自学教程：C++ sqlQuickString函数代码示例

static boolean ctdExists(struct section *section, 	struct sqlConnection *conn, char *geneId)/* Return TRUE if CTD database exists and it has an entry with the gene symbol */{char query[1024];char *geneSymbol;if (isRgdGene(conn))    {    if (sqlTableExists(conn, "rgdGene2Xref") == FALSE) return FALSE;    }else    {    if (sqlTableExists(conn, "kgXref") == FALSE) return FALSE;    }if (sqlTableExists(conn, "hgFixed.ctdSorted") == TRUE)    {    if (isRgdGene(conn))	{	sqlSafef(query, sizeof(query), "select ChemicalId from rgdGene2Xref x, hgFixed.ctdSorted c"	" where x.info=c.GeneSymbol and infoType = 'Name' and rgdGeneId='%s' limit 1", geneId);	geneSymbol = sqlQuickString(conn, query);	}    else        {	sqlSafef(query, sizeof(query), "select ChemicalId from kgXref x, hgFixed.ctdSorted c"	" where x.geneSymbol=c.GeneSymbol and kgId='%s' limit 1", geneId);	geneSymbol = sqlQuickString(conn, query);	}    if (geneSymbol != NULL) return(TRUE);    }return(FALSE);}

static boolean geneReviewsExists(struct section *section,        struct sqlConnection *conn, char *geneId)/* Return TRUE if geneReviewsDetail table exist and have GeneReviews articles * on this one. */{char query[256];char * geneSymbol;char * grSymbol;if (sqlTableExists(conn, "geneReviewsDetail"))    {       sqlSafef(query, sizeof(query), "select geneSymbol from kgXref where kgId = '%s'", geneId);       geneSymbol = sqlQuickString(conn, query);       if (geneSymbol != NULL)          {             sqlSafef(query, sizeof(query), "select  geneSymbol from geneReviewsDetail where geneSymbol='%s'", geneSymbol);             grSymbol = sqlQuickString(conn, query);             if (grSymbol != NULL)                {                  return TRUE;                }           }     }return FALSE;}

char *bamFileNameFromTable(struct sqlConnection *conn, char *table, char *bamSeqName)/* Return file name from table.  If table has a seqName column, then grab the  * row associated with bamSeqName (which can be e.g. '1' not 'chr1' if that is the * case in the bam file). */{boolean checkSeqName = (sqlFieldIndex(conn, table, "seqName") >= 0);if (checkSeqName && bamSeqName == NULL)    errAbort("bamFileNameFromTable: table %s has seqName column, but NULL seqName passed in",	     table);char query[512];if (checkSeqName)    sqlSafef(query, sizeof(query), "select fileName from %s where seqName = '%s'",	  table, bamSeqName);else    sqlSafef(query, sizeof(query), "select fileName from %s", table);char *fileName = sqlQuickString(conn, query);if (fileName == NULL && checkSeqName)    {    if (startsWith("chr", bamSeqName))	sqlSafef(query, sizeof(query), "select fileName from %s where seqName = '%s'",	      table, bamSeqName+strlen("chr"));    else	sqlSafef(query, sizeof(query), "select fileName from %s where seqName = 'chr%s'",	      table, bamSeqName);    fileName = sqlQuickString(conn, query);    }if (fileName == NULL)    {    if (checkSeqName)	errAbort("Missing fileName for seqName '%s' in %s table", bamSeqName, table);    else	errAbort("Missing fileName in %s table", table);    }return fileName;}

void findClosestServer(char **pDb, char **pOrg)/* If db doesn't have a blat server, look for the closest db (or org) that has one, * as hgPcr does. */{char *db = *pDb, *org = *pOrg;struct sqlConnection *conn = hConnectCentral();char query[256];safef(query, sizeof(query), "select db from blatServers where db = '%s'", db);if (!sqlExists(conn, query))    {    safef(query, sizeof(query), "select blatServers.db from blatServers,dbDb "	  "where blatServers.db = dbDb.name and dbDb.genome = '%s'", org);    char *db = sqlQuickString(conn, query);    if (db == NULL)	{	safef(query, sizeof(query), "select blatServers.db from blatServers,dbDb "	      "where blatServers.db = dbDb.name order by dbDb.orderKey,dbDb.name desc");	char *db = sqlQuickString(conn, query);	if (db == NULL)	    errAbort("central database tables blatServers and dbDb are disjoint/empty");	else	    {	    *pDb = db;	    *pOrg = hGenome(db);	    }	}    else	{	*pDb = db;	*pOrg = hGenome(db);	}    }hDisconnectCentral(&conn);}

