openbel-api 0.5.1-java → 0.6.1-java

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (23) hide show
  1. checksums.yaml +4 -4
  2. data/.gemspec +14 -6
  3. data/CHANGELOG.md +32 -0
  4. data/README.md +2 -2
  5. data/VERSION +1 -1
  6. data/app/openbel/api/config.rb +12 -0
  7. data/app/openbel/api/helpers/base.rb +17 -0
  8. data/app/openbel/api/helpers/evidence.rb +74 -0
  9. data/app/openbel/api/helpers/filters.rb +94 -0
  10. data/app/openbel/api/helpers/translators.rb +73 -0
  11. data/app/openbel/api/resources/evidence_transform.rb +1 -13
  12. data/app/openbel/api/routes/authenticate.rb +0 -92
  13. data/app/openbel/api/routes/base.rb +19 -5
  14. data/app/openbel/api/routes/datasets.rb +65 -151
  15. data/app/openbel/api/routes/evidence.rb +10 -95
  16. data/config/config.yml +4 -6
  17. data/lib/openbel/api/evidence/api.rb +8 -0
  18. data/lib/openbel/api/evidence/facet_filter.rb +3 -3
  19. data/lib/openbel/api/evidence/mongo.rb +304 -44
  20. data/lib/openbel/api/evidence/mongo_facet.rb +173 -66
  21. metadata +112 -26
  22. data/config/async_evidence.rb +0 -12
  23. data/config/async_jena.rb +0 -14
data/lib/openbel/api/evidence/mongo_facet.rb CHANGED
@@ -12,10 +12,15 @@ module OpenBEL
12
12
  include FacetFilter
13
13
 
14
14
  def initialize(options = {})
15
- host = options[:host]
16
- port = options[:port]
17
- db = options[:database]
18
- @db = MongoClient.new(host, port).db(db)
15
+ host = options[:host]
16
+ port = options[:port]
17
+ db = options[:database]
18
+ @db = MongoClient.new(
19
+ host,
20
+ port,
21
+ :op_timeout => nil,
22
+ :pool_size => 30
23
+ ).db(db)
19
24
 
20
25
  # Authenticate user if provided.
21
26
  username = options[:username]
@@ -25,90 +30,192 @@ module OpenBEL
25
30
  @db.authenticate(username, password, nil, auth_db)
26
31
  end
27
32
 
28
- @evidence = @db[:evidence]
29
- @evidence_facets = @db[:evidence_facets]
33
+ @evidence = @db[:evidence]
34
+ @evidence_facet_cache = @db[:evidence_facet_cache]
35
+
36
+ # ensure all indexes are created and maintained
37
+ ensure_all_indexes
30
38
  end
31
39
 
32
- def create_facets(_id, query_hash)
33
- # create and save facets, identified by query
34
- facets_doc = _id.merge({
35
- :facets => evidence_facets(query_hash)
36
- })
37
- @evidence_facets.save(facets_doc, :j => true)
40
+ def find_facets(query, filters, facet_value_limit = -1)
41
+ sorted_filters = sort_filters(filters)
42
+ cache_collection = facet_cache_collection(sorted_filters)
43
+
44
+ if no_collection?(cache_collection)
45
+ cache_collection = "evidence_facet_cache_#{EvidenceFacets.generate_uuid}"
46
+ create_aggr = create_aggregation(cache_collection, query)
47
+ @evidence.aggregate(create_aggr[:pipeline], create_aggr[:options])
48
+ @evidence_facet_cache.insert({
49
+ :filters => sorted_filters,
50
+ :cache_collection => cache_collection
51
+ })
52
+ end
53
+
54
+ # set up field projection based on value limit
55
+ field_projection = {
56
+ :_id => 0,
57
+ :category => 1,
58
+ :name => 1,
59
+ :values => 1
60
+ }
61
+ if facet_value_limit > 0
62
+ field_projection[:values] = {:$slice => facet_value_limit}
63
+ end
38
64
 
