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import json
import os
import shutil
import tempfile
import time
from typing import (
Any,
Dict,
List,
)
import pytest
from bioblend import ConnectionError
from . import (
GalaxyTestBase,
test_util,
)
class TestGalaxyWorkflows(GalaxyTestBase.GalaxyTestBase):
@test_util.skip_unless_tool("cat1")
@test_util.skip_unless_tool("cat")
def test_workflow_scheduling(self):
path = test_util.get_abspath(os.path.join("data", "test_workflow_pause.ga"))
workflow = self.gi.workflows.import_workflow_from_local_path(path)
workflow_id = workflow["id"]
history_id = self.gi.histories.create_history(name="TestWorkflowState")["id"]
invocations = self.gi.workflows.get_invocations(workflow_id)
assert len(invocations) == 0
# Try invalid invocation (no input)
with pytest.raises(ConnectionError):
self.gi.workflows.invoke_workflow(workflow["id"])
dataset1_id = self._test_dataset(history_id)
invocation = self.gi.workflows.invoke_workflow(
workflow["id"],
inputs={"0": {"src": "hda", "id": dataset1_id}},
)
assert invocation["state"] == "new"
invocation_id = invocation["id"]
invocations = self.gi.workflows.get_invocations(workflow_id)
assert len(invocations) == 1
assert invocations[0]["id"] == invocation_id
def invocation_steps_by_order_index() -> Dict[int, Dict[str, Any]]:
invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
return {s["order_index"]: s for s in invocation["steps"]}
for _ in range(20):
if 2 in invocation_steps_by_order_index():
break
time.sleep(0.5)
invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
assert invocation["state"] == "ready"
steps = invocation_steps_by_order_index()
pause_step = steps[2]
assert self.gi.workflows.show_invocation_step(workflow_id, invocation_id, pause_step["id"])["action"] is None
self.gi.workflows.run_invocation_step_action(workflow_id, invocation_id, pause_step["id"], action=True)
assert self.gi.workflows.show_invocation_step(workflow_id, invocation_id, pause_step["id"])["action"]
for _ in range(20):
invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
if invocation["state"] == "scheduled":
break
time.sleep(0.5)
invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
assert invocation["state"] == "scheduled"
def test_invoke_workflow_parameters_normalized(self):
path = test_util.get_abspath(os.path.join("data", "paste_columns_subworkflow.ga"))
workflow_id = self.gi.workflows.import_workflow_from_local_path(path)["id"]
history_id = self.gi.histories.create_history(name="TestWorkflowInvokeParametersNormalized")["id"]
dataset_id = self._test_dataset(history_id)
with pytest.raises(ConnectionError):
self.gi.workflows.invoke_workflow(
workflow_id, inputs={"0": {"src": "hda", "id": dataset_id}}, params={"1": {"1|2": "comma"}}
)
self.gi.workflows.invoke_workflow(
workflow_id,
inputs={"0": {"src": "hda", "id": dataset_id}},
params={"1": {"1|2": "comma"}},
parameters_normalized=True,
)
@test_util.skip_unless_galaxy("release_19.09")
@test_util.skip_unless_tool("cat1")
@test_util.skip_unless_tool("cat")
def test_cancelling_workflow_scheduling(self):
path = test_util.get_abspath(os.path.join("data", "test_workflow_pause.ga"))
workflow = self.gi.workflows.import_workflow_from_local_path(path)
workflow_id = workflow["id"]
history_id = self.gi.histories.create_history(name="TestWorkflowState")["id"]
dataset1_id = self._test_dataset(history_id)
invocations = self.gi.workflows.get_invocations(workflow_id)
assert len(invocations) == 0
invocation = self.gi.workflows.invoke_workflow(
workflow["id"],
inputs={"0": {"src": "hda", "id": dataset1_id}},
)
invocation_id = invocation["id"]
invocations = self.gi.workflows.get_invocations(workflow_id)
assert len(invocations) == 1
assert invocations[0]["id"] == invocation_id
invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
assert invocation["state"] in ["new", "ready"]
