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/docId/docIdView/docIdView.c src/hg/encode/docId/docIdView/docIdView.c
index 0fc7955..121bd7a 100644
--- src/hg/encode/docId/docIdView/docIdView.c
+++ src/hg/encode/docId/docIdView/docIdView.c
@@ -1,269 +1,269 @@
 /* docIdView - cgi to show metadata from docId table. */
 
 /* 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 "options.h"
 #include "jksql.h"
 #include "htmshell.h"
 #include "web.h"
 #include "cheapcgi.h"
 #include "cart.h"
 #include "hui.h"
 #include "docId.h"
 #include "mdb.h"
 #include "portable.h"
 #include "trashDir.h"
 #include "dystring.h"
 
 
 /* Global Variables */
 struct cart *cart;             /* CGI and other variables */
 struct hash *oldVars = NULL;
 char *database = "encpipeline_prod";
 char *docIdTable = DEFAULT_DOCID_TABLE;
 //char *docIdDir = "/hive/groups/encode/dcc/pipeline/downloads/docId";
 char *docIdDir = "http://hgdownload-test.soe.ucsc.edu/goldenPath/docId";
 char *docIdDirBeta = "http://hgdownload-test.soe.ucsc.edu/goldenPath/betaDocId";
 
 void addValue(struct dyString *str, char *value)
 {
 if ((value != NULL) && !sameString(value, "None"))
     {
     dyStringPrintf(str, "%s, ", value);
     }
 }
 
 void doStandard(struct cart *theCart)
 {
 cart = theCart;
 cartWebStart(cart, database, "ENCODE DCC Submissions");
 struct sqlConnection *conn = sqlConnect(database);
 struct docIdSub *docIdSub;
 char query[10 * 1024];
 struct sqlResult *sr;
 char **row;
 struct tempName tn;
 trashDirFile(&tn, "docId", "meta", ".txt");
 char *tempFile = tn.forCgi;
 //printf("tempFile is %s\n<BR>", tempFile);
 
     // <Data type> <Cell Type> <Key Metadata> <View>
 printf("<table border=1><tr>");
 printf("<th>date submitted</th>");
 printf("<th>dataType</th>");
 printf("<th>cell type</th>");
 printf("<th>metadata</th>");
 // printf("<th>view</th>");
 printf("<th>fileType</th>");
 printf("<th>file</th>");
 printf("<th>lab</th>");
 printf("<th>assembly</th>");
 printf("<th>subId</th>");
 printf("<th>val-report</th>");
 printf("</tr>\n");
 sqlSafef(query, sizeof query, "select * from %s", docIdTable);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     docIdSub = docIdSubLoad(row);
     verbose(2, "ix %d\n", docIdSub->ix);
     verbose(2, "submitDate %s\n", docIdSub->submitDate);
     verbose(2, "md5sum %s\n", docIdSub->md5sum);
     verbose(2, "valReport %s\n", docIdSub->valReport);
     verbose(2, "metaData %s\n", docIdSub->metaData);
     verbose(2, "submitPath %s\n", docIdSub->submitPath);
     verbose(2, "submitter %s\n", docIdSub->submitter);
 
     cgiDecode(docIdSub->metaData, docIdSub->metaData, strlen(docIdSub->metaData));
     //printf("tempFile %s\n", tempFile);
     FILE *f = mustOpen(tempFile, "w");
     fwrite(docIdSub->metaData, strlen(docIdSub->metaData), 1, f);
     fclose(f);
     //boolean validated = FALSE;
     struct mdbObj *mdbObj = mdbObjsLoadFromFormattedFile(tempFile, NULL);
     unlink(tempFile);
 
     // <Data type> <Cell Type> <Key Metadata> <View>
     char *docIdType = mdbObjFindValue(mdbObj, "type");
     char *docIdComposite = mdbObjFindValue(mdbObj, "composite");
     char buffer[10 * 1024];
     char *cellFromMetaData = mdbObjFindValue(mdbObj, "cell"); 
 
     safef(buffer, sizeof buffer, "%d", docIdSub->ix);
     if (sameString(database, "encpipeline_beta"))
         docIdDir = docIdDirBeta;
 
     printf("<tr>");
     printf("<td>%s</td> ",   docIdSub->submitDate);
     printf("<td>%s</td> ",   mdbObjFindValue(mdbObj, "dataType"));
     printf("<td>%s</td> ",  cellFromMetaData);
-    struct dyString *str = newDyString(100);
+    struct dyString *str = dyStringNew(100);
     addValue(str,  mdbObjFindValue(mdbObj, "antibody"));
     addValue(str,  mdbObjFindValue(mdbObj, "treatment"));
     addValue(str,  mdbObjFindValue(mdbObj, "rnaExtract"));
     addValue(str,  mdbObjFindValue(mdbObj, "localization"));
     printf("<td>%s<a href=docIdView?docId=%s&db=%s&meta=\"\"> ...</a></td>", str->string,buffer, database);
-    freeDyString(&str);
+    dyStringFree(&str);
         
