CLI remove added

sssom/cli.py

@@ -675,5 +675,26 @@ def annotate(input: str, output: TextIO, replace_multivalued: bool, **kwargs):
     )
 
 
+@main.command()
+@input_argument
+@click.option(
+    "--remove-map",
+    type=click.Path(),
+    help="Mapping file path that needs to be removed from input.",
+)
+@output_option
+def remove(input: str, output: TextIO, remove_map: str):
+    """Remove mappings from an input mapping.
+
+    :param input: Input SSSOM tsv file.
+    :param output: Output path.
+    :param remove_map: Mapping to be removed.
+    """
+    input_msdf = parse_sssom_table(input)
+    remove_msdf = parse_sssom_table(remove_map)
+    input_msdf.remove_mappings(remove_msdf)
+    write_table(input_msdf, output)
+
+
 if __name__ == "__main__":
     main()

tests/test_cli.py

@@ -21,6 +21,7 @@
     partition,
     ptable,
     reconcile_prefixes,
+    remove,
     sort,
     split,
     validate,
@@ -33,6 +34,8 @@
     test_out_dir,
 )
 
+from .constants import data_dir
+
 
 class SSSOMCLITestSuite(unittest.TestCase):
     """A test case for the dynamic CLI tests."""
@@ -64,6 +67,7 @@ def test_cli_single_input(self):
                     self.run_sort_rows_columns(runner, test)
                     self.run_filter(runner, test)
                     self.run_annotate(runner, test)
+                    self.run_remove(runner, test)
 
         self.assertTrue(len(test_cases) > 2)
 
@@ -336,3 +340,21 @@ def run_annotate(self, runner: CliRunner, test_case: SSSOMTestCase) -> Result:
         )
         self.run_successful(result, test_case)
         return result
+
+    def run_remove(self, runner: CliRunner, test_case: SSSOMTestCase) -> Result:
+        """Test removal of mappings."""
+        out_file = os.path.join(test_out_dir, "remove_map_test.tsv")
+        in_file = test_case.filepath
+        rm_file = os.path.join(data_dir, "basic3.tsv")
+        result = runner.invoke(
+            remove,
+            [
+                in_file,
+                "-o",
+                os.path.join(test_out_dir, out_file),
+                "--remove-map",
+                rm_file,
+            ],
+        )
+        self.run_successful(result, test_case)
+        return result