Merge pull request #1510 from ScilifelabDataCentre/DDS-1686-Black-ver…

…sion-should-be-the-same-locally-and-on-Github-actions

Dds 1686 Fixed black version on GitHub Actions - update code to black 24.1.1

.github/workflows/python-black.yml

@@ -8,9 +8,14 @@ name: Black
 
 on: [push, pull_request]
 
+env:
+  INPUT_VERSION: 24.1.1
+
 jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - uses: psf/black@stable
+        with:
+          version: ${{ env.INPUT_VERSION }}

SPRINTLOG.md

@@ -343,3 +343,7 @@ _Nothing merged in CLI during this sprint_
 
 - Minor update jinja2 package to address cve ([#1503](https://github.com/ScilifelabDataCentre/dds_web/pull/1503))
 - Minor update jwcrypto package to address cve ([#1504](https://github.com/ScilifelabDataCentre/dds_web/pull/1504))
+
+# 2024-01-29 - 2024-02-09
+
+- Use of a fix version of black and linted files to 24.1.1 ([#1510](https://github.com/ScilifelabDataCentre/dds_web/pull/1510))

dds_web/api/project.py

@@ -1063,9 +1063,9 @@ def give_project_access(project_list, current_user, user):
                             from_user_token=dds_web.security.auth.obtain_current_encrypted_token(),
                         )
             except KeyNotFoundError as keyerr:
-                fix_errors[
-                    proj.public_id
-                ] = "You do not have access to this project. Please contact the responsible unit."
+                fix_errors[proj.public_id] = (
+                    "You do not have access to this project. Please contact the responsible unit."
+                )
 
         return fix_errors
 

dds_web/api/schemas/project_schemas.py

@@ -306,9 +306,9 @@ def return_items(self, data, **kwargs):
                             {
                                 z.name: {
                                     **fileschema.dump(z),
-                                    "url": s3.generate_get_url(key=z.name_in_bucket)
-                                    if url
-                                    else None,
+                                    "url": (
+                                        s3.generate_get_url(key=z.name_in_bucket) if url else None
+                                    ),
                                 }
                                 for z in y
                             }

dds_web/api/user.py

@@ -233,9 +233,9 @@ def invite_user(email, new_user_role, project=None, unit=None):
                                     project=unit_project,
                                 )
                             except ddserr.KeyNotFoundError as keyerr:
-                                projects_not_shared[
-                                    unit_project.public_id
-                                ] = "You do not have access to the project(s)"
+                                projects_not_shared[unit_project.public_id] = (
+                                    "You do not have access to the project(s)"
+                                )
                             else:
                                 goahead = True
                 else:
@@ -258,9 +258,9 @@ def invite_user(email, new_user_role, project=None, unit=None):
                         is_project_owner=new_user_role == "Project Owner",
                     )
                 except ddserr.KeyNotFoundError as keyerr:
-                    projects_not_shared[
-                        project.public_id
-                    ] = "You do not have access to the specified project."
+                    projects_not_shared[project.public_id] = (
+                        "You do not have access to the specified project."
+                    )
                 else:
                     goahead = True
             else:

dds_web/commands.py

@@ -277,15 +277,21 @@ def list_lost_files(project_id: str):
         # Connect to S3
         resource = session.resource(
             service_name="s3",
-            endpoint_url=project.responsible_unit.sto4_endpoint
-            if sto4
-            else project.responsible_unit.sto2_endpoint,
-            aws_access_key_id=project.responsible_unit.sto4_access
-            if sto4
-            else project.responsible_unit.sto2_access,
-            aws_secret_access_key=project.responsible_unit.sto4_secret
-            if sto4
-            else project.responsible_unit.sto2_secret,
+            endpoint_url=(
+                project.responsible_unit.sto4_endpoint
+                if sto4
+                else project.responsible_unit.sto2_endpoint
+            ),
+            aws_access_key_id=(
+                project.responsible_unit.sto4_access
+                if sto4
+                else project.responsible_unit.sto2_access
+            ),
+            aws_secret_access_key=(
+                project.responsible_unit.sto4_secret
+                if sto4
+                else project.responsible_unit.sto2_secret
+            ),
         )
 
