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/sim4big/sim4big.c src/hg/sim4big/sim4big.c index 4b78103..a4c0f52 100644 --- src/hg/sim4big/sim4big.c +++ src/hg/sim4big/sim4big.c @@ -1,336 +1,336 @@ /* sim4big - A wrapper for Sim4 that runs it repeatedly on a multi-sequence .fa file. */ /* Copyright (C) 2011 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 "dystring.h" #include "cheapcgi.h" #include "bed.h" #include "dnaseq.h" #include "fa.h" char *exePath = "sim4"; /* executable name. */ char *tempDir = NULL; /* Temporary dir. */ boolean pslOut; /* PSL format output. */ int dotEvery = 1; /* Output dots every so often. */ void usage() /* Explain usage and exit. */ { errAbort( "sim4big - A wrapper for Sim4 that runs it repeatedly on a multi-sequence .fa file\n" "usage:\n" " sim4big genomic.fa mrna.fa output.bed\n" "options:\n" " -tempDir=someDir\n" " -exe=/path/to/sim4\n" " -psl output is .psl instead of bed format\n" " -dots=N Output a dot every N sequences aligned\n" ); } void tempFile(char *dir, char *root, char *suffix, char result[512]) /* Make a temporary file name. */ { if (dir == NULL) sprintf(result, "%sXXXXXX%s", root, suffix); else sprintf(result, "%s/%sXXXXXX%s", dir, root, suffix); if (mkstemp(result) < 0) errAbort("tempFile: mkstemp failed: %s", strerror(errno)); } void sim4BadLine(struct lineFile *lf) /* Complain about bad line in sim4 file. */ { errAbort("Can't parse line %d of %s. Not usual sim4 format.", lf->lineIx, lf->fileName); } struct block /* A block of an alignment. */ { struct block *next; int qStart, qEnd; /* Query position. */ int tStart, tEnd; /* Target position. */ int percentId; /* Percentage identity. */ }; void outputBlocks(struct block *blockList, FILE *f, boolean isRc, char *qName, int qSize, char *tName, int tSize, boolean psl) /* Output block list to file. */ { int qNumInsert = 0, qBaseInsert = 0, tNumInsert = 0, tBaseInsert = 0; int matchOne, match = 0, mismatch = 0, bases; double scale; struct block *lastBlock = NULL; int score, blockCount = 0; int qTotalStart = BIGNUM, qTotalEnd = 0, tTotalStart = BIGNUM, tTotalEnd = 0; struct block *block; if (blockList == NULL) return; /* Count up overall statistics. */ for (block = blockList; block != NULL; block = block->next) { ++blockCount; scale = 0.01 * block->percentId; bases = block->qEnd - block->qStart; matchOne = round(scale*bases); match += matchOne; mismatch += bases - matchOne; if (lastBlock != NULL) { if (block->qStart != lastBlock->qEnd) { qNumInsert += 1; qBaseInsert += block->qStart - lastBlock->qEnd; } if (block->tStart != lastBlock->tEnd) { tNumInsert += 1; tBaseInsert += block->tStart - lastBlock->tEnd; } qTotalEnd = block->qEnd; tTotalEnd = block->tEnd; } else { qTotalStart = block->qStart; qTotalEnd = block->qEnd; tTotalStart = block->tStart; tTotalEnd = block->tEnd; } lastBlock = block; } if (psl) { fprintf(f, "%d\t%d\t0\t0\t", match, mismatch); fprintf(f, "%d\t%d\t%d\t%d\t", qNumInsert, qBaseInsert, tNumInsert, tBaseInsert); if (isRc) fprintf(f, "-\t"); else