// ============================================================= // // // // File : servercntrl.cxx // // Purpose : // // // // Institute of Microbiology (Technical University Munich) // // http://www.arb-home.de/ // // // // ============================================================= // #include #include #include #include #include #include #include /* The following lines go to servercntrl.h * edit here, not there!! * call 'make proto' to update */ // AISC_MKPT_PROMOTE:#ifndef ARBDB_BASE_H // AISC_MKPT_PROMOTE:#include // AISC_MKPT_PROMOTE:#endif // AISC_MKPT_PROMOTE: // AISC_MKPT_PROMOTE:struct arb_params { // AISC_MKPT_PROMOTE: char *species_name; // AISC_MKPT_PROMOTE: char *extended_name; // AISC_MKPT_PROMOTE: char *alignment; // AISC_MKPT_PROMOTE: char *default_file; // AISC_MKPT_PROMOTE: char *field; // AISC_MKPT_PROMOTE: const char *field_default; // AISC_MKPT_PROMOTE: // AISC_MKPT_PROMOTE: int read_only; // AISC_MKPT_PROMOTE: // AISC_MKPT_PROMOTE: char *job_server; // AISC_MKPT_PROMOTE: char *db_server; // AISC_MKPT_PROMOTE: char *mgr_server; // AISC_MKPT_PROMOTE: char *pt_server; // AISC_MKPT_PROMOTE: // AISC_MKPT_PROMOTE: char *tcp; // AISC_MKPT_PROMOTE:}; // AISC_MKPT_PROMOTE: // AISC_MKPT_PROMOTE:enum SpawnMode { // AISC_MKPT_PROMOTE: WAIT_FOR_TERMINATION, // AISC_MKPT_PROMOTE: SPAWN_ASYNCHRONOUS, // AISC_MKPT_PROMOTE: SPAWN_DAEMONIZED, // AISC_MKPT_PROMOTE:}; #if defined(AISC_MAGIC_NUMBER) # undef AISC_MAGIC_NUMBER #endif #define TRIES 1 static struct gl_struct { aisc_com *link; AISC_Object com; gl_struct() : link(NULp), com(0x10000*1) // faked type id (matches main object, e.g. AN_MAIN or PT_MAIN) { } } glservercntrl; inline void make_async_call(char*& command) { freeset(command, GBS_global_string_copy("( %s ) &", command)); } char *createCallOnSocketHost(const char *host, const char *remotePrefix, const char *command, SpawnMode spawnmode, const char *logfile) { /*! transforms a shell-command * - use ssh if host is not local * - add wrappers for detached execution * @param host socket specification (may be 'host:port', 'host' or ':portOrSocketfile') * @param remotePrefix prefixed to command if it is executed on remote host (e.g. "$ARBHOME/bin/" -> uses value of environment variable ARBHOME on remote host!) * @param command the shell command to execute * @param spawnmode how to spawn: * WAIT_FOR_TERMINATION = run "command" * SPAWN_ASYNCHRONOUS = run "( command ) &" * SPAWN_DAEMONIZED = do not forward kill signals, remove from joblist and redirect output to logfile * @param logfile use with SPAWN_DAEMONIZED (mandatory; NULp otherwise) * @return a SSH system call for remote hosts and direct system calls for the local machine */ arb_assert((remotePrefix[0] == 0) || (strchr(remotePrefix, 0)[-1] == '/')); arb_assert(correlated(spawnmode == SPAWN_DAEMONIZED, logfile)); char *call = NULp; if (host && host[0]) { const char *hostPort = strchr(host, ':'); char *hostOnly = ARB_strpartdup(host, hostPort ? hostPort-1 : NULp); if (hostOnly[0] && !GB_host_is_local(hostOnly)) { char *quotedRemoteCommand = GBK_singlequote(GBS_global_string("%s%s", remotePrefix, command)); call = GBS_global_string_copy("ssh %s -n %s", hostOnly, quotedRemoteCommand); free(quotedRemoteCommand); } free(hostOnly); } if (!call) { call = ARB_strdup(command); make_valgrinded_call(call); // only on local host } switch (spawnmode) { case WAIT_FOR_TERMINATION: break; case