90dc829b2d87b15c4fc4bbc1d814f83d1274ef52
braney
  Fri Sep 4 14:00:05 2026 -0700
Pass element counts, not byte sizes, to the chop routines

chopByWhite, chopString and chopByChar take their last argument as a
count of elements in the output array.  Fifteen call sites passed
sizeof(array) instead.  For an array of pointers that is eight times
the real capacity on a 64-bit build, so the chop could write well past
the end of the array.

Switched each to ArraySize().  Behaviour is unchanged for any input
that already fitted in the array.

Built clean: lib, hg/lib, hg/hgTracks, hg/hgc, hg/utils/hubCheck,
utils/bedScore, parasol/lib, parasol/parasol.  Three directories do not
build, but they fail the same way without this change: checkExp is
missing htslib link flags, and cgapSageFind and affySplice have stale
prototypes in files this does not touch.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

diff --git src/hg/lib/hubSearchText.c src/hg/lib/hubSearchText.c
index 8b5955df15d..7cad7644c9a 100644
--- src/hg/lib/hubSearchText.c
+++ src/hg/lib/hubSearchText.c
@@ -1,398 +1,398 @@
 /* hubSearchText.c was originally generated by the autoSql program, which also 
  * generated hubSearchText.h and hubSearchText.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "rangeTree.h"
 #include "hubSearchText.h"
 #include "hubPublic.h"
 #include "hgConfig.h"
 
 
 char *hubSearchTextCommaSepFieldNames = "hubUrl,db,track,label,textLength,text,parents,parentTypes";
 
 /* definitions for textLength column */
 static char *values_textLength[] = {"Short", "Long", "Meta", NULL};
 static struct hash *valhash_textLength = NULL;
 
 void hubSearchTextStaticLoadWithNull(char **row, struct hubSearchText *ret)
 /* Load a row from hubSearchText table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->hubUrl = row[0];
 ret->db = row[1];
 ret->track = row[2];
 ret->label = row[3];
 ret->textLength = sqlEnumParse(row[4], values_textLength, &valhash_textLength);
 ret->text = row[5];
 ret->parents = row[6];
 ret->parentTypes = row[7];
 }
 
 struct hubSearchText *hubSearchTextLoadWithNull(char **row)
 /* Load a hubSearchText from row fetched with select * from hubSearchText
  * from database.  Dispose of this with hubSearchTextFree(). */
 {
 struct hubSearchText *ret;
 
 AllocVar(ret);
 ret->hubUrl = cloneString(row[0]);
 ret->db = cloneString(row[1]);
 ret->track = cloneString(row[2]);
 ret->label = cloneString(row[3]);
 ret->textLength = sqlEnumParse(row[4], values_textLength, &valhash_textLength);
 ret->text = cloneString(row[5]);
 ret->parents = cloneString(row[6]);
 ret->parentTypes = cloneString(row[7]);
 return ret;
 }
 
 struct hubSearchText *hubSearchTextLoadAll(char *fileName) 
 /* Load all hubSearchText from a whitespace-separated file.
  * Dispose of this with hubSearchTextFreeList(). */
 {
 struct hubSearchText *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[8];
 
 while (lineFileRow(lf, row))
     {
     el = hubSearchTextLoadWithNull(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hubSearchText *hubSearchTextLoadAllByChar(char *fileName, char chopper) 
 /* Load all hubSearchText from a chopper separated file.
  * Dispose of this with hubSearchTextFreeList(). */
 {
 struct hubSearchText *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[8];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = hubSearchTextLoadWithNull(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hubSearchText *hubSearchTextCommaIn(char **pS, struct hubSearchText *ret)
 /* Create a hubSearchText out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new hubSearchText */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->hubUrl = sqlStringComma(&s);
 ret->db = sqlStringComma(&s);
 ret->track = sqlStringComma(&s);
 ret->label = sqlStringComma(&s);
 ret->textLength = sqlEnumComma(&s, values_textLength, &valhash_textLength);
 ret->text = sqlStringComma(&s);
 ret->parents = sqlStringComma(&s);
 ret->parentTypes = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void hubSearchTextFree(struct hubSearchText **pEl)
 /* Free a single dynamically allocated hubSearchText such as created
  * with hubSearchTextLoad(). */
 {
 struct hubSearchText *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->hubUrl);
 freeMem(el->db);
 freeMem(el->track);
 freeMem(el->label);
 freeMem(el->text);
 freeMem(el->parents);
 freeMem(el->parentTypes);
 freez(pEl);
 }
 
 void hubSearchTextFreeList(struct hubSearchText **pList)
 /* Free a list of dynamically allocated hubSearchText's */
 {
 struct hubSearchText *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     hubSearchTextFree(&el);
     }
 *pList = NULL;
 }
 
