e81403a315a24af601884b8a19e89bcecc92f267
galt
  Sat Dec 8 20:04:28 2018 -0800
Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.

diff --git src/hg/hgGene/altSplice.c src/hg/hgGene/altSplice.c
index e2d634e..8d046c4 100644
--- src/hg/hgGene/altSplice.c
+++ src/hg/hgGene/altSplice.c
@@ -1,173 +1,174 @@
 /* altSplice - altSplicing diagram. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "hCommon.h"
 #include "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "hdb.h"
 #include "hvGfx.h"
 #include "portable.h"
 #include "altGraphX.h"
 #include "hgGene.h"
 
 
 static int gpBedBasesShared(struct genePred *gp, struct bed *bed)
 /* Return number of bases genePred and bed share. */
 {
 int intersect = 0;
 int i, blockCount = bed->blockCount;
 int s,e;
 for (i=0; i<blockCount; ++i)
     {
     s = bed->chromStart + bed->chromStarts[i];
     e = s + bed->blockSizes[i];
     intersect += gpRangeIntersection(gp, s, e);
     }
 return intersect;
 }
 
 char *altGraphId(struct sqlConnection *conn, struct genePred *gp)
 /* Return altGraphId that overlaps most with genePred. */
 {
 int rowOffset;
 struct sqlResult *sr;
 char **row;
 struct bed *bestBed = NULL;
 int intersect, bestIntersect = 0;
 char extra[64];
 char *ret = NULL;
 
 safef(extra, sizeof(extra), "strand='%s'", gp->strand);
 sr = hRangeQuery(conn, "agxBed", gp->chrom, gp->txStart, gp->txEnd,
 	extra, &rowOffset);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct bed *bed = bedLoad12(row+rowOffset);
     intersect = gpBedBasesShared(gp, bed);
     if (intersect > bestIntersect)
 	{
 	bestIntersect = intersect;
 	bestBed = bed;
 	}
     else
         bedFree(&bed);
     }
 if (bestBed != NULL)
     {
     ret = cloneString(bestBed->name);
     bedFree(&bestBed);
     }
 return ret;
 }
 
 void makeGrayShades(struct hvGfx *hvg, int maxShade, Color shadesOfGray[])
 /* Make eight shades of gray in display. */
 {
 int i;
 for (i=0; i<=maxShade; ++i)
     {
     int level = 255 - (255*i/maxShade);
     if (level < 0) level = 0;
     shadesOfGray[i] = hvGfxFindColorIx(hvg, level, level, level);
     }
 shadesOfGray[maxShade+1] = MG_RED;
 }
 
 char *altGraphXMakeImage(struct altGraphX *ag)
 /* create a drawing of splicing pattern */
 {
 MgFont *font = mgSmallFont();
 int fontHeight = mgFontLineHeight(font);
 struct spaceSaver *ssList = NULL;
 struct hash *heightHash = NULL;
 int rowCount = 0;
 struct tempName gifTn;
 int pixWidth = atoi(cartUsualString(cart, "pix", DEFAULT_PIX_WIDTH ));
 int pixHeight = 0;
 struct hvGfx *hvg;
 int lineHeight = 0;
 double scale = 0;
 Color shadesOfGray[9];
 int maxShade = ArraySize(shadesOfGray)-1;
 
 scale = (double)pixWidth/(ag->tEnd - ag->tStart);
 lineHeight = 2 * fontHeight +1;
 altGraphXLayout(ag, ag->tStart, ag->tEnd, scale, 100, &ssList, &heightHash, &rowCount);
 hashFree(&heightHash);
 pixHeight = rowCount * lineHeight;
 makeTempName(&gifTn, "hgc", ".png");
 hvg = hvGfxOpenPng(pixWidth, pixHeight, gifTn.forCgi, FALSE);
 makeGrayShades(hvg, maxShade, shadesOfGray);
 hvGfxSetClip(hvg, 0, 0, pixWidth, pixHeight);
 altGraphXDrawPack(ag, ssList, hvg, 0, 0, pixWidth, lineHeight, lineHeight-1,
                   ag->tStart, ag->tEnd, scale,
 		  font, MG_BLACK, shadesOfGray, "Dummy", NULL);
 hvGfxUnclip(hvg);
 hvGfxClose(&hvg);
 printf(
        "<IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d><BR>\n",
        gifTn.forHtml, pixWidth, pixHeight);
 return cloneString(gifTn.forHtml);
 }
 
 static boolean altSpliceExists(struct section *section,
         struct sqlConnection *conn, char *geneId)
 /* Return TRUE if altSplice table exists and has something
  * on this one. */
 {
 char *mark = NULL;
 if (!sqlTableExists(conn, "altGraphX") || !sqlTableExists(conn, "agxBed"))
     return FALSE;
 section->items = altGraphId(conn, curGenePred);
 /* each graph can have different connected components, if there
    is a component take the prefix for matching back to the graph.
    i.e. cut of an '-1' or '-2' */
 if (section->items != NULL)
     if ((mark = strrchr((char *)section->items, '-')) != NULL)
         *mark = '\0';
 return section->items != NULL;
 }
 
 
 static void altSplicePrint(struct section *section,
 	struct sqlConnection *conn, char *geneId)
 /* Print out altSplicing info. */
 {
 char *altId = section->items;
 char query[256];
 struct sqlResult *sr;
 char **row;
 struct altGraphX *ag;
-char table[64];
+char table[HDB_MAX_TABLE_STRING];
 boolean hasBin;
 
-hFindSplitTable(sqlGetDatabase(conn), curGeneChrom, "altGraphX", table, &hasBin);
+if (!hFindSplitTable(sqlGetDatabase(conn), curGeneChrom, "altGraphX", table, sizeof table, &hasBin))
+    errAbort("track altGraphX not found");
 sqlSafef(query, sizeof(query), "select * from %s where name='%s'", table, altId);
 sr = sqlGetResult(conn, query);
 if ((row = sqlNextRow(sr)) != NULL)
     {
     ag = altGraphXLoad(row+hasBin);
     hPrintf("<TABLE><TR><TD BGCOLOR='#888888'>\n");
     altGraphXMakeImage(ag);
     hPrintf("</TD></TR></TABLE><BR>");
     }
 sqlFreeResult(&sr);
 hPrintf("This graph shows alternative splicing observed in mRNAs and "
         "ESTs that is either conserved in mouse, present in full length "
 	"mRNAs, or observed at least three times in ESTs.");
 }
 
 struct section *altSpliceSection(struct sqlConnection *conn,
 	struct hash *sectionRa)
 /* Create altSplice section. */
 {
 struct section *section = sectionNew(sectionRa, "altSplice");
 section->exists = altSpliceExists;
 section->print = altSplicePrint;
 return section;
 }