Merge branch 'master' into respect-config-for-search-api-endpoints-#283

.github/workflows/ci-build.yml

@@ -97,7 +97,7 @@ jobs:
     - name: Setup Python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.9'
+        python-version: '3.9.7'
         architecture: x64
     - name: Checkout DataGateway API
       uses: actions/checkout@v2
@@ -117,7 +117,7 @@ jobs:
     - name: Setup Python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.9'
+        python-version: '3.9.7'
         architecture: x64
     - name: Checkout DataGateway API
       uses: actions/checkout@v2
@@ -137,7 +137,7 @@ jobs:
     - name: Setup Python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.9'
+        python-version: '3.9.7'
         architecture: x64
     - name: Checkout DataGateway API
       uses: actions/checkout@v2
@@ -167,7 +167,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v2
         with:
-          python-version: '3.9'
+          python-version: '3.9.7'
           architecture: x64
 
       # ICAT Ansible clone and install dependencies

CHANGELOG.md

@@ -2,6 +2,21 @@
 
 <!--next-version-placeholder-->
 
+## v1.1.0 (2021-11-19)
+### Feature
+* Add unimplemented endpoint definitions for search API #257 ([`d0e52d9`](https://github.com/ral-facilities/datagateway-api/commit/d0e52d96dd3b94ce54dcc9b81969e777a196922a))
+
+### Documentation
+* Rebuild openapi docs #257 ([`de15357`](https://github.com/ral-facilities/datagateway-api/commit/de1535772db64916f75e16d79be3f3fdf10fc47c))
+
+## v1.0.1 (2021-11-15)
+### Fix
+* Add PID field for study in DB backend #287 ([`18379be`](https://github.com/ral-facilities/datagateway-api/commit/18379becafd23ff2957e556de2bd3fc210a71f5b))
+* Add generation of study.pid #287 ([`f6a8ebc`](https://github.com/ral-facilities/datagateway-api/commit/f6a8ebc6c775ba3f5252d5af5cedc4e1e0e79a40))
+
+### Documentation
+* Add study PID to swagger docs #287 ([`89a9e27`](https://github.com/ral-facilities/datagateway-api/commit/89a9e27b72dfe1d474d49a721f128a643ef2ae36))
+
 ## v1.0.0 (2021-11-03)
 ### Breaking
 * As the API will be approaching production use soon, this seems like a good opportunity to bump the version to 1.0.0. This also serves as a good test that the introduction of automatic versioning actually works  ([`ccf6d29`](https://github.com/ral-facilities/datagateway-api/commit/ccf6d2974216f8979a03e3e223f7c9e84ced05cb))

README.md

@@ -314,10 +314,7 @@ fix: fix bug found with count endpoints #issue-number
 feat: add endpoints for search API #issue-number
 
 # Commit which introduces a breaking change for users
-BREAKING CHANGE: change format of `config.json`, the previous version is no longer supported #issue-number
-
-# You can also use `BREAKING CHANGE:` in the additional information if the commit also adds a new feature, like so:
-feat: my new feature #issue-number
+<commit-type>: change format of `config.json`, the previous version is no longer supported #issue-number
 
