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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 :     our $release_bin = "$fig_disk/dist/releases/current/bin/$ENV{FIGCONFIG_ENV}";
116 :     our $release_lib = "$fig_disk/dist/releases/current/lib/$ENV{FIGCONFIG_ENV}";
117 :    
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", "$fig_disk/FIG/Tmp", 1]);
149 :     push(@$Config, ["temp_url", "http://$hostname/FIG-Tmp", 1]);
150 :     push(@$Config, ["cgi_url", "http://$hostname/FIG", 1]);
151 :     }
152 :    
153 :     sub compute_environment
154 :     {
155 :     #
156 :     # ReleaseTools configuration.
157 :     #
158 :    
159 :     push(@$Env, ["RTROOT", $ENV{FIG_HOME}, 0]);
160 :     push(@$Env, ["RTDIST", "\$RTROOT/dist", 0]);
161 :     push(@$Env, ["RTARCH", $ENV{FIGCONFIG_ENV}, 0]);
162 : olson 1.2 push(@$Env, ["RTCURRENT", "`cat \$RTROOT/CURRENT_RELEASE`", 0]);
163 : olson 1.1 push(@$Env, ["FIG_HOME", $ENV{FIG_HOME}, 0]);
164 :    
165 :     push(@$Env, ["BLASTMAT", "$ENV{FIG_HOME}/BLASTMAT", 0]);
166 :    
167 :     #
168 :     # Determine the path to use.
169 :     #
170 :     # This includes the path into the particular release we're configuring for,
171 :     # and to the environment's bin directory.
172 :     #
173 :    
174 :     my @path = ();
175 :     push(@path, $env_bin);
176 : olson 1.2 push(@path, $fig_bin);
177 : olson 1.1 push(@path, "$fig_disk/bin");
178 :    
179 :     push(@$Env, ["PATH", join(":", @path), 1]);
180 :    
181 : olson 1.2 push(@$Env, ["LD_LIBRARY_PATH", "${env_lib}", 1]);
182 : olson 1.1 }
183 :    
184 :     sub configure_python
185 :     {
186 :     #
187 :     # Determine the PYTHONPATH we're to use.
188 :     #
189 :     # Right now, we don't compute a replacement for the system path,
190 :     # but we're likely going to require that *if* python is
191 :     # distributed with the environment. We're currently not doing that.
192 :     #
193 :     # So we just need to point to any python packages in the release,
194 :     # and to packages that were installed in the environment dir.
195 :     #
196 :    
197 :     my $python = find_python();
198 :     print "Found python at $python\n";
199 :    
200 :     my $py_version = `$python -c 'import sys; print "%d.%d" % (sys.version_info[:2])'`;
201 :     chomp $py_version;
202 :     print "Python version $py_version\n";
203 :    
204 : olson 1.2 $OtherConfig->{python_site_path} = "$ENV{FIGCONFIG_ENV_DIR}/lib/python$py_version/site-packages";
205 :    
206 : olson 1.1 my @path = ();
207 : olson 1.2 push(@path, $OtherConfig->{python_site_path});
208 :     push(@path, "$release_lib");
209 : olson 1.1 push(@path, "$fig_disk/config");
210 :     push(@$Env, ["PYTHONPATH", join(":", @path), 1]);
211 :    
212 :     $OtherConfig->{pythonpath} = join(":", @path);
213 :     }
214 :    
215 :     sub find_in_path
216 :     {
217 : olson 1.5 my($file, @extra) = @_;
218 : olson 1.1 my(@path) = split(":", $ENV{PATH});
219 :    
220 : olson 1.5 for my $p (@path, @extra)
221 : olson 1.1 {
222 :     my $x = "$p/$file";
223 :     if (-x $x)
224 :     {
225 :     return $x;
226 :     }
227 :     }
228 :     return undef;
229 :     }
230 :    
231 :     #
232 :     # Find the name of the python executable we are to use.
233 :     #
234 :     sub find_python
235 :     {
236 :     my $python;
237 :    
238 :     #
239 :     # Special case for the mac.
240 :     #
241 :    
242 :     if ($ENV{FIGCONFIG_ENV} eq "mac")
243 :     {
244 : olson 1.7 #
245 :     # We'd like to use the MacPython that is installed
246 :     # as pythonw.
247 :     #
248 :     if ($python = find_in_path("pythonw", "/usr/local/bin"))
249 : olson 1.1 {
250 : olson 1.7 $OtherConfig->{python_require_poundbang_env} = 1;
251 : olson 1.1 return $python;
252 :     }
253 :    
254 :     #
255 : olson 1.7 # Otherwise, we can live with the regular python.
256 :     # Fall thru to the generic case.
257 : olson 1.1 #
258 : olson 1.7 }
259 :     #
260 :     # Non-mac, just look in the env dir or the path.
261 :     #
262 : olson 1.1
263 : olson 1.7 $python = "$ENV{FIGCONFIG_ENV_DIR}/bin/python";
264 :     if (-x $python)
265 :     {
266 :     return $python;
267 : olson 1.1 }
268 :    
269 : olson 1.7 return find_in_path("python");
270 : olson 1.1 }
271 :    
272 :     #
273 :     # Find the name of the perl executable we are to use.
274 :     #
275 :     sub find_perl
276 :     {
277 :     my $perl;
278 :    
279 :     $perl = "$ENV{FIGCONFIG_ENV_DIR}/bin/perl";
280 :     if (-x $perl)
281 :     {
282 :     return $perl;
283 :     }
284 :    
285 :     warn "We did not find a perl executable in the SEED distribution; some modules may not be found\n";
286 :     return find_in_path("perl");
287 :     }
288 :    
289 :     sub write_bash_init
290 :     {
291 :     my($fh, $env) = @_;
292 :    
293 :     foreach my $item (@$env)
294 :     {
295 :     my($name, $value, $append) = @$item;
296 :    
297 :     if ($append)
298 :     {
299 :     #
300 :     # Write code to detect if the value is set, and act accordingly.
301 :     #
302 :    
303 :     print $fh <<END;
304 :     DELIM=
305 :     if [ -n "\$$name" ] ; then
306 :     DELIM=:
307 :     fi
308 :     $name=\${$name}\${DELIM}$value
309 :     export $name
310 :     END
311 :     }
312 :     else
313 :     {
314 :     print $fh "$name=\"$value\"\n";
315 :     print $fh "export $name\n";
316 :     }
317 :     }
318 :     }
319 :    
320 :     sub write_csh_init
321 :     {
322 :     my($fh, $env) = @_;
323 :    
324 :     foreach my $item (@$env)
325 :     {
326 :     my($name, $value, $append) = @$item;
327 :    
328 :     if ($append)
329 :     {
330 :     #
331 :     # Write code to detect if the value is set, and act accordingly.
332 :     #
333 :    
334 :     print $fh <<END;
335 :     if (\$?$name) then
336 :     setenv $name \${$name}:$value
337 :     else
338 :     setenv $name $value
339 :     endif
340 :     END
341 :     }
342 :     else
343 :     {
344 :     print $fh "setenv $name \"$value\"\n";
345 :     }
346 :     }
347 :    
348 :     }
349 :    
350 :     sub run_script
351 :     {
352 :     my($script) = @_;
353 :    
354 :    
355 :     unless (my $ret = do $script)
356 :     {
357 :     if ($@)
358 :     {
359 :     warn "Error parsing $script: $@\n";
360 :     }
361 :     elsif (!defined($ret))
362 :     {
363 :     warn "Couldn't do $script: $!\n";
364 :     }
365 :     else
366 :     {
367 :     warn "Counldn't run $script\n";
368 :     }
369 :     }
370 :    
371 :    
372 :     }
373 :    
374 :     sub configure_environment_specific
375 :     {
376 :     my $env_script = $ENV{FIGCONFIG_ENV_CONFIG};
377 :    
378 :     if (! -f $env_script)
379 :     {
380 :     warn "No environment-specific configuration file $env_script found, skipping\n";
381 :     return;
382 :     }
383 :    
384 :     run_script($env_script);
385 :     }
386 :    
387 :     #
388 :     # Create any directories that might be missing.
