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/makeDb/hgLoadSample/hgLoadSample.c src/hg/makeDb/hgLoadSample/hgLoadSample.c
index cecc8b6..53a87a9 100644
--- src/hg/makeDb/hgLoadSample/hgLoadSample.c
+++ src/hg/makeDb/hgLoadSample/hgLoadSample.c
@@ -1,224 +1,224 @@
 /* hgLoadBed - Load a generic bed file into database. */
 
 /* Copyright (C) 2013 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 "obscure.h"
 #include "hash.h"
 #include "cheapcgi.h"
 #include "jksql.h"
 #include "dystring.h"
 #include "sample.h"
 #include "hdb.h"
 
 
 /* Command line switches. */
 boolean noBin = FALSE;		/* Suppress bin field. */
 boolean strictTab = FALSE;	/* Separate on tabs. */
 boolean oldTable = FALSE;	/* Don't redo table. */
 char *sqlTable = NULL;		/* Read table from this .sql if non-NULL. */
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgLoadSample - Load a sample 9 (wiggle) file into database\n"
   "usage:\n"
   "   hgLoadSample database track files(s).smp\n"
   "options:\n"
   "   -noBin   suppress bin field\n"
   "   -oldTable add to existing table\n"
   "   -sqlTable=table.sql Create table from .sql file\n"
   "   -tab  Separate by tabs rather than space\n"
   );
 }
 
 int findBedSize(char *fileName)
 /* Read first line of file and figure out how many words in it. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *words[64], *line;
 int wordCount;
 lineFileNeedNext(lf, &line, NULL);
 if (strictTab)
     wordCount = chopTabs(line, words);
 else
     wordCount = chopLine(line, words);
 if (wordCount == 0)
     errAbort("%s appears to be empty", fileName);
 lineFileClose(&lf);
 return wordCount;
 }
 
 struct bedStub
 /* A line in a bed file with chromosome, start, end position parsed out. */
     {
     struct bedStub *next;	/* Next in list. */
     char *chrom;                /* Chromosome . */
     int chromStart;             /* Start position. */
     int chromEnd;		/* End position. */
     char *line;                 /* Line. */
     };
 
 int bedStubCmp(const void *va, const void *vb)
 /* Compare to sort based on query. */
 {
 const struct bedStub *a = *((struct bedStub **)va);
 const struct bedStub *b = *((struct bedStub **)vb);
 int dif;
 dif = strcmp(a->chrom, b->chrom);
 if (dif == 0)
     dif = a->chromStart - b->chromStart;
 return dif;
 }
 
 
 void loadOneBed(char *fileName, int bedSize, struct bedStub **pList)
 /* Load one bed file.  Make sure all lines have bedSize fields.
  * Put results in *pList. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *words[64], *line, *dupe;
 int wordCount;
 struct bedStub *bed;
 
 verbose(1, "Reading %s\n", fileName);
 while (lineFileNext(lf, &line, NULL))
     {
     dupe = cloneString(line);
     if (strictTab)
 	wordCount = chopTabs(line, words);
     else
 	wordCount = chopLine(line, words);
     lineFileExpectWords(lf, bedSize, wordCount);
     AllocVar(bed);
     bed->chrom = cloneString(words[0]);
     bed->chromStart = lineFileNeedNum(lf, words, 1);
     bed->chromEnd = lineFileNeedNum(lf, words, 2);
     bed->line = dupe;
     slAddHead(pList, bed);
     }
 lineFileClose(&lf);
 }
 
 void writeBedTab(char *fileName, struct bedStub *bedList, int bedSize)
 /* Write out bed list to tab-separated file. */
 {
 struct bedStub *bed;
 FILE *f = mustOpen(fileName, "w");
 char *words[64];
 int i, wordCount;
 for (bed = bedList; bed != NULL; bed = bed->next)
     {
     if (!noBin)
         fprintf(f, "%u\t", hFindBin(bed->chromStart, bed->chromEnd));
     if (strictTab)
 	wordCount = chopTabs(bed->line, words);
     else
 	wordCount = chopLine(bed->line, words);
     for (i=0; i<wordCount; ++i)
         {
 	fputs(words[i], f);
 	if (i == wordCount-1)
 	    fputc('\n', f);
 	else
 	    fputc('\t', f);
 	}
     }
 fclose(f);
 }
 
 void loadDatabase(char *database, char *track, int bedSize, struct bedStub *bedList)
 /* Load database from bedList. */
 {
 struct sqlConnection *conn = sqlConnect(database);
-struct dyString *dy = newDyString(1024);
+struct dyString *dy = dyStringNew(1024);
 char *tab = "sample.tab";
 
