Paired redact metadata

q2cli/builtin/tools.py

@@ -1764,3 +1764,42 @@ def signature_verify(input_path, name):
     click.echo(CONFIG.cfg_style('success',
                                 f'Signature {name} on Result '
                                 f'{input_path} verified successfully.'))
+
+
+@tools.command(
+    name='redact-metadata',
+    short_help='Remove metadata from an artifact.',
+    help='Remove all metadata from an artifact and return the artifact '
+         'otherwise unchanged.'
+)
+@click.option(
+    '--input-path',
+    required=True,
+    help='The path to the artifact where you wish to remove the metadata.'
+)
+@click.option(
+    '--output-path',
+    required=True,
+    help='Path to save artifact with redacted metadata to.'
+)
+def redact_metadata(input_path, output_path):
+    from rachis.sdk.result import Result
+    from q2cli.core.config import CONFIG
+
+    artifact = Result.load(input_path)
+
+    try:
+        artifact.redact_metadata()
+    except ValueError as e:
+        click.echo(CONFIG.cfg_style('error', str(e)), err=True)
+        raise click.Abort()
+
+    artifact.save(output_path)
+
+    click.echo(
+        CONFIG.cfg_style(
+            'success',
+            f'Succesfully redacted metadata from {input_path}, and saved to '
+            f'{output_path}.'
+        )
+    )

q2cli/tests/test_tools.py

@@ -31,6 +31,7 @@
 from q2cli.builtin.tools import tools
 from q2cli.commands import RootCommand
 from q2cli.core.usage import ReplayCLIUsage
+from rachis.sdk.result import Visualization
 
 
 class TestCastMetadata(unittest.TestCase):
@@ -2046,5 +2047,67 @@ def test_make_report_duplicate_names(self):
         self.assertIn('Multiple files share the same name', result.output)
 
 
+class TestRedactMetadata(unittest.TestCase):
+    def setUp(self):
+        datadir = datadir = os.path.join(
+            os.path.dirname(os.path.abspath(__file__)), 'data'
+        )
+        self.tax_fp = os.path.join(datadir, 'taxonomy.qza')
+        self.tax_bar_fp = os.path.join(datadir, 'taxa-bar-plots.qzv')
+        self.demux_fp = os.path.join(datadir, 'demux.qza')
+        self.runner = CliRunner()
+        self.tempdir = tempfile.mkdtemp(prefix='qiime2-q2cli-test-temp-')
+        self.redacted_fp = os.path.join(self.tempdir, 'redacted')
+
+    def test_with_metadata(self):
+        redacted_fp = self.redacted_fp + '.qzv'
+        result = self.runner.invoke(tools, [
+            'redact-metadata', '--input-path', self.tax_bar_fp,
+            '--output-path', redacted_fp
+        ])
+
+        redacted_artifact = Visualization.load(redacted_fp)
+        abs_md_paths, _ = redacted_artifact.metadata_paths()
+
+        for path in abs_md_paths:
+            self.assertEqual(os.path.getsize(path), 0)
+
+        success = f'Succesfully redacted metadata from {self.tax_bar_fp}, ' \
+                  f'and saved to {redacted_fp}.\n'
+
+        self.assertEqual(success, result.output)
+
+    def test_fails_already_redacted(self):
+        '''
+        Redacting metadata from an Artifact twice should fail.
+        '''
+        redacted_fp = self.redacted_fp + '.qza'
+        self.runner.invoke(tools, [
+            'redact-metadata', '--input-path', self.tax_fp,
+            '--output-path', self.redacted_fp
+        ])
+
+        result = self.runner.invoke(tools, [
+            'redact-metadata', '--input-path', redacted_fp,
+            '--output-path', os.path.join(self.tempdir, 'bad')
+        ])
+
+        self.assertEqual(result.exit_code, 1)
+        self.assertIn('only redacted metadata', result.output)
+
+    def test_fails_no_metadata(self):
+        '''
+        Redacting metadata from an Artifact with no metadata should fail.
+        '''
+        redacted_fp = self.redacted_fp + '.qza'
+        result = self.runner.invoke(tools, [
+            'redact-metadata', '--input-path', self.demux_fp,
+            '--output-path', redacted_fp
+        ])
+
+        self.assertEqual(result.exit_code, 1)
+        self.assertIn('Artifact without metadata', result.output)
+
+
 if __name__ == "__main__":
     unittest.main()