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/hgLoadWiggle/hgLoadWiggle.c src/hg/makeDb/hgLoadWiggle/hgLoadWiggle.c
index ce3251a..ebf2b96 100644
--- src/hg/makeDb/hgLoadWiggle/hgLoadWiggle.c
+++ src/hg/makeDb/hgLoadWiggle/hgLoadWiggle.c
@@ -1,451 +1,454 @@
 /* hgLoadWiggle - Load a Wiggle track "bed" file into 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 "options.h"
 #include "linefile.h"
 #include "obscure.h"
 #include "hash.h"
 #include "cheapcgi.h"
 #include "jksql.h"
 #include "dystring.h"
 #include "chromInfo.h"
 #include "wiggle.h"
 #include "hdb.h"
 #include "portable.h"
 #include "hgConfig.h"
 
 
 /* Command line switches. */
 static boolean noBin = FALSE;		/* Suppress bin field. */
 static boolean noLoad = FALSE;		/* Do not load table, create tab file */
 static boolean noHistory = FALSE;	/* Do not add history table comments */
 static boolean strictTab = FALSE;	/* Separate on tabs. */
 static boolean oldTable = FALSE;	/* Don't redo table. */
 static boolean noChromInfo = FALSE;	/* don't do size checks */
 static char *pathPrefix = NULL;	/* path prefix instead of /gbdb/hg16/wib */
 static char *chromInfoDb = NULL;	/* DB for chromInfo information */
 static int maxChromNameLength = 0;	/* specify to avoid chromInfo */
 static char *tmpDir = (char *)NULL;	/*location to create a temporary file */
 
 static struct hash *chromHash = NULL;
 
 /* command line option specifications */
 static struct optionSpec optionSpecs[] = {
     {"smallInsertSize", OPTION_INT},
     {"tab", OPTION_BOOLEAN},
     {"noBin", OPTION_BOOLEAN},
     {"noLoad", OPTION_BOOLEAN},
     {"noHistory", OPTION_BOOLEAN},
     {"oldTable", OPTION_BOOLEAN},
     {"pathPrefix", OPTION_STRING},
     {"chromInfoDb", OPTION_STRING},
     {"maxChromNameLength", OPTION_INT},
     {"tmpDir", OPTION_STRING},
     {"noChromInfo", OPTION_BOOLEAN},
     {NULL, 0}
 };
 
 static void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgLoadWiggle - Load a wiggle track definition into database\n"
   "usage:\n"
   "   hgLoadWiggle [options] database track files(s).wig\n"
   "options:\n"
   "   -noBin\tsuppress bin field\n"
   "   -noLoad\tdo not load table, only create .tab file\n"
   "   -noHistory\tdo not add history table comments (for custom tracks)\n"
   "   -oldTable\tadd to existing table\n"
   "   -tab\t\tSeparate by tabs rather than space\n"
   "   -pathPrefix=<path>\t.wib file path prefix to use "
       "(default /gbdb/<DB>/wib)\n"
   "   -chromInfoDb=<DB>\tdatabase to extract chromInfo size information\n"
   "   -maxChromNameLength=N  - specify max chromName length to avoid\n"
   "               - reference to chromInfo table\n"
   "   -tmpDir=<path>  - path to directory for creation of temporary .tab file\n"
   "                   - which will be removed after loading\n"
   "   -verbose=N\tN=2 see # of lines input and SQL create statement,\n"
   "\t\tN=3 see chrom size info, N=4 see details on chrom size info"
   );
 }
 
 static struct hash *loadAllChromInfo(char *database)
 /* Load up all chromosome infos. */
 {
 struct chromInfo *el;
 struct sqlConnection *conn = NULL;
 struct sqlResult *sr = NULL;
 struct hash *ret;
 char **row;
 
 /*	be wary of customTrack db loader pipeline which has special
  *	environment variables for HGDB_HOST and so forth
  */
 conn = hAllocConn(database);
 ret = newHash(0);
 
