自学教程：C++ sqlUpdate函数代码示例

static void initTable(struct sqlConnection *conn, char *table, boolean nuke)/* build tables */{char *sql = NULL;char path[256];if (nuke)    sqlDropTable(conn, table);if (!sqlTableExists(conn, table))    {    safef(path,sizeof(path),"%s/%s.sql",sqlPath,table);    readInGulp(path, &sql, NULL);    sqlUpdate(conn, sql);    }}

static void advanceType(struct sqlConnection *conn, int taxon, char *oldType, char *newType)/* find any remaining type refSeq that couldn't be resolved and demote  * them to type genbank */{ struct dyString *dy = dyStringNew(0);dyStringClear(dy);dyStringPrintf(dy,  "update vgPrb set type='%s', tName=''" " where taxon = %d and state = 'new' and type='%s'" ,newType,taxon,oldType);sqlUpdate(conn, dy->string);dyStringFree(&dy);}

void loadIntoDatabase(char *database, char *createString, char *table, char *tabName)/* Load tabbed file into database table. */{    struct sqlConnection *conn = sqlConnect(database);    struct dyString *ds = newDyString(2048);    dyStringPrintf(ds, createString, table);    sqlRemakeTable(conn, table, ds->string);    dyStringClear(ds);    dyStringPrintf(ds,                   "LOAD data local infile '%s' into table %s", tabName, table);    sqlUpdate(conn, ds->string);    sqlDisconnect(&conn);    freeDyString(&ds);}

static void deleteJoin(struct sqlDeleter* sd, struct sqlConnection *conn,                       char* table, char* column)/* delete by creating a new table with a join */{char query[512], newTmpTable[64], oldTmpTable[64];if (sd->accLoader != NULL)    {    /* build table, free to indicate it's completed */    assert(!sd->deletesDone);    sqlRemakeTable(conn, GB_DELETE_TMP, createGbDeleteTmp);    sqlUpdaterCommit(sd->accLoader, conn);    sqlUpdaterFree(&sd->accLoader);    }sd->deletesDone = TRUE;/* remove existing tmp tables */safef(newTmpTable, sizeof(newTmpTable), "%s_new_tmp", table);safef(oldTmpTable, sizeof(oldTmpTable), "%s_old_tmp", table);sqlDropTable(conn, newTmpTable);sqlDropTable(conn, oldTmpTable);gbSqlDupTableDef(conn, table, newTmpTable);/* do join into new table of entries not in accession table */safef(query, sizeof(query),      "INSERT INTO %s SELECT %s.* FROM %s LEFT JOIN %s "      "ON (%s.%s = %s.acc) WHERE %s.acc IS NULL",      newTmpTable, table, table, GB_DELETE_TMP, table, column,      GB_DELETE_TMP, GB_DELETE_TMP);sqlUpdate(conn, query);/* Now swap the table into place */safef(query, sizeof(query), "RENAME TABLE %s TO %s, %s TO %s",      table, oldTmpTable, newTmpTable, table);sqlUpdate(conn, query);sqlDropTable(conn, oldTmpTable);}

