Merge branch 'master' into add-datagateway-and-panosc-modes-#256

.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))

datagateway_api/src/api_start_utils.py

@@ -27,6 +27,13 @@
 from datagateway_api.src.resources.non_entities.sessions_endpoints import (
     session_endpoints,
 )
+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,
@@ -105,7 +112,11 @@ def create_api_endpoints(flask_app, api, spec):
                 backend,
                 client_pool=icat_client_pool,
             )
-            api.add_resource(get_endpoint_resource, f"/{entity_name.lower()}")
+            api.add_resource(
+                get_endpoint_resource,
+                f"/{entity_name.lower()}",
+                endpoint=f"datagateway_get_{entity_name}",
+            )
             spec.path(resource=get_endpoint_resource, api=api)
 
             get_id_endpoint_resource = get_id_endpoint(
@@ -115,7 +126,9 @@ def create_api_endpoints(flask_app, api, spec):
                 client_pool=icat_client_pool,
             )
             api.add_resource(
-                get_id_endpoint_resource, f"/{entity_name.lower()}/<int:id_>",
+                get_id_endpoint_resource,
+                f"/{entity_name.lower()}/<int:id_>",
+                endpoint=f"datagateway_get_id_{entity_name}",
             )
             spec.path(resource=get_id_endpoint_resource, api=api)
 
@@ -126,7 +139,9 @@ def create_api_endpoints(flask_app, api, spec):
                 client_pool=icat_client_pool,
             )
             api.add_resource(
-                get_count_endpoint_resource, f"/{entity_name.lower()}/count",
+                get_count_endpoint_resource,
+                f"/{entity_name.lower()}/count",
+                endpoint=f"datagateway_count_{entity_name}",
             )
             spec.path(resource=get_count_endpoint_resource, api=api)
 
@@ -137,23 +152,29 @@ def create_api_endpoints(flask_app, api, spec):
                 client_pool=icat_client_pool,
             )
             api.add_resource(
-                get_find_one_endpoint_resource, f"/{entity_name.lower()}/findone",
+                get_find_one_endpoint_resource,
+                f"/{entity_name.lower()}/findone",
+                endpoint=f"datagateway_findone_{entity_name}",
             )
             spec.path(resource=get_find_one_endpoint_resource, api=api)
 
         # Session endpoint
         session_endpoint_resource = session_endpoints(
             backend, client_pool=icat_client_pool,
         )
-        api.add_resource(session_endpoint_resource, "/sessions")
+        api.add_resource(
+            session_endpoint_resource, "/sessions", endpoint="datagateway_sessions",
+        )
         spec.path(resource=session_endpoint_resource, api=api)
 
         # Table specific endpoints
         instrument_facility_cycle_resource = instrument_facility_cycles_endpoint(
             backend, client_pool=icat_client_pool,
         )
         api.add_resource(
-            instrument_facility_cycle_resource, "/instruments/<int:id_>/facilitycycles",
+            instrument_facility_cycle_resource,
+            "/instruments/<int:id_>/facilitycycles",
+            endpoint="datagateway_isis_instrument_facility_cycle",
         )
         spec.path(resource=instrument_facility_cycle_resource, api=api)
 
@@ -163,6 +184,7 @@ def create_api_endpoints(flask_app, api, spec):
         api.add_resource(
             count_instrument_facility_cycle_res,
             "/instruments/<int:id_>/facilitycycles/count",
+            endpoint="datagateway_isis_count_instrument_facility_cycle",
         )
         spec.path(resource=count_instrument_facility_cycle_res, api=api)
 
@@ -173,6 +195,7 @@ def create_api_endpoints(flask_app, api, spec):
             instrument_investigation_resource,
             "/instruments/<int:instrument_id>/facilitycycles/<int:cycle_id>"
             "/investigations",
+            endpoint="datagateway_isis_instrument_investigation",
         )
         spec.path(resource=instrument_investigation_resource, api=api)
 
@@ -183,6 +206,7 @@ def create_api_endpoints(flask_app, api, spec):
             count_instrument_investigation_res,
             "/instruments/<int:instrument_id>/facilitycycles/<int:cycle_id>"
             "/investigations/count",
+            endpoint="datagateway_isis_count_instrument_investigation",
         )
         spec.path(resource=count_instrument_investigation_res, api=api)
 
@@ -191,6 +215,56 @@ def create_api_endpoints(flask_app, api, spec):
         api.add_resource(ping_resource, "/ping")
         spec.path(resource=ping_resource, api=api)
 
