Add option to overwrite files when directory exists

empress/_parameter_descriptions.py

@@ -93,3 +93,5 @@
 OUTPUT_DIR = (
     'Directory to create in which an EMPress visualization will be written.'
 )
+
+OVERWRITE = 'Determines whether to overwrite existing visualization files.'

empress/_plot_utils.py

@@ -39,19 +39,20 @@ def get_bp(newickfmt):
         return parse_newick(treefile.readline())
 
 
-def save_viz(viz, output_dir, q2=True):
+def save_viz(viz, output_dir, q2=True, overwrite=False):
     """Saves an Empress visualization to a filepath.
 
     Parameters
     ----------
     viz : empress.Empress
     output_dir : str
     q2 : bool
+    overwrite : bool
     """
     with open(os.path.join(output_dir, 'empress.html'), 'w') as htmlfile:
         htmlfile.write(str(viz))
 
-    viz.copy_support_files(output_dir)
+    viz.copy_support_files(output_dir, overwrite=overwrite)
 
     if q2:
         import q2templates
@@ -83,22 +84,25 @@ def prepare_pcoa(pcoa, number_of_features):
     return pcoa
 
 
-def check_and_process_files(output_dir, tree_file, feature_metadata):
+def check_and_process_files(output_dir, tree_file, feature_metadata,
+                            overwrite=False):
     """Initial checks and processing of files for standalone CLI plotting.
 
     Parameters
     ----------
     output_dir : str
     tree_file : str
     fm_file : str
+    overwrite: bool
 
     Returns
     -------
     bp.Tree
     pd.DataFrame
     """
     if os.path.isdir(output_dir):
-        raise OSError("Output directory already exists!")
+        if not overwrite:
+            raise OSError("Output directory already exists!")
     with open(str(tree_file), "r") as f:
         tree_newick = parse_newick(f.readline())
     if feature_metadata is not None:

empress/core.py

@@ -244,7 +244,7 @@ def _validate_and_match_data(self, ignore_missing_samples,
             ) = match_tree_and_feature_metadata(self.tree, self.features)
         validate_tree(self.tree)
 
-    def copy_support_files(self, target=None):
+    def copy_support_files(self, target=None, overwrite=False):
         """Copies the support files to a target directory
 
         If an ordination is included Emperor's support files will also be
@@ -260,7 +260,8 @@ def copy_support_files(self, target=None):
             target = self.base_url
 
         # copy the required resources
-        copytree(SUPPORT_FILES, os.path.join(target, 'support_files'))
+        copytree(SUPPORT_FILES, os.path.join(target, 'support_files'),
+                 dirs_exist_ok=overwrite)
 
         if self._emperor is not None:
             self._emperor.copy_support_files(os.path.join(target,

empress/scripts/_cli.py

@@ -30,22 +30,26 @@ def empress():
               help=desc.FM_DESC)
 @click.option("--shear-to-feature-metadata", required=False, default=False,
               help=desc.SHEAR_TO_FM, is_flag=True)
+@click.option("--overwrite", required=False, default=False,
+              help=desc.OVERWRITE, is_flag=True)
 def tree_plot(
     tree: str,
     output_dir: str,
     feature_metadata: str,
     shear_to_feature_metadata: bool,
+    overwrite: bool
 ) -> None:
     tree_newick, fm = check_and_process_files(
         output_dir,
         tree,
-        feature_metadata
+        feature_metadata,
+        overwrite
     )
 
     viz = Empress(tree_newick, feature_metadata=fm,
                   shear_to_feature_metadata=shear_to_feature_metadata)
-    os.makedirs(output_dir)
-    save_viz(viz, output_dir, q2=False)
+    os.makedirs(output_dir, exist_ok=overwrite)
+    save_viz(viz, output_dir, q2=False, overwrite=overwrite)
 
 
 @empress.command(
@@ -68,6 +72,8 @@ def tree_plot(
               help=desc.NUM_FEAT)
 @click.option("--shear-to-table", required=False, default=True,
               help=desc.SHEAR_TO_TBL, is_flag=True)
+@click.option("--overwrite", required=False, default=False,
+              help=desc.OVERWRITE, is_flag=True)
 def community_plot(
     tree: str,
     table: str,
@@ -80,11 +86,13 @@ def community_plot(
     filter_missing_features: bool,
     number_of_pcoa_features: int,
     shear_to_table: bool,
+    overwrite: bool
 ) -> None:
     tree_newick, fm = check_and_process_files(
         output_dir,
         tree,
-        feature_metadata
+        feature_metadata,
+        overwrite
     )
     table = load_table(table)
     sample_metadata = pd.read_csv(sample_metadata, sep="\t", index_col=0)
@@ -104,8 +112,8 @@ def community_plot(
         filter_missing_features=filter_missing_features,
         shear_to_table=shear_to_table,
     )
-    os.makedirs(output_dir)
-    save_viz(viz, output_dir, q2=False)
+    os.makedirs(output_dir, exist_ok=overwrite)
+    save_viz(viz, output_dir, q2=False, overwrite=overwrite)
 
 
 if __name__ == "__main__":

tests/python/test_cli.py

@@ -105,6 +105,18 @@ def test_existing_directory(cls):
         assert not os.path.isdir(f"{output_dir}/support_files")
         assert "empress.html" not in os.listdir(output_dir)
 
+    def test_existing_directory_overwrite(cls):
+        output_dir = "existing_dir_2"
+        os.mkdir(output_dir)
+        result = cls.runner.invoke(
+            empress,
+            ["community-plot", "--tree", cls.tree_loc, "--table",
+             cls.table_loc, "--sample-metadata", cls.sm_loc,
+             "--output-dir", output_dir, "--overwrite"]
+        )
+        assert result.exit_code == 0
+        files_present(output_dir)
+
     def test_tree_plot_basic_cli_abbrev(cls):
         output_dir = "tree_plot_basic_cli_abbrev"
         result = cls.runner.invoke(