39
- # return facets document
40
- facets_doc
65
+ # cursor facets and apply "filter"
66
+ @db[cache_collection].find({}, :fields => field_projection).map { |facet_doc|
67
+ category, name = facet_doc.values_at('category', 'name')
68
+ facet_doc['values'].each do |value|
69
+ value[:filter] = MultiJson.dump({
70
+ :category => category,
71
+ :name => name,
72
+ :value => value['value']
73
+ })
74
+ end
75
+ facet_doc
76
+ }
41
77
  end
42
78
 
43
- def find_facets(query_hash, filters)
44
- _id = {:_id => to_facets_id(filters)}
45
- @evidence_facets.find_one(_id) || create_facets(_id, query_hash)
79
+ def delete_facets(facets)
80
+ # Add zero-filter to facets; clears the default search
81
+ facets = facets.to_a
82
+ facets.unshift([])
83
+
84
+ # Drop facet cache collections
85
+ @evidence_facet_cache.find(
86
+ {:filters => {:$in => facets}},
87
+ :fields => {:_id => 0, :cache_collection => 1}
88
+ ).each do |doc|
89
+ cache_collection = doc['cache_collection']
90
+ @db[cache_collection].drop()
91
+ end
92
+
93
+ # remove filter match entries in evidence_facet_cache
94
+ @evidence_facet_cache.remove({:filters => {:$in => facets}})
46
95
  end
47
96
 
48
- def remove_facets_by_filters(filters = [], options = {})
49
- remove_spec =
50
- if filters.empty?
51
- { :_id => "" }
52
- else
53
- {
54
- :_id => {
55
- :$in => filters.map { |filter|
56
- to_regexp(MultiJson.load(filter))
57
- }
58
- }
59
- }
60
- end
61
- @evidence_facets.remove(remove_spec, :j => true)
97
+ def delete_all_facets
98
+ @evidence_facet_cache.find(
99
+ {},
100
+ :fields => {:_id => 0, :cache_collection => 1}
101
+ ).each do |doc|
102
+ cache_collection = doc['cache_collection']
103
+ @db[cache_collection].drop()
104
+ end
105
+
106
+ # remove all entries in evidence_facet_cache
107
+ @evidence_facet_cache.remove({})
108
+ end
109
+
110
+ def ensure_all_indexes
111
+ @evidence_facet_cache.ensure_index([
112
+ [:"filters.category", Mongo::ASCENDING],
113
+ [:"filters.name", Mongo::ASCENDING]
114
+ ],
115
+ :background => true
116
+ )
62
117
  end
63
118
 
64
119
  private
65
120
 
66
- def to_regexp(filter)
67
- filter_s = "#{filter['category']}|#{filter['name']}|#{filter['value']}"
68
- %r{.*#{Regexp.escape(filter_s)}.*}
121
+ def no_collection?(collection)
122
+ !collection || !@db.collection_names.include?(collection)
69
123
  end
70
124
 
125
+ def sort_filters(filters)
126
+ filters.sort { |f1, f2|
127
+ f1_array = f1.values_at(:category, :name, :value)
128
+ f2_array = f2.values_at(:cat, :name, :value)
71
129
 
72
- def to_facets_id(filters)
73
- filters.map { |filter|
74
- "#{filter['category']}|#{filter['name']}|#{filter['value']}"
75
- }.sort.join(',')
130
+ f1_array <=> f2_array
131
+ }
76
132
  end
77
133
 
78
- def evidence_facets(query_hash = nil)
79
- pipeline =
80
- if query_hash.is_a?(Hash) && !query_hash.empty?
81
- [{:'$match' => query_hash}] + AGGREGATION_PIPELINE
82
- else
83
- AGGREGATION_PIPELINE
84
- end
85
- @evidence.aggregate(pipeline)
134
+ def facet_cache_collection(filters)
135
+ result = @evidence_facet_cache.find_one(
136
+ {:filters => filters},
137
+ :fields => {:cache_collection => 1, :_id => 0}
138
+ )
139
+
140
+ result && result['cache_collection']
86
141
  end
87
142
 
