ran lint commands

app/routes.py

@@ -299,7 +299,7 @@ def make_new_source_contract(form):
         "frequency": form.frequency.data,
         "schema_type": form.schema_type.data,
         "source_type": form.source_type.data,
-        "notification_frequency": form.notification_frequency.data
+        "notification_frequency": form.notification_frequency.data,
     }
 
 
@@ -754,12 +754,15 @@ def download_harvest_errors_by_job(job_id, error_type):
                     [
                         error.id,
                         identifier,
-                        json.loads(source_raw).get("title", None) if source_raw else None,
+                        (
+                            json.loads(source_raw).get("title", None)
+                            if source_raw
+                            else None
+                        ),
                         error.harvest_record_id,
                         error.type,
                         error.message,
-                        error.date_created
-
+                        error.date_created,
                     ]
                     for error, identifier, source_raw in db.get_harvest_record_errors_by_job(
                         job_id, paginate=False
@@ -773,7 +776,7 @@ def download_harvest_errors_by_job(job_id, error_type):
                         "harvest_record_id",
                         "record_error_type",
                         "message",
-                        "date_created"
+                        "date_created",
                     ]
                 ]
 

database/interface.py

@@ -340,17 +340,17 @@ def get_harvest_job_errors_by_job(self, job_id: str) -> list[dict]:
     @paginate
     def get_harvest_record_errors_by_job(self, job_id: str, **kwargs):
         """
-            Retrieves harvest record errors for a given job.
+        Retrieves harvest record errors for a given job.
 
-            This function fetches all records where the harvest status is 'error' and
-            belongs to the specified job. The query returns a tuple containing:
-                - HarvestRecordError object
-                - identifier (retrieved from HarvestRecord)
-                - source_raw (retrieved from HarvestRecord, containing 'title')
+        This function fetches all records where the harvest status is 'error' and
+        belongs to the specified job. The query returns a tuple containing:
+            - HarvestRecordError object
+            - identifier (retrieved from HarvestRecord)
+            - source_raw (retrieved from HarvestRecord, containing 'title')
 
-            Returns:
-                Query: A SQLAlchemy Query object that, when executed, yields tuples of:
-                    (HarvestRecordError, identifier, source_raw).
+        Returns:
+            Query: A SQLAlchemy Query object that, when executed, yields tuples of:
+                (HarvestRecordError, identifier, source_raw).
         """
         subquery = (
             self.db.query(HarvestRecord.id)
@@ -360,12 +360,11 @@ def get_harvest_record_errors_by_job(self, job_id: str, **kwargs):
         )
         query = (
             self.db.query(
-                HarvestRecordError,
-                HarvestRecord.identifier,
-                HarvestRecord.source_raw
+                HarvestRecordError, HarvestRecord.identifier, HarvestRecord.source_raw
+            )
+            .join(
+                HarvestRecord, HarvestRecord.id == HarvestRecordError.harvest_record_id
             )
-            .join(HarvestRecord, 
-                HarvestRecord.id == HarvestRecordError.harvest_record_id)
             .filter(HarvestRecord.id.in_(select(subquery)))
         )
         return query

database/models.py

@@ -79,6 +79,7 @@ class HarvestSource(db.Model):
         nullable=False,
     )
 
+
 class HarvestJob(db.Model):
     __tablename__ = "harvest_job"
 

migrations/env.py

@@ -1,9 +1,8 @@
 import logging
 from logging.config import fileConfig
 
-from flask import current_app
-
 from alembic import context
+from flask import current_app
 
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.
@@ -12,32 +11,31 @@
 # Interpret the config file for Python logging.
 # This line sets up loggers basically.
 fileConfig(config.config_file_name)
-logger = logging.getLogger('alembic.env')
+logger = logging.getLogger("alembic.env")
 
 
 def get_engine():
     try:
         # this works with Flask-SQLAlchemy<3 and Alchemical
-        return current_app.extensions['migrate'].db.get_engine()
+        return current_app.extensions["migrate"].db.get_engine()
     except (TypeError, AttributeError):
         # this works with Flask-SQLAlchemy>=3
-        return current_app.extensions['migrate'].db.engine
+        return current_app.extensions["migrate"].db.engine
 
 
 def get_engine_url():
     try:
-        return get_engine().url.render_as_string(hide_password=False).replace(
-            '%', '%%')
+        return get_engine().url.render_as_string(hide_password=False).replace("%", "%%")
     except AttributeError:
-        return str(get_engine().url).replace('%', '%%')
+        return str(get_engine().url).replace("%", "%%")
 
