Filter prefixes

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()

sssom/io.py

@@ -360,6 +360,8 @@ def filter_file(input: str, output: TextIO, **kwargs) -> MappingSetDataFrame:
             for exp in v[1:]:
                 query += " OR "
                 query += k + " LIKE '" + exp + "') "
+        else:
+            query += ") "
         if multiple_params and idx != len(params):
             query += " AND ("
     return run_sql_query(query=query, inputs=[input], output=output)

sssom/util.py

@@ -149,6 +149,28 @@ def clean_prefix_map(self) -> None:
             self.df = filter_out_prefixes(self.df, missing_prefixes)
         self.prefix_map = new_prefixes
 
+    def remove_mappings(self, msdf: "MappingSetDataFrame"):
+        """Remove mappings in right msdf from left msdf.
+
+        :param msdf: MappingSetDataframe object to be removed from primary msdf object.
+        """
+        self.df = (
+            pd.merge(
+                self.df,
+                msdf.df,
+                on=KEY_FEATURES,
+                how="outer",
+                suffixes=("", "_2"),
+                indicator=True,
+            )
+            .query("_merge == 'left_only'")
+            .drop("_merge", axis=1)
+            .reset_index(drop=True)
+        )
+
+        self.df = self.df[self.df.columns.drop(list(self.df.filter(regex=r"_2")))]
+        self.clean_prefix_map()
+
 
 @dataclass
 class EntityPair:
@@ -990,27 +1012,54 @@ def get_prefixes_used_in_table(df: pd.DataFrame) -> List[str]:
     return list(set(prefixes))
 
 
-def filter_out_prefixes(df: pd.DataFrame, filter_prefixes: List[str]) -> pd.DataFrame:
+def filter_out_prefixes(
+    df: pd.DataFrame, filter_prefixes: List[str], features: list = KEY_FEATURES
+) -> pd.DataFrame:
     """Filter any row where a CURIE in one of the key column uses one of the given prefixes.
 
     :param df: Pandas DataFrame
     :param filter_prefixes: List of prefixes
+    :param features: List of dataframe column names dataframe to consider
     :return: Pandas Dataframe
     """
     filter_prefix_set = set(filter_prefixes)
     rows = []
 
     for _, row in df.iterrows():
-        # Get list of CURIEs from the 3 columns (KEY_FEATURES) for the row.
-        prefixes = {get_prefix_from_curie(curie) for curie in row[KEY_FEATURES]}
-        # Confirm if none of the 3 CURIEs in the list above appear in the filter_prefixes list.
+        prefixes = {get_prefix_from_curie(curie) for curie in row[features]}
+        # Confirm if none of the CURIEs in the list above appear in the filter_prefixes list.
         # If TRUE, append row.
         if not any(prefix in prefixes for prefix in filter_prefix_set):
             rows.append(row)
     if rows:
         return pd.DataFrame(rows)
     else:
-        return pd.DataFrame(columns=KEY_FEATURES)
+        return pd.DataFrame(columns=features)
+
+
+def filter_prefixes(
+    df: pd.DataFrame, filter_prefixes: List[str], features: list = KEY_FEATURES
+) -> pd.DataFrame:
+    """Filter any row where a CURIE in one of the key column uses one of the given prefixes.
+
+    :param df: Pandas DataFrame
+    :param filter_prefixes: List of prefixes
+    :param features: List of dataframe column names dataframe to consider
+    :return: Pandas Dataframe
+    """
+    filter_prefix_set = set(filter_prefixes)
+    rows = []
+
+    for _, row in df.iterrows():
+        prefixes = {get_prefix_from_curie(curie) for curie in row[features]}
+        # Confirm if all of the CURIEs in the list above appear in the filter_prefixes list.
+        # If TRUE, append row.
+        if all(prefix in filter_prefix_set for prefix in prefixes):
+            rows.append(row)
+    if rows:
+        return pd.DataFrame(rows)
+    else:
+        return pd.DataFrame(columns=features)
 
 
 # TODO this is not used anywhere

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

tests/test_utils.py

@@ -1,13 +1,21 @@
 """Test for merging MappingSetDataFrames."""
 import unittest
 
+from sssom.constants import OBJECT_ID, SUBJECT_ID
 from sssom.io import extract_iri
+from sssom.parsers import parse_sssom_table
+from sssom.util import MappingSetDataFrame, filter_out_prefixes, filter_prefixes
 from tests.constants import data_dir
 
 
 class TestIO(unittest.TestCase):
     """A test case for merging msdfs."""
 
+    def setUp(self) -> None:
+        """Set up."""
+        self.msdf = parse_sssom_table(f"{data_dir}/basic.tsv")
+        self.features = [SUBJECT_ID, OBJECT_ID]
+
     def test_broken_predicate_list(self):
         """Test merging of multiple msdfs."""
         pred_filter_list = ["skos:relatedMatch", f"{data_dir}/predicate_list3.txt"]
@@ -18,3 +26,31 @@ def test_broken_predicate_list(self):
             if p_iri:
                 iri_list.extend(p_iri)
         self.assertEqual(3, len(iri_list))
+
+    def test_filter_prefixes(self):
+        """Test filtering MSDF.df by prefixes provided."""
+        prefix_filter_list = ["x", "y"]
+        filtered_df = filter_prefixes(self.msdf.df, prefix_filter_list, self.features)
+        self.assertEqual(len(filtered_df), 40)
+
+    def test_filter_out_prefixes(self):
+        """Test filtering MSDF.df by prefixes provided."""
+        prefix_filter_list = ["x", "y"]
+        filtered_df = filter_out_prefixes(
+            self.msdf.df, prefix_filter_list, self.features
+        )
+        self.assertEqual(len(filtered_df), 5)
+
+    def test_remove_mappings(self):
+        """Test remove mappings."""
+        prefix_filter_list = ["x", "y"]
+        filtered_df = filter_out_prefixes(
+            self.msdf.df, prefix_filter_list, self.features
+        )
+        new_msdf = MappingSetDataFrame(
+            df=filtered_df, prefix_map=self.msdf.prefix_map, metadata=self.msdf.metadata
+        )
+        original_length = len(self.msdf.df)
+        self.msdf.remove_mappings(new_msdf)
+        # len(self.msdf.df) = 141 and len(new_msdf.df) = 5
+        self.assertEqual(len(self.msdf.df), original_length - len(new_msdf.df))