plac8 flake8

api/schemas/views.py

@@ -31,7 +31,7 @@ def format_link(model):
     schema_models.add(model)
     link = '- [{0}](/api/schema/{0})'.format(model.__name__)
     if model.__doc__ and not re.fullmatch(DEFAULT_DOC.format(model.__name__), model.__doc__):
-        link += ': ' + next(l for l in model.__doc__.splitlines() if l)
+        link += ': ' + next(line for line in model.__doc__.splitlines() if line)
     return link
 
 
@@ -40,7 +40,7 @@ def subclass_links(base_model, include_base=True):
     for model in sorted(base_model.__subclasses__(), key=lambda m: m.__name__):
         subclasses = subclass_links(model)
         if include_base:
-            subclasses = [INDENT + l for l in subclasses]
+            subclasses = [INDENT + link for link in subclasses]
         links.extend(subclasses)
     return links
 

share/harvesters/gov_nih.py

@@ -100,7 +100,7 @@ def parse_row(self, row, day_of_week):
 
         if month_column.lower() == u"all":
             return (None, fiscal_year, url)
-        elif re.match('[A-Za-z\s]* [0-9]{4}, WEEK \d+', month_column):
+        elif re.match(r'[A-Za-z\s]* [0-9]{4}, WEEK \d+', month_column):
             date = self.parse_month_column(month_column, day_of_week)
             return (date, fiscal_year, url)
         else:

share/harvesters/oai.py

@@ -68,7 +68,7 @@ def fetch_records(self, url: furl) -> list:
             if not token or not records:
                 break
 
-    def fetch_page(self, url: furl, token: str=None) -> (list, str):
+    def fetch_page(self, url: furl, token: str = None) -> (list, str):
         if token:
             url.args = {'resumptionToken': token, 'verb': 'ListRecords'}
 

share/harvesters/org_biorxiv_html.py

@@ -73,7 +73,7 @@ def fetch_records(self, url, start_date, end_date):
                     el.extract()
 
                 # Links have PKs and dates in them. /content/early/YYYY/MM/DD/PK or /content/early/YYYY/MM/DD/PK.REV
-                identifier = re.match('/content/early/\d{4}/\d{2}/\d{2}/(\d+)(?:\.\d+)?$', link.decode()).group(1)
+                identifier = re.match(r'/content/early/\d{4}/\d{2}/\d{2}/(\d+)(?:\.\d+)?$', link.decode()).group(1)
 
                 yield identifier, str(soup)
 

share/harvesters/org_swbiodiversity.py

@@ -31,7 +31,7 @@ def fetch_records(self, list_url):
 
         record_list = []
         for record in records:
-            record_content = re.findall('collid=(\d+)', record.get('href'))
+            record_content = re.findall(r'collid=(\d+)', record.get('href'))
             if record_content and record_content[0] not in record_list:
                 record_list.append(record_content[0])
         total = len(record_list)

share/management/commands/forceingest.py

@@ -130,8 +130,8 @@ def merge_agents(self, dupes):
         self.describe_smash(winner, losers)
         if self.interactive:
             safe_to_assume_yes = all(
-                loser.name == winner.name and
-                len(loser.identifiers.all()) == 0
+                loser.name == winner.name
+                and len(loser.identifiers.all()) == 0
                 for loser in losers
             )
             if not (safe_to_assume_yes or self.command.input_confirm('OK? (y/n) ')):

share/models/fields.py

@@ -279,8 +279,8 @@ def _check_relationship_model(self, from_model=None, **kwargs):
             self_referential = from_model == to_model
 
