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/hgTracks/encode.c src/hg/hgTracks/encode.c
index 4d71397..f731673 100644
--- src/hg/hgTracks/encode.c
+++ src/hg/hgTracks/encode.c
@@ -1,365 +1,365 @@
 /* encode.c - hgTracks routines that are specific to the ENCODE project */
 
 /* Copyright (C) 2012 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 "hdb.h"
 #include "hui.h"
 #include "hgTracks.h"
 #include "customTrack.h"
 #include "encode.h"
 #include "encode/encodeRna.h"
 #include "encode/encodePeak.h"
 #include "bigBedFilter.h"
 
 extern struct trackLayout tl;
 
 
 char *encodeErgeName(struct track *tg, void *item)
 /* return the actual data name, in form xx/yyyy cut off xx/ return yyyy */
 {
 char *name;
 struct linkedFeatures *lf = item;
 name = strstr(lf->name, "/");
 if (name != NULL)
     name ++;
 if (name != NULL)
     return name;
 return "unknown";
 }
 
 void encodeErgeMethods(struct track *tg)
 /* setup special methods for ENCODE dbERGE II tracks */
 {
 tg->itemName = encodeErgeName;
 }
 
 Color encodeStanfordNRSFColor(struct track *tg, void *item, struct hvGfx *hvg)
 /* color by strand */
 {
 struct bed *thisItem = item;
 int r = tg->color.r;
 int g = tg->color.g;
 int b = tg->color.b;
 
 if (thisItem->strand[0] == '-')
     {
     r = g;
     g = b;
     b = tg->color.r;
     }
 return hvGfxFindColorIx(hvg, r, g, b);
 }
 
 void encodeStanfordNRSFMethods(struct track *tg)
 /* custom methods for ENCODE Stanford NRSF data */
 {
 tg->itemColor = encodeStanfordNRSFColor;
 tg->itemNameColor = encodeStanfordNRSFColor;
 }
 
 
 
 void loadEncodeRna(struct track *tg)
 /* Load up encodeRna from database table to track items. */
 {
 bedLoadItem(tg, "encodeRna", (ItemLoader)encodeRnaLoad);
 }
 
 void freeEncodeRna(struct track *tg)
 /* Free up encodeRna items. */
 {
 encodeRnaFreeList((struct encodeRna**)&tg->items);
 }
 
 Color encodeRnaColor(struct track *tg, void *item, struct hvGfx *hvg)
 /* Return color of encodeRna track item. */
 {
 struct encodeRna *el = item;
 
 if(el->isRmasked)     return MG_BLACK;
 if(el->isTranscribed) return hvGfxFindColorIx(hvg, 0x79, 0xaa, 0x3d);
 if(el->isPrediction)  return MG_RED;
 return MG_BLUE;
 }
 
 char *encodeRnaName(struct track *tg, void *item)
 /* Return RNA gene name. */
 {
 struct encodeRna *el = item;
 char *full = el->name;
 static char abbrev[SMALLBUF];
 char *e;
 
 strcpy(abbrev, skipChr(full));
 subChar(abbrev, '_', ' ');
 abbr(abbrev, " pseudogene");
 if ((e = strstr(abbrev, "-related")) != NULL)
     strcpy(e, "-like");
 return abbrev;
 }
 
 void encodeRnaMethods(struct track *tg)
 /* Make track for rna genes . */
 {
 tg->loadItems = loadEncodeRna;
 tg->freeItems = freeEncodeRna;
 tg->itemName = encodeRnaName;
 tg->itemColor = encodeRnaColor;
 tg->itemNameColor = encodeRnaColor;
 }
 
 static struct linkedFeatures *lfFromEncodePeak(struct slList *item, struct trackDb *tdb,
                                         int scoreMin, int scoreMax)
 /* Translate an {encode,narrow,broad,gapped}Peak item into a linkedFeatures. */
 {
 struct encodePeak *peak = (struct encodePeak *)item;
 struct linkedFeatures *lf;
 struct simpleFeature *sfList = NULL;
 if (!peak)
     return NULL;
 AllocVar(lf);
 lf->start = peak->chromStart;
 lf->end = peak->chromEnd;
 if (peak->peak > -1)
     {
     lf->tallStart = peak->chromStart + peak->peak;
     lf->tallEnd = lf->tallStart + 1;
     }
 lf->filterColor = -1;
 lf->orientation = orientFromChar(peak->strand[0]);
 adjustBedScoreGrayLevel(tdb, (struct bed *)peak, scoreMin, scoreMax);
 lf->grayIx = grayInRange((int)peak->score, scoreMin, scoreMax);
 lf->name = cloneString(peak->name);
 if (peak->blockCount > 0)
     {
     int i;
     for (i = 0; i < peak->blockCount; i++)
 	{
 	struct simpleFeature *sf;
 	AllocVar(sf);
 	sf->start = lf->start + peak->blockStarts[i];
 	sf->end = lf->start + peak->blockStarts[i] + peak->blockSizes[i];
 	sf->grayIx = lf->grayIx;
 	slAddHead(&sfList, sf);
 	}
     slReverse(&sfList);
     }
 else
     {
     AllocVar(sfList);
     sfList->start = lf->start;
     sfList->end = lf->end;
     sfList->grayIx = lf->grayIx;
     }
 lf->components = sfList;
 return lf;
 }
 
