Merge pull request #27 from ral-facilities/15_generate_swagger

Generation of openapi.yaml

common/config.py

@@ -27,5 +27,10 @@ def is_debug_mode(self):
         except:
             sys.exit("Missing config value, debug_mode")
 
+    def is_generate_swagger(self):
+        try:
+            return self.config["generate_swagger"]
+        except:
+            sys.exit("Missing config value, generate_swagger")
 
 config = Config()

config.json

@@ -1,7 +1,8 @@
 {
   "DB_URL": "mysql+pymysql://root:rootpw@localhost:13306/icatdb",
   "log_level": "WARN",
-  "debug_mode": false
+  "debug_mode": false,
+  "generate_swagger": false
 }
 
 

config.json.example

@@ -1,7 +1,8 @@
 {
   "DB_URL": "mysql+pymysql://root:rootpw@localhost:13306/icatdb",
   "log_level": "WARN",
-  "debug_mode": false
+  "debug_mode": false,
+  "generate_swagger": false
 }
 
 

src/main.py

@@ -3,7 +3,6 @@
 
 from common.config import config
 from common.logger_setup import setup_logger
-from src.resources.entities.dataset_type_endpoints import *
 from src.resources.entities.applications_endpoints import *
 from src.resources.entities.datacollection_datafiles_endpoints import *
 from src.resources.entities.datacollection_datasets_endpoints import *
@@ -12,6 +11,7 @@
 from src.resources.entities.datafile_formats_endpoints import *
 from src.resources.entities.datafile_parameters_endpoints import *
 from src.resources.entities.datafiles_endpoints import *
+from src.resources.entities.dataset_type_endpoints import *
 from src.resources.entities.datasets_endpoints import *
 from src.resources.entities.facilities_endpoints import *
 from src.resources.entities.facility_cycles_endpoints import *
@@ -35,18 +35,19 @@
 from src.resources.entities.sample_parameters_endpoints import *
 from src.resources.entities.sample_types_endpoints import *
 from src.resources.entities.samples_endpoints import *
-from src.resources.non_entities.sessions_endpoints import *
 from src.resources.entities.shifts_endpoints import *
 from src.resources.entities.studies_endpoints import *
 from src.resources.entities.study_investigations_endpoints import *
 from src.resources.entities.user_groups_endpoints import *
 from src.resources.entities.users_endpoints import *
+from src.resources.non_entities.sessions_endpoints import *
+from src.swagger.swagger_generator import swagger_gen
 
+swagger_gen.write_swagger_spec()
 
 app = Flask(__name__)
 api = Api(app)
 
-
 setup_logger()
 
 api.add_resource(Applications, "/applications")
@@ -69,7 +70,7 @@
 api.add_resource(DataCollectionParametersWithID, "/datacollectionparameters/<string:id>")
 api.add_resource(DataCollectionParametersCount, "/datacollectionparameters/count")
 api.add_resource(DataCollectionParametersFindOne, "/datacollectionparameters/findOne")
-api.add_resource(Datafiles,"/datafiles")
+api.add_resource(Datafiles, "/datafiles")
 api.add_resource(DatafilesWithID, "/datafiles/<string:id>")
 api.add_resource(DatafilesFindOne, "/datafiles/findOne")
 api.add_resource(DatafilesCount, "/datafiles/count")
@@ -199,6 +200,5 @@
 api.add_resource(UserGroupsCount, "/usergroups/count")
 api.add_resource(UserGroupsFindOne, "/usergroups/findOne")
 
-
 if __name__ == "__main__":
-    app.run(debug=config.is_debug_mode())
+    app.run(debug=config.is_debug_mode())

src/resources/entities/applications_endpoints.py

@@ -5,8 +5,10 @@
 from common.database_helpers import get_row_by_id, delete_row_by_id, update_row_from_id, get_rows_by_filter, \
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class Applications(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/datacollection_datafiles_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import DATACOLLECTIONDATAFILE
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class DataCollectionDatafiles(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/datacollection_datasets_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import DATACOLLECTIONDATASET
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class DataCollectionDatasets(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/datacollection_parameters_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import DATACOLLECTIONPARAMETER
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class DataCollectionParameters(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/datacollections_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import DATACOLLECTION
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class DataCollections(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/datafile_formats_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import DATAFILEFORMAT
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class DatafileFormats(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/datafile_parameters_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import DATAFILEPARAMETER
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class DatafileParameters(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/datafiles_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import DATAFILE
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class Datafiles(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/dataset_type_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import DATASETTYPE
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class DatasetTypes(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/datasets_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import DATASET
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class Datasets(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/facilities_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import FACILITY
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class Facilities(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/facility_cycles_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import FACILITYCYCLE
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class FacilityCycles(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/groupings_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import GROUPING
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class Groupings(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/instrument_scientists_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import INSTRUMENTSCIENTIST
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class InstrumentScientists(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/instruments_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import INSTRUMENT
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class Instruments(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/investigation_groups_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import INVESTIGATIONGROUP
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class InvestigationGroups(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/investigation_instruments_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import INVESTIGATIONINSTRUMENT
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class InvestigationInstruments(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/investigation_parameters_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import INVESTIGATIONPARAMETER
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class InvestigationParameters(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/investigation_types_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import INVESTIGATIONTYPE
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class InvestigationTypes(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/investigation_users_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import INVESTIGATIONUSER
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class InvestigationUsers(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/investigations_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import INVESTIGATION
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class Investigations(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/jobs_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import JOB
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class Jobs(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/keywords_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import KEYWORD
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class Keywords(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/parameter_types_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import PARAMETERTYPE
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class ParameterTypes(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/permissible_string_values_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import PERMISSIBLESTRINGVALUE
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class PermissibleStringValues(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/public_steps_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import PUBLICSTEP
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class PublicSteps(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/publications_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import PUBLICATION
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class Publications(Resource):
     @requires_session_id
     @queries_records

src/resources/entities/related_datafiles_endpoints.py

@@ -5,8 +5,10 @@
     get_filtered_row_count, get_first_filtered_row, create_row_from_json, patch_entities
 from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
 from common.models.db_models import RELATEDDATAFILE
+from src.swagger.swagger_generator import swagger_gen
 
 
+@swagger_gen.resource_wrapper()
 class RelatedDatafiles(Resource):
     @requires_session_id
     @queries_records