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/hgSanger22/hgSanger22.c src/hg/makeDb/hgSanger22/hgSanger22.c
index fe9d548..b209275 100644
--- src/hg/makeDb/hgSanger22/hgSanger22.c
+++ src/hg/makeDb/hgSanger22/hgSanger22.c
@@ -1,308 +1,308 @@
 /* hgSanger22 - Load up database with Sanger 22 annotations. */
 
 /* 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 "hash.h"
 #include "dystring.h"
 #include "cheapcgi.h"
 #include "obscure.h"
 #include "jksql.h"
 #include "sanger22extra.h"
 #include "gff.h"
 #include "genePred.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgSanger22 - Load up database with Sanger 22 annotations\n"
   "usage:\n"
   "   hgSanger22 database transcript.gff cds.gff mrna.fa aa.fa shortArmSize\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 char *createGenePred = 
 "CREATE TABLE %s ( \n"
 "   name varchar(255) not null,	# Name of gene \n"
 "   chrom varchar(255) not null,	# Chromosome name \n"
 "   strand char(1) not null,	# + or - for strand \n"
 "   txStart int unsigned not null,	# Transcription start position \n"
 "   txEnd int unsigned not null,	# Transcription end position \n"
 "   cdsStart int unsigned not null,	# Coding region start \n"
 "   cdsEnd int unsigned not null,	# Coding region end \n"
 "   exonCount int unsigned not null,	# Number of exons \n"
 "   exonStarts longblob not null,	# Exon start positions \n"
 "   exonEnds longblob not null,	# Exon end positions \n"
           "   #Indices \n"
 "   INDEX(name), \n"
 "   INDEX(chrom(12),txStart), \n"
 "   INDEX(chrom(12),txEnd) \n"
 ")";
 
 char *createExtra = 
 "CREATE TABLE %s (\n"
 "    name varchar(255) not null,	# Transcript name\n"
 "    locus varchar(255) not null,	# Possibly biological short name\n"
 "    description longblob not null,	# Description from Sanger gene GFFs\n"
 "    geneType varchar(255) not null,	# Type field from Sanger gene GFFs\n"
 "    cdsType varchar(255) not null,	# Type field from Sanger CDS GFFs\n"
 "              #Indices\n"
 "    PRIMARY KEY(name)\n"
 ")\n";
 
 void loadIntoDatabase(char *database, char *createString, char *table, char *tabName)
 /* Load tabbed file into database table. */
 {
 struct sqlConnection *conn = sqlConnect(database);
-struct dyString *ds = newDyString(2048);
+struct dyString *ds = dyStringNew(2048);
 sqlDyStringPrintf(ds, createString, table);
 sqlRemakeTable(conn, table, ds->string);
 dyStringClear(ds);
 sqlDyStringPrintf(ds, 
    "LOAD data local infile '%s' into table %s", tabName, table);
 sqlUpdate(conn, ds->string);
 sqlDisconnect(&conn);
-freeDyString(&ds);
+dyStringFree(&ds);
 }
 
 boolean lineToGffFields(struct lineFile *lf, char *line, char *fields[9])
 /* Convert first eight space-separated fields to first 8
  * gff items, and stick rest of line in last item. */
 {
 char *s, *word;
 int i;
 
 /* Pretty much ignore comments and blank lines. */
 s = skipLeadingSpaces(line);
 if (s[0] == '#' || s[0] == '0')
     return FALSE;
 
 for (i=0; i<8; ++i)
     {
     word = nextWord(&s);
     if (word == NULL)
 	errAbort("Expecting at least 8 words line %d of %s", lf->lineIx, lf->fileName);
     fields[i] = word;
     }
 fields[8] = skipLeadingSpaces(s);
 return TRUE;
 }
 
 void writeGffLine(FILE *f, char *fields[9])
 /* Output tab-separated line. */
 {
 int i;
 for (i=0; i<8; ++i)
    fprintf(f, "%s\t", fields[i]);
 fprintf(f, "%s\n", fields[8]);
 }
 
 char *findVal(struct lineFile *lf, char *group, char *key)
 /* Return value that matches key in group or NULL. */
 {
 char *s, *var, *val;
 static char buf[512];
 
 if (strlen(group) >= sizeof(buf))
     errAbort("Line too long line %d of %s", lf->lineIx, lf->fileName);
 strcpy(buf, group);
 s = buf;
 for (;;)
     {
     var = nextWord(&s);
     if (var == NULL)
         return "";
     s = skipLeadingSpaces(s);
     if (s == NULL || s[0] == 0)
         errAbort("Unmatched key/val pair in group line %d of %s", lf->lineIx, lf->fileName);
     val = s;
     if (s[0] == '\'' || s[0] == '"')
 	{
         if (!parseQuotedString(val, val, &s))
 	    errAbort("Unmatched quote line %d of %s", lf->lineIx, lf->fileName);
 	}
     else
         {
 	int end;
 	val = nextWord(&s);
 	end = strlen(val) - 1;
 	if (val[end] == ';')
 	     val[end] = 0;
 	}
     s = skipLeadingSpaces(s);
     if (s != NULL && s[0] == ';')
         s += 1;
     if (sameString(key, var))
 	{
 	subChar(val, '\t', ' ');
         return val;
 	}
     }
 }
 
 struct sanger22extra *sanger22extraNew(char *name)
 /* Allocate a new extra.  Don't try to free this though. */
 {
 struct sanger22extra *extra;
 AllocVar(extra);
 extra->name = cloneString(name);
 extra->geneType = extra->cdsType = extra->locus =  extra->description = "";
 return extra;
 }
 
