2020-08-18 09:15:47 +08:00
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#!/bin/sh
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2023-04-26 07:15:06 +08:00
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# Load only once
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if test "x$TEST_NCZARR_SH" = x ; then
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export TEST_NCZARR_SH=1
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2020-08-18 09:15:47 +08:00
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if test "x$SETX" != x; then set -x; fi
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2021-01-29 11:11:01 +08:00
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# Figure out which cloud repo to use
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if test "x$NCZARR_S3_TEST_HOST" = x ; then
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2021-09-28 08:36:33 +08:00
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# export NCZARR_S3_TEST_HOST=stratus.ucar.edu
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export NCZARR_S3_TEST_HOST=s3.us-east-1.amazonaws.com
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2021-01-29 11:11:01 +08:00
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fi
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if test "x$NCZARR_S3_TEST_BUCKET" = x ; then
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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
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export NCZARR_S3_TEST_BUCKET="${S3TESTBUCKET}"
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2021-01-29 11:11:01 +08:00
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fi
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export NCZARR_S3_TEST_URL="https://${NCZARR_S3_TEST_HOST}/${NCZARR_S3_TEST_BUCKET}"
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2023-04-26 07:15:06 +08:00
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if test "x$VALGRIND" != x ; then
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2023-05-01 08:41:31 +08:00
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ZMD="valgrind --leak-check=full ${execdir}/zmapio"
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S3UTIL="valgrind --leak-check=full ${execdir}/s3util"
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2023-04-26 07:15:06 +08:00
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else
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ZMD="${execdir}/zmapio"
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2023-05-01 08:41:31 +08:00
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S3UTIL="${execdir}/s3util"
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2023-04-26 07:15:06 +08:00
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fi
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2020-08-18 09:15:47 +08:00
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# Check settings
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checksetting() {
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if test -f ${TOPBUILDDIR}/libnetcdf.settings ; then
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local PATTERN
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PATTERN="${1}:[ ]*yes"
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if grep "$PATTERN" <${TOPBUILDDIR}/libnetcdf.settings ; then
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HAVE_SETTING=1
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else
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unset HAVE_SETTING
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fi
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fi
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}
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2020-12-17 11:48:02 +08:00
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checkprops() {
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specflag=
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headflag=
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isxfail=
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# determine if this is an xfailtest
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for t in ${XFAILTESTS} ; do
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if test "x${t}" = "x${x}" ; then isxfail=1; fi
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done
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for t in ${SPECTESTS} ; do
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if test "x${t}" = "x${f}" ; then specflag="-s"; fi
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done
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for t in ${HEADTESTS} ; do
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if test "x${t}" = "x${f}" ; then headflag="-h"; fi
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done
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}
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2020-08-18 09:15:47 +08:00
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extfor() {
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case "$1" in
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2021-01-29 11:11:01 +08:00
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file) zext="file" ;;
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zip) zext="zip" ;;
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2020-08-18 09:15:47 +08:00
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s3) zext="s3" ;;
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*) echo "unknown kind: $1" ; exit 1;;
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esac
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}
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deletemap() {
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case "$1" in
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2021-01-29 11:11:01 +08:00
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file) rm -fr $2;;
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zip) rm -f $2;;
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2023-04-26 07:15:06 +08:00
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s3) S3KEY=`${execdir}/zs3parse -k $2`; s3sdkdelete $S3KEY ;;
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2020-12-17 11:48:02 +08:00
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*) echo "unknown kind: $1" ; exit 1;;
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2020-08-18 09:15:47 +08:00
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esac
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}
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2021-01-29 11:11:01 +08:00
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mapstillexists() {
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mapstillexists=0
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2023-04-26 07:15:06 +08:00
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if "${execdir}/zmapio $fileurl" &> /dev/null ; then
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2020-12-17 11:48:02 +08:00
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echo "delete failed: $1"
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2021-01-29 11:11:01 +08:00
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mapstillexists=1
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2020-08-18 09:15:47 +08:00
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fi
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}
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fileargs() {
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2020-12-17 11:48:02 +08:00
