mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
mvdbeek
106 lines
3.0 KiB
Python
106 lines
3.0 KiB
Python
"""Integration tests for workflow syncing."""
|
|
|
|
from galaxy_test.base.populators import (
|
|
DatasetPopulator,
|
|
WorkflowPopulator,
|
|
)
|
|
from galaxy_test.base.uses_shed_api import UsesShedApi
|
|
from .test_containerized_jobs import ContainerizedIntegrationTestCase
|
|
|
|
|
|
class TestDataManagerWorkflowInvocation(ContainerizedIntegrationTestCase, UsesShedApi):
|
|
dataset_populator: DatasetPopulator
|
|
framework_tool_and_types = True
|
|
require_admin_user = False
|
|
admin_user_email = "data-manager@galaxyproject.org"
|
|
container_type = "docker"
|
|
|
|
@classmethod
|
|
def handle_galaxy_config_kwds(cls, config):
|
|
super().handle_galaxy_config_kwds(config)
|
|
config["check_migrate_databases"] = False
|
|
config["admin_users"] = cls.admin_user_email
|
|
|
|
def setUp(self):
|
|
super().setUp()
|
|
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
|
|
self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
|
|
|
|
def test_run_data_manager_workflow(self):
|
|
self.install_repository("devteam", "data_manager_fetch_genome_dbkeys_all_fasta", "4d3eff1bc421")
|
|
self.install_repository("devteam", "data_manager_bwa_mem_index_builder", "9e993022c762")
|
|
with self._different_user(email=self.admin_user_email), self.dataset_populator.test_history() as history_id:
|
|
self.workflow_populator.run_workflow(
|
|
"""
|
|
class: GalaxyWorkflow
|
|
label: Indexing workflow
|
|
inputs:
|
|
dbkey:
|
|
optional: false
|
|
type: string
|
|
display name:
|
|
optional: false
|
|
type: string
|
|
name:
|
|
optional: false
|
|
type: string
|
|
id:
|
|
optional: false
|
|
type: string
|
|
url:
|
|
optional: false
|
|
type: string
|
|
steps:
|
|
fasta_index:
|
|
tool_id: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.4
|
|
tool_version: 0.0.4
|
|
tool_state:
|
|
dbkey_source:
|
|
dbkey_source_selector: new
|
|
reference_source:
|
|
reference_source_selector: url
|
|
sorting:
|
|
sort_selector: as_is
|
|
__data_manager_mode: bundle
|
|
in:
|
|
dbkey_source|dbkey:
|
|
source: dbkey
|
|
dbkey_source|dbkey_name:
|
|
source: display name
|
|
reference_source|user_url:
|
|
source: url
|
|
sequence_id:
|
|
source: id
|
|
sequence_name:
|
|
source: name
|
|
|
|
bwa_mem_index:
|
|
tool_id: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/bwa_mem_index_builder_data_manager/0.0.5
|
|
tool_version: 0.0.5
|
|
tool_state:
|
|
__data_manager_mode: bundle
|
|
in:
|
|
all_fasta_source: fasta_index/out_file
|
|
|
|
test_data:
|
|
dbkey:
|
|
value: wf_bundle
|
|
type: raw
|
|
display name:
|
|
value: display name value
|
|
type: raw
|
|
id:
|
|
value: wf_bundle_id
|
|
type: raw
|
|
name:
|
|
value: workflow bundle
|
|
type: raw
|
|
url:
|
|
value: https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.fasta
|
|
type: raw
|
|
""",
|
|
history_id=history_id,
|
|
wait=True,
|
|
assert_ok=True,
|
|
)
|