 
 static char *encodePeakFilter(char *trackName, struct trackDb *tdb, boolean isCustom)
 {
-struct dyString *extraWhere = newDyString(128);
+struct dyString *extraWhere = dyStringNew(128);
 boolean and = FALSE;
 extraWhere = dyAddFilterAsInt(cart,tdb,extraWhere,SCORE_FILTER,"0:1000","score",&and);
 extraWhere = dyAddFilterAsDouble(cart,tdb,extraWhere,SIGNAL_FILTER,NULL,"signalValue",&and);
 extraWhere = dyAddFilterAsDouble(cart,tdb,extraWhere,PVALUE_FILTER,NULL,"pValue",&and);
 extraWhere = dyAddFilterAsDouble(cart,tdb,extraWhere,QVALUE_FILTER,NULL,"qValue",&and);
 
 if (sameString(extraWhere->string, ""))
     return NULL;
 return dyStringCannibalize(&extraWhere);
 }
 
 void bigNarrowPeakLoadItems(struct track *tg)
 /* Load a set of narrowPeaks from a bigNarrowPeak file. */
 {
 struct linkedFeatures *lfList = NULL;
 enum encodePeakType pt = 0;
 int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "scoreMin", "0"));
 int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "scoreMax", "1000"));
 pt = narrowPeak;
 
 tg->customInt = pt;
 struct bbiFile *bbi =  fetchBbiForTrack(tg);
 
 struct lm *lm = lmInit(0);
 struct bigBedInterval *bb, *bbList =  bigBedIntervalQuery(bbi, chromName, winStart, winEnd, 0, lm);
 int fieldCount = 10;
 char *bedRow[fieldCount];
 char startBuf[16], endBuf[16];
 struct bigBedFilter *filters = NULL;
 struct bigBedFilter *filter;
 
 if ((filter = bigBedMakeNumberFilter(cart, bbi, tg->tdb, SCORE_FILTER, "0:1000", "score")) != NULL)
     slAddHead(&filters, filter);
 if ((filter = bigBedMakeNumberFilter(cart, bbi, tg->tdb, SIGNAL_FILTER, NULL, "signalValue")) != NULL)
     slAddHead(&filters, filter);
 if ((filter = bigBedMakeNumberFilter(cart, bbi, tg->tdb, PVALUE_FILTER, NULL, "pValue")) != NULL)
     slAddHead(&filters, filter);
 if ((filter = bigBedMakeNumberFilter(cart, bbi, tg->tdb, QVALUE_FILTER, NULL, "qValue")) != NULL)
     slAddHead(&filters, filter);
 if (compositeChildHideEmptySubtracks(cart, tg->tdb, NULL, NULL))
    labelTrackAsFiltered(tg);
 
 unsigned filtered = 0;
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
     if (bigBedFilterInterval(bedRow, filters))
         {
         struct encodePeak *peak = encodePeakGeneralLoad(bedRow, pt);
         struct linkedFeatures *lf = lfFromEncodePeak((struct slList *)peak, tg->tdb, scoreMin, scoreMax);
 
         if (lf)
             slAddHead(&lfList, lf);
         else 
             filtered++;
         }
     else
         filtered++;
     }
 if (filtered)
    labelTrackAsFilteredNumber(tg, filtered);
 
