Merge branch 'master' into feature/query-params-search-api-#259

ral-facilities · Nov 19, 2021 · cab9f3f · cab9f3f
2 parents 7b3d039 + fd53e88
commit cab9f3f
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Showing 87 changed files with 214 additions and 229 deletions.
diff --git a/.flake8 b/.flake8
@@ -10,7 +10,7 @@ per-file-ignores =
   test/*: S101
   util/icat_db_generator.py: S311
   datagateway_api/wsgi.py:E402,F401
-  datagateway_api/common/datagateway_api/database/models.py: N815,A003
-  datagateway_api/common/datagateway_api/icat/filters.py: C901
-  datagateway_api/common/search_api/models.py: B950
+  datagateway_api/src/datagateway_api/database/models.py: N815,A003
+  datagateway_api/src/datagateway_api/icat/filters.py: C901
+  datagateway_api/src/search_api/models.py: B950
 enable-extensions=G
diff --git a/.github/workflows/ci-build.yml b/.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

diff --git a/CHANGELOG.md b/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))

diff --git a/datagateway_api/src/api_start_utils.py b/datagateway_api/src/api_start_utils.py
@@ -7,40 +7,34 @@
 from flask_restful import Api
 from flask_swagger_ui import get_swaggerui_blueprint
 
-from datagateway_api.common.config import APIConfigOptions, config
-from datagateway_api.common.datagateway_api.backends import create_backend
-from datagateway_api.common.datagateway_api.database.helpers import db
-from datagateway_api.common.datagateway_api.icat.icat_client_pool import (
-    create_client_pool,
-)
-from datagateway_api.src.resources.datagateway_api.entities.entity_endpoint import (
+from datagateway_api.src.common.config import APIConfigOptions, config
+from datagateway_api.src.datagateway_api.backends import create_backend
+from datagateway_api.src.datagateway_api.database.helpers import db
+from datagateway_api.src.datagateway_api.icat.icat_client_pool import create_client_pool
+from datagateway_api.src.resources.entities.entity_endpoint import (
     get_count_endpoint,
     get_endpoint,
     get_find_one_endpoint,
     get_id_endpoint,
 )
-from datagateway_api.src.resources.datagateway_api.entities.entity_endpoint_dict import (  # noqa: B950
-    endpoints,
-)
-from datagateway_api.src.resources.datagateway_api.non_entities.ping_endpoint import (
-    ping_endpoint,
-)
-from datagateway_api.src.resources.datagateway_api.non_entities.sessions_endpoints import (  # noqa: B950
+from datagateway_api.src.resources.entities.entity_endpoint_dict import endpoints
+from datagateway_api.src.resources.non_entities.ping_endpoint import ping_endpoint
+from datagateway_api.src.resources.non_entities.sessions_endpoints import (
     session_endpoints,
 )
-from datagateway_api.src.resources.datagateway_api.table_endpoints.table_endpoints import (  # noqa: B950
-    count_instrument_facility_cycles_endpoint,
-    count_instrument_investigation_endpoint,
-    instrument_facility_cycles_endpoint,
-    instrument_investigation_endpoint,
-)
-from datagateway_api.src.resources.search_api.search_api_endpoints import (
+from datagateway_api.src.resources.search_api_endpoints import (
     get_files_endpoint,
     get_number_count_endpoint,
     get_number_count_files_endpoint,
     get_search_endpoint,
     get_single_endpoint,
 )
+from datagateway_api.src.resources.table_endpoints.table_endpoints import (
+    count_instrument_facility_cycles_endpoint,
+    count_instrument_investigation_endpoint,
+    instrument_facility_cycles_endpoint,
+    instrument_investigation_endpoint,
+)
 from datagateway_api.src.swagger.apispec_flask_restful import RestfulPlugin
 from datagateway_api.src.swagger.initialise_spec import initialise_spec
 

diff --git a/datagateway_api/common/__init__.py → datagateway_api/src/common/__init__.py b/datagateway_api/common/__init__.py → datagateway_api/src/common/__init__.py
diff --git a/...y_api/common/base_query_filter_factory.py → ...i/src/common/base_query_filter_factory.py b/...y_api/common/base_query_filter_factory.py → ...i/src/common/base_query_filter_factory.py
diff --git a/datagateway_api/common/config.py → datagateway_api/src/common/config.py b/datagateway_api/common/config.py → datagateway_api/src/common/config.py
@@ -35,7 +35,7 @@ class APIConfigOptions(Enum):
 
 
 class Config(object):
-    def __init__(self, path=Path(__file__).parent.parent / "config.json"):
+    def __init__(self, path=Path(__file__).parent.parent.parent / "config.json"):
         self.path = path
         with open(self.path) as target:
             self._config = json.load(target)

diff --git a/datagateway_api/common/constants.py → datagateway_api/src/common/constants.py b/datagateway_api/common/constants.py → datagateway_api/src/common/constants.py
diff --git a/datagateway_api/common/date_handler.py → datagateway_api/src/common/date_handler.py b/datagateway_api/common/date_handler.py → datagateway_api/src/common/date_handler.py
@@ -1,7 +1,7 @@
 from dateutil.parser import parse
 from icat import helper
 
-from datagateway_api.common.exceptions import BadRequestError
+from datagateway_api.src.common.exceptions import BadRequestError
 
 
 class DateHandler:

diff --git a/datagateway_api/common/exceptions.py → datagateway_api/src/common/exceptions.py b/datagateway_api/common/exceptions.py → datagateway_api/src/common/exceptions.py
diff --git a/datagateway_api/common/filters.py → datagateway_api/src/common/filters.py b/datagateway_api/common/filters.py → datagateway_api/src/common/filters.py
@@ -1,7 +1,7 @@
 from abc import ABC, abstractmethod
 import logging
 
-from datagateway_api.common.exceptions import BadRequestError, FilterError
+from datagateway_api.src.common.exceptions import BadRequestError, FilterError
 
 log = logging.getLogger()
 

diff --git a/datagateway_api/common/helpers.py → datagateway_api/src/common/helpers.py b/datagateway_api/common/helpers.py → datagateway_api/src/common/helpers.py
@@ -8,21 +8,16 @@
 from flask_restful import reqparse
 from sqlalchemy.exc import IntegrityError
 
-from datagateway_api.common.datagateway_api.database import models
-from datagateway_api.common.datagateway_api.query_filter_factory import (
-    DataGatewayAPIQueryFilterFactory,
-)
-from datagateway_api.common.date_handler import DateHandler
-from datagateway_api.common.exceptions import (
+from datagateway_api.src.common.date_handler import DateHandler
+from datagateway_api.src.common.exceptions import (
     ApiError,
     AuthenticationError,
     BadRequestError,
     FilterError,
     MissingCredentialsError,
 )
-from datagateway_api.src.resources.datagateway_api.entities.entity_endpoint_dict import (  # noqa: B950
-    endpoints,
-)
+from datagateway_api.src.datagateway_api.database import models
+from datagateway_api.src.resources.entities.entity_endpoint_dict import endpoints
 
 log = logging.getLogger()
 
@@ -103,11 +98,11 @@ def get_filters_from_query_string(api_type):
     :return: The list of filters
     """
     if api_type == "search_api":
-        from datagateway_api.common.search_api.query_filter_factory import (
+        from datagateway_api.src.search_api.query_filter_factory import (
             SearchAPIQueryFilterFactory as QueryFilterFactory,
         )
     elif api_type == "datagateway_api":
-        from datagateway_api.common.datagateway_api.query_filter_factory import (
+        from datagateway_api.src.datagateway_api.query_filter_factory import (
             DataGatewayAPIQueryFilterFactory as QueryFilterFactory,
         )
     else:

diff --git a/datagateway_api/common/logger_setup.py → datagateway_api/src/common/logger_setup.py b/datagateway_api/common/logger_setup.py → datagateway_api/src/common/logger_setup.py
@@ -1,7 +1,7 @@
 import logging.config
 from pathlib import Path
 
-from datagateway_api.common.config import APIConfigOptions, config
+from datagateway_api.src.common.config import APIConfigOptions, config
 
 LOG_FILE_NAME = Path(config.get_config_value(APIConfigOptions.LOG_LOCATION))
 logger_config = {

diff --git a/...ay_api/common/datagateway_api/__init__.py → ...teway_api/src/datagateway_api/__init__.py b/...ay_api/common/datagateway_api/__init__.py → ...teway_api/src/datagateway_api/__init__.py
diff --git a/...way_api/common/datagateway_api/backend.py → ...ateway_api/src/datagateway_api/backend.py b/...way_api/common/datagateway_api/backend.py → ...ateway_api/src/datagateway_api/backend.py
diff --git a/...ay_api/common/datagateway_api/backends.py → ...teway_api/src/datagateway_api/backends.py b/...ay_api/common/datagateway_api/backends.py → ...teway_api/src/datagateway_api/backends.py
@@ -1,7 +1,7 @@
 import sys
 
