lib/tool_subs.pm

   1 # {{{ include
   2
   3 start include statements
   4 use ext::Parallel::ForkManager;
   5 use strict;
   6 use Cwd;
   7 use File::Copy 'cp';
   8 use OSspecific;
   9 use Storable;
  10 use Math::Random;
  11 use ui;
  12 use Data::Dumper;
  13 use Config;
  14 our $AUTOLOAD;
  15 if ( $PsN::config -> {'_'} -> {'use_database'} ) {
  16 # Testing DBD::mysql:
  17   require DBI;
  18 }
  19 end include
  20
  21 # }}} include statements
  22
  23 # {{{ new
  24
  25 start new
  26 {
  27     # The I<retries>, I<picky>, I<nm_version>, I<seed> and I<threads>
  28     # attributes can be specified as either a scalar or as an
  29     # array. The scalar value will be applied to all models whereas
  30     # the array holds values per model. If an array is given it must
  31     # be of the same length as the number of models.
  32     #
  33     # The I<directory> is the folder where the tools stores
  34     # temporary data and runs subtools (or in the modelfit case,
  35     # runs NONMEM). If unsure of what this means, leave it undefined
  36     # and a default will be used, e.g. modelfit_dir3 or something.
  37     #
  38     # The base_directory refers to the directory where the tool
  39     # should place its own directory. Default is current directory.
  40     #
  41     # A more interresting attribute is I<threads> which sets how many
  42     # parallel executions of NONMEM that will run. Some tips are:
  43     # Setting the number of threads higher than the number of nodes in
  44     # your cluster/supercomputer can make your runs slower. The
  45     # biggest limiting factor is the amount of memory needed by
  46     # NONMEM. With smaller runs, just set the thread number to the
  47     # number of nodes available.
  48     #
  49     # The I<directory> is the folder where the tools stores
  50     # temporary data and runs subtools (or in the modelfit case,
  51     # runs NONMEM). Each NONMEM run will have its own sub directory
  52     # NM_run[X] where [X] is an index running from 0 to the number of
  53     # runs-1. If unsure of what this means, leave it undefined and a
  54     # default will be used, e.g. modelfit_dir3 or something.
  55     #
  56     # Next, the I<compress> and I<remove_temp_files> attributes are good
  57     # if you want to save some hard disk space. I<compress> set to 1
  58     # will put all NONMEM output in to an tar/gz archive named
  59     # I<problem_files.tgz> placed in the I<NM_run[X]> directory
  60     # described above. If I<remove_temp_files> is set to 1, the NONMEM
  61     # files: 'FCON', 'FDATA', 'FSTREAM', 'PRDERR' will be removed.
  62     #
  63     # I<clean> is a stronger version of I<remove_temp_files>; it will also
  64     # remove I<NM_run[X]> and all that is in these.
  65     #
  66     # I<retries> is the number of times L</run> will alter initial
  67     # values and (re)execute NONMEM when executions fail. I<retries>
  68     # can either be an integer, specifying the number of retries for
  69     # all models, or it can be an array with the number of retries
  70     # specific for each modelfile as elements. The default value is
  71     # B<5>. The algorithm for altering the initial values works
  72     # roughly like this: For each each new try, a random new initial
  73     # value is drawn from a uniform distribution with limits +-n*10%
  74     # of the original intial estimate and where n i equal to the retry
  75     # number. I.e. the first retry, the borders of the distribution
  76     # are +-10%. The algorithm ensures that the new values are within
  77     # specified boundaries.
  78     #
  79     # =begin html
  80     #
  81     # For a full dexcription of the algorithm, see <a
  82     # href="model/problem/record/init_option.html#set_random_init">set_random_init</a>
  83     # of the <a
  84     # href="model/problem/record/init_option.html">init_option
  85     # class</a>.
  86     #
  87     # =end html
  88     #
  89     # =begin man
  90     #
  91     # For a full dexcription of the algorithm, see I<set_random_init>
  92     # of the I<init_option> class.
  93     #
  94     # =end man
  95     #
  96     # If I<picky> is set to 1, the output from NONMEM will be checked
  97     # more thoroughly. If any of the lines below are found in the
  98     # minimization message, a rerun is initiated.
  99     #
 100     #    ESTIMATE OF THETA IS NEAR THE BOUNDARY AND
 101     #    PARAMETER ESTIMATE IS NEAR ITS BOUNDARY
 102     #    R MATRIX ALGORITHMICALLY SINGULAR
 103     #    S MATRIX ALGORITHMICALLY SINGULAR
 104     #
 105     # I<nm_version> is a string with the version number of NONMEM that
 106     # will be used. The installed versions of NONMEM must be specified
 107     # in OSspecific.pm, the class responsible for system specific
 108     # features settings.
 109     #
 110     # I<logfile> specifies the name of the logfile.
 111     #
 112     # If I<debug> is set to 1(true), (many!) debug messages will be
 113     # printed.
 114     #
 115     # I<extra_files> is an array of strings where each string is a
 116     # file needed for NONMEM execution. Those file will be moved
 117     # to the I<NM_run[X]> directory.
 118     #
 119     # I<seed> is just a way to set a seed number.
 120     #
 121     # If a directory is given as argument to a tool, it will extract
 122     # all information about what has already been run in this
 123     # directory and continue there. If nothing is left to do, it will
 124     # still produce the output as a normal run would. This is useful
 125     # both for resuming crashed runs as well as for extracting
 126     # information form an old run.
