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/gtexAse.c src/hg/lib/gtexAse.c
index ecd17e9..5402ccc 100644
--- src/hg/lib/gtexAse.c
+++ src/hg/lib/gtexAse.c
@@ -1,244 +1,244 @@
 /* gtexAse.c was originally generated by the autoSql program, which also 
  * generated gtexAse.h and gtexAse.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 "gtexAse.h"
 
 
 
 char *gtexAseCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,medianASE,coverage,samples,donors,minASE,q1ASE,q3ASE,maxASE,stdASE";
 
 void gtexAseStaticLoad(char **row, struct gtexAse *ret)
 /* Load a row from gtexAse 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]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->thickStart = sqlUnsigned(row[6]);
 ret->thickEnd = sqlUnsigned(row[7]);
 ret->itemRgb = sqlUnsigned(row[8]);
 ret->medianASE = sqlFloat(row[9]);
 ret->coverage = sqlFloat(row[10]);
 ret->samples = sqlUnsigned(row[11]);
 ret->donors = sqlUnsigned(row[12]);
 ret->minASE = sqlFloat(row[13]);
 ret->q1ASE = sqlFloat(row[14]);
 ret->q3ASE = sqlFloat(row[15]);
 ret->maxASE = sqlFloat(row[16]);
 ret->stdASE = sqlFloat(row[17]);
 }
 
 struct gtexAse *gtexAseLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all gtexAse 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 gtexAseFreeList(). */
 {
 struct gtexAse *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = gtexAseLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void gtexAseSaveToDb(struct sqlConnection *conn, struct gtexAse *el, char *tableName, int updateSize)
 /* Save gtexAse 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);
+struct dyString *update = dyStringNew(updateSize);
 sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s',%u,%u,%u,%g,%g,%u,%u,%g,%g,%g,%g,%g)", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->thickStart,  el->thickEnd,  el->itemRgb,  el->medianASE,  el->coverage,  el->samples,  el->donors,  el->minASE,  el->q1ASE,  el->q3ASE,  el->maxASE,  el->stdASE);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 }
 
 struct gtexAse *gtexAseLoad(char **row)
 /* Load a gtexAse from row fetched with select * from gtexAse
  * from database.  Dispose of this with gtexAseFree(). */
 {
 struct gtexAse *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->thickStart = sqlUnsigned(row[6]);
 ret->thickEnd = sqlUnsigned(row[7]);
 ret->itemRgb = sqlUnsigned(row[8]);
 ret->medianASE = sqlFloat(row[9]);
 ret->coverage = sqlFloat(row[10]);
 ret->samples = sqlUnsigned(row[11]);
 ret->donors = sqlUnsigned(row[12]);
 ret->minASE = sqlFloat(row[13]);
 ret->q1ASE = sqlFloat(row[14]);
 ret->q3ASE = sqlFloat(row[15]);
 ret->maxASE = sqlFloat(row[16]);
 ret->stdASE = sqlFloat(row[17]);
 return ret;
 }
 
 struct gtexAse *gtexAseLoadAll(char *fileName) 
 /* Load all gtexAse from a whitespace-separated file.
  * Dispose of this with gtexAseFreeList(). */
 {
 struct gtexAse *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[18];
 
 while (lineFileRow(lf, row))
     {
     el = gtexAseLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gtexAse *gtexAseLoadAllByChar(char *fileName, char chopper) 
 /* Load all gtexAse from a chopper separated file.
  * Dispose of this with gtexAseFreeList(). */
 {
 struct gtexAse *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[18];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = gtexAseLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gtexAse *gtexAseCommaIn(char **pS, struct gtexAse *ret)
 /* Create a gtexAse out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new gtexAse */
 {
 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->thickStart = sqlUnsignedComma(&s);
 ret->thickEnd = sqlUnsignedComma(&s);
 ret->itemRgb = sqlUnsignedComma(&s);
 ret->medianASE = sqlFloatComma(&s);
 ret->coverage = sqlFloatComma(&s);
 ret->samples = sqlUnsignedComma(&s);
 ret->donors = sqlUnsignedComma(&s);
 ret->minASE = sqlFloatComma(&s);
 ret->q1ASE = sqlFloatComma(&s);
 ret->q3ASE = sqlFloatComma(&s);
 ret->maxASE = sqlFloatComma(&s);
 ret->stdASE = sqlFloatComma(&s);
 *pS = s;
 return ret;
 }
 
 void gtexAseFree(struct gtexAse **pEl)
 /* Free a single dynamically allocated gtexAse such as created
  * with gtexAseLoad(). */
 {
 struct gtexAse *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freez(pEl);
 }
 
 void gtexAseFreeList(struct gtexAse **pList)
 /* Free a list of dynamically allocated gtexAse's */
 {
 struct gtexAse *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     gtexAseFree(&el);
     }
 *pList = NULL;
 }
 
 void gtexAseOutput(struct gtexAse *el, FILE *f, char sep, char lastSep) 
 /* Print out gtexAse.  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);
 fprintf(f, "%u", el->thickStart);
 fputc(sep,f);
 fprintf(f, "%u", el->thickEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->itemRgb);
 fputc(sep,f);
 fprintf(f, "%g", el->medianASE);
 fputc(sep,f);
 fprintf(f, "%g", el->coverage);
 fputc(sep,f);
 fprintf(f, "%u", el->samples);
 fputc(sep,f);
 fprintf(f, "%u", el->donors);
 fputc(sep,f);
 fprintf(f, "%g", el->minASE);
 fputc(sep,f);
 fprintf(f, "%g", el->q1ASE);
 fputc(sep,f);
 fprintf(f, "%g", el->q3ASE);
 fputc(sep,f);
 fprintf(f, "%g", el->maxASE);
 fputc(sep,f);
 fprintf(f, "%g", el->stdASE);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */