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/sageVisCGI/sageVisCGI.c src/hg/sageVisCGI/sageVisCGI.c
index 63b0144..8247797 100644
--- src/hg/sageVisCGI/sageVisCGI.c
+++ src/hg/sageVisCGI/sageVisCGI.c
@@ -1,280 +1,280 @@
 /* Copyright (C) 2013 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 /**
 
 \page sageVisCGI.doxp sageVisCGI cgi program for viewing graphs of sage data
 used standalone or called by the hgc.c program in ~kent/src/hg/hgc/.
 
 <p>sageVisCGI creates graphs on the fly for the sage data of different
 uniGene clusters. The clusters to be graphed are passed via cgi (or command
 line) in the form u=<uniGene number>. There is also an optional 'md' parameter
 which specifies a maximum tag count to go up to, default is 50.
 
 <p>Example
 <br><pre><code>
 sageVisCGI md=20 u=202 u=122566 > out.html
 </code></pre>
 or http://genome-test.soe.ucsc.edu/cgi-bin/sageVisCGI?md=20&u=202&u=122566 .
 
 \sa sageVisCGI.c
 
 */
 #include "common.h"
 #include "hCommon.h"
 #include "dystring.h"
 #include "sage.h"
 #include "sageExp.h"
 #include "gnuPlot2D.h"
 #include "portable.h"
 #include "jksql.h"
 #include "dnautil.h"
 #include "cheapcgi.h"
 #include "htmshell.h"
 #include "knownMore.h"
 #include "hdb.h"
 #include "genePred.h"
 #include "hgConfig.h"
 
 int maxDataVal =0;
 int dataValCeiling;
 
 /**
 Just prints out the <img> tag and filename
 */
 void doPlotPrintOut(char *fileName)
 {
 printf( "<img src=\"%s\">\n", fileName);
 }
 
 
 /**
  * Appends one string to another without having to
  * worry about going over. Assumes that the total length
  * of dest is the strlen(dest) + 1. Wasteful if you want to
  * use it lots of times in a row as it reallocates memory every time
  */
 void dynamicStrncat(char **dest, const char *src)
 {
 ExpandArray(*dest, (strlen(*dest)+1), (strlen(*dest) +strlen(src) + 1));
 strncat(*dest, src, strlen(src));
 }
 
 /**
 Construct a graphPoint from data in sage and current index.
 Assumes that the experiments are stored in order.
 */
 struct graphPoint2D*createSageGraphPoint(struct sage *sg, int i)
 {
 
 struct graphPoint2D *gp = NULL;
 char name[128];
 
 sprintf(name, "Hs.%d", sg->uni);
 AllocVar(gp);
 gp->y = sg->meds[i-1];
 if(gp->y > maxDataVal && gp->y < dataValCeiling)
     maxDataVal = gp->y;
 gp->x = i;
 gp->name = cloneString(name);
 gp->hName = cloneString(name);
 gp->groupName = cloneString(name);
 return gp;
 }
 
 /**
   Uses the sage experiment data (sageExp) and sage data itself (sage)
 to construct the basic gnuPlot2D data type, specifically creating the
 graphPoint2D data lists for each element in sgList */
 struct gnuPlot2D *createSagePlot(struct sageExp *seList, struct sage *sgList)
 {
 struct gnuPlot2D *gp = createGnuPlot2D();
 struct sage *sg = NULL;
 int i;
 for(sg = sgList; sg != NULL; sg = sg->next)
     {
     struct graphPoint2D *gList = NULL;
     for (i=0; i< sg->numExps; i++)
         {
         struct graphPoint2D *gTemp = NULL;
         gTemp = createSageGraphPoint(sg, i+1);
 	slAddHead(&gList, gTemp);
 	}
     gptAddGraphPointList(gp, gList, "linesp");
     }
 return gp;
 }
 
 /* Creates a string which tells gnuPlot what label to put on
    xTics and where to put them. Will Chop "SAGE" from name if present */
 char * constructXticsFromExps(struct sageExp *seList)
 {
 char *ret = cloneString("set xtics rotate(");
 static char buff[256];
 int count =1;
 struct sageExp *se;
 for(se = seList; se != NULL; se = se->next)
     {
     if(se->next == NULL)
 	sprintf(buff, " \"%d)%s\" %d ", count, strstr(se->exp,"SAGE_") ? strstr(se->exp,"_") : se->exp , count);
     else
 	sprintf(buff, " \"%d)%s\" %d, ", count, strstr(se->exp,"SAGE_") ? strstr(se->exp, "_") : se->exp, count);
     dynamicStrncat(&ret, buff);
     count++;
     }
 dynamicStrncat(&ret, ")\n");
 return ret;
 }
 
 /* Prints the header appropriate for the title
  * passed in. Links html to chucks stylesheet for
  * easier maintaince
  */
 void chuckHtmlStart(char *title)
 {
 printf("<html><head>\n%s", getCspMetaHeader());
 //FIXME blueStyle should not be absolute to genome-test and should bae called by:
 // webIncludeResourceFile("blueStyle.css");
 printf("<LINK REL=STYLESHEET TYPE=\"text/css\" href=\"http://genome-test.soe.ucsc.edu/style/blueStyle.css\" title=\"Chuck Style\">\n");
 printf("<title>%s</title>\n</head><body bgcolor=\"#f3f3ff\">",title);
 }
 