 void hubSearchTextOutput(struct hubSearchText *el, FILE *f, char sep, char lastSep) 
 /* Print out hubSearchText.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->hubUrl);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->db);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->track);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->label);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 sqlEnumPrint(f, el->textLength, values_textLength);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->text);
 if (sep == ',') fputc('"',f);
 fputc(sep, f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->parents);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->parentTypes);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 
 /* Restrictions on the size of context chunks returned by getTextContext() */
 #define HST_MAXCONTEXTLENGTH 300
 #define HST_CONTEXTRADIUS 70
 
 static char *getTextContext(char *text, char *searchTerms)
 /* Look for instances of words from searchTerms in the supplied text, grab some surrounding
  * context, and stitch them together into a string that combines overlapping regions. */
 {
 struct dyString *contextString = dyStringNew(0);
 struct rbTree *contextTree = rangeTreeNew();
 char *splitTerms[1024];
 char *cloneTerms = cloneString(searchTerms);
 if (isNotEmpty(cloneTerms))
     strLower(cloneTerms);
 char *lowText = cloneString(text);
 if (isNotEmpty(lowText))
     strLower(lowText);
 int termCount = chopByWhiteRespectDoubleQuotes(cloneTerms, splitTerms, 1024);
 int i;
 for (i=0; i<termCount; i++)
     {
     char *thisTerm = splitTerms[i];
     if (thisTerm[0] == '"')
         {
         thisTerm++;
         trimLastChar(thisTerm);
         }
     char *position = stringIn(thisTerm, lowText);
     if (position == NULL)
         continue;
     int termStart = position - HST_CONTEXTRADIUS - lowText;
     if (termStart < 0)
         termStart = 0;
     int termEnd = position + strlen(thisTerm) + HST_CONTEXTRADIUS - lowText;
     if (termEnd > strlen(lowText))
         termEnd = strlen(lowText);
     rangeTreeAdd(contextTree, termStart, termEnd);
     }
 struct range *rangeResult = rangeTreeList(contextTree);
 int cumulativeSize = 0;
 if (rangeResult != NULL)
     dyStringPrintf(contextString, "...");
 while (rangeResult != NULL)
     {
     char contextChunk[HST_MAXCONTEXTLENGTH+1];
     int copySize = rangeResult->end - rangeResult->start;
     if (copySize > HST_MAXCONTEXTLENGTH)
         copySize = HST_MAXCONTEXTLENGTH;
     safencpy(contextChunk, sizeof(contextChunk), text+rangeResult->start, copySize);
     dyStringPrintf(contextString, " %s ...", contextChunk);
     cumulativeSize += copySize;
     if (cumulativeSize >= HST_MAXCONTEXTLENGTH)
         break;
     rangeResult = rangeResult->next;
     }
 return dyStringCannibalize(&contextString);
 }
 
 
 struct hubSearchText *hubSearchTextLoadWithNullGiveContext(char **row, char *searchTerms)
 /* Load a hubSearchText from row fetched with select * from hubSearchText
  * from database, but instead of loading the entire text field for long text results,
  * only load the pieces that provide context for the supplied searchTerms.
  * Dispose of this with hubSearchTextFree(). */
 {
 struct hubSearchText *hst = hubSearchTextLoadWithNull(row);
 if (hst->textLength == hubSearchTextLong)
     {
     char *longTextContext = getTextContext(hst->text, searchTerms);
     freeMem(hst->text);
     hst->text = longTextContext;
     }
 return hst;
 }
 
 char *modifyTermsForHubSearch(char *hubSearchTerms, bool isStrictSearch)
 /* This won't exactly be pretty.  MySQL treats any sequence of alphanumerics and underscores
  * as a word, and single apostrophes are allowed as long as they don't come back-to-back.
  * Cut down to those characters, then add initial + (for requiring word) and * (for word
  * expansion) as appropriate. */
 {
 char *cloneTerms = cloneString(hubSearchTerms);
 struct dyString *modifiedTerms = dyStringNew(0);
 if (isNotEmpty(cloneTerms))
     {
     int i;
     for (i=0; i<strlen(cloneTerms); i++)
         {
         // allowed punctuation is underscore and apostrophe, and we'll do special handling for hyphen
         if (!isalnum(cloneTerms[i]) && cloneTerms[i] != '_' && cloneTerms[i] != '\'' &&
                 cloneTerms[i] != '-')
             cloneTerms[i] = ' ';
         }
     char *splitTerms[1024];
-    int termCount = chopByWhite(cloneTerms, splitTerms, sizeof(splitTerms));
+    int termCount = chopByWhite(cloneTerms, splitTerms, ArraySize(splitTerms));
     for (i=0; i<termCount; i++)
         {
         char *hyphenatedTerms[1024];
-        int hyphenTerms = chopString(splitTerms[i], "-", hyphenatedTerms, sizeof(hyphenatedTerms));
+        int hyphenTerms = chopString(splitTerms[i], "-", hyphenatedTerms, ArraySize(hyphenatedTerms));
         int j;
         for (j=0; j<hyphenTerms-1; j++)
             {
             dyStringPrintf(modifiedTerms, "+%s ", hyphenatedTerms[j]);
             }
         if (isStrictSearch)
             dyStringPrintf(modifiedTerms, "+%s ", hyphenatedTerms[j]);
         else
             {
             dyStringPrintf(modifiedTerms, "+%s* ", hyphenatedTerms[j]);
             }
         }
     }
 return dyStringCannibalize(&modifiedTerms);
 }
 
