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netcdf-c/nczarr_test/CMakeLists.txt
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.
SET(abs_top_srcdir ${CMAKE_CURRENT_SOURCE_DIR})
remove_definitions(-DDLL_EXPORT)
FILE(READ ${CMAKE_CURRENT_SOURCE_DIR}/../nc_test4/tst_quantize.c QSOURCE)
FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/test_quantize.c "#define TESTNCZARR\n")
FILE(APPEND ${CMAKE_CURRENT_BINARY_DIR}/test_quantize.c "${QSOURCE}")
FILE(READ ${CMAKE_CURRENT_SOURCE_DIR}/../nc_test4/tst_filter_avail.c ASOURCE)
STRING(PREPEND ASOURCE "#define TESTNCZARR\n")
FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/test_filter_avail.c "${ASOURCE}")
FILE(READ ${CMAKE_CURRENT_SOURCE_DIR}/../nc_test4/tst_specific_filters.sh SPSOURCE)
STRING(PREPEND SPSOURCE "#!/bin/bash\n")
STRING(PREPEND SPSOURCE "TESTNCZARR=1\n")
# Replace with FILE(CONFIGURE) when cmake 3.18 is in common use
FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/run_specific_filters.1 "${SPSOURCE}")
CONFIGURE_FILE(${CMAKE_CURRENT_BINARY_DIR}/run_specific_filters.1 ${CMAKE_CURRENT_BINARY_DIR}/run_specific_filters.sh FILE_PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE @ONLY NEWLINE_STYLE LF)
FILE(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/run_specific_filters.1)
FILE(READ ${CMAKE_CURRENT_SOURCE_DIR}/../nc_test4/tst_unknown.sh SPSOURCE)
STRING(PREPEND SPSOURCE "#!/bin/bash\n")
STRING(PREPEND SPSOURCE "TESTNCZARR=1\n")
# Replace with FILE(CONFIGURE) when cmake 3.18 is in common use
FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/run_unknown.1 "${SPSOURCE}")
CONFIGURE_FILE(${CMAKE_CURRENT_BINARY_DIR}/run_unknown.1 ${CMAKE_CURRENT_BINARY_DIR}/run_unknown.sh FILE_PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE @ONLY NEWLINE_STYLE LF)
FILE(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/run_unknown.1)
FILE(GLOB COPY_FILES ${CMAKE_CURRENT_SOURCE_DIR}/*.sh
${CMAKE_CURRENT_SOURCE_DIR}/ref*.cdl
${CMAKE_CURRENT_SOURCE_DIR}/ref*.txt)
FILE(COPY ${COPY_FILES} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ FILE_PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE)
IF(ENABLE_TESTS)
SET(COMMONSRC ut_util.c ut_test.c)
IF(USE_X_GETOPT)
SET(COMMONSRC ${COMMONSRC} XGetopt.c)
ENDIF()
SET(TSTCOMMONSRC tst_utils.c)
IF(USE_X_GETOPT)
SET(TSTCOMMONSRC ${TSTCOMMONSRC} XGetopt.c)
ENDIF()
