080a160c7b9595d516c9c70e83689a09b60839d0
galt
  Mon Jun 3 12:16:53 2013 -0700
fix SQL Injection
diff --git src/hg/lib/altGraphX.c src/hg/lib/altGraphX.c
index 8362dac..3dc7c4f 100644
--- src/hg/lib/altGraphX.c
+++ src/hg/lib/altGraphX.c
@@ -160,97 +160,56 @@
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = altGraphXLoad(row+offSet);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void altGraphXSaveToDb(struct sqlConnection *conn, struct altGraphX *el, char *tableName, int updateSize)
 /* Save altGraphX 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. Note that strings must be escaped to allow insertion into the database.
- * For example "autosql's features include" --> "autosql\'s features include" 
- * If worried about this use altGraphXSaveToDbEscaped() */
+ * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
 {
 struct dyString *update = newDyString(updateSize);
 char  *vTypesArray, *vPositionsArray, *edgeStartsArray, *edgeEndsArray, *edgeTypesArray, *mrnaRefsArray, *mrnaTissuesArray, *mrnaLibsArray;
 vTypesArray = sqlUbyteArrayToString(el->vTypes, el->vertexCount);
 vPositionsArray = sqlSignedArrayToString(el->vPositions, el->vertexCount);
 edgeStartsArray = sqlSignedArrayToString(el->edgeStarts, el->edgeCount);
 edgeEndsArray = sqlSignedArrayToString(el->edgeEnds, el->edgeCount);
 edgeTypesArray = sqlSignedArrayToString(el->edgeTypes, el->edgeCount);
 mrnaRefsArray = sqlStringArrayToString(el->mrnaRefs, el->mrnaRefCount);
 mrnaTissuesArray = sqlSignedArrayToString(el->mrnaTissues, el->mrnaRefCount);
 mrnaLibsArray = sqlSignedArrayToString(el->mrnaLibs, el->mrnaRefCount);
-dyStringPrintf(update, "insert into %s values ( '%s',%d,%d,'%s',%u,'%s',%u,'%s','%s',%u,'%s','%s', NULL ,'%s',%d,'%s','%s','%s')", 
+sqlDyStringPrintf(update, "insert into %s values ( '%s',%d,%d,'%s',%u,'%s',%u,'%s','%s',%u,'%s','%s', NULL ,'%s',%d,'%s','%s','%s')", 
 	tableName,  el->tName,  el->tStart,  el->tEnd,  el->name,  el->id,  el->strand,  el->vertexCount,  vTypesArray ,  vPositionsArray ,  el->edgeCount,  edgeStartsArray ,  edgeEndsArray ,  edgeTypesArray ,  el->mrnaRefCount,  mrnaRefsArray ,  mrnaTissuesArray ,  mrnaLibsArray );
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 freez(&vTypesArray);
 freez(&vPositionsArray);
 freez(&edgeStartsArray);
 freez(&edgeEndsArray);
 freez(&edgeTypesArray);
 freez(&mrnaRefsArray);
 freez(&mrnaTissuesArray);
 freez(&mrnaLibsArray);
 }
 
-void altGraphXSaveToDbEscaped(struct sqlConnection *conn, struct altGraphX *el, char *tableName, int updateSize)
-/* Save altGraphX 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. Automatically 
- * escapes all simple strings (not arrays of string) but may be slower than altGraphXSaveToDb().
- * For example automatically copies and converts: 
- * "autosql's features include" --> "autosql\'s features include" 
- * before inserting into database. */ 
-{
-struct dyString *update = newDyString(updateSize);
-char  *tName, *name, *strand, *vTypesArray, *vPositionsArray, *edgeStartsArray, *edgeEndsArray, *edgeTypesArray, *mrnaRefsArray, *mrnaTissuesArray, *mrnaLibsArray;
-tName = sqlEscapeString(el->tName);
-name = sqlEscapeString(el->name);
-strand = sqlEscapeString(el->strand);
-
-vTypesArray = sqlUbyteArrayToString(el->vTypes, el->vertexCount);
-vPositionsArray = sqlSignedArrayToString(el->vPositions, el->vertexCount);
-edgeStartsArray = sqlSignedArrayToString(el->edgeStarts, el->edgeCount);
-edgeEndsArray = sqlSignedArrayToString(el->edgeEnds, el->edgeCount);
-edgeTypesArray = sqlSignedArrayToString(el->edgeTypes, el->edgeCount);
-mrnaRefsArray = sqlStringArrayToString(el->mrnaRefs, el->mrnaRefCount);
-mrnaTissuesArray = sqlSignedArrayToString(el->mrnaTissues, el->mrnaRefCount);
-mrnaLibsArray = sqlSignedArrayToString(el->mrnaLibs, el->mrnaRefCount);
-dyStringPrintf(update, "insert into %s values ( '%s',%d,%d,'%s',%u,'%s',%u,'%s','%s',%u,'%s','%s', NULL ,'%s',%d,'%s','%s','%s')", 
-	tableName,  tName, el->tStart , el->tEnd ,  name, el->id ,  strand, el->vertexCount ,  vTypesArray ,  vPositionsArray , el->edgeCount ,  edgeStartsArray ,  edgeEndsArray ,  edgeTypesArray , el->mrnaRefCount ,  mrnaRefsArray ,  mrnaTissuesArray ,  mrnaLibsArray );
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-freez(&tName);
-freez(&name);
-freez(&strand);
-freez(&vTypesArray);
-freez(&vPositionsArray);
-freez(&edgeStartsArray);
-freez(&edgeEndsArray);
-freez(&edgeTypesArray);
-freez(&mrnaRefsArray);
-freez(&mrnaTissuesArray);
-freez(&mrnaLibsArray);
-}
 
