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1 : olson 1.1 #
2 :     # FIG bootstrap script.
3 :     #
4 :     # Control is passed here from the toplevel configure (or dists/releases/install depending
5 :     # on how far we've gotten in the process).
6 :     #
7 :     # The configure has set the following environment variables for our use:
8 :     #
9 :     # FIG_HOME Root of the FIGdisk tree we're setting up
10 :     # FIGCONFIG_ENV Name of the environment we're configuring for
11 :     # FIGCONFIG_ENV_DIR Directory in which the binary install tree for $FIGCONFIG_ENV lives
12 :     # FIGCONFIG_RELEASE Release number we're configuring
13 :     # FIGCONFIG_RELEASE_DIR Directory in which that release lives
14 :     #
15 :     # Important note: perl system libraries may not be available when this
16 :     # script is running, if the FIGCONFIG_ENV_DIR is different than it was
17 :     # when the binaries were created. Part of the task of this
18 :     # script is to recognize this case and configure the process
19 :     # environment correctly so that the post-install process as
20 :     # handled by the Makefiles can use perl properly, without concern for paths.
21 :     #
22 :    
23 :     #
24 :     # Look into the FIGCONFIG_ENV_DIR for the PREFIX that this
25 :     # environment was compiled on. If that directory is different
26 :     # than the one we're currently using, rewrite @INC accordingly.
27 :     #
28 :     # We put this into a BEGIN block so that we can later use "use"
29 :     # without worrying about paths.
30 :     #
31 :     # We also set the $perlenv_override to true if we've done this,
32 :     # so we can insert these fixes into the perl tool header.
33 :     #
34 :    
35 :     BEGIN {
36 :    
37 : olson 1.3 print "Here in the perl bootstrap. inc is:\n" . join("\n", @INC), "\n";
38 : olson 1.1
39 :     my $my_prefix, $prefix, $inc, @newInc;
40 :    
41 :     $my_prefix = $ENV{FIGCONFIG_ENV_DIR};
42 :     open(P, "<$my_prefix/PREFIX");
43 :     $prefix = <P>;
44 :     chomp $prefix;
45 :    
46 :    
47 :     # print "Prefix is $prefix myprefix=$my_prefix\n";
48 :    
49 :     if ($prefix ne $my_prefix)
50 :     {
51 :     @newInc = ();
52 :     for $inc (@INC)
53 :     {
54 :     $inc =~ s,^$prefix,$my_prefix,;
55 :     push(@newInc, $inc);
56 :     }
57 :    
58 :     $::perlenv_override = 1;
59 : olson 1.3 @INC = @newInc;
60 : olson 1.1 }
61 :     }
62 :    
63 :    
64 :     use FileHandle;
65 :     use strict;
66 :    
67 :     #
68 :     # Environment definition
69 :     #
70 :     # This list contains triples
71 :     # ($name, $value, $appendFlag). $name is the name of the
72 :     # variable; $value is the value to set, and $appendFlag
73 :     # is nonzero if we need to append this value to an existing
74 :     # environment variable.
75 :     #
76 :    
77 :     our $Env = [];
78 :    
79 :     #
80 :     # FIG configuration information.
81 :     # This list contains tuples [$name, $value, $quote]
82 :     # which are to be set in the FIG_Config modules for
83 :     # both python and perl. $quote is 1 for things that need
84 :     # to be quoted, 0 otherwise.
85 :     #
86 :     our $Config = [];
87 :    
88 :     #
89 :     # Other key/value pairs of stuff we may need to pass
90 :     # to and from the environment-specific configuration modules.
91 :     #
92 :     # Known keys:
93 :     #
94 :     # pythonpath
95 :     #
96 :    
97 :     our $OtherConfig = {};
98 :    
99 :     #
100 :     # Cache values of the various places we may be installing things.
101 :     #
102 :    
103 :     our $fig_disk = $ENV{FIG_HOME};
104 :     our $env_name = $ENV{FIGCONFIG_ENV};
105 : olson 1.7 our $env_dir = "$ENV{FIGCONFIG_ENV_DIR}";
106 : olson 1.1 our $env_bin = "$ENV{FIGCONFIG_ENV_DIR}/bin";
107 :     our $env_lib = "$ENV{FIGCONFIG_ENV_DIR}/lib";
108 : olson 1.2 #
109 :     # We are moving to use a symlink in dist/releases/current for these.
110 :     # This symlink is managed by switch_to_release.
111 :     #
112 :     #our $release_bin = "$ENV{FIGCONFIG_RELEASE_DIR}/bin/$ENV{FIGCONFIG_ENV}";
113 :     #our $release_lib = "$ENV{FIGCONFIG_RELEASE_DIR}/lib/$ENV{FIGCONFIG_ENV}";
114 :    
115 : olson 1.8 our $release_bin = "$fig_disk/dist/releases/current/$ENV{FIGCONFIG_ENV}/bin";
116 :     our $release_lib = "$fig_disk/dist/releases/current/$ENV{FIGCONFIG_ENV}/lib";
117 : olson 1.2
118 :     our $fig_bin = "$fig_disk/FIG/bin";
119 : olson 1.1
120 :     #
121 :     # Location of start/stop servers scripts.
122 :     #
123 :     our $start_servers = "$fig_disk/bin/start-servers";
124 :     our $stop_servers = "$fig_disk/bin/stop-servers";
125 :    
126 :     sub configure_std_fig_environment
127 :     {
128 :     #
129 :     # Populate the Config with the usual stuff we need in FIG_Config.pm.
130 :     #
131 :    
132 :     my $fig = "$fig_disk/FIG";
133 :     my $data = "$fig/Data";
134 :    
135 :     my $hostname = `hostname`;
136 :     chomp $hostname;
137 :    
138 :     push(@$Config, ["fig_disk", $fig_disk, 1]);
139 : olson 1.6 push(@$Config, ["blastmat", "$fig_disk/BLASTMAT", 1]);
140 : olson 1.1 push(@$Config, ["fig", $fig, 1]);
141 : olson 1.2 push(@$Config, ["bin", $fig_bin, 1]);
142 : olson 1.1 push(@$Config, ["ext_bin", $env_bin, 1]);
143 :     push(@$Config, ["data", $data, 1]);
144 :     push(@$Config, ["global", "$data/Global", 1]);
145 :     push(@$Config, ["organisms", "$data/Organisms", 1]);
146 :     push(@$Config, ["RC", "$fig_disk/FIG/ResolutionCenter", 1]);
147 :     push(@$Config, ["NR", "$fig_disk/FIG/NR", 1]);
148 :     push(@$Config, ["temp", "$fig_disk/FIG/Tmp", 1]);
149 : olson 1.11
150 :     my $sandbox;
151 :     if ($ENV{FIGCONFIG_SANDBOX})
152 :     {
153 :     $sandbox = "/$ENV{FIGCONFIG_SANDBOX}";
154 :     }
155 :    
156 :     push(@$Config, ["temp_url", "http://$hostname$sandbox/FIG-Tmp", 1]);
157 :     push(@$Config, ["cgi_url", "http://$hostname$sandbox/FIG", 1]);
158 : golsen 1.9
159 :     #
160 :     # Add values for a relative base href of temp and CGI pages. The latter
161 :     # is used by HHTP.pm to write common page start. It would make the most
162 :     # sense to derive the above 2 values from these. -- GJO
163 :     #
164 :    
165 : olson 1.11 push(@$Config, ["temp_base", "$sandbox/FIG-Tmp/", 1]);
166 :     push(@$Config, ["cgi_base", "$sandbox/FIG/", 1]);
167 : olson 1.1 }
168 :    
169 :     sub compute_environment
170 :     {
171 :     #
172 :     # ReleaseTools configuration.
173 :     #
174 :    
175 :     push(@$Env, ["RTROOT", $ENV{FIG_HOME}, 0]);
176 :     push(@$Env, ["RTDIST", "\$RTROOT/dist", 0]);
177 :     push(@$Env, ["RTARCH", $ENV{FIGCONFIG_ENV}, 0]);
178 : olson 1.2 push(@$Env, ["RTCURRENT", "`cat \$RTROOT/CURRENT_RELEASE`", 0]);
179 : olson 1.1 push(@$Env, ["FIG_HOME", $ENV{FIG_HOME}, 0]);
180 :    
181 :     push(@$Env, ["BLASTMAT", "$ENV{FIG_HOME}/BLASTMAT", 0]);
182 :    
183 :     #
184 :     # Determine the path to use.