char *docIdSubmit(struct sqlConnection *conn, char *docIdTable, struct docIdSub *docIdSub,     char *docIdDir, char *type){verbose(2, "Submitting------/n");verbose(2, "status %d/n", docIdSub->status);verbose(2, "assembly %s/n", docIdSub->assembly);verbose(2, "submitDate %s/n", docIdSub->submitDate);verbose(2, "md5sum %s/n", docIdSub->md5sum);verbose(2, "valReport %s/n", docIdSub->valReport);verbose(2, "valVersion %s/n", docIdSub->valVersion);verbose(2, "metaData %s/n", docIdSub->metaData);verbose(2, "submitPath %s/n", docIdSub->submitPath);verbose(2, "submitter %s/n", docIdSub->submitter);verbose(2, "type %s/n", type);char query[1024 * 1024];fillNull(&docIdSub->valReport);fillNull(&docIdSub->md5sum);sqlSafef(query, sizeof query, "insert into %s (status, assembly, submitDate, md5sum, valReport, valVersion, metaData, submitPath, submitter) values (/"%d/",/"%s/",/"%s/",/"%s/", /"%s/", /"%s/", /"%s/",/"%s/",/"%s/")/n", docIdTable,    docIdSub->status, docIdSub->assembly, docIdSub->submitDate, docIdSub->md5sum, docIdSub->valReport, docIdSub->valVersion, docIdSub->metaData, docIdSub->submitPath, docIdSub->submitter);    //docIdSub->submitDate, docIdSub->md5sum, docIdSub->valReport, "null", docIdSub->submitPath, docIdSub->submitter);//printf("query is %s/n", query);char *response = sqlQuickString(conn, query);printf("submitted got response %s/n", response);sqlSafef(query, sizeof query, "select last_insert_id()");char *docId = cloneString(sqlQuickString(conn, query));printf("submitted got docId %s/n", docId);if (!fileExists(docIdSub->submitPath))    errAbort("cannot open %s/n", docIdSub->submitPath);char *linkToFile = docIdGetPath(docId, docIdDir, type, docIdSub->submitPath);printf("linking %s to file %s/n", docIdSub->submitPath, linkToFile);char *slash = strrchr(linkToFile, '/');if (slash == NULL)    errAbort("can't find slash in path %s/n", linkToFile);*slash = 0;makeDirsOnPath(linkToFile);*slash = '/';if (link(docIdSub->submitPath, linkToFile) < 0)    errnoAbort("can't link %s to file %s/n", docIdSub->submitPath, linkToFile);return docId;}

static char *findGeneId(struct sqlConnection *conn, char *name)/* Given some sort of gene name, see if it is in our primary gene table, and if not * look it up in alias table if we have one. */{/* Just check if it's in the main gene table, and if so return input name. */char *mainTable = genomeSetting("knownGene");char query[256];sqlSafef(query, sizeof(query), "select count(*) from %s where name = '%s'", mainTable, name);if (sqlQuickNum(conn, query) > 0)    return name;else    {    /* check OMIM gene symbol table first */    if (sqlTableExists(conn, "omimGeneSymbol"))    	{    	sqlSafef(query, sizeof(query), "select geneSymbol from omimGeneSymbol where geneSymbol= '%s'", name);    	char *symbol = sqlQuickString(conn, query);    	if (symbol != NULL)	    {    	    sqlSafef(query, sizeof(query), "select kgId from kgXref where geneSymbol = '%s'", symbol);    	    char *kgId = sqlQuickString(conn, query);	    if (kgId != NULL)	    	{    	    	/* The canonical gene is preferred */	        sqlSafef(query, sizeof(query), 		"select c.transcript from knownCanonical c,knownIsoforms i where i.transcript = '%s' and i.clusterId=c.clusterId", kgId);    	        char *canonicalKgId = sqlQuickString(conn, query);	    	if (canonicalKgId != NULL) 		    {		    return canonicalKgId;		    }		else                    return(kgId);		}	    }	}    }char *alias = genomeOptionalSetting("kgAlias");if (alias != NULL && sqlTableExists(conn, alias))     {     sqlSafef(query, sizeof(query), "select kgID from %s where alias = '%s'", alias, name);     char *id = sqlQuickString(conn, query);     if (id == NULL)         hUserAbort("Couldn't find %s in %s.%s or %s.%s", name, database, mainTable, database, alias);     return id;     }else     hUserAbort("Couldn't find %s in %s.%s", name, database, mainTable);return NULL;}