 127
 128   $this -> {'seed'} = defined $parm{'seed'} ? $parm{'seed'} : random_uniform_integer(1,0,10000000);
 129
 130         #Initiate the random generator if a seed is given (which it is, see above)
 131         random_set_seed_from_phrase( $this -> {'seed'} );
 132
 133         # The base_directory refers to the directory where the tool should place its own
 134         # directory
 135         if ( defined $parm{'base_directory'} ) {
 136           $this -> {'base_directory'} = $parm{'base_directory'};
 137         } else {
 138           my ($uniquePath, $file) = OSspecific::absolute_path( '', '' );
 139           $this -> {'base_directory'} = $uniquePath;
 140         }
 141
 142         my @tool_name_full = split( '::', ref $this );
 143         my $tool_name = $tool_name_full[$#tool_name_full];
 144
 145         # The directory is the folder where the tools stores temporary data and
 146         # runs subtools (or in the modelfit case, runs NONMEM)
 147         if ( defined $parm{'directory'} ) {
 148           my $dummy;
 149           ( $this -> {'directory'}, $dummy ) = OSspecific::absolute_path( $parm{'directory'}, '');
 150         } else {
 151           my $file;
 152           $this -> {'directory'} =
 153               OSspecific::unique_path( $tool_name.'_dir' ,
 154                                        $this -> {'base_directory'} );
 155         }
 156
 157
 158   # Create my temporary directory
 159   $this -> _make_dir;
 160   if ( $PsN::config -> {'_'} -> {'use_database'} ) {
 161     my( $found_log, $found_tool_id ) = $this -> read_log;
 162
 163     $this -> register_in_database unless ( $found_tool_id );
 164
 165     $this -> log_object unless ( $found_log and $found_tool_id );
 166   }
 167
 168         debug -> die( message => "No model specified!" )
 169             unless ( defined $this -> {'models'} and scalar @{$this -> {'models'}} > 0 );
 170         foreach my $mod ( @{$this -> {'models'}} ) {
 171           debug -> die( message => "Supplied argument model is not defined" )
 172               unless defined $mod;
 173         }
 174         # Make sure that the filenames are absolute and collect model_ids
 175         my @model_ids;
 176         foreach my $model ( @{$this -> {'models'}} ) {
 177           my $model_id = $model -> model_id;
 178           if( not defined $model_id ) {
 179             $model_id = $model -> register_in_database;
 180           }
 181           my $datas = $model -> datas;
 182           if( defined $datas ) {
 183             foreach my $data ( @{$datas} ) {
 184               my $data_id = $data -> data_id;
 185               if( not defined $data_id ) {
 186                 $data -> register_in_database;
 187               }
 188             }
 189           }
 190
 191           push( @model_ids, $model -> model_id );
 192             my ($directory, $filename) = OSspecific::absolute_path( $model -> directory, $model -> filename );
 193             $model -> filename( $filename );
 194             $model -> directory( $directory );
 195           if ( defined $model -> outputs ) {
 196             my @outputs = @{$model -> outputs};
 197             foreach my $output ( @outputs ) {
 198                 my ($directory, $filename) = OSspecific::absolute_path( $outputs[0] -> directory, $outputs[0] -> filename );
 199                 $output -> filename( $filename );
 200                 $output -> directory( $directory );
 201             }
 202           }
 203           if ( defined $model -> datas ) {
 204             my @datas = @{$model -> datas};
 205             foreach my $data ( @datas ) {
 206                 my ($directory, $filename) = OSspecific::absolute_path( $datas[0] -> directory, $datas[0] -> filename );
 207                 $data -> filename( $filename );
 208                 $data -> directory( $directory );
 209             }
 210           }
 211         }
 212   $this -> {'model_ids'} = \@model_ids;
 213   if ( not -e $this -> {'directory'}."done.database.tool_models" ) {
 214     $this -> register_tm_relation( model_ids       => \@model_ids,
 215                                    prepared_models => 0 );
 216     open( DB, ">".$this -> {'directory'}."done.database.tool_models" );
 217     print DB "";
 218     close( DB );
 219   }
 220 }
 221 end new
 222
 223 # }}} new
 224
 225 # {{{ log_object
 226
 227 start log_object
 228 {
 229   open( OLOG, '>',$self -> {'directory'}.'object.txt' );
 230   $Data::Dumper::Maxdepth = 1;
 231   print OLOG Dumper $self;
 232   $Data::Dumper::Maxdepth = 0;
 233   close( OLOG );
 234 }
 235 end log_object
 236
 237 # }}} log_object
 238
 239 # {{{ read_log
 240 start read_log
 241 {
 242   if( -e $self -> {'directory'}.'object.txt' ) {
 243     $found_log = 1;
 244     open( OLOG, '<'.$self -> {'directory'}.'object.txt' );
 245     my @olog = <OLOG>;
 246     my $str = "(";
 247     for ( my $i = 1; $i < $#olog; $i++ ) {
 248       $str = $str.$olog[$i];
 249     }
 250     $str = $str.")";
 251     my %tmp = eval( $str );
 252
 253     if( exists $tmp{'tool_id'} ) {
 254       $self -> {'tool_id'} = $tmp{'tool_id'};
 255       $found_tool_id = 1;
 256     }
 257     close( OLOG );
 258   }
 259 }
 260 end read_log
 261 # }}} read_log
 262
 263 # {{{ register_in_database
 264
 265 start register_in_database
 266   {
 267     if ( $PsN::config -> {'_'} -> {'use_database'} ) {
 268       my @tool_name_full = split( '::', ref $self );
 269       my $tool_name = $tool_name_full[$#tool_name_full];
 270       my ( $date_str, $time_str );
 271       if ( $Config{osname} eq 'MSWin32' ) {
 272         $date_str = `date /T`;
 273         $time_str = ' '.`time /T`;
 274       } else {
 275         # Assuming UNIX
 276         $date_str = `date`;
 277       }
 278       chomp($date_str);
 279       chomp($time_str);
 280       my $date_time = $date_str.$time_str;
 281       # Backslashes messes up the sql syntax
 282       my $dir_str = $self->{'directory'};
 283       $dir_str =~ s/\\/\//g;
 284
 285       my $dbh = DBI -> connect("DBI:mysql:host=".$PsN::config -> {'_'} -> {'database_server'}.
 286                                ";databse=".$PsN::config -> {'_'} -> {'project'},
 287                                $PsN::config -> {'_'} -> {'user'},
 288                                $PsN::config -> {'_'} -> {'password'},
 289                                {'RaiseError' => 1});
 290       my $sth;
 291       if ( defined $self -> {'parent_tool_id'} ) {
 292         #           print "INSERT INTO tool (parent_tool_id,name,date,directory) ".
 293         #             "VALUES (".$self -> {'parent_tool_id'}.", '".
 294         #               "$tool_name', '$date_time', '$dir_str' )\n";
 295         $sth = $dbh -> prepare("INSERT INTO ".$PsN::config -> {'_'} -> {'project'}.
 296                                ".tool (parent_tool_id,name,date,directory) ".
 297                                "VALUES (".$self -> {'parent_tool_id'}.", '".
 298                                "$tool_name', '$date_time', '$dir_str' )");
 299       } else {
 300         $sth = $dbh -> prepare("INSERT INTO ".$PsN::config -> {'_'} -> {'project'}.
 301                                ".tool (name,date,directory) ".
 302                                "VALUES ('$tool_name', '$date_time', '$dir_str' )");
 303       }
 304       $sth -> execute;
 305       $self -> {'tool_id'} = $sth->{'mysql_insertid'};
 306       $sth -> finish;
 307       $dbh -> disconnect;
 308     }
 309   }
 310 end register_in_database
 311
 312 # }}} register_in_database
 313
 314 # {{{ register_tm_relation
 315
 316 start register_tm_relation
 317   if ( $PsN::config -> {'_'} -> {'use_database'} and
 318        defined $self -> {'tool_id'} and $#model_ids >= 0 ) {
 319     my $dbh = DBI -> connect("DBI:mysql:host=".$PsN::config -> {'_'} -> {'database_server'}.
 320                              ";databse=".$PsN::config -> {'_'} -> {'project'},
 321                              $PsN::config -> {'_'} -> {'user'},
 322                              $PsN::config -> {'_'} -> {'password'},
 323                              {'raiseerror' => 1});
 324     my $sth;
 325     my $values;
 326     my $columns = "( tool_id, model_id, prepared_model )";
 327     foreach my $model_id ( @model_ids ) {
 328       if ( defined $model_id ) {
 329         $values = $values."," if ( defined $values );
 330         if( $prepared_models ) {
 331           $values = $values."(".$self -> {'tool_id'}.", $model_id, 1 )";
 332         } else {
 333           $values = $values."(".$self -> {'tool_id'}.", $model_id, 0 )";
 334         }
 335       }
 336     }
 337     $sth = $dbh -> prepare( "INSERT INTO ".$PsN::config -> {'_'} -> {'project'}.
 338                                ".tool_model $columns VALUES $values" );
 339     $sth -> execute;
 340     $sth -> finish if ( defined $sth );
 341     $dbh -> disconnect;
 342   }
 343 end register_tm_relation
 344
 345 # }}} register_tm_relation
 346
 347 # {{{ copy
 348
 349 start copy
 350 #      {
 351         #%{$tool} = %{$self};
 352         #$tool -> {'models'} = undef;
 353         #$tool -> {'tools'} = undef;
 354         #@{$tool -> {'models'}} = ();
 355         #@{$tool -> {'tools'}} = ();
 356         #foreach my $model ( @{$self -> {'models'}} ) {
 357         #  push( @{$tool -> {'models'}}, $model -> copy );
 358         #}
 359         #foreach my $subtool ( @{$self -> {'tools'}} ) {
 360         #  push( @{$tool -> {'tools'}}, $subtool -> copy );
 361         #}
 362         #bless( $tool, ref( $self ) );
 363
 364         # ! NOTE ! This is not a deep copy ! NOTE !
