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|
Description: removing references to unpackaged SDK in the code
Author: Pierre Gruet <pgt@debian.org>
Forwarded: not-needed
Last-Update: 2022-07-26
--- a/genomicsdb-tiledb/CMakeLists.txt
+++ b/genomicsdb-tiledb/CMakeLists.txt
@@ -125,15 +125,17 @@
#add_subdirectory(${AZURE_FSCLIENT_SOURCE_DIR})
#set(TILEDB_LIB_DEPENDENCIES ${TILEDB_LIB_DEPENDENCIES} azure-storage-lite)
+# Ignoring awssdk, we don't want to download it.
# Build AWS S3 client static libraries
-find_package(S3Client REQUIRED)
-include_directories(${AWSSDK_INCLUDE_DIR})
-set(TILEDB_LIB_DEPENDENCIES ${TILEDB_LIB_DEPENDENCIES} ${AWSSDK_LINK_LIBRARIES})
+#find_package(S3Client REQUIRED)
+#include_directories(${AWSSDK_INCLUDE_DIR})
+#set(TILEDB_LIB_DEPENDENCIES ${TILEDB_LIB_DEPENDENCIES} ${AWSSDK_LINK_LIBRARIES})
+# Ignoring GCS SDK, we don't want to download it.
# Build GCS Storage client static libraries
-find_package(GCSClient REQUIRED)
-include_directories(${GCSSDK_INCLUDE_DIR})
-set(TILEDB_LIB_DEPENDENCIES ${TILEDB_LIB_DEPENDENCIES} ${GCSSDK_LINK_LIBRARIES})
+#find_package(GCSClient REQUIRED)
+#include_directories(${GCSSDK_INCLUDE_DIR})
+#set(TILEDB_LIB_DEPENDENCIES ${TILEDB_LIB_DEPENDENCIES} ${GCSSDK_LINK_LIBRARIES})
# libaws-c-common.a needs dl libs
set(TILEDB_LIB_DEPENDENCIES ${TILEDB_LIB_DEPENDENCIES} ${CMAKE_DL_LIBS})
--- a/genomicsdb-tiledb/core/CMakeLists.txt
+++ b/genomicsdb-tiledb/core/CMakeLists.txt
@@ -33,6 +33,8 @@
# Gather the core source files
file(GLOB_RECURSE TILEDB_CORE_SOURCES "src/*.cc" "src/codec/external/bitshuffle/*.c")
+# Omitting source files related to unpackaged software.
+list(REMOVE_ITEM TILEDB_CORE_SOURCES "${CMAKE_CURRENT_SOURCE_DIR}/src/storage_manager/storage_azure_blob.cc" "${CMAKE_CURRENT_SOURCE_DIR}/src/storage_manager/storage_gcs.cc" "${CMAKE_CURRENT_SOURCE_DIR}/src/storage_manager/storage_hdfs.cc" "${CMAKE_CURRENT_SOURCE_DIR}/src/storage_manager/storage_s3.cc")
if(LZ4_FOUND)
Message(STATUS "Using LZ4 from ${LZ4_LIBRARIES}")
else()
@@ -43,8 +45,8 @@
add_library(TILEDB_CORE_OBJECTS OBJECT ${TILEDB_CORE_SOURCES})
set_property(TARGET TILEDB_CORE_OBJECTS PROPERTY POSITION_INDEPENDENT_CODE ON)
-add_dependencies(TILEDB_CORE_OBJECTS awssdk-ep)
-add_dependencies(TILEDB_CORE_OBJECTS gcssdk-ep)
+#add_dependencies(TILEDB_CORE_OBJECTS awssdk-ep)
+#add_dependencies(TILEDB_CORE_OBJECTS gcssdk-ep)
# Create static and shared libraries
if(USE_HDFS)
@@ -58,7 +60,8 @@
set_target_properties(tiledb_static PROPERTIES OUTPUT_NAME "tiledb")
set_target_properties(tiledb_shared PROPERTIES OUTPUT_NAME "tiledb")
-target_link_libraries(tiledb_static muparserx azure-storage-lite ${AWSSDK_LINK_LIBRARIES} ${GCSSDK_LINK_LIBRARIES})
+#target_link_libraries(tiledb_static muparserx azure-storage-lite ${AWSSDK_LINK_LIBRARIES} ${GCSSDK_LINK_LIBRARIES})
+target_link_libraries(tiledb_static muparserx)
target_link_libraries(tiledb_shared ${TILEDB_LIB_DEPENDENCIES})
# Install libraries
--- a/genomicsdb-tiledb/core/include/storage_manager/storage_manager_config.h
+++ b/genomicsdb-tiledb/core/include/storage_manager/storage_manager_config.h
@@ -41,8 +41,6 @@
#include "storage_fs.h"
#include "storage_posixfs.h"
-#include "storage_hdfs.h"
-#include "storage_gcs.h"
/* ********************************* */
/* CONSTANTS */
@@ -116,8 +114,7 @@
MPI_Comm* mpi_comm = NULL,
int read_method = TILEDB_IO_READ,
int write_methods = TILEDB_IO_WRITE,
- const bool enable_shared_posixfs_optimizations = false,
- const bool use_gcs_hdfs_connector = false);
+ const bool enable_shared_posixfs_optimizations = false);
#else
/**
* Initializes the configuration parameters.
