Merge pull request #243 from ral-facilities/release/v1.1.0

Release `v1.1.0`

Author: VKTB

.github/dependabot.yml

@@ -60,4 +60,4 @@ updates:
     groups:
       pip:
         patterns:
-          - "*"
+          - "*"

.github/workflows/.ci.yml

@@ -21,12 +21,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
 
       - name: Set up Python
-        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
+        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           cache: "pip"
 
       - name: Install dependencies
@@ -46,7 +46,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
 
       - name: Create logging configuration file
         run: cp logging.example.ini logging.ini
@@ -73,7 +73,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
 
       - name: Create logging configuration file
         run: cp logging.example.ini logging.ini
@@ -115,17 +115,17 @@ jobs:
       PUSH_DOCKER_IMAGE_TO_HARBOR: ${{ inputs.push-docker-image-to-harbor != null && inputs.push-docker-image-to-harbor || 'false' }}
     steps:
       - name: Check out repo
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@c1e51972afc2121e065aed6d45c65596fe445f3f # v5.8.0
+        uses: docker/metadata-action@c299e40c65443455700f0fdfc63efafe5b349051 # v5.10.0
         with:
           images: ${{ vars.HARBOR_URL }}/object-storage-api
 
       - name: Login to Harbor
         if: ${{ fromJSON(env.PUSH_DOCKER_IMAGE_TO_HARBOR) }}
-        uses: docker/login-action@184bdaa0721073962dff0199f1fb9940f07167d1 # v3.5.0
+        uses: docker/login-action@5e57cd118135c172c3672efd75eb46360885c0ef # v3.6.0
         with:
           registry: ${{ vars.HARBOR_URL }}
           username: ${{ secrets.HARBOR_USERNAME }}

.github/workflows/release-build.yml

@@ -13,18 +13,18 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repo
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
 
       - name: Login to Harbor
-        uses: docker/login-action@184bdaa0721073962dff0199f1fb9940f07167d1 # v3.5.0
+        uses: docker/login-action@5e57cd118135c172c3672efd75eb46360885c0ef # v3.6.0
         with:
           registry: ${{ vars.HARBOR_URL }}
           username: ${{ secrets.HARBOR_USERNAME }}
           password: ${{ secrets.HARBOR_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@c1e51972afc2121e065aed6d45c65596fe445f3f # v5.8.0
+        uses: docker/metadata-action@c299e40c65443455700f0fdfc63efafe5b349051 # v5.10.0
         with:
           images: ${{ vars.HARBOR_URL }}/object-storage-api
           tags: |

.pylintrc

@@ -59,10 +59,11 @@ ignore-paths=
 # Emacs file locks
 ignore-patterns=^\.#
 
-# List of module names for which member attributes should not be checked
-# (useful for modules/projects where namespaces are manipulated during runtime
-# and thus existing member attributes cannot be deduced by static analysis). It
-# supports qualified module names, as well as Unix pattern matching.
+# List of module names for which member attributes should not be checked and
+# will not be imported (useful for modules/projects where namespaces are
+# manipulated during runtime and thus existing member attributes cannot be
+# deduced by static analysis). It supports qualified module names, as well as
+# Unix pattern matching.
 ignored-modules=
 
 # Python code to execute, usually for sys.path manipulation such as
@@ -86,9 +87,13 @@ load-plugins=
 # Pickle collected data for later comparisons.
 persistent=yes
 
+# Resolve imports to .pyi stubs if available. May reduce no-member messages and
+# increase not-an-iterable messages.
+prefer-stubs=no
+
 # Minimum Python version to use for version dependent checks. Will default to
 # the version used to run pylint.
-py-version=3.12
+py-version=3.13
 
 # Discover python modules and packages in the file system subtree.
 recursive=no
@@ -302,6 +307,9 @@ max-locals=15
 # Maximum number of parents for a class (see R0901).
 max-parents=7
 
+# Maximum number of positional arguments for function / method.
+max-positional-arguments=5
+
 # Maximum number of public methods for a class (see R0904).
 max-public-methods=20
 
@@ -436,7 +444,7 @@ disable=raw-checker-failed,
 # either give multiple identifier separated by comma (,) or put this option
 # multiple time (only on the command line, not in the configuration file where
 # it should appear only once). See also the "--disable" option for examples.
-enable=c-extension-no-member
+enable=
 
