コード例 #1
0
static rc_t OpenTableAndCursor(VDatabase *db, VTable **ptbl, VCursor **pcurs, uint32_t cid[], unsigned ncols)
{
    rc_t rc = VDatabaseCreateTable(db, ptbl, "READ_STATS",
                                   kcmCreate | kcmMD5, "READ_STATS");
    
    if (rc == 0) {
        rc = VTableColumnCreateParams(*ptbl, kcmCreate, kcsCRC32, 0);
        if (rc == 0) {
            rc = VTableCreateCursorWrite(*ptbl, &pcurs, kcmInsert);
            if (rc == 0) {
                unsigned i;
                
                for (i = 0; i < ncols && rc == 0; ++i) {
                    rc = VCursorAddColumn(*pcurs, &cid[i], column_name[i]);
                }
                if (rc == 0) {
                    rc = VCursorOpen(*pcurs);
                    if (rc == 0)
                        return 0;
                }
                VCursorRelease(*pcurs);
            }
        }
        VTableRelease(*ptbl);
    }
    *pcurs = NULL;
    *ptbl = NULL;
    return rc;
}
コード例 #2
0
ファイル: keyring-database.c プロジェクト: Bhumi28/sra-tools
static 
rc_t SaveObjects ( const ObjectTable* data,  VDatabase* db )
{
    VTable* tbl;
    rc_t rc = VDatabaseCreateTable(db, &tbl, "object_inst", kcmCreate | kcmMD5, "OBJECTS");
    if (rc == 0)
    {
        rc_t rc2;
        VCursor *cur;
        rc = VTableCreateCursorWrite( tbl, &cur, kcmInsert );
        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)
            {
                rc = VCursorOpen( cur );
                if (rc == 0)
                {
                    const Object* obj = (const Object*)BSTreeFirst(data);
                    while (rc == 0 && obj != NULL)
                    {
                        rc = VCursorOpenRow( cur );
                        
                        if (rc == 0) rc = VCursorWrite( cur, id_idx,    sizeof(obj->id) * 8,                   &obj->id,                  0, 1);
                        if (rc == 0) rc = VCursorWrite( cur, name_idx,  StringLength(obj->name) * 8,           obj->name->addr,           0, 1);
                        if (rc == 0) rc = VCursorWrite( cur, proj_idx,  StringLength(obj->project) * 8,        obj->project->addr,        0, 1);
                        if (rc == 0) rc = VCursorWrite( cur, dname_idx, StringLength(obj->display_name) * 8,   obj->display_name->addr,   0, 1);
                        if (rc == 0) rc = VCursorWrite( cur, size_idx,  sizeof(obj->size) * 8,                 &obj->size,                0, 1);
                        if (rc == 0) rc = VCursorWrite( cur, csum_idx,  StringLength(obj->encryption_key) * 8, obj->encryption_key->addr, 0, 1);
                        if (rc == 0) rc = VCursorWrite( cur, enc_idx,   StringLength(obj->encryption_key) * 8, obj->encryption_key->addr, 0, 1);
                        
                        if (rc == 0) rc = VCursorCommitRow( cur );
                        if (rc == 0) rc = VCursorCloseRow( cur );
                        
                        obj = (const Object*)BSTNodeNext(&obj->dad);
                    }
                    if (rc == 0) rc = VCursorCommit( cur );
                }
            }
            rc2 = VCursorRelease(cur);
            if (rc == 0)
                rc = rc2;
        }
        
        rc2 = VTableRelease(tbl);
        if (rc == 0)
            rc = rc2;
    }
    return rc;
}
コード例 #3
0
ファイル: keyring-database.c プロジェクト: Bhumi28/sra-tools
static 
rc_t SaveProjects( const ProjectTable* data, VDatabase* db )
{
    VTable* tbl;
    rc_t rc = VDatabaseCreateTable(db, &tbl, "project_inst", kcmCreate | kcmMD5, "PROJECTS");
    if (rc == 0)
    {
        rc_t rc2;
        VCursor *cur;
        rc = VTableCreateCursorWrite( tbl, &cur, kcmInsert );
        if (rc == 0)
        {
            uint32_t id_idx, name_idx, dl_idx, enc_idx;
            rc = VCursorAddColumn( cur, &id_idx, "id" );
            rc = VCursorAddColumn( cur, &name_idx, "name" );
            rc = VCursorAddColumn( cur, &dl_idx, "download_ticket" );
            rc = VCursorAddColumn( cur, &enc_idx, "encryption_key" );
            if (rc == 0)
            {
                rc = VCursorOpen( cur );
                if (rc == 0)
                {
                    const Project* p = (const Project*)BSTreeFirst(data);
                    while (rc == 0 && p != NULL)
                    {
                        rc = VCursorOpenRow( cur );
                        
                        if (rc == 0) rc = VCursorWrite( cur, id_idx,    sizeof(p->id) * 8,                      &p->id,                     0, 1);
                        if (rc == 0) rc = VCursorWrite( cur, name_idx,  StringLength(p->name) * 8,              p->name->addr,              0, 1);
                        if (rc == 0) rc = VCursorWrite( cur, dl_idx,    StringLength(p->download_ticket) * 8,   p->download_ticket->addr,   0, 1);
                        if (rc == 0) rc = VCursorWrite( cur, enc_idx,   StringLength(p->encryption_key) * 8,    p->encryption_key->addr,    0, 1);
                        
                        if (rc == 0) rc = VCursorCommitRow( cur );
                        if (rc == 0) rc = VCursorCloseRow( cur );
                        
                        p = (const Project*)BSTNodeNext(&p->dad);
                    }
                    if (rc == 0)
                        rc = VCursorCommit( cur );
                }
            }
            rc2 = VCursorRelease(cur);
            if (rc == 0)
                rc = rc2;
        }
        
        rc2 = VTableRelease(tbl);
        if (rc == 0)
            rc = rc2;
    }
    return rc;
}
コード例 #4
0
ファイル: wsratbl.c プロジェクト: binlu1981/ncbi-vdb
LIB_EXPORT rc_t CC SRAMgrVOpenTableUpdate(SRAMgr *mgr, SRATable **rslt, const char *spec, va_list args) {
    SRATable *self;
    char path[4096];
    rc_t rc;
    
    if (mgr == NULL)
        return RC(RC_MODULE, RC_TARGET, rcConstructing, rcSelf, rcNull);
    if (spec == NULL || rslt == NULL)
        return RC(RC_MODULE, RC_TARGET, rcConstructing, rcParam, rcNull);
    
    *rslt = NULL;
    
    rc = ResolveTablePath(mgr, path, sizeof(path), spec, args);
    if (rc)
        return rc;
    
    self = calloc(1, sizeof(*self));
    if (self == NULL)
        return RC(RC_MODULE, RC_TARGET, rcConstructing, rcMemory, rcExhausted);
    
    rc = VDBManagerOpenTableUpdate(mgr->vmgr, &self->vtbl, mgr->schema, "%s", path);
    if (rc == 0) {
        rc = VTableOpenMetadataUpdate(self->vtbl, &self->meta);
        if (rc == 0) {
            rc = KMetadataVersion(self->meta, &self->metavers);
            if (rc == 0) {
                rc = VTableCreateCursorWrite(self->vtbl, &self->curs, kcmInsert);
                if (rc == 0) {
                    self->mgr = SRAMgrAttach(mgr);
                    self->mode = mgr->mode;
                    self->read_only = false;
                    KRefcountInit(&self->refcount, 1, "SRATable", "OpenTableUpdate", path);
                    
                    rc = SRATableFillOut ( self, true );
                    if ( rc == 0 )
                    {
                        VectorInit ( & self -> wcol, 0, 16 );
                    
                        *rslt = self;
                        return 0;
                    }
                }
            }
        }
    }
    SRATableWhack(self);
    return rc;
}
コード例 #5
0
rc_t open_write_cursor (VTable * table, VCursor ** cursor,
                        uint32_t * dat, uint32_t * len, 
                        const char * dat_name, const char* len_name)
{
    rc_t rc;

    rc = VTableCreateCursorWrite (table, cursor, kcmInsert);
    if (rc)
    {
        LOGERR (klogErr, rc, "Failed to create Cursor");
        *cursor = NULL;
    }
    else
    {
        do
        {
            rc = VCursorAddColumn (*cursor, dat, dat_name);
            if (rc)
            {
                pLOGERR (klogErr, rc, "Failed to add column $(C)", PLOG_S(C), dat_name);
                break;
            }

            rc = VCursorAddColumn (*cursor, len, len_name);
            if (rc)
            {
                pLOGERR (klogErr, rc, "Failed to add column $(C)", PLOG_S(C), len_name);
                break;
            }       

            rc = VCursorOpen (*cursor);
            if (rc)
            {
                LOGERR (klogErr, rc, "Failed to open cursor");
                break;
            }

            return 0;
        }
        while (0);
    }
    VCursorRelease (*cursor);
    *dat = 0;
    *len = 0;
    *cursor = NULL;
    return rc;
}
コード例 #6
0
/* vtblcp
 */
static
rc_t vtblcp ( const vtblcp_parms *pb, const VTable *stbl, VTable *dtbl, const Vector *v )
{
    const VCursor *scurs;
    rc_t rc = VTableCreateCursorRead ( stbl, & scurs );
    if ( rc != 0 )
        LOGERR ( klogInt, rc, "failed to create empty destination cursor" );
    else
    {
        VCursor *dcurs;
        rc = VTableCreateCursorWrite ( dtbl, & dcurs, kcmInsert );
        if ( rc != 0 )
            LOGERR ( klogInt, rc, "failed to create empty destination cursor" );
        else
        {
            uint32_t count = VectorLength ( v );
            vtblcp_column_map *cm = malloc ( sizeof *cm * count );
            if ( cm == NULL )
            {
                rc = RC ( rcExe, rcVector, rcAllocating, rcMemory, rcExhausted );
                LOGERR ( klogInt, rc, "failed to create column index map" );
            }
            else
            {
                uint32_t rd_filt;
                rc = populate_cursors ( dtbl, dcurs, scurs, cm, v, & rd_filt );

