a53b9958fa734f73aeffb9ddfe2fbad1ca65f90c
galt
  Mon Jan 30 16:18:41 2017 -0800
Check-in of CSP2 Content-Security-Policy work. All C-language CGIs should now support CSP2 in browser to stop major forms of XSS javascript injection. Javascript on pages is gathered together, and then emitted in a single script block at the end with a nonce that tells the browser, this is js that we generated instead of being injected by a hacker. Both inline script from script blocks and inline js event handlers had to be pulled out and separated. You will not see js sprinkled through-out the page now. Older browsers that support CSP1 or that do not understand CSP at all will still work, just without protection. External js libraries loaded at runtime need to be added to the CSP policy header in src/lib/htmshell.c.

diff --git src/hg/hgTracks/extTools.c src/hg/hgTracks/extTools.c
index 76d39dc..50c49d2 100644
--- src/hg/hgTracks/extTools.c
+++ src/hg/hgTracks/extTools.c
@@ -1,293 +1,304 @@
 // Code to parse list of external tools and redirect to it via a hidden form */
 //
 // The link from hgTracks has the form ?hgt.redirectTool=<name>
 // Note that you can add the parameter &debug=1 to the URL to see and modify the hidden form
 // cgi-bin/extTools.ra defines the parameters and labels of the tools
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "dystring.h"
 #include "hCommon.h"
 #include "htmshell.h"
 #include "hash.h"
 #include "web.h"
 #include "ra.h"
 #include "hgTracks.h"
 #include "extTools.h"
 #include "hgFind.h"
 #include "obscure.h"
 #include "net.h"
 
 boolean extToolsEnabled()
 /* Return TRUE if we can display the external tools menu. */
 {
 return fileExists("extTools.ra");
 }
 
 void printExtMenuData() 
 /* print the external tools aka "send to" menu entries as a javascript list to stdout */
 {
 if (!extToolsEnabled())
     return;
 struct extTool *extTools = readExtToolRa("extTools.ra");
 struct extTool *et;
-hPuts("<script>\n");
-hPuts("extTools = [\n");
+struct dyString *dy = dyStringNew(1024);
+dyStringAppend(dy, "extTools = [\n");
 for(et = extTools; et != NULL; et = et->next)
     {
     if (et->dbs!=NULL)
         {
         if (!slNameInList(et->dbs, database))
             continue;
         }
     if (et->notDbs!=NULL)
         {
         if (slNameInList(et->notDbs, database))
             continue;
         }
     char* tool = jsonStringEscape(et->tool);
     char* shortLabel = jsonStringEscape(et->shortLabel);
     char* longLabel = jsonStringEscape(et->longLabel);
-    hPrintf("    ['%s', '%s', '%s', %d]", tool, shortLabel, longLabel, et->maxSize);
+    dyStringPrintf(dy, "    ['%s', '%s', '%s', %d]", tool, shortLabel, longLabel, et->maxSize);
     if (et->next)
-        hPuts(",");
-    hPuts("\n");
+        dyStringAppend(dy, ",");
+    dyStringAppend(dy, "\n");
     }
-hPuts("];\n");
-hPuts("</script>\n");
+dyStringAppend(dy, "];\n");
+
+jsInline(dy->string);
+dyStringFree(&dy);
 
 }
 
 static char *cloneRaSetting(struct hash *hash, char *name, struct lineFile *lf, bool mustExist)
 /* clone a setting out of the ra hash.  errAbort if mustExit and not found, otherwise NULL. */
 {
 char *str;
 if ((str = hashFindVal(hash, name)) == NULL) 
     {
     if (mustExist)
         errAbort("missing required setting '%s' on line %d in file %s\n",
             name, lf->lineIx, lf->fileName);
     else
         return NULL;
     }
 return cloneString(str);
 }
 
 struct extTool *readExtToolRa(char *raFileName) 
 /* parse the extTools.ra file. Inspired by trackHub.c:readGroupRa() */
 {
 struct lineFile *lf = udcWrapShortLineFile(raFileName, NULL, 1*1024*1024);
 struct extTool *list = NULL;
 //struct hash *ra;
 struct slPair *raList;
 while ((raList = raNextStanzAsPairs(lf)) != NULL)
     {
     struct extTool *et;
     AllocVar(et);
 
     struct slPair *paramList = NULL;
 
     struct hash *raHash;
     raHash = hashNew(0);
 
