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/lib/chromGraph.c src/hg/lib/chromGraph.c index 231acc2..5f45262 100644 --- src/hg/lib/chromGraph.c +++ src/hg/lib/chromGraph.c @@ -1,644 +1,648 @@ /* chromGraph.c was originally generated by the autoSql program, which also * generated chromGraph.h and chromGraph.sql. This module links the database and * the RAM representation of objects. */ /* Copyright (C) 2014 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 "dystring.h" #include "obscure.h" #include "jksql.h" #include "sig.h" #include "trackDb.h" #include "bed.h" #include "chromGraph.h" void chromGraphStaticLoad(char **row, struct chromGraph *ret) /* Load a row from chromGraph table into ret. The contents of ret will * be replaced at the next call to this function. */ { ret->chrom = row[0]; ret->chromStart = sqlSigned(row[1]); ret->val = atof(row[2]); } struct chromGraph *chromGraphLoad(char **row) /* Load a chromGraph from row fetched with select * from chromGraph * from database. Dispose of this with chromGraphFree(). */ { struct chromGraph *ret; AllocVar(ret); ret->chrom = cloneString(row[0]); ret->chromStart = sqlSigned(row[1]); ret->val = atof(row[2]); return ret; } struct chromGraph *chromGraphLoadAll(char *fileName) /* Load all chromGraph from a whitespace-separated file. * Dispose of this with chromGraphFreeList(). */ { struct chromGraph *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[3]; while (lineFileRow(lf, row)) { el = chromGraphLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct chromGraph *chromGraphLoadAllByChar(char *fileName, char chopper) /* Load all chromGraph from a chopper separated file. * Dispose of this with chromGraphFreeList(). */ { struct chromGraph *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[3]; while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) { el = chromGraphLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct chromGraph *chromGraphCommaIn(char **pS, struct chromGraph *ret) /* Create a chromGraph out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new chromGraph */ { char *s = *pS; if (ret == NULL) AllocVar(ret); ret->chrom = sqlStringComma(&s); ret->chromStart = sqlSignedComma(&s); ret->val = sqlFloatComma(&s); *pS = s; return ret; } void chromGraphFree(struct chromGraph **pEl) /* Free a single dynamically allocated chromGraph such as created * with chromGraphLoad(). */ { struct chromGraph *el; if ((el = *pEl) == NULL) return; freeMem(el->chrom); freez(pEl); } void chromGraphFreeList(struct chromGraph **pList) /* Free a list of dynamically allocated chromGraph's */ { struct chromGraph *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; chromGraphFree(&el); } *pList = NULL; } void chromGraphOutput(struct chromGraph *el, FILE *f, char sep, char lastSep) /* Print out chromGraph. Separate fields with sep. Follow last field with lastSep. */ { if (sep == ',') fputc('"',f); fprintf(f, "%s", el->chrom); if (sep == ',') fputc('"',f); fputc(sep,f); fprintf(f, "%d", el->chromStart); fputc(sep,f); fprintf(f, "%g", el->val); fputc(lastSep,f); } /* -------------------------------- End autoSql Generated Code -------------------------------- */ int chromGraphCmp(const void *va, const void *vb) /* Compare to sort based on query chromStart. */ { const struct chromGraph *a = *((struct chromGraph **)va); const struct chromGraph *b = *((struct chromGraph **)vb); int dif; dif = strcmp(a->chrom, b->chrom); if (dif == 0) dif = a->chromStart - b->chromStart; return dif; } void chromGraphGetMinMax(struct chromGraph *list, double *pMin, double *pMax) /* Figure out min/max values in list. */ { double minVal = 0, maxVal = 0; if (list != NULL) { struct chromGraph *el; minVal = maxVal = list->val; for (el = list->next; el != NULL; el = el->next) { double val = el->val; if (val < minVal) minVal = val; if (val > maxVal) maxVal = val; } } *pMin = minVal; *pMax = maxVal; } void chromGraphVarName(char *track, char *var, char output[chromGraphVarNameMaxSize]) /* Fill in output with name of cart variable. */ { safef(output, chromGraphVarNameMaxSize, "%s_%s_%s", "cgs", track, var); } void chromGraphDataRange(char *trackName, struct sqlConnection *conn, double *retMin, double *retMax) /* Get min/max values observed from metaChromGraph table */ { char query[256]; struct sqlResult *sr; char **row; sqlSafef(query, sizeof(query), "select minVal,maxVal from metaChromGraph where name='%s'", trackName); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row == NULL) errAbort("%s is not in metaChromGraph", trackName); *retMin = atof(row[0]); *retMax = atof(row[1]); sqlFreeResult(&sr); } struct slName *chromGraphListAll(struct sqlConnection *conn) /* Return list of all chrom graph tables. */ { if (!sqlTableExists(conn, "metaChromGraph")) return NULL; else - return sqlQuickList(conn, NOSQLINJ "select name from metaChromGraph"); + { + char query[1024]; + sqlSafef(query, sizeof query, "select name from metaChromGraph"); + return sqlQuickList(conn, query); + } } char *chromGraphBinaryFileName(char *trackName, struct sqlConnection *conn) /* Get binary file name associated with chromGraph track. Returns NULL * if no such file or track. FreeMem result when done. */ { char query[256]; sqlSafef(query, sizeof(query), "select binaryFile from metaChromGraph where name='%s'", trackName); return sqlQuickString(conn, query); } void chromGraphParseMinMax(char *trackName, char *text, double *pMin, double *pMax) /* Parse out min,max from text. TrackName is just for error reporting */ { struct slName *list = commaSepToSlNames(text); if (slCount(list) != 2) errAbort("minMax must have two values in %s", trackName); *pMin = atof(list->name); *pMax = atof(list->next->name); slFreeList(&list); } void chromGraphSettingsFillFromHash(struct chromGraphSettings *cgs, struct hash *hash, char *trackName) /* Fill in settings from hash table. TrackName is just for error reporting. */ { char *setting; if ((setting = hashFindVal(hash, "maxGapToFill")) != NULL) cgs->maxGapToFill = sqlUnsigned(setting); if ((setting = hashFindVal(hash, "minMax")) != NULL) chromGraphParseMinMax(trackName, setting, &cgs->minVal, &cgs->maxVal); /* They can store min/max separately as well as together... */ if ((setting = hashFindVal(hash, "maxVal")) != NULL) cgs->maxVal = atof(setting); if ((setting = hashFindVal(hash, "minVal")) != NULL) cgs->minVal = atof(setting); if ((setting = hashFindVal(hash, "linesAt")) != NULL) { struct slName *el, *list = commaSepToSlNames(setting); int i; cgs->linesAtCount = slCount(list); if (cgs->linesAtCount <= 0) errAbort("Missing linesAt data in %s", trackName); AllocArray(cgs->linesAt, cgs->linesAtCount); for (i=0,el=list; el!=NULL; ++i,el=el->next) cgs->linesAt[i] = atof(el->name); slFreeList(&list); } if ((setting = hashFindVal(hash, "maxHeightPixels")) != NULL) { struct slName *list = charSepToSlNames(setting, ':'); if (slCount(list) != 3) errAbort("maxHeightPixels in %s must have 3 : separated fields", trackName); cgs->maxPixels = sqlUnsigned(list->name); cgs->pixels = sqlUnsigned(list->next->name); cgs->minPixels = sqlUnsigned(list->next->next->name); } } struct chromGraphSettings *chromGraphSettingsGet(char *trackName, struct sqlConnection *conn, struct trackDb *tdb, struct cart *cart) /* Get settings for chromGraph track. If you pass in all NULLs * you'll get a reasonable default. */ { struct chromGraphSettings *cgs; /* Allocate in memory with default settings */ AllocVar(cgs); cgs->maxGapToFill = chromGraphDefaultGapToFill; cgs->minVal = 0; cgs->maxVal = 100; cgs->minPixels = 8; cgs->pixels = 32; cgs->maxPixels = 128; /* Try and fill in max/min from database. */ if (conn != NULL) { chromGraphDataRange(trackName, conn, &cgs->minVal, &cgs->maxVal); } /* Try and fill in settings from tdb */ if (tdb != NULL) { struct hash *hash = trackDbHashSettings(tdb); chromGraphSettingsFillFromHash(cgs, hash, trackName); } /* Finally try and fill in settings from cart */ if (cart != NULL) { char varName[chromGraphVarNameMaxSize]; chromGraphVarName(trackName, "maxGapToFill", varName); cgs->maxGapToFill = cartUsualInt(cart, varName, cgs->maxGapToFill); chromGraphVarName(trackName, "minVal", varName); cgs->minVal = cartUsualDouble(cart, varName, cgs->minVal); chromGraphVarName(trackName, "maxVal", varName); cgs->maxVal = cartUsualDouble(cart, varName, cgs->maxVal); chromGraphVarName(trackName, "pixels", varName); cgs->pixels = cartUsualInt(cart, varName, cgs->pixels); if (cgs->pixels < cgs->minPixels) cgs->pixels = cgs->minPixels; if (cgs->pixels > cgs->maxPixels) cgs->pixels = cgs->maxPixels; } /* For sanity in various places force max to be greater than min. */ if (cgs->maxVal <= cgs->minVal) cgs->maxVal = cgs->minVal+1; return cgs; } void cgbChromFree(struct cgbChrom **pChrom) /* Free up one cgbChrom */ { struct cgbChrom *chrom = *pChrom; if (chrom != NULL) { freeMem(chrom->name); freez(pChrom); } } void cgbChromFreeList(struct cgbChrom **pList) /* Free a list of dynamically allocated cgbChrom's */ { struct cgbChrom *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; cgbChromFree(&el); } *pList = NULL; } struct cInfo /* Local structure to help us keep track of chromosomes */ { struct cInfo *next; char *name; /* Not allocated here. */ struct chromGraph *start; /* First element in this chrom */ struct chromGraph *end; /* First element not in this chrom */ bits64 offset; /* Offset to start of chrom in file */ }; struct cInfo *cInfoMake(struct chromGraph *cgList, char *fileName) /* Go through cgList and create cInfo list pointing into * start and end of each chromosome. slFreeList this when done. */ { struct chromGraph *cg; int lastPos = -1; struct hash *uniqHash = hashNew(0); struct cInfo *ciList = NULL, *ci = NULL; for (cg = cgList; cg != NULL; cg = cg->next) { if (ci == NULL || !sameString(ci->name, cg->chrom)) { if (hashLookup(uniqHash, cg->chrom) != NULL) errAbort("%s isn't sorted by chrom,start", fileName); hashAdd(uniqHash, cg->chrom, NULL); if (ci != NULL) ci->end = cg; AllocVar(ci); ci->name = cg->chrom; ci->start = cg; slAddHead(&ciList, ci); lastPos = -1; } else { if (cg->chromStart < lastPos) errAbort("%s isn't sorted by chrom,start", fileName); lastPos = cg->chromStart; } } hashFree(&uniqHash); slReverse(&ciList); return ciList; } void chromGraphToBinGetMinMax(struct chromGraph *list, char *fileName, double *retMin, double *retMax) /* Create binary representation of chromGraph list, which should * be sorted. Also return min/max values seen in data*/ { struct chromGraph *el; FILE *f = mustOpen(fileName, "wb"); /* make a .cgm text file in parallel with binary for use by GS * or other programs requiring marker label preservation */ char cgmName[256]; safef(cgmName, sizeof(cgmName), "%s.cgm", fileName); FILE *m = mustOpen(cgmName, "w"); int cgmCount = 0; bits32 sig = chromGraphSig; bits32 endMarker = (bits32)(-1); struct cInfo *ci, *ciList = cInfoMake(list, fileName); bits32 chromCount = slCount(ciList); fpos_t indexPos; double minVal, maxVal; bits32 reserved1=0, reserved2=0, reserved3=0, reserved4=0; /* Start out with file signature and chromosome count */ writeOne(f, sig); writeOne(f, chromCount); /* Figure and write min/max values. */ chromGraphGetMinMax(list, &minVal, &maxVal); writeOne(f, minVal); writeOne(f, maxVal); /* Write out reserved (currently zero) words */ writeOne(f, reserved1); writeOne(f, reserved2); writeOne(f, reserved3); writeOne(f, reserved4); /* Write preliminary version of index, with offsets not filled in */ fgetpos(f, &indexPos); for (ci = ciList; ci != NULL; ci = ci->next) { writeString(f, ci->name); msbFirstWriteBits64(f, ci->offset); } /* Write data. */ for (ci = ciList; ci != NULL; ci = ci->next) { ci->offset = ftell(f); writeString(f, ci->name); for (el = ci->start; el != ci->end; el = el->next) { bits32 pos = el->chromStart; writeOne(f, pos); writeOne(f, el->val); if (el->marker) { fprintf(m, "%s\t%s\t%d\t%f\n", el->marker, ci->name, el->chromStart, el->val); freeMem(el->marker); ++cgmCount; } } writeOne(f, endMarker); } /* Go back and rewrite index. */ fsetpos(f, &indexPos); for (ci = ciList; ci != NULL; ci = ci->next) { writeString(f, ci->name); msbFirstWriteBits64(f, ci->offset); } carefulClose(&f); carefulClose(&m); if (cgmCount < 1) remove(cgmName); slFreeList(&ciList); /* Save return variables */ *retMin = minVal; *retMax = maxVal; } void chromGraphToBin(struct chromGraph *list, char *fileName) /* Create binary representation of chromGraph list, which should * be sorted. */ { double minVal,maxVal; chromGraphToBinGetMinMax(list, fileName, &minVal, &maxVal); } struct