 void getHubSearchResults(struct sqlConnection *conn, char *hubSearchTableName,
         char *hubSearchTerms, bool checkLongText, char *dbFilter, struct hash *hubLookup,
         struct hash **searchResultHashRet, struct slName **hubsToPrintRet, char *extra)
 /* Find hubs, genomes, and tracks that match the provided search terms.
  * Return all hits that satisfy the (optional) supplied assembly filter.
  * if checkLongText is FALSE, skip searching within the long description text entries
  * the string 'extra' is used for additional mysql filter(s) by the caller and
  * must be escaped by them */
 {
 char *cleanSearchTerms = cloneString(hubSearchTerms);
 if (isNotEmpty(cleanSearchTerms))
     tolowers(cleanSearchTerms);
 bool isStrictSearch = FALSE;
 char *modifiedSearchTerms = modifyTermsForHubSearch(cleanSearchTerms, isStrictSearch);
 struct hubSearchText *hubSearchResultsList = NULL;
 struct dyString *query = dyStringNew(100);
 
 sqlDyStringPrintf(query, "select * from %s where ", hubSearchTableName);
 if (isNotEmpty(extra))
     {
     sqlDyStringPrintf(query, "%-s ", extra);
     if (!checkLongText || isNotEmpty(modifiedSearchTerms))
         sqlDyStringPrintf(query, "and ");
     }
 if (!checkLongText)
     {
     sqlDyStringPrintf(query, "textLength = 'Short'"); 
     if (isNotEmpty(modifiedSearchTerms))
        sqlDyStringPrintf(query, "and ");
     }
 
 if (isNotEmpty(modifiedSearchTerms))
     {
     sqlDyStringPrintf(query, "match(text) against ('%s' in boolean mode)"
         " order by match(text) against ('%s' in boolean mode)",
         modifiedSearchTerms, modifiedSearchTerms);
     }
 struct sqlResult *sr = sqlGetResult(conn, dyStringContents(query));
 char **row;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct hubSearchText *hst = hubSearchTextLoadWithNullGiveContext(row, cleanSearchTerms);
     // Skip rows where the long text matched the more lax MySQL search (punctuation just
     // splits terms into two words, so "rna-seq" finds "rna" and "seq" separately, but
     // not the more strict rules used to find context for the search terms.
     if ((hst->textLength == hubSearchTextLong) && isEmpty(hst->text))
         continue;
     char *hubUrl = hst->hubUrl;
     struct hubEntry *hubInfo = hashFindVal(hubLookup, hubUrl);
     if (hubInfo == NULL)
         continue; // Search table evidently includes a hub that's not on this server.  Skip it.
     char *db = cloneString(hst->db);
     tolowers(db);
     if (isNotEmpty(dbFilter))
         {
         if (isNotEmpty(db))
             {
             if (stringIn(dbFilter, db) == NULL)
                 continue;
             }
         else
             {
             // no db in the hubSearchText means this is a top-level hub hit.
             // filter by the db list associated with the hub instead
             char *dbList = cloneString(hubInfo->dbList);
             tolowers(dbList);
             if (stringIn(dbFilter, dbList) == NULL)
                 continue;
             }
         }
     // Add hst to the list to be returned
     slAddHead(&hubSearchResultsList, hst);
     }
 slReverse(&hubSearchResultsList);
 struct slName *hubsToPrint = NULL;
 struct hash *searchResultHash = hashNew(0);
 struct hubSearchText *hst = hubSearchResultsList;
 while (hst != NULL)
     {
     struct hubSearchText *nextHst = hst->next;
     hst->next = NULL;
     struct hashEl *hubHashEnt = hashLookup(searchResultHash, hst->hubUrl);
     if (hubHashEnt == NULL)
         {
         slNameAddHead(&hubsToPrint, hst->hubUrl);
         hashAdd(searchResultHash, hst->hubUrl, hst);
         }
     else
         slAddHead(&(hubHashEnt->val), hst);
     hst = nextHst;
     }
 struct hashEl *hel;
 struct hashCookie cookie = hashFirst(searchResultHash);
 while ((hel = hashNext(&cookie)) != NULL)
     slReverse(&(hel->val));
 *searchResultHashRet = searchResultHash;
 *hubsToPrintRet = hubsToPrint;
 }
 
 char *hubSearchTextTableName()
 {
 return cfgOptionDefault("hubSearchTextTable", "hubSearchText");
 }