                if ( rc == 0 )
                    rc = copy_table ( pb, dcurs, scurs, cm, count, rd_filt );

                free ( cm );
            }

            VCursorRelease ( dcurs );
        }
            
        VCursorRelease ( scurs );
    }

    return rc;
}
コード例 #7
0
static rc_t write_statistic_cmn( VTable * my_table, statistic * data,
                          uint64_t * written, bool show_progress )
{
    VCursor *my_cursor;
    rc_t rc = VTableCreateCursorWrite( my_table, &my_cursor, kcmInsert );
    if ( rc != 0 )
        LogErr( klogInt, rc, "VTableCreateCursorWrite() failed\n" );
    else
    {
        statistic_writer writer;
        rc = make_statistic_writer( &writer, my_cursor );
        if ( rc == 0 )
        {
            rc = write_statistic( &writer, data, written, show_progress );
            if ( rc == 0 )
                rc = whack_statistic_writer( &writer );
        }
        VCursorRelease( my_cursor );
    }
    return rc;
}
コード例 #8
0
rc_t CC KMain(int argc, char* argv[])
{
    const char table[] = "/home/klymenka/REDACT-IN";
    const char name[] = "READ_FILTER";

    rc_t rc = 0;

    bool locked = false;

    VDBManager* mgr;
    VTable *tbl;
    const VCursor *rCursor = NULL;

    int i;

    LogLevelSet("info");

    for (i = 1; i < argc; ++i) {
        if (!strcmp(argv[i], "-+")) {
            if (++i <= argc) {
#if _DEBUGGING
	        KDbgSetString(argv[i]);
#endif
	    }
        }
    }

  /*KDbgSetString("VDB");*/

    if (rc == 0) {
/* +01: ManagerMake */
        LOGMSG(klogInfo, "VDBManagerMakeUpdate");
        rc = VDBManagerMakeUpdate(&mgr, NULL);
        DISP_RC_INT(rc, "while calling VDBManagerMakeUpdate");
    }

    if (rc == 0) {
        rc = VDBManagerWritable(mgr, table);
        if (GetRCState(rc) == rcLocked) {
            LOGMSG(klogInfo, "VDBManagerUnlock");
            rc = VDBManagerUnlock(mgr, table);
            DISP_RC_INT(rc, "while calling VDBManagerUnlock");
            locked = true;
        }
    }

    if (rc == 0) {
/* +02: OpenTable */
        PLOGMSG(klogInfo, (klogInfo,
            "VDBManagerOpenTableUpdate(\"$(t)\")", "t=%s", table));
        rc = VDBManagerOpenTableUpdate
            (mgr, &tbl, NULL, table);
        if (rc != 0) {
            PLOGERR(klogErr, (klogErr, rc,
                "while opening VTable '$(path)'", "path=%s", table));
        }
    }

    if (rc == 0) {
/* +03: CreateCursorRead */
        LOGMSG(klogInfo, "VDBManagerUnlock");
        rc = VTableCreateCursorRead(tbl, &rCursor);
        DISP_RC_INT(rc, "while creating read cursor");

#if 1
        if (rc == 0) {
            uint32_t idx;
            PLOGMSG(klogInfo, (klogInfo,
                "VCursorAddColumn(read cursor, \"$(n)\")", "n=%s", name));
            rc = VCursorAddColumn(rCursor, &idx, name);
            if (rc != 0) {
                PLOGERR(klogErr, (klogErr, rc,
                    "while adding $(name) to read cursor", "name=%s", name));
            }
        }
#endif
        if (rc == 0) {
            LOGMSG(klogInfo, "VCursorOpen(read cursor)");
            rc = VCursorOpen(rCursor);
            DISP_RC_INT(rc, "while opening read cursor");
        }
    }

