Merge branch 'master' into use_classes_for_queries_and_filters

README.md

@@ -20,12 +20,7 @@ The required python libraries:
    - [requests](https://2.python-requests.org/en/master/)
 
 ## Setup and running the API   
-The database connection needs to be set up first, currently it is set in `common/constants.py`  
-
-```python 
-class Constants:
-    DATABASE_URL = "mysql+pymysql://root:rootpw@localhost:13306/icatdb"
-```
+The database connection needs to be set up first. This is set in config.json
 
 
 To run the API from the command line, the enviroment variable `FLASK_APP` should be set to `src/main.py`. Once this is 
@@ -83,15 +78,17 @@ This is illustrated below.
     │   ├── swagger
     │   │   └── openapi.yaml
     │   └── main.py  
-    └── test
-        ├── resources
-        │   ├── entities
-        │   │   └──test_<entity>.py
-        │   └── non_entities
-        │       └── test_<non_entity>.py
-        └── test_base
-            ├── constants.py
-            └── rest_test.py
+    ├── test
+    │   ├── resources
+    │   │   ├── entities
+    │   │   │   └──test_<entity>.py
+    │   │   └── non_entities
+    │   │       └── test_<non_entity>.py
+    │   └── test_base
+    │       ├── constants.py
+    │       └── rest_test.py
+    ├── logs.log
+    └── config.json
  `````
 #### Main:
 The main entry point is in `/src/main.py`. This is where each endpoint route is defined and its 

common/config.py

@@ -0,0 +1,36 @@
+import json
+import sys
+
+
+class Config(object):
+
+    def __init__(self):
+        with open("../config.json") as target:
+            self.config = json.load(target)
+        target.close()
+
+    def get_db_url(self):
+        try:
+            return self.config["DB_URL"]
+        except:
+            sys.exit("Missing config value, DB_URL")
+
+    def get_log_level(self):
+        try:
+            return self.config["log_level"]
+        except:
+            sys.exit("Missing config value, log_level")
+
+    def is_debug_mode(self):
+        try:
+            return self.config["debug_mode"]
+        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()

common/constants.py

@@ -1,2 +1,5 @@
+from common.config import config
+
+
 class Constants:
-    DATABASE_URL = "mysql+pymysql://root:rootpw@localhost:13306/icatdb"
+    DATABASE_URL = config.get_db_url()

common/logger_setup.py

@@ -1,5 +1,5 @@
 import logging.config
-
+from common.config import  config
 
 log_level = "DEBUG"
 LOG_FILE_NAME = "../logs.log"
@@ -9,15 +9,15 @@
         "format": "[%(asctime)s] {%(module)s:%(filename)s:%(funcName)s:%(lineno)d} %(levelname)s -%(message)s  ",
     }},
     "handlers": {"default": {
-        "level": "DEBUG",
+        "level": config.get_log_level(),
         "formatter": "default",
         "class": "logging.handlers.RotatingFileHandler",
         "filename": LOG_FILE_NAME,
         "maxBytes": 5000000,
         "backupCount": 10
     }},
     "root": {
-        "level": log_level,
+        "level": config.get_log_level(),
         "handlers": ["default"]
     }
 }

config.json

@@ -0,0 +1,10 @@
+{
+  "DB_URL": "mysql+pymysql://root:rootpw@localhost:13306/icatdb",
+  "log_level": "WARN",
+  "debug_mode": false,
+  "generate_swagger": false
+}
+
+
+
+

config.json.example

@@ -0,0 +1,10 @@
+{
+  "DB_URL": "mysql+pymysql://root:rootpw@localhost:13306/icatdb",
+  "log_level": "WARN",
+  "debug_mode": false,
+  "generate_swagger": false
+}
+
+
+
+

src/main.py

@@ -1,8 +1,8 @@
 from flask import Flask
 from flask_restful import Api
 
+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 *
@@ -11,6 +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 *
@@ -34,18 +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")
@@ -68,7 +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")
@@ -198,6 +200,5 @@
 api.add_resource(UserGroupsCount, "/usergroups/count")
 api.add_resource(UserGroupsFindOne, "/usergroups/findOne")
 
-
 if __name__ == "__main__":
-    app.run(debug=True)
+    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