netcdf-c/s3cleanup.in
Dennis Heimbigner df3636b959 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.
2023-09-26 16:56:48 -06:00

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#!/bin/sh
# Uncomment to get verbose output
#VERBOSE=1
#VERBOSE=2
if test "x$VERBOSE" = x1 ; then set -x; fi
# Constants passed in from configure.ac/CMakeLists
abs_top_srcdir='@abs_top_srcdir@'
abs_top_builddir='@abs_top_builddir@'
# The process id
puid='@PLATFORMUID@'
# Additional configuration information
. ${abs_top_builddir}/test_common.sh
# Sanity checks
# 1. This requires that the AWS CLI (command line interface) is installed.
if ! which aws ; then
echo ">>>> The s3cleanup script requires the \"aws\" command (i.e. the AWS command line interface program)"
echo ">>>> Try installing \"awscli\" package with apt or equivalent."
exit 0
fi
# 2. Make sure S3TESTSUBTREE is defined
if test "x$S3TESTSUBTREE" = x ; then
echo ">>>> The s3cleanup script requires that S3TESTSUBTREE is defined."
exit 1;
fi
test_cleanup() {
rm -f s3cleanup_${puid}.json
rm -f s3cleanup_${puid}.keys
rm -f ${abs_top_builddir}/s3cleanup_${puid}.uids
}
trap test_cleanup EXIT
rm -f s3cleanup_${puid}.json s3cleanup_${puid}.keys
# Get complete set of keys in ${S3TESTSUBTREE} prefix
unset ALLKEYS
if ! aws s3api list-objects-v2 --bucket ${S3TESTBUCKET} --prefix "${S3TESTSUBTREE}" | grep -F '"Key":' >s3cleanup_${puid}.keys ; then
echo "No keys found"
test_cleanup
exit 0
fi
if test "x$VERBOSE" = x1 ; then set +x; fi
while read -r line; do
KEY=`echo "$line" | sed -e 's|[^"]*"Key":[^"]*"\([^"]*\)".*|\1|'`
# Ignore keys that do not start with ${S3TESTSUBTREE}
PREFIX=`echo "$KEY" | sed -e 's|\([^/]*\)/.*|\1|'`
if test "x$PREFIX" = "x$S3TESTSUBTREE" ; then
ALLKEYS="$ALLKEYS $KEY"
fi
done < s3cleanup_${puid}.keys
if test "x$VERBOSE" = x1 ; then set -x; fi
# get the uid's for all the subtrees to be deleted
UIDS=`cat ${abs_top_builddir}/s3cleanup_${puid}.uids | tr -d '\r' | tr '\n' ' '`
# Capture the keys matching any uid
unset MATCHKEYS
if test "x$VERBOSE" = x1 ; then set +x; fi
for key in $ALLKEYS ; do
for uid in $UIDS ; do
case "$key" in
"$S3TESTSUBTREE/testset_${uid}"*)
# capture the key'
MATCHKEYS="$MATCHKEYS $key"
;;
*) if test "x$VERBOSE" = x1 ; then echo "Ignoring \"$key\""; fi ;;
esac
done
done
if test "x$VERBOSE" = x1 ; then set -x; fi
# We can delete at most 1000 objects at a time, so divide into sets of size 500
REM="$MATCHKEYS"
while test "x$REM" != x ; do
K500=`echo "$REM" | cut -d' ' -f 1-500`
REM=`echo "$REM" | cut -d' ' -f 501-`
unset DELLIST
MATCH=0
FIRST=1
DELLIST="{\"Objects\":["
if test "x$VERBOSE" = x1 ; then set +x; fi
for key in $K500 ; do
if test $FIRST = 0 ; then DELLIST="${DELLIST},"; fi
DELLIST="${DELLIST}
{\"Key\":\"$key\"}"
FIRST=0
MATCH=1
done
if test "x$VERBOSE" = x1 ; then set -x; fi
DELLIST="${DELLIST}],\"Quiet\":false}"
if test "x$MATCH" = x1 ;then
rm -f s3cleanup_${puid}.json
echo "$DELLIST" > s3cleanup_${puid}.json
aws s3api delete-objects --bucket ${S3TESTBUCKET} --delete "file://s3cleanup_${puid}.json"
fi
done
# Final cleanup
test_cleanup