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Merge branch 'dev' into smr/sc-52877/serialization-update-load-schema
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KiterLuc authored Aug 15, 2024
2 parents 1829491 + 5b92634 commit 279b18f
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2 changes: 2 additions & 0 deletions .github/workflows/build-windows.yml
Original file line number Diff line number Diff line change
Expand Up @@ -136,6 +136,8 @@ jobs:
uses: seanmiddleditch/gha-setup-ninja@v4
- name: Prevent vcpkg from building debug variants
run: python $env:GITHUB_WORKSPACE/scripts/ci/patch_vcpkg_triplets.py
- name: Install dependencies from pip
run: python -m pip install pybind11[global]

- name: Configure TileDB
shell: pwsh
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64 changes: 64 additions & 0 deletions HISTORY.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,67 @@
# TileDB v2.25.0 Release Notes

## Announcements

* TileDB 2.25, includes the new current domain feature which allows to specify an area of the domain that is considered to be active for sparse arrays.

## Deprecation announcements

* The HDFS backend is no longer officially tested by TileDB. As announced before, it is scheduled to be removed in version 2.28, to be released in Q4 2024. [#5085](https://github.com/TileDB-Inc/TileDB/pull/5085)
* Support for reading sparse fragments in dense arrays will be removed in version 2.27. Writting sparse fragments in dense arrays was removed in version 2.5. [#5116](https://github.com/TileDB-Inc/TileDB/pull/5116)
* Support for returning the same results multiple times in sparse reads when ranges overlap will be removed in version 2.27. This was possible by setting `sm.merge_overlapping_ranges_experimental` to `false`, but the default `true` behavior has been there since version 2.17.

## New features

* REST support for current domain. [#5136](https://github.com/TileDB-Inc/TileDB/pull/5136)
* Disallow writing outside of the current domain. [#5165](https://github.com/TileDB-Inc/TileDB/pull/5165)
* Current domain: disallow reading outside of current domain. [#5168](https://github.com/TileDB-Inc/TileDB/pull/5168)

## Improvements

* Improve memory consumption for tile structures in dense reader. [#5046](https://github.com/TileDB-Inc/TileDB/pull/5046)

## Defects removed

* Fail early when trying to add members with relative URIs in remote groups. [#5025](https://github.com/TileDB-Inc/TileDB/pull/5025)
* Correct defective return value in `Posix::ls_with_sizes`. [#5037](https://github.com/TileDB-Inc/TileDB/pull/5037)
* Prevent constructing attribute with invalid cell_val_num. [#4952](https://github.com/TileDB-Inc/TileDB/pull/4952)
* Do not mask failures when listing a directory fails on POSIX. [#5043](https://github.com/TileDB-Inc/TileDB/pull/5043)
* Fix write queries using `sm.var_offsets.extra_element=true`. [#5033](https://github.com/TileDB-Inc/TileDB/pull/5033)
* Fix segfaults in WebP queries ran in parallel. [#5065](https://github.com/TileDB-Inc/TileDB/pull/5065)
* Fix exceptions with message: ```unknown exception type; no further information```. [#5080](https://github.com/TileDB-Inc/TileDB/pull/5080)
* Fix check for out of bounds dimension in Dimension::dimension_ptr. [#5094](https://github.com/TileDB-Inc/TileDB/pull/5094)
* Fix array latest schema selection for same MS timestamps schemas. [#5143](https://github.com/TileDB-Inc/TileDB/pull/5143)
* Fix serialization issue with schema evolution for query v3. [#5154](https://github.com/TileDB-Inc/TileDB/pull/5154)

## Configuration changes

* Add `vfs.s3.storage_class` config option to set the storage class of newly uploaded S3 objects. [#5053](https://github.com/TileDB-Inc/TileDB/pull/5053)
* Add `rest.custom_headers.*` config option to set custom headers on REST requests. [#5104](https://github.com/TileDB-Inc/TileDB/pull/5104)
* Add `rest.payer_namespace` config option to set the namespace to be charged for REST requests. [#5105](https://github.com/TileDB-Inc/TileDB/pull/5105)

