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/altSplice/lib/splice.c src/hg/altSplice/lib/splice.c
index 38d1f8a..baaa2bf 100644
--- src/hg/altSplice/lib/splice.c
+++ src/hg/altSplice/lib/splice.c
@@ -1,416 +1,416 @@
 /* splice.c was originally generated by the autoSql program, which also 
  * generated splice.h and splice.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "splice.h"
 #include "geneGraph.h"
 #include "dystring.h"
 
 
 struct path *pathCommaIn(char **pS, struct path *ret)
 /* Create a path out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new path */
 {
 char *s = *pS;
 int i;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->tName = sqlStringComma(&s);
 ret->tStart = sqlSignedComma(&s);
 ret->tEnd = sqlSignedComma(&s);
 ret->type = sqlSignedComma(&s);
 ret->maxVCount = sqlSignedComma(&s);
 ret->vCount = sqlSignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->vertices, ret->vCount);
 for (i=0; i<ret->vCount; ++i)
     {
     ret->vertices[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->upV = sqlSignedComma(&s);
 ret->downV = sqlSignedComma(&s);
 ret->bpCount = sqlSignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void pathFree(struct path **pEl)
 /* Free a single dynamically allocated path such as created
  * with pathLoad(). */
 {
 struct path *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->tName);
 freeMem(el->vertices);
 freez(pEl);
 }
 
 void pathFreeList(struct path **pList)
 /* Free a list of dynamically allocated path's */
 {
 struct path *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     pathFree(&el);
     }
 *pList = NULL;
 }
 
 void pathOutput(struct path *el, FILE *f, char sep, char lastSep) 
 /* Print out path.  Separate fields with sep. Follow last field with lastSep. */
 {
 int i;
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->tStart);
 fputc(sep,f);
 fprintf(f, "%d", el->tEnd);
 fputc(sep,f);
 fprintf(f, "%d", el->type);
 fputc(sep,f);
 fprintf(f, "%d", el->maxVCount);
 fputc(sep,f);
 fprintf(f, "%d", el->vCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->vCount; ++i)
     {
     fprintf(f, "%d", el->vertices[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%d", el->upV);
 fputc(sep,f);
 fprintf(f, "%d", el->downV);
 fputc(sep,f);
 fprintf(f, "%d", el->bpCount);
 fputc(lastSep,f);
 }
 
 struct splice *spliceLoad(char **row)
 /* Load a splice from row fetched with select * from splice
  * from database.  Dispose of this with spliceFree(). */
 {
 struct splice *ret;
 int sizeOne,i;
 char *s;
 
 AllocVar(ret);
 ret->vCount = sqlSigned(row[7]);
 ret->pathCount = sqlSigned(row[10]);
 ret->tName = cloneString(row[0]);
 ret->tStart = sqlSigned(row[1]);
 ret->tEnd = sqlSigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->type = sqlSigned(row[4]);
 strcpy(ret->strand, row[5]);
 ret->agxId = sqlSigned(row[6]);
 sqlSignedDynamicArray(row[8], &ret->vPositions, &sizeOne);
 assert(sizeOne == ret->vCount);
 sqlUbyteDynamicArray(row[9], &ret->vTypes, &sizeOne);
 assert(sizeOne == ret->vCount);
 s = row[11];
 for (i=0; i<ret->pathCount; ++i)
     {
     s = sqlEatChar(s, '{');
     slSafeAddHead(&ret->paths, pathCommaIn(&s, NULL));
     s = sqlEatChar(s, '}');
     s = sqlEatChar(s, ',');
     }
 slReverse(&ret->paths);
 return ret;
 }
 
