netcdf-c/nc_test/test_byterange.sh

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Provide byte-range reading of remote datasets re: issue https://github.com/Unidata/netcdf-c/issues/1251 Assume that you have the URL to a remote dataset which is a normal netcdf-3 or netcdf-4 file. This PR allows the netcdf-c to read that dataset's contents as a netcdf file using HTTP byte ranges if the remote server supports byte-range access. Originally, this PR was set up to access Amazon S3 objects, but it can also access other remote datasets such as those provided by a Thredds server via the HTTPServer access protocol. It may also work for other kinds of servers. Note that this is not intended as a true production capability because, as is known, this kind of access to can be quite slow. In addition, the byte-range IO drivers do not currently do any sort of optimization or caching. An additional goal here is to gain some experience with the Amazon S3 REST protocol. This architecture and its use documented in the file docs/byterange.dox. There are currently two test cases: 1. nc_test/tst_s3raw.c - this does a simple open, check format, close cycle for a remote netcdf-3 file and a remote netcdf-4 file. 2. nc_test/test_s3raw.sh - this uses ncdump to investigate some remote datasets. This PR also incorporates significantly changed model inference code (see the superceded PR https://github.com/Unidata/netcdf-c/pull/1259). 1. It centralizes the code that infers the dispatcher. 2. It adds support for byte-range URLs Other changes: 1. NC_HDF5_finalize was not being properly called by nc_finalize(). 2. Fix minor bug in ncgen3.l 3. fix memory leak in nc4info.c 4. add code to walk the .daprc triples and to replace protocol= fragment tag with a more general mode= tag. Final Note: Th inference code is still way too complicated. We need to move to the validfile() model used by netcdf Java, where each dispatcher is asked if it can process the file. This decentralizes the inference code. This will be done after all the major new dispatchers (PIO, Zarr, etc) have been implemented.
2019-01-02 09:27:36 +08:00
#!/bin/sh
if test "x$srcdir" = x ; then srcdir=`pwd`; fi
. ../test_common.sh
set -e
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.
2022-08-28 10:21:13 +08:00
# Note: thredds-test is currently down and the URLs need to be replaced
# Test Urls
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.
2022-08-28 10:21:13 +08:00
if test "x$FEATURE_THREDDSTEST" = x1 ; then
Fix byterange handling of some URLS re: Issue The byterange handling of the following URLS fails. ### Problem 1: "https://crudata.uea.ac.uk/cru/data/temperature/HadCRUT.4.6.0.0.median.nc#mode=bytes" It turns out that byterange in hdf5 has two possible targets: S3 and not-S3 (e.g. a thredds server or the crudata URL above). Each uses a different HDF5 Virtual File Driver (VFD). I incorrectly set up the byterange code in libhdf5 so that it would choose one or the other of the two VFD's for any netcdf-c library build. The fix is to allow it to choose either one at run-time. ### Problem 2: "https://noaa-goes16.s3.amazonaws.com/ABI-L1b-RadF/2022/001/18/OR_ABI-L1b-RadF-M6C01_G16_s20220011800205_e20220011809513_c20220011809562.nc#mode=bytes,s3" When given what appears to be an S3-related URL, the netcdf-c library code converts it into a canonical, so-called "path" format. In casing out the possible input URL formats, I missed the case where the host contains the bucket ("noaa-goes16"), but not the region. So the fix was to check for this case. ## Misc. Related Changes 1. Since S3 is used in more than just NCZarr, I changed the automake/cmake options to replace "--enable-nczarr-s3" with "--enable-s3", but keeping the former option as a synonym for the latter. This also entailed cleaning up libnetcdf.settings WRT S3 support 2. Added the above URLS as additional test cases ## Misc. Un-Related Changes 1. CURLOPT_PUT is deprecated in favor to CURLOPT_UPLOAD 2. Fix some minor warnings ## Open Problems * Under Ubuntu, either libcrypto or aws-sdk-cpp has a memory leak.
2023-03-03 10:51:02 +08:00
URL3="https://thredds-test.unidata.ucar.edu/thredds/fileServer/pointData/cf_dsg/example/point.nc#mode=bytes"
URL4b="https://thredds-test.unidata.ucar.edu/thredds/fileServer/irma/metar/files/METAR_20170910_0000.nc#bytes"
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.
2022-08-28 10:21:13 +08:00
fi
if test "x$FEATURE_S3TESTS" != xno ; then
Fix byterange handling of some URLS re: Issue The byterange handling of the following URLS fails. ### Problem 1: "https://crudata.uea.ac.uk/cru/data/temperature/HadCRUT.4.6.0.0.median.nc#mode=bytes" It turns out that byterange in hdf5 has two possible targets: S3 and not-S3 (e.g. a thredds server or the crudata URL above). Each uses a different HDF5 Virtual File Driver (VFD). I incorrectly set up the byterange code in libhdf5 so that it would choose one or the other of the two VFD's for any netcdf-c library build. The fix is to allow it to choose either one at run-time. ### Problem 2: "https://noaa-goes16.s3.amazonaws.com/ABI-L1b-RadF/2022/001/18/OR_ABI-L1b-RadF-M6C01_G16_s20220011800205_e20220011809513_c20220011809562.nc#mode=bytes,s3" When given what appears to be an S3-related URL, the netcdf-c library code converts it into a canonical, so-called "path" format. In casing out the possible input URL formats, I missed the case where the host contains the bucket ("noaa-goes16"), but not the region. So the fix was to check for this case. ## Misc. Related Changes 1. Since S3 is used in more than just NCZarr, I changed the automake/cmake options to replace "--enable-nczarr-s3" with "--enable-s3", but keeping the former option as a synonym for the latter. This also entailed cleaning up libnetcdf.settings WRT S3 support 2. Added the above URLS as additional test cases ## Misc. Un-Related Changes 1. CURLOPT_PUT is deprecated in favor to CURLOPT_UPLOAD 2. Fix some minor warnings ## Open Problems * Under Ubuntu, either libcrypto or aws-sdk-cpp has a memory leak.