    if (rc == 0) {
        VCursor *cursor;
        uint32_t idx;
/* +04: CreateCursorWrite */
        LOGMSG(klogInfo, "VTableCreateCursorWrite");
        rc = VTableCreateCursorWrite(tbl, &cursor, kcmInsert);
        DISP_RC_INT(rc, "while creating write cursor");
        if (rc == 0) {
            PLOGMSG(klogInfo, (klogInfo,
                "VCursorAddColumn(write cursor, \"$(n)\")", "n=%s", name));
            rc = VCursorAddColumn(cursor, &idx, name);
            if (rc != 0) {
                PLOGERR(klogErr, (klogErr, rc,
                    "while adding $(name) to write cursor", "name=%s", name));
            }
        }
        if (rc == 0) {
            LOGMSG(klogInfo, "VCursorOpen(write cursor)");
            rc = VCursorOpen(cursor);
            DISP_RC_INT(rc, "while opening write cursor");
        }
#if 1
        for (i = 0; i < 3 && rc == 0; ++i) {
            if (rc == 0) {
                PLOGMSG(klogInfo, (klogInfo,
                    "VCursorOpenRow(write cursor) $(i)", "i=%d", i));
                rc = VCursorOpenRow(cursor);
                DISP_RC_INT(rc, "while opening row to write");
            }
            if (rc == 0) {
                char buffer[1];
                char b;
                switch (i) {
                    case 0:
                        buffer[0] = SRA_READ_FILTER_CRITERIA;
                        buffer[0] = SRA_READ_FILTER_REJECT;
                        break;
                    case 1:
                        buffer[0] = SRA_READ_FILTER_REJECT;
                        buffer[0] = SRA_READ_FILTER_CRITERIA;
                        break;
                    case 2:
                        buffer[0] = SRA_READ_FILTER_REDACTED;
                        break;
                }
                buffer[0] = SRA_READ_FILTER_PASS;
                b = buffer[0];
                PLOGMSG(klogInfo, (klogInfo,
                    "VCursorWrite('$(v)') $(i)", "v=%s,i=%d",
                    b == SRA_READ_FILTER_REDACTED ? "SRA_READ_FILTER_REDACTED" :
                        "?",
                    i));
                rc = VCursorWrite(cursor, idx, 8, buffer, 0, 1);
                DISP_RC_INT(rc, "while writing");
            }
            if (rc == 0) {
                PLOGMSG(klogInfo, (klogInfo,
                    "VCursorCommitRow(write cursor) $(i)", "i=%d", i));
                rc = VCursorCommitRow(cursor);
                DISP_RC_INT(rc, "while committing row");
            }
            PLOGMSG(klogInfo, (klogInfo,
                "VCursorCloseRow(write cursor) $(i)", "i=%d", i));
            {
                rc_t rc2 = VCursorCloseRow(cursor);
                DISP_RC_INT(rc2, "while closing row");
                if (rc == 0)
                {   rc = rc2; }
            }
        }
#endif
        LOGMSG(klogInfo, "VCursorRelease(read cursor)");
/* -03: CreateCursorRead */
        VCursorRelease(rCursor);
        if (rc == 0) {
            LOGMSG(klogInfo, "VCursorCommit(write cursor)");
            rc = VCursorCommit(cursor);
            DISP_RC_INT(rc, "while committing cursor");
        }
        LOGMSG(klogInfo, "VCursorRelease(write cursor)");
/* -04: CreateCursorWrite */
        VCursorRelease(cursor);
    }

    LOGMSG(klogInfo, "VTableRelease");
/* -02: OpenTable */
    VTableRelease(tbl);
    LOGMSG(klogInfo, "VDBManagerLock");
    if (locked) {
        rc_t rc2 = VDBManagerLock(mgr, table);
        DISP_RC_INT(rc2, "while VDBManagerLock");
    }

/* -01: ManagerMake */
    LOGMSG(klogInfo, "VDBManagerRelease");
    VDBManagerRelease(mgr);

    if (rc == 0) {
        LOGMSG(klogInfo, "SUCCESS");
    }
    else { LOGMSG(klogInfo, "FAILURE"); }

    return rc;
}
コード例 #9
0
ファイル: wsratbl.c プロジェクト: binlu1981/ncbi-vdb
LIB_EXPORT rc_t CC SRAMgrVCreateTable ( SRAMgr *self, SRATable **rslt,
    const char *typespec, const char *spec, va_list args )
{
    rc_t rc;

    if ( rslt == NULL )
        rc = RC ( rcSRA, rcTable, rcConstructing, rcParam, rcNull );
    else
    {
        if ( self == NULL )
            rc = RC ( rcSRA, rcTable, rcConstructing, rcSelf, rcNull );
        else if ( spec == NULL )
            rc = RC ( rcSRA, rcTable, rcConstructing, rcString, rcNull );
        else if ( spec [ 0 ] == 0 )
            rc = RC ( rcSRA, rcTable, rcConstructing, rcString, rcEmpty );
        else
        {
            char path [ 4097 ];
            size_t act_size = 0;
            
            rc = string_vprintf(path, 4097, &act_size, spec, args);
            path[act_size] = '\0';
            if ( rc == 0 )
            {
                VTable *vtbl;
                rc = VDBManagerCreateTable ( self -> vmgr, & vtbl, self -> schema,
                                             typespec, ( self -> mode & kcmBitMask ) | kcmCreate, "%s", path );
                if ( rc == 0 )
                {
                    rc = VTableColumnCreateParams ( vtbl, kcmCreate, kcsCRC32, 0 );
                    if ( rc == 0 )
                    {
                        SRATable *tbl = calloc ( 1, sizeof * tbl );
                        if ( tbl == NULL )
                            rc = RC ( rcSRA, rcTable, rcConstructing, rcMemory, rcExhausted );
                        else
                        {
                            tbl -> vtbl = vtbl;

