How to use the bioblend._tests.test_util.get_abspath function in bioblend

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github galaxyproject / bioblend / bioblend / _tests / TestGalaxyWorkflows.py View on Github external
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)
github galaxyproject / bioblend / bioblend / _tests / TestGalaxyObjects.py View on Github external
import tempfile
import uuid
from ssl import SSLError
from urllib.error import URLError
from urllib.request import urlopen

import bioblend
import bioblend.galaxy.objects.galaxy_instance as galaxy_instance
import bioblend.galaxy.objects.wrappers as wrappers
from bioblend.galaxy import dataset_collections
from . import test_util
from .test_util import unittest

bioblend.set_stream_logger('test', level='INFO')
socket.setdefaulttimeout(10.0)
SAMPLE_FN = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
SAMPLE_WF_COLL_FN = test_util.get_abspath(os.path.join('data', 'paste_columns_collections.ga'))
SAMPLE_WF_PARAMETER_INPUT_FN = test_util.get_abspath(os.path.join('data', 'workflow_with_parameter_input.ga'))
FOO_DATA = 'foo\nbar\n'
FOO_DATA_2 = 'foo2\nbar2\n'
SAMPLE_WF_DICT = {
    'deleted': False,
    'id': '9005c5112febe774',
    'inputs': {
        '571': {'label': 'Input Dataset', 'value': ''},
        '572': {'label': 'Input Dataset', 'value': ''},
    },
    'model_class': 'StoredWorkflow',
    'name': 'paste_columns',
    'published': False,
    'steps': {
        '571': {
github galaxyproject / bioblend / bioblend / _tests / TestGalaxyWorkflows.py View on Github external
def test_import_publish_workflow_dict(self):
        path = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
        with open(path, 'r') 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'])
github galaxyproject / bioblend / bioblend / _tests / TestGalaxyWorkflows.py View on Github external
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))
github galaxyproject / bioblend / bioblend / _tests / TestGalaxyWorkflows.py View on Github external
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)
github galaxyproject / bioblend / bioblend / _tests / TestGalaxyWorkflows.py View on Github external
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'])
github galaxyproject / bioblend / bioblend / _tests / TestGalaxyWorkflows.py View on Github external
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, 'r') as f:
                exported_wf_dict = json.load(f)
github galaxyproject / bioblend / bioblend / _tests / TestGalaxyTools.py View on Github external
def test_upload_file_dbkey(self):
        history = self.gi.histories.create_history(name="test_upload_file history")
        fn = test_util.get_abspath("test_util.py")
        file_name = "test1"
        dbkey = "hg19"
        tool_output = self.gi.tools.upload_file(
            fn,
            history_id=history["id"],
            file_name=file_name,
            dbkey=dbkey,
            file_type="txt",
        )
        self._wait_for_and_verify_upload(tool_output, file_name, fn, expected_dbkey=dbkey)