 365         # This function has now been replaced with "copying" the "reference object" in new().
 366
 367 #       my $all_parameters = {};
 368
 369 #       foreach my $valid_p ( keys %{ $self -> {'__valid_parameters'} } ){
 370 #         if( defined $self -> {$valid_p} ) {
 371 #           $all_parameters -> {$valid_p} = $self -> {$valid_p};
 372 #         }
 373 #       }
 374
 375 #       %{$all_parameters} = (%{$all_parameters}, %parameters);
 376
 377 #       use Data::Dumper;
 378 #       $Data::Dumper::Maxdepth = 3;
 379 #       print Dumper( $all_parameters );
 380 #       $Data::Dumper::Maxdepth = 0;
 381
 382 #       my $tool_string = ref $self;
 383
 384 #       $tool = "$tool_string" -> new( %{$all_parameters} );
 385 #      }
 386 end copy
 387
 388 # }}} copy
 389
 390 # {{{ pre_fork_setup
 391
 392 start pre_fork_setup
 393       {
 394         # Runs the pre_fork_setup specific for the subtool
 395         my $sub_pre_fork_setup = $self -> {'subtools'} -> [0];
 396         if ( defined $sub_pre_fork_setup ) {
 397           $sub_pre_fork_setup = $sub_pre_fork_setup.'_pre_fork_setup';
 398           if ( defined( $self -> can( $sub_pre_fork_setup ) ) ) {
 399             $self -> $sub_pre_fork_setup;
 400           }
 401         }
 402       }
 403 end pre_fork_setup
 404
 405 # }}} pre_fork_setup
 406
 407 # {{{ print_results
 408
 409 start print_results
 410 {
 411
 412   # Print results created by 'prepare_results' methods specific to the
 413   # tools. prepare_results and print_results are usually called from
 414   # the tool scripts (e.g. bin/bootstrap)
 415
 416   my $sub_print_results = $self -> {'subtools'} -> [0];
 417
 418   if ( defined $sub_print_results ) {
 419
 420     # Only if we have a subtool, which we allways do, 'modelfit' is as
 421     # usual the inner tool in the basic case.
 422
 423
 424     ### get_dim subroutine recurses through arrays of arrays and
 425     ### returns the number of levels (assumes the same number of
 426     ### levels in alls subarrays).
 427     ###
 428     ### 1st argument is the reference to the toplevel array.
 429     ### 2nd argument is a starting level.
 430     ### 3rd argument is an array giving the size of the arrays at each
 431     ### level (assuming same size arrays at each level)
 432
 433     sub get_dim {
 434       my $arr      = shift;
 435       my $dim      = shift;
 436       my $size_ref = shift;
 437       $dim++;
 438       if ( defined $arr and ref($arr) eq 'ARRAY' ) {
 439         push( @{$size_ref}, scalar @{$arr} );
 440         ( $dim, $size_ref ) = get_dim( $arr->[0], $dim, $size_ref );
 441       }
 442       return ( $dim, $size_ref );
 443     }
 444
 445     ### format_value returns a string for a given number. If the value
 446     ### is not defined it is returned as NaN or NA, depending on the
 447     ### output_style configured. Numbers without decimals get 10
 448     ### digits, Numbers with decimals get 10 digis and 5 decimal
 449     ### values.
 450
 451     sub format_value {
 452       my $val = shift;
 453       if ( not defined $val or $val eq '' ) {
 454         return sprintf("%10s",$PsN::out_miss_data).',';
 455       } else {
 456         $_ = $val;
 457         my $nodot = /.*\..*/ ? 0 : 1;
 458         $_ =~ s/\.//g;
 459         if ( /.*\D+.*/ or $nodot) {
 460           return sprintf("%10s",$val).',';
 461         } else {
 462           return sprintf("%10.5f",$val).',';
 463         }
 464       }
 465     }
 466
 467
 468     ### format_label does the same thing as format value, but does not
 469     ### print out "NA" or "NaN" in case of missing data.
 470
 471     sub format_label {
 472       my $val = shift;
 473       if ( not defined $val or $val eq '' ) {
 474         return ',';
 475       } else {
 476         $_ = $val;
 477         my $nodot = /.*\..*/ ? 0 : 1;
 478         $_ =~ s/\.//g;
 479         if ( /.*\D+.*/ or $nodot) {
 480           return sprintf("%10s",$val).',';
 481         } else {
 482           return sprintf("%10.5f",$val).',';
 483         }
 484       }
 485     }
 486
 487     ### The main part of the method will loop through the 'own'
 488     ### results, each element of the 'own' array is a hash with three
 489     ### keys:
 490     ###
 491     ### 'name' of the result, will be used as header (only if
 492     ### values are defined).
 493     ###
 494     ### 'values' either a single value, a list of values or a table of
 495     ### values.
 496     ###
 497     ### 'lables' either a single value(?), a list of values used as
 498     ### header for the 'values' list or table. It can be a table, Then
 499     ### the first row will be printed before each row in the values
 500     ### table, and the second row will be the header.
 501
 502     debug -> die( message => "No results_file defined" )
 503         unless ( defined $self -> {'results_file'} );
 504
 505     open ( RES, ">".$self -> {'directory'}.$self -> {'results_file'} );
 506
 507     if ( defined $self -> {'results'} ) {
 508       my @all_results = @{$self -> {'results'}};
 509
 510       for ( my $i = 0; $i <= $#all_results; $i++ ) {
 511         if ( defined $all_results[$i]{'own'} ) {
 512           my @my_results = @{$all_results[$i]{'own'}};
 513
 514           for ( my $j = 0; $j <= $#my_results; $j++ ) {
 515             # These size estimates include the problem and sub_problem dimensions:
 516             my ( $ldim, $lsize_ref ) = get_dim( $my_results[$j]{'labels'}, -1, [] );
 517             my ( $vdim, $vsize_ref ) = get_dim( $my_results[$j]{'values'}, -1, [] );
 518             print RES $my_results[$j]{'name'},"\n" if ( $vdim > 1 );
 519
 520             if ( defined $my_results[$j]{'values'} and
 521                  scalar @{$my_results[$j]{'values'}} >= 0 ) {
 522               my @values  = @{$my_results[$j]{'values'}};
 523               my @labels;
 524               if ( defined $my_results[$j]{'labels'} and
 525                    scalar @{$my_results[$j]{'labels'}} >= 0 ) {
 526                 @labels = @{$my_results[$j]{'labels'}};
 527               }
 528
 529               # Print Header Labels
 530               if ( $ldim == 0 ) {
 531                 my $label = \@labels;
 532                 print RES ','.format_label($label),"\n";
 533               } elsif ( $ldim == 2 ) {
 534                 print RES ',';
 535                 for ( my $n = 0; $n < scalar @{$labels[1]}; $n++ ) {
 536                   my $label = $labels[1][$n];
 537                   print RES format_label($label);
 538                 }
 539                 print RES "\n";
 540               }
 541
 542               # Print the values (with labels on each row if ldim == 2:
 543               if ( $vdim == 0 ) {
 544                 print RES ','.format_value(\@values),"\n";
 545               } elsif ( $vdim == 1 ) {
 546                 for ( my $m = 0; $m < scalar @values; $m++ ) {
 547                   my $label = $labels[$m];
 548                   print RES ','.format_label($label);
 549                   my $val = $values[$m];
 550                   print RES ','.format_value($val),"\n";
 551                 }
 552               } elsif ( $vdim == 2 ) {
 553                 for ( my $m = 0; $m < scalar @values; $m++ ) {
 554                   my $label;
 555                   if ( $ldim == 1 ) {
 556                     $label = $labels[$m];
 557                   } elsif ( $ldim == 2 ) {
 558                     $label = $labels[0][$m];
 559                   }
 560                   print RES format_label($label);
 561                   if( defined $values[$m] ){
 562                     for ( my $n = 0; $n < scalar @{$values[$m]}; $n++ ) {
 563                       print RES format_value($values[$m][$n]);
 564                     }
 565                   }
 566                   print RES "\n";
 567                 }
 568               }
 569             }
 570           }
 571         }
 572       }
 573     }
 574     close( RES );
 575   } else {
 576     debug -> warn( level => 2,
 577                    message => "No subtools defined".
 578                    ", using default printing routine" );
 579   }
 580 }
 581 end print_results
 582
 583 # }}} print_results
 584
 585 # {{{ post_fork_analyze
 586
 587 start post_fork_analyze
 588       {
 589         # Runs the post_fork_analyze specific for the subtool
 590         my $sub_post_fork_analyze = $self -> {'subtools'} -> [0];
 591         if ( defined $sub_post_fork_analyze ) {
 592           $sub_post_fork_analyze = $sub_post_fork_analyze.'_post_fork_analyze';
 593           if ( defined( $self -> can( $sub_post_fork_analyze ) ) ) {
 594             $self -> $sub_post_fork_analyze;
 595           }
 596         }
 597         if ( defined $self -> {'results_file'} ) {
 598           #$self -> print_results;
 599         }
 600       }
 601 end post_fork_analyze
 602
 603 # }}} post_fork_analyze
 604
 605 # {{{ setup
 606
 607 start setup
 608
 609 $self -> _prepare_model( model_number => $model_number );
 610
 611 # Run the setup specific for the subtool
 612 my $sub_setup = $self -> {'subtools'} -> [0];
 613 if ( defined $sub_setup ) {
 614   $sub_setup = $sub_setup.'_setup';
 615   $self -> $sub_setup( model_number => $model_number );
 616 }
 617 end setup
 618
 619 # }}} setup
 620
 621 # {{{ _make_dir
 622
 623 start _make_dir
 624        {
 625          mkdir( $self -> {'directory'} ) unless ( -e $self -> {'directory'} );
 626        }
 627 end _make_dir
 628
 629 # }}} _make_dir
 630
 631 # {{{ run
 632
 633 # {{{ documentation
 634
 635 # results structure:
 636
 637 # {results}
 638 #      |
 639 #      |->[0]                                First model
 640 #      |   |
 641 #      |   |->{own}                          The results from this tool on the first model
 642 #      |   |    |
 643 #      |   |    |->[0]
 644 #      |   |    |   |
 645 #      |   |    |   |->{name}                    e.g. 'parameter.estimates'
 646 #      |   |    |   |
 647 #      |   |    |   |->{labels}
 648 #      |   |    |   |     |
 649 #      |   |    |   |     |->[0]...              e.g. ['TH1', 'TH2', 'TH3'] indexed on problem and sub problem
 650 #      |   |    |   |     |->[1]
 651 #      |   |    |   |     |...
 652 #      |   |    |   |     |->[#problems]
 653 #      |   |    |   |
 654 #      |   |    |   |->{values}
 655 #      |   |    |         |
 656 #      |   |    |         |->[0]                 e.g. [0.21, 20.3, 3] indexed as above
 657 #      |   |    |         |->[1]
 658 #      |   |    |         |...
 659 #      |   |    |         |->[#problems]
 660 #      |   |    |
 661 #      |   |    |->[1]
 662 #      |   |    |   |
 663 #      |   |    |   |->{name}                    e.g. 'standard.errors'
 664 #      |   |    |   |->{labels}
 665 #      |   |    |   |->{values}
 666 #      |   |->{subtools}                   The results from the subtools on the first model
 667 #      |           |
 668 #      |           |->[0]                    First sub tool
 669 #      |           |   |
 670 #      |           |   |->[0]                First model of the prepared models sent to the first sub tool
 671 #      |           |   |   |
 672 #      |           |   |   |->{own}          The first sub tools results on the first model
 673 #      |           |   |   |    |
 674 #      |           |   |   |    |->[0]       First result type
 675 #      |           |   |   |    |   |
 676 #      |           |   |   |    |   |->{name}
 677 #      |           |   |   |    |   |->{labels}
 678 #      |           |   |   |    |   |->{values}
 679 #      |           |   |   |    |
 680 #      |           |   |   |    |->[1]       Second result type
 681 #      |           |   |   |    |   |
 682 #      |           |   |   |    |   |->{name}
 683 #      |           |   |   |    |   |->{labels}
 684 #      |           |   |   |    |   |->{values}
 685 #      |           |   |   |->{subtools}   Another tool level
 686 #      |           |   |   |      ...
 687 #      |           |   |->[1]                Second model of the prepared models sent to the first sub tool
 688 #      |           |   |   |
 689 #      |           |   |   |->{own}          The first sub tools results on the second model
 690 #      |           |   |   |    |
 691 #      |           |   |   |    |->[0]       First result type
 692 #      |           |   |   |    |   |
 693 #      |           |   |   |    |   |->{name}
 694 #      |           |   |   |    |   |->{labels}
 695 #      |           |   |   |    |   |->{values}
 696 #      |           |   |   |    |
 697 #      |           |   |   |    |->[1]       Second result type
 698 #      |           |   |   |    |   |
 699 #      |           |   |   |    |   |->{name}
 700 #      |           |   |   |    |   |->{labels}
 701 #      |           |   |   |    |   |->{values}
 702 #      |           |   |   |->{subtools}   Another tool level
 703 #      |           |   |   |      ...
 704 #      |           |   |   |...
 705 #      |           |   |->[#prepared models] Last model of the prepared models sent to the first sub tool
 706 #      |           |   |   |
 707 #      |           |   |   |->{own}          The first sub tools results on the last model
 708 #      |           |   |   |    |
 709 #      |           |   |   |    |->[0]       First result type
 710 #      |           |   |   |    |   |
 711 #      |           |   |   |    |   |->{name}
 712 #      |           |   |   |    |   |->{labels}
 713 #      |           |   |   |    |   |->{values}
 714 #      |           |   |   |    |
 715 #      |           |   |   |    |->[1]       Second result type
 716 #      |           |   |   |    |   |
 717 #      |           |   |   |    |   |->{name}
 718 #      |           |   |   |    |   |->{labels}
 719 #      |           |   |   |    |   |->{values}
 720 #      |           |   |   |->{subtools}   Another tool level
 721 #      |           |   |   |      ...
 722 #      |           |->[1]                    Second sub tool
 723 #      |           |...
 724 #      |           |->[#tools]             Last sub tool
 725 #      |
 726 #      |->[1]                                Second model. All above repeated for this model.
 727 #      |...
 728 #      |->[#models]                          Last model. As above.
 729
 730 # Prepared_models structure:
 731
 732 # {prepared_models}
 733 #      |
 734 #      |->[0]                                First model
 735 #      |   |
 736 #      |   |->{own}                          The prepared models of this tool using the first model as base
 737 #      |   |    |
 738 #      |   |    |->[0]                       First prep model
 739 #      |   |    |->[1]                       Second prep model
 740 #      |   |    |...
 741 #      |   |    |->[#prep_models]            Last prep model
 742 #      |   |
 743 #      |   |->{subtools}                   The prepared models of the subtools on the first model. Only one sub tool per prepared model above.
 744 #      |           |
 745 #      |           |->[0]                    First model of the models (prepared above) sent to the first sub tool
 746 #      |           |   |
 747 #      |           |   |->{own}              The first sub tools prepared models on its first model
 748 #      |           |   |    |
 749 #      |           |   |    |->[0]           First prep model
 750 #      |           |   |    |->[1]           Second prep model
 751 #      |           |   |    |...
 752 #      |           |   |    |->[#prep_models]Last prep model
 753 #      |           |   |
 754 #      |           |   |->{subtools}
 755 #      |           |
 756 #      |           |->[1]                    Second model of the models (prepared above) sent to the first sub tool
 757 #      |           |   |
 758 #      |           |   |->{own}              The first sub tools prepared models on its second model
 759 #      |           |   |    |
 760 #      |           |   |    |->[0]           First prep model
 761 #      |           |   |    |->[1]           Second prep model
 762 #      |           |   |    |...
 763 #      |           |   |    |->[#prep_models]Last prep model
 764 #      |           |   |
 765 #      |           |   |->{subtools}
 766 #      |           |
 767
 768 # }}}
 769
 770 start run
 771     {
 772         my $return_dir = getcwd();
 773         chdir( $self -> {'directory'} );
 774
 775         $self -> pre_fork_setup;
 776
 777         my @models = @{$self -> {'models'}};
 778         # Use the thread number of this tool level:
 779         my $threads = ref( $self -> {'threads'} ) eq 'ARRAY' ?
 780             $self -> {'threads'} -> [0] : $self -> {'threads'};
 781
 782         # No point in using more threads than models
 783         $threads = $#models + 1 if ( $threads > $#models + 1);
 784
 785         # Currently parallel execution is not supported on windows platforms
 786         $threads = 1 if( $Config{osname} eq 'MSWin32' );
 787
 788         # Create new forkmanager
 789         my $pm = ext::Parallel::ForkManager -> new($threads) if ( $threads > 1 );
 790         my $aborting = 0;
 791         $pm -> run_on_finish( sub { my ( $pid, $exit_code, $ident ) = @_;
 792                                     if( $exit_code ){
 793                                       debug -> die( message => "Subtool died, exiting." );
 794                                     }
 795                                   } ) if ( $threads > 1 );
 796
 797         # Store some globals for single-thread mode to make each loop
 798         # over the models see the same (fresh) prepared attributes as
 799         # in the parallel mode.
 800         my @pre_fork_tools;
 801
 802         # THREAD if ( $threads == 1 ) {
 803         # THREAD    if ( defined $self -> {'tools'} ) {
 804         # THREAD        @pre_fork_tools = @{$self -> {'tools'}};
 805         # THREAD    }
 806         # THREAD }
 807
 808         # Loop over the models
 809         for ( my $i = 1; $i <= scalar @models; $i++ ) {
 810             # Spawn new processes
 811             $pm -> start and next if ( $threads > 1 );
 812
 813             # model_number is a member that tells the tool which model
 814             # it is currently working on.
 815             $self -> model_number( $i );
 816
 817             # Reset some globals: (only needed for threads==1)
 818             # THREAD if ( $threads == 1 && defined $self -> {'tools'}) {
 819             # THREAD    @{$self -> {'tools'}} = @pre_fork_tools;
 820             # THREAD }
 821
 822             # Make sure that each process gets a unique random sequence:
 823             random_set_seed_from_phrase(random_uniform_integer(1,0,10000*$i));
 824 #           srand(rand()*10000*$i);
 825
 826             # First, run setup
 827             $self -> setup( model_number => $i );
 828
 829             # Run the subtools
 830             my @tool_results = ();
 831             my @tool_models = ();
 832             if ( defined $self -> {'tools'} ) {
 833                 foreach my $tool (@{$self -> {'tools'}}){
 834                     # There is to date (2004-01-27 no tool that creates more than one internal
 835                     # tool. Hence this is a loop of one cycle. But to be general, again...
 836                     # Run the tool:
 837                     my( $returns, $prep_models ) = $tool -> run;
 838                     # push the sub tool's return values
 839                     push ( @tool_results, $returns );
 840                     if ( defined $prep_models ) {
 841                         push ( @tool_models, $prep_models );
 842                     } else {
 843                       'debug' -> warn(level => 1,
 844                                       message => "inside " . ref($self) . " but no prep_models defined from $tool $i");
 845                     }
 846                     $self -> post_subtool_analyze;
 847                 }
 848
 849             } else {
 850                 debug -> warn( level   => 2,
 851                                message => "No tool object to run from tool object." );
 852             }
 853
 854             $self -> {'results'}[$i-1]{'subtools'}= \@tool_results;
 855             $self -> {'prepared_models'}[$i-1]{'subtools'} = \@tool_models;
 856
 857             # Analyze the results
 858             $self -> analyze( model_number => $i );
 859
 860             Storable::store( $self -> {'prepared_models'},
 861                              $self -> {'directory'}."/m$i/prepared_models.log" );
 862             if ( $threads > 1 ) {
 863                 Storable::store( $self -> {'results'},
 864                                  $self -> {'directory'}."/m$i/results.log" );
 865                   # Maybe redundant to transfer back both prepared_models as well as tools
 866
 867                   # Actually, by principle everything interesting for
 868                   # a parent should be placed in "results" or possibly
 869                   # "prepared_models".
 870
 871                   #Storable::store( $self -> {'tools'},
 872                         #          $self -> {'directory'}."/m$i/tools.log" );
 873                 }
 874             $pm -> finish if ( $threads > 1 );
 875         }
 876         $pm -> wait_all_children if ( $threads > 1 );
 877
 878         for( my $i = 1; $i <= scalar @{$self -> {'models'}}; $i++ ) {
 879           my @prepared_models = @{Storable::retrieve( $self -> {'directory'}.
 880                                                       "/m$i/prepared_models.log" )};
 881           unlink( $self -> {'directory'} . "/m$i/prepared_models.log" );
 882           $self->{'prepared_models'}[$i-1] = $prepared_models[$i-1];
 883         }
 884
 885         if ( $threads > 1 ) {
 886             for( my $i = 1; $i <= scalar @{$self -> {'models'}}; $i++ ) {
 887                 my @model_results = @{Storable::retrieve( $self -> {'directory'}.
 888                                                               "/m$i/results.log" )};
 889 # It is important to keep the number of dimensions: push the first value, not the
 890 # whole array!
 891                 $self->{'results'}[$i-1] = $model_results[$i-1];
 892
 893                 # Read comment aboud tools.log near storable above.
 894
 895                 #push( @{$self -> {'tools'}},
 896                 #      Storable::retrieve( $self -> {'directory'}.
 897                 #                         "/m$i/tools.log" ) );
 898             }
 899           }
 900
 901
 902         # Perform analyses that need to be done after all models have
 903         # been run and processed. Also write a result file if one is
 904         # defined.
