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/customAdjacency.c src/hg/lib/customAdjacency.c index 65349b7..8368c45 100644 --- src/hg/lib/customAdjacency.c +++ src/hg/lib/customAdjacency.c @@ -1,261 +1,261 @@ #include "common.h" #include "errCatch.h" #include "hash.h" #include "linefile.h" #include "portable.h" #include "obscure.h" #include "binRange.h" #include "pipeline.h" #include "jksql.h" #include "net.h" #include "bed.h" #include "psl.h" #include "gff.h" #include "wiggle.h" #include "genePred.h" #include "trackDb.h" #include "hgConfig.h" #include "hdb.h" #include "hui.h" #include "customTrack.h" #include "customPp.h" #include "customFactory.h" #include "trashDir.h" #include "jsHelper.h" #include "encode/encodePeak.h" #include "udc.h" #include "bbiFile.h" #include "bigWig.h" #include "bigBed.h" #include "hgBam.h" #include "vcf.h" #include "makeItemsItem.h" #include "bedDetail.h" #include "pgSnp.h" #include "regexHelper.h" #include "chromInfo.h" #include "adjacency.h" char *ctGenomeOrCurrent(struct customTrack *ct); /*** adjacency Factory - allow adjacency(personal genome SNP) custom tracks ***/ static boolean rowIsAdjacency (char **row, char *db, char *type) /* return TRUE if row looks like a adjacency row */ { return TRUE; #ifdef NOTNOW boolean isAdjacency = rowIsBed(row, 3, db); if (type != NULL && !sameWord(type, "adjacency")) return FALSE; if (!isAdjacency && type == NULL) return FALSE; else if (!isAdjacency) errAbort("Error line 1 of custom track, type is adjacency but first 3 fields are not BED"); if (!isdigit(row[4][0]) && type == NULL) return FALSE; else if (!isdigit(row[4][0])) errAbort("Error line 1 of custom track, type is adjacency but count is not an integer (%s)", row[4]); int count = atoi(row[4]); if (count < 1 && type == NULL) return FALSE; else if (count < 1) errAbort("Error line 1 of custom track, type is adjacency but count is less than 1"); char pattern[128]; /* include count in pattern */ safef(pattern, sizeof(pattern), "^[ACTG-]+(\\/[ACTG-]+){%d}$", count - 1); if (! regexMatchNoCase(row[3], pattern) && type == NULL) return FALSE; else if (! regexMatchNoCase(row[3], pattern)) errAbort("Error line 1 of custom track, type is adjacency with a count of %d but allele is invalid %s", count, row[3]); safef(pattern, sizeof(pattern), "^[0-9]+(,[0-9]+){%d}$", count - 1); if (! regexMatchNoCase(row[5], pattern) && type == NULL) return FALSE; else if (! regexMatchNoCase(row[5], pattern)) errAbort("Error line 1 of custom track, type is adjacency with a count of %d but frequency is invalid (%s)", count, row[5]); safef(pattern, sizeof(pattern), "^[0-9.]+(,[0-9.]+){%d}$", count - 1); if (! regexMatchNoCase(row[6], pattern) && type == NULL) return FALSE; else if (! regexMatchNoCase(row[6], pattern)) errAbort("Error line 1 of custom track, type is adjacency with a count of %d but score is invalid (%s)", count, row[6]); /* if get here must be adjacency format */ return TRUE; #endif } static boolean sameType(char *a, char *b) /* Case-sensitive comparison of first word if multiple words, * so that we can compare types like "bed" vs. "bed 3 ." etc. * Tolerates one null input but not two. */ { if (a == NULL && b == NULL) errAbort("sameType should not be called when both inputs are NULL."); else if (a == NULL || b == NULL) return FALSE; char *aCopy = cloneString(a); char *bCopy = cloneString(b); char *aWord = firstWordInLine(aCopy); char *bWord = firstWordInLine(bCopy); boolean same = sameString(aWord, bWord); freeMem(aCopy); freeMem(bCopy); return same; } static boolean adjacencyRecognizer(struct customFactory *fac, struct customPp *cpp, char *type, struct customTrack *track) /* Return TRUE if looks like we're handling an adjacency track */ { if (type != NULL && !sameType(type, fac->name)) return FALSE; char *line = customFactoryNextRealTilTrack(cpp); if (line == NULL) return FALSE; char *dupe = cloneString(line); char *row[9+3]; int wordCount = chopLine(dupe, row); boolean isAdjacency = FALSE; if (wordCount == 9) { track->fieldCount = wordCount; char *ctDb = ctGenomeOrCurrent(track); isAdjacency = rowIsAdjacency(row, ctDb, type); } freeMem(dupe); customPpReuse(cpp, line); return (isAdjacency); } static struct pipeline *adjacencyLoaderPipe(struct customTrack *track) /* Set up pipeline that will load the adjacency into database. */ { /* running the single command: * hgLoadBed -customTrackLoader -sqlTable=loader/adjacency.sql -renameSqlTable * -trimSqlTable -notItemRgb -tmpDir=/data/tmp * -maxChromNameLength=${nameLength} customTrash tableName stdin */ -struct dyString *tmpDy = newDyString(0); +struct dyString *tmpDy = dyStringNew(0); char *cmd1[] = {"loader/hgLoadBed", "-customTrackLoader", "-sqlTable=loader/adjacency.sql", "-noBin", "-renameSqlTable", "-trimSqlTable", "-notItemRgb", NULL, NULL, NULL, NULL, NULL, NULL}; char *tmpDir = cfgOptionDefault("customTracks.tmpdir", "/data/tmp"); struct stat statBuf; int index = 6; if (stat(tmpDir,&statBuf)) errAbort("can not find custom track tmp load directory: '%s'<BR>\n" "create directory or specify in hg.conf customTracks.tmpdir", tmpDir); dyStringPrintf(tmpDy, "-tmpDir=%s", tmpDir); -cmd1[index++] = dyStringCannibalize(&tmpDy); tmpDy = newDyString(0); +cmd1[index++] = dyStringCannibalize(&tmpDy); tmpDy = dyStringNew(0); dyStringPrintf(tmpDy, "-maxChromNameLength=%d", track->maxChromName); cmd1[index++] = dyStringCannibalize(&tmpDy); cmd1[index++] = CUSTOM_TRASH; cmd1[index++] = track->dbTableName; cmd1[index++] = "stdin"; assert(index <= ArraySize(cmd1)); /* the "/dev/null" file isn't actually used for anything, but it is used * in the pipeLineOpen to properly get a pipe started that isn't simply * to STDOUT which is what a NULL would do here instead of this name. * This function exits if it can't get the pipe created * The dbStderrFile will get stderr messages from hgLoadBed into the * our private error log so we can send it back to the user */ return pipelineOpen1(cmd1, pipelineWrite | pipelineNoAbort, "/dev/null", track->dbStderrFile, 0); } //struct adjacency *adjacencyLineFileLoad(char **row, struct lineFile *lf); void customFactoryCheckChromNameDb(char *genomeDb, char *word, struct lineFile *lf); void pipelineFailExit(struct customTrack *track); /* customTrackAdjacency load item */ static struct adjacency *customTrackAdjacency(char *db, char **row, struct hash *chromHash, struct lineFile *lf) /* Convert a row of strings to adjacency. */ { //struct adjacency *item = adjacencyLineFileLoad(row, lf); struct adjacency *item = adjacencyLoad(row); hashStoreName(chromHash, item->chrom); customFactoryCheckChromNameDb(db, item->chrom, lf); int chromSize = hChromSize(db, item->chrom); if (item->chromEnd > chromSize) lineFileAbort(lf, "chromEnd larger than chrom %s size (%d > %d)", item->chrom, item->chromEnd, chromSize); return item; } /* remember to set all the custom track settings necessary */ static struct customTrack *adjacencyFinish(struct customTrack *track, struct adjacency *itemList) /* Finish up adjacency tracks. */ { struct adjacency *item; char buf[50]; track->tdb->type = cloneString("adjacency"); track->dbTrackType = cloneString("adjacency"); safef(buf, sizeof(buf), "%d", track->fieldCount); ctAddToSettings(track, "fieldCount", cloneString(buf)); safef(buf, sizeof(buf), "%d", slCount(itemList)); ctAddToSettings(track, "itemCount", cloneString(buf)); safef(buf, sizeof(buf), "%s:%u-%u", itemList->chrom, itemList->chromStart, itemList->chromEnd); ctAddToSettings(track, "firstItemPos", cloneString(buf)); /* If necessary add track offsets. */ int offset = track->offset; if (offset != 0) { /* Add track offsets if any */ for (item = itemList; item != NULL; item = item->next) { item->chromStart += offset; item->chromEnd += offset; } track->offset = 0; /* so DB load later won't do this again */ hashMayRemove(track->tdb->settingsHash, "offset"); /* nor the file reader*/ } /* If necessary load database */ customFactorySetupDbTrack(track); struct pipeline *dataPipe = adjacencyLoaderPipe(track); FILE *out = pipelineFile(dataPipe); for (item = itemList; item != NULL; item = item->next) adjacencyOutput(item, out, '\t', '\n'); fflush(out); /* help see error from loader failure */ if(ferror(out) || pipelineWait(dataPipe)) pipelineFailExit(track); /* prints error and exits */ unlink(track->dbStderrFile); /* no errors, not used */ pipelineFree(&dataPipe); return track; } static struct customTrack *adjacencyLoader(struct customFactory *fac, struct hash *chromHash, struct customPp *cpp, struct customTrack *track, boolean dbRequested) /* Load up adjacency data until get next track line. */ { char *line; char *db = ctGenomeOrCurrent(track); struct adjacency *itemList = NULL; if (!dbRequested) errAbort("adjacency custom track type unavailable without custom trash database. Please set that up in your hg.conf"); while ((line = customFactoryNextRealTilTrack(cpp)) != NULL) { char *row[9]; int wordCount = chopLine(line, row); struct lineFile *lf = cpp->fileStack; lineFileExpectAtLeast(lf, track->fieldCount, wordCount); struct adjacency *item = customTrackAdjacency(db, row, chromHash, lf); slAddHead(&itemList, item); } slReverse(&itemList); return adjacencyFinish(track, itemList); } struct customFactory adjacencyFactory = /* Factory for adjacency tracks */ { NULL, "adjacency", adjacencyRecognizer, adjacencyLoader, };