char *spCommentVal(struct sqlConnection *conn, int valId)/* Look up text associated with valId. freeMem result when done. */{char query[256];safef(query, sizeof(query), "select val from commentVal where id=%d", valId);return sqlQuickString(conn, query);}

static char *otherOrgPositionFromDb(struct otherOrg *otherOrg, char *id)/* Get position of id from other organism database, if possible. */{struct hTableInfo *hti = hFindTableInfo(otherOrg->db, NULL,                                        otherOrg->geneTable);if (hti == NULL)    return NULL;  // table  not foundstruct sqlConnection *conn = hAllocConn(otherOrg->db);char query[512];safef(query, sizeof(query),      "select concat(%s, ':', %s+1, '-', %s) from %s "      "where %s = '%s'",      hti->chromField, hti->startField, hti->endField,      otherOrg->geneTable, hti->nameField, id);char *pos = sqlQuickString(conn, query);if (pos != NULL)    {    char posPlus[2048];    safef(posPlus, sizeof(posPlus), "%s&%s=%s&hgFind.matches=%s",          pos,          otherOrg->geneTable, hTrackOpenVis(sqlGetDatabase(conn), otherOrg->geneTable),          id);    hFreeConn(&conn);    freez(&pos);    return cloneString(posPlus);    }else    {    hFreeConn(&conn);    return NULL;    }}

void addImagesMatchingStage(struct visiSearcher *searcher,	struct sqlConnection *conn, int schemeId, int taxon,	char *minAge, int wordIx, int wordCount)/* Given a developmental stage scheme (schemeId) and a specific * stage, return all images that match stage */{struct dyString *dy = dyStringNew(0);char *maxAge;// note in the code below minAge and maxAge are strings//  but they should contain float values.  Putting single-quotes//  around them and escaping their contents is something that will //  protect against sql injection.dyStringClear(dy);sqlDyStringPrintf(dy,     "select age from lifeStage where lifeStageScheme = %d ",     schemeId);sqlDyStringPrintf(dy,    "and age > '%s' order by age", minAge);maxAge = sqlQuickString(conn, dy->string);dyStringClear(dy);sqlDyStringPrintf(dy, "select image.id from specimen,image ");sqlDyStringPrintf(dy, "where specimen.age >= '%s' ", minAge);if (maxAge != NULL)    sqlDyStringPrintf(dy, "and specimen.age < '%s' ", maxAge);dyStringPrintf(dy, "and specimen.taxon = %d ", taxon);dyStringPrintf(dy, "and specimen.id = image.specimen");addImagesMatchingQuery(searcher, conn, dy->string, NULL, NULL,	wordIx, wordCount);dyStringFree(&dy);}

struct visiMatch *removeMutants(struct sqlConnection *conn,	struct visiMatch *matchList)/* Remove images that are associated with mutant genotypes * from list. */{struct visiMatch *match, *next, *newList = NULL;for (match = matchList; match != NULL; match = next)    {    char *genotype;    char query[256];    next = match->next;    sqlSafef(query, sizeof(query),        "select genotype.alleles from image,specimen,genotype "	"where image.id=%d and image.specimen=specimen.id "	"and specimen.genotype=genotype.id", match->imageId);    genotype = sqlQuickString(conn, query);    if (genotype == NULL || genotype[0] == 0 ||    	startsWith("wild type", genotype))	{	slAddHead(&newList, match);	}    freeMem(genotype);    }slReverse(&newList);return newList;}

