void doMiddle(struct cart *theCart)
/* Write header and body of html page. */
{
char *userSeq;
char *db, *organism;
boolean clearUserSeq = cgiBoolean("Clear");
cart = theCart;
dnaUtilOpen();
orgChange = sameOk(cgiOptionalString("changeInfo"),"orgChange");
if (orgChange)
{
cgiVarSet("db", hDefaultDbForGenome(cgiOptionalString("org")));
}
getDbAndGenome(cart, &db, &organism, oldVars);
char *oldDb = cloneString(db);
findClosestServer(&db, &organism);
/* Get sequence - from userSeq variable, or if
* that is empty from a file. */
if (clearUserSeq)
{
cartSetString(cart, "userSeq", "");
cartSetString(cart, "seqFile", "");
}
userSeq = cartUsualString(cart, "userSeq", "");
if (isEmpty(userSeq))
{
userSeq = cartOptionalString(cart, "seqFile");
}
if (isEmpty(userSeq) || orgChange)
{
cartWebStart(theCart, db, "%s BLAT Search", trackHubSkipHubName(organism));
if (differentString(oldDb, db))
printf("<HR><P><EM><B>Note:</B> BLAT search is not available for %s %s; "
"defaulting to %s %s</EM></P><HR>\n",
hGenome(oldDb), hFreezeDate(oldDb), organism, hFreezeDate(db));
askForSeq(organism,db);
cartWebEnd();
}
else
{
blatSeq(skipLeadingSpaces(userSeq), organism);
}
}
void addAssemblyToSupportedList(struct dyString* dy, char* assembly)
{
char* organism = hOrganism(assembly);
char* freezeDate = hFreezeDate(assembly);
dyStringPrintf(dy, "%s %s", organism, freezeDate);
freeMem(organism);
freeMem(freezeDate);
}
void redoDbAndOrgIfNoServer(struct pcrServer *serverList, char **pDb, char **pOrg)
/* Check that database and organism are on our serverList. If not, then update
* them to first thing that is. */
{
struct pcrServer *server, *orgServer = NULL;
char *organism = *pOrg;
char *db = *pDb;
boolean gotDb = FALSE;
/* Find first server for our organism */
for (server = serverList; server != NULL; server = server->next)
{
if (sameString(server->genome, organism))
{
orgServer = server;
break;
}
}
/* If no server, change our organism to the one of the first server in list. */
if (orgServer == NULL)
{
orgServer = serverList;
*pOrg = organism = orgServer->genome;
}
/* Search for our database. */
for (server = serverList; server != NULL; server = server->next)
{
if (sameString(db, server->db))
{
gotDb = TRUE;
break;
}
}
/* If no server for db, change db. */
if (!gotDb)
{
if (differentString(db, orgServer->db))
printf("<HR><P><EM><B>Note:</B> In-Silico PCR is not available for %s %s; "
"defaulting to %s %s</EM></P><HR>\n",
hGenome(db), hFreezeDate(db), organism, hFreezeDate(orgServer->db));
*pDb = db = orgServer->db;
}
}
static void getAssemblyInfo(struct cartJson *cj, struct hash *paramHash)
/* Return useful things from dbDb (or track hub) and assembly description html (possibly NULL).
* If db param is NULL, use db from cart. */
{
char *db = cartJsonOptionalParam(paramHash, "db");
if (db == NULL)
db = cartString(cj->cart, "db");
jsonWriteString(cj->jw, "db", db);
jsonWriteString(cj->jw, "commonName", hGenome(db));
jsonWriteString(cj->jw, "scientificName", hScientificName(db));
jsonWriteString(cj->jw, "dbLabel", hFreezeDate(db));
//#*** TODO: move jsonStringEscape inside jsonWriteString
jsonWriteString(cj->jw, "assemblyDescription", jsonStringEscape(hAssemblyDescription(db)));
}
