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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 : olson 1.14 my @perllib = grep({ $_ ne "." } @INC, "$fig_disk/config", $release_lib,
200 :     "$release_lib/FigKernelPackages");
201 : olson 1.12
202 :     push(@$Env, ["PERL5LIB", join(":", @perllib), 1]);
203 : olson 1.1 }
204 :    
205 :     sub configure_python
206 :     {
207 :     #
208 :     # Determine the PYTHONPATH we're to use.
209 :     #
210 :     # Right now, we don't compute a replacement for the system path,
211 :     # but we're likely going to require that *if* python is
212 :     # distributed with the environment. We're currently not doing that.
213 :     #
214 :     # So we just need to point to any python packages in the release,
215 :     # and to packages that were installed in the environment dir.
216 :     #
217 :    
218 :     my $python = find_python();
219 :     print "Found python at $python\n";
220 :    
221 :     my $py_version = `$python -c 'import sys; print "%d.%d" % (sys.version_info[:2])'`;
222 :     chomp $py_version;
223 :     print "Python version $py_version\n";
224 :    
225 : olson 1.2 $OtherConfig->{python_site_path} = "$ENV{FIGCONFIG_ENV_DIR}/lib/python$py_version/site-packages";
226 :    
227 : olson 1.1 my @path = ();
228 : olson 1.2 push(@path, $OtherConfig->{python_site_path});
229 :     push(@path, "$release_lib");
230 : olson 1.1 push(@path, "$fig_disk/config");
231 :     push(@$Env, ["PYTHONPATH", join(":", @path), 1]);
232 :    
233 :     $OtherConfig->{pythonpath} = join(":", @path);
234 :     }
235 :    
236 :     sub find_in_path
237 :     {
238 : olson 1.5 my($file, @extra) = @_;
239 : olson 1.1 my(@path) = split(":", $ENV{PATH});
240 :    
241 : olson 1.5 for my $p (@path, @extra)
242 : olson 1.1 {
243 :     my $x = "$p/$file";
244 :     if (-x $x)
245 :     {
246 :     return $x;
247 :     }
248 :     }
249 :     return undef;
250 :     }
251 :    
252 :     #
253 :     # Find the name of the python executable we are to use.
254 :     #
255 :     sub find_python
256 :     {
257 :     my $python;
258 :    
259 :     #
260 :     # Special case for the mac.
261 :     #
262 : olson 1.11 # RDO 20040603 - don't do this any more; we want to pick up
263 :     # the python we ship.
264 :     #
265 : olson 1.1
266 : olson 1.11 if (0 && $ENV{FIGCONFIG_ENV} eq "mac")
267 : olson 1.1 {
268 : olson 1.7 #
269 :     # We'd like to use the MacPython that is installed
270 :     # as pythonw.
271 :     #
272 :     if ($python = find_in_path("pythonw", "/usr/local/bin"))
273 : olson 1.1 {
274 : olson 1.7 $OtherConfig->{python_require_poundbang_env} = 1;
275 : olson 1.1 return $python;
276 :     }
277 :    
278 :     #
279 : olson 1.7 # Otherwise, we can live with the regular python.
280 :     # Fall thru to the generic case.
281 : olson 1.1 #
282 : olson 1.7 }
283 :     #
284 :     # Non-mac, just look in the env dir or the path.
285 :     #
286 : olson 1.1
287 : olson 1.7 $python = "$ENV{FIGCONFIG_ENV_DIR}/bin/python";
288 :     if (-x $python)
289 :     {
290 : olson 1.13 #
291 :     # The mac doesn't seem to like the long #! lines, so we'll use poundbang env.
292 :     #
293 :     if ($ENV{FIGCONFIG_ENV} eq "mac")
294 :     {
295 :     $OtherConfig->{python_require_poundbang_env} = 1;
296 :     }
297 : olson 1.7 return $python;
298 : olson 1.1 }
299 :    
300 : olson 1.7 return find_in_path("python");
301 : olson 1.1 }
302 :    
303 :     #
304 :     # Find the name of the perl executable we are to use.
