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https://github.com/Unidata/netcdf-c.git
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231ae96c4b
* 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.
210 lines
6.6 KiB
Makefile
210 lines
6.6 KiB
Makefile
## This is a automake file, part of Unidata's netCDF package.
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# Copyright 2018, see the COPYRIGHT file for more information.
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# This file builds and runs DAP4 tests.
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# Put together AM_CPPFLAGS and AM_LDFLAGS.
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include $(top_srcdir)/lib_flags.am
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TESTS_ENVIRONMENT =
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#TEST_EXTENSIONS = .sh
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#SH_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
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#sh_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
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#LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
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#TESTS_ENVIRONMENT += export SETX=1;
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AM_CPPFLAGS += -I${top_srcdir} -I${top_srcdir}/libnczarr
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AM_LDFLAGS += ${top_builddir}/liblib/libnetcdf.la
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LDADD = ${top_builddir}/liblib/libnetcdf.la
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# Set up the tests; do the .sh first, then .c
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check_PROGRAMS =
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TESTS =
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check_PROGRAMS += ut_map ut_mapapi ut_json ut_projections ut_chunking
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commonsrc = ut_util.c ut_test.c ut_includes.h ut_test.h ut_util.h test_nczarr_utils.h
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tstcommonsrc = tst_utils.c tst_utils.h
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ut_map_SOURCES = ut_map.c ${commonsrc}
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ut_mapapi_SOURCES = ut_mapapi.c ${commonsrc}
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ut_json_SOURCES = ut_json.c ${commonsrc}
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ut_projections_SOURCES = ut_projections.c ${commonsrc}
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ut_chunking_SOURCES = ut_chunking.c ${commonsrc}
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tst_fillonlyz_SOURCES = tst_fillonlyz.c ${tstcommonsrc}
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check_PROGRAMS += tst_zchunks tst_zchunks2 tst_zchunks3 tst_fillonlyz test_quantize
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TESTS += run_ut_chunk.sh
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if BUILD_UTILITIES
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TESTS += run_ut_map.sh
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TESTS += run_ut_mapapi.sh
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TESTS += run_ut_misc.sh
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TESTS += run_ncgen4.sh
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if USE_HDF5
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#TESTS += run_nccopyz.sh
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TESTS += run_fillonlyz.sh
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endif
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check_PROGRAMS += tst_chunkcases
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tst_chunkcases_SOURCES = tst_chunkcases.c ${tstcommonsrc}
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TESTS += run_chunkcases.sh
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TESTS += run_quantize.sh
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TESTS += run_purezarr.sh
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TESTS += run_interop.sh
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TESTS += run_misc.sh
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TESTS += run_nczarr_fill.sh
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TESTS += run_jsonconvention.sh
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TESTS += run_strings.sh
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endif
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if BUILD_UTILITIES
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if ENABLE_NCZARR_ZIP
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TESTS += run_newformat.sh
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endif
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if BUILD_BENCHMARKS
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UTILSRC = bm_utils.c timer_utils.c tst_utils.c bm_utils.h bm_timer.h
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bm_chunks3_SOURCES = bm_chunks3.c ${UTILSRC}
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check_PROGRAMS += bm_chunks3
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# The perf tests need modernization
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if AX_IGNORE
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TESTS += run_perf_chunks1.sh
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endif
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endif # BUILD_BENCHMARKS
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if ENABLE_FILTER_TESTING
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# Do simple filter functionality tests for nczarr
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check_PROGRAMS += tst_nczfilter
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TESTS += run_nczfilter.sh
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# Echo filter tests from nc_test4
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check_PROGRAMS += testfilter testfilter_misc testfilter_order testfilter_repeat testfilter_multi test_filter_avail
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TESTS += run_filter.sh
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TESTS += run_unknown.sh
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TESTS += run_specific_filters.sh
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endif #ENABLE_FILTER_TESTING
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endif #BUILD_UTILITIES
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# These programs are used by the test cases
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noinst_PROGRAMS = zmapio
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zmapio_SOURCES = zmapio.c
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noinst_PROGRAMS += zhex
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zhex_SOURCES = zhex.c
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noinst_PROGRAMS += zisjson
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zisjson_SOURCES = zisjson.c
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noinst_PROGRAMS += zs3parse
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zs3parse_SOURCES = zs3parse.c
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if ENABLE_NCZARR_S3
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noinst_PROGRAMS += s3util
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s3util_SOURCES = s3util.c
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TESTS += run_s3_cleanup.sh
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endif
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# Given a netcdf4|NCZarr file, dump the actual chunk contents.
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# Used to validate nczarr chunking code.
