From a2d7eb094aa78cbec4046d81e3f883e706460b8d Mon Sep 17 00:00:00 2001 From: Jenny V Medina Date: Fri, 1 Mar 2024 15:34:11 -0500 Subject: [PATCH] [ORCA-306] Get and update Challenge submissions (#37) * New update_submission_status and get_submissions methods for Challenges --- Pipfile.lock | 4352 ++++++++++++++++------------ setup.cfg | 1 + src/orca/services/synapse/ops.py | 72 +- tests/services/synapse/test_ops.py | 167 +- 4 files changed, 2761 insertions(+), 1831 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 8b4392b..c619743 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -16,87 +16,94 @@ ] }, "default": { + "a2wsgi": { + "hashes": [ + "sha256:46b2ca427cf9ad538c145e32eb36857e1cbf477b72fe1ed0e3d35e98c06061b9", + "sha256:d29b91d9b18c9308c65e26e0e2bd0cd6af8135ced2bc1d2d03a2b18cc4e32f0c" + ], + "version": "==1.10.2" + }, "aiohttp": { "hashes": [ - "sha256:02ab6006ec3c3463b528374c4cdce86434e7b89ad355e7bf29e2f16b46c7dd6f", - 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+68,7 @@ exclude = # Additional dependencies for specific services all = + challengeutils~=4.3 synapseclient~=2.7 fs-synapse~=1.0 sevenbridges-python~=2.9 diff --git a/src/orca/services/synapse/ops.py b/src/orca/services/synapse/ops.py index d8886d9..42c1347 100644 --- a/src/orca/services/synapse/ops.py +++ b/src/orca/services/synapse/ops.py @@ -1,8 +1,12 @@ +""" +Handles Synapse operations for py-orca services. +""" import logging from dataclasses import field from functools import cached_property -from typing import ClassVar +from typing import ClassVar, List, Union +from challengeutils import utils from pydantic.dataclasses import dataclass from synapseclient import Synapse from synapsefs import SynapseFS @@ -46,7 +50,7 @@ def fs(self) -> SynapseFS: def monitor_evaluation_queue(self, evaluation_id: str) -> bool: """Monitor an evaluation queue in Synapse. - Args: + Arguments: evaluation_id: The Synapse ID of the queue to monitor. Returns: @@ -57,3 +61,67 @@ def monitor_evaluation_queue(self, evaluation_id: str) -> bool: ) submissions_num = sum(1 for submission in received_submissions) return submissions_num > 0 + + def trigger_indexing(self, synapse_view: str) -> None: + """ + Trigger indexing in Synapse. + + Arguments: + syn: A Synapse object. + synapse_view: The Synapse ID of the view. + """ + self.client.tableQuery(f"select * from {synapse_view} limit 1") + + def get_submissions_with_status( + self, submission_view: str, submission_status: str = "RECEIVED" + ) -> List[str]: + """ + Get all submissions with desired submission status in a Synapse + submission view. Status can be one of: + https://rest-docs.synapse.org/rest/org/sagebionetworks/evaluation/model/SubmissionStatusEnum.html + + Arguments: + submission_view: The Synapse ID of the table view to get submissions from. + submission_status: The submission status to filter for. + Defaults to "RECEIVED". + + Returns: + A list of submission IDs. + + """ + # Trigger indexing + self.trigger_indexing(submission_view) + + # Get all submissions for the given ``submission_view`` + query_results = self.client.tableQuery( + f"select * from {submission_view} where status = '{submission_status}'" + ) + + submission_ids = query_results.asDataFrame()["id"].tolist() + + return submission_ids + + def update_submission_status( + self, + submission_id: Union[int, str], + submission_status: str, + ) -> None: + """ + Update the status of a submission in Synapse. + Status can be one of: + https://rest-docs.synapse.org/rest/org/sagebionetworks/evaluation/model/SubmissionStatusEnum.html + + Arguments: + submission_ids: The Synapse ID of the submission. + submission_status: The new status of the submission. + + """ + + # Let's catch for anything that was fed that is NOT a str or int + if type(submission_id) not in [str, int]: + raise TypeError("``submission_id`` must be a string or int.") + + # Update submission status + utils.change_submission_status( + self.client, submissionid=submission_id, status=submission_status + ) diff --git a/tests/services/synapse/test_ops.py b/tests/services/synapse/test_ops.py index f446f59..766def2 100644 --- a/tests/services/synapse/test_ops.py +++ b/tests/services/synapse/test_ops.py @@ -1,31 +1,66 @@ +""" +Tests for Synapse operations conducted by SynapseOps. +""" +from unittest.mock import MagicMock + +import pandas as pd import pytest +from challengeutils import utils from orca.errors import ConfigError from orca.services.synapse import SynapseOps def test_for_an_error_when_accessing_fs_without_credentials( - patch_os_environ, syn_project_id -): + patch_os_environ: pytest.fixture, syn_project_id: str +) -> None: + """ + Test for an error when accessing fs without credentials. + + Arguments: + patch_os_environ: The OS environment patch + syn_project_id: The project ID + + """ ops = SynapseOps() with pytest.raises(ConfigError): ops.fs.listdir(syn_project_id) def test_monitor_evaluation_queue_returns_false_when_there_are_no_new_submissions( - mocker, mocked_ops -): + mocker: pytest.fixture, mocked_ops: MagicMock +) -> None: + """ + Function to test if the monitor evaluation queue returns False + when there are no new submissions. + + Arguments: + mocker: The mocker object for mocking. + mocked_ops: A mocked instance of ``SynapseOps``. + + Returns: + Boolean indicating if there are no new submissions. + """ mock = mocker.patch.object( mocked_ops.client, "getSubmissionBundles", return_value=[] ) result = mocked_ops.monitor_evaluation_queue("foo") mock.assert_called_once_with("foo", status="RECEIVED") - assert result is False + assert not result def test_monitor_evaluation_queue_returns_true_when_there_are_new_submissions( - mocker, mocked_ops -): + mocker: pytest.fixture, mocked_ops: MagicMock +) -> None: + """ + A function to test if the monitor evaluation queue returns True + when there are new submissions. + + Arguments: + mocker: A mocker object. + mocked_ops: A mocked instance of ``SynapseOps``. + + """ mock = mocker.patch.object( mocked_ops.client, "getSubmissionBundles", @@ -34,3 +69,121 @@ def test_monitor_evaluation_queue_returns_true_when_there_are_new_submissions( result = mocked_ops.monitor_evaluation_queue("foo") mock.assert_called_once_with("foo", status="RECEIVED") assert result + + +def test_trigger_indexing(mocker: pytest.fixture, mocked_ops: MagicMock) -> None: + """ + Tests that the ``trigger_indexing`` method in ``SynapseOps`` + triggers indexing in a Synapse table view. + + Arguments: + mocker: A mocker object. + mocked_ops: A mocked instance of ``SynapseOps``. + + """ + # Assigning variable to a fake submission view string + submission_view = "test_view" + + # Using patch to mock the Synapse tableQuery method + with mocker.patch.object(mocked_ops.client, "tableQuery"): + # Calling the function + mocked_ops.trigger_indexing(submission_view) + + # Assertions + mocked_ops.client.tableQuery.assert_called_once_with( + f"select * from {submission_view} limit 1" + ) + + +def test_get_submissions_with_status( + mocker: pytest.fixture, mocked_ops: MagicMock +) -> None: + """ + Tests that the ``get_submissions_with_status`` method in ``SynapseOps`` + returns a list of submission IDs. + + Arguments: + mocker: A mocker object. + mocked_ops: A mocked instance of ``SynapseOps``. + + """ + # Input values + submission_view = "syn111" + submission_status = "RECEIVED" + + input_dict = { + "id": ["submission_1", "submission_2"], + "status": ["RECEIVED", "RECEIVED"], + } + + # Mocking connection to the Synapse API + syn_mock = mocked_ops.client + + # Mocking the table query results + table_mock = MagicMock() + table_mock.asDataFrame.return_value = pd.DataFrame(input_dict) + + # Mock the ``trigger_indexing`` call in SynapseOps() and the tableQuery call + # in ``SynapseOps().get_submissions_with_status`` + with mocker.patch.object(mocked_ops, "trigger_indexing", return_value=None): + with mocker.patch.object(syn_mock, "tableQuery", return_value=table_mock): + # Calling the function to be tested + result = mocked_ops.get_submissions_with_status( + submission_view, submission_status + ) + + # Assertions + syn_mock.tableQuery.assert_called_once_with( + f"select * from {submission_view} where status = '{submission_status}'" + ) + table_mock.asDataFrame.assert_called() + assert result == input_dict["id"] + + +def test_update_submission_status( + mocker: pytest.fixture, mocked_ops: MagicMock +) -> None: + """ + Tests that the ``update_submissions_status`` method in ``SynapseOps`` + updates the status of one or more submissions in Synapse. + + Arguments: + mocker: A mocker object. + mocked_ops: A mocked instance of ``SynapseOps``. + """ + # Input args + submission_status = "APPROVED" + submission_id = "1234" + etag = "0000" + + # Mocking the ``change_submission_status`` call + # in ``SynapseOps.update_submissions_status`` + status_object = mocked_ops.client.evaluation.SubmissionStatus( + id=submission_id, + etag=etag, + submissionAnnotations={"status": [submission_status]}, + ) + mock_change_submission_status = mocker.patch.object( + utils, "change_submission_status", return_value=status_object + ) + + # Calling the function to be tested + mocked_ops.update_submission_status(submission_id, submission_status) + + # Assertions + mock_change_submission_status.assert_called_once_with( + mocked_ops.client, submissionid=submission_id, status=submission_status + ) + + +@pytest.mark.parametrize("submission_id", (111.0, [111])) +def test_update_submission_status_with_wrong_data_type(submission_id) -> None: + """ + Tests that the ``update_submission_status`` method in ``SynapseOps`` + raises an error if the input is the wrong datatype. + + """ + # Expect a custom TypeError for incorrect data types + with pytest.raises(TypeError, match="``submission_id`` must be a string or int."): + # Calling the function to be tested + SynapseOps().update_submission_status(submission_id, "SCORED")