Make direct HTTP requests using clj-http instead of using blend4j (#2)

* Replace blend4j calls with direct API calls with http-kit

* Use clj-http instead of http-kit

* Update

* Changed namespace to org.galaxyproject.clj-blend

* Changed namespace to org.galaxyproject.clj-blend

* Fix namespaces

* Organizing namespaces

* Add more users methods

* Reorganize histories

* update users

* Update user namespace

* Work on downloading history contents

* Added simple test for users namespace

* Remove core ns test and append /api/ to GALAXY_URL when constructing client

* Remove unused reloaded.repl functions

* Remove references to blend4j from README

Author: dfornika

README.md

@@ -1,23 +1,15 @@
 # clj-blend
 
-Clojure library for interacting with Galaxy, CloudMan, and BioCloudCentral. This
-builds on [blend4j][0] with lots of help from [blend][1]. Provides high level
-functionality on top of blend4j, with a focus on smooth interaction with Galaxy.
-
-[0]: https://github.com/jmchilton/blend4j
-[1]: https://github.com/afgane/blend
+Clojure library for interacting with the Galaxy bioinformatics workflow platform.
 
 ## Usage
 
-Requires Java 1.6 or better and [Leiningen 2.x][u1].
+Requires Java 8 or better and [Leiningen 2.x][u1].
 
     $ lein repl
-    > (require '[blend.galaxy.core :as galaxy])
+    > (require '[org.galaxyproject.clj-blend.galaxy.core :as galaxy])
     > (def c (galaxy/get-client "https://main.g2.bx.psu.edu/" "your-api-key"))
-    > (def ds (galaxy/get-datasets-by-type c :bed))
-    > (galaxy/download-dataset c (first ds) "/where/to/put/your/file.bed")
-    > (galaxy/upload-to-history c "http://www.yoursite.com/data" :hg19 :vcf)
-    
+    > (def user (galaxy/get-user-info c))
 
 [u1]: https://github.com/technomancy/leiningen
 

project.clj

@@ -1,8 +1,11 @@
-(defproject clj-blend "0.1.1-SNAPSHOT"
-  :description "Clojure library for interacting with Galaxy, CloudMan, and BioCloudCentral, built on blend4j"
+(defproject clj-blend "0.2.0-SNAPSHOT"
+  :description "Clojure library for interacting with the Galaxy Bioinformatics Workflow Platform"
   :url "http://github.com/chapmanb/clj-blend"
   :license {:name "MIT"
             :url "http://www.opensource.org/licenses/mit-license.html"}
-  :dependencies [[org.clojure/clojure "1.4.0"]
-                 [fs "1.3.2"]
-                 [com.github.jmchilton.blend4j/blend4j "0.1-alpha-1"]])
+  :dependencies [[org.clojure/clojure "1.10.0"]
+                 [clj-http "3.9.1"]
+                 [org.clojure/data.json "0.2.6"]
+                 [org.clojure/data.codec "0.1.1"]
+                 [fs "1.3.2"]]
+  :profiles {:dev {:dependencies [[reloaded.repl "0.2.4"]]}})

src/blend/galaxy/core.clj

@@ -0,0 +1,13 @@
+(ns org.galaxyproject.clj-blend.auth
+  "Galaxy Authentication."
+  (:require [clj-http.client :as client]
+            [clojure.data.json :as json]
+            [org.galaxyproject.clj-blend.util :as util]))
+
+(defn authenticate
+  [server user]
+  (let [b64 (util/b64-encode-str (str (:email user) ":" (:password user)))]
+    (json/read-str
+     (:body (client/get (str (:api-root server) "authenticate/baseauth")
+                        {:headers {"Authorization" (str "Basic " b64)}}))
+     :key-fn util/key-fn)))

src/blend/galaxy/histories.clj

@@ -0,0 +1,33 @@
+(ns org.galaxyproject.clj-blend.core
+  "Top level Galaxy interaction"
+  (:require [clj-http.client :as client]
+            [org.galaxyproject.clj-blend.users :as users]
+            [org.galaxyproject.clj-blend.histories :as histories]
+            [org.galaxyproject.clj-blend.tools :as tools]))
+
+
+(defn authenticate
+  [server user]
+  (client/get (str (:api-root server) "authenticate/baseauth")
+              :headers {"Authorization" (str "Basic " )}))
+
+
+(defn get-client
+  [galaxy-url api-key]
+  {:url (str galaxy-url "/api/") :api-key api-key})
+
+(def get-user-info users/get-current-user)
+
+(defn list-histories
+  [client]
+  [(histories/get-history-most-recently-used client)])
+
+(def get-history-contents-by-type histories/get-history-contents-by-type)
+(def get-history-contents-by-id histories/get-history-contents-by-id)
+
+(def download-history-contents histories/download-history-contents)
+(def upload-to-history tools/upload-to-history)
+
+(comment
+  (def client (get-client "http://localhost:8080" "admin"))
+  )

src/blend/galaxy/tools.clj

@@ -0,0 +1,97 @@
+(ns org.galaxyproject.clj-blend.histories
+  "Retrieve Galaxy history information."
+  (:use [clojure.java.io])
+  (:require [clojure.string :as string]
+            [clj-http.client :as client]
+            [clojure.data.json :as json]
+            [org.galaxyproject.clj-blend.util :as util]
+            [fs.core :as fs]))
+
+(defn get-histories
+  [client]
+  (json/read-str
+   (:body (client/get (str (client :url) "histories")
+                      {:headers {"x-api-key" (client :api-key)}}))
+   :key-fn util/key-fn))
+
+(defn get-history-most-recently-used
+  [client]
+  (json/read-str
+   (:body (client/get (str (client :url) "histories/most_recently_used")
+                      {:headers {"x-api-key" (client :api-key)}}))
+   :key-fn util/key-fn))
+
+(defn get-history-by-id
+  [client history-id]
+  (json/read-str
+   (:body (client/get (str (client :url) "histories/" history-id)
+                      {:headers {"x-api-key" (client :api-key)}}))
+   :key-fn util/key-fn))
+
+(defn create-history
+  [client history]
+  (json/read-str
+   (:body (client/post (str (client :url) "histories")
+                       {:headers {"x-api-key" (client :api-key)}
+                        :content-type :json
+                        :body (json/write-str history)}))
+   :key-fn util/key-fn))
+
+(defn delete-history
+  [client history-id]
+  (json/read-str
+   (:body (client/delete (str (client :url) "histories/" history-id)
+                         {:headers {"x-api-key" (client :api-key)}}))
+   :key-fn util/key-fn))
+
+(defn get-history-contents
+  "Retrieve history datasets, flattened into Clojure maps."
+  [client history-id]
+  (json/read-str
+   (:body (client/get (str (client :url) "histories/" history-id "/contents")
+              {:headers {"x-api-key" (client :api-key)}}))
+   :key-fn util/key-fn))
+
+(defn get-history-contents-by-id
+  "Retrieve a history dataset converted into a clojure map."
+  [client history-id content-id]
+  (json/read-str
+   (:body (client/get (str (client :url) "histories/" history-id "/contents/" content-id)
+              {:headers {"x-api-key" (client :api-key)}}))
+   :key-fn util/key-fn))
+
+(defn get-history-status
+  [client history-id]
+  (select-keys (get-history-by-id client history-id) [:state :state-details]))
+
+(defn- is-ftype?
+  "Check if a dataset is the given filetype, cleanly handling keywords"
+  [ftype dataset]
+  (= (keyword ftype)
+     (keyword (:data-type dataset))))
+
+(defn get-history-contents
+  [client history-id]
+  (json/read-str
+   (:body (client/get (str (client :url) "histories/" history-id "/contents")
+                      {:headers {"x-api-key" (client :api-key)}}))
+   :key-fn util/key-fn))
+
+(defn get-history-contents-by-id
+  [client history-id content-id]
+  (json/read-str
+   (:body (client/get (str (client :url) "histories/" history-id "/contents/" content-id)
+                      {:headers {"x-api-key" (client :api-key)}}))
+   :key-fn util/key-fn))
+
+(defn get-history-contents-by-type
+  "Retrieve datasets from the current active history by filetype."
+  [client history-id ftype]
+  (filter (partial is-ftype? ftype)
+          (get-history-contents client history-id)))
+
+(defn download-history-contents
+  [client history-id content-id download-path]
+  (spit download-path
+        (:body (client/get (str (client :url) "histories/" history-id "/contents/" content-id "/display")
+                           {:headers {"x-api-key" (client :api-key)}}))))

src/blend/galaxy/users.clj

@@ -0,0 +1,32 @@
+(ns org.galaxyproject.clj-blend.tools
+  "Run Galaxy tools through the remote API"
+  (:require [clj-http.client :as client]
+            [clojure.data.json :as json]
+            [clojure.string :as string]
+            [org.galaxyproject.clj-blend.histories :as histories]
+            [org.galaxyproject.clj-blend.util :as util]))
+
+(defn list-tools
+  [client]
+  (json/read-str
+   (:body (client/get (str (client :url) "tools")
+              {:headers {"x-api-key" (client :api-key)}}))
+   :key-fn util/key-fn))
+
+(defn run-tool
+  "Run a remote tool on Galaxy server"
+  [client tool-id params & {:keys [history-id]}]
+  (json/read-str
+   (:body (client/post (str (client :url) "tools")
+              {:headers {"x-api-key" (client :api-key)}}))
+   :key-fn util/key-fn))
+
+(defn upload-to-history
+  "Upload a file via URL to a Galaxy history, defaulting to the current."
+  [client file-url dbkey ftype & {:keys [history-id display-name]}]
+  (run-tool client "upload1"
+            {:file-type (name ftype)
+             :dbkey (name dbkey)
+             "files_0|url_paste" file-url
+             "files_0|NAME" (or display-name (last (string/split file-url #"/")))}
+            :history-id history-id))