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/hgTables/great.c src/hg/hgTables/great.c
index f047d87..7194b90 100644
--- src/hg/hgTables/great.c
+++ src/hg/hgTables/great.c
@@ -1,219 +1,222 @@
 /* great - stuff related to GREAT. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "cheapcgi.h"
 #include "hgTables.h"
 #include "cart.h"
 #include "dystring.h"
 #include "textOut.h"
 #include "trashDir.h"
 
 
 static char* greatData = "greatData/supportedAssemblies.txt";
 
 static struct dyString *getRequestName()
 {
 char *track = cartString(cart, hgtaTrack);
 char *table = cartString(cart, hgtaTable);
 struct dyString *name;
 
 if (differentStringNullOk(track, table))
     name = dyStringCreate("%s:%s", track, table);
 else
     name = dyStringCreate("%s", track);
 return name;
 }
 
 void verifyGreatFormat(const char *output)
 {
 if (!sameString(output, outBed) && !sameString(output, outWigBed))
     {
     htmlOpen("Sorry!");
     errAbort("GREAT requires that the output format be BED format.\n"
          "Some tracks are not available in BED format and thus cannot be passed to GREAT.\n"
          "Please go back and ensure that BED format is chosen.");
     htmlClose();
     }
 }
 
 void addAssemblyToSupportedList(struct dyString* dy, char* assembly)
 {
 char* organism = hOrganism(assembly);
 char* freezeDate = hFreezeDate(assembly);
 dyStringPrintf(dy, "%s %s", organism, freezeDate);
 freeMem(organism);
 freeMem(freezeDate);
 }
 
 void verifyGreatAssemblies()
 {
 // First read in the assembly name and description information into name lists
 struct slName* supportedAssemblies = NULL;
 struct lineFile *lf = lineFileOpen(greatData, TRUE);
 int fieldCount = 1;
 char* row[fieldCount];
 int wordCount;
 while ((wordCount = lineFileChopTab(lf, row)) != 0)
 	{
 	if (wordCount != fieldCount)
 		errAbort("The %s file is not properly formatted.\n", greatData);
 	slNameAddHead(&supportedAssemblies, row[0]);
 	}
 lineFileClose(&lf);
 
 boolean invalidAssembly = TRUE;
 struct slName* currAssembly;
 for (currAssembly = supportedAssemblies; currAssembly != NULL; currAssembly = currAssembly->next)
 	{
 	if (!hDbIsActive(currAssembly->name))
 		{
 		errAbort("Assembly %s in supported assembly file is not an active assembly.\n", currAssembly->name);
 		}
 	if (sameOk(database, currAssembly->name))
 		{
 		invalidAssembly = FALSE;
 		break;
 		}
 	}
 
 if (invalidAssembly)
     {
     slReverse(&supportedAssemblies);
     currAssembly = supportedAssemblies;
     struct dyString* dy = dyStringNew(0);
     addAssemblyToSupportedList(dy, currAssembly->name);
 
     currAssembly = currAssembly->next;
     while (currAssembly != NULL)
 	{
 	dyStringAppend(dy, ", ");
 	if (currAssembly->next == NULL)
 	    dyStringAppend(dy, "and ");
 	addAssemblyToSupportedList(dy, currAssembly->name);
 	currAssembly = currAssembly->next;
 	}
 
-    hPrintf("<script type='text/javascript'>\n");
-    hPrintf("function logSpecies() {\n");
-    hPrintf("try {\n");
-    hPrintf("var r = new XMLHttpRequest();\n");
-    hPrintf("r.open('GET', 'http://great.stanford.edu/public/cgi-bin/logSpecies.php?species=%s');\n", database);
-    hPrintf("r.send(null);\n");
-    hPrintf("} catch (err) { }\n");
-    hPrintf("}\n");
-    hPrintf("window.onload = logSpecies;\n");
-    hPrintf("</script>\n");
+    char javascript[1024];
+    safef(javascript, sizeof javascript,	    
+    "function logSpecies() {\n"
+    " try {\n"
+    "  var r = new XMLHttpRequest();\n"
+    "  r.open('GET', 'http://great.stanford.edu/public/cgi-bin/logSpecies.php?species=%s');\n"
+    "  r.send(null);\n"
+    " } catch (err) { }\n"
+    "}\n"
+    "window.onload = logSpecies;\n"
+    , database);
+    jsInline(javascript);
+
     errAbort("GREAT only supports the %s assemblies."
     "\nPlease go back and ensure that one of those assemblies is chosen.",
 	dyStringContents(dy));
     htmlClose();
 	dyStringFree(&dy);
     }
 
