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/mainPage.c src/hg/hgTables/mainPage.c
index a41bcc9..77573c1 100644
--- src/hg/hgTables/mainPage.c
+++ src/hg/hgTables/mainPage.c
@@ -99,38 +99,39 @@
 
 void makeRegionButtonExtraHtml(char *val, char *selVal, char *extraHtml)
 /* Make region radio button including a little Javascript to save selection state
  * and optional extra html attributes. */
 {
 jsMakeTrackingRadioButtonExtraHtml(hgtaRegionType, "regionType", val, selVal, extraHtml);
 }
 
 void makeRegionButton(char *val, char *selVal)
 /* Make region radio button including a little Javascript
  * to save selection state. */
 {
 makeRegionButtonExtraHtml(val, selVal, NULL);
 }
 
-struct grp *showGroupField(char *groupVar, char *groupScript,
+struct grp *showGroupField(char *groupVar, char *event, char *groupScript,
     struct sqlConnection *conn, boolean allTablesOk)
 /* Show group control. Returns selected group. */
 {
 struct grp *group, *groupList = fullGroupList;
 struct grp *selGroup = findSelectedGroup(groupList, groupVar);
 hPrintf("<B>group:</B>\n");
-hPrintf("<SELECT NAME=%s %s>\n", groupVar, groupScript);
+hPrintf("<SELECT NAME=%s id='%s'>\n", groupVar, groupVar);
+jsOnEventById(event,groupVar,groupScript);
 for (group = groupList; group != NULL; group = group->next)
     {
     if (allTablesOk || differentString(group->name, "allTables"))
         hPrintf(" <OPTION VALUE=%s%s>%s\n", group->name,
                 (group == selGroup ? " SELECTED" : ""),
                 group->label);
     }
 hPrintf("</SELECT>\n");
 return selGroup;
 }
 
 static void addIfExists(struct hash *hash, struct slName **pList, char *name)
 /* Add name to tail of list if it exists in hash. */
 {
 if (hashLookup(hash, name))
@@ -151,56 +152,58 @@
 addIfExists(hash, &dbList, "ultra");
 return dbList;
 }
 
 char *findSelDb()
 /* Find user selected database (as opposed to genome database). */
 {
 struct slName *dbList = getDbListForGenome();
 char *selDb = cartUsualString(cart, hgtaTrack, NULL);
 if (!slNameInList(dbList, selDb))
     selDb = cloneString(dbList->name);
 slFreeList(&dbList);
 return selDb;
 }
 
-struct trackDb *showTrackField(struct grp *selGroup, char *trackVar, char *trackScript,
+struct trackDb *showTrackField(struct grp *selGroup, char *trackVar, char *event, char *trackScript,
                                boolean disableNoGenome)
 /* Show track control. Returns selected track. */
 {
 struct trackDb *track, *selTrack = NULL;
 if (trackScript == NULL)
     trackScript = "";
 if (sameString(selGroup->name, "allTables"))
     {
     char *selDb = findSelDb();
     struct slName *dbList = getDbListForGenome(), *db;
     hPrintf("<B>database:</B>\n");
-    hPrintf("<SELECT NAME=%s %s>\n", trackVar, trackScript);
+    hPrintf("<SELECT NAME=\"%s\" id='%s'>\n", trackVar, trackVar);
+    jsOnEventById(event, trackVar, trackScript);
     for (db = dbList; db != NULL; db = db->next)
 	{
 	hPrintf(" <OPTION VALUE=%s%s>%s\n", db->name,
 		(sameString(db->name, selDb) ? " SELECTED" : ""),
 		db->name);
 	}
     hPrintf("</SELECT>\n");
     }
 else
     {
     boolean allTracks = sameString(selGroup->name, "allTracks");
     hPrintf("<B>track:</B>\n");
-    hPrintf("<SELECT NAME=\"%s\" %s>\n", trackVar, trackScript);
+    hPrintf("<SELECT NAME=\"%s\" id='%s'>\n", trackVar, trackVar);
+    jsOnEventById(event, trackVar, trackScript);
     if (allTracks)
         {
 	selTrack = findSelectedTrack(fullTrackList, NULL, trackVar);
 	slSort(&fullTrackList, trackDbCmpShortLabel);
 	}
     else
 	{
 	selTrack = findSelectedTrack(fullTrackList, selGroup, trackVar);
 	}
     boolean selTrackIsDisabled = FALSE;
     struct trackDb *firstEnabled = NULL;
     for (track = fullTrackList; track != NULL; track = track->next)
 	{
 	if (allTracks || sameString(selGroup->name, track->grp))
 	    {
@@ -292,31 +295,32 @@
 char *selTable;
 
 if (track == NULL)
     nameList = tablesForDb(findSelDb());
 else
     nameList = cartTrackDbTablesForTrack(database, track, useJoiner);
 
