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import os
from datetime import (
datetime,
timedelta,
)
from operator import itemgetter
from typing_extensions import Literal
from bioblend.galaxy.tools.inputs import (
dataset,
inputs,
)
from . import (
GalaxyTestBase,
test_util,
)
class TestGalaxyJobs(GalaxyTestBase.GalaxyTestBase):
def setUp(self):
super().setUp()
self.history_id = self.gi.histories.create_history(name="TestGalaxyJobs")["id"]
self.dataset_contents = "line 1\nline 2\rline 3\r\nline 4"
self.dataset_id = self._test_dataset(self.history_id, contents=self.dataset_contents)
def tearDown(self):
self.gi.histories.delete_history(self.history_id, purge=True)
@test_util.skip_unless_tool("cat1")
def test_wait_for_job(self):
tool_inputs = inputs().set("input1", dataset(self.dataset_id))
tool_output = self.gi.tools.run_tool(history_id=self.history_id, tool_id="cat1", tool_inputs=tool_inputs)
job_id = tool_output["jobs"][0]["id"]
job = self.gi.jobs.wait_for_job(job_id)
assert job["state"] == "ok"
@test_util.skip_unless_tool("random_lines1")
def test_get_jobs(self):
self._run_tool()
self._run_tool()
jobs = self.gi.jobs.get_jobs(tool_id="random_lines1", history_id=self.history_id)
assert len(jobs) == 2
jobs = self.gi.jobs.get_jobs(history_id=self.history_id, state="failed")
assert len(jobs) == 0
yesterday = datetime.today() - timedelta(days=1)
jobs = self.gi.jobs.get_jobs(date_range_max=yesterday.strftime("%Y-%m-%d"), history_id=self.history_id)
assert len(jobs) == 0
tomorrow = datetime.today() + timedelta(days=1)
jobs = self.gi.jobs.get_jobs(date_range_min=tomorrow.strftime("%Y-%m-%d"))
assert len(jobs) == 0
jobs = self.gi.jobs.get_jobs(date_range_min=datetime.today().strftime("%Y-%m-%d"), history_id=self.history_id)
assert len(jobs) == 3
@test_util.skip_unless_galaxy("release_21.05")
def test_get_jobs_with_filtering(self):
path = test_util.get_abspath(os.path.join("data", "paste_columns.ga"))
workflow_id = self.gi.workflows.import_workflow_from_local_path(path)["id"]
dataset = {"src": "hda", "id": self.dataset_id}
invocation1 = self.gi.workflows.invoke_workflow(
workflow_id,
inputs={"Input 1": dataset, "Input 2": dataset},
history_id=self.history_id,
inputs_by="name",
)
invocation2 = self.gi.workflows.invoke_workflow(
workflow_id,
inputs={"Input 1": dataset, "Input 2": dataset},
history_id=self.history_id,
inputs_by="name",
)
self.gi.invocations.wait_for_invocation(invocation1["id"])
self.gi.invocations.wait_for_invocation(invocation2["id"])
all_jobs = self.gi.jobs.get_jobs(history_id=self.history_id, order_by="create_time")
assert len(all_jobs) == 3
job1_id = all_jobs[1]["id"]
jobs = self.gi.jobs.get_jobs(history_id=self.history_id, limit=1, offset=1, order_by="create_time")
assert len(jobs) == 1
assert jobs[0]["id"] == job1_id
jobs = self.gi.jobs.get_jobs(invocation_id=invocation1["id"])
assert len(jobs) == 1
job_id_inv = jobs[0]["id"]
jobs = self.gi.jobs.get_jobs(workflow_id=workflow_id)
assert len(jobs) == 2
assert job_id_inv in [job["id"] for job in jobs]
@test_util.skip_unless_galaxy("release_21.01")
@test_util.skip_unless_tool("random_lines1")
def test_run_and_rerun_random_lines(self):
original_output = self._run_tool(input_format="21.01")
original_job_id = original_output["jobs"][0]["id"]
rerun_output = self.gi.jobs.rerun_job(original_job_id)
original_output_content = self.gi.datasets.download_dataset(original_output["outputs"][0]["id"])
rerun_output_content = self.gi.datasets.download_dataset(rerun_output["outputs"][0]["id"])
assert rerun_output_content == original_output_content
@test_util.skip_unless_galaxy("release_21.01")
@test_util.skip_unless_tool("Show beginning1")
def test_rerun_and_remap(self):
path = test_util.get_abspath(os.path.join("data", "select_first.ga"))
wf = self.gi.workflows.import_workflow_from_local_path(path)
wf_inputs = {
"0": {"src": "hda", "id": self.dataset_id},
"1": "-1",
}
invocation_id = self.gi.workflows.invoke_workflow(wf["id"], inputs=wf_inputs, history_id=self.history_id)["id"]
invocation = self.gi.invocations.wait_for_invocation(invocation_id)
job_steps = [step for step in invocation["steps"] if step["job_id"]]
job_steps.sort(key=itemgetter("order_index"))
try:
self.gi.jobs.wait_for_job(job_steps[0]["job_id"])
except Exception:
pass # indicates the job failed as expected
else:
raise Exception("The job should have failed")
history_contents = self.gi.histories.show_history(self.history_id, contents=True)
assert len(history_contents) == 3
