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/geneBounds/estLibStats/estLibStats.c src/hg/geneBounds/estLibStats/estLibStats.c index 397c72f..baae6bc 100644 --- src/hg/geneBounds/estLibStats/estLibStats.c +++ src/hg/geneBounds/estLibStats/estLibStats.c @@ -1,359 +1,363 @@ /* estLibStats - Calculate some stats on EST libraries given file from polyInfo. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "cheapcgi.h" #include "jksql.h" #include "estOrientInfo.h" void usage() /* Explain usage and exit. */ { errAbort( "estLibStats - Calculate some stats on EST libraries given file from polyInfo\n" "usage:\n" " estLibStats database eiInfo.bed output\n" "options:\n" " -xxx=XXX\n" ); } int scoreEi(struct estOrientInfo *ei, int *retStrand) /* Assign a score to an ei. retStrand if non-null * returns +1 or -1 depending which strand est appears * to be on relative to transcript. */ { int fScore = 0, rScore = 0, score, strand; if (ei->intronOrientation > 0) fScore += ei->intronOrientation * 15; else if (ei->intronOrientation < 0) rScore += -ei->intronOrientation * 15; fScore += ei->sizePolyA; rScore += ei->sizePolyA; if (ei->signalPos > 0) fScore += 8; if (ei->revSignalPos > 0) rScore += 8; if (fScore >= rScore) { score = fScore; strand = 1; } else { score = rScore; strand = -1; } if (score < 6) strand = 0; if (retStrand != NULL) *retStrand = strand; return score; } struct hash *readEstInfo(char *fileName) /* Read in EST info from file. */ { struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[9]; struct hash *hash = newHash(20); while (lineFileRow(lf, row)) { struct estOrientInfo *ei = estOrientInfoLoad(row), *oldEi; oldEi = hashFindVal(hash, ei->name); if (oldEi != NULL) { if (scoreEi(ei, NULL) < scoreEi(oldEi, NULL)) { estOrientInfoFree(&ei); continue; } } hashAdd(hash, ei->name, ei); } return hash; } struct libInfo /* Info on a batch of ESTs */ { struct libInfo *next; char *libName; /* Full name of library. */ char *author; /* Library authors. */ int estCount; /* Total count of ESTs. */ struct estOrientInfo *threePrime; /* List of 3' ESTs. */ struct estOrientInfo *fivePrime; /* List of 5' ESTs. */ struct estOrientInfo *unPrime; /* List of unknown orientation ests. */ }; int libInfoCmp(const void *va, const void *vb) /* Compare to sort based on query. */ { const struct libInfo *a = *((struct libInfo **)va); const struct libInfo *b = *((struct libInfo **)vb); return b->estCount - a->estCount; } struct nameId /* A name/id pair. */ { struct nameId *next; char *id; /* Ascii numerical id. */ char *name; /* Often longish name with white space. */ }; struct hash *readIdHash(char *database, char *table) /* Put an id/name table into a hash keyed by id with * nameId as value. */ { struct sqlConnection *conn = sqlConnect(database); struct hash *hash = newHash(0); char query[256]; struct sqlResult *sr; char **row; struct nameId *nid; sqlSafef(query, sizeof query, "select id,name from %s", table); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { AllocVar(nid); nid->name = cloneString(row[1]); hashAddSaveName(hash, row[0], nid, &nid->id); } sqlFreeResult(&sr); sqlDisconnect(&conn); return hash; } struct libInfo *addEsts(char *database, struct hash *eiHash, struct hash *libHash, struct hash *authorHash, struct hash *liHash) /* Read in all ESTs from mRNA table in database and add them to * library they belong to. */ { struct libInfo *liList = NULL, *li; struct estOrientInfo *ei; struct sqlConnection *conn = sqlConnect(database); struct sqlResult *sr = NULL; char liId[256]; char **row; struct nameId *library, *author; -sr = sqlGetResult(conn, NOSQLINJ "select acc,library,author,direction from mrna where type = 'EST'"); +char query[1024]; +sqlSafef(query, sizeof query, "select acc,library,author,direction from mrna where type = 'EST'"); +sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { library = hashMustFindVal(libHash, row[1]); author = hashMustFindVal(authorHash, row[2]); sprintf(liId, "%s.