2023-03-03 10:51:02 +08:00
URL4a="https://s3.us-east-1.amazonaws.com/noaa-goes16/ABI-L1b-RadC/2017/059/03/OR_ABI-L1b-RadC-M3C13_G16_s20170590337505_e20170590340289_c20170590340316.nc#mode=bytes"
URL4c="https://noaa-goes16.s3.amazonaws.com/ABI-L1b-RadF/2022/001/18/OR_ABI-L1b-RadF-M6C01_G16_s20220011800205_e20220011809513_c20220011809562.nc#mode=bytes,s3"
# Test alternate URL with no specified region and using s3 protocol
URL4e="s3://noaa-goes16/ABI-L1b-RadC/2017/059/03/OR_ABI-L1b-RadC-M3C13_G16_s20170590337505_e20170590340289_c20170590340316.nc#mode=bytes"
fi
if test "x$FEATURE_S3TESTS" = xyes ; then
Fix byterange handling of some URLS re: Issue The byterange handling of the following URLS fails. ### Problem 1: "https://crudata.uea.ac.uk/cru/data/temperature/HadCRUT.4.6.0.0.median.nc#mode=bytes" It turns out that byterange in hdf5 has two possible targets: S3 and not-S3 (e.g. a thredds server or the crudata URL above). Each uses a different HDF5 Virtual File Driver (VFD). I incorrectly set up the byterange code in libhdf5 so that it would choose one or the other of the two VFD's for any netcdf-c library build. The fix is to allow it to choose either one at run-time. ### Problem 2: "https://noaa-goes16.s3.amazonaws.com/ABI-L1b-RadF/2022/001/18/OR_ABI-L1b-RadF-M6C01_G16_s20220011800205_e20220011809513_c20220011809562.nc#mode=bytes,s3" When given what appears to be an S3-related URL, the netcdf-c library code converts it into a canonical, so-called "path" format. In casing out the possible input URL formats, I missed the case where the host contains the bucket ("noaa-goes16"), but not the region. So the fix was to check for this case. ## Misc. Related Changes 1. Since S3 is used in more than just NCZarr, I changed the automake/cmake options to replace "--enable-nczarr-s3" with "--enable-s3", but keeping the former option as a synonym for the latter. This also entailed cleaning up libnetcdf.settings WRT S3 support 2. Added the above URLS as additional test cases ## Misc. Un-Related Changes 1. CURLOPT_PUT is deprecated in favor to CURLOPT_UPLOAD 2. Fix some minor warnings ## Open Problems * Under Ubuntu, either libcrypto or aws-sdk-cpp has a memory leak.
2023-03-03 10:51:02 +08:00
# Requires auth
Mitigate S3 test interference + Unlimited Dimensions in NCZarr 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.
2023-09-27 06:56:48 +08:00
URL3b="s3://${S3TESTBUCKET}/byterangefiles/upload3.nc#bytes"
# Requires auth
Mitigate S3 test interference + Unlimited Dimensions in NCZarr 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.
2023-09-27 06:56:48 +08:00
URL4d="s3://${S3TESTBUCKET}/byterangefiles/upload4.nc#bytes&aws.profile=unidata"
Fix byterange handling of some URLS re: Issue The byterange handling of the following URLS fails. ### Problem 1: "https://crudata.uea.ac.uk/cru/data/temperature/HadCRUT.4.6.0.0.median.nc#mode=bytes" It turns out that byterange in hdf5 has two possible targets: S3 and not-S3 (e.g. a thredds server or the crudata URL above). Each uses a different HDF5 Virtual File Driver (VFD). I incorrectly set up the byterange code in libhdf5 so that it would choose one or the other of the two VFD's for any netcdf-c library build. The fix is to allow it to choose either one at run-time. ### Problem 2: "https://noaa-goes16.s3.amazonaws.com/ABI-L1b-RadF/2022/001/18/OR_ABI-L1b-RadF-M6C01_G16_s20220011800205_e20220011809513_c20220011809562.nc#mode=bytes,s3" When given what appears to be an S3-related URL, the netcdf-c library code converts it into a canonical, so-called "path" format. In casing out the possible input URL formats, I missed the case where the host contains the bucket ("noaa-goes16"), but not the region. So the fix was to check for this case. ## Misc. Related Changes 1. Since S3 is used in more than just NCZarr, I changed the automake/cmake options to replace "--enable-nczarr-s3" with "--enable-s3", but keeping the former option as a synonym for the latter. This also entailed cleaning up libnetcdf.settings WRT S3 support 2. Added the above URLS as additional test cases ## Misc. Un-Related Changes 1. CURLOPT_PUT is deprecated in favor to CURLOPT_UPLOAD 2. Fix some minor warnings ## Open Problems * Under Ubuntu, either libcrypto or aws-sdk-cpp has a memory leak.
2023-03-03 10:51:02 +08:00
fi
URL4f="https://crudata.uea.ac.uk/cru/data/temperature/HadCRUT.4.6.0.0.median.nc#mode=bytes"
if test "x$FEATURE_S3TESTS" = xyes ; then
Mostly revert the filter code to reduce its complexity of use. re: https://github.com/Unidata/netcdf-c/issues/1836 Revert the internal filter code to simplify it. From the user's point of view, the only visible changes should be: 1. The functions that convert text to filter specs have had their signature reverted and have been moved to netcdf_aux.h 2. Some filter API functions now return NC_ENOFILTER when inquiry is made about some filter. Internally,the dispatch table has been modified to get rid of the filter_actions entry and associated complex structures. It has been replaced with inq_var_filter_ids and inq_var_filter_info entries and the dispatch table version has been bumped to 3. Corresponding NOOP and NOTNC4 functions were added to libdispatch/dnotnc4.c. Also, the filter_action entries in dispatch tables were replaced for all dispatch code bases (HDF5, DAP2, etc). This should only impact UDF users. In the process, it became clear that the form of the filters field in NC_VAR_INFO_T was format dependent, so I converted it to be of type void* and pushed its management into the various dispatch code bases. Specifically libhdf5 and libnczarr now manage the filters field in their own way. The auxilliary functions for parsing textual filter specifications were moved to netcdf_aux.h and were renamed to the following: * ncaux_h5filterspec_parse * ncaux_h5filterspec_parselist * ncaux_h5filterspec_free * ncaux_h5filter_fix8 Misc. Other Changes: 1. Document NUG/filters.md updated to reflect the changes above. 2. All the old data types (structs and enums) used by filter_actions actions were deleted. The exception is the NC_H5_Filterspec because it is needed by ncaux_h5filterspec_parselist. 3. Clientside filters were removed -- another enhancement for which no-one ever asked. 4. The ability to remove filters was itself removed. 5. Some functionality needed by nczarr was moved from libhdf5 to libsrc4 e.g. nc4_find_default_chunksizes 6. All the filterx code was removed 7. ncfilter.h and nc4filter.c no longer used Misc. Unrelated Changes: 1. The nczarr_test makefile clean was leaving some directories; so add clean-local to take care of them.
