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[WIP] Feat/nextflow_integration_tests #157

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@nss10 nss10 commented Feb 13, 2025

Link to JIRA ticket if there is one: MIDRC-860

New Features

  • Add integration test to gen3-workflow service

Dependency updates

  • Added nextflow and boto3 as poetry dependencies

@nss10 nss10 requested a review from paulineribeyre February 13, 2025 21:52
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Please find the ci env pod logs here

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could you rename the file gen3workflow instead of gen3workflows

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I will rename the file once all the other review comments in this file are addressed and resolved. Since renaming kind of stirs things up letting git assume that the file with all these comments is deleted.

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Please find the detailed integration test report here

Please find the ci env pod logs here

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Please find the detailed integration test report here

Please find the ci env pod logs here

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Please find the ci env pod logs here

@nss10 nss10 requested a review from paulineribeyre February 25, 2025 00:32
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$$\textcolor{#23d18b}{\tt{tests/test\_aggregate\_mds.py}}$$ $$\textcolor{#23d18b}{\tt{1}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_metadata\_ingestion.py}}$$ $$\textcolor{#23d18b}{\tt{1}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_etl.py}}$$ $$\textcolor{#23d18b}{\tt{1}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_gen3client.py}}$$ $$\textcolor{#23d18b}{\tt{1}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_manifest\_service.py}}$$ $$\textcolor{#23d18b}{\tt{1}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_indexing\_page.py}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#f14c4c}{\tt{2}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#f14c4c}{\tt{2}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_discoverypage.py}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#f14c4c}{\tt{1}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#f14c4c}{\tt{1}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_workspace.py}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#f14c4c}{\tt{1}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#f14c4c}{\tt{1}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_login\_page.py}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#f14c4c}{\tt{2}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#f14c4c}{\tt{2}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_google\_data\_access.py}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#f14c4c}{\tt{1}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#f14c4c}{\tt{1}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_homepage.py}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#f14c4c}{\tt{1}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#f14c4c}{\tt{1}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_pfb\_export.py}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#f14c4c}{\tt{1}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#f14c4c}{\tt{1}}$$
$$\textcolor{#ffa500}{\tt{tests/test\_gen3ff\_landing\_page.py}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#ffa500}{\tt{2}}$$ $$\textcolor{#ffa500}{\tt{2}}$$
$$\textcolor{#ffa500}{\tt{tests/test\_register\_user.py}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#666666}{\tt{0}}$$ $$\textcolor{#ffa500}{\tt{2}}$$ $$\textcolor{#ffa500}{\tt{2}}$$
$$\textcolor{#f14c4c}{\tt{TOTAL}}$$ $$\textcolor{#23d18b}{\tt{79}}$$ $$\textcolor{#f14c4c}{\tt{38}}$$ $$\textcolor{#f14c4c}{\tt{3}}$$ $$\textcolor{#ffa500}{\tt{7}}$$ $$\textcolor{#f14c4c}{\tt{127}}$$

Please find the detailed integration test report here

Please find the ci env pod logs here

"Authorization": f"bearer {self._get_access_token(user)}",
}
if user
else {}
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Suggested change
else {}
else {"Content-Type": "application/json"}

user=self.valid_user,
expected_status=200,
)
assert (
isinstance(response_contents, list) and len(response_contents) > 0
), "Expected the function to return a list of at least one item"
), "Expected the function to return a list of at least one item but received: {response_contents}"
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), "Expected the function to return a list of at least one item but received: {response_contents}"
), f"Expected the function to return a list of at least one item but received: {response_contents}"

)

def create_tes_task(
self, request_body: dict, user: str = "main_account", expected_status=200
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the request_body isn't used

expected_status=401,
)

def test_happy_path_create_tes_tasks(self):
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Could we check that the created task completes successfully, and that the outputs are available and correct?

expected_status=401,
)

def test_happy_path_create_tes_tasks(self):
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Could we merge test_happy_path_create_tes_tasks, test_happy_path_list_tes_tasks and test_happy_path_get_tes_tasks into 1 so we don't create multiple TES tasks that the backend will be busy running (it will slow down any test that waits for a task to complete)?

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