185 :     #
186 :     # This includes the path into the particular release we're configuring for,
187 :     # and to the environment's bin directory.
188 :     #
189 :    
190 :     my @path = ();
191 :     push(@path, $env_bin);
192 : olson 1.2 push(@path, $fig_bin);
193 : olson 1.1 push(@path, "$fig_disk/bin");
194 :    
195 :     push(@$Env, ["PATH", join(":", @path), 1]);
196 :    
197 : olson 1.2 push(@$Env, ["LD_LIBRARY_PATH", "${env_lib}", 1]);
198 : olson 1.11
199 :     push(@$Env, ["PERL5LIB", join(":", grep({ $_ ne "." } @INC)), 1]);
200 : olson 1.1 }
201 :    
202 :     sub configure_python
203 :     {
204 :     #
205 :     # Determine the PYTHONPATH we're to use.
206 :     #
207 :     # Right now, we don't compute a replacement for the system path,
208 :     # but we're likely going to require that *if* python is
209 :     # distributed with the environment. We're currently not doing that.
210 :     #
211 :     # So we just need to point to any python packages in the release,
212 :     # and to packages that were installed in the environment dir.
213 :     #
214 :    
215 :     my $python = find_python();
216 :     print "Found python at $python\n";
217 :    
218 :     my $py_version = `$python -c 'import sys; print "%d.%d" % (sys.version_info[:2])'`;
219 :     chomp $py_version;
220 :     print "Python version $py_version\n";
221 :    
222 : olson 1.2 $OtherConfig->{python_site_path} = "$ENV{FIGCONFIG_ENV_DIR}/lib/python$py_version/site-packages";
223 :    
224 : olson 1.1 my @path = ();
225 : olson 1.2 push(@path, $OtherConfig->{python_site_path});
226 :     push(@path, "$release_lib");
227 : olson 1.1 push(@path, "$fig_disk/config");
228 :     push(@$Env, ["PYTHONPATH", join(":", @path), 1]);
229 :    
230 :     $OtherConfig->{pythonpath} = join(":", @path);
231 :     }
232 :    
233 :     sub find_in_path
234 :     {
235 : olson 1.5 my($file, @extra) = @_;
236 : olson 1.1 my(@path) = split(":", $ENV{PATH});
237 :    
238 : olson 1.5 for my $p (@path, @extra)
239 : olson 1.1 {
240 :     my $x = "$p/$file";
241 :     if (-x $x)
242 :     {
243 :     return $x;
244 :     }
245 :     }
246 :     return undef;
247 :     }
248 :    
249 :     #
250 :     # Find the name of the python executable we are to use.
251 :     #
252 :     sub find_python
253 :     {
254 :     my $python;
255 :    
256 :     #
257 :     # Special case for the mac.
258 :     #
259 : olson 1.11 # RDO 20040603 - don't do this any more; we want to pick up
260 :     # the python we ship.
261 :     #
262 : olson 1.1
263 : olson 1.11 if (0 && $ENV{FIGCONFIG_ENV} eq "mac")
264 : olson 1.1 {
265 : olson 1.7 #
266 :     # We'd like to use the MacPython that is installed
267 :     # as pythonw.
268 :     #
269 :     if ($python = find_in_path("pythonw", "/usr/local/bin"))
270 : olson 1.1 {
271 : olson 1.7 $OtherConfig->{python_require_poundbang_env} = 1;
272 : olson 1.1 return $python;
273 :     }
274 :    
275 :     #
276 : olson 1.7 # Otherwise, we can live with the regular python.
277 :     # Fall thru to the generic case.
278 : olson 1.1 #
279 : olson 1.7 }
280 :     #
281 :     # Non-mac, just look in the env dir or the path.
