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/spm7/spm7.c src/hg/protein/spm7/spm7.c
index 3ae354f..720efdb 100644
--- src/hg/protein/spm7/spm7.c
+++ src/hg/protein/spm7/spm7.c
@@ -1,290 +1,290 @@
 /* spm7 - Creates sorted list of mRNA-SP data file for further duplicates processing */
 
 /* 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 "hCommon.h"
 #include "hdb.h"
 
 char proteinName[20], mrnaName[20];
 FILE *inf;
 char line_in[10000];
 char line[10000];
 char newInfo[10000], oldInfo[10000];
 char *oldMrnaStr, *oldProteinStr, *oldAlignStr;
 char *mrnaStr, *proteinStr, *alignStr;
 
 int aaLen;
 int cdsLen;
 char cond_str[256];
 char *aaStr;
 
 void usage()
 /* Explain usage and exit. */
 {   
 errAbort(
   "spm7 - Create sorted list of mRNA-SP data file for further duplicates processing\n"
   "usage:\n"
   "   spm7 xxxx yyyy\n"
   "      xxxx is the release date of SWISS-PROT data\n"
   "      yyyy is the genome under construction\n"
   "example:\n"
   "   spm7 072003 hg16\n");
 }
     
 int main(int argc, char *argv[])
 {
 char *skippedKgId;
 char *lastValidKgId;
     
 struct sqlConnection *conn2, *conn3;
 struct sqlResult *sr2;
 char query2[256];
 char **row2;
     
 char *proteinID;
 FILE   *o3, *o7;
 char *name, *chrom, *strand, *txStart, *txEnd, *cdsStart, *cdsEnd,
      *exonCount, *exonStarts, *exonEnds;
 
 char *alignID;
 
 char *chp;
 int  i, j;
 
 int  isDuplicate;
     
 char *genomeDBname;
 char *proteinDataDate;
 char proteinsDB[40];
 char spDB[40];
 char *acc;
 
 #define MAX_EXON 1000
 int exStart[MAX_EXON], exEnd[MAX_EXON];
 int exCount;
 
 int aaStart[MAX_EXON], aaEnd[MAX_EXON];
     
 char *sp, *ep;
 
 int  aalen;
 int  cdsS, cdsE;
 int  eS, eE;
  
 if (argc != 3) usage();
     
 proteinDataDate = argv[1];
 genomeDBname    = argv[2];
   
 safef(spDB, sizeof(spDB), "sp%s", proteinDataDate);
 safef(proteinsDB, sizeof(proteinsDB), "proteins%s", proteinDataDate);
  
 o3 = fopen("j.dat", "w");
 o7 = fopen("jj.dat", "w");
 
 conn2= hAllocConn(genomeDBname);
 conn3= hAllocConn(genomeDBname);
     
 inf  = mustOpen("sorted.lis", "r");
 
 strcpy(oldInfo, "");
 
 skippedKgId   = cloneString("");
 lastValidKgId = cloneString("");
 
 isDuplicate   = 0;
 oldMrnaStr    = cloneString("");
 oldAlignStr   = cloneString("");
 oldProteinStr = cloneString("");
 
 mrnaStr       = cloneString("");
 proteinStr    = cloneString("");
 alignStr      = cloneString("");
 
 while (fgets(line_in, 10000, inf) != NULL)
     {
     strcpy(line, line_in);
 
     chp = strstr(line, "\t");	/* chrom */
     chp ++;
 
     chp = strstr(chp, "\t");	/* cds block start position */
     chp ++;
 
     chp = strstr(chp, "\t");	/* cds block end   position */
     *chp = '\0';
     chp++;
     strcpy(newInfo, line);
 
     if (sameString(oldInfo, newInfo))
 	{
 	isDuplicate = 1;
 	}
     else
 	{
 	/* remember previous record as old only if it is not a duplicate */
 	if (!isDuplicate)
 	    {
 	    oldMrnaStr 	  = mrnaStr;
 	    oldProteinStr = proteinStr;
 	    oldAlignStr	  = alignStr;
 	    }
 	strcpy(oldInfo, newInfo);
 	isDuplicate = 0;
 	}
 
     chp = strstr(chp, "\t");	/* priority score */
     chp ++;
 		
     chp = strstr(chp, "\t");	/* mRNA transcription length */ 
     chp ++;
 		
     chp = strstr(chp, "\t");	/* mRNA date */
     chp ++;
 	
     mrnaStr = chp;	
     chp = strstr(chp, "\t");	/* mRNA ID */
     *chp = '\0';
     chp ++;
     mrnaStr = cloneString(mrnaStr);
 
     proteinStr = chp;	
     chp = strstr(chp, "\t");	/* protein ID */
     *chp = '\0';
     chp ++;
     proteinStr = cloneString(proteinStr);
 
     alignID = chp;
 
