resource update june 2024 and krt #47

RichJackson · 2024-07-03T15:48:16Z

new Ontology Upgrade pathway for KRT (used to build this round of resource updates)

…onally clear state on parser change

…he streamlit app

…des. Also provided alternative owl:versionIRI query

…B to avoid commiting large chembl sqllite db to repo

… to this datasource

… weren't properly recalculated in certain places

…ppens when a different parser is selected

…l in favour of the new parquet format moved chembl 34 defaults to correct location

…parser caches. Also added methods to load an instance of the pipeline in a cache aware fashion

…g conflicts may be detected

…ources

… that the cache will repopulate correctly on reload

… target is popped

…er as it now outputs a single parquet file

…ectly, as this also handles deletion

…at that point

…nager init as this was causing bugs with normalisation issues. Instead we rely on the report directly

…urn True if there are multiple mention confidences for a given string, regardless of case sensitivity

RichJackson added 30 commits July 1, 2024 13:18

added OntologyDownloader to facilitate ontology downloading

e4a2f59

updated parser implementations with downloader components

a0ae223

removed obsolete download_ontology_updates.py script

45f1542

added new delete_resource method to ResourceManager

716b005

load_config is now a cached_resource

e201eea

resource_to_df can now also show behaviour, on request

cb27d65

reordered imports

fa75c34

display_parser_selector now only depends on the config. Also can opti…

08e4dd9

…onally clear state on parser change

Do not clear state on _add_new_resource_form parser select

092aaf7

created OntologyUpdateManager to facilitate updating ontologies via t…

3762c1d

…he streamlit app

created OntologyUpdateForm and additional components.py

1c94f7f

created additional page for updating ontology

493c7a6

updated ontology configs with downloader components

8bd3fdb

fixed a bug where some ontologies contain multiple owl:versionInfo no…

2a627d5

…des. Also provided alternative owl:versionIRI query

removed commented out key

e0a75ee

moved DEFAULT_LABEL etc to constants.py to avoid circular imports

96d157d

new ChemblParquetOntologyDownloader handles preprocessing of chembl D…

9639071

…B to avoid commiting large chembl sqllite db to repo

_cached_wget moved to OpenTargetsOntologyDownloader as it is specific…

db225f1

… to this datasource

ChemblOntologyParser deprecated in favour of ChemblParquetOntologyParser

0dd1045

fixed bug in ResourceDiscrepancyManger where unresoveld discrepancies…

7931ef8

… weren't properly recalculated in certain places

ResourceDiscrepancyResolutionForm is now stateful to simplify what ha…

7009716

…ppens when a different parser is selected

reordered pages in krt for a more natural workflow selection

b53de89

update resources for kazu 2.1.0 release. This includes removing chemb…

854910d

…l in favour of the new parquet format moved chembl 34 defaults to correct location

update configuration for kazu 2.1.0 release

d31323c

moved load_config to a location to avoid circular imports

788a2a3

resource manager is now aware of any actions that can invalidate the …

1344e51

…parser caches. Also added methods to load an instance of the pipeline in a cache aware fashion

added simple pipeline testing interface

b7e57f2

added strict mode to find_case_conflicts, so that all potential strin…

c1d27e2

…g conflicts may be detected

string editor uses strict mode on check_for_case_conflicts_across_res…

ec20459

…ources

added clear_invalid_caches, which triggers when save is activated, so…

8e7e0ed

… that the cache will repopulate correctly on reload

RichJackson added 15 commits July 3, 2024 14:53

minor doc improvements

127227f

update OT versions for molecule and measurement

f24f598

update uberon data origin

4dc1abc

using get_selected_parser_name method where appropriate

66f6270

renamed method as it was confusing. also added comment to explain why…

f88f836

… target is popped

using new method name

ce27426

removed superfluous delete function for ChemblParquetOntologyDownload…

ee8a060

…er as it now outputs a single parquet file

using parser.download_ontology rather than calling the downloader dir…

492b53d

…ectly, as this also handles deletion

clear resource mananger cache ofter ont update as it will be invalid …

8b72aac

…at that point

fixed indent which would cause lack of merge report to bug

ece2ce1

stopped reading resources directly from curations path in resource ma…

d7931a1

…nager init as this was causing bugs with normalisation issues. Instead we rely on the report directly

changed log message to ref KRT

248be39

strict mode on conflict analyser: if True, then the function will ret…

7cecbbf

…urn True if there are multiple mention confidences for a given string, regardless of case sensitivity

town crier KRT

58d8621

fixed commit index in test_discrepancy_manager_sync

09b9399

RichJackson merged commit b2ba17a into main Jul 4, 2024
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RichJackson deleted the krt_ontology_upgrade branch July 4, 2024 08:27

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resource update june 2024 and krt #47

resource update june 2024 and krt #47

RichJackson commented Jul 3, 2024

resource update june 2024 and krt #47

resource update june 2024 and krt #47

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RichJackson commented Jul 3, 2024