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/protein/kgBestMrna/kgResultBestMrna.c src/hg/protein/kgBestMrna/kgResultBestMrna.c index e67fc17..1e19d70 100644 --- src/hg/protein/kgBestMrna/kgResultBestMrna.c +++ src/hg/protein/kgBestMrna/kgResultBestMrna.c @@ -1,343 +1,343 @@ /* kgBestMrna - driver program to call blat to select best mRNA for each protein */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include <sys/param.h> #include "common.h" #include "hCommon.h" #include "hdb.h" char proteinName[20], mrnaName[20]; char mrnaNames[500][20]; int mrnaScore[500]; char proteinNameOld[20] = {""}; struct dnaSeq *seq; HGID id; bioSeq *mSeq, qSeq, *pSeq; extern int answer_for_kg; struct dnaSeq *untransList; char line[2000]; char line2[2000]; int mrnaCount; int proteinCount; char mrnaNames[500][20]; char mrnaDates[500][20]; int mrnaScore[500]; int diffIdent[500]; FILE *o3, *o7; char *proteinDataDate; char *genomeRelease; char *genomeReadOnly; char *genomeDBname; char proteinsDB[100]; char spDB[100]; char gbTempDB[100]; /* Explain usage and exit. */ void usage() { errAbort( "usage:\tkgResultBestMrna YYMMDD db ro_db> BestResult.out\n" "\tYYMMDD is the release date of SWISS-PROT data, eg: 031117\n" "\tdb is the genome under construction, eg: kgDB\n" "\tro_db is the actual target genome, e.g.: mm4\n" "kgResultBestMrna - after the cluster run is done, this reads the\n" "\tresults and produces a best.lis listing.\n" "\tExpects to find ./clusterRun and ./out directories in the\n" "\tcurrent working directory."); } int cal_months(char *date) { int year, month, day; int months; sscanf(date, "%d-%d-%d", &year, &month, &day); months = (year - 1970)*12 + month - 1; return(months); } void calScores(char *proteinID, int mrnaCount) { int ixm, maxixm; // index for mRNA int maxScore; int i, ii; char proteinName[20], mrnaName[20]; int diffs[500]; int monthss[500]; int mrnalens[500]; char line[2000]; char mrnaDate[20]; int months; int diff; int mrnalen; char *temp_str; struct dnaSeq *seq; struct sqlConnection *connR; connR = hAllocConn(); ixm = 0; maxScore = 0; strcpy(proteinName, proteinID); maxixm = -1; for (ii=0; ii<mrnaCount; ii++) { strcpy(mrnaName, mrnaNames[ii]); if (hRnaSeqAndIdx(mrnaNames[ii], &mSeq, &id, mrnaDate, connR)== -1) { printf("%s could not be found!!!\n", mrnaNames[ii]);fflush(stdout); exit(1); } strcpy(mrnaDates[ii], mrnaDate); mrnalen = strlen(mSeq->dna); months = cal_months(mrnaDate); diffs[ii] = diffIdent[ii]; mrnalens[ii] = mrnalen; monthss[ii] = months; mrnaScore[ii] = mrnalen + months*2 - diffs[ii]*50; if (mrnaScore[ii] > maxScore) { maxScore = mrnaScore[ii]; maxixm = ii; } } for (i=0; i<mrnaCount; i++) { if (diffIdent[i] != -1) { fprintf(o3, "%10s %10s %8s %5d %5d %5d %5d", proteinName, mrnaNames[i], mrnaDates[i], mrnaScore[i], mrnalens[i], monthss[i], diffs[i]); if (i == maxixm) { fprintf(o3, " *\n"); fprintf(o7, "%s\t%s\n", proteinName, mrnaNames[i]); fflush(o7); } else { fprintf(o3, "\n"); } fflush(o3); } } fprintf(o3, "\n"); fflush(o3); hFreeConn(&connR); } int main(int argc, char *argv[]) { int ixm, maxixm; // index for mRNA int maxScore; char proteinID[20], mrnaName[20]; int monthss[500]; int mrnalens[500]; FILE *inf, *inf2, *outf; int newMrna; int ii= -1; char line[2000]; char mrnaDate[20]; int months; int diff; int mrnalen; int imrna; char dirName[PATH_MAX]; char mrnaFile[PATH_MAX]; char outName[PATH_MAX]; char outDir[PATH_MAX]; char blatCmd[PATH_MAX]; char cwd[PATH_MAX]; struct dnaSeq *seq; HGID id; bioSeq *mSeq, qSeq, *pSeq; struct sqlConnection *conn, *conn2, *conn3; char query[256], query2[256], query3[256]; struct sqlResult *sr, *sr2, *sr3; char **row, **row2, **row3; char *accession; char *displayID; char *division; char *extDB; char *extAC; char *chp0, *chp; int totalCount, matchCount; char *name, *chrom, *strand, *txStart, *txEnd, *cdsStart, *cdsEnd, *exonCount, *exonStarts, *exonEnds; int i; char *mrnaID; FILE *aaOut, *mrnaOut; char *aaSeq, *mrnaSeq; char cond_str[200]; if (argc != 4) usage(); proteinDataDate = argv[1]; genomeRelease = argv[2]; genomeReadOnly = argv[3]; // make sure db connection goes to correct genome // hRnaSeqAndIdx() needs this. hSetDb(genomeReadOnly); sprintf(spDB, "sp%s", proteinDataDate); sprintf(proteinsDB, "proteins%s", proteinDataDate); sprintf(gbTempDB, "%sTemp", genomeRelease); inf = fopen("protein.lis", "r"); if ((FILE *) NULL == inf) errAbort("ERROR: Can not open input file: protein.lis"); o3 = fopen("kgBestMrna.out", "w"); if ((FILE *) NULL == o3) errAbort("ERROR: Can not open output file: kgBestMrna.out"); o7 = fopen("best.lis", "w"); if ((FILE *) NULL == o7) errAbort("ERROR: Can not open output file: best.lis"); conn2= hAllocConn(); conn3= hAllocConn(); proteinCount = 0; snprintf(dirName, (size_t) sizeof(dirName), "%s", "./clusterRun" ); while (fgets(line, 1000, inf) != NULL) { sscanf(line, "%s", proteinID); printf(">%s\n", proteinID); fflush(stdout); - sqlSafefFrag(cond_str, sizeof cond_str, "val='%s'", proteinID); + sqlSafef(cond_str, sizeof cond_str, "val='%s'", proteinID); accession = sqlGetField(conn3, spDB, "displayId","acc", cond_str); - sqlSafefFrag(cond_str, sizeof cond_str, "acc='%s'", accession); + sqlSafef(cond_str, sizeof cond_str, "acc='%s'", accession); aaSeq = sqlGetField(conn3, spDB, "protein","val", cond_str); if (aaSeq == NULL) { printf("no seq found for %s\n", proteinID); fflush(stdout); exit(1); } if ( 0 == (proteinCount % 2000) ) { snprintf(dirName, (size_t) sizeof(dirName), "prot%05d", proteinCount ); snprintf(outDir, (size_t) sizeof(outDir), "prot%05d", proteinCount ); } sqlSafef(query2, sizeof query2, "select mrnaID from %sTemp.spMrna where spID='%s';",genomeRelease, proteinID); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); imrna = 0; while (row2 != NULL) { mrnaID = row2[0]; strcpy(mrnaNames[imrna], mrnaID); - sqlSafefFrag(cond_str, sizeof cond_str, "name='%s'", mrnaID); + sqlSafef(cond_str, sizeof cond_str, "name='%s'", mrnaID); mrnaSeq = sqlGetField(conn3,gbTempDB,"refMrna","seq", cond_str); row2 = sqlNextRow(sr2); imrna++; } mrnaCount = imrna; sqlFreeResult(&sr2); if ( ((char *) NULL) == getcwd(cwd, (size_t) sizeof(cwd)) ) errAbort("ERROR: Can not get current working directory"); snprintf(outName, (size_t) sizeof(outName),"%s/out/%s/b%05d.out", cwd, outDir, proteinCount); inf2 = fopen(outName, "r"); if ((FILE *) NULL == inf2) errAbort("ERROR: Can not open result file: %s, errno: %d", outName, errno); for (i=0; i<mrnaCount; i++) diffIdent[i] = -1; imrna = 0; newMrna = 0; while (fgets(line2, 1000, inf2) != NULL) { if (line2[0] == '>') { newMrna = 1; line2[strlen(line2)-1] = '\0'; chp = line2 + 1; ii=-1; for (i=0; i<mrnaCount; i++) { if (strcmp(chp, mrnaNames[i]) == 0) { ii = i; } } if (ii == -1) { errAbort("ERROR: no mrna registered found", outName, errno); } } chp0 = strstr(line2, "Identities = "); if (chp0 == NULL) continue; if (!newMrna) continue; else newMrna = 0; chp0 = chp0 + strlen("Identities = "); chp = strstr(chp0, "/"); *chp = '\0'; sscanf(chp0, "%d", &matchCount); chp++; chp0 = strstr(chp, " "); *chp0 = '\0'; sscanf(chp, "%d", &totalCount); // some time mulitiple alignments for a single mRNA-protein pair // the first one usually is the best alignment with highest score if (diffIdent[ii] == -1) { diffIdent[ii] = totalCount - matchCount; imrna++; } } fclose(inf2); if (imrna != mrnaCount) { fprintf(stderr, "total mrna count %d %d is different for %s\n", imrna, mrnaCount, proteinID); } calScores(proteinID, mrnaCount); proteinCount++; } hFreeConn(&conn2); hFreeConn(&conn3); fclose(o3); fclose(o7); return(0); }