305 :     #
306 :     sub find_perl
307 :     {
308 :     my $perl;
309 :    
310 :     $perl = "$ENV{FIGCONFIG_ENV_DIR}/bin/perl";
311 :     if (-x $perl)
312 :     {
313 :     return $perl;
314 :     }
315 :    
316 :     warn "We did not find a perl executable in the SEED distribution; some modules may not be found\n";
317 :     return find_in_path("perl");
318 :     }
319 :    
320 :     sub write_bash_init
321 :     {
322 :     my($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 $fh <<END;
335 :     DELIM=
336 :     if [ -n "\$$name" ] ; then
337 :     DELIM=:
338 :     fi
339 : olson 1.10 $name=$value\${DELIM}\${$name}
340 : olson 1.1 export $name
341 :     END
342 :     }
343 :     else
344 :     {
345 :     print $fh "$name=\"$value\"\n";
346 :     print $fh "export $name\n";
347 :     }
348 :     }
349 :     }
350 :    
351 :     sub write_csh_init
352 :     {
353 :     my($fh, $env) = @_;
354 :    
355 :     foreach my $item (@$env)
356 :     {
357 :     my($name, $value, $append) = @$item;
358 :    
359 :     if ($append)
360 :     {
361 :     #
362 :     # Write code to detect if the value is set, and act accordingly.
363 :     #
364 :    
365 :     print $fh <<END;
366 :     if (\$?$name) then
367 : olson 1.10 setenv $name $value:\${$name}
368 : olson 1.1 else
369 :     setenv $name $value
370 :     endif
371 :     END
372 :     }
373 :     else
374 :     {
375 :     print $fh "setenv $name \"$value\"\n";
376 :     }
377 :     }
378 :    
379 :     }
380 :    
381 :     sub run_script
382 :     {
383 :     my($script) = @_;
384 :    
385 :    
386 :     unless (my $ret = do $script)
387 :     {
388 :     if ($@)
389 :     {
390 :     warn "Error parsing $script: $@\n";
391 :     }
392 :     elsif (!defined($ret))
393 :     {
394 :     warn "Couldn't do $script: $!\n";
395 :     }
396 :     else
397 :     {
398 :     warn "Counldn't run $script\n";
399 :     }
400 :     }
401 :    
402 :    
403 :     }
404 :    
405 :     sub configure_environment_specific
406 :     {
407 :     my $env_script = $ENV{FIGCONFIG_ENV_CONFIG};
408 :    
409 :     if (! -f $env_script)
410 :     {
411 :     warn "No environment-specific configuration file $env_script found, skipping\n";
412 :     return;
413 :     }
414 :    
415 :     run_script($env_script);
416 :     }
417 :    
418 :     #
419 :     # Create any directories that might be missing.
420 :     #
421 :    
422 :     sub setup_directories
423 :     {
424 :     my(@needed) = @_;
425 :    
426 :     for my $dir (@needed)
427 :     {
428 :     if (! -d $dir)
429 :     {
430 :     mkdir($dir) or warn "Could not create $dir: $!\n";
431 :     }
432 :     }
433 :     }
434 :    
435 :     sub setup_server_scripts
436 :     {
437 :     #
438 :     # Remove any start/stop servers scripts we might have, and write the stub
439 :     # start.
440 :     #
441 :    
442 :     unlink($start_servers);
443 :     unlink($stop_servers);
444 :    
445 :     open(F, ">$start_servers") or die "Cannot write $start_servers: $!";
446 :     print F "#!/bin/sh\n\n";
447 :     close(F);
448 :     chmod(0775, $start_servers);
449 :    
450 :     open(F, ">$stop_servers") or die "Cannot write $stop_servers: $!";
451 :     print F "#!/bin/sh\n\n";
452 :     close(F);
453 :     chmod(0775, $stop_servers);
454 :    
455 :     }
456 :    
457 : olson 1.7 sub finalize_server_scripts
458 :     {
459 :     #
460 :     # After any environment-specific stuff, call start_services and stop_services.
