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/lib/altGraph.c src/hg/lib/altGraph.c
index ebf19cd..aedded0 100644
--- src/hg/lib/altGraph.c
+++ src/hg/lib/altGraph.c
@@ -1,337 +1,337 @@
 /* altGraph.c was originally generated by the autoSql program, which also 
  * generated altGraph.h and altGraph.sql.  This module links the database and
  * the RAM representation of objects. */
 
 /* Copyright (C) 2014 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 "dystring.h"
 #include "jksql.h"
 #include "altGraph.h"
 #include "geneGraph.h"
 
 
 struct altGraph *altGraphLoad(char **row)
 /* Load a altGraph from row fetched with select * from altGraph
  * from database.  Dispose of this with altGraphFree(). */
 {
 struct altGraph *ret;
 int sizeOne;
 
 AllocVar(ret);
 ret->vertexCount = sqlUnsigned(row[5]);
 ret->edgeCount = sqlUnsigned(row[8]);
 ret->mrnaRefCount = sqlSigned(row[11]);
 ret->id = sqlUnsigned(row[0]);
 ret->tName = cloneString(row[1]);
 ret->tStart = sqlSigned(row[2]);
 ret->tEnd = sqlSigned(row[3]);
 strcpy(ret->strand, row[4]);
 sqlUbyteDynamicArray(row[6], &ret->vTypes, &sizeOne);
 assert(sizeOne == ret->vertexCount);
 sqlSignedDynamicArray(row[7], &ret->vPositions, &sizeOne);
 assert(sizeOne == ret->vertexCount);
 sqlSignedDynamicArray(row[9], &ret->edgeStarts, &sizeOne);
 assert(sizeOne == ret->edgeCount);
 sqlSignedDynamicArray(row[10], &ret->edgeEnds, &sizeOne);
 assert(sizeOne == ret->edgeCount);
 sqlStringDynamicArray(row[12], &ret->mrnaRefs, &sizeOne);
 assert(sizeOne == ret->mrnaRefCount);
 return ret;
 }
 
 struct altGraph *altGraphLoadAll(char *fileName) 
 /* Load all altGraph from a tab-separated file.
  * Dispose of this with altGraphFreeList(). */
 {
 struct altGraph *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[13];
 
 while (lineFileRow(lf, row))
     {
     el = altGraphLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct altGraph *altGraphLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all altGraph from table that satisfy the query given.  
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something = 
  * anotherTable.something'.
  * Dispose of this with altGraphFreeList(). */
 {
 struct altGraph *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = altGraphLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void altGraphSaveToDb(struct sqlConnection *conn, struct altGraph *el, char *tableName, int updateSize)
 /* Save altGraph as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
 {
-struct dyString *update = newDyString(updateSize);
+struct dyString *update = dyStringNew(updateSize);
 char  *vTypesArray, *vPositionsArray, *edgeStartsArray, *edgeEndsArray, *mrnaRefsArray;
 vTypesArray = sqlUbyteArrayToString(el->vTypes, el->vertexCount);
 vPositionsArray = sqlSignedArrayToString(el->vPositions, el->vertexCount);
 edgeStartsArray = sqlSignedArrayToString(el->edgeStarts, el->edgeCount);
 edgeEndsArray = sqlSignedArrayToString(el->edgeEnds, el->edgeCount);
 mrnaRefsArray = sqlStringArrayToString(el->mrnaRefs, el->mrnaRefCount);
 sqlDyStringPrintf(update, "insert into %s values ( %u,'%s',%d,%d,'%s',%u,'%s','%s',%u,'%s','%s',%d,'%s')", 
 	tableName,  el->id,  el->tName,  el->tStart,  el->tEnd,  el->strand,  el->vertexCount,  vTypesArray ,  vPositionsArray ,  el->edgeCount,  edgeStartsArray ,  edgeEndsArray ,  el->mrnaRefCount,  mrnaRefsArray );
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 freez(&vTypesArray);
 freez(&vPositionsArray);
 freez(&edgeStartsArray);
 freez(&edgeEndsArray);
 freez(&mrnaRefsArray);
 }
 