                            rc = VTableOpenMetadataUpdate ( vtbl, & tbl -> meta );
                            if ( rc == 0 )
                                rc = KMetadataVersion ( tbl -> meta, & tbl -> metavers );
                            if ( rc == 0 )
                                rc = VTableCreateCursorWrite ( vtbl, & tbl -> curs, kcmInsert );
                            if ( rc == 0 )
                            {
                                tbl -> mgr = SRAMgrAttach ( self );
                                tbl -> mode = self -> mode;
                                tbl -> read_only = false;
                                KRefcountInit ( & tbl -> refcount, 1, "SRATable", "OpenTableUpdate", path );
                                VectorInit ( & tbl -> wcol, 0, 16 );
                                * rslt = tbl;
                                return 0;
                            }

                            vtbl = NULL;
                            SRATableWhack ( tbl );
                        }
                    }

                    VTableRelease ( vtbl );
                }
            }
        }

        * rslt = NULL;
    }

    return rc;
}
コード例 #10
0
static rc_t static_write(void)
{
    const char *schema_text = "version 1; include 'vdb/vdb.vschema'; table foo #1 { column ascii bar { read = .bar; } physical ascii .bar = bar; }";
    bool force = 1;
    rc_t rc;
    VDBManager *vmgr;
    
    rc = VDBManagerMakeUpdate ( & vmgr, NULL );
    if ( rc != 0 )
        LOGERR ( klogInt, rc, "failed to make VDB manager" );
    else
    {
        VSchema *schema;
        rc = VDBManagerMakeSchema ( vmgr, & schema );
        if ( rc != 0 )
            LOGERR ( klogInt, rc, "failed to make empty schema" );
        else
        {
            rc = VSchemaParseText( schema, "static_schema", schema_text, strlen(schema_text) );
            if ( rc != 0 )
                PLOGERR ( klogErr, (klogErr, rc, "failed to parse schema '$(text)'", "test=%s", schema_text ));
            else
            {
                VTable *vtbl;
                
                rc = VDBManagerCreateTable ( vmgr, & vtbl, schema, "foo", force ? kcmInit : kcmCreate, table_path );
                if ( rc != 0 )
                {
                    PLOGERR ( klogErr, (klogErr, rc, "failed to $(cmode) table '$(path)'"
                             , "cmode=%s,path=%s"
                             , force ? "create or replace" : "create"
                             , table_path
                                        ));
                }
                else
                {
                    VCursor *curs;
                    rc = VTableCreateCursorWrite ( vtbl, & curs, kcmInsert );
                    if ( rc != 0 )
                        LOGERR ( klogInt, rc, "failed to create cursor" );
                    else
                    {
                        uint32_t idx;
                        
                        rc = VCursorAddColumn ( curs, &idx, "bar" );
                        if ( rc != 0 )
                        {
                            PLOGERR ( klogErr, (klogErr, rc, "failed to add column '$(col)' to cursor"
                                     , "col=bar"
                                     ));
                        }
                        else {
                            rc = VCursorOpen ( curs );
                            if ( rc != 0 )
                                LOGERR ( klogErr, rc, "failed to open cursor" );
                            else
                            {
                                int i;
                                
                                for ( i = 0; i != 10 && rc == 0; ++i )
                                {
                                    rc = VCursorOpenRow ( curs );
                                    if ( rc != 0 )
                                        LOGERR ( klogErr, rc, "failed to open cursor row" );
                                    else
                                    {
                                        rc_t rc2;
                                        uint32_t count = sizeof(buff) - 1;
                                        
                                        rc = VCursorWrite ( curs, idx, 8, buff, 0, count );
                                        if ( rc != 0 )
                                        {
                                            int64_t rid = 0;
                                            VCursorRowId ( curs, & rid );
                                            
                                            PLOGERR ( klogInt, (klogInt, rc, "failed to write data to row $(row_id)'"
                                                     , "row_id=%ld"
                                                     , rid
                                                     ));
                                            break;
                                        }
                                        if ( rc == 0 )
                                        {
                                            rc = VCursorCommitRow ( curs );
                                            if ( rc != 0 )
                                                LOGERR ( klogErr, rc, "failed to commit row" );
                                        }
                                        
                                        rc2 = VCursorCloseRow ( curs );
                                        if ( rc2 != 0 )
                                        {
                                            LOGERR ( klogErr, rc2, "failed to close cursor row" );
                                            if ( rc == 0 )
                                                rc = rc2;
                                        }
                                    }
                                }
                                
                                if ( GetRCState ( rc ) == rcDone )
                                    rc = 0;
                                
                                if ( rc == 0 )
                                    rc = VCursorCommit ( curs );
                            }
                        }
                        
                        VCursorRelease ( curs );
                    }
                    
#if 1
                    if ( rc == 0 )
                        rc = VTableReindex ( vtbl );
#endif
                    
