Merge branch 'main' into feature/use-yaml-config#372

CHANGELOG.md

@@ -2,6 +2,18 @@
 
 <!--next-version-placeholder-->
 
+## v5.3.0 (2022-11-16)
+### Feature
+* Add warning for no api ([`3c91635`](https://github.com/ral-facilities/datagateway-api/commit/3c91635bc0c3465d456a4a85c8d6c8793df408c2))
+
+## v5.2.0 (2022-11-03)
+### Feature
+* Add warning that tests only work with ICAT 5 ([`d8825fd`](https://github.com/ral-facilities/datagateway-api/commit/d8825fd71740e2b2d9b387dca175110cee1f9915))
+* Changes to tests so they pass with icat 5 ([`73f3c77`](https://github.com/ral-facilities/datagateway-api/commit/73f3c777f8d3841cf09537140922a9bbdd8dad7c))
+
+### Documentation
+* Update the poetry installation documentation ([`68d4267`](https://github.com/ral-facilities/datagateway-api/commit/68d426722862613358b0b136188d2b61accdc56f))
+
 ## v5.1.1 (2022-09-22)
 ### Fix
 * Update to latest dependencies ([`11a0eeb`](https://github.com/ral-facilities/datagateway-api/commit/11a0eeb3cbc4b5db2a0fa8dcd825dbeceb6ac111))

README.md

@@ -103,15 +103,26 @@ To maintain records of the API's dependencies,
 command:
 
 ```bash
-curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python -
+curl -sSL https://install.python-poetry.org | python3 -
 ```
 
-The installation requires `~/.poetry/env` to be refreshed for changes to be applied.
-Open a new terminal or execute the following command to ensure the installation is
-completed smoothly:
+The installation requires the following to be added to your `~/.bashrc` file so the installation folder is on your path.
+```bash
+export PATH="~/.local/bin:$PATH"
+```
+Then run `source ~/.bashrc` or open a new terminal and check poetry works by running `poetry --version`
 
+If you encounter this error when installing poetry:
+```
+ERROR: No matching distribution found for poetry==1.2.0
+```
+You can try running the installer with python 3.8 with the command below:
 ```bash
-source ~/.poetry/env
+curl -sSL https://install.python-poetry.org | python3.8 -
+```
+Or you can specify the version you want to install from the listed versions with the command below:
+```bash
+curl -sSL https://install.python-poetry.org | python3 - --version 1.2.0
 ```
 
 Before installing the API's dependencies, check the version of `setuptools`:
@@ -259,7 +270,7 @@ python3.8 --version
 pyenv local 3.6.8 3.7.7 3.8.2
 
 # Install Poetry
-curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python -
+curl -sSL https://install.python-poetry.org | python3 -
 
 # Apply changes made to file when installing Poetry
 source ~/.poetry/env
@@ -427,9 +438,11 @@ but covering only the most used aspects of the API).
 
 The configuration file (`config.yaml`) contains two options that will be used during the
 testing of the API. Set `test_user_credentials` and `test_mechanism` appropriately for
+
 your test environment, using `config.yaml.example` as a reference. The tests require a
 connection to an instance of ICAT, so set the rest of the config as needed.
 
+
 By default, this will execute the repo's tests in
 Python 3.6, 3.7, 3.8, 3.9 and 3.10. For most cases, running the tests in a single Python
 version will be sufficient:

datagateway_api/src/common/config.py

@@ -189,6 +189,13 @@ def load(cls, path=Path(__file__).parent.parent.parent / "config.yaml"):
         try:
             with open(path, encoding="utf-8") as target:
                 data = yaml.safe_load(target)
+
+                if "datagateway_api" not in data and "search_api" not in data:
+                    log.warning(
+                        "   WARNING: There is no API specified in the "
+                        "configuration file",
+                    )
+
                 return cls(**data)
         except (IOError, ValidationError) as error:
             sys.exit(f"An error occurred while trying to load the config data: {error}")

datagateway_api/src/datagateway_api/database/models.py

@@ -656,6 +656,8 @@ class INVESTIGATION(Base, EntityHelper, metaclass=EntityMeta):
     typeID = Column(
         "TYPE_ID", ForeignKey("INVESTIGATIONTYPE.ID"), nullable=False, index=True,
     )
+    fileSize = Column("FILESIZE", BigInteger)
+    fileCount = Column("FILECOUNT", BigInteger)
 
     FACILITY = relationship(
         "FACILITY",

noxfile.py

@@ -72,7 +72,16 @@ def safety(session):
             f"--output={requirements.name}",
             external=True,
         )
-        session.run("safety", "check", f"--file={requirements.name}", "--full-report")
+        # Ignore 50916 as the latest version of pydantic does not support
+        # python 3.6 which is still used in production
+        session.run(
+            "safety",
+            "check",
+            f"--file={requirements.name}",
+            "--full-report",
+            "--ignore",
+            "50916",
+        )
 
         try:
             # Due to delete=False, the file must be deleted manually

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "datagateway-api"
-version = "5.1.1"
+version = "5.3.0"
 description = "ICAT API to interface with the DataGateway"
 license = "Apache-2.0"
 readme = "README.md"
@@ -34,18 +34,15 @@ Flask-SQLAlchemy = "^2.4.4"
 requests = "^2.25.1"
 python-dateutil = "^2.8.1"
 pydantic = "^1.8.2"
-dparse = "0.5.2"
 
 [tool.poetry.dev-dependencies]
 pip-tools = "5.3.1"
 Faker = "8.5.1"
 black = "19.10b0"
 flake8 = "^3.8.4"
 flake8-bandit = "^2.1.2"
-flake8-black = "^0.2.1"
 flake8-bugbear = "^20.1.4"
 flake8-import-order = "^0.18.1"
-safety = "^1.9.0"
 flake8-builtins = "^1.5.3"
 flake8-broken-line = "^0.3.0"
 flake8-commas = "^2.0.0"
@@ -58,6 +55,8 @@ pytest-cov = "^2.10.1"
 pytest-icdiff = "^0.5"
 python-semantic-release = "^7.19.2"
 coverage-conditional-plugin = "^0.5.0"
+safety = "^2.2.0"
+flake8-black = "0.2.4"
 
 [tool.poetry.scripts]
 

test/datagateway_api/db/conftest.py

@@ -45,6 +45,8 @@ def create_investigation_db_data(num_entities=1):
         investigation.visitId = str(uuid.uuid1())
         investigation.facilityID = 1
         investigation.typeID = 1
+        investigation.fileSize = 1073741824
+        investigation.fileCount = 3
 
         set_meta_attributes(investigation)
 

test/datagateway_api/db/test_entity_helper.py

@@ -145,6 +145,8 @@ def test_valid_to_dict(self, datafile_entity):
                             "id": None,
                             "createId": None,
                             "createTime": None,
+                            "fileCount": None,
+                            "fileSize": None,
                             "doi": None,
                             "endDate": None,
                             "modId": None,