static boolean colAlreadyThere(struct sqlConnection *conn, char *tableName, char *col)
/* Check to see if there's a field in the table already */
{
char existsSql[128];
safef(existsSql, sizeof(existsSql), "desc %s %s", tableName, col);
return sqlExists(conn, existsSql);
}
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);
}
struct serverTable *findServer(char *db, boolean isTrans)
/* Return server for given database. Db can either be
* database name or description. */
{
if (trackHubDatabase(db))
{
struct serverTable *hubSt = trackHubServerTable(db, isTrans);
if (hubSt != NULL)
return hubSt;
errAbort("Cannot get blat server parameters for track hub with database %s\n", db);
}
static struct serverTable st;
struct sqlConnection *conn = hConnectCentral();
char query[256];
struct sqlResult *sr;
char **row;
char dbActualName[32];
/* If necessary convert database description to name. */
sqlSafef(query, sizeof(query), "select name from dbDb where name = '%s'", db);
if (!sqlExists(conn, query))
{
sqlSafef(query, sizeof(query), "select name from dbDb where description = '%s'", db);
if (sqlQuickQuery(conn, query, dbActualName, sizeof(dbActualName)) != NULL)
db = dbActualName;
}
/* Do a little join to get data to fit into the serverTable. */
sqlSafef(query, sizeof(query), "select dbDb.name,dbDb.description,blatServers.isTrans"
",blatServers.host,blatServers.port,dbDb.nibPath "
"from dbDb,blatServers where blatServers.isTrans = %d and "
"dbDb.name = '%s' and dbDb.name = blatServers.db",
isTrans, db);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) == NULL)
{
errAbort("Can't find a server for %s database %s. Click "
"<A HREF=\"/cgi-bin/hgBlat?%s&command=start&db=%s\">here</A> "
"to reset to default database.",
(isTrans ? "translated" : "DNA"), db,
cartSidUrlString(cart), hDefaultDb());
}
st.db = cloneString(row[0]);
st.genome = cloneString(row[1]);
st.isTrans = atoi(row[2]);
st.host = cloneString(row[3]);
st.port = cloneString(row[4]);
st.nibDir = hReplaceGbdbSeqDir(row[5], st.db);
sqlFreeResult(&sr);
hDisconnectCentral(&conn);
return &st;
}
static void printSeqLink(struct sqlConnection *conn, char *geneId,
char *tableId, char *command, char *label, int colCount)
/* Print out link to mRNA or protein. */
{
char *table = genomeSetting(tableId);
boolean gotHyperlink = FALSE;
webPrintWideCellStart(colCount, HG_COL_TABLE);
if (sqlTableExists(conn, table))
{
char query[512];
safef(query, sizeof(query), "select count(*) from %s where name = '%s'",
table, geneId);
if (sqlExists(conn, query))
{
hPrintf("<A HREF=\"../cgi-bin/hgGene?%s&%s=1&hgg_gene=%s\" class=\"toc\">",
cartSidUrlString(cart), command, geneId);
hPrintf("%s</A>", label);
gotHyperlink = TRUE;
}
}
if (!gotHyperlink)
hPrintf("%s", label);
webPrintLinkCellEnd();
}
