e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/hgGene/gad.c src/hg/hgGene/gad.c
index e349285..7f6b6dc 100644
--- src/hg/hgGene/gad.c
+++ src/hg/hgGene/gad.c
@@ -1,160 +1,163 @@
 /* gad - do GAD section. */
 
+/* Copyright (C) 2013 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 "cheapcgi.h"
 #include "spDb.h"
 #include "hgGene.h"
 #include "hdb.h"
 #include "net.h"
 
 
 static boolean gadExists(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Return TRUE if gadAll table exists and it has an entry with the gene symbol */
 {
 char query[1024];
 char *geneSymbol;
 
 if (sqlTableExists(conn, "gadAll") == TRUE)
     {
     sqlSafef(query, sizeof(query), "select k.geneSymbol from kgXref k, gadAll g"
 	" where k.kgId='%s' and k.geneSymbol = g.geneSymbol", geneId);
     geneSymbol = sqlQuickString(conn, query);
     if (geneSymbol != NULL) return(TRUE);
 /*
     sqlSafefFrag(condStr, sizeof(condStr), 
     "k.kgId='%s' and k.geneSymbol = g.geneSymbol", geneId);
     geneSymbol = sqlGetField(database, "kgXref k, gadAll g", "k.geneSymbol", condStr);
 */
     }
 return(FALSE);
 }
 
 static void gadPrint(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Print out GAD section. */
 {
 int refPrinted = 0;
 boolean showCompleteGadList;
 
 char query[1024];
 struct sqlResult *sr;
 char **row;
 struct dyString *currentCgiUrl;
 char *upperDisease;
 
 char *url = 
 cloneString("http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=gene=");
 char *itemName;
 
 if (url != NULL && url[0] != 0)
     {
     sqlSafef(query, sizeof(query), "select k.geneSymbol from kgXref k, gadAll g"
 	" where k.kgId='%s' and k.geneSymbol = g.geneSymbol", geneId);
     itemName = sqlQuickString(conn, query);
     showCompleteGadList = FALSE;
     if (cgiOptionalString("showAllRef") != NULL)
     	{
         if (sameWord(cgiOptionalString("showAllRef"), "Y") ||
 	    sameWord(cgiOptionalString("showAllRef"), "y") )
 	    {
 	    showCompleteGadList = TRUE;
 	    }
 	}
     currentCgiUrl = cgiUrlString();
    
     printf("<B>Genetic Association Database: ");
     printf("<A HREF=\"%s'%s'\" target=_blank>", url, itemName);
     printf("%s</B></A>\n", itemName);
 
     printf("<BR><B>CDC HuGE Published Literature:  ");
     printf("<A HREF=\"%s%s%s\" target=_blank>", 
            "http://hugenavigator.net/HuGENavigator/searchSummary.do?firstQuery=",
            itemName, 
 	   "&publitSearchType=now&whichContinue=firststart&check=n&dbType=publit&Mysubmit=go");
     printf("%s</B></A>\n", itemName);
 
     /* List diseases associated with the gene */
     sqlSafef(query, sizeof(query),
     "select distinct broadPhen from gadAll where geneSymbol='%s' and association = 'Y' order by broadPhen",
     itemName);
     sr = sqlMustGetResult(conn, query);
     row = sqlNextRow(sr);
     
     if (row != NULL) 
     	{
 	upperDisease = replaceChars(row[0], "'", "''");
 	touppers(upperDisease);
 	printf("<BR><B>Positive Disease Associations:  </B>");
 	printf("<A HREF=\"%s%s%s%s%s\" target=_blank>",
 	"http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=upper(DISEASE)%20like%20'%25",
 	cgiEncode(upperDisease), "%25'%20AND%20upper(GENE)%20%20like%20'%25", itemName, "%25'");
 	printf("%s</B></A>\n", row[0]);
         row = sqlNextRow(sr);
     	}
     while (row != NULL)
         {
 	upperDisease = replaceChars(row[0], "'", "''");
 	touppers(upperDisease);
 	printf(", <A HREF=\"%s%s%s%s%s\" target=_blank>",
 	"http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=upper(DISEASE)%20like%20'%25",
 	cgiEncode(upperDisease), "%25'%20AND%20upper(GENE)%20%20like%20'%25", itemName, "%25'");
 	printf("%s</B></A>\n", row[0]);
         row = sqlNextRow(sr);
 	}
     sqlFreeResult(&sr);
 
     refPrinted = 0;
     sqlSafef(query, sizeof(query), 
        "select broadPhen,reference,title,journal, pubMed, conclusion from gadAll where geneSymbol='%s' and association = 'Y' order by broadPhen",
        itemName);
     sr = sqlMustGetResult(conn, query);
     row = sqlNextRow(sr);
     
     if (row != NULL) printf("<BR><B>Related Studies: </B><OL>");
     while (row != NULL)
         {
         printf("<LI><B>%s </B>", row[0]);
 
 	printf("<br>%s, %s, %s.\n", row[1], row[2], row[3]);
 	if (!sameWord(row[4], ""))
 	    {
 	    printf(" [PubMed ");
 	    printf("<A HREF=\"%s%s%s'\" target=_blank>",
 	    "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=",
 	    row[4],"&query_hl=1&itool=genome.ucsc.edu");
 	    printf("%s</B></A>]\n", row[4]);
 	    }
 	printf("<br><i>%s</i>\n", row[5]);
 	
 	printf("</LI>\n");
         refPrinted++;
         if ((!showCompleteGadList) && (refPrinted >= 3)) break;
 	row = sqlNextRow(sr);
     	}
     sqlFreeResult(&sr);
     printf("</OL>");
     
     if ((!showCompleteGadList) && (row != NULL))
     	{
         printf("<B>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; more ...  </B>");
         printf(
 	      "<A HREF=\"%s?showAllRef=Y&%s&#35;gad\">click here to view the complete list</A> ", 
 	      "hgGene", currentCgiUrl->string);
     	}
     }
 }
 
 struct section *gadSection(struct sqlConnection *conn, 
 	struct hash *sectionRa)
 /* Create gad section. */
 {
 struct section *section = sectionNew(sectionRa, "gad");
 section->exists = gadExists;
 section->print = gadPrint;
 return section;
 }