├── .github └── workflows │ └── main.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── LICENSE ├── MANIFEST.in ├── README.md ├── data ├── DATA_NOTES.md ├── bikg_disease │ └── input │ │ ├── config.json │ │ ├── edges_hierarchy.csv │ │ ├── mappings.csv │ │ ├── nodes.csv │ │ └── nodes_obsolete.csv ├── data_prepper.py └── example_report │ ├── data_docs │ └── local_site │ │ ├── expectations │ │ ├── alignment_steps_report_table.html │ │ ├── connectivity_steps_report_table.html │ │ ├── edges_hierarchy_domain_table.html │ │ ├── edges_hierarchy_post_table.html │ │ ├── edges_hierarchy_table.html │ │ ├── mappings_domain_table.html │ │ ├── mappings_for_input_nodes_table.html │ │ ├── mappings_obsolete_to_current_table.html │ │ ├── mappings_table.html │ │ ├── mappings_updated_table.html │ │ ├── merges_aggregated_table.html │ │ ├── merges_domain_table.html │ │ ├── merges_with_meta_data_table.html │ │ ├── nodes_connected_excluding_seed_table.html │ │ ├── nodes_connected_table.html │ │ ├── nodes_dangling_table.html │ │ ├── nodes_domain_table.html │ │ ├── nodes_merged_table.html │ │ ├── nodes_merged_to_other_table.html │ │ ├── nodes_merged_to_seed_table.html │ │ ├── nodes_obsolete_table.html │ │ ├── nodes_seed_table.html │ │ ├── nodes_table.html │ │ └── nodes_unmapped_table.html │ │ ├── index.html │ │ ├── static │ │ ├── fonts │ │ │ └── HKGrotesk │ │ │ │ ├── HKGrotesk-Bold.otf │ │ │ │ ├── HKGrotesk-BoldItalic.otf │ │ │ │ ├── HKGrotesk-Italic.otf │ │ │ │ ├── HKGrotesk-Light.otf │ │ │ │ ├── HKGrotesk-LightItalic.otf │ │ │ │ ├── HKGrotesk-Medium.otf │ │ │ │ ├── HKGrotesk-MediumItalic.otf │ │ │ │ ├── HKGrotesk-Regular.otf │ │ │ │ ├── HKGrotesk-SemiBold.otf │ │ │ │ └── HKGrotesk-SemiBoldItalic.otf │ │ ├── images │ │ │ ├── favicon.ico │ │ │ ├── glossary_scroller.gif │ │ │ ├── iterative-dev-loop.png │ │ │ ├── logo-long-vector.svg │ │ │ ├── logo-long.png │ │ │ ├── short-logo-vector.svg │ │ │ ├── short-logo.png │ │ │ └── validation_failed_unexpected_values.gif │ │ └── styles │ │ │ ├── data_docs_custom_styles_template.css │ │ │ └── data_docs_default_styles.css │ │ └── validations │ │ ├── alignment_steps_report_table │ │ └── __none__ │ │ │ └── 20220531T014609.275574Z │ │ │ └── 447c503997505199223524eda8359d32.html │ │ ├── connectivity_steps_report_table │ │ └── __none__ │ │ │ └── 20220531T014613.115354Z │ │ │ └── e7c3c0f897f7076cf275d61c765fab40.html │ │ ├── edges_hierarchy_domain_table │ │ └── __none__ │ │ │ └── 20220531T014643.401137Z │ │ │ └── 894501d8f1f6c565e1ae828230799a73.html │ │ ├── edges_hierarchy_post_table │ │ └── __none__ │ │ │ └── 20220531T014544.569975Z │ │ │ └── be18440cd34363ed1c63ca3e0fef2bb1.html │ │ ├── edges_hierarchy_table │ │ └── __none__ │ │ │ └── 20220531T012440.487052Z │ │ │ └── 625eadba9ccaa6b032289f29e62ddade.html │ │ ├── mappings_domain_table │ │ └── __none__ │ │ │ └── 20220531T014636.110307Z │ │ │ └── 8463eb796cc4ce36e6d7d1b4f8ea8227.html │ │ ├── mappings_for_input_nodes_table │ │ └── __none__ │ │ │ └── 