080a160c7b9595d516c9c70e83689a09b60839d0
galt
  Mon Jun 3 12:16:53 2013 -0700
fix SQL Injection
diff --git src/hg/lib/affyTranscriptome.c src/hg/lib/affyTranscriptome.c
index d8009e2..aca35e6 100644
--- src/hg/lib/affyTranscriptome.c
+++ src/hg/lib/affyTranscriptome.c
@@ -1,238 +1,208 @@
 /* affyTranscriptome.c was originally generated by the autoSql program, which also 
  * generated affyTranscriptome.h and affyTranscriptome.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 "affyTranscriptome.h"
 
 
 void affyTranscriptomeStaticLoad(char **row, struct affyTranscriptome *ret)
 /* Load a row from affyTranscriptome table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 int sizeOne,i;
 char *s;
 
 ret->chrom = row[0];
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = row[3];
 ret->score = sqlUnsigned(row[4]);
 strcpy(ret->strand, row[5]);
 ret->sampleCount = sqlUnsigned(row[6]);
 ret->samplePosition = row[7];
 ret->sampleHeight = row[8];
 }
 
 struct affyTranscriptome *affyTranscriptomeLoad(char **row)
 /* Load a affyTranscriptome from row fetched with select * from affyTranscriptome
  * from database.  Dispose of this with affyTranscriptomeFree(). */
 {
 struct affyTranscriptome *ret;
 int sizeOne,i;
 char *s;
 
 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]);
 strcpy(ret->strand, row[5]);
 ret->sampleCount = sqlUnsigned(row[6]);
 ret->samplePosition = cloneString(row[7]);
 ret->sampleHeight = cloneString(row[8]);
 return ret;
 }
 
 struct affyTranscriptome *affyTranscriptomeLoadAll(char *fileName) 
 /* Load all affyTranscriptome from a whitespace-separated file.
  * Dispose of this with affyTranscriptomeFreeList(). */
 {
 struct affyTranscriptome *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[9];
 
 while (lineFileRow(lf, row))
     {
     el = affyTranscriptomeLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct affyTranscriptome *affyTranscriptomeLoadAllByChar(char *fileName, char chopper) 
 /* Load all affyTranscriptome from a chopper separated file.
  * Dispose of this with affyTranscriptomeFreeList(). */
 {
 struct affyTranscriptome *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[9];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = affyTranscriptomeLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct affyTranscriptome *affyTranscriptomeLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all affyTranscriptome 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 affyTranscriptomeFreeList(). */
 {
 struct affyTranscriptome *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = affyTranscriptomeLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void affyTranscriptomeSaveToDb(struct sqlConnection *conn, struct affyTranscriptome *el, char *tableName, int updateSize)
 /* Save affyTranscriptome 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 affyTranscriptomeSaveToDbEscaped() */
+ * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
 {
 struct dyString *update = newDyString(updateSize);
-dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s',%u,%s,%s)", 
+sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s',%u,%s,%s)", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->sampleCount,  el->samplePosition,  el->sampleHeight);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
-void affyTranscriptomeSaveToDbEscaped(struct sqlConnection *conn, struct affyTranscriptome *el, char *tableName, int updateSize)
-/* Save affyTranscriptome 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 affyTranscriptomeSaveToDb().
- * For example automatically copies and converts: 
- * "autosql's features include" --> "autosql\'s features include" 
- * before inserting into database. */ 
-{
-struct dyString *update = newDyString(updateSize);
-char  *chrom, *name, *strand, *samplePosition, *sampleHeight;
-chrom = sqlEscapeString(el->chrom);
-name = sqlEscapeString(el->name);
-strand = sqlEscapeString(el->strand);
-samplePosition = sqlEscapeString(el->samplePosition);
-sampleHeight = sqlEscapeString(el->sampleHeight);
-
-dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s',%u,'%s','%s')", 
-	tableName,  chrom, el->chromStart , el->chromEnd ,  name, el->score ,  strand, el->sampleCount ,  samplePosition,  sampleHeight);
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-freez(&chrom);
-freez(&name);
-freez(&strand);
-freez(&samplePosition);
-freez(&sampleHeight);
-}
-
 struct affyTranscriptome *affyTranscriptomeCommaIn(char **pS, struct affyTranscriptome *ret)
 /* Create a affyTranscriptome out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new affyTranscriptome */
 {
 char *s = *pS;
 int i;
 
 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));
 ret->sampleCount = sqlUnsignedComma(&s);
 ret->samplePosition = sqlStringComma(&s);
 ret->sampleHeight = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void affyTranscriptomeFree(struct affyTranscriptome **pEl)
 /* Free a single dynamically allocated affyTranscriptome such as created
  * with affyTranscriptomeLoad(). */
 {
 struct affyTranscriptome *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->samplePosition);
 freeMem(el->sampleHeight);
 freez(pEl);
 }
 
 void affyTranscriptomeFreeList(struct affyTranscriptome **pList)
 /* Free a list of dynamically allocated affyTranscriptome's */
 {
 struct affyTranscriptome *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     affyTranscriptomeFree(&el);
     }
 *pList = NULL;
 }
 
 void affyTranscriptomeOutput(struct affyTranscriptome *el, FILE *f, char sep, char lastSep) 
 /* Print out affyTranscriptome.  Separate fields with sep. Follow last field with lastSep. */
 {
 int i;
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->sampleCount);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->samplePosition);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->sampleHeight);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */