Remove needless output during tests (#428)

There is a massive amount of text that's printed to stdout as well as
uninformative logging during testing. This PR removes some of that
without changing existing functionality.

It also switches to using a specific logger in several places instead of
directly using e.g. `logging.info`

src/sssom/cli.py

@@ -11,7 +11,7 @@
 .. seealso:: https://click.palletsprojects.com/en/8.0.x/setuptools/
 """
 
-import logging
+import logging as _logging
 import os
 import sys
 from operator import itemgetter
@@ -61,6 +61,8 @@
 )
 from .writers import WRITER_FUNCTIONS, write_table
 
+logging = _logging.getLogger(__name__)
+
 SSSOM_SV_OBJECT = (
     SSSOMSchemaView.instance if hasattr(SSSOMSchemaView, "instance") else SSSOMSchemaView()
 )
@@ -124,15 +126,15 @@
 @click.version_option(__version__)
 def main(verbose: int, quiet: bool):
     """Run the SSSOM CLI."""
-    logger = logging.getLogger()
+    logger = _logging.getLogger()
     if verbose >= 2:
-        logger.setLevel(level=logging.DEBUG)
+        logger.setLevel(level=_logging.DEBUG)
     elif verbose == 1:
-        logger.setLevel(level=logging.INFO)
+        logger.setLevel(level=_logging.INFO)
     else:
-        logger.setLevel(level=logging.WARNING)
+        logger.setLevel(level=_logging.WARNING)
     if quiet:
-        logger.setLevel(level=logging.ERROR)
+        logger.setLevel(level=_logging.ERROR)
 
 
 @main.command()

src/sssom/io.py

@@ -270,7 +270,9 @@ def extract_iri(input: str, converter: Converter) -> List[str]:
 #     return new_msdf
 
 
-def run_sql_query(query: str, inputs: List[str], output: TextIO) -> MappingSetDataFrame:
+def run_sql_query(
+    query: str, inputs: List[str], output: Optional[TextIO] = None
+) -> MappingSetDataFrame:
     """Run a SQL query over one or more SSSOM files.
 
     Each of the N inputs is assigned a table name df1, df2, ..., dfN
@@ -307,11 +309,12 @@ def run_sql_query(query: str, inputs: List[str], output: TextIO) -> MappingSetDa
     new_msdf = MappingSetDataFrame.with_converter(
         df=new_df, converter=msdf.converter, metadata=msdf.metadata
     )
-    write_table(new_msdf, output)
+    if output is not None:
+        write_table(new_msdf, output)
     return new_msdf
 
 
-def filter_file(input: str, output: TextIO, **kwargs) -> MappingSetDataFrame:
+def filter_file(input: str, output: Optional[TextIO] = None, **kwargs) -> MappingSetDataFrame:
     """Filter a dataframe by dynamically generating queries based on user input.
 
     e.g. sssom filter --subject_id x:% --subject_id y:% --object_id y:% --object_id z:% tests/data/basic.tsv
@@ -323,7 +326,7 @@ def filter_file(input: str, output: TextIO, **kwargs) -> MappingSetDataFrame:
 
     :param input: DataFrame to be queried over.
     :param output: Output location.
-    :param **kwargs: Filter options provided by user which generate queries (e.g.: --subject_id x:%).
+    :param kwargs: Filter options provided by user which generate queries (e.g.: --subject_id x:%).
     :raises ValueError: If parameter provided is invalid.
     :return: Filtered MappingSetDataFrame object.
     """
@@ -358,21 +361,22 @@ def filter_file(input: str, output: TextIO, **kwargs) -> MappingSetDataFrame:
 
 
 def annotate_file(
-    input: str, output: TextIO, replace_multivalued: bool = False, **kwargs
+    input: str, output: Optional[TextIO] = None, replace_multivalued: bool = False, **kwargs
 ) -> MappingSetDataFrame:
     """Annotate a file i.e. add custom metadata to the mapping set.
 
     :param input: SSSOM tsv file to be queried over.
     :param output: Output location.
     :param replace_multivalued: Multivalued slots should be
         replaced or not, defaults to False
-    :param **kwargs: Options provided by user
+    :param kwargs: Options provided by user
         which are added to the metadata (e.g.: --mapping_set_id http://example.org/abcd)
     :return: Annotated MappingSetDataFrame object.
     """
     params = {k: v for k, v in kwargs.items() if v}
     are_params_slots(params)
     input_msdf = parse_sssom_table(input)
     msdf = augment_metadata(input_msdf, params, replace_multivalued)
-    write_table(msdf, output)
+    if output is not None:
+        write_table(msdf, output)
     return msdf

src/sssom/parsers.py

@@ -3,7 +3,7 @@
 import io
 import itertools as itt
 import json
-import logging
+import logging as _logging
 import re
 import typing
 from collections import Counter
@@ -68,6 +68,8 @@
     to_mapping_set_dataframe,
 )
 
+logging = _logging.getLogger(__name__)
+
 # * *******************************************************
 # Parsers (from file)
 
@@ -418,7 +420,7 @@ def from_sssom_dataframe(
         mdict, bad_attrs = _get_mdict_ms_and_bad_attrs(row, bad_attrs)
         mlist.append(_prepare_mapping(Mapping(**mdict)))
     for k, v in bad_attrs.most_common():
-        logging.warning(f"No attr for {k} [{v} instances]")
+        logging.debug(f"No attr for {k} [{v} instances]")
     # the autogenerated code's type annotations are _really_ messy. This is in fact okay,
     # so with a heavy heart we employ type:ignore
     ms.mappings = mlist  # type:ignore
@@ -925,7 +927,7 @@ def split_dataframe_by_prefix(
             & (df[OBJECT_ID].str.startswith(object_prefix + ":"))
         ]
         if 0 == len(df_subset):
-            logging.warning(f"No matches ({len(df_subset)} matches found)")
+            logging.debug(f"No matches ({len(df_subset)} matches found)")
             continue
         subconverter = msdf.converter.get_subconverter(
             [subject_prefix, object_prefix, relation_prefix]

src/sssom/util.py

@@ -2,7 +2,7 @@
 
 import itertools as itt
 import json
-import logging
+import logging as _logging
 import os
 import re
 from collections import defaultdict
@@ -63,6 +63,8 @@
 from .sssom_document import MappingSetDocument
 from .typehints import MetadataType, PrefixMap, get_default_metadata
 
+logging = _logging.getLogger(__name__)
+
 #: The key that's used in the YAML section of an SSSOM file
 PREFIX_MAP_KEY = "curie_map"
 

src/sssom/writers.py

@@ -1,7 +1,7 @@
 """Serialization functions for SSSOM."""
 
 import json
-import logging
+import logging as _logging
 from pathlib import Path
 from typing import Any, Callable, Dict, List, Optional, TextIO, Tuple, Union
 
@@ -28,6 +28,8 @@
     sort_df_rows_columns,
 )
 
+logging = _logging.getLogger(__name__)
+
 # noinspection PyProtectedMember
 
 RDF_TYPE = "http://www.w3.org/1999/02/22-rdf-syntax-ns#type"

tests/test_annotate.py

@@ -1,12 +1,9 @@
 """Test for annotating MappingSetDataFrame metadata."""
 
-import sys
 import unittest
 from os.path import join
 
 from sssom.io import annotate_file
-
-# from sssom.io import filter_file
 from sssom.parsers import parse_sssom_table
 from tests.constants import data_dir
 
@@ -26,7 +23,7 @@ def test_annotate(self):
             "mapping_set_id": ("http://w3id.org/my/mapping.sssom.tsv",),
             "mapping_set_version": ("2021-01-01",),
         }
-        annotated_msdf = annotate_file(input=self.input, output=sys.stdout, **kwargs)
+        annotated_msdf = annotate_file(input=self.input, **kwargs)
         validation_msdf = parse_sssom_table(self.validation_file)
 
         self.assertEqual(annotated_msdf.metadata, validation_msdf.metadata)
@@ -38,19 +35,19 @@ def test_annotate_multivalued(self):
         kwargs = {
             "creator_id": ("orcid:0123",),
         }
-        annotated_msdf = annotate_file(input=self.input, output=sys.stdout, **kwargs)
+        annotated_msdf = annotate_file(input=self.input, **kwargs)
 
         self.assertTrue(len(annotated_msdf.metadata["creator_id"]), 3)
 
         # Pass same ORCID.
         kwargs = {
             "creator_id": ("orcid:1234",),
         }
-        annotated_msdf_2 = annotate_file(input=self.input, output=sys.stdout, **kwargs)
+        annotated_msdf_2 = annotate_file(input=self.input, **kwargs)
         self.assertTrue(len(annotated_msdf_2.metadata["creator_id"]), 2)
 
     def test_annotate_fail(self):
         """Pass invalid param to see if it fails."""
         kwargs = {"abcd": ("x:%", "y:%")}
         with self.assertRaises(ValueError):
-            annotate_file(input=self.input, output=sys.stdout, **kwargs)
+            annotate_file(input=self.input, **kwargs)

tests/test_cli.py

@@ -86,11 +86,8 @@ def test_cli_multiple_input(self):
 
     def run_successful(self, result: Result, obj: Any) -> None:
         """Check the test result is successful."""
-        self.assertEqual(
-            result.exit_code,
-            0,
-            f"{obj} did not perform as expected: {result.exception}",
-        )
+        if result.exit_code:
+            raise RuntimeError(f"{obj} failed") from result.exception
 
     def run_convert(self, runner: CliRunner, test_case: SSSOMTestCase) -> Result:
         """Run the convert test."""
@@ -143,7 +140,7 @@ def run_split(self, runner: CliRunner, test_case: SSSOMTestCase) -> Result:
 
     def run_ptable(self, runner: CliRunner, test_case: SSSOMTestCase) -> Result:
         """Run the ptable test."""
-        params = [test_case.filepath]
+        params = [test_case.filepath, "--output", test_case.get_out_file("ptable.tsv")]
         result = runner.invoke(ptable, params)
         self.run_successful(result, test_case)
         return result

tests/test_filter.py

@@ -1,13 +1,10 @@
 """Test for filtering MappingSetDataFrame columns."""
 
-import sys
 import unittest
 from os.path import join
 
 from sssom.constants import PREDICATE_MODIFIER
 from sssom.io import filter_file
-
-# from sssom.io import filter_file
 from sssom.parsers import parse_sssom_table
 from tests.constants import data_dir
 
@@ -25,7 +22,7 @@ def setUp(self) -> None:
     def test_filter(self):
         """Test filtering of rows."""
         kwargs = {"subject_id": ("x:%", "y:%"), "object_id": ("y:%", "z:%", "a:%")}
-        filtered_msdf = filter_file(input=self.input, output=sys.stdout, **kwargs)
+        filtered_msdf = filter_file(input=self.input, **kwargs)
         validation_msdf = parse_sssom_table(self.validation_file)
 
         # Drop empty columns since read_sssom_table drops them by default.
@@ -41,4 +38,4 @@ def test_filter_fail(self):
         """Pass invalid param to see if it fails."""
         kwargs = {"subject_ids": ("x:%", "y:%"), "object_id": ("y:%", "z:%")}
         with self.assertRaises(ValueError):
-            filter_file(input=self.input, output=sys.stdout, **kwargs)
+            filter_file(input=self.input, **kwargs)