 slReverse(&lfList);
 slSort(&lfList, linkedFeaturesCmp);
 tg->items = lfList;
 }
 
 static void encodePeakLoadItemsBoth(struct track *tg, struct customTrack *ct)
 /* Load up an encodePeak table from the regular database or the customTrash one. */
 {
 char *db, *table;
 struct sqlConnection *conn;
 struct sqlResult *sr = NULL;
 char **row;
 char *filterConstraints = NULL;
 int rowOffset;
 struct linkedFeatures *lfList = NULL;
 enum encodePeakType pt = 0;
 int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "scoreMin", "0"));
 int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "scoreMax", "1000"));
 if (ct)
     {
     db = CUSTOM_TRASH;
     table = ct->dbTableName;
     }
 else
     {
     db = database;
     table = tg->tdb->table;
     }
 conn = hAllocConn(db);
 pt = encodePeakInferTypeFromTable(db, table, tg->tdb->type);
 tg->customInt = pt;
 filterConstraints = encodePeakFilter(tg->tdb->track, tg->tdb, (ct!=NULL));
 sr = hRangeQuery(conn, table, chromName, winStart, winEnd, filterConstraints, &rowOffset);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct encodePeak *peak = encodePeakGeneralLoad(row + rowOffset, pt);
     struct linkedFeatures *lf = lfFromEncodePeak((struct slList *)peak, tg->tdb, scoreMin, scoreMax);
 
     if (lf)
         slAddHead(&lfList, lf);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 slReverse(&lfList);
 slSort(&lfList, linkedFeaturesCmp);
 tg->items = lfList;
 }
 
 static void encodePeakLoadItemsNormal(struct track *tg)
 /* Load the encodePeak table form the database. */
 {
 encodePeakLoadItemsBoth(tg, NULL);
 }
 
 static void encodePeakLoadItemsCt(struct track *tg)
 /* Load the encodePeak table form the customTrash database. */
 {
 struct customTrack *ct = tg->customPt;
 encodePeakLoadItemsBoth(tg, ct);
 }
 
 static void encodePeakDrawAt(struct track *tg, void *item,
         struct hvGfx *hvg, int xOff, int y, double scale,
         MgFont *font, Color color, enum trackVisibility vis)
 /* Draw the peak from the linkedFeature.  Currently this doesn't draw any */
 /* sorta shading based on the signalValue/pValue. */
 {
 struct linkedFeatures *lf = item;
 int heightPer = tg->heightPer;
 int shortOff = heightPer/4;
 int shortHeight = heightPer - 2*shortOff;
 char *exonArrows = trackDbSettingClosestToHomeOrDefault(tg->tdb, "exonArrows", "off");
 boolean drawArrows = FALSE;
 if ((exonArrows != NULL) && sameString(exonArrows, "on"))
     drawArrows = TRUE;
 Color rangeColor = shadesOfGray[lf->grayIx];
 Color peakColor = (tg->ixColor != blackIndex()) ? tg->ixColor : getOrangeColor();
 if (drawArrows || lf->tallStart == 0)
     {
     shortOff = 0;
     shortHeight = heightPer;
     }
 if (lf->components)
     {
     struct simpleFeature *sf;
     drawScaledBox(hvg, lf->start, lf->end, scale, xOff, y+(heightPer/2), 1, rangeColor);
     for (sf = lf->components; sf != NULL; sf = sf->next)
 	{
         drawScaledBox(hvg, sf->start, sf->end, scale, xOff, y+shortOff,
                       shortHeight, rangeColor);
 	if (drawArrows)
 	    {
 	    int x1 = round((double)(sf->start-winStart)*scale) + xOff;
 	    int x2 = round((double)(sf->end-winStart)*scale) + xOff;
 	    int w = x2-x1;
             if (w < 1)
                 w = 1;
 
             clippedBarbs(hvg, x1, y + heightPer/2, w, 
                     tl.barbHeight, tl.barbSpacing, lf->orientation,
                     MG_WHITE, FALSE);
             }
 	}
     }
 else
     drawScaledBox(hvg, lf->start, lf->end, scale, xOff, y+shortOff,
 		  shortHeight, rangeColor);
 if ((lf->tallEnd > 0) && (lf->tallStart < lf->end))
     drawScaledBox(hvg, lf->tallStart, lf->tallEnd, scale, xOff, y,
 		  heightPer, peakColor);
 }
 
 char *encodePeakItemName(struct track *tg, void *item)
 /* Get rid of the '.' names */
 {
 struct linkedFeatures *lf = item;
 if (lf->name && sameString(lf->name, "."))
     return "";
 else
     return lf->name;
 }
 
 void encodePeakMethods(struct track *tg)
 /* Methods for ENCODE peak track uses mostly linkedFeatures. */
 {
 linkedFeaturesMethods(tg);
 tg->loadItems = encodePeakLoadItemsNormal;
 tg->drawItemAt = encodePeakDrawAt;
 tg->nextPrevItem = linkedFeaturesLabelNextPrevItem;
 tg->itemName = encodePeakItemName;
 tg->canPack = TRUE;
 }
 
 void encodePeakMethodsCt(struct track *tg)
 /* Methods for ENCODE peak track uses mostly linkedFeatures. */
 {
 encodePeakMethods(tg);
 tg->loadItems = encodePeakLoadItemsCt;
 }