Dicom Viewer Tests

.github/workflows/shared_integration_tests.yaml

@@ -205,6 +205,7 @@ jobs:
             run: |
               mkdir output
               GEN3_INSTANCE_TYPE="ADMINVM_REMOTE" poetry run pytest -n auto -m "not wip" --alluredir allure-results --no-header --dist loadscope ${{ env.TEST_LABEL }}
+              GEN3_INSTANCE_TYPE="ADMINVM_REMOTE" poetry run pytest -m "not wip or sequential" --alluredir allure-results --no-header ${{ env.TEST_LABEL }}
 
           - name: Debug logging
             if: ${{ env.SKIP_TESTS != 'true' }}

gen3-integration-tests/pages/dicom.py

@@ -0,0 +1,32 @@
+import pytest
+from playwright.sync_api import Page, expect
+from utils import logger
+from utils.test_execution import screenshot
+
+
+class DicomPage(object):
+    def __init__(self):
+        self.BASE_URL = f"{pytest.root_url_portal}"
+        # Endpoints
+        self.EXPLORER_ENDPOINT = f"{self.BASE_URL}/explorer"
+        # Locators
+        self.IMAGING_STUDIES_TAB = "//h3[normalize-space()='Imaging Studies']"
+        self.CORNERSTONE_CANVAS = "//*[@class='cornerstone-canvas']"
+
+    def goto_explorer_page(self, page: Page, study_id):
+        page.goto(self.EXPLORER_ENDPOINT)
+        screenshot(page, "ExplorerPage")
+        imaging_studies_tab = page.locator(self.IMAGING_STUDIES_TAB)
+        expect(imaging_studies_tab).to_be_visible(timeout=5000)
+        imaging_studies_tab.click()
+        screenshot(page, "ImagingStudiesPage")
+        STUDY_ID_HREF_XPATH = f"//a[contains(@href, 'StudyInstanceUIDs={study_id}')][1]"
+        study_id_href = page.locator(STUDY_ID_HREF_XPATH)
+        expect(study_id_href).to_be_visible(timeout=5000)
+        href_url = study_id_href.get_attribute("href")
+        page.goto(href_url)
+        logger.info(page.url)
+        assert study_id in page.url, f"Expected {study_id} in {page.url}"
+        cornerstone_canvas = page.locator(self.CORNERSTONE_CANVAS)
+        expect(cornerstone_canvas).to_be_visible(timeout=5000)
+        screenshot(page, "OHIFViewerPage")

gen3-integration-tests/pages/login.py

@@ -103,6 +103,9 @@ def login(
                 .get("topBar", {})
                 .get("useProfileDropdown", "")
             ):
+                accept_button = page.locator(self.POP_UP_ACCEPT_BUTTON)
+                if accept_button:
+                    accept_button.click()
                 page.locator(self.USER_PROFILE_DROPDOWN).click()
             expect(
                 page.get_by_role("link").filter(has_text=logged_in_user)

gen3-integration-tests/pyproject.toml

@@ -46,9 +46,11 @@ markers = [
   "wip: marks tests as `Work In Progress` and skips them in CI pipeline",
   "requires_fence_client: tests for fence clients",
   "requires_google_bucket: tests which require creation of google buckets",
+  "sequential: tests which needs to be run sequentially due to dependencies",
   # services
   "argo_wrapper: tests for argo_wrapper",
   "audit: tests for audit-service",
+  "dicom_viewer: tests for dicom-viewer",
   "fence: test for fence service",
   "frontend_framework: tests for frontend-framework",
   "gen3_client: tests for gen3-client / cdis-data-client",

gen3-integration-tests/services/dicom.py

@@ -0,0 +1,71 @@
+import pytest
+import requests
+from gen3.auth import Gen3Auth
+from gen3.submission import Gen3Submission
+from utils import TEST_DATA_PATH_OBJECT, logger
+
+
+class Dicom(object):
+    def __init__(self):
+        self.BASE_URL = f"{pytest.root_url}"
+        self.DICOM_INSTANCES = "/dicom-server/instances"
+        self.DICOM_STUDIES = "/dicom-server/studies"
+
+    def submit_dicom_file(self, user="main_account", expected_status=200):
+        auth = Gen3Auth(refresh_token=pytest.api_keys[user], endpoint=self.BASE_URL)
+        access_token = auth.get_access_token()
+        url = self.BASE_URL + self.DICOM_INSTANCES
+        with (TEST_DATA_PATH_OBJECT / "dicom/test_file.dcm").open("rb") as file:
+            content = file.read()
+        headers = {
+            "Content-Type": "application/dicom",
+            "Authorization": f"bearer {access_token}",
+        }
+        response = requests.post(url=url, data=content, headers=headers)
+        assert (
+            response.status_code == expected_status
+        ), f"Expected status {expected_status} but got {response.status_code}"
+        if response.status_code == 200:
+            logger.info(response.json())
+            return response.json()
+
+    def get_studies(self, study_instance, user="main_account"):
+        auth = Gen3Auth(refresh_token=pytest.api_keys[user], endpoint=self.BASE_URL)
+        url = self.DICOM_STUDIES + "/" + study_instance
+        response = auth.curl(path=url)
+        assert (
+            response.status_code == 200
+        ), f"Expected status 200 but got {response.status_code}"
+        return response.json()
+
+    def submit_dicom_data(
+        self,
+        case_submitted_id,
+        program,
+        project,
+        study_id,
+        dataset_submitter_id,
+        case_linked_external_data,
+        user="main_account",
+    ):
+        auth = Gen3Auth(refresh_token=pytest.api_keys[user], endpoint=self.BASE_URL)
+        submit_data = {
+            "type": "imaging_study",
+            "datasets": {"submitter_id": dataset_submitter_id},
+            "cases": [
+                {
+                    "submitter_id": case_submitted_id,
+                }
+            ],
+            "image_data_modified": False,
+            "submitter_id": study_id,
+        }
+        Gen3Submission(auth_provider=auth).submit_record(program, project, submit_data)
+
+    def get_dicom_file(self, dicom_file_id, user="main_account", expected_status=200):
+        auth = Gen3Auth(refresh_token=pytest.api_keys[user], endpoint=self.BASE_URL)
+        url = self.DICOM_INSTANCES + "/" + dicom_file_id
+        response = auth.curl(path=url)
+        assert (
+            response.status_code == expected_status
+        ), f"Expected status {expected_status} but got {response.status_code}"

