aab7eb309928e1ffedf18e8cf017dab5c86cfc08
ccpowell
  Thu Aug 8 14:19:17 2019 -0700
Fixing GO subSection links, refs #23939

diff --git src/hg/hgGene/go.c src/hg/hgGene/go.c
index 8733071..290a929 100644
--- src/hg/hgGene/go.c
+++ src/hg/hgGene/go.c
@@ -1,111 +1,147 @@
 /* go - Gene Ontology annotations. */
 
 /* Copyright (C) 2014 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 "spDb.h"
 #include "hgGene.h"
 #include "hdb.h"
 
 
 static boolean goExists(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Return TRUE if GO database exists and has something
  * on this one. */
 {
 char query[512];
 char *fbAcc = getFlyBaseId(conn, geneId);
 boolean useFbGo = (isFly() && fbAcc != NULL && sqlTableExists(conn, "fbGo"));
 if (!sqlDatabaseExists("go"))
     return(FALSE);
 if (useFbGo)
     {
     sqlSafef(query, sizeof(query),
 	  "select count(*) from fbGo where geneId = '%s'",
 	  fbAcc);
     return sqlQuickNum(conn, query) > 0;
     }
 else
     {
     if (swissProtAcc == NULL || !sqlTableExists(conn, "go.goaPart"))
 	return FALSE;
     sqlSafef(query, sizeof(query),
 	  "select count(*) from go.goaPart where dbObjectId = '%s'",
 	  swissProtAcc);
     return sqlQuickNum(conn, query) > 0;
     }
 }
 
 static void goPrint(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Print out GO annotations. */
 {
 struct sqlConnection *goConn = hAllocConn("go");
 char *fbAcc = getFlyBaseId(conn, geneId);
 boolean useFbGo = (isFly() && fbAcc != NULL && sqlTableExists(conn, "fbGo"));
 char *acc = useFbGo ? fbAcc : swissProtAcc;
 char query[512];
 struct sqlResult *sr;
 char **row;
 static char *aspects[3] = {"F", "P", "C"};
 static char *aspectNames[3] = {
     "Molecular Function",
     "Biological Process",
     "Cellular Component",
 };
 int aspectIx;
 
 for (aspectIx = 0; aspectIx < ArraySize(aspects); ++aspectIx)
     {
     boolean hasFirst = FALSE;
     if (useFbGo)
 	sqlSafef(query, sizeof(query),
 	      "select term.acc,term.name"
 	      " from %s.fbGo,term"
 	      " where %s.fbGo.geneId = '%s'"
 	      " and %s.fbGo.goId = term.acc"
 	      " and %s.fbGo.aspect = '%s'",
 	      database, database, acc, database, database, aspects[aspectIx]);
     else
 	sqlSafef(query, sizeof(query),
 	      "select term.acc,term.name"
 	      " from goaPart,term"
 	      " where goaPart.dbObjectId = '%s'"
 	      " and goaPart.goId = term.acc"
 	      " and goaPart.aspect = '%s'"
 	      , acc, aspects[aspectIx]);
     sr = sqlGetResult(goConn, query);
     while ((row = sqlNextRow(sr)) != NULL)
 	{
 	char *goID = row[0];
 	char *goTermName = row[1];
+  /*	if (!hasFirst)
+	    {
+	    hPrintf("<B>good, %s:</B><BR>", aspectNames[aspectIx]);
+	    hasFirst = TRUE; 
+	    }
+		if ( strcmp(aspectNames[aspectIx], "Molecular Function") == 0)
+        		{
+			hPrintf("<A HREF = \"");
+			hPrintf("http://amigo.geneontology.org/amigo/search/ontology?q=%s", goID);
+			hPrintf("\" TARGET=_blank>%s</A> %s<BR>\n", goID, goTermName);
+        		}
+		else if ( strcmp(aspectNames[aspectIx], "Biological Process") == 0)
+                        {
+                        hPrintf("<A HREF = \"");
+                        hPrintf("http://amigo.geneontology.org/amigo/search/bioentity?q=%s", goID);
+                        hPrintf("\" TARGET=_blank>%s</A> %s<BR>\n", goID, goTermName);
+                        }
+		else if ( strcmp(aspectNames[aspectIx], "Cellular Component") == 0)
+                        {
+                        hPrintf("<A HREF = \"");
+                        hPrintf("http://amigo.geneontology.org/amigo/search/annotation?q=%s", goID);
+                        hPrintf("\" TARGET=_blank>%s</A> %s<BR>\n", goID, goTermName);
+                        } */
         if (!hasFirst)
             {
-	    hPrintf("<B>%s:</B><BR>", aspectNames[aspectIx]);
+            hPrintf("<B>good, %s:</B><BR>", aspectNames[aspectIx]);
             hasFirst = TRUE; 
             }
 		hPrintf("<A HREF = \"");
-	hPrintf("http://amigo1.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=%s", goID);
+                if ( strcmp(aspectNames[aspectIx], "Molecular Function") == 0)
+                        {
+                        hPrintf("http://amigo.geneontology.org/amigo/search/ontology?q=%s", goID);
+                        }
+                else if ( strcmp(aspectNames[aspectIx], "Biological Process") == 0)
+                        {
+                        hPrintf("http://amigo.geneontology.org/amigo/search/bioentity?q=%s", goID);
+                        }
+                else if ( strcmp(aspectNames[aspectIx], "Cellular Component") == 0)
+                        {
+                        hPrintf("http://amigo.geneontology.org/amigo/search/annotation?q=%s", goID);
+                        }
+		
                 hPrintf("\" TARGET=_blank>%s</A> %s<BR>\n", goID, goTermName);
+ 
 	}
     if (hasFirst)
         hPrintf("<BR>");
     sqlFreeResult(&sr);
     }
 hFreeConn(&goConn);
 }
 
 struct section *goSection(struct sqlConnection *conn,
 	struct hash *sectionRa)
 /* Create GO annotations section. */
 {
 struct section *section = sectionNew(sectionRa, "go");
 section->exists = goExists;
 section->print = goPrint;
 return section;
 }