Item10044: Initial checkin

git-svn-id: http://svn.foswiki.org/trunk/PhyloWidgetPlugin@10115 0b4bb1d4-4e5a-0410-9cc4-b2b747904278
foswiki · Nov 30, 2010 · 9c62cc7 · 9c62cc7
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diff --git a/PhyloWidgetPlugin.md5 b/PhyloWidgetPlugin.md5
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+501bff97174e9db20a19d4ae3b919841  PhyloWidgetPlugin.tgz
+6a09002f3c29704cfb4cc4968231cf94  PhyloWidgetPlugin_installer
+4aa2f50049e7c574026c035f7136be5f  PhyloWidgetPlugin.zip
diff --git a/PhyloWidgetPlugin.sha1 b/PhyloWidgetPlugin.sha1
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+d32b1587c3b51e2ca330e4012b7f275fb4983e6a  PhyloWidgetPlugin.tgz
+c2b6af7c241b0bcf696c405832759fe15cca6073  PhyloWidgetPlugin_installer
+d6f901c57e74e5766d3d1f9fed64f9ad5f942026  PhyloWidgetPlugin.zip
diff --git a/PhyloWidgetPlugin.tgz b/PhyloWidgetPlugin.tgz
diff --git a/PhyloWidgetPlugin.txt b/PhyloWidgetPlugin.txt
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+%META:TOPICPARENT{name="Plugins"}%
+---+ PhyloWidget Plugin
+
+%SHORTDESCRIPTION%
+
+%INCLUDE{"VarPHYLOWIDGET"}%
+
+%INCLUDE{"VarNEXUSTREES"}%
+
+---++ Installation
+You do not need to install anything in the browser to use this extension. The following instructions are for the administrator who installs the extension on the server.
+
+Open configure, and open the "Extensions" section. Use "Find More Extensions" to get a list of available extensions. Select "Install".
+
+If you have any problems, or if the extension isn't available in =configure=, then you can still install manually from the command-line. See http://foswiki.org/Support/ManuallyInstallingExtensions for more help.
+
+
+---++ Plugin Info
+
+|  Author: | Foswiki:Main.TemiVarghese |
+|  Copyright: | &copy; 2010, Taxonomy Research & Information Network [[http://trin.org.au]] |
+|  License: | GPL ([[http://www.gnu.org/copyleft/gpl.html][GNU General Public License]]) |
+|  Release: | 0.1.1 |
+|  Version: | 20101130 (2010-11-30) |
+|  Change&nbsp;History: | <!-- versions below in reverse order -->&nbsp; |
+|  XX Mmm 20XX (1.0) | Description of change |
+|  Home: | http://foswiki.org/Extensions/%TOPIC% |
+|  Support: | http://foswiki.org/Support/%TOPIC% |
+|  Dependencies: | <table class="foswikiTable" border="1"><tr><th>Name</th><th>Version</th><th>Description</th></tr><tr><td align="left">Bio::NEXUS</td><td align="left">&gt;=0</td><td align="left">Required</td></tr><tr><td align="left">Foswiki::Plugins::DBCachePlugin</td><td align="left">&gt;=0</td><td align="left">Optional, For examples</td></tr></table> |
diff --git a/PhyloWidgetPlugin.zip b/PhyloWidgetPlugin.zip
diff --git a/PhyloWidgetPlugin_installer b/PhyloWidgetPlugin_installer
@@ -0,0 +1,174 @@
+#!perl
+#
+# Install script for PhyloWidgetPlugin
+#
+# Copyright (C) 2004-2007 Foswiki Contributors. All Rights Reserved.
+# Foswiki Contributors are listed in the AUTHORS file in the root of
+# this distribution. NOTE: Please extend that file, not this notice.
+#
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version. For
+# more details read LICENSE in the root of this distribution.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+#
+# As per the GPL, removal of this notice is prohibited.
