pytest_fully_output.txt

============================= test session starts ==============================
platform linux -- Python 3.12.3, pytest-7.4.4, pluggy-1.6.0
rootdir: /home/patch/PycharmProjects/scidk
configfile: pyproject.toml
plugins: cov-7.0.0, playwright-0.4.3, base-url-2.1.0
collected 927 items

tests/test_alert_manager.py ..............                               [  1%]
tests/test_alerts_api.py ............                                    [  2%]
tests/test_annotations_and_selections.py ..                              [  3%]
tests/test_annotations_relationships_syncqueue.py .                      [  3%]
tests/test_annotations_rest_endpoints.py ...........                     [  4%]
tests/test_api_endpoint_registry.py ...................                  [  6%]
tests/test_app_api.py ....                                               [  6%]
tests/test_arrows_import_export.py ..........                            [  7%]
tests/test_auth.py ......................                                [ 10%]
tests/test_auth_multiuser.py ...........................                 [ 13%]
tests/test_auto_lock.py ............                                     [ 14%]
tests/test_backup_automation.py .............                            [ 15%]
tests/test_bioformats_converter.py ...........                           [ 17%]
tests/test_bioformats_interpreters.py ................                   [ 18%]
tests/test_bruker_microct_dataset.py ....                                [ 19%]
tests/test_bruker_skyscan_interpreter.py ..                              [ 19%]
tests/test_chat_api.py .......................................           [ 23%]
tests/test_commit_index_chain.py .                                       [ 23%]
tests/test_commit_neo4j_attempt_flag.py .                                [ 23%]
tests/test_commit_verbose_and_health.py ..                               [ 24%]
tests/test_config_export_import.py ...................                   [ 26%]
tests/test_cross_database_transfer.py ...............                    [ 27%]
tests/test_csv_interpreter.py ..                                         [ 27%]
tests/test_directories_api.py .                                          [ 28%]
tests/test_eda_interpreter.py ...........                                [ 29%]
tests/test_error_and_timeout.py ...                                      [ 29%]
tests/test_files_page_e2e.py .s....Fsss.                                 [ 30%]
tests/test_filesystem.py ...                                             [ 31%]
tests/test_folder_config_precedence.py .                                 [ 31%]
tests/test_folder_hierarchy.py ....                                      [ 31%]
tests/test_fs_list_api.py .                                              [ 31%]
tests/test_fuzzy_matching.py .................                           [ 33%]
tests/test_graph.py ..                                                   [ 33%]
tests/test_graph_combined_schema_api.py .........                        [ 34%]
tests/test_graph_query_api.py ..s.....                                   [ 35%]
tests/test_graph_schema_api.py ..                                        [ 35%]
tests/test_graph_subschema_api.py ..                                     [ 36%]
tests/test_graphrag_endpoints.py ...                                     [ 36%]
tests/test_graphrag_entity_extractor.py .....                            [ 36%]
tests/test_graphrag_errors.py ..                                         [ 37%]
tests/test_graphrag_feedback.py .............                            [ 38%]
tests/test_graphrag_observability.py .                                   [ 38%]
tests/test_graphrag_query_engine.py ......                               [ 39%]
tests/test_graphrag_utilities.py ..                                      [ 39%]
tests/test_health_comprehensive.py ...............                       [ 41%]
tests/test_health_sqlite.py .                                            [ 41%]
tests/test_helpers_example.py ....                                       [ 41%]
tests/test_ilab_plugin.py ...........                                    [ 42%]
tests/test_instances_api.py ..                                           [ 43%]
tests/test_interpreters_effective_and_scan_config.py ..                  [ 43%]
tests/test_interpreters_page.py .                                        [ 43%]
tests/test_interpreters_registry_api.py .....                            [ 43%]
tests/test_ipynb_interpreter.py ......                                   [ 44%]
tests/test_ipynb_ui_render.py .                                          [ 44%]
tests/test_label_endpoint_registry.py ............                       [ 45%]
tests/test_label_instance_count.py ..F                                   [ 46%]
tests/test_labels_api.py ...................................             [ 50%]
tests/test_link_execution_progress.py ...                                [ 50%]
tests/test_links_api.py .........................FF...                   [ 53%]
tests/test_links_integration.py .s.....s.                                [ 54%]