 905         $self -> post_fork_analyze;
 906
 907         chdir($return_dir);
 908         if( $self -> {'clean'} >= 3 ){
 909
 910           my $top_dir = $self -> {'directory'};
 911           foreach my $dir ( <$top_dir/m*> ){
 912             if( $dir =~ /m[0123456789]+/ ){
 913               unlink( <$dir/*> );
 914               rmdir( $dir );
 915             }
 916           }
 917
 918           if( not $self -> {'top_tool'} ){
 919             my $dir = $self -> {'directory'};
 920             unlink( <$dir/*> );
 921             rmdir( $dir );
 922           }
 923         }
 924 #       @results     = @{$self -> {'results'}};
 925 #       @prepared_models = @{$self -> {'prepared_models'}};
 926       }
 927 end run
 928
 929 # }}} run
 930
 931 # {{{ _prepare_model
 932
 933 start _prepare_model
 934       {
 935
 936           my ($newdir, $newfile) = OSspecific::absolute_path( $self -> {'directory'} .  '/m'.$model_number, '' );
 937           debug -> warn( level   => 2,
 938                          message => "Making directory\t\t" . $newdir );
 939           mkdir( $newdir );
 940           if ( defined $self -> models() ) {
 941             my @models = @{$self -> models()};
 942             if ( defined $models[$model_number - 1] ) {
 943               my $model = $models[$model_number - 1];
 944               # copy the msfi files
 945               my @new_names;
 946               if( defined $model -> msfi_names() ){
 947                 foreach my $msfi_files( @{$model -> msfi_names()} ){
 948                   foreach my $msfi_file( @{$msfi_files} ){
 949                     if ( defined $msfi_file ) {
 950                       my ( $dir, $filename ) = OSspecific::absolute_path($model -> directory,
 951                                                                          $msfi_file );
 952                       cp( $dir.$filename, $newdir.$filename );
 953                       push( @new_names, $filename );
 954                     } else {
 955                       push( @new_names, undef );
 956                     }
 957                   }
 958                 }
 959                 $model -> msfi_names( new_names => \@new_names );
 960               }
 961             }
 962           }
 963       }
 964 end _prepare_model
 965
 966 # }}} _prepare_model
 967
 968 # {{{ analyze
 969
 970 start analyze
 971       {
 972         $self -> {'raw_results'}[$model_number-1] =
 973           $self -> {'tools'} -> [0] -> raw_results if( defined $self -> {'tools'} -> [0] );
 974         my $sub_analyze = $self -> {'subtools'} -> [0];
 975         if ( defined $sub_analyze ) {
 976           $sub_analyze = $sub_analyze.'_analyze';
 977           if( defined $self -> can( $sub_analyze ) ){
 978             $self -> $sub_analyze( model_number => $model_number );
 979           }
 980         }
 981       }
 982 end analyze
 983
 984 # }}} analyze
 985
 986 # {{{ _modelfit_raw_results_callback
 987
 988 start _modelfit_raw_results_callback
 989       {
 990         my ($dir,$file) =
 991           OSspecific::absolute_path( $self -> {'directory'},
 992                                      $self -> {'raw_results_file'}[$model_number-1] );
 993         my ($dir,$nonp_file) =
 994           OSspecific::absolute_path( $self -> {'directory'},
 995                                      $self -> {'raw_nonp_file'}[$model_number-1] );
 996         $subroutine = sub {
 997           my $modelfit = shift;
 998           $modelfit -> raw_results_file( $dir.$file );
 999           $modelfit -> raw_nonp_file( $dir.$nonp_file );
1000         };
1001         return $subroutine;
1002       }
1003 end _modelfit_raw_results_callback
1004
1005 # }}} _modelfit_raw_results_callback
1006
1007 # {{{ read_raw_results
1008 start read_raw_results
1009       {
1010         undef $self -> {'raw_results_header'};
1011         for ( my $i = 1; $i <= scalar @{$self->{'models'}}; $i++ ) { # All models
1012           if ( -e $self -> {'directory'}.'raw_results'.$i.'.csv' ) {
1013             open( RRES, $self -> {'directory'}.'raw_results'.$i.'.csv' );
1014             my @file = <RRES>;
1015             close( RRES );
1016             map { chomp; my @tmp = split(',',$_); $_ = \@tmp } @file ;
1017             $self -> {'raw_results_header'} -> [$i-1] = shift @file;
1018             $self -> {'raw_results'} -> [$i-1] = \@file;
1019           }
1020           if ( -e $self -> {'directory'}.'raw_nonp_results'.$i.'.csv' ) {
1021             open( RRES, $self -> {'directory'}.'raw_nonp_results'.$i.'.csv' );
1022             my @file = <RRES>;
1023             close( RRES );
1024             map { chomp; my @tmp = split(',',$_); $_ = \@tmp } @file ;
1025             $self -> {'raw_nonp_results'} -> [$i-1] = \@file;
1026           }
1027         }
1028       }
1029 end read_raw_results
1030 # }}} read_raw_results
1031
1032 # {{{ create_raw_results_rows
1033 start create_raw_results_rows
1034   {
1035
1036     unless( $model -> outputs -> [0] -> parsed ){
1037       $model -> outputs -> [0] -> abort_on_fail(0);
1038       $model -> outputs -> [0] -> _read_problems;
1039     }
1040
1041     if( $model -> outputs -> [0] -> parsed_successfully ){
1042       my @probs = @{$model -> outputs -> [0] -> problem_structure};
1043       my $np = scalar @probs; # #probs
1044       my $model_row = 0;
1045       # ------------  Push model, problem and sub-problem numbers  --------------
1046
1047       for( my $j = 0; $j < $np; $j++ ) {
1048         my $ns = $probs[$j]; # #subprobs
1049         for( my $k = 0; $k < $ns; $k++ ) {
1050           my $row = $model_row++;
1051           push( @{$return_rows[$row]}, ($model_number,($j+1),($k+1)) );
1052         }
1053       }
1054
1055       # ---------------------  Loop all result categories  ----------------------
1056
1057       foreach my $category ( @{$self -> {'raw_results_header'}},'npomega' ){
1058         next if( $category eq 'model' or $category eq 'problem' or $category eq 'subproblem' );
1059         my ( $accessor, $res );
1060
1061         # {{{ Get the values for the category
1062
1063         if ( $category eq 'theta' or $category eq 'omega' or $category eq 'sigma' or
1064              $category eq 'setheta' or $category eq 'seomega' or $category eq 'sesigma' or
1065              $category eq 'npomega' or $category eq 'eigen' ) {
1066           $accessor = $category.'s';
1067           $res = $model -> {'outputs'} -> [0] -> $accessor;
1068         } elsif ( $category eq 'shrinkage_etas' ) {
1069           # Shrinkage does not work for subproblems right now.
1070           $res = $model -> eta_shrinkage;
1071         } elsif ( $category eq 'shrinkage_wres' ) {
1072           # Shrinkage does not work for subproblems right now.
