Update name of field

src/prefixmaps/data/merged.csv

@@ -1,4 +1,4 @@
-context,prefix,namespace,status,source
+context,prefix,namespace,status,expansion_source
 merged,3DMET,http://identifiers.org/3dmet/,canonical,bioregistry
 merged,4DN,http://identifiers.org/4dn/,namespace_alias,bioregistry
 merged,4DN.BIOSOURCE,http://identifiers.org/4dn/,canonical,bioregistry

src/prefixmaps/data/merged.oak.csv

@@ -1,4 +1,4 @@
-context,prefix,namespace,status,source
+context,prefix,namespace,status,expansion_source
 merged.oak,3DMET,http://identifiers.org/3dmet/,canonical,bioregistry
 merged.oak,4DN,http://identifiers.org/4dn/,namespace_alias,bioregistry
 merged.oak,4DN.BIOSOURCE,http://identifiers.org/4dn/,canonical,bioregistry

src/prefixmaps/datamodel/context.py

@@ -71,7 +71,7 @@ class PrefixExpansion:
     status: StatusType
     """Indicates whether the expansion is canonical, a prefix alias, a namespace alias, or both."""
 
-    source: Optional[str] = None
+    expansion_source: Optional[str] = None
     """Indicates the source of the prefix expansion."""
 
     def canonical(self) -> bool:
@@ -156,15 +156,15 @@ def combine(self, context: "Context"):
         :return:
         """
         for pe in context.prefix_expansions:
-            self.add_prefix(pe.prefix, pe.namespace, pe.status, source=context.name)
+            self.add_prefix(pe.prefix, pe.namespace, pe.status, expansion_source=context.name)
 
     def add_prefix(
         self,
         prefix: PREFIX,
         namespace: NAMESPACE,
         status: StatusType = StatusType.canonical,
         preferred: bool = False,
-        source: Optional[str] = None,
+        expansion_source: Optional[str] = None,
     ):
         """
         Adds a prefix expansion to this context.
@@ -180,7 +180,7 @@ def add_prefix(
         :param namespace: namespace to be added
         :param status: the status of the prefix being added
         :param preferred:
-        :param source: An optional annotation to be used when merging contexts together.
+        :param expansion_source: An optional annotation to be used when merging contexts together.
             The source will keep track of the original context that a given prefix
             expansion came from. This is used in :meth:`Context.combine`.
         :return:
@@ -210,7 +210,7 @@ def add_prefix(
                 prefix=prefix,
                 namespace=namespace,
                 status=status,
-                source=source,
+                expansion_source=expansion_source,
             )
         )
 

src/prefixmaps/ingest/etl_runner.py

@@ -90,7 +90,7 @@ def run_etl(output_directory: Union[str, Path]) -> None:
     # Write all contexts
     for name, context in contexts.items():
         with output_directory.joinpath(f"{name}.csv").open("w", encoding="UTF-8") as file:
-            context_to_file(context, file, include_source=context.name in COMBINED)
+            context_to_file(context, file, include_expansion_source=context.name in COMBINED)
 
 
 @click.command

src/prefixmaps/io/writer.py

@@ -15,25 +15,27 @@ def _key(pe: PrefixExpansion):
     return pe.prefix.casefold(), STATUS_TYPE_ORDER[pe.status]
 
 
-def context_to_file(context: Context, file: TextIO, *, include_source: bool = False) -> None:
+def context_to_file(
+    context: Context, file: TextIO, *, include_expansion_source: bool = False
+) -> None:
     """
     Writes a context to a file
 
     :param context:
     :param file:
-    :param include_source: If true, include a "source" column. This is useful for
+    :param include_expansion_source: If true, include a "source" column. This is useful for
         writing merged contexts since it says the highest priority simple context
         from which the row corresponding to a :class:`PrefixExpansion` came.
     :return:
     """
     field_names = ["context", "prefix", "namespace", "status"]
-    if include_source:
-        field_names.append("source")
+    if include_expansion_source:
+        field_names.append("expansion_source")
     writer = DictWriter(file, fieldnames=field_names)
     writer.writeheader()
     for pe in sorted(context.prefix_expansions, key=_key):
         row = vars(pe)
         row["status"] = pe.status.value
-        if not include_source:
-            row.pop("source", None)
+        if not include_expansion_source:
+            row.pop("expansion_source", None)
         writer.writerow(row)