d3853cf1ab1559c73f28a8bf220aac601c16c015
hiram
Wed Dec 4 13:55:17 2024 -0800
when search matches a dbDb name from the genArk table get that result into the dbDb list for selection refs #34862
diff --git src/hg/hgGateway/hgGateway.c src/hg/hgGateway/hgGateway.c
index 75c6365..9455fdf 100644
--- src/hg/hgGateway/hgGateway.c
+++ src/hg/hgGateway/hgGateway.c
@@ -584,49 +584,56 @@
safef(value, sizeof(value), "%s (%s)", dbDb->scientificName, dbDb->genome);
char *bolded = boldTerm(dbDb->scientificName, term, match->offset, match->type);
safef(label, sizeof(label), "%s (%s)", bolded, dbDb->genome);
freeMem(bolded);
}
else if (match->type == ddmtGenome)
{
safecpy(value, sizeof(value), dbDb->genome);
char *bolded = boldTerm(dbDb->genome, term, match->offset, match->type);
safecpy(label, sizeof(label), bolded);
freeMem(bolded);
}
else if (match->type == ddmtDb)
{
safecpy(value, sizeof(value), dbDb->name);
+ // label just in case the bolded doesn't work
+ safef(label, sizeof(label), "%s (%s %s)",
+ dbDb->name, dbDb->genome, dbDb->description);
+ if (sameWord(dbDb->name, term)) // when genArk match, not the same word
+ {
char *bolded = boldTerm(dbDb->name, term, match->offset, match->type);
safef(label, sizeof(label), "%s (%s %s)",
bolded, dbDb->genome, dbDb->description);
freeMem(bolded);
+ }
jsonWriteString(jw, "db", dbDb->name);
}
else if (match->type == ddmtDescription)
{
safef(value, sizeof(value), "%s (%s %s)",
dbDb->name, dbDb->genome, dbDb->description);
char *bolded = boldTerm(dbDb->description, term, match->offset, match->type);
safef(label, sizeof(label), "%s (%s %s)",
dbDb->name, dbDb->genome, bolded);
freeMem(bolded);
jsonWriteString(jw, "db", dbDb->name);
}
else
errAbort("writeDbDbMatch: unrecognized dbDbMatchType value %d (db %s, term %s)",
match->type, dbDb->name, term);
+
jsonWriteString(jw, "label", label);
jsonWriteString(jw, "value", value);
jsonWriteString(jw, "org", dbDb->organism);
jsonWriteNumber(jw, "taxId", dbDb->taxId);
if (isNotEmpty(category))
jsonWriteString(jw, "category", category);
jsonWriteObjectEnd(jw);
}
int wordMatchOffset(char *term, char *target)
/* If some word of target starts with term (case insensitive), return the offset of
* that word in target; otherwise return -1. */
{
if (startsWith(term, target))
return 0;
@@ -1028,65 +1035,93 @@
{
++c;
// the match contains tab-sep accession, hubUrl, asmName, scientificName, commonName
char hubUrl[PATH_LEN+1];
safef(hubUrl, sizeof(hubUrl), "%s/%s", genarkHubUrl, match->hubUrl);
slAddHead(&ret, gHubMatchNew(match->gcAccession, hubUrl, match->asmName, match->scientificName, match->commonName, -1));
if (c > GENARK_LIMIT)
break;
}
if (ret)
slReverse(&ret);
return ret;
}
static struct gHubMatch *filterAssemblyListMatches(struct sqlConnection *conn,
- char *asmListTable, char *term, char *genarkPrefix, boolean wildCard)
+ struct dbDb *dbDbList, struct dbDbMatch **dbDbMatchList, char *asmListTable, char *term, char *genarkPrefix, boolean wildCard)
{
struct gHubMatch *ret = NULL;
struct dyString *query = dyStringNew(64);
/* LIMIT of 100 will allow enough results to include some genArk assemblies */
if (wildCard)
sqlDyStringPrintf(query, "SELECT * FROM %s WHERE MATCH(name, commonName, scientificName, clade, description, refSeqCategory, versionStatus, assemblyLevel) AGAINST ('%s*' IN BOOLEAN MODE) AND browserExists=1 ORDER BY priority LIMIT 100", asmListTable, term);
else
sqlDyStringPrintf(query, "SELECT * FROM %s WHERE MATCH(name, commonName, scientificName, clade, description, refSeqCategory, versionStatus, assemblyLevel) AGAINST ('%s' IN BOOLEAN MODE) AND browserExists=1 ORDER BY priority LIMIT 100", asmListTable, term);
struct sqlResult *sr = sqlGetResult(conn, query->string);
dyStringFree(&query);
char **row;
int c = 0;
while ((row = sqlNextRow(sr)) != NULL)
{
struct assemblyList *el = assemblyListLoadWithNull(row);
if (isGenArk(el->name))
{
++c;
char genarkUrl[PATH_MAX];
safef(genarkUrl, sizeof(genarkUrl), "%s/%s", genarkPrefix, el->hubUrl);
slAddHead(&ret, gHubMatchNew(el->name, genarkUrl, NULL, el->scientificName, el->commonName, *el->priority));
}
+ else
+ {
+ struct dbDb *dbDb;
+ for (dbDb = dbDbList; dbDb != NULL; dbDb = dbDb->next)
+ {
+ if (sameWord(dbDb->name, el->name))
+ {
+ // Make uppercase version of target for case-insensitive matching.
+ int targetLen = strlen(el->name);
+ char targetUpcase[targetLen + 1];
+ safencpy(targetUpcase, sizeof(targetUpcase), el->name, targetLen);
+ touppers(targetUpcase);
+ struct dbDbMatch *extraList = searchDbDb(dbDbList, targetUpcase);
+ struct dbDbMatch *match;
+ boolean canAdd = TRUE;
+ for (match = *dbDbMatchList; match != NULL; match = match->next)
+ {
+ if (sameWord(match->dbDb->name, el->name))
+ {
+ canAdd = FALSE;
+ break;
+ }
+ }
+ if (canAdd)
+ slAddHead(dbDbMatchList, extraList);
+ }
+ }
+ }
if ( c > GENARK_LIMIT) /* limit genArk returns */
break;
}
sqlFreeResult(&sr);
if (ret)
slReverse(&ret);
return ret;
-} /* static struct gHubMatch *filterAssemblyListMatche */
+} /* static struct gHubMatch *filterAssemblyListMatches */
-static struct gHubMatch *searchGenark(char *term)
+static struct gHubMatch *searchGenark(struct dbDb *dbDbList, struct dbDbMatch **dbDbMatchList, char *term)
/* Search through the genark table (or assemblyList table) for hubs
matches term */
{
char *genarkPrefix = cfgOption("genarkHubPrefix");
if (genarkPrefix == NULL)
return NULL;
/* the chopByWhite is going to cannabilize the term string, make a copy */
char *termCopy = cloneString(term);
struct sqlConnection *conn = hConnectCentral();
struct gHubMatch *gHubMatchList = NULL;
char *genarkTbl = genarkTableName();
int colCount = genArkColumnCount();
int termLength = strlen(termCopy);
@@ -1103,55 +1138,55 @@
long long matchCount = sqlQuickLongLong(conn, query->string);
dyStringFree(&query);
boolean wildCard = FALSE;
if (0 == matchCount) /* try prefix search */
{
query = dyStringNew(64);
sqlDyStringPrintf(query, "SELECT COUNT(*) FROM %s WHERE MATCH(name, commonName, scientificName, clade, description, refSeqCategory, versionStatus, assemblyLevel) AGAINST ('%s*' IN BOOLEAN MODE) AND browserExists=1", asmListTable, termCopy);
matchCount = sqlQuickLongLong(conn, query->string);
dyStringFree(&query);
if (matchCount > 0)
wildCard = TRUE;
}
if (matchCount > 0)
- gHubMatchList = filterAssemblyListMatches(conn, asmListTable, termCopy, genarkPrefix, wildCard);
+ gHubMatchList = filterAssemblyListMatches(conn, dbDbList, dbDbMatchList, asmListTable, termCopy, genarkPrefix, wildCard);
} /* 1 == wordCout single word search */
else
{ /* multiple word search */
char *matchAllWords = asmListMatchAllWords(termCopy);
- gHubMatchList = filterAssemblyListMatches(conn, asmListTable, matchAllWords, genarkPrefix, FALSE);
+ gHubMatchList = filterAssemblyListMatches(conn, dbDbList, dbDbMatchList, asmListTable, matchAllWords, genarkPrefix, FALSE);
} /* multiple word search */
} /* termLength > 2 */
else if (sqlTableExists(conn, genarkTbl))
{
char query[1024];
if (colCount > 6)
{
sqlSafef(query, sizeof(query), "select * from %s where "
"(gcAccession like '%%%s%%' or scientificName like '%%%s%%' or commonName like '%%%s%%' or asmName like '%%%s%%') order by priority",
genarkTbl, term, term, term, term);
}
else
{
sqlSafef(query, sizeof(query), "select * from %s where "
"(gcAccession like '%%%s%%' or scientificName like '%%%s%%' or commonName like '%%%s%%' or asmName like '%%%s%%') order by taxId ASC, commonName DESC",
genarkTbl, term, term, term, term);
}
- struct genark *matchList = genarkLoadByQuery(conn, query);
- gHubMatchList = filterGenarkMatches(genarkPrefix, matchList);
+ struct genark *genArkMatch = genarkLoadByQuery(conn, query);
+ gHubMatchList = filterGenarkMatches(genarkPrefix, genArkMatch);
}
hDisconnectCentral(&conn);
return gHubMatchList;
}
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. */
{
pushWarnHandler(htmlVaBadRequestAbort);
pushAbortHandler(htmlVaBadRequestAbort);
char *cgiTerm = cgiOptionalString(SEARCH_TERM);
char *term = skipLeadingSpaces(cgiTerm);
eraseTrailingSpaces(term);
touppers(term);
@@ -1162,42 +1197,45 @@
return term;
}
static void lookupTerm()
/* Look for matches to term in hgcentral and print as JSON for autocomplete if found. */
{
char *term = getSearchTermUpperCase();
// Write JSON response with list of matches
puts("Content-Type:text/javascript\n");
// Before accessing hubs, intialize udc cache location from hg.conf:
setUdcCacheDir();
struct dbDb *dbDbList = hDbDbList();
struct dbDbMatch *matchList = searchDbDb(dbDbList, term);
-struct gHubMatch *gHubMatchList = searchGenark(term);
+struct gHubMatch *gHubMatchList = searchGenark(dbDbList, &matchList, term);
struct aHubMatch *aHubMatchList = searchPublicHubs(dbDbList, term);
struct jsonWrite *jw = jsonWriteNew();
jsonWriteListStart(jw, NULL);
// Write out JSON for dbDb matches, if any; add category if we found assembly hub matches too.
char *category = aHubMatchList ? "UCSC Genome Browser assemblies - annotation tracks curated by UCSC" : NULL;
struct dbDbMatch *match;
for (match = matchList; match != NULL; match = match->next)
writeDbDbMatch(jw, match, term, category);
+
// Write out genark matches, if any, pass term so the matches can be highlighted
+if (slCount(gHubMatchList))
writeGenarkMatches(jw, gHubMatchList, term);
// Write out assembly hub matches, if any.
+if (slCount(aHubMatchList))
writeAssemblyHubMatches(jw, aHubMatchList);
jsonWriteListEnd(jw);
puts(jw->dy->string);
jsonWriteFree(&jw);
}
int main(int argc, char *argv[])
/* Process CGI / command line. */
{
/* Null terminated list of CGI Variables we don't want to save
* permanently. */
char *excludeVars[] = {SEARCH_TERM, CARTJSON_COMMAND, NULL,};
cgiSpoof(&argc, argv);
measureTiming = cgiOptionalInt("measureTiming", 0);
enteredMainTime = clock1000();