Checkpoint back to endpoints/userinfo.

api/test/wfl/integration/modules/aou_test.clj

@@ -4,6 +4,7 @@
             [wfl.api.spec]
             [wfl.util :as util]
             [wfl.module.aou :as aou]
+            [wfl.tools.endpoints :as endpoints]
             [wfl.tools.fixtures :as fixtures]
             [wfl.tools.workloads :as workloads]
             [wfl.service.postgres :as postgres]
@@ -18,7 +19,7 @@
 
 (defn ^:private make-aou-workload-request []
   (-> (workloads/aou-workload-request (UUID/randomUUID))
-      (assoc :creator (:email @workloads/userinfo))))
+      (assoc :creator (:email @endpoints/userinfo))))
 
 (defn ^:private inc-version [sample]
   (update sample :analysis_version_number inc))

api/test/wfl/integration/modules/arrays_test.clj

@@ -2,6 +2,7 @@
   (:require [clojure.test :refer [testing is deftest use-fixtures]]
             [wfl.api.spec]
             [wfl.service.terra :as terra]
+            [wfl.tools.endpoints :as endpoints]
             [wfl.tools.fixtures :as fixtures]
             [wfl.tools.workloads :as workloads])
   (:import (java.util UUID)))
@@ -16,7 +17,7 @@
 
 (defn ^:private make-arrays-workload-request []
   (-> (workloads/arrays-workload-request (UUID/randomUUID))
-      (assoc :creator (:email @workloads/userinfo))))
+      (assoc :creator (:email @endpoints/userinfo))))
 
 (defn ^:private check-inputs
   [workflow]

api/test/wfl/integration/modules/copyfile_test.clj

@@ -5,6 +5,7 @@
             [wfl.module.all :as all]
             [wfl.module.copyfile :as copyfile]
             [wfl.service.cromwell :refer [wait-for-workflow-complete submit-workflow]]
+            [wfl.tools.endpoints :as endpoints]
             [wfl.tools.fixtures :as fixtures]
             [wfl.tools.workloads :as workloads]
             [wfl.util :as util])
@@ -15,7 +16,7 @@
 (defn ^:private make-copyfile-workload-request
   [src dst]
   (-> (workloads/copyfile-workload-request src dst)
-      (assoc :creator (:email @workloads/userinfo))))
+      (assoc :creator (:email @endpoints/userinfo))))
 
 (defn ^:private old-create-copyfile-workload! []
   (let [request (make-copyfile-workload-request "gs://fake/input" "gs://fake/output")]

api/test/wfl/integration/modules/sg_test.clj

@@ -5,6 +5,7 @@
             [wfl.module.sg :as sg]
             [wfl.service.clio :as clio]
             [wfl.service.cromwell :as cromwell]
+            [wfl.tools.endpoints :as endpoints]
             [wfl.tools.fixtures :as fixtures]
             [wfl.tools.workloads :as workloads]
             [wfl.util :as util :refer [absent?]])
@@ -38,7 +39,7 @@
       "gs://broad-gotc-dev-storage/temp_references/gdc/dbsnp_144.hg38.vcf.gz.tbi"
       :input_cram
       "gs://broad-gotc-dev-wfl-sg-test-inputs/pipeline/G96830/NA12878/v23/NA12878.cram"}}]
-   :creator (:email @workloads/userinfo)})
+   :creator (:email @endpoints/userinfo)})
 
 (defn mock-submit-workload
   [{:keys [workflows]} _ _ _ _ _]
@@ -109,7 +110,7 @@
                        :output   "gs://broad-gotc-dev-wfl-ptc-test-outputs/sg-test-output/"
                        :pipeline sg/pipeline
                        :project  @workloads/project
-                       :creator  (:email @workloads/userinfo)}
+                       :creator  (:email @endpoints/userinfo)}
                       workloads/execute-workload!
                       workloads/update-workload!)]
     (is (:finished workload))))

api/test/wfl/integration/modules/wgs_test.clj

@@ -1,8 +1,8 @@
 (ns wfl.integration.modules.wgs-test
   (:require [clojure.set :refer [rename-keys]]
             [clojure.test :refer [deftest testing is] :as clj-test]
-            [wfl.service.cromwell :refer [wait-for-workflow-complete
-                                          submit-workflows]]
+            [wfl.service.cromwell :as cromwell]
+            [wfl.tools.endpoints :as endpoints]
             [wfl.tools.fixtures :as fixtures]
             [wfl.tools.workloads :as workloads]
             [wfl.module.wgs :as wgs]
@@ -21,7 +21,7 @@
 (defn ^:private make-wgs-workload-request []
   (-> (UUID/randomUUID)
       workloads/wgs-workload-request
-      (assoc :creator (:email @workloads/userinfo))))
+      (assoc :creator (:email @endpoints/userinfo))))
 
 (defn ^:private strip-prefix [[k v]]
   [(keyword (util/unprefix (str k) ":ExternalWholeGenomeReprocessing.")) v])
@@ -58,7 +58,7 @@
                 :workflows)))))
 
 (deftest test-start-wgs-workload!
-  (with-redefs-fn {#'submit-workflows mock-submit-workflows}
+  (with-redefs-fn {#'cromwell/submit-workflows mock-submit-workflows}
     #(let [workload (-> (make-wgs-workload-request)
                         workloads/create-workload!
                         workloads/start-workload!)]
@@ -115,13 +115,13 @@
                (UUID/randomUUID))
              inputs))]
     (with-redefs-fn
-      {#'submit-workflows verify-inputs}
+      {#'cromwell/submit-workflows verify-inputs}
       #(-> (make-wgs-workload-request)
            (update :items use-input_bam)
            (workloads/execute-workload!)
            (as-> workload
                  (is (:started workload))
-             (run! go! (:workflows workload)))))))
+                 (run! go! (:workflows workload)))))))
 