2020-09-28 02:43:46 +08:00
# Do not use unless we know it has some permanence (note the segment 'testing' in the URL);
URL4x="https://s3.us-west-2.amazonaws.com/coawst-public/testing/HadCRUT.4.6.0.0.median.nc#mode=bytes,&aws.profile=none"
fi
Fix byterange handling of some URLS re: Issue The byterange handling of the following URLS fails. ### Problem 1: "https://crudata.uea.ac.uk/cru/data/temperature/HadCRUT.4.6.0.0.median.nc#mode=bytes" It turns out that byterange in hdf5 has two possible targets: S3 and not-S3 (e.g. a thredds server or the crudata URL above). Each uses a different HDF5 Virtual File Driver (VFD). I incorrectly set up the byterange code in libhdf5 so that it would choose one or the other of the two VFD's for any netcdf-c library build. The fix is to allow it to choose either one at run-time. ### Problem 2: "https://noaa-goes16.s3.amazonaws.com/ABI-L1b-RadF/2022/001/18/OR_ABI-L1b-RadF-M6C01_G16_s20220011800205_e20220011809513_c20220011809562.nc#mode=bytes,s3" When given what appears to be an S3-related URL, the netcdf-c library code converts it into a canonical, so-called "path" format. In casing out the possible input URL formats, I missed the case where the host contains the bucket ("noaa-goes16"), but not the region. So the fix was to check for this case. ## Misc. Related Changes 1. Since S3 is used in more than just NCZarr, I changed the automake/cmake options to replace "--enable-nczarr-s3" with "--enable-s3", but keeping the former option as a synonym for the latter. This also entailed cleaning up libnetcdf.settings WRT S3 support 2. Added the above URLS as additional test cases ## Misc. Un-Related Changes 1. CURLOPT_PUT is deprecated in favor to CURLOPT_UPLOAD 2. Fix some minor warnings ## Open Problems * Under Ubuntu, either libcrypto or aws-sdk-cpp has a memory leak.
2023-03-03 10:51:02 +08:00
Provide byte-range reading of remote datasets re: issue https://github.com/Unidata/netcdf-c/issues/1251 Assume that you have the URL to a remote dataset which is a normal netcdf-3 or netcdf-4 file. This PR allows the netcdf-c to read that dataset's contents as a netcdf file using HTTP byte ranges if the remote server supports byte-range access. Originally, this PR was set up to access Amazon S3 objects, but it can also access other remote datasets such as those provided by a Thredds server via the HTTPServer access protocol. It may also work for other kinds of servers. Note that this is not intended as a true production capability because, as is known, this kind of access to can be quite slow. In addition, the byte-range IO drivers do not currently do any sort of optimization or caching. An additional goal here is to gain some experience with the Amazon S3 REST protocol. This architecture and its use documented in the file docs/byterange.dox. There are currently two test cases: 1. nc_test/tst_s3raw.c - this does a simple open, check format, close cycle for a remote netcdf-3 file and a remote netcdf-4 file. 2. nc_test/test_s3raw.sh - this uses ncdump to investigate some remote datasets. This PR also incorporates significantly changed model inference code (see the superceded PR https://github.com/Unidata/netcdf-c/pull/1259). 1. It centralizes the code that infers the dispatcher. 2. It adds support for byte-range URLs Other changes: 1. NC_HDF5_finalize was not being properly called by nc_finalize(). 2. Fix minor bug in ncgen3.l 3. fix memory leak in nc4info.c 4. add code to walk the .daprc triples and to replace protocol= fragment tag with a more general mode= tag. Final Note: Th inference code is still way too complicated. We need to move to the validfile() model used by netcdf Java, where each dispatcher is asked if it can process the file. This decentralizes the inference code. This will be done after all the major new dispatchers (PIO, Zarr, etc) have been implemented.
2019-01-02 09:27:36 +08:00
echo ""
testsetup() {
U=$1
# Create and upload test files
rm -f upload4.nc upload3.nc
Improve S3 Documentation and Support ## Improvements to S3 Documentation * Create a new document *quickstart_paths.md* that give a summary of the legal path formats used by netcdf-c. This includes both file paths and URL paths. * Modify *nczarr.md* to remove most of the S3 related text. * Move the S3 text from *nczarr.md* to a new document *cloud.md*. * Add some S3-related text to the *byterange.md* document. Hopefully, this will make it easier for users to find the information they want. ## Rebuild NCZarr Testing In order to avoid problems with running make check in parallel, two changes were made: 1. The *nczarr_test* test system was rebuilt. Now, for each test. any generated files are kept in a test-specific directory, isolated from all other test executions. 2. Similarly, since the S3 test bucket is shared, any generated S3 objects are isolated using a test-specific key path. ## Other S3 Related Changes * Add code to ensure that files created on S3 are reclaimed at end of testing. * Used the bash "trap" command to ensure S3 cleanup even if the test fails. * Cleanup the S3 related configure.ac flag set since S3 is used in several places. So now one should use the option *--enable-s3* instead of *--enable-nczarr-s3*, although the latter is still kept as a deprecated alias for the former. * Get some of the github actions yml to work with S3; required fixing various test scripts adding a secret to access the Unidata S3 bucket. * Cleanup S3 portion of libnetcdf.settings.in and netcdf_meta.h.in and test_common.in. * Merge partial S3 support into dhttp.c. * Create an experimental s3 access library especially for use with Windows. It is enabled by using the options *--enable-s3-internal* (automake) or *-DENABLE_S3_INTERNAL=ON* (CMake). Also add a unit-test for it. * Move some definitions from ncrc.h to ncs3sdk.h ## Other Changes * Provide a default implementation of strlcpy and move this and similar defaults into *dmissing.c*.
