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/utils/hubPublicCheck/hubPublicCheck.c src/hg/utils/hubPublicCheck/hubPublicCheck.c
index 79ad1b0..33e23e7 100644
--- src/hg/utils/hubPublicCheck/hubPublicCheck.c
+++ src/hg/utils/hubPublicCheck/hubPublicCheck.c
@@ -1,172 +1,172 @@
 /* hubPublicCheck - checks that the labels in hubPublic match what is in the hub labels. */
 
 /* 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 "hdb.h"
 #include "udc.h"
 #include "options.h"
 #include "hubConnect.h"
 #include "errCatch.h"
 #include "trackHub.h"
 #include "dystring.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hubPublicCheck - checks that the labels in hubPublic match what is in the hub labels\n"
   "   outputs SQL statements to put the table into compliance\n"
   "usage:\n"
   "   hubPublicCheck tableName \n"
   "options:\n"
   "   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs\n"
   "   -addHub=url           - output statments to add url to table\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"udcDir", OPTION_STRING},
    {"addHub", OPTION_STRING},
    {NULL, 0},
 };
 
 int hubPublicCheck(char *table)
 /* hubPublicCheck - checks that the labels in hubPublic match what is in the hub labels. */
 {
 struct sqlConnection *conn = hConnectCentral();
 char query[512];
 bool hasDescriptionUrl = sqlColumnExists(conn, table, "descriptionUrl");
 if (hasDescriptionUrl)
     sqlSafef(query, sizeof(query), "select hubUrl, shortLabel,longLabel,dbList,descriptionUrl from %s", 
 	table); 
 else
     sqlSafef(query, sizeof(query), "select hubUrl, shortLabel,longLabel,dbList from %s", 
 	table); 
 
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row;
 int differences = 0;
 
 while ((row = sqlNextRow(sr)) != NULL)
     {
     char *url = row[0], *shortLabel = row[1], *longLabel = row[2], *dbList = row[3], *descriptionUrl = row[4];
     struct errCatch *errCatch = errCatchNew();
     boolean gotWarning = FALSE;
     struct trackHub *tHub = NULL;
     
     if (errCatchStart(errCatch))
 	tHub = trackHubOpen(url, "hub_1"); 
     errCatchEnd(errCatch);
     if (errCatch->gotError)
 	{
 	gotWarning = TRUE;
 	warn("%s", errCatch->message->string);
 	}
     errCatchFree(&errCatch);
 
     if (gotWarning)
 	{
 	continue;
 	}
 
     if (!sameString(shortLabel, tHub->shortLabel))
 	{
 	differences++;
 
 	printf("update %s set shortLabel=\"%s\" where hubUrl=\"%s\";\n",table, tHub->shortLabel, url);
 	}
     if (!sameString(longLabel, tHub->longLabel))
 	{
 	differences++;
 
 	printf("update %s set longLabel=\"%s\" where hubUrl=\"%s\";\n",table, tHub->longLabel, url);
 	}
 
     struct dyString *dy = newDyString(1024);
     struct trackHubGenome *genome = tHub->genomeList;
 
     unsigned dbCount = 0;
     for(; genome; genome = genome->next)
         {
         dbCount++;
 	dyStringPrintf(dy, "%s,", trackHubSkipHubName(genome->name));
         }
 
     if (!sameString(dy->string, dbList))
 	{
 	differences++;
 
 	printf("update %s set dbCount=\"%d\" where hubUrl=\"%s\";\n",table, dbCount, url);
 	printf("update %s set dbList=\"%s\" where hubUrl=\"%s\";\n",table, dy->string, url);
 	}
 
     if (hasDescriptionUrl && !isEmpty(tHub->descriptionUrl) && ((descriptionUrl == NULL) || !sameString(descriptionUrl, tHub->descriptionUrl)))
 	{
 	differences++;
 
 	printf("update %s set descriptionUrl=\"%s\" where hubUrl=\"%s\";\n",table, tHub->descriptionUrl, url);
 	}
 
     trackHubClose(&tHub);
     }
 return differences;
 }
 
 int hubPublicAdd(char *table, char *url)
 /* hubPublicAdd -- add url to hubPublic table */
 {
 struct errCatch *errCatch = errCatchNew();
 boolean gotWarning = FALSE;
 struct trackHub *tHub = NULL;
 int dbCount = 0;
 
 if (errCatchStart(errCatch))
     tHub = trackHubOpen(url, "hub_1"); 
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     gotWarning = TRUE;
     warn("%s", errCatch->message->string);
     }
 errCatchFree(&errCatch);
 
 if (gotWarning)
     return 1;
 
 struct dyString *dy = newDyString(1024);
 
 struct trackHubGenome *list;
 for(list = tHub->genomeList; list;  list = list->next)
     {
     dbCount++;
     dyStringPrintf(dy, "%s,", trackHubSkipHubName(list->name));
     }
 
 char *descriptionUrl = tHub->descriptionUrl;
 if (descriptionUrl == NULL)
     descriptionUrl="";
 printf("insert into %s (hubUrl,descriptionUrl,shortLabel,longLabel,registrationTime,dbCount,dbList) values (\"%s\",\"%s\", \"%s\", \"%s\", now(),%d, \"%s\");\n",
     table, url, descriptionUrl, tHub->shortLabel, tHub->longLabel, dbCount, dy->string); 
 
 return 0;
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 2)
     usage();
 udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
 
 char *hubUrl = optionVal("addHub", NULL);
 
 if (hubUrl != NULL)
     return hubPublicAdd(argv[1],hubUrl);
 else
     return hubPublicCheck(argv[1]);
 }