# Base tests
# The tests are set up as a combination of shell scripts and executables that
# must be run in a particular order. It is painful but will use macros to help
# keep it from being too bad.
BUILD_BIN_TEST(ut_map ${COMMONSRC})
BUILD_BIN_TEST(ut_mapapi ${COMMONSRC})
BUILD_BIN_TEST(ut_json ${COMMONSRC})
BUILD_BIN_TEST(ut_projections ${COMMONSRC})
BUILD_BIN_TEST(ut_chunking ${COMMONSRC})
BUILD_BIN_TEST(tst_zchunks ${COMMONSRC})
BUILD_BIN_TEST(tst_zchunks2 ${COMMONSRC})
BUILD_BIN_TEST(tst_zchunks3 ${COMMONSRC})
BUILD_BIN_TEST(tst_fillonlyz ${TSTCOMMONSRC})
TARGET_INCLUDE_DIRECTORIES(ut_map PUBLIC ../libnczarr)
TARGET_INCLUDE_DIRECTORIES(ut_mapapi PUBLIC ../libnczarr)
TARGET_INCLUDE_DIRECTORIES(ut_json PUBLIC ../libnczarr)
TARGET_INCLUDE_DIRECTORIES(ut_projections PUBLIC ../libnczarr)
TARGET_INCLUDE_DIRECTORIES(ut_chunking PUBLIC ../libnczarr)
TARGET_INCLUDE_DIRECTORIES(tst_zchunks PUBLIC ../libnczarr)
TARGET_INCLUDE_DIRECTORIES(tst_zchunks2 PUBLIC ../libnczarr)
TARGET_INCLUDE_DIRECTORIES(tst_zchunks3 PUBLIC ../libnczarr)
TARGET_INCLUDE_DIRECTORIES(tst_fillonlyz PUBLIC ../libnczarr)
# Helper programs for testing
BUILD_BIN_TEST(zmapio ${COMMONSRC})
TARGET_INCLUDE_DIRECTORIES(zmapio PUBLIC ../libnczarr)
BUILD_BIN_TEST(zhex)
BUILD_BIN_TEST(zisjson ${COMMONSRC})
TARGET_INCLUDE_DIRECTORIES(zisjson PUBLIC ../libnczarr)
BUILD_BIN_TEST(zs3parse ${COMMONSRC})
TARGET_INCLUDE_DIRECTORIES(zs3parse PUBLIC ../libnczarr)
if(ENABLE_NCZARR_S3)
BUILD_BIN_TEST(s3util ${COMMONSRC})
TARGET_INCLUDE_DIRECTORIES(s3util PUBLIC ../libnczarr)
endif()
SET(ncdumpchunks_SOURCE ncdumpchunks.c)
IF(USE_X_GETOPT)
SET(ncdumpchunks_SOURCE ${ncdumpchunks_SOURCE} XGetopt.c)
ENDIF()
BUILD_BIN_TEST(ncdumpchunks ${ncdumpchunks_SOURCE})
TARGET_INCLUDE_DIRECTORIES(ncdumpchunks PUBLIC ../libnczarr)
IF(BUILD_UTILITIES)
add_sh_test(nczarr_test run_ut_map)
add_sh_test(nczarr_test run_ut_mapapi)
add_sh_test(nczarr_test run_ut_misc)
add_sh_test(nczarr_test run_ut_chunk)
IF(USE_HDF5)
# add_sh_test(nczarr_test run_nccopyz)
add_sh_test(nczarr_test run_fillonlyz)
ENDIF()
add_sh_test(nczarr_test run_ncgen4)
BUILD_BIN_TEST(tst_chunkcases ${TSTCOMMONSRC})
TARGET_INCLUDE_DIRECTORIES(tst_chunkcases PUBLIC ../libnczarr)
add_sh_test(nczarr_test run_chunkcases)
add_sh_test(nczarr_test run_purezarr)
add_sh_test(nczarr_test run_interop)
add_sh_test(nczarr_test run_misc)
add_sh_test(nczarr_test run_nczarr_fill)
add_sh_test(nczarr_test run_jsonconvention)
add_sh_test(nczarr_test run_strings)
BUILD_BIN_TEST(test_quantize ${TSTCOMMONSRC})
add_sh_test(nczarr_test run_quantize)
if(ENABLE_NCZARR_S3)
add_sh_test(nczarr_test run_s3_cleanup)
ENDIF()
IF(ENABLE_FILTER_TESTING)
build_bin_test(tst_nczfilter)
build_bin_test(testfilter)
build_bin_test(testfilter_misc)
build_bin_test(testfilter_multi)
build_bin_test(testfilter_order)
build_bin_test(testfilter_repeat)
build_bin_test(test_filter_avail)
ADD_SH_TEST(nczarr_test run_nczfilter)
ADD_SH_TEST(nczarr_test run_filter)
ADD_SH_TEST(nczarr_test run_unknown)
ADD_SH_TEST(nczarr_test run_specific_filters)
ENDIF(ENABLE_FILTER_TESTING)
if(ENABLE_NCZARR_ZIP)
add_sh_test(nczarr_test run_newformat)
endif()
ENDIF(BUILD_UTILITIES)
ENDIF(ENABLE_TESTS)
## Specify files to be distributed by 'make dist'
FILE(GLOB CUR_EXTRA_DIST RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/*.c ${CMAKE_CURRENT_SOURCE_DIR}/*.h ${CMAKE_CURRENT_SOURCE_DIR}/*.sh ${CMAKE_CURRENT_SOURCE_DIR}/*.cdl)
SET(CUR_EXTRA_DIST ${CUR_EXTRA_DIST} CMakeLists.txt Makefile.am zmapio.c zhex.c ncdumpchunks.c)
ADD_EXTRA_DIST("${CUR_EXTRA_DIST}")
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