fprintf(f, "+\t"); fprintf(f, "%s\t%d\t%d\t%d\t", qName, qSize, qTotalStart, qTotalEnd); fprintf(f, "%s\t%d\t%d\t%d\t", tName, tSize, tTotalStart, tTotalEnd); fprintf(f, "%d\t", blockCount); for (block = blockList; block != NULL; block = block->next) fprintf(f, "%d,", block->tEnd - block->tStart); fprintf(f, "\t"); for (block = blockList; block != NULL; block = block->next) fprintf(f, "%d,", block->qStart); fprintf(f, "\t"); for (block = blockList; block != NULL; block = block->next) fprintf(f, "%d,", block->tStart); fprintf(f, "\n"); } else /* Output bed line. */ { score = (match - mismatch - qNumInsert*2) * 1000 / (qTotalEnd - qTotalStart); fprintf(f, "%s\t%d\t%d\t%s\t%d\t", tName, tTotalStart, tTotalEnd, qName, score); if (isRc) fprintf(f, "-\t"); else fprintf(f, "+\t"); fprintf(f, "%d\t%d\t0\t%d\t", tTotalStart, tTotalEnd, blockCount); for (block = blockList; block != NULL; block = block->next) fprintf(f, "%d,", block->tEnd - block->tStart); fprintf(f, "\t"); for (block = blockList; block != NULL; block = block->next) fprintf(f, "%d,", block->tStart); fprintf(f, "\n"); } } void parseIntoBed(char *sim4out, char *qName, int qSize, char *tName, int tSize, FILE *f) /* Parse a sim4 output file and put it into bed file. */ { struct lineFile *lf = lineFileOpen(sim4out, TRUE); char *line, *row[3], *parts[3]; int partCount; boolean isRc = FALSE; struct block *blockList = NULL, *block; /* Read header and remember if complemented. */ if (!lineFileNext(lf, &line, NULL)) errAbort("%s is empty", lf->fileName); if (!lineFileNext(lf, &line, NULL) || !startsWith("seq1", line)) errAbort("%s doesn't seem to be a sim4 output file", lf->fileName); lineFileNext(lf, &line, NULL); lineFileNext(lf, &line, NULL); lineFileNext(lf, &line, NULL); if (startsWith("(complement)", line)) isRc = TRUE; else lineFileReuse(lf); /* Parse rest of file into blockList. */ while (lineFileRow(lf, row)) { AllocVar(block); partCount = chopString(row[0], "-", parts, ArraySize(parts)); if (partCount != 2 || !isdigit(parts[0][0]) || !isdigit(parts[1][0])) sim4BadLine(lf); block->qStart = atoi(parts[0]) - 1; block->qEnd = atoi(parts[1]); partCount = chopString(row[1], "(-)", parts, ArraySize(parts)); if (partCount != 2 || !isdigit(parts[0][0]) || !isdigit(parts[1][0])) sim4BadLine(lf); block->tStart = atoi(parts[0]) - 1; block->tEnd = atoi(parts[1]); if (!isdigit(row[2][0])) sim4BadLine(lf); block->percentId = atoi(row[2]); slAddHead(&blockList, block); } lineFileClose(&lf); slReverse(&blockList); outputBlocks(blockList, f, isRc, qName, qSize, tName, tSize, FALSE); slFreeList(&blockList); } void parseIntoPsl(char *lavFile, char *qName, int qSize, char *tName, int tSize, FILE *f) /* Parse a sim4 lav file and put it into something .psl like. */ { struct lineFile *lf = lineFileOpen(lavFile, TRUE); char *line, *words[10]; boolean gotAli = FALSE; int wordCount; struct block *blockList = NULL, *block; boolean isRc = FALSE; /* Check header. */ if (!lineFileNext(lf, &line, NULL)) errAbort("%s is empty", lf->fileName); if (!startsWith("#:lav", line)) errAbort("%s is not a sim4 lav file\n", lf->fileName); /* Search for alignment stanza. */ while (lineFileNext(lf, &line, NULL)) { if (startsWith("a {", line)) { gotAli = TRUE; break; } if (startsWith("(complement)", line)) isRc = TRUE; } if (gotAli) { while (lineFileNext(lf, &line, NULL)) { if (line[0] == '#') continue; if (line[0] == '}') break; wordCount = chopLine(line, words); if (wordCount == 0) continue; if (words[0][0] == 'l') { lineFileExpectWords(lf, 6, wordCount); AllocVar(block); block->qStart = lineFileNeedNum(lf, words, 1) - 1; block->qEnd = lineFileNeedNum(lf, words, 3); block->tStart = lineFileNeedNum(lf, words, 2) - 1; block->tEnd = lineFileNeedNum(lf, words, 4); if (block->qEnd - block->qStart != block->tEnd - block->tStart) errAbort("Block size mismatch line %d of %s", lf->lineIx, lf->fileName); block->percentId = lineFileNeedNum(lf, words, 5); slAddHead(&blockList, block); } } } lineFileClose(&lf); slReverse(&blockList); outputBlocks(blockList, f, isRc, qName, qSize, tName, tSize, TRUE); slFreeList(&blockList); } void dotOut() /* Put out a dot every now and then if user want's to. */ { static int mod = 1; if (dotEvery > 0) { if (--mod <= 0) { fputc('.', stdout); fflush(stdout); mod = dotEvery; } } } void sim4big(char *genomicFile, char *mrnaFile, char *outputFile) /* sim4big - A wrapper for Sim4 that runs it repeatedly on a multi-sequence .fa file. */ { struct lineFile *gLf = lineFileOpen(genomicFile, TRUE), *mLf = NULL; struct dnaSeq gSeq, mSeq; char gTempName[512], mTempName[512], sTempName[512]; char gSeqName[512]; -struct dyString *command = newDyString(512); +struct dyString *command = dyStringNew(512); FILE *f = mustOpen(outputFile, "w"); ZeroVar(&gSeq); ZeroVar(&mSeq); tempFile(tempDir, "g", ".fa", gTempName); tempFile(tempDir, "m", ".fa", mTempName); tempFile(tempDir, "s", ".sim4", sTempName); dyStringPrintf(command, "%s %s %s", exePath, mTempName, gTempName); if (pslOut) dyStringPrintf(command, " A=2"); dyStringPrintf(command, " > %s", sTempName); while (faMixedSpeedReadNext(gLf, &gSeq.dna, &gSeq.size, &gSeq.name)) { strcpy(gSeqName, gSeq.name); /* Save name because calling speedRead again. */ toUpperN(gSeq.dna, gSeq.size); faWrite(gTempName, gSeqName, gSeq.dna, gSeq.size); faFreeFastBuf(); /* Free potentially large buffer. */ mLf = lineFileOpen(mrnaFile, TRUE); while (faMixedSpeedReadNext(mLf, &mSeq.dna, &mSeq.size, &mSeq.name)) { dotOut(); toUpperN(mSeq.dna, mSeq.size); faWrite(mTempName, mSeq.name, mSeq.dna, mSeq.size); mustSystem(command->string); if (pslOut) parseIntoPsl(sTempName, mSeq.name, mSeq.size, gSeqName, gSeq.size, f); else parseIntoBed(sTempName, mSeq.name, mSeq.size, gSeqName, gSeq.size, f); } lineFileClose(&mLf); } if (dotEvery > 0) printf("\n"); lineFileClose(&gLf); -freeDyString(&command); +dyStringFree(&command); carefulClose(&f); remove(gTempName); remove(mTempName); remove(sTempName); } int main(int argc, char *argv[]) /* Process command line. */ { cgiSpoof(&argc, argv); if (argc != 4) usage(); tempDir = cgiUsualString("tempDir", tempDir); exePath = cgiUsualString("exe", exePath); pslOut = cgiBoolean("psl"); dotEvery = cgiUsualInt("dots", dotEvery); sim4big(argv[1], argv[2], argv[3]); return 0; }