+#
+# Author: Crawford Currie http://c-dot.co.uk
+#
+# NOTE TO THE DEVELOPER: THIS FILE IS GENERATED AUTOMATICALLY
+# BY THE BUILD PROCESS DO NOT EDIT IT - IT WILL BE OVERWRITTEN
+#
+use strict;
+use warnings;
+require 5.008;
+
+use File::Spec;
+use Cwd;
+
+=pod
+
+---+ PhyloWidgetPlugin_installer
+This is the installer script. The basic function of this script is to
+locate an archive and unpack it.
+
+It will also check the dependencies listed in DEPENDENCIES and assist
+the user in installing any that are missing. The script also automatically
+maintains the revision histories of any files that are being installed by the
+package but already have ,v files on disc (indicating that they are
+revision controlled).
+
+The script also functions as an *uninstaller* by passing the parameter
+=uninstall= on the command-line. Note that uninstallation does *not* revert
+the history of any topic changed during the installation.
+
+The script allows the definition of PREINSTALL and POSTINSTALL scripts.
+These scripts can be used for example to modify the configuration during
+installation, using the functions described below.
+
+Refer to the documentation of =configure=
+
+=cut
+
+# This is all done in package Foswiki so that reading LocalSite.cfg and Foswiki.cfg
+# will put the config vars into the right namespace.
+package Foswiki;
+
+# The root of package URLs
+my $PACKAGES_URL = 'http://foswiki.org/pub/Extensions';
+
+# Extract MANIFEST and DEPENDENCIES from the __DATA__
+undef $/;
+my @DATA = split( /<<<< (.*?) >>>>\s*\n/, <DATA> );
+shift @DATA;    # remove empty first element
+
+# Establish where we are
+my @path = ( 'tools', 'extender.pl' );
+my $wd = Cwd::cwd();
+$wd =~ /^(.*)$/;    # untaint
+unshift( @path, $1 ) if $1;
+my $script = File::Spec->catfile(@path);
+
+unless ( my $return = do $script ) {
+    my $message = <<MESSAGE;
+************************************************************
+Could not load $script
+MESSAGE
+    if ($@) {
+        $message .= "There was a compile error: $@\n";
+    }
+    elsif (defined $return) {
+        $message .= "There was a file error: $!\n";
+    }
+    else {
+        $message .= "An unspecified error occurred\n";
+    }
+
+    # Try again, using open. This cures some uncooperative platforms.
+    if ( open( F, '<', $script ) ) {
+        local $/;
+        my $data = <F>;
+        close(F);
+        $data =~ /^(.*)$/s;    # untaint
+        eval $1;
+        if ($@) {
+            $message .= "Error when trying to eval the file content: $@\n";
+        }
+        else {
+            print STDERR
+              "'do $script failed, but install was able to proceed: $message";
+            undef $message;
+        }
+    }
+    else {
+        $message .= "Could not open file using open() either: $!\n";
+    }
+    die $message if $message;
+}
+
+sub preuninstall {
+
+    # # No PREUNINSTALL script;
+}
+
+sub postuninstall {
+
+    # # No POSTUNINSTALL script;
+}
+
+sub preinstall {
+
+    # # No PREINSTALL script;
+}
+
+sub postinstall {
+
+    # # No POSTINSTALL script;
+}
+
+Foswiki::Extender::install( $PACKAGES_URL, 'PhyloWidgetPlugin', 'PhyloWidgetPlugin', @DATA );
+
+1;
+
+# MANIFEST and DEPENDENCIES are done this way
+# to make it easy to extract them from this script.
