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GH-1163: Support Somatic Genomes in production. #324

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merged 27 commits into from
Feb 19, 2021
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@tbl3rd tbl3rd commented Feb 17, 2021

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@tbl3rd tbl3rd force-pushed the tbl/GH-1163-prod-clio-url branch 3 times, most recently from c699cbf to 3b9a650 Compare February 18, 2021 18:22
@tbl3rd tbl3rd marked this pull request as ready for review February 19, 2021 00:23
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(-> (service-account-credentials) .refreshAccessToken .getTokenValue))
(some-> (service-account-credentials) .refreshAccessToken .getTokenValue))
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Why some->? If we can't find any service account credentials then we're kind of stuffed? Why not error here instead of getting a 403 later?

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OK. Was propagating from above.

Comment on lines 29 to 33
INTEGRATION := $(DERIVED_MODULE_DIR)/integration.$(TIMESTAMP)
LINT := $(DERIVED_MODULE_DIR)/lint.$(TIMESTAMP)
PREBUILD := $(DERIVED_MODULE_DIR)/prebuild.$(TIMESTAMP)
SYSTEM := $(DERIVED_MODULE_DIR)/system.$(TIMESTAMP)
UNIT := $(DERIVED_MODULE_DIR)/unit.$(TIMESTAMP)
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These were previously sorted in order of execution?

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Execution order is determined by dependence, but OK.

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Correct

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Looks great to me! Thanks for cleaning up the environments :octocat:

api/module.mk Show resolved Hide resolved
api/src/wfl/module/sg.clj Outdated Show resolved Hide resolved
api/src/wfl/module/sg.clj Show resolved Hide resolved
"gs://broad-gotc-dev-wfl-sg-test-inputs/pipeline/G96830/NA12878/v23/NA12878.cram"}}],
:creator (:email @endpoints/userinfo)})
"gs://broad-gotc-dev-wfl-sg-test-inputs/pipeline/G96830/NA12878/v23/NA12878.cram"}}]
:creator "@workloads/email"}) ; quoted to avoid log spam
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enigma…

api/test/wfl/tools/endpoints.clj Show resolved Hide resolved
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@tbl3rd tbl3rd merged commit 8aba8bd into main Feb 19, 2021
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tbl3rd commented Feb 19, 2021

Thank you for the reviews.

@tbl3rd tbl3rd deleted the tbl/GH-1163-prod-clio-url branch March 1, 2021 22:40
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3 participants