Merge branch 'master' into 75_fix_paths

README.md

@@ -13,12 +13,15 @@ ICAT API to interface with the Data Gateway
 
 
 ## Requirements
+All requirements can be installed with `pip install -r requirements.txt`
+
 The required python libraries:  
    - [SQLAlchemy](https://www.sqlalchemy.org/)    
    - [flask-restful](https://github.com/flask-restful/flask-restful/)  
    - [pymysql](https://pymysql.readthedocs.io/en/latest/)  
    - [requests](https://2.python-requests.org/en/master/)
    - [pyyaml](https://pyyaml.org/wiki/PyYAMLDocumentation) (For the swagger generation)
+   - [pip-tools](https://github.com/jazzband/pip-tools) (For generating requirements.txt)
 
 ## Setup and running the API   
 The database connection needs to be set up first. This is set in config.json, an example config file called `config.json.example` is provided.
@@ -116,6 +119,7 @@ and updating them, in a form easily converted to JSON.
 
 
 
-
+## Running Tests
+To run the tests use `python -m unittest discover`
 
 

common/config.py

@@ -35,4 +35,17 @@ def is_generate_swagger(self):
         except:
             sys.exit("Missing config value, generate_swagger")
 
+    def get_host(self):
+        try:
+            return self.config["host"]
+        except:
+            sys.exit("Missing config value, host")
+
+    def get_port(self):
+        try:
+            return self.config["port"]
+        except:
+            sys.exit("Missing config value, port")
+
+
 config = Config()

common/database_helpers.py

@@ -5,7 +5,7 @@
 from sqlalchemy import asc, desc
 from sqlalchemy.orm import aliased
 
-from common.exceptions import MissingRecordError, BadFilterError, BadRequestError
+from common.exceptions import MissingRecordError, BadFilterError, BadRequestError, MultipleIncludeError
 from common.models.db_models import INVESTIGATIONUSER, INVESTIGATION, INSTRUMENT, FACILITYCYCLE, \
     INVESTIGATIONINSTRUMENT, FACILITY
 from common.session_manager import session_manager
@@ -86,6 +86,7 @@ class CreateQuery(Query):
     def __init__(self, table, row):
         super().__init__(table)
         self.row = row
+        self.inserted_row = None
 
     def execute_query(self):
         """Determines if the row is a row object or dictionary then commits it to the table"""
@@ -100,7 +101,8 @@ def execute_query(self):
             record.MOD_ID = "user"  # These will need changing
         self.session.add(record)
         self.commit_changes()
-
+        self.session.refresh(record)
+        self.inserted_row = record
 
 class UpdateQuery(Query):
 
@@ -219,7 +221,10 @@ def __init__(self, included_filters):
         self.included_filters = included_filters["include"]
 
     def apply_filter(self, query):
-        query.include_related_entities = True
+        if not query.include_related_entities:
+            query.include_related_entities = True
+        else:
+            raise MultipleIncludeError("Attempted multiple includes on a single query")
 
 
 class QueryFilterFactory(object):
@@ -292,16 +297,28 @@ def insert_row_into_table(table, row):
         create_query.execute_query()
 
 
-def create_row_from_json(table, json):
+def create_row_from_json(table, data):
     """
     Given a json dictionary create a row in the table from it
     :param table: the table for the row to be inserted into
-    :param json: the dictionary containing the values
-    :return: nothing atm
+    :param data: the dictionary containing the values
+    :return: The inserted row as a dictionary
     """
-    with CreateQuery(table, json) as create_query:
+    with CreateQuery(table, data) as create_query:
         create_query.execute_query()
+        return create_query.inserted_row.to_dict()
 
+def create_rows_from_json(table, data):
+    """
+    Given a List containing dictionary representations of entities, or a dictionary representation of an entity, insert
+    the entities into the table and return the created entities
+    :param table: The table to insert the entities in
+    :param data: The entities to be inserted
+    :return: The inserted entities
+    """
+    if type(data) is list:
+        return [create_row_from_json(table, entity) for entity in data]
+    return create_row_from_json(table, data)
 
 def get_row_by_id(table, id):
     """

common/exceptions.py

@@ -10,6 +10,10 @@ class BadFilterError(ApiError):
     pass
 
 
+class MultipleIncludeError(BadFilterError):
+    pass
+
+
 class AuthenticationError(ApiError):
     pass
 

common/helpers.py

@@ -8,7 +8,7 @@
 
 from common.database_helpers import QueryFilterFactory
 from common.exceptions import MissingRecordError, BadFilterError, AuthenticationError, BadRequestError, \
-    MissingCredentialsError
+    MissingCredentialsError, MultipleIncludeError
 from common.models.db_models import SESSION
 from common.session_manager import session_manager
 