             # Check symmetrical attribute.
-            if (self_referential and self.remote_field.symmetrical and
-                    not self.remote_field.through._meta.auto_created):
+            if (self_referential and self.remote_field.symmetrical
+                    and not self.remote_field.through._meta.auto_created):
                 errors.append(
                     checks.Error(
                         'Many-to-many fields with intermediate tables must not be symmetrical.',
@@ -374,8 +374,9 @@ def _check_relationship_model(self, from_model=None, **kwargs):
         if self.remote_field.through_fields is not None:
             # Validate that we're given an iterable of at least two items
             # and that none of them is "falsy".
-            if not (len(self.remote_field.through_fields) >= 2 and
-                    self.remote_field.through_fields[0] and self.remote_field.through_fields[1]):
+            if not (len(self.remote_field.through_fields) >= 2
+                    and self.remote_field.through_fields[0]
+                    and self.remote_field.through_fields[1]):
                 errors.append(
                     checks.Error(
                         ("Field specifies 'through_fields' but does not "
@@ -429,8 +430,8 @@ def _check_relationship_model(self, from_model=None, **kwargs):
                             )
                         )
                     else:
-                        if not (hasattr(field, 'remote_field') and
-                                getattr(field.remote_field, 'model', None) == related_model):
+                        if not (hasattr(field, 'remote_field')
+                                and getattr(field.remote_field, 'model', None) == related_model):
                             errors.append(
                                 checks.Error(
                                     "'%s.%s' is not a foreign key to '%s'." % (
@@ -477,41 +478,41 @@ def _get_m2m_reverse_attr(self, related, attr):
         return getattr(self, cache_attr)
 
     def contribute_to_class(self, cls, name, **kwargs):
-            # To support multiple relations to self, it's useful to have a non-None
-            # related name on symmetrical relations for internal reasons. The
-            # concept doesn't make a lot of sense externally ("you want me to
-            # specify *what* on my non-reversible relation?!"), so we set it up
-            # automatically. The funky name reduces the chance of an accidental
-            # clash.
-            if self.remote_field.symmetrical and (
-                    self.remote_field.model == "self" or self.remote_field.model == cls._meta.object_name):
-                self.remote_field.related_name = "%s_rel_+" % name
-            elif self.remote_field.is_hidden():
-                # If the backwards relation is disabled, replace the original
-                # related_name with one generated from the m2m field name. Django
-                # still uses backwards relations internally and we need to avoid
-                # clashes between multiple m2m fields with related_name == '+'.
-                self.remote_field.related_name = "_%s_%s_+" % (cls.__name__.lower(), name)
-
-            super(models.ManyToManyField, self).contribute_to_class(cls, name, **kwargs)
-
-            # The intermediate m2m model is not auto created if:
-            #  1) There is a manually specified intermediate, or
-            #  2) The class owning the m2m field is abstract.
-            #  3) The class owning the m2m field has been swapped out.
-            if not cls._meta.abstract:
-                if self.remote_field.through:
-                    def resolve_through_model(_, model, field):
-                        field.remote_field.through = model
-                    lazy_related_operation(resolve_through_model, cls, self.remote_field.through, field=self)
-                elif not cls._meta.swapped:
-                    self.remote_field.through = create_many_to_many_intermediary_model(self, cls)
-
-            # Add the descriptor for the m2m relation.
-            setattr(cls, self.name, ManyToManyDescriptor(self.remote_field, reverse=False))
-
-            # Set up the accessor for the m2m table name for the relation.
-            self.m2m_db_table = curry(self._get_m2m_db_table, cls._meta)
+        # To support multiple relations to self, it's useful to have a non-None
+        # related name on symmetrical relations for internal reasons. The
+        # concept doesn't make a lot of sense externally ("you want me to
+        # specify *what* on my non-reversible relation?!"), so we set it up
+        # automatically. The funky name reduces the chance of an accidental
+        # clash.
+        if self.remote_field.symmetrical and (
+                self.remote_field.model == "self" or self.remote_field.model == cls._meta.object_name):
+            self.remote_field.related_name = "%s_rel_+" % name
+        elif self.remote_field.is_hidden():
+            # If the backwards relation is disabled, replace the original
+            # related_name with one generated from the m2m field name. Django
+            # still uses backwards relations internally and we need to avoid
+            # clashes between multiple m2m fields with related_name == '+'.
+            self.remote_field.related_name = "_%s_%s_+" % (cls.__name__.lower(), name)
+
+        super(models.ManyToManyField, self).contribute_to_class(cls, name, **kwargs)
+
+        # The intermediate m2m model is not auto created if:
+        #  1) There is a manually specified intermediate, or
+        #  2) The class owning the m2m field is abstract.
+        #  3) The class owning the m2m field has been swapped out.
+        if not cls._meta.abstract:
+            if self.remote_field.through:
+                def resolve_through_model(_, model, field):
+                    field.remote_field.through = model
+                lazy_related_operation(resolve_through_model, cls, self.remote_field.through, field=self)
+            elif not cls._meta.swapped:
+                self.remote_field.through = create_many_to_many_intermediary_model(self, cls)
+
+        # Add the descriptor for the m2m relation.
+        setattr(cls, self.name, ManyToManyDescriptor(self.remote_field, reverse=False))
+
+        # Set up the accessor for the m2m table name for the relation.
+        self.m2m_db_table = curry(self._get_m2m_db_table, cls._meta)
 
