addressing review comment on PR

Author: oerc0042

isatools/isatab/defaults.py

@@ -32,8 +32,7 @@ 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"^(https://doi.org/)?(10\.\d{4,9}/[-._;()/:a-z0-9A-Z]+)$")  #
-# _RX_DOI = compile(r"10\.\d{4,9}/[-._;()/:a-z0-9A-Z]+") #
+_RX_DOI = compile(r"^(https://doi.org/)?(10\.\d{4,9}/[-._;()/:a-z0-9A-Z]+)$")
 _RX_PMID = compile(r"(^https://pubmed.ncbi.nlm.nih.gov/)?[0-9]{8}$")
 _RX_PMCID = compile(r"(^https://pmc.ncbi.nlm.nih.gov/articles/)?PMC[0-9]{8}$")
 _RX_CHARACTERISTICS = compile(r"Characteristics\[(.*?)\]")

isatools/isatab/validate/rules/rules_30xx.py

@@ -72,7 +72,6 @@ def check_doi(doi_str):
         :return: None
         """
         if doi_str != "":
-            print("DOI string:", doi_str)
             if not _RX_DOI.match(doi_str):
                 spl = "Found {} in DOI field".format(doi_str)
 
@@ -100,7 +99,7 @@ def check_pubmed_id(pubmed_id_str):
         :return: None
         """
         if pubmed_id_str != "":
-            if _RX_PMID.match(pubmed_id_str) is None:  # and (_RX_PMCID.match(pubmed_id_str) is None)
+            if (_RX_PMID.match(pubmed_id_str) is None) and (_RX_PMCID.match(pubmed_id_str) is None):
                 spl = "Found PubMedID {}".format(pubmed_id_str)
                 validator.add_warning(message="PubMed ID is not valid format", supplemental=spl, code=3003)
                 log.warning("(W) PubMed ID {} is not valid format".format(pubmed_id_str))

tests/isatab/test_isatab.py

@@ -1125,7 +1125,6 @@ def test_isatab_load_issue587(self):
         with open(os.path.join(self._tab_data_dir, "issue587", "i_Investigation.txt")) as fp:
             ISA = isatab.load(fp)
             self.assertEqual(ISA.ontology_source_references[0].name, "1")
-            # self.assertEqual(ISA.ontology_source_references[0].comments[0].value, "onto_stuff")
 
     def test_isatab_load_sdata201414_isa1(self):
         with open(os.path.join(self._tab_data_dir, "sdata201414-isa1", "i_Investigation.txt"), encoding="utf-8") as fp:

tests/model/test_assay.py

@@ -126,13 +126,11 @@ def test_equalities(self):
     def test_to_dict(self, mock_uuid4):
         study = Study(id_="#study/" + mock_uuid4.return_value)
         assay = Assay(
-            # id_="#assay-/" + mock_uuid4.return_value,
             filename="file",
             measurement_type=OntologyAnnotation(term="MT", id_="MT_ID"),
             technology_type=OntologyAnnotation(term="TT", id_="TT_ID"),
         )
 
-        # print("ID:", assay.id)
         self.assertEqual(assay.id, "#assay/" + mock_uuid4.return_value)
 
         expected_dict = {
@@ -162,27 +160,18 @@ def test_to_dict(self, mock_uuid4):
         }
         self.assertEqual(expected_dict, assay.to_dict())
 
-        # assay = Assay()
-        # assay.from_dict(expected_dict, study)
-        # self.assertEqual(assay.to_dict(), expected_dict)
-
-        # expected_dict["unitCategories"] = [
-        #     {"@id": "unit_ID", "annotationValue": "my_unit", "termSource": "", "termAccession": "", "comments": []}
-        # ]
         assay.from_dict(expected_dict, study)
         self.assertEqual(assay.to_dict(), expected_dict)
 
-        # expected_dict["materials"]["samples"] = [{"@id": "my_sample"}]
         indexes.samples = {"my_sample": Sample(id_="my_sample")}
-        # assay = Assay()
+
         assay.from_dict(expected_dict, study)
         self.assertEqual(assay.to_dict(), expected_dict)
 
         # Data Files
         expected_dict["dataFiles"] = [
             {"@id": "my_data_file", "name": "filename", "type": "RawDataFile", "comments": []}
         ]
-        # assay = Assay()
         assay.from_dict(expected_dict, study)
         self.assertEqual(assay.to_dict(), expected_dict)
         indexes.term_sources = {"term_source1": OntologySource(name="term_source1")}