SPAWN_ASYNCHRONOUS: make_async_call(call); break; case SPAWN_DAEMONIZED: { char *quotedLogfile = GBK_singlequote(logfile); char *quotedDaemonizingCall = GBK_singlequote(GBS_global_string("nohup %s >> %s 2>&1 & disown", call, quotedLogfile)); freeset(call, GBS_global_string_copy("bash -c %s", quotedDaemonizingCall)); free(quotedDaemonizingCall); free(quotedLogfile); break; } } return call; } GB_ERROR arb_start_server(const char *arb_tcp_env, int do_sleep) { const char *tcp_id; GB_ERROR error = NULp; if (!(tcp_id = GBS_read_arb_tcp(arb_tcp_env))) { error = GB_await_error(); } else { const char *server = strchr(tcp_id, 0) + 1; char *serverparams = NULp; /* concatenate all params behind server Note : changed behavior on 2007/Mar/09 -- ralf serverparams now is one space if nothing defined in arb_tcp.dat (previously was same as 'server' - most likely a bug) */ { const char *param = strchr(server, 0)+1; size_t plen = strlen(param); size_t alllen = 0; while (plen) { param += plen+1; alllen += plen+1; plen = strlen(param); } ARB_alloc(serverparams, alllen+1); { char *sp = serverparams; param = strchr(server, 0)+1; plen = strlen(param); if (!plen) sp++; else do { memcpy(sp, param, plen); sp[plen] = ' '; sp += plen+1; param += plen+1; plen = strlen(param); } while (plen); sp[-1] = 0; } } { char *command = NULp; const char *port = strchr(tcp_id, ':'); if (!port) { error = GB_export_errorf("Error: Missing ':' in socket definition of '%s' in file $(ARBHOME)/lib/arb_tcp.dat", arb_tcp_env); } else { // When arb is called from arb_launcher, ARB_SERVER_LOG gets set to the name of a logfile. // If ARB_SERVER_LOG is set here -> start servers daemonized here (see #492 for motivation) const char *serverlog = GB_getenv("ARB_SERVER_LOG"); SpawnMode spawnmode = serverlog ? SPAWN_DAEMONIZED : SPAWN_ASYNCHRONOUS; char *plainCommand = GBS_global_string_copy("%s %s '-T%s'", server, serverparams, port); // Note: quotes around -T added for testing only (remove@will) command = createCallOnSocketHost(tcp_id, "$ARBHOME/bin/", plainCommand, spawnmode, serverlog); free(plainCommand); } if (!error) { error = GBK_system(command); if (do_sleep) ARB_sleep(5, SEC); } free(command); } free(serverparams); } return error; } static GB_ERROR arb_wait_for_server(const char *arb_tcp_env, const char *tcp_id, int magic_number, struct gl_struct *serverctrl, int wait) { GB_ERROR error = NULp; serverctrl->link = aisc_open(tcp_id, serverctrl->com, magic_number, &error); if (!error && !serverctrl->link) { // no server running -> start one error = arb_start_server(arb_tcp_env, 0); while (!error && !serverctrl->link && wait) { ARB_sleep(1, SEC); wait--; if ((wait%10) == 0 && wait>0) { printf("Waiting for server '%s' to come up (%i seconds left)\n", arb_tcp_env, wait); } serverctrl->link = aisc_open(tcp_id, serverctrl->com, magic_number, &error); } } return error; } static GB_ERROR check_server_selected(const char *arb_tcp_env) { // check whether arb_tcp_env (normally created by GBS_ptserver_tag for pt-servers) // indicates that no pt-server has been selected by user. // // if so -> provide simple error to reduce confusion. if (strcmp(arb_tcp_env, "ARB_PT_SERVER-1") == 0) { return "No pt-server has been selected."; } return NULp; } GB_ERROR arb_look_and_start_server(long magic_number, const char *arb_tcp_env) { arb_assert(!GB_have_error()); GB_ERROR error = check_server_selected(arb_tcp_env); if (!error) { const char *tcp_id = GBS_read_arb_tcp(arb_tcp_env); const char *arb_tcp_dat = "$(ARBHOME)/lib/arb_tcp.dat"; if (!tcp_id) { error = GBS_global_string("Entry '%s' not found in %s (%s)", arb_tcp_env, arb_tcp_dat, GB_await_error()); } else { const char *file = GBS_scan_arb_tcp_param(tcp_id, "-d"); // find parameter behind '-d' if (!file) { error = GBS_global_string("Parameter -d missing for entry '%s' in %s", arb_tcp_env, arb_tcp_dat); } else { if (strcmp(file, "!ASSUME_RUNNING") == 0) { // assume pt-server is running on a host, w/o access to common network drive // i.e. we cannot check for the existence of the database file } else if (GB_size_of_file(file) <= 0) { if (strncmp(arb_tcp_env, "ARB_NAME_SERVER", 15) == 0) { char *dir = ARB_strdup(file); char *lastSlash = strrchr(dir, '/'); if (lastSlash) { lastSlash[0] = 0; // cut off file { const char *copy_cmd = GBS_global_string("cp %s/names.dat.template %s", dir, file); error = GBK_system(copy_cmd); } if (!error && GB_size_of_file(file) <= 0) { error = GBS_global_string("Cannot copy nameserver template (%s/names.dat.template missing?)", dir); } } else { error = GBS_global_string("Can't determine directory from '%s'", dir); } free(dir); } else if (strncmp(arb_tcp_env, "ARB_PT_SERVER", 13) == 0) { const char *nameOnly = strrchr(file, '/'); if (!nameOnly) nameOnly = file; error = GBS_global_string("PT_server '%s' has not been created yet.\n" " To create it follow these steps:\n" " 1. Start ARB on the whole database you want to use for probe match/design\n" " 2. Go to ARB/Probes/PT_SERVER Admin\n" " 3. Select '%s' and press 'Build server'\n" " 4. Wait (up to hours, depending on your DB size)\n" " 5. Meanwhile read the help file: PT_SERVER: What Why and How", file, nameOnly); } else { error = GBS_global_string("The file '%s' is missing. \nUnable to start %s", file, arb_tcp_env); } } } if (!error) { error = arb_wait_for_server(arb_tcp_env, tcp_id, magic_number, &glservercntrl, 20); if (!error) { if (!glservercntrl.link) { // couldn't start server error = // | "ARB has problems to start a server! Possible reasons may be one\n" "or several of the following list:\n" "- the tcp_id (socket number) is already used by another program\n" " (doesnt apply to user-specific PTSERVERs; check $ARBHOME/lib/arb_tcp.dat versus /etc/services)\n" "- the server exited with error or has crashed.\n" " In case of PTSERVER, the failure might be caused by:\n" " - missing database in $ARBHOME/lib/pts/* (solution: update ptserver database)\n" " - wrong permissions of $ARBHOME/lib/pts/* (no read access)\n" " If you recently installed a new arb version, arb will continue\n" " to use your previous 'arb_tcp.dat', which might be out-of-date.\n" " Backup and remove it, then restart ARB. If it works now,\n" " compare your old 'arb_tcp.dat' with the new one for changes.\n" "- When using remote servers: login or network problems\n" ; } else { aisc_close(glservercntrl.link, glservercntrl.com); glservercntrl.link = NULp; } } } } } arb_assert(!GB_have_error()); return error; } GB_ERROR arb_look_and_kill_server(int magic_number, const char *arb_tcp_env) { GB_ERROR error = check_server_selected(arb_tcp_env); if (!error) { const char *tcp_id = GBS_read_arb_tcp(arb_tcp_env); if (!tcp_id) { error = GB_await_error(); } else { const char *server = strchr(tcp_id, 0)+1; glservercntrl.link = aisc_open(tcp_id, glservercntrl.com, magic_number, &error); if (glservercntrl.link) { aisc_close(glservercntrl.link, glservercntrl.com); glservercntrl.link = NULp; error = GBK_system(GBS_global_string("%s -kill -T%s &", server, tcp_id)); } else { error = "Server is not running"; } } } return error; } const char *arb_look_and_start_ptserver(int magic_number, int ptserver_id, GB_ERROR& error) { // return PT server info string (see GBS_read_arb_tcp for details) // @@@ fix doc // or NULp (in this case 'error' is set) const char *result = NULp; const char *server_tag = GBS_ptserver_tag(ptserver_id); error = arb_look_and_start_server(magic_number, server_tag); if (!error) { result = GBS_read_arb_tcp(server_tag); if (!result) error = GB_await_error(); } arb_assert(contradicted(result, error)); return result; } void arb_print_server_params() { printf("General server parameters (some maybe unused by this server):\n" " -s sets species name to ''\n" " -e sets extended name to ''\n" " -a sets alignment to ''\n" " -d sets default file to ''\n" " -f= sets DB field to '' (using as default)\n" " -r read-only mode\n" " -D sets DB-server to '' [default = ':']\n" " -J sets job-server to '' [default = 'ARB_JOB_SERVER']\n" " -M sets MGR-server to '' [default = 'ARB_MGR_SERVER']\n" " -P sets PT-server to '' [default = 'ARB_PT_SERVER']\n" " -T<[host]:port> sets TCP connection to '<[host]:port>'\n" ); } arb_params *arb_trace_argv(int *argc, const char **argv) { arb_params *erg = ARB_calloc(1); erg->db_server = ARB_strdup(":"); erg->job_server = ARB_strdup("ARB_JOB_SERVER"); erg->mgr_server = ARB_strdup("ARB_MGR_SERVER"); erg->pt_server = ARB_strdup("ARB_PT_SERVER"); int s, d; for (s=d=0; s<*argc; s++) { if (argv[s][0] == '-') { switch (argv[s][1]) { case 's': erg->species_name = ARB_strdup(argv[s]+2); break; case 'e': erg->extended_name = ARB_strdup(argv[s]+2); break; case 'a': erg->alignment = ARB_strdup(argv[s]+2); break; case 'd': erg->default_file = ARB_strdup(argv[s]+2); break; case 'f': { char *eq; erg->field = ARB_strdup(argv[s]+2); eq = strchr(erg->field, '='); if (eq) { erg->field_default = eq+1; eq[0] = 0; } else { erg->field_default = NULp; // this is illegal - error handling done in caller } break; } case 'r': erg->read_only = 1; break; case 'J': freedup(erg->job_server, argv[s]+2); break; case 'D': freedup(erg->db_server, argv[s]+2); break; case 'M': freedup(erg->mgr_server, argv[s]+2); break; case 'P': freedup(erg->pt_server, argv[s]+2); break; case 'T': { const char *ipport = argv[s]+2; if (ipport[0] == ':' && ipport[1] >= '0' && ipport[1] <= '9') { // port only -> assume localhost erg->tcp = GBS_global_string_copy("localhost%s", ipport); } else { erg->tcp = ARB_strdup(ipport); } break; } default: argv[d++] = argv[s]; break; } } else { argv[d++] = argv[s]; } } *argc = d; return erg; } void free_arb_params(arb_params *params) { free(params->species_name); free(params->extended_name); free(params->alignment); free(params->default_file); free(params->field); free(params->job_server); free(params->db_server); free(params->mgr_server); free(params->pt_server); free(params->tcp); free(params); } // -------------------------------------------------------------------------------- #if defined(UNIT_TESTS) && 0 // If you need tests in AISC_COM/C/client.c, put them here instead. #include void TEST_servercntrl() { TEST_REJECT(true); // would fail if test gets activated } #endif // UNIT_TESTS