-sr = sqlGetResult(conn, NOSQLINJ "select * from chromInfo");
+char query[1024];
+sqlSafef(query, sizeof query, "select * from chromInfo");
+sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = chromInfoLoad(row);
     verbose(4, "Add hash %s value %u (%#lx)\n", el->chrom, el->size, (unsigned long)&el->size);
     hashAdd(ret, el->chrom, (void *)(& el->size));
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return ret;
 }
 
 static unsigned chromosomeSize(char *chromosome)
 /* Return full extents of chromosome.  Warn and fill in if none. */
 {
 if (noChromInfo)
     return 0;
 struct hashEl *el = hashLookup(chromHash,chromosome);
 
 if (el == NULL)
     errAbort("Couldn't find size of chromosome %s (note: chrom names are case sensitive)", chromosome);
 return *(unsigned *)el->val;
 }
 
 struct wiggleStub
 /* A line in a wiggle file with chromosome, start, end position parsed out. */
     {
     struct wiggleStub *next;	/* Next in list. */
     char *chrom;                /* Chromosome . */
     int chromStart;             /* Start position. */
     int chromEnd;		/* End position. */
     char *line;                 /* Line. */
     };
 
 static int wiggleStubCmp(const void *va, const void *vb)
 /* Compare to sort based on query. */
 {
 const struct wiggleStub *a = *((struct wiggleStub **)va);
 const struct wiggleStub *b = *((struct wiggleStub **)vb);
 int dif;
 dif = strcmp(a->chrom, b->chrom);
 if (dif == 0)
     dif = a->chromStart - b->chromStart;
 return dif;
 }
 
 
 static void loadOneWiggle(char *fileName, struct wiggleStub **pList)
 /* Load one wiggle file.  Make sure all lines have same number of fields.
  *	The first line is taken as the proper count.
  * Put results in *pList. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *words[64], *line, *dupe;
 int wordCount;
 struct wiggleStub *wiggle;
 int lineCount = 0;
 int wiggleSize = 0;
 
 while (lineFileNext(lf, &line, NULL))
     {
     char *chrName;
     int chrStart;
     int chrEnd;
 
     ++lineCount;
     dupe = cloneString(line);
     if (strictTab)
 	wordCount = chopTabs(line, words);
     else
 	wordCount = chopLine(line, words);
     if (wiggleSize)
 	lineFileExpectWords(lf, wiggleSize, wordCount);
     else
 	{
 	wiggleSize = wordCount;
 	/*	current wiggle standard expects 13 words	*/
 	lineFileExpectWords(lf, 13, wiggleSize);
 	}
     chrName = cloneString(words[0]);
     chrStart = lineFileNeedNum(lf, words, 1);
     chrEnd = lineFileNeedNum(lf, words, 2);
     AllocVar(wiggle);
     wiggle->chrom = chrName;
     wiggle->chromStart = chrStart;
     wiggle->chromEnd = chrEnd;
     wiggle->line = dupe;
     slAddHead(pList, wiggle);
     }
 lineFileClose(&lf);
 verbose(2, "Read %d lines from %s\n", lineCount, fileName);
 }
 
 static void writeWiggleTab(char *fileName, struct wiggleStub *wiggleList,
 	char *database)
 /* Write out wiggle list to tab-separated file. */
 {
 struct wiggleStub *wiggle;
 FILE *f = mustOpen(fileName, "w");
 char *words[64];
 int i, wordCount;
 
 for (wiggle = wiggleList; wiggle != NULL; wiggle = wiggle->next)
     {
     static char *chrom = NULL;
     static unsigned size = 0;
     unsigned start;
     unsigned end;
     unsigned span;
     unsigned count;
     unsigned validCount;
     boolean valid = TRUE;
     if (strictTab)
 	wordCount = chopTabs(wiggle->line, words);
     else
 	wordCount = chopLine(wiggle->line, words);
     start = sqlUnsigned(words[1]);
     end = sqlUnsigned(words[2]);
     span = sqlUnsigned(words[4]);
     count = sqlUnsigned(words[5]);
     validCount = sqlUnsigned(words[10]);
     if (chrom && differentWord(chrom, words[0]))
 	{
 	chrom = words[0];
 	size = chromosomeSize(chrom);
 	verbose(3, "chrom: %s size: %u\n", chrom, size);
 	}
     else if (!chrom)
 	{
 	chrom = words[0];
 	size = chromosomeSize(chrom);
 	verbose(3, "chrom: %s size: %u\n", chrom, size);
 	}
     valid = TRUE;
     if (!noChromInfo && (end > size))
 	{
 	unsigned overrun = 0;
 	unsigned dropCount = 0;
 	overrun = end - size;
 	dropCount = 1 + (overrun / span);
 	warn("WARNING: Exceeded %s size %u > %u. dropping %u data point(s)", chrom, end, size, dropCount);
 	if (dropCount >= count)
 	    valid = FALSE;
 	else
 	    {
 	    count -= dropCount;
 	    if (validCount > count)
 		validCount = count;
 	    if ((end-(dropCount*span)) > start)
 		end -= dropCount*span;
 	    else
 		valid = FALSE;
 	    }
 	}
     if (valid)
 	{
 	if (!noBin)
 	    fprintf(f, "%u\t", hFindBin(wiggle->chromStart, wiggle->chromEnd));
 	for (i=0; i<wordCount; ++i)
 	    {
 	    switch(i)
 		{
 		case 2:
 		    fprintf(f,"%u", end);
 		    break;
 		case 5:
 		    fprintf(f,"%u", count);
 		    break;
 		case 7:
 		    if (pathPrefix )
 			{
 			if (endsWith(pathPrefix, "/"))
 			    fprintf(f,"%s", pathPrefix );
 			else
 			    fprintf(f,"%s/", pathPrefix );
 			}
 		    else
 			fprintf(f,"/gbdb/%s/wib/", database );
 		    fputs(words[i], f);
 		    break;
 		case 10:
 		    fprintf(f,"%u", validCount);
 		    break;
 		default:
 		    fputs(words[i], f);
 		    break;
 		}
 	    if (i == wordCount-1)
 		fputc('\n', f);
 	    else
 		fputc('\t', f);
 	    }
 	}
     }
 fclose(f);
 }
 