 /* First make table definition. */
 if (sqlTable != NULL)
     {
     /* Read from file. */
     char *sql, *s;
     readInGulp(sqlTable, &sql, NULL);
 
     /* Chop of end-of-statement semicolon if need be. */
     s = strchr(sql, ';');
     if (s != NULL) *s = 0;
     
     sqlRemakeTable(conn, track, sql);
     freez(&sql);
     }
 else if (!oldTable)
     {
     /* Create definition statement. */
     verbose(1, "Creating table definition for \n");
     sqlDyStringPrintf(dy, "CREATE TABLE %s (\n", track);
     if (!noBin)
-       dyStringAppend(dy, "  bin smallint unsigned not null,\n");
-    dyStringAppend(dy, "  chrom varchar(255) not null,\n");
-    dyStringAppend(dy, "  chromStart int unsigned not null,\n");
-    dyStringAppend(dy, "  chromEnd int unsigned not null,\n");
+       sqlDyStringPrintf(dy, "  bin smallint unsigned not null,\n");
+    sqlDyStringPrintf(dy, "  chrom varchar(255) not null,\n");
+    sqlDyStringPrintf(dy, "  chromStart int unsigned not null,\n");
+    sqlDyStringPrintf(dy, "  chromEnd int unsigned not null,\n");
     if (bedSize >= 4)
-       dyStringAppend(dy, "  name varchar(255) not null,\n");
+       sqlDyStringPrintf(dy, "  name varchar(255) not null,\n");
     if (bedSize >= 5)
-       dyStringAppend(dy, "  score int unsigned not null,\n");
+       sqlDyStringPrintf(dy, "  score int unsigned not null,\n");
     if (bedSize >= 6)
-       dyStringAppend(dy, "  strand char(1) not null,\n");
+       sqlDyStringPrintf(dy, "  strand char(1) not null,\n");
     if (bedSize >= 7)
-       dyStringAppend(dy, "  sampleCount int unsigned not null,\n");
+       sqlDyStringPrintf(dy, "  sampleCount int unsigned not null,\n");
     if (bedSize >= 8)
-       dyStringAppend(dy, "  samplePosition longblob not null,\n");
+       sqlDyStringPrintf(dy, "  samplePosition longblob not null,\n");
     if (bedSize >= 9)
-       dyStringAppend(dy, "  sampleHeight longblob not null,\n");
-    dyStringAppend(dy, "#Indices\n");
+       sqlDyStringPrintf(dy, "  sampleHeight longblob not null,\n");
+    sqlDyStringPrintf(dy, "#Indices\n");
     if (!noBin)
-       dyStringAppend(dy, "  INDEX(chrom(8),bin),\n");
+       sqlDyStringPrintf(dy, "  INDEX(chrom(8),bin),\n");
     if (bedSize >= 4)
-       dyStringAppend(dy, "  INDEX(name(16)),\n");
-    dyStringAppend(dy, "  INDEX(chrom(8),chromStart)\n");
-    dyStringAppend(dy, ")\n");
+       sqlDyStringPrintf(dy, "  INDEX(name(16)),\n");
+    sqlDyStringPrintf(dy, "  INDEX(chrom(8),chromStart)\n");
+    sqlDyStringPrintf(dy, ")\n");
     sqlRemakeTable(conn, track, dy->string);
     }
 
 verbose(1, "Saving %s\n", tab);
 writeBedTab(tab, bedList, bedSize);
 
 verbose(1, "Loading %s\n", database);
 dyStringClear(dy);
 sqlDyStringPrintf(dy, "load data local infile '%s' into table %s", tab, track);
 sqlUpdate(conn, dy->string);
 sqlDisconnect(&conn);
 }
 
 void hgLoadBed(char *database, char *track, int bedCount, char *bedFiles[])
 /* hgLoadBed - Load a generic bed file into database. */
 {
 int bedSize = findBedSize(bedFiles[0]);
 struct bedStub *bedList = NULL;
 int i;
 
 for (i=0; i<bedCount; ++i)
     loadOneBed(bedFiles[i], bedSize, &bedList);
 verbose(1, "Loaded %d elements\n", slCount(bedList));
 slSort(&bedList, bedStubCmp);
 verbose(1, "Sorted\n");
 loadDatabase(database, track, bedSize, bedList);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 cgiSpoof(&argc, argv);
 if (argc < 4)
     usage();
 noBin = cgiBoolean("noBin");
 strictTab = cgiBoolean("tab");
 uglyf("stringTab = %d\n", strictTab);
 oldTable = cgiBoolean("oldTable");
 sqlTable = cgiOptionalString("sqlTable");
 hgLoadBed(argv[1], argv[2], argc-3, argv+3);
 return 0;
 }