Пример #1
0
int main(int argc, char **argv)
{
    void *value = NULL;

    ajulong length = 0;
    ajulong i = 0;
    ajuint j = 0;

    AjEnum client = ajESqlClientMySQL;

    AjPFile outf = NULL;

    AjPStr user = NULL;
    AjPStr password = NULL;
    AjPStr host = NULL;
    AjPStr port = NULL;
    AjPStr socket = NULL;
    AjPStr dbname = NULL;
    AjPStr statement = NULL;
    AjPStr result = NULL;

    AjPSqlconnection sqlc = NULL;
    AjPSqlstatement sqls = NULL;
    AjISqlrow sqli = NULL;
    AjPSqlrow row = NULL;

    embInit("sqltest", argc, argv);

    user = ajStrNewC("anonymous");
    password = ajStrNew();
    host = ajStrNewC("ensembldb.ensembl.org");
    port = ajStrNewC("3306");
    socket = ajStrNew();
    dbname = ajStrNew();
    statement = ajStrNewC("SHOW PROCESSLIST");
    result = ajStrNew();
    outf = ajAcdGetOutfile("outfile");

    if(!ajSqlInit())
        ajFatal("Library initialisation failed.");

    sqlc =
        ajSqlconnectionNewData(client, user, password, host, port, socket,
                               dbname);

    if(!sqlc)
        ajFatal("Could not connect as user '%S' to server '%S' at port '%S' "
                "to database '%S'", user, host, port, dbname);

    ajFmtPrintF(outf, "Connection to client %d\n",
                ajSqlconnectionGetClient(sqlc));

    sqls = ajSqlstatementNewRun(sqlc, statement);

    if(!sqls)
        ajFatal("SQL Statement did not complete: %S", statement);

    ajFmtPrintF(outf,
                "SQL Statement: %S\n",
                statement);

    ajFmtPrintF(outf,
                "Number of selected rows: %Lu\n",
                ajSqlstatementGetSelectedrows(sqls));

    ajFmtPrintF(outf,
                "Number of columns: %u\n",
                ajSqlstatementGetColumns(sqls));

    sqli = ajSqlrowiterNew(sqls);

    if(!sqli)
        ajFatal("Query Iterator not defined.");

    while(!ajSqlrowiterDone(sqli))
    {
        row = ajSqlrowiterGet(sqli);

        if(row)
        {
            ajDebug("main SQL Row %Lu Columns %u Current %u\n",
                    i, row->Columns, row->Current);

            for(j = 0; j < ajSqlstatementGetColumns(sqls); j++)
            {
                ajStrAssignClear(&result);

                if(ajSqlcolumnNumberGetValue(row, j, &value, &length))
                    ajDebug("main SQL Row %Lu Column %u Value %p Length %d\n",
                            i, j, value, length);

                ajSqlcolumnNumberToStr(row, j, &result);

                ajDebug("main SQL Row %Lu Column %u String '%S'\n",
                        i, j, result);

                ajFmtPrintF(outf, "Row: %Lu Column: %u String: '%S'\n", i, j,
                            result);
            }
        }

        else
            ajDebug("main No row returned!\n");

        i++;
    }

    ajSqlrowiterDel(&sqli);
    ajSqlstatementDel(&sqls);
    ajSqlconnectionDel(&sqlc);

    ajFileClose(&outf);

    ajStrDel(&user);
    ajStrDel(&password);
    ajStrDel(&host);
    ajStrDel(&port);
    ajStrDel(&socket);
    ajStrDel(&dbname);
    ajStrDel(&statement);
    ajStrDel(&result);

    embExit();

    return 0;
}
Пример #2
0
static AjBool karyotypeBandadaptorFetchAllBySQL(EnsPDatabaseadaptor dba,
                                                const AjPStr statement,
                                                EnsPAssemblymapper am,
                                                EnsPSlice slice,
                                                AjPList kblist)
{
    ajuint identifier = 0;
    
    ajuint srid    = 0;
    ajuint srstart = 0;
    ajuint srend   = 0;
    
    AjPStr name  = NULL;
    AjPStr stain = NULL;
    
    AjPSqlstatement sqls = NULL;
    AjISqlrow sqli       = NULL;
    AjPSqlrow sqlr       = NULL;
    
    EnsPCoordsystemadaptor csa = NULL;
    
    EnsPFeature feature = NULL;
    
    EnsPKaryotypeband kb         = NULL;
    EnsPKaryotypebandadaptor kba = NULL;
    
    EnsPSlice srslice   = NULL;
    EnsPSliceadaptor sa = NULL;
    
    if(!dba)
	return ajFalse;
    
    if(!statement)
	return ajFalse;
    
    (void) am;
    
    (void) slice;
    
    if(!kblist)
	return ajFalse;
    
    csa = ensRegistryGetCoordsystemadaptor(dba);