+
+__DATA__
+<<<< MANIFEST >>>>
+data/System/PhyloWidgetPlugin.txt,0644,
+data/System/PhyloNexusViewer.txt,0644,
+data/System/PhyloWidgetExample.txt,0644,
+data/System/PhyloWidgetViewHelper.txt,0644,
+data/System/VarNEXUSTREES.txt,0644,
+data/System/VarPHYLOWIDGET.txt,0644,
+data/System/ViewTrees.txt,0644,
+lib/Foswiki/Plugins/PhyloWidgetPlugin.pm,0644,
+pub/System/PhyloWidgetExample/Tree.nex,0644,
+pub/System/PhyloWidgetPlugin/bare.html,0644,
+pub/System/PhyloWidgetPlugin/img/pw.ico,0644,
+pub/System/PhyloWidgetPlugin/index.html,0644,
+pub/System/PhyloWidgetPlugin/jquery.phylowidget.uncompressed.js,0644,
+pub/System/PhyloWidgetPlugin/lib/core.jar,0644,
+pub/System/PhyloWidgetPlugin/lib/freeloader.jar,0644,
+pub/System/PhyloWidgetPlugin/lib/itext.jar,0644,
+pub/System/PhyloWidgetPlugin/lib/loading.gif,0644,
+pub/System/PhyloWidgetPlugin/lib/pdf.jar,0644,
+pub/System/PhyloWidgetPlugin/lib/phylowidget.jar,0644,
+pub/System/PhyloWidgetPlugin/minimal.txt,0644,
+pub/System/PhyloWidgetPlugin/phylotest.html,0644,
+pub/System/PhyloWidgetPlugin/scripts/phylopopup.js,0644,
+pub/System/PhyloWidgetPlugin/scripts/phylowidget.js,0644,
+pub/System/PhyloWidgetPlugin/style.css,0644,
+pub/System/PhyloWidgetPlugin/test.html,0644,
+pub/System/PhyloWidgetPlugin/zip/phylowidget_src.zip,0644,
+pub/System/PhyloWidgetPlugin/zip/phylowidget_standalone.zip,0644,
+templates/phylonhx.tmpl,0644,
+
+<<<< DEPENDENCIES >>>>
+Bio::NEXUS,>=0,1,cpan,Required
+Foswiki::Plugins::DBCachePlugin,>=0,1,plugin,Optional, For examples
+
diff --git a/PhyloWidgetPlugin_installer.pl b/PhyloWidgetPlugin_installer.pl
@@ -0,0 +1,174 @@
+#!perl
+#
+# Install script for PhyloWidgetPlugin
+#
+# Copyright (C) 2004-2007 Foswiki Contributors. All Rights Reserved.
+# Foswiki Contributors are listed in the AUTHORS file in the root of
+# this distribution. NOTE: Please extend that file, not this notice.
+#
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version. For
+# more details read LICENSE in the root of this distribution.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+#
+# As per the GPL, removal of this notice is prohibited.
+#
+# Author: Crawford Currie http://c-dot.co.uk
+#
+# NOTE TO THE DEVELOPER: THIS FILE IS GENERATED AUTOMATICALLY
+# BY THE BUILD PROCESS DO NOT EDIT IT - IT WILL BE OVERWRITTEN
+#
+use strict;
+use warnings;
+require 5.008;
+
+use File::Spec;
+use Cwd;
+
+=pod
+
+---+ PhyloWidgetPlugin_installer
+This is the installer script. The basic function of this script is to
+locate an archive and unpack it.
+
+It will also check the dependencies listed in DEPENDENCIES and assist
+the user in installing any that are missing. The script also automatically
+maintains the revision histories of any files that are being installed by the
+package but already have ,v files on disc (indicating that they are
+revision controlled).
+
+The script also functions as an *uninstaller* by passing the parameter
+=uninstall= on the command-line. Note that uninstallation does *not* revert
+the history of any topic changed during the installation.
+
+The script allows the definition of PREINSTALL and POSTINSTALL scripts.
+These scripts can be used for example to modify the configuration during
+installation, using the functions described below.
+
+Refer to the documentation of =configure=
+
+=cut
+
+# This is all done in package Foswiki so that reading LocalSite.cfg and Foswiki.cfg
+# will put the config vars into the right namespace.