 struct altGraphX *altGraphXCommaIn(char **pS, struct altGraphX *ret)
 /* Create a altGraphX out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new altGraphX */
 {
 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);
@@ -1031,31 +990,31 @@
 {
 struct evidence *ev = slElementFromIx(ag->evidence, edge);
 return ev->evCount;
 }
 
 struct bed *createBedFromEdges( struct altGraphX *ag, int fpEdge, int cassEdge, int tpEdge)
 /* Put the edges together to from a bed structure. */
 {
 int *vPos = ag->vPositions;
 int *starts = ag->edgeStarts;
 int *ends = ag->edgeEnds;
 struct bed *bed;
 int numBlocks = 3;
 AllocVar(bed);
 bed->chrom = cloneString(ag->tName);
-snprintf(bed->strand, sizeof(bed->strand), "%s", ag->strand);
+safef(bed->strand, sizeof(bed->strand), "%s", ag->strand);
 bed->chromStart = bed->thickStart = vPos[starts[fpEdge]];
 bed->chromEnd = bed->thickEnd = vPos[ends[tpEdge]];
 bed->name = cloneString(ag->name);
 bed->blockCount = numBlocks;
 AllocArray(bed->blockSizes, numBlocks);
 AllocArray(bed->chromStarts, numBlocks);
 bed->blockSizes[0] = vPos[ends[fpEdge]] - vPos[starts[fpEdge]];
 bed->blockSizes[1] = vPos[ends[cassEdge]] - vPos[starts[cassEdge]];
 bed->blockSizes[2] = vPos[ends[tpEdge]] - vPos[starts[tpEdge]];
 bed->chromStarts[0] = vPos[starts[fpEdge]] -bed->chromStart;
 bed->chromStarts[1] = vPos[starts[cassEdge]] - bed->chromStart;
 bed->chromStarts[2] = vPos[starts[tpEdge]] -bed->chromStart;
 bed->score = getEvidenceCount(ag,fpEdge)+ getEvidenceCount(ag, tpEdge);
 
 bed->expCount = numBlocks;
@@ -1757,33 +1716,33 @@
 int width = ag->tEnd - ag->tStart;
 int *tmp = NULL;
 for(i=0; i<ag->vertexCount; i++)
     {
     ag->vPositions[i] = (width - (ag->vPositions[i] - ag->tStart)) + ag->tStart;
     if(ag->vTypes[i] == ggHardEnd)
 	ag->vTypes[i] = ggHardStart;
     else if(ag->vTypes[i] ==ggHardStart)
 	ag->vTypes[i] = ggHardEnd;
     else if(ag->vTypes[i] == ggSoftEnd)
 	ag->vTypes[i] = ggSoftStart;
     else if(ag->vTypes[i] == ggSoftStart)
 	ag->vTypes[i] = ggSoftEnd;
     }
 if(sameString(ag->strand, "+"))
-    snprintf(ag->strand, sizeof(ag->strand), "%s", "-");
+    safef(ag->strand, sizeof(ag->strand), "%s", "-");
 else if(sameString(ag->strand, "-"))
-    snprintf(ag->strand, sizeof(ag->strand), "%s", "+");
+    safef(ag->strand, sizeof(ag->strand), "%s", "+");
 else
     errAbort("altGraphX::altGraphXReverseComplement() - Don't recognize strand: %s", ag->strand);
 tmp = ag->edgeEnds;
 ag->edgeEnds = ag->edgeStarts;
 ag->edgeStarts = tmp;
 }
 
 int altGraphXGetEdgeNum(struct altGraphX *ag, int v1, int v2)
 /** Find the edge index that corresponds to v1 and v2 */
 {
 int eC = ag->edgeCount;
 int i=0;
 for(i=0;i<eC; i++)
     {
     if(ag->edgeStarts[i] == v1 && ag->edgeEnds[i] == v2)