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chore: pin uberon ontology version #388

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merged 2 commits into from
Apr 20, 2023
Merged

chore: pin uberon ontology version #388

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8a56611
pin uberon ontology version
atolopko-czi Apr 18, 2023
17f884b
remove linting ignore
atolopko-czi Apr 18, 2023
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3 changes: 3 additions & 0 deletions tools/cellxgene_census_builder/src/cellxgene_census_builder/build_soma/globals.py
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Expand Up @@ -8,6 +8,9 @@
CENSUS_SCHEMA_VERSION = "0.1.1"

CXG_SCHEMA_VERSION = "3.0.0" # version we write to the census
# NOTE: The UBERON ontology URL needs to manually updated if the CXG Dataset Schema is updated. This is a temporary
# hassle, however, since the TissueMapper, which relies upon this ontology, will eventually be removed from the Builder
CXG_UBERON_ONTOLOGY_URL = "https://github.com/obophenotype/uberon/releases/download/v2022-08-19/uberon.owl"
CXG_SCHEMA_VERSION_IMPORT = [CXG_SCHEMA_VERSION] # versions we can ingest

# Columns expected in the census_datasets dataframe
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11 changes: 5 additions & 6 deletions tools/cellxgene_census_builder/src/cellxgene_census_builder/build_soma/tissue_mapper.py
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Expand Up @@ -12,9 +12,11 @@

This code contains several places that do not pass the lint/static analysis CI for this pipeline, so the analysis is disabled in this prologue.
"""
from typing import List

import owlready2
from typing import List

from .globals import CXG_UBERON_ONTOLOGY_URL


class TissueMapper:
Expand Down Expand Up @@ -120,12 +122,10 @@ class TissueMapper:
"UBERON_0001062", # anatomical entity
]

def __init__(self, uberon_ontology: str = "http://purl.obolibrary.org/obo/uberon.owl"):
# TODO: use the pinned ontology at `single-cell-curation`
self._uberon = owlready2.get_ontology(uberon_ontology)
self._uberon.load()
def __init__(self):
self._cached_tissues = {}
self._cached_labels = {}
self._uberon = owlready2.get_ontology(CXG_UBERON_ONTOLOGY_URL).load()

def get_high_level_tissue(self, tissue_ontology_term_id: str) -> str:
"""
Expand Down Expand Up @@ -246,7 +246,6 @@ def _get_entity_from_id(self, ontology_term_id: str) -> owlready2.entity.ThingCl
"""
Given a readable ontology term id (e.g. "UBERON_0002048"), it returns the associated ontology entity
"""
# TODO: use the pinned ontology at `single-cell-curation`
return self._uberon.search_one(iri=f"http://purl.obolibrary.org/obo/{ontology_term_id}")

@staticmethod
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