 static void loadDatabase(char *database, char *track, struct wiggleStub *wiggleList)
 /* Load database from wiggleList. */
 {
 struct sqlConnection *conn = (struct sqlConnection *)NULL;
-struct dyString *dy = newDyString(1024);
+struct dyString *dy = dyStringNew(1024);
 char *tab = (char *)NULL;
 
 if (! noLoad)
     {
     conn = hAllocConn(database);
     verbose(1, "Connected to database %s for track %s\n", database, track);
     }
 
 if ((char *)NULL != tmpDir)
     tab = cloneString(rTempName(tmpDir,"loadWig",".tab"));
 else
     tab = cloneString("wiggle.tab");
 
 /* First make table definition. */
 if ((!oldTable) && (!noLoad))
     {
     int indexLen = 0;
 
     if (maxChromNameLength)
 	indexLen = maxChromNameLength;
     else
 	indexLen = hGetMinIndexLength(database);
     verbose(2, "INDEX chrom length: %d\n", indexLen);
 
     /* Create definition statement. */
     verbose(1, "Creating wiggle table definition in %s.%s\n",
 	    database, track);
     sqlDyStringPrintf(dy, "CREATE TABLE %s (\n", track);
     if (!noBin)
-       dyStringAppend(dy, "  bin smallint unsigned not null,\n");
-    dyStringAppend(dy, "  chrom varchar(255) not null,\n");
-    dyStringAppend(dy, "  chromStart int unsigned not null,\n");
-    dyStringAppend(dy, "  chromEnd int unsigned not null,\n");
-    dyStringAppend(dy, "  name varchar(255) not null,\n");
-    dyStringAppend(dy, "  span int unsigned not null,\n");
-    dyStringAppend(dy, "  count int unsigned not null,\n");
-    dyStringAppend(dy, "  `offset` int unsigned not null,\n");
-    dyStringAppend(dy, "  file varchar(255) not null,\n");
-    dyStringAppend(dy, "  lowerLimit double not null,\n");
-    dyStringAppend(dy, "  dataRange double not null,\n");
-    dyStringAppend(dy, "  validCount int unsigned not null,\n");
-    dyStringAppend(dy, "  sumData double not null,\n");
-    dyStringAppend(dy, "  sumSquares double not null,\n");
-    dyStringAppend(dy, "#Indices\n");
+       sqlDyStringPrintf(dy, "  bin smallint unsigned not null,\n");
+    sqlDyStringPrintf(dy, 
+    "  chrom varchar(255) not null,\n"
+    "  chromStart int unsigned not null,\n"
+    "  chromEnd int unsigned not null,\n"
+    "  name varchar(255) not null,\n"
+    "  span int unsigned not null,\n"
+    "  count int unsigned not null,\n"
+    "  `offset` int unsigned not null,\n"
+    "  file varchar(255) not null,\n"
+    "  lowerLimit double not null,\n"
+    "  dataRange double not null,\n"
+    "  validCount int unsigned not null,\n"
+    "  sumData double not null,\n"
+    "  sumSquares double not null,\n"
+    "#Indices\n");
     if (!noBin)
-	dyStringPrintf(dy, "  INDEX(chrom(%d),bin)\n", indexLen);
+	sqlDyStringPrintf(dy, "  INDEX(chrom(%d),bin)\n", indexLen);
     else
 	{
-	dyStringPrintf(dy, "  INDEX(chrom(%d),chromStart)\n", indexLen);
+	sqlDyStringPrintf(dy, "  INDEX(chrom(%d),chromStart)\n", indexLen);
 	}
-    dyStringAppend(dy, ")\n");
+    sqlDyStringPrintf(dy, ")\n");
     verbose(2, "%s", dy->string);
     sqlRemakeTable(conn, track, dy->string);
     }
 
