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/estOrientInfo.c src/hg/lib/estOrientInfo.c
index 57cd5e8..8e3e1be 100644
--- src/hg/lib/estOrientInfo.c
+++ src/hg/lib/estOrientInfo.c
@@ -1,217 +1,217 @@
 /* estOrientInfo.c was originally generated by the autoSql program, which also 
  * generated estOrientInfo.h and estOrientInfo.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 "localmem.h"
 #include "estOrientInfo.h"
 
 
 static char *createString = 
     "CREATE TABLE %s (\n"
     "    bin smallint unsigned not null,        # Bin for fast index\n"
     "    chrom varchar(255) not null,	        # Human chromosome or FPC contig\n"
     "    chromStart int unsigned not null,	# Start position in chromosome\n"
     "    chromEnd int unsigned not null,	# End position in chromosome\n"
     "    name varchar(255) not null,	        # Accession of EST\n"
     "    intronOrientation smallint not null,	# Orientation of introns with respect to EST\n"
     "    sizePolyA smallint not null,	        # Number of trailing A's\n"
     "    revSizePolyA smallint not null,	# Number of trailing A's on reverse strand\n"
     "    signalPos smallint not null,	        # Position of start of polyA signal relative to end of EST or 0 if no signal\n"
     "    revSignalPos smallint not null,	# PolyA signal position on reverse strand if any\n"
     "              #Indices\n"
     "    INDEX(chrom(%d),bin),\n"
     "    INDEX(chrom(%d),chromStart),\n"
     "    INDEX(chrom(%d),chromEnd),\n"
     "    INDEX(name(20))\n"
     ")\n";
 
 void estOrientInfoStaticLoad(char **row, struct estOrientInfo *ret)
 /* Load a row from estOrientInfo 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->intronOrientation = sqlSigned(row[4]);
 ret->sizePolyA = sqlSigned(row[5]);
 ret->revSizePolyA = sqlSigned(row[6]);
 ret->signalPos = sqlSigned(row[7]);
 ret->revSignalPos = sqlSigned(row[8]);
 }
 
 struct estOrientInfo *estOrientInfoLoad(char **row)
 /* Load a estOrientInfo from row fetched with select * from estOrientInfo
  * from database.  Dispose of this with estOrientInfoFree(). */
 {
 struct estOrientInfo *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->intronOrientation = sqlSigned(row[4]);
 ret->sizePolyA = sqlSigned(row[5]);
 ret->revSizePolyA = sqlSigned(row[6]);
 ret->signalPos = sqlSigned(row[7]);
 ret->revSignalPos = sqlSigned(row[8]);
 return ret;
 }
 
 struct estOrientInfo *estOrientInfoLoadLm(char **row, struct lm *lm)
 /* Load a estOrientInfo row into local memory struct. */
 {
 struct estOrientInfo *ret;
 
 lmAllocVar(lm, ret);
 ret->chrom = lmCloneString(lm, row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->intronOrientation = sqlSigned(row[4]);
 ret->sizePolyA = sqlSigned(row[5]);
 ret->revSizePolyA = sqlSigned(row[6]);
 ret->signalPos = sqlSigned(row[7]);
 ret->revSignalPos = sqlSigned(row[8]);
 return ret;
 }
 
 struct estOrientInfo *estOrientInfoLoadAll(char *fileName) 
 /* Load all estOrientInfo from a tab-separated file.
  * Dispose of this with estOrientInfoFreeList(). */
 {
 struct estOrientInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[9];
 
 while (lineFileRow(lf, row))
     {
     el = estOrientInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct estOrientInfo *estOrientInfoLoadWhere(struct sqlConnection *conn, char *table, char *where)
 /* Load all estOrientInfo from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with estOrientInfoFreeList(). */
 {
 struct estOrientInfo *list = NULL, *el;
 struct dyString *query = dyStringNew(256);
 struct sqlResult *sr;
 char **row;
 
 sqlDyStringPrintf(query, "select * from %s", table);
 if (where != NULL)
-    dyStringPrintf(query, " where %s", where);
+    sqlDyStringPrintf(query, " where %-s", where);
 sr = sqlGetResult(conn, query->string);
 int off = sqlFieldColumn(sr, "bin") + 1; // offset of data; function returns -1 if no bin
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = estOrientInfoLoad(row+off);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 dyStringFree(&query);
 return list;
 }
 
 struct estOrientInfo *estOrientInfoCommaIn(char **pS, struct estOrientInfo *ret)
 /* Create a estOrientInfo out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new estOrientInfo */
 {
 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->intronOrientation = sqlSignedComma(&s);
 ret->sizePolyA = sqlSignedComma(&s);
 ret->revSizePolyA = sqlSignedComma(&s);
 ret->signalPos = sqlSignedComma(&s);
 ret->revSignalPos = sqlSignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void estOrientInfoFree(struct estOrientInfo **pEl)
 /* Free a single dynamically allocated estOrientInfo such as created
  * with estOrientInfoLoad(). */
 {
 struct estOrientInfo *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freez(pEl);
 }
 
 void estOrientInfoFreeList(struct estOrientInfo **pList)
 /* Free a list of dynamically allocated estOrientInfo's */
 {
 struct estOrientInfo *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     estOrientInfoFree(&el);
     }
 *pList = NULL;
 }
 
 void estOrientInfoOutput(struct estOrientInfo *el, FILE *f, char sep, char lastSep) 
 /* Print out estOrientInfo.  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, "%d", el->intronOrientation);
 fputc(sep,f);
 fprintf(f, "%d", el->sizePolyA);
 fputc(sep,f);
 fprintf(f, "%d", el->revSizePolyA);
 fputc(sep,f);
 fprintf(f, "%d", el->signalPos);
 fputc(sep,f);
 fprintf(f, "%d", el->revSignalPos);
 fputc(lastSep,f);
 }
 
 char *estOrientInfoGetCreateSql(char *table, int chromIdxLen)
 /* Get SQL to create an estOrientInfo table. chromIdxLen is the number of
  * chars at that start of chrom to use for the index. */
 {
-struct dyString *sqlCmd = newDyString(2048);
+struct dyString *sqlCmd = dyStringNew(2048);
 char *sqlCmdStr;
 sqlDyStringPrintf(sqlCmd, createString, table, chromIdxLen, chromIdxLen, chromIdxLen);
 sqlCmdStr = cloneString(sqlCmd->string);
 dyStringFree(&sqlCmd);
 return sqlCmdStr;
 }