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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.
*
* ===========================================================================
*
*/
#include "vdb-copy-includes.h"
#include "matcher_input.h"
#include "helper.h"
#include <sysalloc.h>
#include <stdlib.h>
/* internal definition of a type to be matched */
typedef struct mtype
{
char *name;
uint32_t dflt; /* 0=yes, 1=no (this way for re-ordering) */
uint32_t order;
uint32_t lossy_score;
VTypedecl type_decl;
VTypedesc type_desc;
} mtype;
typedef mtype* p_mtype;
/* internal definition of a pair of source- and dest-type */
typedef struct mpair
{
p_mtype src;
p_mtype dst;
uint32_t compatible; /* 0=yes, 1=no (this way for re-ordering) */
uint32_t distance;
} mpair;
typedef mpair* p_mpair;
/* internal definition of a column */
typedef struct mcol
{
char *name;
uint32_t src_idx; /* index of this column relative to the
read-cursor */
uint32_t dst_idx; /* index of this column relative to the
write-cursor */
bool excluded; /* for excludes via config-file */
bool to_copy; /* this column has a correspondig column
in the list of writable columns of the
destination-schema with writable types */
VTypedecl type_decl; /* type-decl of this column via read-schema */
VTypedesc type_desc; /* type-desc of this column via read-schema */
Vector src_types; /* list of src-types */
Vector dst_types; /* list of dst-types */
Vector pairs; /* list of (src->dst)-pairs... */
/* the src->dst type-pair, that won the type-matching-procedure */
p_mpair type_cast;
} mcol;
typedef mcol* p_mcol;
/* internal definition of the matcher */
typedef struct matcher
{
Vector mcols;
} matcher;
typedef matcher* p_matcher;
/* allocate a type-pair */
static p_mpair matcher_init_pair( const p_mtype src,
const p_mtype dst )
{
p_mpair res = NULL;
if ( src == NULL ) return res;
if ( dst == NULL ) return res;
res = calloc( 1, sizeof( mpair ) );
if ( res != NULL )
{
res->src = src;
res->dst = dst;
}
return res;
}
/* destroys a type-pair */
static void CC matcher_destroy_pair( void* node, void* data )
{
p_mpair pair = (p_mpair)node;
if ( pair != NULL )
free( pair );
}
/* allocate a m-type definition */
static p_mtype matcher_init_type( const char* name,
const bool dflt,
const uint32_t order )
{
p_mtype res = NULL;
if ( name == NULL ) return res;
if ( name[0] == 0 ) return res;
res = calloc( 1, sizeof( mtype ) );
if ( res != NULL )
{
res->name = string_dup_measure ( name, NULL );
res->dflt = ( dflt ? 0 : 1 );
res->order = order;
}
return res;
}
/* destroys a m-type definition */
static void CC matcher_destroy_type( void* node, void* data )
{
p_mtype type = (p_mtype)node;
if ( type != NULL )
{
if ( type->name != NULL )
free( type->name );
free( type );
}
}
/* allocate a matcher-column */
static p_mcol matcher_make_col( const char* name )
{
p_mcol res = NULL;
if ( name == NULL ) return res;
if ( name[0] == 0 ) return res;
res = calloc( 1, sizeof( mcol ) );
/* because of calloc all members are zero! */
if ( res != NULL )
{
res->name = string_dup_measure ( name, NULL );
VectorInit( &(res->src_types), 0, 3 );
VectorInit( &(res->dst_types), 0, 3 );
VectorInit( &(res->pairs), 0, 6 );
res->type_cast = NULL;
}
return res;
}
/* destroys a matcher-column */
static void CC matcher_destroy_col( void* node, void* data )
