ci(he-tme): bump staging to 1.1.0 by ari-nz · Pull Request #450 · aignostics/python-sdk

ari-nz · 2026-02-26T09:37:15Z

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Pull request overview

Updates the staging E2E test configuration for the H&E-TME (“he-tme”) application to reflect a newer deployed version, keeping environment-specific test expectations aligned with what staging runs.

Changes:

Bump HETA_APPLICATION_VERSION for the staging environment from 1.0.0 to 1.1.0 in shared test constants.

codecov · 2026-02-26T10:14:44Z

❌ 1 Tests Failed:

Tests completed	Failed	Passed	Skipped
690	1	689	17

View the top 1 failed test(s) by shortest run time

tests.aignostics.application.cli_test::test_cli_run_submit_and_describe_and_cancel_and_download_and_delete

Stack Traces | 869s run time

runner = <typer.testing.CliRunner object at 0x7f39aeab3620>
tmp_path = PosixPath('.../pytest-20/popen-gw3/test_cli_run_submit_and_descri0')
silent_logging = None
record_property = <function record_property.<locals>.append_property at 0x7f39ae9a00f0>

    @pytest.mark.e2e
    @pytest.mark.long_running
    @pytest.mark.flaky(retries=3, delay=5)
    @pytest.mark.timeout(timeout=60 * 10)
    def test_cli_run_submit_and_describe_and_cancel_and_download_and_delete(  # noqa: PLR0915
        runner: CliRunner, tmp_path: Path, silent_logging, record_property
    ) -> None:
        """Check run submit command runs successfully."""
        record_property("tested-item-id", "TC-APPLICATION-CLI-02")
        csv_content = "external_id;checksum_base64_crc32c;resolution_mpp;width_px;height_px;staining_method;tissue;disease;"
        csv_content += "platform_bucket_url\n"
        csv_content += (
            f"{SPOT_0_FILENAME};{SPOT_0_CRC32C};{SPOT_0_RESOLUTION_MPP};{SPOT_0_WIDTH};{SPOT_0_HEIGHT}"
            f";H&E;LUNG;LUNG_CANCER;{SPOT_0_GS_URL}"
        )
        csv_path = tmp_path / "dummy.csv"
        csv_path.write_text(csv_content)
        result = runner.invoke(
            cli,
            [
                "application",
                "run",
                "submit",
                HETA_APPLICATION_ID,
                str(csv_path),
                "--note",
                "note_of_this_complex_test",
                "--tags",
                "cli-test,test_cli_run_submit_and_describe_and_cancel_and_download_and_delete,further-tag",
                "--deadline",
                (datetime.now(tz=UTC) + timedelta(minutes=10)).isoformat(),
                "--onboard-to-aignostics-portal",
                "--gpu-type",
                PIPELINE_GPU_TYPE,
                "--force",
            ],
        )
        output = normalize_output(result.stdout)
        assert re.search(
            r"Submitted run with id '[0-9a-f-]+' for '",
            output,
        ), f"Output '{output}' doesn't match expected pattern"
        assert result.exit_code == 0
    
        # Extract run ID from the output
        run_id_match = re.search(r"Submitted run with id '([0-9a-f-]+)' for '", output)
        assert run_id_match, f"Failed to extract run ID from output '{output}'"
        run_id = run_id_match.group(1)
    
        # Test that we can find this run by it's note via the query parameter
        list_result = runner.invoke(
            cli,
            [
                "application",
                "run",
                "list",
                "--query",
                "note_of_this_complex_test",
            ],
        )
        assert list_result.exit_code == 0
        list_output = normalize_output(list_result.stdout)
        assert run_id in list_output, f"Run ID '{run_id}' not found when filtering by note via query"
    
        # Test that we can find this run by it's tag via the query parameter
        list_result = runner.invoke(
            cli,
            [
                "application",
                "run",
                "list",
                "--query",
                "test_cli_run_submit_and_describe_and_cancel_and_download_and_delete",
            ],
        )
        assert list_result.exit_code == 0
        list_output = normalize_output(list_result.stdout)
        assert run_id in list_output, f"Run ID '{run_id}' not found when filtering by tag via query"
    