282 :     #
283 : olson 1.1
284 : olson 1.7 $python = "$ENV{FIGCONFIG_ENV_DIR}/bin/python";
285 :     if (-x $python)
286 :     {
287 :     return $python;
288 : olson 1.1 }
289 :    
290 : olson 1.7 return find_in_path("python");
291 : olson 1.1 }
292 :    
293 :     #
294 :     # Find the name of the perl executable we are to use.
295 :     #
296 :     sub find_perl
297 :     {
298 :     my $perl;
299 :    
300 :     $perl = "$ENV{FIGCONFIG_ENV_DIR}/bin/perl";
301 :     if (-x $perl)
302 :     {
303 :     return $perl;
304 :     }
305 :    
306 :     warn "We did not find a perl executable in the SEED distribution; some modules may not be found\n";
307 :     return find_in_path("perl");
308 :     }
309 :    
310 :     sub write_bash_init
311 :     {
312 :     my($fh, $env) = @_;
313 :    
314 :     foreach my $item (@$env)
315 :     {
316 :     my($name, $value, $append) = @$item;
317 :    
318 :     if ($append)
319 :     {
320 :     #
321 :     # Write code to detect if the value is set, and act accordingly.
322 :     #
323 :    
324 :     print $fh <<END;
325 :     DELIM=
326 :     if [ -n "\$$name" ] ; then
327 :     DELIM=:
328 :     fi
329 : olson 1.10 $name=$value\${DELIM}\${$name}
330 : olson 1.1 export $name
331 :     END
332 :     }
333 :     else
334 :     {
335 :     print $fh "$name=\"$value\"\n";
336 :     print $fh "export $name\n";
337 :     }
338 :     }
339 :     }
340 :    
341 :     sub write_csh_init
342 :     {
343 :     my($fh, $env) = @_;
344 :    
345 :     foreach my $item (@$env)
346 :     {
347 :     my($name, $value, $append) = @$item;
348 :    
349 :     if ($append)
350 :     {
351 :     #
352 :     # Write code to detect if the value is set, and act accordingly.
353 :     #
354 :    
355 :     print $fh <<END;
356 :     if (\$?$name) then
357 : olson 1.10 setenv $name $value:\${$name}
358 : olson 1.1 else
359 :     setenv $name $value
360 :     endif
361 :     END
362 :     }
363 :     else
364 :     {
365 :     print $fh "setenv $name \"$value\"\n";
366 :     }
367 :     }
368 :    
369 :     }
370 :    
371 :     sub run_script
372 :     {
373 :     my($script) = @_;
374 :    
375 :    
376 :     unless (my $ret = do $script)
377 :     {
378 :     if ($@)
379 :     {
380 :     warn "Error parsing $script: $@\n";
381 :     }
382 :     elsif (!defined($ret))
383 :     {
384 :     warn "Couldn't do $script: $!\n";
385 :     }
386 :     else
387 :     {
388 :     warn "Counldn't run $script\n";
389 :     }
390 :     }
391 :    
392 :    
393 :     }
394 :    
395 :     sub configure_environment_specific
396 :     {
397 :     my $env_script = $ENV{FIGCONFIG_ENV_CONFIG};
398 :    
399 :     if (! -f $env_script)
400 :     {
401 :     warn "No environment-specific configuration file $env_script found, skipping\n";
402 :     return;
403 :     }
404 :    
405 :     run_script($env_script);
406 :     }
407 :    
408 :     #
409 :     # Create any directories that might be missing.
410 :     #
411 :    
412 :     sub setup_directories
413 :     {
414 :     my(@needed) = @_;
415 :    
416 :     for my $dir (@needed)
417 :     {
418 :     if (! -d $dir)
419 :     {
420 :     mkdir($dir) or warn "Could not create $dir: $!\n";
421 :     }
422 :     }
423 :     }
424 :    
425 :     sub setup_server_scripts
426 :     {
427 :     #
428 :     # Remove any start/stop servers scripts we might have, and write the stub
429 :     # start.
430 :     #
431 :    
432 :     unlink($start_servers);
433 :     unlink($stop_servers);
434 :    
435 :     open(F, ">$start_servers") or die "Cannot write $start_servers: $!";
436 :     print F "#!/bin/sh\n\n";
437 :     close(F);
438 :     chmod(0775, $start_servers);
439 :    
440 :     open(F, ">$stop_servers") or die "Cannot write $stop_servers: $!";
441 :     print F "#!/bin/sh\n\n";
442 :     close(F);
443 :     chmod(0775, $stop_servers);
444 :    
445 :     }
446 :    
447 : olson 1.7 sub finalize_server_scripts
448 :     {
449 :     #
450 :     # After any environment-specific stuff, call start_services and stop_services.
