gered/clj-hl7-fhir
Archived
1
0
Fork 0
Code Issues 1 Pull requests Packages Projects Releases Wiki Activity

update dependencies and some little cleanups

Browse source
This commit is contained in:
Gered 2017-03-01 12:52:40 -05:00
parent 8684899bfa
commit 4ed1dff618
3 changed files with 72 additions and 59 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

24
project.clj
View file

@ -1,10 +1,18 @@
(defproject clj-hl7-fhir "0.3.0"
:description "HL7 FHIR JSON client"
:url "https://github.com/gered/clj-hl7-fhir"
:license {:name "Apache License, Version 2.0"
:url "http://www.apache.org/licenses/LICENSE-2.0"}
:dependencies [[org.clojure/clojure "1.6.0"]
[cheshire "5.3.1"]
[clj-http "0.9.2"]
:description "HL7 FHIR JSON client"
:url "https://github.com/gered/clj-hl7-fhir"
:license {:name "Apache License, Version 2.0"
:url "http://www.apache.org/licenses/LICENSE-2.0"}
:dependencies [[cheshire "5.7.0"]
[clj-http "2.3.0"]
[com.cemerick/url "0.1.1"]
[camel-snake-kebab "0.1.5"]])
[camel-snake-kebab "0.4.0"]]
:profiles {:provided
{:dependencies [[org.clojure/clojure "1.8.0"]]}
:test
{:dependencies [[pjstadig/humane-test-output "0.8.1"]]
:injections [(require 'pjstadig.humane-test-output)
(pjstadig.humane-test-output/activate!)]}})