    /*
    ** AJB: The variable kba, set below, is not used elsewhere
    ** in the function. Needs fixing appropriately.
    */
    
    kba = ensRegistryGetKaryotypebandadaptor(dba);
    
    sa = ensRegistryGetSliceadaptor(dba);
    
    sqls = ensDatabaseadaptorSqlstatementNew(dba, statement);
    
    sqli = ajSqlrowiterNew(sqls);
    
    while(!ajSqlrowiterDone(sqli))
    {
	identifier = 0;
	srid       = 0;
	srstart    = 0;
	srend      = 0;
	name       = ajStrNew();
	stain      = ajStrNew();
	
	sqlr = ajSqlrowiterGet(sqli);
	
	ajSqlcolumnToUint(sqlr, &identifier);
	ajSqlcolumnToUint(sqlr, &srid);
	ajSqlcolumnToUint(sqlr, &srstart);
	ajSqlcolumnToUint(sqlr, &srend);
        ajSqlcolumnToStr(sqlr, &name);
        ajSqlcolumnToStr(sqlr, &stain);
	
	/* Need to get the internal Ensembl Sequence Region identifier. */
	
	srid = ensCoordsystemadaptorGetInternalSeqregionIdentifier(csa, srid);
	
	/*
	** FIXME: karyotype.seq_region_start and karyotype.seq_region_end are
	** defined as signed in the tables.sql file.
	** All other features use unsigned start and end coordinates.
	*/
	
	ensSliceadaptorFetchBySeqregionIdentifier(sa, srid, 0, 0, 0, &srslice);
	
	feature = ensFeatureNewS((EnsPAnalysis) NULL,
				 srslice,
				 srstart,
				 srend,
				 1);
	
	kb = ensKaryotypebandNew(identifier, feature, name, stain);
	
	ajListPushAppend(kblist, (void *) kb);
	
	ensFeatureDel(&feature);
	
	ensSliceDel(&srslice);
	
	ajStrDel(&name);
	ajStrDel(&stain);
    }
    
    ajSqlrowiterDel(&sqli);
    
    ajSqlstatementDel(&sqls);
    
    return ajTrue;
}
Пример #3
0
static AjBool assemblyexceptionadaptorFetchAllBySQL(
    EnsPAssemblyexceptionadaptor aea,
    const AjPStr statement,
    AjPList aes)
{
    ajint ori = 0;

    ajuint identifier = 0;
    ajuint erid       = 0;
    ajuint srid       = 0;
    ajuint erstart    = 0;
    ajuint srstart    = 0;
    ajuint erend      = 0;
    ajuint srend      = 0;

    AjPSqlstatement sqls = NULL;
    AjISqlrow sqli       = NULL;
    AjPSqlrow sqlr       = NULL;

    AjPStr typestr = NULL;

    EnsEAssemblyexceptionType type = ensEAssemblyexceptionTypeNULL;

    EnsPAssemblyexception ae = NULL;

    if(!aea)
        return ajFalse;

    if(!statement)
        return ajFalse;

    if(!aes)
        return ajFalse;

    sqls = ensDatabaseadaptorSqlstatementNew(aea->Adaptor, statement);

    sqli = ajSqlrowiterNew(sqls);

    while(!ajSqlrowiterDone(sqli))
    {
        identifier = 0;
        srid       = 0;
        srstart    = 0;
        srend      = 0;
        typestr    = ajStrNew();
        erid       = 0;
        erstart    = 0;
        erend      = 0;
        ori        = 0;

        type = ensEAssemblyexceptionTypeNULL;

        sqlr = ajSqlrowiterGet(sqli);

        ajSqlcolumnToUint(sqlr, &identifier);
        ajSqlcolumnToUint(sqlr, &srid);
        ajSqlcolumnToUint(sqlr, &srstart);
        ajSqlcolumnToUint(sqlr, &srend);
        ajSqlcolumnToStr(sqlr, &typestr);
        ajSqlcolumnToUint(sqlr, &erid);
        ajSqlcolumnToUint(sqlr, &erstart);
        ajSqlcolumnToUint(sqlr, &erend);
        ajSqlcolumnToInt(sqlr, &ori);

        /* Set the Assembly Exception type. */

        type = ensAssemblyexceptionTypeFromStr(typestr);

        if(!type)
            ajFatal("assemblyexceptionadaptorFetchAllBySQL "
                    "got unexpected Assembly Exception type '%S' "
                    "from database.\n",
                    typestr);

        ae = ensAssemblyexceptionNew(aea,
                                     identifier,
                                     srid,
                                     srstart,
                                     srend,
                                     erid,
                                     erstart,
                                     erend,
                                     ori,
                                     type);

        ajListPushAppend(aes, (void *) ae);

        ajStrDel(&typestr);
    }

    ajSqlrowiterDel(&sqli);

    ensDatabaseadaptorSqlstatementDel(aea->Adaptor, &sqls);

    return ajTrue;
}