080a160c7b9595d516c9c70e83689a09b60839d0
galt
  Mon Jun 3 12:16:53 2013 -0700
fix SQL Injection
diff --git src/hg/lib/dbRIP.c src/hg/lib/dbRIP.c
index 0163be6..8ce2fe6 100644
--- src/hg/lib/dbRIP.c
+++ src/hg/lib/dbRIP.c
@@ -1,352 +1,301 @@
 /* dbRIP.c was originally generated by the autoSql program, which also 
  * generated dbRIP.h and dbRIP.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 "dbRIP.h"
 
 
 void dbRIPStaticLoad(char **row, struct dbRIP *ret)
 /* Load a row from dbRIP table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 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->originalId = row[6];
 ret->forwardPrimer = row[7];
 ret->reversePrimer = row[8];
 ret->polyClass = row[9];
 ret->polyFamily = row[10];
 ret->polySubfamily = row[11];
 ret->polySeq = row[12];
 ret->polySource = row[13];
 ret->reference = row[14];
 ret->ascertainingMethod = row[15];
 ret->remarks = row[16];
 ret->tm = atof(row[17]);
 ret->filledSize = sqlSigned(row[18]);
 ret->emptySize = sqlSigned(row[19]);
 ret->disease = row[20];
 ret->genoRegion = row[21];
 }
 
 struct dbRIP *dbRIPLoad(char **row)
 /* Load a dbRIP from row fetched with select * from dbRIP
  * from database.  Dispose of this with dbRIPFree(). */
 {
 struct dbRIP *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]);
 strcpy(ret->strand, row[5]);
 ret->originalId = cloneString(row[6]);
 ret->forwardPrimer = cloneString(row[7]);
 ret->reversePrimer = cloneString(row[8]);
 ret->polyClass = cloneString(row[9]);
 ret->polyFamily = cloneString(row[10]);
 ret->polySubfamily = cloneString(row[11]);
 ret->polySeq = cloneString(row[12]);
 ret->polySource = cloneString(row[13]);
 ret->reference = cloneString(row[14]);
 ret->ascertainingMethod = cloneString(row[15]);
 ret->remarks = cloneString(row[16]);
 ret->tm = atof(row[17]);
 ret->filledSize = sqlSigned(row[18]);
 ret->emptySize = sqlSigned(row[19]);
 ret->disease = cloneString(row[20]);
 ret->genoRegion = cloneString(row[21]);
 return ret;
 }
 
 struct dbRIP *dbRIPLoadAll(char *fileName) 
 /* Load all dbRIP from a whitespace-separated file.
  * Dispose of this with dbRIPFreeList(). */
 {
 struct dbRIP *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[22];
 