        # Test that we cannot find this run by another tag via the query parameter
        list_result = runner.invoke(
            cli,
            [
                "application",
                "run",
                "list",
                "--query",
                "another_tag",
            ],
        )
        assert list_result.exit_code == 0
        list_output = normalize_output(list_result.stdout)
        assert run_id not in list_output, f"Run ID '{run_id}' found when filtering by another tag via query"
    
        # Test that we can find this run by it's note
        list_result = runner.invoke(
            cli,
            [
                "application",
                "run",
                "list",
                "--note-regex",
                "note_of_this_complex_test",
            ],
        )
        assert list_result.exit_code == 0
        list_output = normalize_output(list_result.stdout)
        assert run_id in list_output, f"Run ID '{run_id}' not found when filtering by note"
    
        # but not another note
        list_result = runner.invoke(
            cli,
            [
                "application",
                "run",
                "list",
                "--note-regex",
                "other_note",
            ],
        )
        assert list_result.exit_code == 0
        list_output = normalize_output(list_result.stdout)
        assert run_id not in list_output, f"Run ID '{run_id}' found when filtering by other note"
    
        # Test that we can find this run by one of its tags
        list_result = runner.invoke(
            cli,
            [
                "application",
                "run",
                "list",
                "--tags",
                "test_cli_run_submit_and_describe_and_cancel_and_download_and_delete",
            ],
        )
        assert list_result.exit_code == 0
        list_output = normalize_output(list_result.stdout)
        assert run_id in list_output, f"Run ID '{run_id}' not found when filtering by one tag"
    
        # but not another tag
        list_result = runner.invoke(
            cli,
            [
                "application",
                "run",
                "list",
                "--tags",
                "other-tag",
            ],
        )
        assert list_result.exit_code == 0
        list_output = normalize_output(list_result.stdout)
        assert run_id not in list_output, f"Run ID '{run_id}' found when filtering by other tag"
    
        # Test that we can find this run by two of its tags
        list_result = runner.invoke(
            cli,
            [
                "application",
                "run",
                "list",
                "--tags",
                "cli-test,test_cli_run_submit_and_describe_and_cancel_and_download_and_delete",
            ],
        )
        assert list_result.exit_code == 0
        list_output = normalize_output(list_result.stdout)
        assert run_id in list_output, f"Run ID '{run_id}' not found when filtering by two tags"
    
        # Test that we can find this run by all of its tags
        list_result = runner.invoke(
            cli,
            [
                "application",
                "run",
                "list",
                "--tags",
                "cli-test,test_cli_run_submit_and_describe_and_cancel_and_download_and_delete,further-tag",
            ],
        )
        assert list_result.exit_code == 0
        list_output = normalize_output(list_result.stdout)
        assert run_id in list_output, f"Run ID '{run_id}' not found when filtering by all tags"
    
        # Test that we cannot find this run by all of its tags and a non-existent tag
        list_result = runner.invoke(
            cli,
            [
                "application",
                "run",
                "list",
                "--tags",
                "cli-test,test_cli_run_submit_and_describe_and_cancel_and_download_and_delete,further-tag,non-existing-tag",
            ],
        )
        assert list_result.exit_code == 0
        list_output = normalize_output(list_result.stdout)
        assert run_id not in list_output, f"Run ID '{run_id}' found when filtering by all tags"
    
        # Test that we can find this run by all of its tags and it's note
        list_result = runner.invoke(
            cli,
            [
                "application",
                "run",
                "list",
                "--note-regex",
                "note_of_this_complex_test",
                "--tags",
                "cli-test,test_cli_run_submit_and_describe_and_cancel_and_download_and_delete,further-tag",
            ],
        )
        assert list_result.exit_code == 0
        list_output = normalize_output(list_result.stdout)
        assert run_id in list_output, f"Run ID '{run_id}' not found when filtering by all tags and note"
    
