diff --git a/Makefile.PL b/Makefile.PL index 87faf8d..1689818 100644 --- a/Makefile.PL +++ b/Makefile.PL @@ -12,18 +12,11 @@ WriteMakefile( : ()), PL_FILES => {}, PREREQ_PM => { - 'Dancer' => 1.3072, - 'Exporter' => 0, - 'HTTP::Async' => 0, - 'HTTP::Request::Common' => 0, - 'LWP::UserAgent' => 0, - 'Moose' => 0, - 'Module::Refresh' => 0, + 'Mojolicious' => 0, 'Test::More' => 0, 'Time::HiRes' => 0, - 'YAML' => 0, - - }, + + }, dist => { COMPRESS => 'gzip -9f', SUFFIX => 'gz', }, clean => { FILES => 'ModelSeedApi-*' }, ); diff --git a/app.pl b/app.pl new file mode 100755 index 0000000..ff428e2 --- /dev/null +++ b/app.pl @@ -0,0 +1,7 @@ +#!/usr/bin/env perl +use strict; +use warnings; + +use lib 'lib'; +use Mojolicious::Commands; +Mojolicious::Commands->start_app("ModelSEED::API"); diff --git a/bin/app.pl b/bin/app.pl deleted file mode 100755 index f73cf96..0000000 --- a/bin/app.pl +++ /dev/null @@ -1,7 +0,0 @@ -#!/usr/bin/env perl -use Dancer; -use lib $ENV{MODEL_SEED_CORE}."/config"; -use local::lib '../local/lib/perl5/'; -use ModelSEEDbootstrap; -use ModelSeedApi; -dance; diff --git a/config.yml b/config.yml deleted file mode 100644 index d1e26a8..0000000 --- a/config.yml +++ /dev/null @@ -1,29 +0,0 @@ -# This is the main configuration file of your Dancer app -# env-related settings should go to environments/$env.yml -# all the settings in this file will be loaded at Dancer's startup. - -# Your application's name -appname: "ModelSeedApi" - -# The default layout to use for your application (located in -# views/layouts/main.tt) -layout: "main" - -# when the charset is set to UTF-8 Dancer will handle for you -# all the magic of encoding and decoding. You should not care -# about unicode within your app when this setting is set (recommended). -charset: "UTF-8" - -# template engine -# simple: default and very basic template engine -# template_toolkit: TT - -template: "simple" - -# template: "template_toolkit" -# engines: -# template_toolkit: -# encoding: 'utf8' -# start_tag: '[%' -# end_tag: '%]' - diff --git a/lib/ModelSEED/API.pm b/lib/ModelSEED/API.pm new file mode 100644 index 0000000..4645a29 --- /dev/null +++ b/lib/ModelSEED/API.pm @@ -0,0 +1,167 @@ +package ModelSEED::API; +use Mojo::Base 'Mojolicious'; +our $VERSION = 0; +use ModelSEED::Auth::Factory; +use ModelSEED::Store; +use IO::String; +use Pod::Text; + + +sub startup { + my $self = shift; + $self->plugin(PODRenderer => { no_perldoc => 1 }); + my $Auth = ModelSEED::Auth::Factory->new->from_config; + my $Store = ModelSEED::Store->new(auth => $Auth); + $self->helper( Store => sub { $Store } ); + my $UuidRegex = qr/[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}/; + my $TopLevelTypes = [qw( + biochemistry + mapping + model + fbaformulation + gapfillingformulation + annotation + )]; + my $r = $self->routes; + # Root path returns POD for this file, + # format pod and send it as html + $r->get('/' => sub { + my $self = shift; + my $buffer; + my $p = Pod::Simple::HTML->new; + $p->output_string($buffer); + $p->parse_file(__FILE__); + $self->render(text => $buffer, format => 'html'); + }); + + $r->add_shortcut(resource => sub { + my ($r, $name, $methods) = @_; + my $resource = $r->route("/")->to("$name#"); + $methods = { map { $_ => 1 } @$methods }; + if ($methods->{post}) { + $resource->post->to('#create')->name("create_$name"); + } + if ($methods->{get}) { + $resource->get->to('#show')->name("remove_$name"); + } + if ($methods->{put}) { + $resource->put->to("#update")->name("remove_$name"); + } + return $resource; + }); + + # All remaining routes are under $VERSION + $r = $r->under("/$VERSION"); + + # Type listing route + $r->get("/" => sub { + my $self = shift; + my $base = $self->req->url->base; + my $data = { + map { $_ => $base . "/$VERSION/" . $_ } + @$TopLevelTypes + }; + return $self->render(json => $data); + }); + + # Typed routes + my $typed = $r->under("/:type" => [ type => $TopLevelTypes ]); + $typed->get("/")->to("Aliases#list"); + + # Typed with :uuid + $typed->get("/:uuid" => [ uuid => $UuidRegex ]) + ->resource("object", [qw(get put)]); + + # Typed with :owner :alias + $typed->under("/#owner/#alias") + ->resource("object", [qw(get put)]); + + # Incomplete :owner , no alias + $typed->get("/:owner")->to("Aliases#list"); +} +1; +__DATA__ + +=head1 ModelSEED::API + +REST API for the ModelSEED + +=head2 Routes + + /0/ + /0/:type + /0/:type/:uuid + /0/:type/:uname + /0/:type/:uname/:alias + +Each route begins with the API version number, +which is currently C<0>. + +=over 4 + +=item C + +=over 4 + +=item GET + +Return a JSON hash where keys are the types and each value is the +URL of the collection resource for that type. + +=back + +=item C + +=over 4 + +=item GET + +Return a JSON list of URLs that are resources available of that type. + +=back + +=item C + +=over 4 + +=item GET + +Return an object of type C<:type> matched by its UUID C<:uuid>. + +=item PUT + +If this object does not exist in the database, inserts the object +and returns 201. Otherwise fails, 403 Forbidden. + +=back + +=item C + +=over 4 + +=item GET + +Return a JSON list of URLs that are resources of the available type +C<:type> that are owned by the user with username C<:uname>. + +=back + +=item C + +=over 4 + +=item GET + +Get an object of type C<:type> owned by user with username +C<:uname> with alias C<:alias>. + +=item PUT + +Inserts the object and returns 201. Otherwise fails, 403 Forbidden. + +=back + +=back + +=cut + diff --git a/lib/ModelSEED/API/Aliases.pm b/lib/ModelSEED/API/Aliases.pm new file mode 100644 index 0000000..c91659a --- /dev/null +++ b/lib/ModelSEED/API/Aliases.pm @@ -0,0 +1,25 @@ +package ModelSEED::API::Aliases; +use Mojo::Base 'Mojolicious::Controller'; + +sub list { + my $self = shift; + my $query = { type => $self->param("type") }; + $query->{owner} = $self->param("owner") if defined $self->param("owner"); + my $aliases = $self->Store->get_aliases($query); + my $base = $self->req->url->base; + foreach my $als (@$aliases) { + my ($t, $o, $a) = ($als->{type}, $als->{owner}, $als->{alias}); + $als = "$base/$t/$o/$a"; + } + return $self->render(json => $aliases); +} + +sub get_config { + +} + +sub put_config { + +} + +1; diff --git a/lib/ModelSEED/API/Object.pm b/lib/ModelSEED/API/Object.pm new file mode 100644 index 0000000..58eff1f --- /dev/null +++ b/lib/ModelSEED/API/Object.pm @@ -0,0 +1,68 @@ +package ModelSEED::API::Object; +use Mojo::Base 'Mojolicious::Controller'; + +# GET +sub show { + my $self = shift; + Mojo::IOLoop->stream($self->tx->connection)->timeout(60); + my $ref = $self->_getBaseObjectRef(); + return $self->render(json => { 'e' => 'Not Found' }, 404) unless defined $ref; + my $url = $self->req->url->to_string; + my $path = $url; + $path =~ s/.