1073           # get ofv just to get the prob-subp structure
1074           $res = $model -> wres_shrinkage;
1075         } else {
1076           $accessor = $category;
1077           $res = $model -> {'outputs'} -> [0] -> $accessor;
1078         }
1079
1080         # {{{ Create entry in raw_line_structure
1081         if( defined $res and ref $res eq 'ARRAY' and $category ne 'npomega' ){
1082           my $prob_num = 0;
1083           foreach my $prob ( @{$res} ){
1084             if( defined $prob and ref $prob eq 'ARRAY' ){
1085               if( defined $prob -> [0] and ref $prob -> [0] eq 'ARRAY' and
1086                   defined $return_rows[$prob_num] ){
1087
1088                 # The last check in the IF above could be put there to
1089                 # avoid a bug. If "output::problem_structure" is
1090                 # correct and output::accessor is correct,
1091                 # $return_rows[$prob_num] should allways be
1092                 # defined. TODO
1093
1094                 my $tmp = scalar @{$return_rows[$prob_num]} . ",". scalar @{$prob -> [0]};
1095                 $raw_line_structure -> {$model_number} -> { $category } = $tmp;
1096
1097               } elsif( defined $prob -> [0] and defined $return_rows[$prob_num]) {
1098                 my $tmp = scalar @{$return_rows[$prob_num]} . ",1";
1099                 $raw_line_structure -> {$model_number} -> { $category } = $tmp;
1100               }
1101             }
1102             $prob_num++;
1103           }
1104         }
1105
1106         # }}}
1107
1108         # }}} Get the values for the category
1109         my $return_array_ref;
1110         if( $category eq 'npomega' ){
1111           $return_array_ref = \@nonp_return_rows;
1112           next;
1113         } else {
1114           $return_array_ref = \@return_rows;
1115         }
1116
1117         my $model_row = 0; # Need to mask previous definition of model_row
1118
1119         if( defined $res ) {
1120           for( my $j = 0; $j < $np; $j++ ) {
1121             my $ns = $probs[$j]; # #subprobs
1122             if( defined $res -> [$j] ) {
1123               for( my $k = 0; $k < $ns; $k++ ) {
1124                 my $row = $model_row++;
1125                 if( ref $res -> [$j] eq 'ARRAY' ){
1126                   if( defined $res -> [$j][$k] ) {
1127                     if ( ref $res -> [$j][$k] eq 'ARRAY' ) {
1128                       push( @{$return_array_ref -> [$row]}, @{$res -> [$j][$k]} );
1129                       push( @{$return_array_ref -> [$row]},
1130                             (undef) x ($max_hash -> {$category} - scalar @{$res -> [$j][$k]})  );
1131                     } else {
1132                       push( @{$return_array_ref -> [$row]}, $res -> [$j][$k] );
1133                     }
1134                   } else {
1135                     push( @{$return_array_ref -> [$row]},
1136                           (undef) x $max_hash -> {$category}  );
1137                   }
1138                 } else {
1139                   push( @{$return_array_ref -> [$row]},
1140                         $res -> [$j] );
1141                 }
1142               }
1143             } else {
1144
1145               # {{{ Push undefs for missing subprobs
1146
1147               for( my $k = 0; $k < $ns; $k++ ) {
1148                 my $row = $model_row++;
1149                 push( @{$return_array_ref -> [$row]},
1150                       (undef) x $max_hash -> {$category}  );
1151               }
1152
1153               # }}} Push undefs for missing subprobs
1154
1155             }
1156
1157           }
1158         } else {
1159
1160           # {{{ Push undefs for missing probs/subprobs
1161
1162           for( my $j = 0; $j < $np; $j++ ) {
1163             my $ns = $probs[$j]; # #subprobs
1164             for( my $k = 0; $k < $ns; $k++ ) {
1165               my $row = $model_row++;
1166               push( @{$return_array_ref -> [$row]},
1167                     (undef) x $max_hash -> {$category}  );
1168             }
1169           }
1170
1171           # }}} Push undefs for missing probs/subprobs
1172
1173         }
1174
1175       }
1176
1177       $raw_line_structure -> {$model_number} -> {'line_numbers'} = scalar @return_rows;
1178
1179     } else {
1180       # Output not parsed successfully.
1181       $return_rows[0] = [ $model_number.
1182                           ",run failed - Could not parse the output file: ".
1183                           $model -> {'outputs'} -> [0] -> filename ];
1184     }
1185   }
1186 end create_raw_results_rows
1187 # }}}
1188
1189 # {{{ post_subtool_analyze
1190
1191 start post_subtool_analyze
1192     {
1193         my $sub_analyze = $self -> {'subtools'} -> [0];
1194         if ( defined $sub_analyze ) {
1195             $sub_analyze = $sub_analyze.'_post_subtool_analyze';
1196             if( defined $self -> can( $sub_analyze ) ){
1197                 $self -> $sub_analyze( model_number => $model_number );
1198             }
1199         }
1200     }
1201 end post_subtool_analyze
1202
1203 # }}} analyze
1204
1205 # {{{ harvest_output
1206
1207 start harvest_output
1208     {
1209
1210       # harvest_output is a complement to AUTOLOAD below. AUTOLOAD is
1211       # currently used to find the AUTOLOAD:ed accessor in any
1212       # existing subtool, model, data or outputobject. It is
1213       # inefficient in that it will have to be called for once for
1214       # each accessor. harvest_output will take a list of accessors
1215       # that it will search for in each object, saving time and
1216       # foremost; memory. Also it will take arguments such as
1217       # "search_models", "search_subtools" that will make things more
1218       # efficient if you know where to search.
1219
1220       unless( $search_models + $search_output + $search_data <= 1 ){
1221         'debug' -> die( message => "This is a PsN bug: Only one of the 'search_' options can and must be specified.".
1222                         "\t search_models: $search_models\n".
1223                         "\t search_data: $search_data\n".