        # Test the describe command with the extracted run ID
        describe_result = runner.invoke(cli, ["application", "run", "describe", run_id])
        assert describe_result.exit_code == 0
        assert f"Run Details for {run_id}" in normalize_output(describe_result.stdout)
>       assert "Status (Termination Reason): PENDING" in normalize_output(
            describe_result.stdout
        ) or "Status (Termination Reason): PROCESSING" in normalize_output(describe_result.stdout)
E       assert ('Status (Termination Reason): PENDING' in "Run Details for 90e422d8-947b-44ed-ac23-a06a90df1c34================================================================================Run ID: 90e422d8-947b-44ed-ac23-a06a90df1c34Application (Version): he-tme (1.1.0)Queue Position: N/AStatus (Termination Reason): TERMINATED (RunTerminationReason.ALL_ITEMS_PROCESSED)Output: NONEError Message (Code): All items of the run finished in error state. Query ......................../runs/90e422d8-947b-44ed-ac23-a06a90df1c34/items to get the error message per item. (API.ALL_ITEMS_ERRORED)Statistics:  - 1 items  - 0 pending  - 0 processing  - 0 skipped  - 0 succeeded  - 1 user errors  - 0 system errorsSubmitted (by): 2026-02-26 13:22:49.647770+00:00 (okta|aignostics-okta-wic|00uj5euu30kszTj9M417)Terminated (duration): 2026-02-26 13:26:59.677007+00:00 (4 minutes and 10.03 seconds)Custom Metadata: {'sdk': {'ci': {'github': {'job': 'test', 'ref': '.../pull/450/merge', 'sha': '1306f3817f698bcd1a0e516b454dd5e510f80c59', 'action': '__self_4', 'run_id': '22443116136', 'run_url': 'https://github..../actions/runs/22443116136', 'ref_name': '450/merge', 'ref_type': 'branch', 'workflow': '+ CI/CD', 'runner_os': 'Linux', 'repository': 'aignostics/python-sd...     Download URL: None    - Name: cell_classification:geojson_polygons      MIME Type: application/octet-stream      Artifact ID: 0ea8dee8-e55f-4871-b568-fa299e5a6804      Download URL: None    - Name: readout_generation:cell_readouts      MIME Type: application/octet-stream      Artifact ID: 6f0e1934-1496-49cc-a029-8a920fd69a78      Download URL: None    - Name: readout_generation:slide_readouts      MIME Type: application/octet-stream      Artifact ID: a4011a9e-cf26-47ff-adcc-f40fe794834b      Download URL: None    - Name: tissue_segmentation:csv_class_information      MIME Type: application/octet-stream      Artifact ID: 1ebf208f-078b-4933-8e65-6c337fc4da8e      Download URL: None    - Name: tissue_segmentation:geojson_polygons      MIME Type: application/octet-stream      Artifact ID: a0d1106a-707d-40a5-80e8-1cbd1f020f39      Download URL: None    - Name: tissue_qc:csv_class_information      MIME Type: application/octet-stream      Artifact ID: 0668c894-dab6-4c10-9705-def8091ec1ea      Download URL: None    - Name: tissue_segmentation:segmentation_map_image      MIME Type: application/octet-stream      Artifact ID: 874d7bd5-e6b2-4f53-9f6b-7b79db0fb9b3      Download URL: None" or 'Status (Termination Reason): PROCESSING' in "Run Details for 90e422d8-947b-44ed-ac23-a06a90df1c34================================================================================Run ID: 90e422d8-947b-44ed-ac23-a06a90df1c34Application (Version): he-tme (1.1.0)Queue Position: N/AStatus (Termination Reason): TERMINATED (RunTerminationReason.ALL_ITEMS_PROCESSED)Output: NONEError Message (Code): All items of the run finished in error state. Query ......................../runs/90e422d8-947b-44ed-ac23-a06a90df1c34/items to get the error message per