 
 [METHOD_ARGS]
@@ -468,6 +476,11 @@ max-nested-blocks=5
 # printed.
 never-returning-functions=sys.exit,argparse.parse_error
 
+# Let 'consider-using-join' be raised when the separator to join on would be
+# non-empty (resulting in expected fixes of the type: ``"- " + " -
+# ".join(items)``)
+suggest-join-with-non-empty-separator=yes
+
 
 [REPORTS]
 
@@ -482,10 +495,10 @@ evaluation=max(0, 0 if fatal else 10.0 - ((float(5 * error + warning + refactor
 # used to format the message information. See doc for all details.
 msg-template=
 
-# Set the output format. Available formats are: text, parseable, colorized,
-# json2 (improved json format), json (old json format) and msvs (visual
-# studio). You can also give a reporter class, e.g.
-# mypackage.mymodule.MyReporterClass.
+# Set the output format. Available formats are: 'text', 'parseable',
+# 'colorized', 'json2' (improved json format), 'json' (old json format), msvs
+# (visual studio) and 'github' (GitHub actions). You can also give a reporter
+# class, e.g. mypackage.mymodule.MyReporterClass.
 #output-format=
 
 # Tells whether to display a full report or only the messages.
@@ -587,7 +600,7 @@ ignored-classes=optparse.Values,thread._local,_thread._local,argparse.Namespace
 # of finding the hint is based on edit distance.
 missing-member-hint=yes
 
-# The minimum edit distance a name should have in order to be considered a
+# The maximum edit distance a name should have in order to be considered a
 # similar match for a missing member name.
 missing-member-hint-distance=1
 

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12.11-alpine3.22@sha256:9b8808206f4a956130546a32cbdd8633bc973b19db2923b7298e6f90cc26db08 AS base
+FROM python:3.13.10-alpine3.23@sha256:65fe04ddc51a8ccbf14ecb882903251e4a124914673001b03c393eb65dd9502a AS base
 
 WORKDIR /app
 

README.md

@@ -10,7 +10,7 @@ This microservice requires a MongoDB and S3 object storage instance to run again
 ### Prerequisites
 
 - Docker and Docker Compose installed (if you want to run the microservice inside Docker)
-- Python 3.12, MongoDB 7.0 and MinIO installed on your machine (if you are not using Docker)
+- Python 3.13, MongoDB 7.0 and MinIO installed on your machine (if you are not using Docker)
 - Public key (must be OpenSSH encoded) to decode JWT access tokens (if JWT authentication/authorization is enabled)
 - [MongoDB Compass](https://www.mongodb.com/products/compass) installed (if you want to interact with the database using
   a GUI)

codecov.yml

@@ -9,3 +9,5 @@ coverage:
         target: 75
 ignore:
   - "test/"
+  - "object_storage_api/v1/*" # ignore routers as they are tested in the e2e tests
+  - "object_storage_api/main.py" # ignore main.py as contains router and is tested in the e2e tests

docker-compose.yml

@@ -43,6 +43,7 @@ services:
     command: minio server /data
     volumes:
       - ./minio/data:/data
+    restart: always
     ports:
       - 9000:9000
       - 9001:9001

object_storage_api/core/exceptions.py

@@ -45,21 +45,21 @@ class DatabaseError(BaseAPIException):
 class InvalidObjectIdError(DatabaseError):
     """The provided value is not a valid ObjectId."""
 
-    status_code = status.HTTP_422_UNPROCESSABLE_ENTITY
+    status_code = status.HTTP_422_UNPROCESSABLE_CONTENT
     response_detail = "Invalid ID given"
 
 
 class InvalidImageFileError(BaseAPIException):
     """The provided image file is not valid."""
 
-    status_code = status.HTTP_422_UNPROCESSABLE_ENTITY
+    status_code = status.HTTP_422_UNPROCESSABLE_CONTENT
     response_detail = "File given is not a valid image"
 
 
 class FileTypeMismatchException(BaseAPIException):
     """The extension and content type of the provided file do not match."""
 