## API changes

### C API

* Add CurrentDomain API support. [#5041](https://github.com/TileDB-Inc/TileDB/pull/5041)

### C++ API

* Current Domain CPP API implementation. [#5056](https://github.com/TileDB-Inc/TileDB/pull/5056)

## Build System Changes

* Backwards compatibility with older CMake versions for libfaketime. [#5049](https://github.com/TileDB-Inc/TileDB/pull/5049)
* Automatic downloading of vcpkg can be disabled by enabling the `TILEDB_DISABLE_AUTO_VCPKG` CMake option, in addition to setting the environment variable with trhe same name. [#5048](https://github.com/TileDB-Inc/TileDB/pull/5048)
* Improve embedding of `magic.mgc` and allow compiling with any libmagic version. [#4989](https://github.com/TileDB-Inc/TileDB/pull/4989)

## Internal Improvements

* Implement actualize function that orders data underlying `alt_var_length_view` [#5087](https://github.com/TileDB-Inc/TileDB/pull/5087)
* Implement a partitioning function to partition cells to fit into fixed size bins [#5092](https://github.com/TileDB-Inc/TileDB/pull/5092)
* Implementation of a `chunk_view` class to provide a subset of C++23 chunk_view, suitable for supporting external sort. [#5035](https://github.com/TileDB-Inc/TileDB/pull/5035)
* Tests that the chunks in a `chunk_view` can be separately sorted. [#5052](https://github.com/TileDB-Inc/TileDB/pull/5052)

# TileDB v2.24.2 Release Notes

## Defects removed
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2 changes: 1 addition & 1 deletion cmake/Options/TileDBToolchain.cmake
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ if (NOT DEFINED CMAKE_TOOLCHAIN_FILE)
# Inspired from https://github.com/Azure/azure-sdk-for-cpp/blob/azure-core_1.10.3/cmake-modules/AzureVcpkg.cmake
message("TILEDB_DISABLE_AUTO_VCPKG is not defined. Fetch a local copy of vcpkg.")
# To help with resolving conflicts, when you update the commit, also update its date.
set(VCPKG_COMMIT_STRING 72010900b7cee36cea77aebb97695095c9358eaf) # 2023-12-05
set(VCPKG_COMMIT_STRING 7aeffc91033ad35cc4e2c152f213a866ec6c11ac) # 2024-07-13
message("Vcpkg commit string used: ${VCPKG_COMMIT_STRING}")
include(FetchContent)
FetchContent_Declare(
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16 changes: 8 additions & 8 deletions ports/README.md
Original file line number Diff line number Diff line change
Expand Up @@ -26,13 +26,13 @@ $ git commit

After copying the port, add an entry to the table below. You should also contribute your changes to vcpkg and/or the upstream package repository.

For ease of review when patching existing ports, you are recommended to make one commit that copies the upstream port unchanged, and another commit that makes the changes you need.