2023-04-26 07:15:06 +08:00
${execdir}/../nczarr_test/s3util -u ${U} -k /byterangefiles clear
${NCGEN} -lb -3 ${srcdir}/nc_enddef.cdl
mv nc_enddef.nc upload3.nc
Improve S3 Documentation and Support ## Improvements to S3 Documentation * Create a new document *quickstart_paths.md* that give a summary of the legal path formats used by netcdf-c. This includes both file paths and URL paths. * Modify *nczarr.md* to remove most of the S3 related text. * Move the S3 text from *nczarr.md* to a new document *cloud.md*. * Add some S3-related text to the *byterange.md* document. Hopefully, this will make it easier for users to find the information they want. ## Rebuild NCZarr Testing In order to avoid problems with running make check in parallel, two changes were made: 1. The *nczarr_test* test system was rebuilt. Now, for each test. any generated files are kept in a test-specific directory, isolated from all other test executions. 2. Similarly, since the S3 test bucket is shared, any generated S3 objects are isolated using a test-specific key path. ## Other S3 Related Changes * Add code to ensure that files created on S3 are reclaimed at end of testing. * Used the bash "trap" command to ensure S3 cleanup even if the test fails. * Cleanup the S3 related configure.ac flag set since S3 is used in several places. So now one should use the option *--enable-s3* instead of *--enable-nczarr-s3*, although the latter is still kept as a deprecated alias for the former. * Get some of the github actions yml to work with S3; required fixing various test scripts adding a secret to access the Unidata S3 bucket. * Cleanup S3 portion of libnetcdf.settings.in and netcdf_meta.h.in and test_common.in. * Merge partial S3 support into dhttp.c. * Create an experimental s3 access library especially for use with Windows. It is enabled by using the options *--enable-s3-internal* (automake) or *-DENABLE_S3_INTERNAL=ON* (CMake). Also add a unit-test for it. * Move some definitions from ncrc.h to ncs3sdk.h ## Other Changes * Provide a default implementation of strlcpy and move this and similar defaults into *dmissing.c*.
2023-04-26 07:15:06 +08:00
${execdir}/../nczarr_test/s3util -u ${U} -k /byterangefiles/upload3.nc -f upload3.nc upload
if test "x$FEATURE_HDF5" = xyes ; then
${NCGEN} -lb -4 ${srcdir}/nc_enddef.cdl
mv nc_enddef.nc upload4.nc
Improve S3 Documentation and Support ## Improvements to S3 Documentation * Create a new document *quickstart_paths.md* that give a summary of the legal path formats used by netcdf-c. This includes both file paths and URL paths. * Modify *nczarr.md* to remove most of the S3 related text. * Move the S3 text from *nczarr.md* to a new document *cloud.md*. * Add some S3-related text to the *byterange.md* document. Hopefully, this will make it easier for users to find the information they want. ## Rebuild NCZarr Testing In order to avoid problems with running make check in parallel, two changes were made: 1. The *nczarr_test* test system was rebuilt. Now, for each test. any generated files are kept in a test-specific directory, isolated from all other test executions. 2. Similarly, since the S3 test bucket is shared, any generated S3 objects are isolated using a test-specific key path. ## Other S3 Related Changes * Add code to ensure that files created on S3 are reclaimed at end of testing. * Used the bash "trap" command to ensure S3 cleanup even if the test fails. * Cleanup the S3 related configure.ac flag set since S3 is used in several places. So now one should use the option *--enable-s3* instead of *--enable-nczarr-s3*, although the latter is still kept as a deprecated alias for the former. * Get some of the github actions yml to work with S3; required fixing various test scripts adding a secret to access the Unidata S3 bucket. * Cleanup S3 portion of libnetcdf.settings.in and netcdf_meta.h.in and test_common.in. * Merge partial S3 support into dhttp.c. * Create an experimental s3 access library especially for use with Windows. It is enabled by using the options *--enable-s3-internal* (automake) or *-DENABLE_S3_INTERNAL=ON* (CMake). Also add a unit-test for it. * Move some definitions from ncrc.h to ncs3sdk.h ## Other Changes * Provide a default implementation of strlcpy and move this and similar defaults into *dmissing.c*.
2023-04-26 07:15:06 +08:00
${execdir}/../nczarr_test/s3util -u ${U} -k /byterangefiles/upload4.nc -f upload4.nc upload
fi
rm -f tst_http_nc3.cdl tst_http_nc4?.cdl
}
testcleanup() {
U=$1
rm -f upload4.nc upload3.nc
Improve S3 Documentation and Support ## Improvements to S3 Documentation * Create a new document *quickstart_paths.md* that give a summary of the legal path formats used by netcdf-c. This includes both file paths and URL paths. * Modify *nczarr.md* to remove most of the S3 related text. * Move the S3 text from *nczarr.md* to a new document *cloud.md*. * Add some S3-related text to the *byterange.md* document. Hopefully, this will make it easier for users to find the information they want. ## Rebuild NCZarr Testing In order to avoid problems with running make check in parallel, two changes were made: 1. The *nczarr_test* test system was rebuilt. Now, for each test. any generated files are kept in a test-specific directory, isolated from all other test executions. 2. Similarly, since the S3 test bucket is shared, any generated S3 objects are isolated using a test-specific key path. ## Other S3 Related Changes * Add code to ensure that files created on S3 are reclaimed at end of testing. * Used the bash "trap" command to ensure S3 cleanup even if the test fails. * Cleanup the S3 related configure.ac flag set since S3 is used in several places. So now one should use the option *--enable-s3* instead of *--enable-nczarr-s3*, although the latter is still kept as a deprecated alias for the former. * Get some of the github actions yml to work with S3; required fixing various test scripts adding a secret to access the Unidata S3 bucket. * Cleanup S3 portion of libnetcdf.settings.in and netcdf_meta.h.in and test_common.in. * Merge partial S3 support into dhttp.c. * Create an experimental s3 access library especially for use with Windows. It is enabled by using the options *--enable-s3-internal* (automake) or *-DENABLE_S3_INTERNAL=ON* (CMake). Also add a unit-test for it. * Move some definitions from ncrc.h to ncs3sdk.h ## Other Changes * Provide a default implementation of strlcpy and move this and similar defaults into *dmissing.c*.
