Python DatasetPopulator.get_history_dataset_content方法代码示例

# 需要导入模块: from base.populators import DatasetPopulator [as 别名]
# 或者: from base.populators.DatasetPopulator import get_history_dataset_content [as 别名]
class DockerizedJobsIntegrationTestCase(integration_util.IntegrationTestCase, RunsEnvironmentJobs):

    framework_tool_and_types = True

    @classmethod
    def handle_galaxy_config_kwds(cls, config):
        cls.jobs_directory = tempfile.mkdtemp()
        config["jobs_directory"] = cls.jobs_directory
        config["job_config_file"] = DOCKERIZED_JOB_CONFIG_FILE
        # Disable tool dependency resolution.
        config["tool_dependency_dir"] = "none"
        config["enable_beta_mulled_containers"] = "true"

    def setUp(self):
        super(DockerizedJobsIntegrationTestCase, self).setUp()
        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
        self.history_id = self.dataset_populator.new_history()

    def test_explicit(self):
        self.dataset_populator.run_tool("mulled_example_explicit", {}, self.history_id)
        self.dataset_populator.wait_for_history(self.history_id, assert_ok=True)
        output = self.dataset_populator.get_history_dataset_content(self.history_id)
        assert "0.7.15-r1140" in output

    def test_mulled_simple(self):
        self.dataset_populator.run_tool("mulled_example_simple", {}, self.history_id)
        self.dataset_populator.wait_for_history(self.history_id, assert_ok=True)
        output = self.dataset_populator.get_history_dataset_content(self.history_id)
        assert "0.7.15-r1140" in output

    def test_docker_job_enviornment(self):
        job_env = self._run_and_get_environment_properties("job_environment_default")

        euid = os.geteuid()
        egid = os.getgid()

        assert job_env.user_id == str(euid), job_env.user_id
        assert job_env.group_id == str(egid), job_env.group_id
        assert job_env.pwd.startswith(self.jobs_directory)
        assert job_env.pwd.endswith("/working")
        assert job_env.home.startswith(self.jobs_directory)
        assert job_env.home.endswith("/home")

    def test_docker_job_environment_legacy(self):
        job_env = self._run_and_get_environment_properties("job_environment_default_legacy")

        euid = os.geteuid()
        egid = os.getgid()

        assert job_env.user_id == str(euid), job_env.user_id
        assert job_env.group_id == str(egid), job_env.group_id
        assert job_env.pwd.startswith(self.jobs_directory)
        assert job_env.pwd.endswith("/working")
        # Should we change env_pass_through to just always include TMP and HOME for docker?
        # I'm not sure, if yes this would change.
        assert job_env.home == "/", job_env.home

# 需要导入模块: from base.populators import DatasetPopulator [as 别名]
# 或者: from base.populators.DatasetPopulator import get_history_dataset_content [as 别名]
 def test_runs_on_mule(self):
     tool_id = 'config_vars'
     expect_server_name = self.expected_server_name
     dataset_populator = DatasetPopulator(self.galaxy_interactor)
     history_id = dataset_populator.new_history()
     payload = dataset_populator.run_tool(
         tool_id=tool_id,
         inputs={'var': 'server_name'},
         history_id=history_id,
     )
     dataset_id = payload['outputs'][0]['id']
     dataset_populator.wait_for_dataset(history_id, dataset_id, assert_ok=True)
     output = dataset_populator.get_history_dataset_content(history_id, dataset_id=dataset_id).strip()
     assert output.startswith(expect_server_name), (
         "Job handler's server name '{output}' does not start with expected string '{expected}'".format(
             output=output,
             expected=expect_server_name,
         )
     )

# 需要导入模块: from base.populators import DatasetPopulator [as 别名]
# 或者: from base.populators.DatasetPopulator import get_history_dataset_content [as 别名]
class MaximumWorkflowJobsPerSchedulingIterationTestCase(integration_util.IntegrationTestCase):

    framework_tool_and_types = True

    def setUp(self):
        super(MaximumWorkflowJobsPerSchedulingIterationTestCase, self).setUp()
        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
        self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
        self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)

