void webPopErrHandlers(void)
/* Pop warn and abort handler for errAbort(). */
{
popWarnHandler();
hDumpStackPopAbortHandler();
popAbortHandler();
}
void errCatchEnd(struct errCatch *errCatch)
/* Restore error handlers and pop self off of catching stack. */
{
popWarnHandler();
popAbortHandler();
struct errCatch **pErrCatchStack = getStack(), *errCatchStack = *pErrCatchStack;
if (errCatch != errCatchStack)
errAbort("Mismatch betweene errCatch and errCatchStack");
*pErrCatchStack = errCatch->next;
}
static char *getSearchTermUpperCase()
/* If we don't have the SEARCH_TERM cgi param, exit with an HTTP Bad Request response.
* If we do, convert it to upper case for case-insensitive matching and return it. */
{
pushAbortHandler(htmlVaBadRequestAbort);
char *term = cgiOptionalString(SEARCH_TERM);
touppers(term);
if (isEmpty(term))
errAbort("Missing required CGI parameter %s", SEARCH_TERM);
popAbortHandler();
return term;
}
char *checkParams(char *database, char *prefix, char *type)
/* If we don't have valid CGI parameters, quit with a Bad Request HTTP response. */
{
pushWarnHandler(htmlVaBadRequestAbort);
pushAbortHandler(htmlVaBadRequestAbort);
if(prefix == NULL || database == NULL)
errAbort("%s", "Missing prefix and/or db CGI parameter");
if (! hDbIsActive(database))
errAbort("'%s' is not a valid, active database", htmlEncode(database));
if (isNotEmpty(type) && differentString(type, ALT_OR_PATCH))
errAbort("'%s' is not a valid type", type);
char *table = NULL;
if (! sameOk(type, ALT_OR_PATCH))
{
struct sqlConnection *conn = hAllocConn(database);
table = connGeneSuggestTable(conn);
hFreeConn(&conn);
if(table == NULL)
errAbort("gene autosuggest is not supported for db '%s'", database);
}
popWarnHandler();
popAbortHandler();
return table;
}
void hDumpStackPopAbortHandler(void)
/* pop the stack dump abort handler from the stack if it's enabled */
{
if (hDumpStackEnabled() && !stackDumpDisabled)
popAbortHandler();
}
static void cartJsonPopErrHandlers()
/* Pop warn and abort handlers for errAbort. */
{
popWarnHandler();
popAbortHandler();
}
void popRHandlers() {
popAbortHandler();
popWarnHandler();
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
cgiSpoof(&argc, argv);
char *prefix = cgiOptionalString("prefix");
char *database = cgiOptionalString("db");
initGenbankTableNames(database);
int exact = cgiOptionalInt("exact", 0);
struct sqlConnection *conn;
char query[2048];
char **row;
struct sqlResult *sr;
int count = 0;
boolean hasKnownCanonical;
struct dyString *str = newDyString(10000);
char *table;
pushAbortHandler(htmlVaBadRequestAbort);
if(prefix == NULL || database == NULL)
errAbort("%s", "Missing prefix and/or db CGI parameter");
conn = hAllocConn(database);
table = connGeneSuggestTable(conn);
if(table == NULL)
errAbort("gene autosuggest is not supported for db '%s'", database);
popAbortHandler();
hasKnownCanonical = sameString(table, "knownCanonical");
puts("Content-Type:text/plain");
puts("\n");
dyStringPrintf(str, "[\n");
if(exact)
{
// NOTE that exact is no longer used by the UI as of v271, but there are still some robots using it so we still support it.
if(hasKnownCanonical)
sqlSafef(query, sizeof(query), "select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
"from knownCanonical k, knownGene kg, kgXref x where k.transcript = x.kgID and k.transcript = kg.name "
"and x.geneSymbol = '%s' order by x.geneSymbol, k.chrom, kg.txEnd - kg.txStart desc", prefix);
else
sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, d.name "
"from %s r, %s g, %s d where r.name2 = '%s' and g.acc = r.name "
"and g.description = d.id order by r.name2, r.chrom, r.txEnd - r.txStart desc", table, gbCdnaInfoTable, descriptionTable, prefix);
}
else
{
// We use a LIKE query b/c it uses the geneSymbol index (substr queries do not use indices in mysql).
// Also note that we take advantage of the fact that searches are case-insensitive in mysql.
// Unfortunately, knownCanonical sometimes has multiple entries for a given gene (e.g. 2 TTn's in mm9 knownCanonical;
// 3 POU5F1's in hg19); we return all of them (#5962).
if(hasKnownCanonical)
sqlSafef(query, sizeof(query), "select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
"from knownCanonical k, knownGene kg, kgXref x where k.transcript = x.kgID and k.transcript = kg.name "
"and x.geneSymbol LIKE '%s%%' order by x.geneSymbol, k.chrom, kg.txStart", prefix);
else
sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, d.name "
"from %s r, %s g, %s d where r.name2 LIKE '%s%%' and g.acc = r.name "
"and g.description = d.id order by r.name2, r.chrom, r.txStart", table, gbCdnaInfoTable, descriptionTable, prefix);
}
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
// ignore funny chroms (e.g. _hap chroms. See redmine #4257.
if(!strchr(row[1], '_'))
{
// We have some very long descriptions, e.g. 4277 chars for hg38 CLOCK, so truncate:
const int maxDesc = 120;
char *description = row[5];
if (strlen(description) > maxDesc + 4)
strcpy(description + maxDesc, "...");
count++;
dyStringPrintf(str, "%s{\"value\": \"%s (%s)\", "
"\"id\": \"%s:%d-%s\", "
"\"geneSymbol\": \"%s\", "
"\"internalId\": \"%s\"}",
count == 1 ? "" : ",\n", row[0], jsonStringEscape(description),
row[1], atoi(row[2])+1, row[3],
jsonStringEscape(row[0]),
jsonStringEscape(row[4]));
}
}
dyStringPrintf(str, "\n]\n");
puts(dyStringContents(str));
cgiExitTime("hgSuggest", enteredMainTime);
return 0;
}