293923a610a014d169a8b4c83a3d91719aab942c
kate
  Wed Aug 24 14:54:08 2016 -0700
Comment out broken link to GTEx portal.  Broad has been alerted.

diff --git src/hg/hgc/gtexClick.c src/hg/hgc/gtexClick.c
index dab7f9a..63f7f5d 100644
--- src/hg/hgc/gtexClick.c
+++ src/hg/hgc/gtexClick.c
@@ -1,141 +1,142 @@
 /* Details pages for GTEx tracks */
 
 /* Copyright (C) 2015 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "hash.h"
 #include "hdb.h"
 #include "hvGfx.h"
 #include "trashDir.h"
 #include "hgc.h"
 #include "hCommon.h"
 
 #include "gtexGeneBed.h"
 #include "gtexTissue.h"
 #include "gtexUi.h"
 #include "gtexInfo.h"
 
 char *geneClassColorCode(char *geneClass)
 /* Get HTML color code used by GENCODE for transcript class
  * WARNING: should share code with gene color handling in hgTracks */
 {
 char *unknown = "#010101";
 if (geneClass == NULL)
     return unknown;
 if (sameString(geneClass, "coding"))
     return "#0C0C78";
 if (sameString(geneClass, "nonCoding"))
     return "#006400";
 if (sameString(geneClass, "pseudo"))
     return "#FF33FF";
 if (sameString(geneClass, "problem"))
     return "#FE0000";
 return unknown;
 }
 
 
 static struct gtexGeneBed *getGtexGene(char *item, char *chrom, int start, int end, char *table)
 /* Retrieve gene info for this item from the main track table */
 {
 struct gtexGeneBed *gtexGene = NULL;
 struct sqlConnection *conn = hAllocConn(database);
 char **row;
 char query[512];
 struct sqlResult *sr;
 if (sqlTableExists(conn, table))
     {
     sqlSafef(query, sizeof query, "SELECT * FROM %s WHERE name = '%s' AND chrom = '%s' "
                                   " and chromStart = %d and chromEnd = %d", 
                                         table, item, chrom, start, end);
     sr = sqlGetResult(conn, query);
     row = sqlNextRow(sr);
     if (row != NULL)
         {
         gtexGene = gtexGeneBedLoad(row);
         }
     sqlFreeResult(&sr);
     }
 hFreeConn(&conn);
 return gtexGene;
 }
 
 char *getGeneDescription(struct gtexGeneBed *gtexGene)
 /* Get description for gene. Needed because knownGene table semantics have changed in hg38 */
 {
 char query[256];
 if (sameString(database, "hg38"))
     {
     char *geneId = cloneString(gtexGene->geneId);
     chopSuffix(geneId);
     sqlSafef(query, sizeof(query), 
         "SELECT kgXref.description FROM kgXref, knownCanonical WHERE "
                 "knownCanonical.protein LIKE '%%%s%%' AND "
                 "knownCanonical.transcript=kgXref.kgID", geneId);
     }
 else
     {
     sqlSafef(query, sizeof(query), 
                 "SELECT kgXref.description FROM kgXref WHERE geneSymbol='%s'", 
                         gtexGene->name);
     }
 struct sqlConnection *conn = hAllocConn(database);
 char *desc = sqlQuickString(conn, query);
 hFreeConn(&conn);
 return desc;
 }
 
 void doGtexGeneExpr(struct trackDb *tdb, char *item)
 /* Details of GTEx gene expression item */
 {
 int start = cartInt(cart, "o");
 int end = cartInt(cart, "t");
 struct gtexGeneBed *gtexGene = getGtexGene(item, seqName, start, end, tdb->table);
 if (gtexGene == NULL)
     errAbort("Can't find gene %s in GTEx gene table %s\n", item, tdb->table);
 
 char *version = gtexVersion(tdb->table);
 genericHeader(tdb, item);
 printf("<b>Gene: </b>");
 char *desc = getGeneDescription(gtexGene);
 if (desc == NULL)
     printf("%s<br>\n", gtexGene->name);
 else
     {
     printf("<a target='_blank' href='%s?db=%s&hgg_gene=%s'>%s</a><br>\n", 
                         hgGeneName(), database, gtexGene->name, gtexGene->name);
     printf("<b>Description:</b> %s<br>\n", desc);
     }
 printf("<b>Ensembl gene ID:</b> %s<br>\n", gtexGene->geneId);
 // The actual transcript model is a union, so this identification is approximate
 // (used just to find a transcript class)
 char *geneClass = gtexGeneClass(gtexGene);
 printf("<b>GENCODE biotype: </b> %s<br>\n", gtexGene->geneType); 
 printf("<b>Gene class: </b><span style='color: %s'>%s</span><br>\n", 
             geneClassColorCode(geneClass), geneClass);
 int tisId;
 float highLevel = gtexGeneHighestMedianExpression(gtexGene, &tisId);
 printf("<b>Highest median expression: </b> %0.2f RPKM in %s<br>\n", 
                 highLevel, gtexGetTissueDescription(tisId, version));
 printf("<b>Total median expression: </b> %0.2f RPKM<br>\n", gtexGeneTotalMedianExpression(gtexGene));
 printf("<b>Score: </b> %d<br>\n", gtexGene->score); 
 printf("<b>Genomic position: "
                 "</b>%s <a href='%s&db=%s&position=%s%%3A%d-%d'>%s:%d-%d</a><br>\n", 
                     database, hgTracksPathAndSettings(), database, 
                     gtexGene->chrom, gtexGene->chromStart+1, gtexGene->chromEnd,
                     gtexGene->chrom, gtexGene->chromStart+1, gtexGene->chromEnd);
 puts("<p>");
 
 // set gtexDetails (e.g. to 'log') to show log transformed details page 
 //      if hgTracks is log-transformed
 boolean doLogTransform = 
         (trackDbSetting(tdb, "gtexDetails") &&
             cartUsualBooleanClosestToHome(cart, tdb, FALSE, GTEX_LOG_TRANSFORM,
                                                 GTEX_LOG_TRANSFORM_DEFAULT));
 struct tempName pngTn;
 if (gtexGeneBoxplot(gtexGene->geneId, gtexGene->name, version, doLogTransform, &pngTn))
     printf("<img src = \"%s\" border=1><br>\n", pngTn.forHtml);
 printf("<br>");
-gtexPortalLink(gtexGene->geneId);
+//gtexPortalLink(gtexGene->geneId);
+// Link broken as of 8/23/16.  Broad has been alerted.
 printTrackHtml(tdb);
 }