1224                         "\t search_output: $search_output");
1225       }
1226
1227       if ( $search_subtools ) {
1228         'debug' -> warn( level => 1,
1229                          message => "\n\nSearching subtools, which is a very untested functionality!!\n\n" );
1230
1231 #       if ( defined $self -> {'tools'} ) {
1232 #         my @tools = @{$self -> {'tools'}};
1233 #         foreach my $tool_ref ( @tools ) {
1234 #           foreach my $tool ( @{$tool_ref} ) {
1235 #             if ( $tool -> can( $accessor ) ) {
1236 #               push( @result, $tool -> $accessor( %accessor_parameters ) );
1237 #             } else {
1238 #               'debug' -> die(message => "Accessor $accessor is not available in the tool " . ref($tool) );
1239 #             }
1240 #           }
1241 #         }
1242 #       } else {
1243 #         'debug' -> warn( level => 1,
1244 #                          message => "Supposed to be run by the sub tools but no sub tools were defined" );
1245 #       }
1246
1247       } else {
1248
1249         sub models_traverse2 {
1250           my %parameters = @_;
1251           my @models = $parameters{'models'} ? @{$parameters{'models'}} : ();
1252           my $search_models = $parameters{'search_models'};
1253           my $search_output = $parameters{'search_output'};
1254           my $search_data   = $parameters{'search_data'};
1255           my $accessor_parameters = $parameters{'accessor_parameters'};
1256           my $accessors = $parameters{'accessors'};
1257           my %results;
1258
1259           for( my $i = 0; $i < scalar (@models); $i++ ){
1260
1261             foreach my $model ( @{$models[$i]{'own'}} ) {
1262
1263               foreach my $accessor( @{$accessors} ) {
1264
1265                 if( $search_models and $model -> can( $accessor ) ) {
1266                   push( @{$results{$accessor}[$i]{'own'}}, $model -> $accessor( %{$accessor_parameters} ) );
1267
1268                 } elsif( $search_data and $model -> datas -> [0] -> can( $accessor ) ) {
1269                   push( @{$results{$accessor}[$i]{'own'}}, $model -> datas -> [0] -> $accessor( %{$accessor_parameters} ) );
1270
1271                 } elsif( $search_output and $model -> outputs -> [0] -> can( $accessor ) ) {
1272                   push( @{$results{$accessor}[$i]{'own'}}, $model -> outputs -> [0] -> $accessor( %{$accessor_parameters} ) );
1273
1274                 } else {
1275                   'debug' -> die( message => "Neither model, data, output have a method for $accessor" );
1276                 }
1277
1278                 if ( defined $models[$i]{'subtools'} ) {
1279                   push( @{$results{$accessor}[$i]{'subtools'}}, models_traverse2( models => $models[$i]{'subtools'} ) );
1280                 }
1281               }
1282
1283               if( $search_data ){
1284                 $model -> datas -> [0] -> flush();
1285               }
1286               if( $search_output ){
1287                 $model -> outputs -> [0] -> flush();
1288               }
1289             }
1290
1291           }
1292           return \%results;
1293         }
1294       }
1295
1296       my @models;
1297
1298       if ( $search_original_models ) {
1299         @models = @{$self -> {'models'}};
1300       } elsif ( defined $self -> {'prepared_models'} ) {
1301         @models = @{$self -> {'prepared_models'}};
1302       } else {
1303         'debug' -> warn( level => 2,
1304                          message => "Trying @accessors, but no prepared models available" );
1305         return {};
1306       }
1307
1308       %result = %{models_traverse2( models => \@models,
1309                                    search_models => $search_models,
1310                                    search_output => $search_output,
1311                                    search_data => $search_data,
1312                                    accessor_parameters => \%accessor_parameters,
1313                                    accessors => \@accessors )};
1314
1315     }
1316 end harvest_output
1317
1318 # }}}
1319
1320 # {{{ AUTOLOAD
1321
1322 start AUTOLOAD
1323       {
1324         debug -> warn( level => 2,
1325                        message => "Caught method $AUTOLOAD" );
1326         debug -> warn( level => 2,
1327                        message => "arguments: @_" );;
1328         my %parm = @_;
1329         my $original_models = $parm{'original_models'};
1330         delete( $parm{'original_models'} );
1331         my $class = $parm{'class'};
1332         $AUTOLOAD =~ s/.*://;
1333         return if $AUTOLOAD eq 'DESTROY';
1334
1335 # TODO: Kolla att orginalmodellen körs med submetod i run!!!!! kolla också var resultaten
1336 # läggs!!!
1337
1338         if ( $class =~ /tool::/ ) {
1339           delete( $parm{'mod_array'} );
1340           delete( $parm{'original_models'} );
1341           delete( $parm{'class'} );
1342           @_ = %parm;
1343           if ( defined $self -> {'tools'} ) {
1344             my @tools = @{$self -> {'tools'}};
1345             my $accessor = $AUTOLOAD;
1346             foreach my $tool_ref ( @tools ) {
1347               foreach my $tool ( @{$tool_ref} ) {
1348                 if ( $tool -> can( $accessor ) ) {
1349                   push( @result, $tool -> $accessor( @_ ) );
1350                 } else {
1351                   'debug' -> die(message => "Accessor $accessor is not available in the tool " . ref($tool) );
1352                 }
1353               }
1354             }
1355           } else {
1356             print "AUTOLOAD in ",ref($self)," caught tool $AUTOLOAD. It was ",
1357               "supposed to be run by the sub tools but no sub tools were defined\n";
1358           }
1359         } else {
1360           my @models;
1361           my @prep_models;
1362           if ( $original_models ) {
1363             @models = @{$self -> {'models'}};
1364           } elsif ( defined $self -> {'prepared_models'} ) {
1365             'debug' -> warn(level => 1,
1366                             message => "Using prepared models" );
1367             @prep_models = @{$self -> {'prepared_models'}};
1368           } else {
1369             print "WARNING: tool -> AUTOLOAD: Trying $AUTOLOAD, but no prepared models available\n";
1370           }
1371
1372           sub models_traverse {
1373             my %parm  = @_;
1374             my $mod_array_ref = $parm{'mod_array'};
1375             my $class     = $parm{'class'};
1376             delete( $parm{'mod_array'} );
1377             delete( $parm{'class'} );
1378             @_ = %parm;
1379             my @mod_array;
1380             @mod_array = defined $mod_array_ref ? @{$mod_array_ref} : ();
1381             my @inner_result = ();
1382             #             my $i = 0;
1383             for ( my $i = 0; $i <= $#mod_array; $i++ ) {
1384               foreach my $model ( @{$mod_array[$i]{'own'}} ) {
1385                 unless ( defined $class ) {
1386                   my $mod_can = defined $model -> can( $AUTOLOAD ) ? 1 : 0;
1387                   my $out_can = (defined $model -> outputs and
1388                                  defined $model -> outputs -> [0] and
1389                                  defined $model -> outputs -> [0] -> can($AUTOLOAD))
1390                     ? 1 : 0;
1391                   my $dat_can = (defined $model -> datas and
1392                                  defined $model -> datas -> [0] and
1393                                  defined $model -> datas -> [0] -> can($AUTOLOAD))
1394                     ? 1 : 0;
1395                   if ( ($mod_can + $out_can + $dat_can) > 1 ) {
1396                     my $classes;
1397                     $classes = 'model ' if $mod_can;
1398                     $classes = $classes.'output ' if $out_can;
1399                     $classes = $classes.'data ' if $dat_can;
1400                     'debug' -> die( message => "Accessor $AUTOLOAD available in multiple classes: $classes" );
1401                   }
1402                   if ( $mod_can + $out_can + $dat_can == 0 ) {
1403                     'debug' -> die( message => "Accessor $AUTOLOAD is not available in any of the model, ".
1404                                     "output or data classes OR no output or data object available".
1405                                     " through this model" );
1406                   }
1407                   if ( $mod_can ) {
1408                     push( @{$inner_result[$i]{'own'}}, $model -> $AUTOLOAD( @_ ) );
1409                   } elsif ( $out_can ) {
1410                     push( @{$inner_result[$i]{'own'}}, $model -> outputs -> [0] -> $AUTOLOAD( @_ ) );
1411                   } elsif ( $dat_can ) {
1412                     push( @{$inner_result[$i]{'own'}}, $model -> datas -> [0] -> $AUTOLOAD( @_ ) );
1413                   }
1414                 } else {
1415                   if ( $class eq 'model' ) {
1416                     push( @{$inner_result[$i]{'own'}}, $model -> $AUTOLOAD( @_ ) );
1417                   } else {
1418                     my $class_accessor = $class.'s';
1419                     push( @{$inner_result[$i]{'own'}}, $model -> $class_accessor -> [0] -> $AUTOLOAD( @_ ) );
1420                   }
1421                 }
1422               }
1423               #               $i++;
1424               if ( defined $mod_array[$i]{'subtools'} ) {
1425                 push( @{$inner_result[$i]{'subtools'}},
1426                       models_traverse( mod_array => $mod_array[$i]{'subtools'},
1427                                        class     => $class,
1428                                        %parm ) );
1429               }
1430             }
1431             return \@inner_result;
1432           }
1433           if ( $original_models ) {
1434             debug -> warn( level => 2,
1435                            message => "Traversing ".scalar $models[0]{'own'}." model(s)" );
1436             @result = @{models_traverse( mod_array => \@models,
1437                                          %parm )};
1438           } else {
1439             @result = @{models_traverse( mod_array => \@prep_models,
1440                                          %parm )};
1441           }
1442         }
1443       }
1444 end AUTOLOAD
1445
1446 # }}} AUTOLOAD