 /**
 Generates the data plot and associated html
 */
 void doCountsPage(struct sageExp *seList, struct sage *sgList)
 {
 struct gnuPlot2D *gp = needMem(sizeof(struct gnuPlot2D*));
 
 char *cmd = NULL;
 double xSize;
 double ySize;
 char *title = NULL;
 char *xTics = NULL;
 char plotSize[256]; // = cloneString("set size .75,.75\n");
 struct tempName pngTn;
 
 chuckHtmlStart("Sage Graph");
 printf("<center>");
 makeTempName(&pngTn, "sageDat", ".png");
 gp = createSagePlot(seList, sgList);
 gp->fileName = pngTn.forCgi;
 xTics = constructXticsFromExps(seList);
 title = cloneString("Sage Data for Unigene Clusters");
 xSize = 0.020*slCount(gp->gpList[0]);
 ySize = 0.075*slCount(sgList);
 if(ySize < 1.25) ySize = 1.25;
 if(xSize <.75) xSize = .75;
 sprintf(plotSize, "set size %g, %g\n", xSize,ySize);
 gp->other = cloneString(plotSize);
 dynamicStrncat(&gp->other, xTics);
 gp->ylabel = cloneString("Median Counts");
 gp->xlabel = cloneString("Experiment");
 gp->title = cloneString(title);
 gp->xMax = slCount(gp->gpList[0]);
 gp->yMax = maxDataVal;
 cmd = gptGenerateCmd(gp);
 gptPlotFromCmd(cmd);
 doPlotPrintOut(pngTn.forHtml);
 htmlEnd();
 }
 
 
 /** load the sage data by constructing a query based on the names in nmList
  */
 struct sage *loadSageData(char *table, struct slName *nmList)
 {
 char *user = cfgOption("db.user");
 char *password = cfgOption("db.password");
 struct sqlConnection *sc = NULL;
-struct dyString *query = newDyString(2048);
+struct dyString *query = dyStringNew(2048);
 struct sage *sgList = NULL, *sg=NULL;
 struct slName *nm =NULL;
 char *db = cgiUsualString("db", "hgFixed");
 char **row;
 int count=0;
 struct sqlResult *sr = NULL;
 sc = sqlConnectRemote("localhost", user, password, db);
 sqlDyStringPrintf(query, "select * from sage where ");
 for(nm=nmList;nm!=NULL;nm=nm->next)
     {
     if (count++)
         {
         sqlDyStringPrintf(query," or uni=%s ", nm->name );
         }
     else
 	{
 	sqlDyStringPrintf(query," uni=%s ", nm->name);
 	}
     }
 sr = sqlGetResult(sc,query->string);
 while((row = sqlNextRow(sr)) != NULL)
     {
     sg = sageLoad(row);
     slAddHead(&sgList,sg);
     }
 sqlFreeResult(&sr);
 sqlDisconnect(&sc);
 slReverse(&sgList);
-freeDyString(&query);
+dyStringFree(&query);
 return sgList;
 }
 
 /** load the sage experiment data
  */
 struct sageExp *loadSageExps(char *tableName, struct slName *nmList)
 {
 char *user = cfgOption("db.user");
 char *password = cfgOption("db.password");
 struct sqlConnection *sc = NULL;
 char query[256];
 struct sageExp *seList = NULL, *se=NULL;
 char **row;
 struct sqlResult *sr = NULL;
 char *db = cgiUsualString("db", "hgFixed");
 sc = sqlConnectRemote("localhost", user, password, db);
 sqlSafef(query, sizeof query, "select * from sageExp order by num");
 sr = sqlGetResult(sc,query);
 while((row = sqlNextRow(sr)) != NULL)
     {
     se = sageExpLoad(row);
     slAddHead(&seList,se);
     }
 sqlFreeResult(&sr);
 sqlDisconnect(&sc);
 slReverse(&seList);
 return seList;
 }
 
 /** print usage and quit */
 void usage()
 {
 errAbort("sageVisCGI - create a graph of median sage counts\n"
 	 "usage:\n\t sageVisCGI u=<uniGeneNum> u=<uniGeneNum2> u=<uniGeneNum3> etc. \n");
 }
 
 /** main html generating function for htmShell */
 void doHtml()
 {
 struct sageExp *seList;
 struct sage *sgList;
 struct slName *unis = cgiStringList("u");
 if(unis == NULL)
     usage();
 dataValCeiling = cgiOptionalInt("md",50);
 seList = loadSageExps("sageExp", unis);
 sgList = loadSageData("sage", unis);
 doCountsPage(seList, sgList);
 sageExpFreeList(&seList);
 sageFreeList(&sgList);
 slFreeList(&unis);
 }
 
 
 int main(int argc, char *argv[])
 {
 cgiSpoof(&argc, argv);
 printf("Content-Type: text/html\n\n");
 htmEmptyShell(doHtml, NULL);
 return 0;
 }