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/makeDb/hgRgdParsePathwayObo/hgRgdParsePathwayObo.c src/hg/makeDb/hgRgdParsePathwayObo/hgRgdParsePathwayObo.c
index 18eb0dc..ee5ce40 100644
--- src/hg/makeDb/hgRgdParsePathwayObo/hgRgdParsePathwayObo.c
+++ src/hg/makeDb/hgRgdParsePathwayObo/hgRgdParsePathwayObo.c
@@ -1,127 +1,127 @@
 /* hgRgdParsePathwayObo - Create a relational database out of RGD pathway .obo file. */
 
 /* Copyright (C) 2011 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 "linefile.h"
 #include "portable.h"
 #include "obscure.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgRgdParsePathwayObo - Parse RGD pathway .obo file\n"
   "usage:\n"
   "   hgRgdParsePathwayObo pathway.obo\n"
   );
 }
 
 char *line;
 int lineSize;
 
 FILE *namef;
 FILE *deff;
 FILE *is_af;
 
 FILE *createAt(char *file)
 /* Open file */
 {
 char path[PATH_LEN];
 safef(path, sizeof(path), "%s", file);
 return mustOpen(path, "w");
 }
 
 void pathwayRecordNext(struct lineFile *lf)
 {
 char emptyString[2] = {""};
 
 char *chp;
 char *pathwayId;
 char *name = NULL;
 char *def, *comment;
 char *is_a;
 
 while (!strstr(line, "[Term]"))
     {
     if (!lineFileNext(lf, &line, &lineSize)) exit(1);
     }
 
 lineFileNext(lf, &line, &lineSize);
 chp = strstr(line, "id: ");
 chp = chp + strlen("id: ");
 pathwayId = strdup(chp);
 
 lineFileNext(lf, &line, &lineSize);
 if (strstr(line, "name: ") != NULL)
     {
     chp = strstr(line, "name: ");
     chp = chp + strlen("name: ");
     name= strdup(chp);
     if (strstr(pathwayId, "PW:") != NULL) fprintf(namef, "%s\t%s\n", pathwayId, name);fflush(namef);
     }
 else
     {
     errAbort("name: expected");
     }
 
 def     = emptyString;
 comment = emptyString;
 
 while (lineFileNext(lf, &line, &lineSize))
     {
     if (strstr(line, "[Term]") != NULL)break;
 
     if (strstr(line, "def: ") != NULL)
     	{
     	chp = strstr(line, "def: ");
     	chp = chp + strlen("def: ") + 1;
     	def = strdup(chp);
     	chp = def + strlen(def);
     	*chp = '\0';
     	if (strstr(pathwayId, "PW:") != NULL) fprintf(deff, "%s\t%s\t%s\n", pathwayId, name, def);fflush(deff);
     	}		
     else
     	{
     	if (strstr(line, "is_a: ") != NULL) 
     	    {
             chp = strstr(line, "is_a: ");
     	    chp = chp + strlen("is_a: ");
 	    is_a = strdup(chp);
             chp = strstr(is_a, " !");
 	    *chp = '\0';
 	    if (strstr(pathwayId, "PW:") != NULL) fprintf(is_af, "%s\t%s\n", pathwayId, is_a);fflush(is_af);
             }  
     	}	
     }
 }
 
 void hgRgdParsePathwayObo(char *datFile)
 /* hgRgdParsePathwayObo - Create a relational database out of .obo pathway file. */
 {
 struct lineFile *lf = lineFileOpen(datFile, TRUE);
 
 namef = createAt("rgdPathway.tab");
 deff  = createAt("rgdPathwayDef.tab");
 is_af = createAt("rgdPathway_isa.tab");
 
 lineFileNext(lf, &line, &lineSize);
 for (;;)
     {
     pathwayRecordNext(lf);
     }
 
 carefulClose(&namef);
 carefulClose(&deff);
 carefulClose(&is_af);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 if (argc != 2)
     usage();
 hgRgdParsePathwayObo(argv[1]);
 return 0;
 }