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/mouseStuff/mafCoverage/mafCoverage.c src/hg/mouseStuff/mafCoverage/mafCoverage.c
index 7b1f285..d6603a0 100644
--- src/hg/mouseStuff/mafCoverage/mafCoverage.c
+++ src/hg/mouseStuff/mafCoverage/mafCoverage.c
@@ -1,521 +1,523 @@
 /* mafCoverage - Analyse coverage by maf files - chromosome by chromosome 
  * and genome-wide.. */
 
 /* 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 "options.h"
 #include "obscure.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "chromInfo.h"
 #include "agpFrag.h"
 #include "memalloc.h"
 #include "maf.h"
 
 #define MAXALIGN 50  /* max number of species to align */
 #define DEFCOUNT 3   /* require 3 species to match before counting as covered */
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "mafCoverage - Analyse coverage by maf files - chromosome by \n"
   "chromosome and genome-wide.\n"
   "usage:\n"
   "   mafCoverage database mafFile\n"
   "Note maf file must be sorted by chromosome,tStart\n"
   "   -restrict=restrict.bed Restrict to parts in restrict.bed\n"
   "   -count=N Number of matching species to count coverage. Default = 3 \n"
   );
 }
 
 struct optionSpec options[] = {
    {"count", OPTION_INT},
    {"restrict", OPTION_STRING},
    {NULL,0}
 };
 struct chromInfo *getAllChromInfo(char *database)
 /* Return list of info for all chromosomes. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr;
 char **row;
 struct chromInfo *ci, *ciList = NULL;
 
-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)
     {
     ci = chromInfoLoad(row);
     slAddHead(&ciList, ci);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 slReverse(&ciList);
 return ciList;
 }
 
 #define maxDepth 100    /* Maximum depth we track, if change this showStats and shortStats need updating. */
 #define restricted 255	/* Special value for masked out. */
 
 struct simpleRange
 /* A range inside of a chromosome. */
    {
    struct simpleRange *next;
    int start;	/* Start (zero based) */
    int end;	/* End (not included) */
    };
 
 struct chromSizes
 /* Sizes of each chromosome, with and without gaps. */
    {
    struct chromSizes *next;
    char *name;	/* Allocated in hash */
    double seqSize;   /* Size without N's. */
    double totalSize; /* Size with N's. */
    double unrestrictedSize;	/* Size unrestricted. */
    double totalDepth;  /* Sum of coverage of all bases. */
    double totalCov;    /* Sum of bases covered at least once. */
    double totalAlign;    /* Sum of aligning bases covered at least once. */
    double totalId;    /* Sum of aligning exact match bases covered at least once. */
 
    double histogram[maxDepth+1]; /* Coverage histogram. */
    double histogramAlign[maxDepth+1]; /* Coverage histogram. */
    boolean completed;   /* True if completed. */
    struct simpleRange *restrictList;	/* List of ranges to restrict to. */
    };
 
 
 void addRestrictions(struct hash *hash, char *fileName)
 /* Add restrictions from maf file */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[3];
 int count = 0;
 while (lineFileRow(lf, row))
     {
     struct chromSizes *cs = hashMustFindVal(hash, row[0]);
     struct simpleRange *r;
     AllocVar(r);
     r->start = lineFileNeedNum(lf, row, 1);
     r->end = lineFileNeedNum(lf, row, 2);
     if (r->start < 0 || r->end > cs->totalSize)
         errAbort("%d-%d doesn't fit into %s size %ld line %d of %s",
 		 r->start, r->end, row[0], (long)cs->totalSize,
 		 lf->lineIx, lf->fileName);
     slAddHead(&cs->restrictList, r);
     ++count;
     }
 printf("Added %d restrictions from %s\n", count, fileName);
 }
 
