e491b3ca6211e825e7f5b4e57a72a3e44574af63
kate
  Mon May 23 15:08:55 2016 -0700
Build patch for hgGene failure on hg38 (trying to access ensGene for GTEx section)

diff --git src/hg/hgGene/gtex.c src/hg/hgGene/gtex.c
index 59ecbbe..f05f2be 100644
--- src/hg/hgGene/gtex.c
+++ src/hg/hgGene/gtex.c
@@ -1,84 +1,100 @@
 /* GTEx - Gene expression from the Genotype Tissue Expression project. */
 
 /* Copyright (C) 2016 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "cart.h"
 #include "cheapcgi.h"
 #include "hdb.h"
 #include "hgGene.h"
 #include "gtexInfo.h"
 #include "gtexTissue.h"
 #include "gtexGeneBed.h"
 #include "gtexUi.h"
 
-static boolean gtexExists(struct section *section, struct sqlConnection *conn, char *geneId)
+static boolean gtexExists(struct section *section, struct sqlConnection *conn, char *ucscId)
 /* Return TRUE if GTEx data exists for this gene */
 {
-// Lookup geneId in knownToEnsembl to get ENST (w/ version), look that up (w/o version) 
-// in ensGene to get ENSG (w/o version), and save it for printer
 char query[512];
 if (!sqlTableExists(conn, "gtexGene"))
     return FALSE;
+
+#define NO_ENSGENE 1
+// NOTE: Can remove this ifdef when/if hg38 ensGene is pushed 
+#ifdef NO_ENSGENE
+if (sameString(database, "hg38"))
+    {
+    // Get ENSG (w/ version) from knownCanonical
+    sqlSafef(query, sizeof(query), 
+        "SELECT SUBSTRING_INDEX(knownCanonical.protein,'.',1) FROM "
+            "knownCanonical, knownIsoforms WHERE "
+            "knownIsoforms.transcript='%s' AND "
+            "knownCanonical.clusterId=knownIsoforms.clusterId", ucscId);
+    }
+else
+#endif
+
+// Lookup ucsc gene ID in knownToEnsembl to get ENST (w/ version), look that up (w/o version) 
+// in ensGene to get ENSG (w/o version), and save it for printer
 sqlSafef(query, sizeof(query), 
     "SELECT ensGene.name2 FROM ensGene, knownToEnsembl WHERE "
         "knownToEnsembl.name='%s' AND "
-            "ensGene.name=SUBSTRING_INDEX(knownToEnsembl.value,'.',1)", geneId);
+        "ensGene.name=SUBSTRING_INDEX(knownToEnsembl.value,'.',1)", ucscId);
 char *ensGene = sqlQuickString(conn, query);
 if (!ensGene)
 return FALSE;
 
 // construct full accession (with version) in gtexGene table
 sqlSafef(query, sizeof(query), 
     "select geneId from gtexGene where geneId like '%s%%'", ensGene);
 ensGene = sqlQuickString(conn, query);
 if (!ensGene)
     return FALSE;
 section->items = ensGene;
 return TRUE;
 }
 
 static void gtexPrint(struct section *section, struct sqlConnection *conn, char *geneId)
 /* Print out GTEx gene expression boxplot */
 {
 char *ensGene = section->items;
 
 // get gtexGene median expression values
 char query[512];
 sqlSafef(query, sizeof(query), "SELECT * from gtexGene WHERE geneId='%s'", ensGene);
 struct gtexGeneBed *gtexGene = gtexGeneBedLoadByQuery(conn, query);
 assert(gtexGene);
 
 int tisId;
 float highestLevel = gtexGeneHighestMedianExpression(gtexGene, &tisId);
 char *highestTissue = gtexGetTissueDescription(tisId, NULL);
 float totalLevel = gtexGeneTotalMedianExpression(gtexGene);
 printf("<b>Highest median expression: </b> %0.2f RPKM in %s\n", highestLevel, highestTissue);
 printf("<br><b>Total median expression: </b> %0.2f RPKM<br><br>\n", totalLevel);
 
 struct tempName pngTn;
 if (gtexGeneBoxplot(ensGene, NULL, GTEX_DEFAULT_VERSION, FALSE, &pngTn))
     hPrintf("<img src = '%s' border=1><br>\n", pngTn.forHtml);
 hPrintf("<br><a target='_blank' href='../cgi-bin/hgTracks?%s&gtexGene=pack'>"
                 "View in GTEx track of Genome Browser</a>", cartSidUrlString(cart));
 
 hPrintf("&nbsp;&nbsp;&nbsp;&nbsp;");
 gtexPortalLink(ensGene);
 }
 
 struct section *gtexSection(struct sqlConnection *conn, struct hash *sectionRa)
 /* Create GTEx gene expression section. */
 {
 struct section *section = sectionNew(sectionRa, "gtex");
 if (section != NULL)
     {
     section->exists = gtexExists;
     section->print = gtexPrint;
     }
 return section;
 }