item. (API.ALL_ITEMS_ERRORED)Statistics:  - 1 items  - 0 pending  - 0 processing  - 0 skipped  - 0 succeeded  - 1 user errors  - 0 system errorsSubmitted (by): 2026-02-26 13:22:49.647770+00:00 (okta|aignostics-okta-wic|00uj5euu30kszTj9M417)Terminated (duration): 2026-02-26 13:26:59.677007+00:00 (4 minutes and 10.03 seconds)Custom Metadata: {'sdk': {'ci': {'github': {'job': 'test', 'ref': '.../pull/450/merge', 'sha': '1306f3817f698bcd1a0e516b454dd5e510f80c59', 'action': '__self_4', 'run_id': '22443116136', 'run_url': 'https://github..../actions/runs/22443116136', 'ref_name': '450/merge', 'ref_type': 'branch', 'workflow': '+ CI/CD', 'runner_os': 'Linux', 'repository': 'aignostics/python-sd...     Download URL: None    - Name: cell_classification:geojson_polygons      MIME Type: application/octet-stream      Artifact ID: 0ea8dee8-e55f-4871-b568-fa299e5a6804      Download URL: None    - Name: readout_generation:cell_readouts      MIME Type: application/octet-stream      Artifact ID: 6f0e1934-1496-49cc-a029-8a920fd69a78      Download URL: None    - Name: readout_generation:slide_readouts      MIME Type: application/octet-stream      Artifact ID: a4011a9e-cf26-47ff-adcc-f40fe794834b      Download URL: None    - Name: tissue_segmentation:csv_class_information      MIME Type: application/octet-stream      Artifact ID: 1ebf208f-078b-4933-8e65-6c337fc4da8e      Download URL: None    - Name: tissue_segmentation:geojson_polygons      MIME Type: application/octet-stream      Artifact ID: a0d1106a-707d-40a5-80e8-1cbd1f020f39      Download URL: None    - Name: tissue_qc:csv_class_information      MIME Type: application/octet-stream      Artifact ID: 0668c894-dab6-4c10-9705-def8091ec1ea      Download URL: None    - Name: tissue_segmentation:segmentation_map_image      MIME Type: application/octet-stream      Artifact ID: 874d7bd5-e6b2-4f53-9f6b-7b79db0fb9b3      Download URL: None")
E        +  where "Run Details for 90e422d8-947b-44ed-ac23-a06a90df1c34================================================================================Run ID: 90e422d8-947b-44ed-ac23-a06a90df1c34Application (Version): he-tme (1.1.0)Queue Position: N/AStatus (Termination Reason): TERMINATED (RunTerminationReason.ALL_ITEMS_PROCESSED)Output: NONEError Message (Code): All items of the run finished in error state. Query ......................../runs/90e422d8-947b-44ed-ac23-a06a90df1c34/items to get the error message per item. (API.ALL_ITEMS_ERRORED)Statistics:  - 1 items  - 0 pending  - 0 processing  - 0 skipped  - 0 succeeded  - 1 user errors  - 0 system errorsSubmitted (by): 2026-02-26 13:22:49.647770+00:00 (okta|aignostics-okta-wic|00uj5euu30kszTj9M417)Terminated (duration): 2026-02-26 13:26:59.677007+00:00 (4 minutes and 10.03 seconds)Custom Metadata: {'sdk': {'ci': {'github': {'job': 'test', 'ref': '.../pull/450/merge', 'sha': '1306f3817f698bcd1a0e516b454dd5e510f80c59', 'action': '__self_4', 'run_id': '22443116136', 'run_url': 'https://github..../actions/runs/22443116136', 'ref_name': '450/merge', 'ref_type': 'branch', 'workflow': '+ CI/CD', 'runner_os': 'Linux', 'repository': 'aignostics/python-sd...     