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/protein/pbCalResStd/pbCalResStd.c src/hg/protein/pbCalResStd/pbCalResStd.c
index 57d2968..7a3d9a4 100644
--- src/hg/protein/pbCalResStd/pbCalResStd.c
+++ src/hg/protein/pbCalResStd/pbCalResStd.c
@@ -1,334 +1,334 @@
 /* pbCalResStd- Calculate the avg frequency and standard deviation of each AA residue for the proteins in a specific genome*/
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #define MAXN 1000000
 #define MAXRES 23
 
 #include "common.h"
 #include "hCommon.h"
 #include "hdb.h"
 #include "spDb.h"
 #include "math.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "pbCalResStd calculates the avg frequency and standard deviation of every AA residues of the proteins in a specific genome\n"
   "usage:\n"
   "   pbCalResStd spDb taxNum gDb\n"
   "      spDb is the SWISS-PROT database name\n"
   "      taxNumis the taxnomy number of the genome\n"
   "      gDb is the genome database name\n"
   "Example: pbCalResStd sp050415 9606 hg17\n"
   );
 }
 
 double measure[MAXN];
 double freq[MAXN][MAXRES];
 double avg[MAXRES];
 double sumJ[MAXRES];
 double sigma[MAXRES];
 double sumJ[MAXRES];
 
 int recordCnt;
 double recordCntDouble;
 double lenDouble;
 double sum;
 
 int calDist(double *measure, int nInput, int nDist, double xMin, double xDelta, char *oFileName)
 /* calculate histogram distribution of a double array of nInput elements */ 
 {
 int distCnt[1000];
 double xDist[1000];
 FILE *o3;
 int i,j;
 int highestCnt, totalCnt;
 
 assert(nDist < ArraySize(distCnt));
 
 o3 = mustOpen(oFileName, "w");
 for (j=0; j<=nDist; j++)
     {
     distCnt[j] = 0;
     xDist[j] = xMin + xDelta * (double)j;
     }
 
 for (i=0; i<nInput; i++)
     {
     if (measure[i] <= xDist[0])
 	{
 	distCnt[0]++;
 	}
     for (j=1; j<nDist; j++)
 	{
 	if ((measure[i] > xDist[j-1]) && (measure[i] <= xDist[j]))
  	    {
 	    distCnt[j]++;
 	    }
 	}
     if (measure[i] > xDist[nDist-1])
 	{
 	distCnt[nDist]++;
 	}
     }
 
 highestCnt = 0;
 totalCnt   = 0;
 for (j=0; j<=nDist; j++)
     {
     if (distCnt[j] > highestCnt) highestCnt = distCnt[j];
     totalCnt = totalCnt + distCnt[j];
     }
     
 if (totalCnt != nInput)
     errAbort("nInput %d is not equal totalCnt %d, aborting ...\n", nInput, totalCnt);
    
 /* do not print out count of the last inteval, which is everything beyond xMax */
 for (j=0; j<nDist; j++)
     {
     fprintf(o3, "%f\t%d\n", xDist[j], distCnt[j]);
     }
 carefulClose(&o3);
    
 return(highestCnt);
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *conn2;
 char query2[256];
 struct sqlResult *sr2;
 char **row2;
 char cond_str[255];
 char *proteinDatabaseName;
 FILE *o1, *o2, *o3;
 FILE *fh[23];
 char temp_str[1000];;
 char *accession;
 char *aaSeq;
 char *chp;
 int i, j, len;
 int ihi, ilow;
 char *answer;
 char *protDisplayId;
 int aaResCnt[30];
 char aaAlphabet[30];
 int aaResFound;
 float fvalue1, fvalue2;
 float p1, p2;
 int icnt, jcnt;
 char *taxon;
 char *database;
 int sortedCnt;
 
 if (argc != 4) usage();
 
 strcpy(aaAlphabet, "WCMHYNFIDQKRTVPGEASLXZB");
 
 proteinDatabaseName = argv[1];
 taxon = argv[2];
 database = argv[3];
 
 o2 = mustOpen("pbResAvgStd.tab", "w");
 
 for (i=0; i<20; i++)
     {
     safef(temp_str, sizeof(temp_str), "%c.txt", aaAlphabet[i]);
     fh[i] = mustOpen(temp_str, "w");
     }
 
 conn  = hAllocConn(hDefaultDb());
 conn2 = hAllocConn(hDefaultDb());
 
 sqlSafef(query2, sizeof(query2), "select proteinID from %s.knownGene;", database);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 icnt = 0;
 jcnt = 0;
 
 for (j=0; j<MAXRES; j++)
     {
     sumJ[j] = 0;
     }
 
 while (row2 != NULL)
     {
     protDisplayId = row2[0];   
-    sqlSafefFrag(cond_str, sizeof(cond_str),  "val='%s'", protDisplayId);
+    sqlSafef(cond_str, sizeof(cond_str),  "val='%s'", protDisplayId);
     accession = sqlGetField(proteinDatabaseName, "displayId", "acc", cond_str);
 
     if (accession == NULL)
 	{
-        sqlSafefFrag(cond_str, sizeof(cond_str),  "acc='%s'", protDisplayId);
+        sqlSafef(cond_str, sizeof(cond_str),  "acc='%s'", protDisplayId);
     	accession = sqlGetField(proteinDatabaseName, "displayId", "acc", cond_str);
 	if (accession == NULL)
 	    {
 	    verbose(2, "'%s' not found.\n", protDisplayId);
 	    goto skip;
 	    }
 	}
     
