Revert "allow for specification of gene identifier"

This reverts commit f44ac0f.

src/phenotype2phenopacket/add/add_genes.py

@@ -68,25 +68,19 @@ def add_genes(
         )
 
 
-def add_genes_to_directory(
-        phenopacket_dir: Path,
-        genes_to_disease: pl.DataFrame,
-        gene_identifier: str,
-        output_dir: Path,
-):
+def add_genes_to_directory(phenopacket_dir: Path, genes_to_disease: pl.DataFrame, output_dir: Path):
     """
     Add known gene-to-phenotype relationships to the interpretations of a directory of phenopackets.
 
     Args:
         phenopacket_dir (Path): Directory containing the phenopacket files.
         genes_to_disease (pl.DataFrame): DataFrame containing genes_to_disease.txt entries.
-        gene_identifier (str): Gene identifier for the phenopacket.
         output_dir (Path): Directory to store the updated phenopackets.
     """
     hgnc_dict = create_hgnc_dict()
     identifier_map = create_gene_identifier_map()
     gene_identifier_updater = GeneIdentifierUpdater(
-        gene_identifier=gene_identifier, hgnc_data=hgnc_dict, identifier_map=identifier_map
+        gene_identifier="ensembl_id", hgnc_data=hgnc_dict, identifier_map=identifier_map
     )
     for phenopacket_path in all_files(phenopacket_dir):
         add_genes(phenopacket_path, genes_to_disease, gene_identifier_updater, output_dir)

src/phenotype2phenopacket/cli_add.py

@@ -28,17 +28,9 @@
     help="Path to output directory.",
     type=Path,
 )
-@click.option(
-    "--gene-identifier",
-    "-g",
-    required=False,
-    help="Gene identifier to update in phenopacket",
-    type=click.Choice(["ensembl_id", "entrez_id", "hgnc_id"]),
-)
 def add_genes_command(
     phenopacket_dir: Path,
     genes_to_disease: Path,
-    gene_identifier: str,
     output_dir: Path,
 ):
     """
@@ -47,14 +39,12 @@ def add_genes_command(
     Args:
         phenopacket_dir (Path): Directory containing the phenopacket files.
         genes_to_disease (Path): Path to the genes_to_disease.txt file.
-        gene_identifier (str): Gene identifier to add in phenopacket
         output_dir (Path): Directory to store the updated phenopackets.
     """
     output_dir.mkdir(exist_ok=True)
     genes_to_disease_df = read_genes_to_disease(genes_to_disease)
     add_genes_to_directory(
         phenopacket_dir,
         genes_to_disease_df,
-        gene_identifier,
         output_dir,
     )