Download URL: None    - Name: cell_classification:geojson_polygons      MIME Type: application/octet-stream      Artifact ID: 0ea8dee8-e55f-4871-b568-fa299e5a6804      Download URL: None    - Name: readout_generation:cell_readouts      MIME Type: application/octet-stream      Artifact ID: 6f0e1934-1496-49cc-a029-8a920fd69a78      Download URL: None    - Name: readout_generation:slide_readouts      MIME Type: application/octet-stream      Artifact ID: a4011a9e-cf26-47ff-adcc-f40fe794834b      Download URL: None    - Name: tissue_segmentation:csv_class_information      MIME Type: application/octet-stream      Artifact ID: 1ebf208f-078b-4933-8e65-6c337fc4da8e      Download URL: None    - Name: tissue_segmentation:geojson_polygons      MIME Type: application/octet-stream      Artifact ID: a0d1106a-707d-40a5-80e8-1cbd1f020f39      Download URL: None    - Name: tissue_qc:csv_class_information      MIME Type: application/octet-stream      Artifact ID: 0668c894-dab6-4c10-9705-def8091ec1ea      Download URL: None    - Name: tissue_segmentation:segmentation_map_image      MIME Type: application/octet-stream      Artifact ID: 874d7bd5-e6b2-4f53-9f6b-7b79db0fb9b3      Download URL: None" = normalize_output("Run Details for 90e422d8-947b-44ed-ac23-a06a90df1c34\n================================================================================\nRun ID: 90e422d8-947b-44ed-ac23-a06a90df1c34\nApplication (Version): he-tme (1.1.0)\nQueue Position: N/A\nStatus (Termination Reason): TERMINATED (RunTerminationReason.ALL_ITEMS_PROCESSED)\nOutput: NONE\nError Message (Code): All items of the run finished in error state. Query ......................../runs/90e422d8-947b-44ed-ac23-a06a90df1c34/items to get the error message per item. (API.ALL_ITEMS_ERRORED)\nStatistics:\n  - 1 items\n  - 0 pending\n  - 0 processing\n  - 0 skipped\n  - 0 succeeded\n  - 1 user errors\n  - 0 system errors\nSubmitted (by): 2026-02-26 13:22:49.647770+00:00 (okta|aignostics-okta-wic|00uj5euu30kszTj9M417)\nTerminated (duration): 2026-02-26 13:26:59.677007+00:00 (4 minutes and 10.03 seconds)\nCustom Metadata: {'sdk': {'ci': {'github': {'job': 'test', 'ref': '.../pull/450/merge', 'sha': '1306f3817f698bcd1a0e516b454dd5e510f80c59', 'action': '__self_4', 'run_id': '22443116136', 'run_url': 'https://github..../actions/runs/22443116136', 'ref_name': '450/merge', 'ref_type': 'branch', 'workflow': '+ CI/CD', 'runner_os': 'Linux',...json_polygons\n      MIME Type: application/octet-stream\n      Artifact ID: 0ea8dee8-e55f-4871-b568-fa299e5a6804\n      Download URL: None\n    - Name: readout_generation:cell_readouts\n      MIME Type: application/octet-stream\n      Artifact ID: 6f0e1934-1496-49cc-a029-8a920fd69a78\n      Download URL: None\n    - Name: readout_generation:slide_readouts\n      MIME Type: application/octet-stream\n      Artifact ID: a4011a9e-cf26-47ff-adcc-f40fe794834b\n      Download URL: None\n    - Name: tissue_segmentation:csv_class_information\n      MIME Type: application/octet-stream\n      Artifact ID: 1ebf208f-078b-4933-8e65-6c337fc4da8e\n      Download URL: None\n    - Name: tissue_segmentation:geojson_polygons\n      MIME Type: application/octet-stream\n      Artifact ID: a0d1106a-707d-40a5-80e8-1cbd1f020f39\n      Download URL: None\n    - Name: tissue_qc:csv_class_information\n      MIME Type: application/octet-stream\n      Artifact ID: 0668c894-dab6-4c10-9705-def8091ec1ea\n      Download URL: None\n    - Name: tissue_segmentation:segmentation_map_image\n      MIME Type: application/octet-stream\n      Artifact ID: 874d7bd5-e6b2-4f53-9f6b-7b79db0fb9b3\n      Download URL: None\n\n")
