[GH-1035] Add terra module to WFL

api/src/wfl/service/terra.clj

@@ -0,0 +1,43 @@
+(ns wfl.service.terra
+  "Analyze data in Terra using the Firecloud/Terra API."
+  (:require [clojure.data.json :as json]
+            [clojure.string :as str]
+            [clj-http.client :as http]
+            [wfl.once :as once]
+            [wfl.util :as util]))
+
+(defn workspace-api-url
+  [terra-url workspace-namespace workspace-name]
+  (str terra-url "/api/workspaces/" workspace-namespace "/" workspace-name))
+
+(defn create-submission
+  "Submit samples in a workspace for analysis with a method configuration in Terra."
+  [terra-url workspace-namespace workspace-name method-configuration-name
+   method-configuration-namespace entity-type entity-name]
+  (let [workspace-url (workspace-api-url terra-url workspace-namespace workspace-name)
+        submission-url (str workspace-url "/submissions")]
+    (->
+      (http/post
+        submission-url
+        {:content-type :application/json
+         :headers   (once/get-auth-header)
+         :body      (json/write-str
+                      {
+                       :methodConfigurationNamespace method-configuration-namespace
+                       :methodConfigurationName method-configuration-name
+                       :entityType entity-type
+                       :entityName entity-name
+                       :useCallCache true
+                       } :escape-slash false)})
+      :body
+      (util/parse-json)
+      :submissionId)))
+
+(defn get-submission
+  "Get information about a Terra Cromwell submission."
+  [terra-url workspace-namespace workspace-name submission-id]
+  (let [workspace-url (workspace-api-url terra-url workspace-namespace workspace-name)
+        submission-url (str workspace-url "/submissions/" submission-id)
+        response (http/get submission-url {:headers (once/get-auth-header)})]
+      (util/parse-json (:body response))))
+

api/src/wfl/util.clj

@@ -42,6 +42,11 @@ vault.client.http/http-client                               ; Keep :clint eastwo
   `(try (do ~@body)
         (catch Exception x#)))
 
+(defn parse-json
+  "Parse the json string STR into a keyword-string map"
+  [str]
+  (json/read-str str :key-fn keyword))
+
 (defn slurp-json
   "Nil or the JSON in FILE."
   [file]

api/test/wfl/integration/terra_test.clj

@@ -0,0 +1,34 @@
+(ns wfl.integration.terra-test
+  (:require [clojure.test          :refer [deftest is testing]]
+            [wfl.service.terra :as terra]
+            [wfl.tools.fixtures :refer [with-temporary-gcs-folder]]))
+
+(def terra-url
+  "https://firecloud-orchestration.dsde-dev.broadinstitute.org")
+
+(def workspace-namespace
+  "general-dev-billing-account")
+
+(def workspace-name
+  "wfl-integration")
+
+(def method-configuration-name
+  "ExternalWholeGenomeReprocessing")
+
+(def method-configuration-namespace
+  "general-dev-billing-account")
+
+(def entity-type
+  "sample")
+
+(def entity-name
+  "NA12878_PLUMBING")
+
+(deftest test-terra-submission
+  (testing "A workflow is created for the entity"
+    (let [submission-id (terra/create-submission terra-url workspace-namespace workspace-name
+                                                method-configuration-name method-configuration-namespace
+                                                entity-type entity-name)
+          submission (terra/get-submission terra-url workspace-namespace workspace-name submission-id)
+          workflow (first (:workflows submission))]
+      (is (= entity-name (get-in workflow [:workflowEntity :entityName]))))))