tests/test_links_page.py .....                                           [ 55%]
tests/test_links_triple_import.py ..............                         [ 56%]
tests/test_logs_api.py ..........                                        [ 57%]
tests/test_logs_endpoint.py .....                                        [ 58%]
tests/test_map_route.py .                                                [ 58%]
tests/test_maps_features.py ...................                          [ 60%]
tests/test_metrics_endpoint.py .                                         [ 60%]
tests/test_neo4j_adapter.py ....                                         [ 60%]
tests/test_neo4j_commit.py .                                             [ 61%]
tests/test_neo4j_commit_flow.py .                                        [ 61%]
tests/test_neo4j_commit_folders.py .                                     [ 61%]
tests/test_neo4j_password_save.py ..                                     [ 61%]
tests/test_neo4j_settings_api.py ..                                      [ 61%]
tests/test_plugin_endpoint_integration.py .........                      [ 62%]
tests/test_plugin_instance_manager.py ..........                         [ 63%]
tests/test_plugin_label_publishing.py .........                          [ 64%]
tests/test_plugin_loader.py ...........                                  [ 65%]
tests/test_plugin_settings.py ..............                             [ 67%]
tests/test_plugin_settings_api.py ..........                             [ 68%]
tests/test_plugin_template_registry.py ............                      [ 69%]
tests/test_plugins_api.py .....                                          [ 70%]
tests/test_progress_indicators.py ...                                    [ 70%]
tests/test_property_removal_and_overwrite.py .........                   [ 71%]
tests/test_providers_api.py .........                                    [ 72%]
tests/test_python_interpreter.py ..                                      [ 72%]
tests/test_rclone_provider.py ...                                        [ 73%]
tests/test_rclone_recursive_hierarchy.py .                               [ 73%]
tests/test_rclone_scan.py .                                              [ 73%]
tests/test_rclone_scan_ingest.py .                                       [ 73%]
tests/test_registry.py ..                                                [ 73%]
tests/test_rescan_idempotency.py .                                       [ 73%]
tests/test_rocrate_export.py ..                                          [ 74%]
tests/test_rocrate_referenced.py ..                                      [ 74%]
tests/test_saved_maps_service.py ..................                      [ 76%]
tests/test_scan_browse_indexed.py .                                      [ 76%]
tests/test_scan_commit_delete.py ..                                      [ 76%]
tests/test_scan_dry_run.py .                                             [ 76%]
tests/test_scan_fs_auto_enter_base.py .                                  [ 76%]
tests/test_scan_nonrecursive_includes_folders.py .                       [ 76%]
tests/test_scan_sources.py ...                                           [ 77%]
tests/test_scans_committed_flag.py .                                     [ 77%]
tests/test_schema.py .............................                       [ 80%]
tests/test_schema_file_folder.py .                                       [ 80%]
tests/test_script_sandbox.py ...............................             [ 83%]
tests/test_scripts.py ......................                             [ 86%]
tests/test_search_api.py ...                                             [ 86%]
tests/test_seed_demo_data.py ..............                              [ 88%]
tests/test_selective_scan_cache.py .                                     [ 88%]
tests/test_sqlite_migrations.py .                                        [ 88%]
tests/test_sqlite_path_index.py ..                                       [ 88%]
tests/test_state_backend_toggle.py ....                                  [ 88%]
tests/test_swagger_api_docs.py ...........                               [ 90%]
tests/test_table_format_registry.py ....................                 [ 92%]
tests/test_table_loader_plugin.py ...................                    [ 94%]
tests/test_tasks_limits_cancel.py ..                                     [ 94%]
tests/test_tasks_scan.py .                                               [ 94%]
tests/test_transparency_analysis_scripts.py ssssssss                     [ 95%]
tests/test_transparency_chat_tools.py .....                              [ 96%]
tests/test_transparency_dependencies.py ..............                   [ 97%]
tests/test_transparency_file_interpretation.py ......                    [ 98%]
tests/test_transparency_plugins_page.py .........                        [ 99%]
tests/contracts/test_api_contracts.py ......                             [ 99%]
tests/e2e/test_demo_recording.py s                                       [ 99%]
tests/e2e/test_persistence.py s                                          [100%]