-    status_code = status.HTTP_422_UNPROCESSABLE_ENTITY
+    status_code = status.HTTP_422_UNPROCESSABLE_CONTENT
     response_detail = "File extension and content type do not match"
 
 
@@ -73,7 +73,7 @@ class UnsupportedFileExtensionException(BaseAPIException):
 class UploadLimitReachedError(BaseAPIException):
     """The limit for the maximum number of attachments or images for the provided `entity_id` has been reached."""
 
-    status_code = status.HTTP_422_UNPROCESSABLE_ENTITY
+    status_code = status.HTTP_422_UNPROCESSABLE_CONTENT
 
     def __init__(self, detail: str, entity_type: str):
         """

object_storage_api/repositories/attachment.py

@@ -61,7 +61,7 @@ def get(self, attachment_id: str, session: Optional[ClientSession] = None) -> Op
         :raises InvalidObjectIdError: If the supplied `attachment_id` is invalid.
         """
 
-        logger.info("Retrieving attachment with ID: %s from the database", attachment_id)
+        logger.info("Retrieving attachment with ID '%s' from the database", attachment_id)
 
         try:
             attachment_id = CustomObjectId(attachment_id)
@@ -73,7 +73,7 @@ def get(self, attachment_id: str, session: Optional[ClientSession] = None) -> Op
 
         if attachment:
             return AttachmentOut(**attachment)
-        raise MissingRecordError(detail=f"No attachment found with ID: {attachment_id}", entity_type="attachment")
+        raise MissingRecordError(detail=f"No attachment found with ID '{attachment_id}'", entity_type="attachment")
 
     def list(self, entity_id: Optional[str], session: Optional[ClientSession] = None) -> list[AttachmentOut]:
         """
@@ -128,7 +128,7 @@ def update(self, attachment_id: str, attachment: AttachmentIn, session: ClientSe
             exc.response_detail = "Attachment not found"
             raise exc
 
-        logger.info("Updating attachment metadata with ID: %s", attachment_id)
+        logger.info("Updating attachment metadata with ID '%s'", attachment_id)
         try:
             self._attachments_collection.update_one(
                 {"_id": attachment_id}, {"$set": attachment.model_dump(by_alias=True)}, session=session
@@ -149,7 +149,7 @@ def delete(self, attachment_id: str, session: Optional[ClientSession] = None) ->
         :raises MissingRecordError: If the supplied `attachment_id` is non-existent.
         :raises InvalidObjectIdError: If the supplied `attachment_id` is invalid.
         """
-        logger.info("Deleting attachment with ID: %s from the database", attachment_id)
+        logger.info("Deleting attachment with ID '%s' from the database", attachment_id)
         try:
             attachment_id = CustomObjectId(attachment_id)
         except InvalidObjectIdError as exc:
@@ -158,7 +158,7 @@ def delete(self, attachment_id: str, session: Optional[ClientSession] = None) ->
             raise exc
         response = self._attachments_collection.delete_one(filter={"_id": attachment_id}, session=session)
         if response.deleted_count == 0:
-            raise MissingRecordError(f"No attachment found with ID: {attachment_id}", entity_type="attachment")
+            raise MissingRecordError(f"No attachment found with ID '{attachment_id}'", entity_type="attachment")
 
     def delete_by_entity_id(self, entity_id: str, session: Optional[ClientSession] = None) -> None:
         """
@@ -167,7 +167,7 @@ def delete_by_entity_id(self, entity_id: str, session: Optional[ClientSession] =
         :param entity_id: The entity ID of the attachments to delete.
         :param session: PyMongo ClientSession to use for database operations.
         """
-        logger.info("Deleting attachments with entity ID: %s from the database", entity_id)
+        logger.info("Deleting attachments with entity ID '%s' from the database", entity_id)
         try:
             entity_id = CustomObjectId(entity_id)
             # Given it is deleting multiple, we are not raising an exception if no attachments were found to be deleted
@@ -184,7 +184,7 @@ def count_by_entity_id(self, entity_id: str, session: Optional[ClientSession] =
         :param entity_id: The entity ID to use to select which documents to count.
         :param session: PyMongo ClientSession to use for database operations.
         """
-        logger.info("Counting number of attachments with entity ID: %s in the database", str(entity_id))
+        logger.info("Counting number of attachments with entity ID '%s' in the database", str(entity_id))
         return self._attachments_collection.count_documents(
             filter={"entity_id": CustomObjectId(entity_id)}, session=session
         )