389 :     #
390 :    
391 :     sub setup_directories
392 :     {
393 :     my(@needed) = @_;
394 :    
395 :     for my $dir (@needed)
396 :     {
397 :     if (! -d $dir)
398 :     {
399 :     mkdir($dir) or warn "Could not create $dir: $!\n";
400 :     }
401 :     }
402 :     }
403 :    
404 :     sub setup_server_scripts
405 :     {
406 :     #
407 :     # Remove any start/stop servers scripts we might have, and write the stub
408 :     # start.
409 :     #
410 :    
411 :     unlink($start_servers);
412 :     unlink($stop_servers);
413 :    
414 :     open(F, ">$start_servers") or die "Cannot write $start_servers: $!";
415 :     print F "#!/bin/sh\n\n";
416 :     close(F);
417 :     chmod(0775, $start_servers);
418 :    
419 :     open(F, ">$stop_servers") or die "Cannot write $stop_servers: $!";
420 :     print F "#!/bin/sh\n\n";
421 :     close(F);
422 :     chmod(0775, $stop_servers);
423 :    
424 :     }
425 :    
426 : olson 1.7 sub finalize_server_scripts
427 :     {
428 :     #
429 :     # After any environment-specific stuff, call start_services and stop_services.
430 :     #
431 :    
432 :     open(F, ">>$start_servers") or die "Cannot write $start_servers: $!";
433 :     print F "\n$fig_bin/start_services\n";
434 :     close(F);
435 :     chmod(0775, $start_servers);
436 :    
437 :     open(F, ">>$stop_servers") or die "Cannot write $stop_servers: $!";
438 :     print F "\n$fig_bin/stop_services\n";
439 :     close(F);
440 :     chmod(0775, $stop_servers);
441 :    
442 :     }
443 :    
444 : olson 1.1 sub write_config_pm
445 :     {
446 :     my($fh, $config) = @_;
447 :    
448 :     print $fh "package FIG_Config;\n\n";
449 :    
450 :     foreach my $item (@$config)
451 :     {
452 :     my($name, $value, $quote) = @$item;
453 :    
454 :     my $q = $quote ? '"' : '';
455 :     printf $fh "\$%-15s = $q$value$q;\n", $name
456 :     }
457 :    
458 :     print $fh "\n1;\n";
459 :     }
460 :    
461 :     sub write_config_py
462 :     {
463 :     my($fh, $config) = @_;
464 :    
465 :     foreach my $item (@$config)
466 :     {
467 :     my($name, $value, $quote) = @$item;
468 :    
469 :     #
470 :     # Ugh. "global" is a keyword in python.
471 :     #
472 :    
473 :     $name = "global_dir" if $name eq "global";
474 :    
475 :     my $q = $quote ? '"' : '';
476 :     printf $fh "%-15s = $q$value$q\n", $name
477 :     }
478 :     }
479 :    
480 :     sub write_tool_hdr_perl
481 :     {
482 :     my($fh) = @_;
483 :    
484 :     my $perl = find_perl();
485 :    
486 :     print $fh "#!$perl\n";
487 :     print $fh "\n";
488 :    
489 :     if ($::perlenv_override)
490 :     {
491 :     #
492 :     # Write the tool header BEGIN block to reset the environment.
493 :     #
494 :    
495 :     print $fh "BEGIN {\n";
496 :     print $fh " \@INC = qw(\n";
497 :     for my $inc (@INC)
498 :     {
499 :     next if $inc eq '.';
500 :     print $fh "\t$inc\n";
501 :     }
502 : olson 1.2 print $fh ");\n";
503 : olson 1.1 print $fh "}\n";
504 :     }
505 :    
506 :     print $fh "use Data::Dumper;\n";
507 :     print $fh "use Carp;\n";
508 :    
509 : olson 1.2 #
510 :     # We generate a comment here that gets expanded by switch_to_release
511 :     # This is part of the effort in making the environment bootstrapping
512 :     # code independent of releases.