=================================== FAILURES ===================================
________________________ test_no_synchronous_scan_in_ui ________________________

    def test_no_synchronous_scan_in_ui():
        """Verify that synchronous /api/scan is NOT used by the Files page UI."""
        from scidk.app import create_app
        app = create_app()
        app.config['TESTING'] = True
    
        with authenticate_test_client(app.test_client(), app) as client:
            resp = client.get('/datasets')
            html = resp.data.decode('utf-8')
    
            # Check that the JavaScript does NOT call /api/scan from provider panel
            # (it should only use /api/tasks)
>           assert "'/api/scan'" not in html or html.count("'/api/scan'") <= 1
E           assert ("'/api/scan'" not in '<!doctype h...dy>\n</html>'
E             "'/api/scan'" is contained here:
E               ait fetch('/api/scan', {
E                         method: 'POST',
E                         headers: { 'Content-Type': 'application/json' },
E                         body: JSON.stringify(payload)
E                       });
E               ...
E             
E             ...Full output truncated (839 lines hidden), use '-vv' to show or 3 <= 1)
E            +  where 3 = <built-in method count of str object at 0x35bc11c0>("'/api/scan'")
E            +    where <built-in method count of str object at 0x35bc11c0> = '<!doctype html>\n<html>\n<head>\n  <meta charset="utf-8" />\n  <title>-SciDK-> Files</title>\n  <style>\n    :root { ...\n\n<!-- Browser notifications for alerts -->\n<script src="/static/js/notifications.js"></script>\n\n</body>\n</html>'.count

tests/test_files_page_e2e.py:222: AssertionError
----------------------------- Captured stderr call -----------------------------
[2026-03-02 11:18:57] [INFO] [root] Logging configured: level=INFO, dir=logs, max_size=50MB, backups=10
[2026-03-02 11:18:57] [INFO] [scidk.app] Graph backend: in-memory
[2026-03-02 11:18:58] [INFO] [scidk.core.label_endpoint_registry] Label endpoint registry initialized
[2026-03-02 11:18:58] [INFO] [scidk.core.plugin_template_registry] Plugin template registry initialized
[2026-03-02 11:18:58] [INFO] [scidk.core.plugin_instance_manager] Plugin instance manager initialized (db: scidk_settings.db)
[2026-03-02 11:18:58] [INFO] [scidk.core.plugin_loader] Discovered 4 plugins: ['example_ilab', 'ilab_table_loader', 'table_loader', 'example_plugin']
[2026-03-02 11:18:58] [INFO] [scidk.core.plugin_loader] Discovered 4 plugins: ['example_ilab', 'ilab_table_loader', 'table_loader', 'example_plugin']
[2026-03-02 11:18:58] [INFO] [scidk.core.label_endpoint_registry] Registered label endpoint: /api/integrations/ilab/services (iLab Services) -> iLabService
[2026-03-02 11:18:58] [INFO] [scidk.core.label_endpoint_registry] Registered label endpoint: /api/integrations/ilab/equipment (iLab Equipment) -> Equipment
[2026-03-02 11:18:58] [INFO] [scidk.core.plugin_loader] Successfully loaded plugin: example_ilab v1.0.0
[2026-03-02 11:18:58] [WARNING] [scidk.core.plugin_template_registry] Template ilab_importer with category 'data_import' missing recommended graph_behavior config keys: ['can_create_label', 'label_source']
[2026-03-02 11:18:58] [INFO] [scidk.core.plugin_template_registry] Registered plugin template: ilab_importer (iLab Data Importer) [category: data_import]
[2026-03-02 11:18:58] [INFO] [plugins.ilab_table_loader] iLab Data Importer plugin template registered successfully
[2026-03-02 11:18:58] [INFO] [scidk.core.plugin_loader] Successfully loaded plugin: ilab_table_loader v1.0.0
[2026-03-02 11:18:58] [INFO] [scidk.core.plugin_template_registry] Registered plugin template: table_loader (Table Loader) [category: data_import]
[2026-03-02 11:18:58] [INFO] [plugins.table_loader] Table Loader plugin template registered successfully
[2026-03-02 11:18:58] [INFO] [scidk.core.plugin_loader] Successfully loaded plugin: table_loader v1.0.0
[2026-03-02 11:18:58] [INFO] [scidk.core.plugin_loader] Successfully loaded plugin: example_plugin v1.0.0
[2026-03-02 11:18:58] [INFO] [apscheduler.scheduler] Adding job tentatively -- it will be properly scheduled when the scheduler starts
[2026-03-02 11:18:58] [INFO] [apscheduler.scheduler] Added job "Daily Backup" to job store "default"
[2026-03-02 11:18:58] [INFO] [apscheduler.scheduler] Scheduler started
___________________ test_instance_count_neo4j_not_configured ___________________