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f="$1"
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2021-02-25 04:46:11 +08:00
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frag="$2"
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if test "x$frag" = x ; then frag="mode=nczarr,$zext" ; fi
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2020-12-20 12:17:46 +08:00
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case "$zext" in
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s3)
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2023-04-26 07:15:06 +08:00
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S3PATH="${NCZARR_S3_TEST_URL}/${S3ISOPATH}"
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2021-02-25 04:46:11 +08:00
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fileurl="${S3PATH}/${f}#${frag}"
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2020-08-18 09:15:47 +08:00
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file=$fileurl
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S3HOST=`${execdir}/zs3parse -h $S3PATH`
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S3BUCKET=`${execdir}/zs3parse -b $S3PATH`
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2020-12-17 11:48:02 +08:00
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S3PREFIX=`${execdir}/zs3parse -k $S3PATH`
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2020-12-20 12:17:46 +08:00
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;;
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*)
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2020-12-17 11:48:02 +08:00
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file="${f}.$zext"
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2021-02-25 04:46:11 +08:00
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fileurl="file://${f}.$zext#${frag}"
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2020-12-20 12:17:46 +08:00
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;;
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esac
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2020-08-18 09:15:47 +08:00
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}
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dumpmap() {
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2021-01-29 11:11:01 +08:00
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zext=$1
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zbase=`basename $2 ".$zext"`
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fileargs $zbase
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${execdir}/zmapio -t int -x objdump $fileurl > $3
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2020-08-18 09:15:47 +08:00
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}
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2021-08-11 04:15:24 +08:00
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# Function to remove selected -s attributes from file;
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# These attributes might be platform dependent
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sclean() {
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cat $1 \
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| sed -e '/:_IsNetcdf4/d' \
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| sed -e '/:_Endianness/d' \
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| sed -e '/_NCProperties/d' \
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| sed -e '/_SuperblockVersion/d' \
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| cat > $2
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}
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2021-04-26 12:02:29 +08:00
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# Make sure execdir and srcdir absolute paths are available
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WD=`pwd`
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cd $srcdir ; abs_srcdir=`pwd` ; cd $WD
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cd $execdir ; abs_execdir=`pwd` ; cd $WD
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Upgrade the nczarr code to match Zarr V2
Re: https://github.com/zarr-developers/zarr-python/pull/716
The Zarr version 2 spec has been extended to include the ability
to choose the dimension separator in chunk name keys. The legal
separators has been extended from {'.'} to {'.' '/'}. So now it
is possible to use a key like "0/1/2/0" for chunk names.
This PR implements this for NCZarr. The V2 spec now says that
this separator can be set on a per-variable basis. For now, I
have chosen to allow this be set only globally by adding a key
named "ZARR.DIMENSION_SEPARATOR=<char>" in the
.daprc/.dodsrc/ncrc file. Currently, the only legal separator
characters are '.' (the default) and '/'. On writing, this key
will only be written if its value is different than the default.
This change caused problems because supporting a separator of '/'
is difficult to parse when keys/paths use '/' as the path separator.
A test case was added for this.
Additionally, make nczarr be enabled default by default. This required
some additional changes so that if zip and/or AWS S3 sdk are unavailable,
then they are disabled for NCZarr.
In addition the following unrelated changes were made.
1. Tested that pure-zarr mode could read an nczarr formatted store.
1. The .rc file handling now merges all known .rc files (.ncrc,.daprc, and .dodsrc) in that order and using those in HOME first, then in current directory. For duplicate entries, the later ones override the earlier ones. This change is to remove some of the conflicts inherent in the current .rc file load process. A set of test cases was also added.
1. Re-order tests in configure.ac and CMakeLists.txt so that if libcurl
is not found then the other options that depend upon it properly
are disabled.
1. I decided that xarray support should be enabled by default for pure
zarr. In order to allow disabling, I added a new mode flag "noxarray".
1. Certain test in nczarr_test depend on use of .dodsrc. In order for these
to work when testing in parallel, some inter-test dependencies needed to
be added.
1. Improved authorization testing to use changes in thredds.ucar.edu
2021-04-25 09:48:15 +08:00
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# Clear out any existing .rc files
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WD=`pwd`
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if test "x$NCAUTH_HOMETEST" != x ; then RCHOME=1; fi
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2021-09-03 07:04:26 +08:00
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# Set plugin path
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2021-12-24 13:18:56 +08:00
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if test "x$FP_USEPLUGINS" = xyes; then
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2021-09-03 07:04:26 +08:00
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# Load the findplugins function
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. ${builddir}/findplugin.sh
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echo "findplugin.sh loaded"
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# Locate the plugin path and the library names; argument order is critical
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Support installation of filters into user-specified location
re: https://github.com/Unidata/netcdf-c/issues/2294
Ed Hartnett suggested that the netcdf library installation process
be extended to install the standard filters into a user specified
location. The user can then set HDF5_PLUGIN_PATH to that location.
