[GH-1641] WFL Release v0.18.0

CHANGELOG.md

@@ -1,3 +1,11 @@
+# Release 0.18.0
+- [GH-1623] workloads/update-workload! should define own transactions ([#597](https://github.com/broadinstitute/wfl/pull/597))
+- [GH-1640] Broken Terra Submission links in completed workflow Slack messages ([#598](https://github.com/broadinstitute/wfl/pull/598))
+- [GH-1639] Pin jinja2 version for mkdocks compatibility ([#596](https://github.com/broadinstitute/wfl/pull/596))
+- [GH-1433] No TDR temporary snapshots in tests ([#595](https://github.com/broadinstitute/wfl/pull/595))
+- [GH-1619] Add workload info to sink logs ([#594](https://github.com/broadinstitute/wfl/pull/594))
+- [GH-1638] Disable link unfurling when Slacking watchers ([#593](https://github.com/broadinstitute/wfl/pull/593))
+
 # Release 0.17.0
 - [GH-1592] [GH-1635] Notify Slack watchers on Terra submission creation ([#591](https://github.com/broadinstitute/wfl/pull/591))
 - [GH-1593] Notify Slack watchers on failed TDR snapshot jobs ([#590](https://github.com/broadinstitute/wfl/pull/590))
@@ -410,4 +418,4 @@
 - [GH-1013] Item Nesting V2 ([#188](https://github.com/broadinstitute/wfl/pull/188))
 - [GH-1034] Fix reference_fasta function ([#194](https://github.com/broadinstitute/wfl/pull/194))
 - [GH-771] WGS updates ([#191](https://github.com/broadinstitute/wfl/pull/191))
-- [GH-819] External Exome Reprocessing ([#139](https://github.com/broadinstitute/wfl/pull/139))
+- [GH-819] External Exome Reprocessing ([#139](https://github.com/broadinstitute/wfl/pull/139))

api/src/wfl/api/workloads.clj

@@ -27,8 +27,8 @@
   (fn [_transaction workload] (:pipeline workload)))
 
 (defmulti update-workload!
-  "(transaction workload) -> workload"
-  (fn [_transaction workload] (:pipeline workload)))
+  "workload-record -> workload"
+  :pipeline)
 
 (defmulti workflows
   "Use db `transaction` to return the workflows managed by the `workload`."
@@ -148,10 +148,10 @@
 
 (defmethod update-workload!
   :default
-  [_ {:keys [pipeline] :as workload}]
+  [{:keys [pipeline] :as workload-record}]
   (throw
    (ex-info "Failed to update workload - no such pipeline"
-            {:workload workload
+            {:workload workload-record
              :pipeline pipeline
              :type     ::invalid-pipeline})))
 

api/src/wfl/executor.clj

@@ -299,7 +299,7 @@
         workflow-link   (-> workflow
                             firecloud/workflow-url
                             (slack/link workflow))
-        submission-link (-> workspace
+        submission-link (-> submission
                             (firecloud/submission-url workspace)
                             (slack/link submission))]
     (str/join \newline

api/src/wfl/module/aou.clj

@@ -314,13 +314,18 @@
 
 (defmethod workloads/update-workload!
   pipeline
-  [tx {:keys [started finished] :as workload}]
-  (letfn [(update! [{:keys [id] :as workload}]
-            (batch/update-workflow-statuses! tx workload)
-            (when (:stopped workload)
-              (batch/update-workload-status! tx workload))
-            (workloads/load-workload-for-id tx id))]
-    (if (and started (not finished)) (update! workload) workload)))
+  [{:keys [id started stopped finished] :as _workload-record}]
+  (jdbc/with-db-transaction [tx (postgres/wfl-db-config)]
+    (letfn [(load-workload []
+              (workloads/load-workload-for-id tx id))
+            (update!       [workload]
+              (batch/update-workflow-statuses! tx workload)
+              (when stopped
+                (batch/update-workload-status! tx workload))
+              (load-workload))]
+      (if (and started (not finished))
+        (update! (load-workload))
+        (load-workload)))))
 
 (defoverload workloads/workflows            pipeline aou-workflows)
 (defoverload workloads/workflows-by-filters pipeline aou-workflows-by-filters)

api/src/wfl/module/batch.clj

@@ -184,13 +184,18 @@
          (mapcat submit-batch!))))
 