*${ref}\/*//; + my $data = $self->Store->get_data($ref); + if ( $path ne "" && defined $data) { + return $self->render(json => { ref => $ref , path => $path, url => $url }); + } elsif(defined $data) { + return $self->render(json => $data); + } else { + return $self->render(json => { 'M' => "Not Found" }, 404); + } +} + +# POST +sub create { + my $self = shift; + return $self->render(text => "Too large file", 500) + if $self->req->is_limit_exceeded; + my $type = $self->param("type"); + my $ref = $self->_getBaseObjectRef(); + my $data = $self->req->json; + my $obj = $self->Store->create($type, $data); + my $rtv = $self->Store->save_object($ref, $obj); + if ($rtv) { + $self->render(json => { M => "Created", S => 201}, status => 201); + } else { + $self->render(json => { M => "Forbidden"}, status => 403); + } +} + +# PUT - update or create new +sub update { + my $self = shift; + return $self->render(text => "Too large file", 500) + if $self->req->is_limit_exceeded; + my $type = $self->param("type"); + my $ref = $self->_getBaseObjectRef(); + my $data = $self->req->json; + my $obj = $self->Store->create($type, $data); + my $rtv = $self->Store->save_object($ref, $obj); + if ($rtv) { + $self->render(json => { M => "Created", S => 201}, status => 201); + } else { + $self->render(json => { M => "Forbidden"}, status => 403); + } +} + +sub _getBaseObjectRef { + my $self = shift; + my $type = $self->param("type"); + my $uuid = $self->param("uuid"); + my $owner = $self->param("owner"); + my $alias = $self->param("alias"); + return "$type/$uuid" if defined $uuid; + return "$type/$owner/$alias" if defined $owner && defined $alias; + return; +} + +1; diff --git a/lib/ModelSeedApi.pm b/lib/ModelSeedApi.pm deleted file mode 100644 index 4d55bb1..0000000 --- a/lib/ModelSeedApi.pm +++ /dev/null @@ -1,78 +0,0 @@ -package ModelSeedApi; -use Dancer ':syntax'; -use ModelSEED::FIGMODEL; -use ModelSEED::CoreApi; -use ServerThing; -use Data::Dumper; -use Try::Tiny; -use Time::HiRes qw(time); -use StatHat; - -our $VERSION = '0'; -our $STAT_EMAIL = $ENV{STATHAT_EMAIL}; -set serializer => 'JSON'; - -my $fbamodel = ServerThing->new("ModelSEED::FBAMODEL"); -my $om = ModelSEED::CoreApi->new({ - database => "/Users/devoid/test.db", - driver => "sqlite", -}); -my $StatHat = StatHat->new(); - -# handle version numbers -any [qw(get post put delete head)] => qr{^/(\d+)} => sub { - my ($version) = splat; - var version => $version; - if($version ne $VERSION) { - # try to look for version supplied - send_error("Unknown api version $version", 404); - } else { - pass(); - } -}; - -prefix "/$VERSION"; - -get "/FBAMODEL.cgi" => sub { - my %params = params; - return $fbamodel->call(\%params); -}; - -get '/docs' => sub { - content_type 'text/html'; - return template 'index'; -}; - -get '/biochemistry/:uuid/full' => sub { - my $uuid = params->{uuid}; - my $data; - my $time = time; - try { - $data = $om->getBiochemistry({ uuid => $uuid, with_all => 1 }); - } catch { - send_error("Not Found", 404); - }; - if($data) { - $StatHat->value('biochemistry/full/read', (time() - $time)); - $StatHat->count('count-biochemistry/full/read', 1); - return $data; - } else { - send_error("Not Found", 404); - } -}; - -put '/biochemistry/:uuid/full' => sub { - my $uuid = params->{uuid}; - my $data = params; - try { - my $bio = ModelSEED::MS::Biochemistry->new($data); - $bio->om($om); - $bio->save(); - } catch { - send_error("Server Error", 500); - }; - return { ok => 200 }; -}; - - -1; diff --git a/public/404.html b/public/404.html deleted file mode 100644 index edf8c2f..0000000 --- a/public/404.html +++ /dev/null @@ -1,18 +0,0 @@ - - - -Error 404 - - - - -