 while (lineFileRow(lf, row))
     {
     el = dbRIPLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct dbRIP *dbRIPLoadAllByChar(char *fileName, char chopper) 
 /* Load all dbRIP from a chopper separated file.
  * Dispose of this with dbRIPFreeList(). */
 {
 struct dbRIP *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[22];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = dbRIPLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct dbRIP *dbRIPLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all dbRIP 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 dbRIPFreeList(). */
 {
 struct dbRIP *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = dbRIPLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void dbRIPSaveToDb(struct sqlConnection *conn, struct dbRIP *el, char *tableName, int updateSize)
 /* Save dbRIP 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 dbRIPSaveToDbEscaped() */
+ * 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','%s','%s','%s','%s','%s','%s',%s,'%s',%s,'%s','%s',%g,%d,%d,'%s','%s')", 
+sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s','%s','%s','%s','%s','%s',%s,'%s',%s,'%s','%s',%g,%d,%d,'%s','%s')", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->originalId,  el->forwardPrimer,  el->reversePrimer,  el->polyClass,  el->polyFamily,  el->polySubfamily,  el->polySeq,  el->polySource,  el->reference,  el->ascertainingMethod,  el->remarks,  el->tm,  el->filledSize,  el->emptySize,  el->disease,  el->genoRegion);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
-void dbRIPSaveToDbEscaped(struct sqlConnection *conn, struct dbRIP *el, char *tableName, int updateSize)
-/* Save dbRIP 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 dbRIPSaveToDb().
- * 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, *originalId, *forwardPrimer, *reversePrimer, *polyClass, *polyFamily, *polySubfamily, *polySeq, *polySource, *reference, *ascertainingMethod, *remarks, *disease, *genoRegion;
-chrom = sqlEscapeString(el->chrom);
-name = sqlEscapeString(el->name);
-strand = sqlEscapeString(el->strand);
-originalId = sqlEscapeString(el->originalId);
-forwardPrimer = sqlEscapeString(el->forwardPrimer);
-reversePrimer = sqlEscapeString(el->reversePrimer);
-polyClass = sqlEscapeString(el->polyClass);
-polyFamily = sqlEscapeString(el->polyFamily);
-polySubfamily = sqlEscapeString(el->polySubfamily);
-polySeq = sqlEscapeString(el->polySeq);
-polySource = sqlEscapeString(el->polySource);
-reference = sqlEscapeString(el->reference);
-ascertainingMethod = sqlEscapeString(el->ascertainingMethod);
-remarks = sqlEscapeString(el->remarks);
-disease = sqlEscapeString(el->disease);
-genoRegion = sqlEscapeString(el->genoRegion);
-
-dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s',%g,%d,%d,'%s','%s')", 
-	tableName,  chrom, el->chromStart , el->chromEnd ,  name, el->score ,  strand,  originalId,  forwardPrimer,  reversePrimer,  polyClass,  polyFamily,  polySubfamily,  polySeq,  polySource,  reference,  ascertainingMethod,  remarks, el->tm , el->filledSize , el->emptySize ,  disease,  genoRegion);
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-freez(&chrom);
-freez(&name);
-freez(&strand);
-freez(&originalId);
-freez(&forwardPrimer);
-freez(&reversePrimer);
-freez(&polyClass);
-freez(&polyFamily);
-freez(&polySubfamily);
-freez(&polySeq);
-freez(&polySource);
-freez(&reference);
-freez(&ascertainingMethod);
-freez(&remarks);
-freez(&disease);
-freez(&genoRegion);
-}
 
 struct dbRIP *dbRIPCommaIn(char **pS, struct dbRIP *ret)
 /* Create a dbRIP out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new dbRIP */
 {
 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));
 ret->originalId = sqlStringComma(&s);
 ret->forwardPrimer = sqlStringComma(&s);
 ret->reversePrimer = sqlStringComma(&s);
 ret->polyClass = sqlStringComma(&s);
 ret->polyFamily = sqlStringComma(&s);
 ret->polySubfamily = sqlStringComma(&s);
 ret->polySeq = sqlStringComma(&s);
 ret->polySource = sqlStringComma(&s);
 ret->reference = sqlStringComma(&s);
 ret->ascertainingMethod = sqlStringComma(&s);
 ret->remarks = sqlStringComma(&s);
 ret->tm = sqlFloatComma(&s);
 ret->filledSize = sqlSignedComma(&s);
 ret->emptySize = sqlSignedComma(&s);
 ret->disease = sqlStringComma(&s);
 ret->genoRegion = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void dbRIPFree(struct dbRIP **pEl)
 /* Free a single dynamically allocated dbRIP such as created
  * with dbRIPLoad(). */
 {
 struct dbRIP *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->originalId);
 freeMem(el->forwardPrimer);
 freeMem(el->reversePrimer);
 freeMem(el->polyClass);
 freeMem(el->polyFamily);
 freeMem(el->polySubfamily);
 freeMem(el->polySeq);
 freeMem(el->polySource);
 freeMem(el->reference);
 freeMem(el->ascertainingMethod);
 freeMem(el->remarks);
 freeMem(el->disease);
 freeMem(el->genoRegion);
 freez(pEl);
 }
 
 void dbRIPFreeList(struct dbRIP **pList)
 /* Free a list of dynamically allocated dbRIP's */
 {
 struct dbRIP *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     dbRIPFree(&el);
     }
 *pList = NULL;
 }
 
 void dbRIPOutput(struct dbRIP *el, FILE *f, char sep, char lastSep) 
 /* Print out dbRIP.  Separate fields with sep. Follow last field with lastSep. */
 {
 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);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->originalId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->forwardPrimer);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->reversePrimer);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->polyClass);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->polyFamily);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->polySubfamily);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->polySeq);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->polySource);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->reference);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->ascertainingMethod);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->remarks);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->tm);
 fputc(sep,f);
 fprintf(f, "%d", el->filledSize);
 fputc(sep,f);
 fprintf(f, "%d", el->emptySize);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->disease);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->genoRegion);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */