Update README.md

README.md

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 # datagateway-api
 ICAT API to interface with the Data Gateway
 
+## Contents
++ [Requirements](#requirements)
++ [Setup](#setup-and-running-the-api)
++ [Project structure](#project-structure)
+    + [Main](#main)
+    + [Endpoints](#endpoints)
+    + [Mapped Classes](#mapped classes)
+
+
+
 
 ## Requirements
-+ [SQLAlchemy](https://www.sqlalchemy.org/)  
-+ [flask-restful](https://github.com/flask-restful/flask-restful/)  
-+ [mypysql](https://pymysql.readthedocs.io/en/latest/)  
-+ [requests](https://2.python-requests.org/en/master/)
+The required python libraries:  
+   - [SQLAlchemy](https://www.sqlalchemy.org/)    
+   - [flask-restful](https://github.com/flask-restful/flask-restful/)  
+   - [mypysql](https://pymysql.readthedocs.io/en/latest/)  
+   - [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 API can then be started by running `src/main.py`
+
+By default the api will run on `http://localhost:5000` and all requests are made here
+
+e.g.
+`http://localhost:5000/sessions`
+
+
+
+## Project structure
+The project consists of 3 main packages: common, src and test. common contains modules shared across test and src such as the database mapping classes.
+src contains the api resources and their http method definitions, and test contains tests for each endpoint.
+
+This is illustrated below.
+
+
+`````
+─── datagateway-api
+    ├── common  
+    │   ├── models
+    │   │   └── db_models.py
+    │   ├── constants.py
+    │   ├── database_helpers.py
+    │   ├── exceptions.py
+    │   └── helpers.py
+    ├── src
+    │   ├── resources
+    │   │   ├── entities
+    │   │   │   └── <entity>_endpoints.py
+    │   │   └── non_entities
+    │   │       └── <non_entity>_endpoints.py
+    │   ├── swagger
+    │   │   └── openapi.yaml
+    │   └── main.py  
+    └── test
+        ├── resources
+        │   ├── entities
+        │   │   └──test_<entity>.py
+        │   └── non_entities
+        │       └── test_<non_entity>.py
+        └── test_base
+            ├── constants.py
+            └── rest_test.py
+ `````
+#### Main:
+The main entry point is in `/src/main.py`. This is where each endpoint route is defined and its 
+related class imported e.g.  
+ `api.add_resource(DatafilesWithID, "/datafiles/<string:id>")`  
+Debugging may also be turned on or off with, `app.run(debug=True)` and `app.run()` respectively.
+When debugging is enabled the api will restart every time code changes are detected.
+
+
+#### Endpoints:  
+The logic for each endpoint are within `/src/resources`. They are split into entities 
+and non entities. Each endpoint has its own file within these folders e.g. the datafile endpoint
+is in `/src/resources/entities/datafiles_endpoints.py`. Inside of this file there is a class for
+each type of endpoint e.g. `/datafiles/count`. Each class is then imported to `/main.py` and added
+as a resource.
+
+
+#### Mapped classes:
+The classes mapped from the database are stored in `/common/models/db_models.py`. Each model was 
+automatically generated using sqlacodegen. A class `EntityHelper` is defined so that each model may
+inherit two methods `to_dict()` and `update_from_dict(dictionary)`, both used for returning entities 
+and updating them, in a form easily converted to JSON.  
+
+
+
+
+
+
+