client = <FlaskClient <Flask 'scidk.app'>>

    def test_instance_count_neo4j_not_configured(client):
        """Test instance count when Neo4j is not configured."""
        # Create a test label
        label_data = {
            'name': 'TestLabel2',
            'properties': [
                {'name': 'name', 'type': 'string'}
            ]
        }
    
        response = client.post('/api/labels', json=label_data)
        assert response.status_code == 200
    
        # Get instance count
        response = client.get('/api/labels/TestLabel2/instance-count')
    
        # Should handle gracefully (either success with 0 or error about Neo4j)
        assert response.status_code in [200, 500]
    
        data = response.get_json()
        assert 'status' in data
    
        if data['status'] == 'error':
            # Error message should mention Neo4j, configuration, or driver issues
            assert 'error' in data
            error_msg = data['error'].lower()
>           assert 'neo4j' in error_msg or 'config' in error_msg or 'connect' in error_msg or 'driver' in error_msg
E           AssertionError: assert ('neo4j' in '{code: neo.clienterror.security.unauthorized} {message: unsupported authentication token, missing key `scheme`}' or 'config' in '{code: neo.clienterror.security.unauthorized} {message: unsupported authentication token, missing key `scheme`}' or 'connect' in '{code: neo.clienterror.security.unauthorized} {message: unsupported authentication token, missing key `scheme`}' or 'driver' in '{code: neo.clienterror.security.unauthorized} {message: unsupported authentication token, missing key `scheme`}')

