fcb3971566d6570959c4cd8022972d8f7c455ebc
chmalee
  Mon Aug 19 13:21:18 2019 -0700
Remove links to lssnp from dbSnp hgc pages, and change lssnp links to mupit on hgGene pages, refs #22953

diff --git src/hg/lib/lsSnpPdbChimera.c src/hg/lib/lsSnpPdbChimera.c
index c3fbf35..a7ce67c 100644
--- src/hg/lib/lsSnpPdbChimera.c
+++ src/hg/lib/lsSnpPdbChimera.c
@@ -132,58 +132,47 @@
 char query[256], buf[32];
 sqlSafef(query, sizeof(query), "SELECT structType FROM lsSnpPdb WHERE (pdbId = \"%s\")",
       pdbId);
 char *structType = sqlNeedQuickQuery(conn, query, buf, sizeof(buf));
 if (sameString(structType, "XRay"))
     return "X-Ray";
 else if (sameString(structType, "NMR"))
     return "NMR";
 else
     return NULL;
 }
 
 boolean lsSnpPdbHasPdb(struct sqlConnection *conn, char *pdbId)
 /* determine if the specified PDB has any entries in LS-SNP */
 {
-if (!sqlTableExists(conn, "lsSnpPdb"))
+if (!sqlTableExists(conn, "knownToMupit"))
     return FALSE;
 char query[256], buf[64];
-sqlSafef(query, sizeof(query), "SELECT chain FROM lsSnpPdb WHERE (pdbId = \"%s\")", pdbId);
+sqlSafef(query, sizeof(query), "SELECT value FROM knownToMupit WHERE value = \"%s\" limit 1", pdbId);
 return (sqlQuickQuery(conn, query, buf, sizeof(buf)) != NULL);
 }
 
-static char *fmtParam(char sep, char *name, char *val)
-/* format a parameter to the URL; WARNING: static return */
-{
-static char param[64];
-safef(param, sizeof(param), "%c%s=%s", sep, name, val);
-return param;
-}
-
 char *lsSnpPdbGetUrlPdbSnp(char *pdbId, char *snpId)
 /* get LS-SNP/PDB URL for a particular PDB and/or SNP.  One or the two
  * ids maybe null */
 {
-char url[256], sep='?';
-safecpy(url, sizeof(url), "http://ls-snp.icm.jhu.edu/ls-snp-pdb/inquire");
+char url[256];
+safecpy(url, sizeof(url), "http://mupit.icm.jhu.edu/MuPIT_Interactive/?structure_id=");
 if (pdbId != NULL)
     {
-    safecat(url, sizeof(url), fmtParam(sep, "pdbId", pdbId));
-    sep = '&';
+    safecat(url, sizeof(url), pdbId);
     }
-if (snpId != NULL)
-    safecat(url, sizeof(url), fmtParam(sep, "snpId", snpId));
 return cloneString(url);
 }
 
 void lsSnpPdbChimeraGenericLink(char *pdbSpec, char *script,
                                 char *trashDirName, char *trashBaseName,
                                 struct tempName *chimerax)
 /* Generate a chimerax file for the given pdbSpec, which can be a PDB id or a
  * URL.  Copies in the lsSnpPdbChimera.py file and then adds optional script python code.
  * Fills in chimerax structure.
  * FIXME: This is an experiment for H1N1 flu browser, this function has
  * nothing to do with LS/SNP.  If we decide to keep this, this should be
  * split into a generic chimera module.
  */
 {
 trashDirFile(chimerax, trashDirName, trashBaseName, ".chimerax");