{
p_mcol col = (p_mcol)node;
if ( col == NULL ) return;
if ( col->name != NULL )
free( col->name );
VectorWhack( &(col->src_types), matcher_destroy_type, NULL );
VectorWhack( &(col->dst_types), matcher_destroy_type, NULL );
VectorWhack( &(col->pairs), matcher_destroy_pair, NULL );
free( col );
}
/* initializes the matcher */
rc_t matcher_init( matcher** self )
{
if ( self == NULL )
return RC( rcVDB, rcNoTarg, rcConstructing, rcSelf, rcNull );
(*self) = calloc( 1, sizeof( matcher ) );
if ( *self == NULL )
return RC( rcVDB, rcNoTarg, rcConstructing, rcMemory, rcExhausted );
VectorInit( &((*self)->mcols), 0, 5 );
return 0;
}
/* destroys the matcher */
rc_t matcher_destroy( matcher* self )
{
if ( self == NULL )
return RC( rcVDB, rcNoTarg, rcDestroying, rcSelf, rcNull );
VectorWhack( &(self->mcols), matcher_destroy_col, NULL );
free( self );
return 0;
}
static p_mcol matcher_find_col( const matcher* self, const char *name )
{
p_mcol res = NULL;
uint32_t idx, count;
count = VectorLength( &(self->mcols) );
for ( idx = 0; idx < count && res == NULL; ++idx )
{
p_mcol col = (p_mcol) VectorGet ( &(self->mcols), idx );
if ( col != NULL )
if ( nlt_strcmp( col->name, name ) == 0 )
res = col;
}
return res;
}
static char * matcher_get_col_cast( const p_mcol col, const char *s_type )
{
char * res;
size_t idx;
uint32_t len = string_measure ( col->name, NULL ) + 4;
len += string_measure ( s_type, NULL );
res = malloc( len );
if ( res == NULL ) return res;
res[ 0 ] = '(';
idx = string_copy_measure ( &(res[ 1 ]), len-1, s_type );
res[ idx + 1 ] = ')';
string_copy_measure ( &(res[ idx + 2 ]), len-(idx+2), col->name );
return res;
}
/* makes a typecast-string for the src/dest-table by column-name */
static rc_t matcher_get_cast( const matcher* self, const char *name,
const bool src, char **cast )
{
p_mcol col;
if ( self == NULL )
return RC( rcVDB, rcNoTarg, rcSearching, rcSelf, rcNull );
if ( cast == NULL || name == NULL )
return RC( rcVDB, rcNoTarg, rcSearching, rcParam, rcNull );
*cast = NULL;
col = matcher_find_col( self, name );
if ( col == NULL ) return 0;
if ( col->type_cast == NULL )
{
/* if the column has no match, just use the undecorated column-name*/
if ( src )
*cast = string_dup_measure ( col->name, NULL );
else
{
if ( col->to_copy && !col->excluded )
*cast = string_dup_measure ( col->name, NULL );
}
}
else
{
/* if the column has a match, construct the type-cast*/
if ( src )
*cast = matcher_get_col_cast( col, col->type_cast->src->name );
else
{
if ( col->to_copy && !col->excluded )
*cast = matcher_get_col_cast( col, col->type_cast->dst->name );
}
}
return 0;
}
/* makes a typecast-string for the source-table by column-name */
rc_t matcher_src_cast( const matcher* self, const char *name, char **cast )
{
return matcher_get_cast( self, name, true, cast );
}
/* makes a typecast-string for the destination-table by column-name */
rc_t matcher_dst_cast( const matcher* self, const char *name, char **cast )
{
return matcher_get_cast( self, name, false, cast );
}
static bool match_type_with_id_vector( const VSchema * s,
const VTypedecl * td, const Vector * id_vector )
{
bool res = false;
uint32_t idx, len;
len = VectorLength( id_vector );
for ( idx = 0; idx < len && !res; ++idx )
{
uint32_t *id = (uint32_t *) VectorGet ( id_vector, idx );
if ( id != NULL )
{