chromGraphBin *chromGraphBinOpen(char *path) /* Open up a chromGraphBin file */ { struct chromGraphBin *cgb; FILE *f = mustOpen(path, "rb"); bits32 sig; bits32 chromCount, i; boolean isSwapped = FALSE; struct cgbChrom *chrom; bits32 reserved1, reserved2, reserved3, reserved4; /* Read in signature and use it to make sure it's the right type * of file, and to tell if we need to swap bytes on integers. */ if (!readOne(f, sig)) errAbort("%s is empty", path); if (sig == chromGraphSig) isSwapped = FALSE; else if (sig == chromGraphSwapSig) isSwapped = TRUE; else errAbort("%s is not a chromGraph binary file", path); /* Allocate object and fill in several fields*/ AllocVar(cgb); cgb->fileName = cloneString(path); cgb->f = f; cgb->isSwapped = isSwapped; cgb->chromHash = hashNew(0); /* Read in chromosome count, swapping if need be. */ mustReadOne(f, chromCount); if (isSwapped) chromCount = byteSwap32(chromCount); /* Read in min/max */ mustReadOne(f, cgb->minVal); mustReadOne(f, cgb->maxVal); /* Read in reserved (currently zero) words */ mustReadOne(f, reserved1); mustReadOne(f, reserved2); mustReadOne(f, reserved3); mustReadOne(f, reserved4); /* Read index into list/hash */ for (i=0; i<chromCount; ++i) { AllocVar(chrom); chrom->name = readString(f); chrom->offset = msbFirstReadBits64(f); slAddHead(&cgb->chromList, chrom); hashAdd(cgb->chromHash, chrom->name, chrom); } slReverse(&cgb->chromList); return cgb; } boolean chromGraphBinSeekToChrom(struct chromGraphBin *cgb, char *chromName) /* Seek to chromosome if have data for it. Otherwise return FALSE. */ { struct cgbChrom *chrom = hashFindVal(cgb->chromHash, chromName); if (chrom == NULL) return FALSE; fseek(cgb->f, chrom->offset, SEEK_SET); chromGraphBinNextChrom(cgb); return TRUE; } void chromGraphBinRewind(struct chromGraphBin *cgb) /* Position file pointer back to the first chromosome */ { fseek(cgb->f, cgb->chromList->offset, SEEK_SET); } void chromGraphBinFree(struct chromGraphBin **pCgb) /* Close down and free up chromGraphBin. */ { struct chromGraphBin *cgb = *pCgb; if (cgb != NULL) { carefulClose(&cgb->f); freeMem(cgb->fileName); hashFree(&cgb->chromHash); cgbChromFreeList(&cgb->chromList); freez(pCgb); } } boolean chromGraphBinNextChrom(struct chromGraphBin *cgb) /* Fetch next chromosome, or FALSE if at end of file. */ { UBYTE size; FILE *f = cgb->f; if (!readOne(f, size)) return FALSE; mustRead(f, cgb->chrom, size); cgb->chrom[size] = 0; return TRUE; } boolean chromGraphBinNextVal(struct chromGraphBin *cgb) /* Fetch next chromStart/val or FALSE if at end of chromosome. */ { FILE *f = cgb->f; mustReadOne(f, cgb->chromStart); if (cgb->isSwapped) cgb->chromStart = byteSwap32(cgb->chromStart); if (cgb->chromStart == (bits32)(-1)) return FALSE; mustReadOne(f, cgb->val); return TRUE; } struct bed3 *chromGraphBinToBed3(char *fileName, double threshold) /* Stream through making list of all places above threshold. */ { struct bed3 *list = NULL, *bed = NULL; struct chromGraphBin *cgb = chromGraphBinOpen(fileName); double val, lastVal = 0; int start, lastStart = 0; while (chromGraphBinNextChrom(cgb)) { /* Set up bed around first point in chromosome. */ char *chrom = cgb->chrom; bed = NULL; if (!chromGraphBinNextVal(cgb)) continue; lastVal = val = cgb->val; lastStart = start = cgb->chromStart; if (val >= threshold) { bed = bed3New(chrom, start, start+1); slAddHead(&list, bed); } /* Loop for next points, extending bed when get transition out, * creating bed when getting transition in. */ while (chromGraphBinNextVal(cgb)) { val = cgb->val; start = cgb->chromStart; if (lastVal >= threshold && val < threshold) { double ratio = (lastVal - threshold)/(lastVal - val); assert(bed != NULL); bed->chromEnd = lastStart + (start-lastStart)*ratio; bed = NULL; } else if (lastVal < threshold && val >= threshold) { double ratio = (threshold - lastVal)/(val - lastVal); int cross = lastStart + (start - lastStart)*ratio; bed = bed3New(chrom, cross, cross+1); slAddHead(&list, bed); } lastVal = val; lastStart = start; } /* Handle last val */ if (bed != NULL && lastVal >= threshold) bed->chromEnd = lastStart+1; } slReverse(&list); return list; }