87
src/clj_hl7_fhir/core.clj
View file

@ -1,11 +1,14 @@
(ns clj-hl7-fhir.core
(:import (java.util Date)
(clojure.lang ExceptionInfo))
(:require [clojure.string :as str]
[cemerick.url :refer [url]]
[cheshire.core :as json])
(:use [camel-snake-kebab]
[clj-hl7-fhir.util]))
(:refer-clojure :exclude [update])
(:require
[camel-snake-kebab.core :as csk]
[cemerick.url :refer [url]]
[cheshire.core :as json]
[clojure.string :as string]
[clj-hl7-fhir.util :as util])
(:import
(java.util Date)
(clojure.lang ExceptionInfo)))
; HACK: using this dynamic/"with"-wrapping type of API design is arguably a "lazy" design.
; in the future I intend to explore reworking the API so as to not require this if
@ -49,30 +52,30 @@
(if (map? (:headers *options*)) {:headers (:headers *options*)})))
(defn- ->fhir-resource-name [x]
(name (->CamelCase x)))
(name (csk/->PascalCase x)))
(defn- fhir-response? [response]
(and (map? response)
(.contains (get-in response [:headers "Content-Type"]) "application/json+fhir")))
(defn- fhir-request [type base-url resource-url & {:keys [params body params-as-body? follow-location?]}]
(let [query (map->query-string params)
url (build-url base-url resource-url (if-not params-as-body? query))
(let [query (util/map->query-string params)
url (util/build-url base-url resource-url (if-not params-as-body? query))
body (if params-as-body? query body)
follow-location? (if (nil? follow-location?) true follow-location?)
http-req-params (get-base-http-req-params)]
(try
(let [response (case type
:get (http-get-json url http-req-params)
:form-post (http-post-form url http-req-params body)
:post (http-post-json url http-req-params body)
:put (http-put-json url http-req-params body)
:delete (http-delete-json url http-req-params body))
:get (util/http-get-json url http-req-params)
:form-post (util/http-post-form url http-req-params body)
:post (util/http-post-json url http-req-params body)
:put (util/http-put-json url http-req-params body)
:delete (util/http-delete-json url http-req-params body))
response-body (:body response)
location (get-in response [:headers "Location"])]
(if location
(if follow-location?
(-> (http-get-json location http-req-params)
(-> (util/http-get-json location http-req-params)
:body
(json/parse-string true))
(if (fhir-response? response)
@ -98,7 +101,7 @@
(if (vector? parameter)
(->> parameter
(map name)
(str/join ".")
(string/join ".")
)
(name parameter))
(if modifier
@ -130,13 +133,13 @@
(sequential? value)
(->> value
(map format-search-value)
(str/join ","))
(string/join ","))
(map? value)
(str (:namespace value) "|" (format-search-value (:value value)))
(instance? Date value)
(->timestamp value)
(util/->timestamp value)
:else
(-> value str escape-parameter)))
@ -210,7 +213,7 @@
(defn- format-resource-url-type [url-path-parts keywordize?]
(if keywordize?
(-> url-path-parts first ->kebab-case keyword)
(-> url-path-parts first csk/->kebab-case keyword)
(-> url-path-parts first ->fhir-resource-name)))
(defn parse-relative-url
@ -221,7 +224,7 @@
the URL cannot be parsed, returns nil"
[relative-url & [keywordize?]]
(let [parts (-> (strip-query-params relative-url)
(str/split #"/"))]
(string/split #"/"))]
(cond
(= 2 (count parts))
{:type (format-resource-url-type parts keywordize?)
@ -241,11 +244,11 @@
the URL cannot be parsed, returns nil."
[absolute-url & [keywordize?]]
(let [{:keys [path]} (url absolute-url)
parts (str/split path #"/")
parts (string/split path #"/")
has-version? (= "_history" (second (reverse parts)))]
(cond
(and (> (count parts) 4)
(= "_history" (second-last parts))
(= "_history" (util/second-last parts))
has-version?)
(let [versioned-url-parts (take-last 4 parts)]
{:type (format-resource-url-type versioned-url-parts keywordize?)
@ -263,7 +266,7 @@
passed in is not a string (or an empty string) an exception is thrown."
[^String resource-url]
(if (and (string? resource-url)
(not (str/blank? resource-url)))
(not (string/blank? resource-url)))
(boolean
(try
(url resource-url)
@ -297,8 +300,8 @@
"combines a base URL to a FHIR server and a relative FHIR resource URL into an
absolute resource URL."
[base-url relative-url]
(if-not (or (str/blank? base-url)
(str/blank? relative-url))
(if-not (or (string/blank? base-url)
(string/blank? relative-url))
(-> (url base-url relative-url)
(.toString))))
@ -350,7 +353,7 @@
[bundle]
(if-let [next-url (get-bundle-next-page-url bundle)]
(let [http-req-params (get-base-http-req-params)]
(http-get-json next-url http-req-params))))
(util/http-get-json next-url http-req-params))))
(defn- concat-bundle-entries [bundle other-bundle]
(if (nil? bundle)
@ -400,7 +403,7 @@
reference:
contained resources: http://www.hl7.org/implement/standards/fhir/references.html#contained"
[containing-resource ref-id]
(if-not (str/blank? ref-id)
(if-not (string/blank? ref-id)
(if-let [parsed-id (if (.startsWith ref-id "#") (subs ref-id 1))]
(->> (:contained containing-resource)
(filter #(= parsed-id (:id %)))
@ -453,7 +456,7 @@
url-components (if version
["/" resource-name id "_history" version]
["/" resource-name id])]
(get-resource base-url (apply join-paths url-components)))))
(get-resource base-url (apply util/join-paths url-components)))))
(defn get-relative-resource
"gets a single resource from a FHIR server. the server to be queried will be taken from the
@ -479,10 +482,10 @@
url-components ["/" resource-name]]
(fhir-request :get
base-url
(apply join-paths url-components)
(apply util/join-paths url-components)
:params (merge
{:_id id}
(build-params-map params)))))
(util/build-params-map params)))))
(defn history
"returns a bundle containing the history of a single FHIR resource. note that this history can
@ -501,8 +504,8 @@
url-components ["/" resource-name id "_history"]]
(fhir-request :get
base-url
(apply join-paths url-components)
:params (build-params-map params))))
(apply util/join-paths url-components)
:params (util/build-params-map params))))
(defn search
"searches for resources on a FHIR server. multiple parameters are ANDed together. use of the search
@ -521,11 +524,11 @@
url-components ["/" resource-name "/_search"]]
(fhir-request :form-post
base-url
(apply join-paths url-components)
(apply util/join-paths url-components)
:params-as-body? true
:params (merge
(search-params->query-map where)
(build-params-map params)))))
(util/build-params-map params)))))
(defn search-and-fetch
"same as search, but automatically fetches all pages of resources returning a single bundle
@ -551,7 +554,7 @@
return-resource? (if (nil? return-resource?) true return-resource?)]
(fhir-request :post
base-url
(apply join-paths uri-components)
(apply util/join-paths uri-components)
:body resource
:follow-location? return-resource?)))
@ -574,7 +577,7 @@
return-resource? (if (nil? return-resource?) true return-resource?)]
(fhir-request :put
base-url
(apply join-paths uri-components)
(apply util/join-paths uri-components)
:body resource
:follow-location? return-resource?)))
@ -589,7 +592,7 @@
uri-components ["/" resource-name id]]
(fhir-request :delete
base-url
(apply join-paths uri-components))))
(apply util/join-paths uri-components))))
(defn deleted?
"checks if a resource has been deleted or not. this is based on FHIR servers returning
@ -597,7 +600,7 @@
[base-url type id]
(let [resource-name (->fhir-resource-name type)
url-components ["/" resource-name id]
relative-url (apply join-paths url-components)]
relative-url (apply util/join-paths url-components)]
(try
(fhir-request :get
base-url
@ -651,13 +654,13 @@
(:valueDecimal extension))
(defmethod get-extension-value :valueDateTime [extension]
(parse-timestamp (:valueDateTime extension)))
(util/parse-timestamp (:valueDateTime extension)))
(defmethod get-extension-value :valueDate [extension]
(parse-date (:valueDate extension)))
(util/parse-date (:valueDate extension)))
(defmethod get-extension-value :valueInstant [extension]
(parse-timestamp (:valueInstant extension)))
(util/parse-timestamp (:valueInstant extension)))
(defmethod get-extension-value :valueString [extension]
(:valueString extension))

20
src/clj_hl7_fhir/util.clj
View file

@ -1,10 +1,12 @@
(ns clj-hl7-fhir.util
(:import (java.util TimeZone Date)
(java.text SimpleDateFormat))
(:require [clojure.string :as str]
[clj-http.client :as http]
[cemerick.url :refer [url url-encode]]
[cheshire.core :as json]))
(:require
[cemerick.url :refer [url url-encode]]
[cheshire.core :as json]
[clj-http.client :as http]
[clojure.string :as string])
(:import
(java.util TimeZone Date)
(java.text SimpleDateFormat)))
(def tz (TimeZone/getDefault))
(def iso8601-timestamp "yyyy-MM-dd'T'HH:mm:ssXXX")
@ -35,7 +37,7 @@
(format-date date iso8601-date))
(defn parse-formatted-timestamp [^String timestamp ^String format]
(if-not (str/blank? timestamp)
(if-not (string/blank? timestamp)
(let [df (SimpleDateFormat. format)]
(.setTimeZone df tz)
(.parse df timestamp))))
@ -84,8 +86,8 @@
(defn join-paths [& paths]
(as-> paths x
(remove nil? x)
(str/join "/" x)
(str/replace x #"(/+)" "/")))
(string/join "/" x)
(string/replace x #"(/+)" "/")))
(defn build-url [base-url path & [params]]
(-> (url base-url)