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/hgGene/sequence.c src/hg/hgGene/sequence.c
index 5205b21..6f34544 100644
--- src/hg/hgGene/sequence.c
+++ src/hg/hgGene/sequence.c
@@ -1,241 +1,241 @@
 /* sequence.c - Handle sequence stuff - formerly a section, now part of links. */
 
 /* 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 "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "cheapcgi.h"
 #include "hui.h"
 #include "hdb.h"
 #include "web.h"
 #include "dnautil.h"
 #include "dbDb.h"
 #include "axtInfo.h"
 #include "obscure.h"
 #include "hCommon.h"
 #include "hgGene.h"
 
 
 static void printGenomicAnchor(char *table, char *itemName,
 	char *chrom, int start, int end)
 /* Print genomic sequence anchor. */
 {
 hPrintf("<A HREF=\"%s?%s", hgcName(),
    cartSidUrlString(cart));
 hPrintf("&g=htcGeneInGenome&i=%s", itemName);
 hPrintf("&c=%s&l=%d&r=%d", chrom, start, end);
 hPrintf("&o=%s&table=%s", table, table);
 hPrintf("\" class=\"toc\">");
 }
 
 void printGenomicSeqLink(struct sqlConnection *conn, char *geneId,
 	char *chrom, int start, int end)
 /* Figure out known genes table, position of gene, link it. */
 {
 char *table = genomeSetting("knownGene");
 if (globalTdb)
     table = globalTdb->table;
 webPrintWideCellStart(3, HG_COL_TABLE);
 printGenomicAnchor(table, geneId, chrom, start, end);
 hPrintf("Genomic Sequence (%s:", chrom);
 printLongWithCommas(stdout, start+1);
 hPrintf("-");
 printLongWithCommas(stdout, end);
 hPrintf(")</A>");
 webPrintLinkCellEnd();
 }
 
 static void printSeqLink(struct sqlConnection *conn, char *geneId,
 	char *tableId, char *command, char *label, int colCount)
 /* Print out link to mRNA or protein. */
 {
 char *table = genomeSetting(tableId);
 boolean gotHyperlink = FALSE;
 webPrintWideCellStart(colCount, HG_COL_TABLE);
 if (sqlTableExists(conn, table))
     {
     char query[512];
     sqlSafef(query, sizeof(query), "select count(*) from %s where name = '%s'",
     	table, geneId);
     if (sqlExists(conn, query))
         {
 	hPrintf("<A HREF=\"../cgi-bin/hgGene?%s&%s=1&hgg_gene=%s\" class=\"toc\">",
 	       cartSidUrlString(cart), command, geneId);
 	hPrintf("%s</A>", label);
 	gotHyperlink = TRUE;
 	}
     }
 if (!gotHyperlink)
     hPrintf("%s", label);
 webPrintLinkCellEnd();
 }
 
 
 void printMrnaSeqLink(struct sqlConnection *conn, char *geneId)
 /* Print out link to fetch mRNA. */
 {
 char *title = "mRNA";
 char *tableId = "knownGene";
 if (genomeOptionalSetting("knownGeneMrna") != NULL)
     {
     title = "mRNA (may differ from genome)";
     tableId = "knownGeneMrna";
     }
 printSeqLink(conn, geneId, tableId, hggDoGetMrnaSeq, title, 2);
 }
 
 void printProteinSeqLink(struct sqlConnection *conn, char *geneId)
 /* Print out link to fetch protein. */
 {
 char *table = genomeSetting("knownGenePep");
 char query[256];
 char title[128];
 sqlSafef(query, sizeof(query), 
 	"select length(seq) from %s where name='%s'" , table,  geneId);
 int protSize = sqlQuickNum(conn, query);
 if (protSize > 0)
     {
     safef(title, sizeof(title), "Protein (%d aa)", protSize);
     printSeqLink(conn, geneId, "knownGenePep", hggDoGetProteinSeq,
 	    title, 1);
     }
 else
     {
     webPrintLinkCellStart();
     hPrintf("No protein");
     webPrintLinkCellEnd();
     }
 }
 
 
 void sequenceTablePrint(struct section *section, struct sqlConnection *conn,
 	char *geneId)
 /* Print the sequence table. */
 {
 char *table = genomeSetting("knownGene");
-struct dyString *query = newDyString(0);
+struct dyString *query = dyStringNew(0);
 char **row;
 struct sqlResult *sr;
 char *chrom;
 int start,end;
 
