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/encode/hgEncodeApi/hgEncodeApi.c src/hg/encode/hgEncodeApi/hgEncodeApi.c
index 0e1f859..348a1b1 100644
--- src/hg/encode/hgEncodeApi/hgEncodeApi.c
+++ src/hg/encode/hgEncodeApi/hgEncodeApi.c
@@ -1,172 +1,172 @@
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 /* hgEncodeApi - a web API to selected ENCODE resources
 
 The API requests here are intended to follow the REST architectural approach.  
 Each API request accesses a resource, and no state is maintained. While implemented
 as a CGI, to follow the REST paradigm, access should be via resource identifiers translated
 from the CGI command and parameters via Apache rewriting.
 
 Initial implementation is limited to a few requests needed by UCSC applications, 
 and only supports JSON format responses.
 
 Example use (with rewriting) might be:
 
 http://api.wgEncode.ucsc.edu/cv/cells
     hgEncodeApi?cmd=cv&type=cellType
 
 http://api.wgEncode.ucsc.edu/cv/cells/K562
     hgEncodeApi?cmd=cv&type=cellType&term=K562
 
 http://api.wgEncode.ucsc.edu/cv/cells/organism=mouse
     hgEncodeApi?cmd=cv&type=cellType&organism=mouse
 
 Note: full RESTful style would limit response lists to specified count, providing
 URL's and next/previous links in a paging style (not implemented here).
 */
 
 /*
 Some additional requests in the same style (TBD):
 http://api.wgEncode.ucsc.edu/cv/assays
 http://api.wgEncode.ucsc.edu/cv/assays/ChipSeq
 http://api.wgEncode.ucsc.edu/cv/antibodies
 http://api.wgEncode.ucsc.edu/cv/antibodies/Pol2
 http://api.wgEncode.ucsc.edu/experiments
 http://api.wgEncode.ucsc.edu/experiments/2312
 http://api.wgEncode.ucsc.edu/experiments/assembly=hg19
 */
 
 #include "common.h"
 #include "hdb.h"
 #include "htmshell.h"
 #include "mdb.h"
 #include "hPrint.h"
 #include "dystring.h"
 #include "api.h"
 #include "encode/encodeExp.h"
 #include "cv.h"
 
 /* Requests */
 
 void cvResource(struct dyString *output)
 /* Retrieve CV entries from CV file and format as JSON to output. 
    Initially supporting only cellType, dataType, and antibody (type= parameter).
    Allows specifying cv file with file= parameter
         e.g. http://genome.ucsc.edu/cgi-bin/hgApi?db=hg19&cmd=cv&file=cv.ra&type=dataType
 */
 {
 char *type = cgiString("type");
 char *cvFile = cgiOptionalString("file");
 if (cvFile != NULL)
     cvFileDeclare(cvFile);
 if (differentString(type, "dataType") &&
     differentString(type, "cellType") &&
     differentString(type, "antibody"))
         {
         warn("Unsupported CV type %s (must be dataType, cellType, antibody)", type);
         errAbort("Unsupported 'cmd' parameter");
         }
 dyStringPrintf(output, "[\n");
 struct hash *typeHash = (struct hash *)cvTermHash(cvTermNormalized(type));
 struct hashCookie hc = hashFirst(typeHash);
 struct hashEl *hel;
 while ((hel = hashNext(&hc)) != NULL)
     {
     cvTermJson(output, type, hel->val);
     dyStringAppend(output,",");
     }
 output->string[dyStringLen(output)-1] = 0;
 output->stringSize--;
 dyStringPrintf(output, "\n]\n");
 }
 
 void experimentsResource(struct dyString *output)
 /* Retrieve experiments from database, optionally filtering by assembly (db= parameter)
    e.g. http://genome.ucsc.edu/cgi-bin/hgEncodeApi?cmd=experiments&db=hg19
 */
 {
 struct sqlConnection *connExp = sqlConnect(ENCODE_EXP_DATABASE);
 if (!sqlTableExists(connExp, ENCODE_EXP_TABLE))
     {
     errAbort("Experiment table not found on server");
     }
 
 int *ids = NULL;
 struct sqlConnection *conn;
 char *database = cgiOptionalString("db");
 if (database)
     {
     // Get ids of all experiments in metadata of this database
     // so those not in this assembly can be filtered out
     struct sqlResult *sr;
     char **row;
     char query[256];
     int id, maxId;
     if (!hDbExists(database))
         errAbort("Invalid database '%s'", database);
     int idOffset = encodeExpIdOffset();
     maxId = encodeExpIdMax(connExp);
     conn = hAllocConn(database);
     sqlSafef(query, sizeof(query), "select distinct(%s) from %s where %s='%s'",
                     MDB_VAL, MDB_DEFAULT_NAME, MDB_VAR, MDB_VAR_DCC_ACCESSION);
     sr = sqlGetResult(conn, query);
     AllocArray(ids, maxId + 1); // ids start with 1
     while ((row = sqlNextRow(sr)) != NULL)
         {
         id = sqlUnsigned(row[0] + idOffset);
         if (id <= maxId) 
             ids[id] = 1;
         }
     sqlFreeResult(&sr);
     hFreeConn(&conn);
     }
 struct encodeExp *exp = NULL, *exps = encodeExpLoadAllFromTable(connExp, ENCODE_EXP_TABLE);
 dyStringPrintf(output, "[\n");
 while ((exp = slPopHead(&exps)) != NULL)
     {
     // filter out experiments not in the selected database
     if (database && ids[exp->ix] == 0)
         continue;
     // filter out unaccessioned or deaccessioned experiments
     if (!encodeExpIsAccessioned(exp))
         continue;
     encodeExpJson(output, exp);
     dyStringAppend(output,",\n");
     }
 output->string[dyStringLen(output)-2] = '\n';
 output->string[dyStringLen(output)-1] = ']';
 dyStringPrintf(output, "\n");
 sqlDisconnect(&connExp);
 }
 
 int main(int argc, char *argv[])
 /* Process command line */
 {
 long enteredMainTime = clock1000();
-struct dyString *output = newDyString(10000);
+struct dyString *output = dyStringNew(10000);
 
 cgiSpoof(&argc, argv);
 pushWarnHandler(htmlVaBadRequestAbort);
 pushAbortHandler(htmlVaBadRequestAbort);
 
 char *cmd = cgiString("cmd");
 char *jsonp = cgiOptionalString("jsonp");
 if (!strcmp(cmd, "cv"))
     {
     cvResource(output);
     }
 else if (!strcmp(cmd, "experiments"))
     {
     experimentsResource(output);
     }
 else
     {
     warn("unknown cmd: %s",cmd);
     errAbort("Unsupported 'cmd' parameter");
     }
 
 apiOut(dyStringContents(output), jsonp);
 cgiExitTime("hgEncodeApi", enteredMainTime);
 return 0;
 }