     // the "param" field is there more than once, so cannot use a hash for it
     struct slPair *raPair;
     for (raPair = raList; raPair != NULL; raPair = raPair->next)
         {
         if (sameWord(raPair->name, "param"))
             {
             // split the val into parameter name and value
             char *paramArr[2];
             int fCount = chopByWhite(raPair->val, paramArr, 2);
             // hacky way to allow spaces in parameter names and values
             char *name = replaceChars(paramArr[0], "%20", " ");
             char *val;
             if (fCount==2)
                 val = cloneString(paramArr[1]);
             else
                 val = cloneString("");
             val = replaceChars(val, "%20", " ");
             slPairAdd(&paramList, name, val);
             }
         else
             // add all other name/val pairs to the hash
             hashAdd(raHash, raPair->name, cloneString(raPair->val));
         }
 
     // pull out the required fields from the hash
     et->tool = cloneRaSetting(raHash, "tool", lf, TRUE);
     et->shortLabel = cloneRaSetting(raHash, "shortLabel", lf, TRUE);
     et->longLabel = cloneRaSetting(raHash, "longLabel", lf, TRUE);
     et->url = cloneRaSetting(raHash, "url", lf, TRUE);
     et->dbs = NULL;
 
     // optional fields
     et->email = cloneRaSetting(raHash, "email", lf, FALSE);
     if (hashFindVal(raHash, "onlyDbs"))
         et->dbs = commaSepToSlNames(hashFindVal(raHash, "onlyDbs"));
     if (hashFindVal(raHash, "notDbs"))
         et->notDbs = commaSepToSlNames(hashFindVal(raHash, "notDbs"));
 
     char *isHttpGet = hashFindVal(raHash, "isHttpGet");
     if (isHttpGet && \
      (sameString(isHttpGet, "yes") || sameString(isHttpGet, "on") || sameString(isHttpGet, "true")))
             et->isHttpGet = TRUE;
 
     char *maxSize = hashFindVal(raHash, "maxSize");
     if (maxSize!=NULL)
         et->maxSize = sqlUnsignedOrError(maxSize, "Error: maxSize %s for tool %s is not a number", \
                 maxSize, et->tool);
 
     slReverse(&paramList);
     et->params = paramList;
 
     slAddHead(&list, et);
     freeHashAndVals(&raHash);
     slPairFree(&raList);
     }
 
 if (list)
     slReverse(&list);
 lineFileClose(&lf);
 return list;
 }
 
 void extToolRedirect(struct cart *cart, char *tool)
 /* redirect to an external tool, sending the data specified in the ext tools config file */
 {
 bool debug = cgiVarExists("debug");
 
 struct extTool *extTools = readExtToolRa("extTools.ra");
 struct extTool *et;
 for (et = extTools; et != NULL; et = et->next)
     if (sameWord(et->tool, tool))
         break;
 if (et==NULL)
     errAbort("No configuration found for tool %s", tool);
 
+
 // construct an invisible CGI form with the given parameters
-printf("<html><body>\n");
+printf("<html>\n<head>\n");
+generateCspMetaHeader(stdout);
+printf("</head>\n<body>\n");
 
 if (debug)
     printf("Target URL: %s<p>", et->url);
 
 char *chromName;
 int winStart, winEnd;
 char *db = cartString(cart, "db");
 char *pos = cartString(cart, "position");
 