## List of port overlays

| Port | Reason |
|----------------------------|---------------------------------------------------------------------------------------------------------|
| `libmagic` | Updating to the upstream port deferred due to failures. |
| `pcre2` | To be removed alongside libmagic. |
| `azure-storage-common-cpp` | Patching to disable default features on libxml2 (https://github.com/Azure/azure-sdk-for-cpp/pull/5221). |
| `libfaketime` | Port does not yet exist upstream |
| `vcpkg-cmake-config` | Patching to fix build issues with CMake 3.29.1. (https://github.com/microsoft/vcpkg/pull/38017) |
| `google-cloud-cpp` | Patching to remove dependency on GMock. (https://github.com/microsoft/vcpkg/pull/39802) |
| Port | Reason |
|---------------|----------------------------------------------------------------------------------------------------------------------------|
| `aws-c-io` | Patching to fix MinGW build failures. (https://github.com/awslabs/aws-c-io/pull/664) |
| `aws-sdk-cpp` | Patching to fix MinGW build failures, and to avoid building test-only SDKs (https://github.com/aws/aws-sdk-cpp/pull/3061). |
| `libmagic` | Updating to the upstream port deferred due to failures. |
| `libfaketime` | Port does not yet exist upstream |
22 changes: 22 additions & 0 deletions ports/aws-c-io/fix-pointer-mismatch.patch
Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
diff --git a/source/windows/secure_channel_tls_handler.c b/source/windows/secure_channel_tls_handler.c
index b62b1a0..48f4556 100644
--- a/source/windows/secure_channel_tls_handler.c
+++ b/source/windows/secure_channel_tls_handler.c
@@ -53,7 +53,7 @@ struct secure_channel_ctx {
struct aws_tls_ctx ctx;
struct aws_string *alpn_list;
SCHANNEL_CRED credentials;
- PCERT_CONTEXT pcerts;
+ PCCERT_CONTEXT pcerts;
HCERTSTORE cert_store;
HCERTSTORE custom_trust_store;
HCRYPTPROV crypto_provider;
@@ -188,7 +188,7 @@ static int s_manually_verify_peer_cert(struct aws_channel_handler *handler) {
int result = AWS_OP_ERR;
CERT_CONTEXT *peer_certificate = NULL;
HCERTCHAINENGINE engine = NULL;
- CERT_CHAIN_CONTEXT *cert_chain_ctx = NULL;
+ PCCERT_CHAIN_CONTEXT cert_chain_ctx = NULL;

/* get the peer's certificate so we can validate it.*/
SECURITY_STATUS status =
34 changes: 34 additions & 0 deletions ports/aws-c-io/portfile.cmake
Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
vcpkg_from_github(
OUT_SOURCE_PATH SOURCE_PATH
REPO awslabs/aws-c-io
REF "v${VERSION}"
SHA512 b5dc81635ce775c3783df2d4f6ccf0890b1e1669bddb1c10f6d200203684e84504ca87099cb88874010df28f98f658da5a4eacb9e4df0408d40d845f3d394f48
HEAD_REF master
PATCHES
"fix-pointer-mismatch.patch"
)

vcpkg_cmake_configure(
SOURCE_PATH "${SOURCE_PATH}"
OPTIONS
"-DCMAKE_MODULE_PATH=${CURRENT_INSTALLED_DIR}/share/aws-c-common" # use extra cmake files
-DBUILD_TESTING=FALSE
)

vcpkg_cmake_install()

string(REPLACE "dynamic" "shared" subdir "${VCPKG_LIBRARY_LINKAGE}")
vcpkg_cmake_config_fixup(CONFIG_PATH "lib/${PORT}/cmake/${subdir}" DO_NOT_DELETE_PARENT_CONFIG_PATH)
vcpkg_cmake_config_fixup(CONFIG_PATH "lib/${PORT}/cmake")
vcpkg_replace_string("${CURRENT_PACKAGES_DIR}/share/${PORT}/${PORT}-config.cmake" [[/${type}/]] "/")

file(REMOVE_RECURSE
"${CURRENT_PACKAGES_DIR}/debug/include"
"${CURRENT_PACKAGES_DIR}/debug/lib/${PORT}"
"${CURRENT_PACKAGES_DIR}/debug/share"
"${CURRENT_PACKAGES_DIR}/lib/${PORT}"
)

vcpkg_copy_pdbs()