 
 class ShareManyToManyField(ShareRelatedField, TypedManyToManyField):

share/models/jobs.py

@@ -302,7 +302,7 @@ class Meta:
 
 
 class LockableQuerySet(models.QuerySet):
-    LOCK_ACQUIRED = re.sub('\s\s+', ' ', '''
+    LOCK_ACQUIRED = re.sub(r'\s\s+', ' ', '''
         pg_try_advisory_lock(%s::REGCLASS::INTEGER, "{0.model._meta.db_table}"."{0.column}")
     ''').strip()
 

share/models/validators.py

@@ -56,7 +56,7 @@ def __call__(self, value):
                 self.validate_node(node, refs, nodes)
             except exceptions.ValidationError as e:
                 e.path.appendleft(i)  # Hack to add in a leading slash
-                raise ValidationError('{} at /@graph/{}'.format(e.message, i, '/'.join(str(x) for x in e.path)))
+                raise ValidationError('{} at /@graph/{}'.format(e.message, '/'.join(str(x) for x in e.path)))
 
         if refs['blank'] - nodes['blank']:
             raise ValidationError('Unresolved references {}'.format(json.dumps([

share/regulate/steps/normalize_iris.py

@@ -74,6 +74,6 @@ def regulate_node(self, node):
                 self.info('Discarding identifier based on invalid authority "{}"'.format(ret['authority']), node.id)
                 node.delete()
 
-        except InvalidIRI as e:
+        except InvalidIRI:
             self.info('Discarding identifier based on unrecognized IRI "{}"'.format(old_iri), node.id)
             node.delete()

share/search/__init__.py

@@ -58,13 +58,11 @@ def pks_to_reindex(self, model, pks):
                 Q(
                     outgoing_creative_work_relations__type=parent_relation,
                     outgoing_creative_work_relations__related_id__in=pks
-                ) |
-                Q(
+                ) | Q(
                     outgoing_creative_work_relations__type=parent_relation,
                     outgoing_creative_work_relations__related__outgoing_creative_work_relations__type=parent_relation,
                     outgoing_creative_work_relations__related__outgoing_creative_work_relations__related_id__in=pks
-                ) |
-                Q(
+                ) | Q(
                     outgoing_creative_work_relations__type=parent_relation,
                     outgoing_creative_work_relations__related__outgoing_creative_work_relations__type=parent_relation,
                     outgoing_creative_work_relations__related__outgoing_creative_work_relations__related__outgoing_creative_work_relations__type=parent_relation,

share/search/daemon.py

@@ -126,7 +126,7 @@ def _action_loop(self, model_name, timeout=5):
                 logger.info('%r: Prepared %d %ss to be indexed in %.02fs', self, len(msgs), model_name, time.time() - start)
         except Exception as e:
             client.captureException()
-            logger.exception('%r: _action_loop(%s) encountered an unexpected error', self, model_name)
+            logger.exception('%r: _action_loop(%s) encountered an unexpected error (%s)', self, model_name, e)
             self.stop()
 
     def _actions(self, msgs, timeout=5):
@@ -168,7 +168,7 @@ def _index_loop(self):
                     logger.debug('%r: Recieved no messages for %.02fs', self, time.time() - start)
         except Exception as e:
             client.captureException()
-            logger.exception('%r: _index_loop encountered an unexpected error', self)
+            logger.exception('%r: _index_loop encountered an unexpected error (%s)', self, e)
             self.stop()
 
     def __repr__(self):

share/tasks/jobs.py

@@ -377,7 +377,7 @@ def _apply_changes(self, job, graph, normalized_datum):
                     matches = change_set_builder.matches
 