2023-04-26 07:15:06 +08:00
${execdir}/../nczarr_test/s3util -u ${U} -k /byterangefiles clear
}
testbytes() {
TAG="$1"
EXPECTED="$2"
U="$3"
Improve S3 Documentation and Support ## Improvements to S3 Documentation * Create a new document *quickstart_paths.md* that give a summary of the legal path formats used by netcdf-c. This includes both file paths and URL paths. * Modify *nczarr.md* to remove most of the S3 related text. * Move the S3 text from *nczarr.md* to a new document *cloud.md*. * Add some S3-related text to the *byterange.md* document. Hopefully, this will make it easier for users to find the information they want. ## Rebuild NCZarr Testing In order to avoid problems with running make check in parallel, two changes were made: 1. The *nczarr_test* test system was rebuilt. Now, for each test. any generated files are kept in a test-specific directory, isolated from all other test executions. 2. Similarly, since the S3 test bucket is shared, any generated S3 objects are isolated using a test-specific key path. ## Other S3 Related Changes * Add code to ensure that files created on S3 are reclaimed at end of testing. * Used the bash "trap" command to ensure S3 cleanup even if the test fails. * Cleanup the S3 related configure.ac flag set since S3 is used in several places. So now one should use the option *--enable-s3* instead of *--enable-nczarr-s3*, although the latter is still kept as a deprecated alias for the former. * Get some of the github actions yml to work with S3; required fixing various test scripts adding a secret to access the Unidata S3 bucket. * Cleanup S3 portion of libnetcdf.settings.in and netcdf_meta.h.in and test_common.in. * Merge partial S3 support into dhttp.c. * Create an experimental s3 access library especially for use with Windows. It is enabled by using the options *--enable-s3-internal* (automake) or *-DENABLE_S3_INTERNAL=ON* (CMake). Also add a unit-test for it. * Move some definitions from ncrc.h to ncs3sdk.h ## Other Changes * Provide a default implementation of strlcpy and move this and similar defaults into *dmissing.c*.
2023-04-26 07:15:06 +08:00
K=`${NCDUMP} -k "$U" | tr -d '\r\n'`
Provide byte-range reading of remote datasets re: issue https://github.com/Unidata/netcdf-c/issues/1251 Assume that you have the URL to a remote dataset which is a normal netcdf-3 or netcdf-4 file. This PR allows the netcdf-c to read that dataset's contents as a netcdf file using HTTP byte ranges if the remote server supports byte-range access. Originally, this PR was set up to access Amazon S3 objects, but it can also access other remote datasets such as those provided by a Thredds server via the HTTPServer access protocol. It may also work for other kinds of servers. Note that this is not intended as a true production capability because, as is known, this kind of access to can be quite slow. In addition, the byte-range IO drivers do not currently do any sort of optimization or caching. An additional goal here is to gain some experience with the Amazon S3 REST protocol. This architecture and its use documented in the file docs/byterange.dox. There are currently two test cases: 1. nc_test/tst_s3raw.c - this does a simple open, check format, close cycle for a remote netcdf-3 file and a remote netcdf-4 file. 2. nc_test/test_s3raw.sh - this uses ncdump to investigate some remote datasets. This PR also incorporates significantly changed model inference code (see the superceded PR https://github.com/Unidata/netcdf-c/pull/1259). 1. It centralizes the code that infers the dispatcher. 2. It adds support for byte-range URLs Other changes: 1. NC_HDF5_finalize was not being properly called by nc_finalize(). 2. Fix minor bug in ncgen3.l 3. fix memory leak in nc4info.c 4. add code to walk the .daprc triples and to replace protocol= fragment tag with a more general mode= tag. Final Note: Th inference code is still way too complicated. We need to move to the validfile() model used by netcdf Java, where each dispatcher is asked if it can process the file. This decentralizes the inference code. This will be done after all the major new dispatchers (PIO, Zarr, etc) have been implemented.
2019-01-02 09:27:36 +08:00
if test "x$K" != "x$EXPECTED" ; then
echo "test_http: -k flag mismatch: expected=$EXPECTED have=$K"
exit 1
fi
rm -f tst_http_$TAG.cdl
Provide byte-range reading of remote datasets re: issue https://github.com/Unidata/netcdf-c/issues/1251 Assume that you have the URL to a remote dataset which is a normal netcdf-3 or netcdf-4 file. This PR allows the netcdf-c to read that dataset's contents as a netcdf file using HTTP byte ranges if the remote server supports byte-range access. Originally, this PR was set up to access Amazon S3 objects, but it can also access other remote datasets such as those provided by a Thredds server via the HTTPServer access protocol. It may also work for other kinds of servers. Note that this is not intended as a true production capability because, as is known, this kind of access to can be quite slow. In addition, the byte-range IO drivers do not currently do any sort of optimization or caching. An additional goal here is to gain some experience with the Amazon S3 REST protocol. This architecture and its use documented in the file docs/byterange.dox. There are currently two test cases: 1. nc_test/tst_s3raw.c - this does a simple open, check format, close cycle for a remote netcdf-3 file and a remote netcdf-4 file. 2. nc_test/test_s3raw.sh - this uses ncdump to investigate some remote datasets. This PR also incorporates significantly changed model inference code (see the superceded PR https://github.com/Unidata/netcdf-c/pull/1259). 1. It centralizes the code that infers the dispatcher. 2. It adds support for byte-range URLs Other changes: 1. NC_HDF5_finalize was not being properly called by nc_finalize(). 2. Fix minor bug in ncgen3.l 3. fix memory leak in nc4info.c 4. add code to walk the .daprc triples and to replace protocol= fragment tag with a more general mode= tag. Final Note: Th inference code is still way too complicated. We need to move to the validfile() model used by netcdf Java, where each dispatcher is asked if it can process the file. This decentralizes the inference code. This will be done after all the major new dispatchers (PIO, Zarr, etc) have been implemented.