 struct splice *spliceLoadAll(char *fileName) 
 /* Load all splice from a whitespace-separated file.
  * Dispose of this with spliceFreeList(). */
 {
 struct splice *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileRow(lf, row))
     {
     el = spliceLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct splice *spliceLoadAllByChar(char *fileName, char chopper) 
 /* Load all splice from a chopper separated file.
  * Dispose of this with spliceFreeList(). */
 {
 struct splice *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = spliceLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct splice *spliceCommaIn(char **pS, struct splice *ret)
 /* Create a splice out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new splice */
 {
 char *s = *pS;
 int i;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->tName = sqlStringComma(&s);
 ret->tStart = sqlSignedComma(&s);
 ret->tEnd = sqlSignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->type = sqlSignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->agxId = sqlSignedComma(&s);
 ret->vCount = sqlSignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->vPositions, ret->vCount);
 for (i=0; i<ret->vCount; ++i)
     {
     ret->vPositions[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->vTypes, ret->vCount);
 for (i=0; i<ret->vCount; ++i)
     {
     ret->vTypes[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->pathCount = sqlSignedComma(&s);
 s = sqlEatChar(s, '{');
 for (i=0; i<ret->pathCount; ++i)
     {
     s = sqlEatChar(s, '{');
     if(s[0] != '}')        slSafeAddHead(&ret->paths, pathCommaIn(&s,NULL));
     s = sqlEatChar(s, '}');
     s = sqlEatChar(s, ',');
     }
 slReverse(&ret->paths);
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 *pS = s;
 return ret;
 }
 
 void spliceFree(struct splice **pEl)
 /* Free a single dynamically allocated splice such as created
  * with spliceLoad(). */
 {
 struct splice *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->tName);
 freeMem(el->name);
 freeMem(el->vPositions);
 freeMem(el->vTypes);
 pathFreeList(&el->paths);
 freez(pEl);
 }
 
 void spliceFreeList(struct splice **pList)
 /* Free a list of dynamically allocated splice's */
 {
 struct splice *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     spliceFree(&el);
     }
 *pList = NULL;
 }
 
 void spliceOutput(struct splice *el, FILE *f, char sep, char lastSep) 
 /* Print out splice.  Separate fields with sep. Follow last field with lastSep. */
 {
 int i;
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->tStart);
 fputc(sep,f);
 fprintf(f, "%d", el->tEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->type);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->agxId);
 fputc(sep,f);
 fprintf(f, "%d", el->vCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->vCount; ++i)
     {
     fprintf(f, "%d", el->vPositions[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->vCount; ++i)
     {
     fprintf(f, "%u", el->vTypes[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%d", el->pathCount);
 fputc(sep,f);
 /* Loading path list. */
     {
     struct path *it = el->paths;
     if (sep == ',') fputc('{',f);
     for (i=0; i<el->pathCount; ++i)
         {
         fputc('{',f);
         pathCommaOut(it,f);
         it = it->next;
         fputc('}',f);
         fputc(',',f);
         }
     if (sep == ',') fputc('}',f);
     }
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 enum ggEdgeType pathEdgeType(unsigned char *vTypes, int v1, int v2)
 /* Return edge type. */
 {
 if( (vTypes[v1] == ggHardStart || vTypes[v1] == ggSoftStart)  
     && (vTypes[v2] == ggHardEnd || vTypes[v2] == ggSoftEnd)) 
     return ggExon;
 else if( (vTypes[v1] == ggHardEnd || vTypes[v1] == ggSoftEnd)  
 	 && (vTypes[v2] == ggHardStart || vTypes[v2] == ggSoftStart)) 
     return ggSJ;
 else
     return ggIntron;
 }
 
 struct bed *pathToBed(struct path *path, struct splice *splice,
 		      int source, int sink, boolean spoofEnds)
 /* Construct a bed for the path. If spoofEnds is TRUE,
    ensure that there is at least a 1bp exon at splice
    sites. */
 {
 struct bed *bed = NULL;
 int vertIx = 0;
 int *verts = path->vertices;
 int *vPos = splice->vPositions;
 unsigned char *vTypes = splice->vTypes;
 int i = 0;
-struct dyString *buff = newDyString(256);
+struct dyString *buff = dyStringNew(256);
 
