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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 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
}
#!/usr/bin/env python
import os
from bioblend import galaxy
admin_email = os.environ.get('GALAXY_DEFAULT_ADMIN_USER', 'admin@galaxy.org')
admin_pass = os.environ.get('GALAXY_DEFAULT_ADMIN_PASSWORD', 'admin')
url = "http://localhost:8080"
gi = galaxy.GalaxyInstance(url=url, email=admin_email, password=admin_pass)
wf = galaxy.workflows.WorkflowClient(gi)
for filepath in os.listdir('/home/galaxy/'):
if filepath.endswith('.ga'):
wf.import_workflow_from_local_path( os.path.join('/home/galaxy/', filepath) )
def __init__(self, url, api, library_id, folder_id, should_link,
non_local):
self.gi = galaxy.GalaxyInstance(url=url, key=api)
self.library_id = library_id
self.folder_id = folder_id
self.should_link = should_link
self.non_local = non_local
self.memo_path = {}
self.prepopulate_memo()
def setup_data_libraries(gi, data, training=False, legacy=False):
"""
Load files into a Galaxy data library.
By default all test-data tools from all installed tools
will be linked into a data library.
"""
log.info("Importing data libraries.")
jc = galaxy.jobs.JobsClient(gi)
config = galaxy.config.ConfigClient(gi)
version = config.get_version()
if legacy:
create_func = create_legacy
else:
version_major = version.get("version_major", "16.01")
create_func = create_batch_api if version_major >= "18.05" else create_legacy
library_def = yaml.safe_load(data)
def normalize_items(has_items):
# Synchronize Galaxy batch format with older training material style.
if "files" in has_items:
items = has_items.pop("files")
has_items["items"] = items
def galaxy_connection(self):
return galaxy.GalaxyInstance(url=self.base_url, key=self.api_key)
def setup_data_libraries(gi, data, training=False, legacy=False):
"""
Load files into a Galaxy data library.
By default all test-data tools from all installed tools
will be linked into a data library.
"""
log.info("Importing data libraries.")
jc = galaxy.jobs.JobsClient(gi)
config = galaxy.config.ConfigClient(gi)
version = config.get_version()
if legacy:
create_func = create_legacy
else:
version_major = version.get("version_major", "16.01")
create_func = create_batch_api if version_major >= "18.05" else create_legacy
library_def = yaml.safe_load(data)
def normalize_items(has_items):
# Synchronize Galaxy batch format with older training material style.
if "files" in has_items:
items = has_items.pop("files")
has_items["items"] = items
#!/usr/bin/env python
from bioblend import galaxy
import json
import time
with open('/etc/gx-api-creds.json', 'r') as handle:
secrets = json.load(handle)
api_key = secrets['api_key']
url = secrets['url']
handlers = secrets['handlers']
history_name = "Nagios Run %s" % time.time()
gi = galaxy.GalaxyInstance(url, api_key)
history = gi.histories.create_history(name=history_name)
history_id = history['id']
jobs = []
# Run all of the jobs.
try:
for handler in handlers:
job = gi.tools.run_tool(history_id, 'echo_main_' + handler, {'echo': handler})
jobs.append({
'handler': handler,
'job': job,
'started': time.time()
})
# Check all the jobs
"""
Return a Galaxy connection, given a user or an API key.
If not given gets the arguments from the file.
If either is missing raise ValueError.
"""
if file:
file_content = load_yaml_file(file)
else:
file_content = dict()
url = args.galaxy or file_content.get('galaxy_instance')
galaxy_url = check_url(url, log)
api_key = args.api_key or file_content.get('api_key')
if args.user and args.password:
return galaxy.GalaxyInstance(url=galaxy_url, email=args.user, password=args.password)
elif api_key:
return galaxy.GalaxyInstance(url=galaxy_url, key=api_key)
elif not login_required:
return galaxy.GalaxyInstance(url=galaxy_url)
else:
raise ValueError("Missing api key or user & password combination, in order to make a galaxy connection.")