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/near/hgExpDistance/hgExpDistance_fq.c src/hg/near/hgExpDistance/hgExpDistance_fq.c index f625e0c..117a052 100644 --- src/hg/near/hgExpDistance/hgExpDistance_fq.c +++ src/hg/near/hgExpDistance/hgExpDistance_fq.c @@ -1,432 +1,432 @@ /* hgExpDistance_fq1 - Create table that measures expression distance between pairs. Multi-threaded version that uses a synQueue within the spawning thread to write distances to the filehandle */ /* 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 "synQueue.h" #include "options.h" #include "dystring.h" #include "jksql.h" #include "bed.h" #include "hgRelate.h" #include <pthread.h> #define DEFTHREADS 4 #define GENEDISTS 1000 /* global vars accessible by every thread */ struct microData *geneList = NULL; int geneCount = 0; float *weights = NULL; struct synQueue *synQ = NULL; pthread_mutex_t mutexDotOut; int numThreads; int dotEvery = 0; void usage() /* Explain usage and exit. */ { errAbort( "hgExpDistance - Create table that measures expression distance between pairs\n" "usage:\n" " hgExpDistance database expPosTable expNameTable distanceTable\n" "example:\n" " hgExpDistance hg15 affyUcla affyUclaExp dest.tab\n" "options:\n" " -weights=weight.tab - Two column file <weight><id> for experiments\n" " -lookup=table - Lookup table like knownToAffyUcla\n" " -dots=N - Print out a dot every N genes\n" " -targetIndex - Index target as well as query\n" " -threads=N - number of threads in distance computation: default = 4\n" ); } static struct optionSpec options[] = { {"weights", OPTION_STRING}, {"lookup", OPTION_STRING}, {"dots", OPTION_INT}, {"targetIndex", OPTION_BOOLEAN}, {"threads", OPTION_INT}, {NULL, 0}, }; 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 distanceTableCreate(struct sqlConnection *conn, char *tableName) /* Create a scored-ref table with the given name. */ { static char *createString = "CREATE TABLE %s (\n" " query varchar(255) not null, # Name of query sequence\n" " target varchar(255) not null, # Name of target sequence\n" " distance float not null # Distance in expression space\n" ")\n"; -struct dyString *dy = newDyString(1024); +struct dyString *dy = dyStringNew(1024); sqlDyStringPrintf(dy, createString, tableName); sqlRemakeTable(conn, tableName, dy->string); dyStringFree(&dy); } struct microData /* Name/score pair. */ { struct microData *next; char *name; /* Name - allocated in hash. */ int expCount; /* Count of experiments. */ float *expScores; /* One score for each experiment. */ }; struct microDataDistance /* pairwise distance between two expts */ { char *name1; char *name2; float distance; }; int cmpMicroDataDistance(const void *va, const void *vb) /* Compare to sort based on distance field, closest first. */ { const struct microDataDistance *a = (struct microDataDistance *)va; const struct microDataDistance *b = (struct microDataDistance *)vb; float dif = a->distance - b->distance; if (dif < 0) return -1; else if (dif > 0) return 1; else return 0; } float *getWeights(int count) /* Get weights - all 1.0 by default, or read from file otherwise. */ { float *weights; float total = 0.0; int observed = 0; int i; char *fileName = optionVal("weights", NULL); /* Initialize all to 1.0. */ AllocArray(weights, count); for (i=0; i<count; ++i) weights[i] = 1.0; /* Read from file if it exists. */ if (fileName != NULL) { struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[2]; while (lineFileRow(lf, row)) { int ix = atoi(row[1]); float val = atof(row[0]); if (ix < 0 || ix > count || val <= 0) errAbort("%s does not seem to be a good weight file on line %d", lf->fileName, lf->lineIx); weights[ix] = val; total += val; ++observed; } lineFileClose(&lf); printf("%d genes, %d weights, %f total