Error 404

-
-

Page Not Found

Sorry, this is the void.

-
- - - \ No newline at end of file diff --git a/public/500.html b/public/500.html deleted file mode 100644 index 03e2dbc..0000000 --- a/public/500.html +++ /dev/null @@ -1,18 +0,0 @@ - - - -Error 500 - - - - -

Error 500

-
-

Internal Server Error

Wooops, something went wrong

-
- - - \ No newline at end of file diff --git a/public/css/error.css b/public/css/error.css deleted file mode 100644 index 003ee2a..0000000 --- a/public/css/error.css +++ /dev/null @@ -1,70 +0,0 @@ -body { - font-family: Lucida,sans-serif; -} - -h1 { - color: #AA0000; - border-bottom: 1px solid #444; -} - -h2 { color: #444; } - -pre { - font-family: "lucida console","monaco","andale mono","bitstream vera sans mono","consolas",monospace; - font-size: 12px; - border-left: 2px solid #777; - padding-left: 1em; -} - -footer { - font-size: 10px; -} - -span.key { - color: #449; - font-weight: bold; - width: 120px; - display: inline; -} - -span.value { - color: #494; -} - -/* these are for the message boxes */ - -pre.content { - background-color: #eee; - color: #000; - padding: 1em; - margin: 0; - border: 1px solid #aaa; - border-top: 0; - margin-bottom: 1em; -} - -div.title { - font-family: "lucida console","monaco","andale mono","bitstream vera sans mono","consolas",monospace; - font-size: 12px; - background-color: #aaa; - color: #444; - font-weight: bold; - padding: 3px; - padding-left: 10px; -} - -pre.content span.nu { - color: #889; - margin-right: 10px; -} - -pre.error { - background: #334; - color: #ccd; - padding: 1em; - border-top: 1px solid #000; - border-left: 1px solid #000; - border-right: 1px solid #eee; - border-bottom: 1px solid #eee; -} - diff --git a/public/css/style.css b/public/css/style.css deleted file mode 100644 index 706c3e5..0000000 --- a/public/css/style.css +++ /dev/null @@ -1,189 +0,0 @@ - -body { -margin: 0; -margin-bottom: 25px; -padding: 0; -background-color: #ddd; -background-image: url("/images/perldancer-bg.jpg"); -background-repeat: no-repeat; -background-position: top left; - -font-family: "Lucida Grande", "Bitstream Vera Sans", "Verdana"; -font-size: 13px; -color: #333; -} - -h1 { -font-size: 28px; -color: #000; -} - -a {color: #03c} -a:hover { -background-color: #03c; -color: white; -text-decoration: none; -} - -#page { -background-color: #ddd; -width: 750px; -margin: auto; -margin-left: auto; -padding-left: 0px; -margin-right: auto; -} - -#content { -background-color: white; -border: 3px solid #aaa; -border-top: none; -padding: 25px; -width: 500px; -} - -#sidebar { -float: right; -width: 175px; -} - -#header, #about, #getting-started { -padding-left: 75px; -padding-right: 30px; -} - - -#header { -background-image: url("/images/perldancer.jpg"); -background-repeat: no-repeat; -background-position: top left; -height: 64px; -} -#header h1, #header h2 {margin: 0} -#header h2 { -color: #888; -font-weight: normal; -font-size: 16px; -} - -#about h3 { -margin: 0; -margin-bottom: 10px; -font-size: 14px; -} - -#about-content { -background-color: #ffd; -border: 1px solid #fc0; -margin-left: -11px; -} -#about-content table { -margin-top: 10px; -margin-bottom: 10px; -font-size: 11px; -border-collapse: collapse; -} -#about-content td { -padding: 10px; -padding-top: 3px; -padding-bottom: 3px; -} -#about-content td.name {color: #555} -#about-content td.value {color: #000} - -#about-content.failure { -background-color: #fcc; -border: 1px solid #f00; -} -#about-content.failure p { -margin: 0; -padding: 10px; -} - -#getting-started { -border-top: 1px solid #ccc; -margin-top: 25px; -padding-top: 15px; -} -#getting-started h1 { -margin: 0; -font-size: 20px; -} -#getting-started h2 { -margin: 0; -font-size: 14px; -font-weight: normal; -color: #333; -margin-bottom: 25px; -} -#getting-started ol { -margin-left: 0; -padding-left: 0; -} -#getting-started li { -font-size: 18px; -color: #888; -margin-bottom: 25px; -} -#getting-started li h2 { -margin: 0; -font-weight: normal; -font-size: 18px; -color: #333; -} -#getting-started li p { -color: #555; -font-size: 13px; -} - -#search { -margin: 0; -padding-top: 10px; -padding-bottom: 10px; -font-size: 11px; -} -#search input { -font-size: 11px; -margin: 2px; -} -#search-text {width: 170px} - -#sidebar ul { -margin-left: 0; -padding-left: 0; -} -#sidebar ul h3 { -margin-top: 25px; -font-size: 16px; -padding-bottom: 10px; -border-bottom: 1px solid #ccc; -} -#sidebar li { -list-style-type: none; -} -#sidebar ul.links li { -margin-bottom: 5px; -} - -h1, h2, h3, h4, h5 { -font-family: sans-serif; -margin: 1.2em 0 0.6em 0; -} - -p { -line-height: 1.5em; -margin: 1.6em 0; -} - -code, tt { - font-family: 'Andale Mono', Monaco, 'Liberation Mono', 'Bitstream Vera Sans Mono', 'DejaVu Sans Mono', monospace; -} - -#footer { -clear: both; -padding-top: 2em; -text-align: center; -padding-right: 160px; -font-family: sans-serif; -font-size: 10px; -} diff --git a/public/dispatch.cgi b/public/dispatch.cgi deleted file mode 100755 index 3bb7f2a..0000000 --- a/public/dispatch.cgi +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env perl -use Dancer ':syntax'; -use FindBin '$RealBin'; -use Plack::Runner; - -# For some reason Apache SetEnv directives dont propagate -# correctly to the dispatchers, so forcing PSGI and env here -# is safer. -set apphandler => 'PSGI'; -set environment => 'production'; - -my $psgi = path($RealBin, '..', 'bin', 'app.pl'); -die "Unable to read startup script: $psgi" unless -r $psgi; - -Plack::Runner->run($psgi); diff --git a/public/dispatch.fcgi b/public/dispatch.fcgi deleted file mode 100755 index 8c42e3a..0000000 --- a/public/dispatch.fcgi +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env perl -use Dancer ':syntax'; -use FindBin '$RealBin'; -use Plack::Handler::FCGI; - -# For some reason Apache SetEnv directives dont propagate -# correctly to the dispatchers, so forcing PSGI and env here -# is safer. -set apphandler => 'PSGI'; -set environment => 'production'; - -my $psgi = path($RealBin, '..', 'bin', 'app.pl'); -my $app = do($psgi); -die "Unable to read startup script: $@" if $@; -my $server = Plack::Handler::FCGI->new(nproc => 5, detach => 1); - -$server->run($app); diff --git a/public/favicon.ico b/public/favicon.ico deleted file mode 100644 index 96c7465..0000000 Binary files a/public/favicon.ico and /dev/null differ diff --git a/public/images/header.png b/public/images/header.png deleted file mode 100644 index e3977af..0000000 Binary files a/public/images/header.png and /dev/null differ diff --git a/public/images/logo.png b/public/images/logo.png deleted file mode 100644 index abd5dc8..0000000 Binary files