E        +    where "Run Details for 90e422d8-947b-44ed-ac23-a06a90df1c34\n================================================================================\nRun ID: 90e422d8-947b-44ed-ac23-a06a90df1c34\nApplication (Version): he-tme (1.1.0)\nQueue Position: N/A\nStatus (Termination Reason): TERMINATED (RunTerminationReason.ALL_ITEMS_PROCESSED)\nOutput: NONE\nError Message (Code): All items of the run finished in error state. Query ......................../runs/90e422d8-947b-44ed-ac23-a06a90df1c34/items to get the error message per item. (API.ALL_ITEMS_ERRORED)\nStatistics:\n  - 1 items\n  - 0 pending\n  - 0 processing\n  - 0 skipped\n  - 0 succeeded\n  - 1 user errors\n  - 0 system errors\nSubmitted (by): 2026-02-26 13:22:49.647770+00:00 (okta|aignostics-okta-wic|00uj5euu30kszTj9M417)\nTerminated (duration): 2026-02-26 13:26:59.677007+00:00 (4 minutes and 10.03 seconds)\nCustom Metadata: {'sdk': {'ci': {'github': {'job': 'test', 'ref': '.../pull/450/merge', 'sha': '1306f3817f698bcd1a0e516b454dd5e510f80c59', 'action': '__self_4', 'run_id': '22443116136', 'run_url': 'https://github..../actions/runs/22443116136', 'ref_name': '450/merge', 'ref_type': 'branch', 'workflow': '+ CI/CD', 'runner_os': 'Linux',...json_polygons\n      MIME Type: application/octet-stream\n      Artifact ID: 0ea8dee8-e55f-4871-b568-fa299e5a6804\n      Download URL: None\n    - Name: readout_generation:cell_readouts\n      MIME Type: application/octet-stream\n      Artifact ID: 6f0e1934-1496-49cc-a029-8a920fd69a78\n      Download URL: None\n    - Name: readout_generation:slide_readouts\n      MIME Type: application/octet-stream\n      Artifact ID: a4011a9e-cf26-47ff-adcc-f40fe794834b\n      Download URL: None\n    - Name: tissue_segmentation:csv_class_information\n      MIME Type: application/octet-stream\n      Artifact ID: 1ebf208f-078b-4933-8e65-6c337fc4da8e\n      Download URL: None\n    - Name: tissue_segmentation:geojson_polygons\n      MIME Type: application/octet-stream\n      Artifact ID: a0d1106a-707d-40a5-80e8-1cbd1f020f39\n      Download URL: None\n    - Name: tissue_qc:csv_class_information\n      MIME Type: application/octet-stream\n      Artifact ID: 0668c894-dab6-4c10-9705-def8091ec1ea\n      Download URL: None\n    - Name: tissue_segmentation:segmentation_map_image\n      MIME Type: application/octet-stream\n      Artifact ID: 874d7bd5-e6b2-4f53-9f6b-7b79db0fb9b3\n      Download URL: None\n\n" = <Result okay>.stdout
E        +  and   "Run Details for 90e422d8-947b-44ed-ac23-a06a90df1c34================================================================================Run ID: 90e422d8-947b-44ed-ac23-a06a90df1c34Application (Version): he-tme (1.1.0)Queue Position: N/AStatus (Termination Reason): TERMINATED (RunTerminationReason.ALL_ITEMS_PROCESSED)Output: NONEError Message (Code): All items of the run finished in error state. Query ......................../runs/90e422d8-947b-44ed-ac23-a06a90df1c34/items to get the error message per item. (API.ALL_ITEMS_ERRORED)Statistics:  - 1 items  - 0 pending  - 0 processing  - 0 skipped  - 0 succeeded  - 1 user errors  - 0 system errorsSubmitted (by): 2026-02-26 13:22:49.647770+00:00 (okta|aignostics-okta-wic|00uj5euu30kszTj9M417)Terminated (duration): 2026-02-26 13:26:59.677007+00:00 (4 minutes and 10.03 seconds)Custom Metadata: {'sdk': {'ci': {'github': {'job': 'test', 'ref': '.../pull/450/merge', 'sha': '1306f3817f698bcd1a0e516b454dd5e510f80c59', 'action': '__self_4', 'run_id': '22443116136', 'run_url': 'https://github..../actions/runs/22443116136', 'ref_name': '450/merge', 'ref_type': 'branch', 'workflow': '+ CI/CD', 'runner_os': 'Linux', 'repository': 'aignostics/python-sd...     