self.gi.workflows.cancel_invocation(workflow_id, invocation_id)
invocation = self.gi.invocations.wait_for_invocation(invocation_id, check=False)
assert invocation["state"] == "cancelled"
def test_import_export_workflow_from_local_path(self):
with pytest.raises(TypeError):
self.gi.workflows.import_workflow_from_local_path(None) # type: ignore[arg-type]
path = test_util.get_abspath(os.path.join("data", "paste_columns.ga"))
imported_wf = self.gi.workflows.import_workflow_from_local_path(path)
assert isinstance(imported_wf, dict)
assert imported_wf["name"] == "paste_columns"
assert imported_wf["url"].startswith("/api/workflows/")
assert not imported_wf["deleted"]
assert not imported_wf["published"]
with pytest.raises(TypeError):
self.gi.workflows.export_workflow_to_local_path(None, None, None) # type: ignore[arg-type]
export_dir = tempfile.mkdtemp(prefix="bioblend_test_")
try:
self.gi.workflows.export_workflow_to_local_path(imported_wf["id"], export_dir)
dir_contents = os.listdir(export_dir)
assert len(dir_contents) == 1
export_path = os.path.join(export_dir, dir_contents[0])
with open(export_path) as f:
exported_wf_dict = json.load(f)
finally:
shutil.rmtree(export_dir)
assert isinstance(exported_wf_dict, dict)
def test_import_publish_workflow_from_local_path(self):
path = test_util.get_abspath(os.path.join("data", "paste_columns.ga"))
imported_wf = self.gi.workflows.import_workflow_from_local_path(path, publish=True)
assert isinstance(imported_wf, dict)
assert not imported_wf["deleted"]
assert imported_wf["published"]
def test_import_export_workflow_dict(self):
path = test_util.get_abspath(os.path.join("data", "paste_columns.ga"))
with open(path) as f:
wf_dict = json.load(f)
imported_wf = self.gi.workflows.import_workflow_dict(wf_dict)
assert isinstance(imported_wf, dict)
assert imported_wf["name"] == "paste_columns"
assert imported_wf["url"].startswith("/api/workflows/")
assert not imported_wf["deleted"]
assert not imported_wf["published"]
exported_wf_dict = self.gi.workflows.export_workflow_dict(imported_wf["id"])
assert isinstance(exported_wf_dict, dict)
def test_import_publish_workflow_dict(self):
path = test_util.get_abspath(os.path.join("data", "paste_columns.ga"))
with open(path) as f:
wf_dict = json.load(f)
imported_wf = self.gi.workflows.import_workflow_dict(wf_dict, publish=True)
assert isinstance(imported_wf, dict)
assert not imported_wf["deleted"]
assert imported_wf["published"]
def test_get_workflows(self):
path = test_util.get_abspath(os.path.join("data", "paste_columns.ga"))
workflow = self.gi.workflows.import_workflow_from_local_path(path)
all_wfs = self.gi.workflows.get_workflows()
assert len(all_wfs) > 0
wfs_with_name = self.gi.workflows.get_workflows(name=workflow["name"])
wf_list = [w for w in wfs_with_name if w["id"] == workflow["id"]]
assert len(wf_list) == 1
wf_data = wf_list[0]
if "create_time" in workflow: # Galaxy >= 20.01
assert wf_data["create_time"] == workflow["create_time"]
else: # Galaxy <= 22.01
assert wf_data["url"] == workflow["url"]
def test_show_workflow(self):
path = test_util.get_abspath(os.path.join("data", "paste_columns.ga"))
wf = self.gi.workflows.import_workflow_from_local_path(path)
wf_data = self.gi.workflows.show_workflow(wf["id"])
assert wf_data["id"] == wf["id"]
assert wf_data["name"] == wf["name"]
assert wf_data["url"] == wf["url"]
assert len(wf_data["steps"]) == 3
assert wf_data["inputs"] is not None
def test_update_workflow_name(self):
path = test_util.get_abspath(os.path.join("data", "paste_columns.ga"))
wf = self.gi.workflows.import_workflow_from_local_path(path)
new_name = "new name"
updated_wf = self.gi.workflows.update_workflow(wf["id"], name=new_name)
assert updated_wf["name"] == new_name
@test_util.skip_unless_galaxy("release_21.01")
def test_update_workflow_published(self):
path = test_util.get_abspath(os.path.join("data", "paste_columns.ga"))
wf = self.gi.workflows.import_workflow_from_local_path(path)
assert not wf["published"]
updated_wf = self.gi.workflows.update_workflow(wf["id"], published=True)
assert updated_wf["published"]
updated_wf = self.gi.workflows.update_workflow(wf["id"], published=False)
assert not updated_wf["published"]
@test_util.skip_unless_galaxy(
"release_19.09"
) # due to Galaxy bug fixed in https://github.com/galaxyproject/galaxy/pull/9014
def test_show_workflow_versions(self):
path = test_util.get_abspath(os.path.join("data", "paste_columns.ga"))
wf = self.gi.workflows.import_workflow_from_local_path(path)
wf_data = self.gi.workflows.show_workflow(wf["id"])
assert wf_data["version"] == 0
new_name = "new name"
self.gi.workflows.update_workflow(wf["id"], name=new_name)
updated_wf = self.gi.workflows.show_workflow(wf["id"])
assert updated_wf["name"] == new_name
assert updated_wf["version"] == 1
updated_wf = self.gi.workflows.show_workflow(wf["id"], version=0)
assert updated_wf["name"] == "paste_columns"
assert updated_wf["version"] == 0
updated_wf = self.gi.workflows.show_workflow(wf["id"], version=1)
assert updated_wf["name"] == new_name
assert updated_wf["version"] == 1
@test_util.skip_unless_galaxy("release_19.09")
def test_extract_workflow_from_history(self):
path = test_util.get_abspath(os.path.join("data", "paste_columns.ga"))
wf = self.gi.workflows.import_workflow_from_local_path(path)
history_id = self.gi.histories.create_history(name="test_wf_invocation")["id"]
dataset1_id = self._test_dataset(history_id)
dataset = {"src": "hda", "id": dataset1_id}
invocation_id = self.gi.workflows.invoke_workflow(
wf["id"],
inputs={"Input 1": dataset, "Input 2": dataset},
history_id=history_id,
inputs_by="name",
)["id"]
invocation = self.gi.invocations.wait_for_invocation(invocation_id)
wf1 = self.gi.workflows.show_workflow(invocation["workflow_id"])
datasets = self.gi.histories.show_history(invocation["history_id"], contents=True)
dataset_hids = [dataset["hid"] for dataset in datasets]
job_ids = [step["job_id"] for step in invocation["steps"] if step["job_id"]]
for job_id in job_ids:
self.gi.jobs.wait_for_job(job_id)
new_workflow_name = "My new workflow!"
wf2 = self.gi.workflows.extract_workflow_from_history(
history_id=invocation["history_id"],
workflow_name=new_workflow_name,
job_ids=job_ids,
dataset_hids=dataset_hids,
)
wf2 = self.gi.workflows.show_workflow(wf2["id"])
assert wf2["name"] == new_workflow_name
assert len(wf1["steps"]) == len(wf2["steps"])
for i in range(len(wf1["steps"])):
assert wf1["steps"][str(i)]["type"] == wf2["steps"][str(i)]["type"]
assert wf1["steps"][str(i)]["tool_id"] == wf2["steps"][str(i)]["tool_id"]
def test_show_versions(self):
path = test_util.get_abspath(os.path.join("data", "paste_columns.ga"))
wf = self.gi.workflows.import_workflow_from_local_path(path)
versions = self.gi.workflows.show_versions(wf["id"])
assert len(versions) == 1
version = versions[0]
assert version["version"] == 0
assert "update_time" in version
assert "steps" in version
@test_util.skip_unless_galaxy("release_21.01")
def test_refactor_workflow(self):
actions: List[Dict[str, Any]] = [
{"action_type": "add_input", "type": "data", "label": "foo"},
{"action_type": "update_step_label", "label": "bar", "step": {"label": "foo"}},
]
path = test_util.get_abspath(os.path.join("data", "paste_columns.ga"))
wf = self.gi.workflows.import_workflow_from_local_path(path)
response = self.gi.workflows.refactor_workflow(wf["id"], actions, dry_run=True)
assert len(response["action_executions"]) == len(actions)
assert response["dry_run"] is True
updated_steps = response["workflow"]["steps"]
assert len(updated_steps) == 4
assert {step["label"] for step in updated_steps.values()} == {"bar", None, "Input 1", "Input 2"}
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