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/cdwFakeManifestFromSubmit/cdwFakeManifestFromSubmit.c src/hg/cirm/cdw/cdwFakeManifestFromSubmit/cdwFakeManifestFromSubmit.c
index 3344160..83c6f51 100644
--- src/hg/cirm/cdw/cdwFakeManifestFromSubmit/cdwFakeManifestFromSubmit.c
+++ src/hg/cirm/cdw/cdwFakeManifestFromSubmit/cdwFakeManifestFromSubmit.c
@@ -1,132 +1,132 @@
 /* cdwFakeManifestFromSubmit - Create a fake submission based on a real one that is in the 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 "options.h"
 #include "portable.h"
 #include "cdw.h"
 #include "cdwLib.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "cdwFakeManifestFromSubmit - Create a fake submission based on a real one that is in the warehouse\n"
   "usage:\n"
   "   cdwFakeManifestFromSubmit submitId outDir\n"
   "This will create an out directory populated with manifest.txt and validated.txt\n"
   "and with symbolic links back to cdw files.\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 void fprint2(FILE *f1, FILE *f2, char *format, ...)
 /* Print out to two files */
 #if defined(__GNUC__)
 __attribute__((format(printf, 3, 4)))
 #endif
 ;
 
 void fprint2(FILE *f1, FILE *f2, char *format, ...)
 /* Print out to two files */
 {
 va_list args;
 va_start(args, format);
 vfprintf(f1, format, args);
 va_end(args);
 va_start(args, format);
 vfprintf(f2, format, args);
 va_end(args);
 }
 
 
 void printSharedHeader(FILE *f)
 /* Print out part of header shared by manifest and validated.txt */
 {
 fprintf(f, "#file_name\tformat\toutput_type\texperiment\tenriched_in\tucsc_db\treplicate\tpart\tpaired_end");
 }
 
 void cdwFakeManifestFromSubmit(char *submitIdString, char *outDir)
 /* cdwFakeManifestFromSubmit - Create a fake submission based on a real one that is in the warehouse. */
 {
 struct sqlConnection *conn = cdwConnect();
 char query[512];
 sqlSafef(query, sizeof(query), "select * from cdwSubmit where id=%s", submitIdString);
 struct cdwSubmit *submit = cdwSubmitLoadByQuery(conn, query);
 if (submit == NULL)
     errAbort("Can't find submission %s", submitIdString);
 
 uglyf("%d files in query\n", submit->newFiles);
 sqlSafef(query, sizeof(query), "select * from cdwFile where submitId=%s", submitIdString);
 struct cdwFile *ef, *efList = cdwFileLoadByQuery(conn, query);
 
 FILE *maniF = NULL, *valiF = NULL;
 for (ef = efList; ef != NULL; ef = ef->next)
     {
     struct cdwValidFile *vf = cdwValidFileFromFileId(conn, ef->id);
     if (vf != NULL)
         {
 	/* First time through create out directory and open output files. */
 	if (maniF == NULL)
 	    {
 	    char *fakeVersion = "##validateManifest version 1.7";
 	    makeDirsOnPath(outDir);
 	    setCurrentDir(outDir);
 	    maniF = mustOpen("manifest.txt", "w");
 	    printSharedHeader(maniF);
 	    fprintf(maniF, "\n");
 	    fprintf(maniF, "%s\n", fakeVersion);
 	    valiF = mustOpen("validated.txt", "w");
 	    printSharedHeader(valiF);
 	    fprintf(valiF, "\tmd5_sum\tsize\tmodified\tvalid_key\n");
 	    fprintf(valiF, "%s\n", fakeVersion);
 	    }
 
 	/* Figure out file names */
 	char cdwPath[PATH_LEN], rootName[FILENAME_LEN], ext[FILEEXT_LEN];
 	safef(cdwPath, sizeof(cdwPath), "%s%s", cdwRootDir, ef->cdwFileName);
 	splitPath(ef->cdwFileName, NULL, rootName, ext);
 	char localPath[PATH_LEN];
 	safef(localPath, sizeof(localPath), "%s%s", rootName, ext);
 
 	/* Create sym-linked file and write to manifest */
 	symlink(cdwPath, localPath);
 	fprint2(maniF, valiF, "%s", localPath);
 
 	/* Write other columns shared between manifest and validated */
 	fprint2(maniF, valiF, "\t%s", vf->format);
 	fprint2(maniF, valiF, "\t%s", naForEmpty(vf->outputType));
 	fprint2(maniF, valiF, "\t%s", naForEmpty(vf->experiment));
 	fprint2(maniF, valiF, "\t%s", naForEmpty(vf->enrichedIn));
 	fprint2(maniF, valiF, "\t%s", naForEmpty(vf->ucscDb));
 	fprint2(maniF, valiF, "\t%s", naForEmpty(vf->replicate));
 	fprint2(maniF, valiF, "\t%s", naForEmpty(vf->part));
 	fprint2(maniF, valiF, "\t%s", naForEmpty(vf->pairedEnd));
 	fprintf(maniF, "\n");
 
 	/* Print out remaining fields in validated.txt */
 	fprintf(valiF, "\t%s\t%lld\t%lld\n", ef->md5, ef->size, ef->updateTime);
 	}
     }
 carefulClose(&maniF);
 carefulClose(&valiF);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 cdwFakeManifestFromSubmit(argv[1], argv[2]);
 return 0;
 }