[GH-1172] Start System Test for sarscov2_illumina_all Automation
#334
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
ehigham
force-pushed
the
ehigham/GH-1172-sarscov2-illumina-full
branch
2 times, most recently
from
b03dd34
to
4da8383
Compare
ehigham
force-pushed
the
ehigham/GH-1172-sarscov2-illumina-full
branch
from
4da8383
to
b855da3
Compare
ehigham
commented
Mar 1, 2021
ehigham
changed the title
sarscov2_illumina_all automationsarscov2_illumina_all Automation
instead and therefore the values will be strings. Change `rename-gather` to reflect this.
tbl3rd
approved these changes
Mar 2, 2021
… an ingest request from the inputs`
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
RR: https://broadinstitute.atlassian.net/browse/GH-1172
This PR includes the start of an end-to-end system test for the
sarscov2_illumina_all. The test aims to test creating, starting and stopping a workload to automate pipeline submission from and to the source and sink TDR datasets. We don't have much of this functionality yet so this test just sketches the expected behaviour.In the test, I've expended on
rename-gatheras a means of converting pipeline names to dataset names (and vice versa). I'm currently using it to conform build a dataset ingest request from inputs.The mapping (
dataset-from-inputs.edn) defines how to construct a row in the dataset table from the inputs of the pipeline.rename-gatheris an interpreter for this mapping. There are issues which I'll solve another time, namely how to coerce between json and a map.There's some code duplication in dataset ingest code as it's not clear how to group this yet or if it will need to be split up, say if we want to record what the dataset ingest job IDs were if WFL crashes.