44ccfacbe3a3d4b300f80d48651c77837a4b571e
galt
  Tue Apr 26 11:12:02 2022 -0700
SQL INJECTION Prevention Version 2 - this improves our methods by making subclauses of SQL that get passed around be both easy and correct to use. The way that was achieved was by getting rid of the obscure and not well used functions sqlSafefFrag and sqlDyStringPrintfFrag and replacing them with the plain versions of those functions, since these are not needed anymore. The new version checks for NOSQLINJ in unquoted %-s which is used to include SQL clauses, and will give an error the NOSQLINJ clause is not present, and this will automatically require the correct behavior by developers. sqlDyStringPrint is a very useful function, however because it was not enforced, users could use various other dyString functions and they operated without any awareness or checking for SQL correct use. Now those dyString functions are prohibited and it will produce an error if you try to use a dyString function on a SQL string, which is simply detected by the presence of the NOSQLINJ prefix.

diff --git src/hg/hgGene/altSplice.c src/hg/hgGene/altSplice.c
index 05530be..6c229a3 100644
--- src/hg/hgGene/altSplice.c
+++ src/hg/hgGene/altSplice.c
@@ -1,174 +1,174 @@
 /* altSplice - altSplicing diagram. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ 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);
+sqlSafef(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[HDB_MAX_TABLE_STRING];
 boolean 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;
 }