 verbose(1, "Saving %s\n", tab);
 writeWiggleTab(tab, wiggleList, database);
 
 if (! noLoad)
     {
     char comment[256];
     char pathAdded[192];
     verbose(1, "Loading %s\n", database);
     dyStringClear(dy);
     sqlDyStringPrintf(dy, "load data local infile '%s' into table %s", tab, track);
     sqlUpdate(conn, dy->string);
     if (pathPrefix)
 	safef(pathAdded, sizeof(pathAdded), "%s/", pathPrefix);
     else
 	safef(pathAdded, sizeof(pathAdded), "/gbdb/%s/wib/", database);
     if (oldTable)
 	safef(comment, sizeof(comment),
 	    "adding to wiggle table %s from %s/%s with wib path %s", track,
 		getCurrentDir(), tab, pathAdded);
     else
 	safef(comment, sizeof(comment),
 	    "new wiggle table %s from %s/%s with wib path %s", track,
 		getCurrentDir(), tab, pathAdded);
     if (! noHistory)
 	hgHistoryComment(conn, "%s", comment);
     verbose(2, "#\t%s\n", comment);
     hFreeConn(&conn);
     /*	if temp dir specified, unlink file to make it disappear */
     if ((char *)NULL != tmpDir)
 	unlink(tab);
     }
 else
     verbose(1, "noLoad option requested, see resulting file: %s\n", tab);
 }
 
 static void hgLoadWiggle(char *database, char *track,
 	int wiggleCount, char *wiggleFiles[])
 /* hgLoadWiggle - Load a generic wiggle file into database. */
 {
 struct wiggleStub *wiggleList = NULL;
 int i;
 
 if (!noChromInfo)
     {
     if (chromInfoDb)
 	chromHash = loadAllChromInfo(chromInfoDb);
     else
 	chromHash = loadAllChromInfo(database);
 
     if (verboseLevel() > 2)
 	{
 	struct hashCookie cookie;
 	struct hashEl *el;
 
 	cookie = hashFirst(chromHash);
 
 	verbose(3,"chrom\tsize\n");
 	while ((el = hashNext(&cookie)) != NULL)
 	    {
 	    unsigned size;
 	    size = chromosomeSize(el->name);
 	    verbose(3,"%s\t%u\n", el->name, size);
 	    }
 	}
     }
 
 for (i=0; i<wiggleCount; ++i)
     loadOneWiggle(wiggleFiles[i], &wiggleList);
 slSort(&wiggleList, wiggleStubCmp);
 loadDatabase(database, track, wiggleList);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, optionSpecs);
 
 if (argc < 4)
     usage();
 noBin = optionExists("noBin");
 noLoad = optionExists("noLoad");
 noHistory = optionExists("noHistory");
 strictTab = optionExists("tab");
 noChromInfo = optionExists("noChromInfo");
 oldTable = optionExists("oldTable");
 pathPrefix = optionVal("pathPrefix",NULL);
 chromInfoDb = optionVal("chromInfoDb",NULL);
 maxChromNameLength = optionInt("maxChromNameLength",0);
 tmpDir = optionVal("tmpDir", tmpDir);
 
 verbose(2, "noBin: %s, noLoad: %s, noHistory: %s, tab: %s, oldTable: %s\n",
 	noBin ? "TRUE" : "FALSE",
 	noLoad ? "TRUE" : "FALSE",
 	noHistory ? "TRUE" : "FALSE",
 	strictTab ? "TRUE" : "FALSE",
 	oldTable ? "TRUE" : "FALSE");
 if (pathPrefix)
     verbose(2, " pathPrefix: %s\n", pathPrefix);
 if (chromInfoDb)
     verbose(2, "chromInfoDb: %s\n", chromInfoDb);
 hgLoadWiggle(argv[1], argv[2], argc-3, argv+3);
 if (verboseLevel() > 1)
     printVmPeak();
 return 0;
 }