20220531T014602.573691Z │ │ │ └── 9f005e8c5446e66a675987ad67830449.html │ │ ├── mappings_obsolete_to_current_table │ │ └── __none__ │ │ │ └── 20220531T014606.817315Z │ │ │ └── 38051fcd5968316dd98365913a42c383.html │ │ ├── mappings_table │ │ └── __none__ │ │ │ └── 20220531T012433.441834Z │ │ │ └── 28d859e50c34b64f80451f3093bcd896.html │ │ ├── mappings_updated_table │ │ └── __none__ │ │ │ └── 20220531T014553.556352Z │ │ │ └── d3dc362ad9ce646c377872db0b8bd86d.html │ │ ├── merges_aggregated_table │ │ └── __none__ │ │ │ └── 20220531T014550.772044Z │ │ │ └── e953db51e67893a980cb41aaccf24ace.html │ │ ├── merges_domain_table │ │ └── __none__ │ │ │ └── 20220531T014641.269467Z │ │ │ └── 3ea223d545c9c2077f9d8e82f363bf38.html │ │ ├── merges_with_meta_data_table │ │ └── __none__ │ │ │ └── 20220531T014547.900897Z │ │ │ └── cb4525b4f113747c5649d0d8e9aba16c.html │ │ ├── nodes_connected_excluding_seed_table │ │ └── __none__ │ │ │ └── 20220531T014539.567626Z │ │ │ └── c490f1e9c83d9fc22374d14fb0f20bcb.html │ │ ├── nodes_connected_table │ │ └── __none__ │ │ │ └── 20220531T014537.188188Z │ │ │ └── 3a244397315dbbf6c66726da2760ecd2.html │ │ ├── nodes_dangling_table │ │ └── __none__ │ │ │ └── 20220531T014542.045863Z │ │ │ └── 3f1d021431ea460d9897fb437bfec1d1.html │ │ ├── nodes_domain_table │ │ └── __none__ │ │ │ └── 20220531T014633.618450Z │ │ │ └── 7896b7c522346100cceefc80cd9da6db.html │ │ ├── nodes_merged_table │ │ └── __none__ │ │ │ └── 20220531T014530.372251Z │ │ │ └── 80bf758adafb7e083519bc709e20cf3b.html │ │ ├── nodes_merged_to_other_table │ │ └── __none__ │ │ │ └── 20220531T014535.346079Z │ │ │ └── 57e656876dcca3dbbba3b9170e7d9b23.html │ │ ├── nodes_merged_to_seed_table │ │ └── __none__ │ │ │ └── 20220531T014533.120785Z │ │ │ └── fc7b178891615fc1a32971cc63a96174.html │ │ ├── nodes_obsolete_table │ │ └── __none__ │ │ │ └── 20220531T012431.986243Z │ │ │ └── 15472abaaed9cb9b9af3ec9568b12da7.html │ │ ├── nodes_seed_table │ │ └── __none__ │ │ │ └── 20220531T014523.604709Z │ │ │ └── 87ec812f47b15b9dbf4c996e9cba3249.html │ │ ├── nodes_table │ │ └── __none__ │ │ │ └── 20220531T012429.973109Z │ │ │ └── e78b97003cef381050feafa16638744c.html │ │ └── nodes_unmapped_table │ │ └── __none__ │ │ └── 20220531T014527.330180Z │ │ └── 1800465361cedc87e04ad05f1e2b9c76.html │ ├── data_profile_reports │ ├── alignment_steps_report_report.html │ ├── connectivity_steps_report_report.html │ ├── edges_hierarchy_domain_report.html │ ├── edges_hierarchy_post_report.html │ ├── edges_hierarchy_report.html │ ├── mappings_domain_report.html │ ├── mappings_for_input_nodes_report.html │ ├── mappings_obsolete_to_current_report.html │ ├── mappings_report.html │ ├── mappings_updated_report.html │ ├── merges_aggregated_report.html │ ├── merges_domain_report.html │ ├── merges_with_meta_data_report.html │ ├── nodes_connected_excluding_seed_report.html │ ├── nodes_connected_report.html │ ├── nodes_dangling_report.html │ ├── nodes_domain_report.html │ ├── nodes_merged_report.html │ ├── nodes_merged_to_other_report.html │ ├── nodes_merged_to_seed_report.html │ ├── nodes_obsolete_report.html │ ├── nodes_report.html │ ├── nodes_seed_report.html │ └── nodes_unmapped_report.html │ ├── images │ ├── __init__.py │ ├── alignment_merges_cluster_size_bins.png │ ├── alignment_merges_nss_analysis.png │ ├── alignment_node_status.png │ ├── alignment_pipeline_steps_report_gantt_chart.png │ ├── alignment_step_node_analysis_stacked_bar_chart.png │ ├── check.png │ ├── connectivity_edges_hierarchy_child_parent.png │ ├── connectivity_edges_hierarchy_status.png │ ├── connectivity_node_status.png │ ├── connectivity_pipeline_steps_report_gantt_chart.png │ ├── connectivity_step_node_analysis_stacked_bar_chart.png │ ├── delete.png │ ├── ge-long-logo.png │ ├── icon_alignment.png │ ├── icon_connectivity.png │ ├── icon_data_profiling.png │ ├── icon_data_tests.png │ ├── icon_input.png │ ├── icon_output.png │ ├── icon_overview.png │ ├── input_edges_hierarchy_connected_nss_analysis_chart.png │ ├── input_mappings_mapped_nss_analysis.png │ ├── input_mappings_type_analysis.png │ ├── input_node_status.png │ ├── input_nodes_nodes_general_analysis.png │ ├── input_nodes_obsolete_nodes_obsolete_general_analysis.png │ ├── onto_merger_logo.jpg │ ├── output_edges_hierarchy_connected_nss_analysis_chart.png │ ├── output_mappings_mapped_nss_analysis.png │ ├── output_mappings_type_analysis.png │ ├── output_node_status.png │ ├── output_nodes_domain_nodes_general_analysis.png │ ├── overview_node_status.png │ ├── overview_pipeline_steps_report_gantt_chart.png │ ├── pandas_profiling_logo.png │ └── pandas_profiling_logo_2.png │ ├── index.html │ └── logs │ └── onto-merger.logger ├── dev_doc_gen.sh ├── docs ├── Makefile ├── requirements_1.txt └── source │ ├── _static │ ├── alignment_steps_report.png │ ├── bikg_disease_duplicated_disconnected_nodes.png │ ├── bikg_disease_mapping_ckd.png │ ├── bikg_disease_sources.png │ ├── bikg_disease_sources_full.png │ ├── bikg_with_disease_ont.png │ ├── config.json │ ├── examples │ │ ├── edges_hierarchy.csv │ │ ├── mappings.csv │ │ └── nodes.csv │ ├── ge_overview.png │ ├── ge_table.png │ ├── map_via_mapped_parent.png │ └── tree.txt │ ├── api │ ├── onto_merger.AlignmentManager.rst │ ├── onto_merger.DataManager.rst │ ├── onto_merger.Pipeline.rst │ ├── onto_merger.connect_nodes.rst │ ├── onto_merger.get_logger.rst │ ├── onto_merger.pipeline.Pipeline.rst │ ├── onto_merger.produce_merged_node_id_list.rst │ ├── onto_merger.produce_node_id_table_from_edge_table.rst │ ├── onto_merger.produce_table_nodes_dangling.rst │ ├── onto_merger.produce_table_nodes_only_connected.rst │ ├── onto_merger.produce_table_seed_ontology_hierarchy.rst │ ├── onto_merger.produce_table_with_namespace_column_for_node_ids.rst │ └── onto_merger.setup_logger.rst │ ├── conf.py │ ├── index.rst │ ├── modules │ ├── pipeline.rst │ └── root.rst │ └── notes │ ├── alignment.rst │ ├── alignment_configuration.rst │ ├── analysis.rst │ ├── connectivity.rst │ ├── data.rst │ ├── data_testing.rst │ ├── installation.rst │ ├── intro_short.rst │ ├── introduction.rst │ ├── pipeline.rst │ └── resources.rst ├── images └── onto_merger_logo.jpg ├── onto_merger ├── __init__.py ├── alignment │ ├── __init__.py │ ├── alignment_manager.py │ ├── hierarchy_utils.py │ ├── mapping_utils.py │ ├── merge_utils.py │ ├── networkit_utils.py │ └── networkx_utils.py ├── alignment_config │ ├── __init__.py │ ├── json_schema.py │ └── validator.py ├── analyser │ ├── __init__.py │ ├── analysis_utils.py │ ├── constants.py │ ├── pandas_profiler.py │ ├── plotly_utils.py │ ├── report_analyser.py │ └── report_analyser_utils.py ├── data │ ├── __init__.py │ ├── constants.py │ ├── data_manager.py │ └── dataclasses.py ├── data_testing │ ├── __init__.py │ ├── ge_expectation_helper.py │ ├── ge_runner.py │ └── ge_utils.py ├── logger │ ├── __init__.py │ └── log.py ├── main.py ├── pipeline │ ├── __init__.py │ └── pipeline.py ├── report │ ├── __init__.py │ ├── constants.py │ ├── data │ │ ├── __init__.py │ │ ├── section_summary_descriptions │ │ │ ├── __init__.py │ │ │ ├── alignment_summary_about.html │ │ │ ├── connectivity_summary_about.html │ │ │ ├── data_profiling_summary_about.html │ │ │ ├── data_tests_summary_about.html │ │ │ ├── input_summary_about.html │ │ │ ├── output_summary_about.html │ │ │ └── overview_summary_about.html │ │ └── table_column_descriptions │ │ │ ├── __init__.py │ │ │ ├── alignment_steps_detail.csv │ │ │ ├── connectivity_steps_detail.csv │ │ │ ├── edges_hierarchy_connected_nss_analysis.csv │ │ │ ├── mappings_mapped_nss_analysis.csv │ │ │ ├── merges_nss_analysis.csv │ │ │ ├── node_summary.csv │ │ │ └── nodes_general_analysis.csv │ ├── report_generator.py │ ├── section_data_loader.py │ └── templates │ │ ├── __init__.py │ │ ├── assets │ │ ├── __init__.py │ │ ├── bootstrap-theme.min.css │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.css │ │ ├── bootstrap.min.css │ │ ├── bootstrap.min.js │ │ ├── jquery.min.js │ │ ├── onto_merge_style.css │ │ └── script.js │ │ ├── data_content │ │ ├── __init__.py │ │ ├── table_column_description.html │ │ ├── table_description.html │ │ ├── table_edge_analysis.html │ │ ├── table_edge_path_length_description.html │ │ ├── table_frequency.html │ │ ├── table_mapping_analysis.html │ │ ├── table_merge_analysis.html │ │ ├── table_merge_analysis_aggregated_for_canonical.html │ │ ├── table_merge_cluster_mutliple_nss_in_same_cluster.html │ │ ├── table_merge_cluster_size_distribution.html │ │ ├── table_node_analysis.html │ │ ├── table_node_coverage_by_edge.html │ │ ├── table_node_status.html │ │ ├── table_node_status_overview.html │ │ ├── table_overview_hierarchy_edge_children_count_comparison.html │ │ ├── table_overview_hierarchy_edge_general_comparison.html │ │ ├── table_overview_node_summary.html │ │ ├── table_steps_alignment.html │ │ ├── table_steps_connectivity.html │ │ ├── table_summary_two_col.html │ │ ├── table_summary_two_col_no_bold.html │ │ ├── table_summary_two_col_striped.html │ │ ├── table_third_party_data.html │ │ └── table_validation_summary.html │ │ ├── images │ │ ├── __init__.py │ │ ├── check.png │ │ ├── delete.png │ │ ├── ge-long-logo.png │ │ ├── icon_alignment.png │ │ ├── icon_connectivity.png │ │ ├── icon_data_profiling.png │ │ ├── icon_data_tests.png │ │ ├── icon_input.png │ │ ├── icon_output.png │ │ ├── icon_overview.png │ │ ├── onto_merger_logo.jpg │ │ ├── pandas_profiling_logo.png │ │ └── pandas_profiling_logo_2.png │ │ ├── report.html │ │ ├── report_content │ │ ├── __init__.py │ │ ├── content.html │ │ ├── footer.html │ │ ├── javascript.html │ │ ├── navigation.html │ │ └── style.html │ │ ├── section_content │ │ ├── __init__.py │ │ ├── section-generic.html │ │ └── section-header.html │ │ └── subsection_content │ │ ├── __init__.py │ │ ├── alignment-details.html │ │ ├── alignment-merge-analyses.html │ │ ├── alignment-merge-analysis-clusters.html │ │ ├── alignment-merge-analysis.html │ │ ├── alignment-node-analysis.html │ │ ├── attributions.html │ │ ├── connectivity-details.html │ │ ├── connectivity-edge-analysis.html │ │ ├── connectivity-node-analysis.html │ │ ├── dataset-entity-analysis-with-chart-and-description.html │ │ ├── dataset-nodes.html │ │ ├── dataset-summary.html │ │ ├── edges-analysis.html │ │ ├── horizontal-rule.html │ │ ├── mapping-analysis.html │ │ ├── node-status.html │ │ ├── overview-configuration.html │ │ ├── overview-edge-summary.html │ │ ├── overview-node-summary.html │ │ ├── overview-project-org.html │ │ ├── overview-validation.html │ │ ├── section-summary.html │ │ ├── subsection-runtime.html │ │ └── table-description-accordion.html └── version.py ├── pyproject.toml ├── requirements.txt ├── setup.cfg ├── setup.py ├── tests ├── __init__.py ├── fixtures.py ├── integration │ ├── __init__.py │ ├── analysis_table_files.csv │ ├── image_and_figure_files.csv │ ├── test_alignment_manager.py │ └── test_pipeline.py ├── test_data │ └── input │ │ ├── config.json │ │ ├── edges_hierarchy.csv │ │ ├── mappings.csv │ │ ├── nodes.csv │ │ └── nodes_obsolete.csv ├── test_data_invalid │ └── input │ │ └── config.json └── unit │ ├── __init__.py │ ├── alignment │ ├── __init__.py │ ├── test_analysis_utils.py │ ├── test_hierarchy_utils.py │ ├── test_mapping_utils.py │ ├── test_merge_utils.py │ └── test_networkit_utils.py │ ├── alignment_config │ ├── __init__.py │ └── test_validator.py │ ├── analyser │ ├── __init__.py │ ├── test_analysis_util.py │ └── test_profiler.py │ ├── data │ ├── __init__.py │ ├── test_data_manager.py │ └── test_dataclasses.py │ └── data_testing │ ├── __init__.py │ ├── test_ge_expectation_helper.py │ ├── test_ge_runner.py │ └── test_ge_utils.py └── tox.ini /.github/workflows/main.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstraZeneca/onto_merger/HEAD/.github/workflows/main.yaml -------------------------------------------------------------------------------- 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