vcpkg_install_copyright(FILE_LIST "${SOURCE_PATH}/LICENSE")
24 changes: 24 additions & 0 deletions ports/aws-c-io/vcpkg.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
{
"name": "aws-c-io",
"version": "0.14.9",
"description": "Handles all IO and TLS work for application protocols.",
"homepage": "https://github.com/awslabs/aws-c-io",
"license": "Apache-2.0",
"supports": "!(windows & arm) & !uwp",
"dependencies": [
"aws-c-cal",
"aws-c-common",
{
"name": "s2n",
"platform": "!uwp & !windows"
},
{
"name": "vcpkg-cmake",
"host": true
},
{
"name": "vcpkg-cmake-config",
"host": true
}
]
}
14 changes: 14 additions & 0 deletions ports/aws-sdk-cpp/find-dependency.patch
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
diff --git a/toolchains/core-config.cmake b/toolchains/core-config.cmake
index d90bfaf747..ab14402577 100644
--- a/toolchains/core-config.cmake
+++ b/toolchains/core-config.cmake
@@ -15,5 +15,9 @@ if (AWSSDK_CRYPTO_IN_SOURCE_BUILD)
find_dependency(crypto)
find_dependency(ssl)
endif()
+find_dependency(ZLIB)
+if("@ENABLE_CURL_CLIENT@")
+ find_dependency(CURL)
+endif()
set(BUILD_SHARED_LIBS ${BUILD_SHARED_LIBS_PREV})
include("${CMAKE_CURRENT_LIST_DIR}/@[email protected]")
22 changes: 22 additions & 0 deletions ports/aws-sdk-cpp/fix-aws-root.patch
Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
diff --git a/cmake/AWSSDKConfig.cmake b/cmake/AWSSDKConfig.cmake
--- a/cmake/AWSSDKConfig.cmake (revision 2f90f9fd6c56460bd382243aa215fcddcb5883c8)
+++ b/cmake/AWSSDKConfig.cmake (date 1636913220527)
@@ -54,18 +54,14 @@
string(REPLACE ";" "${AWS_MODULE_DIR};" SYSTEM_MODULE_PATH "${CMAKE_SYSTEM_PREFIX_PATH}${AWS_MODULE_DIR}")
list(APPEND CMAKE_MODULE_PATH ${AWS_MODULE_PATH} ${SYSTEM_MODULE_PATH})

-# On Windows, dlls are treated as runtime target and installed in bindir
if (WIN32 AND AWSSDK_INSTALL_AS_SHARED_LIBS)
- set(AWSSDK_INSTALL_LIBDIR "${AWSSDK_INSTALL_BINDIR}")
# If installed CMake scripts are associated with dll library, define USE_IMPORT_EXPORT for customers
add_definitions(-DUSE_IMPORT_EXPORT)
endif()


# Compute the default installation root relative to this file.
-# from prefix/lib/cmake/AWSSDK/xx.cmake to prefix
get_filename_component(AWSSDK_DEFAULT_ROOT_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
-get_filename_component(AWSSDK_DEFAULT_ROOT_DIR "${AWSSDK_DEFAULT_ROOT_DIR}" PATH)
get_filename_component(AWSSDK_DEFAULT_ROOT_DIR "${AWSSDK_DEFAULT_ROOT_DIR}" PATH)
get_filename_component(AWSSDK_DEFAULT_ROOT_DIR "${AWSSDK_DEFAULT_ROOT_DIR}" PATH)
get_filename_component(AWS_NATIVE_SDK_ROOT "${CMAKE_CURRENT_SOURCE_DIR}" ABSOLUTE)
14 changes: 14 additions & 0 deletions ports/aws-sdk-cpp/fix-winsock-headers.patch
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
diff --git a/src/aws-cpp-sdk-core/source/http/windows/WinHttpSyncHttpClient.cpp b/src/aws-cpp-sdk-core/source/http/windows/WinHttpSyncHttpClient.cpp
index b8ab519..7cd91e9 100644
--- a/src/aws-cpp-sdk-core/source/http/windows/WinHttpSyncHttpClient.cpp
+++ b/src/aws-cpp-sdk-core/source/http/windows/WinHttpSyncHttpClient.cpp
@@ -19,6 +19,9 @@