 /* Print the current position. */
 webPrintLinkTableStart();
 printGenomicSeqLink(conn, geneId, curGeneChrom, curGeneStart, curGeneEnd);
 printMrnaSeqLink(conn,geneId);
 printProteinSeqLink(conn,geneId);
 webPrintLinkTableEnd();
 
 /* Print out any additional positions. */
 sqlDyStringPrintf(query, "select chrom,txStart,txEnd from %s", table);
 sqlDyStringPrintf(query, " where name = '%s'", curGeneId);
 sqlDyStringPrintf(query, " and (chrom != '%s'", curGeneChrom);
 sqlDyStringPrintf(query, " or txStart != %d", curGeneStart);
 sqlDyStringPrintf(query, " or txEnd != %d)", curGeneEnd);
 sr = sqlGetResult(conn, query->string);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct sqlConnection *conn2 = hAllocConn(database);
     chrom = row[0];
     start = atoi(row[1]);
     end = atoi(row[2]);
     webPrintLinkTableStart();
     printGenomicSeqLink(conn2, geneId, chrom, start, end);
     webPrintLinkTableEnd();
     hFreeConn(&conn2);
     }
 sqlFreeResult(&sr);
-freeDyString(&query);
+dyStringFree(&query);
 }
 
 struct section *sequenceSection(struct sqlConnection *conn,
 	struct hash *sectionRa)
 /* Create sequence section. */
 {
 struct section *section = sectionNew(sectionRa, "sequence");
 section->print = sequenceTablePrint;
 return section;
 }
 
 void showSeqFromTable(struct sqlConnection *conn, char *geneId,
 	char *geneName, char *table)
 /* Show some sequence from given table. */
 {
 char query[512];
 struct sqlResult *sr;
 char **row;
 hPrintf("<TT><PRE>");
 
 sqlSafef(query, sizeof(query), 
     "select seq from %s where name = '%s'", table, geneId);
 sr = sqlGetResult(conn, query);
 if ((row = sqlNextRow(sr)) != NULL)
     {
     char *seq = row[0];
     hPrintf(">%s (%s) length=%d\n", geneId, geneName, (seq!=NULL) ? (int)strlen(seq): 0);
     writeSeqWithBreaks(stdout, seq, strlen(seq), 60);
     }
 sqlFreeResult(&sr);
 hPrintf("</PRE></TT>");
 }
 
 static void showSeq(struct sqlConnection *conn, char *geneId,
 	char *geneName, char *tableId)
 /* Show some sequence. */
 {
 char *table = genomeSetting(tableId);
 showSeqFromTable(conn, geneId, geneName, table);
 }
 
 static void showMrnaFromGenePred(struct sqlConnection *conn, 
 	char *geneId, char *geneName)
 /* Get mRNA sequence for gene from gene prediction. */
 {
 char *table = genomeSetting("knownGene");
 struct sqlResult *sr;
 char **row;
 char query[256];
 boolean hasBin = hIsBinned(sqlGetDatabase(conn), table);
 
 hPrintf("<TT><PRE>");
 sqlSafef(query, sizeof(query), 
     "select * from %s where name='%s'"
     " and chrom='%s' and txStart=%d and txEnd=%d", 
     table, geneId, curGeneChrom, curGeneStart, curGeneEnd);
 sr = sqlGetResult(conn, query);
 if ((row = sqlNextRow(sr)) != NULL)
     {
     struct genePred *gene = genePredLoad(row+hasBin);
     struct bed *bed = bedFromGenePred(gene);
     struct dnaSeq *seq = hSeqForBed(sqlGetDatabase(conn), bed);
     hPrintf(">%s (%s predicted mRNA)\n", geneId, geneName);
     writeSeqWithBreaks(stdout, seq->dna, seq->size, 50);
     dnaSeqFree(&seq);
     bedFree(&bed);
     genePredFree(&gene);
     }
 else
     errAbort("Couldn't find %s at %s:%d-%d", geneId, 
     	curGeneChrom, curGeneStart, curGeneEnd);
 sqlFreeResult(&sr);
 hPrintf("</TT></PRE>");
 }
 
 void doGetMrnaSeq(struct sqlConnection *conn, char *geneId, char *geneName)
 /* Get mRNA sequence in a simple page. */
 {
 if (genomeOptionalSetting("knownGeneMrna") != NULL)
     showSeq(conn, geneId, geneName, "knownGeneMrna");
 else
     showMrnaFromGenePred(conn, geneId, geneName);
 }
 
 void doGetProteinSeq(struct sqlConnection *conn, char *geneId, char *geneName)
 /* Get mRNA sequence in a simple page. */
 {
 showSeq(conn, geneId, geneName, "knownGenePep");
 }