VTypedecl cast;
uint32_t distance;
res = VTypedeclToType ( td, s, *id, &cast, &distance );
}
}
return res;
}
/* checks if a column with the given name has at least one type
that is also in the given typelist... */
bool matcher_src_has_type( const matcher* self, const VSchema * s,
const char *name, const Vector *id_vector )
{
bool res = false;
p_mcol col;
VTypedecl td;
if ( self == NULL || s == NULL || name == NULL || id_vector == NULL )
return res;
col = matcher_find_col( self, name );
if ( col == NULL ) return res; /* column not found */
if ( col->type_cast == NULL ) return res; /* column has no typecast */
/* we use the destination-type-cast */
if ( VSchemaResolveTypedecl ( s, &td, "%s", col->type_cast->dst->name ) == 0 )
res = match_type_with_id_vector( s, &td, id_vector );
/*
if ( res )
KOutMsg( "redact-type found on (%s)%s\n", col->type_cast->dst->name, name );
*/
return res;
}
static void matcher_report_types( const char * s, const Vector *v )
{
uint32_t idx, len;
len = VectorLength( v );
if ( len > 0 )
{
KOutMsg( "%s: ", s );
for ( idx = 0; idx < len; ++idx )
{
p_mtype item = (p_mtype) VectorGet ( v, idx );
if ( item != NULL )
KOutMsg( "[ %s ] ", item->name );
}
KOutMsg( "\n" );
}
}
static void matcher_report_pair( const p_mpair pair )
{
if ( pair->src == NULL || pair->dst == NULL )
return;
if ( pair->compatible == 0 )
KOutMsg( "[%s](l=%u/o=%u/d=%u) --> [%s] (c) dist=%u\n",
pair->src->name,
pair->src->lossy_score, pair->src->order, pair->src->dflt,
pair->dst->name, pair->distance );
else
KOutMsg( "[%s](l=%u/o=%u/d=%u) --> [%s] dist=%u\n",
pair->src->name,
pair->src->lossy_score, pair->src->order, pair->src->dflt,
pair->dst->name, pair->distance );
}
static void matcher_report_pairs( const Vector *v )
{
uint32_t idx, len;
len = VectorLength( v );
for ( idx = 0; idx < len; ++idx )
matcher_report_pair( (p_mpair) VectorGet ( v, idx ) );
}
static void matcher_report_col( const p_mcol item )
{
KOutMsg( "----------------------------------\n" );
if ( item->to_copy )
KOutMsg( "col: %s (c)\n", item->name );
else
KOutMsg( "col: %s\n", item->name );
matcher_report_types( " src", &(item->src_types ) );
matcher_report_types( " dst", &(item->dst_types ) );
matcher_report_pairs( &(item->pairs ) );
KOutMsg( "\n" );
}
rc_t matcher_report( matcher* self, const bool only_copy_columns )
{
uint32_t idx, len;
if ( self == NULL )
return RC( rcExe, rcNoTarg, rcResolving, rcSelf, rcNull );
len = VectorLength( &(self->mcols) );
for ( idx = 0; idx < len; ++idx )
{
p_mcol item = (p_mcol) VectorGet ( &(self->mcols), idx );
if ( item != NULL )
{
if ( only_copy_columns )
{
if ( item->to_copy )
matcher_report_col( item );
}
else
matcher_report_col( item );
}
}
return 0;
}
static rc_t matcher_append_type( const char *name, const bool dflt,
const uint32_t order,
const VSchema *schema, Vector *v )
{
rc_t rc = 0;
p_mtype t = matcher_init_type( name, dflt, order );
if ( t == NULL )
rc = RC( rcExe, rcNoTarg, rcResolving, rcMemory, rcExhausted );
if ( rc == 0 )
{
rc = VectorAppend( v, NULL, t );
if ( rc == 0 )
{
rc = VSchemaResolveTypedecl( schema, &(t->type_decl), "%s", name );
if ( rc == 0 )
{
rc = VSchemaDescribeTypedecl( schema, &(t->type_desc), &(t->type_decl) );
}
}
}
return rc;
}
static rc_t matcher_read_col_src_types( p_mcol col,
const KNamelist *names, const uint32_t dflt_idx, const VSchema *schema )
