oba-client 2.0.2 → 2.0.3
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.
- data/History.md +3 -0
- data/lib/oba-client.rb +12 -11
- metadata +4 -4
data/History.md
CHANGED
data/lib/oba-client.rb
CHANGED
|
@@ -9,7 +9,7 @@ require "uri"
|
|
|
9
9
|
# things we do: get text, and parse it. We can do both independently or
|
|
10
10
|
# serially.
|
|
11
11
|
class OBAClient
|
|
12
|
-
VERSION = "2.0.
|
|
12
|
+
VERSION = "2.0.3"
|
|
13
13
|
|
|
14
14
|
##
|
|
15
15
|
# A high HTTP read timeout, as the service sometimes takes awhile to respond.
|
|
@@ -117,8 +117,7 @@ class OBAClient
|
|
|
117
117
|
ONTOLOGY_BEANS_XPATH = "/success/data/annotatorResultBean/ontologies/ontologyUsedBean"
|
|
118
118
|
|
|
119
119
|
##
|
|
120
|
-
# Attributes for mapping concepts (
|
|
121
|
-
# attribute. See also {ANNOTATION_CONCEPT_ATTRIBUTES}.
|
|
120
|
+
# Attributes for mapping concepts (only one type).
|
|
122
121
|
CONCEPT_ATTRIBUTES = {
|
|
123
122
|
:id => lambda {|c| c.xpath("id").text.to_i},
|
|
124
123
|
:localConceptId => lambda {|c| c.xpath("localConceptId").text},
|
|
@@ -146,7 +145,7 @@ class OBAClient
|
|
|
146
145
|
|
|
147
146
|
|
|
148
147
|
##
|
|
149
|
-
#
|
|
148
|
+
# Attributes for mapping and mgrep contexts (both will add
|
|
150
149
|
# additional attributes).
|
|
151
150
|
CONTEXT_ATTRIBUTES = {
|
|
152
151
|
:contextName => lambda {|c| c.xpath("contextName").text},
|
|
@@ -156,7 +155,7 @@ class OBAClient
|
|
|
156
155
|
}
|
|
157
156
|
|
|
158
157
|
##
|
|
159
|
-
#
|
|
158
|
+
# Attributes for annotation contexts.
|
|
160
159
|
ANNOTATION_CONTEXT_ATTRIBUTES = {
|
|
161
160
|
:score => lambda {|c| c.xpath("score").text.to_i},
|
|
162
161
|
:concept => lambda {|c| parse_concept(c.xpath("concept").first)},
|
|
@@ -164,14 +163,14 @@ class OBAClient
|
|
|
164
163
|
}
|
|
165
164
|
|
|
166
165
|
##
|
|
167
|
-
#
|
|
166
|
+
# Attributes for mapping contexts.
|
|
168
167
|
MAPPED_CONTEXT_ATTRIBUTES = CONTEXT_ATTRIBUTES.merge(
|
|
169
|
-
:mappingType
|
|
168
|
+
:mappingType => lambda {|c| c.xpath("mappingType").text},
|
|
170
169
|
:mappedConcept => lambda {|c| parse_concept(c.xpath("mappedConcept").first)}
|
|
171
170
|
)
|
|
172
171
|
|
|
173
172
|
##
|
|
174
|
-
#
|
|
173
|
+
# Attributes for mgrep contexts.
|
|
175
174
|
MGREP_CONTEXT_ATTRIBUTES = CONTEXT_ATTRIBUTES.merge(
|
|
176
175
|
:name => lambda {|c| c.xpath("term/name").text},
|
|
177
176
|
:localConceptId => lambda {|c| c.xpath("term/localConceptId").text},
|
|
@@ -179,10 +178,12 @@ class OBAClient
|
|
|
179
178
|
:dictionaryId => lambda {|c| c.xpath("term/dictionaryId").text}
|
|
180
179
|
)
|
|
181
180
|
|
|
181
|
+
##
|
|
182
|
+
# Map the bean type to the set of attributes we parse from it.
|
|
182
183
|
CONTEXT_CLASSES = {
|
|
183
|
-
"annotationContextBean"
|
|
184
|
-
"mgrepContextBean"
|
|
185
|
-
"mappingContextBean"
|
|
184
|
+
"annotationContextBean" => ANNOTATION_CONTEXT_ATTRIBUTES,
|
|
185
|
+
"mgrepContextBean" => MGREP_CONTEXT_ATTRIBUTES,
|
|
186
|
+
"mappingContextBean" => MAPPED_CONTEXT_ATTRIBUTES,
|
|
186
187
|
}
|
|
187
188
|
|
|
188
189
|
##
|
metadata
CHANGED
|
@@ -1,13 +1,13 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: oba-client
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
hash:
|
|
4
|
+
hash: 9
|
|
5
5
|
prerelease: false
|
|
6
6
|
segments:
|
|
7
7
|
- 2
|
|
8
8
|
- 0
|
|
9
|
-
-
|
|
10
|
-
version: 2.0.
|
|
9
|
+
- 3
|
|
10
|
+
version: 2.0.3
|
|
11
11
|
platform: ruby
|
|
12
12
|
authors:
|
|
13
13
|
- Rob Tirrell
|
|
@@ -15,7 +15,7 @@ autorequire:
|
|
|
15
15
|
bindir: bin
|
|
16
16
|
cert_chain: []
|
|
17
17
|
|
|
18
|
-
date: 2010-07-
|
|
18
|
+
date: 2010-07-16 00:00:00 -07:00
|
|
19
19
|
default_executable:
|
|
20
20
|
dependencies:
|
|
21
21
|
- !ruby/object:Gem::Dependency
|