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df3636b959
This PR started as an attempt to add unlimited dimensions to NCZarr. It did that, but this exposed significant problems with test interference. So this PR is mostly about fixing -- well mitigating anyway -- test interference. The problem of test interference is now documented in the document docs/internal.md. The solutions implemented here are also describe in that document. The solution is somewhat fragile but multiple cleanup mechanisms are provided. Note that this feature requires that the AWS command line utility must be installed. ## Unlimited Dimensions. The existing NCZarr extensions to Zarr are modified to support unlimited dimensions. NCzarr extends the Zarr meta-data for the ".zgroup" object to include netcdf-4 model extensions. This information is stored in ".zgroup" as dictionary named "_nczarr_group". Inside "_nczarr_group", there is a key named "dims" that stores information about netcdf-4 named dimensions. The value of "dims" is a dictionary whose keys are the named dimensions. The value associated with each dimension name has one of two forms Form 1 is a special case of form 2, and is kept for backward compatibility. Whenever a new file is written, it uses format 1 if possible, otherwise format 2. * Form 1: An integer representing the size of the dimension, which is used for simple named dimensions. * Form 2: A dictionary with the following keys and values" - "size" with an integer value representing the (current) size of the dimension. - "unlimited" with a value of either "1" or "0" to indicate if this dimension is an unlimited dimension. For Unlimited dimensions, the size is initially zero, and as variables extend the length of that dimension, the size value for the dimension increases. That dimension size is shared by all arrays referencing that dimension, so if one array extends an unlimited dimension, it is implicitly extended for all other arrays that reference that dimension. This is the standard semantics for unlimited dimensions. Adding unlimited dimensions required a number of other changes to the NCZarr code-base. These included the following. * Did a partial refactor of the slice handling code in zwalk.c to clean it up. * Added a number of tests for unlimited dimensions derived from the same test in nc_test4. * Added several NCZarr specific unlimited tests; more are needed. * Add test of endianness. ## Misc. Other Changes * Modify libdispatch/ncs3sdk_aws.cpp to optionally support use of the AWS Transfer Utility mechanism. This is controlled by the ```#define TRANSFER```` command in that file. It defaults to being disabled. * Parameterize both the standard Unidata S3 bucket (S3TESTBUCKET) and the netcdf-c test data prefix (S3TESTSUBTREE). * Fixed an obscure memory leak in ncdump. * Removed some obsolete unit testing code and test cases. * Uncovered a bug in the netcdf-c handling of big-endian floats and doubles. Have not fixed yet. See tst_h5_endians.c. * Renamed some nczarr_tests testcases to avoid name conflicts with nc_test4. * Modify the semantics of zmap\#ncsmap_write to only allow total rewrite of objects. * Modify the semantics of zodom to properly handle stride > 1. * Add a truncate operation to the libnczarr zmap code.
171 lines
6.2 KiB
Makefile
171 lines
6.2 KiB
Makefile
# This is part of the netCDF package. Copyright 2005-2019 University
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# Corporation for Atmospheric Research/Unidata See COPYRIGHT file for
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# conditions of use.
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#
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# This directory holds tests for netCDF-4. It is skipped if netCDF-4
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# is not enabled.
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#
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# Ed Hartnett, Ward Fisher
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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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# Un comment to use a more verbose test driver
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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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TEST_EXTENSIONS = .sh
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# Link to our assembled library.
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LDADD = ${top_builddir}/liblib/libnetcdf.la
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# These are netCDF-4 C test programs which are built and run.
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NC4_TESTS = tst_dims tst_dims2 tst_dims3 tst_files tst_files4 \
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tst_vars tst_varms tst_unlim_vars tst_converts tst_converts2 tst_grps \
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tst_grps2 tst_compounds tst_compounds2 tst_compounds3 tst_opaques \
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tst_strings tst_strings2 tst_interops tst_interops4 tst_interops5 \
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tst_interops6 tst_interops_dims tst_enums tst_coords tst_coords2 \
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tst_coords3 tst_vars3 tst_vars4 tst_chunks tst_chunks2 tst_utf8 \
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tst_fills tst_fills2 tst_fillbug tst_xplatform tst_xplatform2 \
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tst_endian_fill tst_atts t_type cdm_sea_soundings tst_camrun tst_vl \
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tst_atts1 tst_atts2 tst_vars2 tst_files5 tst_files6 tst_sync \
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tst_h_scalar tst_rename tst_rename2 tst_rename3 tst_h5_endians \
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tst_atts_string_rewrite tst_hdf5_file_compat tst_fill_attr_vanish \
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tst_rehash tst_filterparser tst_bug324 tst_types tst_atts3 \
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tst_put_vars tst_elatefill tst_udf tst_put_vars_two_unlim_dim \
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tst_bug1442 tst_quantize tst_h_transient_types
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if HAS_PAR_FILTERS
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NC4_TESTS += tst_alignment
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endif
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NC4_TESTS += tst_h_strbug tst_h_refs
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# Build test programs plus programs used in test scripts.
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check_PROGRAMS = $(NC4_TESTS) tst_empty_vlen_unlim tst_charvlenbug tst_vlenstr
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TESTS = $(NC4_TESTS) run_empty_vlen_test.sh
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XFAIL_TESTS =
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# Add these if large file tests are turned on.
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if LARGE_FILE_TESTS
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check_PROGRAMS += tst_large tst_large2
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TESTS += tst_large tst_large2
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endif
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# If the v2 API was built, add its test program.
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if BUILD_V2
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check_PROGRAMS += tst_v2
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TESTS += tst_v2
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endif # BUILD_V2
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# The rest of the tests require ncgen/ncdump.