wieght\n", count, observed, total); } return weights; } double expDistance(struct microData *a, struct microData *b, float *weights) /* Return normalized distance between a and b. */ { double totalWeight = 0.0, totalDistance = 0.0, distance, weight; double aVal, bVal; int i, count = a->expCount; assert(a->expCount == b->expCount); for (i=0; i<count; ++i) { aVal = a->expScores[i]; bVal = b->expScores[i]; if (aVal >= -9999 && bVal >= -9999) { if (aVal > bVal) distance = aVal - bVal; else distance = bVal - aVal; weight = weights[i]; totalWeight += weight; totalDistance += distance*weight; } } assert(totalDistance >= 0); if (totalWeight <= 0.0) return count; /* No data at all - everything is far apart. */ else return totalDistance/totalWeight; } void calcDistances(struct microDataDistance *geneDistArray, struct microData *curGene, struct microData *GeneList, float *weights) { struct microData *gene; struct microDataDistance *geneDistPtr = geneDistArray; for (gene = GeneList; gene != NULL; gene = gene->next, geneDistPtr++) { geneDistPtr->name1 = curGene->name; geneDistPtr->name2 = gene->name; geneDistPtr->distance = expDistance(curGene, gene, weights); } } struct microData *lookupGenes(struct sqlConnection *conn, char *table, struct microData *oldList) /* Use gene list to lookup */ { struct microData *newList = NULL, *gene, *geneCopy, *next; struct hash *hash = newHash(0); struct sqlResult *sr; char **row; char query[256]; /* Load up hash from lookup table. We are doing inverse lookup on it * actually. */ sqlSafef(query, sizeof(query), "select name,value from %s", table); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *geneName = row[0]; char *expName = row[1]; hashAdd(hash, expName, cloneString(geneName)); } /* Move genes in oldList that hit hash to newList. * If more than one new gene hits then make a (shallow) * dupe of it and put it on newList too. This would * be a nightmare if we were actually going to free this * memory, but as a simple file filter there's no need. */ for (gene = oldList; gene != NULL; gene = next) { struct hashEl *hel; next = gene->next; hel = hashLookup(hash, gene->name); if (hel != NULL) { gene->name = hel->val; slAddHead(&newList, gene); while ((hel = hashLookupNext(hel)) != NULL) { geneCopy = CloneVar(gene); geneCopy->name = hel->val; slAddHead(&newList, geneCopy); } } } slReverse(&newList); return newList; } void *computeDistance(void *thread_ID) { struct microDataDistance *geneDistArray = NULL; struct microData *curGene; int baseGenesPerThread, genesPerThread, rmdrPerThread, rmdr, xtra; int subListSize; int i; /* offset = thread ID */ int offset = *((int *)thread_ID); /* create subList size for each thread to process */ baseGenesPerThread = geneCount / numThreads; rmdr = geneCount % numThreads; rmdrPerThread = rmdr / numThreads; xtra = rmdr % numThreads; genesPerThread = baseGenesPerThread + rmdrPerThread; subListSize = (offset == numThreads-1) ? genesPerThread + xtra : genesPerThread; /* each thread positions initial current gene */ curGene = geneList; for (i = 0; i < offset*genesPerThread; i++) curGene = curGene->next; /* compute the pairwise experiment distances */ for (i = 0; i < subListSize; i++, curGene = curGene->next) { AllocArray(geneDistArray, geneCount); calcDistances(geneDistArray, curGene, geneList, weights); qsort(geneDistArray, geneCount, sizeof(geneDistArray[0]), cmpMicroDataDistance); synQueuePut( synQ, geneDistArray ); pthread_mutex_lock( &mutexDotOut ); dotOut(); pthread_mutex_unlock( &mutexDotOut ); } pthread_exit(NULL); } void hgExpDistance(char *database, char *posTable, char *expTable, char *outTable) /* hgExpDistance - Create table that measures expression distance between pairs. */ { struct sqlConnection *conn = sqlConnect(database); struct sqlResult *sr; char