 /* Get currently selected table.  If it isn't in our list
  * then revert to first in list. */
 selTable = cartUsualString(cart, varName, nameList->name);
 if (!slNameInListUseCase(nameList, selTable))
     selTable = nameList->name;
 
 /* Print out label and drop-down list. */
 hPrintf("<B>table: </B>");
-hPrintf("<SELECT NAME=\"%s\" %s>\n", varName, onChangeTable());
+hPrintf("<SELECT NAME=\"%s\" id='%s'>\n", varName, varName);
+jsOnEventById("change", varName, onChangeTable());
 struct trackDb *selTdb = NULL;
 for (name = nameList; name != NULL; name = name->next)
     {
     struct trackDb *tdb = NULL;
     if (track != NULL)
 	tdb = findTdbForTable(database,track,name->name, ctLookupName);
     hPrintf("<OPTION VALUE=\"%s\"", name->name);
     // Disable options for related tables that are noGenome -- if a non-positional table
     // is selected then we output its entire contents.
     if (cartTrackDbIsNoGenome(database, name->name) &&
         (track == NULL || differentString(track->table, name->name)))
         hPrintf(" DISABLED"NO_GENOME_CLASS);
     else if (sameString(selTable, name->name))
         {
         hPrintf(" SELECTED");
@@ -377,51 +381,50 @@
     hPrintf(" <OPTION VALUE=%s", ot->name);
     if (sameString(ot->name, outputType))
 	hPrintf(" SELECTED");
     if (sameString(ot->name, outBed) || sameString(ot->name, outWigBed))
         hPrintf(" id=\"outBed\"");
     hPrintf(">%s\n", ot->label);
     }
 hPrintf("</SELECT>\n");
 hPrintf(" ");
 
 if (!cfgOptionBooleanDefault("hgta.disableSendOutput", FALSE))
     {
     hPrintf(" Send output to ");
     struct dyString *dy = dyStringNew(256);
     dyStringAppend(dy, 
-	"onclick=\"document.getElementById('checkboxGreat').checked=false;");
+	"document.getElementById('checkboxGreat').checked=false;");
     if (isGenomeSpaceEnabled())
 	dyStringAppend(dy, 
 	      	  "document.getElementById('checkboxGenomeSpace').checked=false;");
     dyStringAppend(dy, 
-	      	  "return true;\"");
-    cgiMakeCheckBoxIdAndJS("sendToGalaxy", doGalaxy(),
-        "checkboxGalaxy", dy->string);
+	      	  "return true;");
+    cgiMakeCheckBoxWithId("sendToGalaxy", doGalaxy(), "checkboxGalaxy");
+    jsOnEventById("click", "checkboxGalaxy", dy->string);
     hPrintf("<A HREF=\""GALAXY_URL_BASE"\" target=_BLANK>Galaxy</A>\n");
     nbSpaces(2);
-    cgiMakeCheckBoxIdAndJS("sendToGreat", doGreat(),
-        "checkboxGreat",
-        "onclick=\"return onSelectGreat();\"");
+    cgiMakeCheckBoxWithId("sendToGreat", doGreat(), "checkboxGreat");
+    jsOnEventById("click", "checkboxGreat", "return onSelectGreat();");
     hPrintf(" <A HREF=\"http://great.stanford.edu\" target=_BLANK>GREAT</A>");
     if (isGenomeSpaceEnabled())
 	{
 	nbSpaces(2);
-	cgiMakeCheckBoxIdAndJS("sendToGenomeSpace", doGenomeSpace(),
-	    "checkboxGenomeSpace",
-	    "onclick=\"document.getElementById('checkboxGreat').checked=false;"
-		      "document.getElementById('checkboxGalaxy').checked=false; return true;\"");
+	cgiMakeCheckBoxWithId("sendToGenomeSpace", doGenomeSpace(), "checkboxGenomeSpace");
+	jsOnEventById("click", "checkboxGenomeSpace", 
+	    "document.getElementById('checkboxGreat').checked=false;"
+	    "document.getElementById('checkboxGalaxy').checked=false; return true;");
 	hPrintf(" <A HREF=\"http://www.genomespace.org\" target=_BLANK>GenomeSpace</A>");
 	}
     }
 