88
- AGGREGATION_PIPELINE = [
89
- {
90
- :'$project' => {
91
- :_id => 0,
92
- :facets => 1
93
- }
94
- },
95
- {
96
- :'$unwind' => '$facets'
97
- },
143
+ def create_aggregation(out_collection, match_query = {}, options = {})
144
+ pipeline = CREATE_AGGREGATION[:pipeline] + [{ :$out => out_collection }]
145
+ unless match_query.empty?
146
+ pipeline.unshift({ :$match => match_query })
147
+ end
148
+
98
149
  {
99
- :'$group' => {
100
- :_id => '$facets',
101
- :count => {
102
- :'$sum' => 1
150
+ :pipeline => pipeline,
151
+ :options => CREATE_AGGREGATION[:options].merge(options)
152
+ }
153
+ end
154
+
155
+ # Define the aggregation pipeline
156
+ CREATE_AGGREGATION = {
157
+ :pipeline => [
158
+ {
159
+ :$project => {
160
+ :_id => 0,
161
+ :facets => 1
162
+ }
163
+ },
164
+ {
165
+ :$unwind => '$facets'
166
+ },
167
+ {
168
+ :$group => {
169
+ :_id => '$facets',
170
+ :count => {
171
+ :$sum => 1
172
+ }
173
+ }
174
+ },
175
+ {
176
+ :$sort => {
177
+ :count => -1
178
+ }
179
+ },
180
+ {
181
+ :$group => {
182
+ :_id => {
183
+ :category => '$_id.category',
184
+ :name => '$_id.name'
185
+ },
186
+ :values => {
187
+ :$push => {
188
+ :value => '$_id.value',
189
+ :count => '$count'
190
+ }
191
+ }
192
+ }
193
+ },
194
+ {
195
+ :$project => {
196
+ :category => '$_id.category',
197
+ :name => '$_id.name',
198
+ :values => { :$slice => ['$values', 1000] }
103
199
  }
104
200
  }
105
- },
106
- {
107
- :'$sort' => {
108
- :count => -1
109
- }
201
+ ],
202
+ :options => {
203
+ :allowDiskUse => true
110
204
  }
111
- ]
205
+ }
206
+
207
+ # Define UUID implementation based on Ruby.
208
+ if RUBY_ENGINE =~ /^jruby/i
209
+ java_import 'java.util.UUID'
210
+ define_singleton_method(:generate_uuid) do
211
+ Java::JavaUtil::UUID.random_uuid.to_s
212
+ end
213
+ else
214
+ require 'uuid'
215
+ define_singleton_method(:generate_uuid) do
216
+ UUID.generate
217
+ end
218
+ end
112
219
  end
113
220
  end
114
221
  end
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: openbel-api
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.5.1
4
+ version: 0.6.1
5
5
  platform: java
6
6
  authors:
7
7
  - Anthony Bargnesi
@@ -10,14 +10,14 @@ authors:
10
10
  autorequire:
11
11
  bindir: bin
12
12
  cert_chain: []
13
- date: 2015-12-18 00:00:00.000000000 Z
13
+ date: 2016-03-16 00:00:00.000000000 Z
14
14
  dependencies:
15
15
  - !ruby/object:Gem::Dependency
16
16
  requirement: !ruby/object:Gem::Requirement
17
17
  requirements:
18
18
  - - '='
19
19
  - !ruby/object:Gem::Version
20
- version: 0.4.1
20
+ version: 0.6.0
21
21
  name: bel
22
22
  prerelease: false
23
23
  type: :runtime
@@ -25,7 +25,105 @@ dependencies:
25
25
  requirements:
26
26
  - - '='
27
27
  - !ruby/object:Gem::Version
28
- version: 0.4.1
28
+ version: 0.6.0
29
+ - !ruby/object:Gem::Dependency
30
