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/kgBestRef2/kgPrepBestRef2.c src/hg/protein/kgBestRef2/kgPrepBestRef2.c index 714a4ca..9c850a8 100644 --- src/hg/protein/kgBestRef2/kgPrepBestRef2.c +++ src/hg/protein/kgBestRef2/kgPrepBestRef2.c @@ -1,223 +1,223 @@ /* * kgPrepBestRef2 - prepare input files for blat run 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 "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]; char *proteinDataDate; char *kgTempDb; char *db; char proteinsDB[100]; char spDB[100]; char gbTempDB[100]; char *clusterDir = "./clusterRun"; /* Explain usage and exit. */ void usage() { errAbort( "usage:\tkgPrepBestRef YYMMDD tempDb db\n" "\tYYMMDD is the release date of SWISS-PROT data, eg: 031117\n" "\ttempDb is the temporary db for kg construction, eg: kgMm4ATemp\n" "\tdb is the genome under construction, eg: mm4\n" "kgPrepBestRef - read a list of proteins from protRef.lis and get\n" "\tcorresponding mRNAs from dbTemp.refRef to prepare input files\n" "\tfor blat run. Creates files ./clusterRun/protN/[mp]NNNN.fa\n" "\tand result directories: ./out/protN/ (2000 results per directory)\n" "\tCreates files rawJobList and protRef.lis."); } 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); } int main(int argc, char *argv[]) { char proteinID[20]; FILE *IN, *OUT; char line[2000]; int imrna; char dirName[1000]; char protName[1000]; char mrnaFile[1000]; char outName[1000]; char outDir[1000]; char blatCmd[1000]; HGID id; bioSeq *mSeq; struct sqlConnection *conn2, *conn3; char query2[256]; struct sqlResult *sr2; char **row2; char *mrnaID; FILE *aaOut, *mrnaOut; char *aaSeq; char cond_str[200]; if (argc != 4) usage(); proteinDataDate = argv[1]; kgTempDb = argv[2]; db = argv[3]; sprintf(spDB, "sp%s", proteinDataDate); sprintf(proteinsDB, "proteins%s", proteinDataDate); sprintf(gbTempDB, "%s", kgTempDb); IN = fopen("protRef.lis", "r"); OUT = fopen("rawJobList", "w"); conn2= hAllocConn(db); conn3= hAllocConn(db); proteinCount = 0; snprintf(dirName, (size_t) sizeof(dirName), "./out" ); mkdir(dirName, S_IRUSR | S_IWUSR | S_IXUSR | S_IRGRP | S_IWGRP | S_IXGRP | S_IROTH | S_IWOTH | S_IXOTH ); snprintf(dirName, (size_t) sizeof(dirName), "%s", clusterDir ); mkdir(dirName, S_IRUSR | S_IWUSR | S_IXUSR | S_IRGRP | S_IWGRP | S_IXGRP | S_IROTH | S_IWOTH | S_IXOTH ); if (chdir(dirName)) errAbort("ERROR: Can not change dir to %s\n", dirName); while (fgets(line, 1000, IN) != NULL) { sscanf(line, "%s", proteinID); printf(">%s\n", proteinID); - sqlSafefFrag(cond_str, sizeof cond_str, "acc='%s'", proteinID); + sqlSafef(cond_str, sizeof cond_str, "acc='%s'", proteinID); aaSeq = sqlGetField(spDB, "protein","val", cond_str); if (aaSeq == NULL) { aaSeq = sqlGetField(spDB, "varProtein","val", cond_str); } if (aaSeq == NULL) { printf("no seq found for %s\n", proteinID); fflush(stdout); exit(1); } /* 2000 results per output directory. 4000 input files for each * ./protN directory */ if ( 0 == (proteinCount % 2000) ) { snprintf(dirName, (size_t)sizeof(dirName), "../out/prot%05d", proteinCount); if (mkdir(dirName, S_IRUSR | S_IWUSR | S_IXUSR | S_IRGRP | S_IWGRP | S_IXGRP | S_IROTH | S_IWOTH | S_IXOTH )) { if (errno != EEXIST) errAbort("ERROR: Can not create dir %s\n", dirName); } snprintf(dirName, (size_t) sizeof(dirName), "prot%05d", proteinCount ); if (mkdir(dirName, S_IRUSR | S_IWUSR | S_IXUSR | S_IRGRP | S_IWGRP | S_IXGRP | S_IROTH | S_IWOTH | S_IXOTH )) { if (errno != EEXIST) errAbort("ERROR: Can not create dir %s\n", dirName); } snprintf(outDir, (size_t) sizeof(outDir), "out/prot%05d", proteinCount); } snprintf(protName, (size_t) sizeof(protName), \ "%s/p%05d.fa", dirName, proteinCount ); aaOut = fopen(protName, "w"); fprintf(aaOut, ">%s\n%s\n", proteinID, aaSeq); fclose(aaOut); sqlSafef(query2, sizeof query2, "select mrnaID from %s.spRef where spID='%s';",kgTempDb, proteinID); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); imrna = 0; snprintf(mrnaFile, (size_t) sizeof(mrnaFile), \ "%s/m%05d.fa", dirName, proteinCount ); mrnaOut = NULL; while (row2 != NULL) { mrnaID = row2[0]; strcpy(mrnaNames[imrna], mrnaID); printf("%s\t%s\n", proteinID, mrnaID);fflush(stdout); sprintf(cond_str, "name='%s'", mrnaID); if (hRnaSeqAndIdx(mrnaID, &mSeq, &id, conn3)== -1) { printf("%s could not be found!!!\n", mrnaID);fflush(stdout); } else { if (mrnaOut == NULL)mrnaOut = fopen(mrnaFile, "w"); fprintf(mrnaOut, ">%s\n%s\n", mrnaID, mSeq->dna); } row2 = sqlNextRow(sr2); imrna++; } mrnaCount = imrna; if (mrnaOut != NULL)fclose(mrnaOut); sqlFreeResult(&sr2); snprintf(outName, (size_t) sizeof(outName),"./%s/b%05d.out", outDir, proteinCount); snprintf(blatCmd, (size_t) sizeof(blatCmd), "blat {check in exists %s/%s} {check in exists %s/%s} {check out line %s} -noHead -t=dnax -q=prot", \ clusterDir, mrnaFile, clusterDir, protName, outName); if (mrnaOut != NULL) { fprintf(OUT, "%s\n", blatCmd); proteinCount++; } } hFreeConn(&conn2); hFreeConn(&conn3); fclose(IN); fclose(OUT); return(0); }