Code

resource update june 2024 and krt#47

Code

Merged

RichJackson merged 45 commits intomainAstraZeneca/KAZU:mainfrom krt_ontology_upgradeAstraZeneca/KAZU:krt_ontology_upgradeCopy head branch name to clipboardJul 4, 2024

+3,266-2,230

Commits

Commits on Jul 1, 2024

• added OntologyDownloader to facilitate ontology downloading

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  e4a2f59

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• updated parser implementations with downloader components

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• removed obsolete download_ontology_updates.py script

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• added new delete_resource method to ResourceManager

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• load_config is now a cached_resource

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• resource_to_df can now also show behaviour, on request

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• reordered imports

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• display_parser_selector now only depends on the config. Also can optionally clear state on parser change

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• Do not clear state on _add_new_resource_form parser select

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• created OntologyUpdateManager to facilitate updating ontologies via the streamlit app

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• created OntologyUpdateForm and additional components.py

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• created additional page for updating ontology

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• updated ontology configs with downloader components

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• fixed a bug where some ontologies contain multiple owl:versionInfo nodes. Also provided alternative owl:versionIRI query

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• removed commented out key

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• moved DEFAULT_LABEL etc to constants.py to avoid circular imports

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• new ChemblParquetOntologyDownloader handles preprocessing of chembl DB to avoid commiting large chembl sqllite db to repo

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• _cached_wget moved to OpenTargetsOntologyDownloader as it is specific to this datasource

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• ChemblOntologyParser deprecated in favour of ChemblParquetOntologyParser

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• fixed bug in ResourceDiscrepancyManger where unresoveld discrepancies weren't properly recalculated in certain places

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• ResourceDiscrepancyResolutionForm is now stateful to simplify what happens when a different parser is selected

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• reordered pages in krt for a more natural workflow selection

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Commits on Jul 3, 2024

• update resources for kazu 2.1.0 release. This includes removing chembl in favour of the new parquet format

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• update configuration for kazu 2.1.0 release

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• moved load_config to a location to avoid circular imports

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• resource manager is now aware of any actions that can invalidate the parser caches. Also added methods to load an instance of the pipeline in a cache aware fashion

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• added simple pipeline testing interface

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• added strict mode to find_case_conflicts, so that all potential string conflicts may be detected

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• string editor uses strict mode on check_for_case_conflicts_across_resources

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• added clear_invalid_caches, which triggers when save is activated, so that the cache will repopulate correctly on reload

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• minor doc improvements

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• update OT versions for molecule and measurement

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• update uberon data origin

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• using get_selected_parser_name method where appropriate

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• renamed method as it was confusing. also added comment to explain why target is popped

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• using new method name

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• removed superfluous delete function for ChemblParquetOntologyDownloader as it now outputs a single parquet file

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• using parser.download_ontology rather than calling the downloader directly, as this also handles deletion

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• clear resource mananger cache ofter ont update as it will be invalid at that point

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• fixed indent which would cause lack of merge report to bug

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• stopped reading resources directly from curations path in resource manager init as this was causing bugs with normalisation issues. Instead we rely on the report directly

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• changed log message to ref KRT

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• strict mode on conflict analyser: if True, then the function will return True if there

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• town crier KRT

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Commits on Jul 4, 2024

• fixed commit index in test_discrepancy_manager_sync

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