451 :     #
452 :    
453 :     open(F, ">>$start_servers") or die "Cannot write $start_servers: $!";
454 :     print F "\n$fig_bin/start_services\n";
455 :     close(F);
456 :     chmod(0775, $start_servers);
457 :    
458 :     open(F, ">>$stop_servers") or die "Cannot write $stop_servers: $!";
459 :     print F "\n$fig_bin/stop_services\n";
460 :     close(F);
461 :     chmod(0775, $stop_servers);
462 :    
463 :     }
464 :    
465 : olson 1.1 sub write_config_pm
466 :     {
467 :     my($fh, $config) = @_;
468 :    
469 :     print $fh "package FIG_Config;\n\n";
470 :    
471 :     foreach my $item (@$config)
472 :     {
473 :     my($name, $value, $quote) = @$item;
474 :    
475 :     my $q = $quote ? '"' : '';
476 :     printf $fh "\$%-15s = $q$value$q;\n", $name
477 :     }
478 :    
479 :     print $fh "\n1;\n";
480 :     }
481 :    
482 :     sub write_config_py
483 :     {
484 :     my($fh, $config) = @_;
485 :    
486 :     foreach my $item (@$config)
487 :     {
488 :     my($name, $value, $quote) = @$item;
489 :    
490 :     #
491 :     # Ugh. "global" is a keyword in python.
492 :     #
493 :    
494 :     $name = "global_dir" if $name eq "global";
495 :    
496 :     my $q = $quote ? '"' : '';
497 :     printf $fh "%-15s = $q$value$q\n", $name
498 :     }
499 :     }
500 :    
501 :     sub write_tool_hdr_perl
502 :     {
503 :     my($fh) = @_;
504 :    
505 :     my $perl = find_perl();
506 :    
507 :     print $fh "#!$perl\n";
508 :     print $fh "\n";
509 :    
510 :     if ($::perlenv_override)
511 :     {
512 :     #
513 :     # Write the tool header BEGIN block to reset the environment.
514 :     #
515 :    
516 :     print $fh "BEGIN {\n";
517 :     print $fh " \@INC = qw(\n";
518 :     for my $inc (@INC)
519 :     {
520 :     next if $inc eq '.';
521 :     print $fh "\t$inc\n";
522 :     }
523 : olson 1.2 print $fh ");\n";
524 : olson 1.1 print $fh "}\n";
525 :     }
526 :    
527 :     print $fh "use Data::Dumper;\n";
528 :     print $fh "use Carp;\n";
529 :    
530 : olson 1.2 #
531 :     # We generate a comment here that gets expanded by switch_to_release
532 :     # This is part of the effort in making the environment bootstrapping
533 :     # code independent of releases.
534 :     #
535 :    
536 :     #print $fh "use lib \"$release_lib\";\n";
537 :     #print $fh "use lib \"$release_lib/FigKernelPackages\";\n";
538 :    
539 :     print $fh "# Following block is expanded by switch_to_release to add use lib directives\n";
540 :     print $fh "# to point at the correct locations in the release directory.\n";
541 :     print $fh "#BEGIN switch_to_release generated code\n";
542 :     print $fh "#END switch_to_release generated code\n";
543 :     print $fh "\n";
544 :    
545 : olson 1.1 print $fh "use lib \"$fig_disk/config\";\n";
546 :    
547 :     print $fh "use FIG_Config;\n";
548 :     print $fh "\n";
549 : olson 1.11 print $fh "#### END tool_hdr ####\n\n"
550 : olson 1.1 }
551 :    
552 :     sub write_tool_hdr_python
553 :     {
554 :     my($fh) = @_;
555 :    
556 :     my $python = find_python();
557 :    
558 : olson 1.4 if ($OtherConfig->{python_require_poundbang_env})
559 :     {
560 :     print $fh "#!/usr/bin/env $python\n";
561 :     }
562 :     else
563 :     {
564 :     print $fh "#!$python\n";
565 :     }
566 : olson 1.1 print $fh "\n";
567 :    
568 : olson 1.11 print $fh "import sys, os\n";
569 : olson 1.2
570 :    
571 :     print $fh "sys.path.append('$OtherConfig->{python_site_path}')\n";
572 :    
573 : olson 1.11 #
574 :     # Append the perl path to the environment, for use later with CallPerl.