 void showStats(struct chromSizes *cs)
 /* Print out stats. */
 {
 int i, j;
 printf("%-6s ", cs->name);
 printLongWithCommas(stdout,cs->unrestrictedSize);
 printf("    Depth ");
 printLongWithCommas(stdout,cs->totalDepth);
 printf(" %5.2f%%    Coverage ", 100.0 * cs->totalDepth/cs->unrestrictedSize);
 printLongWithCommas(stdout,cs->totalCov);
 printf(" %5.2f%%    Align ", 100.0 * cs->totalCov/cs->unrestrictedSize);
 printLongWithCommas(stdout,cs->totalAlign);
 printf(" %5.2f%%    Exact Match ", 100.0 * cs->totalAlign/cs->unrestrictedSize);
 printLongWithCommas(stdout,cs->totalId);
 printf(" %5.2f%%    MisMatch ", 100.0 * cs->totalId/cs->unrestrictedSize);
 printLongWithCommas(stdout,cs->totalAlign - cs->totalId);
 printf(" %5.2f%%    \n", 100.0 * (cs->totalAlign - cs->totalId)/cs->unrestrictedSize);
 for (i=1; i<10; ++i)
     {
     double sum = cs->histogram[i];
     if (sum > 0)
         printf("%2d  %10.0f %5.3f%%\n", i, sum, 100.0 * sum/cs->unrestrictedSize);
     }
 for (i=0; i<100; i += 10)
     {
     double sum = 0;
     for (j=0; j<10; ++j)
         {
 	int ix = i+j;
 	sum += cs->histogram[ix];
 	}
     if (sum > 0)
         printf("%2d to %2d:  %10f %5.3f%%\n", i, i+9, sum, 100.0 * sum/cs->unrestrictedSize);
     }
 if (cs->histogram[100] > 0)
     printf(">=100  %10f %5.3f%%\n", cs->histogram[100], 
 	100.0 * cs->histogram[100]/cs->unrestrictedSize);
 printf("\n");
 }
 
 void shortStats(struct chromSizes *cs)
 /* Display short form of stats. */
 {
 int i;
 double totalCov, tenOrMore=0, hundredOrMore=0;
 totalCov = cs->totalCov;
 // twoOrMore = totalCov - cs->histogram[1]; not necessary
 for (i=10; i<=100; ++i)
     tenOrMore += cs->histogram[i];
 hundredOrMore = cs->histogram[100];
 if (totalCov > 0 || cs->totalAlign > 0 || tenOrMore > 0 || hundredOrMore > 0)
     {
     printf("%s\t", cs->name); 
     printLongWithCommas(stdout,cs->totalCov);
     printf("\t%1.2f\t",totalCov * 100.0 / cs->unrestrictedSize); 
     printLongWithCommas(stdout,cs->totalAlign);
     printf("\t%1.2f\t",cs->totalAlign * 100.0 / cs->unrestrictedSize);
     printLongWithCommas(stdout,cs->totalId);
     printf("\t%1.2f\t",cs->totalId * 100.0 / cs->unrestrictedSize);
     printLongWithCommas(stdout,cs->totalAlign - cs->totalId);
     printf("\t%1.2f\n",(cs->totalAlign - cs->totalId) * 100.0 / cs->unrestrictedSize);
     }
 }
 
 void getChromSizes(char *database, struct hash **retHash, 
 	struct chromSizes **retList)
 /* Return hash of chromSizes.  Also calculates size without
  * gaps. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct chromInfo *ci, *ciList = getAllChromInfo(database);
 struct sqlResult *sr;
 char **row;
 struct chromSizes *cs, *csList = NULL;
 struct hash *hash = newHash(8);
 int rowOffset;
 
 for (ci = ciList; ci != NULL; ci = ci->next)
     {
     AllocVar(cs);
     hashAddSaveName(hash, ci->chrom, cs, &cs->name);
     slAddHead(&csList, cs);
     cs->totalSize = ci->size;
     sr = hChromQuery(conn, "gold", ci->chrom, NULL, &rowOffset);
     while ((row = sqlNextRow(sr)) != NULL)
         {
 	struct agpFrag frag;
 	agpFragStaticLoad(row + rowOffset, &frag);
 	cs->seqSize += frag.chromEnd - frag.chromStart;
 	}
     sqlFreeResult(&sr);
     }
 hFreeConn(&conn);
 slReverse(&csList);
 *retHash = hash;
 *retList = csList;
 }
 
 void incNoOverflow(UBYTE *cov, int size)
 /* Add one to each member of cov, so long as it's
  * not over maxDepth. */
 {
 UBYTE c;
 while (--size >= 0)
    {
    c = *cov;
    if (c < maxDepth)
        {
        ++c;
        *cov = c;
        }
    ++cov;
    }
 }
 