-from datagateway_api.common.datagateway_api.database.backend import DatabaseBackend
-from datagateway_api.common.datagateway_api.icat.backend import PythonICATBackend
+from datagateway_api.src.datagateway_api.database.backend import DatabaseBackend
+from datagateway_api.src.datagateway_api.icat.backend import PythonICATBackend
 
 
 def create_backend(backend_type):

diff --git a/...mmon/datagateway_api/database/__init__.py → .../src/datagateway_api/database/__init__.py b/...mmon/datagateway_api/database/__init__.py → .../src/datagateway_api/database/__init__.py
diff --git a/...ommon/datagateway_api/database/backend.py → ...i/src/datagateway_api/database/backend.py b/...ommon/datagateway_api/database/backend.py → ...i/src/datagateway_api/database/backend.py
@@ -5,9 +5,14 @@
 from sqlalchemy import inspect
 from sqlalchemy.exc import SQLAlchemyError
 
-from datagateway_api.common.constants import Constants
-from datagateway_api.common.datagateway_api.backend import Backend
-from datagateway_api.common.datagateway_api.database.helpers import (
+from datagateway_api.src.common.constants import Constants
+from datagateway_api.src.common.exceptions import AuthenticationError, DatabaseError
+from datagateway_api.src.common.helpers import (
+    get_entity_object_from_name,
+    queries_records,
+)
+from datagateway_api.src.datagateway_api.backend import Backend
+from datagateway_api.src.datagateway_api.database.helpers import (
     create_rows_from_json,
     db,
     delete_row_by_id,
@@ -24,9 +29,7 @@
     requires_session_id,
     update_row_from_id,
 )
-from datagateway_api.common.datagateway_api.database.models import SESSION
-from datagateway_api.common.exceptions import AuthenticationError, DatabaseError
-from datagateway_api.common.helpers import get_entity_object_from_name, queries_records
+from datagateway_api.src.datagateway_api.database.models import SESSION
 
 
 log = logging.getLogger()

diff --git a/...ommon/datagateway_api/database/filters.py → ...i/src/datagateway_api/database/filters.py b/...ommon/datagateway_api/database/filters.py → ...i/src/datagateway_api/database/filters.py
@@ -2,16 +2,16 @@
 
 from sqlalchemy import asc, desc
 
-from datagateway_api.common.exceptions import FilterError, MultipleIncludeError
-from datagateway_api.common.filters import (
+from datagateway_api.src.common.exceptions import FilterError, MultipleIncludeError
+from datagateway_api.src.common.filters import (
     DistinctFieldFilter,
     IncludeFilter,
     LimitFilter,
     OrderFilter,
     SkipFilter,
     WhereFilter,
 )
-from datagateway_api.common.helpers import get_entity_object_from_name
+from datagateway_api.src.common.helpers import get_entity_object_from_name
 
 
 log = logging.getLogger()

diff --git a/...ommon/datagateway_api/database/helpers.py → ...i/src/datagateway_api/database/helpers.py b/...ommon/datagateway_api/database/helpers.py → ...i/src/datagateway_api/database/helpers.py
@@ -6,28 +6,26 @@
 from flask_sqlalchemy import SQLAlchemy
 from sqlalchemy.orm import aliased
 
-from datagateway_api.common.datagateway_api.database.filters import (
+from datagateway_api.src.common.exceptions import (
+    AuthenticationError,
+    BadRequestError,
+    MissingRecordError,
+)
+from datagateway_api.src.common.helpers import map_distinct_attributes_to_results
+from datagateway_api.src.datagateway_api.database.filters import (
     DatabaseDistinctFieldFilter,
     DatabaseIncludeFilter as IncludeFilter,
     DatabaseWhereFilter as WhereFilter,
 )
-from datagateway_api.common.datagateway_api.database.models import (
+from datagateway_api.src.datagateway_api.database.models import (
     FACILITY,
     FACILITYCYCLE,
     INSTRUMENT,
     INVESTIGATION,
     INVESTIGATIONINSTRUMENT,
     SESSION,
 )
-from datagateway_api.common.datagateway_api.filter_order_handler import (
-    FilterOrderHandler,
-)
-from datagateway_api.common.exceptions import (
-    AuthenticationError,
-    BadRequestError,
-    MissingRecordError,
-)
-from datagateway_api.common.helpers import map_distinct_attributes_to_results
+from datagateway_api.src.datagateway_api.filter_order_handler import FilterOrderHandler
 
 
 log = logging.getLogger()

diff --git a/...common/datagateway_api/database/models.py → ...pi/src/datagateway_api/database/models.py b/...common/datagateway_api/database/models.py → ...pi/src/datagateway_api/database/models.py
@@ -21,8 +21,8 @@
 from sqlalchemy.orm import relationship
 from sqlalchemy.orm.collections import InstrumentedList
 
