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/genark.c src/hg/lib/genark.c
index bd2707d..b475faf 100644
--- src/hg/lib/genark.c
+++ src/hg/lib/genark.c
@@ -1,290 +1,290 @@
 /* genark.c was originally generated by the autoSql program, which also 
  * generated genark.h and genark.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "genark.h"
 #include "hgConfig.h"
 #include "hdb.h"
 
 
 
 char *genarkCommaSepFieldNames = "gcAccession,hubUrl,asmName,scientificName,commonName,taxId";
 
 void genarkStaticLoad(char **row, struct genark *ret)
 /* Load a row from genark table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->gcAccession = row[0];
 ret->hubUrl = row[1];
 ret->asmName = row[2];
 ret->scientificName = row[3];
 ret->commonName = row[4];
 ret->taxId = sqlSigned(row[5]);
 }
 
 struct genark *genarkLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all genark from table that satisfy the query given.  
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something = 
  * anotherTable.something'.
  * Dispose of this with genarkFreeList(). */
 {
 struct genark *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = genarkLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void genarkSaveToDb(struct sqlConnection *conn, struct genark *el, char *tableName, int updateSize)
 /* Save genark as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. This function automatically escapes quoted strings for mysql. */
 {
-struct dyString *update = newDyString(updateSize);
+struct dyString *update = dyStringNew(updateSize);
 sqlDyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s',%d)", 
 	tableName,  el->gcAccession,  el->hubUrl,  el->asmName,  el->scientificName,  el->commonName,  el->taxId);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 }
 
 struct genark *genarkLoad(char **row)
 /* Load a genark from row fetched with select * from genark
  * from database.  Dispose of this with genarkFree(). */
 {
 struct genark *ret;
 
 AllocVar(ret);
 ret->gcAccession = cloneString(row[0]);
 ret->hubUrl = cloneString(row[1]);
 ret->asmName = cloneString(row[2]);
 ret->scientificName = cloneString(row[3]);
 ret->commonName = cloneString(row[4]);
 ret->taxId = sqlSigned(row[5]);
 return ret;
 }
 
 struct genark *genarkLoadAll(char *fileName) 
 /* Load all genark from a whitespace-separated file.
  * Dispose of this with genarkFreeList(). */
 {
 struct genark *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[6];
 
 while (lineFileRow(lf, row))
     {
     el = genarkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct genark *genarkLoadAllByChar(char *fileName, char chopper) 
 /* Load all genark from a chopper separated file.
  * Dispose of this with genarkFreeList(). */
 {
 struct genark *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[6];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = genarkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct genark *genarkCommaIn(char **pS, struct genark *ret)
 /* Create a genark out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new genark */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->gcAccession = sqlStringComma(&s);
 ret->hubUrl = sqlStringComma(&s);
 ret->asmName = sqlStringComma(&s);
 ret->scientificName = sqlStringComma(&s);
 ret->commonName = sqlStringComma(&s);
 ret->taxId = sqlSignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void genarkFree(struct genark **pEl)
 /* Free a single dynamically allocated genark such as created
  * with genarkLoad(). */
 {
 struct genark *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->gcAccession);
 freeMem(el->hubUrl);
 freeMem(el->asmName);
 freeMem(el->scientificName);
 freeMem(el->commonName);
 freez(pEl);
 }
 
 void genarkFreeList(struct genark **pList)
 /* Free a list of dynamically allocated genark's */
 {
 struct genark *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     genarkFree(&el);
     }
 *pList = NULL;
 }
 
 void genarkOutput(struct genark *el, FILE *f, char sep, char lastSep) 
 /* Print out genark.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->gcAccession);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->hubUrl);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->asmName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->scientificName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->commonName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->taxId);
 fputc(lastSep,f);
 }
 
 void genarkJsonOutput(struct genark *el, FILE *f) 
 /* Print out genark in JSON format. */
 {
 fputc('{',f);
 fputc('"',f);
 fprintf(f,"gcAccession");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->gcAccession);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"hubUrl");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->hubUrl);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"asmName");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->asmName);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"scientificName");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->scientificName);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"commonName");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->commonName);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"taxId");
 fputc('"',f);
 fputc(':',f);
 fprintf(f, "%d", el->taxId);
 fputc('}',f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 char *genarkUrl(char *accession)
 /* Return the URL to the genark assembly with this accession if present,
  * otherwise return NULL
  * */
 {
 char *genarkPrefix = cfgOption("genarkHubPrefix");
 
 if (genarkPrefix == NULL)
     return NULL;
 
 struct sqlConnection *conn = hConnectCentral();
 if (!sqlTableExists(conn, genarkTableName()))
     return NULL;
 
 char *url = NULL;
 char query[4096];
 char buffer[4096];
 sqlSafef(query, sizeof query, "select hubUrl from %s where gcAccession='%s'", genarkTableName(), accession);
 if (sqlQuickQuery(conn, query, buffer, sizeof buffer))
     {
     char buffer2[4096];
     safef(buffer2, sizeof buffer2, "%s/%s", genarkPrefix, buffer);
 
     url = cloneString(buffer2);
     }
 
 hDisconnectCentral(&conn);
 
 return url;
 }
 
 static char *_genarkTableName = NULL;
 
 char *genarkTableName()
 /* return the genark table name from the environment, 
  * or hg.conf, or use the default.  Cache the result */
 {
 if (_genarkTableName == NULL)
     _genarkTableName = cfgOptionEnvDefault("HGDB_GENARK_STATUS_TABLE",
 	    genarkTableConfVariable, defaultGenarkTableName);
 
 return _genarkTableName;
 }