 (deftest test-submitted-workflow-inputs
   (letfn [(prefixed? [prefix key] (str/starts-with? (str key) (str prefix)))
@@ -137,7 +137,7 @@
                (verify-workflow-inputs (into {} (map strip-prefix in)))
                (UUID/randomUUID))
              inputs))]
-    (with-redefs-fn {#'submit-workflows verify-submitted-inputs}
+    (with-redefs-fn {#'cromwell/submit-workflows verify-submitted-inputs}
       (fn []
         (->
          (make-wgs-workload-request)
@@ -167,7 +167,7 @@
             (let [request (-> (make-wgs-workload-request)
                               (assoc :items [{:inputs {key value}}]))]
               (testing (str "default inputs when given only " key)
-                (with-redefs-fn {#'submit-workflows verify-submitted-inputs}
+                (with-redefs-fn {#'cromwell/submit-workflows verify-submitted-inputs}
                   #(workloads/execute-workload! request)))))]
     (test-with-input :input_bam (:input_cram workloads/wgs-inputs))
     (test-with-input :input_cram (:input_cram workloads/wgs-inputs))))
@@ -182,7 +182,7 @@
               (verify-workflow-options options)
               (is (= defaults (select-keys options (keys defaults))))
               (map (fn [_] (UUID/randomUUID)) inputs)))]
-    (with-redefs-fn {#'submit-workflows verify-submitted-options}
+    (with-redefs-fn {#'cromwell/submit-workflows verify-submitted-options}
       (fn []
         (->
          (make-wgs-workload-request)

api/test/wfl/integration/modules/xx_test.clj

@@ -5,7 +5,9 @@
             [wfl.module.xx :as xx]
             [wfl.module.batch :as batch]
             [wfl.service.cromwell :as cromwell]
+            [wfl.tools.endpoints :as endpoints]
             [wfl.tools.fixtures :as fixtures]
+            [wfl.tools.endpoints :as endpoints]
             [wfl.tools.workloads :as workloads]
             [wfl.util :as util :refer [absent?]])
   (:import (java.time OffsetDateTime)
@@ -16,7 +18,7 @@
 (defn ^:private make-xx-workload-request []
   (-> (UUID/randomUUID)
       workloads/xx-workload-request
-      (assoc :creator (:email @workloads/userinfo))))
+      (assoc :creator (:email @endpoints/userinfo))))
 
 (defn mock-submit-workload [{:keys [workflows]} _ _ _ _ _]
   (let [now       (OffsetDateTime/now)
@@ -78,7 +80,7 @@
                        :output   "gs://broad-gotc-dev-wfl-ptc-test-outputs/xx-test-output/"
                        :pipeline xx/pipeline
                        :project  @workloads/project
-                       :creator  (:email @workloads/userinfo)}
+                       :creator  (:email @endpoints/userinfo)}
                       workloads/execute-workload!
                       workloads/update-workload!)]
     (is (:finished workload))))

api/test/wfl/integration/workloads_test.clj

@@ -2,6 +2,7 @@
   (:require [clojure.test :refer [deftest testing is] :as clj-test]
             [clojure.test :refer :all]
             [wfl.module.copyfile :as copyfile]
+            [wfl.tools.endpoints :as endpoints]
             [wfl.tools.fixtures :as fixtures]
             [wfl.tools.workloads :as workloads]))
 
@@ -10,7 +11,7 @@
 (defn ^:private make-copyfile-workload-request-with-project
   [src dst project]
   (-> (workloads/copyfile-workload-request src dst)
-      (assoc :creator (:email @workloads/userinfo) :project project)))
+      (assoc :creator (:email @endpoints/userinfo) :project project)))
 
 (deftest test-loading-copyfile-workloads-with-project
   (let [upper-project "TEST-PROJECT"

api/test/wfl/system/v1_endpoint_test.clj

@@ -59,7 +59,7 @@
                     (endpoints/create-workload request)]
                 (is uuid "workloads should be been assigned a uuid")
                 (is created "should have a created timestamp")
-                (is (= (:email @workloads/userinfo) creator)
+                (is (= (:email @endpoints/userinfo) creator)
                     "creator inferred from auth token")
                 (is (not started) "hasn't been started in cromwell")
                 (letfn [(included [m] (select-keys m [:pipeline :project]))]
@@ -125,7 +125,7 @@
       (is uuid    "workloads should have a uuid")
       (is created "should have a created timestamp")
       (is started "should have a started timestamp")
-      (is (= (:email @workloads/userinfo) creator)
+      (is (= (:email @endpoints/userinfo) creator)
           "creator inferred from auth token")
       (letfn [(included [m] (select-keys m [:pipeline :project]))]
         (is (= (included request) (included workload))))

api/test/wfl/tools/endpoints.clj

@@ -3,8 +3,12 @@
             [clojure.data.json :as json]
             [wfl.auth :as auth]
             [wfl.environment :as env]
+            [wfl.service.google.storage :as gcs]
             [wfl.util :as util]))
 
+(def userinfo
+  (delay (gcs/userinfo {:headers (auth/get-auth-header)})))
+
 (def ^:private wfl-url
   "The WFL server URL to test."
   (delay (env/getenv "WFL_WFL_URL")))

api/test/wfl/tools/workloads.clj

@@ -22,9 +22,6 @@
 
 (def clio-url (delay (env/getenv "WFL_CLIO_URL")))
 
-(def userinfo
-  (delay (gcs/userinfo {:headers (auth/get-auth-header)})))
-
 (def ^:private git-branch
   (delay (util/shell! "git" "branch" "--show-current")))