         # Retry if it was just the wrong place at the wrong time
-        except (exceptions.IngestConflict, OperationalError) as e:
+        except (exceptions.IngestConflict, OperationalError):
             job.retries = (job.retries or 0) + 1
             job.save(update_fields=('retries',))
             if job.retries > self.MAX_RETRIES:

share/transform/chain/links.py

@@ -716,7 +716,7 @@ def checksum(cls, digits):
         for lower, upper in cls.BOUNDS:
             if (not lower or lower < literal) and (not upper or upper > literal):
                 return
-        raise InvalidIRI('\'{0}\' is outside reserved {1} range.'.format(digits, cls.FORMAT, lower, upper))
+        raise InvalidIRI('\'{0}\' is outside reserved {1} range.'.format(digits, cls.FORMAT))
 
     def _parse(self, obj):
         match = re.search(self.ISNI_RE, obj.upper())
@@ -924,7 +924,7 @@ class InfoURILink(AbstractIRILink):
     # https://tools.ietf.org/html/rfc4452
 
     SCHEME = 'info'
-    INFO_RE = re.compile('^\s*info:([\w-]+)(/\S+)\s*$')
+    INFO_RE = re.compile(r'^\s*info:([\w-]+)(/\S+)\s*$')
 
     @classmethod
     def hint(cls, obj):
@@ -946,8 +946,8 @@ def _parse(self, obj):
 class ISBNLink(AbstractIRILink):
     SCHEME = 'urn'
     AUTHORITY = 'isbn'
-    ISBN10_RE = re.compile('^(?:urn:\/\/isbn\/|ISBN:? ?)?(\d\d?)-(\d{3,7})-(\d{1,6})-(\d|x)$', re.I)
-    ISBN13_RE = re.compile('^(?:urn://isbn/|ISBN:? ?)?(978|979)-(\d\d?)-(\d{3,5})-(\d{2,5})-(\d)$', re.I)
+    ISBN10_RE = re.compile(r'^(?:urn:\/\/isbn\/|ISBN:? ?)?(\d\d?)-(\d{3,7})-(\d{1,6})-(\d|x)$', re.I)
+    ISBN13_RE = re.compile(r'^(?:urn://isbn/|ISBN:? ?)?(978|979)-(\d\d?)-(\d{3,5})-(\d{2,5})-(\d)$', re.I)
 
     @classmethod
     def hint(cls, obj):

share/transform/chain/utils.py

@@ -123,9 +123,9 @@ def get_emails(s):
     # Removing lines that start with '//' because the regular expression
     # mistakenly matches patterns like 'http://[email protected]' as '//[email protected]'.
     # Adopted from code by Dennis Ideler [email protected]
-    regex = re.compile(("([a-z0-9!#$%&'*+\/=?^_`{|}~-]+(?:\.[a-z0-9!#$%&'*+\/=?^_`"
-                        "{|}~-]+)*(@|\sat\s)(?:[a-z0-9](?:[a-z0-9-]*[a-z0-9])?(\.|"
-                        "\sdot\s))+[a-z0-9](?:[a-z0-9-]*[a-z0-9])?)"))
+    regex = re.compile((r"([a-z0-9!#$%&'*+\/=?^_`{|}~-]+(?:\.[a-z0-9!#$%&'*+\/=?^_`"
+                        r"{|}~-]+)*(@|\sat\s)(?:[a-z0-9](?:[a-z0-9-]*[a-z0-9])?(\.|"
+                        r"\sdot\s))+[a-z0-9](?:[a-z0-9-]*[a-z0-9])?)"))
     s = s.lower()
     result = re.findall(regex, s)
     if result:

