mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-11-02 11:48:57 +08:00
Nicola Soranzo
959f4a5aa4
by runnig: ```shell make pyupgrade ruff check --fix . make format ``` Also update ruff configuration to: - Enable UP006 and UP035 error codes for PEP 585 type annotations - Ignore UP045 for the packages which need to stay compatible with Python 3.8 - Add tool-util-models paths to those that need to stay compatible with Python 3.8
246 lines
12 KiB
Python
246 lines
12 KiB
Python
""" """
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import base64
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from typing import (
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Any,
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)
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import requests
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from galaxy_test.base.api_asserts import assert_status_code_is_ok
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from galaxy_test.base.populators import (
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DatasetPopulator,
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skip_without_tool,
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)
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from ._framework import ApiTestCase
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class TestToolExecution(ApiTestCase):
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dataset_populator: DatasetPopulator
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def setUp(self):
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super().setUp()
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self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
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@skip_without_tool("gx_int")
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def test_validation(self):
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with self.dataset_populator.test_history() as history_id:
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self._assert_request_validates("gx_int", history_id, {"parameter": 5})
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self._assert_request_invalid("gx_int", history_id, {"parameter": None})
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self._assert_request_invalid("gx_int", history_id, {"parameter": "5"})
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@skip_without_tool("gx_int")
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def test_execution(self):
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with self.dataset_populator.test_history() as history_id:
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response = self._run("gx_int", history_id, {"parameter": 5})
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assert_status_code_is_ok(response)
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response_json = response.json()
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tool_request_id = response_json.get("tool_request_id")
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task_result = response_json["task_result"]
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history_tool_requests = self.dataset_populator.get_history_tool_requests(history_id)
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assert tool_request_id in [tr["id"] for tr in history_tool_requests]
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self.dataset_populator.wait_on_task_object(task_result)
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state = self.dataset_populator.wait_on_tool_request(tool_request_id)
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assert state
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jobs = self.galaxy_interactor.jobs_for_tool_request(tool_request_id)
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self.dataset_populator.wait_for_jobs(jobs, assert_ok=True)
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@skip_without_tool("gx_data")
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def test_execution_with_src_urls(self):
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with self.dataset_populator.test_history() as history_id:
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response = self._run(
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"gx_data",
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history_id,
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{
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"parameter": {
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"src": "url",
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"url": "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt",
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"ext": "txt",
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}
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},
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)
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assert_status_code_is_ok(response)
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response_json = response.json()
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tool_request_id = response_json.get("tool_request_id")
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task_result = response_json["task_result"]
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self.dataset_populator.wait_on_task_object(task_result)
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state = self.dataset_populator.wait_on_tool_request(tool_request_id)
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assert state, str(self.dataset_populator.get_tool_request(tool_request_id))
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jobs = self.galaxy_interactor.jobs_for_tool_request(tool_request_id)
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self.dataset_populator.wait_for_jobs(jobs, assert_ok=True)
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if len(jobs) != 1:
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raise Exception(f"Found incorrect number of jobs for tool request - was expecting a single job {jobs}")
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assert len(jobs) == 1, jobs
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job_id = jobs[0]["id"]
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job_outputs = self.galaxy_interactor.job_outputs(job_id)
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assert len(job_outputs) == 1
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job_output = job_outputs[0]
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assert job_output["name"] == "output"
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content = self.dataset_populator.get_history_dataset_content(history_id, dataset=job_output["dataset"])
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assert content == "Hello World!"
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# verify input was not left deferred and materialized before the job started
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input_dataset_details = self.dataset_populator.get_history_dataset_details(history_id, hid=1)
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assert input_dataset_details["state"] == "ok", input_dataset_details
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@skip_without_tool("gx_data")
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def test_execution_with_deferred_src_urls(self):
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with self.dataset_populator.test_history() as history_id:
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response = self._run(
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"gx_data",
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history_id,
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{
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"parameter": {
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"src": "url",
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"url": "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt",
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"ext": "txt",
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"deferred": True,
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}
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},
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)
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assert_status_code_is_ok(response)
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response_json = response.json()
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tool_request_id = response_json.get("tool_request_id")
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task_result = response_json["task_result"]
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self.dataset_populator.wait_on_task_object(task_result)
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state = self.dataset_populator.wait_on_tool_request(tool_request_id)
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assert state, str(self.dataset_populator.get_tool_request(tool_request_id))
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jobs = self.galaxy_interactor.jobs_for_tool_request(tool_request_id)
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self.dataset_populator.wait_for_jobs(jobs, assert_ok=True)
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if len(jobs) != 1:
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raise Exception(f"Found incorrect number of jobs for tool request - was expecting a single job {jobs}")
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assert len(jobs) == 1, jobs
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job_id = jobs[0]["id"]
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job_outputs = self.galaxy_interactor.job_outputs(job_id)
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assert len(job_outputs) == 1
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job_output = job_outputs[0]
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assert job_output["name"] == "output"
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content = self.dataset_populator.get_history_dataset_content(history_id, dataset=job_output["dataset"])
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assert content == "Hello World!"
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# verify input was left deferred and infer must have been materialized just for the job
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input_dataset_details = self.dataset_populator.get_history_dataset_details(history_id, hid=1)
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assert input_dataset_details["state"] == "deferred", input_dataset_details
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@skip_without_tool("gx_data_collection_list")
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def test_execution_with_deferred_list(self):
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with self.dataset_populator.test_history() as history_id:
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input_b64_1 = base64.b64encode(b"Hello World!\n").decode("utf-8")
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input_b64_2 = base64.b64encode(b"It is me - a collection!\n").decode("utf-8")
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response = self._run(
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"gx_data_collection_list",
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history_id,
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{
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"parameter": {
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"class": "Collection",
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"collection_type": "list",
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"elements": [
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{
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"class": "File",
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"identifier": "mycoolelement",
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"url": f"base64://{input_b64_1}",
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"ext": "txt",
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"deferred": True,
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},
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{
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"class": "File",
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"identifier": "mycoolelement2",
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"url": f"base64://{input_b64_2}",
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"ext": "txt",
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"deferred": False,
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},
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],
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},
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},
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)
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assert_status_code_is_ok(response)
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response_json = response.json()
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tool_request_id = response_json.get("tool_request_id")
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task_result = response_json["task_result"]
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self.dataset_populator.wait_on_task_object(task_result)
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state = self.dataset_populator.wait_on_tool_request(tool_request_id)
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assert state, str(self.dataset_populator.get_tool_request(tool_request_id))
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jobs = self.galaxy_interactor.jobs_for_tool_request(tool_request_id)
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self.dataset_populator.wait_for_jobs(jobs, assert_ok=True)
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if len(jobs) != 1:
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raise Exception(f"Found incorrect number of jobs for tool request - was expecting a single job {jobs}")
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assert len(jobs) == 1, jobs
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job_id = jobs[0]["id"]
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job_outputs = self.galaxy_interactor.job_outputs(job_id)
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assert len(job_outputs) == 1
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job_output = job_outputs[0]
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assert job_output["name"] == "output"
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content = self.dataset_populator.get_history_dataset_content(history_id, dataset=job_output["dataset"])
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assert content == "Hello World!\nIt is me - a collection!\n"
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@skip_without_tool("gx_data_collection")
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def test_execution_with_deferred_nested_list(self):
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with self.dataset_populator.test_history() as history_id:
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input_b64_1 = base64.b64encode(b"Hello World!\n").decode("utf-8")
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input_b64_2 = base64.b64encode(b"It is me - a collection!\n").decode("utf-8")
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response = self._run(
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"gx_data_collection",
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history_id,
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{
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"parameter": {
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"class": "Collection",
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"collection_type": "list:list",
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"elements": [
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{
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# Why is this needed? Planemo doesn't require this class right?
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# wait is it needed?
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"class": "Collection",
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"identifier": "outer_element",
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"collection_type": "list",
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"elements": [
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{
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"class": "File",
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"identifier": "mycoolelement",
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"url": f"base64://{input_b64_1}",
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"ext": "txt",
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"deferred": True,
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},
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{
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"class": "File",
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"identifier": "mycoolelement2",
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"url": f"base64://{input_b64_2}",
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"ext": "txt",
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"deferred": False,
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},
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],
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}
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],
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},
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},
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)
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assert_status_code_is_ok(response)
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response_json = response.json()
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tool_request_id = response_json.get("tool_request_id")
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task_result = response_json["task_result"]
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self.dataset_populator.wait_on_task_object(task_result)
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state = self.dataset_populator.wait_on_tool_request(tool_request_id)
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assert state, str(self.dataset_populator.get_tool_request(tool_request_id))
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jobs = self.galaxy_interactor.jobs_for_tool_request(tool_request_id)
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self.dataset_populator.wait_for_jobs(jobs, assert_ok=True)
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if len(jobs) != 1:
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raise Exception(f"Found incorrect number of jobs for tool request - was expecting a single job {jobs}")
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assert len(jobs) == 1, jobs
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job_id = jobs[0]["id"]
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job_outputs = self.galaxy_interactor.job_outputs(job_id)
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assert len(job_outputs) == 1
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job_output = job_outputs[0]
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assert job_output["name"] == "output"
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content = self.dataset_populator.get_history_dataset_content(history_id, dataset=job_output["dataset"])
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assert content == "Hello World!\nIt is me - a collection!\n"
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def _assert_request_validates(self, tool_id: str, history_id: str, inputs: dict[str, Any]):
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response = self._run(tool_id, history_id, inputs)
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assert response.status_code == 200
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def _assert_request_invalid(self, tool_id: str, history_id: str, inputs: dict[str, Any]):
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response = self._run(tool_id, history_id, inputs)
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assert response.status_code == 400
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def _run(self, tool_id: str, history_id: str, inputs: dict[str, Any]) -> requests.Response:
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return self.dataset_populator.tool_request_raw(tool_id, inputs, history_id)
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