    @classmethod
    def handle_galaxy_config_kwds(cls, config):
        config["maximum_workflow_jobs_per_scheduling_iteration"] = 1

    def do_test(self):
        workflow_id = self.workflow_populator.upload_yaml_workflow("""
class: GalaxyWorkflow
steps:
  - type: input_collection
  - tool_id: collection_creates_pair
    state:
      input1:
        $link: 0
  - tool_id: collection_paired_test
    state:
      f1:
        $link: 1#paired_output
  - tool_id: cat_list
    state:
      input1:
        $link: 2#out1
""")
        with self.dataset_populator.test_history() as history_id:
            hdca1 = self.dataset_collection_populator.create_list_in_history(history_id, contents=["a\nb\nc\nd\n", "e\nf\ng\nh\n"]).json()
            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
            inputs = {
                '0': {"src": "hdca", "id": hdca1["id"]},
            }
            invocation_id = self.workflow_populator.invoke_workflow(history_id, workflow_id, inputs)
            self.workflow_populator.wait_for_workflow(history_id, workflow_id, invocation_id)
            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
            self.assertEqual("a\nc\nb\nd\ne\ng\nf\nh\n", self.dataset_populator.get_history_dataset_content(history_id, hid=0))

# 需要导入模块: from base.populators import DatasetPopulator [as 别名]
# 或者: from base.populators.DatasetPopulator import get_history_dataset_content [as 别名]

#.........这里部分代码省略.........
            assert self._update(history_id, {str_key: False}).status_code == 400

        for bool_key in ['deleted', 'importable', 'published']:
            assert self._update(history_id, {bool_key: "a string"}).status_code == 400

        assert self._update(history_id, {"tags": "a simple string"}).status_code == 400
        assert self._update(history_id, {"tags": [True]}).status_code == 400

    def test_invalid_keys(self):
        invalid_history_id = "1234123412341234"

        assert self._get("histories/%s" % invalid_history_id).status_code == 400
        assert self._update(invalid_history_id, {"name": "new name"}).status_code == 400
        assert self._delete("histories/%s" % invalid_history_id).status_code == 400
        assert self._post("histories/deleted/%s/undelete" % invalid_history_id).status_code == 400

    def test_create_anonymous_fails(self):
        post_data = dict(name="CannotCreate")
        # Using lower-level _api_url will cause key to not be injected.
        histories_url = self._api_url("histories")
        create_response = post(url=histories_url, data=post_data)
        self._assert_status_code_is(create_response, 403)

    def test_import_export(self):
        history_name = "for_export"
        history_id = self.dataset_populator.new_history(name=history_name)
        self.dataset_populator.new_dataset(history_id, content="1 2 3")
        imported_history_id = self._reimport_history(history_id, history_name)

        contents_response = self._get("histories/%s/contents" % imported_history_id)
        self._assert_status_code_is(contents_response, 200)
        contents = contents_response.json()
        assert len(contents) == 1
        imported_content = self.dataset_populator.get_history_dataset_content(
            history_id=imported_history_id,
            dataset_id=contents[0]["id"]
        )
        assert imported_content == "1 2 3\n"

    def test_import_export_collection(self):
        from nose.plugins.skip import SkipTest
        raise SkipTest("Collection import/export not yet implemented")

        history_name = "for_export_with_collections"
        history_id = self.dataset_populator.new_history(name=history_name)
        self.dataset_collection_populator.create_list_in_history(history_id, contents=["Hello", "World"])

        imported_history_id = self._reimport_history(history_id, history_name)

        contents_response = self._get("histories/%s/contents" % imported_history_id)
        self._assert_status_code_is(contents_response, 200)
        contents = contents_response.json()
        assert len(contents) == 3

    def _reimport_history(self, history_id, history_name):
        # Ensure the history is ready to go...
        self.dataset_populator.wait_for_history(history_id, assert_ok=True)

        # Export the history.
        download_path = self._export(history_id)

        # Create download for history
        full_download_url = "%s%s?key=%s" % (self.url, download_path, self.galaxy_interactor.api_key)
        download_response = get(full_download_url)
        self._assert_status_code_is(download_response, 200)

# 需要导入模块: from base.populators import DatasetPopulator [as 别名]
# 或者: from base.populators.DatasetPopulator import get_history_dataset_content [as 别名]

#.........这里部分代码省略.........
        bam_path = TestDataResolver().get_filename("1.bam")
        with open(bam_path, "rb") as fh:
            details = self._upload_and_get_details(fh, file_type="auto")
        assert details["state"] == "ok"
        assert details["file_ext"] == "bam", details

    def test_fetch_metadata(self):
        table = ONE_TO_SIX_WITH_SPACES
        details = self._upload_and_get_details(table, api='fetch', dbkey="hg19", info="cool upload", tags=["name:data", "group:type:paired-end"])
        assert details.get("genome_build") == "hg19"
        assert details.get("misc_info") == "cool upload", details
        tags = details.get("tags")
        assert len(tags) == 2, details
        assert "group:type:paired-end" in tags
        assert "name:data" in tags