share/transformers/edu_ageconsearch.py

@@ -121,7 +121,7 @@ def get_agent_emails(self, ctx, agent_key, email_key):
             agent_email = next((x for x in emails if agent in x), None)
 
             if agent_email:
-                agent_object['email'] = re.compile('\((\S+?)\)').search(agent_email).group(1)
+                agent_object['email'] = re.compile(r'\((\S+?)\)').search(agent_email).group(1)
             agent_objects.append(agent_object)
 
         return agent_objects

share/transformers/oai.py

@@ -310,7 +310,7 @@ class RootParser(OAICreativeWork):
             type_map = root_type_map
 
         if property_list:
-            logger.debug('Attaching addition properties %s to transformer for %s'.format(property_list, self.config.label))
+            logger.debug('Attaching addition properties %s to transformer for %s', property_list, self.config.label)
             for prop in property_list:
                 if prop in RootParser._extra:
                     logger.warning('Skipping property %s, it already exists', prop)

share/transformers/org_neurovault.py

@@ -39,7 +39,7 @@ class CreativeWork(Parser):
     def parse_names(self, authors):
         if not authors:
             return []
-        return re.split(',\s|\sand\s', authors)
+        return re.split(r',\s|\sand\s', authors)
 
 
 class NeurovaultTransformer(ChainTransformer):

tests/api/test_sources_endpoint.py

@@ -18,8 +18,8 @@
 
 
 def exceptionCallback(request, uri, headers):
-        time.sleep(6)
-        return (400, headers, uri)
+    time.sleep(6)
+    return (400, headers, uri)
 
 
 @pytest.fixture

tests/api/test_validator.py

@@ -264,7 +264,7 @@ class TestValidator:
                           "'INSTITUTION', 'Institution', 'ORGANIZATION', "
                           "'Organization', 'PERSON', 'Person', 'agent', "
                           "'consortium', 'department', 'institution', 'organization', 'person'"
-                          "] at /@graph/1",
+                          "] at /@graph/1/agent/@type",
                 'source': {'pointer': '/data/attributes/data'},
                 'status': '400'
             }]

tests/share/harvesters/test_swbiodiversity_harvester.py

@@ -107,7 +107,7 @@ def test_swbiodiversity_harvester():
                            body=main_page, content_type='text/html', match_querystring=True)
     collection = furl(url)
     collection.args['collid'] = 223
-    httpretty.register_uri(httpretty.GET, url + ';collid=(\d+)',
+    httpretty.register_uri(httpretty.GET, url + r';collid=(\d+)',
                            body=collection_page, content_type='text/html', match_querystring=True)
     start = pendulum.utcnow() - timedelta(days=3)
     end = pendulum.utcnow()

tests/validation/test_changeset.py

@@ -153,7 +153,7 @@ class TestJSONLDValidator:
             }]
         }
     }, {
-        'out': "1 is not of type 'string' at /@graph/0",
+        'out': "1 is not of type 'string' at /@graph/0/name",
         'in': {
             '@graph': [{
                 '@id': '_:123',
@@ -185,7 +185,7 @@ class TestJSONLDValidator:
             }]
         }
     }, {
-        'out': "'throughtugs' is not one of ['THROUGHTAGS', 'ThroughTags', 'throughtags'] at /@graph/0",
+        'out': "'throughtugs' is not one of ['THROUGHTAGS', 'ThroughTags', 'throughtags'] at /@graph/0/tags/0/@type",
         'in': {
             '@graph': [{
                 '@id': '_:123',
@@ -208,7 +208,7 @@ class TestJSONLDValidator:
             }]
         }
     }, {
-        'out': "'giraffe' is not a 'uri' at /@graph/0",
+        'out': "'giraffe' is not a 'uri' at /@graph/0/uri",
         'in': {
             '@graph': [{
                 '@id': '_:123',