[GH-1172] Bulk Ingest Workflow Outputs

api/src/wfl/mime_type.clj

@@ -1,17 +1,29 @@
 (ns wfl.mime-type
   (:require [clojure.string :as str]
-            [ring.util.mime-type :as mime-type]))
+            [ring.util.mime-type :as mime-type]
+            [wfl.util :as util]))
 
 (def ^:private mime-types
   "mime-types for file extensions commonly used in computational biology."
-  (let [bio-mimes {"bam"   "application/octet-stream"
-                   "cram"  "application/octet-stream"
-                   "fasta" "application/octet-stream"
-                   "vcf"   "text/plain"}]
-    (merge mime-type/default-mime-types bio-mimes)))
+  (let [extensions
+        {"bam"     "application/octet-stream"
+         "cram"    "application/octet-stream"
+         "fasta"   "application/octet-stream"
+         "genbank" "application/octet-stream"
+         "ready"   "text/plain"
+         "tsv"     "text/tab-separated-values"
+         "vcf"     "text/plain"}]
+    (merge mime-type/default-mime-types extensions)))
+
+;; visible for testing
+(defn ext-mime-type-no-default
+  "Look up the mime-type of the filename by file extension."
+  [filename]
+  (loop [filename (util/basename filename)]
+    (if-let [ext (util/extension filename)]
+      (or (mime-types ext) (recur (util/remove-extension filename))))))
 
 (defn ext-mime-type
   "Look up the mime-type of the filename by file extension."
   [filename]
-  (if-let [ext (last (str/split filename #"\."))]
-    (mime-types ext)))
+  (or (ext-mime-type-no-default filename) "application/octet-stream"))

api/src/wfl/service/datarepo.clj

@@ -6,7 +6,9 @@
             [wfl.environment   :as env]
             [wfl.mime-type     :as mime-type]
             [wfl.util          :as util])
-  (:import (java.util.concurrent TimeUnit)))
+  (:import (java.util.concurrent TimeUnit)
+           (java.time OffsetDateTime)
+           (java.sql Timestamp)))
 
 (defn ^:private datarepo-url [& parts]
   (let [url (util/slashify (env/getenv "WFL_TERRA_DATA_REPO_URL"))]
@@ -33,15 +35,38 @@
       util/response-body-json
       :id))
 
+;; While TDR does assign `loadTag`s, they're not always unique - submitting
+;; requests in parallel can cause bad things to happen. Use this to create a
+;; unique `loadTag` instead.
+(defn ^:private new-load-tag []
+  (str (Timestamp/from (.toInstant (OffsetDateTime/now)))))
+
 (defn ingest-file
   "Ingest `source` file as `target` using `dataset-id` and `profile-id`."
   [dataset-id profile-id source target]
   (ingest "files" dataset-id {:description (util/basename source)
-                              :profileId   profile-id
+                              :loadTag     (new-load-tag)
                               :mime_type   (mime-type/ext-mime-type source)
+                              :profileId   profile-id
                               :source_path source
                               :target_path target}))
 
+(defn bulk-ingest
+  "Ingest `source` file as `target` using `dataset-id` and `profile-id`."
+  [dataset-id profile-id source->target]
+  (letfn [(make-file-load [source target]
+            {:description (util/basename source)
+             :mimeType    (mime-type/ext-mime-type source)
+             :sourcePath  source
+             :targetPath  target})]
+    (ingest
+     "files/bulk/array"
+     dataset-id
+     {:profileId          profile-id
+      :loadArray          (map #(apply make-file-load %) source->target)
+      :loadTag            (new-load-tag)
+      :maxFailedFileLoads 0})))
+
 (defn ingest-table
   "Ingest TABLE at PATH to DATASET-ID and return the job ID."
   [dataset-id path table]
@@ -94,20 +119,3 @@
       util/response-body-json
       :id
       poll-job))
-
-(comment
-  (def successful-file-ingest-response
-    {:description     "something derived from file name + extension?"
-     :path            "/zero-test/NA12878_PLUMBING.g.vcf.gz"
-     :directoryDetail nil
-     :collectionId    "f359303e-15d7-4cd8-a4c7-c50499c90252"
-     :fileDetail      {:datasetId "f359303e-15d7-4cd8-a4c7-c50499c90252"
-                       :mimeType  "text/plain"
-                       :accessUrl "gs://broad-jade-dev-data-bucket/f359303e-15d7-4cd8-a4c7-c50499c90252/271cd32c-2e86-4f46-9eb1-f3ddb44a6c1f"}
-     :fileType        "file"
-     :created         "2019-11-26T15:41:06.508Z"
-     :checksums       [{:checksum "591d9cec" :type "crc32c"}
-                       {:checksum "24f38b33c6eac4dd3569e0c4547ced88" :type "md5"}]
-     :size            3073329
-     :fileId          "271cd32c-2e86-4f46-9eb1-f3ddb44a6c1f"}))
-

