fix!: use better name for CLI source option (#153)

README.md

@@ -59,15 +59,15 @@ The Disease Normalizer currently uses data from the following sources:
 
 As described above, all source data other than OMIM can be acquired automatically.
 
-To update one source, simply set `--normalizer` to the source you wish to update. The normalizer will check to see if local source data is up-to-date, acquire the most recent data if not, and use it to populate the database.
+To update one source, simply set `--sources` to the source you wish to update. The normalizer will check to see if local source data is up-to-date, acquire the most recent data if not, and use it to populate the database.
 
 For example, run the following to acquire the latest NCIt data if necessary, and update the NCIt disease records in the normalizer database:
 
 ```commandline
-disease_norm_update --normalizer="ncit"
+disease_norm_update --sources="ncit"
 ```
 
-To update multiple sources, you can use the `--normalizer` option with the source names separated by spaces.
+To update multiple sources, you can use the `--sources` option with the source names separated by spaces.
 
 #### Update all sources
 

disease/cli.py

@@ -112,22 +112,22 @@ def dump_database(output_directory: Path, db_url: str) -> None:
         click.get_current_context().exit(1)
 
 
-def _update_normalizers(
-    normalizers: Collection[SourceName],
+def _update_sources(
+    sources: Collection[SourceName],
     db: AbstractDatabase,
     update_merged: bool,
     from_local: bool,
 ) -> None:
     """Update selected normalizer sources.
 
-    :param normalizers: names of sources to update
+    :param sources: names of sources to update
     :param db: database instance
     :param update_merged: if true, retain processed records to use in updating merged
         records
     :param from_local: if true, use locally available data only
     """
     processed_ids = list()
-    for n in normalizers:
+    for n in sources:
         delete_time = _delete_source(n, db)
         _load_source(n, db, delete_time, processed_ids, from_local)
 
@@ -229,9 +229,7 @@ def _load_merge(db: AbstractDatabase, processed_ids: Set[str]) -> None:
 
 
 @click.command()
-@click.option(
-    "--normalizer", help="The normalizer(s) you wish to update separated by spaces."
-)
+@click.option("--sources", help="The source(s) you wish to update separated by spaces.")
 @click.option("--aws_instance", is_flag=True, help="Using AWS DynamodDB instance.")
 @click.option("--db_url", help="URL endpoint for the application database.")
 @click.option("--update_all", is_flag=True, help="Update all normalizer sources.")
@@ -246,8 +244,8 @@ def _load_merge(db: AbstractDatabase, processed_ids: Set[str]) -> None:
     default=False,
     help="Use most recent local source data instead of fetching latest versions.",
 )
-def update_normalizer_db(
-    normalizer: str,
+def update_db(
+    sources: str,
     aws_instance: bool,
     db_url: str,
     update_all: bool,
@@ -257,7 +255,7 @@ def update_normalizer_db(
     """Update selected normalizer source(s) in the disease database.
 
     \f
-    :param normalizer: names of sources to update, comma-separated
+    :param sources: names of sources to update, comma-separated
     :param aws_instance: if true, use cloud instance
     :param db_url: URI pointing to database
     :param update_all: if true, update all sources (ignore `normalizer` parameter)
@@ -267,8 +265,8 @@ def update_normalizer_db(
     db = create_db(db_url, aws_instance)
 
     if update_all:
-        _update_normalizers(list(SourceName), db, update_merged, from_local)
-    elif not normalizer:
+        _update_sources(list(SourceName), db, update_merged, from_local)
+    elif not sources:
         if update_merged:
             _load_merge(db, set())
         else:
@@ -279,19 +277,19 @@ def update_normalizer_db(
             click.echo(ctx.get_help())
             ctx.exit()
     else:
-        normalizers = normalizer.lower().split()
+        sources_split = sources.lower().split()
 
-        if len(normalizers) == 0:
-            raise Exception("Must enter a normalizer")
+        if len(sources_split) == 0:
+            raise Exception("Must enter one or more source names")
 
-        non_sources = set(normalizers) - set(SOURCES_LOWER_LOOKUP)
+        non_sources = set(sources_split) - set(SOURCES_LOWER_LOOKUP)
 
         if len(non_sources) != 0:
             raise Exception(f"Not valid source(s): {non_sources}")
 
-        sources_to_update = {SourceName(SOURCES_LOWER_LOOKUP[s]) for s in normalizers}
-        _update_normalizers(sources_to_update, db, update_merged, from_local)
+        sources_to_update = {SourceName(SOURCES_LOWER_LOOKUP[s]) for s in sources_split}
+        _update_sources(sources_to_update, db, update_merged, from_local)
 
 
 if __name__ == "__main__":
-    update_normalizer_db()
+    update_db()

setup.cfg

@@ -37,7 +37,7 @@ disease =
 
 [options.entry_points]
 console_scripts =
-    disease_norm_update = disease.cli:update_normalizer_db
+    disease_norm_update = disease.cli:update_db
     disease_norm_update_remote = disease.cli:update_from_remote
     disease_norm_dump = disease.cli:dump_database
     disease_norm_check_db = disease.cli:check_db