     /* get rid of "end-of-line" character at the end of the string */
     alignStr = trimSpaces(alignID);
 
     if (isDuplicate)
 	{
 	/* only put out records for valid KG entries */
 	if (!sameString(oldMrnaStr, skippedKgId) || sameString(oldMrnaStr, lastValidKgId))
 	    {
 	    fprintf(o7, "%s\t%s\t%s\t%s\n", oldMrnaStr, oldProteinStr, mrnaStr, proteinStr);
 	    }
 	}
     else
 	{
 	sqlSafef(query2, sizeof(query2), "select * from %sTemp.knownGene0 where alignID='%s';", genomeDBname, alignID);
 	sr2 = sqlMustGetResult(conn2, query2);
     	row2 = sqlNextRow(sr2);
     	while (row2 != NULL)
 	    {
  	    name 	= row2[0];
 	    chrom 	= row2[1];
 	    strand	= row2[2];
  	    txStart 	= row2[3];
 	    txEnd       = row2[4];
 	    cdsStart    = row2[5]; 
 	    cdsEnd	= row2[6];
 	    exonCount   = row2[7]; 
 	    exonStarts  = row2[8]; 
 	    exonEnds    = row2[9];	
 
 	    proteinID = row2[10];
 	    alignID   = row2[11];
 
 	    sscanf(exonCount, "%d", &exCount);
 	    sp = cloneString(exonStarts);
 	    ep = cloneString(exonEnds);
 	
             sscanf(cdsStart, "%d", &cdsS);
             sscanf(cdsEnd, "%d", &cdsE);
 
 	    aalen = 0;
 	    j=0;
 	    for (i=0; i<exCount; i++)
 		{
 		chp = strstr(sp, ",");
 		*chp = '\0';
 		sscanf(sp, "%d", &(exStart[i]));
 		chp++;
 		sp = chp;
 
 		chp = strstr(ep, ",");
 		*chp = '\0';
 		sscanf(ep, "%d", &(exEnd[i]));
 	
 		eS = exStart[i];
 		eE = exEnd[i];
 		
 		if (cdsS > eS)
 		    {
 		    eS = cdsS;
 		    }
 		if (cdsE < eE)
 		    {
 		    eE = cdsE;
 		    }
 		if (eS > eE) 
 		    {
 		    eS = 0;
 		    eE = 0;
 		    }
 	        if (eS != eE)
 		    {
 		    aaStart[j] = aalen;
 		    aaEnd[j] = aaStart[j] + (eE- eS +1)/3 -1;
 		    aalen = aalen + (eE- eS +1)/3;
 			
 		    j++;
 		    }
 		
 		chp++;
 		ep = chp;
 		}
 		
 	    cdsLen = aalen;
 
-            sqlSafefFrag(cond_str, sizeof(cond_str), "val='%s'", proteinID);
+            sqlSafef(cond_str, sizeof(cond_str), "val='%s'", proteinID);
             acc = sqlGetField(spDB, "displayId", "acc", cond_str);
 
-            sqlSafefFrag(cond_str, sizeof(cond_str), "acc='%s'", acc);
+            sqlSafef(cond_str, sizeof(cond_str), "acc='%s'", acc);
             aaStr=sqlGetField(spDB, "protein", "val", cond_str);
     	    aaLen = strlen(aaStr);
 
             if ((cdsLen >  50) || ((cdsLen * 100)/aaLen > 50))
 		{
 		fprintf(o3,"%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n",
  		    	name,
 			chrom,
 		        strand,
  	    		txStart,
 	    		txEnd,
 	 	   	cdsStart,
 	    		cdsEnd,
 		    	exonCount,
 		    	exonStarts,
 	    		exonEnds,
 			
 			proteinID,
 			alignID);
 		lastValidKgId = cloneString(name);
 		}
 	    else
 		{
 		printf("skipping %s %d \n", name, cdsLen);
 		skippedKgId = cloneString(name);
 		} 
 	    row2 = sqlNextRow(sr2);
 	    }
 	sqlFreeResult(&sr2);
 	}
     }
 hFreeConn(&conn2);
 hFreeConn(&conn3);
 fclose(o3);
 fclose(o7);
     
 mustSystem("cat j.dat|sort|uniq  >knownGene.tab");
 mustSystem("cat jj.dat|sort|uniq >duplicate.tab");
 mustSystem("rm j.dat");
 mustSystem("rm jj.dat");
 return(0);
 }