#include <Windows.h>
#include <winhttp.h>
+#ifdef __MINGW32__
+#include <WinSock2.h>
+#endif
#include <mstcpip.h> // for tcp_keepalive
#include <sstream>
#include <iostream>
31 changes: 31 additions & 0 deletions ports/aws-sdk-cpp/fix_find_curl.patch
Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
diff --git a/cmake/external_dependencies.cmake b/cmake/external_dependencies.cmake
index acf16c0..3a49fb4 100644
--- a/cmake/external_dependencies.cmake
+++ b/cmake/external_dependencies.cmake
@@ -80,23 +80,12 @@ if(NOT NO_HTTP_CLIENT AND NOT USE_CRT_HTTP_CLIENT)
set(BUILD_CURL 1)
message(STATUS " Building Curl as part of AWS SDK")
else()
- include(FindCURL)
+ find_package(CURL REQUIRED)
if(NOT CURL_FOUND)
message(FATAL_ERROR "Could not find curl")
+ else()
+ set(CURL_LIBRARIES CURL::libcurl)
endif()
-
- # When built from source using cmake, curl does not include
- # CURL_INCLUDE_DIRS or CURL_INCLUDE_DIRS so we need to use
- # find_package to fix it
- if ("${CURL_INCLUDE_DIRS}" STREQUAL "" AND "${CURL_LIBRARIES}" STREQUAL "")
- message(STATUS "Could not find curl include or library path, falling back to find with config.")
- find_package(CURL)
- set(CURL_LIBRARIES CURL::libcurl)
- else ()
- message(STATUS " Curl include directory: ${CURL_INCLUDE_DIRS}")
- List(APPEND EXTERNAL_DEPS_INCLUDE_DIRS ${CURL_INCLUDE_DIRS})
- set(CLIENT_LIBS ${CURL_LIBRARIES})
- endif ()
set(CLIENT_LIBS_ABSTRACT_NAME curl)
message(STATUS " Curl target link: ${CURL_LIBRARIES}")
endif()
73 changes: 73 additions & 0 deletions ports/aws-sdk-cpp/generateFeatures.ps1
Original file line number Diff line number Diff line change
@@ -0,0 +1,73 @@
[CmdletBinding()]
param(
[Parameter(Mandatory=$true)][string]$SourcesRef,
[Parameter(Mandatory=$false)][string]$PortDirectory = $PSScriptRoot,
[Parameter(Mandatory=$false)][string]$vcpkg = "$PSScriptRoot/../../vcpkg"
)

$ErrorActionPreference = "Stop"

$ManifestIn = "$PortDirectory/vcpkg.in.json"
$ManifestOut = "$PortDirectory/vcpkg.json"

$ExtractedSources = "${env:TEMP}/aws-sdk-cpp-generateFeatures-$SourcesRef"
if (-not (Test-Path $ExtractedSources)) {
if (Test-Path "$ExtractedSources.tmp") {
Remove-Item -Force "$ExtractedSources.tmp"
}
git clone --depth=1 "https://github.com/aws/aws-sdk-cpp" "$ExtractedSources.tmp" | Out-Host
git -c "$ExtractedSources.tmp" checkout $SourcesRef
Move-Item "$ExtractedSources.tmp" "$ExtractedSources"
}
Write-Host "Using sources directory: $ExtractedSources"


$subfolders = Get-ChildItem -Path "$ExtractedSources\generated\src\aws-cpp-sdk-*", "$ExtractedSources\src\aws-cpp-sdk*" | Sort-Object -Property Name

$manifest = Get-Content $ManifestIn | ConvertFrom-Json
$manifest | Add-Member `
-NotePropertyName '$note' `
-NotePropertyValue 'Automatically generated by generateFeatures.ps1'
$manifest | Add-Member -NotePropertyName 'features' -NotePropertyValue @{}

function GetDescription($dir, $modulename)
{
if (Test-Path "$dir\CMakeLists.txt")
{
$descs = @(Select-String -Path "$dir\CMakeLists.txt" -Pattern "`"C\+\+ SDK for the AWS [^`"]*`"")
if ($descs.count -eq 1) {
$desc = $descs[0].Matches.Value -replace "`"",""
"$desc"
}
else { "C++ SDK for the AWS $modulename service" }
}
else { "C++ SDK for the AWS $modulename service" }
}

