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

@@ -25,10 +25,9 @@
 
 from sssom.constants import (
     DEFAULT_VALIDATION_TYPES,
-    MAPPING_SET_SLOTS,
-    MAPPING_SLOTS,
     PREFIX_MAP_MODES,
     SchemaValidationType,
+    SSSOMSchemaView,
 )
 from sssom.context import get_default_metadata
 
@@ -628,7 +627,7 @@ def decorator(f):
 @main.command()
 @input_argument
 @output_option
-@dynamically_generate_sssom_options(MAPPING_SLOTS)
+@dynamically_generate_sssom_options(SSSOMSchemaView().mapping_slots)
 def filter(input: str, output: TextIO, **kwargs):
     """Filter a dataframe by dynamically generating queries based on user input.
 
@@ -659,7 +658,7 @@ def filter(input: str, output: TextIO, **kwargs):
     type=bool,
     help="Multivalued slots should be replaced or not. [default: False]",
 )
-@dynamically_generate_sssom_options(MAPPING_SET_SLOTS)
+@dynamically_generate_sssom_options(SSSOMSchemaView().mapping_set_slots)
 def annotate(input: str, output: TextIO, replace_multivalued: bool, **kwargs):
     """Annotate metadata of a mapping set.
 

sssom/constants.py

@@ -11,15 +11,6 @@
 
 HERE = pathlib.Path(__file__).parent.resolve()
 
-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"
 
@@ -42,16 +33,6 @@
     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"
@@ -177,3 +158,19 @@ class SchemaValidationType(str, Enum):
     SchemaValidationType.JsonSchema,
     SchemaValidationType.PrefixMapCompleteness,
 ]
+
+
+class SSSOMSchemaView:
+    """
+    SchemaView class from linkml which is instantiated when necessary.
+
+    Reason for this: https://github.com/mapping-commons/sssom-py/issues/322
+    Implemented via PR: https://github.com/mapping-commons/sssom-py/pull/323
+    """
+
+    entity_reference = "EntityReference"
+    yaml = pkg_resources.resource_filename("sssom_schema", "schema/sssom_schema.yaml")
+    view = SchemaView(yaml)
+    dict = schema_as_dict(view.schema)
+    mapping_slots = dict["classes"]["mapping"]["slots"]
+    mapping_set_slots = dict["classes"]["mapping set"]["slots"]

sssom/context.py

@@ -7,7 +7,7 @@
 
 from linkml.generators.jsonldcontextgen import ContextGenerator
 
-from sssom.constants import SCHEMA_YAML
+from sssom.constants import SSSOMSchemaView
 
 from .external_context import sssom_external_context
 from .typehints import Metadata, MetadataType, PrefixMap
@@ -29,7 +29,7 @@ def get_jsonld_context():
 
     :return: JSON-LD context
     """
-    sssom_context = ContextGenerator(SCHEMA_YAML).serialize()
+    sssom_context = ContextGenerator(SSSOMSchemaView().yaml).serialize()
     return json.loads(sssom_context, strict=False)
 
 

sssom/parsers.py

@@ -30,8 +30,6 @@
     MAPPING_JUSTIFICATION,
     MAPPING_JUSTIFICATION_UNSPECIFIED,
     MAPPING_SET_ID,
-    MAPPING_SET_SLOTS,
-    MAPPING_SLOTS,
     OBJECT_ID,
     OBJECT_LABEL,
     OBJECT_SOURCE,
@@ -43,6 +41,7 @@
     SUBJECT_LABEL,
     SUBJECT_SOURCE,
     SUBJECT_SOURCE_ID,
+    SSSOMSchemaView,
 )
 
 from .context import (
@@ -310,6 +309,9 @@ def _get_mdict_ms_and_bad_attrs(
 ) -> Tuple[dict, MappingSet, Counter]:
 
     mdict = {}
+    schema_view = SSSOMSchemaView()
+    mapping_slots = schema_view.mapping_slots
+    mapping_set_slots = schema_view.mapping_set_slots
 
     for k, v in row.items():
         if v and v == v:
@@ -318,11 +320,11 @@ 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