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if BUILD_UTILITIES
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check_PROGRAMS += renamegroup
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TESTS += run_grp_rename.sh tst_misc.sh
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check_PROGRAMS += tst_fillonly
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TESTS += test_fillonly.sh
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# H5 and nczarr Fixed string support
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TESTS += tst_fixedstring.sh
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# Szip Tests (requires ncdump)
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if HAVE_H5Z_SZIP
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check_PROGRAMS += test_szip h5testszip
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TESTS += tst_szip.sh
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endif
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# Filter Tests (requires ncdump and ncgen and HDF5)
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if USE_HDF5
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if ENABLE_FILTER_TESTING
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extradir =
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check_PROGRAMS += test_filter test_filter_misc test_filter_order test_filter_repeat
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check_PROGRAMS += tst_multifilter tst_filter_vlen
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TESTS += tst_filter.sh
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TESTS += tst_specific_filters.sh
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TESTS += tst_bloscfail.sh
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if ISMINGW
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XFAIL_TESTS += tst_filter.sh
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endif # ISMINGW
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TESTS += tst_filter_vlen.sh
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TESTS += tst_filter_misc.sh
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if AX_MANUAL
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# This test is too dangerous to run in a parallel make environment.
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# It causes race conditions. So suppress and only test by hand.
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TESTS += tst_unknown.sh
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endif
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if AX_MANUAL
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# The tst_filterinstall test can only be run after an install
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# occurred with --with-plugin-dir enabled. So there is no point
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#in running it via make check. It is kept here so it can be
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# manually invoked if desired
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TESTS += tst_filterinstall.sh
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endif
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endif # ENABLE_FILTER_TESTING
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endif # USE_HDF5
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endif # BUILD_UTILITIES
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# This are extra tests that will only be run if netcdf-4 is configured
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# with --enable-parallel-tests.
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if TEST_PARALLEL4
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check_PROGRAMS += tst_mpi_parallel tst_parallel tst_parallel3 \
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tst_parallel4 tst_parallel5 tst_nc4perf tst_mode tst_simplerw_coll_r \
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tst_mode tst_parallel_zlib tst_parallel_compress tst_quantize_par \
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tst_parallel6
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TESTS += run_par_test.sh
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endif # TEST_PARALLEL4
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EXTRA_DIST = run_par_test.sh.in ref_tst_compounds.nc \
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ref_tst_xplatform2_1.nc ref_tst_xplatform2_2.nc ref_tst_dims.nc \
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ref_tst_interops4.nc CMakeLists.txt run_grp_rename.sh \
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run_empty_vlen_test.sh ref_hdf5_compat1.nc ref_hdf5_compat2.nc \
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ref_hdf5_compat3.nc tst_misc.sh tdset.h5 tst_szip.sh ref_szip.h5 \
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ref_szip.cdl tst_filter.sh bzip2.cdl noop.cdl ref_filtered.cdl \
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ref_unfiltered.cdl ref_bzip2.c findplugin.in ref_unfilteredvv.cdl \
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ref_filteredvv.cdl ref_multi.cdl \
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ref_ncgenF.cdl ref_nccopyF.cdl \
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ref_filter_repeat.txt ref_fillonly.cdl test_fillonly.sh \
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ref_filter_order_create.txt ref_filter_order_read.txt \
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ref_any.cdl tst_specific_filters.sh tst_unknown.sh \
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tst_virtual_datasets.c noop1.cdl unknown.cdl \
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tst_broken_files.c ref_bloscx.cdl tst_bloscfail.sh \
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tst_fixedstring.sh ref_fixedstring.h5 ref_fixedstring.cdl \
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tst_filterinstall.sh tst_filter_vlen.sh tst_filter_misc.sh
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CLEANFILES = tst_mpi_parallel.bin cdm_sea_soundings.nc bm_chunking.nc \
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tst_floats_1D.cdl floats_1D_3.nc floats_1D.cdl tst_*.nc tmp_*.txt \
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tst_floats2_*.cdl tst_ints2_*.cdl tst_shorts2_*.cdl tst_elena_*.cdl \
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tst_simple*.cdl tst_chunks.cdl pr_A1.* tauu_A1.* usi_01.* thetau_01.* \
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tst_*.h5 tst_grp_rename.cdl tst_grp_rename.dmp ref_grp_rename.cdl \
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foo1.nc tst_*.h4 test.nc testszip.nc test.h5 szip_dump.cdl \
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perftest.txt bigmeta.nc bigvars.nc *.gz MSGCPP_*.nc \
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floats*.nc floats*.cdl shorts*.nc shorts*.cdl ints*.nc ints*.cdl \
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testfilter_reg.nc filterrepeat.txt tmp_fillonly.nc \
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testfilter_order.nc crfilterorder.txt rdfilterorder.txt 1 \
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tmp_*.txt tmp_*.nc tmp*.dump tmp*.cdl tmp*.txt tmp*.tmp \
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tmp_bzip2.c bzip2.nc noop.nc tmp_*.dmp tmp_*.cdl
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DISTCLEANFILES = findplugin.sh run_par_test.sh
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clean-local:
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rm -fr testdir_* testset_*
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# If valgrind is present, add valgrind targets.
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@VALGRIND_CHECK_RULES@
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# The (otherwise unused) program build_fixedstring.c
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# is used to generate the test file ref_fixedstring.h5.
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# That test file is build and included as part of the distribution,
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# so the build_fixedstring.c program generally does not need to
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# be executed unless the test file needs to be modified..
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check_PROGRAMS += build_fixedstring
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ref_fixedstring.h5: build_fixedstring.c
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${srcdir}/buildfixedstring
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