query[256]; char **row; struct hash *expHash = hashNew(16); int realExpCount = -1; struct microData *gene; int rc, t; pthread_t *threads = NULL; pthread_attr_t attr; int *threadID = NULL; void *status; char *tempDir = "."; int arrayNum; struct microDataDistance *geneDistPtr = NULL; struct microDataDistance *geneDistArray = NULL; int geneIx; FILE *f = NULL; /* Get list/hash of all items with expression values. */ sqlSafef(query, sizeof(query), "select name,expCount,expScores from %s", posTable); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *name = row[0]; if (!hashLookup(expHash, name)) { int expCount = sqlUnsigned(row[1]); int commaCount; float *expScores = NULL; sqlFloatDynamicArray(row[2], &expScores, &commaCount); if (expCount != commaCount) errAbort("expCount and expScores don't match on %s in %s", name, posTable); if (realExpCount == -1) realExpCount = expCount; if (expCount != realExpCount) errAbort("In %s some rows have %d experiments others %d", name, expCount, realExpCount); AllocVar(gene); gene->expCount = expCount; gene->expScores = expScores; hashAddSaveName(expHash, name, gene, &gene->name); slAddHead(&geneList, gene); } } sqlFreeResult(&sr); conn = sqlConnect(database); slReverse(&geneList); geneCount = slCount(geneList); printf("Have %d elements in %s\n", geneCount, posTable); weights = getWeights(realExpCount); if (optionExists("lookup")) geneList = lookupGenes(conn, optionVal("lookup", NULL), geneList); geneCount = slCount(geneList); printf("Got %d unique elements in %s\n", geneCount, posTable); sqlDisconnect(&conn); /* Disconnect because next step is slow. */ if (geneCount < 1) errAbort("ERROR: unique gene count less than one ?"); f = hgCreateTabFile(tempDir, outTable); synQ = synQueueNew(); /* instantiate threads */ AllocArray( threadID, numThreads ); AllocArray( threads, numThreads ); pthread_attr_init( &attr ); pthread_mutex_init( &mutexDotOut, NULL ); pthread_attr_setdetachstate( &attr, PTHREAD_CREATE_JOINABLE ); for (t = 0; t < numThreads; t++) { threadID[t] = t; rc = pthread_create( &threads[t], &attr, computeDistance, (void *) &threadID[t]); if (rc) errAbort("ERROR: in pthread_create() %d\n", rc ); } /* this thread will write to the file from the queue */ for (arrayNum = 0; arrayNum < geneCount; arrayNum++) { geneDistArray = (struct microDataDistance *)synQueueGet( synQ ); geneDistPtr = geneDistArray; /* Print out closest GENEDISTS distances in tab file. */ for (geneIx=0; geneIx < GENEDISTS && geneIx < geneCount; ++geneIx, geneDistPtr++) if (geneDistPtr != NULL) fprintf(f, "%s\t%s\t%f\n", geneDistPtr->name1, geneDistPtr->name2, geneDistPtr->distance); else errAbort("ERROR: writing distance %d to file\n", geneIx); freeMem( geneDistArray ); } /* synchronize all threads */ for (t = 0; t < numThreads; t++) { rc = pthread_join( threads[t], &status); if (rc) errAbort("ERROR: in pthread_join() %d\n", rc ); } printf("Made %s.tab\n", outTable); slFreeList( &geneList ); pthread_mutex_destroy( &mutexDotOut ); pthread_attr_destroy( &attr ); /* Create and load table. */ conn = sqlConnect(database); distanceTableCreate(conn, outTable); hgLoadTabFile(conn, tempDir, outTable, &f); printf("Loaded %s\n", outTable); /* Add indices. */ sqlSafef(query, sizeof(query), "alter table %s add index(query(12))", outTable); sqlUpdate(conn, query); printf("Made query index\n"); if (optionExists("targetIndex")) { sqlSafef(query, sizeof(query), "alter table %s add index(target(12))", outTable); sqlUpdate(conn, query); printf("Made target index\n"); } hgRemoveTabFile(tempDir, outTable); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); dotEvery = optionInt("dots", 0); numThreads = optionInt("threads", DEFTHREADS); if (argc != 5) usage(); hgExpDistance(argv[1], argv[2], argv[3], argv[4]); return 0; }