+    # Search API endpoints
+    # TODO - make conditional respect new config style when implemented
+    if True:
+        # TODO - Use config value when new config style is implemented
+        search_api_extension = "search_api"
+        search_api_entity_endpoints = ["datasets", "documents", "instruments"]
+
+        for entity_name in search_api_entity_endpoints:
+            get_search_endpoint_resource = get_search_endpoint(entity_name)
+            api.add_resource(
+                get_search_endpoint_resource,
+                f"/{search_api_extension}/{entity_name}",
+                endpoint=f"search_api_get_{entity_name}",
+            )
+            spec.path(resource=get_endpoint_resource, api=api)
+
+            get_single_endpoint_resource = get_single_endpoint(entity_name)
+            api.add_resource(
+                get_single_endpoint_resource,
+                f"/{search_api_extension}/{entity_name}/<int:pid>",
+                endpoint=f"search_api_get_single_{entity_name}",
+            )
+            spec.path(resource=get_single_endpoint_resource, api=api)
+
+            get_number_count_endpoint_resource = get_number_count_endpoint(entity_name)
+            api.add_resource(
+                get_number_count_endpoint_resource,
+                f"/{search_api_extension}/{entity_name}/count",
+                endpoint=f"search_api_count_{entity_name}",
+            )
+            spec.path(resource=get_number_count_endpoint_resource, api=api)
+
+        get_files_endpoint_resource = get_files_endpoint("datasets")
+        api.add_resource(
+            get_files_endpoint_resource,
+            f"/{search_api_extension}/datasets/<int:pid>/files",
+            endpoint="search_api_get_dataset_files",
+        )
+        spec.path(resource=get_files_endpoint_resource, api=api)
+
+        get_number_count_files_endpoint_resource = get_number_count_files_endpoint(
+            "datasets",
+        )
+        api.add_resource(
+            get_number_count_files_endpoint_resource,
+            f"/{search_api_extension}/datasets/<int:pid>/files/count",
+            endpoint="search_api_count_dataset_files",
+        )
+        spec.path(resource=get_number_count_files_endpoint_resource, api=api)
+
 
 def openapi_config(spec):
     # Reorder paths (e.g. get, patch, post) so openapi.yaml only changes when there's a

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/resources/search_api_endpoints.py

@@ -1,9 +1,10 @@
 from flask_restful import Resource
 
 
-# TODO - Might need kwargs on get_endpoint(), get_id_endpoint(), get_count_endpoint(),
-# get_files_endpoint(), get_count_files_endpoint() for client handling?
-def get_endpoint(name):
+# TODO - Might need kwargs on get_search_endpoint(), get_single_endpoint(),
+# get_number_count_endpoint(), get_files_endpoint(), get_number_count_files_endpoint()
+# for client handling?
+def get_search_endpoint(name):
     """
     TODO - Add docstring
     """
@@ -30,7 +31,7 @@ def get(self):
     return Endpoint
 
 
-def get_id_endpoint(name):
+def get_single_endpoint(name):
     """
     TODO - Add docstring
     """
@@ -46,7 +47,7 @@ def get(self, pid):
     return EndpointWithID
 
 
-def get_count_endpoint(name):
+def get_number_count_endpoint(name):
     """
     TODO - Add docstring
     """
@@ -78,7 +79,7 @@ def get(self, pid):
     return FilesEndpoint
 
 
-def get_count_files_endpoint(name):
+def get_number_count_files_endpoint(name):
     """
     TODO - Add docstring
     """

datagateway_api/src/swagger/openapi.yaml

@@ -1659,6 +1659,8 @@ components:
           type: string
         name:
           type: string
+        pid:
+          type: string
         startDate:
           format: datetime
           type: string
@@ -11013,5 +11015,13 @@ paths:
       summary: Ping API connection method
       tags:
       - Ping
+  /search_api/datasets/{pid}: {}
+  /search_api/datasets/count: {}
+  /search_api/documents/{pid}: {}
+  /search_api/documents/count: {}
+  /search_api/instruments/{pid}: {}
+  /search_api/instruments/count: {}
+  /search_api/datasets/{pid}/files: {}
+  /search_api/datasets/{pid}/files/count: {}
 security:
 - session_id: []

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_endpoint_rules.py

@@ -58,6 +58,51 @@ def test_entity_endpoints(self, flask_test_app, endpoint_ending, expected_method
                 ["GET"],
                 id="count ISIS investigations",
             ),
+            pytest.param(
+                "/search_api/datasets", ["GET"], id="Search API search datasets",
+            ),
+            pytest.param(
+                "/search_api/documents", ["GET"], id="Search API search documents",
+            ),
+            pytest.param(
+                "/search_api/instruments", ["GET"], id="Search API search instruments",
+            ),
+            pytest.param(
+                "/search_api/datasets/<int:pid>",
+                ["GET"],
+                id="Search API get single dataset",
+            ),
+            pytest.param(
+                "/search_api/documents/<int:pid>",
+                ["GET"],
+                id="Search API get single document",
+            ),
+            pytest.param(
+                "/search_api/instruments/<int:pid>",
+                ["GET"],
+                id="Search API get single instrument",
+            ),
+            pytest.param(
+                "/search_api/datasets/count", ["GET"], id="Search API dataset count",
+            ),
+            pytest.param(
+                "/search_api/documents/count", ["GET"], id="Search API document count",
+            ),
+            pytest.param(
+                "/search_api/instruments/count",
+                ["GET"],
+                id="Search API instrument count",
+            ),
+            pytest.param(
+                "/search_api/datasets/<int:pid>/files",
+                ["GET"],
+                id="Search API get dataset files",
+            ),
+            pytest.param(
+                "/search_api/datasets/<int:pid>/files/count",
+                ["GET"],
+                id="Search API dataset files count",
+            ),
         ],
     )
     def test_non_entity_endpoints(

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)