575 :     #
576 :    
577 :     my $perlpath = join(":", @INC, "$fig_disk/config");
578 :     print $fh <<END;
579 :     if os.getenv("PERL5LIB", "") != "":
580 :     _delim = ":"
581 :     else:
582 :     _delim = ""
583 :     os.environ["PERL5LIB"] = "$perlpath" + _delim + os.getenv("PERL5LIB", "")
584 :    
585 :     END
586 :    
587 : olson 1.2 print $fh "# Following block is expanded by switch_to_release to add use lib directives\n";
588 :     print $fh "# to point at the correct locations in the release directory.\n";
589 :     print $fh "#BEGIN switch_to_release generated code\n";
590 :     print $fh "#END switch_to_release generated code\n";
591 :     print $fh "\n";
592 :    
593 :     print $fh "sys.path.append('$fig_disk/config')\n";
594 :    
595 : olson 1.1 print $fh "import FIG_Config\n";
596 :     print $fh "\n";
597 : olson 1.11 print $fh "#### END tool_hdr_py ####\n\n"
598 : olson 1.1 }
599 :    
600 :     setup_directories("$fig_disk/bin",
601 :     "$fig_disk/config");
602 :    
603 :     setup_server_scripts();
604 :    
605 :    
606 :     find_python();
607 :    
608 :     compute_environment();
609 :     configure_std_fig_environment();
610 :     configure_python();
611 :     configure_environment_specific();
612 : olson 1.7
613 :     finalize_server_scripts();
614 : olson 1.1
615 :     #
616 :     # Write the shell startup to the figdisk.
617 :     #
618 :     open(FH, ">$fig_disk/config/fig-user-env.sh") or die "Cannot write $fig_disk/config/fig-user-env.sh: $!";
619 :     write_bash_init(\*FH, $Env);
620 :     close(FH);
621 :    
622 :     open(FH, ">$fig_disk/config/fig-user-env.csh") or die "Cannot write $fig_disk/config/fig-user-env.csh: $!";
623 :     write_csh_init(\*FH, $Env);
624 :     close(FH);
625 :    
626 :     #
627 :     # Write the FIG_Config file.
628 :     #
629 :    
630 :     open(FH, ">$fig_disk/config/FIG_Config.pm") or die "Cannot write $fig_disk/config/FIG_Config.pm: $!";
631 :     write_config_pm(\*FH, $Config);
632 :     close(FH);
633 :    
634 :     open(FH, ">$fig_disk/config/FIG_Config.py") or die "Cannot write $fig_disk/config/FIG_Config.py: $!";
635 :     write_config_py(\*FH, $Config);
636 :     close(FH);
637 :    
638 :     #
639 :     # Write the tool headers
640 :     #
641 :    
642 : olson 1.2 open(FH, ">$fig_disk/config/base_tool_hdr") or die "Cannot write $fig_disk/config/tool_hdr: $!";
643 : olson 1.1 write_tool_hdr_perl(\*FH);
644 :     close(FH);
645 :    
646 : olson 1.2 open(FH, ">$fig_disk/config/base_tool_hdr_py") or die "Cannot write $fig_disk/config/tool_hdr_py: $!";
647 : olson 1.1 write_tool_hdr_python(\*FH);
648 :     close(FH);
649 :    
650 : olson 1.2 unshift(@INC, "$ENV{FIGCONFIG_RELEASE_DIR}");
651 :    
652 :     require FigCommon::SwitchRelease;
653 : olson 1.1
654 : olson 1.2 &FigCommon::SwitchRelease::switch_to_release($fig_disk, $ENV{FIGCONFIG_ENV}, $ENV{FIGCONFIG_RELEASE});

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