cloudos-cli 2.17.0__py3-none-any.whl

tests/test_jobs/test_send_job.py

@@ -0,0 +1,84 @@
+"""pytest is added for checking Job.workflow_id"""
+from io import StringIO
+import sys
+import mock
+import responses
+from responses import matchers
+from cloudos_cli.jobs import Job
+from tests.functions_for_pytest import load_json_file
+
+INPUT = "tests/test_data/send_job.json"
+APIKEY = 'vnoiweur89u2ongs'
+CLOUDOS_URL = 'http://cloudos.lifebit.ai'
+WORKSPACE_ID = 'lv89ufc838sdig'
+PROJECT_NAME = "lifebit-testing"
+WORKFLOW_NAME = "nf-core-deepvariant"
+INPUT_PROJECT = "tests/test_data/projects.json"
+INPUT_WORKFLOW = "tests/test_data/workflows.json"
+PAGE_SIZE = 10
+PAGE = 1
+ARCHIVED_STATUS = "false"
+
+param_dict = {
+    "config": "cloudos_cli/examples/rnatoy.config"
+    }
+
+
+@mock.patch('cloudos_cli.clos', mock.MagicMock())
+@responses.activate
+def test_send_job():
+    """
+    Test 'send_job' to work as intended
+    API request is mocked and replicated with json files
+    """
+    create_json_project = load_json_file(INPUT_PROJECT)
+    create_json_workflow = load_json_file(INPUT_WORKFLOW)
+    create_json = load_json_file(INPUT)
+    params_job = {"teamId": WORKSPACE_ID}
+    params_workflows = {
+        "teamId": WORKSPACE_ID,
+        "pageSize": PAGE_SIZE,
+        "page": PAGE,
+        "archived.status": ARCHIVED_STATUS}
+    header = {
+            "Content-type": "application/json",
+            "apikey": APIKEY
+        }
+    search_str = f"teamId={WORKSPACE_ID}"
+    search_str_workflows = f"teamId={WORKSPACE_ID}&pageSize={PAGE_SIZE}&page={PAGE}&archived.status={ARCHIVED_STATUS}"
+    # mock GET method with the .json
+    responses.add(
+            responses.POST,
+            url=f"{CLOUDOS_URL}/api/v1/jobs?{search_str}",
+            body=create_json,
+            headers=header,
+            match=[matchers.query_param_matcher(params_job)],
+            status=200)
+    responses.add(
+            responses.GET,
+            url=f"{CLOUDOS_URL}/api/v1/projects?{search_str}",
+            body=create_json_project,
+            headers=header,
+            match=[matchers.query_param_matcher(params_job)],
+            status=200)
+    responses.add(
+            responses.GET,
+            url=f"{CLOUDOS_URL}/api/v3/workflows?{search_str_workflows}",
+            body=create_json_workflow,
+            headers=header,
+            match=[matchers.query_param_matcher(params_workflows)],
+            status=200)
+    # start cloudOS service
+    job = Job(apikey=APIKEY,
+              cloudos_url=CLOUDOS_URL,
+              workspace_id=WORKSPACE_ID,
+              cromwell_token=None,
+              project_name=PROJECT_NAME,
+              workflow_name=WORKFLOW_NAME)
+    output = StringIO()
+    sys.stdout = output
+    job_json = job.send_job(param_dict["config"])
+    result_string = output.getvalue().rstrip()
+
+    assert isinstance(job_json, str)
+    assert "Job successfully launched to CloudOS, please check the following link:" in result_string

tests/test_jobs/test_workflow_id.py

@@ -0,0 +1,67 @@
+"""pytest is added for checking Job.workflow_id"""
+import mock
+import responses
+from responses import matchers
+from cloudos_cli.jobs import Job
+from tests.functions_for_pytest import load_json_file
+
+INPUT_PROJECT = "tests/test_data/projects.json"
+INPUT_WORKFLOW = "tests/test_data/workflows.json"
+APIKEY = 'vnoiweur89u2ongs'
+CLOUDOS_URL = 'http://cloudos.lifebit.ai'
+WORKSPACE_ID = 'lv89ufc838sdig'
+PROJECT_NAME = "lifebit-testing"
+WORKFLOW_NAME = "nf-core-deepvariant"
+PAGE_SIZE = 10
+PAGE = 1
+ARCHIVED_STATUS = "false"
+
+
+@mock.patch('cloudos_cli.clos', mock.MagicMock())
+@responses.activate
+def test_workflow_id():
+    """
+    Test 'workflow_id' to work as intended
+    API request is mocked and replicated with json files
+    """
+    create_json_project = load_json_file(INPUT_PROJECT)
+    create_json_workflow = load_json_file(INPUT_WORKFLOW)
+    params = {"teamId": WORKSPACE_ID}
+    params_workflows = {
+        "teamId": WORKSPACE_ID,
+        "pageSize": PAGE_SIZE,
+        "page": PAGE,
+        "archived.status": ARCHIVED_STATUS}
+    header = {
+        "Accept": "application/json, text/plain, */*",
+        "Content-Type": "application/json;charset=UTF-8",
+        "apikey": APIKEY
+    }
+    search_str = f"teamId={WORKSPACE_ID}"
+    search_str_workflows = f"teamId={WORKSPACE_ID}&pageSize={PAGE_SIZE}&page={PAGE}&archived.status={ARCHIVED_STATUS}"
+    # mock GET method with the .json
+    responses.add(
+            responses.GET,
+            url=f"{CLOUDOS_URL}/api/v1/projects?{search_str}",
+            body=create_json_project,
+            headers=header,
+            match=[matchers.query_param_matcher(params)],
+            status=200)
+    responses.add(
+            responses.GET,
+            url=f"{CLOUDOS_URL}/api/v3/workflows?{search_str_workflows}",
+            body=create_json_workflow,
+            headers=header,
+            match=[matchers.query_param_matcher(params_workflows)],
+            status=201)
+    # start cloudOS service
+    job = Job(apikey=APIKEY,
+              cloudos_url=CLOUDOS_URL,
+              workspace_id=WORKSPACE_ID,
+              cromwell_token=None,
+              project_name=PROJECT_NAME,
+              workflow_name=WORKFLOW_NAME)
+    # get mock response
+    wf_id = job.workflow_id
+    # check the response
+    assert wf_id == "111XXX111"