@@ -40,12 +40,9 @@
 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,
@@ -59,8 +56,6 @@
     PREDICATE_MODIFIER_NOT,
     PREFIX_MAP_MODES,
     RDFS_SUBCLASS_OF,
-    SCHEMA_DICT,
-    SCHEMA_YAML,
     SEMAPV,
     SKOS_BROAD_MATCH,
     SKOS_CLOSE_MATCH,
@@ -72,6 +67,7 @@
     SUBJECT_ID,
     SUBJECT_LABEL,
     SUBJECT_SOURCE,
+    SSSOMSchemaView,
 )
 from .context import (
     SSSOM_BUILT_IN_PREFIXES,
@@ -832,7 +828,7 @@ def inject_metadata_into_df(msdf: MappingSetDataFrame) -> MappingSetDataFrame:
     :return: MappingSetDataFrame with metadata as columns
     """
     # TODO Check if 'k' is a valid 'slot' for 'mapping' [sssom.yaml]
-    with open(SCHEMA_YAML) as file:
+    with open(schema_view_object.yaml) as file:
         schema = yaml.safe_load(file)
     slots = schema["classes"]["mapping"]["slots"]
     if msdf.metadata is not None and msdf.df is not None:
@@ -957,8 +953,8 @@ def to_mapping_set_dataframe(doc: MappingSetDocument) -> MappingSetDataFrame:
     data = []
     slots_with_double_as_range = [
         s
-        for s in SCHEMA_DICT["slots"].keys()
-        if SCHEMA_DICT["slots"][s]["range"] == "double"
+        for s in schema_dict["slots"].keys()
+        if schema_dict["slots"][s]["range"] == "double"
     ]
     if doc.mapping_set.mappings is not None:
         for mapping in doc.mapping_set.mappings:
@@ -991,19 +987,19 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) ->
     map_dict = {}
     slots_with_double_as_range = [
         s
-        for s in SCHEMA_DICT["slots"].keys()
-        if SCHEMA_DICT["slots"][s]["range"] == "double"
+        for s in schema_dict["slots"].keys()
+        if schema_dict["slots"][s]["range"] == "double"
     ]
     for property in map_obj:
         if map_obj[property] is not None:
             if isinstance(map_obj[property], list):
                 # IF object is an enum
                 if (
-                    SCHEMA_DICT["slots"][property]["range"]
-                    in SCHEMA_DICT["enums"].keys()
+                    schema_dict["slots"][property]["range"]
+                    in schema_dict["enums"].keys()
                 ):
                     # IF object is a multivalued enum
-                    if SCHEMA_DICT["slots"][property]["multivalued"]:
+                    if schema_dict["slots"][property]["multivalued"]:
                         map_dict[property] = "|".join(
                             enum_value.code.text for enum_value in map_obj[property]
                         )
@@ -1019,8 +1015,8 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) ->
             else:
                 # IF object is an enum
                 if (
-                    SCHEMA_DICT["slots"][property]["range"]
-                    in SCHEMA_DICT["enums"].keys()
+                    schema_dict["slots"][property]["range"]
+                    in schema_dict["enums"].keys()
                 ):
                     map_dict[property] = map_obj[property].code.text
                 else:
@@ -1040,6 +1036,18 @@ class NoCURIEException(ValueError):
 
 
 CURIE_RE = re.compile(r"[A-Za-z0-9_.]+[:][A-Za-z0-9_]")
+schema_view_object = SSSOMSchemaView()
+schema_view = schema_view_object.view
+schema_dict = schema_view_object.dict
+mapping_set_slots = schema_view_object.mapping_set_slots
+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 == schema_view_object.entity_reference
+]
 
 
 def is_curie(string: str) -> bool:
@@ -1100,7 +1108,7 @@ def get_prefixes_used_in_table(df: pd.DataFrame) -> List[str]:
     """Get a list of prefixes used in CURIEs in key feature columns in a dataframe."""
     prefixes = SSSOM_BUILT_IN_PREFIXES
     if not df.empty:
-        for col in ENTITY_REFERENCE_SLOTS:
+        for col in entity_reference_slots:
             if col in df.columns:
                 for v in df[col].values:
                     pref = get_prefix_from_curie(str(v))
@@ -1266,7 +1274,7 @@ def is_multivalued_slot(slot: str) -> bool:
     # view = SchemaView('schema/sssom.yaml')
     # return view.get_slot(slot).multivalued
 