Download URL: None    - Name: cell_classification:geojson_polygons      MIME Type: application/octet-stream      Artifact ID: 0ea8dee8-e55f-4871-b568-fa299e5a6804      Download URL: None    - Name: readout_generation:cell_readouts      MIME Type: application/octet-stream      Artifact ID: 6f0e1934-1496-49cc-a029-8a920fd69a78      Download URL: None    - Name: readout_generation:slide_readouts      MIME Type: application/octet-stream      Artifact ID: a4011a9e-cf26-47ff-adcc-f40fe794834b      Download URL: None    - Name: tissue_segmentation:csv_class_information      MIME Type: application/octet-stream      Artifact ID: 1ebf208f-078b-4933-8e65-6c337fc4da8e      Download URL: None    - Name: tissue_segmentation:geojson_polygons      MIME Type: application/octet-stream      Artifact ID: a0d1106a-707d-40a5-80e8-1cbd1f020f39      Download URL: None    - Name: tissue_qc:csv_class_information      MIME Type: application/octet-stream      Artifact ID: 0668c894-dab6-4c10-9705-def8091ec1ea      Download URL: None    - Name: tissue_segmentation:segmentation_map_image      MIME Type: application/octet-stream      Artifact ID: 874d7bd5-e6b2-4f53-9f6b-7b79db0fb9b3      Download URL: None" = normalize_output("Run Details for 90e422d8-947b-44ed-ac23-a06a90df1c34\n================================================================================\nRun ID: 90e422d8-947b-44ed-ac23-a06a90df1c34\nApplication (Version): he-tme (1.1.0)\nQueue Position: N/A\nStatus (Termination Reason): TERMINATED (RunTerminationReason.ALL_ITEMS_PROCESSED)\nOutput: NONE\nError Message (Code): All items of the run finished in error state. Query ......................../runs/90e422d8-947b-44ed-ac23-a06a90df1c34/items to get the error message per item. (API.ALL_ITEMS_ERRORED)\nStatistics:\n  - 1 items\n  - 0 pending\n  - 0 processing\n  - 0 skipped\n  - 0 succeeded\n  - 1 user errors\n  - 0 system errors\nSubmitted (by): 2026-02-26 13:22:49.647770+00:00 (okta|aignostics-okta-wic|00uj5euu30kszTj9M417)\nTerminated (duration): 2026-02-26 13:26:59.677007+00:00 (4 minutes and 10.03 seconds)\nCustom Metadata: {'sdk': {'ci': {'github': {'job': 'test', 'ref': '.../pull/450/merge', 'sha': '1306f3817f698bcd1a0e516b454dd5e510f80c59', 'action': '__self_4', 'run_id': '22443116136', 'run_url': 'https://github..../actions/runs/22443116136', 'ref_name': '450/merge', 'ref_type': 'branch', 'workflow': '+ CI/CD', 'runner_os': 'Linux',...json_polygons\n      MIME Type: application/octet-stream\n      Artifact ID: 0ea8dee8-e55f-4871-b568-fa299e5a6804\n      Download URL: None\n    - Name: readout_generation:cell_readouts\n      MIME Type: application/octet-stream\n      Artifact ID: 6f0e1934-1496-49cc-a029-8a920fd69a78\n      Download URL: None\n    - Name: readout_generation:slide_readouts\n      MIME Type: application/octet-stream\n      Artifact ID: a4011a9e-cf26-47ff-adcc-f40fe794834b\n      Download URL: None\n    - Name: tissue_segmentation:csv_class_information\n      MIME Type: application/octet-stream\n      Artifact ID: 1ebf208f-078b-4933-8e65-6c337fc4da8e\n      Download URL: None\n    - Name: tissue_segmentation:geojson_polygons\n      MIME Type: application/octet-stream\n      Artifact ID: a0d1106a-707d-40a5-80e8-1cbd1f020f39\n      Download URL: None\n    - Name: tissue_qc:csv_class_information\n      MIME Type: application/octet-stream\n      Artifact ID: 0668c894-dab6-4c10-9705-def8091ec1ea\n      Download URL: None\n    - Name: tissue_segmentation:segmentation_map_image\n      MIME Type: application/octet-stream\n      Artifact ID: 874d7bd5-e6b2-4f53-9f6b-7b79db0fb9b3\n      Download URL: None\n\n")