void doLabContacts(struct cart *theCart){char *subId = cartString(theCart, "lab");cartWebStart(cart, database, "ENCODE DCC:  Contacts for submission: %s",subId);struct sqlConnection *conn = sqlConnect(database);char query[10 * 1024];struct sqlResult *sr;char **row;printf("<a href=docIdView?db=%s> Return </a><BR>", database);safef(query, sizeof query, "select user_id from %s where id = %s ", "projects",subId);char *userId = sqlQuickString(conn, query);safef(query, sizeof query, "select name,email,pi from %s where id = '%s' ", "users",userId);sr = sqlGetResult(conn, query);printf("<pre>");while ((row = sqlNextRow(sr)) != NULL)    {    printf("Name:  %s/nEmail: %s/nPI:    %s", row[0], row[1], row[2]);    }sqlFreeResult(&sr);sqlDisconnect(&conn);cartWebEnd();}

void addImagesMatchingStage(struct visiSearcher *searcher,	struct sqlConnection *conn, int schemeId, int taxon,	char *minAge, int wordIx, int wordCount)/* Given a developmental stage scheme (schemeId) and a specific * stage, return all images that match stage */{struct dyString *dy = dyStringNew(0);char *maxAge;dyStringClear(dy);dyStringPrintf(dy,     "select age from lifeStage where lifeStageScheme = %d ",     schemeId);dyStringPrintf(dy,    "and age > %s order by age", minAge);maxAge = sqlQuickString(conn, dy->string);dyStringClear(dy);dyStringPrintf(dy, "select image.id from specimen,image ");dyStringPrintf(dy, "where specimen.age >= %s ", minAge);if (maxAge != NULL)    dyStringPrintf(dy, "and specimen.age < %s ", maxAge);dyStringPrintf(dy, "and specimen.taxon = %d ", taxon);dyStringPrintf(dy, "and specimen.id = image.specimen");addImagesMatchingQuery(searcher, conn, dy->string, NULL, NULL,	wordIx, wordCount);dyStringFree(&dy);}

static void mrnaDescriptionsPrint(struct section *section, 	struct sqlConnection *conn, char *geneId)/* Print out mrna descriptions annotations. */{struct psl *psl, *pslList = section->items;for (psl = pslList; psl != NULL; psl = psl->next)    {    if (basesShared(curGenePred, psl) > 12)	/* Filter out possible little noisy flecks. */        {	char query[512];	char *description;	safef(query, sizeof(query),	    "select description.name from gbCdnaInfo,description"	    " where gbCdnaInfo.acc='%s' and gbCdnaInfo.description = description.id"	    , psl->qName);	description = sqlQuickString(conn, query);	if (description != NULL)	    {	    char *url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"	    		"?cmd=Search&db=Nucleotide&term=%s&doptcmdl=GenBank"			"&tool=genome.ucsc.edu";	    hPrintf("<A HREF=/"");	    hPrintf(url, psl->qName);	    hPrintf("/" TARGET=_blank>");	    hPrintf("%s</A> - ", psl->qName);	    hPrintf("%s<BR>", description);	    }	freeMem(description);	}    }}

void getEcHtml(char *ecNumber)/* fetch ec codes and descriptions and output html */{char query[1024];struct sqlConnection *conn = hAllocConn("ec");char *level1 = NULL;char *level2 = NULL;char *level3 = NULL;//char *level4 = NULL;struct ecAttribute attr;char **row = NULL;struct sqlResult *sr = NULL;if (ecNumber == NULL)    return;if (conn == NULL)    return;sqlSafef(query,sizeof(query), "select distinct e.description from ecAttribute a , ecCode e where a.ec = /"%s/" and a.level1 = e.level1 and e.level2 = 0 ",ecNumber);level1 = sqlQuickString(conn, query);sqlSafef(query,sizeof(query), "select distinct e.description from ecAttribute a , ecCode e where a.ec = /"%s/" and a.level1 = e.level1 and a.level2 = e.level2 and e.level3 = 0 ",ecNumber);level2 = sqlQuickString(conn, query);sqlSafef(query,sizeof(query), "select distinct e.description from ecAttribute a , ecCode e where a.ec = /"%s/" and a.level1 = e.level1 and a.level2 = e.level2 and a.level3 = e.level3 and e.level4 = 0 ",ecNumber);level3 = sqlQuickString(conn, query);//sqlSafef(query,sizeof(query), "select distinct description from ecAttribute a where a.ec = /"%s/" ",ecNumber);//level4 = sqlQuickString(conn, query);printf("[ %s / %s / %s ] <BR>",        (level1 != NULL) ? level1 :"n/a",         (level2 != NULL) ? level2 :"n/a",         (level3 != NULL) ? level3 :"n/a"//        (level4 != NULL) ? level4 :"n/a"        );sqlSafef(query,sizeof(query), "select * from ecAttribute a where a.ec = /"%s/"",ecNumber);sr = sqlGetResult(conn, query);while ((row = sqlNextRow(sr)) != NULL)    {    char *attrDesc = NULL;    struct sqlConnection *conn2 = hAllocConn("ec");    ecAttributeStaticLoad(row, &attr);    sqlSafef(query,sizeof(query), "select description from ecAttributeCode where type = /"%s/" ",attr.type);    attrDesc = sqlQuickString(conn2, query);    if (differentString(attr.type, "DR"))        printf("<B>EC %s:</B> %s<BR>", attrDesc != NULL ? attrDesc : "n/a",attr.description);    hFreeConn(&conn2);    }hFreeConn(&conn);}