tests/test_label_instance_count.py:73: AssertionError
---------------------------- Captured stderr setup -----------------------------
[2026-03-02 11:19:35] [INFO] [root] Logging configured: level=INFO, dir=logs, max_size=50MB, backups=10
[2026-03-02 11:19:35] [INFO] [scidk.app] Graph backend: in-memory
[2026-03-02 11:19:35] [INFO] [scidk.core.label_endpoint_registry] Label endpoint registry initialized
[2026-03-02 11:19:35] [INFO] [scidk.core.plugin_template_registry] Plugin template registry initialized
[2026-03-02 11:19:35] [INFO] [scidk.core.plugin_instance_manager] Plugin instance manager initialized (db: scidk_settings.db)
[2026-03-02 11:19:35] [INFO] [scidk.core.plugin_loader] Discovered 4 plugins: ['example_ilab', 'ilab_table_loader', 'table_loader', 'example_plugin']
[2026-03-02 11:19:35] [INFO] [scidk.core.plugin_loader] Discovered 4 plugins: ['example_ilab', 'ilab_table_loader', 'table_loader', 'example_plugin']
[2026-03-02 11:19:35] [INFO] [scidk.core.label_endpoint_registry] Registered label endpoint: /api/integrations/ilab/services (iLab Services) -> iLabService
[2026-03-02 11:19:35] [INFO] [scidk.core.label_endpoint_registry] Registered label endpoint: /api/integrations/ilab/equipment (iLab Equipment) -> Equipment
[2026-03-02 11:19:35] [INFO] [scidk.core.plugin_loader] Successfully loaded plugin: example_ilab v1.0.0
[2026-03-02 11:19:35] [WARNING] [scidk.core.plugin_template_registry] Template ilab_importer with category 'data_import' missing recommended graph_behavior config keys: ['can_create_label', 'label_source']
[2026-03-02 11:19:35] [INFO] [scidk.core.plugin_template_registry] Registered plugin template: ilab_importer (iLab Data Importer) [category: data_import]
[2026-03-02 11:19:35] [INFO] [plugins.ilab_table_loader] iLab Data Importer plugin template registered successfully
[2026-03-02 11:19:35] [INFO] [scidk.core.plugin_loader] Successfully loaded plugin: ilab_table_loader v1.0.0
[2026-03-02 11:19:35] [INFO] [scidk.core.plugin_template_registry] Registered plugin template: table_loader (Table Loader) [category: data_import]
[2026-03-02 11:19:35] [INFO] [plugins.table_loader] Table Loader plugin template registered successfully
[2026-03-02 11:19:35] [INFO] [scidk.core.plugin_loader] Successfully loaded plugin: table_loader v1.0.0
[2026-03-02 11:19:35] [INFO] [scidk.core.plugin_loader] Successfully loaded plugin: example_plugin v1.0.0
[2026-03-02 11:19:35] [INFO] [apscheduler.scheduler] Adding job tentatively -- it will be properly scheduled when the scheduler starts
[2026-03-02 11:19:35] [INFO] [apscheduler.scheduler] Added job "Daily Backup" to job store "default"
[2026-03-02 11:19:35] [INFO] [apscheduler.scheduler] Scheduler started
_______________________ test_enrich_link_with_properties _______________________

client = <FlaskClient <Flask 'scidk.app'>>

    def test_enrich_link_with_properties(client):
        """Test enriching link relationships with specific properties."""
        # Create labels
        client.post('/api/labels', json={
            'name': 'Source',
            'properties': [{'name': 'uuid', 'type': 'string'}],
            'relationships': []
        })
        client.post('/api/labels', json={
            'name': 'Target',
            'properties': [{'name': 'uuid', 'type': 'string'}],
            'relationships': []
        })
    
        # Create an Active import link with source_database
        payload = {
            'name': 'Test Import Link',
            'source_label': 'Source',
            'target_label': 'Target',
            'match_strategy': 'graph_import',
            'match_config': {
                'source_database': 'TestDB',
                'source_uid_property': 'uuid',
                'target_uid_property': 'uuid'
            },
            'relationship_type': 'LINKS_TO',
            'relationship_props': {},
            'status': 'active'
        }
        create_resp = client.post('/api/links', json=payload)
>       assert create_resp.status_code in [200, 201]
E       assert 400 in [200, 201]
E        +  where 400 = <WrapperTestResponse streamed [400 BAD REQUEST]>.status_code