 slNameFreeList(&supportedAssemblies);
 }
 
 void doGreatTopLevel()
 /* intermediate page for formats printed directly from top form */
 {
 struct dyString *name = getRequestName();
 
 htmlOpen("Send BED data to GREAT as %s", dyStringContents(name));
 freeDyString(&name);
 verifyGreatAssemblies();
 startGreatForm();
 cgiMakeHiddenVar(hgtaDoTopSubmit, "get output");
 printGreatSubmitButtons();
 hPrintf("<div style='height:.9em;'></div>\n");
 htmlClose();
 }
 
 void startGreatForm()
 /* Start form for GREAT */
 {
 hPrintf("<FORM ACTION=\"%s\" NAME='greatForm' METHOD=POST>\n", getScriptName());
 }
 
 void printGreatSubmitButtons()
 /* print submit button to create data and then send query results to GREAT. */
 {
 cartSetString(cart, hgtaCompressType, textOutCompressNone);
 cartSetString(cart, hgtaOutFileName, "");
 
 cgiMakeHiddenVar(hgtaCompressType, textOutCompressNone);
 cgiMakeHiddenVar(hgtaOutFileName, "");
 
 cgiMakeHiddenVar(hgtaDoGreatOutput, "on");
 cgiMakeHiddenVar(hgtaPrintCustomTrackHeaders, "on");
 cgiMakeButton(hgtaDoGreatQuery, "Send query to GREAT");
 hPrintf("</FORM>\n");
 hPrintf(" ");
 /* new form as action is different */
 hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", cgiScriptName());
 cgiMakeButton(hgtaDoMainPage, "Cancel");
 hPrintf("</FORM>\n");
 }
 
 boolean doGreat()
 /* has the send to GREAT checkbox been selected? */
 {
 return cartUsualBoolean(cart, "sendToGreat", FALSE);
 }
 
 void doSubmitToGreat(const char *path)
 /* Send a URL to GREAT that it can use to retrieve the results. */
 {
 struct dyString *requestName = getRequestName();
 struct dyString *requestURL = dyStringCreate("http://%s/%s", cgiServerNamePort(), path);
 struct dyString *greatRequest;
 
 // archive server for hg18
 if (sameWord("hg18", database))
   greatRequest = dyStringCreate(
     "<meta http-equiv='refresh' content='0;url=http://bejerano.stanford.edu/great/public-2.0.2/cgi-bin/greatStart.php?requestURL=%s&requestSpecies=%s&requestName=%s&requestSender=UCSC%%20Table%%20Browser'>",
     dyStringContents(requestURL), database, dyStringContents(requestName));
 else
   greatRequest = dyStringCreate(
     "<meta http-equiv='refresh' content='0;url=http://great.stanford.edu/public/cgi-bin/greatStart.php?requestURL=%s&requestSpecies=%s&requestName=%s&requestSender=UCSC%%20Table%%20Browser'>",
     dyStringContents(requestURL), database, dyStringContents(requestName));
 
 hPrintf("<b>GREAT</b> is processing BED data from \"%s\"...please wait.\n", dyStringContents(requestName));
 hWrites(dyStringContents(greatRequest));
 freeDyString(&greatRequest);
 freeDyString(&requestName);
 freeDyString(&requestURL);
 }
 
 void doGetGreatOutput(void (*dispatch)())
 {
 struct tempName tn;
 int saveStdout;
 FILE *f;
 
 trashDirFile(&tn, "great", cartSessionId(cart), ".bed");
 f = fopen(tn.forCgi, "w");
 
 /* We want to capture hgTables stdout output to a trash file
  * which will later be fetched by Great via URL. */
 /* Workaround because stdout stream is not assignable on some operating systems */
 fflush(stdout);
 saveStdout = dup(STDOUT_FILENO);
 dup2(fileno(f),STDOUT_FILENO);   /* closes STDOUT before setting it again */
 fclose(f);
 
 dispatch();  /* this writes to stdout */
 
 /* restore stdout */
 fflush(stdout);
 dup2(saveStdout ,STDOUT_FILENO);  /* closes STDOUT before setting it back to saved descriptor */
 close(saveStdout);
 
 cartRemove(cart, hgtaDoGreatOutput);
 htmlOpen("Table Browser integration with GREAT");
 doSubmitToGreat(tn.forCgi);
 htmlClose();
 }