diff --git a/test/integration/test_data_manager_workflow_bundle.py b/test/integration/test_data_manager_workflow_bundle.py new file mode 100644 index 000000000000..dd7262906646 --- /dev/null +++ b/test/integration/test_data_manager_workflow_bundle.py @@ -0,0 +1,105 @@ +"""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, + )