assert history_contents[1]["state"] == "error"
assert history_contents[2]["state"] == "paused"
# resume the paused step job
resumed_outputs = self.gi.jobs.resume_job(job_steps[-1]["job_id"])
assert resumed_outputs[0]["name"] == "out_file1"
# the following does not pass stably - the job goes back to paused too quickly
# history_contents_resumed = self.gi.histories.show_history(self.history_id, contents=True)
# assert history_contents_resumed[2]["state"] != "paused"
# now rerun and remap with correct input param
failed_job_id = self.gi.datasets.show_dataset(history_contents[1]["id"])["creating_job"]
tool_inputs_update = {"lineNum": "1"}
rerun_job = self.gi.jobs.rerun_job(failed_job_id, remap=True, tool_inputs_update=tool_inputs_update)
new_job_id = rerun_job["jobs"][0]["id"]
# Wait for the last dataset in the history to be unpaused and complete
last_dataset = self.gi.histories.show_history(self.history_id, contents=True)[-1]
last_job_id = self.gi.datasets.show_dataset(last_dataset["id"])["creating_job"]
self.gi.jobs.wait_for_job(new_job_id)
self.gi.jobs.resume_job(last_job_id) # last_job can get stuck on paused - resume it in case
self.gi.jobs.wait_for_job(last_job_id)
assert last_dataset["hid"] == 3
assert last_dataset["id"] == history_contents[2]["id"]
self._wait_and_verify_dataset(last_dataset["id"], b"line 1\tline 1\n")
@test_util.skip_unless_galaxy("release_19.05")
@test_util.skip_unless_tool("random_lines1")
def test_get_common_problems(self):
job_id = self._run_tool()["jobs"][0]["id"]
response = self.gi.jobs.get_common_problems(job_id)
assert response == {"has_duplicate_inputs": False, "has_empty_inputs": True}
@test_util.skip_unless_tool("random_lines1")
def test_get_inputs(self):
job_id = self._run_tool()["jobs"][0]["id"]
response = self.gi.jobs.get_inputs(job_id)
assert response == [{"name": "input", "dataset": {"src": "hda", "id": self.dataset_id}}]
@test_util.skip_unless_tool("random_lines1")
def test_get_outputs(self):
output = self._run_tool()
job_id, output_id = output["jobs"][0]["id"], output["outputs"][0]["id"]
response = self.gi.jobs.get_outputs(job_id)
assert response == [{"name": "out_file1", "dataset": {"src": "hda", "id": output_id}}]
@test_util.skip_unless_galaxy("release_20.05")
@test_util.skip_unless_tool("random_lines1")
def test_get_destination_params(self):
job_id = self._run_tool()["jobs"][0]["id"]
# In Galaxy 20.05 and 20.09 we need to wait for the job, otherwise
# `get_destination_params()` receives a 500 error code. Fixed upstream
# in https://github.com/galaxyproject/galaxy/commit/3e7f03cd1f229b8c9421ade02002728a33e131d8
self.gi.jobs.wait_for_job(job_id)
response = self.gi.jobs.get_destination_params(job_id)
assert "Runner" in response
assert "Runner Job ID" in response
assert "Handler" in response
@test_util.skip_unless_tool("random_lines1")
def test_search_jobs(self):
job_id = self._run_tool()["jobs"][0]["id"]
inputs = {
"num_lines": "1",
"input": {"src": "hda", "id": self.dataset_id},
"seed_source|seed_source_selector": "set_seed",
"seed_source|seed": "asdf",
}
response = self.gi.jobs.search_jobs("random_lines1", inputs)
assert job_id in [job["id"] for job in response]
@test_util.skip_unless_galaxy("release_20.01")
@test_util.skip_unless_tool("random_lines1")
def test_report_error(self):
output = self._run_tool()
job_id, output_id = output["jobs"][0]["id"], output["outputs"][0]["id"]
response = self.gi.jobs.report_error(job_id, output_id, "Test error")
# expected response when the Galaxy server does not have mail configured
assert response == {
"messages": [
[
"An error occurred sending the report by email: Mail is not configured for this Galaxy instance",
"danger",
]
]
}
@test_util.skip_unless_galaxy("release_20.05")
def test_show_job_lock(self):
status = self.gi.jobs.show_job_lock()
assert not status
@test_util.skip_unless_galaxy("release_20.05")
def test_update_job_lock(self):
status = self.gi.jobs.update_job_lock(active=True)
assert status
status = self.gi.jobs.update_job_lock(active=False)
assert not status
def test_cancel_job(self):
job_id = self._run_tool()["jobs"][0]["id"]
self.gi.jobs.cancel_job(job_id)
job = self.gi.jobs.wait_for_job(job_id, check=False)
assert job["state"] in ("deleted", "deleting")
def _run_tool(self, input_format: Literal["21.01", "legacy"] = "legacy") -> dict:
return super()._run_random_lines1(self.history_id, self.dataset_id, input_format=input_format)
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