\n" unless scalar(@ARGV)==2; main(@ARGV); sub main { my ($base_filename, $title) = @_; my $diagrams = generate_diagrams($base_filename); my $data = {'title' => $title, 'diagrams' => $diagrams}; # The HTML file open(my $fh, '>', $base_filename.'.html') or die "Couldn't open the output file"; generate_html($fh, $data); close($fh); # The Markdown file open($fh, '>', $base_filename.'.md') or die "Couldn't open the output file"; generate_markdown($fh, $data); close($fh); # The RST file open($fh, '>', $base_filename.'.rst') or die "Couldn't open the output file"; generate_rst($fh, $data); close($fh); } sub generate_diagrams { my $base_filename = shift; # Creates a temporary JSON config file my ($fh, $json_filename) = tempfile(UNLINK => 1); print STDERR "json: $json_filename\n"; print $fh $display_config_json; close($fh); my @confs = Bio::EnsEMBL::Hive::Utils::Config->default_config_files(); push @confs, $json_filename; # Creates a temporary pipe-config file my ($pipe_fh, $pipe_filename) = tempfile('tXXXXXXX', UNLINK => 1, DIR => '.', SUFFIX => '.pm'); my $package_name = File::Basename::basename($pipe_filename); $package_name =~ s/\.pm//; print STDERR "pipeconfig: $pipe_filename\n"; close($pipe_fh); # The example files my @example_files = glob($base_filename.'/*.txt'); my @data = sort {$a->[0] <=> $b->[0]} map {[parse_one_file($_)]} @example_files; my @diagrams; foreach my $record (@data) { unless ($record->[3]) { push @diagrams, [@$record]; next; } # Write the pipeconfig file open(my $pipe_fh, '>', $pipe_filename); print $pipe_fh sprintf($pipeconfig_template, $package_name, $record->[3]); close($pipe_fh); # The diagram warn $record->[0]; my $img = sprintf('%s/%d.png', $base_filename, $record->[0]); system($ehrd.'/scripts/generate_graph.pl', -pipeconfig => $pipe_filename, -output => $img, map {-config_file => $_} @confs); push @diagrams, [@$record, $img]; } return \@diagrams; } sub parse_one_file { my $file_name = shift; open(my $fh, '<', $file_name) or die "Couldnt open file [$file_name]"; my $data; { local $/ = undef; $data = <$fh>; } close($fh); my ($title, $description, $code) = split( /^--*-$/m, $data); chomp $title; $title =~ s/^\R*//; chomp $description; $description =~ s/^\R*//; die "Wrong format in '$data'" unless $title and $description; if ($code) { chomp $code; $code =~ s/^\R*//; } my $id = $file_name; $id =~ s/[^0-9]//g; return ($id, $title, $description, $code); } sub generate_html { my ($output_fh, $data) = @_; print $output_fh "<html><body><h1>".$data->{'title'}."</h1>\n"; print $output_fh "<ol>\n"; my $in_group = 0; foreach my $record (@{$data->{'diagrams'}}) { if ($record->[3]) { print $output_fh sprintf(q{<li><a href="#%d">%s</a></li>}, $record->[0], $record->[1]), "\n"; } else { if ($in_group) { print $output_fh q{</ol></li>}, "\n"; } print $output_fh sprintf(q{<li><a href="#%d">%s</a><ol>}, $record->[0], $record->[1]), "\n"; $in_group = 1; } } if ($in_group) { print $output_fh q{</ol></li>}, "\n"; } print $output_fh "</ol><table>\n"; foreach my $record (@{$data->{'diagrams'}}) { if ($record->[3]) { print $output_fh sprintf(q{<tr id="%d"><td><h3>%s</h3><p>%s</p><pre>%s</pre></td><td><img src='%s'></td></tr>}, $record->[0], $record->[1], $record->[2], encode_entities($record->[3]), $record->[4], ), "\n"; } else { print $output_fh sprintf(q{<tr id="%d"><td><h2>%s</h2><p>%s</p></td><td></td></tr>}, $record->[0], $record->[1], $record->[2], ), "\n"; } } print $output_fh "</table></body></html>\n"; } sub generate_markdown { my ($output_fh, $data) = @_; print $output_fh "# ".$data->{'title'}."\n\n"; print $output_fh "## Index\n\n"; my $i = 1; my $j = 1; foreach my $record (@{$data->{'diagrams'}}) { if ($record->[3]) { print $output_fh sprintf(" %s. [%s](#%s) \n", chr(96+$j), $record->[1], $record->[0]); $j++; } else { print $output_fh sprintf("%d. [%s](#%s) \n", $i, $record->[1], $record->[0]); $j = 1; $i++; } } print $output_fh "\n"; foreach my $record (@{$data->{'diagrams'}}) { if ($record->[3]) { print $output_fh sprintf("### <a name='%s'></a>%s\n\n%s\n\n```\n%s\n```\n![diagram](%s)\n", $record->[0], $record->[1], $record->[2], $record->[3], $record->[4], ), "\n"; } else { print $output_fh sprintf("## <a name='%s'></a>%s\n\n%s\n\n", $record->[0], $record->[1], $record->[2], ), "\n"; } } } sub _rst_underline { my ($str, $char) = @_; return $str . "\n" . ($char x length($str)) . "\n\n"; } sub generate_rst { my ($output_fh, $data) = @_; print $output_fh _rst_underline($data->{'title'}, '='); print $output_fh ".. contents::\n\n"; foreach my $record (@{$data->{'diagrams'}}) { if ($record->[3]) { print $output_fh _rst_underline($record->[1], '~'); print $output_fh $record->[2], "\n\n"; my $s = $record->[3]; $s =~ s/^/ /gms; print $output_fh "::\n\n", $s, "\n\n"; print $output_fh ".. figure:: ", $record->[4], "\n\n"; } else { print $output_fh _rst_underline($record->[1], '-'); print $output_fh $record->[2], "\n\n"; } } } __DATA__ =pod =head1 NAME scripts/make_branch_glossary.pl =head1 DESCRIPTION An internal eHive script for regenerating the document that lists all (most ?) of the dataflow patterns. =head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2017] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =head1 CONTACT Please subscribe to the Hive mailing list: http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users to discuss Hive-related questions or to be notified of our updates =cut

#!/usr/bin/env perl use strict; use warnings; use File::Temp qw/tempfile/; use Getopt::Long; use HTML::Entities; use List::Util qw(min); #use Bio::EnsEMBL::Hive::Version; use Bio::EnsEMBL::Hive::Utils::Config; # Finding out own path in order to reference own components (including own modules): use Cwd (); use File::Basename (); BEGIN { $ENV{'EHIVE_ROOT_DIR'} ||= File::Basename::dirname( File::Basename::dirname( Cwd::realpath($0) ) ); unshift @INC, $ENV{'EHIVE_ROOT_DIR'}.'/modules'; } my $ehrd = $ENV{'EHIVE_ROOT_DIR'} or die "Environment variable 'EHIVE_ROOT_DIR' not defined, please check your setup"; chdir $ehrd.'/docs'; my $pipeconfig_template = q{ package %s; use strict; use warnings; use base ('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf'); sub pipeline_analyses { my ($self) = @_; my $all_analyses = [%s]; map {$_->{-module} = 'Bio::EnsEMBL::Hive::RunnableDB::Dummy'} @$all_analyses; return $all_analyses; } 1; }; my $display_config_json = q{ { "Graph": {"Pad": 0, "DisplayStats": 0, "DisplayDBIDs": 0, "DisplayDetails": 0 } } }; die "Usage: $0 \n" unless scalar(@ARGV)==2; main(@ARGV); sub main { my ($base_filename, $title) = @_; my $diagrams = generate_diagrams($base_filename); my $data = {'title' => $title, 'diagrams' => $diagrams}; # The HTML file open(my $fh, '>', $base_filename.'.html') or die "Couldn't open the output file"; generate_html($fh, $data); close($fh); # The Markdown file open($fh, '>', $base_filename.'.md') or die "Couldn't open the output file"; generate_markdown($fh, $data); close($fh); # The RST file open($fh, '>', $base_filename.'.rst') or die "Couldn't open the output file"; generate_rst($fh, $data); close($fh); } sub generate_diagrams { my $base_filename = shift; # Creates a temporary JSON config file my ($fh, $json_filename) = tempfile(UNLINK => 1); print STDERR "json: $json_filename\n"; print $fh $display_config_json; close($fh); my @confs = Bio::EnsEMBL::Hive::Utils::Config->default_config_files(); push @confs, $json_filename; # Creates a temporary pipe-config file my ($pipe_fh, $pipe_filename) = tempfile('tXXXXXXX', UNLINK => 1, DIR => '.', SUFFIX => '.pm'); my $package_name = File::Basename::basename($pipe_filename); $package_name =~ s/\.pm//; print STDERR "pipeconfig: $pipe_filename\n"; close($pipe_fh); # The example files my @example_files = glob($base_filename.'