static char *getCgapId(struct sqlConnection *conn)/* Get cgap ID. */{char query[256];sqlSafef(query, sizeof(query), 	"select cgapId from cgapAlias where alias=/"%s/"", curGeneName);return sqlQuickString(conn, query);}

char *xyzCellVal(struct column *col, struct genePos *gp,                 struct sqlConnection *conn)/* Make comma separated list of matches to association table. */{    char query[1000];    sqlSafef(query, sizeof(query), "select %s from %s where %s = '%s'",             col->valField, col->table, col->keyField, gp->name);    return sqlQuickString(conn, query);}

void checkForGeoMirrorRedirect(struct cart *cart)// Implement Geo/IP based redirection.{char *thisNodeStr = geoMirrorNode();if (thisNodeStr)   // if geo-mirroring is enabled    {    char *redirectCookie = findCookieData("redirect");    char *redirect = cgiOptionalString("redirect");    // if we're not already redirected    if (redirect == NULL && redirectCookie == NULL)         {        int thisNode = sqlUnsigned(thisNodeStr);        struct sqlConnection *centralConn = hConnectCentral();        char *ipStr = cgiRemoteAddr();        int node = defaultNode(centralConn, ipStr);        // if our node is not the node that's closest.        if (thisNode != node)            {	    char *geoSuffix = cfgOptionDefault("browser.geoSuffix","");            char query[1056];            sqlSafef(query, sizeof query, "select domain from gbNode%s where node = %d", geoSuffix, node);            char *newDomain = sqlQuickString(centralConn, query);            char *oldDomain = cgiServerName();            char *port = cgiServerPort();            char *uri = cgiRequestUri();            char *sep = strchr(uri, '?') ? "&" : "?";            int newUriSize = strlen(uri) + 1024;            char *newUri = needMem(newUriSize);            char *oldUri = needMem(newUriSize);            safef(oldUri, newUriSize, "http%s://%s:%s%s%sredirect=manual&source=%s", 		cgiServerHttpsIsOn() ? "s" : "", oldDomain, port, uri, sep, oldDomain);            safef(newUri, newUriSize, "http%s://%s:%s%s%sredirect=manual&source=%s", 		cgiServerHttpsIsOn() ? "s" : "", newDomain, port, uri, sep, oldDomain);	    printf("<TR><TD COLSPAN=3 id='redirectTd' onclick=/"javascript:document.getElementById('redirectTd').innerHTML='';/">"	    "<div style=/"margin: 10px 25%%; border-style:solid; border-width:thin; border-color:#97D897;/">"	    "<h3 style=/"background-color: #97D897; text-align: left; margin-top:0px; margin-bottom:0px;/">"	    "&nbsp;You might want to navigate to your nearest mirror - %s"	    "</h3> "	    "<ul style=/"margin:5px;/">",	    newDomain);	    	    printf("<li>User settings (sessions and custom tracks) <B>will differ</B> between sites."		"<idiv style=/"float:right;/"><a href=/"../goldenPath/help/genomeEuro.html#sessions/">Read more.</a></idiv>");	    printf("<li>Take me to  <a href=/"%s/">%s</a> </li>",		newUri, newDomain);	    printf("<li>Let me stay here   <a href=/"%s/">%s</a>",		oldUri, oldDomain );	    printf("</div></TD></TR>/n");            exit(0);            }        hDisconnectCentral(&centralConn);        }    }}