void dbRIPSaveToDbEscaped(struct sqlConnection *conn, struct dbRIP *el, char *tableName, int updateSize)/* Save dbRIP as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size. * of a string that would contain the entire query. Automatically * escapes all simple strings (not arrays of string) but may be slower than dbRIPSaveToDb(). * For example automatically copies and converts: * "autosql's features include" --> "autosql/'s features include" * before inserting into database. */{    struct dyString *update = newDyString(updateSize);    char  *chrom, *name, *strand, *originalId, *forwardPrimer, *reversePrimer, *polyClass, *polyFamily, *polySubfamily, *polySeq, *polySource, *reference, *ascertainingMethod, *remarks, *disease, *genoRegion;    chrom = sqlEscapeString(el->chrom);    name = sqlEscapeString(el->name);    strand = sqlEscapeString(el->strand);    originalId = sqlEscapeString(el->originalId);    forwardPrimer = sqlEscapeString(el->forwardPrimer);    reversePrimer = sqlEscapeString(el->reversePrimer);    polyClass = sqlEscapeString(el->polyClass);    polyFamily = sqlEscapeString(el->polyFamily);    polySubfamily = sqlEscapeString(el->polySubfamily);    polySeq = sqlEscapeString(el->polySeq);    polySource = sqlEscapeString(el->polySource);    reference = sqlEscapeString(el->reference);    ascertainingMethod = sqlEscapeString(el->ascertainingMethod);    remarks = sqlEscapeString(el->remarks);    disease = sqlEscapeString(el->disease);    genoRegion = sqlEscapeString(el->genoRegion);    dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s',%g,%d,%d,'%s','%s')",                   tableName,  chrom, el->chromStart , el->chromEnd ,  name, el->score ,  strand,  originalId,  forwardPrimer,  reversePrimer,  polyClass,  polyFamily,  polySubfamily,  polySeq,  polySource,  reference,  ascertainingMethod,  remarks, el->tm , el->filledSize , el->emptySize ,  disease,  genoRegion);    sqlUpdate(conn, update->string);    freeDyString(&update);    freez(&chrom);    freez(&name);    freez(&strand);    freez(&originalId);    freez(&forwardPrimer);    freez(&reversePrimer);    freez(&polyClass);    freez(&polyFamily);    freez(&polySubfamily);    freez(&polySeq);    freez(&polySource);    freez(&reference);    freez(&ascertainingMethod);    freez(&remarks);    freez(&disease);    freez(&genoRegion);}

void ggMrnaBlockSaveToDbEscaped(struct sqlConnection *conn, struct ggMrnaBlock *el, char *tableName, int updateSize)/* Save ggMrnaBlock as a row to the table specified by tableName.  * As blob fields may be arbitrary size updateSize specifies the approx size. * of a string that would contain the entire query. Automatically  * escapes all simple strings (not arrays of string) but may be slower than ggMrnaBlockSaveToDb(). * For example automatically copies and converts:  * "autosql's features include" --> "autosql/'s features include"  * before inserting into database. */ {struct dyString *update = newDyString(updateSize);dyStringPrintf(update, "insert into %s values ( %d,%d,%d,%d)", 	tableName, el->qStart , el->qEnd , el->tStart , el->tEnd );sqlUpdate(conn, update->string);freeDyString(&update);}

void ggMrnaAliSaveToDb(struct sqlConnection *conn, struct ggMrnaAli *el, char *tableName, int updateSize)/* Save ggMrnaAli as a row to the table specified by tableName.  * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. Note that strings must be escaped to allow insertion into the database. * For example "autosql's features include" --> "autosql/'s features include"  * If worried about this use ggMrnaAliSaveToDbEscaped() */{struct dyString *update = newDyString(updateSize);dyStringPrintf(update, "insert into %s values ( '%s',%d,%d,'%s','%s',%d,%d,%u,%d,%d,%d,%d, NULL )", 	tableName,  el->tName,  el->tStart,  el->tEnd,  el->strand,  el->qName,  el->qStart,  el->qEnd,  el->baseCount,  el->orientation,  el->hasIntrons,  el->milliScore,  el->blockCount);sqlUpdate(conn, update->string);freeDyString(&update);}

void polyGenotypeSaveToDb(struct sqlConnection *conn, struct polyGenotype *el, char *tableName, int updateSize)/* Save polyGenotype as a row to the table specified by tableName.  * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. Note that strings must be escaped to allow insertion into the database. * For example "autosql's features include" --> "autosql/'s features include"  * If worried about this use polyGenotypeSaveToDbEscaped() */{struct dyString *update = newDyString(updateSize);dyStringPrintf(update, "insert into %s values ( '%s','%s',%d,%d,%d,%d,%g,%g)", 	tableName,  el->name,  el->ethnicGroup,  el->plusPlus,  el->plusMinus,  el->minusMinus,  el->sampleSize,  el->alleleFrequency,  el->unbiasedHeterozygosity);sqlUpdate(conn, update->string);freeDyString(&update);}