 AllocVar(bed);
 bed->chrom = cloneString(splice->tName);
 bed->chromStart = BIGNUM;
 bed->chromEnd = 0;
 safef(bed->strand, sizeof(bed->strand), "%s", splice->strand);
 bed->score = splice->type;
 AllocArray(bed->chromStarts, path->vCount);
 AllocArray(bed->blockSizes, path->vCount);
 
 /* If necessary tack on a fake exon. */
 if(spoofEnds && verts[vertIx] != source && verts[vertIx+1] <= splice->vCount &&
    pathEdgeType(vTypes, verts[vertIx], verts[vertIx+1]) != ggExon)
     {
     bed->blockSizes[bed->blockCount] = 1;
     bed->chromStarts[bed->blockCount] = vPos[verts[vertIx]] - 1;
     bed->chromStart = bed->thickStart = min(bed->chromStart, vPos[verts[vertIx]] - 1 );
     bed->chromEnd = bed->thickEnd = max(bed->chromEnd, vPos[verts[vertIx+1]]);
     bed->blockCount++;
     }
 
 /* For each edge that is an exon count up the base pairs. */
 for(vertIx = 0; vertIx < path->vCount - 1; vertIx++)
     {
     if(verts[vertIx] != source && verts[vertIx] <= splice->vCount)
 	{
 	/* If exon add up the base pairs. */
 	if(pathEdgeType(vTypes, verts[vertIx], verts[vertIx+1]) == ggExon)
 	    {
 	    bed->blockSizes[bed->blockCount] = vPos[verts[vertIx+1]] - vPos[verts[vertIx]];
 	    bed->chromStarts[bed->blockCount] = vPos[verts[vertIx]];
 	    bed->chromStart = bed->thickStart = min(bed->chromStart, vPos[verts[vertIx]]);
 	    bed->chromEnd = bed->thickEnd = max(bed->chromEnd, vPos[verts[vertIx+1]]);
 	    bed->blockCount++;
 	    }
 	}
     }
 
 /* if spoofing ends tack on a 1bp exon as necessary. */
 vertIx = path->vCount - 2;
 if(spoofEnds && verts[vertIx] != source && verts[vertIx+1] <= splice->vCount &&
    pathEdgeType(vTypes, verts[vertIx], verts[vertIx+1]) != ggExon)
     {
     bed->blockSizes[bed->blockCount] = 1;
     bed->chromStarts[bed->blockCount] = vPos[verts[vertIx+1]];
     bed->chromStart = bed->thickStart = min(bed->chromStart, vPos[verts[vertIx+1]]);
     bed->chromEnd = bed->thickEnd = max(bed->chromEnd, vPos[verts[vertIx+1]]+1);
     bed->blockCount++;
     }
 
 /* Fix up the name and adjust the chromStarts. */
 dyStringPrintf(buff, "%s.%d.", splice->name, slIxFromElement(splice->paths, path));
 for(i = 0; i < path->vCount; i++)
     {
     if(path->vertices[i] != sink && path->vertices[i] <= splice->vCount)
 	dyStringPrintf(buff, "%d,", path->vertices[i]);
     }
 if(splice->type == alt5Prime || splice->type == alt3Prime ||
    splice->type == altRetInt || splice->type == altCassette)
     {
     int pathIx = slIxFromElement(splice->paths, path);
     if(pathIx == 0)
 	dyStringPrintf(buff, "-Ex");
     else if(pathIx == 1)
 	dyStringPrintf(buff, "-Inc");
     }
 bed->name = cloneString(buff->string);
 for(i = 0; i < bed->blockCount; i++)
     bed->chromStarts[i] -= bed->chromStart;
 
 /* If we don't have any blocks, quit now. */
 if(bed->blockCount == 0)
     bedFree(&bed);
 dyStringFree(&buff);
 return bed;
 }