@@ -144,8 +141,7 @@
const char* home,
int read_method = TILEDB_IO_READ,
int write_method = TILEDB_IO_WRITE,
- const bool enable_shared_posixfs_optimizations = false,
- const bool use_gcs_hdfs_connector = false);
+ const bool enable_shared_posixfs_optimizations = false);
#endif
/* ********************************* */
--- a/genomicsdb-tiledb/core/src/c_api/tiledb.cc
+++ b/genomicsdb-tiledb/core/src/c_api/tiledb.cc
@@ -115,8 +115,7 @@
#endif
tiledb_config->read_method_,
tiledb_config->write_method_,
- tiledb_config->enable_shared_posixfs_optimizations_,
- tiledb_config->use_gcs_hdfs_connector_) == TILEDB_SMC_ERR) {
+ tiledb_config->enable_shared_posixfs_optimizations_) == TILEDB_SMC_ERR) {
delete storage_manager_config;
free(*tiledb_ctx);
*tiledb_ctx = NULL;
--- a/genomicsdb-tiledb/core/src/storage_manager/storage_manager_config.cc
+++ b/genomicsdb-tiledb/core/src/storage_manager/storage_manager_config.cc
@@ -31,9 +31,7 @@
* This file implements the StorageManagerConfig class.
*/
-#include "storage_azure_blob.h"
-#include "storage_gcs.h"
-#include "storage_s3.h"
+//#include "storage_azure_blob.h"
#include "storage_manager_config.h"
#include "tiledb_constants.h"
#include "utils.h"
@@ -89,8 +87,7 @@
#endif
int read_method,
int write_method,
- const bool enable_shared_posixfs_optimizations,
- const bool use_gcs_hdfs_connector) {
+ const bool enable_shared_posixfs_optimizations) {
// Initialize home
if (home != NULL && strstr(home, "://")) {
if (fs_ != NULL) {
@@ -98,7 +95,8 @@
fs_ = NULL;
}
home_ = std::string(home, strlen(home));
- if (is_azure_blob_storage_path(home_)) {
+ // We are not supporting azure nor s3.
+ /*if (is_azure_blob_storage_path(home_)) {
try {
fs_ = new AzureBlob(home_);
} catch(std::system_error& ex) {
@@ -114,15 +112,7 @@
tiledb_smc_errmsg = "S3 Storage intialization failed for home=" + home_;
return TILEDB_SMC_ERR;
}
- } else if (is_gcs_path(home_) && !is_env_set("TILEDB_USE_GCS_HDFS_CONNECTOR") && !use_gcs_hdfs_connector) {
- try {
- fs_ = new GCS(home_);
- } catch(std::system_error& ex) {
- PRINT_ERROR(ex.what());
- tiledb_smc_errmsg = "GCS Storage intialization failed for home=" + home_;
- return TILEDB_SMC_ERR;
- }
- } else if (is_supported_cloud_path(home_)) {
+ } else */if (is_supported_cloud_path(home_)) {
try {
#ifdef USE_HDFS
fs_ = new HDFS(home_);
--- a/genomicsdb-tiledb/test/CMakeLists.txt
+++ b/genomicsdb-tiledb/test/CMakeLists.txt
@@ -35,6 +35,8 @@
# Get test source files
file(GLOB_RECURSE TILEDB_TEST_SOURCES "src/*/test*.cc")
+# Remove tests about unsupported software
+list(REMOVE_ITEM TILEDB_TEST_SOURCES "${CMAKE_CURRENT_SOURCE_DIR}/src/storage_manager/test_azure_blob_storage.cc" "${CMAKE_CURRENT_SOURCE_DIR}/src/storage_manager/test_gcs_storage.cc" "${CMAKE_CURRENT_SOURCE_DIR}/src/storage_manager/test_s3_storage.cc")
# Add TILEDB_TEST_DIR macro
add_definitions(-DTILEDB_TEST_DIR="${CMAKE_CURRENT_SOURCE_DIR}")
--- a/genomicsdb-tiledb/test/src/storage_manager/test_storage_buffer.cc
+++ b/genomicsdb-tiledb/test/src/storage_manager/test_storage_buffer.cc
@@ -32,11 +32,11 @@
#include "catch.h"
-#include "storage_azure_blob.h"
+//#include "storage_azure_blob.h"
#include "storage_buffer.h"
-#include "storage_gcs.h"
+//#include "storage_gcs.h"
#include "storage_posixfs.h"
-#include "storage_s3.h"
+//#include "storage_s3.h"
#include "utils.h"
TEST_CASE_METHOD(TempDir, "Test Storage Buffer Basic", "[basic]") {
@@ -184,16 +184,17 @@
// Buffered write
std::string filename = get_temp_dir()+"/buffered_file";
- if (is_gcs_path(filename)) {
+// We are not supporting gcs, azure nor s3 in the Debian packaging.
+/* if (is_gcs_path(filename)) {
fs = std::make_shared<GCS>(filename);
} else if (is_azure_blob_storage_path(filename)) {
fs = std::make_shared<AzureBlob>(filename);
} else if (is_s3_storage_path(filename)) {
fs = std::make_shared<S3>(filename);
- } else {
+ } else {*/
fs = std::make_shared<PosixFS>();
is_posix = true;
- }
+// }
auto write_chunk_size = fs->get_upload_buffer_size()?fs->get_upload_buffer_size():10240; // default chunk
auto read_chunk_size = fs->get_download_buffer_size()?fs->get_download_buffer_size():5120; // default chunk
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