tests/test_links_api.py:605: AssertionError
---------------------------- Captured stderr setup -----------------------------
[2026-03-02 11:20:29] [INFO] [root] Logging configured: level=INFO, dir=logs, max_size=50MB, backups=10
[2026-03-02 11:20:29] [INFO] [scidk.app] Graph backend: in-memory
[2026-03-02 11:20:30] [INFO] [scidk.core.label_endpoint_registry] Label endpoint registry initialized
[2026-03-02 11:20:30] [INFO] [scidk.core.plugin_template_registry] Plugin template registry initialized
[2026-03-02 11:20:30] [INFO] [scidk.core.plugin_instance_manager] Plugin instance manager initialized (db: scidk_settings.db)
[2026-03-02 11:20:30] [INFO] [scidk.core.plugin_loader] Discovered 4 plugins: ['example_ilab', 'ilab_table_loader', 'table_loader', 'example_plugin']
[2026-03-02 11:20:30] [INFO] [scidk.core.plugin_loader] Discovered 4 plugins: ['example_ilab', 'ilab_table_loader', 'table_loader', 'example_plugin']
[2026-03-02 11:20:30] [INFO] [scidk.core.label_endpoint_registry] Registered label endpoint: /api/integrations/ilab/services (iLab Services) -> iLabService
[2026-03-02 11:20:30] [INFO] [scidk.core.label_endpoint_registry] Registered label endpoint: /api/integrations/ilab/equipment (iLab Equipment) -> Equipment
[2026-03-02 11:20:30] [INFO] [scidk.core.plugin_loader] Successfully loaded plugin: example_ilab v1.0.0
[2026-03-02 11:20:30] [WARNING] [scidk.core.plugin_template_registry] Template ilab_importer with category 'data_import' missing recommended graph_behavior config keys: ['can_create_label', 'label_source']
[2026-03-02 11:20:30] [INFO] [scidk.core.plugin_template_registry] Registered plugin template: ilab_importer (iLab Data Importer) [category: data_import]
[2026-03-02 11:20:30] [INFO] [plugins.ilab_table_loader] iLab Data Importer plugin template registered successfully
[2026-03-02 11:20:30] [INFO] [scidk.core.plugin_loader] Successfully loaded plugin: ilab_table_loader v1.0.0
[2026-03-02 11:20:30] [INFO] [scidk.core.plugin_template_registry] Registered plugin template: table_loader (Table Loader) [category: data_import]
[2026-03-02 11:20:30] [INFO] [plugins.table_loader] Table Loader plugin template registered successfully
[2026-03-02 11:20:30] [INFO] [scidk.core.plugin_loader] Successfully loaded plugin: table_loader v1.0.0
[2026-03-02 11:20:30] [INFO] [scidk.core.plugin_loader] Successfully loaded plugin: example_plugin v1.0.0
[2026-03-02 11:20:30] [INFO] [apscheduler.scheduler] Adding job tentatively -- it will be properly scheduled when the scheduler starts
[2026-03-02 11:20:30] [INFO] [apscheduler.scheduler] Added job "Daily Backup" to job store "default"
[2026-03-02 11:20:30] [INFO] [apscheduler.scheduler] Scheduler started
____________________ test_enrich_link_with_empty_properties ____________________

client = <FlaskClient <Flask 'scidk.app'>>

    def test_enrich_link_with_empty_properties(client):
        """Test enriching link relationships with no specific properties (uses SET r +=)."""
        # Create labels
        client.post('/api/labels', json={
            'name': 'Source',
            'properties': [{'name': 'uuid', 'type': 'string'}],
            'relationships': []
        })
        client.post('/api/labels', json={
            'name': 'Target',
            'properties': [{'name': 'uuid', 'type': 'string'}],
            'relationships': []
        })
    
        # Create an Active import link
        payload = {
            'name': 'Test Import Link 2',
            'source_label': 'Source',
            'target_label': 'Target',
            'match_strategy': 'graph_import',
            'match_config': {
                'source_database': 'TestDB',
                'source_uid_property': 'uuid',
                'target_uid_property': 'uuid'
            },
            'relationship_type': 'LINKS_TO',
            'relationship_props': {},
            'status': 'active'
        }
        create_resp = client.post('/api/links', json=payload)
>       link_id = create_resp.get_json()['link']['id']
E       KeyError: 'link'

