Fixes #305 and #306 (#308)

* Fixes validate  #306

* fix for #305

* blank values for prefixes shouls not be added.

* undo refactor and change logic

* changed metadata check logic

* changed logic to get pref from meta

* formatted

* casting issue

* mypy fix

* mypy fix

* edits after discussion with Nico on PR

Author: hrshdhgd

sssom/context.py

@@ -17,7 +17,7 @@
 # EXTERNAL_CONTEXT_PATH = HERE / "sssom.external.context.jsonld"
 
 SSSOM_URI_PREFIX = "https://w3id.org/sssom/"
-SSSOM_BUILT_IN_PREFIXES = ["sssom", "owl", "rdf", "rdfs", "skos"]
+SSSOM_BUILT_IN_PREFIXES = ["sssom", "owl", "rdf", "rdfs", "skos", "semapv"]
 DEFAULT_MAPPING_SET_ID = f"{SSSOM_URI_PREFIX}mappings/{uuid.uuid4()}"
 DEFAULT_LICENSE = f"{SSSOM_URI_PREFIX}license/unspecified"
 

sssom/util.py

@@ -73,7 +73,12 @@
     SUBJECT_LABEL,
     SUBJECT_SOURCE,
 )
-from .context import SSSOM_URI_PREFIX, get_default_metadata, get_jsonld_context
+from .context import (
+    SSSOM_BUILT_IN_PREFIXES,
+    SSSOM_URI_PREFIX,
+    get_default_metadata,
+    get_jsonld_context,
+)
 from .sssom_document import MappingSetDocument
 from .typehints import Metadata, MetadataType, PrefixMap
 
@@ -145,15 +150,22 @@ def __str__(self) -> str:  # noqa:D105
 
     def clean_prefix_map(self) -> None:
         """Remove unused prefixes from the internal prefix map based on the internal dataframe."""
-        prefixes_in_map = get_prefixes_used_in_table(self.df)
+        all_prefixes = []
+        prefixes_in_table = get_prefixes_used_in_table(self.df)
+        if self.metadata:
+            prefixes_in_metadata = get_prefixes_used_in_metadata(self.metadata)
+            all_prefixes = list(set(prefixes_in_table + prefixes_in_metadata))
+        else:
+            all_prefixes = prefixes_in_table
+
         new_prefixes: PrefixMap = dict()
         missing_prefixes = []
-        for prefix in prefixes_in_map:
+        for prefix in all_prefixes:
             if prefix in self.prefix_map:
                 new_prefixes[prefix] = self.prefix_map[prefix]
             else:
                 logging.warning(
-                    f"{prefix} is used in the data frame but does not exist in prefix map"
+                    f"{prefix} is used in the SSSOM mapping set but it does not exist in the prefix map"
                 )
                 missing_prefixes.append(prefix)
         if missing_prefixes:
@@ -1086,11 +1098,34 @@ def curie_from_uri(uri: str, prefix_map: Mapping[str, str]) -> str:
 
 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 = []
+    prefixes = SSSOM_BUILT_IN_PREFIXES
     if not df.empty:
-        for col in KEY_FEATURES:
-            for v in df[col].values:
-                prefixes.append(get_prefix_from_curie(v))
+        for col in ENTITY_REFERENCE_SLOTS:
+            if col in df.columns:
+                for v in df[col].values:
+                    pref = get_prefix_from_curie(str(v))
+                    if pref != "" and not None:
+                        prefixes.append(pref)
+    return list(set(prefixes))
+
+
+def get_prefixes_used_in_metadata(meta: MetadataType) -> List[str]:
+    """Get a list of prefixes used in CURIEs in the metadata."""
+    prefixes = SSSOM_BUILT_IN_PREFIXES
+    if meta:
+        for v in meta.values():
+            if type(v) is list:
+                prefixes.extend(
+                    [
+                        get_prefix_from_curie(x)
+                        for x in v
+                        if get_prefix_from_curie(x) != ""
+                    ]
+                )
+            else:
+                pref = get_prefix_from_curie(str(v))
+                if pref != "" and not None:
+                    prefixes.append(pref)
     return list(set(prefixes))
 
 
@@ -1374,6 +1409,7 @@ def get_all_prefixes(msdf: MappingSetDataFrame) -> list:
                         [
                             get_prefix_from_curie(s)
                             for s in list(set(msdf.df[slot].to_list()))  # type: ignore
+                            if get_prefix_from_curie(s) != ""
                         ]
                     )
                 )