static struct slName* getExonFrames(char *table, struct sqlConnection *conn, struct bed *bedList)/* get real exonFrames if they are available */{struct slName* list = NULL;struct bed *bed;for (bed = bedList;  bed != NULL;  bed = bed->next)    {    // be super specific, the same name may align to multiple locations    //  or even the same location with alternate splicing or exon structure.        // convert bed block coordinates to exonStarts, exonEnds    int i;    struct dyString *exonStarts = newDyString(256);    struct dyString *exonEnds = newDyString(256);    for( i = 0 ; i < bed->blockCount; i++ )	{	int exonStart = bed->chromStart + bed->chromStarts[i];	int exonEnd = exonStart + bed->blockSizes[i];	dyStringPrintf(exonStarts, "%d,", exonStart);	dyStringPrintf(exonEnds,   "%d,", exonEnd);	}    char sql[4096+strlen(exonStarts->string)+strlen(exonEnds->string)];    sqlSafef(sql, sizeof sql, "select exonFrames "	"from %s where " 	"name = '%s' and "  	"chrom = '%s' and "	"strand = '%c' and "	"txStart = %d and "	"txEnd = %d and "	"cdsStart = %d and "	"cdsEnd = %d and "        "exonCount = %d and "        "exonStarts = '%s' and "        "exonEnds = '%s'"	, 	table, 	bed->name,	bed->chrom,	bed->strand[0],	bed->chromStart,	bed->chromEnd,	bed->thickStart,	bed->thickEnd,	bed->blockCount,	exonStarts->string,	exonEnds->string	);    char *exonFrames = sqlQuickString(conn, sql);    slNameAddHead(&list, exonFrames);    dyStringFree(&exonStarts);    dyStringFree(&exonEnds);    }slReverse(&list);return list;}

boolean edwSubmitShouldStop(struct sqlConnection *conn, unsigned submitId)/* Return TRUE if there's an error message on submit, indicating we should stop. */{char query[256];sqlSafef(query, sizeof(query), "select errorMessage from edwSubmit where id=%u", submitId);char *errorMessage = sqlQuickString(conn, query);boolean ret = isNotEmpty(errorMessage);freez(&errorMessage);return ret;}

char *getCdsString(struct sqlConnection *conn, char *acc)/* get the CDS string for an accession, or null if not found */{char query[256];safef(query, sizeof(query),      "SELECT cds.name FROM gbCdnaInfo,cds WHERE (gbCdnaInfo.acc = '%s') AND (gbCdnaInfo.cds != 0) AND (gbCdnaInfo.cds = cds.id)",      acc);return sqlQuickString(conn, query);}

char *hubNameFromUrl(char *hubUrl)/* Given the URL for a hub, return its hub_# name. */{char query[PATH_LEN*4];sqlSafef(query, sizeof(query), "select concat('hub_', id) from %s where hubUrl = '%s'",         getHubStatusTableName(), hubUrl);struct sqlConnection *conn = hConnectCentral();char *name = sqlQuickString(conn, query);hDisconnectCentral(&conn);return name;}

/*	Return is an array of integers, last one of value zero to indicate the *	end of the array.  In case of nothing found in trackDb, return *	a NULL pointer indicating no results.  * *      If the value is 'first' then use the first span value from the table. *      Assumes that all values in the table are the same. */int *wiggleSpanList(struct sqlConnection *conn, struct trackDb *tdb){char *tdbDefault = cloneString(trackDbSettingOrDefault(tdb, SPANLIST, "NONE"));int *ret = (int *)NULL;if (sameWord("NONE",tdbDefault))    {    struct hashEl *hel;    /*	if not found in trackDb, maybe it is in tdb->settings     *	(custom tracks keep settings here)     */    if ((tdb->settings != (char *)NULL) &&	(tdb->settingsHash != (struct hash *)NULL))	{	if ((hel = hashLookup(tdb->settingsHash, SPANLIST)) != NULL)	    {	    freeMem(tdbDefault);	    tdbDefault = cloneString((char *)hel->val);	    }	}    }/* if we still don't have a spanList, or we got "first" for spanList, * make up spanList by choosing the first span we find in the table *///if (sameWord("NONE",tdbDefault) || sameWord("first",tdbDefault))else if( sameWord("first",tdbDefault))    {    char query[1024];    snprintf(query, sizeof(query), "SELECT span FROM %s limit 1", tdb->table );    char *tmpSpan = sqlQuickString(conn, query);    AllocArray(ret,2);    ret[0] = sqlUnsigned(tmpSpan);    ret[1] = 0;    freeMem(tmpSpan);    }else     {    /*	If something found, let's parse it	*/    int i;    char *words[MAX_SPAN_COUNT];    int wc;    wc = chopCommas(tdbDefault,words);    AllocArray(ret,wc+1);	/*	+ 1 for the extra zero	*/    for ( i = 0; i < wc; ++i )	ret[i] = sqlUnsigned(words[i]);    intSort(wc,ret);    ret[wc] = 0;	/*	end of list	*/    }freeMem(tdbDefault);return(ret);}	/*	int *wiggleSpanList(struct trackDb *tdb)	*/