void dbRIPSaveToDb(struct sqlConnection *conn, struct dbRIP *el, char *tableName, int updateSize)/* Save dbRIP as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. Note that strings must be escaped to allow insertion into the database. * For example "autosql's features include" --> "autosql/'s features include" * If worried about this use dbRIPSaveToDbEscaped() */{    struct dyString *update = newDyString(updateSize);    dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s','%s','%s','%s','%s','%s',%s,'%s',%s,'%s','%s',%g,%d,%d,'%s','%s')",                   tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->originalId,  el->forwardPrimer,  el->reversePrimer,  el->polyClass,  el->polyFamily,  el->polySubfamily,  el->polySeq,  el->polySource,  el->reference,  el->ascertainingMethod,  el->remarks,  el->tm,  el->filledSize,  el->emptySize,  el->disease,  el->genoRegion);    sqlUpdate(conn, update->string);    freeDyString(&update);}

void hapmapPrimateAllelesSaveToDb(struct sqlConnection *conn, struct hapmapPrimateAlleles *el, char *tableName, int updateSize)/* Save hapmapPrimateAlleles as a row to the table specified by tableName.  * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. Note that strings must be escaped to allow insertion into the database. * For example "autosql's features include" --> "autosql/'s features include"  * If worried about this use hapmapPrimateAllelesSaveToDbEscaped() */{struct dyString *update = newDyString(updateSize);dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%c','%c','%c','%s',%u,'%c','%s',%u,'%s',%u,'%c','%s',%u)", 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->refAllele,  el->otherAllele,  el->chimpChrom,  el->chimpPos,  el->chimpStrand,  el->chimpAllele,  el->chimpQual,  el->rhesusChrom,  el->rhesusPos,  el->rhesusStrand,  el->rhesusAllele,  el->rhesusQual);sqlUpdate(conn, update->string);freeDyString(&update);}

void cnpSharpCutoffSaveToDb(struct sqlConnection *conn, struct cnpSharpCutoff *el, char *tableName, int updateSize)/* Save cnpSharpCutoff as a row to the table specified by tableName.  * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. Note that strings must be escaped to allow insertion into the database. * For example "autosql's features include" --> "autosql/'s features include"  * If worried about this use cnpSharpCutoffSaveToDbEscaped() */{struct dyString *update = newDyString(updateSize);dyStringPrintf(update, "insert into %s values ( '%s',%u,%g)", 	tableName,  el->sample,  el->batch,  el->value);sqlUpdate(conn, update->string);freeDyString(&update);}

