change option names

docs/source/install.rst

@@ -145,7 +145,7 @@ Load data
 
 To load all source data, and then generate normalized records, use the following shell command: ::
 
-    gene-normalizer update --update_all --update_merged
+    gene-normalizer update --all --normalize
 
 This will download the latest available versions of all source data files, extract and transform recognized gene concepts, load them into the database, and construct normalized concept groups. For more specific update commands, see :ref:`Loading and updating data <loading_and_updating_data>`.
 

docs/source/managing_data/loading_and_updating_data.rst

@@ -11,21 +11,21 @@ Loading and updating data
 Refreshing all data
 -------------------
 
-Calling the Gene Normalizer update command with the ``--update_all`` and ``--update_merged`` flags will delete all existing data, fetch new source data if available, and then perform a complete reload of the database (including merged records):
+Calling the Gene Normalizer update command with the ``--all`` and ``--normalize`` flags will delete all existing data, fetch new source data if available, and then perform a complete reload of the database (including merged records):
 
 .. code-block:: shell
 
-    gene-normalizer update --update_all --update_merged
+    gene-normalizer update --all --normalize
 
 
 Reload individual sources
 -------------------------
 
-To update specific sources, provide them as arguments to the ``update`` command. While it is possible to update individual source data without also updating the normalized record data, that may affect the proper function of the normalized query endpoints, so it is recommended to include the ``--update_merged`` flag as well.
+To update specific sources, provide them as arguments to the ``update`` command. While it is possible to update individual source data without also updating the normalized record data, that may affect the proper function of the normalized query endpoints, so it is recommended to include the ``--normalize`` flag as well.
 
 .. code-block:: shell
 
-    gene-normalizer update --update_merged HGNC NCBI
+    gene-normalizer update --normalize HGNC NCBI
 
 
 Use local data
@@ -35,7 +35,7 @@ The Gene Normalizer will fetch the latest available data from all sources if loc
 
 .. code-block:: shell
 
-    gene-normalizer update --update_all --use_existing
+    gene-normalizer update --all --use_existing
 
 
 Check DB health

src/gene/cli.py

@@ -22,12 +22,8 @@ def cli() -> None:
 
 @cli.command()
 @click.argument("sources", nargs=-1)
-@click.option("--update_all", is_flag=True, help="Update all normalizer sources.")
-@click.option(
-    "--update_merged",
-    is_flag=True,
-    help="Update concepts for normalize endpoint from accepted sources.",
-)
+@click.option("--all", is_flag=True, help="Update records for all sources.")
+@click.option("--normalize", is_flag=True, help="Update normalized concepts.")
 @click.option("--db_url", help="URL endpoint for the application database.")
 @click.option("--aws_instance", is_flag=True, help="Using AWS DynamodDB instance.")
 @click.option(
@@ -40,34 +36,35 @@ def update(
     sources: Tuple[str],
     aws_instance: bool,
     db_url: str,
-    update_all: bool,
-    update_merged: bool,
+    all: bool,
+    normalize: bool,
     use_existing: bool,
 ) -> None:
     """Update provided normalizer SOURCES in the gene database.
 
     Valid SOURCES are "HGNC", "NCBI", and "Ensembl" (case is irrelevant). SOURCES are
-    optional, but if not provided, either --update_all or --update_merged must be used.
+    optional, but if not provided, either --all or --normalize must be used.
 
-    For example, the following command will update NCBI and HGNC data:
+    For example, the following command will update NCBI and HGNC source records:
 
     % gene-normalizer update HGNC NCBI
 
-    To completely reload all data, use the --update_all and --update_merged options:
+    To completely reload all source records and construct normalized concepts, use the
+    --all and --normalize options:
 
-    % gene-normalizer update --update_all --update_merged
+    % gene-normalizer update --all --normalize
 
     \f
     :param sources: tuple of raw names of sources to update
     :param aws_instance: if true, use cloud instance
     :param db_url: URI pointing to database
-    :param update_all: if True, update all sources (ignore ``sources``)
-    :param update_merged: if True, update normalized records
+    :param all: if True, update all sources (ignore ``sources``)
+    :param normalize: if True, update normalized records
     :param use_existing: if True, use most recent local data instead of fetching latest version
     """  # noqa: D301
-    if (not sources) and (not update_all) and (not update_merged):
+    if (not sources) and (not all) and (not normalize):
         click.echo(
-            "Error: must provide SOURCES or at least one of --update_all, --update_merged\n"
+            "Error: must provide SOURCES or at least one of --all, --normalize\n"
         )
         ctx = click.get_current_context()
         click.echo(ctx.get_help())
@@ -76,7 +73,7 @@ def update(
     db = create_db(db_url, aws_instance)
 
     processed_ids = None
-    if update_all:
+    if all:
         processed_ids = update_all_sources(db, use_existing, silent=False)
     elif sources:
         parsed_sources = []
@@ -100,7 +97,7 @@ def update(
         if len(sources) == len(SourceName):
             processed_ids = working_processed_ids
 
-    if update_merged:
+    if normalize:
         update_normalized(db, processed_ids, silent=False)