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/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
#ifndef _h_helper_
#define _h_helper_
#ifdef __cplusplus
extern "C" {
#endif
#ifndef _h_vdb_copy_includes_
#include "vdb-copy-includes.h"
#endif
#ifndef _h_vdb_redactval_
#include "redactval.h"
#endif
#ifndef _h_config_values_
#include "config_values.h"
#endif
int64_t strtoi64( const char* str, char** endp, uint32_t base );
uint64_t strtou64( const char* str, char** endp, uint32_t base );
/*
* calls the given manager to create a new SRA-schema
* takes the list of user-supplied schema's (which can be empty)
* and let the created schema parse all of them
*/
rc_t helper_parse_schema( const VDBManager *my_manager,
VSchema **new_schema,
const KNamelist *schema_list );
/*
* tries to interpret the given string in path as a accession
* and returns the path of the found accession back in path
* if it is possible, if not the original value of path remains unchanged
* rc = 0 if the given path is a file-system-path or we are not
* (weakly) linked against the sra-path-library
rc_t helper_resolve_accession( const KDirectory *my_dir,
char ** path );
*/
/*
* calls VTableTypespec to discover the table-name out of the schema
* the given table has to be opened!
*/
rc_t helper_get_schema_tab_name( const VTable *my_table, char ** name ) ;
/*
* reads a string out of a vdb-table:
* needs a open cursor, a row-idx and the index of the column
* it opens the row, requests a pointer via VCursorCellData()
* malloc's the dst-pointer and copies the string into it
* a 0-termination get's attached
* finally it closes the row
*/
rc_t helper_read_vdb_string( const VCursor* src_cursor,
const uint64_t row_idx,
const uint32_t col_idx,
char ** dst );
/*
* reads a int64 out of a vdb-table:
* needs a open cursor, row-id already set, row opened
* it copies the data via memmove where to the dst-pointer
* points to / the size in the vdb-table can be smaller
*/
rc_t helper_read_vdb_int_row_open( const VCursor* src_cursor,
const uint32_t col_idx, uint64_t * dst );
/*
* reads a int64 out of a vdb-table:
* needs a open cursor, it opens the row,
* calls helper_read_vdb_int_row_open()
* finally it closes the row
*/
rc_t helper_read_vdb_int( const VCursor* src_cursor,
const uint64_t row_idx,
const uint32_t col_idx,
uint64_t * dst );
/*
* reads a string out of a KConfig-object:
* needs a cfg-object, and the full name of the key(node)
* it opens the node, discovers the size, malloc's the string,
* reads the string and closes the node
*/
rc_t helper_read_cfg_str( const KConfig *cfg,
const char * key,
char ** value );
/*
* reads a uint64 out of a KConfig-object:
* needs a cfg-object, and the full name of the key(node)
* it calls helper_read_cfg_str() to read the node as string
* and converts it via strtoll() into a uint64
*/
rc_t helper_read_cfg_int( const KConfig *cfg,
const char * key,
uint64_t * value );
/*
* tries to detect if the given name of a schema-table is
* a schema-legacy-table, it needs the vdb-manager to
* open a sra-schema and request this schema to list all
* legacy tables, then it searches in that list for the
* given table-name
*/
rc_t helper_is_tablename_legacy( const VDBManager *my_manager,
const char * tabname, bool * flag );
/*
* this function tries to read 3 strings out of cfg-nodes
* (1) the name of the schema-file to be used to copy to
* (2) the name of the table to be used inside the schema
* (3) a list of columns that should not be copied
* if (3) cannot be found it is not a error
* it needs as input the cfg-object, the name of the
* (src)legacy-platform and the name of the
* (src)schema-table
*/
rc_t helper_get_legacy_write_schema_from_config( KConfig *cfg,
const char * platform,
const char * src_schema,
char ** legacy_schema_file, char ** legacy_schema_tab,
char ** legacy_dont_copy );
/*
* this function creates a config-manager, by passing in
* a KDirectory-object representing the given path
* this will include the the given path into the search
* for *.kfg - files
*/
rc_t helper_make_config_mgr( KConfig **config_mgr, const char * path );
/*
* this function tries to read the lossynes-score of a vdb-type
* out of a config-object
* it constructs a node-name-string like this:
* "/VDBCOPY/SCORE/INSDC/2na/bin"
* INSDC/2na/bin is the name of the type with ":" replaced by "/"
* it reads the value by calling helper_read_cfg_str()
*/
uint32_t helper_rd_type_score( const KConfig *cfg,
const char *type_name );
/*
* this function tries to remove the given path
*/
rc_t helper_remove_path( KDirectory * directory, const char * path );
/*
* looks into the path for chars like '/', '\\' or '.'
* to detect that it is rather a path and not and accession
*/
bool helper_is_this_a_filesystem_path( const char * path );
/*
* reads global config-values, from the config-manager
*/
void helper_read_redact_values( KConfig * config_mgr,
redact_vals * rvals );
/*
* reads global config-values, if not found via config-manager
* use the defines from definition.h
*/
void helper_read_config_values( KConfig * config_mgr,
p_config_values config );
/*
* detects if the given table uses md5-checksum's
*/
bool helper_detect_src_md5( const VTable * src_tab );
KCreateMode helper_assemble_CreateMode( const VTable * src_tab,
bool force_init, uint8_t md5_mode );
KChecksum helper_assemble_ChecksumMode( uint8_t ctx_blob_checksum );
#ifdef __cplusplus
}
#endif
#endif
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