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 found
struct 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);
}
char *spRefTitle(struct sqlConnection *conn, int refId)
/* Get title of reference. This can be NULL legitimately. */
{
char query[256];
safef(query, sizeof(query),
"select title from reference where id=%d", refId);
return sqlQuickString(conn, query);
}
char *spRefPubMed(struct sqlConnection *conn, int refId)
/* Get PubMed id. May be NULL legitimately. */
{
char query[256];
safef(query, sizeof(query),
"select pubMed from reference where id=%d", refId);
return sqlQuickString(conn, query);
}
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);
}
char *genoQuery(char *id, char *settingName, struct sqlConnection *conn)
/* Look up sql query in genome.ra given by settingName,
* plug id into it, and return. */
{
char query[256];
char *sql = genomeSetting(settingName);
sqlSafef(query, sizeof(query), sql, id);
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;\">"
" 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(¢ralConn);
}
}
}
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 *spIdToAcc(struct sqlConnection *conn, char *id)
/* Convert SwissProt ID (things like HXA1_HUMAN) to
* accession. Returns NULL if the conversion fails.
* (doesn't abort). */
{
char query[256];
safef(query, sizeof(query), "select acc from displayId where val = '%s'",
id);
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;
}
char *spOrganelle(struct sqlConnection *conn, char *acc)
/* Return text description of organelle. FreeMem this when done.
* This may return NULL if it's not an organelle. */
{
char query[256];
safef(query, sizeof(query),
"select organelle.val from info,organelle "
"where info.acc = '%s' and info.organelle = organelle.id"
, acc);
return sqlQuickString(conn, query);
}
char *spAccFromEmbl(struct sqlConnection *conn, char *acc)
/* Get SwissProt accession associated with EMBL mRNA. */
{
char query[256];
int emblId;
safef(query, sizeof(query), "select id from extDb where val = 'EMBL'");
emblId = sqlNeedQuickNum(conn, query);
safef(query, sizeof(query),
"select acc from extDbRef where extAcc1 = '%s' and extDb = %d"
, acc, emblId);
return sqlQuickString(conn, query);
}
/* 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);
}