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AM_CPPFLAGS += -I$(top_srcdir)/libnczarr
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noinst_PROGRAMS += ncdumpchunks
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ncdumpchunks_SOURCES = ncdumpchunks.c
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EXTRA_DIST = CMakeLists.txt \
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run_ut_map.sh run_ut_mapapi.sh run_ut_misc.sh run_ut_chunk.sh run_ncgen4.sh \
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run_nccopyz.sh run_fillonlyz.sh run_chunkcases.sh test_nczarr.sh run_perf_chunks1.sh run_s3_cleanup.sh \
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run_purezarr.sh run_interop.sh run_misc.sh \
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run_filter.sh run_specific_filters.sh \
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run_newformat.sh run_nczarr_fill.sh run_quantize.sh \
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run_jsonconvention.sh run_nczfilter.sh run_unknown.sh
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EXTRA_DIST += \
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ref_ut_map_create.cdl ref_ut_map_writedata.cdl ref_ut_map_writemeta2.cdl ref_ut_map_writemeta.cdl \
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ref_ut_map_readmeta.txt ref_ut_map_readmeta2.txt ref_ut_map_search.txt \
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ref_ut_mapapi_create.cdl ref_ut_mapapi_data.cdl ref_ut_mapapi_meta.cdl ref_ut_mapapi_search.txt \
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ref_t_meta_dim1.cdl ref_t_meta_var1.cdl \
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ref_ut_json_build.txt ref_ut_json_parse.txt \
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ref_ut_proj.txt ref_ut_testmap_create.cdl \
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ref_perdimspecs.cdl ref_fillonly.cdl \
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ref_whole.cdl ref_whole.txt \
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ref_skip.cdl ref_skip.txt ref_skipw.cdl \
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ref_rem.cdl ref_rem.dmp ref_ndims.cdl ref_ndims.dmp \
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ref_misc1.cdl ref_misc1.dmp ref_misc2.cdl \
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ref_avail1.cdl ref_avail1.dmp ref_avail1.txt \
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ref_xarray.cdl ref_purezarr.cdl ref_purezarr_base.cdl ref_nczarr2zarr.cdl \
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ref_bzip2.cdl ref_filtered.cdl ref_multi.cdl \
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ref_any.cdl ref_oldformat.cdl ref_oldformat.zip ref_newformatpure.cdl \
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ref_groups.h5 ref_byte.zarr.zip ref_byte_fill_value_null.zarr.zip \
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ref_groups_regular.cdl ref_byte.cdl ref_byte_fill_value_null.cdl \
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ref_jsonconvention.cdl ref_jsonconvention.zmap \
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ref_string.cdl
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# Interoperability files
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EXTRA_DIST += ref_power_901_constants_orig.zip ref_power_901_constants.cdl ref_quotes_orig.zip ref_quotes.cdl
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CLEANFILES = ut_*.txt ut*.cdl tmp*.nc tmp*.cdl tmp*.txt tmp*.dmp tmp*.zip tmp*.nc tmp*.dump tmp*.tmp tmp_ngc.c ref_zarr_test_data.cdl tst_*.nc.zip ref_quotes.zip ref_power_901_constants.zip
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BUILT_SOURCES = test_quantize.c test_filter_avail.c run_specific_filters.sh run_filterinstall.sh
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test_quantize.c: $(top_srcdir)/nc_test4/tst_quantize.c
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rm -f $@
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echo "#define TESTNCZARR" > $@
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cat $(top_srcdir)/nc_test4/tst_quantize.c >> $@
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test_filter_avail.c: $(top_srcdir)/nc_test4/tst_filter_avail.c
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rm -f $@
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echo "#define TESTNCZARR" > $@
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cat $(top_srcdir)/nc_test4/tst_filter_avail.c >> $@
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run_unknown.sh: $(top_srcdir)/nc_test4/tst_unknown.sh
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rm -f $@ run_unknown.tmp
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echo "#!/bin/bash" > run_unknown.tmp
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echo "TESTNCZARR=1" >> run_unknown.tmp
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cat $(top_srcdir)/nc_test4/tst_unknown.sh >> run_unknown.tmp
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tr -d '\r' < run_unknown.tmp > $@
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chmod a+x $@
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rm -f run_unknown.tmp
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run_specific_filters.sh: $(top_srcdir)/nc_test4/tst_specific_filters.sh
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rm -f $@ run_specific_filters.tmp
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echo "#!/bin/bash" > run_specific_filters.tmp
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echo "TESTNCZARR=1" >> run_specific_filters.tmp
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cat $(top_srcdir)/nc_test4/tst_specific_filters.sh >> run_specific_filters.tmp
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tr -d '\r' < run_specific_filters.tmp > $@
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chmod a+x $@
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rm -f run_specific_filters.tmp
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run_filterinstall.sh: $(top_srcdir)/nc_test4/tst_filterinstall.sh
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rm -f $@ run_filterinstall.tmp
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echo "#!/bin/bash" > run_filterinstall.tmp
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echo "TESTNCZARR=1" >> run_filterinstall.tmp
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cat $(top_srcdir)/nc_test4/tst_filterinstall.sh >> run_filterinstall.tmp
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tr -d '\r' < run_filterinstall.tmp > $@
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chmod a+x $@
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rm -f run_filterinstall.tmp
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# Remove directories
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clean-local:
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rm -fr tmp_*.nc tmp_*.zarr tst_quantize*.zarr tmp*.file results.file results.s3 results.zip
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rm -fr rcmiscdir ref_power_901_constants.file
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DISTCLEANFILES = findplugin.sh test_quantize.c run_specific_filters.sh run_filterinstall.sh
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# If valgrind is present, add valgrind targets.
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@VALGRIND_CHECK_RULES@
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