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/kgPick/kgPick.c src/hg/protein/kgPick/kgPick.c index 07596f1..3d397eb 100644 --- src/hg/protein/kgPick/kgPick.c +++ src/hg/protein/kgPick/kgPick.c @@ -1,223 +1,223 @@ /* kgPick - select the best repersentative mRNA/protein pair from KG candidates having identical CDS Structure */ /* 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 printedMrna[40], printedProt[40], printedCds[40]; void usage() /* Explain usage and exit. */ { errAbort( "kgPick - select the best repersentative mRNA/protein pair\n" "usage:\n" " kgPick tempDb outfile\n" " tempDb is the temp KG DB name\n" " roDb is the read only genome DB name\n" " spDb is the proteinsYYMMDDt DB name\n" " outfile is the output file name\n" " dupOutfile is the duplicate mrna/prot output file name\n" "example: kgPick kgHg17ETemp hg17 proteins050415 kg2.tmp dupSpMrna.tmp\n"); } /* convert a possible compund mrnaID ("protID_mrnaID") to just the mrnaID. */ char *convert(char *compound) { char *chp; chp = compound; if ((*chp == 'N') && (*(chp+1) == 'M') && (*(chp+2) == '_')) { return compound; } else { chp = strstr(compound, "_"); if (chp == NULL) return compound; chp ++; } return chp; } void printKg(struct sqlConnection *conn, struct sqlConnection *conn2, char *kgTempDb, char *spDb, char *cdsId, char *mrnaID, char *protAcc, char *alignID, FILE *outf) { char query[256]; struct sqlResult *sr; char **row; int i; char condStr[256]; char *displayId; sqlSafef(query, sizeof(query), "select * from %s.kgCandidate where alignID='%s'", kgTempDb, alignID); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); while (row != NULL) { fprintf(outf, "%s\t", convert(row[0])); for (i=1; i<10; i++) { fprintf(outf, "%s\t", row[i]); } /* get protein display ID */ - sqlSafefFrag(condStr, sizeof condStr, "acc='%s'", protAcc); + sqlSafef(condStr, sizeof condStr, "acc='%s'", protAcc); displayId = sqlGetField(spDb, "displayId", "val", condStr); if (displayId == NULL) displayId = protAcc; fprintf(outf, "%s\t%s\t%s\n", displayId, alignID, cdsId); /* remember what have been printed */ safecpy(printedCds, sizeof(printedCds), cdsId); safecpy(printedMrna, sizeof(printedCds), row[0]); safecpy(printedProt, sizeof(printedProt), displayId); row = sqlNextRow(sr); } sqlFreeResult(&sr); } int main(int argc, char *argv[]) { struct sqlConnection *conn2, *conn3, *conn4, *conn5; char query2[256], query3[256]; struct sqlResult *sr2, *sr3; char **row2, **row3; char condStr[256]; char *kgTempDb; char *outfileName, *dupOutfileName; FILE *outf, *dupOutf; char *score; char *protAcc; char *ranking; char *cdsId, *mrnaID, *alignID; char *protDbId; char *spDb; boolean gotRefseq, gotNonRef; boolean isRefseq; int printCnt; char *roDb; char *refseqId; if (argc != 6) usage(); kgTempDb = argv[1]; roDb = argv[2]; spDb = argv[3]; outfileName = argv[4]; dupOutfileName = argv[5]; outf = mustOpen(outfileName, "w"); dupOutf = mustOpen(dupOutfileName, "w"); conn2= hAllocConn(roDb); conn3= hAllocConn(roDb); conn4= hAllocConn(roDb); conn5= hAllocConn(roDb); strcpy(printedCds, ""); strcpy(printedMrna, ""); strcpy(printedProt, ""); /* go through each unique cds structure */ sqlSafef(query2, sizeof(query2), "select distinct cdsId from %s.kgCandidateZ", kgTempDb); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); while (row2 != NULL) { /* get all mrna/prot pairs with this CDS structure */ cdsId = row2[0]; /* ranking reflects CDS quaility and preference for RefSeq and MGC */ /* Swiss-Prot is prefered than TrEMBL */ /* finally, higher prot-Mrna alignment score is prefered */ sqlSafef(query3, sizeof(query3), "select * from %s.kgCandidateZ where cdsId='%s' order by ranking, protDbId, score desc", kgTempDb, cdsId); sr3 = sqlMustGetResult(conn3, query3); row3 = sqlNextRow(sr3); gotRefseq = FALSE; gotNonRef = FALSE; printCnt = 0; while (row3 != NULL) { cdsId = row3[0]; ranking = row3[1]; protDbId = row3[2]; score = row3[3]; mrnaID = row3[4]; protAcc = row3[5]; alignID = row3[6]; isRefseq = FALSE; if ((mrnaID[0] == 'N') && (mrnaID[1] == 'M') && (mrnaID[2] == '_')) { isRefseq = TRUE; } if (isRefseq) { /* print one qualified RefSeq */ if (!gotRefseq) { /* double check again to see if the RefSeq is still valid */ - sqlSafefFrag(condStr, sizeof condStr, "name='%s'", mrnaID); + sqlSafef(condStr, sizeof condStr, "name='%s'", mrnaID); refseqId = sqlGetField(roDb, "refGene", "name", condStr); if (refseqId != NULL) { if (printCnt < 1) { printKg(conn4, conn5, kgTempDb, spDb, cdsId, mrnaID, protAcc, alignID, outf); printCnt++; gotRefseq = TRUE; } } else { fprintf(stderr, "%s no longer found in refGene.\n", mrnaID); } } } else { /* print out only one non-RefSeq entry for this CDS structure */ if (!gotRefseq && (!gotNonRef)) { printKg(conn4, conn5, kgTempDb, spDb, cdsId, mrnaID, protAcc, alignID, outf); printCnt++; gotNonRef = TRUE; } } /* save duplicates of mrna/prot that has same CDS but does not make it to final KG set */ if (sameWord(printedCds, cdsId)) { if ( (!sameWord(printedMrna, mrnaID)) || (!sameWord(printedProt, protAcc)) ) { fprintf(dupOutf, "%s\t%s\t%s\t%s\n", convert(printedMrna), printedProt, convert(mrnaID), protAcc); } } row3 = sqlNextRow(sr3); } sqlFreeResult(&sr3); row2 = sqlNextRow(sr2); } sqlFreeResult(&sr2); hFreeConn(&conn2); hFreeConn(&conn3); fclose(outf); fclose(dupOutf); return(0); }