 
 struct altGraph *altGraphCommaIn(char **pS, struct altGraph *ret)
 /* Create a altGraph out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new altGraph */
 {
 char *s = *pS;
 int i;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->id = sqlUnsignedComma(&s);
 ret->tName = sqlStringComma(&s);
 ret->tStart = sqlSignedComma(&s);
 ret->tEnd = sqlSignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->vertexCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->vTypes, ret->vertexCount);
 for (i=0; i<ret->vertexCount; ++i)
     {
     ret->vTypes[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->vPositions, ret->vertexCount);
 for (i=0; i<ret->vertexCount; ++i)
     {
     ret->vPositions[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->edgeCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->edgeStarts, ret->edgeCount);
 for (i=0; i<ret->edgeCount; ++i)
     {
     ret->edgeStarts[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->edgeEnds, ret->edgeCount);
 for (i=0; i<ret->edgeCount; ++i)
     {
     ret->edgeEnds[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->mrnaRefCount = sqlSignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->mrnaRefs, ret->mrnaRefCount);
 for (i=0; i<ret->mrnaRefCount; ++i)
     {
     ret->mrnaRefs[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 *pS = s;
 return ret;
 }
 
 void altGraphFree(struct altGraph **pEl)
 /* Free a single dynamically allocated altGraph such as created
  * with altGraphLoad(). */
 {
 struct altGraph *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->tName);
 freeMem(el->vTypes);
 freeMem(el->vPositions);
 freeMem(el->edgeStarts);
 freeMem(el->edgeEnds);
 /* All strings in mrnaRefs are allocated at once, so only need to free first. */
 if (el->mrnaRefs != NULL)
     freeMem(el->mrnaRefs[0]);
 freeMem(el->mrnaRefs);
 freez(pEl);
 }
 
 void altGraphFreeList(struct altGraph **pList)
 /* Free a list of dynamically allocated altGraph's */
 {
 struct altGraph *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     altGraphFree(&el);
     }
 *pList = NULL;
 }
 
 void altGraphOutput(struct altGraph *el, FILE *f, char sep, char lastSep) 
 /* Print out altGraph.  Separate fields with sep. Follow last field with lastSep. */
 {
 int i;
 fprintf(f, "%u", el->id);
 fputc(sep,f);
 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->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->vertexCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->vertexCount; ++i)
     {
     fprintf(f, "%u", el->vTypes[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->vertexCount; ++i)
     {
     fprintf(f, "%d", el->vPositions[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%u", el->edgeCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->edgeCount; ++i)
     {
     fprintf(f, "%d", el->edgeStarts[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->edgeCount; ++i)
     {
     fprintf(f, "%d", el->edgeEnds[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%d", el->mrnaRefCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->mrnaRefCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->mrnaRefs[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 
 static boolean isEndVertice(bool **em, int vertexCount, int vertice, 
 	unsigned char *vTypes)
 /* check to see if there are any edges coming out of this vertice */
 {
 int i;
 for(i=0; i<vertexCount; i++)
     {
     if(em[vertice][i] && (vTypes[i] != ggUnused))
 	return FALSE;
     }
 return TRUE;
 }
 
 void countPathsFromVertice(bool **em, unsigned char *vTypes, int vertexCount, int vertice, int *pathCount)
 /* recursively count paths from vertice */
 {
 int i=0;
 /* check for termination */
 if( isEndVertice(em, vertexCount, vertice, vTypes))
     {
     (*pathCount)++;
     }
 else
     {
     /* recursively call for all vertices that are connected to from this vertex */
     for(i = 0; i < vertexCount; i++)
 	{
 	if(em[vertice][i] && vTypes[i] != ggUnused)
 	    {
 	    countPathsFromVertice(em, vTypes, vertexCount, i, pathCount);
 	    }
 	}
     }
 }
 
 int altGraphNumAltSplices(struct altGraph *ag)
 /* Count number of times that exons have more than one edge through them */
 {
 int pathCount=0;
 int i=0;
 int vertexCount = ag->vertexCount;
 bool **em;
 
 /* construct the edge matrix */
 AllocArray(em, vertexCount);
 for (i=0; i<vertexCount; ++i)
     {
     AllocArray(em[i], vertexCount);
     }
 for (i=0; i<ag->edgeCount; ++i)
     em[ag->edgeStarts[i]][ag->edgeEnds[i]] = TRUE;
 
 /* recursively count all possible paths */
 countPathsFromVertice(em, ag->vTypes, vertexCount, 0, &pathCount);
 
 /* clean up */
 for(i = 0; i < vertexCount; i++)
     freez(&em[i]);
 freez(&em);
 
 return pathCount;
 }