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/parasol/lib/jobResult.c src/parasol/lib/jobResult.c
index d5d6eac..a24f870 100644
--- src/parasol/lib/jobResult.c
+++ src/parasol/lib/jobResult.c
@@ -1,207 +1,207 @@
 /* jobResult.c was originally generated by the autoSql program, which also 
  * generated jobResult.h and jobResult.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "paraCommon.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "sqlNum.h"
 #include "sqlList.h"
 #include "jobResult.h"
 
 void jobResultStaticLoad(char **row, struct jobResult *ret)
 /* Load a row from jobResult table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 ret->status = sqlSigned(row[0]);
 ret->host = row[1];
 ret->jobId = row[2];
 ret->exe = row[3];
 ret->usrTicks = sqlSigned(row[4]);
 ret->sysTicks = sqlSigned(row[5]);
 ret->submitTime = sqlUnsigned(row[6]);
 ret->startTime = sqlUnsigned(row[7]);
 ret->endTime = sqlUnsigned(row[8]);
 ret->user = row[9];
 ret->errFile = row[10];
 }
 
 struct jobResult *jobResultLoad(char **row)
 /* Load a jobResult from row fetched with select * from jobResult
  * from database.  Dispose of this with jobResultFree(). */
 {
 struct jobResult *ret;
 
 AllocVar(ret);
 ret->status = sqlSigned(row[0]);
 ret->host = cloneString(row[1]);
 ret->jobId = cloneString(row[2]);
 ret->exe = cloneString(row[3]);
 ret->usrTicks = sqlSigned(row[4]);
 ret->sysTicks = sqlSigned(row[5]);
 ret->submitTime = sqlUnsigned(row[6]);
 ret->startTime = sqlUnsigned(row[7]);
 ret->endTime = sqlUnsigned(row[8]);
 ret->user = cloneString(row[9]);
 ret->errFile = cloneString(row[10]);
 return ret;
 }
 
 struct jobResult *jobResultLoadAll(char *fileName, off_t *resultBookMark, off_t resultsSize) 
 /* Load all jobResult from a tab-separated file, starting from bookMark, ending at resultsSize.
  * Dispose of this with jobResultFreeList(). */
 {
 struct jobResult *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, FALSE);
 int lineSize, wordCount;
 char *row[11], *line;
 off_t bookMark = *resultBookMark;
 lineFileSeek(lf, bookMark, SEEK_SET);
 if (bookMark > resultsSize)
     errAbort("bookMark (%llu) > resultsSize (%llu)", 
       (unsigned long long) bookMark,
       (unsigned long long) resultsSize);
 if (bookMark == resultsSize)
     return list;
 while (lineFileNext(lf, &line, &lineSize))
     {
     bookMark = lineFileTell(lf);
     if (bookMark >= resultsSize)
 	break;
     char lastChar = line[lineSize-1];
     if (lastChar != '\n')
     	{
 	// warn("Skipping incomplete last line of %s", fileName);
 	break;
 	}
     line[lineSize-1] = 0;
     wordCount = chopLine(line, row);
     lineFileExpectWords(lf, ArraySize(row), wordCount);
     el = jobResultLoad(row);
     slAddHead(&list, el);
     }
 bookMark = lineFileTell(lf);
 lineFileClose(&lf);
 slReverse(&list);
 *resultBookMark = bookMark;
 return list;
 }
 
 #ifdef USING_SQL
 struct jobResult *jobResultLoadWhere(struct sqlConnection *conn, char *table, char *where)
 /* Load all jobResult from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with jobResultFreeList(). */
 {
 struct jobResult *list = NULL, *el;
 struct dyString *query = dyStringNew(256);
 struct sqlResult *sr;
 char **row;
 
 // should be changed to sqlDyStringPrintf for NOSQLINJ
 // but that would perhaps require moving this code to someplace under hg/ ?
-dyStringPrintf(query, "select * from %s", table);
+sqlDyStringPrintf(query, "select * from %s", table);
 if (where != NULL)
-    dyStringPrintf(query, " where %s", where);
+    sqlDyStringPrintf(query, " where %-s", where);
 sr = sqlGetResult(conn, query->string);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = jobResultLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 dyStringFree(&query);
 return list;
 }
 #endif /* USEING_SQL */
 
 struct jobResult *jobResultCommaIn(char **pS, struct jobResult *ret)
 /* Create a jobResult out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new jobResult */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->status = sqlSignedComma(&s);
 ret->host = sqlStringComma(&s);
 ret->jobId = sqlStringComma(&s);
 ret->exe = sqlStringComma(&s);
 ret->usrTicks = sqlSignedComma(&s);
 ret->sysTicks = sqlSignedComma(&s);
 ret->submitTime = sqlUnsignedComma(&s);
 ret->startTime = sqlUnsignedComma(&s);
 ret->endTime = sqlUnsignedComma(&s);
 ret->user = sqlStringComma(&s);
 ret->errFile = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void jobResultFree(struct jobResult **pEl)
 /* Free a single dynamically allocated jobResult such as created
  * with jobResultLoad(). */
 {
 struct jobResult *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->host);
 freeMem(el->jobId);
 freeMem(el->exe);
 freeMem(el->user);
 freeMem(el->errFile);
 freez(pEl);
 }
 
 void jobResultFreeList(struct jobResult **pList)
 /* Free a list of dynamically allocated jobResult's */
 {
 struct jobResult *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     jobResultFree(&el);
     }
 *pList = NULL;
 }
 
 void jobResultOutput(struct jobResult *el, FILE *f, char sep, char lastSep) 
 /* Print out jobResult.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%d", el->status);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->host);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->jobId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->exe);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->usrTicks);
 fputc(sep,f);
 fprintf(f, "%d", el->sysTicks);
 fputc(sep,f);
 fprintf(f, "%u", el->submitTime);
 fputc(sep,f);
 fprintf(f, "%u", el->startTime);
 fputc(sep,f);
 fprintf(f, "%u", el->endTime);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->user);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->errFile);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }