000226be7ecaa7674455d3968af3590ff2a047b3
kate
  Thu Apr 28 13:13:40 2016 -0700
Add GTEx gene expression boxplot to hg38 and hg19 hgGene pages. Remove old GTEx link. refs #17244

diff --git src/hg/hgGene/gtex.c src/hg/hgGene/gtex.c
new file mode 100644
index 0000000..db90050
--- /dev/null
+++ src/hg/hgGene/gtex.c
@@ -0,0 +1,62 @@
+/* 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 "gtexUi.h"
+
+static boolean gtexExists(struct section *section, struct sqlConnection *conn, char *geneId)
+/* 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;
+sqlSafef(query, sizeof(query), 
+    "SELECT ensGene.name2 FROM ensGene, knownToEnsembl WHERE "
+        "knownToEnsembl.name='%s' AND "
+        "ensGene.name=SUBSTRING_INDEX(knownToEnsembl.value,'.',1)", geneId);
+char *ensGene = sqlQuickString(conn, query);
+if (!ensGene)
+    return FALSE;
+sqlSafef(query, sizeof(query), 
+    "select geneId from gtexGene where geneId like '%s%%'", ensGene);
+ensGene = sqlQuickString(conn, query);
+if (!ensGene)
+    return FALSE;
+section->items = cloneString(ensGene);
+return TRUE;
+}
+
+static void gtexPrint(struct section *section, struct sqlConnection *conn, char *geneId)
+/* Print out GTEx gene expression boxplot */
+{
+struct tempName pngTn;
+char *ensGene = section->items;
+if (gtexGeneBoxplot(ensGene, NULL, GTEX_DEFAULT_VERSION, FALSE, &pngTn))
+    hPrintf("<IMG SRC = \"%s\" BORDER=1><BR>\n", pngTn.forHtml);
+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;
+}
+