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 parse [xml])

(defn execute-request [uri timeout parse-xml parameters text]
  (let [parameters (assoc parameters :textToAnnotate text)]
    (binding [*connect-timeout* timeout]
      (let [response (res/post uri {} parameters)] 
        (if parse-xml 
          (parse (response :body-seq)) 
          (response :body-seq))))))

(defn annotate 
  ([] (annotate {}))
  ([options] 
    (let [uri       (clojure.core/get options :uri     default-uri)
          timeout   (clojure.core/get options :timeout default-timeout)
          parse-xml (                 options :parse-xml)]
      (when-let [ontologies (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)