E        +    where "Run Details for 90e422d8-947b-44ed-ac23-a06a90df1c34\n================================================================================\nRun ID: 90e422d8-947b-44ed-ac23-a06a90df1c34\nApplication (Version): he-tme (1.1.0)\nQueue Position: N/A\nStatus (Termination Reason): TERMINATED (RunTerminationReason.ALL_ITEMS_PROCESSED)\nOutput: NONE\nError Message (Code): All items of the run finished in error state. Query ......................../runs/90e422d8-947b-44ed-ac23-a06a90df1c34/items to get the error message per item. (API.ALL_ITEMS_ERRORED)\nStatistics:\n  - 1 items\n  - 0 pending\n  - 0 processing\n  - 0 skipped\n  - 0 succeeded\n  - 1 user errors\n  - 0 system errors\nSubmitted (by): 2026-02-26 13:22:49.647770+00:00 (okta|aignostics-okta-wic|00uj5euu30kszTj9M417)\nTerminated (duration): 2026-02-26 13:26:59.677007+00:00 (4 minutes and 10.03 seconds)\nCustom Metadata: {'sdk': {'ci': {'github': {'job': 'test', 'ref': '.../pull/450/merge', 'sha': '1306f3817f698bcd1a0e516b454dd5e510f80c59', 'action': '__self_4', 'run_id': '22443116136', 'run_url': 'https://github..../actions/runs/22443116136', 'ref_name': '450/merge', 'ref_type': 'branch', 'workflow': '+ CI/CD', 'runner_os': 'Linux',...json_polygons\n      MIME Type: application/octet-stream\n      Artifact ID: 0ea8dee8-e55f-4871-b568-fa299e5a6804\n      Download URL: None\n    - Name: readout_generation:cell_readouts\n      MIME Type: application/octet-stream\n      Artifact ID: 6f0e1934-1496-49cc-a029-8a920fd69a78\n      Download URL: None\n    - Name: readout_generation:slide_readouts\n      MIME Type: application/octet-stream\n      Artifact ID: a4011a9e-cf26-47ff-adcc-f40fe794834b\n      Download URL: None\n    - Name: tissue_segmentation:csv_class_information\n      MIME Type: application/octet-stream\n      Artifact ID: 1ebf208f-078b-4933-8e65-6c337fc4da8e\n      Download URL: None\n    - Name: tissue_segmentation:geojson_polygons\n      MIME Type: application/octet-stream\n      Artifact ID: a0d1106a-707d-40a5-80e8-1cbd1f020f39\n      Download URL: None\n    - Name: tissue_qc:csv_class_information\n      MIME Type: application/octet-stream\n      Artifact ID: 0668c894-dab6-4c10-9705-def8091ec1ea\n      Download URL: None\n    - Name: tissue_segmentation:segmentation_map_image\n      MIME Type: application/octet-stream\n      Artifact ID: 874d7bd5-e6b2-4f53-9f6b-7b79db0fb9b3\n      Download URL: None\n\n" = <Result okay>.stdout

.../aignostics/application/cli_test.py:586: AssertionError

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sonarqubecloud · 2026-02-26T13:37:31Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

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Copilot AI review requested due to automatic review settings February 26, 2026 09:37

ari-nz requested a review from helmut-hoffer-von-ankershoffen as a code owner February 26, 2026 09:37

Copilot AI reviewed Feb 26, 2026

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blanca-pablos self-requested a review February 26, 2026 11:43

blanca-pablos approved these changes Feb 26, 2026

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ci(he-tme): bump staging to 1.1.0

8c6e6e6

ari-nz force-pushed the chore/he-tme-version-bump branch from 8aefaf9 to 8c6e6e6 Compare February 26, 2026 12:58

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ci(he-tme): bump staging to 1.1.0#450

ci(he-tme): bump staging to 1.1.0#450
ari-nz wants to merge 1 commit intomainfrom
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