-from datagateway_api.common.date_handler import DateHandler
-from datagateway_api.common.exceptions import DatabaseError, FilterError
+from datagateway_api.src.common.date_handler import DateHandler
+from datagateway_api.src.common.exceptions import DatabaseError, FilterError
 
 Base = declarative_base()
 
@@ -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)

diff --git a/...n/datagateway_api/filter_order_handler.py → ...c/datagateway_api/filter_order_handler.py b/...n/datagateway_api/filter_order_handler.py → ...c/datagateway_api/filter_order_handler.py
@@ -1,6 +1,6 @@
 import logging
 
-from datagateway_api.common.datagateway_api.icat.filters import (
+from datagateway_api.src.datagateway_api.icat.filters import (
     PythonICATLimitFilter,
     PythonICATOrderFilter,
     PythonICATSkipFilter,

diff --git a/...i/common/datagateway_api/icat/__init__.py → ..._api/src/datagateway_api/icat/__init__.py b/...i/common/datagateway_api/icat/__init__.py → ..._api/src/datagateway_api/icat/__init__.py
diff --git a/...pi/common/datagateway_api/icat/backend.py → ...y_api/src/datagateway_api/icat/backend.py b/...pi/common/datagateway_api/icat/backend.py → ...y_api/src/datagateway_api/icat/backend.py
@@ -2,9 +2,11 @@
 
 from icat.exception import ICATError, ICATSessionError
 
-from datagateway_api.common.constants import Constants
-from datagateway_api.common.datagateway_api.backend import Backend
-from datagateway_api.common.datagateway_api.icat.helpers import (
+from datagateway_api.src.common.constants import Constants
+from datagateway_api.src.common.exceptions import AuthenticationError, PythonICATError
+from datagateway_api.src.common.helpers import queries_records
+from datagateway_api.src.datagateway_api.backend import Backend
+from datagateway_api.src.datagateway_api.icat.helpers import (
     create_entities,
     delete_entity_by_id,
     get_cached_client,
@@ -23,8 +25,6 @@
     update_entities,
     update_entity_by_id,
 )
-from datagateway_api.common.exceptions import AuthenticationError, PythonICATError
-from datagateway_api.common.helpers import queries_records
 
 
 log = logging.getLogger()

diff --git a/...pi/common/datagateway_api/icat/filters.py → ...y_api/src/datagateway_api/icat/filters.py b/...pi/common/datagateway_api/icat/filters.py → ...y_api/src/datagateway_api/icat/filters.py
@@ -1,8 +1,8 @@
 import logging
 
-from datagateway_api.common.config import config
-from datagateway_api.common.exceptions import FilterError
-from datagateway_api.common.filters import (
+from datagateway_api.src.common.config import config
+from datagateway_api.src.common.exceptions import FilterError
+from datagateway_api.src.common.filters import (
     DistinctFieldFilter,
     IncludeFilter,
     LimitFilter,

diff --git a/...pi/common/datagateway_api/icat/helpers.py → ...y_api/src/datagateway_api/icat/helpers.py b/...pi/common/datagateway_api/icat/helpers.py → ...y_api/src/datagateway_api/icat/helpers.py
@@ -14,22 +14,20 @@
     ICATValidationError,
 )
 
-from datagateway_api.common.datagateway_api.filter_order_handler import (
-    FilterOrderHandler,
-)
-from datagateway_api.common.datagateway_api.icat.filters import (
-    PythonICATLimitFilter,
-    PythonICATWhereFilter,
-)
-from datagateway_api.common.datagateway_api.icat.lru_cache import ExtendedLRUCache
-from datagateway_api.common.datagateway_api.icat.query import ICATQuery
-from datagateway_api.common.date_handler import DateHandler
-from datagateway_api.common.exceptions import (
+from datagateway_api.src.common.date_handler import DateHandler
+from datagateway_api.src.common.exceptions import (
     AuthenticationError,
     BadRequestError,
     MissingRecordError,
     PythonICATError,
 )
+from datagateway_api.src.datagateway_api.filter_order_handler import FilterOrderHandler
+from datagateway_api.src.datagateway_api.icat.filters import (
+    PythonICATLimitFilter,
+    PythonICATWhereFilter,
+)
+from datagateway_api.src.datagateway_api.icat.lru_cache import ExtendedLRUCache
+from datagateway_api.src.datagateway_api.icat.query import ICATQuery
 
 log = logging.getLogger()