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/cirm/cdw/cdwAddAssembly/cdwAddAssembly.c src/hg/cirm/cdw/cdwAddAssembly/cdwAddAssembly.c
index 5b9dcee..d62e802 100644
--- src/hg/cirm/cdw/cdwAddAssembly/cdwAddAssembly.c
+++ src/hg/cirm/cdw/cdwAddAssembly/cdwAddAssembly.c
@@ -1,89 +1,89 @@
 /* cdwAddAssembly - Add an assembly to database.. */
 
 /* Copyright (C) 2014 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 "hash.h"
 #include "cheapcgi.h"
 #include "options.h"
 #include "jksql.h"
 #include "twoBit.h"
 #include "cdwValid.h"
 #include "cdw.h"
 #include "cdwLib.h"
 
 char *givenMd5;    /* If set then just symlink the twobit file rather than copy */
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "cdwAddAssembly - Add an assembly to database.\n"
   "usage:\n"
   "   cdwAddAssembly taxon name ucscDb twoBitFile\n"
   "options:\n"
   "   -givenMd5=MD5SUM - if set then use the given MD5SUM\n"
   "                     rather than calculating it.  Just to speed up testing."
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {"givenMd5", OPTION_STRING},
    {NULL, 0},
 };
 
 
 void cdwAddAssembly(char *taxonString, char *name, char *ucscDb, char *twoBitFile)
 /* cdwAddAssembly - Add an assembly to database.. */
 {
 /* Convert taxon to integer. */
 int taxon = sqlUnsigned(taxonString);
 
 
 /* See if we have assembly with this name already and abort with error if we do. */
 struct sqlConnection *conn = sqlConnect(cdwDatabase);
 char query[256 + PATH_LEN];
 sqlSafef(query, sizeof(query), "select id from cdwAssembly where name='%s'", name);
 int asmId = sqlQuickNum(conn, query);
 if (asmId != 0)
    errAbort("Assembly %s already exists", name);
 
 /* Get total sequence size from twoBit file, which also makes sure it exists in right format. */
 struct twoBitFile *tbf = twoBitOpen(twoBitFile);
 long long baseCount = twoBitTotalSize(tbf);
 long long realBaseCount = twoBitTotalSizeNoN(tbf);
 int seqCount = tbf->seqCount;
 twoBitClose(&tbf);
 
 /* Create file record and add tags. */
 struct cdwFile *ef= cdwGetLocalFile(conn, twoBitFile, givenMd5);
 struct dyString *tags = dyStringNew(0);
 cgiEncodeIntoDy("ucsc_db", ucscDb, tags);
 cgiEncodeIntoDy("format", "2bit", tags);
 cgiEncodeIntoDy("valid_key", cdwCalcValidationKey(ef->md5, ef->size), tags);
 cdwUpdateFileTags(conn, ef->id, tags);
 dyStringFree(&tags);
 
 /* Insert info into cdwAssembly record. */
 sqlSafef(query, sizeof(query), 
    "insert cdwAssembly (taxon,name,ucscDb,twoBitId,baseCount,realBaseCount,seqCount) "
                 "values(%d, '%s', '%s', %lld, %lld, %lld, %d)"
 		, taxon, name, ucscDb, (long long)ef->id, baseCount, realBaseCount, seqCount);
 sqlUpdate(conn, query);
 cdwAddQaJob(conn, ef->id, 0);
 
 sqlDisconnect(&conn);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 5)
     usage();
 givenMd5 = optionVal("givenMd5", NULL);
 cdwAddAssembly(argv[1], argv[2], argv[3], argv[4]);
 return 0;
 }