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/cgapSageTrack.c src/hg/hgTracks/cgapSageTrack.c index 6172583..af90c1b 100644 --- src/hg/hgTracks/cgapSageTrack.c +++ src/hg/hgTracks/cgapSageTrack.c @@ -1,312 +1,315 @@ /* cgapSageTrack - module for CGAP SAGE track. */ /* 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 "hash.h" #include "linefile.h" #include "jksql.h" #include "hdb.h" #include "hgTracks.h" #include "hCommon.h" #include "cgapSage/cgapSage.h" #include "cgapSage/cgapSageLib.h" static int grayIxForCgap(double tpm) /* Return a grayIx based on the score. */ { int val = (int)ceil(tpm); return grayInRange(val, 0, 150); } static struct hash *libTissueHash(struct sqlConnection *conn) /* Read two columns of a table and hash em up. */ { struct hash *ret = newHash(9); struct sqlResult *sr = NULL; -char query[49] = NOSQLINJ "select libId,tissue from cgapSageLib"; +char query[49]; char **row; +sqlSafef(query, sizeof query, "select libId,tissue from cgapSageLib"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) hashAdd(ret, row[0], cloneString(row[1])); sqlFreeResult(&sr); return ret; } struct cgapSageTpmHashEl /* A convenience struct for computing means. */ { double total; long freqTotal; long libTotals; int count; }; static boolean keepThisLib(char *tissue, char *libId) /* Tissue filtering code checks cart. */ { char *tissueHl = cartUsualString(cart, "cgapSage.tissueHl", "All"); if (!tissue) errAbort("NULL tissue or libId passed into keepThisLib()"); if (sameString(tissueHl, "All") || sameString(tissue, tissueHl)) return TRUE; return FALSE; } static struct hash *combineCgapSages(struct cgapSage *tag, struct hash *libHash, struct hash *libTotHash) /* Go through the each lib for a tag and combine it's score using a hash for */ /* repeated tissues. */ { struct hash *tpmHash = newHash(5); int i; for (i = 0; i < tag->numLibs; i++) { char libId[16]; char *libName; int libTotTags = 0; struct cgapSageTpmHashEl *tpm; safef(libId, sizeof(libId), "%d", tag->libIds[i]); libName = hashMustFindVal(libHash, libId); tpm = hashFindVal(tpmHash, libName); libTotTags = hashIntVal(libTotHash, libId); if (keepThisLib(libName, libId)) { if (tpm) { tpm->count++; tpm->freqTotal += tag->freqs[i]; tpm->total += tag->tagTpms[i]; tpm->libTotals += libTotTags; } else { AllocVar(tpm); tpm->count = 1; tpm->total = tag->tagTpms[i]; tpm->freqTotal = tag->freqs[i]; tpm->libTotals = libTotTags; hashAdd(tpmHash, libName, tpm); } } } return tpmHash; } static struct linkedFeatures *skeletonLf(struct cgapSage *tag) /* Fill in everything except the name and score. */ { struct linkedFeatures *lf; struct simpleFeature *sf; AllocVar(lf); AllocVar(sf); lf->start = sf->start = tag->chromStart; lf->end = sf->end = tag->chromEnd; lf->tallStart = tag->thickStart; lf->tallEnd = tag->thickEnd; lf->orientation = orientFromChar(tag->strand[0]); lf->components = sf; return lf; } static void addSimpleFeature(struct linkedFeatures *lf) /* Make a dumb simpleFeature out of a single linkedFeatures. */ { struct simpleFeature *sf; AllocVar(sf); sf->start = lf->start; sf->end = lf->end; sf->grayIx = lf->grayIx; lf->components = sf; } static char *cgapSageMapItemName(struct track *tg, void *item) /* Use what's in the ->extra for the name. */ { struct linkedFeatures *lf = item; return (char *)lf->extra; } static void cgapSageMapItem(struct track *tg, struct hvGfx *hvg, void *item, char *itemName, char *mapItemName, int start, int end, int x, int y, int width, int height) { struct linkedFeatures *lf = item; mapBoxHgcOrHgGene(hvg, start, end, x, y, width, height, tg->track, itemName, NULL, NULL, TRUE, (char *)lf->extra); } int cgapLinkedFeaturesCmp(const void *va, const void *vb) /* Compare to sort based on chrom,chromStart. */ { const struct linkedFeatures *a = *((struct linkedFeatures **)va); const struct linkedFeatures *b = *((struct linkedFeatures **)vb); return (int)b->score - (int)a->score; } static struct linkedFeatures *cgapSageToLinkedFeatures(struct cgapSage *tag, struct hash *libHash, struct hash *libTotHash, enum trackVisibility vis) /* Convert a single CGAP tag to a list of linkedFeatures. */ { struct linkedFeatures *libList = NULL; struct linkedFeatures *skel = skeletonLf(tag); int i; if (vis == tvDense) /* Just use the skeleton one. */ { int tagTotal = 0; int freqTotal = 0; int libsUsed = 0; for (i = 0; i < tag->numLibs; i++) { char libId[16]; char *libName; safef(libId, sizeof(libId), "%d", tag->libIds[i]); libName = hashMustFindVal(libHash, libId); if (keepThisLib(libName, libId)) { int libTotal = hashIntVal(libTotHash, libId); tagTotal += libTotal; freqTotal += tag->freqs[i]; libsUsed++; } } if (libsUsed > 0) { skel->name = cloneString("whatever"); skel->score = (float)((double)freqTotal * (1000000/tagTotal)); skel->grayIx = grayIxForCgap(skel->score); addSimpleFeature(skel); libList = skel; } } else if (vis == tvPack) { /* If it's pack mode, average tissues into one linkedFeature. */ struct hash *tpmHash = combineCgapSages(tag, libHash, libTotHash); struct hashEl *tpmList = hashElListHash(tpmHash); struct hashEl *tpmEl; slSort(&tpmList, slNameCmp); for (tpmEl = tpmList; tpmEl != NULL; tpmEl = tpmEl->next) { struct linkedFeatures *tiss = CloneVar(skel); struct cgapSageTpmHashEl *tpm = (struct cgapSageTpmHashEl *)tpmEl->val; char link[256]; char *encTissName = NULL; double score = 0; int len = strlen(tpmEl->name) + 32; tiss->name = needMem(len); safef(tiss->name, len, "%s (%d)", tpmEl->name, tpm->count); encTissName = cgiEncode(tpmEl->name); safef(link, sizeof(link), "i=%s&tiss=%s", tag->name, encTissName); score = (double)tpm->freqTotal*(1000000/(double)tpm->libTotals); tiss->score = (float)score; tiss->grayIx = grayIxForCgap(score); tiss->extra = cloneString(link); freeMem(encTissName); addSimpleFeature(tiss); slAddHead(&libList, tiss); } hashElFreeList(&tpmList); freeHashAndVals(&tpmHash); } else /* full mode */ { for (i = 0; i < tag->numLibs; i++) { char libId[16]; char *libName; char link[256]; struct linkedFeatures *lf; safef(libId, sizeof(libId), "%d", tag->libIds[i]); libName = hashMustFindVal(libHash, libId); if (keepThisLib(libName, libId)) { lf = CloneVar(skel); lf->name = cloneString(libName); safef(link, sizeof(link), "i=%s&lib=%s", tag->name, libId); lf->score = (float)tag->tagTpms[i]; lf->grayIx = grayIxForCgap(tag->tagTpms[i]); lf->extra = cloneString(link); addSimpleFeature(lf); slAddHead(&libList, lf); } } } slSort(&libList, cgapLinkedFeaturesCmp); slReverse(&libList); return libList; } struct hash *getTotTagsHashFromTable(struct sqlConnection *conn) /* Load the cgapSageLib table for the db then call getTotTagsHash. */ { -struct cgapSageLib *libs = cgapSageLibLoadByQuery(conn, NOSQLINJ "select * from cgapSageLib"); +char query[1024]; +sqlSafef(query, sizeof query, "select * from cgapSageLib"); +struct cgapSageLib *libs = cgapSageLibLoadByQuery(conn, query); struct hash *libTotHash = getTotTagsHash(libs); cgapSageLibFreeList(&libs); return libTotHash; } void cgapSageLoadItems(struct track *tg) /* This function loads the beds in the current window into a linkedFeatures list. */ /* Each bed entry may turn into multiple linkedFeatures because one is made for */ /* each library at a given tag (bed). */ { struct linkedFeatures *itemList = NULL; struct sqlConnection *conn = hAllocConn(database); struct hash *libHash = libTissueHash(conn); struct hash *libTotHash = getTotTagsHashFromTable(conn); struct sqlResult *sr = NULL; char **row; int rowOffset; sr = hOrderedRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset); if ((winEnd - winStart) > CGAP_SAGE_DENSE_GOVERNOR) tg->visibility = tvDense; while ((row = sqlNextRow(sr)) != NULL) { struct cgapSage *tag = cgapSageLoad(row+rowOffset); struct linkedFeatures *oneLfList = cgapSageToLinkedFeatures(tag, libHash, libTotHash, tg->visibility); itemList = slCat(oneLfList, itemList); } slReverse(&itemList); sqlFreeResult(&sr); hFreeConn(&conn); tg->items = itemList; } /***** All the drawing/color-related stuff. ******/ static Color cgapShadesOfRed[10+1]; /* This will go from white to darker red. */ static Color cgapSageItemColor(struct track *tg, void *item, struct hvGfx *hvg) /* Return color to draw CGAP SAGE item */ { struct linkedFeatures *thisItem = item; return cgapShadesOfRed[thisItem->grayIx]; } void cgapSageDrawItems(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis) /* Initialize the colors, then do the normal drawing. */ { static struct rgbColor lowerColor = {205, 191, 191}; static struct rgbColor cgapRed = {205, 0, 0}; hvGfxMakeColorGradient(hvg, &lowerColor, &cgapRed, 10, cgapShadesOfRed); genericDrawItems(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis); } void cgapSageMethods(struct track *tg) /* Make track for simple repeats. */ { linkedFeaturesMethods(tg); tg->loadItems = cgapSageLoadItems; tg->itemColor = cgapSageItemColor; tg->drawItems = cgapSageDrawItems; tg->mapItemName = cgapSageMapItemName; tg->mapItem = cgapSageMapItem; }