Merge pull request #539 from ptth222/doi-regex-fix

Update defaults.py
ISA-tools · Mar 7, 2024 · e5f6fd2 · e5f6fd2
2 parents 4bb3e83 + 2275ee9
commit e5f6fd2
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/isatools/isatab/defaults.py b/isatools/isatab/defaults.py
@@ -34,7 +34,7 @@ def pbar(x):
 _RX_I_FILE_NAME = compile(r'i_(.*?)\.txt')
 _RX_DATA = compile(r'data\[(.*?)\]')
 _RX_COMMENT = compile(r'Comment\[(.*?)\]')
-_RX_DOI = compile(r'(10[.][0-9]{4,}(?:[.][0-9]+)*/(?:(?![%"#? ])\\S)+)')
+_RX_DOI = compile(r'10.\d{4,9}/[-._;()/:a-z0-9A-Z]+')
 _RX_PMID = compile(r'[0-9]{8}')
 _RX_PMCID = compile(r'PMC[0-9]{8}')
 _RX_CHARACTERISTICS = compile(r'Characteristics\[(.*?)\]')

diff --git a/tests/isatab/validate/test_core.py b/tests/isatab/validate/test_core.py
@@ -17,7 +17,7 @@ def test_b_ii_s_3(self):
         data_path = path.join(path.dirname(path.abspath(__file__)), '..', '..', 'data', 'tab', 'BII-S-3')
         with open(path.join(data_path, 'i_gilbert.txt'), 'r') as data_file:
             r = validate(fp=data_file, config_dir=self.default_conf, origin="")
-        self.assertEqual(len(r['warnings']), 12)
+        self.assertEqual(len(r['warnings']), 10)
 
     def test_mtbls267(self):
         data_path = path.join(path.dirname(path.abspath(__file__)), '..', '..', 'data', 'tab', 'MTBLS267-partial')
@@ -82,7 +82,7 @@ def is_investigation(investigation_df):
         data_path = path.join(path.dirname(path.abspath(__file__)), '..', '..', 'data', 'tab', 'BII-S-3')
         with open(path.join(data_path, 'i_gilbert.txt'), 'r') as data_file:
             r = validate(data_file, rules=rules)
-        self.assertEqual(len(r['warnings']), 12)
+        self.assertEqual(len(r['warnings']), 10)
 
         rule = '12000'
         expected_error = {