tests/test_links_api.py:652: KeyError
---------------------------- Captured stderr setup -----------------------------
[2026-03-02 11:20:30] [INFO] [root] Logging configured: level=INFO, dir=logs, max_size=50MB, backups=10
[2026-03-02 11:20:30] [INFO] [scidk.app] Graph backend: in-memory
[2026-03-02 11:20:31] [INFO] [scidk.core.label_endpoint_registry] Label endpoint registry initialized
[2026-03-02 11:20:31] [INFO] [scidk.core.plugin_template_registry] Plugin template registry initialized
[2026-03-02 11:20:31] [INFO] [scidk.core.plugin_instance_manager] Plugin instance manager initialized (db: scidk_settings.db)
[2026-03-02 11:20:31] [INFO] [scidk.core.plugin_loader] Discovered 4 plugins: ['example_ilab', 'ilab_table_loader', 'table_loader', 'example_plugin']
[2026-03-02 11:20:31] [INFO] [scidk.core.plugin_loader] Discovered 4 plugins: ['example_ilab', 'ilab_table_loader', 'table_loader', 'example_plugin']
[2026-03-02 11:20:31] [INFO] [scidk.core.label_endpoint_registry] Registered label endpoint: /api/integrations/ilab/services (iLab Services) -> iLabService
[2026-03-02 11:20:31] [INFO] [scidk.core.label_endpoint_registry] Registered label endpoint: /api/integrations/ilab/equipment (iLab Equipment) -> Equipment
[2026-03-02 11:20:31] [INFO] [scidk.core.plugin_loader] Successfully loaded plugin: example_ilab v1.0.0
[2026-03-02 11:20:31] [WARNING] [scidk.core.plugin_template_registry] Template ilab_importer with category 'data_import' missing recommended graph_behavior config keys: ['can_create_label', 'label_source']
[2026-03-02 11:20:31] [INFO] [scidk.core.plugin_template_registry] Registered plugin template: ilab_importer (iLab Data Importer) [category: data_import]
[2026-03-02 11:20:31] [INFO] [plugins.ilab_table_loader] iLab Data Importer plugin template registered successfully
[2026-03-02 11:20:31] [INFO] [scidk.core.plugin_loader] Successfully loaded plugin: ilab_table_loader v1.0.0
[2026-03-02 11:20:31] [INFO] [scidk.core.plugin_template_registry] Registered plugin template: table_loader (Table Loader) [category: data_import]
[2026-03-02 11:20:31] [INFO] [plugins.table_loader] Table Loader plugin template registered successfully
[2026-03-02 11:20:31] [INFO] [scidk.core.plugin_loader] Successfully loaded plugin: table_loader v1.0.0
[2026-03-02 11:20:31] [INFO] [scidk.core.plugin_loader] Successfully loaded plugin: example_plugin v1.0.0
[2026-03-02 11:20:31] [INFO] [apscheduler.scheduler] Adding job tentatively -- it will be properly scheduled when the scheduler starts
[2026-03-02 11:20:31] [INFO] [apscheduler.scheduler] Added job "Daily Backup" to job store "default"
[2026-03-02 11:20:31] [INFO] [apscheduler.scheduler] Scheduler started
=============================== warnings summary ===============================
tests/test_label_instance_count.py: 2 warnings
tests/test_labels_api.py: 13 warnings
tests/test_link_execution_progress.py: 2 warnings
  /home/patch/PycharmProjects/scidk/.venv/lib/python3.12/site-packages/neo4j/_sync/driver.py:547: DeprecationWarning: Relying on Driver's destructor to close the session is deprecated. Please make sure to close the session. Use it as a context (`with` statement) or make sure to call `.close()` explicitly. Future versions of the driver will not close drivers automatically.
    _deprecation_warn(

tests/test_links_api.py: 10 warnings
tests/test_links_integration.py: 15 warnings
tests/test_scripts.py: 6 warnings
tests/test_transparency_chat_tools.py: 12 warnings
tests/test_transparency_file_interpretation.py: 6 warnings
tests/test_transparency_plugins_page.py: 27 warnings
  /home/patch/PycharmProjects/scidk/scidk/core/script_validators.py:40: DeprecationWarning: ast.Str is deprecated and will be removed in Python 3.14; use ast.Constant instead
    isinstance(tree.body[0].value, (ast.Str, ast.Constant))):

tests/test_links_api.py: 9 warnings
tests/test_links_integration.py: 15 warnings
tests/test_transparency_chat_tools.py: 12 warnings
tests/test_transparency_file_interpretation.py: 6 warnings
tests/test_transparency_plugins_page.py: 27 warnings
  /home/patch/PycharmProjects/scidk/scidk/core/script_validators.py:43: DeprecationWarning: ast.Str is deprecated and will be removed in Python 3.14; use ast.Constant instead
    if isinstance(tree.body[0].value, ast.Str):