 hPrintf("</TD></TR>\n");
 }
 
 struct outputType otAllFields = { NULL,	outPrimaryTable,"all fields from selected table", };
 struct outputType otSelected =  { NULL, outSelectedFields,
                                   "selected fields from primary and related tables",  };
 struct outputType otSequence =  { NULL, outSequence,    "sequence", };
 struct outputType otPal =       { NULL, outPalOptions,
                                   "CDS FASTA alignment from multiple alignment", };
 struct outputType otGff =         { NULL, outGff,         "GTF - gene transfer format", };
 struct outputType otBed =         { NULL, outBed,         "BED - browser extensible data", };
@@ -521,69 +524,69 @@
 /* Put up table with main controls for main page. */
 {
 struct grp *selGroup;
 boolean isWig = FALSE, isPositional = FALSE, isMaf = FALSE, isBedGr = FALSE,
         isChromGraphCt = FALSE, isPal = FALSE, isArray = FALSE, isBam = FALSE, isVcf = FALSE, isHalSnake = FALSE, isLongTabix = FALSE;
 boolean gotClade = hGotClade();
 struct hTableInfo *hti = NULL;
 
 hPrintf("<TABLE BORDER=0>\n");
 
 /* Print clade, genome and assembly line. */
     {
     if (gotClade)
         {
         hPrintf("<TR><TD><B>clade:</B>\n");
-        printCladeListHtml(hGenome(database), onChangeClade());
+        printCladeListHtml(hGenome(database), "change", onChangeClade());
         nbSpaces(3);
         hPrintf("<B>genome:</B>\n");
-        printGenomeListForCladeHtml(database, onChangeOrg());
+        printGenomeListForCladeHtml(database, "change", onChangeOrg());
         }
     else
         {
         hPrintf("<TR><TD><B>genome:</B>\n");
-        printGenomeListHtml(database, onChangeOrg());
+        printGenomeListHtml(database, "change", onChangeOrg());
         }
     nbSpaces(3);
     hPrintf("<B>assembly:</B>\n");
-    printAssemblyListHtml(database, onChangeDb());
+    printAssemblyListHtml(database, "change", onChangeDb());
     hPrintf("</TD></TR>\n");
     }
 
 /* Print group and track line. */
     {
     hPrintf("<TR><TD>");
-    selGroup = showGroupField(hgtaGroup, onChangeGroupOrTrack(), conn, hAllowAllTables());
+    selGroup = showGroupField(hgtaGroup, "change", onChangeGroupOrTrack(), conn, hAllowAllTables());
     nbSpaces(3);
-    curTrack = showTrackField(selGroup, hgtaTrack, onChangeGroupOrTrack(), FALSE);
+    curTrack = showTrackField(selGroup, hgtaTrack, "change", onChangeGroupOrTrack(), FALSE);
     nbSpaces(3);
     boolean hasCustomTracks = FALSE;
     struct trackDb *t;
     for (t = fullTrackList;  t != NULL;  t = t->next)
         {
         if (isCustomTrack(t->table))
             {
             hasCustomTracks = TRUE;
             break;
             }
         }
-    hOnClickButton("document.customTrackForm.submit();return false;",
+    hOnClickButton("showMainCtlTbl_Ct", "document.customTrackForm.submit();return false;",
                    hasCustomTracks ? CT_MANAGE_BUTTON_LABEL : CT_ADD_BUTTON_LABEL);
 
     hPrintf(" ");
     if (hubConnectTableExists())
-	hOnClickButton("document.trackHubForm.submit();return false;", "track hubs");
+	hOnClickButton("showMainCtlTbl_Hub", "document.trackHubForm.submit();return false;", "track hubs");
 
     hPrintf("</TD></TR>\n");
     }
 
 /* Print table line. */
     {
     hPrintf("<TR><TD>");
     curTable = showTableField(curTrack, hgtaTable, TRUE);
     if (isHubTrack(curTable) || (strchr(curTable, '.') == NULL))  /* In same database */
         {
         hti = getHti(database, curTable, conn);
         isPositional = htiIsPositional(hti);
         }
     isLongTabix = isLongTabixTable( curTable);
     isBam = isBamTable( curTable);
@@ -651,32 +654,34 @@
         hPrintf("&nbsp;<span"NO_GENOME_CLASS">genome (unavailable for selected track)</span>"
                 "&nbsp;");
         }
     else
         {
         makeRegionButton(hgtaRegionTypeGenome, regionType);
         hPrintf("&nbsp;genome&nbsp;");
         }
     if (doEncode)
         {
 	makeRegionButton(hgtaRegionTypeEncode, regionType);
 	hPrintf("&nbsp;ENCODE Pilot regions&nbsp;");
 	}
     makeRegionButton(hgtaRegionTypeRange, regionType);
     hPrintf("&nbsp;position&nbsp;");
-    hPrintf("<INPUT TYPE=TEXT NAME=\"%s\" SIZE=26 VALUE=\"%s\" onFocus=\"%s\">\n",
-    	hgtaRange, range, jsRadioUpdate(hgtaRegionType, "regionType", "range"));
+    hPrintf("<INPUT TYPE=TEXT NAME=\"%s\" id='%s' SIZE=26 VALUE=\"%s\">\n",
+    	hgtaRange, hgtaRange, range);
+    jsOnEventById("focus", hgtaRange, 
+	jsRadioUpdate(hgtaRegionType, "regionType", "range"));
     cgiMakeButton(hgtaDoLookupPosition, "lookup");
     hPrintf("&nbsp;");
     if (userRegionsFileName() != NULL)
 	{
 	makeRegionButton(hgtaRegionTypeUserRegions, regionType);
 	hPrintf("&nbsp;defined regions&nbsp;");
 	cgiMakeButton(hgtaDoSetUserRegions, "change");
 	hPrintf("&nbsp;");
 	cgiMakeButton(hgtaDoClearUserRegions, "clear");
 	}
     else
 	cgiMakeButton(hgtaDoSetUserRegions, "define regions");
     hPrintf("</TD></TR>\n");
     }
 else
@@ -926,53 +931,60 @@
   "our <A HREF=\"../goldenPath/help/mysql.html\">public "
   "MySQL server</A>. "
   "To examine the biological function of your set through annotation "
   "enrichments, send the data to "
   "<A HREF=\"http://great.stanford.edu\" target=_BLANK>GREAT</A>. "
   "%s"
   "Refer to the "
   "<A HREF=\"../goldenPath/credits.html\">Credits</A> page for the list of "
   "contributors and usage restrictions associated with these data. "
   "All tables can be downloaded in their entirety from the "
   "<A HREF=\"http://hgdownload.cse.ucsc.edu/downloads.html\""
   ">Sequence and Annotation Downloads</A> page."
    , getGenomeSpaceText()
    );
 
-hPrintf("<script type=\"text/javascript\">\n");
 // When GREAT is selected, disable the other checkboxes and force output to BED
-hPrintf("function onSelectGreat() {\n");
-hPrintf("document.getElementById('checkboxGalaxy').checked=false;\n");
+struct dyString *js = dyStringNew(1024);
+dyStringPrintf(js,
+    "function onSelectGreat() {\n"
+    " document.getElementById('checkboxGalaxy').checked=false;\n");
 if (isGenomeSpaceEnabled())
-    hPrintf("document.getElementById('checkboxGenomeSpace').checked=false;\n");
-hPrintf("document.getElementById('outBed').selected=true;\n");
-hPrintf("return true;\n");
-hPrintf("}\n");
+    dyStringPrintf(js,
+    " document.getElementById('checkboxGenomeSpace').checked=false;\n");
+dyStringPrintf(js,
+    " document.getElementById('outBed').selected=true;\n"
+    " return true;\n"
+    "}\n");
+jsInline(js->string);
+
 // Disable/enable noGenome tracks depending on whether region is genome.
-hPrintf("function maybeDisableNoGenome() {\n"
+dyStringClear(js);
+dyStringPrintf(js,
+    "function maybeDisableNoGenome() {\n"
     "   var regionTypeSelected = $('input[name=\"hgta_regionType\"]:checked').val();\n"
     "   var regionIsGenome = (regionTypeSelected === 'genome');\n"
     "   var $noGenomeOptions = $('select[name=\"hgta_track\"] option.hgtaNoGenome');\n"
     "   $noGenomeOptions.attr('disabled', regionIsGenome)\n"
     "                   .css('color', regionIsGenome ? '' : 'black');\n"
     "}\n"
     "$(document).ready(function() {\n"
     // once when the page loads, and every time the user changes the region type:
     "    maybeDisableNoGenome();\n"
     "    $('input[name=\"hgta_regionType\"]').change(maybeDisableNoGenome);\n"
-        "});\n"
-        "</script>\n");
+    "});\n");
+jsInline(js->string);
 
 /* Main form. */
 hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n",
 	getScriptName(), cartUsualString(cart, "formMethod", "POST"));
 cartSaveSession(cart);
 jsInit();
 showMainControlTable(conn);
 hPrintf("</FORM>\n");
 
 /* Hidden form - for benefit of javascript. */
     {
     static char *saveVars[] = {
       "clade", "org", "db", hgtaGroup, hgtaTrack, hgtaTable, hgtaRegionType,
       hgtaRange, hgtaOutputType, hgtaOutFileName};
     jsCreateHiddenForm(cart, getScriptName(), saveVars, ArraySize(saveVars));