4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/gsid/gsidSubj3/clinical.c src/hg/gsid/gsidSubj3/clinical.c
index 770e99e..0aa80c6 100644
--- src/hg/gsid/gsidSubj3/clinical.c
+++ src/hg/gsid/gsidSubj3/clinical.c
@@ -1,140 +1,140 @@
 /* clinical - do Clinical section. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "cheapcgi.h"
 #include "spDb.h"
 #include "gsidSubj3.h"
 #include "hdb.h"
 #include "net.h"
 
 
 static boolean clinicalExists(struct section *section,
 	struct sqlConnection *conn, char *subjId)
 /* Return TRUE if clinicalAll table exists and it has an entry with the gene symbol */
 {
 if (sqlTableExists(conn, "gsidClinicRec") == TRUE)
     {
     return(TRUE);
     }
 return(FALSE);
 }
 
 static void clinicalPrint(struct section *section,
 	struct sqlConnection *conn, char *subjId)
 /* Print out Clinical section. */
 {
 char bigQuery[2000];
 
 struct sqlResult *sr;
 char **row;
 char *specimenId, *labCode, *daysCollection, *hivQuan, *cd4Count;
 char *naString = strdup("N/A");
 printf("<TABLE BGCOLOR='#222222' CELLSPACING=1 CELLPADDING=3><TR>\n");
 
 printf("<TR>\n");
 printf("<TD align=left BGCOLOR=\"#8686D1\"><B style='color:#FFFFFF;'>Days After Estimated<BR>Infection (DAEI)*</B></TD>\n");
 printf("<TD align=center BGCOLOR=\"#8686D1\"><B style='color:#FFFFFF;'>HIV-1 RNA<BR>copies/mL</B></TD>\n");
 printf("<TD align=center BGCOLOR=\"#8686D1\"><B style='color:#FFFFFF;'>CD4<BR>cells/microliter</B></TD>\n");
 printf("</TR>\n");
 
 /* complex query to ensure date is correctly sorted */
 sqlSafef(bigQuery, sizeof(bigQuery),
 "select specimenId, labCode, daysCollection, hivQuan, cd4Count from gsidClinicRec where subjId='%s' order by daysCollection",
 subjId);
 
 sr = sqlMustGetResult(conn, bigQuery);
 row = sqlNextRow(sr);
 
 /* special processing if this subject does not have any clinical data */
 if (row == NULL)
     {
     /*specimenId     = row[0];
     labCode        = row[1];
     daysCollection = row[2];
     hivQuan        = row[3];
     cd4Count       = row[4];
     */
 
     daysCollection = naString;
     hivQuan = naString;
     cd4Count = naString;
 
     printf("<TR>");
     printf("<TD align=right BGCOLOR=\"#D9F8E4\">%s</TD>\n", daysCollection);
     printf("<TD align=right BGCOLOR=\"#D9F8E4\">%s</TD>\n", hivQuan);
 
     printf("<TD align=right BGCOLOR=\"#D9F8E4\">%s</TD>\n", cd4Count);
     printf("</TR>");
     }
 
 while (row != NULL)
     {
     specimenId     = row[0];
     labCode        = row[1];
     daysCollection = row[2];
     hivQuan        = row[3];
     cd4Count       = row[4];
 
     if (daysCollection == NULL) daysCollection = naString;
     if (hivQuan  == NULL) hivQuan = naString;
     if (cd4Count == NULL) cd4Count = naString;
 
     printf("<TR>");
     printf("<TD align=right BGCOLOR=\"#D9F8E4\">%s</TD>\n", daysCollection);
     //printf("<TD align=right BGCOLOR=\"#D9F8E4\">%s</TD>\n", cd4Count);
     if (sameWord(hivQuan, "1000000"))
 	{
     	printf("<TD align=right BGCOLOR=\"#D9F8E4\">&gt;&nbsp;1000000</TD>\n");
     	}
     else
         {
         if (sameWord(hivQuan, "200"))
 	    {
     	    printf("<TD align=right BGCOLOR=\"#D9F8E4\">&lt;&nbsp;400</TD>\n");
     	    }
     	else
 	    {
             printf("<TD align=right BGCOLOR=\"#D9F8E4\">%s</TD>\n", hivQuan);
     	    }
 	}
 
     if (sameWord(cd4Count, "0"))
 	{
     	printf("<TD align=right BGCOLOR=\"#D9F8E4\">N/A</TD>\n");
     	}
     else
 	{
     	printf("<TD align=right BGCOLOR=\"#D9F8E4\">%s</TD>\n", cd4Count);
     	}
 
     printf("</TR>");
 
     row = sqlNextRow(sr);
     }
 sqlFreeResult(&sr);
 printf("</TR></TABLE>");
 printf("<br>* Estimated Study Day of Infection (ESDI), ");
 printf("click <a href=\"http://www.gsid.org/downloads/methods_and_conventions.pdf\" target=_blank> here </a>");
 printf(" for further explanation.\n");
 printf("<br>* Days After Estimated Infection (DAEI), ");
 printf("click <a href=\"http://www.gsid.org/downloads/methods_and_conventions.pdf\" target=_blank> here </a>");
 printf(" for further explanation.\n");
 return;
 }
 
 struct section *clinicalSection(struct sqlConnection *conn,
 	struct hash *sectionRa)
 /* Create clinical section. */
 {
 struct section *section = sectionNew(sectionRa, "clinical");
 section->exists = clinicalExists;
 section->print = clinicalPrint;
 return section;
 }