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/protein/spXref3/spXref3.c src/hg/protein/spXref3/spXref3.c
index 0152fbd..3fcdfd4 100644
--- src/hg/protein/spXref3/spXref3.c
+++ src/hg/protein/spXref3/spXref3.c
@@ -1,119 +1,119 @@
 /* spXref3 - get xref data of proteins in SWISS-PROT, TrEMBL, TrEMBL-NEW and HUGO
    and create spXref3.tab file to be imported into proteinxxxx database */
 
 /* 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"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "spXref3 - get xref data of proteins in SWISS-PROT, TrEMBL, TrEMBL-NEW and HUGO.\n"
   "          Output is placed in file spXref3.tab.\n"
   "usage:\n"
   "   spXref3 xxxx \n"
   "      xxxx is the release date of SWISS-PROT data\n"
   "example: spXref3 070403\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *conn2, *conn3;
 char query[256], query2[256];
 struct sqlResult *sr, *sr2;
 char **row, **row2;
 
 char *hugoSymbol;
 char *hugoDesc;
     
 char *chp;
 char *proteinDataDate;
 
 char *bioentry_id;
 char *biodatabase_id;
 char *display_id;
 char *accession;
 char *entry_version;
 char *division;     
 char *description;
 
 char cond_str[100]; 
 char *ontology_term_id;
 
 char proteinDatabaseName[40];    
 FILE *o1;
 char empty_str[1] = {""};
 
 if (argc != 2) usage();
 proteinDataDate = argv[1];
 
 o1 = fopen("spXref3.tab", "w");
 
 conn = hAllocConn(hDefaultDb());
 conn2= hAllocConn(hDefaultDb());
 conn3= hAllocConn(hDefaultDb());
    
 sprintf(proteinDatabaseName, "biosql%s", proteinDataDate);
 sqlSafefFrag(cond_str, sizeof cond_str, "term_name = 'description'");
 ontology_term_id = sqlGetField(proteinDatabaseName, "ontology_term", 
                                "ontology_term_id", cond_str); 
 
 sprintf(proteinDatabaseName, "proteins%s", proteinDataDate);
 sqlSafef(query2, sizeof query2, "select * from biosql%s.bioentry;", proteinDataDate);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     bioentry_id 	= row2[0];    
     biodatabase_id 	= row2[1]; 
     display_id		= row2[2];     
     accession		= row2[3];      
     entry_version	= row2[4];  
     division		= row2[5];
 			       
     sqlSafef(query, sizeof query,
 	    "select qualifier_value from biosql%s.bioentry_qualifier_value where bioentry_id=%s and ontology_term_id=%s;",
 	    proteinDataDate, bioentry_id, ontology_term_id);
 
     sqlSafefFrag(cond_str, sizeof cond_str, "swissprot='%s'", accession);
     hugoSymbol = sqlGetField(proteinDatabaseName, "hugo", "symbol", cond_str);
     hugoDesc = sqlGetField(proteinDatabaseName, "hugo", "name", cond_str);
 
     if (hugoSymbol==NULL) hugoSymbol = empty_str;
     if (hugoDesc==NULL)   hugoDesc   = empty_str;
 
     sr = sqlMustGetResult(conn, query);
     row = sqlNextRow(sr);
     while (row != NULL)
     	{
     	description = row[0];
 	chp = strstr(description, "(");
 	if (chp != NULL)
 	    {
 	    *chp = '\0';
 	    }
 	fprintf(o1, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n", 
 		accession, 
 		display_id,  
 		division,
 		bioentry_id, 
 		biodatabase_id,
 		description,
 		hugoSymbol,
 		hugoDesc
 	       );
 	row = sqlNextRow(sr);
 	}
     sqlFreeResult(&sr);
     row2 = sqlNextRow(sr2);
     }
 fclose(o1);
 sqlFreeResult(&sr2);
 hFreeConn(&conn);
 hFreeConn(&conn2);
 hFreeConn(&conn3);
 return(0);
 }