gistfile1.clj

(ns oba-client
  (:use [clojure-http.resourcefully :as res]
        [clojure.contrib.str-utils :only [str-join]])
  (:refer-clojure :exclude [get]))

(def default-timeout 30) 
(def default-uri     "http://rest.bioontology.org/obs/annotator")

(def all-annotator-parameters #{
 	"email"
  "filterNumber"
  "format"
  "isStopWordsCaseSensitive"
  "isVirtualOntologyID"
  "levelMax"
  "longestOnly"
  "ontologiesToExpand"
  "ontologiesToKeepInResult"
  "mappingTypes"
  "minTermSize"
  "scored"
  "semanticTypes"
  "stopWords"
  "wholeWordOnly"
  "withDefaultStopWords"
  "withSynonyms"})

(defn execute-request [uri timeout parse-xml parameters text]
  (let [parameters (assoc parameters "textToAnnotate" text)
        response (res/post uri {} parameters)]
    (println response)))

(defn annotate 
  ([] (annotate {}))
  ([options] 
    (let [uri       (get options "uri"     default-uri)
          timeout   (get options "timeout" default-timeout)
          parse-xml (get options "parse-xml")]
      (when-let [ontologies (get options "ontologies")]
        (do (assoc options "ontologiesToExpand"       ontologies)
  					(assoc options "ontologiesToKeepInResult" ontologies)))
      (let [parameters (select-keys options all-annotator-parameters)]
        (doseq [[k v] parameters] 
          (if (vector? v) (assoc parameters k (str-join ", " v))))
        (partial execute-request uri timeout parse-xml parameters)))))

(defn annotate-text []
  ((annotate) "hello!? out there?!"))

(annotate-text)