1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
|
## SETUP
[ 'rubygems', 'sinatra', 'rest_client', 'sinatra/url_for', 'datamapper', 'dm-more', 'do_sqlite3', 'builder', 'api_key' ].each do |lib|
require lib
end
# reload
## MODELS
class Dataset
include DataMapper::Resource
property :id, Serial
property :name, String, :unique => true
has n, :associations
end
class Association
include DataMapper::Resource
property :id, Serial
property :compound_uri, Text
property :feature_uri, Text
belongs_to :dataset
end
# automatically create the tables
configure :test do
DataMapper.setup(:default, 'sqlite3::memory:')
[Dataset, Association].each do |model|
model.auto_migrate!
end
end
@db = "datasets.sqlite3"
configure :development, :production do
DataMapper::setup(:default, "sqlite3://#{Dir.pwd}/#{@db}")
unless FileTest.exists?("#{@db}")
[Dataset, Association].each do |model|
model.auto_migrate!
end
end
puts @db
end
## Authentification
helpers do
def protected!
response['WWW-Authenticate'] = %(Basic realm="Testing HTTP Auth") and \
throw(:halt, [401, "Not authorized\n"]) and \
return unless authorized?
end
def authorized?
@auth ||= Rack::Auth::Basic::Request.new(request.env)
@auth.provided? && @auth.basic? && @auth.credentials && @auth.credentials == ['api', API_KEY]
end
end
## REST API
get '/' do
Dataset.all.collect{ |d| url_for("/", :full) + d.id.to_s }.join("\n")
end
get '/:id' do
begin
dataset = Dataset.get(params[:id])
builder do |xml|
xml.instruct!
xml.dataset do
xml.uri url_for("/", :full) + dataset.id.to_s
xml.name dataset.name
dataset.associations.each do |a|
xml.association do
xml.compound a.compound_uri
xml.feature a.feature_uri
end
end
end
end
rescue
status 404
"Cannot find dataset with ID #{params[:id]}."
end
end
get '/:id/compounds' do
dataset = Dataset.get(params[:id])
compounds = []
features = {}
dataset.associations.each do |a|
compounds << a.compound_uri
if features[a.compound_uri]
features[a.compound_uri] << a.feature_uri
else
features[a.compound_uri] = [a.feature_uri]
end
end
compounds.uniq!
builder do |xml|
xml.instruct!
xml.dataset do
xml.uri url_for("/", :full) + dataset.id.to_s
xml.name dataset.name
xml.compounds do
compounds.each do |p|
xml.compound do
xml.uri p
xml.features do
features[p].each do |c|
xml.feature c
end
end
end
end
end
end
end
end
put '/:id' do
#protected!
#begin
dataset = Dataset.get params[:id]
#compound_uri = RestClient.post COMPOUNDS_SERVICE_URI, :name => params[:compound_name]
#feature_uri = RestClient.post FEATURES_SERVICE_URI, :name => params[:feature_name], :value => params[:feature_value]
compound_uri = params[:compound_uri]
puts params.to_yaml
feature_uri = params[:feature_uri]
Association.create(:compound_uri => compound_uri.to_s, :feature_uri => feature_uri.to_s, :dataset_id => dataset.id)
url_for("/", :full) + dataset.id.to_s
#rescue
#status 500
#"Failed to update dataset #{params[:id]}."
#end
end
post '/' do
#protected!
dataset = Dataset.find_or_create :name => params[:name]
if dataset.id.nil?
status 500
"Failed to create new dataset."
else
url_for("/", :full) + dataset.id.to_s
end
end
delete '/:id' do
# dangerous, because other datasets might refer to it
protected!
begin
dataset = Dataset.get(params[:id])
dataset.associations.each { |a| a.destroy }
dataset.destroy
"Successfully deleted dataset #{params[:id]}."
rescue
status 500
"Can not delete dataset #{params[:id]}."
end
end
|
