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/hgGene/domains.c src/hg/hgGene/domains.c
index e36859e..3ce7cdb 100644
--- src/hg/hgGene/domains.c
+++ src/hg/hgGene/domains.c
@@ -1,243 +1,243 @@
 /* domains - do protein domains section. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "trashDir.h"
 #include "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "spDb.h"
 #include "hgGene.h"
 #include "hdb.h"
 #include "lsSnpPdbChimera.h"
 
 
 static boolean domainsExists(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Return TRUE if there's some pfam domains in swissProt on this one. 
  * on this one. */
 {
 return swissProtAcc != NULL;
 }
 
 void modBaseAnchor(char *swissProtAcc)
 /* Print out anchor to modBase. */
 {
 hPrintf("<A HREF=\"http://salilab.org/modbase/search?databaseID=%s\" TARGET=_blank>", swissProtAcc);
 //hPrintf("<A HREF=\"http://salilab.org/modbase-cgi/model_search.cgi?searchkw=name&kword=%s\" TARGET=_blank>", swissProtAcc);
 }
 
 static void domainsPrint(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Print out protein domains. */
 {
 char *db = sqlGetDatabase(conn);
 struct slName *el, *list;
 list = spExtDbAcc1List(spConn, swissProtAcc, "Interpro");
 if (list != NULL)
     {
     char query[256], **row, **row2;
     struct sqlResult *sr, *sr2;
     hPrintf("<B>InterPro Domains: </B> ");
     hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/protein/%s\" TARGET=_blank>",
     	swissProtAcc);
     hPrintf("Graphical view of domain structure</A><BR>");
     sqlSafef(query, sizeof(query),
     	"select extAcc1,extAcc2 from extDbRef,extDb"
 	" where extDbRef.acc = '%s'"
 	" and extDb.val = 'Interpro' and extDb.id = extDbRef.extDb"
 	, swissProtAcc);
     sr = sqlGetResult(spConn, query);
     while ((row = sqlNextRow(sr)) != NULL)
         {
 	//hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/entry/%s\" TARGET=_blank>", row[0]);
 	//hPrintf("%s</A> - %s<BR>\n", row[0], row[1]);
         char interPro[256];
         char *pdb = hPdbFromGdb(db);
         safef(interPro, 128, "%s.interProXref", pdb);
         if (hTableExists(db, interPro))
                 {
                 sqlSafef(query, sizeof(query),
                         "select description from %s where accession = '%s' and interProId = '%s'",
                         interPro, swissProtAcc, row[0]);
                 sr2 = sqlGetResult(conn, query);
                 if ((row2 = sqlNextRow(sr2)) != NULL)
                     {
                     hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/entry/%s\" TARGET=_blank>", row[0]);
                     hPrintf("%s</A> - %s <BR>\n", row[0], row2[0]);
                     }
                 sqlFreeResult(&sr2);
                 }
             else
                 {
                 hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/entry/%s\" TARGET=_blank>", row[0]);
                 hPrintf("%s</A> - %s<BR>\n", row[0], row[1]);
                 }
 	}
     hPrintf("<BR>\n");
     slFreeList(&list);
     }
 if (kgVersion == KG_III)
     {
     /* Do Pfam domains here. */
     list = getPfamDomainList(conn, geneId);
     if (list != NULL)
     	{
     	hPrintf("<B>Pfam Domains:</B><BR>");
     	for (el = list; el != NULL; el = el->next)
 	    {
 	    char query[256];
 	    char *description;
 	    sqlSafef(query, sizeof(query), 
 	          "select description from pfamDesc where pfamAC='%s'", el->name);
 	    description = sqlQuickString(conn, query);
 	    if (description == NULL)
 	    	description = cloneString("n/a");
 	    hPrintf("<A HREF=\"http://pfam.xfam.org/family?acc=%s\" TARGET=_blank>", 
 	    	    el->name);
 	    hPrintf("%s</A> - %s<BR>\n", el->name, description);
 	    freez(&description);
 	    }
         slFreeList(&list);
         hPrintf("<BR>\n");
 	}
     
     /* Do SCOP domains here */
     list = getDomainList(conn, geneId,  "Scop");
     if (list != NULL)
     	{
     	hPrintf("<B>SCOP Domains:</B><BR>");
     	for (el = list; el != NULL; el = el->next)
 	    {
 	    char query[256];
 	    char *description;
 	    sqlSafef(query, sizeof(query), 
 	          "select description from scopDesc where acc='%s'", el->name);
 	    description = sqlQuickString(conn, query);
 	    if (description == NULL)
 	    	description = cloneString("n/a");
 	    hPrintf("<A HREF=\"http://scop.berkeley.edu/sunid=%s\" TARGET=_blank>", 
 	    	    el->name);
 	    hPrintf("%s</A> - %s<BR>\n", el->name, description);
 	    freez(&description);
 	    }
         slFreeList(&list);
         hPrintf("<BR>\n");
 	}
     }
 else
     {
     list = spExtDbAcc1List(spConn, swissProtAcc, "Pfam");
     if (list != NULL)
     	{
     	char *pfamDescSql = genomeSetting("pfamDescSql");
     	hPrintf("<B>Pfam Domains:</B><BR>");
     	for (el = list; el != NULL; el = el->next)
 	    {
 	    char query[256];
 	    char *description;
 	    sqlSafef(query, sizeof(query), pfamDescSql, el->name);
 	    description = sqlQuickString(conn, query);
 	    if (description == NULL)
 	    	description = cloneString("n/a");
 		hPrintf("<A HREF=\"http://pfam.xfam.org/family?acc=%s\" TARGET=_blank>", 
 	    	        el->name);
 	    hPrintf("%s</A> - %s<BR>\n", el->name, description);
 	    freez(&description);
 	    }
     	slFreeList(&list);
     	hPrintf("<BR>\n");
     	}
     }
 
 list = spExtDbAcc1List(spConn, swissProtAcc, "PDB");
 if (list != NULL)
     {
     struct sqlConnection *conn2 = sqlConnect(db);
     char query[256], **row;
     struct sqlResult *sr;
     int column = 0, maxColumn=3, rowCount=0;
     hPrintf("<B>Protein Data Bank (PDB) 3-D Structure</B><BR>");
     sqlSafef(query, sizeof(query),
     	"select extAcc1,extAcc2 from extDbRef,extDb"
 	" where extDbRef.acc = '%s'"
 	" and extDb.val = 'PDB' and extDb.id = extDbRef.extDb"
 	, swissProtAcc);
     sr = sqlGetResult(spConn, query);
     hPrintf("<TABLE><TR>\n");
     while ((row = sqlNextRow(sr)) != NULL)
         {
 	if (++column > maxColumn)
 	    {
 	    hPrintf("</TR><TR>");
 	    column = 1;
 	    if (rowCount == 0)
 	        {
 		hPrintf("<TD ALIGN=CENTER COLSPAN=4><I>To conserve bandwidth, only the images from the first %d structures are shown.</I>", maxColumn);
 		hPrintf("</TR><TR>");
 		}
 	    ++rowCount;
 	    }
 	hPrintf("<TD>");
 	hPrintf("<A HREF=\"http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=%s\" TARGET=_blank>", row[0]);
 	if (rowCount < 1)
 	    hPrintf("<IMG SRC=\"http://www.rcsb.org/pdb/images/%s_asym_r_250.jpe\"><BR>", row[0]);
         hPrintf("%s</A> - %s ", row[0], row[1]);
         // include links LS-SNP and to launch viewer in PDB chimera
         struct tempName chimerax;
         lsSnpPdbChimeraSnpAnn(conn, row[0], NULL, &chimerax);
         hPrintf(" <A HREF=\"%s\">Chimera</A>", chimerax.forHtml);
         if (lsSnpPdbHasPdb(conn2, row[0]))
             hPrintf(" <A HREF=\"%s\" TARGET=_blank>LS-SNP</A>", lsSnpPdbGetUrlPdbSnp(row[0], NULL));
 	hPrintf("</TD>\n");
 	}
     hPrintf("</TR></TABLE>\n");
     hPrintf("<A href=\"../goldenPath/help/chimera.html\" TARGET=_blank>Chimera help</A>\n");
     hPrintf("<BR><BR>\n");
     slFreeList(&list);
     sqlDisconnect(&conn2);
     }
 
 /* Do modBase link. */
     {
     hPrintf("<B>ModBase Predicted Comparative 3D Structure on ");
     modBaseAnchor(swissProtAcc);
     hPrintf("%s", swissProtAcc);
     hPrintf("</A></B><BR>\n");
 
     hPrintf("<TABLE><TR>");
     hPrintf("<TD>");
     modBaseAnchor(swissProtAcc);
-    hPrintf("\n<IMG SRC=\"http://salilab.org/modbaseimages/image/modbase.jpg?database_id=%s\"></A></TD>", swissProtAcc);
+    hPrintf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s\"></A></TD>", swissProtAcc);
     hPrintf("<TD>");
     modBaseAnchor(swissProtAcc);
-    hPrintf("\n<IMG SRC=\"http://salilab.org/modbaseimages/image/modbase.jpg?database_id=%s&axis=x&degree=90\"></A></TD>", swissProtAcc);
+    hPrintf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s&axis=x&degree=90\"></A></TD>", swissProtAcc);
     hPrintf("<TD>");
     modBaseAnchor(swissProtAcc);
-    hPrintf("\n<IMG SRC=\"http://salilab.org/modbaseimages/image/modbase.jpg?database_id=%s&axis=y&degree=90\"></A></TD>", swissProtAcc);
+    hPrintf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s&axis=y&degree=90\"></A></TD>", swissProtAcc);
     hPrintf("</TR><TR>\n");
     hPrintf("<TD ALIGN=CENTER>Front</TD>");
     hPrintf("<TD ALIGN=CENTER>Top</TD>");
     hPrintf("<TD ALIGN=CENTER>Side</TD>");
     hPrintf("</TR></TABLE>\n");
     hPrintf("<I>The pictures above may be empty if there is no "
             "ModBase structure for the protein.  The ModBase structure "
 	    "frequently covers just a fragment of the protein.  You may "
 	    "be asked to log onto ModBase the first time you click on the "
 	    "pictures. It is simplest after logging in to just click on "
 	    "the picture again to get to the specific info on that model.</I>");
     }
 }
 
 struct section *domainsSection(struct sqlConnection *conn, 
 	struct hash *sectionRa)
 /* Create domains section. */
 {
 struct section *section = sectionNew(sectionRa, "domains");
 section->exists = domainsExists;
 section->print = domainsPrint;
 return section;
 }