+package Foswiki;
+
+# The root of package URLs
+my $PACKAGES_URL = 'http://foswiki.org/pub/Extensions';
+
+# Extract MANIFEST and DEPENDENCIES from the __DATA__
+undef $/;
+my @DATA = split( /<<<< (.*?) >>>>\s*\n/, <DATA> );
+shift @DATA;    # remove empty first element
+
+# Establish where we are
+my @path = ( 'tools', 'extender.pl' );
+my $wd = Cwd::cwd();
+$wd =~ /^(.*)$/;    # untaint
+unshift( @path, $1 ) if $1;
+my $script = File::Spec->catfile(@path);
+
+unless ( my $return = do $script ) {
+    my $message = <<MESSAGE;
+************************************************************
+Could not load $script
+MESSAGE
+    if ($@) {
+        $message .= "There was a compile error: $@\n";
+    }
+    elsif (defined $return) {
+        $message .= "There was a file error: $!\n";
+    }
+    else {
+        $message .= "An unspecified error occurred\n";
+    }
+
+    # Try again, using open. This cures some uncooperative platforms.
+    if ( open( F, '<', $script ) ) {
+        local $/;
+        my $data = <F>;
+        close(F);
+        $data =~ /^(.*)$/s;    # untaint
+        eval $1;
+        if ($@) {
+            $message .= "Error when trying to eval the file content: $@\n";
+        }
+        else {
+            print STDERR
+              "'do $script failed, but install was able to proceed: $message";
+            undef $message;
+        }
+    }
+    else {
+        $message .= "Could not open file using open() either: $!\n";
+    }
+    die $message if $message;
+}
+
+sub preuninstall {
+
+    # # No PREUNINSTALL script;
+}
+
+sub postuninstall {
+
+    # # No POSTUNINSTALL script;
+}
+
+sub preinstall {
+
+    # # No PREINSTALL script;
+}
+
+sub postinstall {
+
+    # # No POSTINSTALL script;
+}
+
+Foswiki::Extender::install( $PACKAGES_URL, 'PhyloWidgetPlugin', 'PhyloWidgetPlugin', @DATA );
+
+1;
+
+# MANIFEST and DEPENDENCIES are done this way
+# to make it easy to extract them from this script.
+
+__DATA__
+<<<< MANIFEST >>>>
+data/System/PhyloWidgetPlugin.txt,0644,
+data/System/PhyloNexusViewer.txt,0644,
+data/System/PhyloWidgetExample.txt,0644,
+data/System/PhyloWidgetViewHelper.txt,0644,
+data/System/VarNEXUSTREES.txt,0644,
+data/System/VarPHYLOWIDGET.txt,0644,
+data/System/ViewTrees.txt,0644,
+lib/Foswiki/Plugins/PhyloWidgetPlugin.pm,0644,
+pub/System/PhyloWidgetExample/Tree.nex,0644,
+pub/System/PhyloWidgetPlugin/bare.html,0644,
+pub/System/PhyloWidgetPlugin/img/pw.ico,0644,
+pub/System/PhyloWidgetPlugin/index.html,0644,
+pub/System/PhyloWidgetPlugin/jquery.phylowidget.uncompressed.js,0644,
+pub/System/PhyloWidgetPlugin/lib/core.jar,0644,
+pub/System/PhyloWidgetPlugin/lib/freeloader.jar,0644,
+pub/System/PhyloWidgetPlugin/lib/itext.jar,0644,
+pub/System/PhyloWidgetPlugin/lib/loading.gif,0644,
+pub/System/PhyloWidgetPlugin/lib/pdf.jar,0644,
+pub/System/PhyloWidgetPlugin/lib/phylowidget.jar,0644,
+pub/System/PhyloWidgetPlugin/minimal.txt,0644,
+pub/System/PhyloWidgetPlugin/phylotest.html,0644,
+pub/System/PhyloWidgetPlugin/scripts/phylopopup.js,0644,
+pub/System/PhyloWidgetPlugin/scripts/phylowidget.js,0644,
+pub/System/PhyloWidgetPlugin/style.css,0644,
+pub/System/PhyloWidgetPlugin/test.html,0644,
+pub/System/PhyloWidgetPlugin/zip/phylowidget_src.zip,0644,
+pub/System/PhyloWidgetPlugin/zip/phylowidget_standalone.zip,0644,
+templates/phylonhx.tmpl,0644,
+
+<<<< DEPENDENCIES >>>>
+Bio::NEXUS,>=0,1,cpan,Required
+Foswiki::Plugins::DBCachePlugin,>=0,1,plugin,Optional, For examples
+