void tellSubscribers(struct sqlConnection *conn, char *submitDir, char *submitFileName, unsigned id)/* Tell subscribers that match about file of given id */{char query[256];sqlSafef(query, sizeof(query), "select tags from edwFile where id=%u", id);char *tagsString = sqlQuickString(conn, query);struct hash *tagHash=NULL;struct cgiVar *tagList=NULL;if (!isEmpty(tagsString))    cgiParseInputAbort(tagsString, &tagHash, &tagList);char **row;struct sqlResult *sr = sqlGetResult(conn, "NOSQLINJ select * from edwSubscriber order by runOrder,id");while ((row = sqlNextRow(sr)) != NULL)    {    struct edwSubscriber *subscriber = edwSubscriberLoad(row);    if (wildMatch(subscriber->filePattern, submitFileName)        && wildMatch(subscriber->dirPattern, submitDir))	{	/* Might have to check for tags match, which involves db load and a cgi vs. cgi compare */	boolean tagsOk = TRUE;	if (!isEmpty(subscriber->tagPattern))	    {	    if (tagHash == NULL)  // if we're nonempty they better be too	        tagsOk = FALSE;	    else	        {		if (!allTagsWildMatch(subscriber->tagPattern, tagHash))		    tagsOk = FALSE;		}	    }	if (tagsOk)	    {	    int maxNumSize=16;	// more than enough digits base ten.	    int maxCommandSize = strlen(subscriber->onFileEndUpload) + maxNumSize + 1;	    char command[maxCommandSize];	    safef(command, sizeof(command), subscriber->onFileEndUpload, id);	    verbose(2, "system(%s)/n", command);	    int err = system(command);	    if (err != 0)	        warn("err %d from system(%s)/n", err, command);	    }	}    edwSubscriberFree(&subscriber);    }sqlFreeResult(&sr);freez(&tagsString);slFreeList(&tagList);hashFree(&tagHash);}

void submitToDir(struct sqlConnection *conn, struct sqlConnection *conn2, struct sqlConnection *connSp,    char *outDir, char *inJax)/* Create directory full of visiGeneLoad .ra/.tab files from * jackson database connection.  Creates a pair of files for * each submission set.   Returns outDir. */{struct dyString *query = dyStringNew(0);struct slName *ref, *refList = sqlQuickList(conn, NOSQLINJ "select distinct(_Refs_key) from GXD_Assay");int refCount = 0;makeDir(outDir);for (ref = refList; ref != NULL; ref = ref->next)    {    char path[PATH_LEN];    char *pub=NULL;    boolean skip;    /* Check that it isn't on our skip list - one that we     * have already in the database from a higher resolution     * source. */    dyStringClear(query);    sqlDyStringPrintf(query, "select title from BIB_Refs where _Refs_key = %s",     	ref->name);    pub = sqlQuickString(conn, query->string);    if (!pub)	{	verbose(1,"ref %s: missing title from BIB_Refs, ref skipped/n",ref->name);	continue;	}    skip = oneSubmissionSet ?  oneSubmissionSet != sqlSigned(ref->name) : FALSE;    if (!skip)	{	safef(path, sizeof(path), "%s/%s", outDir, ref->name);	submitRefToFiles(conn, conn2, connSp, ref->name, path, inJax);	refCount += 1;	if (testMax != 0 && refCount >= testMax)	     errAbort("Reached testMax %d output dirs [%s]/n", testMax, path);	}    freeMem(pub);    }    verbose(1,"refCount=%d/n",refCount);slNameFreeList(&refList);dyStringFree(&query);}