This PR provides that capability using:
````
configure option: --with-plugin-dir=<absolute directory path>
cmake option: -DPLUGIN_INSTALL_DIR=<absolute directory path>
````
Currently, the following plugins are always installed, if
available: bzip2, zstd, blosc.
If NCZarr is enabled, then additional plugins are installed:
fletcher32, shuffle, deflate, szip.
Additionally, the necessary codec support is installed
for each of the above filters that is installed.
## Changes:
1. Cleanup handling of built-in bzip2.
2. Add documentation to docs/filters.md
3. Re-factor the NCZarr codec libraries
4. Add a test, although it can only be exercised after
the library is installed, so it cannot be used during
normal testing.
5. Cleanup use of HDF5_PLUGIN_PATH in the filter test cases.
2022-04-30 04:31:55 +08:00
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# Find misc in order to determine HDF5_PLUGIN+PATH.
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2021-09-03 07:04:26 +08:00
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# Assume all test filters are in same plugin dir
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findplugin h5misc
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Support installation of filters into user-specified location
re: https://github.com/Unidata/netcdf-c/issues/2294
Ed Hartnett suggested that the netcdf library installation process
be extended to install the standard filters into a user specified
location. The user can then set HDF5_PLUGIN_PATH to that location.
This PR provides that capability using:
````
configure option: --with-plugin-dir=<absolute directory path>
cmake option: -DPLUGIN_INSTALL_DIR=<absolute directory path>
````
Currently, the following plugins are always installed, if
available: bzip2, zstd, blosc.
If NCZarr is enabled, then additional plugins are installed:
fletcher32, shuffle, deflate, szip.
Additionally, the necessary codec support is installed
for each of the above filters that is installed.
## Changes:
1. Cleanup handling of built-in bzip2.
2. Add documentation to docs/filters.md
3. Re-factor the NCZarr codec libraries
4. Add a test, although it can only be exercised after
the library is installed, so it cannot be used during
normal testing.
5. Cleanup use of HDF5_PLUGIN_PATH in the filter test cases.
2022-04-30 04:31:55 +08:00
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echo "final HDF5_PLUGIN_DIR=${HDF5_PLUGIN_DIR}"
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export HDF5_PLUGIN_PATH="${HDF5_PLUGIN_DIR}"
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2021-12-24 13:18:56 +08:00
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fi # USEPLUGINS
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2021-09-03 07:04:26 +08:00
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Upgrade the nczarr code to match Zarr V2
Re: https://github.com/zarr-developers/zarr-python/pull/716
The Zarr version 2 spec has been extended to include the ability
to choose the dimension separator in chunk name keys. The legal
separators has been extended from {'.'} to {'.' '/'}. So now it
is possible to use a key like "0/1/2/0" for chunk names.
This PR implements this for NCZarr. The V2 spec now says that
this separator can be set on a per-variable basis. For now, I
have chosen to allow this be set only globally by adding a key
named "ZARR.DIMENSION_SEPARATOR=<char>" in the
.daprc/.dodsrc/ncrc file. Currently, the only legal separator
characters are '.' (the default) and '/'. On writing, this key
will only be written if its value is different than the default.
This change caused problems because supporting a separator of '/'
is difficult to parse when keys/paths use '/' as the path separator.
A test case was added for this.
Additionally, make nczarr be enabled default by default. This required
some additional changes so that if zip and/or AWS S3 sdk are unavailable,
then they are disabled for NCZarr.
In addition the following unrelated changes were made.
1. Tested that pure-zarr mode could read an nczarr formatted store.
1. The .rc file handling now merges all known .rc files (.ncrc,.daprc, and .dodsrc) in that order and using those in HOME first, then in current directory. For duplicate entries, the later ones override the earlier ones. This change is to remove some of the conflicts inherent in the current .rc file load process. A set of test cases was also added.
1. Re-order tests in configure.ac and CMakeLists.txt so that if libcurl
is not found then the other options that depend upon it properly
are disabled.
1. I decided that xarray support should be enabled by default for pure
zarr. In order to allow disabling, I added a new mode flag "noxarray".
1. Certain test in nczarr_test depend on use of .dodsrc. In order for these
to work when testing in parallel, some inter-test dependencies needed to
be added.