 
 # add your model's MetaData object here
 # for 'autogenerate' support
 # from myapp import mymodel
 # target_metadata = mymodel.Base.metadata
-config.set_main_option('sqlalchemy.url', get_engine_url())
-target_db = current_app.extensions['migrate'].db
+config.set_main_option("sqlalchemy.url", get_engine_url())
+target_db = current_app.extensions["migrate"].db
 
 # other values from the config, defined by the needs of env.py,
 # can be acquired:
@@ -46,7 +44,7 @@ def get_engine_url():
 
 
 def get_metadata():
-    if hasattr(target_db, 'metadatas'):
+    if hasattr(target_db, "metadatas"):
         return target_db.metadatas[None]
     return target_db.metadata
 
@@ -64,9 +62,7 @@ def run_migrations_offline():
 
     """
     url = config.get_main_option("sqlalchemy.url")
-    context.configure(
-        url=url, target_metadata=get_metadata(), literal_binds=True
-    )
+    context.configure(url=url, target_metadata=get_metadata(), literal_binds=True)
 
     with context.begin_transaction():
         context.run_migrations()
@@ -84,23 +80,21 @@ def run_migrations_online():
     # when there are no changes to the schema
     # reference: http://alembic.zzzcomputing.com/en/latest/cookbook.html
     def process_revision_directives(context, revision, directives):
-        if getattr(config.cmd_opts, 'autogenerate', False):
+        if getattr(config.cmd_opts, "autogenerate", False):
             script = directives[0]
             if script.upgrade_ops.is_empty():
                 directives[:] = []
-                logger.info('No changes in schema detected.')
+                logger.info("No changes in schema detected.")
 
-    conf_args = current_app.extensions['migrate'].configure_args
+    conf_args = current_app.extensions["migrate"].configure_args
     if conf_args.get("process_revision_directives") is None:
         conf_args["process_revision_directives"] = process_revision_directives
 
     connectable = get_engine()
 
     with connectable.connect() as connection:
         context.configure(
-            connection=connection,
-            target_metadata=get_metadata(),
-            **conf_args
+            connection=connection, target_metadata=get_metadata(), **conf_args
         )
 
         with context.begin_transaction():

migrations/versions/c04b66d4d5b9_add_notification_frequency.py

@@ -5,28 +5,34 @@
 Create Date: 2025-02-07 09:55:49.013498
 
 """
-from alembic import op
-import sqlalchemy as sa
 
+import sqlalchemy as sa
+from alembic import op
 
 # revision identifiers, used by Alembic.
-revision = 'c04b66d4d5b9'
+revision = "c04b66d4d5b9"
 down_revision = None
 branch_labels = None
 depends_on = None
 
 
 def upgrade():
     # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('harvest_source', schema=None) as batch_op:
-        batch_op.add_column(sa.Column('notification_frequency', sa.Enum('on_error', 'always', name='notification_frequency'), nullable=False))
+    with op.batch_alter_table("harvest_source", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "notification_frequency",
+                sa.Enum("on_error", "always", name="notification_frequency"),
+                nullable=False,
+            )
+        )
 
     # ### end Alembic commands ###
 
 
 def downgrade():
     # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('harvest_source', schema=None) as batch_op:
-        batch_op.drop_column('notification_frequency')
+    with op.batch_alter_table("harvest_source", schema=None) as batch_op:
+        batch_op.drop_column("notification_frequency")
 
     # ### end Alembic commands ###

tests/integration/harvest_job_flows/test_harvest_job_full_flow.py

@@ -1,6 +1,6 @@
 import json
 import os
-from unittest.mock import patch, MagicMock
+from unittest.mock import MagicMock, patch
 
 from harvester.harvest import harvest_job_starter
 from harvester.utils.general_utils import download_file