{
uint32_t count;
rc_t rc = KNamelistCount( names, &count );
if ( rc == 0 )
{
uint32_t idx;
for ( idx = 0; idx < count && rc == 0; ++idx )
{
const char *name;
rc = KNamelistGet( names, idx, &name );
if ( rc == 0 )
rc = matcher_append_type( name, ( idx == dflt_idx ), idx,
schema, &(col->src_types) );
}
}
return rc;
}
static rc_t matcher_read_src_types( matcher* self, const VTable *table,
const VSchema *schema )
{
rc_t rc = 0;
uint32_t idx, len;
if ( self == NULL )
return RC( rcExe, rcNoTarg, rcResolving, rcSelf, rcNull );
if ( table == NULL || schema == NULL )
return RC( rcExe, rcNoTarg, rcResolving, rcParam, rcNull );
len = VectorLength( &(self->mcols) );
for ( idx = 0; idx < len && rc == 0; ++idx )
{
p_mcol item = (p_mcol) VectorGet ( &(self->mcols), idx );
if ( item != NULL )
{
uint32_t dflt_idx;
KNamelist *names;
rc = VTableListReadableDatatypes( table, item->name, &dflt_idx, &names );
if ( rc == 0 )
{
rc = matcher_read_col_src_types( item, names, dflt_idx, schema );
KNamelistRelease( names );
}
}
}
return rc;
}
static rc_t matcher_read_dst_types( matcher* self, const VTable *table,
const VSchema *schema )
{
rc_t rc = 0;
uint32_t idx, len;
if ( self == NULL )
return RC( rcExe, rcNoTarg, rcResolving, rcSelf, rcNull );
if ( table == NULL || schema == NULL )
return RC( rcExe, rcNoTarg, rcResolving, rcParam, rcNull );
len = VectorLength( &(self->mcols) );
for ( idx = 0; idx < len && rc == 0; ++idx )
{
p_mcol item = (p_mcol) VectorGet ( &(self->mcols), idx );
if ( item != NULL )
{
KNamelist *names;
rc = VTableListWritableDatatypes ( (VTable*)table, item->name, &names );
if ( rc == 0 )
{
uint32_t type_count;
rc = KNamelistCount( names, &type_count );
if ( rc == 0 && type_count > 0 )
{
uint32_t type_idx;
item->to_copy = true; /* !!! this column has to be copied */
for ( type_idx = 0; type_idx < type_count && rc == 0; ++type_idx )
{
const char *name;
rc = KNamelistGet( names, type_idx, &name );
if ( rc == 0 )
rc = matcher_append_type( name, false, idx,
schema, &(item->dst_types) );
}
}
KNamelistRelease( names );
}
}
}
return rc;
}
static rc_t matcher_make_column_matrix( p_mcol col )
{
rc_t rc = 0;
uint32_t src_idx, src_len;
src_len = VectorLength( &(col->src_types) );
for ( src_idx = 0; src_idx < src_len && rc == 0; ++src_idx )
{
p_mtype src_type = (p_mtype) VectorGet ( &(col->src_types), src_idx );
if ( src_type )
{
uint32_t dst_idx, dst_len;
dst_len = VectorLength( &(col->dst_types) );
for ( dst_idx = 0; dst_idx < dst_len && rc == 0; ++dst_idx )
{
p_mtype dst_type = (p_mtype) VectorGet ( &(col->dst_types), dst_idx );
if ( dst_type )
{
p_mpair pair = matcher_init_pair( src_type, dst_type );
if ( pair != NULL )
rc = VectorAppend( &(col->pairs), NULL, pair );
else
rc = RC( rcVDB, rcNoTarg, rcConstructing, rcMemory, rcExhausted );
}
}
}
}
return rc;
}
static rc_t matcher_make_type_matrix( matcher* self )
{
rc_t rc = 0;
uint32_t idx, len;
if ( self == NULL )
return RC( rcExe, rcNoTarg, rcResolving, rcSelf, rcNull );
len = VectorLength( &(self->mcols) );
for ( idx = 0; idx < len && rc == 0; ++idx )
{
p_mcol col = (p_mcol) VectorGet ( &(self->mcols), idx );
if ( col != NULL )
if ( col->to_copy )
rc = matcher_make_column_matrix( col );
}
return rc;
}
static int64_t CC matcher_match_cb( const void ** p1, const void ** p2, void *data )
{
int64_t res = 0;
const p_mpair pair_1 = (p_mpair)(*p1);
const p_mpair pair_2 = (p_mpair)(*p2);
if ( pair_1 == NULL || pair_2 == NULL )
return res;
/* first we order by compatibility */
res = (int64_t)( pair_1->compatible ) - (int64_t)( pair_2->compatible );
if ( res == 0 )
{
/* second we order by lossy-ness, lowest value first */
res = ( pair_1->src->lossy_score ) - ( pair_2->src->lossy_score );
if ( res == 0 )
{
/* if the lossy-ness is the same, we order by distance */
res = (int64_t)( pair_1->distance ) - (int64_t)( pair_2->distance );
if ( res == 0 )
{
/* if the distance is the same, we order by default-value */
res = (int64_t)( pair_1->src->dflt ) - (int64_t)( pair_2->src->dflt );
if ( res == 0 )
/* if there is not default-value, we use the org. order */
res = (int64_t)( pair_1->src->order ) - (int64_t)( pair_2->src->order );
}
}
}
return res;
}
static void CC matcher_enter_type_score_cb( void * item, void * data )
{
p_mtype type = (p_mtype)item;
const KConfig *cfg = (const KConfig *)data;
if ( type != NULL && cfg != NULL )
type->lossy_score = helper_rd_type_score( cfg, type->name );
}
static void CC matcher_measure_dist_cb( void * item, void * data )
{
p_mpair pair = (p_mpair)item;
const VSchema *schema = (const VSchema *)data;
if ( pair != NULL && schema != NULL )
{
bool compatible = VTypedeclCommonAncestor ( &(pair->src->type_decl),
schema, &(pair->dst->type_decl), NULL, &(pair->distance) );
pair->compatible = ( compatible ? 0 : 1 );
}
}
static void matcher_match_column( p_mcol col,
const VSchema *schema, const KConfig *cfg )
{
uint32_t pair_count = VectorLength( &(col->pairs) );
col->type_cast = NULL;
if ( col->excluded ) return;
/* call VTypedeclCommonAncestor for every type-pair */
VectorForEach ( &(col->pairs), false,
matcher_measure_dist_cb, (void*)schema );
/* if we have more than one pair left... */
if ( pair_count > 1 )
{
/* enter the lossy-ness into the src-types... */
VectorForEach ( &(col->src_types), false,
matcher_enter_type_score_cb, (void*)cfg );
/* reorder the remaining pair's by:
compatibility, lossy-ness, distance, default, order */
VectorReorder ( &(col->pairs), matcher_match_cb, NULL );
}
/* pick the winner = first item in the vector */
if ( pair_count > 0 )
{
col->type_cast = (p_mpair)VectorFirst ( &(col->pairs) );
/* if the winner is not a compatible pair, we have no cast ! */
if ( col->type_cast->compatible != 0 )
col->type_cast = NULL;
}
}
static rc_t matcher_match_matrix( matcher* self,
const VSchema *schema, const KConfig *cfg )
{
rc_t rc = 0;
uint32_t idx, len;
if ( self == NULL )
return RC( rcExe, rcNoTarg, rcResolving, rcSelf, rcNull );
if ( schema == NULL || cfg == NULL )
return RC( rcExe, rcNoTarg, rcResolving, rcParam, rcNull );
len = VectorLength( &(self->mcols) );
for ( idx = 0; idx < len; ++idx )
{
p_mcol col = (p_mcol) VectorGet ( &(self->mcols), idx );
if ( col != NULL )
if ( col->to_copy )
matcher_match_column( col, schema, cfg );
}
return rc;
}
static rc_t matcher_build_column_vector( matcher* self, const char * columns )
{
const KNamelist *list;
uint32_t count, idx;
rc_t rc = nlt_make_namelist_from_string( &list, columns );
if ( rc != 0 ) return rc;
rc = KNamelistCount( list, &count );
if ( rc == 0 )
for ( idx = 0; idx < count && rc == 0; ++idx )
{
const char *s;
rc = KNamelistGet( list, idx, &s );
