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/outside/hgKegg3/hgKegg3.c src/hg/makeDb/outside/hgKegg3/hgKegg3.c
index 0763dd6..c6b772b 100644
--- src/hg/makeDb/outside/hgKegg3/hgKegg3.c
+++ src/hg/makeDb/outside/hgKegg3/hgKegg3.c
@@ -1,125 +1,125 @@
 /* hgKegg3 - creates keggPathway.tab and keggMapDesc.tab files for KG links to KEGG Pathway Map */
 
 /* 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 "hCommon.h"
 #include "hdb.h"
 #include "options.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgKegg3 - creates keggPathway.tab and keggMapDesc.tab files for KG links to KEGG Pathway Map"
   "usage:\n"
   "   hgKegg3 kgTempDb roDb\n"
   "      kgTempDb is the KG build temp database name\n"
   "      roDb is the read only genome database name\n"
   "example: hgKegg3 kgMm6ATemp mm6\n");
 }
 
 char *table = (char *)NULL;	/*name of table containing knownGenes or other gene prediction*/
 static struct optionSpec options[] = {
    {"table", OPTION_STRING},
    {NULL, 0},
 };
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *conn3;
 char query[256], query3[256];
 struct sqlResult *sr, *sr3;
 char **row, **row3;
 
 FILE *o1, *o2;
 
 char *locusID;	/* LocusLink ID */
 
 char *kgTempDbName, *roDbName; 
 char cond_str[200];
 char *kgId;
 char *mapID;
 char *desc;
 char *mRNA;
 
 optionInit(&argc, argv, options);
 if (argc != 3)  usage();
 kgTempDbName    = argv[1];
 roDbName 	= argv[2];
 
 conn = hAllocConn(roDbName);
 conn3= hAllocConn(roDbName);
 
 o1 = fopen("j.dat",  "w");
 o2 = fopen("jj.dat", "w");
     
 table = optionVal("table", "knownGene");
 sqlSafef(query, sizeof(query), "select name from %s.%s", roDbName, table);
 sr = sqlMustGetResult(conn, query);
 row = sqlNextRow(sr);
 while (row != NULL)
     {
     kgId = row[0];
 	
     sqlSafefFrag(cond_str, sizeof(cond_str), "kgId='%s'", kgId);
     mRNA = sqlGetField(roDbName, "kgXref", "mRNA", cond_str);
     
     sqlSafefFrag(cond_str, sizeof(cond_str), "mrna='%s'", mRNA);
     locusID = sqlGetField("entrez", "entrezMrna", "geneId", cond_str);
     
     /* look for RefSeq if not found in mRNAs */
     if (locusID == NULL)
     	{
     	sqlSafefFrag(cond_str, sizeof(cond_str), "refseq='%s'", mRNA);
     	locusID = sqlGetField("entrez", "entrezRefseq", "geneId", cond_str);
 	}
 
     if (locusID != NULL)
 	{
         sqlSafef(query3, sizeof(query3), "select * from %s.keggList where locusID = '%s'", kgTempDbName, locusID);
         sr3 = sqlGetResult(conn3, query3);
         while ((row3 = sqlNextRow(sr3)) != NULL)
             {
             mapID   = row3[1];
 	    desc    = row3[2];
 	    fprintf(o1, "%s\t%s\t%s\n", kgId, locusID, mapID);
 	    fprintf(o2, "%s\t%s\n", mapID, desc);
 	    row3 = sqlNextRow(sr3);
             }
         sqlFreeResult(&sr3);
 	}
     else
         {
 	/* printf("%s not found in Entrez.\n", kgId);fflush(stdout);*/
         if (differentString(table, "knownGene"))
             {
             sqlSafefFrag(cond_str, sizeof(cond_str), "name='%s'", kgId);
             locusID = sqlGetField(roDbName, table, "name2", cond_str);
             sqlSafef(query3, sizeof(query3), "select * from %s.keggList where locusID = '%s'", kgTempDbName, kgId);
             sr3 = sqlGetResult(conn3, query3);
             while ((row3 = sqlNextRow(sr3)) != NULL)
                 {
                 mapID   = row3[1];
                 desc    = row3[2];
                 fprintf(o1, "%s\t%s\t%s\n", kgId, locusID, mapID);
                 fprintf(o2, "%s\t%s\n", mapID, desc);
                 row3 = sqlNextRow(sr3);
                 }
             sqlFreeResult(&sr3);
             }
         }
     row = sqlNextRow(sr);
     }
 
 fclose(o1);
 fclose(o2);
 hFreeConn(&conn);
 
 mustSystem("cat j.dat|sort|uniq >keggPathway.tab");
 mustSystem("cat jj.dat|sort|uniq >keggMapDesc.tab");
 mustSystem("rm j.dat");
 mustSystem("rm jj.dat");
 return(0);
 }