    def test_upload_multiple_files_1(self):
        with self.dataset_populator.test_history() as history_id:
            payload = self.dataset_populator.upload_payload(history_id, "Test123",
                dbkey="hg19",
                extra_inputs={
                    "files_1|url_paste": "SecondOutputContent",
                    "files_1|NAME": "SecondOutputName",
                    "files_1|file_type": "tabular",
                    "files_1|dbkey": "hg18",
                    "file_count": "2",
                }
            )
            run_response = self.dataset_populator.tools_post(payload)
            self.dataset_populator.wait_for_tool_run(history_id, run_response)
            datasets = run_response.json()["outputs"]

            assert len(datasets) == 2, datasets
            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0])
            assert content.strip() == "Test123"
            assert datasets[0]["file_ext"] == "txt"
            assert datasets[0]["genome_build"] == "hg19", datasets

            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1])
            assert content.strip() == "SecondOutputContent"
            assert datasets[1]["file_ext"] == "tabular"
            assert datasets[1]["genome_build"] == "hg18", datasets

    def test_upload_multiple_files_2(self):
        with self.dataset_populator.test_history() as history_id:
            payload = self.dataset_populator.upload_payload(history_id, "Test123",
                file_type="tabular",
                dbkey="hg19",
                extra_inputs={
                    "files_1|url_paste": "SecondOutputContent",
                    "files_1|NAME": "SecondOutputName",
                    "files_1|file_type": "txt",
                    "files_1|dbkey": "hg18",
                    "file_count": "2",
                }
            )
            run_response = self.dataset_populator.tools_post(payload)
            self.dataset_populator.wait_for_tool_run(history_id, run_response)
            datasets = run_response.json()["outputs"]

            assert len(datasets) == 2, datasets
            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0])
            assert content.strip() == "Test123"
            assert datasets[0]["file_ext"] == "tabular", datasets
            assert datasets[0]["genome_build"] == "hg19", datasets

# 需要导入模块: from base.populators import DatasetPopulator [as 别名]
# 或者: from base.populators.DatasetPopulator import get_history_dataset_content [as 别名]

#.........这里部分代码省略.........
                "files_1|space_to_tab": "Yes",
                "files_2|url_paste": "log\rcontent",
                "files_2|type": "upload_dataset",
            })

            roadmaps_content = self._get_roadmaps_content(history_id, dataset)
            assert roadmaps_content.strip() == "roadmaps\ncontent", roadmaps_content

    def test_upload_dbkey(self):
        with self.dataset_populator.test_history() as history_id:
            payload = self.dataset_populator.upload_payload(history_id, "Test123", dbkey="hg19")
            run_response = self.dataset_populator.tools_post(payload)
            self.dataset_populator.wait_for_tool_run(history_id, run_response)
            datasets = run_response.json()["outputs"]
            assert datasets[0].get("genome_build") == "hg19", datasets[0]

    def test_upload_multiple_files_1(self):
        with self.dataset_populator.test_history() as history_id:
            payload = self.dataset_populator.upload_payload(history_id, "Test123",
                dbkey="hg19",
                extra_inputs={
                    "files_1|url_paste": "SecondOutputContent",
                    "files_1|NAME": "SecondOutputName",
                    "files_1|file_type": "tabular",
                    "files_1|dbkey": "hg18",
                    "file_count": "2",
                }
            )
            run_response = self.dataset_populator.tools_post(payload)
            self.dataset_populator.wait_for_tool_run(history_id, run_response)
            datasets = run_response.json()["outputs"]

            assert len(datasets) == 2, datasets
            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0])
            assert content.strip() == "Test123"
            assert datasets[0]["file_ext"] == "txt"
            assert datasets[0]["genome_build"] == "hg19", datasets

            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1])
            assert content.strip() == "SecondOutputContent"
            assert datasets[1]["file_ext"] == "tabular"
            assert datasets[1]["genome_build"] == "hg18", datasets

    def test_upload_multiple_files_2(self):
        with self.dataset_populator.test_history() as history_id:
            payload = self.dataset_populator.upload_payload(history_id, "Test123",
                file_type="tabular",
                dbkey="hg19",
                extra_inputs={
                    "files_1|url_paste": "SecondOutputContent",
                    "files_1|NAME": "SecondOutputName",
                    "files_1|file_type": "txt",
                    "files_1|dbkey": "hg18",
                    "file_count": "2",
                }
            )
            run_response = self.dataset_populator.tools_post(payload)
            self.dataset_populator.wait_for_tool_run(history_id, run_response)
            datasets = run_response.json()["outputs"]

            assert len(datasets) == 2, datasets
            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0])
            assert content.strip() == "Test123"
            assert datasets[0]["file_ext"] == "tabular", datasets
            assert datasets[0]["genome_build"] == "hg19", datasets