$featureDependencies = @{}
Select-String -Path "$ExtractedSources\cmake\sdksCommon.cmake" -Pattern "list\(APPEND SDK_DEPENDENCY_LIST `"([\w-]+):([\w-,]+)`"\)" -AllMatches `
| ForEach-Object { $_.Matches } `
| ForEach-Object { $featureDependencies[$_.Groups[1].Value] = @($_.Groups[2].Value -split "," `
| Where-Object { $_ -ne "core" }) }

foreach ($subfolder in $subfolders)
{
$modulename = $subfolder.name -replace "^aws-cpp-sdk-",""
if ($modulename -match "-tests`$") { continue }
if ($modulename -match "-sample`$") { continue }
if ($modulename -eq "core") { continue }

$lowermodulename = $modulename.ToLower()

$featureObj = @{ description = (GetDescription $subfolder $modulename) }

if ($featureDependencies.ContainsKey($lowermodulename)) {
$featureObj.dependencies = ,@{ name = "aws-sdk-cpp"; "default-features" = $false; "features" = $featureDependencies[$lowermodulename] }
}

$manifest.features.Add("$lowermodulename", $featureObj)
}

[IO.File]::WriteAllText($ManifestOut, (ConvertTo-Json -Depth 10 -InputObject $manifest))

& $vcpkg format-manifest --feature-flags=-manifests $ManifestOut
20 changes: 20 additions & 0 deletions ports/aws-sdk-cpp/lock-curl-http-and-tls-settings.patch
Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
diff --git a/src/aws-cpp-sdk-core/CMakeLists.txt b/src/aws-cpp-sdk-core/CMakeLists.txt
index c44546b0e..b66888362 100644
--- a/src/aws-cpp-sdk-core/CMakeLists.txt
+++ b/src/aws-cpp-sdk-core/CMakeLists.txt
@@ -113,13 +113,8 @@ if(ENABLE_CURL_CLIENT)
int main() {
CURL* handle = curl_easy_init();
return curl_easy_setopt(handle, CURLOPT_PROXY_SSLCERT, \"client.pem\"); }")
- if (CMAKE_CROSSCOMPILING)
- check_c_source_compiles("${CHECK_CURL_HAS_H2}" CURL_HAS_H2)
- check_c_source_compiles("${CHECK_CURL_HAS_TLS_PROXY}" CURL_HAS_TLS_PROXY)
- else()
- check_c_source_runs("${CHECK_CURL_HAS_H2}" CURL_HAS_H2)
- check_c_source_runs("${CHECK_CURL_HAS_TLS_PROXY}" CURL_HAS_TLS_PROXY)
- endif()
+ set(CURL_HAS_H2 OFF)
+ set(CURL_HAS_TLS_PROXY ON)
elseif(ENABLE_WINDOWS_CLIENT)
# NOTE: HTTP/2 is not supported when using IXML_HTTP_REQUEST_2
if(USE_IXML_HTTP_REQUEST_2)
25 changes: 25 additions & 0 deletions ports/aws-sdk-cpp/no-test-deps.patch
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
diff --git a/cmake/sdks.cmake b/cmake/sdks.cmake
index 75283cdd1b6..71d383e3323 100644
--- a/cmake/sdks.cmake
+++ b/cmake/sdks.cmake
@@ -34,12 +34,14 @@ if(BUILD_ONLY)
endforeach()
endif()

- get_dependencies_for_test(${TARGET} DEPENDENCY_LIST)
- if(DEPENDENCY_LIST)
- STRING(REPLACE "," ";" LIST_RESULT ${DEPENDENCY_LIST})
- foreach(DEPENDENCY IN LISTS LIST_RESULT)
- list(APPEND SDK_DEPENDENCY_BUILD_LIST ${DEPENDENCY})
- endforeach()
+ if(ENABLE_TESTING)
+ get_dependencies_for_test(${TARGET} DEPENDENCY_LIST)
+ if(DEPENDENCY_LIST)
+ STRING(REPLACE "," ";" LIST_RESULT ${DEPENDENCY_LIST})
+ foreach(DEPENDENCY IN LISTS LIST_RESULT)
+ list(APPEND SDK_DEPENDENCY_BUILD_LIST ${DEPENDENCY})
+ endforeach()
+ endif()
endif()
endforeach()
LIST(REMOVE_DUPLICATES SDK_BUILD_LIST)
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