adding field Performer, associated test

ISA-tools · Apr 12, 2023 · 27c5797 · 27c5797
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Showing 4 changed files with 17 additions and 3 deletions.
diff --git a/README.md b/README.md
@@ -31,7 +31,7 @@ The *ISA API*  aims to provide you, the developer, with a set of tools to help y
 ----
 ### Read the Publication...
 
-Read our **open access [publication](https://doi.org/10.1093/gigascience/giab060) "SA API: An open platform for interoperable life science experimental metadata", published in GigaScience** as a `technical note`
+Read our **open access [publication](https://doi.org/10.1093/gigascience/giab060) "ISA API: An open platform for interoperable life science experimental metadata", published in GigaScience** as a `technical note`
 
 *David Johnson, Dominique Batista, Keeva Cochrane, Robert P. Davey, Anthony Etuk, Alejandra Gonzalez-Beltran, Kenneth Haug, Massimiliano Izzo, Martin Larralde, Thomas N. Lawson, Alice Minotto, Pablo Moreno, Venkata Chandrasekhar Nainala, Claire O'Donovan, Luca Pireddu, Pierrick Roger, Felix Shaw, Christoph Steinbeck, Ralf J. M. Weber, Susanna-Assunta Sansone, Philippe Rocca-Serra.
 ISA API: An open platform for interoperable life science experimental metadata. 2020.11.13.382119; doi:

diff --git a/isatools/isatab/load/core.py b/isatools/isatab/load/core.py
@@ -25,9 +25,10 @@
 )
 
 
-def load(isatab_path_or_ifile, skip_load_tables=False):
+def load(isatab_path_or_ifile: object, skip_load_tables: object = False) -> object:
     """Load an ISA-Tab into ISA Data Model objects
 
+    :rtype: object
     :param isatab_path_or_ifile: Full path to an ISA-Tab directory or file-like
     buffer object pointing to an investigation file
     :param skip_load_tables: Whether or not to skip loading the table files

diff --git a/isatools/isatab/validate/rules/rules_40xx.py b/isatools/isatab/validate/rules/rules_40xx.py
@@ -341,7 +341,7 @@ def load_table_checks(df, filename):
                            'Data Transformation Name',
                            'Derived Spectral Data File', 'Normalization Name',
                            'Derived Array Data File', 'Image File', "Free Induction Decay Data File",
-                           'Metabolite Assignment File',  "Date", "Array Data Matrix File",
+                           'Metabolite Assignment File', "Performer", "Date", "Array Data Matrix File",
                            'Free Induction Decay File', "Derived Array Data Matrix File",
                            'Acquisition Parameter Data File']) \
                 and not _RX_CHARACTERISTICS.match(column) \

diff --git a/tests/validators/test_validate_test_data.py b/tests/validators/test_validate_test_data.py
@@ -349,3 +349,16 @@ def test_validate_testdata_treatment_sequence_json(self):
             validator = Draft4Validator(treatment_sequence_schema,
                                         resolver=resolver)
             validator.validate(json.load(test_case_fp))
+
+
+class TestPerformerValidation(unittest.TestCase):
+    def test_ptx(self):
+        filepath = os.path.join(utils.TAB_DATA_DIR, 'TEST-PTX', 'i_investigation.txt')
+        with open(filepath) as fp:
+            investigation = isatab.load(fp)
+            print(investigation.title)
+            report = isatab.validate(fp)
+            print(report["errors"])
+
+        # self.assertTrue(len(report["errors"]) == 0)
+        # self.assertEqual(len(report["errors"]), 0)