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/tigrCmrGene.c src/hg/lib/tigrCmrGene.c
index 9d3382b..be1eea3 100644
--- src/hg/lib/tigrCmrGene.c
+++ src/hg/lib/tigrCmrGene.c
@@ -1,287 +1,287 @@
 /* tigrCmrGene.c was originally generated by the autoSql program, which also 
  * generated tigrCmrGene.h and tigrCmrGene.sql.  This module links the database and
  * the RAM representation of objects. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "tigrCmrGene.h"
 
 
 void tigrCmrGeneStaticLoad(char **row, struct tigrCmrGene *ret)
 /* Load a row from tigrCmrGene table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->bin = sqlSigned(row[0]);
 ret->chrom = row[1];
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->name = row[4];
 ret->score = sqlUnsigned(row[5]);
 strcpy(ret->strand, row[6]);
 ret->tigrCommon = row[7];
 ret->tigrGene = row[8];
 ret->tigrECN = row[9];
 ret->primLocus = row[10];
 ret->tigrLength = sqlUnsigned(row[11]);
 ret->tigrPepLength = sqlUnsigned(row[12]);
 ret->tigrMainRole = row[13];
 ret->tigrSubRole = row[14];
 ret->swissProt = row[15];
 ret->genbank = row[16];
 ret->tigrMw = atof(row[17]);
 ret->tigrPi = atof(row[18]);
 ret->tigrGc = atof(row[19]);
 ret->goTerm = row[20];
 }
 
 struct tigrCmrGene *tigrCmrGeneLoad(char **row)
 /* Load a tigrCmrGene from row fetched with select * from tigrCmrGene
  * from database.  Dispose of this with tigrCmrGeneFree(). */
 {
 struct tigrCmrGene *ret;
 
 AllocVar(ret);
 ret->bin = sqlSigned(row[0]);
 ret->chrom = cloneString(row[1]);
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->name = cloneString(row[4]);
 ret->score = sqlUnsigned(row[5]);
 strcpy(ret->strand, row[6]);
 ret->tigrCommon = cloneString(row[7]);
 ret->tigrGene = cloneString(row[8]);
 ret->tigrECN = cloneString(row[9]);
 ret->primLocus = cloneString(row[10]);
 ret->tigrLength = sqlUnsigned(row[11]);
 ret->tigrPepLength = sqlUnsigned(row[12]);
 ret->tigrMainRole = cloneString(row[13]);
 ret->tigrSubRole = cloneString(row[14]);
 ret->swissProt = cloneString(row[15]);
 ret->genbank = cloneString(row[16]);
 ret->tigrMw = atof(row[17]);
 ret->tigrPi = atof(row[18]);
 ret->tigrGc = atof(row[19]);
 ret->goTerm = cloneString(row[20]);
 return ret;
 }
 
 struct tigrCmrGene *tigrCmrGeneLoadAll(char *fileName) 
 /* Load all tigrCmrGene from a whitespace-separated file.
  * Dispose of this with tigrCmrGeneFreeList(). */
 {
 struct tigrCmrGene *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[21];
 
 while (lineFileRow(lf, row))
     {
     el = tigrCmrGeneLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct tigrCmrGene *tigrCmrGeneLoadAllByChar(char *fileName, char chopper) 
 /* Load all tigrCmrGene from a chopper separated file.
  * Dispose of this with tigrCmrGeneFreeList(). */
 {
 struct tigrCmrGene *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[21];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = tigrCmrGeneLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct tigrCmrGene *tigrCmrGeneLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all tigrCmrGene 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 tigrCmrGeneFreeList(). */
 {
 struct tigrCmrGene *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = tigrCmrGeneLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void tigrCmrGeneSaveToDb(struct sqlConnection *conn, struct tigrCmrGene *el, char *tableName, int updateSize)
 /* Save tigrCmrGene 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. Strings are automatically escaped to allow insertion into the database. */
 {
-struct dyString *update = newDyString(updateSize);
+struct dyString *update = dyStringNew(updateSize);
 sqlDyStringPrintf(update, "insert into %s values ( %d,'%s',%u,%u,'%s',%u,'%s',%s,'%s','%s','%s',%u,%u,%s,%s,'%s','%s',%f,%f,%f,'%s')", 
 	tableName,  el->bin,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->tigrCommon,  el->tigrGene,  el->tigrECN,  el->primLocus,  el->tigrLength,  el->tigrPepLength,  el->tigrMainRole,  el->tigrSubRole,  el->swissProt,  el->genbank,  el->tigrMw,  el->tigrPi,  el->tigrGc,  el->goTerm);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 }
 
 
 struct tigrCmrGene *tigrCmrGeneCommaIn(char **pS, struct tigrCmrGene *ret)
 /* Create a tigrCmrGene out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new tigrCmrGene */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->bin = sqlSignedComma(&s);
 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->tigrCommon = sqlStringComma(&s);
 ret->tigrGene = sqlStringComma(&s);
 ret->tigrECN = sqlStringComma(&s);
 ret->primLocus = sqlStringComma(&s);
 ret->tigrLength = sqlUnsignedComma(&s);
 ret->tigrPepLength = sqlUnsignedComma(&s);
 ret->tigrMainRole = sqlStringComma(&s);
 ret->tigrSubRole = sqlStringComma(&s);
 ret->swissProt = sqlStringComma(&s);
 ret->genbank = sqlStringComma(&s);
 ret->tigrMw = sqlFloatComma(&s);
 ret->tigrPi = sqlFloatComma(&s);
 ret->tigrGc = sqlFloatComma(&s);
 ret->goTerm = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void tigrCmrGeneFree(struct tigrCmrGene **pEl)
 /* Free a single dynamically allocated tigrCmrGene such as created
  * with tigrCmrGeneLoad(). */
 {
 struct tigrCmrGene *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->tigrCommon);
 freeMem(el->tigrGene);
 freeMem(el->tigrECN);
 freeMem(el->primLocus);
 freeMem(el->tigrMainRole);
 freeMem(el->tigrSubRole);
 freeMem(el->swissProt);
 freeMem(el->genbank);
 freeMem(el->goTerm);
 freez(pEl);
 }
 
 void tigrCmrGeneFreeList(struct tigrCmrGene **pList)
 /* Free a list of dynamically allocated tigrCmrGene's */
 {
 struct tigrCmrGene *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     tigrCmrGeneFree(&el);
     }
 *pList = NULL;
 }
 
 void tigrCmrGeneOutput(struct tigrCmrGene *el, FILE *f, char sep, char lastSep) 
 /* Print out tigrCmrGene.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%d", el->bin);
 fputc(sep,f);
 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->tigrCommon);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tigrGene);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tigrECN);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->primLocus);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->tigrLength);
 fputc(sep,f);
 fprintf(f, "%u", el->tigrPepLength);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tigrMainRole);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tigrSubRole);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->swissProt);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->genbank);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->tigrMw);
 fputc(sep,f);
 fprintf(f, "%f", el->tigrPi);
 fputc(sep,f);
 fprintf(f, "%f", el->tigrGc);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->goTerm);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */