static
rc_t RestoreReadMake ( RestoreRead **objp, const VTable *tbl, const VCursor* native_curs )
{
rc_t rc;
char name[]="PRIMARY_ALIGNMENT";
/* create the object */
RestoreRead *obj = malloc ( sizeof * obj );
memset(obj,0,sizeof * obj);
if ( obj == NULL )
{
*objp=0;
rc = RC ( rcXF, rcFunction, rcConstructing, rcMemory, rcExhausted );
}
else
{
rc = VCursorLinkedCursorGet(native_curs,name,&obj->curs);
if(rc == 0){
VCursorAddRef(obj->curs);
} else {
/* get at the parent database */
const VDatabase *db;
rc = VTableOpenParentRead ( tbl, & db );
if ( rc == 0 )
{
const VTable *patbl;
/* open the primary alignment table */
rc = VDatabaseOpenTableRead ( db, & patbl, name );
VDatabaseRelease ( db );
if ( rc == 0 )
{
/* create a cursor */
rc = VTableCreateCachedCursorRead( patbl, &obj->curs, 32*1024*1024UL );
VTableRelease ( patbl );
if ( rc == 0 )
{
/* add columns to cursor */
rc = VCursorAddColumn ( obj -> curs, & obj -> read_idx, "( INSDC:4na:bin ) READ" );
if ( rc == 0 )
{
rc = VCursorOpen ( obj -> curs );
if ( rc == 0 )
{
VCursorLinkedCursorSet( native_curs, name, obj->curs );
SUB_DEBUG( ( "SUB.Make in 'seq-restore-read.c'\n" ) );
* objp = obj;
return 0;
}
}
VCursorRelease ( obj -> curs );
}
}
}
free ( obj );
}
}
return rc;
}
static rc_t vdb_prepare_cursor( const p_dump_context ctx, const VTable * tbl, fastq_ctx * fctx )
{
rc_t rc;
/* first we try to open READ/QUALITY/NAME */
rc = VTableCreateCachedCursorRead( tbl, &fctx->cursor, ctx->cur_cache_size );
DISP_RC( rc, "VTableCreateCursorRead( 1st ) failed" );
if ( rc == 0 )
{
rc = VCursorAddColumn( fctx->cursor, &fctx->idx_read, "(INSDC:dna:text)READ" );
if ( rc == 0 && ctx->format == df_fastq )
rc = VCursorAddColumn( fctx->cursor, &fctx->idx_qual, "(INSDC:quality:text:phred_33)QUALITY" );
else
fctx->idx_qual = INVALID_COLUMN;
if ( rc == 0 )
rc = VCursorAddColumn( fctx->cursor, &fctx->idx_name, "(ascii)NAME" );
if ( rc == 0 )
rc = VCursorOpen ( fctx->cursor );
if ( rc != 0 )
{
VCursorRelease( fctx->cursor );
rc = VTableCreateCachedCursorRead( tbl, &fctx->cursor, ctx->cur_cache_size );
DISP_RC( rc, "VTableCreateCursorRead( 2nd ) failed" );
if ( rc == 0 )
{
rc = VCursorAddColumn( fctx->cursor, &fctx->idx_read, "(INSDC:dna:text)READ" );
if ( rc == 0 && ctx->format == df_fastq )
rc = VCursorAddColumn( fctx->cursor, &fctx->idx_qual, "(INSDC:quality:text:phred_33)QUALITY" );
else
fctx->idx_qual = INVALID_COLUMN;
if ( rc == 0 )
rc = VCursorOpen ( fctx->cursor );
fctx->idx_name = INVALID_COLUMN;
}
}
}
return rc;
}
rc_t AlignRefTableCursor(const VTable* table, const VCursor *native_curs, const VCursor** ref_cursor,const VTable **reftbl)
{
rc_t rc = 0;
char ref_tbl_name[512] = "REFERENCE";
const KMetadata* meta;
const VCursor *curs;
if( (rc = VTableOpenMetadataRead(table, &meta)) == 0 ) {
const KMDataNode* node;
if( (rc = KMetadataOpenNodeRead(meta, &node, "CONFIG/REF_TABLE")) == 0 ) {
size_t sz;
rc = KMDataNodeReadCString(node, ref_tbl_name, sizeof(ref_tbl_name), &sz);
ref_tbl_name[sz] = '\0';
KMDataNodeRelease(node);
}
KMetadataRelease(meta);
}
rc = VCursorLinkedCursorGet(native_curs,ref_tbl_name,&curs);
if(rc != 0){
const VDatabase *db;
const VTable *tbl;
/* get at the parent database */
rc = VTableOpenParentRead ( table, & db );
if(rc != 0) return rc;
/* open the table */
rc = VDatabaseOpenTableRead ( db, &tbl, ref_tbl_name);
VDatabaseRelease ( db );
if(rc != 0) return rc;
/* create a cursor */
rc = VTableCreateCachedCursorRead(tbl, &curs,256*1024*1024);
if(reftbl){
*reftbl = tbl;
} else {
VTableRelease(tbl);
}
if(rc != 0) return rc;
rc = VCursorPermitPostOpenAdd( curs );
if(rc != 0) return rc;
rc = VCursorOpen( curs );
if(rc != 0) return rc;
if(native_curs){
rc = VCursorLinkedCursorSet(native_curs,ref_tbl_name,curs);
}
if(rc != 0) return rc;
} else {
VCursorAddRef(curs);
}
*ref_cursor = curs;
return 0;
}
static
rc_t init_self( self_t *self, VTable const * const srctbl, char const column[] )
{
VDatabase const * db;
rc_t rc = VTableOpenParentRead( srctbl, &db );
if ( rc == 0 )
{
VTable const * tbl;
rc = VDatabaseOpenTableRead( db, &tbl, "SEQUENCE" );
VDatabaseRelease( db );
if ( rc == 0 )
{
bool has_column = does_table_have_column( tbl, column );
if ( !has_column )
VTableRelease( tbl );
else
{
VCursor const * curs;
#if CURSOR_CACHE_SIZE
rc = VTableCreateCachedCursorRead( tbl, &curs, CURSOR_CACHE_SIZE );
#else
rc = VTableCreateCursorRead( tbl, &curs );
#endif
VTableRelease( tbl );
if ( rc == 0 )
{
uint32_t col_idx;
rc = VCursorAddColumn( curs, &col_idx, "%s", column );
if ( rc == 0 )
{
rc = VCursorOpen( curs );
if ( rc == 0 )
{
self->curs = curs;
self->col_idx = col_idx;
return 0;
}
if ( GetRCObject( rc ) == (enum RCObject)rcColumn && GetRCState( rc ) == rcUndefined )
rc = 0;
}
VCursorRelease( curs );
}
}
}
}
return rc;
}
static
rc_t open_RR_cursor( Read_Restorer * obj, const VTable *tbl, const VCursor* native_curs, const char * tablename )
{
rc_t rc = VCursorLinkedCursorGet( native_curs, tablename, &obj->curs );
if ( rc != 0 )
{
/* get at the parent database */
const VDatabase *db;
rc = VTableOpenParentRead ( tbl, & db );
if ( rc == 0 )
{
const VTable *patbl;
/* open the primary alignment table */
rc = VDatabaseOpenTableRead ( db, & patbl, tablename );
VDatabaseRelease ( db );
if ( rc == 0 )
{
/* create a cursor */
rc = VTableCreateCachedCursorRead( patbl, &obj->curs, 32*1024*1024UL );
/* rc = VTableCreateCursorRead( patbl, &obj->curs ); */
VTableRelease ( patbl );
if ( rc == 0 )
rc = VCursorLinkedCursorSet( native_curs, tablename, obj->curs );
}
}
}
if ( rc == 0 )
{
/* add columns to cursor */
rc = VCursorAddColumn ( obj -> curs, & obj -> read_idx, "( INSDC:4na:bin ) READ" );
if ( GetRCState(rc) == rcExists )
rc = 0;
if ( rc == 0 )
{
rc = VCursorOpen ( obj -> curs );
}
}
return rc;
}
static
rc_t LoadObjects ( ObjectTable* data, const VDatabase* db )
{
const VTable* tbl;
rc_t rc = VDatabaseOpenTableRead(db, &tbl, "OBJECTS");
if (rc == 0)
{
rc_t rc2;
const VCursor *cur;
rc = VTableCreateCachedCursorRead( tbl, &cur, CursorCacheSize );
if (rc == 0)
{
uint32_t id_idx, name_idx, proj_idx, dname_idx, size_idx, csum_idx, enc_idx;
if (rc == 0) rc = VCursorAddColumn( cur, &id_idx, "id" );
if (rc == 0) rc = VCursorAddColumn( cur, &name_idx, "name" );
if (rc == 0) rc = VCursorAddColumn( cur, &proj_idx, "project" );
if (rc == 0) rc = VCursorAddColumn( cur, &dname_idx, "display_name" );
if (rc == 0) rc = VCursorAddColumn( cur, &size_idx, "size" );
if (rc == 0) rc = VCursorAddColumn( cur, &csum_idx, "checksum" );
if (rc == 0) rc = VCursorAddColumn( cur, &enc_idx, "encryption_key" );
if (rc == 0 && HasData(tbl))
{
rc = VCursorOpen( cur );
if (rc == 0)
{
int64_t first;
uint64_t count;
rc = VCursorIdRange( cur, 0, &first, &count );
if (rc == 0)
{
uint64_t i;
for (i=0; i < count; ++i)
{
const void* ptr;
uint32_t elem_count;
uint32_t id;
String name;
String project;
String display_name;
uint64_t size;
String checksum;
String encryption_key;
rc = VCursorSetRowId(cur, first + i);
if (rc == 0) rc = VCursorOpenRow( cur );
if (rc == 0) rc = VCursorCellData( cur, id_idx, NULL, &ptr, NULL, NULL);
if (rc == 0) id = *(uint32_t*)ptr;
if (rc == 0) rc = VCursorCellData( cur, name_idx, NULL, &ptr, NULL, &elem_count);
if (rc == 0) StringInit(&name, (const char*)ptr, elem_count, elem_count);
if (rc == 0) rc = VCursorCellData( cur, proj_idx, NULL, &ptr, NULL, &elem_count);
if (rc == 0) StringInit(&project, (const char*)ptr, elem_count, elem_count);
if (rc == 0) rc = VCursorCellData( cur, dname_idx, NULL, &ptr, NULL, &elem_count);
if (rc == 0) StringInit(&display_name, (const char*)ptr, elem_count, elem_count);
if (rc == 0) rc = VCursorCellData( cur, size_idx, NULL, &ptr, NULL, NULL);
if (rc == 0) size = *(uint32_t*)ptr;
if (rc == 0) rc = VCursorCellData( cur, enc_idx, NULL, &ptr, NULL, &elem_count);
if (rc == 0) StringInit(&encryption_key, (const char*)ptr, elem_count, elem_count);
if (rc == 0) rc = VCursorCellData( cur, csum_idx, NULL, &ptr, NULL, &elem_count);
if (rc == 0) StringInit(&checksum, (const char*)ptr, elem_count, elem_count);
if (rc == 0) rc = KeyRingDataInsertObject(data, id, &name, &project, &display_name, size, &checksum, &encryption_key);
if (rc == 0) rc = VCursorCloseRow( cur );
if (rc != 0)
break;
}
}
}
}
rc2 = VCursorRelease(cur);
if (rc == 0)
rc = rc2;
}
rc2 = VTableRelease(tbl);
if (rc == 0)
rc = rc2;
}
return rc;
}
static
rc_t LoadProjects( ProjectTable* data, const VDatabase* db )
{
const VTable* tbl;
rc_t rc = VDatabaseOpenTableRead(db, &tbl, "PROJECTS");
if (rc == 0)
{
rc_t rc2;
const VCursor *cur;
rc = VTableCreateCachedCursorRead( tbl, &cur, CursorCacheSize );
if (rc == 0)
{
uint32_t id_idx, name_idx, dl_idx, enc_idx;
rc = VCursorAddColumn( cur, &id_idx, "id" );
if (rc == 0) rc = VCursorAddColumn( cur, &name_idx, "name" );