 //    printf("<td>%s</td> ",   mdbObjFindValue(mdbObj, "view"));
     printf("<td>%s</td> ",   mdbObjFindValue(mdbObj, "type"));
     printf("<td><a href=%s> %s</a></td>", 
         docIdGetPath(buffer, docIdDir, docIdType, NULL) , 
         docIdDecorate(docIdComposite, cellFromMetaData, docIdSub->ix));
     char *lab = mdbObjFindValue(mdbObj, "lab");
     char *subId = mdbObjFindValue(mdbObj, "subId");
     printf("<td><a href=docIdView?docId=%s&db=%s&lab=\"%s\"> %s</a></td>",buffer, database, subId, lab);
     printf("<td>%s</td> ",   mdbObjFindValue(mdbObj, "assembly"));
     printf("<td>%s</td> ",   subId);
     printf("<td><a href=docIdView?docId=%s&db=%s&report=\"\"> report</a></td>", buffer, database);
     printf("</tr>\n");
     }
 
 printf("</table>");
 sqlFreeResult(&sr);
 sqlDisconnect(&conn);
 cartWebEnd();
 }
 
 void doDocIdMeta(struct cart *theCart)
 {
 char *docId = cartString(theCart, "docId");
 cartWebStart(cart, database, "ENCODE DCC:  Metadata for docId %s",docId);
 struct sqlConnection *conn = sqlConnect(database);
 char query[10 * 1024];
 struct sqlResult *sr;
 char **row;
 struct tempName tn;
 trashDirFile(&tn, "docId", "meta", ".txt");
 char *tempFile = tn.forCgi;
 boolean beenHere = FALSE;
 
 printf("<a href=docIdView?db=%s> Return </a><BR>", database);
 sqlSafef(query, sizeof query, "select * from %s where ix=%s", docIdTable,docId);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     if (beenHere)
         errAbort("found more than one record with ix value %s in table %s", 
             docId, docIdTable);
     beenHere = TRUE;
 
     struct docIdSub *docIdSub = docIdSubLoad(row);
     cgiDecode(docIdSub->metaData, docIdSub->metaData, strlen(docIdSub->metaData));
     //printf("tempFile is %s\n<BR>", tempFile);
     FILE *f = mustOpen(tempFile, "w");
     fwrite(docIdSub->metaData, strlen(docIdSub->metaData), 1, f);
     fclose(f);
     boolean validated;
     struct mdbObj *mdbObj = mdbObjsLoadFromFormattedFile(tempFile, &validated);
     unlink(tempFile);
 
     if (mdbObj->next)
         errAbort("got more than one metaObj from metaData");
 
     for(; mdbObj; mdbObj = mdbObj->next)
         {
         printf("<BR>object: %s\n", mdbObj->obj);
         struct mdbVar *vars = mdbObj->vars;
         for(; vars; vars = vars->next)
             {
             printf("<BR>%s %s\n", vars->var, vars->val);
             }
         }
     }
 
 cartWebEnd();
 }
 
 void doDocIdReport(struct cart *theCart)
 {
 char *docId = cartString(theCart, "docId");
 cartWebStart(cart, database, "ENCODE DCC:  Validation report for docId %s",docId);
 struct sqlConnection *conn = sqlConnect(database);
 char query[10 * 1024];
 struct sqlResult *sr;
 char **row;
 boolean beenHere = FALSE;
 
 printf("<a href=docIdView?db=%s> Return </a><BR>", database);
 sqlSafef(query, sizeof query, "select * from %s where ix=%s", docIdTable,docId);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     if (beenHere)
         errAbort("found more than one record with ix value %s in table %s", 
             docId, docIdTable);
     beenHere = TRUE;
 
     struct docIdSub *docIdSub = docIdSubLoad(row);
     cgiDecode(docIdSub->valReport, docIdSub->valReport, strlen(docIdSub->valReport));
     //printf("tempFile is %s\n<BR>", tempFile);
     printf("<pre>%s", docIdSub->valReport);
     }
 
 cartWebEnd();
 }
 
 void doLabContacts(struct cart *theCart)
 {
 char *subId = cartString(theCart, "lab");
 cartWebStart(cart, database, "ENCODE DCC:  Contacts for submission: %s",subId);
 struct sqlConnection *conn = sqlConnect(database);
 char query[10 * 1024];
 struct sqlResult *sr;
 char **row;
 
 printf("<a href=docIdView?db=%s> Return </a><BR>", database);
 sqlSafef(query, sizeof query, "select user_id from %s where id = %s ", "projects",subId);
 char *userId = sqlQuickString(conn, query);
 
 sqlSafef(query, sizeof query, "select name,email,pi from %s where id = '%s' ", "users",userId);
 sr = sqlGetResult(conn, query);
 printf("<pre>");
 while ((row = sqlNextRow(sr)) != NULL)
     {
     printf("Name:  %s\nEmail: %s\nPI:    %s", row[0], row[1], row[2]);
     }
 
 sqlFreeResult(&sr);
 sqlDisconnect(&conn);
 cartWebEnd();
 }
 
 void doMiddle(struct cart *theCart)
 /* Set up globals and make web page */
 {
 if (cgiVarExists("docId"))
     {
     if (cgiVarExists("meta"))
         doDocIdMeta(theCart);
     else if (cgiVarExists("report"))
         doDocIdReport(theCart);
     else if (cgiVarExists("lab"))
         doLabContacts(theCart);
     }
 else 
     doStandard(theCart);
 }
 
 
 
 /* Null terminated list of CGI Variables we don't want to save
  * permanently. */
 char *excludeVars[] = {"Submit", "submit", "docId", NULL,};
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 cgiSpoof(&argc, argv);
 if (cgiVarExists("db"))
     {
     database=cgiOptionalString("db");
     }
 
 cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
 return 0;
 }