513 :     #
514 :    
515 :     #print $fh "use lib \"$release_lib\";\n";
516 :     #print $fh "use lib \"$release_lib/FigKernelPackages\";\n";
517 :    
518 :     print $fh "# Following block is expanded by switch_to_release to add use lib directives\n";
519 :     print $fh "# to point at the correct locations in the release directory.\n";
520 :     print $fh "#BEGIN switch_to_release generated code\n";
521 :     print $fh "#END switch_to_release generated code\n";
522 :     print $fh "\n";
523 :    
524 : olson 1.1 print $fh "use lib \"$fig_disk/config\";\n";
525 :    
526 :     print $fh "use FIG_Config;\n";
527 :     print $fh "\n";
528 :     }
529 :    
530 :     sub write_tool_hdr_python
531 :     {
532 :     my($fh) = @_;
533 :    
534 :     my $python = find_python();
535 :    
536 : olson 1.4 if ($OtherConfig->{python_require_poundbang_env})
537 :     {
538 :     print $fh "#!/usr/bin/env $python\n";
539 :     }
540 :     else
541 :     {
542 :     print $fh "#!$python\n";
543 :     }
544 : olson 1.1 print $fh "\n";
545 :    
546 :     print $fh "import sys\n";
547 : olson 1.2
548 :    
549 :     print $fh "sys.path.append('$OtherConfig->{python_site_path}')\n";
550 :    
551 :     print $fh "# Following block is expanded by switch_to_release to add use lib directives\n";
552 :     print $fh "# to point at the correct locations in the release directory.\n";
553 :     print $fh "#BEGIN switch_to_release generated code\n";
554 :     print $fh "#END switch_to_release generated code\n";
555 :     print $fh "\n";
556 :    
557 :     print $fh "sys.path.append('$fig_disk/config')\n";
558 :    
559 : olson 1.1 print $fh "import FIG_Config\n";
560 :     print $fh "\n";
561 :     }
562 :    
563 :     setup_directories("$fig_disk/bin",
564 :     "$fig_disk/config");
565 :    
566 :     setup_server_scripts();
567 :    
568 :    
569 :     find_python();
570 :    
571 :     compute_environment();
572 :     configure_std_fig_environment();
573 :     configure_python();
574 :     configure_environment_specific();
575 : olson 1.7
576 :     finalize_server_scripts();
577 : olson 1.1
578 :     #
579 :     # Write the shell startup to the figdisk.
580 :     #
581 :     open(FH, ">$fig_disk/config/fig-user-env.sh") or die "Cannot write $fig_disk/config/fig-user-env.sh: $!";
582 :     write_bash_init(\*FH, $Env);
583 :     close(FH);
584 :    
585 :     open(FH, ">$fig_disk/config/fig-user-env.csh") or die "Cannot write $fig_disk/config/fig-user-env.csh: $!";
586 :     write_csh_init(\*FH, $Env);
587 :     close(FH);
588 :    
589 :     #
590 :     # Write the FIG_Config file.
591 :     #
592 :    
593 :     open(FH, ">$fig_disk/config/FIG_Config.pm") or die "Cannot write $fig_disk/config/FIG_Config.pm: $!";
594 :     write_config_pm(\*FH, $Config);
595 :     close(FH);
596 :    
597 :     open(FH, ">$fig_disk/config/FIG_Config.py") or die "Cannot write $fig_disk/config/FIG_Config.py: $!";
598 :     write_config_py(\*FH, $Config);
599 :     close(FH);
600 :    
601 :     #
602 :     # Write the tool headers
603 :     #
604 :    
605 : olson 1.2 open(FH, ">$fig_disk/config/base_tool_hdr") or die "Cannot write $fig_disk/config/tool_hdr: $!";
606 : olson 1.1 write_tool_hdr_perl(\*FH);
607 :     close(FH);
608 :    
609 : olson 1.2 open(FH, ">$fig_disk/config/base_tool_hdr_py") or die "Cannot write $fig_disk/config/tool_hdr_py: $!";
610 : olson 1.1 write_tool_hdr_python(\*FH);
611 :     close(FH);
612 :    
613 : olson 1.2 unshift(@INC, "$ENV{FIGCONFIG_RELEASE_DIR}");
614 :    
615 :     require FigCommon::SwitchRelease;
616 : olson 1.1
617 : olson 1.2 &FigCommon::SwitchRelease::switch_to_release($fig_disk, $ENV{FIGCONFIG_ENV}, $ENV{FIGCONFIG_RELEASE});

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