 void closeChromCov(char *fileName, struct chromSizes *cs, UBYTE **pCov1, UBYTE **pCov2, UBYTE **pCov3)
 /* Fill in cs->histogram from cov, and free cov. */
 {
 UBYTE *cov = *pCov1, *align = *pCov2, *id = *pCov3,  c;
 int i, size = cs->totalSize;
 for (i=0; i<size; ++i)
    {
    c = cov[i];
    if (c > 0 && c != restricted)
        {
        cs->histogram[c] += 1;
        cs->totalCov += 1;
        }
    c = align[i];
    if (c > 0 && c != restricted)
        {
        cs->histogramAlign[c] += 1;
        cs->totalAlign += 1;
        }
    c = id[i];
    if (c > 0 && c != restricted)
        {
        cs->totalId += 1;
        }
    }
 freez(pCov1);
 freez(pCov2);
 freez(pCov3);
 if (cs->completed)
      errAbort("maf file not sorted by chromosome in %s .", fileName);
 cs->completed = TRUE;
 showStats(cs);
 }
 
 
 void restrictCov(UBYTE *cov, int size, struct simpleRange *restrictList)
 /* Set areas that are restricted (not in restrict list) to restricted
  * value. Assumes cov is all zero to begin with. */
 {
 struct simpleRange *r;
 memset(cov, restricted, size);
 for (r = restrictList; r != NULL; r = r->next)
     {
     assert(r->start >= 0);
     assert(r->end <= size);
     memset(cov + r->start, 0, r->end - r->start);
     }
 }
 
 void restrictGaps(char *database, UBYTE *cov, int size, char *chrom)
 /* Mark gaps as off-limits. */
 {
 int rowOffset;
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr = hChromQuery(conn, "gap", chrom, NULL, &rowOffset);
 char **row;
 int s,e;
 
 while ((row = sqlNextRow(sr)) != NULL)
     {
     s = sqlUnsigned(row[1+rowOffset]);
     e = sqlUnsigned(row[2+rowOffset]);
     assert(s >= 0);
     assert(e <= size);
     memset(cov + s, restricted, e - s);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 int calcUnrestrictedSize(UBYTE *cov, int size)
 /* Figure out number of bases not restricted. */
 {
 int count = 0;
 int i;
 for (i=0; i<size; ++i)
     if (cov[i] != restricted)
         ++count;
 return count;
 }
 
 
 void scanMaf(char *database, char *fileName, struct hash *chromHash, boolean covRestrict, int spCount)
 /* Scan through maf file (which must be sorted by
  * chromosome) and fill in coverage histograms on 
  * each chromosome. */
 {
 struct mafFile *mf = mafOpen(fileName);
 struct mafAli *ali = NULL;
 struct mafComp *comp = NULL;
 struct chromSizes *lastCs = NULL, *cs = NULL;
 char *chrom = NULL;
 int start = 0, end = 0, size = 0, j, k;
 int idStart = 0, idEnd = 0, idSize = 0;
 UBYTE *cov = NULL;
 UBYTE *align = NULL;
 UBYTE *id = NULL;
 char *tPtr[MAXALIGN];
 bool hit = FALSE;
 
 while ((ali = mafNext(mf)) != NULL)
     {
     int cCount = slCount(ali->components);
     int i = 1;
     int nextStart, idNextStart;
 
     comp = ali->components; 
     tPtr[0] = comp->text;
     chrom = strchr(comp->src,'.')+1;
     if (chrom == NULL)
          chrom = comp->src;
     start = comp->start;
     idStart = comp->start;
     nextStart = idNextStart = start;
     cs = hashMustFindVal(chromHash, chrom);
     if (cs != lastCs)
         {
 	if (lastCs != NULL)
 	    closeChromCov(fileName, lastCs, &cov, &align, &id);
 	AllocArray(cov, cs->totalSize);
 	AllocArray(align, cs->totalSize);
 	AllocArray(id, cs->totalSize);
 	if (covRestrict)
             {
 	    restrictCov(cov, cs->totalSize, cs->restrictList);
 	    restrictCov(align, cs->totalSize, cs->restrictList);
 	    restrictCov(id, cs->totalSize, cs->restrictList);
             }
 	restrictGaps(database, cov, cs->totalSize, chrom);
 	restrictGaps(database, align, cs->totalSize, chrom);
 	restrictGaps(database, id, cs->totalSize, chrom);
 	cs->unrestrictedSize = calcUnrestrictedSize(cov, cs->totalSize);
 	lastCs = cs;
 	}
     /* don't count if few alignments than spCount */
     if ((ali->components->next == NULL) || (cCount < spCount))
         {
         mafAliFree(&ali);
         continue;
         }
     //printf("coverage %d, size %d\n", start, comp->size);
     incNoOverflow(cov+start, comp->size);
     for (comp = ali->components->next; comp != NULL; comp = comp->next)
         {
 	if (comp->size > 0)	// do not process e lines
 	    {
 	    tPtr[i] = comp->text;
 	    i++;
 	    assert (i < MAXALIGN-1);
 	    }
 	else
 	    --cCount;
         }
     size = 0;
     assert(cs != NULL);
     /* count gapless columns */
     for (j = 0 ; j<ali->textSize ; j++)
         {
 	hit = TRUE;
         /* look for aligning bases in query seqs , abort if any is a gap */
         for (i = 1 ; i < cCount ; i++)
             {
             if (tPtr[i][j] == '-' || tPtr[0][j] == '-')
                 {
      //   printf("align %d, size %d\n", start, size);
                 incNoOverflow(align+start, size);
                 cs->totalDepth += size;
                 start = nextStart;
                 size = 0;
                 hit = FALSE;
                 break;
                 }
             }
         if (hit)
             size++;
         /* if there is a gap in the target, start a new alignment block*/
         if (tPtr[0][j] != '-')
             nextStart++;
         }
     assert(cs!=NULL);
     end = start+size;
     if (end > cs->totalSize)
 	{
         if (cs->name != NULL)
             errAbort("End %d past end %ld of %f\n", end, (long)cs->totalSize, ali->score);
         else
             {
             if (ali!=NULL)
                 errAbort("End %d past end %ld %f\n", end, (long)cs->totalSize, ali->score );
             else
                 errAbort("End %d past end %ld \n", end, (long)cs->totalSize);
             }
 	}
     incNoOverflow(align+start, size-1);
     cs->totalDepth += size-1;
 
