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/vaccine.c src/hg/gsid/gsidSubj3/vaccine.c
index 3a17bff..0a14e9f 100644
--- src/hg/gsid/gsidSubj3/vaccine.c
+++ src/hg/gsid/gsidSubj3/vaccine.c
@@ -1,199 +1,199 @@
 /* vaccine - do Vacceine and HIV Status 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 vaccineExists(struct section *section, 
 	struct sqlConnection *conn, char *subjId)
 /* Return TRUE if vaccineAll table exists and it has an entry with the gene symbol */
 {
 if (sqlTableExists(conn, "gsidSubjInfo") == TRUE)
     {
     return(TRUE);
     }
 return(FALSE);
 }
 
 void vxprintf(char *templ, char *string)
 /* print "N/A" if the string to be printed is NULL */
 {
 if (string == NULL) 
     printf(templ, "N/A");
 else
     printf(templ, string);
 }
 
 static void vaccinePrint(struct section *section, 
 	struct sqlConnection *conn, char *subjId)
 /* Print out Vaccine section. */
 {
 char *immunStatus = NULL;
 char *daysInfectF = NULL;
 char *daysInfectL = NULL;
 char *injections  = NULL;
 
 char *startDate       = NULL;
 char *lastSeroNegDay  = NULL;
 char *firstSeroPosDay = NULL;
 char *firstRNAPosDay  = NULL;
 char *ESDBasis	      = NULL;
 char *seqDay	      = NULL;
 
 char *art_daei        = NULL;
 char *art_sequencing  = NULL;
  
 char query[256];
 struct sqlResult *sr;
 char **row;
 
 printf("<TABLE>");
 
 sqlSafef(query, sizeof(query), 
       "select art_daei, art_sequencing from hgFixed.artDaei where subjId='%s'", 
       subjId);
 sr = sqlMustGetResult(conn, query);
 row = sqlNextRow(sr);
 if (row != NULL) 
     {
     art_daei       = cloneString(row[0]);
     art_sequencing = cloneString(row[1]);
     }
 sqlFreeResult(&sr);
 
 sqlSafef(query, sizeof(query), 
       "select immunStatus, daysInfectF, daysInfectL, injections from gsidSubjInfo where subjId='%s'", 
       subjId);
 sr = sqlMustGetResult(conn, query);
 row = sqlNextRow(sr);
 if (row != NULL) 
     {
     immunStatus  = cloneString(row[0]);
     daysInfectF	 = cloneString(row[1]);
     daysInfectL  = cloneString(row[2]);
     injections   = cloneString(row[3]);
     }
 sqlFreeResult(&sr);
 
 sqlSafef(query, sizeof(query), 
       "select startDate,lastSeroNegDay,firstSeroPosDay,firstRNAPosDay,ESDBasis,seqDay from hgFixed.testDates where subjId='%s'", subjId);
 sr = sqlMustGetResult(conn, query);
 row = sqlNextRow(sr);
 if (row != NULL) 
     {
     startDate 	    = cloneString(row[0]);
     lastSeroNegDay  = cloneString(row[1]);
     firstSeroPosDay = cloneString(row[2]);
     firstRNAPosDay  = cloneString(row[3]);
     ESDBasis        = cloneString(row[4]);
     seqDay    	    = cloneString(row[5]);
     }
 sqlFreeResult(&sr);
 
 printf("<TR>");
 printf("<TD>");
 printf("<B>Vaccine/Placebo:</B> %s%s", immunStatus, GSBLANKS);
 printf("</TD>");
     
 printf("<TD>");
 vxprintf("<B>ART at Sequencing?</B> %s", art_sequencing);
 printf("</TD>");
 printf("</TR>");
 
 printf("<TR>");
 printf("<TD>");
 /* !!! currently all subjects in the database are infected. */
 /* update this when non-infected subjects addded into DB */
 
 printf("<B>HIV Status:</B> %s%s", "Infected", GSBLANKS);
 printf("</TD>");
     
 printf("<TD>");
 vxprintf("<B>DAEI for ART Start:</B> %s", art_daei);
 printf("</TD>");
 printf("</TR>");
 
 /* removed the following item per GSID user feedback */
 /*printf("<TD>");
 printf("<B>Days of infection relative to last negative date:</B> %s\n", 
        daysInfectL);
 printf("</TD>");
 */
     
 printf("<TR>");
 printf("<TD>");
 printf("<B>Injections:</B> &nbsp;%s%s", injections, GSBLANKS);
 printf("</TD>");
     
 printf("<TD>");
 
 if (sameWord(lastSeroNegDay, "-1"))
     printf("<B>Study Day of Last Serology-Negative HIV Test: </B> %s\n", 
 	   "N/A");
 else
     vxprintf("<B>Study Day of Last Serology-Negative HIV Test: </B> %s\n", 
 	     lastSeroNegDay);
 printf("</TD>");
 printf("</TR>");
 
 printf("<TR>");
 printf("<TD>");
 vxprintf("<B>Date of Study Start:</B> %s\n", 
        startDate);
 printf("</TD>");
 
 printf("<TD>");
 vxprintf("<B>Study Day of First Serology-Positive HIV Test:</B> %s\n", 
        firstSeroPosDay);
 printf("</TD>");
 printf("</TR>");
 
 printf("<TR>");
 printf("<TD>");
 vxprintf("<B>Estimated Study Day of Infection (ESDI)*:</B> %s\n", 
 	daysInfectF);
 printf("</TD>");
 
 printf("<TD>");
 vxprintf("<B>Study Day of First RNA-positive HIV Test (NAT):</B> %s\n", firstRNAPosDay);
 printf("</TD>");
 printf("</TR>");
 
 printf("<TR>");
 printf("<TD>");
 if (sameWord(seqDay, "-1"))
     printf("<B>Study Day of Sequencing:</B> N/A\n");
 else
     vxprintf("<B>Study Day of Sequencing:</B> %s\n", seqDay);
 printf("</TD>");
 
 printf("<TD>");
 vxprintf("<B>Basis for ESDI:</B> %s\n", 
         ESDBasis);
 printf("</TD>");
 printf("</TR>");
 
 printf("</TABLE>");
 return;
 }
 
 struct section *vaccineSection(struct sqlConnection *conn, 
 	struct hash *sectionRa)
 /* Create vaccine section. */
 {
 struct section *section = sectionNew(sectionRa, "vaccine");
 section->exists = vaccineExists;
 section->print = vaccinePrint;
 return section;
 }