 void processOneGff(char *gffName, FILE *f, char *exonType, struct hash *extraHash,
 	struct sanger22extra **pExtraList, boolean isCds)
 /* Parse through a GFF and store it in f, hash, and list. */
 {
 char *line, *name, *group, *fields[9];
 struct lineFile *lf = lineFileOpen(gffName, TRUE);
 struct sanger22extra *extra;
 
 while (lineFileNext(lf, &line, NULL))
     {
     if (lineToGffFields(lf, line, fields))
 	{
 	fields[0] = "chr22";
 	group = fields[8];
 	fields[8] = name = findVal(lf, group, "Sequence");
 	if (name == NULL)
 	    continue;
 	if (endsWith(name, ".mRNA"))
 	    chopSuffix(name);
 	if (sameString(fields[2], "exon"))
 	    {
 	    fields[2] = exonType;
 	    writeGffLine(f, fields);
 	    if ((extra = hashFindVal(extraHash, name)) == NULL)
 		{
 		extra = sanger22extraNew(name);
 		hashAdd(extraHash, name, extra);
 		slAddHead(pExtraList, extra);
 		}
 	    if (isCds)
 		extra->cdsType = cloneString(fields[1]);
 	    else
 		extra->geneType = cloneString(fields[1]);
 	    }
 	else if (sameString(fields[2], "Sequence"))
 	    {
 	    if ((extra = hashFindVal(extraHash, name)) == NULL)
 		{
 		extra = sanger22extraNew(name);
 		hashAdd(extraHash, name, extra);
 		slAddHead(pExtraList, extra);
 		}
 	    if (extra->description[0] == 0)
 		extra->description = cloneString(findVal(lf, group, "Description"));
 	    if (extra->locus[0] == 0)
 	        extra->locus = cloneString(findVal(lf, group, "Locus"));
 	    }
 	}
     }
 lineFileClose(&lf);
 }
 
 struct sanger22extra *makeFixedGffAndReadExtra(char *txGff, char *cdsGff, 
 	char *fixedGff, struct hash *extraHash)
 /* Combine txGff and cdsGff into something our regular GFF to
  * genePred routine can handle. */
 {
 FILE *f = mustOpen(fixedGff, "w");
 struct sanger22extra *extraList = NULL;
 
 processOneGff(txGff, f, "exon", extraHash, &extraList, FALSE);
 processOneGff(cdsGff, f, "CDS", extraHash, &extraList, TRUE);
 carefulClose(&f);
 slReverse(&extraList);
 return extraList;
 }
 
 void saveExtras(char *fileName, struct sanger22extra *extraList)
 /* Save out extras to tab-separated file. */
 {
 struct sanger22extra *extra;
 FILE *f = mustOpen(fileName, "w");
 for (extra = extraList; extra != NULL; extra = extra->next)
     sanger22extraTabOut(extra, f);
 carefulClose(&f);
 }
 
 void genePredOffset(struct genePred *gp, int offset)
 /* Add fixed offset to gene prediction. */
 {
 int i;
 gp->txStart += offset;
 gp->txEnd += offset;
 gp->cdsStart += offset;
 gp->cdsEnd += offset;
 for (i=0; i<gp->exonCount; ++i)
     {
     gp->exonStarts[i] += offset;
     gp->exonEnds[i] += offset;
     }
 }
 
 void gffIntoDatabase(char *database, char *fileName, char *table, int offset)
 /* Load a gff file into database. */
 {
 struct gffFile *gff = gffFileNew("");
 struct gffGroup *group;
 struct genePred *gpList = NULL, *gp;
 FILE *f;
 char *tabName = "genePred.tab";
 
 /* Load fixed gff and convert it to genePred. */
 gffFileAdd(gff, fileName, 0);
 gffGroupLines(gff);
 for (group = gff->groupList; group != NULL; group = group->next)
     {
     gp = genePredFromGroupedGff(gff, group, group->name, "exon", 
                                 genePredCdsStatFld|genePredExonFramesFld,
                                 genePredGxfDefaults);
     if (gp != NULL)
 	{
 	slAddHead(&gpList, gp);
 	genePredOffset(gp, offset);
 	}
     }
 slSort(&gpList, genePredCmp);
 
 /* Create tab-delimited file. */
 f = mustOpen(tabName, "w");
 for (gp = gpList; gp != NULL; gp = gp->next)
     genePredTabOut(gp, f);
 carefulClose(&f);
 
 /* Load into database. */
 loadIntoDatabase(database, createGenePred, "sanger22", tabName);
 }
 
 void hgSanger22(char *database, char *txGff, char *cdsGff, char *mrnaFa, char *aaFa,
 	int shortArmSize)
 /* hgSanger22 - Load up database with Sanger 22 annotations. */
 {
 char *fixedGff = "fixed.gff";
 char *extraBed = "extras.bed";
 struct hash *extraHash = newHash(0);
 struct sanger22extra *extraList;
 
 extraList = makeFixedGffAndReadExtra(txGff, cdsGff, fixedGff, extraHash);
 saveExtras(extraBed, extraList);
 loadIntoDatabase(database, sanger22extraCreate, "sanger22extra", extraBed);
 gffIntoDatabase(database, fixedGff, "sanger22", shortArmSize);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 cgiSpoof(&argc, argv);
 if (argc != 7)
     usage();
 hgSanger22(argv[1], argv[2], argv[3], argv[4], argv[5], atoi(argv[6]));
 return 0;
 }