Omics fixes

[drernie]

1. Use 'list_objects' if cannot call 'list_object_versions'
2. Do NOT fail if the user cannot read the workflow config folder (causes many errors)
3. Add integration test to check Omics access (will need to be removed, as it requires sales credentials)

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 24.19%. Comparing base (2edbba0) to head (e32beb2).

Additional details and impacted files

@@             Coverage Diff             @@
##           master    #3924       +/-   ##
===========================================
- Coverage   36.58%   24.19%   -12.39%     
===========================================
  Files         719      684       -35     
  Lines       31980    26040     -5940     
  Branches     4707     4707               
===========================================
- Hits        11700     6301     -5399     
+ Misses      19116    18575      -541     
  Partials     1164     1164               

Flag	Coverage Δ
api-python	?
catalog	10.61% <ø> (ø)
lambda	87.74% <ø> (ø)

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[drernie]

1. Can we add some sort of standard option to NOT always have to read the workflow config? This drove me crazy at the NextFlow summit.
2. The integration test is horrible, in that it requires the sales profile to test against Omics. Should I just delete it, or is there a saner way to test the "versions not allowed" use case?

[sir-sigurd]

this PR needs to be split at least into two parts: list objects logic change and workflow logic changes

[sir-sigurd]

I see no reason to not having unit tests instead

[drernie]

I have no idea how to test permission errors.

[sir-sigurd]

https://botocore.amazonaws.com/v1/documentation/api/latest/reference/stubber.html#botocore.stub.Stubber.add_client_error

you could find some example of its usage in the existing tests

[sir-sigurd]

@drernie
why don't you use master branch as base of your PR?

[drernie]

why don't you use master branch as base of your PR?

I wasn’t thinking clearly when I created the branch, and now I don’t know how to change it.

…

On Apr 2, 2024, at 23:26, Sergey Fedoseev ***@***.***> wrote: @drernie <https://github.com/drernie> why don't you use master branch as base of your PR? — Reply to this email directly, view it on GitHub <#3924 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAE2T5JSEX5BNQI7TV3C2LY3OOJVAVCNFSM6AAAAABFUSFBOSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZTGY2TMNJTG4>. You are receiving this because you were mentioned.

[sir-sigurd]

wasn’t thinking clearly when I created the branch, and now I don’t know how to change it.

you could start from scratch and force push here

[sir-sigurd]

it's still too broad

Suggested change

	except botocore.exceptions.ClientError as e:
	except botocore.exceptions.ClientError as e:
	if e.response["Error"]["Code"] != "AccessDenied":
	raise

[drernie]

Fixed in new PR

[drernie]

Let me just start over, rather than risk messing up git with my lack of skill:
#3927