Fixed test_write_report() log path issue

dandi/bids_validator_xs.py

@@ -434,7 +434,7 @@ def validate_all(
 
 def write_report(
     validation_result,
-    report_path="bids-validator-report_{}.log",
+    report_path="/var/tmp/bids-validator-report_{}.log",
     datetime_format="%Y%m%d-%H%M%S",
 ):
     """Write a human-readable report based on the validation result.
@@ -458,6 +458,12 @@ def write_report(
     """
 
     report_path = report_path.format(datetime.datetime.now().strftime(datetime_format))
+    report_path = os.path.abspath(os.path.expanduser(report_path))
+    try:
+        os.makedirs(os.path.dirname(report_path))
+    except OSError:
+        pass
+
     total_file_count = len(validation_result["path_listing"])
     validated_files_count = total_file_count - len(validation_result["path_tracking"])
     with open(report_path, "w") as f:
@@ -601,6 +607,7 @@ def validate_bids(
     schema_version=None,
     force_select=False,
     debug=False,
+    report_path=False,
 ):
     """
     Validate paths according to BIDS schema.
@@ -623,6 +630,10 @@ def validate_bids(
         If None, the `dataset_description.json` fie will be queried for the dataset schema version.
     force_select : bool, optional
         Whether to fall back to newest version of schema if no version is given or found.
+    report_path : bool or str, optional
+        If `True` a log will be written using the standard output path of `.write_report()`.
+        If string, the string will be used as the output path.
+        If the variable evaluates as False, no log will be written.
 
     Examples
     --------
@@ -644,6 +655,11 @@ def validate_bids(
         regex_schema,
         debug=debug,
     )
-    write_report(validation_result)
+
+    if report_path:
+        if isinstance(report_path, str):
+            write_report(validation_result, report_path=report_path)
+        else:
+            write_report(validation_result)
 
     return validation_result

dandi/cli/cmd_validate.py

@@ -10,15 +10,29 @@
 @devel_option(
     "--schema", help="Validate against new BIDS schema version", metavar="VERSION"
 )
+@click.option("--report", help="Specify path to write a report under.")
+@click.option(
+    "--report-flag",
+    "-r",
+    is_flag=True,
+    help="Whether to write a report under a"
+    "unique path in the current directory. Only usable if `--report` is not already used.",
+)
 @click.argument("paths", nargs=-1, type=click.Path(exists=True, dir_okay=True))
 @devel_debug_option()
 @map_to_click_exceptions
-def validate_bids(paths, schema=None, devel_debug=False):
+def validate_bids(
+    paths, schema=None, devel_debug=False, report=False, report_flag=False
+):
     """Validate BIDS paths."""
     from ..validate import validate_bids as validate_bids_
 
+    if report_flag and not report:
+        report = report_flag
+
     validate_bids_(
         *paths,
+        report=report,
         schema_version=schema,
         devel_debug=devel_debug,
     )

dandi/tests/test_bids_validator_xs.py

@@ -230,7 +230,7 @@ def test_load_all():
         assert "mandatory" in list(entry.keys())
 
 
-def test_write_report():
+def test_write_report(tmp_path):
     from dandi.bids_validator_xs import write_report
 
     validation_result = {}
@@ -273,8 +273,8 @@ def test_write_report():
     ]
 
     report_path = os.path.join(
-        os.path.abspath(os.path.dirname(__file__)),
-        "data/output_bids_validator_xs_write.log",
+        tmp_path,
+        "output_bids_validator_xs_write.log",
     )
     expected_report_path = os.path.join(
         os.path.abspath(os.path.dirname(__file__)),
@@ -288,7 +288,7 @@ def test_write_report():
     assert report_text == expected_report_text
 
 
-def test_bids_datasets(bids_examples):
+def test_bids_datasets(bids_examples, tmp_path):
     from dandi.bids_validator_xs import validate_bids
 
     whitelist = [
@@ -327,6 +327,16 @@ def test_bids_datasets(bids_examples):
         for f in files:
             selected_path = os.path.join(root, f)
             selected_paths.append(selected_path)
+    # Does terminal debug output work?
     result = validate_bids(selected_paths, schema_version=schema_path, debug=True)
+    # Does default log path specification work?
+    result = validate_bids(selected_paths, schema_version=schema_path, report_path=True)
+    # Does custom log path specification work?
+    result = validate_bids(
+        selected_paths,
+        schema_version=schema_path,
+        debug=True,
+        report_path=os.path.join(tmp_path, "test_bids.log"),
+    )
     # Have all files been validated?
     assert len(result["path_tracking"]) == 0

dandi/validate.py

@@ -9,6 +9,7 @@ def validate_bids(
     *paths: str,
     schema_version: Optional[str] = None,
     devel_debug: bool = False,
+    report: Optional[str] = None,
 ) -> Any:
     """Validate BIDS paths.
 
@@ -20,18 +21,20 @@ def validate_bids(
         BIDS schema version to use, this setting will override the version specified in the dataset.
     devel_debug : bool, optional
         Whether to trigger debugging in the BIDS validator.
+    report_path : bool or str, optional
+        If `True` a log will be written using the standard output path of `.write_report()`.
+        If string, the string will be used as the output path.
+        If the variable evaluates as False, no log will be written.
 
     Notes
     -----
     Can be used from bash, as:
-        DANDI_DEVEL=1 dandi validate-bids --schema="1.7.0+012+dandi001" /data/paths
+        DANDI_DEVEL=1 dandi validate-bids --schema="1.7.0+012+dandi001" --report="my.log" /my/path
     """
     from .bids_validator_xs import validate_bids as validate_bids_
 
     return validate_bids_(
-        paths,
-        schema_version=schema_version,
-        debug=devel_debug,
+        paths, schema_version=schema_version, debug=devel_debug, report_path=report
     )