gen3-integration-tests/tests/test_dicom_viewer.py

@@ -0,0 +1,102 @@
+import pytest
+import utils.gen3_admin_tasks as gat
+from gen3.auth import Gen3Auth
+from pages.dicom import DicomPage
+from pages.login import LoginPage
+from playwright.sync_api import Page
+from services.dicom import Dicom
+from services.graph import GraphDataTools
+from utils import logger
+
+
+@pytest.mark.skipif(
+    "midrc" not in pytest.namespace, reason="DICOM test is specific to MIDRC"
+)
+@pytest.mark.dicom_viewer
+@pytest.mark.sequential
+class TestDicomViewer(object):
+    auth = Gen3Auth(refresh_token=pytest.api_keys["main_account"])
+    sd_tools = GraphDataTools(auth=auth, program_name="DEV", project_code="DICOM_test")
+    dicom = Dicom()
+    dicom_page = DicomPage()
+    login_page = LoginPage()
+    file_id = ""
+    study_id = ""
+
+    @classmethod
+    def setup_class(cls):
+        cls.sd_tools.delete_all_records()
+        file_res = cls.dicom.submit_dicom_file()
+        cls.file_id = file_res["ID"]
+        study_instance = file_res["ParentStudy"]
+        study_res = cls.dicom.get_studies(study_instance=study_instance)
+        cls.study_id = study_res["MainDicomTags"]["StudyInstanceUID"]
+        cls.sd_tools.submit_all_test_records()
+        logger.info("Running first etl")
+        gat.run_gen3_job("etl", test_env_namespace=pytest.namespace)
+        for key, item in cls.sd_tools.test_records.items():
+            if key == "dataset":
+                dataset_submitter_id = item.props["submitter_id"]
+            if key == "case":
+                case_linked_external_data = item.props["linked_external_data"]
+                case_submitted_id = item.props["submitter_id"]
+        cls.dicom.submit_dicom_data(
+            program="DEV",
+            project="DICOM_test",
+            study_id=cls.study_id,
+            dataset_submitter_id=dataset_submitter_id,
+            case_submitted_id=case_submitted_id,
+            case_linked_external_data=case_linked_external_data,
+        )
+        logger.info("Running second etl")
+        gat.run_gen3_job("etl", test_env_namespace=pytest.namespace)
+
+    @classmethod
+    def teardown_class(cls):
+        cls.sd_tools.delete_all_records()
+
+    def test_check_uploaded_dicom_file(self, page: Page):
+        """
+        Scenario: Verify Uploaded Dicom file
+        Steps:
+            1. Goto Exploration page and click on Imaging Studies tab
+            2. Find the xref containing the study id
+            3. Click on the button of the href
+            4. Verify OHIF viewer page is launched for the study id
+        """
+        # Login with main_account
+        self.login_page.go_to(page)
+        self.login_page.login(page, user="main_account")
+
+        # Goto explorer page
+        self.dicom_page.goto_explorer_page(page=page, study_id=self.study_id)
+
+    def test_unauthorized_user_cannot_post_dicom_file(self):
+        """
+        Scenario: Unauthorized user cannot submit dicom file
+        Steps:
+            1. Submit a dicom file using dummy_one user
+            2. Expect 403 in response, since dummy_one user doesn't have permission to submit dicom file
+        """
+        self.dicom.submit_dicom_file(user="dummy_one", expected_status=403)
+
+    def test_unauthorized_user_cannot_get_dicom_file(self):
+        """
+        Scenario: Unauthorized user cannot get dicom file
+        Steps:
+             1. Get dicom file deatils using dummy_one user
+             2. Expect 403 in response, since dummy_one user doesn't have permission to get dicom file
+        """
+        self.dicom.get_dicom_file(
+            dicom_file_id=self.file_id, user="dummy_one", expected_status=403
+        )
+
+    def test_unauthorized_user_cannot_get_non_exist_dicom_file(self):
+        """
+        Scenario: Unauthorized user cannot get non-exist dicom file
+        Steps:
+             1. Get non-exist dicom file deatils using dummy_one user
+             2. Expect 404 in response, since the dicom file doesn't exists
+        """
+        non_exist_id = "538a3dfd-219a25e0-8443a0b7-d1f512a6-2348ff25"
+        self.dicom.get_dicom_file(dicom_file_id=non_exist_id, expected_status=404)