 BREAKING CHANGE: this feature means X functionality has been removed
 ```

datagateway_api/src/common/config.py

@@ -17,6 +17,24 @@
 log = logging.getLogger()
 
 
+def validate_extension(extension):
+    """
+    Checks that the API extension starts and does not end with a '/'. An error is
+    raised, at which point the application exits, if the extension does not meet
+    these validation rules.
+
+    :param extension: The extension for the API
+    """
+    extension = extension.strip()
+
+    if not extension.startswith("/"):
+        raise ValueError("must start with '/'")
+    if extension.endswith("/"):
+        raise ValueError("must not end with '/'")
+
+    return extension
+
+
 class DataGatewayAPI(BaseModel):
     """
     Configuration model class that implements pydantic's BaseModel class to allow for
@@ -34,16 +52,18 @@ class DataGatewayAPI(BaseModel):
     icat_check_cert: Optional[StrictBool]
     icat_url: Optional[StrictStr]
 
+    _validate_extension = validator("extension", allow_reuse=True)(validate_extension)
+
     @validator("db_url", always=True)
     def require_db_config_value(cls, value, values):  # noqa: B902, N805
         """
         By default the `db_url` config field is optional so that it does not have to be
         present in the config file if `backend` is set to `python_icat`. However, if the
         `backend` is set to `db`, this validator esentially makes the `db_url` config
-        field mandatory. This means that if the an error is raised, at which point the
+        field mandatory. This means that an error is raised, at which point the
         application exits, if a `db_url` config value is not present in the config file.
 
-        :param cls: :class:`APIConfig` pointer
+        :param cls: :class:`DataGatewayAPI` pointer
         :param value: The value of the given config field
         :param values: The config field values loaded before the given config field
         """
@@ -62,13 +82,13 @@ def require_db_config_value(cls, value, values):  # noqa: B902, N805
     def require_icat_config_value(cls, value, values):  # noqa: B902, N805
         """
         By default the above config fields that are passed to the `@validator` decorator
-        are optional so that they not have to be present in the config file if `backend`
-        is set to `db`. However, if the `backend` is set to `python_icat`, this
-        validator esentially makes these config fields mandatory. This means that an
-        error is raised, at which point the application exits, if any of these config
+        are optional so that they do not have to be present in the config file if
+        `backend` is set to `db`. However, if the `backend` is set to `python_icat`,
+        this validator esentially makes these config fields mandatory. This means that
+        an error is raised, at which point the application exits, if any of these config
         values are not present in the config file.
 
-        :param cls: :class:`APIConfig` pointer
+        :param cls: :class:`DataGatewayAPI` pointer
         :param value: The value of the given config field
         :param values: The config field values loaded before the given config field
         """
@@ -112,6 +132,8 @@ class SearchAPI(BaseModel):
     icat_check_cert: StrictBool
     icat_url: StrictStr
 
+    _validate_extension = validator("extension", allow_reuse=True)(validate_extension)
+
 
 class TestUserCredentials(BaseModel):
     username: StrictStr
@@ -158,6 +180,7 @@ def load(cls, path=Path(__file__).parent.parent.parent / "config.json"):
         model. Exits the application if it fails to locate the JSON config file or
         the APIConfig model validation fails.
 
+        :param cls: :class:`APIConfig` pointer
         :param path: path to the configuration file
         :return: APIConfig model object that contains the config data
         """
@@ -168,5 +191,28 @@ def load(cls, path=Path(__file__).parent.parent.parent / "config.json"):
         except (IOError, ValidationError) as error:
             sys.exit(f"An error occurred while trying to load the config data: {error}")
 
+    @validator("search_api")
+    def validate_api_extensions(cls, value, values):  # noqa: B902, N805
+        """
+        Checks that the DataGateway API and Search API extensions are not the same. An
+        error is raised, at which point the application exits, if the extensions are the
+        same.
+
+        :param cls: :class:`APIConfig` pointer
+        :param value: The value of the given config field
+        :param values: The config field values loaded before the given config field
+        """
+        if (
+            "datagateway_api" in values
+            and values["datagateway_api"] is not None
+            and value is not None
+            and values["datagateway_api"].extension == value.extension
+        ):
+            raise ValueError(
+                "extension cannot be the same as datagateway_api extension",
+            )
+
+        return value
+
 
 config = APIConfig.load()

datagateway_api/src/datagateway_api/database/models.py

@@ -1229,6 +1229,7 @@ class STUDY(Base, EntityHelper, metaclass=EntityMeta):
     modId = Column("MOD_ID", String(255), nullable=False)
     modTime = Column("MOD_TIME", DateTime, nullable=False)
     name = Column("NAME", String(255), nullable=False)
+    pid = Column("PID", String(255))
     startDate = Column("STARTDATE", DateTime)
     status = Column("STATUS", Integer)
     userID = Column("USER_ID", ForeignKey("USER_.ID"), index=True)

datagateway_api/src/swagger/openapi.yaml

@@ -1659,6 +1659,8 @@ components:
           type: string
         name:
           type: string
+        pid:
+          type: string
         startDate:
           format: datetime
           type: string

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "datagateway-api"
-version = "1.0.0"
+version = "1.1.0"
 description = "ICAT API to interface with the DataGateway"
 license = "Apache-2.0"
 readme = "README.md"

test/test_config.py

@@ -77,6 +77,28 @@ def test_load_with_datagateway_api_icat_backend_and_missing_icat_config_data(
             with pytest.raises(SystemExit):
                 APIConfig.load("test/path")
 
+    def test_load_with_invalid_api_extension_does_not_start_with_slash(
+        self, test_config_data,
+    ):
+        test_config_data["datagateway_api"]["extension"] = "datagateway-api"
+        with patch("builtins.open", mock_open(read_data=json.dumps(test_config_data))):
+            with pytest.raises(SystemExit):
+                APIConfig.load("test/path")
+
+    def test_load_with_invalid_api_extension_ends_with_slash(
+        self, test_config_data,
+    ):
+        test_config_data["search_api"]["extension"] = "/search-api/"
+        with patch("builtins.open", mock_open(read_data=json.dumps(test_config_data))):
+            with pytest.raises(SystemExit):
+                APIConfig.load("test/path")
+
+    def test_load_with_same_api_extensions(self, test_config_data):
+        test_config_data["search_api"]["extension"] = "/datagateway-api"
+        with patch("builtins.open", mock_open(read_data=json.dumps(test_config_data))):
+            with pytest.raises(SystemExit):
+                APIConfig.load("test/path")
+
     def test_set_backend_type(self, test_config):
         test_config.datagateway_api.set_backend_type("backend_name_changed")
 

test/test_query_filter.py

@@ -1,6 +1,5 @@
 import pytest
 
-
 import datagateway_api.src.common.config as config
 from datagateway_api.src.common.exceptions import ApiError
 from datagateway_api.src.common.filters import QueryFilter

util/icat_db_generator.py

@@ -420,6 +420,8 @@ def generate_user_groups(i):
 class StudyGenerator(Generator):
     tier = 3
     amount = UserGenerator.amount
+    pid_faker = Faker()
+    pid_faker.seed_instance(SEED)
 
     def generate(self):
         for i in range(1, self.amount):
@@ -431,6 +433,7 @@ def generate_studies(i):
         apply_common_attributes(study, i)
         study.startDate = get_start_date(i)
         study.status = faker.random_int(0, 1)
+        study.pid = StudyGenerator.pid_faker.isbn10(separator="-")
         study.userID = i
         post_entity(study)