@@ -63,6 +63,9 @@ def wrapper_gets_records(*args, **kwargs):
         except MissingRecordError as e:
             log.exception(e)
             return "No such record in table", 404
+        except MultipleIncludeError as e:
+            log.exception(e)
+            return "Bad request, only one include filter may be given per request", 400
         except BadFilterError as e:
             log.exception(e)
             return "Invalid filter requested", 400
@@ -78,7 +81,6 @@ def wrapper_gets_records(*args, **kwargs):
         except BadRequestError as e:
             log.exception(e)
             return "Bad request", 400
-
     return wrapper_gets_records
 
 
@@ -109,6 +111,8 @@ def is_valid_json(string):
         json_object = json.loads(string)
     except ValueError:
         return False
+    except TypeError:
+        return False
     return True
 
 

config.json.example

@@ -2,7 +2,9 @@
   "DB_URL": "mysql+pymysql://root:rootpw@localhost:13306/icatdb",
   "log_level": "WARN",
   "debug_mode": false,
-  "generate_swagger": false
+  "generate_swagger": false,
+  "host": "127.0.0.1",
+  "port": "5000"
 }
 
 

requirements.in

@@ -0,0 +1,5 @@
+flask_restful == 0.3.7
+sqlalchemy == 1.3.8
+pymysql == 0.9.3
+pyyaml == 5.1.2
+flask-cors == 3.0.8

requirements.txt

@@ -0,0 +1,20 @@
+#
+# This file is autogenerated by pip-compile
+# To update, run:
+#
+#    pip-compile
+#
+aniso8601==8.0.0          # via flask-restful
+click==7.0                # via flask
+flask-cors==3.0.8
+flask==1.1.1              # via flask-cors, flask-restful
+flask_restful==0.3.7
+itsdangerous==1.1.0       # via flask
+jinja2==2.10.1            # via flask
+markupsafe==1.1.1         # via jinja2
+pymysql==0.9.3
+pytz==2019.2              # via flask-restful
+pyyaml==5.1.2
+six==1.12.0               # via flask-cors, flask-restful
+sqlalchemy==1.3.8
+werkzeug==0.16.0          # via flask

src/main.py

@@ -1,4 +1,5 @@
 from flask import Flask
+from flask_cors import CORS
 from flask_restful import Api
 
 from common.config import config
@@ -49,6 +50,7 @@
 swagger_gen.write_swagger_spec()
 
 app = Flask(__name__)
+cors = CORS(app)
 app.url_map.strict_slashes = False
 api = Api(app)
 
@@ -215,4 +217,6 @@
                  "/instruments/<int:instrument_id>/facilitycycles/<int:cycle_id>/investigations/count")
 
 if __name__ == "__main__":
+    app.run(host=config.get_host(), port=config.get_port())
     app.run(debug=config.is_debug_mode())
+

src/resources/entities/applications_endpoints.py

@@ -3,7 +3,7 @@
 from flask_restful import Resource
 
 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
+    get_filtered_row_count, get_first_filtered_row, create_rows_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
 
@@ -18,8 +18,7 @@ def get(self):
     @requires_session_id
     @queries_records
     def post(self):
-        create_row_from_json(APPLICATION, request.json)
-        return get_row_by_id(APPLICATION, request.json["id"].to_dict()), 200
+        return create_rows_from_json(APPLICATION, request.json), 200
 
     @requires_session_id
     @queries_records

src/resources/entities/datacollection_datafiles_endpoints.py

@@ -2,7 +2,7 @@
 from flask_restful import Resource
 
 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
+    get_filtered_row_count, get_first_filtered_row, create_rows_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
@@ -18,8 +18,8 @@ def get(self):
     @requires_session_id
     @queries_records
     def post(self):
-        create_row_from_json(DATACOLLECTIONDATAFILE, request.json)
-        return get_row_by_id(DATACOLLECTIONDATAFILE, request.json["id"].to_dict()), 200
+        return create_rows_from_json(DATACOLLECTIONDATAFILE, request.json), 200
+
 