2019-01-02 09:27:36 +08:00
# Now test the reading of at least the metadata
${NCDUMP} -h "$U" >tst_http_$TAG.cdl
Provide byte-range reading of remote datasets re: issue https://github.com/Unidata/netcdf-c/issues/1251 Assume that you have the URL to a remote dataset which is a normal netcdf-3 or netcdf-4 file. This PR allows the netcdf-c to read that dataset's contents as a netcdf file using HTTP byte ranges if the remote server supports byte-range access. Originally, this PR was set up to access Amazon S3 objects, but it can also access other remote datasets such as those provided by a Thredds server via the HTTPServer access protocol. It may also work for other kinds of servers. Note that this is not intended as a true production capability because, as is known, this kind of access to can be quite slow. In addition, the byte-range IO drivers do not currently do any sort of optimization or caching. An additional goal here is to gain some experience with the Amazon S3 REST protocol. This architecture and its use documented in the file docs/byterange.dox. There are currently two test cases: 1. nc_test/tst_s3raw.c - this does a simple open, check format, close cycle for a remote netcdf-3 file and a remote netcdf-4 file. 2. nc_test/test_s3raw.sh - this uses ncdump to investigate some remote datasets. This PR also incorporates significantly changed model inference code (see the superceded PR https://github.com/Unidata/netcdf-c/pull/1259). 1. It centralizes the code that infers the dispatcher. 2. It adds support for byte-range URLs Other changes: 1. NC_HDF5_finalize was not being properly called by nc_finalize(). 2. Fix minor bug in ncgen3.l 3. fix memory leak in nc4info.c 4. add code to walk the .daprc triples and to replace protocol= fragment tag with a more general mode= tag. Final Note: Th inference code is still way too complicated. We need to move to the validfile() model used by netcdf Java, where each dispatcher is asked if it can process the file. This decentralizes the inference code. This will be done after all the major new dispatchers (PIO, Zarr, etc) have been implemented.
2019-01-02 09:27:36 +08:00
# compare
diff -wb tst_http_$TAG.cdl ${srcdir}/ref_tst_http_$TAG.cdl
}
Provide byte-range reading of remote datasets re: issue https://github.com/Unidata/netcdf-c/issues/1251 Assume that you have the URL to a remote dataset which is a normal netcdf-3 or netcdf-4 file. This PR allows the netcdf-c to read that dataset's contents as a netcdf file using HTTP byte ranges if the remote server supports byte-range access. Originally, this PR was set up to access Amazon S3 objects, but it can also access other remote datasets such as those provided by a Thredds server via the HTTPServer access protocol. It may also work for other kinds of servers. Note that this is not intended as a true production capability because, as is known, this kind of access to can be quite slow. In addition, the byte-range IO drivers do not currently do any sort of optimization or caching. An additional goal here is to gain some experience with the Amazon S3 REST protocol. This architecture and its use documented in the file docs/byterange.dox. There are currently two test cases: 1. nc_test/tst_s3raw.c - this does a simple open, check format, close cycle for a remote netcdf-3 file and a remote netcdf-4 file. 2. nc_test/test_s3raw.sh - this uses ncdump to investigate some remote datasets. This PR also incorporates significantly changed model inference code (see the superceded PR https://github.com/Unidata/netcdf-c/pull/1259). 1. It centralizes the code that infers the dispatcher. 2. It adds support for byte-range URLs Other changes: 1. NC_HDF5_finalize was not being properly called by nc_finalize(). 2. Fix minor bug in ncgen3.l 3. fix memory leak in nc4info.c 4. add code to walk the .daprc triples and to replace protocol= fragment tag with a more general mode= tag. Final Note: Th inference code is still way too complicated. We need to move to the validfile() model used by netcdf Java, where each dispatcher is asked if it can process the file. This decentralizes the inference code. This will be done after all the major new dispatchers (PIO, Zarr, etc) have been implemented.
2019-01-02 09:27:36 +08:00
tests3auth() {
TAG="$1"
EXPECTED="$2"
U="$3"
Improve S3 Documentation and Support ## Improvements to S3 Documentation * Create a new document *quickstart_paths.md* that give a summary of the legal path formats used by netcdf-c. This includes both file paths and URL paths. * Modify *nczarr.md* to remove most of the S3 related text. * Move the S3 text from *nczarr.md* to a new document *cloud.md*. * Add some S3-related text to the *byterange.md* document. Hopefully, this will make it easier for users to find the information they want. ## Rebuild NCZarr Testing In order to avoid problems with running make check in parallel, two changes were made: 1. The *nczarr_test* test system was rebuilt. Now, for each test. any generated files are kept in a test-specific directory, isolated from all other test executions. 2. Similarly, since the S3 test bucket is shared, any generated S3 objects are isolated using a test-specific key path. ## Other S3 Related Changes * Add code to ensure that files created on S3 are reclaimed at end of testing. * Used the bash "trap" command to ensure S3 cleanup even if the test fails. * Cleanup the S3 related configure.ac flag set since S3 is used in several places. So now one should use the option *--enable-s3* instead of *--enable-nczarr-s3*, although the latter is still kept as a deprecated alias for the former. * Get some of the github actions yml to work with S3; required fixing various test scripts adding a secret to access the Unidata S3 bucket. * Cleanup S3 portion of libnetcdf.settings.in and netcdf_meta.h.in and test_common.in. * Merge partial S3 support into dhttp.c. * Create an experimental s3 access library especially for use with Windows. It is enabled by using the options *--enable-s3-internal* (automake) or *-DENABLE_S3_INTERNAL=ON* (CMake). Also add a unit-test for it. * Move some definitions from ncrc.h to ncs3sdk.h ## Other Changes * Provide a default implementation of strlcpy and move this and similar defaults into *dmissing.c*.
2023-04-26 07:15:06 +08:00
K=`${NCDUMP} -k "$U" | tr -d '\r\n'`
if test "x$K" != "x$EXPECTED" ; then
echo "test_http: -k flag mismatch: expected=$EXPECTED have=$K"
exit 1
fi
rm -f tmp_${TAG}.cdl
# Now test the reading of at least the metadata
${NCDUMP} -n nc_enddef "$U" >tmp_${TAG}.cdl
# compare
diff -wb tmp_$TAG.cdl ${srcdir}/nc_enddef.cdl
}
if test "x$FEATURE_S3TESTS" = xyes ; then
Mitigate S3 test interference + Unlimited Dimensions in NCZarr 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.