-    sqlSafefFrag(cond_str, sizeof(cond_str),  "accession='%s'", accession);
+    sqlSafef(cond_str, sizeof(cond_str),  "accession='%s'", accession);
     answer = sqlGetField("proteins040115", "spXref2", "biodatabaseID", cond_str);
     if (answer == NULL)
 	{
 	/* this protein might be a variant splice protein, and then it won't be in spXref2 */
 	goto skip;
 	}
     if (answer[0] != '1')
 	{
 	/* printf("%s not in SWISS-PROT\n", protDisplayId);fflush(stdout); */
 	goto skip;
 	}
     
-    sqlSafefFrag(cond_str, sizeof(cond_str),  "acc='%s'", accession);
+    sqlSafef(cond_str, sizeof(cond_str),  "acc='%s'", accession);
     aaSeq = sqlGetField(proteinDatabaseName, "protein", "val", cond_str);
     if (aaSeq == NULL)
 	{
 	printf("Can't find peptide sequence for %s, exiting ...\n", protDisplayId);
 	fflush(stdout);
 	exit(1);
 	}
 
     len  = strlen(aaSeq);
     if (len < 100) goto skip;
 
     lenDouble = (double)len;
 
     for (j=0; j<MAXRES; j++)
     	{
     	aaResCnt[j] = 0;
 	}
 
     chp = aaSeq;
     for (i=0; i<len; i++)
 	{
 	aaResFound = 0;
 	for (j=0; j<MAXRES; j++)
 	    {
 	    if (*chp == aaAlphabet[j])
 		{
 		aaResFound = 1;
 		aaResCnt[j] ++;
 		}
 	    }
 	if (!aaResFound)
 	    {
 	    fprintf(stderr, "%c %d not a valid AA residue.\n", *chp, *chp);
 	    }
 	chp++;
 	}
 
     for (j=0; j<MAXRES; j++)
 	{	
 	freq[icnt][j] = (double)aaResCnt[j]/lenDouble;
 	sumJ[j] = sumJ[j] + freq[icnt][j];
 	}
 
     for (j=0; j<20; j++)
 	{
 	fprintf(fh[j], "%15.7f\t%s\n", freq[icnt][j], accession);fflush(fh[j]);
 	}
     icnt++;
     if (icnt >= MAXN)
 	errAbort("Too many proteins - please set MAXN to be more than %d\n", MAXN);
 		
 skip:
     row2 = sqlNextRow(sr2);
     }
 
 recordCnt = icnt;
 recordCntDouble = (double)recordCnt;
 
 for (j=0; j<20; j++)
     {
     carefulClose(&(fh[j]));
     }
 
 sqlFreeResult(&sr2);
 hFreeConn(&conn);
 hFreeConn(&conn2);
 
 for (j=0; j<MAXRES; j++)
     {
     avg[j] = sumJ[j]/recordCntDouble;
     }
 
 for (j=0; j<20; j++)
     {
     sum = 0.0;
     for (i=0; i<recordCnt; i++)
      	{
 	sum = sum + (freq[i][j] - avg[j]) * (freq[i][j] - avg[j]);
 	}
     sigma[j] = sqrt(sum/(double)(recordCnt-1));
     fprintf(o2, "%c\t%f\t%f\n", aaAlphabet[j], avg[j], sigma[j]);
     }
 
 carefulClose(&o2);
 
 o1 = mustOpen("pbAnomLimit.tab", "w");
 for (j=0; j<20; j++)
     {
     safef(temp_str, sizeof(temp_str), "cat %c.txt|sort|uniq > %c.srt",  aaAlphabet[j], aaAlphabet[j]);
     mustSystem(temp_str);
 
     /* figure out how many unique entries */
     safef(temp_str, sizeof(temp_str), "wc %c.srt > %c.tmp",  aaAlphabet[j], aaAlphabet[j]);
     mustSystem(temp_str);
     safef(temp_str, sizeof(temp_str), "%c.tmp",  aaAlphabet[j]);
     o3 = mustOpen(temp_str, "r");
     mustGetLine(o3, temp_str, 1000);
     chp = temp_str;
     while (*chp == ' ') chp++;
     while (*chp != ' ') chp++;
     *chp = '\0';
     sscanf(temp_str, "%d", &sortedCnt);
     safef(temp_str, sizeof(temp_str), "rm %c.tmp", aaAlphabet[j]);
     mustSystem(temp_str);
 
     /* cal hi and low cutoff threshold */
     ilow = (int)((float)sortedCnt * 0.025);
     ihi  = (int)((float)sortedCnt * 0.975);
     
     safef(temp_str, sizeof(temp_str), "%c.srt",  aaAlphabet[j]);
     o2 = mustOpen(temp_str, "r");
     i=0;
     for (i=0; i<ilow; i++)
 	{
 	mustGetLine(o2, temp_str, 1000);
 	}
     sscanf(temp_str, "%f", &fvalue1);
 
     mustGetLine(o2, temp_str, 1000);
     sscanf(temp_str, "%f", &fvalue2);
     p1 = (fvalue1 + fvalue2)/2.0;
 
     for (i=ilow+1; i<ihi; i++)
 	{
 	mustGetLine(o2, temp_str, 1000);
 	}
     sscanf(temp_str, "%f", &fvalue1);
 
     mustGetLine(o2, temp_str, 1000);
     sscanf(temp_str, "%f", &fvalue2);
     p2 = (fvalue1 + fvalue2)/2.0;
     carefulClose(&o2);
 
     fprintf(o1, "%c\t%f\t%f\n", aaAlphabet[j], p1, p2);fflush(stdout);
 
     for (i=0; i<recordCnt; i++)
 	{
 	measure[i] = freq[i][j]; 
 	}
     safef(temp_str, sizeof(temp_str), "pbAaDist%c.tab", aaAlphabet[j]);
     calDist(measure,  recordCnt,    51,     0.0, 0.005, temp_str);
     }
     
 carefulClose(&o1);
 
 return(0);
 }