     @requires_session_id
     @queries_records

src/resources/entities/datacollection_datasets_endpoints.py

@@ -2,7 +2,7 @@
 from flask_restful import Resource
 
 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
+    get_filtered_row_count, get_first_filtered_row, create_rows_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
@@ -18,8 +18,7 @@ def get(self):
     @requires_session_id
     @queries_records
     def post(self):
-        create_row_from_json(DATACOLLECTIONDATASET, request.json)
-        return get_row_by_id(DATACOLLECTIONDATASET, request.json["id"].to_dict()), 200
+        return create_rows_from_json(DATACOLLECTIONDATASET, request.json), 200
 
     @requires_session_id
     @queries_records

src/resources/entities/datacollection_parameters_endpoints.py

@@ -2,7 +2,7 @@
 from flask_restful import Resource
 
 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
+    get_filtered_row_count, get_first_filtered_row, patch_entities, create_rows_from_json
 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
@@ -18,8 +18,7 @@ def get(self):
     @requires_session_id
     @queries_records
     def post(self):
-        create_row_from_json(DATACOLLECTIONPARAMETER, request.json)
-        return get_row_by_id(DATACOLLECTIONPARAMETER, request.json["id"].to_dict()), 200
+        return create_rows_from_json(DATACOLLECTIONPARAMETER, request.json), 200
 
     @requires_session_id
     @queries_records

src/resources/entities/datacollections_endpoints.py

@@ -2,7 +2,7 @@
 from flask_restful import Resource
 
 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
+    get_filtered_row_count, get_first_filtered_row, create_rows_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
@@ -18,8 +18,7 @@ def get(self):
     @requires_session_id
     @queries_records
     def post(self):
-        create_row_from_json(DATACOLLECTION, request.json)
-        return get_row_by_id(DATACOLLECTION, request.json["id"].to_dict()), 200
+        return create_rows_from_json(DATACOLLECTION, request.json), 200
 
     @requires_session_id
     @queries_records

src/resources/entities/datafile_formats_endpoints.py

@@ -2,7 +2,7 @@
 from flask_restful import Resource
 
 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
+    get_filtered_row_count, get_first_filtered_row, create_rows_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
@@ -18,8 +18,7 @@ def get(self):
     @requires_session_id
     @queries_records
     def post(self):
-        create_row_from_json(DATAFILEFORMAT, request.json)
-        return get_row_by_id(DATAFILEFORMAT, request.json["id"].to_dict()), 200
+        return create_rows_from_json(DATAFILEFORMAT, request.json), 200
 
     @requires_session_id
     @queries_records

src/resources/entities/datafile_parameters_endpoints.py

@@ -2,7 +2,7 @@
 from flask_restful import Resource
 
 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
+    get_filtered_row_count, get_first_filtered_row, create_rows_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
@@ -18,8 +18,7 @@ def get(self):
     @requires_session_id
     @queries_records
     def post(self):
-        create_row_from_json(DATAFILEPARAMETER, request.json)
-        return get_row_by_id(DATAFILEPARAMETER, request.json["id"].to_dict()), 200
+        return create_rows_from_json(DATAFILEPARAMETER, request.json), 200
 
     @requires_session_id
     @queries_records

src/resources/entities/datafiles_endpoints.py

@@ -2,7 +2,7 @@
 from flask_restful import Resource
 
 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
+    get_filtered_row_count, get_first_filtered_row, create_rows_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
@@ -18,8 +18,7 @@ def get(self):
     @requires_session_id
     @queries_records
     def post(self):
-        create_row_from_json(DATAFILE, request.json)
-        return "", 200
+        return create_rows_from_json(DATAFILE, request.json), 200
 
     @requires_session_id
     @queries_records

src/resources/entities/dataset_type_endpoints.py

@@ -2,7 +2,7 @@
 from flask_restful import Resource
 
 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
+    get_filtered_row_count, get_first_filtered_row, create_rows_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
@@ -18,8 +18,7 @@ def get(self):
     @requires_session_id
     @queries_records
     def post(self):
-        create_row_from_json(DATASETTYPE, request.json)
-        return get_row_by_id(DATASETTYPE, request.json["id"].to_dict()), 200
+        return create_rows_from_json(DATASETTYPE, request.json), 200
 
     @requires_session_id
     @queries_records