 // Try to deal with virt chrom position used by hgTracks.
 if (startsWith("virt:", cartUsualString(cart, "position", "")))
     pos = cartString(cart, "nonVirtPosition");
 
 findGenomePos(db, pos, &chromName, &winStart, &winEnd, cart);
 int len = winEnd-winStart;
 
 char start1[255];
 safef(start1, sizeof(start1), "%d", winStart+1);
 
 char *url = replaceInUrl(et->url, "", cart, db, chromName, winStart, winEnd, NULL, TRUE);
 
 char *method = "POST";
 if (et->isHttpGet)
     method = "GET";
 
 printf("<form id=\"redirForm\" method=\"%s\" action=\"%s\">\n", method, url);
 
 struct slPair *slp;
 
 if (et->maxSize!=0 && len > et->maxSize)
     {
     printf("Sorry, this tool accepts only a sequence with less than %d base pairs<p>\n"
       "Please zoom in some more.<p>\n", et->maxSize);
     return;
     }
 
 printf("You're being redirected from the UCSC Genome Browser to the site %s<br>\n", url);
 if (et->email)
     printf("Please contact %s for questions on this tool.<br>\n", et->email);
 
 boolean submitDone = FALSE;
 for (slp=et->params; slp!=NULL; slp=slp->next)
     {
     char* val = slp->val;
     if (sameWord(val, "$db"))
         val = db;
     if (sameWord(val, "$position"))
         val = pos;
     if (sameWord(val, "$start1"))
         val = start1;
     if (sameWord(val, "$returnUrl"))
         {
         // get the full URL of this hgTracks page, so external page can construct a custom track
         // and link back to us
         char* host = getenv("HTTP_HOST");
         char* reqUrl = getenv("REQUEST_URI");
         // remove everything after ? in URL
         char *e = strchr(reqUrl, '?');
         if (e) *e = 0; 
 
         char url[4000];
         // cannot find a way to find out if the request came in via http or https
         safef(url, sizeof(url), "http://%s%s", host, reqUrl);
         val = url;
         }
     // half the current window size
     if (stringIn("$halfLen", val))
         {
         char buf[64];
         safef(buf, sizeof(buf), "%d", len/2);
         val = replaceChars(val, "$halfLen", buf);
         }
     if (sameWord(val, "$seq") || sameWord(val, "$faSeq"))
         {
         static struct dnaSeq *seq = NULL;
         seq = hDnaFromSeq(db, chromName, winStart, winEnd, dnaLower);
         if (sameWord(val, "$seq"))
             val = seq->dna;
         else
             {
             val = catTwoStrings(">sequence\n",seq->dna);
             freez(&seq);
             }
         }
     // any remaining $-expression might be one of the general ones
     if (stringIn("$", val))
         {
         val = replaceInUrl(val, "", cart, db, chromName, winStart, winEnd, NULL, TRUE);
         }
 
     // output
     if (debug)
         {
         printf("%s: ", slp->name);
         printf("<input name=\"%s\" value=\"%s\"><p>\n", slp->name, val);
         }
     else
         {
         // parameter named submit is a special case
         if (sameWord(slp->name, "submit"))
             {
             submitDone = TRUE;
             printf("<input type=\"submit\" value=\"%s\" style=\"position: absolute; left: -9999px; "
                 "width: 1px; height: 1px;\">\n", val);
             }
         else
             printf("<input type=\"hidden\" name=\"%s\" value=\"%s\">\n", slp->name, val);
         }
     }
 
 // a hidden submit button, see
 // http://stackoverflow.com/questions/477691/submitting-a-form-by-pressing-enter-without-a-submit-button
 if (debug)
     printf("<input type=\"submit\">\n");
 else if (!submitDone)
     printf("<input type=\"submit\" style=\"position: absolute; left: -9999px; width: 1px; height: 1px;\">\n");
 printf("</form>\n");
 // a little javascript that clicks the submit button
 if (!debug)
-    printf("<script>document.getElementById(\"redirForm\").submit();</script>\n");
+    {
+    struct dyString *dy = dyStringNew(256);
+    dyStringPrintf(dy, "document.getElementById(\"redirForm\").submit();");
+    jsInline(dy->string);
+    dyStringFree(&dy);
+    }
+jsInlineFinish();
 printf("</body></html>\n");
 }