void genotypeSaveToDb(struct sqlConnection *conn, struct genotype *el, char *tableName, int updateSize)/* Save genotype as a row to the table specified by tableName.  * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. Note that strings must be escaped to allow insertion into the database. * For example "autosql's features include" --> "autosql/'s features include"  * If worried about this use genotypeSaveToDbEscaped() */{struct dyString *update = newDyString(updateSize);dyStringPrintf(update, "insert into %s values ( '%s','%s','%s',%d,'%c','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s')", 	tableName,  el->rsId,  el->SNPalleles,  el->chrom,  el->chromStart,  el->strand,  el->assembly,  el->center,  el->protLSID,  el->assayLSID,  el->panelLSID,  el->NA06985,  el->NA06991,  el->NA06993,  el->NA06993_dup,  el->NA06994,  el->NA07000,  el->NA07019,  el->NA07022,  el->NA07029,  el->NA07034,  el->NA07048,  el->NA07055,  el->NA07056,  el->NA07345,  el->NA07348,  el->NA07357,  el->NA10830,  el->NA10831,  el->NA10835,  el->NA10838,  el->NA10839,  el->NA10846,  el->NA10847,  el->NA10851,  el->NA10854,  el->NA10855,  el->NA10856,  el->NA10857,  el->NA10859,  el->NA10860,  el->NA10861,  el->NA10863,  el->NA11829,  el->NA11830,  el->NA11831,  el->NA11832,  el->NA11839,  el->NA11840,  el->NA11881,  el->NA11882,  el->NA11992,  el->NA11993,  el->NA11993_dup,  el->NA11994,  el->NA11995,  el->NA12003,  el->NA12003_dup,  el->NA12004,  el->NA12005,  el->NA12006,  el->NA12043,  el->NA12044,  el->NA12056,  el->NA12057,  el->NA12144,  el->NA12145,  el->NA12146,  el->NA12154,  el->NA12155,  el->NA12156,  el->NA12156_dup,  el->NA12234,  el->NA12236,  el->NA12239,  el->NA12248,  el->NA12248_dup,  el->NA12249,  el->NA12264,  el->NA12707,  el->NA12716,  el->NA12717,  el->NA12740,  el->NA12750,  el->NA12751,  el->NA12752,  el->NA12753,  el->NA12760,  el->NA12761,  el->NA12762,  el->NA12763,  el->NA12801,  el->NA12802,  el->NA12812,  el->NA12813,  el->NA12814,  el->NA12815,  el->NA12864,  el->NA12865,  el->NA12872,  el->NA12873,  el->NA12874,  el->NA12875,  el->NA12878,  el->NA12891,  el->NA12892);sqlUpdate(conn, update->string);freeDyString(&update);}

static void loadDatabase(char* database,                         char* table,                         struct traceInfo* traceInfoList)/* Load the trace information into the database. */{struct sqlConnection *conn = NULL;FILE *tmpFh = NULL; struct traceInfo* trace = NULL;char query[512];/* Write it as tab-delimited file. */printf("Writing tab-delimited file %s/n", TMP_TAB_FILE);tmpFh = mustOpen(TMP_TAB_FILE, "w");for (trace = traceInfoList; trace != NULL; trace = trace->next)    {    traceInfoTabOut(trace, tmpFh);    }carefulClose(&tmpFh);/* Import into database. */printf("Importing into %d rows into %s/n",       slCount(traceInfoList), database);conn = sqlConnect(database);if (!sqlTableExists(conn, table))    errAbort("You need to create the table first (with %s.sql)", table);sqlSafef(query, sizeof query, "delete from %s", table);sqlUpdate(conn, query);sqlSafef(query, sizeof query, "load data local infile '%s' into table %s", TMP_TAB_FILE,        table);sqlUpdate(conn, query);sqlDisconnect(&conn);unlink(TMP_TAB_FILE);printf("Import complete/n");}

static void markNoneVgPrbAli(struct sqlConnection *conn, int fromTaxon, char *db, char *table)/* mark records in vgPrbAli that did not find any alignment for db */{struct dyString *dy = dyStringNew(0);dyStringClear(dy);dyStringPrintf(dy,"update %s a, vgPrb e"" set a.status = 'none'"" where a.status = 'new'"" and a.db = '%s' and e.taxon = %d"" and a.vgPrb = e.id"    ,table,db,fromTaxon);sqlUpdate(conn, dy->string);dyStringFree(&dy);}

static int getLocalHost(struct sqlConnection *conn)/* Make up record for local host if it is not there already. */{char query[256];sqlSafef(query, sizeof(query), "select id from edwHost where name = '%s'", localHostName);int hostId = sqlQuickNum(conn, query);if (hostId == 0)    {    sqlSafef(query, sizeof(query), "insert edwHost(name, firstAdded) values('%s', %lld)",	localHostName,  edwNow());    sqlUpdate(conn, query);    hostId = sqlLastAutoId(conn);    }return hostId;}