     /* count percent id */
     idSize = 0;
     assert(cs != NULL);
     for (k = 0 ; k<ali->textSize ; k++)
         {
 	hit = TRUE;
         char tc = toupper(tPtr[0][k]);
         for (i = 1 ; i < cCount ; i++)
             {
             if (toupper(tPtr[i][k]) != tc || tc == '-' || tc == 'N')
                 {
                 incNoOverflow(id+idStart, idSize);
                 idStart = idNextStart;
                 idSize = 0;
                 hit = FALSE;
                 break;
                 }
             }
         if (hit)
             idSize++;
         /* skip over gaps */
         if (tc != '-')
             idNextStart++;
         }
     assert(cs!=NULL);
     idEnd = idStart+idSize;
     if (idEnd > cs->totalSize)
 	{
         if (cs->name != NULL)
             errAbort("End %d past end %ld of %f\n", idEnd, (long)cs->totalSize, ali->score);
         else
             {
             if (ali!=NULL)
                 errAbort("End %d past end %ld %f\n", idEnd, (long)cs->totalSize, ali->score );
             else
                 errAbort("End %d past end %ld \n", idEnd, (long)cs->totalSize);
             }
 	}
     incNoOverflow(id+idStart, idSize-1);
     mafAliFree(&ali);
     }
 closeChromCov(fileName, cs, &cov, &align, &id);
 }
 
 struct chromSizes *genoSize(struct chromSizes *chromSizes)
 /* Sum up all chromSizes and return result. */
 {
 struct chromSizes *cs, *g;
 int i;
 AllocVar(g);
 g->name = "all";
 for (cs = chromSizes; cs != NULL; cs = cs->next)
     {
     g->unrestrictedSize += cs->unrestrictedSize;
     g->seqSize += cs->seqSize;
     g->totalSize += cs->totalSize;
     g->totalDepth += cs->totalDepth;
     g->totalCov += cs->totalCov;
     g->totalAlign += cs->totalAlign;
     g->totalId += cs->totalId;
     for (i=0; i<=maxDepth; ++i)
         g->histogram[i] += cs->histogram[i];
     }
 return g;
 }
 
 void mafCoverage(char *database, char *mafFile, char *restrictFile, int spCount)
 /* mafCoverage - Analyse coverage by maf files - chromosome by 
  * chromosome and genome-wide.. */
 {
 struct chromSizes *cs, *csList = NULL;
 struct hash *chromHash = NULL;
 struct chromSizes *genome;
 
 getChromSizes(database, &chromHash, &csList);
 if (restrictFile != NULL)
     addRestrictions(chromHash, restrictFile);
 scanMaf(database, mafFile, chromHash, restrictFile != NULL, spCount);
 genome = genoSize(csList);
 showStats(genome);
 
 printf("\n");
 shortStats(genome);
 for (cs = csList; cs != NULL; cs = cs->next)
     shortStats(cs);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 pushCarefulMemHandler(950000000);
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 mafCoverage(argv[1], argv[2], optionVal("restrict", NULL), optionInt("count",DEFCOUNT));
 return 0;
 }