chore: remove deprecated ontology processing code (#818)

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 5.0.0
+current_version = 5.0.2
 commit = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<prerel>rc)\.(?P<prerelversion>\d+))?
 serialize = 

.github/workflows/ontology_process.yml → .github/workflows/gencode_process.yml

@@ -1,10 +1,9 @@
-name: Updates to Ontology Files
+name: Updates to GENCODE Files
 
 on:
   push:
     paths:
-      - '**/cellxgene_schema_cli/cellxgene_schema/ontology_files/gene_info.yml'
-      - '**/cellxgene_schema_cli/cellxgene_schema/ontology_files/owl_info.yml'
+      - '**/cellxgene_schema_cli/cellxgene_schema/gencode_files/gene_info.yml'
     branches-ignore:
       - main
 
@@ -16,19 +15,10 @@ jobs:
         uses: actions/checkout@v3
         with:
           ref: ${{ github.event.pull_request.head.ref }}
-      - name: ontology changes
-        uses: dorny/paths-filter@v2
-        id: filter
-        with:
-          filters: |
-            owl_info:
-              - 'cellxgene_schema_cli/cellxgene_schema/ontology_files/owl_info.yml'
-            gene_info:
-              - 'cellxgene_schema_cli/cellxgene_schema/ontology_files/gene_info.yml'
-      - name: Set up Python 3.8
+      - name: Set up Python 3.10
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: "3.10"
       - name: Python cache
         uses: actions/cache@v1
         with:
@@ -43,21 +33,14 @@ jobs:
         run: |
           git config user.name github-actions
           git config user.email [email protected]
-      - name: owl-processing
-        if: ${{ steps.filter.outputs.owl_info == 'true' }}
-        run: |
-          make download-ontologies -C cellxgene_schema_cli
-          git add ./cellxgene_schema_cli/cellxgene_schema/ontology_files/all_ontology.json.gz
       - name: gene-processing
-        if: ${{ steps.filter.outputs.gene_info == 'true' }}
         run: |
           make gene-processing -C cellxgene_schema_cli
           git add ./cellxgene_schema_cli/cellxgene_schema/ontology_files/genes_*.csv.gz
           git add ./cellxgene_schema_cli/cellxgene_schema/ontology_files/*_diff.txt
       - name: Commit
-        if: ${{ steps.filter.outputs.gene_info == 'true'  || steps.filter.outputs.owl_info == 'true' }}
         run: |
-          git commit -m "AUTO: update ontologies"
+          git commit -m "AUTO: update gencode files"
           git push
 
   unit-tests:

.github/workflows/schema-version-bump.yml

@@ -91,7 +91,7 @@ jobs:
         id: changed-files
         uses: tj-actions/changed-files@v36
         with:
-          files: cellxgene_schema_cli/cellxgene_schema/ontology_files/*.csv.gz
+          files: cellxgene_schema_cli/cellxgene_schema/gencode_files/*.csv.gz
       - name: Run Dry-Run Script
         if: steps.changed-files.outputs.any_changed == 'true'
         run: python3 -m scripts.schema_bump_dry_run_genes.gene_bump_dry_run

cellxgene_schema_cli/Makefile

@@ -1,9 +1,5 @@
 .PHONY: update-references
-update-references: download-ontologies gene-processing clean
-
-.PHONY: download-ontologies
-download-ontologies:
-	python3 ./scripts/ontology_processing.py
+update-references: gene-processing clean
 
 .PHONY: gene-processing
 gene-processing:

cellxgene_schema_cli/cellxgene_schema/__init__.py

@@ -1 +1 @@
-__version__ = "5.0.0"
+__version__ = "5.0.2"

cellxgene_schema_cli/cellxgene_schema/env.py

@@ -1,10 +1,8 @@
 import os
 
 PACKAGE_ROOT = os.path.dirname(os.path.realpath(__file__))
-ONTOLOGY_DIR = os.path.join(PACKAGE_ROOT, "ontology_files")
-GENE_INFO_YAML = os.path.join(ONTOLOGY_DIR, "gene_info.yml")
-OWL_INFO_YAML = os.path.join(ONTOLOGY_DIR, "owl_info.yml")
-PARSED_ONTOLOGIES_FILE = os.path.join(ONTOLOGY_DIR, "all_ontology.json.gz")
+GENCODE_DIR = os.path.join(PACKAGE_ROOT, "gencode_files")
+GENE_INFO_YAML = os.path.join(GENCODE_DIR, "gene_info.yml")
 SCHEMA_DEFINITIONS_DIR = os.path.join(PACKAGE_ROOT, "schema_definitions")
 SCHEMA_DEFINITION_FILE = os.path.join(SCHEMA_DEFINITIONS_DIR, "schema_definition.yaml")
 SCHEMA_REFERENCE_BASE_URL = "https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema"

cellxgene_schema_cli/cellxgene_schema/ontology.py → cellxgene_schema_cli/cellxgene_schema/gencode.py

@@ -41,10 +41,10 @@ class GeneChecker:
     """Handles checking gene ids, retrieves symbols"""
 
