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/toDev64/toDev64.c src/hg/utils/toDev64/toDev64.c index 8f3f90f..f28ea91 100644 --- src/hg/utils/toDev64/toDev64.c +++ src/hg/utils/toDev64/toDev64.c @@ -1,302 +1,302 @@ /* safePush - Push database tables from one machine to another. This is a * little more careful than mypush.. */ /* 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 "obscure.h" #include "dystring.h" #include "jksql.h" #include "hash.h" #include "options.h" #include "hgConfig.h" /* Command line flags - all default to false. */ boolean oldOk, chrom, prefix, allTables, test; char *dev32 = "hgwdevold"; /* Old dev machine. */ char *dev64 = "hgwdev"; /* New dev machine. */ char *mysqlDataDir = "/var/lib/mysql"; void usage() /* Explain usage and exit. */ { errAbort( "toDev64 - A program that copies data from the old hgwdev database to the\n" "new hgwdev database.\n" "usage:\n" " toDev64 database table\n" "options:\n" " -chrom - if set will copy tables split by chromosome\n" " -prefix - if set will copy all tables that start with 'table'\n" " -oldOk - if set will let you overwrite a new table on the dest with\n" " an older source table\n" " -allTables - if set will copy all tables in database. The table\n" " table parameter should be 'all' in this case\n" " -test - if set it not will actually do the copy. (It just\n" " prints the commands it will execute.)\n" ); } char *user, *password; /* Database user and password. */ static struct optionSpec options[] = { {"oldOk", OPTION_BOOLEAN}, {"chrom", OPTION_BOOLEAN}, {"prefix", OPTION_BOOLEAN}, {"allTables", OPTION_BOOLEAN}, {"test", OPTION_BOOLEAN}, {NULL, 0}, }; boolean isAllGoodChars(char *s) /* Return TRUE if all characters are alphanumeric or _ */ { char c; while ((c = *s++) != 0) if (!isalnum(c) && c != '_') return FALSE; return TRUE; } void forceAllGoodChars(char *s) /* Make sure all chars are good or abort */ { if (!isAllGoodChars(s)) errAbort("Illegal characters in %s, only letters, numbers, and _ allowed", s); } void execAndCheck(char *command) /* Do a system on command, and abort with error message if * it fails */ { puts(command); if (!test) { int err = system(command); if (err != 0) errAbort("system call failed error code %d", err); } } boolean is5(char *host) /* Return TRUE if we seem to be version 5.0 of mysql or later */ { struct sqlConnection *conn = sqlConnectRemote(host, user, password, NULL); int version = sqlMajorVersion(conn); sqlDisconnect(&conn); verbose(2, "%s is version %d\n", host, version); return (version >= 5); } void flushTables(char *host) /* Issue mysqladmin flush command. */ { char command[2048]; safef(command, sizeof(command), "mysqladmin --user=hguser --password=hguserstuff flush-tables"); execAndCheck(command); } void pushAllTables(char *sourceHost, char *destHost, char *database) /* Do the big rsync on database from sourceHost to destHost */ { char command[2048]; if (sqlDatabaseExists(database)) errAbort("Database %s already exists", database); safef(command, sizeof(command), "rsync -avr --progress --rsh=rsh %s:%s/%s %s/", sourceHost, mysqlDataDir, database, mysqlDataDir); execAndCheck(command); } struct hash *tableTimeHash(char *host, boolean is5, char *database, char *tablePattern) /* Get hash of tables and the time they were last updated. */ { struct hash *hash = hashNew(0); struct sqlConnection *conn = sqlConnectRemote(host, user, password, database); char query[512]; struct sqlResult *sr; char **row; sqlSafef(query, sizeof(query), "show table status like '%s'", tablePattern); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *table = row[0]; char *time = (is5 ? row[12] : row[11]); verbose(3, "%s:%s.%s %s\n", host, database, table, time); hashAdd(hash, table, cloneString(time)); } sqlDisconnect(&conn); return hash; } void pushTable(char *sourceHost, struct hash *sourceTimes, char *destHost, struct hash *destTimes, char *database, char *table, boolean missingTableOk) /* Push a single table */ { char command[2048]; if (!oldOk) { char *sTime = hashFindVal(sourceTimes, table); char *dTime = hashFindVal(destTimes, table); if (sTime == NULL) { if (missingTableOk) return; else errAbort("Table %s missing in %s:%s", table, sourceHost, database); } if (dTime != NULL) { int s = sqlDateToUnixTime(sTime); int d = sqlDateToUnixTime(dTime); verbose(2, "%s.