Resolve #403 speed issue, but at 45 minutes, the best we can do (#406)

.gitignore

@@ -1,4 +1,5 @@
 # Python build, virtual environments, and buildouts
+.venv
 venv
 __pycache__/
 dist/

setup.cfg

@@ -38,12 +38,12 @@ install_requires =
     itsdangerous==2.0.1
     jinja2==3.0.1
     jsonschema==3.0.0
-    lxml>=4.5
+    lxml==4.6.3
     nltk==3.5
-    numpy>=1.18
+    numpy==1.21.2
     openapi-schema-validator==0.1.4
     openpyxl~=3.0.7
-    pandas~=1.4.4
+    pandas==1.3.4
     python-dateutil>=2.8
     python-jose[cryptography]
     pytz==2020.1
@@ -86,7 +86,7 @@ dev =
     pre-commit
     sphinx
     sphinxcontrib-napoleon
-    tox
+    tox==3.28.0
     flask_testing==0.8.0
     sphinx-rtd-theme==0.5.0
     sphinx-argparse==0.2.5
@@ -103,6 +103,7 @@ dev =
     types-requests
     types-six
     types-waitress
+    virtualenv==20.8.1
 
 # 👉 Note: The ``-stubs`` and ``types-`` dependencies above ↑ in the ``dev``
 # extra must be duplicated in ``.pre-commit-config.yaml`` in order for ``tox``

src/pds_doi_service/api/util.py

@@ -14,7 +14,7 @@
 """
 import datetime
 import typing
-from collections import Iterable
+from typing import Iterable
 
 import six
 

src/pds_doi_service/core/actions/update.py

@@ -247,7 +247,6 @@ def _update_dois(self, dois):
         return updated_dois
 
     def _get_doi_record_from_pds_identifier(self, pds_identifier):
-
         # Get the record from the transaction database for the current DOI value
         transaction_record = self._list_action.transaction_for_identifier(pds_identifier)
 
@@ -265,7 +264,6 @@ def _get_doi_record_from_pds_identifier(self, pds_identifier):
         return existing_dois[0]
 
     def _get_doi_record_from_doi_identifier(self, doi_identifier):
-
         # Get the record from the transaction database for the current DOI value
         transaction_record = self._list_action.transaction_for_doi(doi_identifier)
 

src/pds_doi_service/core/input/input_util.py

@@ -40,7 +40,6 @@
 
 
 class DOIInputUtil:
-
     MANDATORY_COLUMNS = [
         "title",
         "publication_date",

src/pds_doi_service/core/outputs/test/doi_validator_test.py

@@ -401,8 +401,9 @@ def test_identifier_validation_doi_id_mismatch(self):
             self._doi_validator._check_identifier_fields(doi_obj)
 
     def test_site_url_validation(self):
-        """ """
-        # Test with an unreachable (fake) URL
+        """
+        Test validation of site URLs with an unreachable (fake) URL.
+        """
         doi_obj = Doi(
             title=self.title + " different",
             publication_date=self.transaction_date,

src/pds_doi_service/core/util/config_parser.py

@@ -83,7 +83,7 @@ def get_config_defaults_filepath():
     def _resolve_relative_path(parser):
         # resolve relative path with sys.prefix base path
         for section in parser.sections():
-            for (key, val) in parser.items(section):
+            for key, val in parser.items(section):
                 if key.endswith("_file") or key.endswith("_dir"):
                     parser[section][key] = os.path.abspath(os.path.join(sys.prefix, val))
 

src/pds_doi_service/core/util/test/contributors_util_test.py

@@ -10,7 +10,6 @@ class ContributorsUtilTestCase(unittest.TestCase):
     )
 
     def test_authorized_contributor(self):
-
         authorized_contributor = (
             "Cartography and Imaging Sciences Discipline" in self._doi_contributor_util.get_permissible_values()
         )