2023-09-27 06:56:48 +08:00
testsetup https://s3.us-east-1.amazonaws.com/${S3TESTBUCKET}
fi
echo "*** Testing reading NetCDF-3 file with http"
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.
2022-08-28 10:21:13 +08:00
if test "x$FEATURE_THREDDSTEST" = x1 ; then
echo "***Test remote classic file"
testbytes nc3 classic "$URL3"
fi
if test "x$FEATURE_HDF5" = xyes ; then
Fix byterange handling of some URLS re: Issue The byterange handling of the following URLS fails. ### Problem 1: "https://crudata.uea.ac.uk/cru/data/temperature/HadCRUT.4.6.0.0.median.nc#mode=bytes" It turns out that byterange in hdf5 has two possible targets: S3 and not-S3 (e.g. a thredds server or the crudata URL above). Each uses a different HDF5 Virtual File Driver (VFD). I incorrectly set up the byterange code in libhdf5 so that it would choose one or the other of the two VFD's for any netcdf-c library build. The fix is to allow it to choose either one at run-time. ### Problem 2: "https://noaa-goes16.s3.amazonaws.com/ABI-L1b-RadF/2022/001/18/OR_ABI-L1b-RadF-M6C01_G16_s20220011800205_e20220011809513_c20220011809562.nc#mode=bytes,s3" When given what appears to be an S3-related URL, the netcdf-c library code converts it into a canonical, so-called "path" format. In casing out the possible input URL formats, I missed the case where the host contains the bucket ("noaa-goes16"), but not the region. So the fix was to check for this case. ## Misc. Related Changes 1. Since S3 is used in more than just NCZarr, I changed the automake/cmake options to replace "--enable-nczarr-s3" with "--enable-s3", but keeping the former option as a synonym for the latter. This also entailed cleaning up libnetcdf.settings WRT S3 support 2. Added the above URLS as additional test cases ## Misc. Un-Related Changes 1. CURLOPT_PUT is deprecated in favor to CURLOPT_UPLOAD 2. Fix some minor warnings ## Open Problems * Under Ubuntu, either libcrypto or aws-sdk-cpp has a memory leak.
2023-03-03 10:51:02 +08:00
echo "***Test remote netcdf-4 files: non-s3"
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.
2022-08-28 10:21:13 +08:00
if test "x$FEATURE_THREDDSTEST" = x1 ; then
testbytes nc4b netCDF-4 "$URL4b"
fi
Fix byterange handling of some URLS re: Issue The byterange handling of the following URLS fails. ### Problem 1: "https://crudata.uea.ac.uk/cru/data/temperature/HadCRUT.4.6.0.0.median.nc#mode=bytes" It turns out that byterange in hdf5 has two possible targets: S3 and not-S3 (e.g. a thredds server or the crudata URL above). Each uses a different HDF5 Virtual File Driver (VFD). I incorrectly set up the byterange code in libhdf5 so that it would choose one or the other of the two VFD's for any netcdf-c library build. The fix is to allow it to choose either one at run-time. ### Problem 2: "https://noaa-goes16.s3.amazonaws.com/ABI-L1b-RadF/2022/001/18/OR_ABI-L1b-RadF-M6C01_G16_s20220011800205_e20220011809513_c20220011809562.nc#mode=bytes,s3" When given what appears to be an S3-related URL, the netcdf-c library code converts it into a canonical, so-called "path" format. In casing out the possible input URL formats, I missed the case where the host contains the bucket ("noaa-goes16"), but not the region. So the fix was to check for this case. ## Misc. Related Changes 1. Since S3 is used in more than just NCZarr, I changed the automake/cmake options to replace "--enable-nczarr-s3" with "--enable-s3", but keeping the former option as a synonym for the latter. This also entailed cleaning up libnetcdf.settings WRT S3 support 2. Added the above URLS as additional test cases ## Misc. Un-Related Changes 1. CURLOPT_PUT is deprecated in favor to CURLOPT_UPLOAD 2. Fix some minor warnings ## Open Problems * Under Ubuntu, either libcrypto or aws-sdk-cpp has a memory leak.
2023-03-03 10:51:02 +08:00
testbytes nc4f netCDF-4 "$URL4f"
fi
if test "x$URL3B" != x ; then
Fix byterange handling of some URLS re: Issue The byterange handling of the following URLS fails. ### Problem 1: "https://crudata.uea.ac.uk/cru/data/temperature/HadCRUT.4.6.0.0.median.nc#mode=bytes" It turns out that byterange in hdf5 has two possible targets: S3 and not-S3 (e.g. a thredds server or the crudata URL above). Each uses a different HDF5 Virtual File Driver (VFD). I incorrectly set up the byterange code in libhdf5 so that it would choose one or the other of the two VFD's for any netcdf-c library build. The fix is to allow it to choose either one at run-time. ### Problem 2: "https://noaa-goes16.s3.amazonaws.com/ABI-L1b-RadF/2022/001/18/OR_ABI-L1b-RadF-M6C01_G16_s20220011800205_e20220011809513_c20220011809562.nc#mode=bytes,s3" When given what appears to be an S3-related URL, the netcdf-c library code converts it into a canonical, so-called "path" format. In casing out the possible input URL formats, I missed the case where the host contains the bucket ("noaa-goes16"), but not the region. So the fix was to check for this case. ## Misc. Related Changes 1. Since S3 is used in more than just NCZarr, I changed the automake/cmake options to replace "--enable-nczarr-s3" with "--enable-s3", but keeping the former option as a synonym for the latter. This also entailed cleaning up libnetcdf.settings WRT S3 support 2. Added the above URLS as additional test cases ## Misc. Un-Related Changes 1. CURLOPT_PUT is deprecated in favor to CURLOPT_UPLOAD 2. Fix some minor warnings ## Open Problems * Under Ubuntu, either libcrypto or aws-sdk-cpp has a memory leak.