         # List the lost files
@@ -340,15 +346,21 @@ def list_lost_files(project_id: str):
                 # Connect to S3
                 resource_unit = session.resource(
                     service_name="s3",
-                    endpoint_url=proj.responsible_unit.sto4_endpoint
-                    if sto4
-                    else proj.responsible_unit.sto2_endpoint,
-                    aws_access_key_id=proj.responsible_unit.sto4_access
-                    if sto4
-                    else proj.responsible_unit.sto2_access,
-                    aws_secret_access_key=proj.responsible_unit.sto4_secret
-                    if sto4
-                    else proj.responsible_unit.sto2_secret,
+                    endpoint_url=(
+                        proj.responsible_unit.sto4_endpoint
+                        if sto4
+                        else proj.responsible_unit.sto2_endpoint
+                    ),
+                    aws_access_key_id=(
+                        proj.responsible_unit.sto4_access
+                        if sto4
+                        else proj.responsible_unit.sto2_access
+                    ),
+                    aws_secret_access_key=(
+                        proj.responsible_unit.sto4_secret
+                        if sto4
+                        else proj.responsible_unit.sto2_secret
+                    ),
                 )
 
                 # List the lost files
@@ -411,15 +423,17 @@ def add_missing_bucket(project_id: str):
     # Connect to S3
     resource = session.resource(
         service_name="s3",
-        endpoint_url=project.responsible_unit.sto4_endpoint
-        if sto4
-        else project.responsible_unit.sto2_endpoint,
-        aws_access_key_id=project.responsible_unit.sto4_access
-        if sto4
-        else project.responsible_unit.sto2_access,
-        aws_secret_access_key=project.responsible_unit.sto4_secret
-        if sto4
-        else project.responsible_unit.sto2_secret,
+        endpoint_url=(
+            project.responsible_unit.sto4_endpoint
+            if sto4
+            else project.responsible_unit.sto2_endpoint
+        ),
+        aws_access_key_id=(
+            project.responsible_unit.sto4_access if sto4 else project.responsible_unit.sto2_access
+        ),
+        aws_secret_access_key=(
+            project.responsible_unit.sto4_secret if sto4 else project.responsible_unit.sto2_secret
+        ),
     )
 
     # Check if bucket exists
@@ -474,15 +488,17 @@ def delete_lost_files(project_id: str):
     # Connect to S3
     resource = session.resource(
         service_name="s3",
-        endpoint_url=project.responsible_unit.sto4_endpoint
-        if sto4
-        else project.responsible_unit.sto2_endpoint,
-        aws_access_key_id=project.responsible_unit.sto4_access
-        if sto4
-        else project.responsible_unit.sto2_access,
-        aws_secret_access_key=project.responsible_unit.sto4_secret
-        if sto4
-        else project.responsible_unit.sto2_secret,
+        endpoint_url=(
+            project.responsible_unit.sto4_endpoint
+            if sto4
+            else project.responsible_unit.sto2_endpoint
+        ),
+        aws_access_key_id=(
+            project.responsible_unit.sto4_access if sto4 else project.responsible_unit.sto2_access
+        ),
+        aws_secret_access_key=(
+            project.responsible_unit.sto4_secret if sto4 else project.responsible_unit.sto2_secret
+        ),
     )
 