tests/test_links_api.py: 9 warnings
tests/test_links_integration.py: 15 warnings
tests/test_transparency_chat_tools.py: 12 warnings
tests/test_transparency_file_interpretation.py: 6 warnings
tests/test_transparency_plugins_page.py: 27 warnings
  /home/patch/PycharmProjects/scidk/scidk/core/script_validators.py:44: DeprecationWarning: Attribute s is deprecated and will be removed in Python 3.14; use value instead
    return tree.body[0].value.s

tests/test_transparency_chat_tools.py: 3 warnings
tests/test_transparency_dependencies.py: 17 warnings
tests/test_transparency_file_interpretation.py: 4 warnings
tests/test_transparency_plugins_page.py: 7 warnings
  /home/patch/PycharmProjects/scidk/scidk/core/script_validators.py:76: DeprecationWarning: ast.Str is deprecated and will be removed in Python 3.14; use ast.Constant instead
    if node.args and isinstance(node.args[0], (ast.Str, ast.Constant)):

tests/test_transparency_chat_tools.py: 3 warnings
tests/test_transparency_dependencies.py: 17 warnings
tests/test_transparency_file_interpretation.py: 4 warnings
tests/test_transparency_plugins_page.py: 7 warnings
  /home/patch/PycharmProjects/scidk/scidk/core/script_validators.py:78: DeprecationWarning: ast.Str is deprecated and will be removed in Python 3.14; use ast.Constant instead
    if isinstance(node.args[0], ast.Str):

tests/test_transparency_chat_tools.py: 3 warnings
tests/test_transparency_dependencies.py: 17 warnings
tests/test_transparency_file_interpretation.py: 4 warnings
tests/test_transparency_plugins_page.py: 7 warnings
  /home/patch/PycharmProjects/scidk/scidk/core/script_validators.py:79: DeprecationWarning: Attribute s is deprecated and will be removed in Python 3.14; use value instead
    value = node.args[0].s

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
SKIPPED [1] tests/test_files_page_e2e.py:33: UI redesigned - test needs updating for new tree explorer
SKIPPED [1] tests/test_files_page_e2e.py:229: UI redesigned - test needs updating for new tree explorer
SKIPPED [1] tests/test_files_page_e2e.py:244: UI redesigned - test needs updating for new tree explorer
SKIPPED [1] tests/test_files_page_e2e.py:259: UI redesigned - test needs updating for new tree explorer
SKIPPED [1] tests/test_graph_query_api.py:25: Mocking challenge - test works in real scenario
SKIPPED [1] tests/test_links_integration.py:32: Requires scripts/links/ directory with multiple demo scripts - currently only 1 exists
SKIPPED [1] tests/test_links_integration.py:130: Demo scripts semantic-similarity-link and author-collaboration-link no longer exist - only sample_to_imagingdataset
SKIPPED [3] tests/test_transparency_analysis_scripts.py: Phase 7: AnalysisContext not yet implemented
SKIPPED [2] tests/test_transparency_analysis_scripts.py: Phase 7: Analysis validation not yet implemented
SKIPPED [3] tests/test_transparency_analysis_scripts.py: Phase 8: Results page integration not yet implemented
SKIPPED [1] tests/e2e/test_demo_recording.py:35: BASE_URL is not set; start the server locally and export BASE_URL to run E2E smoke.
SKIPPED [1] tests/e2e/test_persistence.py:68: BASE_URL is not set; start the server locally and export BASE_URL to run E2E smoke.
FAILED tests/test_files_page_e2e.py::test_no_synchronous_scan_in_ui - assert ...
FAILED tests/test_label_instance_count.py::test_instance_count_neo4j_not_configured
FAILED tests/test_links_api.py::test_enrich_link_with_properties - assert 400...
FAILED tests/test_links_api.py::test_enrich_link_with_empty_properties - KeyE...
===== 4 failed, 906 passed, 17 skipped, 324 warnings in 401.31s (0:06:41) ======