void loadOneTable(char *database, struct sqlConnection *conn, char *tempName, char *tableName)/* Load .tab file tempName into tableName and remove tempName. */{    struct dyString *query = newDyString(1024);    verbose(1, "Loading up table %s/n", tableName);    if (sqlTableExists(conn, tableName))    {        sqlDyStringPrintf(query, "DROP table %s", tableName);        sqlUpdate(conn, query->string);    }    /* Create first part of table definitions, the fields. */    dyStringClear(query);    sqlDyStringPrintf(query, createRmskOut, tableName);    /* Create the indexes */    if (!noSplit)    {        dyStringAppend(query, "   INDEX(bin))/n");    }    else    {        int indexLen = hGetMinIndexLength(database);        sqlDyStringPrintf(query, "   INDEX(genoName(%d),bin))/n", indexLen);    }    sqlUpdate(conn, query->string);    /* Load database from tab-file. */    dyStringClear(query);    sqlDyStringPrintf(query, "LOAD data local infile '%s' into table %s",                      tempName, tableName);    sqlUpdate(conn, query->string);    remove(tempName);}

void tigrCmrGeneSaveToDb(struct sqlConnection *conn, struct tigrCmrGene *el, char *tableName, int updateSize)/* Save tigrCmrGene as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. Note that strings must be escaped to allow insertion into the database. * For example "autosql's features include" --> "autosql/'s features include" * If worried about this use tigrCmrGeneSaveToDbEscaped() */{    struct dyString *update = newDyString(updateSize);    dyStringPrintf(update, "insert into %s values ( %d,'%s',%u,%u,'%s',%u,'%s',%s,'%s','%s','%s',%u,%u,%s,%s,'%s','%s',%f,%f,%f,'%s')",                   tableName,  el->bin,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->tigrCommon,  el->tigrGene,  el->tigrECN,  el->primLocus,  el->tigrLength,  el->tigrPepLength,  el->tigrMainRole,  el->tigrSubRole,  el->swissProt,  el->genbank,  el->tigrMw,  el->tigrPi,  el->tigrGc,  el->goTerm);    sqlUpdate(conn, update->string);    freeDyString(&update);}

void makeItemsItemSaveToDb(struct sqlConnection *conn, struct makeItemsItem *el, char *tableName, int updateSize)/* Save makeItemsItem as a row to the table specified by tableName.  * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. Note that strings must be escaped to allow insertion into the database. * For example "autosql's features include" --> "autosql/'s features include"  * If worried about this use makeItemsItemSaveToDbEscaped() */{struct dyString *update = newDyString(updateSize);dyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s',%u,'%s',%u,%u,%u,%s,%u)", 	tableName,  el->bin,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->thickStart,  el->thickEnd,  el->itemRgb,  el->description,  el->id);sqlUpdate(conn, update->string);freeDyString(&update);}

static void populateMissingVgPrbAli(struct sqlConnection *conn, int taxon, char *db, char *table)/* populate vgPrbAli for db */{struct dyString *dy = dyStringNew(0);dyStringClear(dy);dyStringPrintf(dy,"insert into %s"" select distinct '%s', e.id, 'new' from vgPrb e"" left join %s a on e.id = a.vgPrb and a.db = '%s'"" where a.vgPrb is NULL "" and e.taxon = %d"    ,table,db,table,db,taxon);sqlUpdate(conn, dy->string);dyStringFree(&dy);}

void edwAddSubmitJob(struct sqlConnection *conn, char *userEmail, char *url, boolean update)/* Add submission job to table and wake up daemon. */{/* Create command and add it to edwSubmitJob table. */char command[strlen(url) + strlen(userEmail) + 256];safef(command, sizeof(command), "edwSubmit %s'%s' %s", (update ? "-update " : ""), url, userEmail);char query[strlen(command)+128];sqlSafef(query, sizeof(query), "insert edwSubmitJob (commandLine) values('%s')", command);sqlUpdate(conn, query);/* Write sync signal (any string ending with newline) to fifo to wake up daemon. */FILE *fifo = mustOpen("../userdata/edwSubmit.fifo", "w");fputc('/n', fifo);carefulClose(&fifo);}

