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/makeDb/hgKgMrna/hgKgMrna.c src/hg/makeDb/hgKgMrna/hgKgMrna.c index b7154c1..f7f5e88 100644 --- src/hg/makeDb/hgKgMrna/hgKgMrna.c +++ src/hg/makeDb/hgKgMrna/hgKgMrna.c @@ -1,595 +1,599 @@ /* hgKgMrna - is a modified version of hgRefSeqMrna to be used as part of the building process of Known Genes track. It loads all mRNA alignments and other info into refGene tables in a temporary working genome database. */ /* 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 "linefile.h" #include "hash.h" #include "cheapcgi.h" #include "fa.h" #include "psl.h" #include "jksql.h" #include "hdb.h" #include "hgRelate.h" #include "obscure.h" /* Variables that can be set from command line. */ boolean clTest = FALSE; boolean clDots = 100; char *proteinDB; void usage() /* Explain usage and exit. */ { errAbort( "hgKgMrna - Load mRNA alignments and other info into refGene tables\n" " into a TEMPORARY database to build Known Genes track.\n" "usage:\n" " hgKgMrna rn3Temp mrna.fa mrna.ra tight_mrna.psl loc2ref mrnaPep.fa mim2loc proteins070403\n"); } -char *refLinkTableDef = -NOSQLINJ "CREATE TABLE refLink (\n" -" name varchar(255) not null, # Name displayed in UI\n" -" product varchar(255) not null, # Name of protein product\n" -" mrnaAcc varchar(255) not null, # mRNA accession\n" -" protAcc varchar(255) not null, # protein accession\n" -" geneName int unsigned not null, # pointer to geneName table\n" -" prodName int unsigned not null, # pointer to product name table\n" -" locusLinkId int unsigned not null, # Locus Link ID\n" -" omimId int unsigned not null, # Locus Link ID\n" -" #Indices\n" -" PRIMARY KEY(mrnaAcc(12)),\n" -" index(name(10)),\n" -" index(protAcc(10)),\n" -" index(locusLinkId),\n" -" index(omimId),\n" -" index(prodName),\n" -" index(geneName)\n" -")"; - -char *refGeneTableDef = -NOSQLINJ "CREATE TABLE refGene ( \n" -" name varchar(255) not null, # mrna accession of gene \n" -" chrom varchar(255) not null, # Chromosome name \n" -" strand char(1) not null, # + or - for strand \n" -" txStart int unsigned not null, # Transcription start position \n" -" txEnd int unsigned not null, # Transcription end position \n" -" cdsStart int unsigned not null, # Coding region start \n" -" cdsEnd int unsigned not null, # Coding region end \n" -" exonCount int unsigned not null, # Number of exons \n" -" exonStarts longblob not null, # Exon start positions \n" -" exonEnds longblob not null, # Exon end positions \n" - " #Indices \n" -" INDEX(name(10)), \n" -" INDEX(chrom(12),txStart), \n" -" INDEX(chrom(12),txEnd) \n" -")"; - -char *refPepTableDef = -NOSQLINJ "CREATE TABLE refPep (\n" -" name varchar(255) not null, # Accession of sequence\n" -" seq longblob not null, # Peptide sequence\n" -" #Indices\n" -" PRIMARY KEY(name(32))\n" -")\n"; - -char *refMrnaTableDef = -NOSQLINJ "CREATE TABLE refMrna (\n" -" name varchar(255) not null, # Accession of sequence\n" -" seq longblob not null, # Nucleotide sequence\n" -" #Indices\n" -" PRIMARY KEY(name(32))\n" -")\n"; - struct hash *loadNameTable(struct sqlConnection *conn, char *tableName, int hashSize) /* Create a hash and load it up from table. */ { char query[128]; struct sqlResult *sr; char **row; struct hash *hash = newHash(hashSize); sqlSafef(query, sizeof query, "select id,name from %s", tableName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { hashAdd(hash, row[1], intToPt(sqlUnsigned(row[0]))); } sqlFreeResult(&sr); return hash; } int putInNameTable(struct hash *hash, FILE *f, char *name) /* Add to name table if it isn't there already. * Return ID of name in table. */ { struct hashEl *hel; if (name == NULL) return 