 (defn update-workload!
-  "Use transaction TX to batch-update WORKLOAD statuses."
-  [tx {:keys [started finished] :as workload}]
-  (letfn [(update! [{:keys [id] :as workload}]
-            (batch-update-workflow-statuses! tx workload)
-            (update-workload-status! tx workload)
-            (workloads/load-workload-for-id tx id))]
-    (if (and started (not finished)) (update! workload) workload)))
+  "Batch-update `workload-record` statuses."
+  [{:keys [id started finished] :as _workload-record}]
+  (jdbc/with-db-transaction [tx (postgres/wfl-db-config)]
+    (letfn [(load-workload []
+              (workloads/load-workload-for-id tx id))
+            (update!       [workload]
+              (batch-update-workflow-statuses! tx workload)
+              (update-workload-status! tx workload)
+              (load-workload))]
+      (if (and started (not finished))
+        (update! (load-workload))
+        (load-workload)))))
 
 (defn stop-workload!
   "Use transaction TX to stop the WORKLOAD."

api/src/wfl/module/sg.clj

@@ -1,8 +1,8 @@
 (ns wfl.module.sg
   "Handle Somatic Genomes."
   (:require [clojure.data.json          :as json]
-            [clojure.spec.alpha         :as s]
             [clojure.set                :as set]
+            [clojure.spec.alpha         :as s]
             [clojure.string             :as str]
             [wfl.api.workloads          :as workloads :refer [defoverload]]
             [wfl.jdbc                   :as jdbc]
@@ -13,6 +13,7 @@
             [wfl.service.clio           :as clio]
             [wfl.service.cromwell       :as cromwell]
             [wfl.service.google.storage :as gcs]
+            [wfl.service.postgres       :as postgres]
             [wfl.util                   :as util]
             [wfl.wfl                    :as wfl])
   (:import [java.time OffsetDateTime]))
@@ -210,19 +211,22 @@
   (run! (partial register-workflow-in-clio workload output) workflows))
 
 (defn update-sg-workload!
-  "Use transaction `tx` to batch-update `workload` statuses."
-  [tx {:keys [started finished] :as workload}]
-  (letfn [(update! [{:keys [id] :as workload}]
-            (batch/batch-update-workflow-statuses! tx workload)
-            (batch/update-workload-status! tx workload)
-            (workloads/load-workload-for-id tx id))]
-    (if (and started (not finished))
-      (let [workload' (update! workload)]
-        (when (:finished workload')
-          (register-workload-in-clio workload'
-                                     (workloads/workflows tx workload')))
-        workload')
-      workload)))
+  "Batch-update `workload-record` statuses."
+  [{:keys [id started finished] :as _workload-record}]
+  (jdbc/with-db-transaction [tx (postgres/wfl-db-config)]
+    (letfn [(load-workload []
+              (workloads/load-workload-for-id tx id))
+            (update!       [workload]
+              (batch/batch-update-workflow-statuses! tx workload)
+              (batch/update-workload-status! tx workload)
+              (load-workload))]
+      (if (and started (not finished))
+        (let [{:keys [finished] :as updated} (update! (load-workload))]
+          (when finished
+            (register-workload-in-clio updated
+                                       (workloads/workflows tx updated)))
+          updated)
+        (load-workload)))))
 
 (defoverload workloads/create-workload!     pipeline create-sg-workload!)
 (defoverload workloads/start-workload!      pipeline start-sg-workload!)

api/src/wfl/module/staged.clj

@@ -125,18 +125,25 @@
     (if-not started (start workload (utc-now)) workload)))
 
 (defn ^:private update-staged-workload
-  "Use transaction `tx` to update `workload` statuses."
-  [tx {:keys [started finished] :as workload}]
-  (letfn [(update! [{:keys [id source executor sink] :as workload} now]
+  "Update `workload-record` stages."
+  [{:keys [id started finished] :as _workload-record}]
+  (letfn [(load-workload [tx]
+            (workloads/load-workload-for-id tx id))
+          (update! [{:keys [source executor sink] :as workload} now]
             (-> workload
                 (source/update-source!)
                 (executor/update-executor!)
                 (sink/update-sink!))
-            (patch-workload tx workload {:updated now})
-            (when (every? stage/done? [source executor sink])
-              (patch-workload tx workload {:finished now}))
-            (workloads/load-workload-for-id tx id))]
-    (if (and started (not finished)) (update! workload (utc-now)) workload)))
+            (jdbc/with-db-transaction [tx (postgres/wfl-db-config)]
+              (patch-workload tx workload {:updated now})
+              (when (every? stage/done? [source executor sink])
+                (patch-workload tx workload {:finished now}))
+              (load-workload tx)))]
+    (let [workload (jdbc/with-db-transaction [tx (postgres/wfl-db-config)]
+                     (load-workload tx))]
+      (if (and started (not finished))
+        (update! workload (utc-now))
+        workload))))
 
 (defn ^:private stop-staged-workload
   "Use transaction `tx` to stop the `workload` looking for new data."

api/src/wfl/server.clj

@@ -79,41 +79,39 @@
       (wrap-json-response {:pretty true})))
 
 (defn ^:private do-update!
-  "Update `_workload` in a database transaction. "
-  [{:keys [id] :as _workload}]
-  (jdbc/with-db-transaction [tx (postgres/wfl-db-config)]
-    (let [workload (workloads/load-workload-for-id tx id)]
-      (try
-        (workloads/update-workload! tx workload)
-        (catch UserException e
-          (log/warning "Error updating workload"
-                       :workload  (workloads/to-log workload)
-                       :exception e)
-          (slack/notify-watchers workload (.getMessage e)))))))
+  "Update `workload-record` and notify watchers on UserException."
+  [workload-record]
+  (try
+    (workloads/update-workload! workload-record)
+    (catch UserException e
+      (log/warning "UserException while updating workload"
+                   :workload  (workloads/to-log workload-record)
+                   :exception e)
+      (slack/notify-watchers workload-record (.getMessage e)))))
 
 (defn ^:private try-update
-  "Try to update the workflows in `workload` with a backstop."
-  [workload]
+  "Try to update `workload-record` with backstop."
+  [workload-record]
   (try
-    (log/info "Updating workload"
-              :workload (workloads/to-log workload))
-    (do-update! workload)
+    (log/info "Updating workload" :workload (workloads/to-log workload-record))
+    (do-update! workload-record)
     (catch Throwable t
       (log/error "Failed to update workload"
-                 :workload  (workloads/to-log workload)
+                 :workload  (workloads/to-log workload-record)
                  :throwable t))))
 
 (defn ^:private update-workloads
   "Update the active workflows in the active workloads."
   []
   (try
     (log/info "Finding workloads to update...")
-    (run! try-update
-          (jdbc/with-db-transaction [tx (postgres/wfl-db-config)]
-            (jdbc/query tx (str/join \space
-                                     ["SELECT * FROM workload"
-                                      "WHERE started IS NOT NULL"
-                                      "AND finished IS NULL"]))))
+    (let [query   (str/join \space
+                            ["SELECT * FROM workload"
+                             "WHERE started IS NOT NULL"
+                             "AND finished IS NULL"])
+          records (jdbc/with-db-transaction [tx (postgres/wfl-db-config)]
+                    (jdbc/query tx query))]
+      (run! try-update records))
     (catch Throwable t
       (log/error "Failed to update workloads" :throwable t))))
 

api/src/wfl/service/slack.clj

@@ -32,10 +32,13 @@
 ;; https://api.slack.com/methods/chat.postMessage#errors
 ;;
 (defn ^:private post-message
-  "Post `message` to `channel`."
+  "Post `message` to `channel` with link unfurling disabled."
   [channel message]
   (let [headers {:Authorization (str "Bearer " (env/getenv "WFL_SLACK_TOKEN"))}
-        body    (json/write-str {:channel channel :text message})]
+        body    (json/write-str {:channel      channel
+                                 :text         message
+                                 :unfurl_links false
+                                 :unfurl_media false})]
     (-> "https://slack.com/api/chat.postMessage"
         (http/post {:headers      headers
                     :content-type :application/json

api/src/wfl/sink.clj

@@ -6,7 +6,7 @@
             [clojure.set                :as set]
             [clojure.spec.alpha         :as s]
             [clojure.string             :as str]
-            [wfl.api.workloads          :refer [defoverload]]
+            [wfl.api.workloads          :as workloads :refer [defoverload]]
             [wfl.environment            :as env]
             [wfl.jdbc                   :as jdbc]
             [wfl.log                    :as log]
@@ -199,21 +199,20 @@
   "Write outputs from consumable `executor` workflows
    to `entityType` table in `workspace`."
   [{executor :executor
-    {:keys [fromOutputs workspace entityType details] :as sink} :sink :as _workload}]
+    {:keys [fromOutputs workspace entityType details] :as sink} :sink :as workload}]
   (when-let [[_ {:keys [uuid] :as workflow}] (stage/peek-queue executor)]
-    (log/debug {:action     "Attempting to sink workflow outputs"
-                :workflow   uuid
-                :entityType entityType})
     (let [entityName (throw-or-entity-name-from-workflow workflow sink)
           entity     [entityType entityName]
           attributes (terra-workspace-sink-to-attributes workflow fromOutputs)]
       (when (entity-exists? workspace entity)
         (firecloud/delete-entities workspace [entity]))
       (rawls/batch-upsert workspace [(conj entity attributes)])
       (stage/pop-queue! executor)
-      (log/debug {:action   "Sunk workflow outputs"
-                  :workflow uuid
-                  :entity   entity})
+      (log/info "Sunk workflow outputs to Terra workspace"
+                :workload   (workloads/to-log workload)
+                :workflow   uuid
+                :workspace  workspace
+                :entityType entityType)
       (jdbc/with-db-transaction [tx (postgres/wfl-db-config)]
         (jdbc/insert! tx details {:entity   entityName
                                   :updated  (util/utc-now)
@@ -421,7 +420,7 @@
 (defn ^:private update-datarepo-sink
   "Pull a workflow off the `_workload`'s `executor` queue and write its
   outputs as new rows in a TDR dataset table."
-  [{:keys [executor sink uuid labels] :as _workload}]
+  [{:keys [executor sink] :as workload}]
   (when-let [[_ workflow] (stage/peek-queue executor)]
     (start-ingesting-outputs sink workflow)
     (stage/pop-queue! executor))
@@ -430,10 +429,12 @@
     (try
       (let [result (datarepo/job-result job)]
         (if (< (:bad_row_count result) 1)
-          (log/info "Sunk workflow outputs to dataset"
-                    :labels labels :workload uuid)
-          (throw (UserException. "Row failed to sink to dataset"
-                                 {:job job :workflow workflow}))))
+          (log/info "Sunk all workflow outputs to TDR dataset"
+                    :workload (workloads/to-log workload)
+                    :job-id   job
+                    :workflow workflow)
+          (throw (UserException. "Row failed to sink to TDR dataset"
+                                 {:job-id job :workflow workflow}))))
       (finally
         (pop-job-queue! sink record)))))
 

api/test/wfl/integration/datarepo_test.clj

@@ -88,17 +88,18 @@
               (is (== 1 (count row-ids))
                   "Single input row should have been written to the dataset")
               (testing "creating snapshot after completed ingest"
-                (fixtures/with-temporary-snapshot
-                  (snapshots/unique-snapshot-request tdr-profile
-                                                     dataset
-                                                     table-name
-                                                     row-ids)
-                  #(let [snapshot        (datarepo/snapshot %)
-                         expected-prefix (str (:name dataset) "_" table-name)]
-                     (is (= % (:id snapshot)))
-                     (is (str/starts-with? (:name snapshot) expected-prefix)
-                         (str "Snapshot name should start with "
-                              "dataset name and table name"))))))))))))
+                (let [request         (snapshots/unique-snapshot-request
+                                       tdr-profile
+                                       dataset
+                                       table-name
+                                       row-ids)
+                      snapshot-id     (datarepo/create-snapshot request)
+                      snapshot        (datarepo/snapshot snapshot-id)
+                      expected-prefix (str (:name dataset) "_" table-name)]
+                  (is (= snapshot-id (:id snapshot)))
+                  (is (str/starts-with? (:name snapshot) expected-prefix)
+                      (str "Snapshot name should start with "
+                           "dataset name and table name")))))))))))
 
 (deftest test-flattened-query-result
   (let [samplesheets (-> (datarepo/snapshot (:id testing-snapshot))

api/test/wfl/tools/fixtures.clj

@@ -193,18 +193,6 @@
    datarepo/delete-snapshots-then-dataset
    f))
 
-;; Recommendation: only call this within a temporary dataset.
-;; If calling within a fixed dataset, running the same test concurrently
-;; may fail due to exclusive dataset locking on snapshot deletion.
-;;
-(defn with-temporary-snapshot
-  "Create a temporary Terra Data Repository Snapshot with `snapshot-request`"
-  [snapshot-request f]
-  (util/bracket
-   #(datarepo/create-snapshot snapshot-request)
-   datarepo/delete-snapshot
-   f))
-
 (defn with-temporary-workspace
   "Create and use a temporary Terra Workspace."
   ([workspace-prefix group f]

api/test/wfl/tools/workloads.clj

@@ -285,7 +285,7 @@
 (def start-workload!      (evalT wfl.api.workloads/start-workload!))
 (def stop-workload!       (evalT wfl.api.workloads/stop-workload!))
 (def execute-workload!    (evalT wfl.api.workloads/execute-workload!))
-(def update-workload!     (evalT wfl.api.workloads/update-workload!))
+(def update-workload!     wfl.api.workloads/update-workload!)
 (def workflows            (evalT wfl.api.workloads/workflows))
 (def workflows-by-filters (evalT wfl.api.workloads/workflows-by-filters))
 

docs/requirements.txt

@@ -1,3 +1,4 @@
 pymdown-extensions==8.0.1
 markdown-include==0.6.0
 mkdocs-material==7.2.4
+jinja2==3.0.3

version

@@ -1 +1 @@
-0.17.0
+0.18.0