int edwGetHost(struct sqlConnection *conn, char *hostName)/* Look up host name in table and return associated ID.  If not found * make up new table entry. */{/* If it's already in table, just return ID. */char query[512];sqlSafef(query, sizeof(query), "select id from edwHost where name='%s'", hostName);int hostId = sqlQuickNum(conn, query);if (hostId > 0)    return hostId;sqlSafef(query, sizeof(query), "insert edwHost (name, firstAdded, paraFetchStreams) values('%s', %lld, 10)",        hostName, edwNow());sqlUpdate(conn, query);return sqlLastAutoId(conn);}

void edwRunOnIds(char *program, char *queryString)/* edwRunOnIds - Run a edw command line program (one that takes startId endId as it's two parameters) for a range of ids,  * putting it on edwJob queue. */{struct sqlConnection *conn = edwConnectReadWrite();struct slName *id, *idList = sqlQuickList(conn, queryString);for (id = idList; id != NULL; id = id->next)    {    char query[512];    sqlSafef(query, sizeof(query), "insert into %s (commandLine) values ('%s %s %s')",	runTable, program, id->name, id->name);    sqlUpdate(conn, query);    }}

void gtexGeneBedSaveToDb(struct sqlConnection *conn, struct gtexGeneBed *el, char *tableName, int updateSize)/* Save gtexGeneBed as a row to the table specified by tableName.  * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */{struct dyString *update = newDyString(updateSize);char  *expScoresArray;expScoresArray = sqlFloatArrayToString(el->expScores, el->expCount);sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s','%s',%u,'%s')", 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->geneId,  el->geneType,  el->expCount,  expScoresArray );sqlUpdate(conn, update->string);freeDyString(&update);freez(&expScoresArray);}

void edwFileResetTags(struct sqlConnection *conn, struct edwFile *ef, char *newTags)/* Reset tags on file, strip out old validation and QA,  schedule new validation and QA. *//* Remove existing QA records and rerun QA agent on given file.   */{long long fileId = ef->id;/* Update database to let people know format revalidation is in progress. */char query[4*1024];sqlSafef(query, sizeof(query), "update edwFile set errorMessage = '%s' where id=%lld",     "Revalidation in progress.", fileId); sqlUpdate(conn, query);/* Update tags for file in edwFile table. */sqlSafef(query, sizeof(query), "update edwFile set tags='%s' where id=%lld", newTags, fileId);sqlUpdate(conn, query);    /* Get rid of records referring to file in other validation and qa tables. */sqlSafef(query, sizeof(query), "delete from edwFastqFile where fileId=%lld", fileId);sqlUpdate(conn, query);sqlSafef(query, sizeof(query),    "delete from edwQaPairSampleOverlap where elderFileId=%lld or youngerFileId=%lld",    fileId, fileId);sqlUpdate(conn, query);sqlSafef(query, sizeof(query),    "delete from edwQaPairCorrelation where elderFileId=%lld or youngerFileId=%lld",    fileId, fileId);sqlUpdate(conn, query);sqlSafef(query, sizeof(query), "delete from edwQaEnrich where fileId=%lld", fileId);sqlUpdate(conn, query);sqlSafef(query, sizeof(query), "delete from edwQaContam where fileId=%lld", fileId);sqlUpdate(conn, query);sqlSafef(query, sizeof(query), "delete from edwQaRepeat where fileId=%lld", fileId);sqlUpdate(conn, query);sqlSafef(query, sizeof(query),     "delete from edwQaPairedEndFastq where fileId1=%lld or fileId2=%lld",    fileId, fileId);sqlUpdate(conn, query);/* schedule validator */edwAddQaJob(conn, ef->id);}