-    return slot in MULTIVALUED_SLOTS
+    return slot in multivalued_slots
 
 
 def reconcile_prefix_and_data(
@@ -1329,7 +1337,7 @@ def reconcile_prefix_and_data(
     # Data editing
     if len(data_switch_dict) > 0:
         # Read schema file
-        slots = SCHEMA_DICT["slots"]
+        slots = schema_dict["slots"]
         entity_reference_columns = [
             k for k, v in slots.items() if v["range"] == "EntityReference"
         ]
@@ -1359,7 +1367,7 @@ def sort_df_rows_columns(
     """
     if by_columns and len(df.columns) > 0:
         column_sequence = [
-            col for col in SCHEMA_DICT["slots"].keys() if col in df.columns
+            col for col in schema_dict["slots"].keys() if col in df.columns
         ]
         df = df.reindex(column_sequence, axis=1)
     if by_rows and len(df) > 0:
@@ -1380,7 +1388,7 @@ def get_all_prefixes(msdf: MappingSetDataFrame) -> list:
         metadata_keys = list(msdf.metadata.keys())
         df_columns_list = msdf.df.columns.to_list()  # type: ignore
         all_keys = metadata_keys + df_columns_list
-        ent_ref_slots = [s for s in all_keys if s in ENTITY_REFERENCE_SLOTS]
+        ent_ref_slots = [s for s in all_keys if s in entity_reference_slots]
 
         for slot in ent_ref_slots:
             if slot in metadata_keys:
@@ -1437,7 +1445,7 @@ def augment_metadata(
     if msdf.metadata:
         for k, v in meta.items():
             # If slot is multivalued, add to list.
-            if k in MULTIVALUED_SLOTS and not replace_multivalued:
+            if k in multivalued_slots and not replace_multivalued:
                 tmp_value: list = []
                 if isinstance(msdf.metadata[k], str):
                     tmp_value = [msdf.metadata[k]]
@@ -1450,7 +1458,7 @@ def augment_metadata(
                     )
                 tmp_value.extend(v)
                 msdf.metadata[k] = list(set(tmp_value))
-            elif k in MULTIVALUED_SLOTS and replace_multivalued:
+            elif k in multivalued_slots and replace_multivalued:
                 msdf.metadata[k] = list(v)
             else:
                 msdf.metadata[k] = v[0]
@@ -1469,10 +1477,10 @@ def are_params_slots(params: dict) -> bool:
     if len(empty_params) > 0:
         logging.info(f"Parameters: {empty_params.keys()} has(ve) no value.")
 
-    legit_params = all(p in MAPPING_SET_SLOTS for p in params.keys())
+    legit_params = all(p in mapping_set_slots for p in params.keys())
     if not legit_params:
-        invalids = [p for p in params if p not in MAPPING_SET_SLOTS]
+        invalids = [p for p in params if p not in mapping_set_slots]
         raise ValueError(
-            f"The params are invalid: {invalids}. Should be any of the following: {MAPPING_SET_SLOTS}"
+            f"The params are invalid: {invalids}. Should be any of the following: {mapping_set_slots}"
         )
     return True

sssom/validators.py

@@ -8,12 +8,11 @@
 from linkml.validators.sparqlvalidator import SparqlDataValidator  # noqa: F401
 from sssom_schema import MappingSet
 
+from sssom.constants import SchemaValidationType, SSSOMSchemaView
 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]
@@ -37,7 +36,8 @@ def validate_json_schema(msdf: MappingSetDataFrame) -> None:
 
     :param msdf: MappingSetDataFrame to eb validated.
     """
-    validator = JsonSchemaDataValidator(SCHEMA_YAML)
+    schema_view_object = SSSOMSchemaView()
+    validator = JsonSchemaDataValidator(schema_view_object.yaml)
     mapping_set = to_mapping_set_document(msdf).mapping_set
     validator.validate_object(mapping_set, MappingSet)
 

sssom/writers.py

@@ -16,9 +16,9 @@
 # from .sssom_datamodel import slots
 from sssom_schema import slots
 
+from sssom.constants import SSSOMSchemaView
 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,
@@ -284,7 +284,7 @@ def to_rdf_graph(msdf: MappingSetDataFrame) -> Graph:
     # os.remove("sssom.ttl")  # remove the intermediate file.
     graph = rdflib_dumper.as_rdf_graph(
         element=doc.mapping_set,
-        schemaview=SchemaView(SCHEMA_YAML),
+        schemaview=SchemaView(SSSOMSchemaView().yaml),
         prefix_map=msdf.prefix_map,
     )
     return graph

tests/test_resources.py

@@ -5,12 +5,12 @@
 import os
 import unittest
 
-from sssom.constants import SCHEMA_YAML
+from sssom.constants import SSSOMSchemaView
 
 
 class TestResources(unittest.TestCase):
     """A test case for resource availability checks."""
 
     def test_exists(self):
         """Test the schema YAML file is available to the package."""
-        self.assertTrue(os.path.exists(SCHEMA_YAML))
+        self.assertTrue(os.path.exists(SSSOMSchemaView().yaml))