461 :     #
462 :    
463 :     open(F, ">>$start_servers") or die "Cannot write $start_servers: $!";
464 :     print F "\n$fig_bin/start_services\n";
465 :     close(F);
466 :     chmod(0775, $start_servers);
467 :    
468 :     open(F, ">>$stop_servers") or die "Cannot write $stop_servers: $!";
469 :     print F "\n$fig_bin/stop_services\n";
470 :     close(F);
471 :     chmod(0775, $stop_servers);
472 :    
473 :     }
474 :    
475 : olson 1.1 sub write_config_pm
476 :     {
477 :     my($fh, $config) = @_;
478 :    
479 :     print $fh "package FIG_Config;\n\n";
480 :    
481 :     foreach my $item (@$config)
482 :     {
483 :     my($name, $value, $quote) = @$item;
484 :    
485 :     my $q = $quote ? '"' : '';
486 :     printf $fh "\$%-15s = $q$value$q;\n", $name
487 :     }
488 :    
489 :     print $fh "\n1;\n";
490 :     }
491 :    
492 :     sub write_config_py
493 :     {
494 :     my($fh, $config) = @_;
495 :    
496 :     foreach my $item (@$config)
497 :     {
498 :     my($name, $value, $quote) = @$item;
499 :    
500 :     #
501 :     # Ugh. "global" is a keyword in python.
502 :     #
503 :    
504 :     $name = "global_dir" if $name eq "global";
505 :    
506 :     my $q = $quote ? '"' : '';
507 :     printf $fh "%-15s = $q$value$q\n", $name
508 :     }
509 :     }
510 :    
511 :     sub write_tool_hdr_perl
512 :     {
513 :     my($fh) = @_;
514 :    
515 :     my $perl = find_perl();
516 :    
517 :     print $fh "#!$perl\n";
518 :     print $fh "\n";
519 :    
520 :     if ($::perlenv_override)
521 :     {
522 :     #
523 :     # Write the tool header BEGIN block to reset the environment.
524 :     #
525 :    
526 :     print $fh "BEGIN {\n";
527 :     print $fh " \@INC = qw(\n";
528 :     for my $inc (@INC)
529 :     {
530 :     next if $inc eq '.';
531 :     print $fh "\t$inc\n";
532 :     }
533 : olson 1.2 print $fh ");\n";
534 : olson 1.1 print $fh "}\n";
535 :     }
536 :    
537 :     print $fh "use Data::Dumper;\n";
538 :     print $fh "use Carp;\n";
539 :    
540 : olson 1.2 #
541 :     # We generate a comment here that gets expanded by switch_to_release
542 :     # This is part of the effort in making the environment bootstrapping
543 :     # code independent of releases.
544 :     #
545 :    
546 :     #print $fh "use lib \"$release_lib\";\n";
547 :     #print $fh "use lib \"$release_lib/FigKernelPackages\";\n";
548 :    
549 :     print $fh "# Following block is expanded by switch_to_release to add use lib directives\n";
550 :     print $fh "# to point at the correct locations in the release directory.\n";
551 :     print $fh "#BEGIN switch_to_release generated code\n";
552 :     print $fh "#END switch_to_release generated code\n";
553 :     print $fh "\n";
554 :    
555 : olson 1.1 print $fh "use lib \"$fig_disk/config\";\n";
556 :    
557 :     print $fh "use FIG_Config;\n";
558 :     print $fh "\n";
559 : olson 1.11 print $fh "#### END tool_hdr ####\n\n"
560 : olson 1.1 }
561 :    
562 :     sub write_tool_hdr_python
563 :     {
564 :     my($fh) = @_;
565 :    
566 :     my $python = find_python();
567 :    
568 : olson 1.4 if ($OtherConfig->{python_require_poundbang_env})
569 :     {
570 :     print $fh "#!/usr/bin/env $python\n";
571 :     }
572 :     else
573 :     {
574 :     print $fh "#!$python\n";
575 :     }
576 : olson 1.1 print $fh "\n";
577 :    
578 : olson 1.11 print $fh "import sys, os\n";
579 : olson 1.2
580 :    
581 :     print $fh "sys.path.append('$OtherConfig->{python_site_path}')\n";
582 :    
583 : olson 1.11 #
584 :     # Append the perl path to the environment, for use later with CallPerl.
585 :     #
586 :    
587 : olson 1.14 my $perlpath = join(":", @INC, "$fig_disk/config", $release_lib, "$release_lib/FigKernelPackages");
588 : olson 1.11 print $fh <<END;
589 :     if os.getenv("PERL5LIB", "") != "":
590 :     _delim = ":"
591 :     else:
592 :     _delim = ""
593 :     os.environ["PERL5LIB"] = "$perlpath" + _delim + os.getenv("PERL5LIB", "")
594 :    
595 :     END
596 :    
597 : olson 1.2 print $fh "# Following block is expanded by switch_to_release to add use lib directives\n";
598 :     print $fh "# to point at the correct locations in the release directory.\n";
599 :     print $fh "#BEGIN switch_to_release generated code\n";
600 :     print $fh "#END switch_to_release generated code\n";
601 :     print $fh "\n";
602 :    
603 :     print $fh "sys.path.append('$fig_disk/config')\n";
604 :    
605 : olson 1.1 print $fh "import FIG_Config\n";
606 :     print $fh "\n";
607 : olson 1.11 print $fh "#### END tool_hdr_py ####\n\n"
608 : olson 1.1 }
609 :    
610 :     setup_directories("$fig_disk/bin",
611 :     "$fig_disk/config");
612 :    
613 :     setup_server_scripts();
614 :    
615 :    
616 :     find_python();
617 :    
618 :     compute_environment();
619 :     configure_std_fig_environment();
620 :     configure_python();
621 :     configure_environment_specific();
622 : olson 1.7
623 :     finalize_server_scripts();
624 : olson 1.1
625 :     #
626 :     # Write the shell startup to the figdisk.
627 :     #
628 :     open(FH, ">$fig_disk/config/fig-user-env.sh") or die "Cannot write $fig_disk/config/fig-user-env.sh: $!";
629 :     write_bash_init(\*FH, $Env);
630 :     close(FH);
631 :    
632 :     open(FH, ">$fig_disk/config/fig-user-env.csh") or die "Cannot write $fig_disk/config/fig-user-env.csh: $!";
633 :     write_csh_init(\*FH, $Env);
634 :     close(FH);
635 :    
636 :     #
637 :     # Write the FIG_Config file.
638 :     #
639 :    
640 :     open(FH, ">$fig_disk/config/FIG_Config.pm") or die "Cannot write $fig_disk/config/FIG_Config.pm: $!";
641 :     write_config_pm(\*FH, $Config);
642 :     close(FH);
643 :    
644 :     open(FH, ">$fig_disk/config/FIG_Config.py") or die "Cannot write $fig_disk/config/FIG_Config.py: $!";
645 :     write_config_py(\*FH, $Config);
646 :     close(FH);
647 :    
648 :     #
649 :     # Write the tool headers
650 :     #
651 :    
652 : olson 1.2 open(FH, ">$fig_disk/config/base_tool_hdr") or die "Cannot write $fig_disk/config/tool_hdr: $!";
653 : olson 1.1 write_tool_hdr_perl(\*FH);
654 :     close(FH);
655 :    
656 : olson 1.2 open(FH, ">$fig_disk/config/base_tool_hdr_py") or die "Cannot write $fig_disk/config/tool_hdr_py: $!";
657 : olson 1.1 write_tool_hdr_python(\*FH);
658 :     close(FH);
659 :    
660 : olson 1.2 unshift(@INC, "$ENV{FIGCONFIG_RELEASE_DIR}");
661 :    
662 :     require FigCommon::SwitchRelease;
663 : olson 1.1
664 : olson 1.2 &FigCommon::SwitchRelease::switch_to_release($fig_disk, $ENV{FIGCONFIG_ENV}, $ENV{FIGCONFIG_RELEASE});

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