api/src/wfl/service/google/pubsub.clj

@@ -163,6 +163,17 @@
 
 (defn set-iam-policy
   "Set the IAM policy for the given Pub/Sub `resource` with the specified
+   `policy` bindings. A Pub/Sub `resource` is a topic, a subscription or a
+   snapshot."
+  [resource policy]
+  (http/post
+   (pubsub-url resource ":setIamPolicy")
+   {:headers      (auth/get-auth-header)
+    :content-type :json
+    :body         (json/write-str {:policy policy} :escape-slash false)}))
+
+(defn add-iam-policy
+  "Augment the IAM policy for the given Pub/Sub `resource` with the specified
    role->member bindings. A Pub/Sub `resource` is a topic, a subscription or a
    snapshot.
 
@@ -173,11 +184,8 @@
    role->members - map from a Google Cloud Pub/Sub role to a list of members.
                    See https://cloud.google.com/pubsub/docs/access-control#permissions_and_roles"
   [resource role->members]
-  (letfn [(make-binding [[role members]] {:role role :members members})]
-    (http/post
-     (pubsub-url resource ":setIamPolicy")
-     {:headers      (auth/get-auth-header)
-      :content-type :json
-      :body         (json/write-str
-                     {:policy {:bindings (map make-binding role->members)}}
-                     :escape-slash false)})))
+  (letfn [(make-binding [[role members]] [{:role role :members members}])]
+    (set-iam-policy
+     resource
+     (-> (get-iam-policy resource)
+         (update :bindings #(concat % (map make-binding role->members)))))))

api/src/wfl/service/google/storage.clj

@@ -67,16 +67,20 @@
   (gs-url bucket name))
 
 (defn iam
-  "Return IamPolicy response for URL."
-  [url]
-  (let [[bucket _] (parse-gs-url url)]
-    (-> {:method       :get             ; :debug true :debug-body true
-         :url          (str bucket-url bucket "/iam")
-         ;; :query-params {:project project :prefix prefix}
-         :content-type :application/json
-         :headers      (auth/get-auth-header)}
-        http/request :body
-        (json/read-str :key-fn keyword))))
+  "Return IamPolicy response for `bucket`."
+  [bucket]
+  (-> (str bucket-url bucket "/iam")
+      (http/get {:headers (auth/get-auth-header)})
+      util/response-body-json))
+
+(defn set-iam
+  "Set IamPolicy `bucket` to `policy`."
+  [bucket policy]
+  (-> (str bucket-url bucket "/iam")
+      (http/put {:headers      (auth/get-auth-header)
+                 :content-type :application/json
+                 :body         (json/write-str policy :escape-slash false)})
+      util/response-body-json))
 
 (defn list-buckets
   "The buckets in PROJECT named with optional PREFIX."
@@ -242,6 +246,13 @@
   ([email url]
    (apply add-object-reader email (parse-gs-url url))))
 
+(defn add-storage-object-viewer
+  "Give service-account `email` the \"Storage Object Viewer\" role in `bucket`."
+  [email bucket]
+  (let [new-binding [{:role   "roles/storage.objectViewer"
+                      :members [(str "serviceAccount:" email)]}]]
+    (set-iam bucket (update (iam bucket) :bindings cons new-binding))))
+
 (defn patch-bucket!
   "Patch BUCKET in PROJECT with METADATA."
   [project bucket metadata]

api/src/wfl/util.clj

@@ -34,15 +34,11 @@
 (defn parse-int [s] (do-or-nil (Integer/parseInt s)))
 (defn parse-boolean [s] (do-or-nil (Boolean/valueOf s)))
 
-(defn parse-json [^String object]
+(defn parse-json
   "Parse json `object` into keyword->object map recursively"
+  [^String object]
   (json/read-str object :key-fn keyword))
 
-(defn parse-json
-  "Parse the json string STR into a keyword-string map"
-  [str]
-  (json/read-str str :key-fn keyword))
-
 (defn response-body-json [response]
   "Return the :body of the http `response` as JSON"
   (-> response :body (or "null") parse-json))
@@ -82,6 +78,12 @@
     (subs filename 0 idx)
     filename))
 
+(defn extension
+  "Return the (last) file extension from `filename`, if one exists."
+  [filename]
+  (if-let [idx (str/last-index-of filename ".")]
+    (subs filename (inc idx) (count filename))))
+
 (defn basename
   "Strip directory from `filename`."
   [filename]