%s source time %s (%d), dest time %s (%d)\n", database, table, sTime, s, dTime, d); if (d > s) errAbort("%s.%s is newer on %s than on %s", database, table, destHost, sourceHost); if (d == s) { warn("%s.%s has same timestamp on %s and %s. Skipping...", database, table, destHost, sourceHost); return; } } } safef(command, sizeof(command), "rsync -av --progress --rsh=rsh %s:%s/%s/%s.* %s/%s/", sourceHost, mysqlDataDir, database, table, mysqlDataDir, database); execAndCheck(command); } struct slName *tablesLike(char *host, char *database, char *pattern) /* Get list of tables matching SQL wildcard pattern */ { struct slName *list = NULL; struct sqlConnection *conn = sqlConnectRemote(host, user, password, database); char query[512]; struct sqlResult *sr; char **row; sqlSafef(query, sizeof(query), "show tables like '%s'", pattern); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) slNameAddHead(&list, row[0]); sqlFreeResult(&sr); sqlDisconnect(&conn); slReverse(&list); return list; } void pushSomeTables(char *sourceHost, boolean sourceIs5, char *destHost, boolean destIs5, char *database, char *table, boolean missingTableOk) /* Push selected tables in database. */ { struct hash *sourceTimes = NULL, *destTimes = NULL; struct slName *tableList = NULL, *tableEl; char pattern[512]; if (chrom) { if (prefix) safef(pattern, sizeof(pattern), "chr%%\\_%s%%", table); else safef(pattern, sizeof(pattern), "chr%%\\_%s", table); tableList = tablesLike(sourceHost, database, pattern); } else if (prefix) { safef(pattern, sizeof(pattern), "%s%%", table); tableList = tablesLike(sourceHost, database, pattern); } else { safef(pattern, sizeof(pattern), "%s", table); tableList = slNameNew(table); } if (!oldOk) { sourceTimes = tableTimeHash(sourceHost, sourceIs5, database, pattern); destTimes = tableTimeHash(destHost, destIs5, database, pattern); } for (tableEl = tableList; tableEl != NULL; tableEl = tableEl->next) pushTable(sourceHost, sourceTimes, destHost, destTimes, database, tableEl->name, missingTableOk); } void pushDatabase(char *sourceHost, boolean sourceIs5, char *destHost, boolean destIs5, char *database, char *table, boolean missingTableOk) /* Push table from single database. Possibly push all tables. */ { if (allTables) pushAllTables(sourceHost, destHost, database); else pushSomeTables(sourceHost, sourceIs5, destHost, destIs5, database, table, missingTableOk); } void pushToHost(char *sourceHost, char *database, char *table, char *destHost) /* Do push of database and table from source to one host */ { boolean sourceIs5 = is5(sourceHost); boolean destIs5 = is5(destHost); if (sourceIs5 || destIs5) errAbort("Sorry, can't yet handle mySQL 5"); if (sourceIs5 && !destIs5) errAbort("%s is running Mysql pre-5, and %s is running MySQL post-5, sorry", destHost, sourceHost); forceAllGoodChars(sourceHost); forceAllGoodChars(destHost); forceAllGoodChars(database); forceAllGoodChars(table); pushDatabase(sourceHost, sourceIs5, destHost, destIs5, database, table, TRUE); flushTables(destHost); } void toDev64(char *database, char *table) /* Push from old hgwdev to new hgwdev */ { char *envHost = getenv("HOST"); /* Various error checks */ if (envHost == NULL) errAbort("Couldn't find HOST environment variable, sorry."); if (!sameString(envHost, dev64)) errAbort("You can only run this machine from %s", dev64); if (allTables && !sameString(table, "all")) errAbort("Expecting 'all' for table with -allTables"); if (sameWord(table, "mysql")) errAbort("Please contact cluster-admin to update 'mysql' database"); if (prefix && strlen(table) < 3) errAbort("You can only use -prefix if have at least 3 letters in table name."); pushToHost(dev32, database, table, dev64); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 3) usage(); oldOk = optionExists("oldOk"); chrom = optionExists("chrom"); prefix = optionExists("prefix"); allTables = optionExists("allTables"); test = optionExists("test"); user = "hguser"; password = "hguserstuff"; toDev64(argv[1], argv[2]); return 0; }