view env/lib/python3.9/site-packages/bioblend/_tests/TestGalaxyWorkflows.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

import json
import os
import shutil
import tempfile
import time

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"]
        dataset1_id = self._test_dataset(history_id)

        invocations = self.gi.workflows.get_invocations(workflow_id)
        self.assertEqual(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)
        self.assertEqual(len(invocations), 1)
        self.assertEqual(invocations[0]["id"], invocation_id)

        def invocation_steps_by_order_index():
            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(.5)

        invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
        self.assertEqual(invocation['state'], "ready")

        steps = invocation_steps_by_order_index()
        pause_step = steps[2]
        self.assertIsNone(
            self.gi.workflows.show_invocation_step(workflow_id, invocation_id, pause_step["id"])["action"])
        self.gi.workflows.run_invocation_step_action(workflow_id, invocation_id, pause_step["id"], action=True)
        self.assertTrue(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(.5)

        invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
        self.assertEqual(invocation["state"], "scheduled")

    @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)
        self.assertEqual(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)
        self.assertEqual(len(invocations), 1)
        self.assertEqual(invocations[0]["id"], invocation_id)

        invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
        self.assertIn(invocation['state'], ['new', 'ready'])

        self.gi.workflows.cancel_invocation(workflow_id, invocation_id)
        invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
        self.assertEqual(invocation['state'], 'cancelled')

    def test_import_export_workflow_from_local_path(self):
        with self.assertRaises(Exception):
            self.gi.workflows.import_workflow_from_local_path(None)
        path = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
        imported_wf = self.gi.workflows.import_workflow_from_local_path(path)
        self.assertIsInstance(imported_wf, dict)
        self.assertEqual(imported_wf['name'], 'paste_columns')
        self.assertTrue(imported_wf['url'].startswith('/api/workflows/'))
        self.assertFalse(imported_wf['deleted'])
        self.assertFalse(imported_wf['published'])
        with self.assertRaises(Exception):
            self.gi.workflows.export_workflow_to_local_path(None, None, None)
        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)
            self.assertEqual(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)
        self.assertIsInstance(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)
        self.assertIsInstance(imported_wf, dict)
        self.assertFalse(imported_wf['deleted'])
        self.assertTrue(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)
        self.assertIsInstance(imported_wf, dict)
        self.assertEqual(imported_wf['name'], 'paste_columns')
        self.assertTrue(imported_wf['url'].startswith('/api/workflows/'))
        self.assertFalse(imported_wf['deleted'])
        self.assertFalse(imported_wf['published'])
        exported_wf_dict = self.gi.workflows.export_workflow_dict(imported_wf['id'])
        self.assertIsInstance(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)
        self.assertIsInstance(imported_wf, dict)
        self.assertFalse(imported_wf['deleted'])
        self.assertTrue(imported_wf['published'])

    def test_get_workflows(self):
        path = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
        wf = self.gi.workflows.import_workflow_from_local_path(path)
        all_wfs = self.gi.workflows.get_workflows()
        self.assertGreater(len(all_wfs), 0)
        wf_data = self.gi.workflows.get_workflows(workflow_id=wf['id'])[0]
        self.assertEqual(wf['id'], wf_data['id'])
        self.assertEqual(wf['name'], wf_data['name'])
        self.assertEqual(wf['url'], wf_data['url'])
        wf_data_list = self.gi.workflows.get_workflows(name=wf['name'])
        self.assertTrue(any(_['id'] == wf['id'] for _ in wf_data_list))

    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'])
        self.assertEqual(wf_data['id'], wf['id'])
        self.assertEqual(wf_data['name'], wf['name'])
        self.assertEqual(wf_data['url'], wf['url'])
        self.assertEqual(len(wf_data['steps']), 3)
        self.assertIsNotNone(wf_data['inputs'])

    @test_util.skip_unless_galaxy('release_18.05')
    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)
        self.assertEqual(updated_wf['name'], new_name)

    @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'])
        self.assertEqual(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'])
        self.assertEqual(updated_wf['name'], new_name)
        self.assertEqual(updated_wf['version'], 1)
        updated_wf = self.gi.workflows.show_workflow(wf['id'], version=0)
        self.assertEqual(updated_wf['name'], 'paste_columns')
        self.assertEqual(updated_wf['version'], 0)
        updated_wf = self.gi.workflows.show_workflow(wf['id'], version=1)
        self.assertEqual(updated_wf['name'], new_name)
        self.assertEqual(updated_wf['version'], 1)

    def test_run_workflow(self):
        path = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
        wf = self.gi.workflows.import_workflow_from_local_path(path)
        # Try invalid run of workflow
        with self.assertRaises(Exception):
            self.gi.workflows.run_workflow(wf['id'], None)

    def test_invoke_workflow(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}
        invoke_response = self.gi.workflows.invoke_workflow(
            wf['id'],
            inputs={'Input 1': dataset, 'Input 2': dataset},
            history_id=history_id,
            inputs_by='name',
        )
        assert invoke_response['state'] == 'new', invoke_response