     GENE_FILES = {
-        SupportedOrganisms.HOMO_SAPIENS: os.path.join(env.ONTOLOGY_DIR, "genes_homo_sapiens.csv.gz"),
-        SupportedOrganisms.MUS_MUSCULUS: os.path.join(env.ONTOLOGY_DIR, "genes_mus_musculus.csv.gz"),
-        SupportedOrganisms.SARS_COV_2: os.path.join(env.ONTOLOGY_DIR, "genes_sars_cov_2.csv.gz"),
-        SupportedOrganisms.ERCC: os.path.join(env.ONTOLOGY_DIR, "genes_ercc.csv.gz"),
+        SupportedOrganisms.HOMO_SAPIENS: os.path.join(env.GENCODE_DIR, "genes_homo_sapiens.csv.gz"),
+        SupportedOrganisms.MUS_MUSCULUS: os.path.join(env.GENCODE_DIR, "genes_mus_musculus.csv.gz"),
+        SupportedOrganisms.SARS_COV_2: os.path.join(env.GENCODE_DIR, "genes_sars_cov_2.csv.gz"),
+        SupportedOrganisms.ERCC: os.path.join(env.GENCODE_DIR, "genes_ercc.csv.gz"),
     }
 
     def __init__(self, species: SupportedOrganisms):

cellxgene_schema_cli/cellxgene_schema/ontology_files/gene_info.yml → cellxgene_schema_cli/cellxgene_schema/gencode_files/gene_info.yml

@@ -1,4 +1,4 @@
-# Changes to this file will trigger a run of the ontology_process.yml GHA job, which will run the gene_processing.py script.
+# Changes to this file will trigger a run of the gencode_process.yml GHA job, which will run the gene_processing.py script.
 ercc:
   description: ercc
   url: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/cms_095047.txt

cellxgene_schema_cli/cellxgene_schema/validate.py

@@ -15,7 +15,7 @@
 from pandas.core.computation.ops import UndefinedVariableError
 from scipy import sparse
 
-from . import ontology, schema
+from . import gencode, schema
 from .utils import SPARSE_MATRIX_TYPES, get_matrix_format, getattr_anndata, read_h5ad
 
 logger = logging.getLogger(__name__)
@@ -31,8 +31,8 @@ def __init__(self, ignore_labels=False):
         self.schema_version: str = None
         self.ignore_labels = ignore_labels
 
-        # Values will be instances of ontology.GeneChecker,
-        # keys will be one of ontology.SupportedOrganisms
+        # Values will be instances of gencode.GeneChecker,
+        # keys will be one of gencode.SupportedOrganisms
         self.gene_checkers = dict()
 
     def reset(self):
@@ -292,7 +292,7 @@ def _validate_feature_id(self, feature_id: str, df_name: str):
         :rtype none
         """
 
-        organism = ontology.get_organism_from_feature_id(feature_id)
+        organism = gencode.get_organism_from_feature_id(feature_id)
 
         if not organism:
             self.errors.append(
@@ -302,7 +302,7 @@ def _validate_feature_id(self, feature_id: str, df_name: str):
             return
 
         if organism not in self.gene_checkers:
-            self.gene_checkers[organism] = ontology.GeneChecker(organism)
+            self.gene_checkers[organism] = gencode.GeneChecker(organism)
 
         if not self.gene_checkers[organism].is_valid_id(feature_id):
             self.errors.append(f"'{feature_id}' is not a valid feature ID in '{df_name}'.")

cellxgene_schema_cli/cellxgene_schema/write_labels.py

@@ -3,7 +3,7 @@
 from typing import Dict, List, Optional
 
 import pandas as pd
-from cellxgene_schema import ontology
+from cellxgene_schema import gencode
 from cellxgene_schema.env import SCHEMA_REFERENCE_BASE_URL, SCHEMA_REFERENCE_FILE_NAME
 from cellxgene_schema.validate import ONTOLOGY_PARSER, Validator
 
@@ -169,12 +169,12 @@ def _get_mapping_dict_feature_id(self, ids: List[str]) -> Dict[str, str]:
         mapping_dict = {}
 
         for i in ids:
-            organism = ontology.get_organism_from_feature_id(i)
+            organism = gencode.get_organism_from_feature_id(i)
             mapping_dict[i] = self.validator.gene_checkers[organism].get_symbol(i)
 
         return mapping_dict
 
-    def _get_mapping_dict_feature_reference(self, ids: List[str]) -> Dict[str, Optional[ontology.SupportedOrganisms]]:
+    def _get_mapping_dict_feature_reference(self, ids: List[str]) -> Dict[str, Optional[gencode.SupportedOrganisms]]:
         """
         Creates a mapping dictionary of gene/feature IDs and NCBITaxon curies
 
@@ -187,7 +187,7 @@ def _get_mapping_dict_feature_reference(self, ids: List[str]) -> Dict[str, Optio
         mapping_dict = {}
 
         for i in ids:
-            organism = ontology.get_organism_from_feature_id(i)
+            organism = gencode.get_organism_from_feature_id(i)
             mapping_dict[i] = organism.value
 
         return mapping_dict
@@ -227,7 +227,7 @@ def _get_mapping_dict_feature_length(self, ids: List[str]) -> Dict[str, int]:
 
         for i in ids:
             if i.startswith("ENS"):
-                organism = ontology.get_organism_from_feature_id(i)
+                organism = gencode.get_organism_from_feature_id(i)
                 mapping_dict[i] = self.validator.gene_checkers[organism].get_length(i)
             else:
                 mapping_dict[i] = 0

cellxgene_schema_cli/requirements.txt

@@ -3,10 +3,10 @@ cellxgene-ontology-guide==0.4.0
 click==8.1.3
 Cython==0.29.34
 numpy==1.23.2
-owlready2==0.40.0
 pandas==1.4.4
 PyYaml==6.0
 wheel==0.40.0
+scipy<1.13.0    # scipy 1.13.0 is not compatible with anndata <=0.10.6, revisit before next release
 semver==3.0.0
 xxhash==3.3.0
 matplotlib==3.7.3