SchemaView object should be instantiated when needed & not globally.

.github/workflows/pypi-publish.yml

@@ -11,10 +11,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3.0.2
+    - uses: actions/checkout@v3
 
     - name: Set up Python
-      uses: actions/setup-python@v3.1.2
+      uses: actions/setup-python@v4.3.0
       with:
         python-version: 3.9
 

sssom/cli.py

@@ -20,14 +20,15 @@
 import click
 import pandas as pd
 import yaml
+from linkml_runtime.utils.schema_as_dict import schema_as_dict
+from linkml_runtime.utils.schemaview import SchemaView
 from rdflib import Graph
 from scipy.stats import chi2_contingency
 
 from sssom.constants import (
     DEFAULT_VALIDATION_TYPES,
-    MAPPING_SET_SLOTS,
-    MAPPING_SLOTS,
     PREFIX_MAP_MODES,
+    SCHEMA_YAML,
     SchemaValidationType,
 )
 from sssom.context import get_default_metadata
@@ -62,6 +63,11 @@
 )
 from .writers import write_table
 
+SCHEMA_VIEW = SchemaView(SCHEMA_YAML)
+SCHEMA_DICT = schema_as_dict(SCHEMA_VIEW.schema)
+MAPPING_SLOTS = SCHEMA_DICT["classes"]["mapping"]["slots"]
+MAPPING_SET_SLOTS = SCHEMA_DICT["classes"]["mapping set"]["slots"]
+
 # Click input options common across commands
 input_argument = click.argument("input", required=True, type=click.Path())
 

sssom/constants.py

@@ -4,24 +4,17 @@
 from enum import Enum
 
 import pkg_resources
-from linkml_runtime.utils.schema_as_dict import schema_as_dict
-from linkml_runtime.utils.schemaview import SchemaView
 
 # from linkml_runtime.utils.introspection import package_schemaview
 
 HERE = pathlib.Path(__file__).parent.resolve()
 
+OWL_EQUIV_CLASS = "http://www.w3.org/2002/07/owl#equivalentClass"
+RDFS_SUBCLASS_OF = "http://www.w3.org/2000/01/rdf-schema#subClassOf"
+
 SCHEMA_YAML = pkg_resources.resource_filename(
     "sssom_schema", "schema/sssom_schema.yaml"
 )
-SCHEMA_VIEW = SchemaView(SCHEMA_YAML)
-# SCHEMA_VIEW = package_schemaview("sssom_schema")
-SCHEMA_DICT = schema_as_dict(SCHEMA_VIEW.schema)
-MAPPING_SLOTS = SCHEMA_DICT["classes"]["mapping"]["slots"]
-MAPPING_SET_SLOTS = SCHEMA_DICT["classes"]["mapping set"]["slots"]
-
-OWL_EQUIV_CLASS = "http://www.w3.org/2002/07/owl#equivalentClass"
-RDFS_SUBCLASS_OF = "http://www.w3.org/2000/01/rdf-schema#subClassOf"
 
 DEFAULT_MAPPING_PROPERTIES = [
     "http://www.geneontology.org/formats/oboInOwl#hasDbXref",
@@ -42,16 +35,6 @@
     PREFIX_MAP_MODE_SSSOM_DEFAULT_ONLY,
     PREFIX_MAP_MODE_MERGED,
 ]
-ENTITY_REFERENCE = "EntityReference"
-
-MULTIVALUED_SLOTS = [
-    c for c in SCHEMA_VIEW.all_slots() if SCHEMA_VIEW.get_slot(c).multivalued
-]
-ENTITY_REFERENCE_SLOTS = [
-    c
-    for c in SCHEMA_VIEW.all_slots()
-    if SCHEMA_VIEW.get_slot(c).range == ENTITY_REFERENCE
-]
 
 # Slot Constants
 MIRROR_FROM = "mirror_from"

sssom/parsers.py

@@ -17,6 +17,8 @@
 import yaml
 from deprecation import deprecated
 from linkml_runtime.loaders.json_loader import JSONLoader
+from linkml_runtime.utils.schema_as_dict import schema_as_dict
+from linkml_runtime.utils.schemaview import SchemaView
 from rdflib import Graph, URIRef
 
 # from .sssom_datamodel import Mapping, MappingSet
@@ -30,15 +32,14 @@
     MAPPING_JUSTIFICATION,
     MAPPING_JUSTIFICATION_UNSPECIFIED,
     MAPPING_SET_ID,
-    MAPPING_SET_SLOTS,
-    MAPPING_SLOTS,
     OBJECT_ID,
     OBJECT_LABEL,
     OBJECT_SOURCE,
     OBJECT_SOURCE_ID,
     OWL_EQUIV_CLASS,
     PREDICATE_ID,
     RDFS_SUBCLASS_OF,
+    SCHEMA_YAML,
     SUBJECT_ID,
     SUBJECT_LABEL,
     SUBJECT_SOURCE,
@@ -310,6 +311,10 @@ def _get_mdict_ms_and_bad_attrs(
 ) -> Tuple[dict, MappingSet, Counter]:
 