     # Get list of lost files

dds_web/security/project_user_keys.py

@@ -1,4 +1,5 @@
 """ Code for generating and maintaining project and user related keys """
+
 import os
 
 import argon2

dds_web/web/root.py

@@ -3,6 +3,7 @@
 Most of the app routes are in `dds_web/web/user.py`.
 Here we have the routes that are not specific to a user.
 """
+
 from datetime import datetime, timedelta
 import functools
 import threading

dds_web/web/user.py

@@ -596,9 +596,9 @@ def password_reset_completed():
                 unit_admins_to_contact = users
             else:
                 if project.responsible_unit.external_display_name not in units_to_contact:
-                    units_to_contact[
-                        project.responsible_unit.external_display_name
-                    ] = project.responsible_unit.contact_email
+                    units_to_contact[project.responsible_unit.external_display_name] = (
+                        project.responsible_unit.contact_email
+                    )
 
         if len(unit_admins_to_contact) > 0:
             for unit_admin in unit_admins_to_contact:

migrations/versions/02acefb3057a_add_done_to_project.py

@@ -5,6 +5,7 @@
 Create Date: 2022-08-17 08:32:57.578324
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/0c9c237cced5_unit_quota_and_warning.py

@@ -5,6 +5,7 @@
 Create Date: 2023-01-10 14:30:57.089391
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/1256117ad629_add_password_reset.py

@@ -5,6 +5,7 @@
 Create Date: 2022-03-14 16:23:44.287254
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/19b877061c98_add_motd.py

@@ -5,6 +5,7 @@
 Create Date: 2022-04-05 13:49:44.087517
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/1ab892d08e16_change_public_id_length.py

@@ -5,6 +5,7 @@
 Create Date: 2022-04-13 06:16:56.046361
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/1e56b6212479_add_sto4_columns.py

@@ -5,6 +5,7 @@
 Create Date: 2023-07-26 10:40:22.591583
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/1fbd604872e9_add_column_created_at.py

@@ -5,6 +5,7 @@
 Create Date: 2022-04-08 14:32:26.800385
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/2cefec51b9bb_add_tbhours_since_start.py

@@ -5,6 +5,7 @@
 Create Date: 2023-06-02 12:07:01.372912
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/399801a80e7a_change_researchuser_count_column.py

@@ -5,6 +5,7 @@
 Create Date: 2023-05-29 09:37:31.007336
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/3d610b382383_remove_cost_from_usage_table.py

@@ -5,6 +5,7 @@
 Create Date: 2023-11-03 08:36:35.425045
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/53bb37a3cd84_add_num_unique_proj_owners.py

@@ -5,6 +5,7 @@
 Create Date: 2023-05-30 13:24:52.406907
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/666003748d14_change_active_nullable_and_default.py

@@ -5,6 +5,7 @@
 Create Date: 2022-02-24 16:35:34.228040
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/6e9b74878553_add_busy_to_project.py

@@ -5,6 +5,7 @@
 Create Date: 2022-09-07 09:09:06.081829
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/879b99e7f212_unit_personnel_added.py

@@ -5,6 +5,7 @@
 Create Date: 2023-05-29 07:51:05.491352
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/908382be548a_add_column_active_to_motd.py

@@ -3,6 +3,7 @@
 Revises: cd1903e5f2b0
 Create Date: 2022-06-13 12:34:34.981373
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/93ec6983ce8d_number_of_inactive_projects_added.py

@@ -5,6 +5,7 @@
 Create Date: 2023-05-30 08:47:53.926692
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/a5a40d843415_changed_sensitive.py

@@ -5,6 +5,7 @@
 Create Date: 2022-02-19 10:32:31.626236
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.orm.session import Session

migrations/versions/aec752f1e0a5_tb_uploaded_since_start_added.py

@@ -5,6 +5,7 @@
 Create Date: 2023-05-31 14:09:07.327919
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/b01fc48f5939_add_totp.py

@@ -5,6 +5,7 @@
 Create Date: 2022-04-13 14:27:49.319000
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/b976f6cda95c_add_reporting_table.py

@@ -5,6 +5,7 @@
 Create Date: 2023-01-26 10:02:37.535695
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/bb2f428feb9b_rename_safespring_columns.py

@@ -5,6 +5,7 @@
 Create Date: 2023-07-26 07:11:20.429058
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql

migrations/versions/c1e908241401_total_number_of_projects_added.py

@@ -5,6 +5,7 @@
 Create Date: 2023-05-29 11:27:10.843043
 
 """
+
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql