How to use bioblend - 10 common examples

def main():
    args = parse_args()
    web_protocol, fqdn, ftp_protocol, port, api_key = \
    args.protocol, args.fqdn, args.ftp_protocol, args.port, args.api_key
    if args.http_auth_username:
        GalaxyInstance.make_delete_request = inject_auth(make_delete_request, args.http_auth_username, args.http_auth_password)
        GalaxyInstance.make_post_request = inject_auth(make_post_request, args.http_auth_username, args.http_auth_password)
        GalaxyInstance.make_put_request = inject_auth(make_put_request, args.http_auth_username, args.http_auth_password)
        GalaxyInstance.make_get_request = inject_auth(GalaxyInstance.make_get_request, args.http_auth_username, args.http_auth_password)
    url = web_protocol + "://" + fqdn
    new_api_key, user_email, password = create_user(url, api_key)
    tmpfile = NamedTemporaryFile()
    tmpfile.write("1\n2\n3\n")
    if ftp_protocol == "ftp":
        ftp_upload_file(fqdn, user_email, password, port, tmpfile.name)
    else:
        sftp_upload_file(fqdn, user_email, password, port, tmpfile.name)
    if not successfull_upload(url, new_api_key, tmpfile.name):
        sys.exit("{ftp_protocol} upload to galaxy server {fqdn} failed.".format(ftp_protocol = ftp_protocol, fqdn = fqdn))

def _gi(args):
    gi = galaxy.GalaxyInstance(args.host, key=args.api_key)
    name = "histexport-user-%d" % random.randint(0, 1000000)

    user = gi.users.create_local_user(name, "%s@galaxytesting.dev" % name, "pass123")
    user_id = user["id"]
    api_key = gi.users.create_user_apikey(user_id)
    user_gi = galaxy.GalaxyInstance(args.host, api_key)
    return user_gi

def _gi(args):
    gi = galaxy.GalaxyInstance(args.host, key=args.api_key)
    name = "wftest-user-%d" % random.randint(0, 1000000)

    user = gi.users.create_local_user(name, "%s@galaxytesting.dev" % name, "pass123")
    user_id = user["id"]
    api_key = gi.users.create_user_apikey(user_id)
    user_gi = galaxy.GalaxyInstance(args.host, api_key)
    return user_gi

def setUp(self):
        self.GALAXY_HISTORY_ID = str(uuid.uuid4())
        self.GALAXY_DATASET_ID = str(uuid.uuid4())
        self.GALAXY_DATASET_FILESIZE = 1024
        self.MISCELLANEOUS_STRING = "Coffee is tasty"

        self.galaxy_instance = GalaxyInstanceFactory(api_key=str(uuid.uuid4()))
        self.show_history_mock = mock.patch.object(
            galaxy.histories.HistoryClient, "show_history"
        ).start()
        self.show_dataset_mock = mock.patch.object(
            galaxy.histories.HistoryClient, "show_dataset"
        ).start()

        self.history_content_entry = {
            "name": "Test History Content Entry",
            "url": "www.example.com/history_content_entry",
            "type": "file",
            "id": self.GALAXY_DATASET_ID
        }

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)

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': {

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'])

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_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 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'])