1. Improved authorization testing to use changes in thredds.ucar.edu
2021-04-25 09:48:15 +08:00
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resetrc() {
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if test "x$RCHOME" = x1 ; then
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rm -f ${HOME}/.dodsrc ${HOME}/.daprc ${HOME}/.ncrc
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fi
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rm -f ${WD}/.dodsrc ${WD}/.daprc ${WD}/.ncrc
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unset NCRCENV_IGNORE
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unset NCRCENV_RC
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unset DAPRCFILE
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}
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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
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s3sdkdelete() {
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if test -f ${execdir}/s3util ; then
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${S3UTIL} ${PROFILE} -u "${NCZARR_S3_TEST_URL}" -k "$1" clear
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elif which aws ; then
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aws s3api delete-object --endpoint-url=https://${NCZARR_S3_TEST_HOST} --bucket=${NCZARR_S3_TEST_BUCKET} --key="/${S3ISOPATH}/$1"
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else
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echo "**** Could not delete ${NCZAR_S3_TEST_URL}"
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fi
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}
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s3sdkcleanup() {
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if test -f ${execdir}/s3util ; then
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${S3UTIL} ${PROFILE} -u "${NCZARR_S3_TEST_URL}" -k "$1" clear
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elif which aws ; then
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aws s3api delete-object --endpoint-url=https://${NCZARR_S3_TEST_HOST} --bucket=${NCZARR_S3_TEST_BUCKET} --key="/${S3ISOPATH}/$1"
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else
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echo "**** Could not delete ${NCZAR_S3_TEST_URL}"
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fi
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}
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# Create an isolation path for S3; build on the isolation directory
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s3isolate() {
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if test "x$S3ISOPATH" = x ; then
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if test "x$ISOPATH" = x ; then isolate "$1"; fi
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S3ISODIR="$ISODIR"
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S3ISOTESTSET="${S3TESTSUBTREE}/testset_"
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if test "x$NOISOPATH" = x ; then S3ISOTESTSET="${S3ISOTESTSET}${TESTUID}"; fi
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S3ISOPATH="${S3ISOTESTSET}/$S3ISODIR"
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fi
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2023-04-26 07:15:06 +08:00
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}
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2023-05-10 11:13:49 +08:00
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GDBB="gdb -batch -ex r -ex bt -ex q --args"
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|
|
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|
Upgrade the nczarr code to match Zarr V2
Re: https://github.com/zarr-developers/zarr-python/pull/716
The Zarr version 2 spec has been extended to include the ability
to choose the dimension separator in chunk name keys. The legal
separators has been extended from {'.'} to {'.' '/'}. So now it
is possible to use a key like "0/1/2/0" for chunk names.
This PR implements this for NCZarr. The V2 spec now says that
this separator can be set on a per-variable basis. For now, I
have chosen to allow this be set only globally by adding a key
named "ZARR.DIMENSION_SEPARATOR=<char>" in the
.daprc/.dodsrc/ncrc file. Currently, the only legal separator
characters are '.' (the default) and '/'. On writing, this key
will only be written if its value is different than the default.
This change caused problems because supporting a separator of '/'
is difficult to parse when keys/paths use '/' as the path separator.
A test case was added for this.
Additionally, make nczarr be enabled default by default. This required
some additional changes so that if zip and/or AWS S3 sdk are unavailable,
then they are disabled for NCZarr.
In addition the following unrelated changes were made.
1. Tested that pure-zarr mode could read an nczarr formatted store.
1. The .rc file handling now merges all known .rc files (.ncrc,.daprc, and .dodsrc) in that order and using those in HOME first, then in current directory. For duplicate entries, the later ones override the earlier ones. This change is to remove some of the conflicts inherent in the current .rc file load process. A set of test cases was also added.
1. Re-order tests in configure.ac and CMakeLists.txt so that if libcurl
is not found then the other options that depend upon it properly
are disabled.
1. I decided that xarray support should be enabled by default for pure
zarr. In order to allow disabling, I added a new mode flag "noxarray".
1. Certain test in nczarr_test depend on use of .dodsrc. In order for these
to work when testing in parallel, some inter-test dependencies needed to
be added.
1. Improved authorization testing to use changes in thredds.ucar.edu
2021-04-25 09:48:15 +08:00
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resetrc
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2023-04-26 07:15:06 +08:00
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|
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|
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|
fi #TEST_NCZARR_SH
|