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/synMap/createSlamParaSpec.c src/hg/synMap/createSlamParaSpec.c
index d6de87a..f13dcb6 100644
--- src/hg/synMap/createSlamParaSpec.c
+++ src/hg/synMap/createSlamParaSpec.c
@@ -1,187 +1,188 @@
 /* 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 <sys/stat.h>
 #include <sys/types.h>
 #include "synMap.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "dystring.h"
 
 
 int maxFaSize = BIGNUM;
 boolean dontCheckLargeSize = FALSE;
 boolean dontCheckSmallSize = FALSE;
 void usage()
 {
 errAbort("createSlamParaSpec - constructs a spec file for use on parasol\n"
 	 "UCSC's kilo-cluster with slam and runSlam.\n"
 	 "usage:\n\t"
 	 "createSlamParaSpec <maxFaSize> <resultsDir> <refNibDir> <alignNibDir> <synMapFile> <specOutFile> <db> <makeSubDirs{true|false}> <refPrefix> <alignPrefix> <binPrefix> <skipLargeSizeChecks> <skipSmallSizeChecks>\n");
 }
 
 FILE *jobList = NULL;
 char *stitchName(char *chrom, unsigned int start, unsigned int end)
 /* stitch chrom, start, end into chrom:start-end */
 {
 char buff[512];
 if(strstr(chrom, "chr") != NULL)
     snprintf(buff, sizeof(buff), "%s:%u-%u", chrom, start, end);
 else
     snprintf(buff, sizeof(buff), "chr%s:%u-%u", chrom, start, end);
 return cloneString(buff);
 }
 
 void makeSubDirs(char *db)
 /* create a subdir for each chrom in database */
 {
 struct sqlConnection *conn = NULL;
 struct sqlResult *sr = NULL;
 char **row;
-char *query = NOSQLINJ "select chrom from chromInfo";
+char query[1024];
+sqlSafef(query, sizeof query, "select chrom from chromInfo");
 hSetDb(db);
 conn = hAllocConn();
 sr = sqlGetResult(conn, query);
 while((row = sqlNextRow(sr)) != NULL)
     {
     mkdir(row[0], 1);
     chmod(row[0],0777);
     }
 mkdir("log", 1);
 chmod("log",0777);
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 
 void outputRequieredFiles(struct synMap *smList, char *refPrefix, char *alignPrefix, char *resultsDir)
 {
 FILE *out = mustOpen("requiredFiles.txt","w");
 struct synMap *sm = NULL;
 char *out1 = NULL, *out2 = NULL;
 for(sm = smList; sm != NULL; sm = sm->next)
     {
     out1 = stitchName(sm->chromA, sm->chromStartA, sm->chromEndA);
     fprintf(out, "%s/%s/%s.%s.gff\n", 	    resultsDir, sm->chromA, refPrefix, out1);
     freez(&out1);
     }
 carefulClose(&out);
 }
 