0; if ((hel = hashLookup(hash, name)) != NULL) return ptToInt(hel->val); else { // It appears like this program is dead code that is no longer used. // I don't want to make a potential bogus change to track the removal // of hgNextId(), so a landmine is added. Code can be change to determine // max id from table if ever needed. markd 2010-12-15 #if 1 errAbort("code hasn't been updated to work, please see markd"); return 0; #else int id = hgNextId(); fprintf(f, "%u\t%s\n", id, name); hashAdd(hash, name, intToPt(id)); return id; #endif } } struct refSeqInfo /* Information on one refSeq. */ { struct refSeqInfo *next; char *mrnaAcc; /* Accession of mRNA. */ char *proteinAcc; /* Accession of protein. */ char *geneName; /* Gene name */ char *productName; /* Product name (long name for protein) or NULL. */ int locusLinkId; /* LocusLink id (of mRNA) */ int omimId; /* OMIM id (or 0) */ int size; /* mRNA size. */ int cdsStart, cdsEnd; /* start/end of coding region (mRNA coords) */ int ngi; /* Nucleotide GI number. */ struct psl *pslList; /* List of aligments. */ int geneNameId; /* Id of gene name in table. */ int productNameId; /* Id of product name in table. */ }; struct hash *hashNextRa(struct lineFile *lf) /* Read in a record of a .ra file into a hash */ { struct hash *hash = newHash(5); char *line, *firstWord; int lineSize; int lineCount = 0; while (lineFileNext(lf, &line, &lineSize)) { if (line[0] == 0) break; ++lineCount; firstWord = nextWord(&line); hashAdd(hash, firstWord, cloneString(line)); } if (lineCount == 0) freeHash(&hash); return hash; } void dotOut() /* Print dot to standard output and flush it so user can * see it right away. */ { fputc('.', stdout); fflush(stdout); } void parseCds(char *gbCds, int start, int end, int *retStart, int *retEnd) /* Parse genBank style cds string into something we can use... */ { char *s = gbCds; char *startP, *endP; endP = gbCds + strlen(gbCds) - 1; if (*endP == ',') { printf("\n^^^%s\n", gbCds); fflush(stdout); } while (!isdigit(*endP)) endP--; while (isdigit(*endP)) endP--; endP++; startP = gbCds; if (*s == '<') { s++; startP = s; } else { if (*s == 'j') { while (!isdigit(*s)) s++; startP = s; } } s = strchr(s, '.'); if (s == NULL || s[1] != '.') { //errAbort("Malformed GenBank cds %s", gbCds); goto skip; } start = atoi(startP) - 1; end = atoi(endP); skip: *retStart = start; *retEnd = end; } char *unburyAcc(struct lineFile *lf, char *longNcbiName) /* Return accession given a long style NCBI name. * Cannibalizes the longNcbiName. */ { char *parts[5]; int partCount; partCount = chopByChar(longNcbiName, '|', parts, ArraySize(parts)); if (partCount < 4) errAbort("Badly formed longNcbiName line %d of %s\n", lf->lineIx, lf->fileName); chopSuffix(parts[3]); return parts[3]; } char *accWithoutSuffix(char *acc) /* Function to strip the suffix from an accession in order to make it consistent with our notation here. We ignore the suffix. Eg. NM_123456.1 becomes NM_123456 */ { char *fixedAcc = acc; char *dotIndex = strchr(acc, '.'); if (dotIndex) { char *accNum = NULL; int dotPos = dotIndex - acc; /* stupid C pointer arith. No other way to do get the string length up to the period. */ accNum = needMem(dotPos + 1); strncpy(accNum, acc, dotPos); accNum[dotPos] = 0; /* Null terminate */ fixedAcc = accNum; } return fixedAcc; } void writeSeqTable(char *faName, FILE *out, boolean unburyAccession, boolean isPep) /* Write out contents of fa file to name/sequence pairs in tabbed out file. */ { struct lineFile *lf = lineFileOpen(faName, TRUE); bioSeq seq; int dotMod = 0; printf("Reading %s\n", faName); while (faSomeSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name, !isPep)) { if (clDots > 0 && ++dotMod == clDots ) { dotMod = 0; dotOut(); } if (unburyAccession) { seq.name = unburyAcc(lf, seq.name); } seq.name = accWithoutSuffix(seq.name); fprintf(out, "%s\t%s\n", seq.name, seq.dna); } if (clDots) printf("\n"); lineFileClose(&lf); } struct exon /* Keep track of an exon. */ { struct exon *next; int start, end; }; struct exon *pslToExonList(struct psl *psl) /* Convert psl to exon list, merging together blocks * separated by small inserts as necessary. */ { struct exon *exonList = NULL, *exon = NULL; int i, tStart, tEnd; for (i=0; i<psl->blockCount; ++i) { tStart = psl->tStarts[i]; tEnd = tStart + psl->blockSizes[i]; if (exon == NULL || tStart - exon->end > genePredStdInsertMergeSize) { AllocVar(exon); slAddHead(&exonList, exon); exon->start = tStart; } exon->end = tEnd; } slReverse(&exonList); return exonList; } void processRefSeq(char *database, char *faFile, char *raFile, char *pslFile, char *loc2refFile, char *pepFile, char *mim2locFile) /* hgRefSeqMrna - Load refSeq mRNA alignments and other info into * refSeqGene table. */ { struct lineFile *lf; struct hash *raHash, *rsiHash = newHash(0); struct hash *loc2mimHash = newHash(0); struct refSeqInfo *rsiList = NULL, *rsi; char *s, *line, *row[5]; int wordCount, dotMod = 0; int noLocCount = 0; int rsiCount = 0; int noProtCount = 0; struct psl *psl; struct sqlConnection *conn = hgStartUpdate(database); struct hash *productHash = loadNameTable(conn, "productName", 16); struct hash *geneHash = loadNameTable(conn, "geneName", 16); char *kgName = "refGene"; FILE *kgTab = hgCreateTabFile(".", kgName); FILE *productTab = hgCreateTabFile(".", "productName"); FILE *geneTab = hgCreateTabFile(".", "geneName"); FILE *refLinkTab = hgCreateTabFile(".", "refLink"); FILE *refPepTab = hgCreateTabFile(".", "refPep"); FILE *refMrnaTab = hgCreateTabFile(".", "refMrna"); struct exon *exonList = NULL, *exon; char *answer; char cond_str[200]; +char query[1024]; +sqlSafef(query, sizeof query, +"CREATE TABLE refLink (\n" +" name varchar(255) not null, # Name displayed in UI\n" +" product varchar(255) not null, # Name of protein product\n" +" mrnaAcc varchar(255) not null, # mRNA accession\n" +" protAcc varchar(255) not null, # protein accession\n" +" geneName int unsigned not null, # pointer to geneName table\n" +" prodName int unsigned not null, # pointer to product name table\n" +" locusLinkId int unsigned not null, # Locus Link ID\n" +" omimId int unsigned not null, # Locus Link ID\n" +" #Indices\n" +" PRIMARY KEY(mrnaAcc(12)),\n" +" index(name(10)),\n" +" index(protAcc(10)),\n" +" index(locusLinkId),\n" +" index(omimId),\n" +" index(prodName),\n" +" index(geneName)\n" +")"); /* Make refLink and other tables table if they don't exist already. */ -sqlMaybeMakeTable(conn, "refLink", refLinkTableDef); -sqlUpdate(conn, NOSQLINJ "delete from refLink"); -sqlMaybeMakeTable(conn, "refGene", refGeneTableDef); -sqlUpdate(conn, NOSQLINJ "delete from refGene"); -sqlMaybeMakeTable(conn, "refPep", refPepTableDef); -sqlUpdate(conn, NOSQLINJ "delete from refPep"); -sqlMaybeMakeTable(conn, "refMrna", refMrnaTableDef); -sqlUpdate(conn, NOSQLINJ "delete from refMrna"); +sqlMaybeMakeTable(conn, "refLink", query); +sqlSafef(query, sizeof query, "delete from refLink"); +sqlUpdate(conn, query); + +sqlSafef(query, sizeof query, +"CREATE TABLE refGene ( \n" +" name varchar(255) not null, # mrna accession of gene \n" +" chrom varchar(255) not null, # Chromosome name \n" +" strand char(1) not null, # + or - for strand \n" +" txStart int unsigned not null, # Transcription start position \n" +" txEnd int unsigned not null, # Transcription end position \n" +" cdsStart int unsigned not null, # Coding region start \n" +" cdsEnd int unsigned not null, # Coding region end \n" +" exonCount int unsigned not null, # Number of exons \n" +" exonStarts longblob not null, # Exon start positions \n" +" exonEnds longblob not null, # Exon end positions \n" + " #Indices \n" +" INDEX(name(10)), \n" +" INDEX(chrom(12),txStart), \n" +" INDEX(chrom(12),txEnd) \n" +")"); +sqlMaybeMakeTable(conn, "refGene", query); +sqlSafef(query, sizeof query, "delete from refGene"); +sqlUpdate(conn, query); + +sqlSafef(query, sizeof query, +"CREATE TABLE refPep (\n" +" name varchar(255) not null, # Accession of sequence\n" +" seq longblob not null, # Peptide sequence\n" +" #Indices\n" +" PRIMARY KEY(name(32))\n" +")\n"); +sqlMaybeMakeTable(conn, "refPep", query); +sqlSafef(query, sizeof query, "delete from refPep"); +sqlUpdate(conn, query); + +sqlSafef(query, sizeof query, +"CREATE TABLE refMrna (\n" +" name varchar(255) not null, # Accession of sequence\n" +" seq longblob not null, # Nucleotide sequence\n" +" #Indices\n" +" PRIMARY KEY(name(32))\n" +")\n"); +sqlMaybeMakeTable(conn, "refMrna", query); +sqlSafef(query, sizeof query, "delete from refMrna"); +sqlUpdate(conn, query); /* Scan through locus link to omim ID file and put in hash. */ { char *row[2]; printf("Scanning %s\n", mim2locFile); lf = lineFileOpen(mim2locFile, TRUE); while (lineFileRow(lf, row)) { hashAdd(loc2mimHash, row[1], intToPt(atoi(row[0]))); } lineFileClose(&lf); } /* Scan through .ra file and make up start of refSeqInfo * objects in hash and list. */ printf("Scanning %s\n", raFile); lf = lineFileOpen(raFile, TRUE); while ((raHash = hashNextRa(lf)) != NULL) { if (clDots > 0 && ++dotMod == clDots ) { dotMod = 0; dotOut(); } AllocVar(rsi); slAddHead(&rsiList, rsi); if ((s = hashFindVal(raHash, "acc")) == NULL) errAbort("No acc near line %d of %s", lf->lineIx, lf->fileName); rsi->mrnaAcc = cloneString(s); if ((s = hashFindVal(raHash, "siz")) == NULL) errAbort("No siz near line %d of %s", lf->lineIx, lf->fileName); rsi->size = atoi(s); if ((s = hashFindVal(raHash, "gen")) != NULL) rsi->geneName = cloneString(s); //!!!else //!!! warn("No gene name for %s", rsi->mrnaAcc); if ((s = hashFindVal(raHash, "cds")) != NULL) parseCds(s, 0, rsi->size, &rsi->cdsStart, &rsi->cdsEnd); else rsi->cdsEnd = rsi->size; if ((s = hashFindVal(raHash, "ngi")) != NULL) rsi->ngi = atoi(s); rsi->geneNameId = putInNameTable(geneHash, geneTab, rsi->geneName); s = hashFindVal(raHash, "pro"); if (s != NULL) rsi->productName = cloneString(s); rsi->productNameId = putInNameTable(productHash, productTab, s); hashAdd(rsiHash, rsi->mrnaAcc, rsi); freeHashAndVals(&raHash); } lineFileClose(&lf); if (clDots) printf("\n"); /* Scan through loc2ref filling in some gaps in rsi. */ printf("Scanning %s\n", loc2refFile); lf = lineFileOpen(loc2refFile, TRUE); while (lineFileNext(lf, &line, NULL)) { char *mrnaAcc; if (line[0] == '#') continue; wordCount = chopTabs(line, row); if (wordCount < 5) errAbort("Expecting at least 5 tab-separated words line %d of %s", lf->lineIx, lf->fileName); mrnaAcc = row[1]; mrnaAcc = accWithoutSuffix(mrnaAcc); if (mrnaAcc[2] != '_') warn("%s is and odd name %d of %s", mrnaAcc, lf->lineIx, lf->fileName); if ((rsi = hashFindVal(rsiHash, mrnaAcc)) != NULL) { rsi->locusLinkId = lineFileNeedNum(lf, row, 0); rsi->omimId = ptToInt(hashFindVal(loc2mimHash, row[0])); rsi->proteinAcc = cloneString(accWithoutSuffix(row[4])); } } lineFileClose(&lf); /* Report how many seem to be missing from loc2ref file. * Write out knownInfo file. */ printf("Writing %s\n", "refLink.tab"); for (rsi = rsiList; rsi != NULL; rsi = rsi->next) { ++rsiCount; if (rsi->locusLinkId == 0) ++noLocCount; if (rsi->proteinAcc == NULL) ++noProtCount; fprintf(refLinkTab, "%s\t%s\t%s\t%s\t%u\t%u\t%u\t%u\n", emptyForNull(rsi->geneName), emptyForNull(rsi->productName), emptyForNull(rsi->mrnaAcc), emptyForNull(rsi->proteinAcc), rsi->geneNameId, rsi->productNameId, rsi->locusLinkId, rsi->omimId); } if (noLocCount) printf("Missing locusLinkIds for %d of %d\n", noLocCount, rsiCount); if (noProtCount) printf("Missing protein accessions for %d of %d\n", noProtCount, rsiCount); /* Process alignments and write them out as genes. */ lf = pslFileOpen(pslFile); dotMod = 0; while ((psl = pslNext(lf)) != NULL) { if (hashFindVal(rsiHash, psl->qName) != NULL) { if (clDots > 0 && ++dotMod == clDots ) { dotMod = 0; dotOut(); } - sqlSafefFrag(cond_str, sizeof cond_str, "extAC='%s'", psl->qName); + sqlSafef(cond_str, sizeof cond_str, "extAC='%s'", psl->qName); answer = sqlGetField(proteinDB, "spXref2", "displayID", cond_str); if (answer == NULL) { fprintf(stderr, "%s NOT FOUND.\n", psl->qName); fflush(stderr); } if (answer != NULL) { struct genePred *gp = NULL; exonList = pslToExonList(psl); fprintf(kgTab, "%s\t%s\t%c\t%d\t%d\t", psl->qName, psl->tName, psl->strand[0], psl->tStart, psl->tEnd); rsi = hashMustFindVal(rsiHash, psl->qName); gp = genePredFromPsl(psl, rsi->cdsStart, rsi->cdsEnd, genePredStdInsertMergeSize); if (!gp) errAbort("Cannot convert psl (%s) to genePred.\n", psl->qName); fprintf(kgTab, "%d\t%d\t", gp->cdsStart, gp->cdsEnd); fprintf(kgTab, "%d\t", slCount(exonList)); fflush(kgTab); for (exon = exonList; exon != NULL; exon = exon->next) fprintf(kgTab, "%d,", exon->start); fprintf(kgTab, "\t"); for (exon = exonList; exon != NULL; exon = exon->next) fprintf(kgTab, "%d,", exon->end); fprintf(kgTab, "\n"); slFreeList(&exonList); } } else { fprintf(stderr, "%s found in psl, but not in .fa or .ra data files.\n", psl->qName); fflush(stderr); } } if (clDots) printf("\n"); if (!clTest) { writeSeqTable(pepFile, refPepTab, FALSE, TRUE); writeSeqTable(faFile, refMrnaTab, FALSE, FALSE); } carefulClose(&kgTab); carefulClose(&productTab); carefulClose(&geneTab); carefulClose(&refLinkTab); carefulClose(&refPepTab); carefulClose(&refMrnaTab); if (!clTest) { printf("Loading database with %s\n", kgName); fflush(stdout); hgLoadTabFile(conn, ".", kgName, NULL); printf("Loading database with %s\n", "productName"); fflush(stdout); hgLoadTabFile(conn, ".", "productName", NULL); printf("Loading database with %s\n", "geneName"); fflush(stdout); hgLoadTabFile(conn, ".", "geneName", NULL); printf("Loading database with %s\n", "refLink"); fflush(stdout); hgLoadTabFile(conn, ".", "refLink", NULL); printf("Loading database with %s\n", "refPep"); fflush(stdout); hgLoadTabFile(conn, ".", "refPep", NULL); printf("Loading database with %s\n", "refMrna"); fflush(stdout); hgLoadTabFile(conn, ".", "refMrna", NULL); } } void hgRefSeqMrna(char *database, char *faFile, char *raFile, char *pslFile, char *loc2refFile, char *pepFile, char *mim2locFile) /* hgRefSeqMrna - Load refSeq mRNA alignments and other info into * refSeqGene table. */ { //catch anyone trying to load data into actual genome database if (strstr(database, "Temp") == NULL) { errAbort("hgKgMrna is meant to load mrna data into a Temporary database only, exiting ...\n"); } processRefSeq(database, faFile, raFile, pslFile, loc2refFile, pepFile, mim2locFile); } int main(int argc, char *argv[]) /* Process command line. */ { cgiSpoof(&argc, argv); clTest = cgiBoolean("test"); clDots = cgiOptionalInt("dots", clDots); if (argc != 9) usage(); proteinDB = argv[8]; hgRefSeqMrna(argv[1], argv[2], argv[3], argv[4], argv[5], argv[6], argv[7]); return 0; }