                    VTableRelease ( vtbl );
                }
            }
            
            VSchemaRelease ( schema );
        }
        
        VDBManagerRelease ( vmgr );
    }
    
    return rc;
}
コード例 #11
0
ファイル: rowwritetest.c プロジェクト: gconcepcion/sratoolkit
rc_t run (const char * table_path, uint64_t N )
{
    static const char *colInf[] = {
        "C1: Same value, same length",
        "C2: Var. value, same length",
        "C3: Var. value, var. legnth",
        "C4: Same value except I row",
        "C5: Same value except L row" };
    rc_t rc;
    uint64_t row = 0;
    VDBManager *mgr = NULL;
    VSchema *schema = NULL;
    VTable *table = NULL;
    VCursor *cursor;
    uint32_t idx[COLUMNS];
    uint64_t total[COLUMNS];
    int i = 0, j = 0, prev = 0;
    char *buffer[BUFFERS];
    



    /* Initialize arrays */
    memset(&idx, 0, sizeof idx);
    memset(&total, 0, sizeof total);
    for (i = 0; i < BUFFERS; ++i) {
        char c;
        size_t sz = ROWLEN + 1;
        if (i == (BUFFERS - 1))
            sz += ROWLEN;
        buffer[i] = malloc(sz);
        for (j = 0, c = 0; j < sz - 1; ++j, ++c) {
            if (c >= ROWLEN)
                c -= ROWLEN;
            buffer[i][j] = '0' + c;
        }
        buffer[i][j] = '\0';
    }
    /* Create manager */
    rc = VDBManagerMakeUpdate(&mgr, NULL);
    if (rc != 0) {
        LOGERR(klogInt, rc, "failed to open vdb library");
    }
    /* Initialize schema */
    if (rc == 0) {
        rc = VDBManagerMakeSchema(mgr, &schema);
        if (rc != 0)
            LOGERR(klogInt, rc, "failed to create empty schema");
    }
    if (rc == 0) {
        char text[512] = "table Table #1 {\n";
        char col [128];
        for (i = 1; i <=  COLUMNS; ++i) {
            sprintf(col,
                "  column ascii C%d = .C%d; physical ascii .C%d = C%d;\n",
                i, i, i, i);
            strcat(text, col);
        }
        strcat(text, "};");
        STSMSG(1,("Parsing schema:\n%s", text));
        rc = VSchemaParseText(schema, "Schema", text, strlen(text));
        if (rc != 0)
            LOGERR(klogInt, rc, "failed to parse schema");
    }
    /* Create table */
    if (rc == 0) {
        STSMSG(1,("Creating %s", tablePath));
        rc = VDBManagerCreateTable(mgr, &table, schema, "Table", kcmInit,
            tablePath);
        if (rc != 0)
            LOGERR(klogInt, rc, "failed to create table");
    }
    /* Initialize cursor */
    if (rc == 0) {
        rc = VTableCreateCursorWrite(table, &cursor, kcmInsert);
        if (rc != 0)
            LOGERR(klogInt, rc, "failed to create cursor");
    }
    for (i = 0; rc == 0 && i < COLUMNS; ++i) {
        char col[3];
        sprintf(col, "C%d", i + 1);
        STSMSG(2,("Adding column %s to cursor", col));
        rc = VCursorAddColumn(cursor, &idx[i], col);
        if (rc != 0)
            PLOGERR(klogInt, (klogInt, rc,
                              "failed to add $(c) to cursor", "c=%s", col));
    }
    if (rc == 0) {
        rc = VCursorOpen(cursor);
        if (rc != 0)
            LOGERR(klogInt, rc, "failed to open cursor");
    }
    /* Write data */
    for (row = 0; row < N && rc == 0; ++row) {
        int max = 2 * ROWLEN - 1;
        int sz = 0;
        if ((row % 2) == 0) {
            int min = 1;
            sz = min + (int) (max * (rand() / (RAND_MAX + 1.0)));
            prev = sz;
            buffer[1][0] = '1';
        }
        else {
            sz = max + 1 - prev;
            buffer[1][0] = '2';
        }
        rc = Quitting();
        if (rc == 0) {
            KStsLevel lvl = 2;
            if (row > 0 && ((row % ROWS) == 0)) {
                lvl = 1;
            }
            STSMSG (lvl, ("Writing row %ji / %ji",
                          row + 1, N));
            rc = VCursorOpenRow(cursor);
            if (rc != 0)
                LOGERR(klogInt, rc, "failed to open row");
        }
        for (j = 0; j < COLUMNS && rc == 0; ++j) {
            uint32_t count = 0;
            int buf = j;
            switch (j) {
                case 0:
                case 1:
                    count = strlen(buffer[j]);
                    break;
                case 2:
                    count = sz;
                    break;
                case 3:
                    buf = 0;
                    if (row == 0)
                        buf = 1;
                    count = strlen(buffer[buf]);
                    break;
                case 4:
                    buf = 0;
                    if (row == (N - 1))
                        buf = 1;
                    count = strlen(buffer[buf]);
                    break;
                default:
                    assert(0);
                    break;
            }
            STSMSG (3, ("Row %ji/Col.%d: %sd %.*s\n",
                        row + 1, j + 1, count, count, buffer[buf]));
            rc = VCursorWrite
                (cursor, idx[j], 8, buffer[buf], 0, count);
            if (rc != 0)
                PLOGERR(klogInt, (klogInt, rc, "failed to write row[$i]", "i=%d", j + 1));
            total[j] += count;
        }
        if (rc == 0) {
            rc = VCursorCommitRow(cursor);
            if (rc != 0)
                LOGERR(klogInt, rc, "failed to commit row");
        }
        if (rc == 0) {
            rc = VCursorCloseRow(cursor);
            if (rc != 0)
                LOGERR(klogInt, rc, "failed to close row");
        }
    }
    if (rc == 0) {
        STSMSG (1, ("Commiting cursor\n"));
        rc = VCursorCommit(cursor);
        if (rc != 0)
            LOGERR(klogInt, rc, "failed to commit cursor");
    }
    /* Cleanup */
    VCursorRelease(cursor);
    VTableRelease(table);
    VSchemaRelease(schema);
    VDBManagerRelease(mgr);
    for (i = 0; i < BUFFERS; ++i) {
        free(buffer[i]);
    }
    /* Log */
    if (rc == 0) {
        PLOGMSG(klogInfo, (klogInfo, "$(t)", "t=%s", tablePath));
        PLOGMSG(klogInfo,(klogInfo, 
            "$(n)($(N)) rows written - $(b) bytes per row",
                          PLOG_I64(n) "," PLOG_X64(N) ",b=%d", N, N, ROWLEN));
        for (i = 0; i < COLUMNS; ++i) {
            PLOGMSG(klogInfo,(klogInfo, 
                              "$(i): $(n)($(N)) bytes",
                              "i=%s," PLOG_I64(n) "," PLOG_X64(N),
                              colInf[i], total[i], total[i]));
        }
    }
    if (rc == 0) {
        KDirectory *dir = NULL;
        uint64_t sizes[COLUMNS];
        memset(&sizes, 0, sizeof sizes);
        rc = KDirectoryNativeDir(&dir);
        if (rc != 0)
            LOGERR(klogInt, rc, "failed to KDirectoryNativeDir");
        else {
            for (i = 1; i <= COLUMNS; ++i) {
                uint64_t size = 0;
#define  FORMAT    "%s/col/%s/data"
#define KFORMAT "$(d)/col/$(n)/data", "d=%s,n=%s"
#define  STATUS(action) (action FORMAT, tablePath, name)
                char name[3];