if ( rc == 0 )
{
p_mcol new_col = matcher_make_col( s );
if ( new_col == NULL )
rc = RC( rcExe, rcNoTarg, rcResolving, rcMemory, rcExhausted );
if ( rc == 0 )
rc = VectorAppend( &(self->mcols), NULL, new_col );
}
}
KNamelistRelease( list );
return rc;
}
static rc_t matcher_exclude_columns( matcher* self, const char * columns )
{
const KNamelist *list;
uint32_t len, idx;
rc_t rc;
if ( columns == NULL ) return 0;
rc = nlt_make_namelist_from_string( &list, columns );
len = VectorLength( &(self->mcols) );
for ( idx = 0; idx < len; ++idx )
{
p_mcol col = (p_mcol) VectorGet ( &(self->mcols), idx );
if ( col != NULL )
col->excluded = nlt_is_name_in_namelist( list, col->name );
}
KNamelistRelease( list );
return rc;
}
rc_t matcher_execute( matcher* self, const p_matcher_input in )
{
VSchema * dflt_schema;
const VTable * src_table;
rc_t rc;
if ( self == NULL )
return RC( rcExe, rcNoTarg, rcResolving, rcSelf, rcNull );
if ( in->manager == NULL || in->add_schemas == NULL ||
in->cfg == NULL || in->columns == NULL ||
in->src_path == NULL || in->dst_path == NULL ||
in->dst_tabname == NULL )
return RC( rcExe, rcNoTarg, rcResolving, rcParam, rcNull );
rc = matcher_build_column_vector( self, in->columns );
if ( rc != 0 ) return rc;
rc = matcher_exclude_columns( self, in->excluded_columns );
if ( rc != 0 ) return rc;
rc = helper_parse_schema( in->manager, &dflt_schema, in->add_schemas );
if ( rc != 0 ) return rc;
rc = VDBManagerOpenTableRead( in->manager, &src_table, dflt_schema, "%s", in->src_path );
if ( rc == 0 )
{
const VSchema * src_schema;
rc = VTableOpenSchema ( src_table, &src_schema );
if ( rc == 0 )
{
rc = matcher_read_src_types( self, src_table, src_schema );
if ( rc == 0 )
{
if ( in->legacy_schema != NULL )
rc = VSchemaParseFile ( dflt_schema, "%s", in->legacy_schema );
if ( rc == 0 )
{
VTable * dst_table;
KCreateMode cmode = kcmParents;
const VSchema * dst_schema = src_schema;
if ( in->legacy_schema != NULL )
dst_schema = dflt_schema;
if ( in->force_unlock )
VDBManagerUnlock ( in->manager, "%s", in->dst_path );
if ( in->force_kcmInit )
cmode |= kcmInit;
else
cmode |= kcmCreate;
rc = VDBManagerCreateTable( in->manager, &dst_table,
dst_schema, in->dst_tabname, cmode, "%s", in->dst_path );
if ( rc == 0 )
{
rc = matcher_read_dst_types( self, dst_table, dst_schema );
if ( rc == 0 )
{
rc = matcher_make_type_matrix( self );
if ( rc == 0 )
rc = matcher_match_matrix( self, src_schema, in->cfg );
}
VTableRelease( dst_table );
if ( !(in->force_kcmInit) )
KDirectoryRemove ( in->dir, true, "%s", in->dst_path );
}
}
}
VSchemaRelease( src_schema );
}
VTableRelease( src_table );
}
VSchemaRelease( dflt_schema );
return rc;
}
rc_t matcher_db_execute( matcher* self, const VTable * src_tab, VTable * dst_tab,
const VSchema * schema, const char * columns,
const char * kfg_path )
{
KConfig * cfg;
rc_t rc = helper_make_config_mgr( &cfg, kfg_path );
if ( rc == 0 )
{
rc = matcher_build_column_vector( self, columns );
if ( rc != 0 ) return rc;
rc = matcher_read_src_types( self, src_tab, schema );
if ( rc == 0 )
{
rc = matcher_read_dst_types( self, dst_tab, schema );
if ( rc == 0 )
{
rc = matcher_make_type_matrix( self );
if ( rc == 0 )
rc = matcher_match_matrix( self, schema, cfg );
}
}
KConfigRelease( cfg );
}
return rc;
}
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