Merge 1744618 into cf45830

q2_types/feature_data/_format.py

@@ -132,6 +132,7 @@ class DNAFASTAFormat(model.TextFileFormat):
     def _validate_lines(self, max_lines):
         FASTADNAValidator = re.compile(r'[ACGTURYKMSWBDHVN]+\r?\n?')
         last_line_was_ID = False
+        ids = {}
 
         with open(str(self), 'rb') as fh:
             try:
@@ -143,18 +144,33 @@ def _validate_lines(self, max_lines):
                     return
                 if first[0] != ord(b'>'):
                     raise ValidationError("First line of file is not a valid "
-                                          "FASTA ID. FASTA IDs must start "
-                                          "with '>'")
+                                          "description. Descriptions must "
+                                          "start with '>'")
                 fh.seek(0)
                 for line_number, line in enumerate(fh, 1):
                     if line_number >= max_lines:
                         return
                     line = line.decode('utf-8-sig')
                     if line.startswith('>'):
                         if last_line_was_ID:
-                            raise ValidationError('Multiple consecutive IDs '
-                                                  'starting on line '
-                                                  f'{line_number-1!r}')
+                            raise ValidationError('Multiple consecutive '
+                                                  'descriptions starting on '
+                                                  f'line {line_number-1!r}')
+                        line = line.split()
+                        if line[0] == '>':
+                            if len(line) == 1:
+                                raise ValidationError(
+                                    f'Description on line {line_number} is '
+                                    'missing an ID.')
+                            else:
+                                raise ValidationError(
+                                    f'ID on line {line_number} starts with a '
+                                    'space. IDs may not start with spaces')
+                        if line[0] in ids:
+                            raise ValidationError(
+                                f'ID on line {line_number} is a duplicate of '
+                                f'another ID on line {ids[line[0]]}.')
+                        ids[line[0]] = line_number
                         last_line_was_ID = True
                     elif re.fullmatch(FASTADNAValidator, line):
                         last_line_was_ID = False

q2_types/feature_data/tests/data/dna-sequences-duplicate-id.fasta

@@ -0,0 +1,5 @@
+>SEQUENCE1
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+>SEQUENCE1
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGT

q2_types/feature_data/tests/data/dna-sequences-id-starts-with-space.fasta

@@ -0,0 +1 @@
+> this_id_starts_with_a_space

q2_types/feature_data/tests/data/dna-sequences-no-id.fasta

@@ -0,0 +1 @@
+>

q2_types/feature_data/tests/test_format.py

@@ -169,7 +169,8 @@ def test_dna_fasta_format_consecutive_IDs(self):
         filepath = self.get_data_path('dna-sequences-consecutive-ids.fasta')
         format = DNAFASTAFormat(filepath, mode='r')
 
-        with self.assertRaisesRegex(ValidationError, 'consecutive IDs.*1'):
+        with self.assertRaisesRegex(
+                ValidationError, 'consecutive descriptions.*1'):
             format.validate()
 
     def test_dna_fasta_format_missing_initial_ID(self):
@@ -201,6 +202,28 @@ def test_dna_sequences_directory_format(self):
 
         format.validate()
 
+    def test_dna_fasta_format_duplicate_ids(self):
+        filepath = self.get_data_path('dna-sequences-duplicate-id.fasta')
+        format = DNAFASTAFormat(filepath, mode='r')
+
+        with self.assertRaisesRegex(ValidationError, '3.*duplicate.*1'):
+            format.validate()
+
+    def test_dna_fasta_format_no_id(self):
+        filepath = self.get_data_path('dna-sequences-no-id.fasta')
+        format = DNAFASTAFormat(filepath, mode='r')
+
+        with self.assertRaisesRegex(ValidationError, '1.*missing an ID'):
+            format.validate()
+
+    def test_dna_fasta_format_id_starts_with_space(self):
+        filepath = self.get_data_path(
+            'dna-sequences-id-starts-with-space.fasta')
+        format = DNAFASTAFormat(filepath, mode='r')
+
+        with self.assertRaisesRegex(ValidationError, '1 starts with a space'):
+            format.validate()
+
     def test_paired_dna_sequences_directory_format(self):
         filepath = self.get_data_path('dna-sequences.fasta')
         temp_dir = self.temp_dir.name