2023-03-03 10:51:02 +08:00
echo "***Test remote netcdf-3 file: s3 auth"
tests3auth nc3b classic "$URL3b"
fi
Fix byterange handling of some URLS re: Issue The byterange handling of the following URLS fails. ### Problem 1: "https://crudata.uea.ac.uk/cru/data/temperature/HadCRUT.4.6.0.0.median.nc#mode=bytes" It turns out that byterange in hdf5 has two possible targets: S3 and not-S3 (e.g. a thredds server or the crudata URL above). Each uses a different HDF5 Virtual File Driver (VFD). I incorrectly set up the byterange code in libhdf5 so that it would choose one or the other of the two VFD's for any netcdf-c library build. The fix is to allow it to choose either one at run-time. ### Problem 2: "https://noaa-goes16.s3.amazonaws.com/ABI-L1b-RadF/2022/001/18/OR_ABI-L1b-RadF-M6C01_G16_s20220011800205_e20220011809513_c20220011809562.nc#mode=bytes,s3" When given what appears to be an S3-related URL, the netcdf-c library code converts it into a canonical, so-called "path" format. In casing out the possible input URL formats, I missed the case where the host contains the bucket ("noaa-goes16"), but not the region. So the fix was to check for this case. ## Misc. Related Changes 1. Since S3 is used in more than just NCZarr, I changed the automake/cmake options to replace "--enable-nczarr-s3" with "--enable-s3", but keeping the former option as a synonym for the latter. This also entailed cleaning up libnetcdf.settings WRT S3 support 2. Added the above URLS as additional test cases ## Misc. Un-Related Changes 1. CURLOPT_PUT is deprecated in favor to CURLOPT_UPLOAD 2. Fix some minor warnings ## Open Problems * Under Ubuntu, either libcrypto or aws-sdk-cpp has a memory leak.
2023-03-03 10:51:02 +08:00
if test "x$URL4a" != x ; then
echo "***Test remote netdf-4 file: s3"
testbytes nc4a netCDF-4 "$URL4a"
fi
if test "x$URL4c" != x ; then
echo "***Test remote netcdf-4 file: s3"
testbytes nc4c netCDF-4 "$URL4c"
fi
if test "x$URL4d" != x ; then
echo "***Test remote netcdf-4 file: s3 auth"
tests3auth nc4d netCDF-4 "$URL4d"
fi
if test "x$URL4e" != x ; then
Fix byterange handling of some URLS re: Issue The byterange handling of the following URLS fails. ### Problem 1: "https://crudata.uea.ac.uk/cru/data/temperature/HadCRUT.4.6.0.0.median.nc#mode=bytes" It turns out that byterange in hdf5 has two possible targets: S3 and not-S3 (e.g. a thredds server or the crudata URL above). Each uses a different HDF5 Virtual File Driver (VFD). I incorrectly set up the byterange code in libhdf5 so that it would choose one or the other of the two VFD's for any netcdf-c library build. The fix is to allow it to choose either one at run-time. ### Problem 2: "https://noaa-goes16.s3.amazonaws.com/ABI-L1b-RadF/2022/001/18/OR_ABI-L1b-RadF-M6C01_G16_s20220011800205_e20220011809513_c20220011809562.nc#mode=bytes,s3" When given what appears to be an S3-related URL, the netcdf-c library code converts it into a canonical, so-called "path" format. In casing out the possible input URL formats, I missed the case where the host contains the bucket ("noaa-goes16"), but not the region. So the fix was to check for this case. ## Misc. Related Changes 1. Since S3 is used in more than just NCZarr, I changed the automake/cmake options to replace "--enable-nczarr-s3" with "--enable-s3", but keeping the former option as a synonym for the latter. This also entailed cleaning up libnetcdf.settings WRT S3 support 2. Added the above URLS as additional test cases ## Misc. Un-Related Changes 1. CURLOPT_PUT is deprecated in favor to CURLOPT_UPLOAD 2. Fix some minor warnings ## Open Problems * Under Ubuntu, either libcrypto or aws-sdk-cpp has a memory leak.
2023-03-03 10:51:02 +08:00
echo "***Test remote netcdf-4 file: s3 noauth"
testbytes nc4e netCDF-4 "$URL4e"
fi
# Cleanup
if test "x$FEATURE_S3TESTS" = xyes ; then
Mitigate S3 test interference + Unlimited Dimensions in NCZarr 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.
2023-09-27 06:56:48 +08:00
testcleanup https://s3.us-east-1.amazonaws.com/${S3TESTBUCKET}
fi
Provide byte-range reading of remote datasets re: issue https://github.com/Unidata/netcdf-c/issues/1251 Assume that you have the URL to a remote dataset which is a normal netcdf-3 or netcdf-4 file. This PR allows the netcdf-c to read that dataset's contents as a netcdf file using HTTP byte ranges if the remote server supports byte-range access. Originally, this PR was set up to access Amazon S3 objects, but it can also access other remote datasets such as those provided by a Thredds server via the HTTPServer access protocol. It may also work for other kinds of servers. Note that this is not intended as a true production capability because, as is known, this kind of access to can be quite slow. In addition, the byte-range IO drivers do not currently do any sort of optimization or caching. An additional goal here is to gain some experience with the Amazon S3 REST protocol. This architecture and its use documented in the file docs/byterange.dox. There are currently two test cases: 1. nc_test/tst_s3raw.c - this does a simple open, check format, close cycle for a remote netcdf-3 file and a remote netcdf-4 file. 2. nc_test/test_s3raw.sh - this uses ncdump to investigate some remote datasets. This PR also incorporates significantly changed model inference code (see the superceded PR https://github.com/Unidata/netcdf-c/pull/1259). 1. It centralizes the code that infers the dispatcher. 2. It adds support for byte-range URLs Other changes: 1. NC_HDF5_finalize was not being properly called by nc_finalize(). 2. Fix minor bug in ncgen3.l 3. fix memory leak in nc4info.c 4. add code to walk the .daprc triples and to replace protocol= fragment tag with a more general mode= tag. Final Note: Th inference code is still way too complicated. We need to move to the validfile() model used by netcdf Java, where each dispatcher is asked if it can process the file. This decentralizes the inference code. This will be done after all the major new dispatchers (PIO, Zarr, etc) have been implemented.
2019-01-02 09:27:36 +08:00
exit