0df623bc76a0c81c38aed0ea9945808a605935b6
kate
  Thu May 18 17:01:41 2017 -0700
Protect against bad barChart files (where #expScores doesn't match expCount. refs #18736

diff --git src/hg/lib/barChartBed.c src/hg/lib/barChartBed.c
index 9784bc0..380400c 100644
--- src/hg/lib/barChartBed.c
+++ src/hg/lib/barChartBed.c
@@ -1,68 +1,71 @@
 /* barChartBed.c was originally generated by the autoSql program, which also 
  * generated barChartBed.h and barChartBed.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 "barChartBed.h"
 
 
 
 char *barChartBedCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,name2,expCount,expScores,_dataOffset,_dataLen";
 
+#ifdef NOT_SAFE
 struct barChartBed *barChartBedLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all barChartBed 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 barChartBedFreeList(). */
 {
 struct barChartBed *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = barChartBedLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
+#endif
 
 void barChartBedSaveToDb(struct sqlConnection *conn, struct barChartBed *el, char *tableName, int updateSize)
 /* Save barChartBed 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. This function automatically escapes quoted strings for mysql. */
 {
 struct dyString *update = newDyString(updateSize);
 char  *expScoresArray;
 expScoresArray = sqlFloatArrayToString(el->expScores, el->expCount);
 sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s',%u,'%s',%lld,%d)", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->name2,  el->expCount,  expScoresArray ,  el->_dataOffset,  el->_dataLen);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 freez(&expScoresArray);
 }
 
+#ifdef NOT_SAFE
 struct barChartBed *barChartBedLoad(char **row)
 /* Load a barChartBed from row fetched with select * from barChartBed
  * from database.  Dispose of this with barChartBedFree(). */
 {
 struct barChartBed *ret;
 
 AllocVar(ret);
 ret->expCount = sqlUnsigned(row[7]);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->name2 = cloneString(row[6]);
@@ -100,30 +103,32 @@
 {
 struct barChartBed *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[11];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = barChartBedLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
+#endif
+
 struct barChartBed *barChartBedCommaIn(char **pS, struct barChartBed *ret)
 /* Create a barChartBed out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new barChartBed */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
@@ -274,79 +279,84 @@
 struct bed *barChartSimpleBedLoad(char **row)
 /* Load a bed from row containing barChart bed fields. 
  * This reuses autoSql barChartBedLoad, but with a full-size bed.
  Dispose of this with bedFree() */
 {
 struct bed *ret;
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 // name2 is in row[6]
 ret->expCount = sqlUnsigned(row[7]);
-{
 int sizeOne;
 sqlFloatDynamicArray(row[8], &ret->expScores, &sizeOne);
-assert(sizeOne == ret->expCount);
+if (sizeOne != ret->expCount)
+    {
+    warn("expScores mismatch");
+    return NULL;
     }
 return ret;
 }
 
 struct barChartBed *barChartBedLoadOptionalOffsets(char **row, boolean hasOffsets)
 /* Load a barChartBed from row fetched with select * from barChartBed
  * from database or file.  Also supports schema lacking file offet and length for details.
 .  Dispose of this with barChartBedFree(). */
 {
 struct barChartBed *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->name2 = cloneString(row[6]);
 ret->expCount = sqlUnsigned(row[7]);
-{
 int sizeOne;
 sqlFloatDynamicArray(row[8], &ret->expScores, &sizeOne);
-assert(sizeOne == ret->expCount);
+if (sizeOne != ret->expCount)
+    {
+    warn("expScores mismatch");
+    return NULL;
     }
 if (hasOffsets)
     {
     ret->_dataOffset = sqlLongLong(row[9]);
     ret->_dataLen = sqlSigned(row[10]);
     }
 return ret;
 }
 
 float barChartTotalValue(struct barChartBed *bed)
 /* Return total of all category values */
 {
 int i;
 float sum = 0.0;
 for (i=0; i<bed->expCount; i++)
     sum += bed->expScores[i];
 return sum;
 }
 
 float barChartMaxValue(struct barChartBed *bed, int *categIdRet)
 /* Return value and id of category with highest value for this item */
 {
 int i;
 float maxScore = 0.0;
-assert(categIdRet);
+if (!categIdRet)
+    return maxScore;
 for (i=0; i<bed->expCount; i++)
     {
     float score = bed->expScores[i];
     if (score > maxScore)
         {
         maxScore = score;
         *categIdRet = i;
         }
     }
 return maxScore;
 }