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/kgCheck/kgCheck.c src/hg/protein/kgCheck/kgCheck.c index a1cfea7..4da0d53 100644 --- src/hg/protein/kgCheck/kgCheck.c +++ src/hg/protein/kgCheck/kgCheck.c @@ -1,210 +1,210 @@ /* kgCheck - From the initial gene candidates, */ /* go through various criteria on gene-check results and keep the ones that pass the criteria */ /* 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" void usage() /* Explain usage and exit. */ { errAbort( "kgCheck - from gene candidates, go through various criteria and keep the ones that pass the criteria \n" "usage:\n" " kgCheck tempDb genomeDb candidateTable chkTable outfile\n" " tempDb is the temp KG DB name\n" " genomeDb is the genome DB where refGene and mgcGenes tables are\n" " candidateTable is the gene candidates table in tempDb\n" " checkTable is the table (in tempDb) storing gene-check results\n" " outfile is the output file name\n" "example: kgCheck kgMm6ATemp mm6 kgCandidate0 kgCandidate.tab\n"); } int main(int argc, char *argv[]) { struct sqlConnection *conn, *conn2, *conn3; char query2[256], query3[256]; struct sqlResult *sr2, *sr3; char **row2, **row3; char condStr[255]; char *answer; char *kgTempDb; char *outfileName; FILE *outf; int i; char *chp; char *acc2; char *name, *txStart, *txEnd; char *chrom; char *acc, *stat; char *frame, *start, *stop; char *causes; char *genomeDb; char *geneName; char srcType; int alignCnt = 0; char *candTable, *chkTable; int orfStop, cdsGap, cdsSplice, numCdsIntrons; boolean passed; float ranking; if (argc != 6) usage(); kgTempDb = argv[1]; genomeDb = argv[2]; candTable = argv[3]; chkTable = argv[4]; outfileName = argv[5]; outf = mustOpen(outfileName, "w"); conn = hAllocConn(genomeDb); conn2= hAllocConn(genomeDb); conn3= hAllocConn(genomeDb); /* go through each protein */ sqlSafef(query2, sizeof(query2), "select * from %s.%s", kgTempDb, candTable); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); while (row2 != NULL) { name = row2[0]; chrom = row2[1]; txStart = row2[3]; txEnd = row2[4]; /* retrieve gene-check results */ sqlSafef(query3, sizeof(query3), "select * from %s.%s where acc='%s' and chrStart=%s and chrEnd = %s", kgTempDb, chkTable, name, txStart, txEnd); sr3 = sqlMustGetResult(conn3, query3); row3 = sqlNextRow(sr3); { passed = FALSE; ranking = 3; acc = row3[0]; stat = row3[5]; frame = row3[6]; start = row3[7]; stop = row3[8]; orfStop = atoi(row3[9]); cdsGap = atoi(row3[10]); cdsSplice = atoi(row3[12]); numCdsIntrons = atoi(row3[18]); causes = row3[21]; ranking = 9; /* all genes passed gene-check with status ok are considered good */ if (sameWord(stat, "ok")) { passed = TRUE; ranking = 1; } else { /* frame, start, orfStop, and stop conditions must be met for KG candidates */ if ((sameWord(frame, "ok")) && (sameWord(start, "ok")) && (orfStop == 0) && (sameWord(stop, "ok")) ) { ranking = 2; /* accept cdsSplice = 0 or (cdsSplice = 1 and numCdsIntrons > 1) */ if ((cdsSplice == 0) || ((numCdsIntrons > 1) && (cdsSplice == 1))) { passed = TRUE; } /* if cdsGap > 0, degrade it ranking by 1. If cdsGap is not a multiple of 3, degrade its ranking further */ if (cdsGap > 0) { ranking = ranking + 1; if ((cdsGap - (cdsGap/3)*3) != 0) ranking = ranking + 1; } } } /* give RefSeq entries 0.5 advantage in its ranking */ - sqlSafefFrag(condStr, sizeof(condStr), "name='%s'", acc); + sqlSafef(condStr, sizeof(condStr), "name='%s'", acc); answer = sqlGetField(genomeDb, "refGene", "name", condStr); if (answer != NULL) { ranking = ranking - 0.5; } else { chp = strstr(acc, "_"); if (chp != NULL) { acc2 = chp + 1; } else { acc2 = acc; } - sqlSafefFrag(condStr, sizeof(condStr), "name='%s'", acc2); + sqlSafef(condStr, sizeof(condStr), "name='%s'", acc2); /* If it is an MGC gene, give it a 0.3 advantable */ answer = sqlGetField(genomeDb, "mgcGenes", "name", condStr); if (answer != NULL) { ranking = ranking - 0.3; } } /* print out entries, with their rankings, that passed the above criteria */ if (passed) { /*for (i=0; i<10; i++) { fprintf(outf, "%s\t", row2[i]); } */ geneName = strdup(row2[0]); chp = strstr(geneName, "_"); if (chp != NULL) { if (strstr(geneName, "NM_") != NULL) { srcType = 'R'; /* src is RefSeq */ } else { chp++; /* keep the composite name, so that kgGetCds can process correctly */ /* geneName = chp; */ srcType = 'U'; /* src is UCSC prot/mrna alignment */ } } else { srcType = 'G'; /* src is GenBank */ } alignCnt++; fprintf(outf, "%s\t", geneName); for (i= 1; i<10; i++) fprintf(outf, "%s\t", row2[i]); fprintf(outf, "%c%d\t", srcType, alignCnt); fprintf(outf, "%.2f\n", ranking); } row3 = sqlNextRow(sr3); } sqlFreeResult(&sr3); row2 = sqlNextRow(sr2); } sqlFreeResult(&sr2); hFreeConn(&conn); hFreeConn(&conn2); hFreeConn(&conn3); fclose(outf); return(0); }