if (rc == 0) rc = VCursorAddColumn( cur, &dl_idx, "download_ticket" );
if (rc == 0) rc = VCursorAddColumn( cur, &enc_idx, "encryption_key" );
if (rc == 0 && HasData(tbl))
{
rc = VCursorOpen( cur );
if (rc == 0)
{
int64_t first;
uint64_t count;
rc = VCursorIdRange( cur, 0, &first, &count );
if (rc == 0)
{
uint64_t i;
for (i=0; i < count; ++i)
{
const void* ptr;
uint32_t elem_count;
uint32_t id;
String name;
String download_ticket;
String encryption_key;
rc = VCursorSetRowId(cur, first + i);
if (rc == 0) rc = VCursorOpenRow( cur );
if (rc == 0) rc = VCursorCellData( cur, id_idx, NULL, &ptr, NULL, NULL);
if (rc == 0) id = *(uint32_t*)ptr;
if (rc == 0) rc = VCursorCellData( cur, name_idx, NULL, &ptr, NULL, &elem_count);
if (rc == 0) StringInit(&name, (const char*)ptr, elem_count, elem_count);
if (rc == 0) rc = VCursorCellData( cur, dl_idx, NULL, &ptr, NULL, &elem_count);
if (rc == 0) StringInit(&download_ticket, (const char*)ptr, elem_count, elem_count);
if (rc == 0) rc = VCursorCellData( cur, enc_idx, NULL, &ptr, NULL, &elem_count);
if (rc == 0) StringInit(&encryption_key, (const char*)ptr, elem_count, elem_count);
if (rc == 0) rc = KeyRingDataInsertProject(data, id, &name, &download_ticket, &encryption_key);
if (rc == 0) rc = VCursorCloseRow( cur );
if (rc != 0)
break;
}
}
}
}
rc2 = VCursorRelease(cur);
if (rc == 0)
rc = rc2;
}
rc2 = VTableRelease(tbl);
if (rc == 0)
rc = rc2;
}
return rc;
}
static rc_t cg_dump_src_dst_rows_vdb( cg_dump_opts * opts, const VDBManager * mgr, const char * src, cg_dump_ctx * cg_ctx )
{
const VDatabase * db;
rc_t rc = VDBManagerOpenDBRead( mgr, &db, NULL, "%s", src );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot open database" );
}
else
{
rc = parse_sg_lookup( cg_ctx->lookup, db ); /* in sg_lookup.c */
if ( rc == 0 )
{
const VTable * seq;
rc = VDatabaseOpenTableRead( db, &seq, "SEQUENCE" );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot open SEQUENCE-table" );
}
else
{
const VTable * prim;
rc = VDatabaseOpenTableRead( db, &prim, "PRIMARY_ALIGNMENT" );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot open PRIMARY-ALIGNMENT-table" );
}
else
{
if ( opts->cursor_cache > 0 )
rc = VTableCreateCachedCursorRead( seq, &cg_ctx->seq_cur, opts->cursor_cache );
else
rc = VTableCreateCursorRead( seq, &cg_ctx->seq_cur );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot create cursor for SEQUENCE-table" );
}
else
{
/*
if ( opts->cursor_cache > 0 )
rc = VTableCreateCachedCursorRead( prim, &cg_ctx->prim_cur, opts->cursor_cache );
else
rc = VTableCreateCursorRead( prim, &cg_ctx->prim_cur );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot create cursor for PRIMARY_ALIGNMENT-table" );
}
*/
if ( rc == 0 )
{
rc = cg_dump_src_dst_rows_cur( opts, cg_ctx ); /* <================== */
/* VCursorRelease( cg_ctx->prim_cur ); */
}
VCursorRelease( cg_ctx->seq_cur );
}
/* VTableRelease( prim ); */
}
VTableRelease( seq );
}
}
VDatabaseRelease( db );
}
return rc;
}