%s", library->id, author->id); if ((li = hashFindVal(liHash, liId)) == NULL) { AllocVar(li); li->libName = library->name; li->author = author->name; hashAdd(liHash, liId, li); slAddHead(&liList, li); } li->estCount += 1; if ((ei = hashFindVal(eiHash, row[0])) != NULL) { switch (row[3][0]) { case '5': slAddHead(&li->fivePrime, ei); break; case '3': slAddHead(&li->threePrime, ei); break; case '0': slAddHead(&li->unPrime, ei); break; default: errAbort("Unknown type '%s' for %s", row[3], row[0]); break; } } } sqlFreeResult(&sr); sqlDisconnect(&conn); slSort(&liList, libInfoCmp); return liList; } void sumStrandAndScore(struct estOrientInfo *eiList, int *retStrand, int *retScore) /* Return sum of strand and score. */ { struct estOrientInfo *ei; int strand = 0, score = 0, strand1, score1; for (ei = eiList; ei != NULL; ei = ei->next) { score1 = scoreEi(ei, &strand1); score += score1; strand += strand1; } *retScore = score; *retStrand = strand; } void labelGroup(FILE *f, char *name) /* Print label of a couple elements. */ { fprintf(f, "%s\torient\tsplice+\tsplice-\tsignal+\tsignal-\tpolyA+\tpolyA-\t", name); } void printGroupStats(FILE *f, struct estOrientInfo *eiList) /* Print stats from list. */ { int splicePlus=0, spliceMinus=0, signalPlus=0, signalMinus=0, polyPlus=0, polyMinus=0; int all = 0, orient = 0, strand; struct estOrientInfo *ei; for (ei=eiList; ei != NULL; ei = ei->next) { ++all; scoreEi(ei, &strand); if (strand != 0) ++orient; if (ei->intronOrientation > 0) ++splicePlus; else if (ei->intronOrientation < 0) ++spliceMinus; if (ei->signalPos > 0) ++signalPlus; if (ei->revSignalPos > 0) ++signalMinus; if (ei->sizePolyA >= 6) ++polyPlus; if (ei->revSizePolyA >= 6) ++polyMinus; } fprintf(f, "%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t", all, orient, splicePlus, spliceMinus, signalPlus, signalMinus, polyPlus, polyMinus); } #ifdef NEEDSWORK void addSizeAndDates(struct estInfo *eiList, long *size, int *count, char **minDate, char **maxDate) /* Fold in size and date info from this est list. */ { struct estInfo *ei; for (ei = eiList; ei != NULL; ei = ei->next) { *size += ei->size; if (*minDate == NULL || strcmp(ei->date, *minDate) < 0) *minDate = ei->date; if (*maxDate == NULL || strcmp(ei->date, *maxDate) > 0) *maxDate = ei->date; *count += 1; } } #endif /* NEEDSWORK */ void printLibStats(struct libInfo *liList, char *fileName) /* Write stats on libs to file. */ { struct libInfo *li; FILE *f = mustOpen(fileName, "w"); #ifdef NEEDSWORK fprintf(f, "#ests\tsize\tstartDate\tendngDate\t"); #else fprintf(f, "#ests\t"); #endif /* NEEDSWORK */ labelGroup(f, "3'"); labelGroup(f, "5'"); labelGroup(f, "?"); fprintf(f, "library\tauthor\n"); for (li = liList; li != NULL; li = li->next) { #ifdef NEEDSWORK char *minDate = NULL, *maxDate = NULL; long totalSize = 0; int count = 0, avgSize = 0; #endif /* NEEDSWORK */ if (li->estCount == 0) continue; fprintf(f, "%d\t", li->estCount); #ifdef NEEDSWORK addSizeAndDates(li->threePrime, &totalSize, &count, &minDate, &maxDate); addSizeAndDates(li->fivePrime, &totalSize, &count, &minDate, &maxDate); addSizeAndDates(li->unPrime, &totalSize, &count, &minDate, &maxDate); if (count > 0) avgSize = totalSize/count; fprintf(f, "%d\t%s\t%s\t", avgSize, minDate, maxDate); #endif /* NEEDSWORK */ printGroupStats(f, li->threePrime); printGroupStats(f, li->fivePrime); printGroupStats(f, li->unPrime); fprintf(f, "%s\t", li->libName); fprintf(f, "%s\n", li->author); } carefulClose(&f); } #ifdef NEEDSWORK void addSizes(char *database, struct hash *eiHash, struct hash *dateHash) /* Add and date info to ests in eiHash. Date strings are stored in dateHash */ { struct sqlConnection *conn = sqlConnect(database); struct sqlResult *sr = NULL; char **row; -sr = sqlGetResult(conn, NOSQLINJ "select acc,size,gb_date from seq"); +char query[1024]; +sqlSafef(query, sizeof query, "select acc,size,gb_date from seq"); +sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *acc = row[0]; struct estInfo *ei = hashFindVal(eiHash, acc); if (ei != NULL) { ei->size = sqlUnsigned(row[1]); ei->date = hashStoreName(dateHash, row[2]); } } sqlFreeResult(&sr); sqlDisconnect(&conn); } #endif /* NEEDSWORK */ void estLibStats(char *database, char *eiInfoBed, char *output) /* estLibStats - Calculate some stats on EST libraries given file from polyInfo. */ { struct hash *eiHash = NULL, *liHash = newHash(0); struct hash *libHash = NULL, *authorHash = NULL; #ifdef NEEDSWORK struct hash *dateHash = newHash(0); #endif /* NEEDSWORK */ struct libInfo *liList = NULL; libHash = readIdHash(database, "library"); authorHash = readIdHash(database, "author"); printf("Read libs and authors\n"); eiHash = readEstInfo(eiInfoBed); printf("Read %s\n", eiInfoBed); #ifdef NEEDSWORK addSizes(database, eiHash, dateHash); #endif /* NEEDSWORK */ printf("Added size info\n"); liList = addEsts(database, eiHash, libHash, authorHash, liHash); printf("Read in 3' and other info from %s\n", database); printLibStats(liList, output); } int main(int argc, char *argv[]) /* Process command line. */ { cgiSpoof(&argc, argv); if (argc != 4) usage(); estLibStats(argv[1], argv[2], argv[3]); return 0; }