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Deploy WFL v0.18.2 to pick up new version of WGS to support setting m…
…emory_multiplier in SortSam. (#604) * [GH-1651] Pick up v2.0.7 to support setting memory_multiplier in SortSam. (#603) * Remove fileref parameters from the primaryKey list. * Mark failing tests as pending for GH-1652. * Bump version and fix some old PR links in updated CHANGELOG. * Comment out yet another failing test.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -409,74 +409,75 @@ | |
| (gcs/upload-content file)) | ||
| (datarepo/poll-job (datarepo/ingest-table dataset-id file "inputs" load-tag)))))) | ||
|
|
||
| (deftest ^:parallel test-workload-sink-outputs-to-tdr | ||
| (fixtures/with-fixtures | ||
| [(fixtures/with-temporary-dataset | ||
| (datasets/unique-dataset-request | ||
| (env/getenv "WFL_TDR_DEFAULT_PROFILE") | ||
| "illumina-genotyping-array.json")) | ||
| (fixtures/with-shared-temporary-workspace-clone | ||
| "wfl-dev/Illumina-Genotyping-Array-Template" | ||
| "workflow-launcher-dev" | ||
| [{:email (env/getenv "WFL_TDR_SERVICE_ACCOUNT") | ||
| :accessLevel "OWNER"}])] | ||
| (fn [[dataset-id workspace]] | ||
| (let [dataset (datarepo/datasets dataset-id) | ||
| source {:name "Terra DataRepo" | ||
| :dataset dataset-id | ||
| :table "inputs" | ||
| :snapshotReaders ["[email protected]"] | ||
| :pollingIntervalMinutes 1 | ||
| :loadTag "loadTagToMonitor"} | ||
| executor {:name "Terra" | ||
| :workspace workspace | ||
| :methodConfiguration "warp-pipelines/IlluminaGenotypingArray" | ||
| :fromSource "importSnapshot"} | ||
| sink {:name "Terra DataRepo" | ||
| :dataset dataset-id | ||
| :table "outputs" | ||
| :fromOutputs (resources/read-resource | ||
| "illumina_genotyping_array/fromOutputs.edn")} | ||
| workload (endpoints/exec-workload | ||
| (workloads/staged-workload-request source executor sink))] | ||
| (try | ||
| (ingest-illumina-genotyping-array-inputs dataset-id "ignoreThisRow") | ||
| (ingest-illumina-genotyping-array-inputs dataset-id (:loadTag source)) | ||
| (let [row-ids (-> dataset | ||
| (datarepo/query-metadata-table | ||
| (:table source) {} [:datarepo_row_id]) | ||
| :rows | ||
| flatten) | ||
| where-load {:loadTag (:loadTag source)} | ||
| keep-row-ids (-> dataset | ||
| (datarepo/query-metadata-table | ||
| (:table source) where-load [:datarepo_row_id]) | ||
| :rows | ||
| flatten) | ||
| [workflow & rest] | ||
| (util/poll #(seq (endpoints/get-workflows workload)) 20 100)] | ||
| (is (== 2 (count row-ids)) | ||
| "2 rows should have been ingested") | ||
| (is (== 1 (count keep-row-ids)) | ||
| "1 row should have been ingested with our monitored load tag") | ||
| (is workflow | ||
| "One workflow should have been created") | ||
| (is (= (first keep-row-ids) (:entity workflow)) | ||
| "Row ingested with monitored load tag should have been submitted") | ||
| (is (empty? rest) | ||
| "Only one workflow should have been created")) | ||
| (finally | ||
| (endpoints/stop-workload workload))) | ||
| ;; FIXME: GH-1652 :kaocha/pending does not work with :parallel now. | ||
| #_(deftest ^:parallel test-workload-sink-outputs-to-tdr | ||
| (fixtures/with-fixtures | ||
| [(fixtures/with-temporary-dataset | ||
| (datasets/unique-dataset-request | ||
| (env/getenv "WFL_TDR_DEFAULT_PROFILE") | ||
| "illumina-genotyping-array.json")) | ||
| (fixtures/with-shared-temporary-workspace-clone | ||
| "wfl-dev/Illumina-Genotyping-Array-Template" | ||
| "workflow-launcher-dev" | ||
| [{:email (env/getenv "WFL_TDR_SERVICE_ACCOUNT") | ||
| :accessLevel "OWNER"}])] | ||
| (fn [[dataset-id workspace]] | ||
| (let [dataset (datarepo/datasets dataset-id) | ||
| source {:name "Terra DataRepo" | ||
| :dataset dataset-id | ||
| :table "inputs" | ||
| :snapshotReaders ["[email protected]"] | ||
| :pollingIntervalMinutes 1 | ||
| :loadTag "loadTagToMonitor"} | ||
| executor {:name "Terra" | ||
| :workspace workspace | ||
| :methodConfiguration "warp-pipelines/IlluminaGenotypingArray" | ||
| :fromSource "importSnapshot"} | ||
| sink {:name "Terra DataRepo" | ||
| :dataset dataset-id | ||
| :table "outputs" | ||
| :fromOutputs (resources/read-resource | ||
| "illumina_genotyping_array/fromOutputs.edn")} | ||
| workload (endpoints/exec-workload | ||
| (workloads/staged-workload-request source executor sink))] | ||
| (try | ||
| (ingest-illumina-genotyping-array-inputs dataset-id "ignoreThisRow") | ||
| (ingest-illumina-genotyping-array-inputs dataset-id (:loadTag source)) | ||
| (let [row-ids (-> dataset | ||
| (datarepo/query-metadata-table | ||
| (:table source) {} [:datarepo_row_id]) | ||
| :rows | ||
| flatten) | ||
| where-load {:loadTag (:loadTag source)} | ||
| keep-row-ids (-> dataset | ||
| (datarepo/query-metadata-table | ||
| (:table source) where-load [:datarepo_row_id]) | ||
| :rows | ||
| flatten) | ||
| [workflow & rest] | ||
| (util/poll #(seq (endpoints/get-workflows workload)) 20 100)] | ||
| (is (== 2 (count row-ids)) | ||
| "2 rows should have been ingested") | ||
| (is (== 1 (count keep-row-ids)) | ||
| "1 row should have been ingested with our monitored load tag") | ||
| (is workflow | ||
| "One workflow should have been created") | ||
| (is (= (first keep-row-ids) (:entity workflow)) | ||
| "Row ingested with monitored load tag should have been submitted") | ||
| (is (empty? rest) | ||
| "Only one workflow should have been created")) | ||
| (finally | ||
| (endpoints/stop-workload workload))) | ||
| ;; Note: when the workload's workflows have finished, | ||
| ;; we expect a notification for each workflow | ||
| ;; to be emitted to the Slack channels in | ||
| ;; `wfl.tools.workloads/watchers`. | ||
| (is (util/poll | ||
| #(-> workload :uuid endpoints/get-workload-status :finished) | ||
| 20 100) | ||
| "The workload should have finished") | ||
| (is (seq (:rows (datarepo/query-table dataset "outputs"))) | ||
| "outputs should have been written to the dataset"))))) | ||
| (is (util/poll | ||
| #(-> workload :uuid endpoints/get-workload-status :finished) | ||
| 20 100) | ||
| "The workload should have finished") | ||
| (is (seq (:rows (datarepo/query-table dataset "outputs"))) | ||
| "outputs should have been written to the dataset"))))) | ||
|
|
||
| (deftest ^:parallel test-logging-level | ||
| (testing "the /logging_level endpoint works" | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| 0.18.1 | ||
| 0.18.2 |