static struct genePred *getCurGenePred(struct sqlConnection *conn)
/* Return current gene in genePred. */
{
char *track = genomeSetting("knownGene");
char table[HDB_MAX_TABLE_STRING];
boolean hasBin;
char query[256];
struct sqlResult *sr;
char **row;
struct genePred *gp = NULL;
if (!hFindSplitTable(sqlGetDatabase(conn), curGeneChrom, track, table, sizeof table, &hasBin))
errAbort("track %s not found", track);
bool hasAttrId = sqlColumnExists(conn, table, "alignId");
sqlSafef(query, sizeof(query),
"select * from %s where name = '%s' "
"and chrom = '%s' and txStart=%d and txEnd=%d"
, table, curGeneId, curGeneChrom, curGeneStart, curGeneEnd);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
gp = genePredLoad(row + hasBin);
#define ALIGNIDFIELD 11 // Gencode Id
if (hasAttrId)
curAlignId = cloneString(row[ALIGNIDFIELD]);
else
curAlignId = gp->name;
}
sqlFreeResult(&sr);
if (gp == NULL)
errAbort("getCurGenePred: Can't find %s", query);
return gp;
}
int hubPublicCheck(char *table)
/* hubPublicCheck - checks that the labels in hubPublic match what is in the hub labels. */
{
struct sqlConnection *conn = hConnectCentral();
char query[512];
bool hasDescriptionUrl = sqlColumnExists(conn, table, "descriptionUrl");
if (hasDescriptionUrl)
sqlSafef(query, sizeof(query), "select hubUrl, shortLabel,longLabel,dbList,descriptionUrl from %s",
table);
else
sqlSafef(query, sizeof(query), "select hubUrl, shortLabel,longLabel,dbList from %s",
table);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
int differences = 0;
while ((row = sqlNextRow(sr)) != NULL)
{
char *url = row[0], *shortLabel = row[1], *longLabel = row[2], *dbList = row[3], *descriptionUrl = row[4];
struct errCatch *errCatch = errCatchNew();
boolean gotWarning = FALSE;
struct trackHub *tHub = NULL;
if (errCatchStart(errCatch))
tHub = trackHubOpen(url, "hub_1");
errCatchEnd(errCatch);
if (errCatch->gotError)
{
gotWarning = TRUE;
warn("%s", errCatch->message->string);
}
errCatchFree(&errCatch);
if (gotWarning)
{
continue;
}
if (!sameString(shortLabel, tHub->shortLabel))
{
differences++;
printf("update %s set shortLabel=\"%s\" where hubUrl=\"%s\";\n",table, tHub->shortLabel, url);
}
if (!sameString(longLabel, tHub->longLabel))
{
differences++;
printf("update %s set longLabel=\"%s\" where hubUrl=\"%s\";\n",table, tHub->longLabel, url);
}
struct hashCookie cookie = hashFirst(tHub->genomeHash);
struct dyString *dy = newDyString(1024);
struct hashEl *hel;
while ((hel = hashNext(&cookie)) != NULL)
dyStringPrintf(dy, "%s,", trackHubSkipHubName(hel->name));
if (!sameString(dy->string, dbList))
{
differences++;
printf("update %s set dbList=\"%s\" where hubUrl=\"%s\";\n",table, dy->string, url);
}
if (hasDescriptionUrl && !isEmpty(tHub->descriptionUrl) && ((descriptionUrl == NULL) || !sameString(descriptionUrl, tHub->descriptionUrl)))
{
differences++;
printf("update %s set descriptionUrl=\"%s\" where hubUrl=\"%s\";\n",table, tHub->descriptionUrl, url);
}
trackHubClose(&tHub);
}
return differences;
}
