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/encode3/encodeDataWarehouse/edwAddQaEnrichTarget/edwAddQaEnrichTarget.c src/hg/encode3/encodeDataWarehouse/edwAddQaEnrichTarget/edwAddQaEnrichTarget.c
index ba23ae3..d4692be 100644
--- src/hg/encode3/encodeDataWarehouse/edwAddQaEnrichTarget/edwAddQaEnrichTarget.c
+++ src/hg/encode3/encodeDataWarehouse/edwAddQaEnrichTarget/edwAddQaEnrichTarget.c
@@ -1,91 +1,91 @@
 /* edwAddQaEnrichTarget - Add a new enrichment target to warehouse.. */
 
 /* 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 "linefile.h"
 #include "hash.h"
 #include "cheapcgi.h"
 #include "options.h"
 #include "twoBit.h"
 #include "bigBed.h"
 #include "encodeDataWarehouse.h"
 #include "encode3/encode3Valid.h"
 #include "edwLib.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "edwAddQaEnrichTarget - Add a new enrichment target to warehouse.\n"
   "usage:\n"
   "   edwAddQaEnrichTarget name db path\n"
   "where name is target name, db is a UCSC db name like 'hg19' or 'mm9' and path is absolute\n"
   "path to a simple non-blocked bed file with non-overlapping items.\n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 void edwAddQaEnrichTarget(char *name, char *db, char *path)
 /* edwAddQaEnrichTarget - Add a new enrichment target to warehouse. */
 {
 /* Figure out if we have this genome assembly */
 struct sqlConnection *conn = edwConnectReadWrite();
 char query[256 + PATH_LEN];
 sqlSafef(query, sizeof(query), "select id from edwAssembly where ucscDb='%s'", db);
 int assemblyId = sqlQuickNum(conn, query);
 if (assemblyId == 0)
     errAbort("Assembly %s doesn't exist in warehouse. Typo or time for edwAddAssembly?", db);
 
 /* See if we have target with this name and assembly already and abort with error if we do. */
 sqlSafef(query, sizeof(query), "select id from edwQaEnrichTarget where name='%s' and assemblyId=%d", 
     name, assemblyId);
 int targetId = sqlQuickNum(conn, query);
 if (targetId != 0)
    errAbort("Target %s already exists", name);
 
 /* Load up file as list of beds and compute total size.  Assumes bed is nonoverlapping. */
 struct bbiFile *bbi = bigBedFileOpen(path);
 if (bbi->definedFieldCount > 9)
     errAbort("Can't handle blocked bigBeds");
 struct bbiSummaryElement sum = bbiTotalSummary(bbi);
 long long targetSize = sum.validCount;
 bigBedFileClose(&bbi);
 
 /* Add target file to database. */
 struct edwFile *ef = edwGetLocalFile(conn, path, NULL);
 
 /* Add tags. */
 struct dyString *tags = dyStringNew(0);
 cgiEncodeIntoDy("ucsc_db", db, tags);
 cgiEncodeIntoDy("format", "bigBed", tags);
 cgiEncodeIntoDy("valid_key", encode3CalcValidationKey(ef->md5, ef->size), tags);
 cgiEncodeIntoDy("enriched_in", name, tags);
 edwUpdateFileTags(conn, ef->id, tags);
 dyStringFree(&tags);
 
 /* Add record describing target to database. */
 sqlSafef(query, sizeof(query), 
    "insert edwQaEnrichTarget (assemblyId,name,fileId,targetSize) values(%d, '%s', %lld, %lld)"
    , assemblyId, name, (long long)ef->id, targetSize);
 sqlUpdate(conn, query);
 
 edwAddQaJob(conn, ef->id);
 
 printf("Added target %s, id %u,  size %lld\n", name, sqlLastAutoId(conn), targetSize);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 4)
     usage();
 edwAddQaEnrichTarget(argv[1], argv[2], argv[3]);
 return 0;
 }