a/public/images/logo.png and /dev/null differ diff --git a/public/images/perldancer-bg.jpg b/public/images/perldancer-bg.jpg deleted file mode 100644 index 6ee6b77..0000000 Binary files a/public/images/perldancer-bg.jpg and /dev/null differ diff --git a/public/images/perldancer.jpg b/public/images/perldancer.jpg deleted file mode 100644 index 3f9e718..0000000 Binary files a/public/images/perldancer.jpg and /dev/null differ diff --git a/public/javascripts/jquery.js b/public/javascripts/jquery.js deleted file mode 100644 index 7c24308..0000000 --- a/public/javascripts/jquery.js +++ /dev/null @@ -1,154 +0,0 @@ -/*! - * jQuery JavaScript Library v1.4.2 - * http://jquery.com/ - * - * Copyright 2010, John Resig - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * Includes Sizzle.js - * http://sizzlejs.com/ - * Copyright 2010, The Dojo Foundation - * Released under the MIT, BSD, and GPL Licenses. - * - * Date: Sat Feb 13 22:33:48 2010 -0500 - */ -(function(A,w){function ma(){if(!c.isReady){try{s.documentElement.doScroll("left")}catch(a){setTimeout(ma,1);return}c.ready()}}function Qa(a,b){b.src?c.ajax({url:b.src,async:false,dataType:"script"}):c.globalEval(b.text||b.textContent||b.innerHTML||"");b.parentNode&&b.parentNode.removeChild(b)}function X(a,b,d,f,e,j){var i=a.length;if(typeof b==="object"){for(var o in b)X(a,o,b[o],f,e,d);return a}if(d!==w){f=!j&&f&&c.isFunction(d);for(o=0;o)[^>]*$|^#([\w-]+)$/,Ua=/^.[^:#\[\.,]*$/,Va=/\S/, -Wa=/^(\s|\u00A0)+|(\s|\u00A0)+$/g,Xa=/^<(\w+)\s*\/?>(?:<\/\1>)?$/,P=navigator.userAgent,xa=false,Q=[],L,$=Object.prototype.toString,aa=Object.prototype.hasOwnProperty,ba=Array.prototype.push,R=Array.prototype.slice,ya=Array.prototype.indexOf;c.fn=c.prototype={init:function(a,b){var d,f;if(!a)return this;if(a.nodeType){this.context=this[0]=a;this.length=1;return this}if(a==="body"&&!b){this.context=s;this[0]=s.body;this.selector="body";this.length=1;return this}if(typeof a==="string")if((d=Ta.exec(a))&& -(d[1]||!b))if(d[1]){f=b?b.ownerDocument||b:s;if(a=Xa.exec(a))if(c.isPlainObject(b)){a=[s.createElement(a[1])];c.fn.attr.call(a,b,true)}else a=[f.createElement(a[1])];else{a=sa([d[1]],[f]);a=(a.cacheable?a.fragment.cloneNode(true):a.fragment).childNodes}return c.merge(this,a)}else{if(b=s.getElementById(d[2])){if(b.id!==d[2])return T.find(a);this.length=1;this[0]=b}this.context=s;this.selector=a;return this}else if(!b&&/^\w+$/.test(a)){this.selector=a;this.context=s;a=s.getElementsByTagName(a);return c.merge(this, -a)}else return!b||b.jquery?(b||T).find(a):c(b).find(a);else if(c.isFunction(a))return T.ready(a);if(a.selector!==w){this.selector=a.selector;this.context=a.context}return c.makeArray(a,this)},selector:"",jquery:"1.4.2",length:0,size:function(){return this.length},toArray:function(){return R.call(this,0)},get:function(a){return a==null?this.toArray():a<0?this.slice(a)[0]:this[a]},pushStack:function(a,b,d){var f=c();c.isArray(a)?ba.apply(f,a):c.merge(f,a);f.prevObject=this;f.context=this.context;if(b=== -"find")f.selector=this.selector+(this.selector?" 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-

Documentation

-
diff --git a/views/layouts/main.tt b/views/layouts/main.tt deleted file mode 100644 index f0e7e47..0000000 --- a/views/layouts/main.tt +++ /dev/null @@ -1,68 +0,0 @@ - - - - -ModelSeedApi - - - - - - - - -
-<% content %> -
- - -