 void createSlamParaSpec(int maxFaSize, char *resultsDir, char *refNibDir, char *alignNibDir, char *synMapFile, char *specOut, char *db, 
 			char *subDirs, char *refPrefix, char *alignPrefix, char *binPrefix)
 /* top level function to write everything out */
 {
 struct synMap *smList = NULL, *sm = NULL;
 struct synMap *tmpList = NULL, *smNext = NULL;
-struct dyString *command = newDyString(4096);
+struct dyString *command = dyStringNew(4096);
 char *out1 = NULL, *out2 = NULL;
 FILE *out = NULL;
 int synSize = 0;
 float minSize = 0;
 smList = synMapLoadAll(synMapFile);
 out = mustOpen(specOut, "w");
 if(sameString(subDirs,"true") || sameString(subDirs,"TRUE"))
     makeSubDirs(db);
 for(sm = smList; sm != NULL; sm = smNext)
     {
      minSize = .05 * (sm->chromEndA - sm->chromStartA); 
      synSize = sm->chromEndB - sm->chromStartB; 
      smNext = sm->next; 
      if((synSize >= (int)minSize || dontCheckSmallSize))
  	{ 
  	slAddHead(&tmpList, sm); 
  	} 
     else
 	{
 	if(synSize < (int)minSize && !dontCheckSmallSize)
 	    warn("Size too small for: %s:%d-%d", sm->chromA, sm->chromStartA, sm->chromEndA);
 	else
 	    errAbort("createSlamParaSpec::createSlamParaSpec() - Confused, shouldn't be aborting for : %s:%d-%d but I am...", 
 		     sm->chromA, sm->chromStartA, sm->chromEndA);
 	synMapFree(&sm);
 	}
     }
 slReverse(&tmpList);
 smList = tmpList;
 for(sm = smList; sm != NULL; sm = sm->next)
     {
     int faTotal = 0;
     faTotal += sm->chromEndB - sm->chromStartB;
     dyStringClear(command);
     out1 = stitchName(sm->chromA, sm->chromStartA, sm->chromEndA);
     out2 = stitchName(sm->chromB, sm->chromStartB, sm->chromEndB);
 /* switch back to this command when we are sure that .gff file will be produced every time. */
 /*     dyStringPrintf(command, "%s/runSlam %s %s %s/%s %s %s {check out exists %s/%s/%s.%s.gff} {check out exists %s/%s/%s.%s.merged.gff} %s %s", */
 /* 		   binPrefix, */
 /* 		   refNibDir, alignNibDir, resultsDir, sm->chromA,  */
 /* 		   refPrefix, alignPrefix, */
 /* 		   resultsDir, sm->chromA, refPrefix, out1,  */
 /* 		   resultsDir, sm->chromA, alignPrefix, out2,  */
 /* 		   out1,  */
 /* 		   out2); */
     dyStringPrintf(command, "%s/runSlam %d %s %s %s/%s %s %s {check out exists %s/%s/%s.%s_%s.%s.log} dummy.txt %s %s",
 		   maxFaSize,
 		   binPrefix,
 		   refNibDir, alignNibDir, resultsDir, sm->chromA, 
 		   refPrefix, alignPrefix,
 		   resultsDir, sm->chromA, refPrefix, out1, 
 		   alignPrefix, out2, 
 		   out1, 
 		   out2);
     fprintf(jobList, "%s/runSlam %d %s %s %s/%s %s %s  %s/%s/%s.%s.gff %s/%s/%s.%s.merged.gff %s %s",
 	    maxFaSize,
 	    binPrefix,
 	    refNibDir, alignNibDir, resultsDir, sm->chromA, 
 	    refPrefix, alignPrefix,
 	    resultsDir, sm->chromA, refPrefix, out1, 
 	    resultsDir, sm->chromA, alignPrefix, out2, 
 	    out1, 
 	    out2);
     while(sm->next && sameString(sm->next->chromA, sm->chromA) 
 	  && sm->next->chromStartA == sm->chromStartA && sm->next->chromEndA == sm->chromEndA)
 	{
 	char *alignBit = NULL;
 	sm = sm->next;
 	faTotal += sm->chromEndB - sm->chromStartB;
 	alignBit = stitchName(sm->chromB, sm->chromStartB, sm->chromEndB);
 	dyStringPrintf(command, " %s", alignBit);
 	fprintf(jobList, " %s", alignBit);
 	freez(&alignBit);
 	}
     if(command->stringSize < (3.5*1024) && 
        (faTotal <= maxFaSize || dontCheckLargeSize) )
 	{
 	fprintf(out, "%s\n", command->string);
 	fprintf(jobList, "\n");
 	}
     else if(command->stringSize >= (3.5*1024))
 	warn("Command %s is too long %d characters, skipping\n",command->string, command->stringSize);
     else
 	warn("Size too large for: %s:%d-%d, %d counted, %d allowed", sm->chromA, sm->chromStartA, sm->chromEndA,
 	     faTotal, maxFaSize);
     freez(&out1);
     freez(&out2);
     }
 dyStringFree(&command);
 carefulClose(&out);
 synMapFreeList(&smList);
 }
 
 int main(int argc, char *argv[])
 {
 if(argc != 14)
     {
     warn("Only %d arguments, expecting 14", argc);
     usage();
     }
 jobList = mustOpen("jobList.txt", "w");
 if(sameString(argv[12], "true"))
     dontCheckLargeSize = TRUE;
 if(sameString(argv[13], "true"))
     dontCheckSmallSize = TRUE;
 createSlamParaSpec(atoi(argv[1]), argv[2], argv[3], argv[4], argv[5], argv[6], argv[7], argv[8], argv[9], argv[10], argv[11]);
 carefulClose(&jobList);
 return 0;
 }