+ requirement: !ruby/object:Gem::Requirement
31
+ requirements:
32
+ - - '='
33
+ - !ruby/object:Gem::Version
34
+ version: 1.99.0
35
+ name: json-ld
36
+ prerelease: false
37
+ type: :runtime
38
+ version_requirements: !ruby/object:Gem::Requirement
39
+ requirements:
40
+ - - '='
41
+ - !ruby/object:Gem::Version
42
+ version: 1.99.0
43
+ - !ruby/object:Gem::Dependency
44
+ requirement: !ruby/object:Gem::Requirement
45
+ requirements:
46
+ - - '='
47
+ - !ruby/object:Gem::Version
48
+ version: 1.99.0
49
+ name: rdf-json
50
+ prerelease: false
51
+ type: :runtime
52
+ version_requirements: !ruby/object:Gem::Requirement
53
+ requirements:
54
+ - - '='
55
+ - !ruby/object:Gem::Version
56
+ version: 1.99.0
57
+ - !ruby/object:Gem::Dependency
58
+ requirement: !ruby/object:Gem::Requirement
59
+ requirements:
60
+ - - '='
61
+ - !ruby/object:Gem::Version
62
+ version: 1.99.0
63
+ name: rdf-rdfa
64
+ prerelease: false
65
+ type: :runtime
66
+ version_requirements: !ruby/object:Gem::Requirement
67
+ requirements:
68
+ - - '='
69
+ - !ruby/object:Gem::Version
70
+ version: 1.99.0
71
+ - !ruby/object:Gem::Dependency
72
+ requirement: !ruby/object:Gem::Requirement
73
+ requirements:
74
+ - - '='
75
+ - !ruby/object:Gem::Version
76
+ version: 1.99.0
77
+ name: rdf-rdfxml
78
+ prerelease: false
79
+ type: :runtime
80
+ version_requirements: !ruby/object:Gem::Requirement
81
+ requirements:
82
+ - - '='
83
+ - !ruby/object:Gem::Version
84
+ version: 1.99.0
85
+ - !ruby/object:Gem::Dependency
86
+ requirement: !ruby/object:Gem::Requirement
87
+ requirements:
88
+ - - '='
89
+ - !ruby/object:Gem::Version
90
+ version: 1.99.0.1
91
+ name: rdf-trig
92
+ prerelease: false
93
+ type: :runtime
94
+ version_requirements: !ruby/object:Gem::Requirement
95
+ requirements:
96
+ - - '='
97
+ - !ruby/object:Gem::Version
98
+ version: 1.99.0.1
99
+ - !ruby/object:Gem::Dependency
100
+ requirement: !ruby/object:Gem::Requirement
101
+ requirements:
102
+ - - '='
103
+ - !ruby/object:Gem::Version
104
+ version: 1.99.0
105
+ name: rdf-trix
106
+ prerelease: false
107
+ type: :runtime
108
+ version_requirements: !ruby/object:Gem::Requirement
109
+ requirements:
110
+ - - '='
111
+ - !ruby/object:Gem::Version
112
+ version: 1.99.0
113
+ - !ruby/object:Gem::Dependency
114
+ requirement: !ruby/object:Gem::Requirement
115
+ requirements:
116
+ - - '='
117
+ - !ruby/object:Gem::Version
118
+ version: 1.99.0
119
+ name: rdf-turtle
120
+ prerelease: false
121
+ type: :runtime
122
+ version_requirements: !ruby/object:Gem::Requirement
123
+ requirements:
124
+ - - '='
125
+ - !ruby/object:Gem::Version
126
+ version: 1.99.0
29
127
  - !ruby/object:Gem::Dependency
30
128
  requirement: !ruby/object:Gem::Requirement
31
129
  requirements:
@@ -45,7 +143,7 @@ dependencies:
45
143
  requirements:
46
144
  - - '='
47
145
  - !ruby/object:Gem::Version
48
- version: 0.4.1
146
+ version: 0.4.2
49
147
  name: bel-rdf-jena
50
148
  prerelease: false
51
149
  type: :runtime
@@ -53,13 +151,13 @@ dependencies:
53
151
  requirements:
54
152
  - - '='
55
153
  - !ruby/object:Gem::Version
56
- version: 0.4.1
154
+ version: 0.4.2
57
155
  - !ruby/object:Gem::Dependency
58
156
  requirement: !ruby/object:Gem::Requirement
59
157
  requirements:
60
158
  - - '='
61
159
  - !ruby/object:Gem::Version
62
- version: 1.99.0
160
+ version: 1.99.1
63
161
  name: rdf
64
162
  prerelease: false
65
163
  type: :runtime
@@ -67,7 +165,7 @@ dependencies:
67
165
  requirements:
68
166
  - - '='
69
167
  - !ruby/object:Gem::Version
70
- version: 1.99.0
168
+ version: 1.99.1
71
169
  - !ruby/object:Gem::Dependency
72
170
  requirement: !ruby/object:Gem::Requirement
73
171
  requirements:
@@ -171,7 +269,7 @@ dependencies:
171
269
  requirements:
172
270
  - - '='
173
271
  - !ruby/object:Gem::Version
174
- version: 2.15.3
272
+ version: 3.1.0
175
273
  name: puma
176
274
  prerelease: false
177
275
  type: :runtime
@@ -179,7 +277,7 @@ dependencies:
179
277
  requirements:
180
278
  - - '='
181
279
  - !ruby/object:Gem::Version
182
- version: 2.15.3
280
+ version: 3.1.0
183
281
  - !ruby/object:Gem::Dependency
184
282
  requirement: !ruby/object:Gem::Requirement
185
283
  requirements:
@@ -264,20 +362,6 @@ dependencies:
264
362
  - - '='
265
363
  - !ruby/object:Gem::Version
266
364
  version: 1.5.2
267
- - !ruby/object:Gem::Dependency
268
- requirement: !ruby/object:Gem::Requirement
269
- requirements:
270
- - - '='
271
- - !ruby/object:Gem::Version
272
- version: 1.8.0
273
- name: rest-client
274
- prerelease: false
275
- type: :runtime
276
- version_requirements: !ruby/object:Gem::Requirement
277
- requirements:
278
- - - '='
279
- - !ruby/object:Gem::Version
280
- version: 1.8.0
281
365
  description: The OpenBEL API provides a RESTful API over HTTP to manage BEL knowledge.
282
366
  email: abargnesi@selventa.com
283
367
  executables:
@@ -296,7 +380,11 @@ files:
296
380
  - app/openbel/api/app.rb
297
381
  - app/openbel/api/config.rb
298
382
  - app/openbel/api/config.ru
383
+ - app/openbel/api/helpers/base.rb
384
+ - app/openbel/api/helpers/evidence.rb
385
+ - app/openbel/api/helpers/filters.rb
299
386
  - app/openbel/api/helpers/pager.rb
387
+ - app/openbel/api/helpers/translators.rb
300
388
  - app/openbel/api/middleware/auth.rb
301
389
  - app/openbel/api/resources/adapters/basic_json.rb
302
390
  - app/openbel/api/resources/annotation.rb
@@ -333,8 +421,6 @@ files:
333
421
  - app/openbel/api/version.rb
334
422
  - bin/openbel-api
335
423
  - bin/openbel-config
336
- - config/async_evidence.rb
337
- - config/async_jena.rb
338
424
  - config/config.yml
339
425
  - config/server_config.rb
340
426
  - lib/openbel/api/cache/cache.rb