                sprintf(name, "C%d", i);
                STSMSG (1, STATUS("checking "));
                rc = KDirectoryFileSize(dir, &size, FORMAT, tablePath, name);
                if (rc != 0) {
                    if (GetRCState(rc) == rcNotFound) {
                        STSMSG (2, STATUS("not found "));
                        rc = 0;
                    }
                    else
                        PLOGERR(klogInt, (klogInt, rc,
                                          "failed to check " KFORMAT, tablePath, name));
                }
                else {
                    STSMSG (2, STATUS("found "));
                }
                PLOGMSG(klogInfo, (klogInfo, "Size of $(d)/col/$(n)/data = $(s)",
                                   "d=%s,n=%s," PLOG_I64(s), tablePath, name, size));
                sizes[i - 1] = size;
            }
        }
        KDirectoryRelease(dir);
        if (rc == 0) {
            puts("");
            KOutMsg("%ld rows, %d bytes per row:\n", N, ROWLEN);
            for (i = 0; i < COLUMNS; ++i) {
                puts(colInf[i]);
            }
            puts("");
            for (i = 0; i < COLUMNS; ++i) {
                int64_t over = sizes[i] - total[i];
                KOutMsg("C%d: %9ld bytes written; "
                    "%9ld in 'data'", i + 1, total[i], sizes[i]);
                if (over > 0) {
                    double p = 100.0 * over / sizes[i];
                    printf(": %7ld extra bytes (%.4f%%)\n", over, p);
                }
                else {
                    puts("");
                }
            }
        }
    }

    return rc;
}
コード例 #12
0
static rc_t DbInit(rc_t rc, const CmdLine* args, Db* db)
{
    const char name[] = "READ_FILTER";

    assert(args && db);

    memset(db, 0, sizeof *db);

    if (rc != 0)
    {   return rc; }

    db->table = args->table;

    if (rc == 0) {
        rc = VDBManagerMakeUpdate(&db->mgr, NULL);
        DISP_RC(rc, "while calling VDBManagerMakeUpdate");
    }

    if (rc == 0) {
        rc = VDBManagerWritable(db->mgr, args->table);
        if (rc != 0) {
            if (GetRCState(rc) == rcLocked)
            {
                rc = VDBManagerUnlock(db->mgr, args->table);
                if (rc != 0) {
                    PLOGERR(klogErr, (klogErr, rc,
                        "while calling VDBManagerUnlock('$(table)')",
                        "table=%s", args->table));
                }
                db->locked = true;
            }
            else {
                PLOGERR(klogErr, (klogErr, rc,
                    "while calling VDBManagerWritable('$(table)')",
                    "table=%s", args->table));
                if (rc == RC(rcDB, rcPath, rcAccessing, rcPath, rcReadonly)) {
                    PLOGERR(klogErr, (klogErr, rc,
                        "N.B. It is possible '$(table)' was not locked properly"
                        , "table=%s", args->table));
                }
            }
        }
    }

