added validation positive for emty files

q2_amr/amrfinderplus/types/_format.py

@@ -71,7 +71,7 @@ def amr_dna_tab_path_maker(self):
 
 
 class ARMFinderPlusAnnotationFormat(model.TextFileFormat):
-    def _validate(self, n_records=None):
+    def _validate(self):
         header_coordinates = [
             "Protein identifier",
             "Contig id",
@@ -98,16 +98,19 @@ def _validate(self, n_records=None):
             "Hierarchy node",
         ]
         header = header_coordinates[:1] + header_coordinates[5:]
-        header_obs = pd.read_csv(str(self), sep="\t", nrows=0).columns.tolist()
-        if header != header_obs and header_coordinates != header_obs:
-            raise ValidationError(
-                "Header line does not match ARMFinderPlusAnnotation format. Must "
-                "consist of the following values: "
-                + ", ".join(header_coordinates)
-                + ".\nWhile Contig id, Start, Stop and Strand are optional."
-                + ".\n\nFound instead: "
-                + ", ".join(header_obs)
-            )
+        try:
+            header_obs = pd.read_csv(str(self), sep="\t", nrows=0).columns.tolist()
+            if header != header_obs and header_coordinates != header_obs:
+                raise ValidationError(
+                    "Header line does not match ARMFinderPlusAnnotation format. Must "
+                    "consist of the following values: "
+                    + ", ".join(header_coordinates)
+                    + ".\nWhile Contig id, Start, Stop and Strand are optional."
+                    + ".\n\nFound instead: "
+                    + ", ".join(header_obs)
+                )
+        except pd.errors.EmptyDataError:
+            pass
 
     def _validate_(self, level):
         self._validate()

q2_amr/amrfinderplus/types/tests/test_types_formats_transformers.py

@@ -5,6 +5,9 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
+import os
+import tempfile
+
 from qiime2.core.exceptions import ValidationError
 from qiime2.plugin.testing import TestPluginBase
 
@@ -40,6 +43,14 @@ def test_amrfinderplus_annotation_format_validate_positive_coordinates(self):
         format = ARMFinderPlusAnnotationFormat(filepath, mode="r")
         format.validate()
 
+    def test_amrfinderplus_annotation_format_validate_positive_empty(self):
+        with tempfile.TemporaryDirectory() as temp_dir:
+            temp_file_path = os.path.join(temp_dir, "amr_annotations.tsv")
+            with open(temp_file_path, "w"):
+                pass
+            format = ARMFinderPlusAnnotationFormat(temp_file_path, mode="r")
+            format.validate()
+
     def test_amrfinderplus_annotation_format_validation_error(self):
         with self.assertRaises(ValidationError) as context:
             path = self.get_data_path("annotation_wrong/amr_annotation.tsv")