     mdict = {}
+    schema_view = SchemaView(SCHEMA_YAML)
+    schema_dict = schema_as_dict(schema_view.schema)
+    mapping_slots = schema_dict["classes"]["mapping"]["slots"]
+    mapping_set_slots = schema_dict["classes"]["mapping set"]["slots"]
 
     for k, v in row.items():
         if v and v == v:
@@ -318,11 +323,11 @@ def _get_mdict_ms_and_bad_attrs(
                 k = str(k)
             v = _address_multivalued_slot(k, v)
             # if hasattr(Mapping, k):
-            if k in MAPPING_SLOTS:
+            if k in mapping_slots:
                 mdict[k] = v
                 ok = True
             # if hasattr(MappingSet, k):
-            if k in MAPPING_SET_SLOTS:
+            if k in mapping_set_slots:
                 ms[k] = v
                 ok = True
             if not ok:

sssom/util.py

@@ -31,6 +31,8 @@
 import yaml
 from jsonschema import ValidationError
 from linkml_runtime.linkml_model.types import Uriorcurie
+from linkml_runtime.utils.schema_as_dict import schema_as_dict
+from linkml_runtime.utils.schemaview import SchemaView
 
 # from .sssom_datamodel import Mapping as SSSOM_Mapping
 # from .sssom_datamodel import slots
@@ -40,12 +42,9 @@
 from .constants import (
     COMMENT,
     CONFIDENCE,
-    ENTITY_REFERENCE_SLOTS,
     MAPPING_JUSTIFICATION,
     MAPPING_SET_ID,
-    MAPPING_SET_SLOTS,
     MAPPING_SET_SOURCE,
-    MULTIVALUED_SLOTS,
     OBJECT_CATEGORY,
     OBJECT_ID,
     OBJECT_LABEL,
@@ -59,7 +58,6 @@
     PREDICATE_MODIFIER_NOT,
     PREFIX_MAP_MODES,
     RDFS_SUBCLASS_OF,
-    SCHEMA_DICT,
     SCHEMA_YAML,
     SEMAPV,
     SKOS_BROAD_MATCH,
@@ -1040,6 +1038,19 @@ class NoCURIEException(ValueError):
 
 
 CURIE_RE = re.compile(r"[A-Za-z0-9_.]+[:][A-Za-z0-9_]")
+SCHEMA_VIEW = SchemaView(SCHEMA_YAML)
+ENTITY_REFERENCE = "EntityReference"
+ENTITY_REFERENCE_SLOTS = [
+    c
+    for c in SCHEMA_VIEW.all_slots()
+    if SCHEMA_VIEW.get_slot(c).range == ENTITY_REFERENCE
+]
+SCHEMA_DICT = schema_as_dict(SCHEMA_VIEW.schema)
+MAPPING_SLOTS = SCHEMA_DICT["classes"]["mapping"]["slots"]
+MAPPING_SET_SLOTS = SCHEMA_DICT["classes"]["mapping set"]["slots"]
+MULTIVALUED_SLOTS = [
+    c for c in SCHEMA_VIEW.all_slots() if SCHEMA_VIEW.get_slot(c).multivalued
+]
 
 
 def is_curie(string: str) -> bool:

sssom/validators.py

@@ -8,12 +8,11 @@
 from linkml.validators.sparqlvalidator import SparqlDataValidator  # noqa: F401
 from sssom_schema import MappingSet
 
+from sssom.constants import SCHEMA_YAML, SchemaValidationType
 from sssom.context import add_built_in_prefixes_to_prefix_map
 from sssom.parsers import to_mapping_set_document
 from sssom.util import MappingSetDataFrame, get_all_prefixes
 
-from .constants import SCHEMA_YAML, SchemaValidationType
-
 
 def validate(
     msdf: MappingSetDataFrame, validation_types: List[SchemaValidationType]

sssom/writers.py

@@ -16,9 +16,9 @@
 # from .sssom_datamodel import slots
 from sssom_schema import slots
 
+from sssom.constants import SCHEMA_YAML
 from sssom.validators import check_all_prefixes_in_curie_map
 
-from .constants import SCHEMA_YAML
 from .parsers import to_mapping_set_document
 from .util import (
     PREFIX_MAP_KEY,

tests/test_sort.py

@@ -2,11 +2,17 @@
 
 import unittest
 
-from sssom.constants import SCHEMA_DICT
+from linkml_runtime.utils.schema_as_dict import schema_as_dict
+from linkml_runtime.utils.schemaview import SchemaView
+
+from sssom.constants import SCHEMA_YAML
 from sssom.parsers import parse_sssom_table
 from sssom.util import sort_df_rows_columns
 from tests.constants import data_dir
 
+SCHEMA_VIEW = SchemaView(SCHEMA_YAML)
+SCHEMA_DICT = schema_as_dict(SCHEMA_VIEW.schema)
+
 
 class TestSort(unittest.TestCase):
     """A test case for sorting msdf columns."""