Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

feat(#3): add schemas downloading from aidbox url #13

Merged
merged 5 commits into from
Jul 29, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ generate_reflect_config:
COMPILE_OPTS := \
--no-fallback \
--features=clj_easy.graal_build_time.InitClojureClasses \
--enable-url-protocols=http,https \
-H:ReflectionConfigurationFiles=$(project_dir)/META/reflect-config.json \
-H:Name=aidbox-sdk
compile_native_image: generate_reflect_config
Expand Down
6 changes: 3 additions & 3 deletions deps.edn
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
{:paths ["src"]
:deps {org.clojure/data.json {:mvn/version "2.5.0"}

com.github.clj-easy/graal-build-time {:mvn/version "1.0.5"}
:deps {com.github.clj-easy/graal-build-time {:mvn/version "1.0.5"}
org.clj-commons/clj-http-lite {:mvn/version "1.0.13"}
org.clojure/clojure {:mvn/version "1.11.3"}
org.clojure/data.json {:mvn/version "2.5.0"}
org.clojure/tools.cli {:mvn/version "1.1.230"}}

:aliases
Expand Down
3 changes: 1 addition & 2 deletions dev/user.clj
Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,6 @@
(count (gen/apply-constraints mcodes
bases))

(vec (gen/retrieve-schemas' source'))
(contains? (->> (gen/retrieve-schemas' source')
(filter gen/base-schema?)
(gen/prepared-schemas)
Expand All @@ -71,6 +70,6 @@
(vector-to-map))
"http://hl7.org/fhir/StructureDefinition/Observation")

(gen/build-all! source' target)
(gen/build-all! (io/as-url "http://localhost:8765/sdk/fhir-packages") target)

:rcf)
38 changes: 30 additions & 8 deletions src/aidbox_sdk/core.clj
Original file line number Diff line number Diff line change
Expand Up @@ -2,24 +2,43 @@
(:gen-class)
(:require
[clojure.java.io :as io]
[clojure.tools.cli :as cli]
[aidbox-sdk.generator :as generator]))

(set! *warn-on-reflection* true)

(defn url
(defn url?
"Safe version of as-url function"
[s]
(try
(io/as-url s)
(catch java.net.MalformedURLException _ nil)
(catch java.net.URISyntaxException _ nil)))
(let [_ (io/as-url s)]
true)
(catch java.net.MalformedURLException _ false)
(catch java.net.URISyntaxException _ false)))

(defn resource [path]
(or (url path)
(io/as-file path)))
(if (url? path)
{:type :url :source path}
{:type :file :source path}))

(def cli-options
[["-a" "--auth BASE64_string" "Base64 of username:password"
:validate [(complement nil?) "auth token is required"]]
["-h" "--help"]])

(defn -main [& args]
(let [[input output] args]
(let [{:keys [options summary]} (cli/parse-opts args cli-options)
[input output] args]
(when (:help options)
(println "Generate Aidbox SDK from FHIR schemas")
(println)
(println "USAGE")
(println "aidbox-sdk <input-source> <output-dir> [options]")
(println)
(println "OPTIONS")
(println summary)
(System/exit 0))

(cond
(nil? input)
(binding [*out* *err*]
Expand All @@ -33,5 +52,8 @@
(do
(println "Building FHIR SDK...")
(generator/build-all!
options
(resource input)
(io/as-file output))))))
(io/as-file output))
(println "Finished succesfully!")
(System/exit 0)))))
50 changes: 23 additions & 27 deletions src/aidbox_sdk/generator.clj
Original file line number Diff line number Diff line change
@@ -1,15 +1,16 @@
(ns aidbox-sdk.generator
(:refer-clojure :exclude [namespace])
(:require [aidbox-sdk.generator.dotnet.templates :as dotnettpl]
[aidbox-sdk.generator.helpers :refer [->pascal-case safe-conj
uppercase-first-letter
vector-to-map]]
[aidbox-sdk.schema :as schema]
[clojure.java.io :as io]
[clojure.set :as set]
[clojure.string :as str]
[clojure.walk])
(:import [java.util.zip ZipEntry ZipOutputStream]))
(:require
[aidbox-sdk.generator.dotnet.templates :as dotnettpl]
[aidbox-sdk.generator.helpers :refer [->pascal-case
safe-conj
uppercase-first-letter
vector-to-map]]
[aidbox-sdk.schema :as schema]
[clojure.java.io :as io]
[clojure.set :as set]
[clojure.string :as str]
[clojure.walk]))

;;
;; FHIR
Expand Down Expand Up @@ -645,20 +646,6 @@
(delete-directory! dir)
(create-directory! dir))

;; FIXME do we need it?
(defn zip-dir! [path zip-name]
(with-open [zip (ZipOutputStream. (io/output-stream zip-name))]
(doseq [f (file-seq (io/file path)) :when (.isFile f)]
(.putNextEntry zip (ZipEntry. (str/replace-first (.getPath f) path "")))
(io/copy f zip)
(.closeEntry zip)))
(io/file zip-name))

;; FIXME do we need it?
(defn copy-files! [src-dir target-dir]
(doseq [file (remove #(.isDirectory %) (file-seq src-dir))]
(io/copy file (io/file target-dir (.getName file)))))

;;
;; main
;;
Expand Down Expand Up @@ -692,18 +679,21 @@
(conj schema {:backbone-elements
(flat-backbones (:backbone-elements schema) [])})))))

(defn build-all! [input output]
(defn build-all! [ctx input output]
(let [search-parameters-dir (io/file output "search")
all-schemas (schema/retrieve input)
all-schemas (schema/retrieve input {:auth (:auth ctx)})
;; search-params-schemas (retrieve-search-params source-dir)
search-params-schemas all-schemas
constraints (->> all-schemas
(filter #(and
(constraint? %)
(not (from-extension? %)))))]

(prepare-target-directory! output)

;; create base namespace (all FHIR datatypes) file
(println "---")
(println "Generating base namespace")
(->> all-schemas
(filter base-schema?)
(prepared-schemas)
Expand All @@ -713,6 +703,7 @@
(io/file output "Base.cs")))

;; create spezialization files
(println "Generating resource classes")
(doseq [item (->> all-schemas
(filter base-schema?)
(filter domain-resource?)
Expand All @@ -727,6 +718,7 @@
(generate-resource-namespace item)))

;; create resource map file
(println "Generating resource map")
(->> all-schemas
(filter base-schema?)
(filter domain-resource?)
Expand All @@ -751,6 +743,7 @@
(:class-file-content item)))

;; create constraints
(println "Generating constraints classes")
(doseq [{:keys [name schema file-content]}
(->> (apply-constraints
constraints
Expand All @@ -767,8 +760,11 @@
(assoc schema
:url name'))})))]
(save-to-file!
(io/file output (package->directory (:package schema)) (str (->pascal-case (url->resource-type name)) ".cs"))
(io/file output
(package->directory (:package schema))
(str (->pascal-case (url->resource-type name)) ".cs"))
file-content))

(println "Generating common SDK files")
(doseq [file dotnettpl/files]
(spit (io/file output (:name file)) (:content file)))))
7 changes: 7 additions & 0 deletions src/aidbox_sdk/generator/helpers.clj
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
(ns aidbox-sdk.generator.helpers
(:require
[clojure.data.json :as json]
[clojure.string :as str]))

(defn words
Expand All @@ -24,3 +25,9 @@
(into {})))

(defn safe-conj [a b] (conj a (or b {})))

(defn rand-int-between [min max]
(int (+ min (Math/floor (rand (- max min))))))

(defn parse-json [s]
(json/read-str s :key-fn keyword))
73 changes: 54 additions & 19 deletions src/aidbox_sdk/schema.clj
Original file line number Diff line number Diff line change
@@ -1,13 +1,12 @@
(ns aidbox-sdk.schema
(:require [aidbox-sdk.schema.verify :as verify]
[clojure.data.json :as json]
[aidbox-sdk.generator.helpers :refer [rand-int-between parse-json]]
[clj-http.lite.client :as http.client]
[clojure.java.io :as io]
[clojure.string :as str]))

(defn get-packages-from-directory
"Returns all packages in the given directory, including files in subdirectories.
NOTE: right now it'll filter out all files which do not contains hl7.fhir
in their name."
"Returns all packages in the given directory, including files in subdirectories. "
[path]
(let [packages (->> path
file-seq
Expand All @@ -28,11 +27,10 @@
;; see https://github.com/Aidbox/aidbox-sdk/issues/10
(defn parse-package [path]
(println "Parsing package:" (str path))
(with-open [rdr (create-gzip-reader path)]
(->> rdr
(with-open [reader (create-gzip-reader path)]
(->> reader
line-seq
(mapv (fn [line]
(json/read-str line :key-fn keyword))))))
(mapv parse-json))))

(defn remove-invalid-schemas [schemas]
(remove #(nil? (:package-meta %)) schemas))
Expand All @@ -48,23 +46,60 @@
(assoc % :package))
schemas))

(defmulti retrieve (fn [resource _] (:type resource)))

(defmulti retrieve class)

;; ! According to an example here:
;; ! https://clojuredocs.org/clojure.java.io/file
;; ! it's possible to create a File instance from url, which may lead to bugs
(defmethod retrieve java.io.File
[source]
(defmethod retrieve :file
[{:keys [source]} opts]
(println "Retrieving packages from: " (str source))
(->> (get-packages-from-directory source)
(->> (get-packages-from-directory (io/as-file source))
(mapv parse-package)
(verify/check-compatibility!)
(flatten)
(remove-invalid-schemas)
(prepare-schemas)
(merge-duplicates)))

(defmethod retrieve java.net.URL
[source]
(do "something"))
(defn- next-timeout
"Timeout calculation for retrying like in kafka.
https://kafka.js.org/docs/retry-detailed"
[timeout]
(let [factor 0.2
multiplier 2]
(* (rand-int-between
(* timeout (- 1 factor))
(* timeout (+ 1 factor)))
multiplier)))

(defn- retry [f & {:keys [timeout trials]
:or {timeout 3000
trials 3}}]
(if (zero? (dec trials))
(f)
(try
(f)
(catch Throwable _
(Thread/sleep ^long timeout)
(retry f {:timeout (next-timeout timeout)
:trials (dec trials)})))))

(defn fetch-n-parse [url opts]
(let [result (retry #(http.client/get url {:headers {"Authorization" (str "Basic " (:auth opts))}}))]
(some-> result :body parse-json)))

(defn skip-root-package [packages]
(rest packages))

(defmethod retrieve :url
[{:keys [source]} opts]
(let [extract-link (fn [package] (-> package :href))
extract-name (fn [package] (str (:name package) "#" (:version package)))
fhir-packages (do
(println "Downloading list of dependencies from:" source)
(-> (fetch-n-parse source opts)
(skip-root-package)))]

(->> fhir-packages
(pmap (fn [package]
(println "Downloading schemas for:" (extract-name package))
(fetch-n-parse (extract-link package) opts)))
(flatten))))