static int getLocalSubmit(struct sqlConnection *conn)/* Get the submission that covers all of our local additions. */{int dirId = getLocalSubmitDir(conn);char query[256];sqlSafef(query, sizeof(query), "select id from edwSubmit where submitDirId='%d'", dirId);int submitId = sqlQuickNum(conn, query);if (submitId == 0)    {    sqlSafef(query, sizeof(query), "insert edwSubmit (submitDirId,startUploadTime) values(%d,%lld)",	dirId, edwNow());    sqlUpdate(conn, query);    submitId = sqlLastAutoId(conn);    }return submitId;}

int edwGetSubmitDir(struct sqlConnection *conn, int hostId, char *submitDir)/* Get submitDir from database, creating it if it doesn't already exist. */{/* If it's already in table, just return ID. */char query[512];sqlSafef(query, sizeof(query), "select id from edwSubmitDir where url='%s'", submitDir);int dirId = sqlQuickNum(conn, query);if (dirId > 0)    return dirId;sqlSafef(query, sizeof(query),    "insert edwSubmitDir (url, firstAdded, hostId) values('%s', %lld, %d)",    submitDir, edwNow(), hostId);sqlUpdate(conn, query);return sqlLastAutoId(conn);}

static void insertHubUrlInStatus(char *url)/* add a url to the hubStatus table */{struct sqlConnection *conn = hConnectCentral();char query[4096];char *statusTable = getHubStatusTableName();if (sqlFieldIndex(conn, statusTable, "firstAdded") >= 0)    sqlSafef(query, sizeof(query), "insert into %s (hubUrl,firstAdded) values (/"%s/",now())",	statusTable, url);else    sqlSafef(query, sizeof(query), "insert into %s (hubUrl) values (/"%s/")",	statusTable, url);sqlUpdate(conn, query);hDisconnectCentral(&conn);}

void cdwRetryJob(char *database, char *jobTable)/* cdwRetryJob - Add jobs that failed back to a cdwJob format queue.. */{/* Figure out thresholds for age. */long long now = cdwNow();long long maxTimeThreshold = now - 24*3600 * maxTime;/* Get list of all jobs ordered by ID with most recent job first. */struct sqlConnection *conn = sqlConnect(database);char query[512];sqlSafef(query, sizeof(query), "select * from %s order by id desc", jobTable);struct cdwJob *job, *jobList = cdwJobLoadByQuery(conn, query);/* Loop through job list looking for commandLines that failed or timed out  in their * most recent attempt. */struct hash *jobHash = hashNew(0);struct slRef *failRef, *failRefList = NULL;for (job = jobList; job != NULL; job = job->next)    {    if (hashLookup(jobHash, job->commandLine) == NULL)        {	hashAdd(jobHash, job->commandLine, job);	if (job->id >= minId && job->startTime != 0)	    {	    boolean timedOut = (job->startTime < maxTimeThreshold && job->endTime == 0);	    if (job->returnCode != 0 || timedOut)	        {		refAdd(&failRefList, job);		}	    }	}    }/* Loop through failed list printing or retrying */for (failRef = failRefList; failRef != NULL; failRef = failRef->next)    {    job = failRef->val;    if (dry)	printf("%s/n", job->commandLine);    else	{	sqlSafef(query, sizeof(query), 	    "insert into %s (commandLine) values ('%s')",  jobTable, job->commandLine);	sqlUpdate(conn, query);	}    } }

void edwCreateNewUser(char *email)/* Create new user, checking that user does not already exist. */{/* Now make sure user is not already in user table. */struct sqlConnection *conn = edwConnectReadWrite();struct dyString *query = dyStringNew(0);sqlDyStringPrintf(query, "select count(*) from edwUser where email = '%s'", email);if (sqlQuickNum(conn, query->string) > 0)    errAbort("User %s already exists", email);/* Do database insert. */dyStringClear(query);sqlDyStringPrintf(query, "insert into edwUser (email) values('%s')", email);sqlUpdate(conn, query->string);sqlDisconnect(&conn);}