/*.txt'); my @data = sort {$a->[0] <=> $b->[0]} map {[parse_one_file($_)]} @example_files; my @diagrams; foreach my $record (@data) { unless ($record->[3]) { push @diagrams, [@$record]; next; } # Write the pipeconfig file open(my $pipe_fh, '>', $pipe_filename); print $pipe_fh sprintf($pipeconfig_template, $package_name, $record->[3]); close($pipe_fh); # The diagram warn $record->[0]; my $img = sprintf('%s/%d.png', $base_filename, $record->[0]); system($ehrd.'/scripts/generate_graph.pl', -pipeconfig => $pipe_filename, -output => $img, map {-config_file => $_} @confs); push @diagrams, [@$record, $img]; } return \@diagrams; } sub parse_one_file { my $file_name = shift; open(my $fh, '<', $file_name) or die "Couldnt open file [$file_name]"; my $data; { local $/ = undef; $data = <$fh>; } close($fh); my ($title, $description, $code) = split( /^--*-$/m, $data); chomp $title; $title =~ s/^\R*//; chomp $description; $description =~ s/^\R*//; die "Wrong format in '$data'" unless $title and $description; if ($code) { chomp $code; $code =~ s/^\R*//; } my $id = $file_name; $id =~ s/[^0-9]//g; return ($id, $title, $description, $code); } sub generate_html { my ($output_fh, $data) = @_; print $output_fh "<html><body><h1>".$data->{'title'}."</h1>\n"; print $output_fh "<ol>\n"; my $in_group = 0; foreach my $record (@{$data->{'diagrams'}}) { if ($record->[3]) { print $output_fh sprintf(q{<li><a href="#%d">%s</a></li>}, $record->[0], $record->[1]), "\n"; } else { if ($in_group) { print $output_fh q{</ol></li>}, "\n"; } print $output_fh sprintf(q{<li><a href="#%d">%s</a><ol>}, $record->[0], $record->[1]), "\n"; $in_group = 1; } } if ($in_group) { print $output_fh q{</ol></li>}, "\n"; } print $output_fh "</ol><table>\n"; foreach my $record (@{$data->{'diagrams'}}) { if ($record->[3]) { print $output_fh sprintf(q{<tr id="%d"><td><h3>%s</h3><p>%s</p><pre>%s</pre></td><td><img src='%s'></td></tr>}, $record->[0], $record->[1], $record->[2], encode_entities($record->[3]), $record->[4], ), "\n"; } else { print $output_fh sprintf(q{<tr id="%d"><td><h2>%s</h2><p>%s</p></td><td></td></tr>}, $record->[0], $record->[1], $record->[2], ), "\n"; } } print $output_fh "</table></body></html>\n"; } sub generate_markdown { my ($output_fh, $data) = @_; print $output_fh "# ".$data->{'title'}."\n\n"; print $output_fh "## Index\n\n"; my $i = 1; my $j = 1; foreach my $record (@{$data->{'diagrams'}}) { if ($record->[3]) { print $output_fh sprintf(" %s. [%s](#%s) \n", chr(96+$j), $record->[1], $record->[0]); $j++; } else { print $output_fh sprintf("%d. [%s](#%s) \n", $i, $record->[1], $record->[0]); $j = 1; $i++; } } print $output_fh "\n"; foreach my $record (@{$data->{'diagrams'}}) { if ($record->[3]) { print $output_fh sprintf("### <a name='%s'></a>%s\n\n%s\n\n```\n%s\n```\n![diagram](%s)\n", $record->[0], $record->[1], $record->[2], $record->[3], $record->[4], ), "\n"; } else { print $output_fh sprintf("## <a name='%s'></a>%s\n\n%s\n\n", $record->[0], $record->[1], $record->[2], ), "\n"; } } } sub _rst_underline { my ($str, $char) = @_; return $str . "\n" . ($char x length($str)) . "\n\n"; } sub generate_rst { my ($output_fh, $data) = @_; print $output_fh _rst_underline($data->{'title'}, '='); print $output_fh ".. contents::\n\n"; foreach my $record (@{$data->{'diagrams'}}) { if ($record->[3]) { print $output_fh _rst_underline($record->[1], '~'); print $output_fh $record->[2], "\n\n"; my $s = $record->[3]; $s =~ s/^/ /gms; print $output_fh "::\n\n", $s, "\n\n"; print $output_fh ".. figure:: ", $record->[4], "\n\n"; } else { print $output_fh _rst_underline($record->[1], '-'); print $output_fh $record->[2], "\n\n"; } } } __DATA__ =pod =head1 NAME scripts/make_branch_glossary.pl =head1 DESCRIPTION An internal eHive script for regenerating the document that lists all (most ?) of the dataflow patterns. =head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2017] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =head1 CONTACT Please subscribe to the Hive mailing list: http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users to discuss Hive-related questions or to be notified of our updates =cut