C++ (Cpp) gbMetaDataDeleteFromIdTables Examples

Example #1

File: gbIgnoreDelete.c Project: CEpBrowser/CEpBrowser--from-UCSC-CGI-BIN

static void deleteFromTables(char *db, struct sqlConnection *conn,
                             struct sqlDeleter* deleter, unsigned srcDb,
                             struct dbLoadOptions* options)
/* deleted acc in a sqlDeleter from all tables. */
{
/* order is important here */
gbAlignDataDeleteFromTables(db, conn, srcDb, GB_MRNA, deleter, options);
gbAlignDataDeleteFromTables(db, conn, srcDb, GB_EST, deleter, options);

gbMetaDataDeleteFromIdTables(conn, options, deleter);
gbMetaDataDeleteFromTables(conn, options, srcDb, deleter);
sqlDeleterDel(deleter, conn, "gbStatus", "acc");
}

Example #2

File: gbMetaData.c Project: ucsc-mus-strain-cactus/kent

void gbMetaDataDeleteOutdated(struct sqlConnection *conn,
                              struct gbSelect* select,
                              struct gbStatusTbl* statusTbl,
                              struct dbLoadOptions* options,
                              char *tmpDir)
/* Delete outdated metadata.  Also delete genePred table entries for genes
 * where metadata changed but sequence has not.  These will have the genePred
 * records reloaded.*/
{
setGeneTblFlags(conn, options);
struct sqlDeleter* deleter = sqlDeleterNew(tmpDir, (gbVerbose >= 4));
struct sqlDeleter* geneTblDeleter = NULL;
struct sqlDeleter* derivedTblDeleter = NULL;
if (partitionMayHaveGeneTbls(select))
    geneTblDeleter = sqlDeleterNew(tmpDir, (gbVerbose >= 4));
if (select->type == GB_MRNA)
    derivedTblDeleter = sqlDeleterNew(tmpDir, (gbVerbose >= 4));
struct gbStatus* status;
gSrcDb = select->release->srcDb;
gOptions = options;
strcpy(gTmpDir, tmpDir);

/* Delete any meta modified from id tables */
for (status = statusTbl->seqChgList; status != NULL; status = status->next)
    {
    if (status->stateChg & GB_META_CHG)
        sqlDeleterAddAcc(deleter, status->acc);
    }
for (status = statusTbl->metaChgList; status != NULL; status = status->next)
    {
    assert(!(status->stateChg&GB_SEQ_CHG));
    if (status->stateChg&GB_META_CHG)
        sqlDeleterAddAcc(deleter, status->acc);
    else if (status->stateChg&GB_REBUILD_DERIVED)
        sqlDeleterAddAcc(derivedTblDeleter, status->acc);
    if (geneTblDeleter != NULL)
        {
        // need to just try, since we can set the status->isMgcFull
        // flag until we are reading the ra.
        sqlDeleterAddAcc(geneTblDeleter, status->acc);
        }
    }
for (status = statusTbl->deleteList; status != NULL; status = status->next)
    sqlDeleterAddAcc(deleter, status->acc);
for (status = statusTbl->orphanList; status != NULL; status = status->next)
    sqlDeleterAddAcc(deleter, status->acc);
gbMetaDataDeleteFromIdTables(conn, options, deleter);
sqlDeleterFree(&deleter);

/* remove deleted and orphans from metadata. */
deleter = sqlDeleterNew(tmpDir, (gbVerbose >= 4));
for (status = statusTbl->deleteList; status != NULL; status = status->next)
    sqlDeleterAddAcc(deleter, status->acc);
for (status = statusTbl->orphanList; status != NULL; status = status->next)
    sqlDeleterAddAcc(deleter, status->acc);

// must do gene tbls before other tables
if (geneTblDeleter != NULL)
    deleteFromGeneTbls(conn, select, geneTblDeleter);
gbMetaDataDeleteFromTables(conn, options, select->release->srcDb, deleter);

sqlDeleterFree(&deleter);
sqlDeleterFree(&geneTblDeleter);
sqlDeleterFree(&derivedTblDeleter);

/* If we are cleaning up the ext table, we need to get rid of any
 * refseq peptides in gbSeq that are no longer referenced.  We don't
 * do it other times as these are not reachable directly.
 */
if ((select->release->srcDb == GB_REFSEQ)
    && (gOptions->flags & DBLOAD_EXT_FILE_UPDATE))
    refSeqPepClean(conn);
}