    if (rc == 0) {
        db->locked = true; /* has to be locked in production mode */
        rc = VDBManagerOpenTableUpdate (db->mgr, &db->tbl, NULL, args->table);
        if (rc != 0) {
	    VDatabase *vdb;
	    rc_t rc2 = VDBManagerOpenDBUpdate ( db->mgr, &vdb, NULL , args->table );
	    if( rc2 == 0) {
		rc2 = VDatabaseOpenTableUpdate ( vdb, &db->tbl, "SEQUENCE" );
		if (rc2 == 0 ) rc = 0;
		VDatabaseRelease ( vdb );
	    }
        }
	if(rc != 0){
            PLOGERR(klogErr, (klogErr, rc,
                "while opening VTable '$(table)'", "table=%s", args->table));
	}
    } 
    if( rc == 0) {
        rc = VTableCreateCursorRead(db->tbl, &db->rCursor);
        DISP_RC(rc, "while creating read cursor");
        if (rc == 0) {
            rc = VCursorAddColumn(db->rCursor, &db->rFilterIdx, "%s", name);
            if (rc != 0) {
                PLOGERR(klogErr, (klogErr, rc,
                    "while adding $(name) to read cursor", "name=%s", name));
            }
        }
        if (rc == 0) {
            rc = VCursorOpen(db->rCursor);
            DISP_RC(rc, "while opening read cursor");
        }
    }
    if (rc == 0) {
        rc = VTableCreateCursorWrite(db->tbl, &db->wCursor, kcmInsert);
        DISP_RC(rc, "while creating write cursor");
        if (rc == 0) {
            rc = VCursorAddColumn(db->wCursor, &db->wIdx, "%s", name);
            if (rc != 0) {
                PLOGERR(klogErr, (klogErr, rc,
                    "while adding $(name) to write cursor", "name=%s", name));
            }
        }
        if (rc == 0) {
            rc = VCursorOpen(db->wCursor);
            DISP_RC(rc, "while opening write cursor");
        }
    }

    return rc;
}
コード例 #13
0
ファイル: sortreadtest.c プロジェクト: Jingyu9/sra-tools
rc_t open (param_block * pb)
{
    rc_t rc;

    rc = KDirectoryNativeDir (&pb->pwd);
    if (rc)
        LOGERR (klogFatal, rc, "Failed to open file system");
    else
    {
        rc = KDirectoryOpenFileRead (pb->pwd, &pb->file, "%s", pb->file_path);
        if (rc)
            LOGERR (klogFatal, rc, "Failed to open input file");
        else
        {
            rc = KMMapMakeRead (&pb->mmap, pb->file);
            if (rc)
                LOGERR (klogFatal, rc, "unable to map file");
            else
            {
                rc = VDBManagerMakeUpdate (&pb->mgr, pb->pwd);
                if (rc)
                    LOGERR (klogFatal, rc, "Failed to open DB Manager");
                else
                {
                    rc = VDBManagerMakeSchema (pb->mgr, &pb->schema);
                    if (rc)
                        LOGERR (klogFatal, rc, "Failed to create a schema object");
                    else
                    {
                        VSchemaAddIncludePath (pb->schema, "interfaces");

                        rc = VSchemaParseFile (pb->schema, "%s", pb->schema_path);
                        if (rc)
                            LOGERR (klogFatal, rc, "Failed to parse schema");
                        else
                        {
                            rc = VDBManagerCreateTable (pb->mgr, &pb->table, pb->schema,
                                                        TYPESPEC, kcmCreate, "%s", pb->table_path);
                            if (rc)
                                LOGERR (klogFatal, rc, "Failed to create table");
                            else
                            {
                                rc = VTableCreateCursorWrite (pb->table, &pb->cursor, kcmCreate);
                                if (rc)
                                    LOGERR (klogFatal, rc, "Failed to create cursor");
                                else
                                {
                                    rc = VCursorAddColumn (pb->cursor, &pb->idx, "READ");
                                    if (rc)
                                        LOGERR (klogFatal, rc, "Failed to add READ to cursor");
                                    else
                                    {
                                        rc = VCursorOpen (pb->cursor);
                                        if (rc)
                                            LOGERR (klogFatal, rc, "Failed to open cursor");
                                        else
                                        {
                                            rc = write_rows (pb);
                                            if (rc == 0)
                                                VCursorCommit (pb->cursor);
                                        }
                                    }
                                    VCursorRelease (pb->cursor);
                                }
                                VTableRelease (pb->table);
                            }
                        }
                        VSchemaRelease (pb->schema);
                    }
                    VDBManagerRelease (pb->mgr);
                }
                KMMapRelease (pb->mmap);
            }
            KFileRelease (pb->file);
        }
        KDirectoryRelease (pb->pwd);
    }
    return rc;
}