" = x; then
alias pwd='pwd -W'
fi
# We assume that TOPSRCDIR and TOPBUILDDIR are defined
# At the top of this shell script
top_srcdir="$TOPSRCDIR"
top_builddir="$TOPBUILDDIR"
# Currently not used, but left as a Visual Studio placeholder.
# VS=Debug
# srcdir may or may not be defined, but if not, then create it
if test "x$srcdir" = x ; then
# we need to figure out our directory
# pick off the last component as the relative name of this directory
srcdir=`pwd`
current=`basename $srcdir`
srcdir="${top_srcdir}/$current"
fi
# We also assume we are executing in builddir
builddir=`pwd`
# execdir is an alias for builddir
execdir="${builddir}"
# pick off the last component as the relative name of this directory
thisdir=`basename $srcdir`
WD=`pwd`
# Absolutize paths of interest
cd $srcdir; srcdir=`pwd` ; cd $WD
cd $top_srcdir; top_srcdir=`pwd` ; cd $WD
cd $builddir; builddir=`pwd` ; cd $WD
cd $top_builddir; top_builddir=`pwd` ; cd $WD
cd $execdir; execdir=`pwd` ; cd $WD
# For sun os
export srcdir top_srcdir builddir top_builddir execdir
# Figure out executable extension (probably a better way)
if test -e "${top_builddir}/ncdump${VS}/ncdump.exe" ; then
ext=".exe"
else
ext=""
fi
# We need to locate certain executables (and other things),
# capture absolute paths, and make visible
export NCDUMP="${top_builddir}/ncdump${VS}/ncdump${ext}"
export NCCOPY="${top_builddir}/ncdump${VS}/nccopy${ext}"
export NCGEN="${top_builddir}/ncgen${VS}/ncgen${ext}"
export NCGEN3="${top_builddir}/ncgen3${VS}/ncgen3${ext}"
export NCPATHCVT="${top_builddir}/ncdump${VS}/ncpathcvt${ext}"
# Temporary hacks (until we have a test_utils directory)
# to locate certain specific test files
ncgen3c0="${top_srcdir}/ncgen3/c0.cdl"
ncgenc0="${top_srcdir}/ncgen/c0.cdl"
ncgenc04="${top_srcdir}/ncgen/c0_4.cdl"
# Set LC_ALL
if test "x$FP_ISMSVC" = xyes || test "x$FP_ISCYGWIN" = xyes; then export LC_ALL="en_US.utf8"; fi
# Set HOME
if test "x$FP_ISMSVC" = xyes || test "x$FP_MINGW" = xyes; then
if test "x$HOME" = x ; then
HOME=`echo $USERPROFILE |tr '\\\' '/'`
export HOME
fi
fi
# Test for filter availability
avail() {
if test yes = `${execdir}/../ncdump/ncfilteravail $1` ; then return 0 ; else echo "filter $1 not available" ; return 1; fi
}
# Thredds-test is no longer available
#FEATURE_THREDDSTEST=1
# Make sure we are in builddir (not execdir)
cd $builddir
fi #TEST_COMMON_SH